@article {pmid29880023, year = {2018}, author = {Méheust, R and Watson, AK and Lapointe, FJ and Papke, RT and Lopez, P and Bapteste, E}, title = {Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {75}, doi = {10.1186/s13059-018-1454-9}, pmid = {29880023}, issn = {1474-760X}, support = {#615274//FP7 Ideas: European Research Council/International ; 1716046//National Science Foundation/International ; NNX15AM09G/NASA/NASA/United States ; OGP249644//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Amino Acids/genetics ; Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; }, abstract = {BACKGROUND: Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. We use network analyses to show that the evolution of novel genes exclusive to Haloarchaea also contributed to the evolution of this group.

RESULTS: We report the creation of 320 novel composite genes, both early in the evolution of Haloarchaea during haloarchaeal genesis and later in diverged haloarchaeal groups. One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. These latter genes, largely involved in metabolic functions but also in oxygenic lifestyle, constitute a different gene pool from the laterally acquired bacterial genes formerly identified. These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points.

CONCLUSIONS: Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes.}, } @article {pmid27028821, year = {2016}, author = {Naumoff, DG}, title = {[GH10 Family of Glycoside Hydrolases: Structure and Evolutionary Connections].}, journal = {Molekuliarnaia biologiia}, volume = {50}, number = {1}, pages = {151-160}, doi = {10.7868/S0026898415060208}, pmid = {27028821}, issn = {0026-8984}, mesh = {Bacteria/*enzymology/*genetics ; Bacterial Proteins/chemistry/classification/genetics ; Catalytic Domain/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Glycoside Hydrolases/chemistry/*classification/*genetics ; }, abstract = {Evolutionary connections were analyzed for endo-β-xylanases, which possess the GH10 family catalytic domains. A homology search yielded thrice as many proteins as are available from the Carbohydrate-Active Enzymes (CAZy) database. Lateral gene transfer was shown to play an important role in evolution of bacterial proteins of the family, especially in the phyla Acidobacteria, Cyanobacteria, Planctomycetes, Spirochaetes, and Verrucomicrobia. In the case of Verrucomicrobia, 23 lateral transfers from organisms of other phyla were detected. Evolutionary relationships were observed between the GH10 family domains and domains with the TIM-barrel tertiary structure from several other glycosidase families. The GH39 family of glycoside hydrolases showed the closest relationship. Unclassified homologs were grouped into 12 novel families of putative glycoside hydrolases (GHL51-GHL62).}, } @article {pmid30319562, year = {2018}, author = {Sand, KK and Jelavić, S}, title = {Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life?.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2217}, doi = {10.3389/fmicb.2018.02217}, pmid = {30319562}, issn = {1664-302X}, abstract = {A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.}, } @article {pmid29617810, year = {2018}, author = {Murillo, T and Ramírez-Vargas, G and Riedel, T and Overmann, J and Andersen, JM and Guzmán-Verri, C and Chaves-Olarte, E and Rodríguez, C}, title = {Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms.}, journal = {Genome biology and evolution}, volume = {10}, number = {3}, pages = {982-998}, doi = {10.1093/gbe/evy059}, pmid = {29617810}, issn = {1759-6653}, mesh = {Clostridium Infections/*genetics/microbiology ; Clostridium difficile/*genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genome, Bacterial ; Genotype ; Humans ; Mutation ; Virulence/genetics ; }, abstract = {Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301-8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.}, } @article {pmid30237791, year = {2018}, author = {Chelkha, N and Levasseur, A and Pontarotti, P and Raoult, D and Scola, B and Colson, P}, title = {A Phylogenomic Study of Acanthamoeba polyphaga Draft Genome Sequences Suggests Genetic Exchanges With Giant Viruses.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2098}, doi = {10.3389/fmicb.2018.02098}, pmid = {30237791}, issn = {1664-302X}, abstract = {Acanthamoeba are ubiquitous phagocytes predominant in soil and water which can ingest many microbes. Giant viruses of amoebae are listed among the Acanthamoeba-resisting microorganisms. Their sympatric lifestyle within amoebae is suspected to promote lateral nucleotide sequence transfers. Some Acanthamoeba species have shown differences in their susceptibility to giant viruses. Until recently, only the genome of a single Acanthamoeba castellanii Neff was available. We analyzed the draft genome sequences of Acanthamoeba polyphaga through several approaches, including comparative genomics, phylogeny, and sequence networks, with the aim of detecting putative nucleotide sequence exchanges with giant viruses. We identified a putative sequence trafficking between this Acanthamoeba species and giant viruses, with 366 genes best matching with viral genes. Among viruses, Pandoraviruses provided the greatest number of best hits with 117 (32%) for A. polyphaga. Then, genes from mimiviruses, Mollivirus sibericum, marseilleviruses, and Pithovirus sibericum were best hits in 67 (18%), 35 (9%), 24 (7%), and 2 (0.5%) cases, respectively. Phylogenetic reconstructions showed in a few cases that the most parsimonious evolutionary scenarios were a transfer of gene sequences from giant viruses to A. polyphaga. Nevertheless, in most cases, phylogenies were inconclusive regarding the sense of the sequence flow. The number and nature of putative nucleotide sequence transfers between A. polyphaga, and A. castellanii ATCC 50370 on the one hand, and pandoraviruses, mimiviruses and marseilleviruses on the other hand were analyzed. The results showed a lower number of differences within the same giant viral family compared to between different giant virus families. The evolution of 10 scaffolds that were identified among the 14 Acanthamoeba sp. draft genome sequences and that harbored ≥ 3 genes best matching with viruses showed a conservation of these scaffolds and their 46 viral genes in A. polyphaga, A. castellanii ATCC 50370 and A. pearcei. In contrast, the number of conserved genes decreased for other Acanthamoeba species, and none of these 46 genes were present in three of them. Overall, this work opens up several potential avenues for future studies on the interactions between Acanthamoeba species and giant viruses.}, } @article {pmid30223892, year = {2018}, author = {Sitaraman, R}, title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {163}, doi = {10.1186/s40168-018-0551-z}, pmid = {30223892}, issn = {2049-2618}, abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.}, } @article {pmid27357338, year = {2016}, author = {Glöckner, G and Lawal, HM and Felder, M and Singh, R and Singer, G and Weijer, CJ and Schaap, P}, title = {The multicellularity genes of dictyostelid social amoebas.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12085}, doi = {10.1038/ncomms12085}, pmid = {27357338}, issn = {2041-1723}, support = {BB/G020426/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {*Biological Evolution ; Cell Differentiation/genetics ; Dictyostelium/*genetics ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genes, Essential ; Whole Genome Sequencing ; }, abstract = {The evolution of multicellularity enabled specialization of cells, but required novel signalling mechanisms for regulating cell differentiation. Early multicellular organisms are mostly extinct and the origins of these mechanisms are unknown. Here using comparative genome and transcriptome analysis across eight uni- and multicellular amoebozoan genomes, we find that 80% of proteins essential for the development of multicellular Dictyostelia are already present in their unicellular relatives. This set is enriched in cytosolic and nuclear proteins, and protein kinases. The remaining 20%, unique to Dictyostelia, mostly consists of extracellularly exposed and secreted proteins, with roles in sensing and recognition, while several genes for synthesis of signals that induce cell-type specialization were acquired by lateral gene transfer. Across Dictyostelia, changes in gene expression correspond more strongly with phenotypic innovation than changes in protein functional domains. We conclude that the transition to multicellularity required novel signals and sensors rather than novel signal processing mechanisms.}, } @article {pmid28405008, year = {2017}, author = {Dunning Hotopp, JC and Slatko, BE and Foster, JM}, title = {Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {857}, doi = {10.1038/s41598-017-00814-4}, pmid = {28405008}, issn = {2045-2322}, support = {DP2 OD007372/OD/NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Helminth ; Nematoda/genetics/microbiology ; *Symbiosis ; Wolbachia/genetics/pathogenicity ; }, abstract = {Lateral gene transfer (LGT) from microbial symbionts to invertebrate animals is described at an increasing rate, particularly between Wolbachia endosymbionts and their diverse invertebrate hosts. We sought to assess the use of a capture system to cost-effectively sequence such LGT from the host genome. The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depleted B. malayi (p-value: <2e-16). Using a sequencing depth threshold of two or three standard deviations above the mean, 96.9% or 96.7% of positions, respectively, are predicted in the same manner between the two datasets, with 24.7% or 42.5% of the known 49.0 kbp of LGT sequence predicted correctly, respectively. Prior qPCR results for nuwts showed similar correlations for both datasets supporting our conclusion that oligonucleotide-based capture methods can be used to obtain sequences from Wolbachia-host LGT. However, at least 121 positions had a minority of the reads supporting the endosymbiont reference base call using the capture data, illustrating that sequence reads from endosymbiont-host LGTs can confound endosymbiont genome projects, erroneously altering the called consensus genome, a problem that is irrespective to the sequencing technology or platform.}, } @article {pmid28364120, year = {2017}, author = {Chamosa, LS and Álvarez, VE and Nardelli, M and Quiroga, MP and Cassini, MH and Centrón, D}, title = {Lateral Antimicrobial Resistance Genetic Transfer is active in the open environment.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {513}, doi = {10.1038/s41598-017-00600-2}, pmid = {28364120}, issn = {2045-2322}, mesh = {Alleles ; Argentina ; Bacteria/*drug effects/*genetics ; *Drug Resistance, Bacterial ; *Environmental Microbiology ; Gene Frequency ; *Gene Transfer, Horizontal ; Integrases/genetics ; Public Health Surveillance ; }, abstract = {Historically, the environment has been viewed as a passive deposit of antimicrobial resistance mechanisms, where bacteria show biological cost for maintenance of these genes. Thus, in the absence of antimicrobial pressure, it is expected that they disappear from environmental bacterial communities. To test this scenario, we studied native IntI1 functionality of 11 class 1 integron-positive environmental strains of distant genera collected in cold and subtropical forests of Argentina. We found natural competence and successful site-specific insertion with no significant fitness cost of both aadB and bla VIM-2 antimicrobial resistance gene cassettes, in a model system without antibiotic pressure. A bidirectional flow of antimicrobial resistance gene cassettes between natural and nosocomial habitats is proposed, which implies an active role of the open environment as a reservoir, recipient and source of antimicrobial resistance mechanisms, outlining an environmental threat where novel concepts of rational use of antibiotics are extremely urgent and mandatory.}, } @article {pmid27727237, year = {2016}, author = {Bordenstein, SR and Bordenstein, SR}, title = {Eukaryotic association module in phage WO genomes from Wolbachia.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13155}, doi = {10.1038/ncomms13155}, pmid = {27727237}, issn = {2041-1723}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R21 HD086833/HD/NICHD NIH HHS/United States ; }, mesh = {Ankyrin Repeat ; Bacteriophages/*genetics ; Conserved Sequence ; Eukaryota/*metabolism ; Furin/metabolism ; Gene Transfer, Horizontal ; Genes, Viral ; *Genome, Viral ; Models, Biological ; Phylogeny ; Spider Venoms/chemistry ; Tetratricopeptide Repeat ; Viral Proteins/metabolism ; Wolbachia/*virology ; }, abstract = {Viruses are trifurcated into eukaryotic, archaeal and bacterial categories. This domain-specific ecology underscores why eukaryotic viruses typically co-opt eukaryotic genes and bacteriophages commonly harbour bacterial genes. However, the presence of bacteriophages in obligate intracellular bacteria of eukaryotes may promote DNA transfers between eukaryotes and bacteriophages. Here we report a metagenomic analysis of purified bacteriophage WO particles of Wolbachia and uncover a eukaryotic association module in the complete WO genome. It harbours predicted domains, such as the black widow latrotoxin C-terminal domain, that are uninterrupted in bacteriophage genomes, enriched with eukaryotic protease cleavage sites and combined with additional domains to forge one of the largest bacteriophage genes to date (14,256 bp). To the best of our knowledge, these eukaryotic-like domains have never before been reported in packaged bacteriophages and their phylogeny, distribution and sequence diversity imply lateral transfers between bacteriophage/prophage and animal genomes. Finally, the WO genome sequences and identification of attachment sites will potentially advance genetic manipulation of Wolbachia.}, } @article {pmid29923454, year = {2018}, author = {Yair, Y and Gophna, U}, title = {Repeat modularity as a beneficial property of multiple CRISPR-Cas systems.}, journal = {RNA biology}, volume = {}, number = {}, pages = {1-3}, doi = {10.1080/15476286.2018.1474073}, pmid = {29923454}, issn = {1555-8584}, abstract = {CRISPR-Cas systems are a highly effective immune mechanism for prokaryotes, providing defense against invading foreign DNA. By definition, all CRISPR-Cas systems have short repeats interspersing their spacers. These repeats play a key role in preventing cleavage of self DNA and in the integration of new spacers. Here we focus on the phenomenon of repeat modularity, namely the unexpectedly high degree of repeat conservation across different systems within a genome or between different species. We hypothesize that modularity can be beneficial for CRISPR-Cas containing organisms, because it facilitates horizontal acquisition of 'pre-immunized' CRISPR arrays and allows the utilization of spacers acquired by one system for use by other systems within the same cell.}, } @article {pmid28262486, year = {2017}, author = {Eme, L and Gentekaki, E and Curtis, B and Archibald, JM and Roger, AJ}, title = {Lateral Gene Transfer in the Adaptation of the Anaerobic Parasite Blastocystis to the Gut.}, journal = {Current biology : CB}, volume = {27}, number = {6}, pages = {807-820}, doi = {10.1016/j.cub.2017.02.003}, pmid = {28262486}, issn = {1879-0445}, mesh = {Acclimatization ; Blastocystis/genetics/*physiology ; Blastocystis Infections/*parasitology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Intestinal Diseases/*parasitology ; Intestines/*parasitology ; *Microbiota ; }, abstract = {Blastocystis spp. are the most prevalent eukaryotic microbes found in the intestinal tract of humans. Here we present an in-depth investigation of lateral gene transfer (LGT) in the genome of Blastocystis sp. subtype 1. Using rigorous phylogeny-based methods and strict validation criteria, we show that ∼2.5% of the genes of this organism were recently acquired by LGT. We identify LGTs both from prokaryote and eukaryote donors. Several transfers occurred specifically in ancestors of a subset of Blastocystis subtypes, demonstrating that LGT is an ongoing process. Functional predictions reveal that these genes are involved in diverse metabolic pathways, many of which appear related to adaptation of Blastocystis to the gut environment. Specifically, we identify genes involved in carbohydrate scavenging and metabolism, anaerobic amino acid and nitrogen metabolism, oxygen-stress resistance, and pH homeostasis. A number of the transferred genes encoded secreted proteins that are potentially involved in infection, escaping host defense, or most likely affect the prokaryotic microbiome and the inflammation state of the gut. We also show that Blastocystis subtypes differ in the nature and copy number of LGTs that could relate to variation in their prevalence and virulence. Finally, we identified bacterial-derived genes encoding NH3-dependent nicotinamide adenine dinucleotide (NAD) synthase in Blastocystis and other protozoan parasites, which are promising targets for drug development. Collectively, our results suggest new avenues for research into the role of Blastocystis in intestinal disease and unequivocally demonstrate that LGT is an important mechanism by which eukaryotic microbes adapt to new environments.}, } @article {pmid29954096, year = {2018}, author = {Andrews, M and De Meyer, S and James, EK and Stępkowski, T and Hodge, S and Simon, MF and Young, JPW}, title = {Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance.}, journal = {Genes}, volume = {9}, number = {7}, pages = {}, doi = {10.3390/genes9070321}, pmid = {29954096}, issn = {2073-4425}, abstract = {Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their &lsquo;host&rsquo;. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.}, } @article {pmid29922518, year = {2018}, author = {Hernandez, AM and Ryan, JF}, title = {Horizontally transferred genes in the ctenophore Mnemiopsis leidyi.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5067}, doi = {10.7717/peerj.5067}, pmid = {29922518}, issn = {2167-8359}, abstract = {Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.}, } @article {pmid29914363, year = {2018}, author = {Dunning Hotopp, JC}, title = {Grafting or pruning in the animal tree: lateral gene transfer and gene loss?.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {470}, doi = {10.1186/s12864-018-4832-5}, pmid = {29914363}, issn = {1471-2164}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; ABI-1457957//National Science Foundation/ ; 1-R01-CA206188//National Cancer Institute/ ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate.

RESULTS: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes.

CONCLUSIONS: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.}, } @article {pmid29868902, year = {2018}, author = {Bertelli, C and Tilley, KE and Brinkman, FSL}, title = {Microbial genomic island discovery, visualization and analysis.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bby042}, pmid = {29868902}, issn = {1477-4054}, abstract = {Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.}, } @article {pmid29813058, year = {2018}, author = {Hendrickson, HL and Barbeau, D and Ceschin, R and Lawrence, JG}, title = {Chromosome architecture constrains horizontal gene transfer in bacteria.}, journal = {PLoS genetics}, volume = {14}, number = {5}, pages = {e1007421}, doi = {10.1371/journal.pgen.1007421}, pmid = {29813058}, issn = {1553-7404}, support = {R01-GM7809204/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Chromosome Inversion ; Chromosomes/*genetics ; DNA Replication ; Gene Rearrangement/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; *Selection, Genetic ; }, abstract = {Despite significant frequencies of lateral gene transfer between species, higher taxonomic groups of bacteria show ecological and phenotypic cohesion. This suggests that barriers prevent panmictic dissemination of genes via lateral gene transfer. We have proposed that most bacterial genomes have a functional architecture imposed by Architecture IMparting Sequences (AIMS). AIMS are defined as 8 base pair sequences preferentially abundant on leading strands, whose abundance and strand-bias are positively correlated with proximity to the replication terminus. We determined that inversions whose endpoints lie within a single chromosome arm, which would reverse the polarity of AIMS in the inverted region, are both shorter and less frequent near the replication terminus. This distribution is consistent with the increased selection on AIMS function in this region, thus constraining DNA rearrangement. To test the hypothesis that AIMS also constrain DNA transfer between genomes, AIMS were identified in genomes while ignoring atypical, potentially laterally-transferred genes. The strand-bias of AIMS within recently acquired genes was negatively correlated with the distance of those genes from their genome's replication terminus. This suggests that selection for AIMS function prevents the acquisition of genes whose AIMS are not found predominantly in the permissive orientation. This constraint has led to the loss of at least 18% of genes acquired by transfer in the terminus-proximal region. We used completely sequenced genomes to produce a predictive road map of paths of expected horizontal gene transfer between species based on AIMS compatibility between donor and recipient genomes. These results support a model whereby organisms retain introgressed genes only if the benefits conferred by their encoded functions outweigh the detriments incurred by the presence of foreign DNA lacking genome-wide architectural information.}, } @article {pmid29786161, year = {2018}, author = {Simbaqueba, J and Catanzariti, AM and González, C and Jones, DA}, title = {Evidence for horizontal gene transfer and separation of effector recognition from effector function revealed by analysis of effector genes shared between cape-gooseberry- and tomato-infecting formae speciales of Fusarium oxysporum.}, journal = {Molecular plant pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mpp.12700}, pmid = {29786161}, issn = {1364-3703}, abstract = {RNAseq reads from cape-gooseberry plants (Physalis peruviana) infected with Fusarium oxysporum f. sp. physali (Foph) were mapped against the lineage-specific transcriptome of Fusarium oxysporum f. sp. lycopersici (Fol) to look for putative effector genes. Homologues of Fol SIX1 (designated SIX1a and SIX1b), SIX7, SIX10, SIX12, SIX15 and Ave1 were identified. The near identity of the Foph and Fol SIX7, SIX10 and SIX12 genes and their intergenic regions suggest that this gene cluster may have undergone recent lateral transfer. Foph SIX1a and SIX1b were tested for their ability to complement a SIX1 knockout mutant of Fol. This mutant has reduced pathogenicity on susceptible tomato plants, but is able to infect otherwise resistant tomato plants carrying the I-3 gene for Fusarium wilt resistance (SIX1 corresponds to Avr3). Neither, SIX1a nor SIX1b could restore full pathogenicity on susceptible tomato plants, suggesting that any role they may play in pathogenicity is likely to be specific to cape gooseberry. SIX1b, but not SIX1a, was able to restore avirulence on tomato plants carrying I-3. These findings separate the recognition of SIX1 from its role as an effector and suggest direct recognition by I-3. A hypervariable region of SIX1 undergoing diversifying selection within the F. oxysporum species complex is likely to play an important role in SIX1 recognition. These findings also indicate that I-3 could potentially be deployed as a transgene in cape gooseberry to protect this emerging crop from Foph. Alternatively, cape gooseberry germplasm could be explored for I-3 homologues capable of providing resistance to Foph. This article is protected by copyright. All rights reserved.}, } @article {pmid29751066, year = {2018}, author = {Gupta, S and Lemenze, A and Donnelly, RJ and Connell, ND and Kadouri, DE}, title = {Keeping it together: absence of genetic variation and DNA incorporation by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus during predation.}, journal = {Research in microbiology}, volume = {169}, number = {4-5}, pages = {237-243}, doi = {10.1016/j.resmic.2018.03.002}, pmid = {29751066}, issn = {1769-7123}, abstract = {The use of predatory bacteria as a potential live therapeutic to control human infection is gaining increased attention. Earlier work with Micavibrio spp. and Bdellovibrio spp. has demonstrated the ability of these predators to control drug-resistant Gram-negative pathogens, Tier-1 select agents and biofilms. Additional studies also confirmed that introducing high doses of the predators into animals does not negatively impact animal well-being and might assist in reducing bacterial burden in vivo. The survival of predators requires extreme proximity to the prey cell, which might bring about horizontal transfer of genetic material, such as genes encoding for pathogenic genetic islands that would indirectly facilitate the spread of genetic material to other organisms. In this study, we examined the genetic makeup of several lab isolates of the predators Bdellovibriobacteriovorus and Micavibrioaeruginosavorus that were cultured repeatedly and stored over a course of 13 years. We also conducted controlled experiments in which the predators were sequentially co-cultured on Klebsiella pneumoniae followed by genetic analysis of the predator. In both cases, we saw little genetic variation and no evidence of horizontally transferred chromosomal DNA from the prey during predator-prey interaction. Culturing the predators repeatedly did not cause any change in predation efficacy.}, } @article {pmid29728072, year = {2018}, author = {Gambetta, GA and Matthews, MA and Syvanen, M}, title = {The Xylella fastidosa RTX operons: evidence for the evolution of protein mosaics through novel genetic exchanges.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {329}, doi = {10.1186/s12864-018-4731-9}, pmid = {29728072}, issn = {1471-2164}, support = {01-0712//California Department of Food and Agriculture (US)/ ; 2005-34442-15841//USDA/ ; }, abstract = {BACKGROUND: Xylella fastidiosa (Xf) is a gram negative bacterium inhabiting the plant vascular system. In most species this bacterium lives as a benign symbiote, but in several agriculturally important plants (e.g. coffee, citrus, grapevine) Xf is pathogenic. Xf has four loci encoding homologues to hemolysin RTX proteins, virulence factors involved in a wide range of plant pathogen interactions.

RESULTS: We show that all four genes are expressed during pathogenesis in grapevine. The sequences from these four genes have a complex repetitive structure. At the C-termini, sequence diversity between strains is what would be expected from orthologous genes. However, within strains there is no N-terminal homology, indicating these loci encode RTXs of different functions and/or specificities. More striking is that many of the orthologous loci between strains share this extreme variation at the N-termini. Thus these RTX orthologues are most easily visualized as fusions between the orthologous C-termini and different N-termini. Further, the four genes are found in operons having a peculiar structure with an extensively duplicated module encoding a small protein with homology to the N-terminal region of the full length RTX. Surprisingly, some of these small peptides are most similar not to their corresponding full length RTX, but to the N-termini of RTXs from other Xf strains, and even other remotely related species.

CONCLUSIONS: These results demonstrate that these genes are expressed in planta during pathogenesis. Their structure suggests extensive evolutionary restructuring through horizontal gene transfers and heterologous recombination mechanisms. The sum of the evidence suggests these repetitive modules are a novel kind of mobile genetic element.}, } @article {pmid29705204, year = {2018}, author = {Godde, JS and Baichoo, S and Mungloo-Dilmohamud, Z and Jaufeerally-Fakim, Y}, title = {Comparison of genomic islands in cyanobacteria: Evidence of bacteriophage-mediated horizontal gene transfer from eukaryotes.}, journal = {Microbiological research}, volume = {211}, number = {}, pages = {31-46}, doi = {10.1016/j.micres.2018.03.005}, pmid = {29705204}, issn = {1618-0623}, abstract = {A number of examples of putative eukaryote-to-prokaryote horizontal gene transfer (HGT) have been proposed in the past using phylogenetic analysis in support of these claims but none have attempted to map these gene transfers to the presence of genomic islands (GIs) in the host. Two of these cases have been examined in detail, including an ATP sulfurylase (ATPS) gene and a class I fructose bisphosphate aldolase (FBA I) gene that were putatively transferred to cyanobacteria of the genus Prochlorococcus from either green or red algae, respectively. Unlike previous investigations of HGT, parametric methods were initially used to detect genomic islands, then more traditional phylogenomic and phylogenetic methods were used to confirm or deny the HGT status of these genes. The combination of these three methods of analysis- detection of GIs, the determination of genomic neighborhoods, as well as traditional phylogeny, lends strong support to the claim that trans-domain HGT has occurred in only one of these cases and further suggests a new insight into the method of transmission of FBA I, namely that cyanophage-mediated transfer may have been responsible for the HGT event in question. The described methods were then applied to a range of prochlorococcal genomes in order to characterize a candidate for eukaryote-to-prokaryote HGT that had not been previously studied by others. Application of the same methodology used to confirm or deny HGT for ATPS and FBA I identified a ⊗12 fatty acid desaturase (FAD) gene that was likely transferred to Prochlorococcus from either green or red algae.}, } @article {pmid29697049, year = {2018}, author = {Stairs, CW and Eme, L and Muñoz-Gómez, SA and Cohen, A and Dellaire, G and Shepherd, JN and Fawcett, JP and Roger, AJ}, title = {Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.34292}, pmid = {29697049}, issn = {2050-084X}, support = {MOP 341174//Canadian Institutes of Health Research/Canada ; MOP 142349//Canadian Institutes of Health Research/Canada ; R15 GM096398/GM/NIGMS NIH HHS/United States ; 1R15GM096398-01//National Institutes of Health/ ; NSERC-CGS-D//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN 05616//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Under hypoxic conditions, some organisms use an electron transport chain consisting of only complex I and II (CII) to generate the proton gradient essential for ATP production. In these cases, CII functions as a fumarate reductase that accepts electrons from a low electron potential quinol, rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction in eukaryotes, we investigated the origin and function of rquA, a gene encoding an RQ biosynthetic enzyme. RquA is very patchily distributed across eukaryotes and bacteria adapted to hypoxia. Phylogenetic analyses suggest lateral gene transfer (LGT) of rquA from bacteria to eukaryotes occurred at least twice and the gene was transferred multiple times amongst protists. We demonstrate that RquA functions in the mitochondrion-related organelles of the anaerobic protist Pygsuia and is correlated with the presence of RQ. These analyses reveal the role of gene transfer in the evolutionary remodeling of mitochondria in adaptation to hypoxia.}, } @article {pmid29651978, year = {2018}, author = {Vigliotti, C and Bicep, C and Bapteste, E and Lopez, P and Corel, E}, title = {Tracking the Rules of Transmission and Introgression with Networks.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.MTBP-0008-2016}, pmid = {29651978}, issn = {2165-0497}, abstract = {Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs. One interest of these networks is that they can consider a rich diversity of important players in microbial evolution that are usually excluded from evolutionary studies, like plasmids and viruses. These methods bring forward the notion of "gene externalization," which is defined as the presence of redundant copies of prokaryotic genes on mobile genetic elements (MGEs), and therefore emphasizes a related although distinct process from lateral gene transfer between microbial cells. This chapter introduces guidelines to the construction of these networks, reviews their analysis, and illustrates their possible biological interpretations and uses. The application to human gut microbiomes shows that sequences present in a higher diversity of MGEs have both biased functions and a broader microbial and human host range. These results suggest that an "externalized gut metagenome" is partly common to humans and benefits the gut microbial community. We conclude that testing relationships between microbial genes, microbes, and their animal hosts, using network-based methods, could help to unravel additional mechanisms of transmission in holobionts.}, } @article {pmid29630596, year = {2018}, author = {Druzhinina, IS and Chenthamara, K and Zhang, J and Atanasova, L and Yang, D and Miao, Y and Rahimi, MJ and Grujic, M and Cai, F and Pourmehdi, S and Salim, KA and Pretzer, C and Kopchinskiy, AG and Henrissat, B and Kuo, A and Hundley, H and Wang, M and Aerts, A and Salamov, A and Lipzen, A and LaButti, K and Barry, K and Grigoriev, IV and Shen, Q and Kubicek, CP}, title = {Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.}, journal = {PLoS genetics}, volume = {14}, number = {4}, pages = {e1007322}, doi = {10.1371/journal.pgen.1007322}, pmid = {29630596}, issn = {1553-7404}, mesh = {Basidiomycota/classification/enzymology/genetics ; Cell Wall/*metabolism/microbiology ; Fungal Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Glycoside Hydrolases/genetics/metabolism ; Host-Pathogen Interactions ; Hyphae/enzymology/genetics/ultrastructure ; Hypocreales/classification/enzymology/genetics ; Microscopy, Electron, Scanning ; Phylogeny ; Plants/*metabolism/microbiology ; Trichoderma/enzymology/*genetics/physiology ; }, abstract = {Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.}, } @article {pmid29628918, year = {2018}, author = {Shen, Y and Cai, J and Davies, MR and Zhang, C and Gao, K and Qiao, D and Jiang, H and Yao, W and Li, Y and Zeng, M and Chen, M}, title = {Identification and Characterization of Fluoroquinolone Non-susceptible Streptococcus pyogenes Clones Harboring Tetracycline and Macrolide Resistance in Shanghai, China.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {542}, doi = {10.3389/fmicb.2018.00542}, pmid = {29628918}, issn = {1664-302X}, abstract = {Streptococcus pyogenes, also known as group A Streptococcus (GAS), is one of the top 10 infectious causes of death worldwide. Macrolide and tetracycline resistant GAS has emerged as a major health concern in China coinciding with an ongoing scarlet fever epidemic. Furthermore, increasing rates of fluoroquinolone (FQ) non-susceptibility within GAS from geographical regions outside of China has also been reported. Fluoroquinolones are the third most commonly prescribed antibiotic in China and is an therapeutic alternative for multi-drug resistant GAS. The purpose of this study was to investigate the epidemiological and molecular features of GAS fluoroquinolone (FQ) non-susceptibility in Shanghai, China. GAS (n = 2,258) recovered between 2011 and 2016 from children and adults were tested for FQ-non-susceptibility. Efflux phenotype and mutations in parC, parE, gyrA, and gyrB were investigated and genetic relationships were determined by emm typing, pulsed-field gel electrophoresis and phylogenetic analysis. The frequency of GAS FQ-non-susceptibility was 1.3% (30/2,258), with the phenotype more prevalent in GAS isolated from adults (14.3%) than from children (1.2%). Eighty percent (24/30) of FQ-non-susceptible isolates were also resistant to both macrolides (ermB) and tetracycline (tetM) including the GAS sequence types emm12, emm6, emm11, and emm1. Genomic fingerprinting analysis of the 30 isolates revealed that non-susceptibility may arise in various genetic backgrounds even within a single emm type. No efflux phenotype was observed in FQ non-susceptible isolates, and molecular analysis of the quinolone resistance-determining regions (QRDRs) identified several sequence polymorphisms in ParC and ParE, and none in GyrA and GyrB. Expansion of this analysis to 152 publically available GAS whole genome sequences from Hong Kong predicted 7.9% (12/152) of Hong Kong isolates harbored a S79F ParC mutation, of which 66.7% (8/12) were macrolide and tetracycline resistant. Phylogenetic analysis of the parC QRDR sequences suggested the possibility that FQ resistance may be acquired through inter-species lateral gene transfer. This study reports the emergence of macrolide, tetracycline, and fluoroquinolone multidrug-resistant clones across several GAS emm types including emm1 and emm12, warranting continual surveillance given the extensive use of fluoroquinolones in clinical use.}, } @article {pmid29625982, year = {2018}, author = {Westbye, AB and Kater, L and Wiesmann, C and Ding, H and Yip, CK and Beatty, JT}, title = {The Protease ClpXP and the PAS Domain Protein DivL Regulate CtrA and Gene Transfer Agent Production in Rhodobacter capsulatus.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, doi = {10.1128/AEM.00275-18}, pmid = {29625982}, issn = {1098-5336}, abstract = {Several members of the Rhodobacterales (Alphaproteobacteria) produce a conserved horizontal gene transfer vector, called the gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system used to study GTA biology is the Rhodobacter capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls the production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that dysregulation of the CckA-ChpT-CtrA phosphorelay either by the loss of the PAS domain protein DivL or by substitution of the autophosphorylation residue of the hybrid histidine kinase CckA decreased CtrA phosphorylation and greatly increased RcGTA protein production in R. capsulatus We show that the loss of the ClpXP protease or the three C-terminal residues of CtrA results in increased CtrA levels in R. capsulatus and identify ClpX(P) to be essential for the maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in the RhodobacteralesIMPORTANCE Members of the Rhodobacterales are abundant in ocean and freshwater environments. The conserved GTA produced by many Rhodobacterales may have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay; however, several questions about GTA regulation remain. Our identification that a short DivL homologue and ClpXP regulate CtrA in R. capsulatus extends the model of CtrA regulation from Caulobacter crescentus to a member of the Rhodobacterales We found that the magnitude of RcGTA production greatly depends on DivL and CckA kinase activity, adding yet another layer of regulatory complexity to RcGTA. RcGTA is known to undergo CckA-dependent maturation, and we extend the understanding of this process by showing that the ClpX chaperone is required for formation of tailed, DNA-containing particles.}, } @article {pmid29558455, year = {2018}, author = {Shalev, Y and Soucy, SM and Papke, RT and Gogarten, JP and Eichler, J and Gophna, U}, title = {Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.}, journal = {Genes}, volume = {9}, number = {3}, pages = {}, doi = {10.3390/genes9030172}, pmid = {29558455}, issn = {2073-4425}, abstract = {Within the Haloferax genus, both the surface (S)-layer protein, and the glycans that can decorate it, vary between species, which can potentially result in many different surface types, analogous to bacterial serotypes. This variation may mediate phenotypes, such as sensitivity to different viruses and mating preferences. Here, we describe S-layer glycoproteins found in multiple Haloferax strains and perform comparative genomics analyses of major and alternative glycosylation clusters of isolates from two coastal sites. We analyze the phylogeny of individual glycosylation genes and demonstrate that while the major glycosylation cluster tends to be conserved among closely related strains, the alternative cluster is highly variable. Thus, geographically- and genetically-related strains may exhibit diverse surface structures to such an extent that no two isolates present an identical surface profile.}, } @article {pmid29543982, year = {2018}, author = {Leger, MM and Eme, L and Stairs, CW and Roger, AJ}, title = {Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115).}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {5}, pages = {e1700242}, doi = {10.1002/bies.201700242}, pmid = {29543982}, issn = {1521-1878}, abstract = {In a recent BioEssays paper [W. F. Martin, BioEssays 2017, 39, 1700115], William Martin sharply criticizes evolutionary interpretations that involve lateral gene transfer (LGT) into eukaryotic genomes. Most published examples of LGTs in eukaryotes, he suggests, are in fact contaminants, ancestral genes that have been lost from other extant lineages, or the result of artefactual phylogenetic inferences. Martin argues that, except for transfers that occurred from endosymbiotic organelles, eukaryote LGT is insignificant. Here, in reviewing this field, we seek to correct some of the misconceptions presented therein with regard to the evidence for LGT in eukaryotes.}, } @article {pmid29515543, year = {2018}, author = {Ward, LM and Hemp, J and Shih, PM and McGlynn, SE and Fischer, WW}, title = {Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {260}, doi = {10.3389/fmicb.2018.00260}, pmid = {29515543}, issn = {1664-302X}, abstract = {The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.}, } @article {pmid29440578, year = {2018}, author = {Watson, BNJ and Staals, RHJ and Fineran, PC}, title = {CRISPR-Cas-Mediated Phage Resistance Enhances Horizontal Gene Transfer by Transduction.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, doi = {10.1128/mBio.02406-17}, pmid = {29440578}, issn = {2150-7511}, abstract = {A powerful contributor to prokaryotic evolution is horizontal gene transfer (HGT) through transformation, conjugation, and transduction, which can be advantageous, neutral, or detrimental to fitness. Bacteria and archaea control HGT and phage infection through CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immunity. Although the benefits of resisting phage infection are evident, this can come at a cost of inhibiting the acquisition of other beneficial genes through HGT. Despite the ability of CRISPR-Cas to limit HGT through conjugation and transformation, its role in transduction is largely overlooked. Transduction is the phage-mediated transfer of bacterial DNA between cells and arguably has the greatest impact on HGT. We demonstrate that in Pectobacterium atrosepticum, CRISPR-Cas can inhibit the transduction of plasmids and chromosomal loci. In addition, we detected phage-mediated transfer of a large plant pathogenicity genomic island and show that CRISPR-Cas can inhibit its transduction. Despite these inhibitory effects of CRISPR-Cas on transduction, its more common role in phage resistance promotes rather than diminishes HGT via transduction by protecting bacteria from phage infection. This protective effect can also increase transduction of phage-sensitive members of mixed populations. CRISPR-Cas systems themselves display evidence of HGT, but little is known about their lateral dissemination between bacteria and whether transduction can contribute. We show that, through transduction, bacteria can acquire an entire chromosomal CRISPR-Cas system, including cas genes and phage-targeting spacers. We propose that the positive effect of CRISPR-Cas phage immunity on enhancing transduction surpasses the rarer cases where gene flow by transduction is restricted.IMPORTANCE The generation of genetic diversity through acquisition of DNA is a powerful contributor to microbial evolution and occurs through transformation, conjugation, and transduction. Of these, transduction, the phage-mediated transfer of bacterial DNA, is arguably the major route for genetic exchange. CRISPR-Cas adaptive immune systems control gene transfer by conjugation and transformation, but transduction has been mostly overlooked. Our results indicate that CRISPR-Cas can impede, but typically enhances the transduction of plasmids, chromosomal genes, and pathogenicity islands. By limiting wild-type phage replication, CRISPR-Cas immunity increases transduction in both phage-resistant and -sensitive members of mixed populations. Furthermore, we demonstrate mobilization of a chromosomal CRISPR-Cas system containing phage-targeting spacers by generalized transduction, which might partly account for the uneven distribution of these systems in nature. Overall, the ability of CRISPR-Cas to promote transduction reveals an unexpected impact of adaptive immunity on horizontal gene transfer, with broader implications for microbial evolution.}, } @article {pmid29428427, year = {2018}, author = {Poey, ME and Laviña, M}, title = {Horizontal transfer of class 1 integrons from uropathogenic Escherichia coli to E. coli K12.}, journal = {Microbial pathogenesis}, volume = {117}, number = {}, pages = {16-22}, doi = {10.1016/j.micpath.2018.02.006}, pmid = {29428427}, issn = {1096-1208}, abstract = {Class 1 integrons are genetic elements that carry a variable set of antibiotic resistance genes, being frequently found in clinical Gram-negative isolates. It is generally assumed that they easily spread horizontally among bacteria, thus contributing to the appearance of multidrug resistant clones. However, there are few experimental studies on the lateral transfer of these elements performed with bacterial collections that had been gathered following an epidemiological design. In this work, a collection with these characteristics, comprising uropathogenic Escherichia coli (UPEC) isolates bearing class 1 integrons, was employed to study the horizontal transfer of the integron to an E. coli K12 strain by means of conjugation and transduction experiments. Donor and resultant strains were characterized for their antibiotic resistances, presence of sul1, sul2 and sul3 genes, integron cassette arrays, plasmid replicons and tra region. Conjugation assays were carried out using 45 UPEC isolates as integron donors and transconjugants were obtained in 18 cases (40%). P1-transduction experiments only added the integron transfer from a single donor isolate. Thus, a collection of E. coli K12 strains carrying the class 1 integron from 19 UPEC isolates was generated. In all cases, the integron was co-transferred with at least one low-copy-number plasmid, generally of the F replicon type. Several variables were searched for that could be related to the ability to horizontally transfer the integron. Although no strict correlation was observed, the phylogenetic background of the donor strain and the presence of the sul2 gene appeared as candidates to influence the process. Therefore, there appears that besides being carried by mobile genetic elements, class 1 integrons may be influenced by other factors to accomplish their horizontal transfer, a topic that requires further studies.}, } @article {pmid29346651, year = {2018}, author = {Corel, E and Méheust, R and Watson, AK and McInerney, JO and Lopez, P and Bapteste, E}, title = {Bipartite Network Analysis of Gene Sharings in the Microbial World.}, journal = {Molecular biology and evolution}, volume = {35}, number = {4}, pages = {899-913}, doi = {10.1093/molbev/msy001}, pmid = {29346651}, issn = {1537-1719}, abstract = {Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of "gene externalization," affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.}, } @article {pmid29301977, year = {2018}, author = {Dunning Hotopp, JC and Klasson, L}, title = {The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {1}, pages = {373-374}, doi = {10.1534/g3.117.300164}, pmid = {29301977}, issn = {2160-1836}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; }, abstract = {In "Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element," Leung et al. (2017) improved contigs attributed to the Muller F element from the original CAF1 assembly, and used them to conclude that most of the sequence expansion of the fourth chromosome of D. ananassae is due to a higher transposon load than previously thought, but is not due to Wolbachia DNA integrations. While we do not disagree with the first conclusion, the authors base their second conclusion on the lack of homology detected between their improved CAF1 genome assembly attributed to D. ananassae and reference Wolbachia genomes. While the consensus CAF1 genome assembly lacks any sequence similarity to the reference genome of the Wolbachia endosymbiont of Drosophila melanogaster (wMel), numerous studies from multiple laboratories provide experimental support for a large lateral/horizontal gene transfer (LGT) of a Wolbachia genome into this D. ananassae line. As such, we strongly suspect that the original whole genome assembly was either constructed after the removal of all Wolbachia reads, or that Wolbachia sequences were directly removed from the contigs in the CAF1 assembly. Hence, Leung et al. (2017) could not have identified the Wolbachia LGT using the CAF1 assembly. This manuscript by Leung et al. (2017) highlights that an assembly of the Wolbachia sequence reads and their mate pairs was erroneously attributed solely to the Wolbachia endosymbiont, albeit before we understood the extent of LGT in D. ananassae As such, we recommend that the sequences deposited at the National Center for Biotechnology Information (NCBI) under PRJNA13365 should not be attributed to Wolbachia endosymbiont of D. ananassae, but should have their taxonomy reclassified by NCBI as "Unclassified sequences." As our knowledge about genome biology improves, we need to reconsider and reanalyze earlier genomes removing the prejudice introduced from now defunct paradigms.}, } @article {pmid29277876, year = {2018}, author = {Rödelsperger, C}, title = {Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {419-432}, doi = {10.1007/978-1-4939-7463-4_16}, pmid = {29277876}, issn = {1940-6029}, abstract = {Nematodes, such as Caenorhabditis elegans, form one of the most species-rich animal phyla. By now more than 30 nematode genomes have been published allowing for comparative genomic analyses at various different time-scales. The majority of a nematode's gene repertoire is represented by either duplicated or so-called orphan genes of unknown origin. This indicates the importance of mechanisms that generate new genes during the course of evolution. While it is certain that nematodes have acquired genes by horizontal gene transfer from various donors, this process only explains a small portion of the nematode gene content. As evolutionary genomic analyses strongly support that most orphan genes are indeed protein-coding, future studies will have to decide, whether they are result from extreme divergence or evolved de novo from previously noncoding sequences. In this contribution, I summarize several studies investigating gene loss and gain in nematodes and discuss the strengths and weaknesses of individual approaches and datasets. These approaches can be used to ask nematode-specific questions such as associated with the evolution of parasitism or with switches in mating systems, but also can complement studies in other animal phyla like vertebrates and insects to broaden our general view on genome evolution.}, } @article {pmid29272410, year = {2018}, author = {Brito, PH and Chevreux, B and Serra, CR and Schyns, G and Henriques, AO and Pereira-Leal, JB}, title = {Genetic Competence Drives Genome Diversity in Bacillus subtilis.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {108-124}, doi = {10.1093/gbe/evx270}, pmid = {29272410}, issn = {1759-6653}, abstract = {Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them.}, } @article {pmid29240843, year = {2017}, author = {Dan, H and Ikeda, N and Fujikami, M and Nakabachi, A}, title = {Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189779}, doi = {10.1371/journal.pone.0189779}, pmid = {29240843}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*pathogenicity ; Animals ; Bacterial Infections/*microbiology ; Citrus/*parasitology ; Female ; Hemiptera/*microbiology/physiology ; Host-Parasite Interactions ; Host-Pathogen Interactions ; *Insect Vectors ; Ovary/*microbiology ; Plant Diseases/*microbiology ; }, abstract = {The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Liviidae) is a serious pest worldwide, transmitting Candidatus Liberibacter spp. (Alphaproteobacteria), the causative agents of a devastating citrus disease known as huanglongbing or greening disease. In a symbiotic organ called the bacteriome, D. citri possesses an organelle-like defensive symbiont, Candidatus Profftella armatura (Betaproteobacteria), and a nutritional symbiont, Ca. Carsonella ruddii (Gammaproteobacteria). Drastically reduced symbiont genomes and metabolic complementarity among the symbionts and D. citri indicate their mutually indispensable association. Moreover, horizontal gene transfer between the Profftella and Liberibacter lineages suggests ecological and evolutionary interactions between the bacteriome symbiont and the HLB pathogen. Using fluorescence in situ hybridization, we examined the behavior of Profftella and Carsonella during transovarial transmission and the development of D. citri. In the bacteriomes of sexually-mature female adults, symbionts transformed from an extremely elongated tubular form into spherical or short-rod forms, which migrated toward the ovary. The symbionts then formed mosaic masses, which entered at the posterior pole of the vitellogenic oocytes. After anatrepsis, Carsonella and Profftella migrated to the central and peripheral parts of the mass, respectively. Following the appearance of host nuclei, the mass cellularized, segregating Carsonella and Profftella in the central syncytium and peripheral uninucleate bacteriocytes, respectively. Subsequently, the uninucleate bacteriocytes harboring Profftella assembled at the posterior pole, while the syncytium, containing Carsonella, sat on the anterior side facing the germ band initiating katatrepsis. During dorsal closure, the syncytium was divided into uninuclear bacteriocytes, which surrounded the mass of bacteriocytes containing Profftella. Once fully surrounded, the bacteriocyte mass containing Profftella was fused into a syncytium. Prior to hatching, a pair of wing-like protrusions arose from both lateral sides of the bacteriome, which continued to grow throughout the nymphal stages. These findings provide a foundation for better understanding the intricate relationship between D. citri and its microbiota.}, } @article {pmid29202688, year = {2017}, author = {Abrahamian, M and Kagda, M and Ah-Fong, AMV and Judelson, HS}, title = {Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {241}, doi = {10.1186/s12862-017-1087-8}, pmid = {29202688}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Cytosol ; Eukaryotic Cells/*metabolism ; Genes ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Oomycetes/metabolism ; Phosphorylation ; Phylogeny ; Phytophthora infestans/metabolism ; Serine/*biosynthesis ; Stramenopiles/*enzymology/*metabolism ; }, abstract = {BACKGROUND: An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides.

RESULTS: Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin.

CONCLUSIONS: Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology.}, } @article {pmid29177480, year = {2017}, author = {Wang, Z and Wu, M}, title = {Comparative Genomic Analysis of Acanthamoeba Endosymbionts Highlights the Role of Amoebae as a "Melting Pot" Shaping the Rickettsiales Evolution.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3214-3224}, doi = {10.1093/gbe/evx246}, pmid = {29177480}, issn = {1759-6653}, mesh = {Acanthamoeba/*microbiology/physiology ; Alphaproteobacteria/classification/*genetics/physiology ; Biological Evolution ; Gene Transfer, Horizontal ; Phylogeny ; Symbiosis ; }, abstract = {Amoebae have been considered as a genetic "melting pot" for its symbionts, facilitating genetic exchanges of the bacteria that co-inhabit the same host. To test the "melting pot" hypothesis, we analyzed six genomes of amoeba endosymbionts within Rickettsiales, four of which belong to Holosporaceae family and two to Candidatus Midichloriaceae. For the first time, we identified plasmids in obligate amoeba endosymbionts, which suggests conjugation as a potential mechanism for lateral gene transfers (LGTs) that underpin the "melting pot" hypothesis. We found strong evidence of recent LGTs between the Rickettsiales amoeba endosymbionts, suggesting that the LGTs are continuous and ongoing. In addition, comparative genomic and phylogenomic analyses revealed pervasive and recurrent LGTs between Rickettsiales and distantly related amoeba-associated bacteria throughout the Rickettsiales evolution. Many of these exchanged genes are important for amoeba-symbiont interactions, including genes in transport system, antibiotic resistance, stress response, and bacterial virulence, suggesting that LGTs have played important roles in the adaptation of endosymbionts to their intracellular habitats. Surprisingly, we found little evidence of LGTs between amoebae and their bacterial endosymbionts. Our study strongly supports the "melting pot" hypothesis and highlights the role of amoebae in shaping the Rickettsiales evolution.}, } @article {pmid29142104, year = {2017}, author = {Stubenrauch, CJ and Dougan, G and Lithgow, T and Heinz, E}, title = {Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.}, journal = {Open biology}, volume = {7}, number = {11}, pages = {}, doi = {10.1098/rsob.170144}, pmid = {29142104}, issn = {2046-2441}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Enteropathogenic Escherichia coli/*genetics ; Escherichia coli Proteins/chemistry/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Molecular Chaperones/chemistry/*genetics ; Protein Folding ; }, abstract = {Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC) Escherichia coli, and further focus on a so far undescribed chaperone-usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic E. coli strain worldwide. Deletion of the TAM from a naive strain of E. coli results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms, Yersinia and Enterobacter We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer.}, } @article {pmid29120392, year = {2017}, author = {Drezen, JM and Josse, T and Bézier, A and Gauthier, J and Huguet, E and Herniou, EA}, title = {Impact of Lateral Transfers on the Genomes of Lepidoptera.}, journal = {Genes}, volume = {8}, number = {11}, pages = {}, doi = {10.3390/genes8110315}, pmid = {29120392}, issn = {2073-4425}, abstract = {Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera. Large DNA viruses, such as baculoviruses and the symbiotic viruses of parasitic wasps (bracoviruses), have the potential to mediate these transfers in Lepidoptera. In particular, using ultra-deep sequencing, newly integrated transposons have been identified within baculovirus genomes. Bacterial genes have also been acquired by genomes of Lepidoptera, as in other insects and nematodes. In addition, insertions of bracovirus sequences were present in the genomes of certain moth and butterfly lineages, that were likely corresponding to rearrangements of ancient integrations. The viral genes present in these sequences, sometimes of hymenopteran origin, have been co-opted by lepidopteran species to confer some protection against pathogens.}, } @article {pmid29100762, year = {2017}, author = {Novick, RP and Ram, G}, title = {Staphylococcal pathogenicity islands-movers and shakers in the genomic firmament.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {197-204}, doi = {10.1016/j.mib.2017.08.001}, pmid = {29100762}, issn = {1879-0364}, support = {R01 AI022159/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/physiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; *Interspersed Repetitive Sequences ; Staphylococcus/*genetics/*pathogenicity ; Transduction, Genetic ; Virulence Factors/*genetics/*metabolism ; }, abstract = {The staphylococcal pathogenicity islands (SaPIs) are highly mobile 15kb genomic islands that carry superantigen genes and other virulence factors and are mobilized by helper phages. Helper phages counteract the SaPI repressor to induce the SaPI replication cycle, resulting in encapsidation in phage like particles, enabling high frequency transfer. The SaPIs split from a protophage lineage in the distant past, have evolved a variety of novel and salient features, and have become an invaluable component of the staphylococcal genome. This review focuses on recent studies describing three different mechanisms of SaPI interference with helper phage reproduction and other studies demonstrating that helper phage mutations to resistance against this interference impact phage evolution. Also described are recent results showing that SaPIs contribute in a major way to lateral transfer of host genes as well as enabling their own transfer. SaPI-like elements, readily identifiable in the bacterial genome, are widespread throughout the Gram-positive cocci, though functionality has thus far been demonstrated for only a single one of these.}, } @article {pmid29080779, year = {2018}, author = {Steel, M and Kauffman, S}, title = {A note on random catalytic branching processes.}, journal = {Journal of theoretical biology}, volume = {437}, number = {}, pages = {222-224}, doi = {10.1016/j.jtbi.2017.10.024}, pmid = {29080779}, issn = {1095-8541}, mesh = {*Algorithms ; Artificial Cells/*metabolism ; Computer Simulation ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Markov Chains ; *Models, Genetic ; Origin of Life ; Prokaryotic Cells/*metabolism ; }, abstract = {A variety of evolutionary processes in biology can be viewed as settings where organisms 'catalyse' the formation of new types of organisms. One example, relevant to the origin of life, is where transient biological colonies (e.g. prokaryotes or protocells) give rise to new colonies via lateral gene transfer. In this short note, we describe and analyse a simple random process which models such settings. By applying theory from general birth-death processes, we describe how the survival of a population under catalytic diversification depends on interplay of the catalysis rate and the initial population size. We also note how such process can also be viewed within the framework of 'self-sustaining autocatalytic networks'.}, } @article {pmid29068466, year = {2017}, author = {Martin, WF}, title = {Too Much Eukaryote LGT.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700115}, pmid = {29068466}, issn = {1521-1878}, mesh = {Animals ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Mitochondria/genetics ; Phylogeny ; Plants/classification/genetics ; Plastids/genetics ; Prokaryotic Cells/cytology/metabolism ; Symbiosis/*genetics ; }, abstract = {The realization that prokaryotes naturally and frequently disperse genes across steep taxonomic boundaries via lateral gene transfer (LGT) gave wings to the idea that eukaryotes might do the same. Eukaryotes do acquire genes from mitochondria and plastids and they do transfer genes during the process of secondary endosymbiosis, the spread of plastids via eukaryotic algal endosymbionts. From those observations it, however, does not follow that eukaryotes transfer genes either in the same ways as prokaryotes do, or to a quantitatively similar degree. An important illustration of the difference is that eukaryotes do not exhibit pangenomes, though prokaryotes do. Eukaryotes reveal no detectable cumulative effects of LGT, though prokaryotes do. A critical analysis suggests that something is deeply amiss with eukaryote LGT theories.}, } @article {pmid29061896, year = {2017}, author = {Hall, JPJ and Brockhurst, MA and Harrison, E}, title = {Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1735}, pages = {}, doi = {10.1098/rstb.2016.0424}, pmid = {29061896}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.}, } @article {pmid29052138, year = {2017}, author = {Zhu, C and Wang, Y and Cai, C and Cai, Q}, title = {Bacterial Infection and Associated Cancers.}, journal = {Advances in experimental medicine and biology}, volume = {1018}, number = {}, pages = {181-191}, doi = {10.1007/978-981-10-5765-6_11}, pmid = {29052138}, issn = {0065-2598}, mesh = {Bacterial Infections/complications/epidemiology/*microbiology ; Biofilms/growth & development ; Carcinogenesis/*genetics ; Gene Transfer, Horizontal/ethics ; Helicobacter pylori/genetics/*pathogenicity ; Humans ; Microbiota/genetics ; Neoplasms/complications/epidemiology/*microbiology ; }, abstract = {Bacterial infections were traditionally not considered as major causes of cancer. However, increasing evidence in the past decades has suggested that several cancers are highly associated with bacterial infection. The bacterial infections have evolved some unique strategies including lateral gene transfer, biofilm and microbiome to induce genome instability and chronic inflammation, as well as escape of immune surveillance for carcinogenesis. Here we summarize and highlight the recent progress on understanding of how bacterial infection plays a role in tumor formation and malignancy.}, } @article {pmid28961181, year = {2017}, author = {Rancurel, C and Legrand, L and Danchin, EGJ}, title = {Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, doi = {10.3390/genes8100248}, pmid = {28961181}, issn = {2073-4425}, abstract = {Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.}, } @article {pmid28827361, year = {2017}, author = {Monier, A and Chambouvet, A and Milner, DS and Attah, V and Terrado, R and Lovejoy, C and Moreau, H and Santoro, AE and Derelle, É and Richards, TA}, title = {Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {E7489-E7498}, doi = {10.1073/pnas.1708097114}, pmid = {28827361}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; WT105618MA//Wellcome Trust/United Kingdom ; }, mesh = {Cell Membrane/virology ; Chlorophyta/virology ; Gene Transfer, Horizontal/*genetics ; Genes, Viral/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions/*genetics ; Nitrogen/*metabolism ; Phytoplankton/*virology ; Viral Proteins/*metabolism ; }, abstract = {Phytoplankton community structure is shaped by both bottom-up factors, such as nutrient availability, and top-down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.}, } @article {pmid28731472, year = {2017}, author = {Vigil-Stenman, T and Ininbergs, K and Bergman, B and Ekman, M}, title = {High abundance and expression of transposases in bacteria from the Baltic Sea.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2611-2623}, doi = {10.1038/ismej.2017.114}, pmid = {28731472}, issn = {1751-7370}, mesh = {Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Baltic States ; Gene Transfer, Horizontal ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/*microbiology ; Transposases/*genetics/metabolism ; }, abstract = {Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.}, } @article {pmid27703668, year = {2016}, author = {Koehorst, JJ and Saccenti, E and Schaap, PJ and Martins Dos Santos, VAP and Suarez-Diez, M}, title = {Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {1987}, doi = {10.12688/f1000research.9416.3}, pmid = {27703668}, issn = {2046-1402}, abstract = {A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic boundaries, and it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness.}, } @article {pmid28689895, year = {2017}, author = {Kim, JS and Kim, S and Park, J and Shin, E and Yun, YS and Lee, DY and Kwak, HS and Seong, WK and Chung, GT and Kim, J}, title = {Plasmid-mediated transfer of CTX-M-55 extended-spectrum beta-lactamase among different strains of Salmonella and Shigella spp. in the Republic of Korea.}, journal = {Diagnostic microbiology and infectious disease}, volume = {89}, number = {1}, pages = {86-88}, doi = {10.1016/j.diagmicrobio.2017.03.014}, pmid = {28689895}, issn = {1879-0070}, mesh = {Animals ; *Gene Transfer, Horizontal ; Humans ; Plasmids/*analysis/classification ; Republic of Korea ; Salmonella/*enzymology/*genetics/isolation & purification ; Shigella/*enzymology/*genetics/isolation & purification ; beta-Lactamases/*genetics ; }, abstract = {We screened 10 CTX-M-55-producing Shigella and Salmonella isolates from a national surveillance in Korea. The blaCTX-M-55 was located on the IncI1 (n=5), IncA/C (n=4) and IncZ (n=1) plasmids, downstream of ISEcp1, IS26-ISEcp1 and ISEcp1-IS5 sequences, respectively. These results indicate that CTX-M-55 has disseminated to other bacteria by lateral plasmid transfer.}, } @article {pmid28604829, year = {2017}, author = {Kim, BJ and Kim, GN and Kim, BR and Shim, TS and Kook, YH and Kim, BJ}, title = {Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179237}, doi = {10.1371/journal.pone.0179237}, pmid = {28604829}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; DNA-Directed RNA Polymerases/*genetics ; *Gene Transfer, Horizontal ; Humans ; Multilocus Sequence Typing ; Mycobacterium/*classification/*genetics ; *Phylogeny ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M. massiliense Type II genotypes (0%, 0/46), showing a discrepancy between the 2 typing methods. Further MLST analysis based on the partial sequencing of seven housekeeping genes, argH, cya, glpK, gnd, murC, pta and purH, as well as erm(41) PCR proved that these 6 Rec-mas strains consisted of two distinct genotypes belonging to M. massiliense and not M. abscessus. The complete rpoB sequencing analysis showed that these 6 Rec-mas strains have an identical hybrid rpoB gene, of which a 478 bp partial rpoB fragment may be laterally transferred from M. abscessus. Notably, five of the 6 Rec-mas strains showed complete identical sequences in a total of nine genes, including the seven MLST genes, hsp65, and rpoB, suggesting their clonal propagation in South Korea. In conclusion, we identified 6 M. massiliense smooth strains of 2 phylogenetically distinct genotypes with a specific hybrid rpoB gene laterally transferred from M. abscessus from Korean patients. Their clinical relevance and bacteriological traits remain to be elucidated.}, } @article {pmid28588130, year = {2017}, author = {McDonald, BR and Currie, CR}, title = {Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces.}, journal = {mBio}, volume = {8}, number = {3}, pages = {}, doi = {10.1128/mBio.00644-17}, pmid = {28588130}, issn = {2150-7511}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/biosynthesis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Point Mutation ; Streptomyces/*genetics/metabolism ; }, abstract = {Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces, with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.}, } @article {pmid28578314, year = {2017}, author = {Mina, JG and Thye, JK and Alqaisi, AQI and Bird, LE and Dods, RH and Grøftehauge, MK and Mosely, JA and Pratt, S and Shams-Eldin, H and Schwarz, RT and Pohl, E and Denny, PW}, title = {Functional and phylogenetic evidence of a bacterial origin for the first enzyme in sphingolipid biosynthesis in a phylum of eukaryotic protozoan parasites.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {29}, pages = {12208-12219}, doi = {10.1074/jbc.M117.792374}, pmid = {28578314}, issn = {1083-351X}, support = {MR/K018779/1//Medical Research Council/United Kingdom ; BB/D52396X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M024156/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Catalytic Domain ; Computational Biology ; Conserved Sequence ; Dimerization ; Endoplasmic Reticulum/*enzymology ; Gene Deletion ; Gene Duplication ; Gene Transfer, Horizontal ; Isoenzymes/chemistry/genetics/isolation & purification/metabolism ; *Models, Molecular ; Peptide Fragments/chemistry/genetics/metabolism ; *Phylogeny ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Transport ; Protozoan Proteins/chemistry/genetics/isolation & purification/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Sequence Alignment ; Serine C-Palmitoyltransferase/chemistry/genetics/isolation & purification/*metabolism ; Structural Homology, Protein ; Toxoplasma/*enzymology ; }, abstract = {Toxoplasma gondii is an obligate, intracellular eukaryotic apicomplexan protozoan parasite that can cause fetal damage and abortion in both animals and humans. Sphingolipids are essential and ubiquitous components of eukaryotic membranes that are both synthesized and scavenged by the Apicomplexa. Here we report the identification, isolation, and analyses of the Toxoplasma serine palmitoyltransferase, an enzyme catalyzing the first and rate-limiting step in sphingolipid biosynthesis: the condensation of serine and palmitoyl-CoA. In all eukaryotes analyzed to date, serine palmitoyltransferase is a highly conserved heterodimeric enzyme complex. However, biochemical and structural analyses demonstrated the apicomplexan orthologue to be a functional, homodimeric serine palmitoyltransferase localized to the endoplasmic reticulum. Furthermore, phylogenetic studies indicated that it was evolutionarily related to the prokaryotic serine palmitoyltransferase, identified in the Sphingomonadaceae as a soluble homodimeric enzyme. Therefore this enzyme, conserved throughout the Apicomplexa, is likely to have been obtained via lateral gene transfer from a prokaryote.}, } @article {pmid28570771, year = {2017}, author = {Gavelis, GS and Keeling, PJ and Leander, BS}, title = {How exaptations facilitated photosensory evolution: Seeing the light by accident.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {7}, pages = {}, doi = {10.1002/bies.201600266}, pmid = {28570771}, issn = {1521-1878}, mesh = {Adaptation, Physiological/physiology ; Animals ; Eukaryota/physiology ; Evolution, Molecular ; Gene Transfer, Horizontal/physiology ; Humans ; Light ; Organelles/physiology ; Photoreceptor Cells/*physiology ; Symbiosis/physiology ; Vision, Ocular/*physiology ; }, abstract = {Exaptations are adaptations that have undergone a major change in function. By recruiting genes from sources originally unrelated to vision, exaptation has allowed for sudden and critical photosensory innovations, such as lenses, photopigments, and photoreceptors. Here we review new or neglected findings, with an emphasis on unicellular eukaryotes (protists), to illustrate how exaptation has shaped photoreception across the tree of life. Protist phylogeny attests to multiple origins of photoreception, as well as the extreme creativity of evolution. By appropriating genes and even entire organelles from foreign organisms via lateral gene transfer and endosymbiosis, protists have cobbled photoreceptors and eyespots from a diverse set of ingredients. While refinement through natural selection is paramount, exaptation helps illustrate how novelties arise in the first place, and is now shedding light on the origins of photoreception itself.}, } @article {pmid28550453, year = {2017}, author = {Weiss, RA}, title = {Exchange of Genetic Sequences Between Viruses and Hosts.}, journal = {Current topics in microbiology and immunology}, volume = {407}, number = {}, pages = {1-29}, doi = {10.1007/82_2017_21}, pmid = {28550453}, issn = {0070-217X}, abstract = {Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.}, } @article {pmid28540258, year = {2017}, author = {Moses, AS and Millar, JA and Bonazzi, M and Beare, PA and Raghavan, R}, title = {Horizontally Acquired Biosynthesis Genes Boost Coxiella burnetii's Physiology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {174}, doi = {10.3389/fcimb.2017.00174}, pmid = {28540258}, issn = {2235-2988}, support = {R03 AI123464/AI/NIAID NIH HHS/United States ; R15 AI126385/AI/NIAID NIH HHS/United States ; }, mesh = {Biotin/*biosynthesis/genetics ; Coxiella burnetii/*genetics/growth & development/*metabolism ; Fatty Acids/biosynthesis/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Glutamic Acid/biosynthesis/genetics ; Heme/biosynthesis/genetics ; Lipopolysaccharides/biosynthesis/genetics ; Metabolic Networks and Pathways/genetics ; RNA, Ribosomal, 16S/classification/genetics ; Viral Proteins/genetics ; }, abstract = {Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C. burnetii are different from that of Coxiella-like bacteria found in ticks. Horizontally acquired genes that allow C. burnetii to infect and grow within mammalian cells likely facilitated the host shift; however, because of its obligate intracellular replication, C. burnetii would have lost most genes that have been rendered redundant due to the availability of metabolites within the host cell. Based on these observations, we reasoned that horizontally derived biosynthetic genes that have been retained in the reduced genome of C. burnetii are ideal candidates to begin to uncover its intracellular metabolic requirements. Our analyses identified a large number of putative foreign-origin genes in C. burnetii, including tRNAGlu2 that is potentially required for heme biosynthesis, and genes involved in the production of lipopolysaccharide-a virulence factor, and of critical metabolites such as fatty acids and biotin. In comparison to wild-type C. burnetii, a strain that lacks tRNAGlu2 exhibited reduced growth, indicating its importance to Coxiella's physiology. Additionally, by using chemical agents that block heme and biotin biosyntheses, we show that these pathways are promising targets for the development of new anti-Coxiella therapies.}, } @article {pmid28511421, year = {2017}, author = {Mandal, SK and Mandal, A and Fleming, JC and Goecks, T and Meador, A and Fowler, BT}, title = {Surgical Outcome of Epicanthus and Telecanthus Correction by Double Z-Plasty and Trans-Nasal Fixation with Prolene Suture in Blepharophimosis Syndrome.}, journal = {Journal of clinical and diagnostic research : JCDR}, volume = {11}, number = {3}, pages = {NC05-NC08}, doi = {10.7860/JCDR/2017/25651.9496}, pmid = {28511421}, issn = {2249-782X}, abstract = {INTRODUCTION: Blepharophimosis Syndrome (BPES) is a complex and rare disease characterized by epicanthus inversus, telecanthus, lateral ectropion, narrowed or shortened inter-palpebral fissure distance and ptosis. It is mostly bilateral and may or may not be symmetrical. It is typically inherited as an autosomal dominant trait. In sporadic cases, the disease may occur without a prior family history as a genetic mutation from a deletion or translocation of the FOXL2 gene, which maps to chromosome 3q23. Surgical treatment of this disease poses an oculoplastic challenge due to multiple complex eyelid deformities.

AIM: To evaluate the functional and cosmetic outcome of telecanthus and epicanthus correction by a Mustarde's rectangular double Z-Plasty and trans-nasal fixation using 1-0 prolene suture in BPES.

MATERIALS AND METHODS: This was prospective, interventional study of 16 patients over a period of three years. In this study, all patients had BPES with prominent epicanthus and telecanthus. Mustarde's double Z-plasty and trans-nasal fixation with 1-0 prolene suture was performed in the first of a two-stage operation. If ectropion was present, the lateral ectropion was corrected by a base-out flap transfer from the upper eyelid to the lower eyelid. After three months, a 2nd stage was undertaken, involving a lateral canthoplasty for horizontal widening of a short palpebral fissure and a tarso frontalis sling with silicone rod for correction of moderate to severe ptosis. Patients were followed up for six months to one year with postoperative ophthalmologic examinations and photographs.

RESULTS: Out of 16 patients, 10 were females and six were males. All the patients had bilateral involvement. In this study preoperative Inner Intercanthal Distance (IICD) ranged from 38 mm to 42 mm and the mean IICD was 41.2±0.57 mm. Postoperative IICD ranged from 31 mm to 34 mm. Horizontal Palpebral Fissure Length (HPFL) ranged from 20 mm to 23 mm and the mean value of HPFL was 21.50 mm preoperatively. Postoperative HPFL ranged from 26 mm to 29 mm and had a mean value of 28.50 mm, which was much improved after a combined correction of telecanthus and lateral canthoplasty. The mean preoperative IICD and HPFL ratio was 1.77 and was reduced to a postoperative value of 1.2. The Marginal Reflex Distance1 (MRD-1) test value improved from +1.25 mm to +3.50 mm postoperatively after placement of a tarsofrontalis sling with silicone rod using the Fox's Pentagon technique. In this study, two eyes had minimal unequal correction but were cosmetically and functionally acceptable. Correction of IICD is possible up to 6 mm. No major complication e.g., CSF rhinorrhea was noted in this series and preoperative prominent epicanthal folds were abolished.

CONCLUSION: Here we propose a two-staged procedure involving a combined Mustarde's double Z-plasty with transnasal fixation using a 1-0 prolene suture with a flap transfer from the upper lid to the lower lid in the first stage and a lateral canthoplasty with a tarsofrontalis sling and silicone rod in the second stage. This technique is effective to correct epicanthus, telecanthus, ptosis and lateral ectropion in BPES with good cosmetic and functional outcome.}, } @article {pmid28477267, year = {2017}, author = {Toribio-Fernández, R and Bella, JL and Martínez-Rodríguez, P and Funkhouser-Jones, LJ and Bordenstein, SR and Pita, M}, title = {Chromosomal localization of Wolbachia inserts in the genomes of two subspecies of Chorthippus parallelus forming a Pyrenean hybrid zone.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {25}, number = {3-4}, pages = {215-225}, doi = {10.1007/s10577-017-9557-9}, pmid = {28477267}, issn = {1573-6849}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R21 HD086833/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; *Chromosomes, Bacterial ; *Genome, Insect ; Grasshoppers/*genetics ; Heterochromatin ; *Hybridization, Genetic ; In Situ Hybridization, Fluorescence ; Male ; *Mutagenesis, Insertional ; *Polytene Chromosomes ; Sequence Analysis, DNA ; Wolbachia/*genetics ; }, abstract = {Wolbachia are endosymbiotic bacteria of arthropods and nematodes that can manipulate the reproduction of various host organisms to facilitate their own maternal transmission. Moreover, Wolbachia's presence in host germ cells may contribute to the many cases of lateral gene transfer from Wolbachia to host genomes that have been described. A previous study in Chorthippus parallelus, a well-known orthopteroid forming a hybrid zone in the Pyrenees, identified Wolbachia sequences from two major supergroups in the genomes of infected and uninfected Chorthippus parallelus parallelus (Cpp) and Chorthippus parallelus erythropus (Cpe) subspecies. In this study, we map the Wolbachia genomic inserts to specific regions on the chromosomes of Cpp and Cpe by fluorescent in situ hybridization (FISH) using tyramides to increase the accuracy and detection of these insertions. Additionally, we consider some of the possible roles that these bacterial inserts play in the organization and function of the grasshopper genome, as well as how they can serve as markers for phylogenetic relationships of these organisms.}, } @article {pmid28451760, year = {2017}, author = {Cardona, G and Pons, JC}, title = {Reconstruction of LGT networks from tri-LGT-nets.}, journal = {Journal of mathematical biology}, volume = {75}, number = {6-7}, pages = {1669-1692}, doi = {10.1007/s00285-017-1131-8}, pmid = {28451760}, issn = {1432-1416}, mesh = {Computer Simulation ; Evolution, Molecular ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Mathematical Concepts ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic networks have gained attention from the scientific community due to the evidence of the existence of evolutionary events that cannot be represented using trees. A variant of phylogenetic networks, called LGT networks, models specifically lateral gene transfer events, which cannot be properly represented with generic phylogenetic networks. In this paper we treat the problem of the reconstruction of LGT networks from substructures induced by three leaves, which we call tri-LGT-nets. We first restrict ourselves to a class of LGT networks that are both mathematically treatable and biologically significant, called BAN-LGT networks. Then, we study the decomposition of such networks in subnetworks with three leaves and ask whether or not this decomposition determines the network. The answer to this question is negative, but if we further impose time-consistency (species involved in a later gene transfer must coexist) the answer is affirmative, up to some redundancy that can never be recovered but is fully characterized.}, } @article {pmid28406168, year = {2017}, author = {Zeman, M and Mašlaňová, I and Indráková, A and Šiborová, M and Mikulášek, K and Bendíčková, K and Plevka, P and Vrbovská, V and Zdráhal, Z and Doškař, J and Pantůček, R}, title = {Staphylococcus sciuri bacteriophages double-convert for staphylokinase and phospholipase, mediate interspecies plasmid transduction, and package mecA gene.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46319}, doi = {10.1038/srep46319}, pmid = {28406168}, issn = {2045-2322}, abstract = {Staphylococcus sciuri is a bacterial pathogen associated with infections in animals and humans, and represents a reservoir for the mecA gene encoding methicillin-resistance in staphylococci. No S. sciuri siphophages were known. Here the identification and characterization of two temperate S. sciuri phages from the Siphoviridae family designated ϕ575 and ϕ879 are presented. The phages have icosahedral heads and flexible noncontractile tails that end with a tail spike. The genomes of the phages are 42,160 and 41,448 bp long and encode 58 and 55 ORFs, respectively, arranged in functional modules. Their head-tail morphogenesis modules are similar to those of Staphylococcus aureus ϕ13-like serogroup F phages, suggesting their common evolutionary origin. The genome of phage ϕ575 harbours genes for staphylokinase and phospholipase that might enhance the virulence of the bacterial hosts. In addition both of the phages package a homologue of the mecA gene, which is a requirement for its lateral transfer. Phage ϕ879 transduces tetracycline and aminoglycoside pSTS7-like resistance plasmids from its host to other S. sciuri strains and to S. aureus. Furthermore, both of the phages efficiently adsorb to numerous staphylococcal species, indicating that they may contribute to interspecies horizontal gene transfer.}, } @article {pmid28303404, year = {2017}, author = {Ito, D and Ihara, Y and Nishihara, H and Masuda, S}, title = {Phylogenetic analysis of proteins involved in the stringent response in plant cells.}, journal = {Journal of plant research}, volume = {130}, number = {4}, pages = {625-634}, doi = {10.1007/s10265-017-0922-8}, pmid = {28303404}, issn = {1618-0860}, mesh = {Bacteria/enzymology/*genetics ; Chloroplasts/genetics/physiology ; Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Gene Transfer, Horizontal ; Ligases/genetics ; Phosphoprotein Phosphatases/genetics ; Phylogeny ; Plant Cells/enzymology/physiology ; Plant Proteins/*genetics ; Plants/enzymology/*genetics ; }, abstract = {The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear. Here, we investigated the origin and evolution of genes involved in the stringent response in plants. Phylogenetic analysis and primary structures of RSH homologs from different plant phyla (including Embryophyta, Charophyta, Chlorophyta, Rhodophyta and Glaucophyta) indicate that RSH gene families were introduced into plant cells by at least two independent lateral gene transfers from the bacterial Deinococcus-Thermus phylum and an unidentified bacterial phylum; alternatively, they were introduced into a proto-plant cell by a lateral gene transfer from the endosymbiotic cyanobacterium followed by gene loss of an ancestral RSH gene in the cyanobacterial linage. Phylogenetic analysis of gppA/ppx families indicated that plant gppA/ppx homologs form an individual cluster in the phylogenetic tree, and show a sister relationship with some bacterial gppA/ppx homologs. Although RSHs contain a plastidial transit peptide at the N terminus, GppA/Ppx homologs do not, suggesting that plant GppA/Ppx homologs function in the cytosol. These results reveal that a proto-plant cell obtained genes for the stringent response by lateral gene transfer events from different bacterial phyla and have utilized them to control metabolism in plastids and the cytosol.}, } @article {pmid28235827, year = {2017}, author = {Dupont, PY and Cox, MP}, title = {Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {4}, pages = {1301-1314}, doi = {10.1534/g3.116.038448}, pmid = {28235827}, issn = {2160-1836}, mesh = {Automation ; *Data Accuracy ; Epichloe/*genetics ; *Gene Transfer, Horizontal ; Genes, Fungal ; Genetic Variation ; Genomics/*standards ; Phylogeny ; Species Specificity ; Statistics as Topic ; }, abstract = {Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.}, } @article {pmid28189637, year = {2017}, author = {Sieber, KB and Bromley, RE and Dunning Hotopp, JC}, title = {Lateral gene transfer between prokaryotes and eukaryotes.}, journal = {Experimental cell research}, volume = {358}, number = {2}, pages = {421-426}, doi = {10.1016/j.yexcr.2017.02.009}, pmid = {28189637}, issn = {1090-2422}, support = {DP2 OD007372/OD/NIH HHS/United States ; R01 CA206188/CA/NCI NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; 1-R01-CA206188/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Humans ; Mitochondria/metabolism ; Prokaryotic Cells/*cytology ; }, abstract = {Lateral gene transfer (LGT) is an all-encompassing term for the movement of DNA between diverse organisms. LGT is synonymous with horizontal gene transfer, and the terms are used interchangeably throughout the scientific literature. While LGT has been recognized within the bacteria domain of life for decades, inter-domain LGTs are being increasingly described. LGTs between bacteria and complex multicellular organisms are of interest because they challenge the long-held dogma that such transfers could only occur in closely-related, single-celled organisms. Scientists will continue to challenge our understanding of LGT as we sequence more, diverse organisms, as we sequence more endosymbiont-colonized arthropods, and as we continue to appreciate LGT events, both young and old.}, } @article {pmid28185583, year = {2016}, author = {Khan, MA and Mahmudi, O and Ullah, I and Arvestad, L and Lagergren, J}, title = {Probabilistic inference of lateral gene transfer events.}, journal = {BMC bioinformatics}, volume = {17}, number = {Suppl 14}, pages = {431}, doi = {10.1186/s12859-016-1268-2}, pmid = {28185583}, issn = {1471-2105}, mesh = {Biological Evolution ; Entomoplasmataceae/classification/genetics ; Gene Transfer, Horizontal/*genetics ; *Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge.

RESULTS: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT.

CONCLUSIONS: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.}, } @article {pmid28154557, year = {2017}, author = {Cong, Y and Chan, YB and Phillips, CA and Langston, MA and Ragan, MA}, title = {Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {21}, doi = {10.3389/fmicb.2017.00021}, pmid = {28154557}, issn = {1664-302X}, support = {R01 AA018776/AA/NIAAA NIH HHS/United States ; }, abstract = {Bacteria and archaea can exchange genetic material across lineages through processes of lateral genetic transfer (LGT). Collectively, these exchange relationships can be modeled as a network and analyzed using concepts from graph theory. In particular, densely connected regions within an LGT network have been defined as genetic exchange communities (GECs). However, it has been problematic to construct networks in which edges solely represent LGT. Here we apply term frequency-inverse document frequency (TF-IDF), an alignment-free method originating from document analysis, to infer regions of lateral origin in bacterial genomes. We examine four empirical datasets of different size (number of genomes) and phyletic breadth, varying a key parameter (word length k) within bounds established in previous work. We map the inferred lateral regions to genes in recipient genomes, and construct networks in which the nodes are groups of genomes, and the edges natively represent LGT. We then extract maximum and maximal cliques (i.e., GECs) from these graphs, and identify nodes that belong to GECs across a wide range of k. Most surviving lateral transfer has happened within these GECs. Using Gene Ontology enrichment tests we demonstrate that biological processes associated with metabolism, regulation and transport are often over-represented among the genes affected by LGT within these communities. These enrichments are largely robust to change of k.}, } @article {pmid28151042, year = {2017}, author = {Paul, D and Garg, A and Bhattacharjee, A}, title = {Occurrence of blaNDM-1 and blaNDM-5 in a Tertiary Referral Hospital of North India.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {23}, number = {7}, pages = {815-821}, doi = {10.1089/mdr.2016.0124}, pmid = {28151042}, issn = {1931-8448}, mesh = {Acinetobacter/drug effects/enzymology/*genetics/isolation & purification ; Acinetobacter Infections/drug therapy/epidemiology/microbiology/transmission ; Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/enzymology/*genetics/isolation & purification ; Escherichia coli Infections/drug therapy/epidemiology/microbiology/transmission ; Female ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Humans ; India/epidemiology ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Plasmids/chemistry/metabolism ; Pseudomonas Infections/drug therapy/epidemiology/microbiology/transmission ; Pseudomonas aeruginosa/drug effects/enzymology/*genetics/isolation & purification ; Tertiary Care Centers ; Transcription, Genetic ; beta-Lactamases/*genetics/metabolism ; }, abstract = {Antimicrobial resistance poses a great challenge to clinicians leaving very limited treatment options available. A panel of carbapenem-resistant bacterial isolates was selected based on Rapidec Carba NP test from a total of 900 samples, which were collected from different specialities hospitals of Kanpur, India. Carba NP-positive isolates were screened for carbapenemases, extended-spectrum beta-lactamases (ESBLs), quinolone resistance, and 16s methyltransferase genes. Presence of diverse blaNDM (blaNDM-1 and blaNDM-5) were detected and horizontal transferability was determined by transformation and conjugation assay. Elimination of blaNDM-1 and blaNDM-5 harboring plasmid was done by treating the isolates with sodium dodecyl sulfate. The transcriptional response of blaNDM-1 and blaNDM-5 under the exposure of imipenem, meropenem, and ertapenem stress was determined by quantitative real-time polymerase chain reaction. blaNDM harboring isolates were found to be horizontally transferable through IncFrepB and K type plasmid and could be successfully eliminated after the single treatment with sodium dodecyl sulfate. A distinct pattern of transcriptional response was observed for blaNDM-1 and blaNDM-5 under the pressure of carbapenem antibiotics where an upregulated expression of both blaNDM-1 and blaNDM-5 was observed. Minimum inhibitory concentration (MIC) results revealed that blaNDM harboring strains showed a high MIC range against imipenem, meropenem, ertapenem, cefepime, and aztreonam. Thus, prudent action should be taken to control the spread of these multidrug-resistant determinants or at least slowing down their lateral transfer in the hospital settings.}, } @article {pmid28137804, year = {2017}, author = {Ramírez-Vargas, G and Quesada-Gómez, C and Acuña-Amador, L and López-Ureña, D and Murillo, T and Del Mar Gamboa-Coronado, M and Chaves-Olarte, E and Thomson, N and Rodríguez-Cavallini, E and Rodríguez, C}, title = {A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements.}, journal = {Antimicrobial agents and chemotherapy}, volume = {61}, number = {4}, pages = {}, doi = {10.1128/AAC.02054-16}, pmid = {28137804}, issn = {1098-6596}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Clostridium Infections/*epidemiology/microbiology/transmission ; Clostridium difficile/classification/drug effects/*genetics/isolation & purification ; Costa Rica/epidemiology ; DNA Gyrase/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/*genetics ; *Endemic Diseases ; Gene Expression ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; *Interspersed Repetitive Sequences ; Metronidazole/pharmacology ; *Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Vancomycin/pharmacology ; }, abstract = {The antimicrobial resistance (AMR) rates and levels recorded for Clostridium difficile are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human C. difficile isolates of the NAPCR1/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibilities of 38 NAPCR1 isolates to 10 antibiotics from seven classes using Etests or macrodilution tests and examined 31 NAPCR1 whole-genome sequences to identify single nucleotide polymorphisms (SNPs) and genes that could explain the resistance phenotypes observed. The NAPCR1 isolates were multidrug resistant (MDR) and commonly exhibited very high resistance levels. By sequencing their genomes, we showed that they possessed resistance-associated SNPs in gyrA and rpoB and carried eight to nine acquired antimicrobial resistance (AMR) genes. Most of these genes were located on known or novel mobile genetic elements shared by isolates recovered at different hospitals and at different time points. Metronidazole and vancomycin remain the first-line treatment options for these isolates. Overall, the NAPCR1 lineage showed an enhanced ability to acquire AMR genes through lateral gene transfer. On the basis of this finding, we recommend further vigilance and the adoption of improved control measures to limit the dissemination of this lineage and the emergence of more C. difficile MDR strains.}, } @article {pmid28127891, year = {2017}, author = {Vera, MA and Brune, A}, title = {Hand over that gun: lateral gene transfer provides an amoeba with a bacterial weapon.}, journal = {Environmental microbiology}, volume = {19}, number = {3}, pages = {847-848}, doi = {10.1111/1462-2920.13680}, pmid = {28127891}, issn = {1462-2920}, mesh = {*Amoeba ; Bacteria ; *Gene Transfer, Horizontal ; Weapons ; }, } @article {pmid28096488, year = {2017}, author = {Keen, EC and Bliskovsky, VV and Malagon, F and Baker, JD and Prince, JS and Klaus, JS and Adhya, SL}, title = {Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation.}, journal = {mBio}, volume = {8}, number = {1}, pages = {}, doi = {10.1128/mBio.02115-16}, pmid = {28096488}, issn = {2150-7511}, mesh = {*Bacteriolysis ; Coliphages/*growth & development ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*virology ; *Gene Transfer, Horizontal ; Maryland ; Plasmids ; *Transformation, Bacterial ; Wyoming ; }, abstract = {Bacteriophages infect an estimated 1023 to 1025 bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications.

IMPORTANCE: Bacteriophages (phages), viruses that infect bacteria, are the planet's most numerous biological entities and kill vast numbers of bacteria in natural environments. Many of these bacteria carry plasmids, extrachromosomal DNA elements that frequently encode antibiotic resistance. However, it is largely unknown whether plasmids are destroyed during phage infection or released intact upon phage lysis, whereupon their encoded resistance could be acquired and manifested by other bacteria (transformation). Because phages are being developed to combat antibiotic-resistant bacteria and because transformation is a principal form of horizontal gene transfer, this question has important implications for biomedicine and microbial evolution alike. Here we report the isolation and characterization of two novel Escherichia coli phages, dubbed "superspreaders," that promote extensive plasmid transformation and efficiently disperse antibiotic resistance genes. Our work suggests that phage superspreaders are not suitable for use in medicine but may help drive bacterial evolution in natural environments.}, } @article {pmid28010735, year = {2016}, author = {Druzhinina, IS and Kubicek, EM and Kubicek, CP}, title = {Several steps of lateral gene transfer followed by events of 'birth-and-death' evolution shaped a fungal sorbicillinoid biosynthetic gene cluster.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {269}, doi = {10.1186/s12862-016-0834-6}, pmid = {28010735}, issn = {1471-2148}, mesh = {Ascomycota/classification/*genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Penicillium/classification/*genetics/metabolism ; Phylogeny ; Polyketide Synthases/genetics ; Polyketides/*metabolism ; }, abstract = {BACKGROUND: Sorbicillinoids are a family of complex cyclic polyketides produced by only a small number of distantly related ascomycete fungi such as Trichoderma (Sordariomycetes) and Penicillium (Eurotiomycetes). In T. reesei, they are synthesized by a gene cluster consisting of eight genes including two polyketide synthases (PKS). To reconstruct the evolutionary origin of this gene cluster, we examined the occurrence of these eight genes in ascomycetes.

RESULTS: A cluster comprising at least six of them was only found in Hypocreales (Acremonium chrysogenum, Ustilaginoidea virens, Trichoderma species from section Longibrachiatum) and in Penicillium rubens (Eurotiales). In addition, Colletotrichum graminicola contained the two pks (sor1 and sor2), but not the other sor genes. A. chrysogenum was the evolutionary eldest species in which sor1, sor2, sor3, sor4 and sor6 were present. Sor5 was gained by lateral gene transfer (LGT) from P. rubens. In the younger Hypocreales (U. virens, Trichoderma spp.), the cluster evolved by vertical transfer, but sor2 was lost and regained by LGT from C. graminicola. SorB (=sor2) and sorD (=sor4) were symplesiomorphic in P. rubens, whereas sorA, sorC and sorF were obtained by LGT from A. chrysogenum, and sorE by LGT from Pestalotiopsis fici (Xylariales). The sorbicillinoid gene cluster in Trichoderma section Longibrachiatum is under strong purifying selection. The T. reesei sor genes are expressed during fast vegetative growth, during antagonism of other fungi and regulated by the secondary metabolism regulator LAE1.

CONCLUSIONS: Our findings pinpoint the evolution of the fungal sorbicillinoid biosynthesis gene cluster. The core cluster arose in early Hypocreales, and was complemented by LGT. During further speciation in the Hypocreales, it became subject to birth and death evolution in selected lineages. In P. rubrens (Eurotiales), two cluster genes were symplesiomorphic, and the whole cluster formed by LGT from at least two different fungal donors.}, } @article {pmid27956257, year = {2017}, author = {Khowal, S and Siddiqui, MZ and Ali, S and Khan, MT and Khan, MA and Naqvi, SH and Wajid, S}, title = {A report on extensive lateral genetic reciprocation between arsenic resistant Bacillus subtilis and Bacillus pumilus strains analyzed using RAPD-PCR.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {443-454}, doi = {10.1016/j.ympev.2016.12.010}, pmid = {27956257}, issn = {1095-9513}, mesh = {Arsenic/*toxicity ; Bacillus pumilus/*drug effects/*genetics/isolation & purification ; Bacillus subtilis/*drug effects/*genetics/isolation & purification ; Evolution, Molecular ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Likelihood Functions ; Phylogeny ; Polymerase Chain Reaction/*methods ; Random Amplified Polymorphic DNA Technique/*methods ; Soil ; }, abstract = {The study involves isolation of arsenic resistant bacteria from soil samples. The characterization of bacteria isolates was based on 16S rRNA gene sequences. The phylogenetic consanguinity among isolates was studied employing rpoB and gltX gene sequence. RAPD-PCR technique was used to analyze genetic similarity between arsenic resistant isolates. In accordance with the results Bacillus subtilis and Bacillus pumilus strains may exhibit extensive horizontal gene transfer. Arsenic resistant potency in Bacillus sonorensis and high arsenite tolerance in Bacillus pumilus strains was identified. The RAPD-PCR primer OPO-02 amplified a 0.5kb DNA band specific to B. pumilus 3ZZZ strain and 0.75kb DNA band specific to B. subtilis 3PP. These unique DNA bands may have potential use as SCAR (Sequenced Characterized Amplified Region) molecular markers for identification of arsenic resistant B. pumilus and B. subtilis strains.}, } @article {pmid27902886, year = {2017}, author = {Nývltová, E and Šut'ák, R and Žárský, V and Harant, K and Hrdý, I and Tachezy, J}, title = {Lateral gene transfer of p-cresol- and indole-producing enzymes from environmental bacteria to Mastigamoeba balamuthi.}, journal = {Environmental microbiology}, volume = {19}, number = {3}, pages = {1091-1102}, doi = {10.1111/1462-2920.13636}, pmid = {27902886}, issn = {1462-2920}, mesh = {Animals ; Archamoebae/*genetics ; Bacteria/genetics ; Carboxy-Lyases ; Cresols/*metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Indoles/*metabolism ; Operon ; S-Adenosylmethionine/metabolism ; }, abstract = {p-Cresol and indole are volatile biologically active products of the bacterial degradation of tyrosine and tryptophan respectively. They are typically produced by bacteria in animal intestines, soil and various sediments. Here, we demonstrate that the free-living eukaryote Mastigamoeba balamuthi and its pathogenic relative Entamoeba histolytica produce significant amounts of indole via tryptophanase activity. Unexpectedly, M. balamuthi also produces p-cresol in concentrations that are bacteriostatic to non-p-cresol-producing bacteria. The ability of M. balamuthi to produce p-cresol, which has not previously been observed in any eukaryotic microbe, was gained due to the lateral acquisition of a bacterial gene for 4-hydroxyphenylacetate decarboxylase (HPAD). In bacteria, the genes for HPAD and the S-adenosylmethionine-dependent activating enzyme (AE) are present in a common operon. In M. balamuthi, HPAD displays a unique fusion with the AE that suggests the operon-mediated transfer of genes from a bacterial donor. We also clarified that the tyrosine-to-4-hydroxyphenylacetate conversion proceeds via the Ehrlich pathway. The acquisition of the bacterial HPAD gene may provide M. balamuthi a competitive advantage over other microflora in its native habitat.}, } @article {pmid27896732, year = {2017}, author = {de Oliveira Martins, L and Posada, D}, title = {Species Tree Estimation from Genome-Wide Data with guenomu.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1525}, number = {}, pages = {461-478}, doi = {10.1007/978-1-4939-6622-6_18}, pmid = {27896732}, issn = {1940-6029}, mesh = {Algorithms ; Bayes Theorem ; Computational Biology/*methods ; Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; *Phylogeny ; }, abstract = {The history of particular genes and that of the species that carry them can be different for a variety of reasons. In particular, gene trees and species trees can differ due to well-known evolutionary processes such as gene duplication and loss, lateral gene transfer, or incomplete lineage sorting. Species tree reconstruction methods have been developed to take this incongruence into account; these can be divided grossly into supertree and supermatrix approaches. Here we introduce a new Bayesian hierarchical model that we have recently developed and implemented in the program guenomu. The new model considers multiple sources of gene tree/species tree disagreement. Guenomu takes as input posterior distributions of unrooted gene tree topologies for multiple gene families, in order to estimate the posterior distribution of rooted species tree topologies.}, } @article {pmid27896730, year = {2017}, author = {Chan, CX and Beiko, RG and Ragan, MA}, title = {Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1525}, number = {}, pages = {421-432}, doi = {10.1007/978-1-4939-6622-6_16}, pmid = {27896730}, issn = {1940-6029}, support = {//CIHR/Canada ; }, mesh = {Algorithms ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomics ; Phylogeny ; }, abstract = {Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships. These types of approach have been used to elucidate the nature and extent of LGT and its physiological and ecological consequences throughout the Tree of Life. Advances in DNA sequencing technology have led to enormous increases in the number of sequenced genomes, including ultra-deep sampling of specific taxonomic groups and single cell-based sequencing of unculturable "microbial dark matter." Environmental shotgun sequencing enables the study of LGT among organisms that share the same habitat.This abundance of genomic data offers new opportunities for scientific discovery, but poses two key problems. As ever more genomes are generated, the assembly and annotation of each individual genome receives less scrutiny; and with so many genomes available it is tempting to include them all in a single analysis, but thousands of genomes and millions of genes can overwhelm key algorithms in the analysis pipeline. Identifying LGT events of interest therefore depends on choosing the right dataset, and on algorithms that appropriately balance speed and accuracy given the size and composition of the chosen set of genomes.}, } @article {pmid27889804, year = {2017}, author = {Furukawa, R and Nakagawa, M and Kuroyanagi, T and Yokobori, SI and Yamagishi, A}, title = {Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases.}, journal = {Journal of molecular evolution}, volume = {84}, number = {1}, pages = {51-66}, doi = {10.1007/s00239-016-9768-2}, pmid = {27889804}, issn = {1432-1432}, mesh = {Amino Acid Sequence/genetics ; Amino Acyl-tRNA Synthetases/*genetics ; Archaea/genetics ; Bacteria/genetics ; Base Sequence/genetics ; Biological Evolution ; Computer Simulation ; Eukaryota/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; Phylogeny ; Sequence Alignment/methods ; }, abstract = {The three-domain phylogenetic system of life has been challenged, particularly with regard to the position of Eukarya. The recent increase of known genome sequences has allowed phylogenetic analyses of all extant organisms using concatenated sequence alignment of universally conserved genes; these data supported the two-domain hypothesis, which place eukaryal species as ingroups of the Domain Archaea. However, the origin of Eukarya is complicated: the closest archaeal species to Eukarya differs in single-gene phylogenetic analyses depending on the genes. In this report, we performed molecular phylogenetic analyses of 23 aminoacyl-tRNA synthetases (ARS). Cytoplasmic ARSs in 12 trees showed a monophyletic Eukaryotic branch. One ARS originated from TACK superphylum. One ARS originated from Euryarchaeota and three originated from DPANN superphylum. Four ARSs originated from different bacterial species. The other 8 cytoplasmic ARSs were split into two or three groups in respective trees, which suggested that the cytoplasmic ARSs were replaced by secondary ARSs, and the original ARSs have been lost during evolution of Eukarya. In these trees, one original cytoplasmic ARS was derived from Euryarchaeota and three were derived from DPANN superphylum. Our results strongly support the two-domain hypothesis. We discovered that rampant-independent lateral gene transfers from several archaeal species of DPANN superphylum have contributed to the formation of Eukaryal cells. Based on our phylogenetic analyses, we proposed a model for the establishment of Eukarya.}, } @article {pmid27863503, year = {2016}, author = {Danchin, EG}, title = {Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?.}, journal = {BMC biology}, volume = {14}, number = {1}, pages = {101}, doi = {10.1186/s12915-016-0330-x}, pmid = {27863503}, issn = {1741-7007}, mesh = {Eukaryota/genetics ; *Gene Transfer, Horizontal ; Genome ; *Ice ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Lateral gene transfer (LGT) is the transmission of genes, sometimes across species barriers, outwith the classic vertical inheritance from parent to offspring. LGT is recognized as an important phenomenon that has shaped the genomes and biology of prokaryotes. Whether LGT in eukaryotes is important and widespread remains controversial. A study in BMC Biology concludes that LGT in eukaryotes is neither continuous nor prevalent and suggests a rule of thumb for judging when apparent LGT may reflect contamination.See research article: http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0315-9 .}, } @article {pmid27824124, year = {2016}, author = {Watanabe, T and Kojima, H and Fukui, M}, title = {Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36262}, doi = {10.1038/srep36262}, pmid = {27824124}, issn = {2045-2322}, mesh = {Bacteria/classification/*enzymology/genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Evolution, Molecular ; Fresh Water/*microbiology ; Gene Transfer, Horizontal ; Lakes ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Adenylylsulfate reductase is a heterodimeric complex of two subunits, AprB and AprA, and is a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. Common use of aprA as a functional marker gene has revealed the diversity of sulfur-cycle prokaryotes in diverse environments. In this study, we established a comprehensive sequence set of apr genes and employed it to reanalyze apr phylogeny, evaluate the coverage of a widely used primer set (AprA-1-FW/AprA-5-RV), and categorize environmental aprA sequences. Phylogenetic tree construction revealed new members of Apr lineage II and several previously unrecognized lateral gene transfer events. Using the established phylogenetic tree, we classified all previously reported aprA sequences amplified from freshwater lakes with the primer pair AprA-1-FW/AprA-5-RV in addition to the aprA sequences newly retrieved from freshwater lakes; the obtained results were complemented by 16S rRNA clone library analysis. Apr-based classifications of some of operational taxonomic units were supported by 16S rRNA-based analysis. This study updates our knowledge on the phylogeny of aprBA and shows the identities of several sulfur-cycle bacteria, which could not be classified to a known taxa until now. The established apr sequence set is publicly available and can be applied to assign environmental sequences to known lineages.}, } @article {pmid27811174, year = {2016}, author = {Maumus, F and Blanc, G}, title = {Study of Gene Trafficking between Acanthamoeba and Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses.}, journal = {Genome biology and evolution}, volume = {8}, number = {11}, pages = {3351-3363}, doi = {10.1093/gbe/evw260}, pmid = {27811174}, issn = {1759-6653}, mesh = {Acanthamoeba/*genetics/virology ; DNA Viruses/classification/*genetics/pathogenicity ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Protozoan ; *Genes, Viral ; Phylogeny ; }, abstract = {The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain unicellular eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. These findings prompted us to search the genome of Acanthamoeba castellanii strain Neff (Neff), one of the most prolific hosts in the discovery of giant NCLDVs, for possible DNA inserts of viral origin. We report the identification of 267 markers of lateral gene transfer with viruses, approximately half of which are clustered in Neff genome regions of viral origins, transcriptionally inactive or exhibit nucleotide-composition signatures suggestive of a foreign origin. The integrated viral genes had diverse origin among relatives of viruses that infect Neff, including Mollivirus, Pandoravirus, Marseillevirus, Pithovirus, and Mimivirus However, phylogenetic analysis suggests the existence of a yet-undiscovered family of amoeba-infecting NCLDV in addition to the five already characterized. The active transcription of some apparently anciently integrated virus-like genes suggests that some viral genes might have been domesticated during the amoeba evolution. These insights confirm that genomic insertion of NCLDV DNA is a common theme in eukaryotes. This gene flow contributed fertilizing the eukaryotic gene repertoire and participated in the occurrence of orphan genes, a long standing issue in genomics. Search for viral inserts in eukaryotic genomes followed by environmental screening of the original viruses should be used to isolate radically new NCLDVs.}, } @article {pmid27765015, year = {2016}, author = {LaRoche-Johnston, F and Monat, C and Cousineau, B}, title = {Recent horizontal transfer, functional adaptation and dissemination of a bacterial group II intron.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {223}, doi = {10.1186/s12862-016-0789-7}, pmid = {27765015}, issn = {1471-2148}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; DNA Transposable Elements ; Enterococcus faecalis/*genetics ; *Gene Transfer, Horizontal ; *Introns ; Lactococcus lactis/*genetics ; Mutation ; Phylogeny ; RNA Splicing ; RNA, Catalytic/genetics ; }, abstract = {BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer.

RESULTS: We characterized the functional and evolutionary relationship between the model group II intron from Lactococcus lactis, Ll.LtrB, and Ef.PcfG, a newly discovered intron from a clinical strain of Enterococcus faecalis. Ef.PcfG was found to be homologous to Ll.LtrB and to splice and mobilize in its native environment as well as in L. lactis. Interestingly, Ef.PcfG was shown to splice at the same level as Ll.LtrB but to be significantly less efficient to invade the Ll.LtrB recognition site. We also demonstrated that specific point mutations between the IEPs of both introns correspond to functional adaptations which developed in L. lactis as a response to selective pressure on mobility efficiency independently of splicing. The sequence of all the homologous full-length variants of Ll.LtrB were compared and shown to share a conserved pattern of mutation acquisition.

CONCLUSIONS: This work shows that Ll.LtrB and Ef.PcfG are homologous and have a common origin resulting from a recent lateral transfer event followed by further adaptation to the new target site and/or host environment. We hypothesize that Ef.PcfG is the ancestor of Ll.LtrB and was initially acquired by L. lactis, most probably by conjugation, via a single event of horizontal transfer. Strong selective pressure on homing site invasion efficiency then led to the emergence of beneficial point mutations in the IEP, enabling the successful establishment and survival of the group II intron in its novel lactococcal environment. The current colonization state of Ll.LtrB in L. lactis was probably later achieved through recurring episodes of conjugation-based horizontal transfer as well as independent intron mobility events. Overall, our data provide the first evidence of functional adaptation of a group II intron upon invading a new host, offering strong experimental support to the theory that bacterial group II introns, in sharp contrast to their organellar counterparts, behave mostly as mobile elements.}, } @article {pmid27751184, year = {2016}, author = {Ku, C and Martin, WF}, title = {A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule.}, journal = {BMC biology}, volume = {14}, number = {1}, pages = {89}, doi = {10.1186/s12915-016-0315-9}, pmid = {27751184}, issn = {1741-7007}, mesh = {Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Prokaryotic Cells/*metabolism ; }, abstract = {BACKGROUND: The literature harbors many claims for lateral gene transfer (LGT) from prokaryotes to eukaryotes. Such claims are typically founded in analyses of genome sequences. It is undisputed that many genes entered the eukaryotic lineage via the origin of mitochondria and the origin of plastids. Claims for lineage-specific LGT to eukaryotes outside the context of organelle origins and claims of continuous LGT to eukaryotic lineages are more problematic. If eukaryotes acquire genes from prokaryotes continuously during evolution, then sequenced eukaryote genomes should harbor evidence for recent LGT, like prokaryotic genomes do.

RESULTS: Here we devise an approach to investigate 30,358 eukaryotic sequences in the context of 1,035,375 prokaryotic homologs among 2585 phylogenetic trees containing homologs from prokaryotes and eukaryotes. Prokaryote genomes reflect a continuous process of gene acquisition and inheritance, with abundant recent acquisitions showing 80-100 % amino acid sequence identity to their phylogenetic sister-group homologs from other phyla. By contrast, eukaryote genomes show no evidence for either continuous or recent gene acquisitions from prokaryotes. We find that, in general, genes in eukaryotic genomes that share ≥70 % amino acid identity to prokaryotic homologs are genome-specific; that is, they are not found outside individual genome assemblies.

CONCLUSIONS: Our analyses indicate that eukaryotes do not acquire genes through continual LGT like prokaryotes do. We propose a 70 % rule: Coding sequences in eukaryotic genomes that share more than 70 % amino acid sequence identity to prokaryotic homologs are most likely assembly or annotation artifacts. The findings further uncover that the role of differential loss in eukaryote genome evolution has been vastly underestimated.}, } @article {pmid27708147, year = {2016}, author = {Hofstatter, PG and Tice, AK and Kang, S and Brown, MW and Lahr, DJ}, title = {Evolution of bacterial recombinase A (recA) in eukaryotes explained by addition of genomic data of key microbial lineages.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1840}, pages = {}, doi = {10.1098/rspb.2016.1453}, pmid = {27708147}, issn = {1471-2954}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {Amoebozoa/enzymology/genetics ; Bacterial Proteins/*genetics ; Dictyostelium/enzymology/genetics ; Eukaryota/enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Rec A Recombinases/*genetics ; }, abstract = {Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria-eukaryote) and/or secondary (eukaryote-eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.}, } @article {pmid27706829, year = {2017}, author = {Gillings, MR}, title = {Lateral gene transfer, bacterial genome evolution, and the Anthropocene.}, journal = {Annals of the New York Academy of Sciences}, volume = {1389}, number = {1}, pages = {20-36}, doi = {10.1111/nyas.13213}, pmid = {27706829}, issn = {1749-6632}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents ; Bacteria/drug effects/*genetics ; Bacterial Infections/genetics ; *Biological Evolution ; DNA, Bacterial/analysis ; Ecosystem ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Humans ; Phenotype ; }, abstract = {Lateral gene transfer (LGT) has significantly influenced bacterial evolution since the origins of life. It helped bacteria generate flexible, mosaic genomes and enables individual cells to rapidly acquire adaptive phenotypes. In turn, this allowed bacteria to mount strong defenses against human attempts to control their growth. The widespread dissemination of genes conferring resistance to antimicrobial agents has precipitated a crisis for modern medicine. Our actions can promote increased rates of LGT and also provide selective forces to fix such events in bacterial populations. For instance, the use of selective agents induces the bacterial SOS response, which stimulates LGT. We create hotspots for lateral transfer, such as wastewater systems, hospitals, and animal production facilities. Conduits of gene transfer between humans and animals ensure rapid dissemination of recent transfer events, as does modern transport and globalization. As resistance to antibacterial compounds becomes universal, there is likely to be increasing selection pressure for phenotypes with adverse consequences for human welfare, such as enhanced virulence, pathogenicity, and transmission. Improved understanding of the ecology of LGT could help us devise strategies to control this fundamental evolutionary process.}, } @article {pmid27648812, year = {2017}, author = {Popa, O and Landan, G and Dagan, T}, title = {Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction.}, journal = {The ISME journal}, volume = {11}, number = {2}, pages = {543-554}, doi = {10.1038/ismej.2016.116}, pmid = {27648812}, issn = {1751-7370}, support = {281357//European Research Council/International ; }, mesh = {Bacteria/classification/*genetics/virology ; Bacteriophages/*physiology ; Biological Evolution ; *Gene Transfer, Horizontal ; Genome, Bacterial/*genetics ; Host Specificity ; Phylogeny ; *Transduction, Genetic ; }, abstract = {Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage-mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species. Our results thus demonstrate that DNA transfer via transduction occurs within the context of phage-host specificity, but that this tight constraint can be breached, on rare occasions, to produce long-range LGTs of profound evolutionary consequences.}, } @article {pmid27630250, year = {2016}, author = {Pinhassi, J and DeLong, EF and Béjà, O and González, JM and Pedrós-Alió, C}, title = {Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {80}, number = {4}, pages = {929-954}, doi = {10.1128/MMBR.00003-16}, pmid = {27630250}, issn = {1098-5557}, mesh = {Aquatic Organisms/metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Gene Expression/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; Ion Transport/*physiology ; Light ; Rhodopsins, Microbial/genetics/*metabolism ; Seawater/microbiology ; Sodium-Potassium-Exchanging ATPase/genetics/metabolism ; }, abstract = {The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.}, } @article {pmid27604878, year = {2016}, author = {Gilbert, MJ and Miller, WG and Yee, E and Kik, M and Zomer, AL and Wagenaar, JA and Duim, B}, title = {Comparative Genomics of Campylobacter iguaniorum to Unravel Genetic Regions Associated with Reptilian Hosts.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {3022-3029}, doi = {10.1093/gbe/evw218}, pmid = {27604878}, issn = {1759-6653}, mesh = {Animals ; Base Composition ; Campylobacter/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Host-Pathogen Interactions/genetics ; Reptiles/microbiology ; Selection, Genetic ; }, abstract = {Campylobacter iguaniorum is most closely related to the species C fetus, C hyointestinalis, and C lanienae Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C iguaniorum strain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated from a green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-associated C fetus subsp. testudinum In contrast to C fetus, C iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C iguaniorum Instead, multiple predicted glycosylation regions were identified in C iguaniorum One of these regions is > 50 kb with deviant G + C content, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C iguaniorum shared highest homology with C hyointestinalis and C fetus. As in reptile-associated C fetus subsp. testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C iguaniorum and related Campylobacter taxa.}, } @article {pmid27600442, year = {2016}, author = {Willems, M and Lord, E and Laforest, L and Labelle, G and Lapointe, FJ and Di Sciullo, AM and Makarenkov, V}, title = {Using hybridization networks to retrace the evolution of Indo-European languages.}, journal = {BMC evolutionary biology}, volume = {16}, number = {}, pages = {180}, doi = {10.1186/s12862-016-0745-6}, pmid = {27600442}, issn = {1471-2148}, mesh = {Algorithms ; Computational Biology ; Databases, Factual ; Europe ; India ; *Language ; Linguistics ; *Models, Theoretical ; Phylogeny ; }, abstract = {BACKGROUND: Curious parallels between the processes of species and language evolution have been observed by many researchers. Retracing the evolution of Indo-European (IE) languages remains one of the most intriguing intellectual challenges in historical linguistics. Most of the IE language studies use the traditional phylogenetic tree model to represent the evolution of natural languages, thus not taking into account reticulate evolutionary events, such as language hybridization and word borrowing which can be associated with species hybridization and horizontal gene transfer, respectively. More recently, implicit evolutionary networks, such as split graphs and minimal lateral networks, have been used to account for reticulate evolution in linguistics.

RESULTS: Striking parallels existing between the evolution of species and natural languages allowed us to apply three computational biology methods for reconstruction of phylogenetic networks to model the evolution of IE languages. We show how the transfer of methods between the two disciplines can be achieved, making necessary methodological adaptations. Considering basic vocabulary data from the well-known Dyen's lexical database, which contains word forms in 84 IE languages for the meanings of a 200-meaning Swadesh list, we adapt a recently developed computational biology algorithm for building explicit hybridization networks to study the evolution of IE languages and compare our findings to the results provided by the split graph and galled network methods.

CONCLUSION: We conclude that explicit phylogenetic networks can be successfully used to identify donors and recipients of lexical material as well as the degree of influence of each donor language on the corresponding recipient languages. We show that our algorithm is well suited to detect reticulate relationships among languages, and present some historical and linguistic justification for the results obtained. Our findings could be further refined if relevant syntactic, phonological and morphological data could be analyzed along with the available lexical data.}, } @article {pmid27565162, year = {2016}, author = {Dang, UJ and Devault, AM and Mortimer, TD and Pepperell, CS and Poinar, HN and Golding, GB}, title = {Estimation of Gene Insertion/Deletion Rates with Missing Data.}, journal = {Genetics}, volume = {204}, number = {2}, pages = {513-529}, doi = {10.1534/genetics.116.191973}, pmid = {27565162}, issn = {1943-2631}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; *Evolution, Molecular ; Gardnerella vaginalis/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; INDEL Mutation/*genetics ; Mutagenesis, Insertional/genetics ; *Mutation Rate ; Mycobacterium/genetics ; }, abstract = {Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.}, } @article {pmid27508073, year = {2016}, author = {Koonin, EV}, title = {Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {}, doi = {10.12688/f1000research.8737.1}, pmid = {27508073}, issn = {2046-1402}, abstract = {The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of 'lateral genomics' to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT) dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller's ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.}, } @article {pmid27485833, year = {2016}, author = {Jaffe, AL and Corel, E and Pathmanathan, JS and Lopez, P and Bapteste, E}, title = {Bipartite graph analyses reveal interdomain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {5072-5081}, doi = {10.1111/1462-2920.13477}, pmid = {27485833}, issn = {1462-2920}, mesh = {Archaea/classification/*genetics/isolation & purification ; Bacteria/classification/*genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Membrane Proteins/*genetics/metabolism ; Phylogeny ; Symbiosis ; }, abstract = {Based on their small size and genomic properties, ultrasmall prokaryotic groups like the Candidate Phyla Radiation have been proposed as possible symbionts dependent on other bacteria or archaea. In this study, we use a bipartite graph analysis to examine patterns of sequence similarity between draft and complete genomes from ultrasmall bacteria and other complete prokaryotic genomes, assessing whether the former group might engage in significant gene transfer (or even endosymbioses) with other community members. Our results provide preliminary evidence for many lateral gene transfers with other prokaryotes, including members of the archaea, and report the presence of divergent, membrane-associated proteins among these ultrasmall taxa. In particular, these divergent genes were found in TM6 relatives of the intracellular parasite Babela massiliensis.}, } @article {pmid27453035, year = {2016}, author = {Cong, Y and Chan, YB and Ragan, MA}, title = {A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30308}, doi = {10.1038/srep30308}, pmid = {27453035}, issn = {2045-2322}, mesh = {Computational Biology/methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Analysis, Protein/*methods ; }, abstract = {Lateral genetic transfer (LGT) plays an important role in the evolution of microbes. Existing computational methods for detecting genomic regions of putative lateral origin scale poorly to large data. Here, we propose a novel method based on TF-IDF (Term Frequency-Inverse Document Frequency) statistics to detect not only regions of lateral origin, but also their origin and direction of transfer, in sets of hierarchically structured nucleotide or protein sequences. This approach is based on the frequency distributions of k-mers in the sequences. If a set of contiguous k-mers appears sufficiently more frequently in another phyletic group than in its own, we infer that they have been transferred from the first group to the second. We performed rigorous tests of TF-IDF using simulated and empirical datasets. With the simulated data, we tested our method under different parameter settings for sequence length, substitution rate between and within groups and post-LGT, deletion rate, length of transferred region and k size, and found that we can detect LGT events with high precision and recall. Our method performs better than an established method, ALFY, which has high recall but low precision. Our method is efficient, with runtime increasing approximately linearly with sequence length.}, } @article {pmid27452976, year = {2016}, author = {Cong, Y and Chan, YB and Ragan, MA}, title = {Exploring lateral genetic transfer among microbial genomes using TF-IDF.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29319}, doi = {10.1038/srep29319}, pmid = {27452976}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Databases, Genetic ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; *Genome, Microbial ; Phylogeny ; }, abstract = {Many microbes can acquire genetic material from their environment and incorporate it into their genome, a process known as lateral genetic transfer (LGT). Computational approaches have been developed to detect genomic regions of lateral origin, but typically lack sensitivity, ability to distinguish donor from recipient, and scalability to very large datasets. To address these issues we have introduced an alignment-free method based on ideas from document analysis, term frequency-inverse document frequency (TF-IDF). Here we examine the performance of TF-IDF on three empirical datasets: 27 genomes of Escherichia coli and Shigella, 110 genomes of enteric bacteria, and 143 genomes across 12 bacterial and three archaeal phyla. We investigate the effect of k-mer size, gap size and delineation of groups on the inference of genomic regions of lateral origin, finding an interplay among these parameters and sequence divergence. Because TF-IDF identifies donor groups and delineates regions of lateral origin within recipient genomes, aggregating these regions by gene enables us to explore, for the first time, the mosaic nature of lateral genes including the multiplicity of biological sources, ancestry of transfer and over-writing by subsequent transfers. We carry out Gene Ontology enrichment tests to investigate which biological processes are potentially affected by LGT.}, } @article {pmid27446814, year = {2016}, author = {Cenci, U and Ducatez, M and Kadouche, D and Colleoni, C and Ball, SG}, title = {Was the Chlamydial Adaptative Strategy to Tryptophan Starvation an Early Determinant of Plastid Endosymbiosis?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {6}, number = {}, pages = {67}, doi = {10.3389/fcimb.2016.00067}, pmid = {27446814}, issn = {2235-2988}, mesh = {Amino Acids/metabolism ; Biological Evolution ; Chlamydia/enzymology/genetics/*metabolism ; Cyanobacteria/metabolism ; Escherichia coli/metabolism ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Phylogeny ; Plants/enzymology/metabolism/microbiology ; Plastids/genetics/*metabolism/*microbiology ; Symbiosis ; Tryptophan/biosynthesis/*deficiency/genetics/*metabolism ; }, abstract = {Chlamydiales were recently proposed to have sheltered the future cyanobacterial ancestor of plastids in a common inclusion. The intracellular pathogens are thought to have donated those critical transporters that triggered the efflux of photosynthetic carbon and the consequent onset of symbiosis. Chlamydiales are also suspected to have encoded glycogen metabolism TTS (Type Three Secretion) effectors responsible for photosynthetic carbon assimilation in the eukaryotic cytosol. We now review the reasons underlying other chlamydial lateral gene transfers evidenced in the descendants of plastid endosymbiosis. In particular we show that half of the genes encoding enzymes of tryptophan synthesis in Archaeplastida are of chlamydial origin. Tryptophan concentration is an essential cue triggering two alternative modes of replication in Chlamydiales. In addition, sophisticated tryptophan starvation mechanisms are known to act as antibacterial defenses in animal hosts. We propose that Chlamydiales have donated their tryptophan operon to the emerging plastid to ensure increased synthesis of tryptophan by the plastid ancestor. This would have allowed massive expression of the tryptophan rich chlamydial transporters responsible for symbiosis. It would also have allowed possible export of this valuable amino-acid in the inclusion of the tryptophan hungry pathogens. Free-living single cell cyanobacteria are devoid of proteins able to transport this amino-acid. We therefore investigated the phylogeny of the Tyr/Trp transporters homologous to E. coli TyrP/Mre and found yet another LGT from Chlamydiales to Archaeplastida thereby considerably strengthening our proposal.}, } @article {pmid27363362, year = {2016}, author = {Bernard, G and Chan, CX and Ragan, MA}, title = {Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28970}, doi = {10.1038/srep28970}, pmid = {27363362}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Computer Simulation ; Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genomics/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.}, } @article {pmid27333878, year = {2016}, author = {Gilbert, MJ and Miller, WG and Yee, E and Zomer, AL and van der Graaf-van Bloois, L and Fitzgerald, C and Forbes, KJ and Méric, G and Sheppard, SK and Wagenaar, JA and Duim, B}, title = {Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {2006-2019}, doi = {10.1093/gbe/evw146}, pmid = {27333878}, issn = {1759-6653}, mesh = {Animals ; Campylobacter Infections/*genetics/microbiology ; Campylobacter fetus/*genetics/pathogenicity ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Host-Pathogen Interactions/*genetics ; Humans ; Mammals/genetics/microbiology ; Phylogeny ; Reptiles/genetics/microbiology ; Species Specificity ; }, abstract = {Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C fetus was performed. The genomes of C fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C fetus subspecies, but a clear distinction between mammal- and reptile-associated C fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C fetus subsp. testudinum strains. Within C fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C fetus Overall, this study shows that reptile-associated C fetus subsp. testudinum is genetically divergent from mammal-associated C fetus subspecies.}, } @article {pmid27330141, year = {2016}, author = {Xu, T and Qin, S and Hu, Y and Song, Z and Ying, J and Li, P and Dong, W and Zhao, F and Yang, H and Bao, Q}, title = {Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {23}, number = {4}, pages = {325-338}, doi = {10.1093/dnares/dsw023}, pmid = {27330141}, issn = {1756-1663}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Instability ; Phylogeny ; *Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid ; Spirulina/classification/*genetics ; }, abstract = {Arthrospira platensis is a multi-cellular and filamentous non-N2-fixing cyanobacterium that is capable of performing oxygenic photosynthesis. In this study, we determined the nearly complete genome sequence of A. platensis YZ. A. platensis YZ genome is a single, circular chromosome of 6.62 Mb in size. Phylogenetic and comparative genomic analyses revealed that A. platensis YZ was more closely related to A. platensis NIES-39 than Arthrospira sp. PCC 8005 and A. platensis C1. Broad gene gains were identified between A. platensis YZ and three other Arthrospira speices, some of which have been previously demonstrated that can be laterally transferred among different species, such as restriction-modification systems-coding genes. Moreover, unprecedented extensive chromosomal rearrangements among different strains were observed. The chromosomal rearrangements, particularly the chromosomal inversions, were analysed and estimated to be closely related to palindromes that involved long inverted repeat sequences and the extensively distributed type IIR restriction enzyme in the Arthrospira genome. In addition, species from genus Arthrospira unanimously contained the highest rate of repetitive sequence compared with the other species of order Oscillatoriales, suggested that sequence duplication significantly contributed to Arthrospira genome phylogeny. These results provided in-depth views into the genomic phylogeny and structural variation of A. platensis, as well as provide a valuable resource for functional genomics studies.}, } @article {pmid27324571, year = {2016}, author = {Naamala, J and Jaiswal, SK and Dakora, FD}, title = {Microsymbiont diversity and phylogeny of native bradyrhizobia associated with soybean (Glycine max L. Merr.) nodulation in South African soils.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {5}, pages = {336-344}, doi = {10.1016/j.syapm.2016.05.009}, pmid = {27324571}, issn = {1618-0984}, mesh = {Base Sequence ; *Bradyrhizobium/classification/genetics/isolation & purification ; DNA Gyrase/genetics ; DNA, Bacterial/genetics ; Genes, Essential/genetics ; Genetic Variation/genetics ; Molecular Typing ; Oxidoreductases/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; South Africa ; Soybeans/*microbiology ; Symbiosis ; Transcription Factors/genetics ; }, abstract = {The genetic diversity and identification of slow- and fast-growing soybean root nodule bacterial isolates from different agro-climatic regions in Mpumalanga, Limpopo and Gauteng Provinces of South Africa were evaluated. The 16S-rDNA-RFLP analysis of 100 rhizobial isolates and eight reference type strains placed the isolates into six major clusters, and revealed their site-dependent genomic diversity. Sequence analysis of single and concatenated housekeeping genes (atpD, glnII and gyrB), as well as the symbiotic gene nifH captured a considerably higher level of genetic diversity and indicated the dominance of Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum in Mpumalanga, Limpopo and Gauteng Provinces. Gene sequence similarities of isolates with type strains of Bradyrhizobium ranged from 97.3 to 100% for the 16S rDNA, and 83.4 to 100% for the housekeeping genes. The glnII gene phylogeny showed discordance with the other genes, suggesting lateral gene transfer or recombination events. Concatenated gene sequence analysis showed that most of the isolates did not align with known type strains and might represent new species from South Africa. This underscores the high genetic variability associated with soybean Bradyrhizobium in South African soils, and the presence of an important reservoir of novel soybean-nodulating bradyrhizobia in the country. In this study, the grouping of isolates was influenced by site origin, with Group I isolates originating from Limpopo Province and Groups II and III from Mpumlanga Province in the 16S rDNA-RFLP analysis.}, } @article {pmid27312952, year = {2016}, author = {Barbosa, EG and Crisp, A and Broadbent, SE and Carrillo, M and Boschetti, C and Tunnacliffe, A}, title = {A functional difference between native and horizontally acquired genes in bdelloid rotifers.}, journal = {Gene}, volume = {590}, number = {1}, pages = {186-191}, doi = {10.1016/j.gene.2016.06.019}, pmid = {27312952}, issn = {1879-0038}, mesh = {Alternative Splicing ; Amino Acid Sequence ; Animals ; Biological Evolution ; Gene Expression Profiling ; Gene Ontology ; *Gene Transfer, Horizontal ; *Genome, Helminth ; Molecular Sequence Annotation ; RNA, Helminth/*genetics/metabolism ; RNA, Messenger/*genetics/metabolism ; RNA, Spliced Leader/*genetics/metabolism ; Rotifera/*genetics ; Sequence Alignment ; *Trans-Splicing ; Transcriptome ; Transgenes ; }, abstract = {The form of RNA processing known as SL trans-splicing involves the transfer of a short conserved sequence, the spliced leader (SL), from a noncoding SL RNA to the 5' ends of mRNA molecules. SL trans-splicing occurs in several animal taxa, including bdelloid rotifers (Rotifera, Bdelloidea). One striking feature of these aquatic microinvertebrates is the large proportion of foreign genes, i.e. those acquired by horizontal gene transfer from other organisms, in their genomes. However, whether such foreign genes behave similarly to native genes has not been tested in bdelloids or any other animal. We therefore used a combination of experimental and computational methods to examine whether transcripts of foreign genes in bdelloids were SL trans-spliced, like their native counterparts. We found that many foreign transcripts contain SLs, use similar splice acceptor sequences to native genes, and are able to undergo alternative trans-splicing. However, a significantly lower proportion of foreign mRNAs contains SL sequences than native transcripts. This demonstrates a novel functional difference between foreign and native genes in bdelloids and suggests that SL trans-splicing is not essential for the expression of foreign genes, but is acquired during their domestication.}, } @article {pmid27239333, year = {2016}, author = {Romero, M and Cerritos, R and Ximenez, C}, title = {Horizontal Gene Transfers from Bacteria to Entamoeba Complex: A Strategy for Dating Events along Species Divergence.}, journal = {Journal of parasitology research}, volume = {2016}, number = {}, pages = {3241027}, doi = {10.1155/2016/3241027}, pmid = {27239333}, issn = {2090-0023}, abstract = {Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasite Entamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genus Entamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of some Entamoeba species was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence between E. histolytica and E. nuttallii probably occurred 5.93 million years ago (Mya); this lineage diverged from E. dispar 9.97 Mya, while the ancestor of the latter separated from E. invadens 68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of the Entamoeba genus.}, } @article {pmid27233666, year = {2016}, author = {Ahmed, MZ and Breinholt, JW and Kawahara, AY}, title = {Evidence for common horizontal transmission of Wolbachia among butterflies and moths.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {118}, doi = {10.1186/s12862-016-0660-x}, pmid = {27233666}, issn = {1471-2148}, mesh = {Animals ; Biodiversity ; Butterflies/*microbiology ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Geography ; Likelihood Functions ; Moths/*microbiology ; Phylogeny ; Wolbachia/genetics/*physiology ; }, abstract = {BACKGROUND: Wolbachia is one of the most widespread bacteria on Earth. Previous research on Wolbachia-host interactions indicates that the bacterium is typically transferred vertically, from mother to offspring, through the egg cytoplasm. Although horizontal transmission of Wolbachia from one species to another is reported to be common in arthropods, limited direct ecological evidence is available. In this study, we examine horizontal transmission of Wolbachia using a multilocus sequence typing (MLST) strains dataset and used Wolbachia and Lepidoptera genomes to search for evidence for lateral gene transfer (LGT) in Lepidoptera, one of the most diverse cosmopolitan insect orders. We constructed a phylogeny of arthropod-associated MLST Wolbachia strains and calibrated the age of Wolbachia strains associated with lepidopteran species.

RESULTS: Our results reveal inter-specific, inter-generic, inter-familial, and inter-ordinal horizontal transmission of Wolbachia strains, without discernible geographic patterns. We found at least seven probable cases of horizontal transmission among 31 species within Lepidoptera and between Lepidoptera and other arthropod hosts. The divergence time analysis revealed that Wolbachia is recently (22.6-4.7 mya, 95 % HPD) introduced in Lepidoptera. Analysis of nine Lepidoptera genomes (Bombyx mori, Danaus plexippus, Heliconius melpomene, Manduca sexta, Melitaea cinxia, Papilio glaucus, P. polytes, P. xuthus and Plutella xylostella) yielded one possible instance of Wolbachia LGT.

CONCLUSIONS: Our results provide evidence of high incidence of identical and multiple strains of Wolbachia among butterflies and moths, adding Lepidoptera to the growing body of evidence for common horizontal transmission of Wolbachia. This study demonstrates interesting dynamics of this remarkable and influential microorganism.}, } @article {pmid27193376, year = {2016}, author = {Cenci, U and Moog, D and Curtis, BA and Tanifuji, G and Eme, L and Lukeš, J and Archibald, JM}, title = {Heme pathway evolution in kinetoplastid protists.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {109}, doi = {10.1186/s12862-016-0664-6}, pmid = {27193376}, issn = {1471-2148}, support = {MOP-115141//CIHR/Canada ; }, mesh = {Animals ; Biological Evolution ; Eukaryota/classification/*physiology ; Gene Transfer, Horizontal ; Heme/*metabolism ; Kinetoplastida/classification/*genetics/*physiology ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetoplastids have emerged from free-living, non-pathogenic ancestors on multiple occasions during the evolutionary history of the group. Interestingly, in both parasitic and free-living kinetoplastids, the heme pathway-a core metabolic pathway in a wide range of organisms-is incomplete or entirely absent. Indeed, Kinetoplastea investigated thus far seem to bypass the need for heme biosynthesis by acquiring heme or intermediate metabolites directly from their environment.

RESULTS: Here we report the existence of a near-complete heme biosynthetic pathway in Perkinsela spp., kinetoplastids that live as obligate endosymbionts inside amoebozoans belonging to the genus Paramoeba/Neoparamoeba. We also use phylogenetic analysis to infer the evolution of the heme pathway in Kinetoplastea.

CONCLUSION: We show that Perkinsela spp. is a deep-branching kinetoplastid lineage, and that lateral gene transfer has played a role in the evolution of heme biosynthesis in Perkinsela spp. and other Kinetoplastea. We also discuss the significance of the presence of seven of eight heme pathway genes in the Perkinsela genome as it relates to its endosymbiotic relationship with Paramoeba.}, } @article {pmid27190138, year = {2016}, author = {Lin, X and Faridi, N and Casola, C}, title = {An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers.}, journal = {Genome biology and evolution}, volume = {8}, number = {4}, pages = {1252-1266}, doi = {10.1093/gbe/evw076}, pmid = {27190138}, issn = {1759-6653}, mesh = {Animals ; Arthropods/*genetics ; Coniferophyta/*genetics ; Cycadopsida/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; Phylogeny ; *Retroelements ; }, abstract = {Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants.}, } @article {pmid27139503, year = {2016}, author = {Jensen, L and Grant, JR and Laughinghouse, HD and Katz, LA}, title = {Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa.}, journal = {Evolution; international journal of organic evolution}, volume = {70}, number = {6}, pages = {1322-1333}, doi = {10.1111/evo.12935}, pmid = {27139503}, issn = {1558-5646}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Germ Cells ; Phylogeny ; }, abstract = {A sequestered germline in Metazoa has been argued to be an obstacle to lateral gene transfer (LGT), though few studies have specifically assessed this claim. Here, we test the hypothesis that the origin of a sequestered germline reduced LGT events in Bilateria (i.e., triploblast lineages) as compared to early-diverging Metazoa (i.e., Ctenophora, Cnidaria, Porifera, and Placozoa). We analyze single-gene phylogenies generated with over 900 species sampled from among Bacteria, Archaea, and Eukaryota to identify well-supported interdomain LGTs. We focus on ancient interdomain LGT (i.e., those between prokaryotes and multiple lineages of Metazoa) as systematic errors in single-gene tree reconstruction create uncertainties for interpreting eukaryote-to-eukaryote transfer. The breadth of the sampled Metazoa enables us to estimate the timing of LGTs, and to examine the pattern before versus after the evolution of a sequestered germline. We identified 58 LGTs found only in Metazoa and prokaryotes (i.e., bacteria and/or archaea), and seven genes transferred from prokaryotes into Metazoa plus one other eukaryotic clade. Our analyses indicate that more interdomain transfers occurred before the development of a sequestered germline, consistent with the hypothesis that this feature is an obstacle to LGT.}, } @article {pmid27128469, year = {2016}, author = {Yoshida, S and Cui, S and Ichihashi, Y and Shirasu, K}, title = {The Haustorium, a Specialized Invasive Organ in Parasitic Plants.}, journal = {Annual review of plant biology}, volume = {67}, number = {}, pages = {643-667}, doi = {10.1146/annurev-arplant-043015-111702}, pmid = {27128469}, issn = {1545-2123}, mesh = {Biological Transport ; Convolvulaceae/growth & development/*physiology ; Orobanchaceae/growth & development/*physiology ; *Plant Roots ; *Plant Stems ; Plant Weeds/growth & development/*physiology ; }, abstract = {Parasitic plants thrive by infecting other plants. Flowering plants evolved parasitism independently at least 12 times, in all cases developing a unique multicellular organ called the haustorium that forms upon detection of haustorium-inducing factors derived from the host plant. This organ penetrates into the host stem or root and connects to its vasculature, allowing exchange of materials such as water, nutrients, proteins, nucleotides, pathogens, and retrotransposons between the host and the parasite. In this review, we focus on the formation and function of the haustorium in parasitic plants, with a specific emphasis on recent advances in molecular studies of root parasites in the Orobanchaceae and stem parasites in the Convolvulaceae.}, } @article {pmid27075453, year = {2016}, author = {Ghatak, S and Blom, J and Das, S and Sanjukta, R and Puro, K and Mawlong, M and Shakuntala, I and Sen, A and Goesmann, A and Kumar, A and Ngachan, SV}, title = {Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {7}, pages = {945-956}, doi = {10.1007/s10482-016-0693-6}, pmid = {27075453}, issn = {1572-9699}, mesh = {Aeromonas caviae/drug effects/*genetics/pathogenicity ; Aeromonas hydrophila/drug effects/*genetics/pathogenicity ; Aeromonas veronii/drug effects/*genetics/pathogenicity ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Genotype ; Homologous Recombination ; Humans ; Microbial Sensitivity Tests ; Phylogeny ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.}, } @article {pmid27065965, year = {2016}, author = {Panda, P and Vanga, BR and Lu, A and Fiers, M and Fineran, PC and Butler, R and Armstrong, K and Ronson, CW and Pitman, AR}, title = {Pectobacterium atrosepticum and Pectobacterium carotovorum Harbor Distinct, Independently Acquired Integrative and Conjugative Elements Encoding Coronafacic Acid that Enhance Virulence on Potato Stems.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {397}, doi = {10.3389/fmicb.2016.00397}, pmid = {27065965}, issn = {1664-302X}, abstract = {Integrative and conjugative elements (ICEs) play a central role in the evolution of bacterial virulence, their transmission between bacteria often leading to the acquisition of virulence factors that alter host range or aggressiveness. Much is known about the functions of the virulence determinants that ICEs harbor, but little is understood about the cryptic effects of ICEs on their host cell. In this study, the importance of horizontally acquired island 2 (HAI2), an ICE in the genome of Pectobacterium atrosepticum SCRI1043, was studied using a strain in which the entire ICE had been removed by CRISPR-Cas-mediated genome editing. HAI2 encodes coronafacic acid, a virulence factor that enhances blackleg disease of potato stems caused by P. atrosepticum SCRI1043. As expected, deletion of HAI2 resulted in reduced blackleg symptoms in potato stems. A subsequent screen for HAI2-related ICEs in other strains of the Pectobacterium genus revealed their ubiquitous nature in P. atrosepticum. Yet, HAI2-related ICEs were only detected in the genomes of a few P. carotovorum strains. These strains were notable as blackleg causing strains belonging to two different subspecies of P. carotovorum. Sequence analysis of the ICEs in different strains of both P. atrosepticum and P. carotovorum confirmed that they were diverse and were present in different locations on the genomes of their bacterial host, suggesting that the cfa cluster was probably acquired independently on a number of occasions via chromosomal insertion of related ICEs. Excision assays also demonstrated that the ICEs in both P. atrosepticum and P. carotovorum are mobilized from the host chromosome. Thus, the future spread of these ICEs via lateral gene transfer might contribute to an increase in the prevalence of blackleg-causing strains of P. carotovorum.}, } @article {pmid27048805, year = {2016}, author = {Hemme, CL and Green, SJ and Rishishwar, L and Prakash, O and Pettenato, A and Chakraborty, R and Deutschbauer, AM and Van Nostrand, JD and Wu, L and He, Z and Jordan, IK and Hazen, TC and Arkin, AP and Kostka, JE and Zhou, J}, title = {Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02234-15}, doi = {10.1128/mBio.02234-15}, pmid = {27048805}, issn = {2150-7511}, mesh = {Gammaproteobacteria/*genetics/metabolism ; *Gene Transfer, Horizontal ; Groundwater/analysis/*microbiology ; Metals, Heavy/*analysis/metabolism ; Microbiota ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {UNLABELLED: Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

IMPORTANCE: Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.}, } @article {pmid26997548, year = {2016}, author = {Wang, GH and Jia, LY and Xiao, JH and Huang, DW}, title = {Discovery of a new Wolbachia supergroup in cave spider species and the lateral transfer of phage WO among distant hosts.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {41}, number = {}, pages = {1-7}, doi = {10.1016/j.meegid.2016.03.015}, pmid = {26997548}, issn = {1567-7257}, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Bacteriophages/classification/*genetics ; Caves ; Chaperonin 60/genetics ; China ; Cytoskeletal Proteins/genetics ; Electron Transport Complex IV/genetics ; Gene Expression ; Gene Transfer, Horizontal ; Host Specificity ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Spiders/*microbiology ; Symbiosis/physiology ; Wolbachia/classification/*genetics/virology ; }, abstract = {Wolbachia are widespread intracellular bacteria infecting the major classes of arthropods and some filarial nematodes. In arthropods, Wolbachia have evolved various intriguing reproductive manipulations, including cytoplasmic incompatibility, parthenogenesis, feminization, and male killing. Sixteen supergroups of Wolbachia have been identified, named A-Q (except G). Though Wolbachia present great diversity in arthropods, spiders, especially cave spiders, are still a poorly surveyed group of Wolbachia hosts. Here, we report a novel Wolbachia supergroup from nine Telema cave spiders (Araneae: Telemidae) based on five molecular markers (16S rRNA, ftsZ, gltA, groEL, and coxA). In addition, phage WO, which was previously reported only in Wolbachia supergroups A, B, and F, infects this new Wolbachia supergroup. We detected a 100% infection rate for phage WO and Wolbachia in Telema species. The phylogenetic trees of phage WO and Wolbachia are not congruent, which suggests that horizontal transfer of phage WO has occurred in these secluded species. Additionally, these data indicate Telema-Wolbachia-phage WO may be a good model for exploring the horizontal transfer history of WO among different host species.}, } @article {pmid26938861, year = {2016}, author = {Martins-Pinheiro, M and Lima, WC and Asif, H and Oller, CA and Menck, CF}, title = {Evolutionary and Functional Relationships of the dha Regulon by Genomic Context Analysis.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150772}, doi = {10.1371/journal.pone.0150772}, pmid = {26938861}, issn = {1932-6203}, mesh = {Aerobiosis ; Algorithms ; Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; Fermentation ; Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Glyceraldehyde/*analogs & derivatives/chemistry ; Glycerol/chemistry/metabolism ; Likelihood Functions ; Molecular Sequence Data ; Phylogeny ; Propane/*chemistry ; Propylene Glycols/*chemistry ; *Regulon ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {3-hydroxypropionaldehyde (3-HPA) and 1,3-propanediol (1,3-PD) are subproducts of glycerol degradation and of economical interest as they are used for polymers synthesis, such as polyesters and polyurethanes. Some few characterized bacterial species (mostly from Firmicutes and Gamma-proteobacteria groups) are able to catabolize these monomers from glycerol using the gene products from the dha regulon. To expand our knowledge and direct further experimental studies on the regulon and related genes for the anaerobic glycerol metabolism, an extensive genomic screening was performed to identify the presence of the dha genes in fully sequenced prokaryotic genomes. Interestingly, this work shows that although only few bacteria species are known to produce 3-HPA or 1,3-PD, the incomplete regulon is found in more than 100 prokaryotic genomes. However, the complete pathway is found only in a few dozen species belonging to five different taxonomic groups, including one Archaea species, Halalkalicoccus jeotgali. Phylogenetic analysis and conservation of both gene synteny and primary sequence similarity reinforce the idea that these genes have a common origin and were possibly acquired by lateral gene transfer (LGT). Besides the evolutionary aspect, the identification of homologs from several different organisms may predict potential alternative targets for faster or more efficient biological synthesis of 3-HPA or 1,3-PD.}, } @article {pmid26925045, year = {2016}, author = {von Wintersdorff, CJ and Penders, J and van Niekerk, JM and Mills, ND and Majumder, S and van Alphen, LB and Savelkoul, PH and Wolffs, PF}, title = {Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {173}, doi = {10.3389/fmicb.2016.00173}, pmid = {26925045}, issn = {1664-302X}, abstract = {The emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. It is becoming increasingly recognized that not only antibiotic resistance genes (ARGs) encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria-and also mobile genetic elements and bacteriophages-form a reservoir of ARGs (the resistome) from which pathogenic bacteria can acquire resistance via horizontal gene transfer (HGT). HGT has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important ARGs. Of the three canonical mechanisms of HGT, conjugation is thought to have the greatest influence on the dissemination of ARGs. While transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. Understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. Here, we will discuss the concept of the resistome, provide examples of HGT of clinically relevant ARGs and present an overview of the current knowledge of the contributions the various HGT mechanisms make to the spread of antibiotic resistance.}, } @article {pmid26914459, year = {2016}, author = {Ikeda-Ohtsubo, W and Strassert, JF and Köhler, T and Mikaelyan, A and Gregor, I and McHardy, AC and Tringe, SG and Hugenholtz, P and Radek, R and Brune, A}, title = {'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.}, journal = {Environmental microbiology}, volume = {18}, number = {8}, pages = {2548-2564}, doi = {10.1111/1462-2920.13234}, pmid = {26914459}, issn = {1462-2920}, mesh = {Animals ; Deltaproteobacteria/*classification/genetics/*isolation & purification ; Desulfovibrio/genetics ; Formate Dehydrogenases/genetics ; Gene Transfer, Horizontal/genetics ; Hypermastigia/*microbiology ; In Situ Hybridization, Fluorescence ; Intestines/*microbiology ; Isoptera/*parasitology ; Nitrogen Fixation/genetics ; Phylogeny ; Symbiosis ; }, abstract = {Termite gut flagellates are typically colonized by specific bacterial symbionts. Here we describe the phylogeny, ultrastructure and subcellular location of 'Candidatus Adiutrix intracellularis', an intracellular symbiont of Trichonympha collaris in the termite Zootermopsis nevadensis. It represents a novel, deep-branching clade of uncultured Deltaproteobacteria widely distributed in intestinal tracts of termites and cockroaches. Fluorescence in situ hybridization and transmission electron microscopy localized the endosymbiont near hydrogenosomes in the posterior part and near the ectosymbiont 'Candidatus Desulfovibrio trichonymphae' in the anterior part of the host cell. The draft genome of 'Ca. Adiutrix intracellularis' obtained from a metagenomic library revealed the presence of a complete gene set encoding the Wood-Ljungdahl pathway, including two homologs of fdhF encoding hydrogenase-linked formate dehydrogenases (FDHH) and all other components of the recently described hydrogen-dependent carbon dioxide reductase (HDCR) complex, which substantiates previous claims that the symbiont is capable of reductive acetogenesis from CO2 and H2 . The close phylogenetic relationship between the HDCR components and their homologs in homoacetogenic Firmicutes and Spirochaetes suggests that the deltaproteobacterium acquired the capacity for homoacetogenesis via lateral gene transfer. The presence of genes for nitrogen fixation and the biosynthesis of amino acids and cofactors indicate the nutritional nature of the symbiosis.}, } @article {pmid26907990, year = {2016}, author = {Lu, B and Leong, HW}, title = {GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.}, journal = {Journal of bioinformatics and computational biology}, volume = {14}, number = {1}, pages = {1640003}, doi = {10.1142/S0219720016400035}, pmid = {26907990}, issn = {1757-6334}, mesh = {Corynebacterium diphtheriae/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Genomics/*methods ; Pseudomonas aeruginosa/genetics ; Salmonella typhi/genetics ; Sequence Analysis, DNA ; *Support Vector Machine ; }, abstract = {Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes.}, } @article {pmid26859724, year = {2016}, author = {Keroack, CD and Wurster, JI and Decker, CG and Williams, KM and Slatko, BE and Foster, JM and Williams, SA}, title = {Absence of the Filarial Endosymbiont Wolbachia in Seal Heartworm (Acanthocheilonema spirocauda) but Evidence of Ancient Lateral Gene Transfer.}, journal = {The Journal of parasitology}, volume = {102}, number = {3}, pages = {312-318}, doi = {10.1645/15-872}, pmid = {26859724}, issn = {1937-2345}, mesh = {Acanthocheilonema/genetics/*microbiology ; Acanthocheilonemiasis/microbiology/parasitology/*veterinary ; Animals ; Biological Evolution ; Blotting, Western ; DNA Barcoding, Taxonomic ; DNA, Helminth/chemistry/isolation & purification ; Female ; *Gene Transfer, Horizontal/physiology ; Hydroxymethylbilane Synthase/genetics ; Phoca/*parasitology ; Phylogeny ; Polymerase Chain Reaction/methods ; Pseudogenes ; Sequence Analysis, DNA ; Symbiosis ; Wolbachia/*genetics/immunology/physiology ; }, abstract = {The symbiotic relationship of Wolbachia spp. was first observed in insects and subsequently in many parasitic filarial nematodes. This bacterium is believed to provide metabolic and developmental assistance to filarial parasitic nematodes, although the exact nature of this relationship remains to be fully elucidated. While Wolbachia is present in most filarial nematodes in the family Onchocercidae, it is absent in several disparate species such as the human parasite Loa loa . All tested members of the genus Acanthocheilonema, such as Acanthocheilonema viteae, have been shown to lack Wolbachia. Consistent with this, we show that Wolbachia is absent from the seal heartworm (Acanthocheilonema spirocauda), but lateral gene transfer (LGT) of DNA sequences between Wolbachia and A. spirocauda has occurred, indicating a past evolutionary association. Seal heartworm is an important pathogen of phocid seals and understanding its basic biology is essential for conservation of the host. The findings presented here may allow for the development of future treatments or diagnostics for the disease and also aid in clarification of the complicated nematode-Wolbachia relationship.}, } @article {pmid26836814, year = {2016}, author = {Benoit, JB and Adelman, ZN and Reinhardt, K and Dolan, A and Poelchau, M and Jennings, EC and Szuter, EM and Hagan, RW and Gujar, H and Shukla, JN and Zhu, F and Mohan, M and Nelson, DR and Rosendale, AJ and Derst, C and Resnik, V and Wernig, S and Menegazzi, P and Wegener, C and Peschel, N and Hendershot, JM and Blenau, W and Predel, R and Johnston, PR and Ioannidis, P and Waterhouse, RM and Nauen, R and Schorn, C and Ott, MC and Maiwald, F and Johnston, JS and Gondhalekar, AD and Scharf, ME and Peterson, BF and Raje, KR and Hottel, BA and Armisén, D and Crumière, AJ and Refki, PN and Santos, ME and Sghaier, E and Viala, S and Khila, A and Ahn, SJ and Childers, C and Lee, CY and Lin, H and Hughes, DS and Duncan, EJ and Murali, SC and Qu, J and Dugan, S and Lee, SL and Chao, H and Dinh, H and Han, Y and Doddapaneni, H and Worley, KC and Muzny, DM and Wheeler, D and Panfilio, KA and Vargas Jentzsch, IM and Vargo, EL and Booth, W and Friedrich, M and Weirauch, MT and Anderson, MA and Jones, JW and Mittapalli, O and Zhao, C and Zhou, JJ and Evans, JD and Attardo, GM and Robertson, HM and Zdobnov, EM and Ribeiro, JM and Gibbs, RA and Werren, JH and Palli, SR and Schal, C and Richards, S}, title = {Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {10165}, doi = {10.1038/ncomms10165}, pmid = {26836814}, issn = {2041-1723}, support = {GM070559-9/GM/NIGMS NIH HHS/United States ; 616346//European Research Council/International ; R01 GM070559/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; 260986//European Research Council/International ; UL1 TR001427/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Bedbugs/*genetics ; *Ectoparasitic Infestations ; *Feeding Behavior ; Gene Transfer, Horizontal/*genetics ; Genome ; Host-Parasite Interactions/*genetics ; Humans ; Insecticide Resistance/*genetics ; *Insecticides ; Sequence Analysis, DNA ; }, abstract = {The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.}, } @article {pmid26812112, year = {2016}, author = {Subbarayan, S and Marimuthu, SK and Nachimuthu, SK and Zhang, W and Subramanian, S}, title = {Characterization and cytotoxic activity of apoptosis-inducing pierisin-5 protein from white cabbage butterfly.}, journal = {International journal of biological macromolecules}, volume = {87}, number = {}, pages = {16-27}, doi = {10.1016/j.ijbiomac.2016.01.072}, pmid = {26812112}, issn = {1879-0003}, mesh = {ADP Ribose Transferases/*genetics/isolation & purification/*toxicity ; Animals ; Apoptosis/*drug effects ; Butterflies/*genetics/growth & development ; Cell Cycle/drug effects ; Cell Proliferation/drug effects ; Conserved Sequence ; DNA Fragmentation/drug effects ; Evolution, Molecular ; Gene Dosage ; Gene Expression Regulation, Developmental ; HeLa Cells ; Hep G2 Cells ; Humans ; Insect Proteins/*genetics/isolation & purification/*toxicity ; Mice ; Mitochondria/drug effects ; Rats ; Sequence Analysis ; }, abstract = {In this study, caspase-dependent apoptosis-inducing pierisin-5 gene was identified and characterized from cabbage white butterfly, Pieris canidia. A thousand-fold increase in expression of pierisin-5 gene was observed from second to third instar larvae, gradually decreasing before pupation. Pierisin-5 was purified from the fifth-instar larvae and was found to exhibit cytotoxicity against HeLa and HepG2 human cancer cell lines. Pierisin-5 showed growth inhibition and several morphological changes such as cell shrinkage, chromatin condensation and apoptotic body formation with programmed cell death in HeLa and HepG2 cells. Moreover, DNA fragmentation was observed after gel electrophoresis analysis. Caspase substrate assay showed further cleavage of Ac-DEVD-pNA, suggesting the activation of Caspase-3. Flow cytometry analysis revealed the cell cycle arrest at G1 phase and increased the percentage of apoptotic cells in cancer cell lines treated with pierisin-5. These findings suggest that pierisin-5 could significantly induce apoptosis in cancer cell lines and is mediated by activation of caspase-3 in the mitochondrial pathway. Phylogenetic analysis using pierisin proteins from Pierid butterflies, ADP-ribosylating toxins from bacteria, human, rat, and mouse indicated the possibility of horizontal transfer of pierisin genes from bacteria to butterflies. The single copy of pierisin gene unlike other insect toxin genes also supports lateral transfer.}, } @article {pmid26715630, year = {2016}, author = {Martinson, EO and Martinson, VG and Edwards, R and Mrinalini, and Werren, JH}, title = {Laterally Transferred Gene Recruited as a Venom in Parasitoid Wasps.}, journal = {Molecular biology and evolution}, volume = {33}, number = {4}, pages = {1042-1052}, doi = {10.1093/molbev/msv348}, pmid = {26715630}, issn = {1537-1719}, support = {R01 GM098667/GM/NIGMS NIH HHS/United States ; R01GM098667/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chitinases/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Insect ; Host-Parasite Interactions/genetics ; Microsporidia/genetics ; *Phylogeny ; Wasp Venoms/*genetics ; Wasps/genetics/pathogenicity ; }, abstract = {Parasitoid wasps use venom to manipulate the immunity and metabolism of their host insects in a variety of ways to provide resources for their offspring. Yet, how genes are recruited and evolve to perform venom functions remain open questions. A recently recognized source of eukaryotic genome innovation is lateral gene transfer (LGT). Glycoside hydrolase family 19 (GH19) chitinases are widespread in bacteria, microsporidia, and plants where they are used in nutrient acquisition or defense, but have previously not been known in metazoans. In this study, a GH19 chitinase LGT is described from the unicellular microsporidia/Rozella clade into parasitoid wasps of the superfamily Chalcidoidea, where it has become recruited as a venom protein. The GH19 chitinase is present in 15 species of chalcidoid wasps representing four families, and phylogenetic analysis indicates that it was laterally transferred near or before the origin of Chalcidoidea (∼95 Ma). The GH19 chitinase gene is highly expressed in the venom gland of at least seven species, indicating a role in the complex host manipulations performed by parasitoid wasp venom. RNAi knockdown in the model parasitoid Nasonia vitripennis reveals that-following envenomation-the GH19 chitinase induces fly hosts to upregulate genes involved in an immune response to fungi. A second, independent LGT of GH19 chitinase from microsporidia into mosquitoes was also found, also supported by phylogenetic reconstructions. Besides these two LGT events, GH19 chitinase is not found in any other sequenced animal genome, or in any fungi outside the microsporidia/Rozella clade.}, } @article {pmid26709836, year = {2016}, author = {Mallet, J and Besansky, N and Hahn, MW}, title = {How reticulated are species?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {2}, pages = {140-149}, doi = {10.1002/bies.201500149}, pmid = {26709836}, issn = {1521-1878}, support = {BB/G006903/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI076584/AI/NIAID NIH HHS/United States ; R01 AI76584/AI/NIAID NIH HHS/United States ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Genomics/methods ; Organisms, Genetically Modified/genetics ; *Phylogeny ; Plants/genetics ; }, abstract = {Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.}, } @article {pmid26691555, year = {2015}, author = {Cardona, G and Pons, JC and Rosselló, F}, title = {A reconstruction problem for a class of phylogenetic networks with lateral gene transfers.}, journal = {Algorithms for molecular biology : AMB}, volume = {10}, number = {}, pages = {28}, doi = {10.1186/s13015-015-0059-z}, pmid = {26691555}, issn = {1748-7188}, abstract = {BACKGROUND: Lateral, or Horizontal, Gene Transfers are a type of asymmetric evolutionary events where genetic material is transferred from one species to another. In this paper we consider LGT networks, a general model of phylogenetic networks with lateral gene transfers which consist, roughly, of a principal rooted tree with its leaves labelled on a set of taxa, and a set of extra secondary arcs between nodes in this tree representing lateral gene transfers. An LGT network gives rise in a natural way to a principal phylogenetic subtree and a set of secondary phylogenetic subtrees, which, roughly, represent, respectively, the main line of evolution of most genes and the secondary lines of evolution through lateral gene transfers.

RESULTS: We introduce a set of simple conditions on an LGT network that guarantee that its principal and secondary phylogenetic subtrees are pairwise different and that these subtrees determine, up to isomorphism, the LGT network. We then give an algorithm that, given a set of pairwise different phylogenetic trees [Formula: see text] on the same set of taxa, outputs, when it exists, the LGT network that satisfies these conditions and such that its principal phylogenetic tree is [Formula: see text] and its secondary phylogenetic trees are [Formula: see text].}, } @article {pmid26690249, year = {2015}, author = {Dilthey, A and Lercher, MJ}, title = {Horizontally transferred genes cluster spatially and metabolically.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {72}, doi = {10.1186/s13062-015-0102-5}, pmid = {26690249}, issn = {1745-6150}, mesh = {Gammaproteobacteria/*genetics/metabolism ; *Gene Regulatory Networks ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Multigene Family ; }, abstract = {BACKGROUND: Genomic uptake of DNA by prokaryotes often encompasses more than a single gene. In many cases, several horizontally transferred genes may be acquired together. Accordingly, we expect that horizontally transferred genes cluster spatially in the genome more often than expected if transfers were independent. Further, genes that depend on each other functionally may be unlikely to have beneficial fitness effects when taken up individually by a foreign genome. Hence, we also expect the co-acquisition of functionally related genes, resulting in the clustering of horizontally transferred genes in functional networks.

RESULTS: Analysing spatial and metabolic clustering of recent horizontal (or lateral) gene transfers among 21 γ-proteobacteria, we confirm both predictions. When comparing two datasets of predicted transfers that differ in their expected false-positive rate, we find that the more stringent dataset shows a stronger enrichment of clustered pairs.

CONCLUSIONS: The enrichment of interdependent metabolic genes among predicted transfers supports a biologically significant role of horizontally transferred genes in metabolic adaptation. Our results further suggest that spatial and metabolic clustering may be used as a benchmark for methods that predict recent horizontal gene transfers.}, } @article {pmid26666222, year = {2015}, author = {Filée, J and Rouault, JD and Harry, M and Hua-Van, A}, title = {Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1061}, doi = {10.1186/s12864-015-2060-9}, pmid = {26666222}, issn = {1471-2164}, mesh = {Animals ; *DNA Transposable Elements ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; Genome, Insect ; Phylogeny ; Rhodnius/*genetics ; }, abstract = {BACKGROUND: The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species.

RESULTS: Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable elements in this genome.

CONCLUSION: These data provide a new insight into the evolution of transposons in the genomes of hematophagous insects and bring additional evidences that lateral exchanges of mobile genetics elements occur frequently in the R. prolixus genome.}, } @article {pmid26598659, year = {2015}, author = {Boothby, TC and Tenlen, JR and Smith, FW and Wang, JR and Patanella, KA and Nishimura, EO and Tintori, SC and Li, Q and Jones, CD and Yandell, M and Messina, DN and Glasscock, J and Goldstein, B}, title = {Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {52}, pages = {15976-15981}, doi = {10.1073/pnas.1510461112}, pmid = {26598659}, issn = {1091-6490}, support = {K12 GM000678/GM/NIGMS NIH HHS/United States ; K12GM000678/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA, Viral/chemistry/genetics ; *Gene Transfer, Horizontal ; Genome/*genetics ; *Genomic Library ; Phylogeny ; Sequence Analysis, DNA/*methods ; Tardigrada/classification/*genetics ; }, abstract = {Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.}, } @article {pmid26535725, year = {2015}, author = {Andrade, BS and Góes-Neto, A}, title = {Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {14105-14114}, doi = {10.4238/2015.October.29.30}, pmid = {26535725}, issn = {1676-5680}, mesh = {Agaricales/*enzymology/*genetics ; Cacao/microbiology ; DNA-Directed DNA Polymerase/*genetics ; DNA-Directed RNA Polymerases/*genetics ; *Gene Transfer, Horizontal ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/microbiology ; Plasmids/genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {The filamentous fungus Moniliophthora perniciosa is a hemibiotrophic basidiomycete that causes witches' broom disease of cacao (Theobroma cacao L.). Many fungal mitochondrial plasmids are DNA and RNA polymerase-encoding invertrons with terminal inverted repeats and 5'-linked proteins. The aim of this study was to carry out comparative and phylogenetic analyses of DNA and RNA polymerases for all known linear mitochondrial plasmids in fungi. We performed these analyses at both gene and protein levels and assessed differences between fungal and viral polymerases in order to test the lateral gene transfer (LGT) hypothesis. We analyzed all mitochondrial plasmids of the invertron type within the fungal clade, including five from Ascomycota, seven from Basidiomycota, and one from Chytridiomycota. All phylogenetic analyses generated similar tree topologies regardless of the methods and datasets used. It is likely that DNA and RNA polymerase genes were inserted into the mitochondrial genomes of the 13 fungal species examined in our study as a result of different LGT events. These findings are important for a better understanding of the evolutionary relationships between fungal mitochondrial plasmids.}, } @article {pmid26518052, year = {2016}, author = {Tijet, N and Muller, MP and Matukas, LM and Khan, A and Patel, SN and Melano, RG}, title = {Lateral dissemination and inter-patient transmission of blaKPC-3: role of a conjugative plasmid in spreading carbapenem resistance.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {71}, number = {2}, pages = {344-347}, doi = {10.1093/jac/dkv356}, pmid = {26518052}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; Blotting, Southern ; Citrobacter freundii/*enzymology/genetics/isolation & purification ; Conjugation, Genetic ; Cross Infection/microbiology ; Disk Diffusion Antimicrobial Tests ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae Infections/*microbiology ; Escherichia coli/*enzymology/genetics/isolation & purification ; Female ; Gene Transfer, Horizontal ; Genotype ; Humans ; Klebsiella pneumoniae/*enzymology/genetics/isolation & purification ; Middle Aged ; Multilocus Sequence Typing ; Plasmids/*analysis ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *beta-Lactam Resistance ; beta-Lactamases/genetics/*secretion ; }, abstract = {OBJECTIVES: The objective of this study was to describe the nosocomial spread of carbapenemase-producing enterobacteria and characterize a plasmid involved in KPC dissemination.

METHODS: Two Klebsiella pneumoniae, one Escherichia coli and one Citrobacter freundii isolated from two patients were studied. Susceptibility profiles were obtained using Etest. Carbapenemase activity was detected using the Carba NP test. β-Lactamase gene content was screened by PCR and sequencing. K. pneumoniae isolates were genotyped by MLST and PFGE. KPC plasmid sizes were estimated by S1-DNA digestion and PFGE-Southern blot. Plasmids were sequenced using Illumina's technology and Sanger sequencing.

RESULTS: Two patients sharing a room on a surgical unit were positive for carbapenemase-producing K. pneumoniae. One patient was also colonized with carbapenemase-producing C. freundii and E. coli. Neither patient had known risk factors for carbapenemase acquisition, although one patient had recent surgery at another Toronto hospital; the other patient's husband had surgery in New York City 3 years prior to her presentation. An extensive investigation was conducted at both hospitals, but no additional cases were identified. blaKPC-3 was detected in all clinical isolates. Variable carbapenem resistance levels were observed. Both K. pneumoniae belonged to the same clone by PFGE and MLST (ST277). pKPC-SMH (∼ 53 kb) was identified in all the clinical isolates, showing identity only with structurally similar IncN plasmids.

CONCLUSIONS: We describe intra- and inter-patient dissemination of blaKPC. The involvement of a clone related to the successful K. pneumoniae ST258 and the blaKPC-3 gene detected in an active Tn4401 transposon carried on a conjugative broad-host-range plasmid increased the potential for this horizontal transmission.}, } @article {pmid26472620, year = {2016}, author = {Elling, FJ and Becker, KW and Könneke, M and Schröder, JM and Kellermann, MY and Thomm, M and Hinrichs, KU}, title = {Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment.}, journal = {Environmental microbiology}, volume = {18}, number = {2}, pages = {692-707}, doi = {10.1111/1462-2920.13086}, pmid = {26472620}, issn = {1462-2920}, mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/metabolism ; Biomarkers/metabolism ; Biomass ; Black Sea ; Ecology ; Gene Transfer, Horizontal ; Membrane Lipids/metabolism ; Oxidation-Reduction ; Phylogeny ; Quinones/*chemistry ; Terpenes/*chemistry ; }, abstract = {The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.}, } @article {pmid26433693, year = {2015}, author = {Vos, M and Hesselman, MC and Te Beek, TA and van Passel, MWJ and Eyre-Walker, A}, title = {Rates of Lateral Gene Transfer in Prokaryotes: High but Why?.}, journal = {Trends in microbiology}, volume = {23}, number = {10}, pages = {598-605}, doi = {10.1016/j.tim.2015.07.006}, pmid = {26433693}, issn = {1878-4380}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Prokaryotic Cells/*metabolism ; }, abstract = {Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.}, } @article {pmid26433010, year = {2015}, author = {Lemaire, B and Van Cauwenberghe, J and Chimphango, S and Stirton, C and Honnay, O and Smets, E and Muasya, AM}, title = {Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {11}, pages = {}, doi = {10.1093/femsec/fiv118}, pmid = {26433010}, issn = {1574-6941}, mesh = {Alphaproteobacteria/classification/enzymology/*genetics/physiology ; Betaproteobacteria/classification/enzymology/*genetics/physiology ; Carbon-Carbon Lyases/*genetics ; Ecosystem ; Evolution, Molecular ; Fabaceae/*microbiology/physiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; South Africa ; Symbiosis ; }, abstract = {The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.}, } @article {pmid26385192, year = {2015}, author = {Morrow, JL and Frommer, M and Royer, JE and Shearman, DC and Riegler, M}, title = {Wolbachia pseudogenes and low prevalence infections in tropical but not temperate Australian tephritid fruit flies: manifestations of lateral gene transfer and endosymbiont spillover?.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {202}, doi = {10.1186/s12862-015-0474-2}, pmid = {26385192}, issn = {1471-2148}, mesh = {Animals ; Australia ; Cloning, Molecular ; Gene Transfer, Horizontal ; Haplotypes ; Multilocus Sequence Typing ; Phylogeny ; Pseudogenes ; Tephritidae/*classification/*microbiology/physiology ; Wolbachia/*genetics/*isolation & purification/physiology ; }, abstract = {BACKGROUND: Maternally inherited Wolbachia bacteria infect many insect species. They can also be transferred horizontally into uninfected host lineages. A Wolbachia spillover from an infected source population must occur prior to the establishment of heritable infections, but this spillover may be transient. In a previous study of tephritid fruit fly species of tropical Australia we detected a high incidence of identical Wolbachia strains in several species as well as Wolbachia pseudogenes. Here, we have investigated this further by analysing field specimens of 24 species collected along a 3,000 km climate gradient of eastern Australia.

RESULTS: Wolbachia sequences were detected in individuals of nine of the 24 (37 %) species. Seven (29 %) species displayed four distinct Wolbachia strains based on characterisation of full multi locus sequencing (MLST) profiles; the strains occurred as single and double infections in a small number of individuals (2-17 %). For the two remaining species all individuals had incomplete MLST profiles and Wolbachia pseudogenes that may be indicative of lateral gene transfer into host genomes. The detection of Wolbachia was restricted to northern Australia, including in five species that only occur in the tropics. Within the more widely distributed Bactrocera tryoni and Bactrocera neohumeralis, Wolbachia also only occurred in the north, and was not linked to any particular mitochondrial haplotypes.

CONCLUSIONS: The presence of Wolbachia pseudogenes at high prevalence in two species in absence of complete MLST profiles may represent footprints of historic infections that have been lost. The detection of identical low prevalence strains in a small number of individuals of seven species may question their role as reproductive manipulator and their vertical inheritance. Instead, the findings may be indicative of transient infections that result from spillover events from a yet unknown source. These spillover events appear to be restricted to northern Australia, without proliferation in host lineages further south. Our study highlights that tropical fruit fly communities contain Wolbachia pseudogenes and may be exposed to frequent horizontal Wolbachia transfer. It also emphasises that global estimates of Wolbachia frequencies may need to consider lateral gene transfer and Wolbachia spillover that may be regionally restricted, transient and not inherited.}, } @article {pmid26323765, year = {2015}, author = {Szöllősi, GJ and Davín, AA and Tannier, E and Daubin, V and Boussau, B}, title = {Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140335}, doi = {10.1098/rstb.2014.0335}, pmid = {26323765}, issn = {1471-2970}, mesh = {Computer Simulation ; Cyanobacteria/genetics ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; *Genome, Fungal ; Models, Genetic ; *Phylogeny ; }, abstract = {Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.}, } @article {pmid26323756, year = {2015}, author = {Katz, LA}, title = {Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140324}, doi = {10.1098/rstb.2014.0324}, pmid = {26323756}, issn = {1471-2970}, support = {R15 GM113177/GM/NIGMS NIH HHS/United States ; 1R15GM113177/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Eukaryotic Cells ; Gene Transfer, Horizontal ; Genetics, Microbial ; Photosynthesis/genetics ; Symbiosis/*genetics/*physiology ; }, abstract = {While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence-absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.}, } @article {pmid26319575, year = {2015}, author = {Rauch, C and Vries, Jd and Rommel, S and Rose, LE and Woehle, C and Christa, G and Laetz, EM and Wägele, H and Tielens, AG and Nickelsen, J and Schumann, T and Jahns, P and Gould, SB}, title = {Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2602-2607}, doi = {10.1093/gbe/evv173}, pmid = {26319575}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; Gastropoda/*genetics ; Gene Transfer, Horizontal ; Photosynthesis/genetics ; Plastids/*genetics ; }, abstract = {Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals' digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For almost two decades, lateral gene transfer (LGT) from algae to slugs appeared to offer a solution, but RNA-seq analysis, later supported by genome sequencing of slug DNA, failed to find any evidence for such LGT events. Yet, isolated reports continue to be published and are readily discussed by the popular press and social media, making the data on LGT and its support for kleptoplast longevity appear controversial. However, when we take a sober look at the methods used, we realize that caution is warranted in how the results are interpreted. There is no evidence that the evolution of kleptoplasty in sea slugs involves LGT events. Based on what we know about photosystem maintenance in embryophyte plastids, we assume kleptoplasts depend on nuclear genes. However, studies have shown that some isolated algal plastids are, by nature, more robust than those of land plants. The evolution of kleptoplasty in green sea slugs involves many promising and unexplored phenomena, but there is no evidence that any of these require the expression of slug genes of algal origin.}, } @article {pmid26291765, year = {2015}, author = {Suzuki, K and Moriguchi, K and Yamamoto, S}, title = {Horizontal DNA transfer from bacteria to eukaryotes and a lesson from experimental transfers.}, journal = {Research in microbiology}, volume = {166}, number = {10}, pages = {753-763}, doi = {10.1016/j.resmic.2015.08.001}, pmid = {26291765}, issn = {1769-7123}, mesh = {Animals ; Bacteria/*genetics ; DNA, Bacterial/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Phylogeny ; Type IV Secretion Systems/genetics/metabolism ; }, abstract = {Horizontal gene transfer (HGT) is widespread among bacteria and plays a key role in genome dynamics. HGT is much less common in eukaryotes, but is being reported with increasing frequency in eukaryotes. The mechanism as to how eukaryotes acquired genes from distantly related organisms remains obscure yet. This paper cites examples of bacteria-derived genes found in eukaryotic organisms, and then describes experimental DNA transports to eukaryotes by bacterial type 4 secretion systems in optimized conditions. The mechanisms of the latter are efficient, quite reproducible in vitro and predictable, and thereby would provide insight into natural HGT and to the development of new research tools.}, } @article {pmid26287458, year = {2015}, author = {Ku, C and Nelson-Sathi, S and Roettger, M and Sousa, FL and Lockhart, PJ and Bryant, D and Hazkani-Covo, E and McInerney, JO and Landan, G and Martin, WF}, title = {Endosymbiotic origin and differential loss of eukaryotic genes.}, journal = {Nature}, volume = {524}, number = {7566}, pages = {427-432}, doi = {10.1038/nature14963}, pmid = {26287458}, issn = {1476-4687}, mesh = {Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; Eukaryota/classification/*genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome/genetics ; Mitochondria/genetics ; *Models, Genetic ; Organelles/*genetics ; Phylogeny ; Plastids/genetics ; Prokaryotic Cells/metabolism ; Proteome/genetics ; Symbiosis/*genetics ; Time Factors ; }, abstract = {Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.}, } @article {pmid26282127, year = {2015}, author = {McDonald, MJ and Chou, CH and Swamy, KB and Huang, HD and Leu, JY}, title = {The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {163}, doi = {10.1186/s12862-015-0441-y}, pmid = {26282127}, issn = {1471-2148}, mesh = {Amino Acids/genetics ; Biological Evolution ; *Codon ; Escherichia coli/*genetics ; Escherichia coli O157/genetics ; Gene Dosage ; *Gene Transfer, Horizontal ; Protein Biosynthesis ; RNA, Transfer/*genetics ; Shigella/classification/genetics ; }, abstract = {BACKGROUND: The introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition. Problems can arise if the genes introduced by LGT use codons that are not suited to the host's translational machinery. Here we investigate compensatory adaptation of E. coli in response to the introduction of large volumes of codons that are rarely used by the host genome.

RESULTS: We analyze genome sequences from the E. coli/Shigella complex, and find that certain tRNA genes are present in multiple copies in two pathogenic Shigella and O157:H7 subgroups of E. coli. Furthermore, we show that the codons that correspond to these multi-copy number tRNA genes are enriched in the high copy number Selfish Genetic Elements (SGE's) in Shigella and laterally introduced genes in O157:H7. We analyze the duplicate copies and find evidence for the selective retention of tRNA genes introduced by LGT in response to the changed codon content of the genome.

CONCLUSION: These data support a model where the relatively rapid influx of LGT genes and SGE's introduces a large number of genes maladapted to the host's translational machinery. Under these conditions, it becomes advantageous for the host to retain tRNA genes that are required for the incorporation of amino acids at these codons. Subsequently, the increased number of copies of these specific tRNA genes adjusts the cellular tRNA pool to the demands set by global shifts in codon usage.}, } @article {pmid26262891, year = {2015}, author = {Kang, F and Hu, X and Liu, J and Gao, Y}, title = {Noncovalent Binding of Polycyclic Aromatic Hydrocarbons with Genetic Bases Reducing the in Vitro Lateral Transfer of Antibiotic Resistant Genes.}, journal = {Environmental science & technology}, volume = {49}, number = {17}, pages = {10340-10348}, doi = {10.1021/acs.est.5b02293}, pmid = {26262891}, issn = {1520-5851}, mesh = {Ampicillin Resistance/*genetics ; *Base Pairing ; Binding Sites ; Fluorescence ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Microscopy, Atomic Force ; Plasmids/genetics ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Spectroscopy, Fourier Transform Infrared ; Thermodynamics ; }, abstract = {In current studies of noncovalent interactions of polycyclic aromatic hydrocarbons (PAHs) with genetic units, the impact of such interactions on gene transfer has not been explored. In this study, we examined the association of some widely occurring PAHs (phenanthrene, pyrene, benzo[g,h,i]perylene, and other congeners) with antibiotic resistant plasmids (pUC19). Small molecular PAHs (e.g., phenanthrene) bind effectively with plasmids to form a loosely clew-like plasmid-PAH complex (16.5-49.5 nm), resulting in reduced transformation of ampicillin resistance gene (Ampr). The in vitro transcription analysis demonstrated that reduced transformation of Ampr in plasmids results from the PAH-inhibited Ampr transcription to RNA. Fluorescence microtitration coupled with Fourier transform infrared spectroscopy (FTIR) and theoretical interaction models showed that adenine in plasmid has a stronger capacity to sequester small Phen and Pyre molecules via a π-π attraction. Changes in Gibbs free energy (ΔG) suggest that the CT-PAH model reliably depicts the plasmid-PAH interaction through a noncovalently physical sorption mechanism. Considering the wide occurrence of PAHs and antibiotic resistant genes (ARGs) in the environment, our findings suggest that small-sized PAHs can well affect the behavior of ARGs via above-described noncovalent interactions.}, } @article {pmid26254486, year = {2015}, author = {Choi, JY and Bubnell, JE and Aquadro, CF}, title = {Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2362-2382}, doi = {10.1093/gbe/evv158}, pmid = {26254486}, issn = {1759-6653}, support = {R01 GM095793/GM/NIGMS NIH HHS/United States ; R01GM095793/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila/*microbiology ; *Evolution, Molecular ; Female ; *Genetic Variation ; *Genome, Bacterial ; Genome, Mitochondrial ; Genomics ; Heterozygote ; Polymorphism, Genetic ; Sequence Alignment ; Wolbachia/*genetics ; }, abstract = {Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered.}, } @article {pmid26248371, year = {2015}, author = {Zhang, S and Ma, R and Liu, X and Zhang, X and Sun, B}, title = {Modulation of ccrAB Expression and SCCmec Excision by an Inverted Repeat Element and SarS in Methicillin-Resistant Staphylococcus aureus.}, journal = {Antimicrobial agents and chemotherapy}, volume = {59}, number = {10}, pages = {6223-6232}, doi = {10.1128/AAC.01041-15}, pmid = {26248371}, issn = {1098-6596}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Inverted Repeat Sequences ; Methicillin/*pharmacology ; Methicillin-Resistant Staphylococcus aureus/drug effects/*genetics/metabolism ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Binding ; Recombinases/chemistry/*genetics/metabolism ; Repressor Proteins ; Sequence Alignment ; beta-Lactam Resistance ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious human pathogen that can cause a broad spectrum of infections. MRSA strains are resistant to almost the entire family of β-lactam antibiotics due to the acquisition of staphylococcal cassette chromosome mec (SCCmec). The chromosome cassette recombinases A and B, encoded by ccrAB genes located on SCCmec, play a key role in the excision of SCCmec. Studies have shown that ccrAB genes are expressed in only a minority of cells, suggesting the involvement of a subtle regulatory mechanism in ccrAB expression which has not been uncovered. Here, we found that an inverted repeat (IR) element, existing extensively and conservatively within the ccrAB promoter of different SCCmec types, played a repressive role in ccrAB expression and SCCmec excision in MRSA strain N315. Replacement of the IR sequence led to a significant increase in ccrAB expression and curing of SCCmec from strain N315 cells. In addition, we identified the transcriptional regulator SarS using DNA-affinity chromatography and further demonstrated that SarS can bind to the IR sequence and upregulate ccrAB expression and SCCmec excision. These findings reveal a molecular mechanism regulating ccrAB expression and SCCmec excision and may provide mechanic insights into the lateral transfer of SCCmec and spread of antibiotic resistance in S. aureus.}, } @article {pmid26185097, year = {2015}, author = {Chiara, M and Caruso, M and D'Erchia, AM and Manzari, C and Fraccalvieri, R and Goffredo, E and Latorre, L and Miccolupo, A and Padalino, I and Santagada, G and Chiocco, D and Pesole, G and Horner, DS and Parisi, A}, title = {Comparative Genomics of Listeria Sensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2154-2172}, doi = {10.1093/gbe/evv131}, pmid = {26185097}, issn = {1759-6653}, mesh = {DNA, Bacterial/chemistry ; Ethanolamine/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Italy ; Listeria/classification/*genetics/isolation & purification/metabolism ; Phylogeny ; Propylene Glycols/metabolism ; Repetitive Sequences, Nucleic Acid ; Riboflavin/biosynthesis ; }, abstract = {Historically, genome-wide and molecular characterization of the genus Listeria has concentrated on the important human pathogen Listeria monocytogenes and a small number of closely related species, together termed Listeria sensu strictu. More recently, a number of genome sequences for more basal, and nonpathogenic, members of the Listeria genus have become available, facilitating a wider perspective on the evolution of pathogenicity and genome level evolutionary dynamics within the entire genus (termed Listeria sensu lato). Here, we have sequenced the genomes of additional Listeria fleischmannii and Listeria newyorkensis isolates and explored the dynamics of genome evolution in Listeria sensu lato. Our analyses suggest that acquisition of genetic material through gene duplication and divergence as well as through lateral gene transfer (mostly from outside Listeria) is widespread throughout the genus. Novel genetic material is apparently subject to rapid turnover. Multiple lines of evidence point to significant differences in evolutionary dynamics between the most basal Listeria subclade and all other congeners, including both sensu strictu and other sensu lato isolates. Strikingly, these differences are likely attributable to stochastic, population-level processes and contribute to observed variation in genome size across the genus. Notably, our analyses indicate that the common ancestor of Listeria sensu lato lacked flagella, which were acquired by lateral gene transfer by a common ancestor of Listeria grayi and Listeria sensu strictu, whereas a recently functionally characterized pathogenicity island, responsible for the capacity to produce cobalamin and utilize ethanolamine/propane-2-diol, was acquired in an ancestor of Listeria sensu strictu.}, } @article {pmid26173980, year = {2015}, author = {Wong, DH and Beiko, RG}, title = {Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {526}, doi = {10.1186/s12864-015-1752-5}, pmid = {26173980}, issn = {1471-2164}, mesh = {Bacteria/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Contig Mapping ; Energy Metabolism/genetics ; Enzymes/genetics/metabolism ; *Gene Transfer, Horizontal ; Phosphorus/*metabolism ; Sewage/microbiology ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways.

RESULTS: The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture.

CONCLUSIONS: Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.}, } @article {pmid26124240, year = {2015}, author = {de la Mora, J and Uchida, K and del Campo, AM and Camarena, L and Aizawa, S and Dreyfus, G}, title = {Structural Characterization of the Fla2 Flagellum of Rhodobacter sphaeroides.}, journal = {Journal of bacteriology}, volume = {197}, number = {17}, pages = {2859-2866}, doi = {10.1128/JB.00170-15}, pmid = {26124240}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics/*metabolism ; Flagella/*ultrastructure ; Flagellin/*genetics/metabolism ; Gene Expression Regulation, Bacterial/*physiology ; Polymorphism, Genetic ; Rhodobacter sphaeroides/genetics/metabolism/*ultrastructure ; }, abstract = {UNLABELLED: Rhodobacter sphaeroides is a free-living alphaproteobacterium that contains two clusters of functional flagellar genes in its genome: one acquired by horizontal gene transfer (fla1) and one that is endogenous (fla2). We have shown that the Fla2 system is normally quiescent and under certain conditions produces polar flagella, while the Fla1 system is always active and produces a single flagellum at a nonpolar position. In this work we purified and characterized the structure and analyzed the composition of the Fla2 flagellum. The number of polar filaments per cell is 4.6 on average. By comparison with the Fla1 flagellum, the prominent features of the ultra structure of the Fla2 HBB are the absence of an H ring, thick and long hooks, and a smoother zone at the hook-filament junction. The Fla2 helical filaments have a pitch of 2.64 μm and a diameter of 1.4 μm, which are smaller than those of the Fla1 filaments. Fla2 filaments undergo polymorphic transitions in vitro and showed two polymorphs: curly (right-handed) and coiled. However, in vivo in free-swimming cells, we observed only a bundle of filaments, which should probably be left-handed. Together, our results indicate that Fla2 cell produces multiple right-handed polar flagella, which are not conventional but exceptional.

IMPORTANCE: R. sphaeroides possesses two functional sets of flagellar genes. The fla1 genes are normally expressed in the laboratory and were acquired by horizontal transfer. The fla2 genes are endogenous and are expressed in a Fla1(-) mutant grown phototrophically and in the absence of organic acids. The Fla1 system produces a single lateral or subpolar flagellum, and the Fla2 system produces multiple polar flagella. The two kinds of flagella are never expressed simultaneously, and both are used for swimming in liquid media. The two sets of genes are certainly ready for responding to specific environmental conditions. The characterization of the Fla2 system will help us to understand its role in the physiology of this microorganism.}, } @article {pmid26101080, year = {2015}, author = {Sheppard, SK and Maiden, MC}, title = {The evolution of Campylobacter jejuni and Campylobacter coli.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {7}, number = {8}, pages = {a018119}, doi = {10.1101/cshperspect.a018119}, pmid = {26101080}, issn = {1943-0264}, support = {087622//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological/genetics ; Campylobacter coli/*genetics/physiology ; Campylobacter jejuni/*genetics/physiology ; *Evolution, Molecular ; Recombination, Genetic ; }, abstract = {The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure.}, } @article {pmid26048565, year = {2015}, author = {Wijayawardena, BK and Minchella, DJ and DeWoody, JA}, title = {Horizontal gene transfer in schistosomes: A critical assessment.}, journal = {Molecular and biochemical parasitology}, volume = {201}, number = {1}, pages = {57-65}, doi = {10.1016/j.molbiopara.2015.05.008}, pmid = {26048565}, issn = {1872-9428}, mesh = {Animals ; Computational Biology ; *Gene Transfer, Horizontal ; *Host-Parasite Interactions ; Phylogeny ; Schistosoma/*genetics ; Sequence Homology ; }, abstract = {Horizontal gene transfer (HGT), the movement of genetic material between distinct evolutionary lineages, has long been known as a principal force of diversification and adaptation of prokaryotes. More recently, genomic and transcriptomic datasets have suggested gene transfers among various eukaryotic taxa (e.g., Porifera, Cnidaria, Nematoda, Arthropoda, Rotifera, Craniata, and Plantae). Although the exact mechanism of eukaryotic HGT is often unknown, host-parasite interactions may provide ample opportunities for HGT. Schistosomes are trematode blood parasites with complex life cycles that have been repeatedly implicated in HGT. We employed molecular, bioinformatic and phylogenetic approaches to critically analyze 13 published reports of direct HGTs between schistosomes and their hosts to better understand host-parasite co-evolution. Our research suggests that reported cases of schistosome-associated HGT may be due to technical artifacts as opposed to biological reality as we were unable to substantiate them. HGT clearly occurs in eukaryotic organisms, but the burden of proof is high and we emphasize the importance of multiple lines of evidence to conclusively document HGT.}, } @article {pmid26047475, year = {2015}, author = {Kim, JI and Yoon, HS and Yi, G and Kim, HS and Yih, W and Shin, W}, title = {The Plastid Genome of the Cryptomonad Teleaulax amphioxeia.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129284}, doi = {10.1371/journal.pone.0129284}, pmid = {26047475}, issn = {1932-6203}, mesh = {Chloroplast Proteins/genetics ; Cryptophyta/*genetics ; DNA, Chloroplast/chemistry/genetics ; DNA, Circular/chemistry/genetics ; Gene Order ; Gene Transfer, Horizontal ; Genes, Chloroplast/*genetics ; Genome, Plastid/*genetics ; Photosynthesis/genetics ; Photosystem I Protein Complex/genetics ; Photosystem II Protein Complex/genetics ; Phylogeny ; Plastids/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Teleaulax amphioxeia is a photosynthetic unicellular cryptophyte alga that is distributed throughout marine habitats worldwide. This alga is an important plastid donor to the dinoflagellate Dinophysis caudata through the ciliate Mesodinium rubrum in the marine food web. To better understand the genomic characteristics of T. amphioxeia, we have sequenced and analyzed its plastid genome. The plastid genome sequence of T. amphioxeia is similar to that of Rhodomonas salina, and they share significant synteny. This sequence exhibits less similarity to that of Guillardia theta, the representative plastid genome of photosynthetic cryptophytes. The gene content and order of the three photosynthetic cryptomonad plastid genomes studied is highly conserved. The plastid genome of T. amphioxeia is composed of 129,772 bp and includes 143 protein-coding genes, 2 rRNA operons and 30 tRNA sequences. The DNA polymerase III gene (dnaX) was most likely acquired via lateral gene transfer (LGT) from a firmicute bacterium, identical to what occurred in R. salina. On the other hand, the psbN gene was independently encoded by the plastid genome without a reverse transcriptase gene as an intron. To clarify the phylogenetic relationships of the algae with red-algal derived plastids, phylogenetic analyses of 32 taxa were performed, including three previously sequenced cryptophyte plastid genomes containing 93 protein-coding genes. The stramenopiles were found to have branched out from the Chromista taxa (cryptophytes, haptophytes, and stramenopiles), while the cryptophytes and haptophytes were consistently grouped into sister relationships with high resolution.}, } @article {pmid26039986, year = {2015}, author = {Wilson, AC and Duncan, RP}, title = {Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10255-10261}, doi = {10.1073/pnas.1423305112}, pmid = {26039986}, issn = {1091-6490}, mesh = {Amino Acids/chemistry ; Amino Acids, Branched-Chain/chemistry ; Animals ; Bacteria/genetics ; Buchnera/genetics ; Cell Lineage ; Cytoplasm/metabolism ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Hemiptera/*genetics/*microbiology ; Pantothenic Acid/chemistry ; *Symbiosis ; }, abstract = {The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research.}, } @article {pmid26039278, year = {2015}, author = {Khater, S and Mohanty, D}, title = {In silico identification of AMPylating enzymes and study of their divergent evolution.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10804}, doi = {10.1038/srep10804}, pmid = {26039278}, issn = {2045-2322}, mesh = {Adenosine Monophosphate/*metabolism ; Amino Acid Motifs ; *Biological Evolution ; Conserved Sequence ; Gene Transfer, Horizontal ; Genomic Islands ; Genomics/methods ; Humans ; Markov Chains ; Models, Molecular ; Multigene Family ; Phylogeny ; Protein Conformation ; Protein Interaction Domains and Motifs ; *Protein Processing, Post-Translational ; Substrate Specificity ; Support Vector Machine ; }, abstract = {AMPylation is a novel post-translational modification (PTM) involving covalent attachment of an AMP moiety to threonine/tyrosine side chains of a protein. AMPylating enzymes belonging to three different families, namely Fic/Doc, GS-ATase and DrrA have been experimentally characterized. Involvement of these novel enzymes in a myriad of biological processes makes them interesting candidates for genome-wide search. We have used SVM and HMM to develop a computational protocol for identification of AMPylation domains and their classification into various functional subfamilies catalyzing AMPylation, deAMPylation, phosphorylation and phosphocholine transfer. Our analysis has not only identified novel PTM catalyzing enzymes among unannotated proteins, but has also revealed how this novel enzyme family has evolved to generate functional diversity by subtle changes in sequence/structures of the proteins. Phylogenetic analysis of Fic/Doc has revealed three new isofunctional subfamilies, thus adding to their functional divergence. Also, frequent occurrence of Fic/Doc proteins on highly mobile and unstable genomic islands indicated their evolution via extensive horizontal gene transfers. On the other hand phylogenetic analyses indicate lateral evolution of GS-ATase family and an early duplication event responsible for AMPylation and deAMPylation activity of GS-ATase. Our analysis also reveals molecular basis of substrate specificity of DrrA proteins.}, } @article {pmid26025427, year = {2015}, author = {Gawryluk, RM and Eme, L and Roger, AJ}, title = {Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.}, journal = {Molecular phylogenetics and evolution}, volume = {91}, number = {}, pages = {12-16}, doi = {10.1016/j.ympev.2015.05.010}, pmid = {26025427}, issn = {1095-9513}, mesh = {ATP Citrate (pro-S)-Lyase/classification/*genetics ; Animals ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; Gene Deletion ; *Gene Fusion ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {ATP citrate lyase (ACL) is an enzyme critical to the generation of cytosolic acetyl-CoA in eukaryotes. In most studied organisms, ACL activity is conferred in combination by two proteins, ACLA and ACLB (dsACL); however, animals encode a single-subunit ACL (ssACL) - the result of a gene fusion event. Through phylogenetic analyses, we investigated the evolution of ACL in a broad range of eukaryotes, including numerous microbes (protists). We show that the fused form is not restricted to animals, and is instead widely distributed among eukaryotes. Furthermore, ssACL and dsACL are patchily distributed and appear to be mutually exclusive; both types arose early in eukaryotic evolution. Finally, we present several compelling hypotheses of lateral gene transfer and gene loss, along with the secondary gene fission of ssACL in Ascomycota. Collectively, our in-depth analyses suggest that a complex suite of evolutionary events, usually considered rare, has shaped the evolution of ACL in eukaryotes.}, } @article {pmid26020646, year = {2015}, author = {Ravenhall, M and Škunca, N and Lassalle, F and Dessimoz, C}, title = {Inferring horizontal gene transfer.}, journal = {PLoS computational biology}, volume = {11}, number = {5}, pages = {e1004095}, doi = {10.1371/journal.pcbi.1004095}, pmid = {26020646}, issn = {1553-7358}, mesh = {Base Composition ; Computational Biology ; Computer Simulation ; DNA, Bacterial/genetics ; Databases, Genetic ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genomics/statistics & numerical data ; Humans ; Models, Genetic ; Models, Statistical ; Phylogeny ; }, abstract = {Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events.}, } @article {pmid27774277, year = {2015}, author = {Martin, DP and Murrell, B and Golden, M and Khoosal, A and Muhire, B}, title = {RDP4: Detection and analysis of recombination patterns in virus genomes.}, journal = {Virus evolution}, volume = {1}, number = {1}, pages = {vev003}, doi = {10.1093/ve/vev003}, pmid = {27774277}, issn = {2057-1577}, support = {K24 AI100665/AI/NIAID NIH HHS/United States ; U01 GM110749/GM/NIGMS NIH HHS/United States ; U19 AI090970/AI/NIAID NIH HHS/United States ; }, abstract = {RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 Mb) than those that could be analysed by older versions of the program. RDP4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. Other novelties in RDP4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of 'recombination aware' phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility. It can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.}, } @article {pmid25994183, year = {2015}, author = {Labeeuw, L and Martone, PT and Boucher, Y and Case, RJ}, title = {Ancient origin of the biosynthesis of lignin precursors.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {23}, doi = {10.1186/s13062-015-0052-y}, pmid = {25994183}, issn = {1745-6150}, mesh = {Alcohols/chemistry ; Aldehyde Oxidoreductases/metabolism ; Arabidopsis/genetics ; Biological Evolution ; Chlamydomonas/*genetics ; Chlorella/*genetics ; Computational Biology ; Dinoflagellida/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Haptophyta/genetics ; Lignin/*biosynthesis ; Likelihood Functions ; Photosynthesis ; Phylogeny ; Selaginellaceae/genetics ; }, abstract = {BACKGROUND: Lignin plays an important role in plant structural support and water transport, and is considered one of the hallmarks of land plants. The recent discovery of lignin or its precursors in various algae has raised questions on the evolution of its biosynthetic pathway, which could be much more ancient than previously thought. To determine the taxonomic distribution of the lignin biosynthesis genes, we screened all publicly available genomes of algae and their closest non-photosynthetic relatives, as well as representative land plants. We also performed phylogenetic analysis of these genes to decipher the evolution and origin(s) of lignin biosynthesis.

RESULTS: Enzymes involved in making p-coumaryl alcohol, the simplest lignin monomer, are found in a variety of photosynthetic eukaryotes, including diatoms, dinoflagellates, haptophytes, cryptophytes as well as green and red algae. Phylogenetic analysis of these enzymes suggests that they are ancient and spread to some secondarily photosynthetic lineages when they acquired red and/or green algal endosymbionts. In some cases, one or more of these enzymes was likely acquired through lateral gene transfer (LGT) from bacteria.

CONCLUSIONS: Genes associated with p-coumaryl alcohol biosynthesis are likely to have evolved long before the transition of photosynthetic eukaryotes to land. The original function of this lignin precursor is therefore unlikely to have been related to water transport. We suggest that it participates in the biological defense of some unicellular and multicellular algae.}, } @article {pmid25986903, year = {2015}, author = {Sanchez-Alberola, N and Campoy, S and Emerson, D and Barbé, J and Erill, I}, title = {An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria.}, journal = {Journal of bacteriology}, volume = {197}, number = {16}, pages = {2622-2630}, doi = {10.1128/JB.00035-15}, pmid = {25986903}, issn = {1098-5530}, mesh = {Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Betaproteobacteria/classification/*genetics/metabolism ; Comparative Genomic Hybridization ; Consensus Sequence ; DNA, Bacterial/genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Protein Structure, Tertiary ; *Regulon ; *SOS Response (Genetics) ; Sequence Alignment ; Serine Endopeptidases/genetics/*metabolism ; Transcriptional Activation ; }, abstract = {UNLABELLED: The SOS response is a transcriptional regulatory network governed by the LexA repressor that activates in response to DNA damage. In the Betaproteobacteria, LexA is known to target a palindromic sequence with the consensus sequence CTGT-N8-ACAG. We report the characterization of a LexA regulon in the iron-oxidizing betaproteobacterium Sideroxydans lithotrophicus. In silico and in vitro analyses show that LexA targets six genes by recognizing a binding motif with the consensus sequence GAACGaaCGTTC, which is strongly reminiscent of the Bacillus subtilis LexA-binding motif. We confirm that the closely related Gallionella capsiferriformans shares the same LexA-binding motif, and in silico analyses indicate that this motif is also conserved in the Nitrosomonadales and the Methylophilales. Phylogenetic analysis of LexA and the alpha subunit of DNA polymerase III (DnaE) reveal that the organisms harboring this noncanonical LexA form a compact taxonomic cluster within the Betaproteobacteria. However, their lexA gene is unrelated to the standard Betaproteobacteria lexA, and there is evidence of its spread through lateral gene transfer. In contrast to other reported cases of noncanonical LexA-binding motifs, the regulon of S. lithotrophicus is comparable in size and function to that of many other Betaproteobacteria, suggesting that a convergent SOS regulon has reevolved under the control of a new LexA protein. Analysis of the DNA-binding domain of S. lithotrophicus LexA reveals little sequence similarity with that of other LexA proteins targeting similar binding motifs, suggesting that network structure may limit site evolution or that structural constrains make the B. subtilis-type motif an optimal interface for multiple LexA sequences.

IMPORTANCE: Understanding the evolution of transcriptional systems enables us to address important questions in microbiology, such as the emergence and transfer potential of different regulatory systems to regulate virulence or mediate responses to stress. The results reported here constitute the first characterization of a noncanonical LexA protein regulating a standard SOS regulon. This is significant because it illustrates how a complex transcriptional program can be put under the control of a novel transcriptional regulator. Our results also reveal a substantial degree of plasticity in the LexA recognition domain, raising intriguing questions about the space of protein-DNA interfaces and the specific evolutionary constrains faced by these elements.}, } @article {pmid25943580, year = {2015}, author = {Bishnoi, R and Khatri, I and Subramanian, S and Ramya, TN}, title = {Prevalence of the F-type lectin domain.}, journal = {Glycobiology}, volume = {25}, number = {8}, pages = {888-901}, doi = {10.1093/glycob/cwv029}, pmid = {25943580}, issn = {1460-2423}, mesh = {Amino Acid Sequence ; Amphibians/classification/genetics ; Animals ; Bacteria/chemistry/classification/genetics ; Birds/classification/genetics ; Fucose/chemistry ; Gene Expression ; *Gene Transfer, Horizontal ; Lancelets/chemistry/classification/genetics ; Lectins/*chemistry/genetics ; Mammals/classification/genetics ; Models, Molecular ; Molecular Sequence Data ; Mollusca/chemistry/classification/genetics ; *Phylogeny ; Protein Structure, Tertiary ; Reptiles/classification/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {F-type lectins are fucolectins with characteristic fucose and calcium-binding sequence motifs and a unique lectin fold (the "F-type" fold). F-type lectins are phylogenetically widespread with selective distribution. Several eukaryotic F-type lectins have been biochemically and structurally characterized, and the F-type lectin domain (FLD) has also been studied in the bacterial proteins, Streptococcus mitis lectinolysin and Streptococcus pneumoniae SP2159. However, there is little knowledge about the extent of occurrence of FLDs and their domain organization, especially, in bacteria. We have now mined the extensive genomic sequence information available in the public databases with sensitive sequence search techniques in order to exhaustively survey prokaryotic and eukaryotic FLDs. We report 437 FLD sequence clusters (clustered at 80% sequence identity) from eukaryotic, eubacterial and viral proteins. Domain architectures are diverse but mostly conserved in closely related organisms, and domain organizations of bacterial FLD-containing proteins are very different from their eukaryotic counterparts, suggesting unique specialization of FLDs to suit different requirements. Several atypical phylogenetic associations hint at lateral transfer. Among eukaryotes, we observe an expansion of FLDs in terms of occurrence and domain organization diversity in the taxa Mollusca, Hemichordata and Branchiostomi, perhaps coinciding with greater emphasis on innate immune strategies in these organisms. The naturally occurring FLDs with diverse domain organizations that we have identified here will be useful for future studies aimed at creating designer molecular platforms for directing desired biological activities to fucosylated glycoconjugates in target niches.}, } @article {pmid25886068, year = {2015}, author = {Buchberger, T and Lamparter, T}, title = {Streptophyte phytochromes exhibit an N-terminus of cyanobacterial origin and a C-terminus of proteobacterial origin.}, journal = {BMC research notes}, volume = {8}, number = {}, pages = {144}, doi = {10.1186/s13104-015-1082-3}, pmid = {25886068}, issn = {1756-0500}, mesh = {Algorithms ; Archaea/classification/genetics/metabolism ; Bacteroidetes/classification/genetics/metabolism ; Biological Evolution ; Cyanobacteria/classification/genetics/metabolism ; Fungi/classification/genetics/metabolism ; Gene Duplication ; Gene Expression ; Gene Transfer, Horizontal ; Histidine Kinase ; *Phylogeny ; Phytochrome A/*chemistry/genetics/metabolism ; Phytochrome B/*chemistry/genetics/metabolism ; Plant Proteins/*chemistry/genetics/metabolism ; Protein Kinases/*chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Proteobacteria/classification/genetics/metabolism ; Streptophyta/classification/*genetics/metabolism ; }, abstract = {BACKGROUND: Phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. Prototypical phytochromes exhibit an N-terminal tridomain (PGP) consisting of PAS, GAF and PHY domains and a C-terminal histidine kinase (HK).

RESULTS: The mode of evolution of streptophyte, fungal and diatom phytochromes from bacteria is analyzed using two programs for sequence alignment and six programs for tree construction. Our results suggest that Bacteroidetes present the most ancient types of phytochromes. We found many examples of lateral gene transfer and rearrangements of PGP and HK sequences. The PGP and HK of streptophyte phytochromes seem to have different origins. In the most likely scenario, PGP was inherited from cyanobacteria, whereas the C-terminal portion originated from a proteobacterial protein with multiple PAS domains and a C-terminal HK. The plant PhyA and PhyB lineages go back to an early gene duplication event before the diversification of streptophytes. Fungal and diatom PGPs could have a common prokaryotic origin within proteobacteria. Early gene duplication is also obvious in fungal phytochromes.

CONCLUSIONS: The dominant question of the origin of plant phytochromes is difficult to tackle because the patterns differ among phylogenetic trees. We could partially overcome this problem by combining several alignment and tree construction algorithms and comparing many trees. A rearrangement of PGP and HK can directly explain the insertion of the two PAS domains by which streptophyte phytochromes are distinguished from all other phytochromes.}, } @article {pmid25863176, year = {2015}, author = {Szydlowski, L and Boschetti, C and Crisp, A and Barbosa, EG and Tunnacliffe, A}, title = {Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae.}, journal = {Gene}, volume = {566}, number = {2}, pages = {125-137}, doi = {10.1016/j.gene.2015.04.007}, pmid = {25863176}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cellulase/genetics/*metabolism ; Cellulose/*metabolism ; DNA ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Molecular Sequence Data ; Polymerase Chain Reaction ; Prokaryotic Cells ; Rotifera/*enzymology ; Sequence Homology, Amino Acid ; }, abstract = {The bdelloid rotifer, Adineta ricciae, an anhydrobiotic microinvertebrate, exhibits a high rate of horizontal gene transfer (HGT), with as much as 10% of its transcriptome being of foreign origin. Approximately 80% of these foreign transcripts are involved in metabolic processes, and therefore bdelloids represent a useful model for assessing the contribution of HGT to biochemical diversity. To validate this concept, we focused on cellulose digestion, an unusual activity in animals, which is represented by at least 16 genes encoding cellulolytic enzymes in A. ricciae. These genes have been acquired from a variety of different donor organisms among the bacteria and fungi, demonstrating that bdelloids use diverse genetic resources to construct a novel biochemical pathway. A variable complement of the cellulolytic gene set was found in five other bdelloid species, indicating a dynamic process of gene acquisition, duplication and loss during bdelloid evolution. For example, in A. ricciae, gene duplications have led to the formation of three copies of a gene encoding a GH45 family glycoside hydrolase, at least one of which encodes a functional enzyme; all three of these gene copies are present in a close relative, Adineta vaga, but only one copy was found in each of four Rotaria species. Furthermore, analysis of expression levels of the cellulolytic genes suggests that a bacterial-origin cellobiase is upregulated upon desiccation. In summary, bdelloid rotifers have apparently developed cellulolytic functions by the acquisition and domestication of multiple foreign genes.}, } @article {pmid25851957, year = {2015}, author = {De Vooght, L and Caljon, G and Van Hees, J and Van Den Abbeele, J}, title = {Paternal Transmission of a Secondary Symbiont during Mating in the Viviparous Tsetse Fly.}, journal = {Molecular biology and evolution}, volume = {32}, number = {8}, pages = {1977-1980}, doi = {10.1093/molbev/msv077}, pmid = {25851957}, issn = {1537-1719}, mesh = {Animals ; Enterobacteriaceae/*physiology ; *Evolution, Molecular ; Female ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial/*physiology ; Male ; Reproduction/physiology ; Symbiosis/*physiology ; *Tsetse Flies/microbiology/physiology ; }, abstract = {Sodalis glossinidius, a maternally inherited secondary symbiont of the tsetse fly, is a bacterium in the early/intermediate state of the transition toward symbiosis, representing an important model for investigating establishment and evolution of insect-bacteria symbiosis. The absence of phylogenetic congruence in tsetse-Sodalis coevolution and the existence of Sodalis genotypic diversity in field flies are suggestive for a horizontal transmission route. However, to date no natural mechanism for the horizontal transfer of this symbiont has been identified. Using novel methodologies for the stable fluorescent-labeling and introduction of modified Sodalis in tsetse flies, we unambiguously show that male-borne Sodalis is 1) horizontally transferred to females during mating and 2) subsequently vertically transmitted to the progeny, that is, paternal transmission. This mixed mode of transmission has major consequences regarding Sodalis' genome evolution as it can lead to coinfections creating opportunities for lateral gene transfer which in turn could affect the interaction with the tsetse host.}, } @article {pmid25769111, year = {2015}, author = {Cavalier-Smith, T}, title = {Mixed heterolobosean and novel gregarine lineage genes from culture ATCC 50646: Long-branch artefacts, not lateral gene transfer, distort α-tubulin phylogeny.}, journal = {European journal of protistology}, volume = {51}, number = {2}, pages = {121-137}, doi = {10.1016/j.ejop.2014.12.001}, pmid = {25769111}, issn = {1618-0429}, mesh = {*Artifacts ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Eukaryota/*classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Phylogeny ; Tubulin/*genetics ; }, abstract = {Contradictory and confusing results can arise if sequenced 'monoprotist' samples really contain DNA of very different species. Eukaryote-wide phylogenetic analyses using five genes from the amoeboflagellate culture ATCC 50646 previously implied it was an undescribed percolozoan related to percolatean flagellates (Stephanopogon, Percolomonas). Contrastingly, three phylogenetic analyses of 18S rRNA alone, did not place it within Percolozoa, but as an isolated deep-branching excavate. I resolve that contradiction by sequence phylogenies for all five genes individually, using up to 652 taxa. Its 18S rRNA sequence (GQ377652) is near-identical to one from stained-glass windows, somewhat more distant from one from cooling-tower water, all three related to terrestrial actinocephalid gregarines Hoplorhynchus and Pyxinia. All four protein-gene sequences (Hsp90; α-tubulin; β-tubulin; actin) are from an amoeboflagellate heterolobosean percolozoan, not especially deeply branching. Contrary to previous conclusions from trees combining protein and rRNA sequences or rDNA trees including Eozoa only, this culture does not represent a major novel deep-branching eukaryote lineage distinct from Heterolobosea, and thus lacks special significance for deep eukaryote phylogeny, though the rDNA sequence is important for gregarine phylogeny. α-Tubulin trees for over 250 eukaryotes refute earlier suggestions of lateral gene transfer within eukaryotes, being largely congruent with morphology and other gene trees.}, } @article {pmid25733873, year = {2015}, author = {Ku, C and Nelson-Sathi, S and Roettger, M and Garg, S and Hazkani-Covo, E and Martin, WF}, title = {Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10139-10146}, doi = {10.1073/pnas.1421385112}, pmid = {25733873}, issn = {1091-6490}, support = {232975//European Research Council/International ; }, mesh = {Alleles ; Animals ; Chloroplasts/genetics ; Computational Biology ; Cyanobacteria/genetics ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Humans ; Mitochondria/genetics ; Phylogeny ; Plastids/genetics ; Recombination, Genetic ; Symbiosis/*genetics ; }, abstract = {Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners--the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)--and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic--and plant and algal--lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller's ratchet--the origin of eukaryotic recombination, or sex--might have required surprisingly little evolutionary innovation.}, } @article {pmid25688108, year = {2015}, author = {Degli Esposti, M and Rosas-Pérez, T and Servín-Garcidueñas, LE and Bolaños, LM and Rosenblueth, M and Martínez-Romero, E}, title = {Molecular evolution of cytochrome bd oxidases across proteobacterial genomes.}, journal = {Genome biology and evolution}, volume = {7}, number = {3}, pages = {801-820}, doi = {10.1093/gbe/evv032}, pmid = {25688108}, issn = {1759-6653}, mesh = {Bacterial Proteins/classification/*genetics ; Cytochromes/classification/*genetics ; Electron Transport Complex IV ; *Evolution, Molecular ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Multigene Family ; Oxidoreductases/classification/*genetics ; Phylogeny ; Proteobacteria/classification/*genetics ; }, abstract = {This work is aimed to resolve the complex molecular evolution of cytochrome bd ubiquinol oxidase, a nearly ubiquitous bacterial enzyme that is involved in redox balance and bioenergetics. Previous studies have created an unclear picture of bd oxidases phylogenesis without considering the existence of diverse types of bd oxidases. Integrated approaches of genomic and protein analysis focused on proteobacteria have generated a molecular classification of diverse types of bd oxidases, which produces a new scenario for interpreting their evolution. A duplication of the original gene cluster of bd oxidase might have occurred in the ancestors of extant α-proteobacteria of the Rhodospirillales order, such as Acidocella, from which the bd-I type of the oxidase might have diffused to other proteobacterial lineages. In contrast, the Cyanide-Insensitive Oxidase type may have differentiated into recognizable subtypes after another gene cluster duplication. These subtypes are widespread in the genomes of α-, β-, and γ-proteobacteria, with occasional instances of lateral gene transfer. In resolving the evolutionary pattern of proteobacterial bd oxidases, this work sheds new light on the basal taxa of α-proteobacteria from which the γ-proteobacterial lineage probably emerged.}, } @article {pmid25630351, year = {2015}, author = {Lossouarn, J and Nesbø, CL and Mercier, C and Zhaxybayeva, O and Johnson, MS and Charchuck, R and Farasin, J and Bienvenu, N and Baudoux, AC and Michoud, G and Jebbar, M and Geslin, C}, title = {'Ménage à trois': a selfish genetic element uses a virus to propagate within Thermotogales.}, journal = {Environmental microbiology}, volume = {17}, number = {9}, pages = {3278-3288}, doi = {10.1111/1462-2920.12783}, pmid = {25630351}, issn = {1462-2920}, mesh = {Bacteria/genetics/isolation & purification/*virology ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA, Viral/genetics ; Gene Dosage/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Hydrothermal Vents/*microbiology/virology ; Mitomycin/pharmacology ; Plasmids/*genetics ; Siphoviridae/*genetics ; }, abstract = {Prokaryotic viruses play a major role in the microbial ecology and evolution. However, the virosphere associated with deep-sea hydrothermal ecosystems remains largely unexplored. Numerous instances of lateral gene transfer have contributed to the complex and incongruent evolutionary history of Thermotogales, an order well represented in deep-sea hydrothermal vents. The presence of clustered regularly interspaced short palindromic repeats (CRISPR) loci has been reported in all Thermotogales genomes, suggesting that these bacteria have been exposed to viral infections that could have mediated gene exchange. In this study, we isolated and characterized the first virus infecting bacteria from the order Thermotogales, Marinitoga piezophila virus 1 (MPV1). The host, Marinitoga piezophila is a thermophilic, anaerobic and piezophilic bacterium isolated from a deep-sea hydrothermal chimney. MPV1 is a temperate Siphoviridae-like virus with a 43.7 kb genome. Surprisingly, we found that MPV1 virions carry not only the viral DNA but preferentially package a plasmid of 13.3 kb (pMP1) also carried by M. piezophila. This 'ménage à trois' highlights potential relevance of selfish genetic elements in facilitating lateral gene transfer in the deep-sea biosphere.}, } @article {pmid25601290, year = {2015}, author = {Méheust, R and Lopez, P and Bapteste, E}, title = {Metabolic bacterial genes and the construction of high-level composite lineages of life.}, journal = {Trends in ecology & evolution}, volume = {30}, number = {3}, pages = {127-129}, doi = {10.1016/j.tree.2015.01.001}, pmid = {25601290}, issn = {1872-8383}, mesh = {Archaea/*classification/*genetics ; Bacteria/*genetics ; Euryarchaeota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Archaeal/*genetics ; Genes, Bacterial/*genetics ; }, abstract = {Understanding how major organismal lineages originated is fundamental for understanding processes by which life evolved. Major evolutionary transitions, like eukaryogenesis, merging genetic material from distantly related organisms, are rare events, hence difficult ones to explain causally. If most archaeal lineages emerged after massive acquisitions of bacterial genes, a rule however arises: metabolic bacterial genes contributed to all major evolutionary transitions.}, } @article {pmid25573905, year = {2015}, author = {Nývltová, E and Stairs, CW and Hrdý, I and Rídl, J and Mach, J and Pačes, J and Roger, AJ and Tachezy, J}, title = {Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes.}, journal = {Molecular biology and evolution}, volume = {32}, number = {4}, pages = {1039-1055}, doi = {10.1093/molbev/msu408}, pmid = {25573905}, issn = {1537-1719}, support = {MOP-62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Anaerobiosis/genetics ; Archamoebae/enzymology/*genetics/metabolism ; Cell Membrane Structures/genetics/metabolism ; Energy Metabolism/*genetics ; Enzymes/genetics/isolation & purification ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Organelles/enzymology/*genetics/metabolism ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism of evolution for protists adapting to oxygen-poor environments. Specifically, modifications of energy metabolism in anaerobic forms of mitochondria (e.g., hydrogenosomes) are likely to have been associated with gene transfer from prokaryotes. An interesting question is whether the products of transferred genes were directly targeted into the ancestral organelle or initially operated in the cytosol and subsequently acquired organelle-targeting sequences. Here, we identified key enzymes of hydrogenosomal metabolism in the free-living anaerobic amoebozoan Mastigamoeba balamuthi and analyzed their cellular localizations, enzymatic activities, and evolutionary histories. Additionally, we characterized 1) several canonical mitochondrial components including respiratory complex II and the glycine cleavage system, 2) enzymes associated with anaerobic energy metabolism, including an unusual D-lactate dehydrogenase and acetyl CoA synthase, and 3) a sulfate activation pathway. Intriguingly, components of anaerobic energy metabolism are present in at least two gene copies. For each component, one copy possesses an mitochondrial targeting sequence (MTS), whereas the other lacks an MTS, yielding parallel cytosolic and hydrogenosomal extended glycolysis pathways. Experimentally, we confirmed that the organelle targeting of several proteins is fully dependent on the MTS. Phylogenetic analysis of all extended glycolysis components suggested that these components were acquired by LGT. We propose that the transformation from an ancestral organelle to a hydrogenosome in the M. balamuthi lineage involved the lateral acquisition of genes encoding extended glycolysis enzymes that initially operated in the cytosol and that established a parallel hydrogenosomal pathway after gene duplication and MTS acquisition.}, } @article {pmid25547755, year = {2014}, author = {Thiergart, T and Landan, G and Martin, WF}, title = {Concatenated alignments and the case of the disappearing tree.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {266}, doi = {10.1186/s12862-014-0266-0}, pmid = {25547755}, issn = {1471-2148}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Conserved Sequence/genetics ; Evolution, Molecular ; Fungi/classification/genetics ; Gene Transfer, Horizontal ; *Genome ; *Phylogeny ; Plants/classification/genetics ; }, abstract = {BACKGROUND: Analyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of generating genetic diversity, there are open questions as to whether concatenation amplifies or averages phylogenetic signals residing in individual genes. Here we investigate concatenations of prokaryotic and eukaryotic datasets to investigate possible sources of incongruence in phylogenetic trees and to examine the level of overlap between individual and concatenated alignments.

RESULTS: We analyzed prokaryotic datasets comprising 248 invidual gene trees from 315 genomes at three taxonomic depths spanning gammaproteobacteria, proteobacteria, and prokaryotes (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual gene trees from 85 genomes at two taxonomic depths: across plants-animals-fungi and within fungi. Consistent with previous findings, the branches in trees made from concatenated alignments are, in general, not supported by any of their underlying individual gene trees, even though the concatenation trees tend to possess high bootstrap proportions values. For the prokaryote data, this observation is independent of phylogenetic depth and sequence conservation. The eukaryotic data show much better agreement between concatenation and single gene trees. LGT frequencies in trees were estimated using established methods. Sequence length in individual alignments, but not sequence divergence, was found to correlate with the generation of branches that correspond to the concatenated tree.

CONCLUSIONS: The weak correspondence of concatenation trees with single gene trees gives rise to the question where the phylogenetic signal in concatenated trees is coming from. The eukaryote data reveals a better correspondence between individual and concatenation trees than the prokaryote data. The question of whether the lack of correspondence between individual genes and the concatenation tree in the prokaryotic data is due to LGT or phylogenetic artefacts remains unanswered. If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence.}, } @article {pmid25541486, year = {2015}, author = {Mansfield, MJ and Adams, JB and Doxey, AC}, title = {Botulinum neurotoxin homologs in non-Clostridium species.}, journal = {FEBS letters}, volume = {589}, number = {3}, pages = {342-348}, doi = {10.1016/j.febslet.2014.12.018}, pmid = {25541486}, issn = {1873-3468}, mesh = {Botulinum Toxins/*genetics/isolation & purification ; Clostridium/chemistry/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Multigene Family ; Protein Structure, Tertiary ; Tetanus Toxin/*genetics/isolation & purification ; Weissella/chemistry/*genetics ; }, abstract = {Clostridial neurotoxins (CNTs) are the deadliest toxins known and the causative agents of botulism and tetanus. Despite their structural and functional complexity, no CNT homologs are currently known outside Clostridium. Here, we report the first homologs of Clostridium CNTs within the genome of the rice fermentation organism Weissella oryzae SG25. One gene in W. oryzae S25 encodes a protein with a four-domain architecture and HExxH protease motif common to botulinum neurotoxins (BoNTs). An adjacent gene with partial similarity to CNTs is also present, and both genes seem to have been laterally transferred into the W. oryzae genome from an unknown source. Identification of mobile, CNT-related genes outside of Clostridium has implications for our understanding of the evolution of this important toxin family.}, } @article {pmid25496002, year = {2014}, author = {Klasson, L and Kumar, N and Bromley, R and Sieber, K and Flowers, M and Ott, SH and Tallon, LJ and Andersson, SG and Dunning Hotopp, JC}, title = {Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {1097}, doi = {10.1186/1471-2164-15-1097}, pmid = {25496002}, issn = {1471-2164}, support = {DP2 OD007372/OD/NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; *DNA Replication ; DNA, Bacterial/*biosynthesis/*genetics ; Drosophila/*genetics/*microbiology ; Female ; Gene Dosage ; *Gene Transfer, Horizontal ; Genome, Insect/genetics ; Heterozygote ; Male ; Polytene Chromosomes/genetics ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) from bacterial Wolbachia endosymbionts has been detected in ~20% of arthropod and nematode genome sequencing projects. Many of these transfers are large and contain a substantial part of the Wolbachia genome.

RESULTS: Here, we re-sequenced three D. ananassae genomes from Asia and the Pacific that contain large LGTs from Wolbachia. We find that multiple copies of the Wolbachia genome are transferred to the Drosophila nuclear genome in all three lines. In the D. ananassae line from Indonesia, the copies of Wolbachia DNA in the nuclear genome are nearly identical in size and sequence yielding an even coverage of mapped reads over the Wolbachia genome. In contrast, the D. ananassae lines from Hawaii and India show an uneven coverage of mapped reads over the Wolbachia genome suggesting that different parts of these LGTs are present in different copy numbers. In the Hawaii line, we find that this LGT is underrepresented in third instar larvae indicative of being heterochromatic. Fluorescence in situ hybridization of mitotic chromosomes confirms that the LGT in the Hawaii line is heterochromatic and represents ~20% of the sequence on chromosome 4 (dot chromosome, Muller element F).

CONCLUSIONS: This collection of related lines contain large lateral gene transfers composed of multiple Wolbachia genomes that constitute >2% of the D. ananassae genome (~5 Mbp) and partially explain the abnormally large size of chromosome 4 in D. ananassae.}, } @article {pmid25483352, year = {2015}, author = {Hirt, RP and Alsmark, C and Embley, TM}, title = {Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites.}, journal = {Current opinion in microbiology}, volume = {23}, number = {}, pages = {155-162}, doi = {10.1016/j.mib.2014.11.018}, pmid = {25483352}, issn = {1879-0364}, support = {268701//European Research Council/International ; 045404//Wellcome Trust/United Kingdom ; 075796//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Eukaryota/*chemistry/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; *Prokaryotic Cells ; Proteome/*analysis ; }, abstract = {Our knowledge of the extent and functional impact of lateral gene transfer (LGT) from prokaryotes to eukaryotes, outside of endosymbiosis, is still rather limited. Here we review the recent literature, focusing mainly on microbial parasites, indicating that LGT from diverse prokaryotes has played a significant role in the evolution of a number of lineages, and by extension throughout eukaryotic evolution. As might be expected, taxonomic biases for donor prokaryotes indicate that shared habitat is a major factor driving transfers. The LGTs identified predominantly affect enzymes from metabolic pathways, but over a third of LGT are genes for putative proteins of unknown function. Finally, we discuss the difficulties in analysing LGT among eukaryotes and suggest that high-throughput methodologies integrating different approaches are needed to achieve a more global understanding of the importance of LGT in eukaryotic evolution.}, } @article {pmid25480150, year = {2014}, author = {Castanera, R and Pérez, G and López, L and Sancho, R and Santoyo, F and Alfaro, M and Gabaldón, T and Pisabarro, AG and Oguiza, JA and Ramírez, L}, title = {Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {1071}, doi = {10.1186/1471-2164-15-1071}, pmid = {25480150}, issn = {1471-2164}, mesh = {Base Sequence ; DNA Helicases/classification/genetics/metabolism ; DNA Transposable Elements/*genetics ; Expressed Sequence Tags ; Fungal Proteins/classification/genetics/metabolism ; *Genome, Fungal ; Phylogeny ; Pleurotus/*genetics ; Protein Structure, Tertiary ; Retroelements/genetics ; Sequence Alignment ; Transcriptome ; }, abstract = {BACKGROUND: Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species.

RESULTS: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons.

CONCLUSION: P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.}, } @article {pmid25477875, year = {2014}, author = {Degnan, SM}, title = {Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {638}, doi = {10.3389/fmicb.2014.00638}, pmid = {25477875}, issn = {1664-302X}, abstract = {Since the origin of the animal kingdom, marine animals have lived in association with viruses, prokaryotes and unicellular eukaryotes, often as symbionts. This long and continuous interaction has provided ample opportunity not only for the evolution of intimate interactions such as sharing of metabolic pathways, but also for horizontal gene transfer (HGT) of non-metazoan genes into metazoan genomes. The number of demonstrated cases of inter-kingdom HGT is currently small, such that it is not yet widely appreciated as a significant player in animal evolution. Sessile marine invertebrates that vertically inherit bacterial symbionts, that have no dedicated germ line, or that bud or excise pluripotent somatic cells during their life history may be particularly receptive to HGT from their symbionts. Closer scrutiny of the growing number of genomes being accrued for these animals may thus reveal HGT as a regular source of novel variation that can function to extend the host phenotype metabolically, morphologically, or even behaviorally. Taxonomic identification of symbionts will help to address the intriguing question of whether past HGT events may constrain contemporary symbioses.}, } @article {pmid25477419, year = {2014}, author = {Gillespie, JJ and Driscoll, TP and Verhoeve, VI and Utsuki, T and Husseneder, C and Chouljenko, VN and Azad, AF and Macaluso, KR}, title = {Genomic diversification in strains of Rickettsia felis Isolated from different arthropods.}, journal = {Genome biology and evolution}, volume = {7}, number = {1}, pages = {35-56}, doi = {10.1093/gbe/evu262}, pmid = {25477419}, issn = {1759-6653}, support = {R01 AI043006/AI/NIAID NIH HHS/United States ; R56AI104923/AI/NIAID NIH HHS/United States ; R01 AI017828/AI/NIAID NIH HHS/United States ; HHSN272200900040C/AI/NIAID NIH HHS/United States ; HHSN272200900040C//PHS HHS/United States ; R01AI017828/AI/NIAID NIH HHS/United States ; P30GM110760/GM/NIGMS NIH HHS/United States ; R01AI043006/AI/NIAID NIH HHS/United States ; P30 GM110760/GM/NIGMS NIH HHS/United States ; R56 AI104923/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arthropods/microbiology ; Bacterial Proteins/*genetics ; Cats ; Gene Transfer, Horizontal ; Genomics ; Hemolysin Proteins/*genetics ; Humans ; Phylogeny ; Plasmids/genetics ; Rickettsia felis/*genetics/pathogenicity ; Rickettsiaceae Infections/*genetics/*microbiology/transmission ; Siphonaptera/microbiology ; }, abstract = {Rickettsia felis (Alphaproteobacteria: Rickettsiales) is the causative agent of an emerging flea-borne rickettsiosis with worldwide occurrence. Originally described from the cat flea, Ctenocephalides felis, recent reports have identified R. felis from other flea species, as well as other insects and ticks. This diverse host range for R. felis may indicate an underlying genetic variability associated with host-specific strains. Accordingly, to determine a potential genetic basis for host specialization, we sequenced the genome of R. felis str. LSU-Lb, which is an obligate mutualist of the parthenogenic booklouse Liposcelis bostrychophila (Insecta: Psocoptera). We also sequenced the genome of R. felis str. LSU, the second genome sequence for cat flea-associated strains (cf. R. felis str. URRWXCal2), which are presumably facultative parasites of fleas. Phylogenomics analysis revealed R. felis str. LSU-Lb diverged from the flea-associated strains. Unexpectedly, R. felis str. LSU was found to be divergent from R. felis str. URRWXCal2, despite sharing similar hosts. Although all three R. felis genomes contain the pRF plasmid, R. felis str. LSU-Lb carries an additional unique plasmid, pLbaR (plasmid of L. bostrychophila associated Rickettsia), nearly half of which encodes a unique 23-gene integrative conjugative element. Remarkably, pLbaR also encodes a repeats-in-toxin-like type I secretion system and associated toxin, heretofore unknown from other Rickettsiales genomes, which likely originated from lateral gene transfer with another obligate intracellular parasite of arthropods, Cardinium (Bacteroidetes). Collectively, our study reveals unexpected genomic diversity across three R. felis strains and identifies several diversifying factors that differentiate facultative parasites of fleas from obligate mutualists of booklice.}, } @article {pmid25371435, year = {2015}, author = {Groussin, M and Hobbs, JK and Szöllősi, GJ and Gribaldo, S and Arcus, VL and Gouy, M}, title = {Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees.}, journal = {Molecular biology and evolution}, volume = {32}, number = {1}, pages = {13-22}, doi = {10.1093/molbev/msu305}, pmid = {25371435}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Computational Biology/*methods ; Computer Simulation ; Evolution, Molecular ; Genotype ; Gram-Positive Bacteria/enzymology/genetics ; Phenotype ; Phylogeny ; Proteins/*genetics ; }, abstract = {The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the species phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using species tree-aware gene trees on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify.}, } @article {pmid25331432, year = {2015}, author = {Blesa, A and César, CE and Averhoff, B and Berenguer, J}, title = {Noncanonical cell-to-cell DNA transfer in Thermus spp. is insensitive to argonaute-mediated interference.}, journal = {Journal of bacteriology}, volume = {197}, number = {1}, pages = {138-146}, doi = {10.1128/JB.02113-14}, pmid = {25331432}, issn = {1098-5530}, mesh = {Argonaute Proteins/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/*physiology ; Gene Expression Regulation, Bacterial/physiology ; Gene Transfer, Horizontal/*physiology ; Plasmids ; Thermus thermophilus/cytology/genetics/*metabolism ; }, abstract = {Horizontal gene transfer drives the rapid evolution of bacterial populations. Classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. However, some species have nonconserved transfer mechanisms that are not well known. This is the case for the ancient extreme thermophile Thermus thermophilus. In this work, we show that T. thermophilus strains are capable of exchanging large DNA fragments by a novel mechanism that requires cell-to-cell contacts and employs components of the natural transformation machinery. This process facilitates the bidirectional transfer of virtually any DNA locus but favors by 10-fold loci found in the megaplasmid over those in the chromosome. In contrast to naked DNA acquisition by transformation, the system does not activate the recently described DNA-DNA interference mechanism mediated by the prokaryotic Argonaute protein, thus allowing the organism to distinguish between DNA transferred from a mate and exogenous DNA acquired from unknown hosts. This Argonaute-mediated discrimination may be tentatively viewed as a strategy for safe sharing of potentially "useful" traits by the components of a given population of Thermus spp. without increasing the genome sizes of its individuals.}, } @article {pmid25261830, year = {2014}, author = {Alonso, R and Girbau, C and Martinez-Malaxetxebarria, I and Fernández-Astorga, A}, title = {Multilocus sequence typing reveals genetic diversity of foodborne Arcobacter butzleri isolates in the North of Spain.}, journal = {International journal of food microbiology}, volume = {191}, number = {}, pages = {125-128}, doi = {10.1016/j.ijfoodmicro.2014.09.012}, pmid = {25261830}, issn = {1879-3460}, mesh = {Alleles ; Animals ; Arcobacter/*genetics ; Bacteriocins/genetics ; *Food Microbiology ; Gene Transfer, Horizontal ; *Genetic Variation ; Glutamate-Ammonia Ligase/genetics ; Humans ; *Multilocus Sequence Typing ; Spain ; }, abstract = {The emerging pathogen Arcobacter butzleri is being increasingly isolated from different animal food products but the routes of its transmission to human are not well established yet. Typing methods would be useful in gaining such knowledge. Here we report the great genetic diversity observed among A. butzleri isolates from different food products. Forty-five isolates were analyzed by Multilocus Sequence Typing (MLST). A total of 157 alleles were identified across all seven loci, ranging from 16 alleles at glnA to 31 at glyA. MLST differentiated the isolates into 34 sequence types (STs), with the majority of isolates containing a unique sequence type. Seventy-four new alleles were identified, which resulted in the assignment of 33 new STs. No association of alleles or STs with food source was observed. For the first time, lateral gene transfer from Arcobacter skirrowii to A. butzleri at the glyA locus is also reported.}, } @article {pmid25221566, year = {2014}, author = {Sagy, O and Shamir, R and Rechavi, O}, title = {Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {275}, doi = {10.3389/fgene.2014.00275}, pmid = {25221566}, issn = {1664-8021}, abstract = {Genome sequencing requires insertion of random fragments of the sequenced organism's DNA into a unicellular host, most often Escherichia coli bacteria. This manipulation was found in the past to be analogous to naturally occurring horizontal gene transfer, and moreover has proved valuable to understanding toxicity of foreign genetic elements to E. coli. Sequencing of the Caenorhabditis elegans genome was similarly achieved via DNA transformation into E. coli. However, numerous attempts have proven a significant percentage of the genome unclonable using bacteria, although clonable via yeast. We examined the genomic segments that were not clonable in bacteria but were clonable in yeast, and observed that, in line with previous hypotheses, such sequences are more repetitive on average compared with the entire C. elegans genome. In addition, we found that these gap-sequences encode significantly more for DNA transposons. Surprisingly, we discovered that although the vast majority of the C. elegans genome is clonable in bacteria (77.5%), almost all the thousands of sequences that encode for PIWI-interacting small RNAs, or 21U-RNAs (91.6%) were only clonable in yeast. These results might help understanding why most piRNAs in C. elegans are physically clustered on particular loci on chromosome IV. In worms and in a large number of other organisms, piRNAs serve to distinguish "Self" from "Non-Self" sequences, and thus to protect the integrity of the genome against foreign genetic elements, such as transposons. We discuss the possible implications of these discoveries.}, } @article {pmid25173757, year = {2014}, author = {Mortimer, TD and Pepperell, CS}, title = {Genomic signatures of distributive conjugal transfer among mycobacteria.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2489-2500}, doi = {10.1093/gbe/evu175}, pmid = {25173757}, issn = {1759-6653}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; T32 GM07215/GM/NIGMS NIH HHS/United States ; }, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Humans ; Mycobacterium/classification/*genetics/isolation & purification ; Mycobacterium Infections/microbiology ; Phylogeny ; Recombination, Genetic ; }, abstract = {Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis. We have tested popular LGT detection methods on whole-genome sequence data from experimental DCT transconjugants and used the best performing methods to compare genomic signatures of DCT with those of LGT through natural transformation, conjugative plasmids, and mobile genetic elements (MGE). We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT. We used the best performing methods to characterize LGT in Mycobacterium canettii, the mycobacterial species most closely related to Mycobacterium tuberculosis. Patterns of LGT among M. canettii were highly distinctive. Gene flow appeared unidirectional, from lineages with minimal evidence of LGT to isolates with a substantial proportion (6-13%) of sites identified as recombinant. Among M. canettii isolates with evidence of LGT, recombinant fragments were larger and more evenly distributed relative to bacteria that undergo LGT through natural transformation, conjugative plasmids, and MGE. Spatial bias in M. canettii was also unusual in that patterns of recombinant fragment sharing mirrored overall phylogenetic structure. Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.}, } @article {pmid25168586, year = {2014}, author = {Ioannidis, P and Lu, Y and Kumar, N and Creasy, T and Daugherty, S and Chibucos, MC and Orvis, J and Shetty, A and Ott, S and Flowers, M and Sengamalay, N and Tallon, LJ and Pick, L and Dunning Hotopp, JC}, title = {Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {738}, doi = {10.1186/1471-2164-15-738}, pmid = {25168586}, issn = {1471-2164}, mesh = {Animals ; Bacteria/genetics ; Bacterial Proteins/genetics ; Computational Biology/methods ; Female ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal ; Heteroptera/*genetics/microbiology ; Insect Proteins/*genetics ; Introduced Species ; Male ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, RNA/*methods ; Symbiosis ; }, abstract = {BACKGROUND: Halyomorpha halys (Stål) (Insecta:Hemiptera;Pentatomidae), commonly known as the Brown Marmorated Stink Bug (BMSB), is an invasive pest of the mid-Atlantic region of the United States, causing economically important damage to a wide range of crops. Native to Asia, BMSB was first observed in Allentown, PA, USA, in 1996, and this pest is now well-established throughout the US mid-Atlantic region and beyond. In addition to the serious threat BMSB poses to agriculture, BMSB has become a nuisance to homeowners, invading home gardens and congregating in large numbers in human-made structures, including homes, to overwinter. Despite its significance as an agricultural pest with limited control options, only 100 bp of BMSB sequence data was available in public databases when this project began.

RESULTS: Transcriptome sequencing was undertaken to provide a molecular resource to the research community to inform the development of pest control strategies and to provide molecular data for population genetics studies of BMSB. Using normalized, strand-specific libraries, we sequenced pools of all BMSB life stages on the Illumina HiSeq. Trinity was used to assemble 200,000 putative transcripts in >100,000 components. A novel bioinformatic method that analyzed the strand-specificity of the data reduced this to 53,071 putative transcripts from 18,573 components. By integrating multiple other data types, we narrowed this further to 13,211 representative transcripts.

CONCLUSIONS: Bacterial endosymbiont genes were identified in this dataset, some of which have a copy number consistent with being lateral gene transfers between endosymbiont genomes and Hemiptera, including ankyrin-repeat related proteins, lysozyme, and mannanase. Such genes and endosymbionts may provide novel targets for BMSB-specific biocontrol. This study demonstrates the utility of strand-specific sequencing in generating shotgun transcriptomes and that rapid sequencing shotgun transcriptomes is possible without the need for extensive inbreeding to generate homozygous lines. Such sequencing can provide a rapid response to pest invasions similar to that already described for disease epidemiology.}, } @article {pmid25146649, year = {2014}, author = {Grant, JR and Katz, LA}, title = {Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2350-2360}, doi = {10.1093/gbe/evu179}, pmid = {25146649}, issn = {1759-6653}, support = {R15 GM097722/GM/NIGMS NIH HHS/United States ; 1R15GM097722-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Entamoeba/*classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Parabasalidea/*classification/*genetics ; *Phylogeny ; }, abstract = {Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence--a taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence--to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our approach, using an automated phylogenomic pipeline to build taxon-rich gene trees, suggests that LGT is more extensive than previously thought. Our analyses reveal that genes have frequently entered the Entamoeba genome via nonvertical events, including at least 116 genes acquired directly from bacteria or archaea, plus an additional 22 genes in which Entamoeba plus one other eukaryote are nested among bacteria and/or archaea. These genes may make good candidates for novel therapeutics, as drugs targeting these genes are less likely to impact the human host. Although we recognize the challenges of inferring intradomain transfers given systematic errors in gene trees, we find 109 genes supporting LGT from a eukaryote to Entamoeba spp., and 178 genes unique to Entamoeba spp. and one other eukaryotic taxon (i.e., presence/absence data). Inspection of these intradomain LGTs provide evidence of a common sister relationship between genes of Entamoeba (Amoebozoa) and parabasalids (Excavata). We speculate that this indicates a past close relationship (e.g., symbiosis) between ancestors of these extant lineages.}, } @article {pmid25108459, year = {2014}, author = {Shanker, A and Pardasani, KR}, title = {Insilico model for prediction of lateral gene transfer in Rhodopseudomonas paulistris.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {6}, number = {4}, pages = {323-330}, doi = {10.1007/s12539-012-0071-7}, pmid = {25108459}, issn = {1867-1462}, mesh = {Alphaproteobacteria/genetics ; Bacterial Proteins/*genetics ; Bradyrhizobium/genetics ; Computer Simulation ; Cyanobacteria/genetics ; DNA, Ribosomal/analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Least-Squares Analysis ; Models, Biological ; Oxidoreductases/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodobacter/genetics ; Rhodopseudomonas/*genetics ; Sequence Analysis, DNA ; }, abstract = {Study of evolutionary phenomenon is of great interest to biologists in discovering the secrets of life. The presence of reticulation events due to lateral gene transfer (LGT) among species poses new challenges for such evolutionary studies. In this paper an attempt has been made to develop an insilico model to predict LGT in the Rhodopseudomonas paulistris. Neighbour Joining method is employed to generate phylogenetic tree of 26 sequences of Alphaproteobacteria and one sequence of Cyanobacteria used as an out group. Then Least Squares approach is employed to predict the reticulation branches. Three reticulation branches were detected among these 27 sequences. The lateral gene transfer was predicted between Rhodopseudomonas paulistris 99 D and Rhodobacter sphaeroides, Rhodopseudomonas paulistris HMD 88 and Bradyrhizobium japonicum USDA and Bradyrhizobium japonicum USDA and Rhodobacter blasticus. The results obtained are in agreement with the results obtained by earlier research workers.}, } @article {pmid26988457, year = {2014}, author = {Piccin-Santos, V and Brandão, MM and Bittencourt-Oliveira, Mdo C}, title = {Phylogenetic study of Geitlerinema and Microcystis (Cyanobacteria) using PC-IGS and 16S-23S ITS as markers: investigation of horizontal gene transfer.}, journal = {Journal of phycology}, volume = {50}, number = {4}, pages = {736-743}, doi = {10.1111/jpy.12204}, pmid = {26988457}, issn = {1529-8817}, abstract = {Selection of genes that have not been horizontally transferred for prokaryote phylogenetic inferences is regarded as a challenging task. The markers internal transcribed spacer of ribosomal genes (16S-23S ITS) and phycocyanin intergenic spacer (PC-IGS), based on the operons of ribosomal and phycocyanin genes respectively, are among the most used markers in cyanobacteria. The region of the ribosomal genes has been considered stable, whereas the phycocyanin operon may have undergone horizontal transfer. To investigate the occurrence of horizontal transfer of PC-IGS, phylogenetic trees of Geitlerinema and Microcystis strains were generated using PC-IGS and 16S-23S ITS and compared. Phylogenetic trees based on the two markers were mostly congruent for Geitlerinema and Microcystis, indicating a common evolutionary history among ribosomal and phycocyanin genes with no evidence for horizontal transfer of PC-IGS. Thus, PC-IGS is a suitable marker, along with 16S-23S ITS for phylogenetic studies of cyanobacteria.}, } @article {pmid24998348, year = {2014}, author = {Filée, J}, title = {Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of the iceberg?.}, journal = {Virology}, volume = {466-467}, number = {}, pages = {53-59}, doi = {10.1016/j.virol.2014.06.004}, pmid = {24998348}, issn = {1096-0341}, mesh = {Chromosomes/genetics ; Cryptophyta/genetics/virology ; DNA Primase/genetics ; DNA Viruses/classification/*genetics ; DNA, Viral/genetics ; Eukaryota/*genetics/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome/*genetics ; Genome, Viral/*genetics ; Genomics ; Host-Pathogen Interactions ; Phylogeny ; Viral Proteins/*genetics ; }, abstract = {Giant Viruses are a widespread group of viruses, characterized by huge genomes composed of a small subset of ancestral, vertically inherited core genes along with a large body of highly variable genes. In this study, I report the acquisition of 23 core ancestral Giant Virus genes by diverse eukaryotic species including various protists, a moss and a cnidarian. The viral genes are inserted in large scaffolds or chromosomes with intron-rich, eukaryotic-like genomic contexts, refuting the possibility of DNA contaminations. Some of these genes are expressed and in the cryptophyte alga Guillardia theta, a possible non-homologous displacement of the eukaryotic DNA primase by a viral D5 helicase/primase is documented. As core Giant Virus genes represent only a tiny fraction of the total genomic repertoire of these viruses, these results suggest that Giant Viruses represent an underestimated source of new genes and functions for their hosts.}, } @article {pmid24998344, year = {2014}, author = {Dorman, CJ}, title = {H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria.}, journal = {Plasmid}, volume = {75}, number = {}, pages = {1-11}, doi = {10.1016/j.plasmid.2014.06.004}, pmid = {24998344}, issn = {1095-9890}, mesh = {Amino Acid Sequence ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Interspersed Repetitive Sequences/*genetics ; Molecular Sequence Data ; Plasmids/*genetics ; }, abstract = {Horizontal gene transfer plays an important role in the evolution of bacterial species, conferring new genetic traits on the recipient bacterium that extend its range of phenotypes and plasmids make important contributions to this process. However, the inappropriate expression of newly acquired genes may lead to a loss of competitive fitness, resulting in the elimination of the new gene-bacterium combination. It is thought that transcriptional silencing of horizontally acquired genes offers a route out of this dilemma and that nucleoid-associated proteins, especially those related to the H-NS protein, play a particularly important role in the silencing process. The discovery that many plasmids express orthologues of nucleoid-associated proteins adds an interesting dimension to current models of regulatory integration following lateral transfer of DNA. Other horizontally acquired genetic elements, such as genomic islands, also express nucleoid-associated proteins of their own. Here the interactions of H-NS-like nucleoid-associated proteins encoded by the core genome, genomic islands and plasmids are described.}, } @article {pmid24990676, year = {2014}, author = {Bruto, M and Prigent-Combaret, C and Luis, P and Moënne-Loccoz, Y and Muller, D}, title = {Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1789}, pages = {20140848}, doi = {10.1098/rspb.2014.0848}, pmid = {24990676}, issn = {1471-2954}, mesh = {Biological Evolution ; Carbon-Carbon Lyases/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Introns ; Phylogeny ; Pseudomonas fluorescens/genetics ; Selection, Genetic ; Stramenopiles/genetics ; }, abstract = {Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes-as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.}, } @article {pmid24967627, year = {2014}, author = {Iranzo, J and Gómez, MJ and López de Saro, FJ and Manrubia, S}, title = {Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.}, journal = {PLoS computational biology}, volume = {10}, number = {6}, pages = {e1003680}, doi = {10.1371/journal.pcbi.1003680}, pmid = {24967627}, issn = {1553-7358}, mesh = {DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; *Models, Genetic ; }, abstract = {Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated.}, } @article {pmid24951673, year = {2014}, author = {Bello-Ortí, B and Aragon, V and Pina-Pedrero, S and Bensaid, A}, title = {Genome comparison of three serovar 5 pathogenic strains of Haemophilus parasuis: insights into an evolving swine pathogen.}, journal = {Microbiology (Reading, England)}, volume = {160}, number = {Pt 9}, pages = {1974-1984}, doi = {10.1099/mic.0.079483-0}, pmid = {24951673}, issn = {1465-2080}, mesh = {Animals ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Haemophilus Infections/microbiology/veterinary ; Haemophilus parasuis/classification/*genetics/isolation & purification ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Serogroup ; Swine ; Swine Diseases/microbiology ; }, abstract = {Haemophilus parasuis is the causative agent of Glässer's disease, a systemic disorder characterized by polyarthritis, polyserositis and meningitis in pigs. Although it is well known that H. parasuis serovar 5 is the most prevalent serovar associated with the disease, the genetic differences among strains are only now being discovered. Genomes from two serovar 5 strains, SH0165 and 29755, are already available. Here, we present the draft genome of a third H. parasuis serovar 5 strain, the formal serovar 5 reference strain Nagasaki. An in silico genome subtractive analysis with full-length predicted genes of the three H. parasuis serovar 5 strains detected 95, 127 and 95 strain-specific genes (SSGs) for Nagasaki, SH0165 and 29755, respectively. We found that the genomic diversity within these three strains was high, in part because of a high number of mobile elements. Furthermore, a detailed analysis of large sequence polymorphisms (LSPs), encompassing regions ranging from 2 to 16 kb, revealed LSPs in virulence-related elements, such as a Toll-IL receptor, the AcrA multidrug efflux protein, an ATP-binding cassette (ABC) transporter, lipopolysaccharide-synthetizing enzymes and a tripartite ATP-independent periplasmic (TRAP) transporter. The whole-genome codon adaptation index (CAI) was also calculated and revealed values similar to other well-known bacterial pathogens. In addition, whole-genome SNP analysis indicated that nucleotide changes tended to be increased in membrane-related genes. This analysis provides further evidence that the genome of H. parasuis has been subjected to multiple lateral gene transfers (LGTs) and to fine-tuning of virulence factors, and has the potential for accelerated genome evolution.}, } @article {pmid24898731, year = {2014}, author = {Strese, A and Backlund, A and Alsmark, C}, title = {A recently transferred cluster of bacterial genes in Trichomonas vaginalis--lateral gene transfer and the fate of acquired genes.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {119}, doi = {10.1186/1471-2148-14-119}, pmid = {24898731}, issn = {1471-2148}, mesh = {Bacteria/classification/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Protozoan ; Multigene Family ; Phylogeny ; Trichomonas vaginalis/*genetics ; }, abstract = {BACKGROUND: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome.

RESULTS: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation.

CONCLUSIONS: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.}, } @article {pmid24889424, year = {2015}, author = {Rapa, RA and Islam, A and Monahan, LG and Mutreja, A and Thomson, N and Charles, IG and Stokes, HW and Labbate, M}, title = {A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.}, journal = {Environmental microbiology}, volume = {17}, number = {4}, pages = {1090-1102}, doi = {10.1111/1462-2920.12512}, pmid = {24889424}, issn = {1462-2920}, mesh = {Amino Acid Sequence ; Bacterial Adhesion/genetics ; Base Sequence ; Cholera/*microbiology ; Cholera Toxin/genetics ; DNA Damage/genetics/*radiation effects ; DNA Repair/*genetics ; DNA-Directed DNA Polymerase/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Genomic Islands/*genetics ; Humans ; Molecular Sequence Data ; Rec A Recombinases/*genetics ; Recombination, Genetic ; Ultraviolet Rays/adverse effects ; Vibrio cholerae/genetics/*pathogenicity ; Virulence Factors/genetics ; }, abstract = {Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V. cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V. cholerae strain containing multiple genes involved in DNA repair including the recombination repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in Escherichia coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V. cholerae and emphasizes the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains.}, } @article {pmid24843024, year = {2014}, author = {Wybouw, N and Dermauw, W and Tirry, L and Stevens, C and Grbić, M and Feyereisen, R and Van Leeuwen, T}, title = {A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning.}, journal = {eLife}, volume = {3}, number = {}, pages = {e02365}, pmid = {24843024}, issn = {2050-084X}, mesh = {Alanine/analogs & derivatives/metabolism ; Animals ; *Animals, Genetically Modified ; Bacteria/*genetics ; Cysteine Synthase/genetics/metabolism ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Glycosides/*metabolism ; Hydrogen Cyanide/toxicity ; Lyases/genetics/metabolism ; Phylogeny ; Tetranychidae/*genetics ; Transcription, Genetic ; }, abstract = {Cyanogenic glucosides are among the most widespread defense chemicals of plants. Upon plant tissue disruption, these glucosides are hydrolyzed to a reactive hydroxynitrile that releases toxic hydrogen cyanide (HCN). Yet many mite and lepidopteran species can thrive on plants defended by cyanogenic glucosides. The nature of the enzyme known to detoxify HCN to β-cyanoalanine in arthropods has remained enigmatic. Here we identify this enzyme by transcriptome analysis and functional expression. Phylogenetic analysis showed that the gene is a member of the cysteine synthase family horizontally transferred from bacteria to phytophagous mites and Lepidoptera. The recombinant mite enzyme had both β-cyanoalanine synthase and cysteine synthase activity but enzyme kinetics showed that cyanide detoxification activity was strongly favored. Our results therefore suggest that an ancient horizontal transfer of a gene originally involved in sulfur amino acid biosynthesis in bacteria was co-opted by herbivorous arthropods to detoxify plant produced cyanide.DOI: http://dx.doi.org/10.7554/eLife.02365.001.}, } @article {pmid24839025, year = {2014}, author = {Trejo-Becerril, C and Pérez-Cárdenas, E and Dueñas-González, A}, title = {In vivo rat model to study horizontal tumor progression.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1165}, number = {}, pages = {175-185}, doi = {10.1007/978-1-4939-0856-1_12}, pmid = {24839025}, issn = {1940-6029}, mesh = {Animals ; Cell Line, Tumor ; DNA/blood/genetics ; Disease Models, Animal ; *Disease Progression ; Female ; *Gene Transfer Techniques ; Humans ; In Situ Hybridization, Fluorescence ; Microdissection ; Neoplasms/blood/*genetics/*pathology ; Polymerase Chain Reaction ; Rats ; Rats, Wistar ; Sequence Analysis, DNA ; }, abstract = {Most cancer deaths are due to metastases. Metastasis is an extraordinarily complex process by which cancer cells complete a sequential series of steps before they transform into a clinically detectable lesion. These steps typically include separation from the primary tumor, invasion through surrounding tissues and basement membranes, entry and survival in the circulation, lymphatic or peritoneal space, and arrest in a distant target organ and the formation of secondary tumors in distant organs.While proposed or accepted models and mechanisms of metastatic progression, have been demonstrated in experimental systems, none of them sufficiently explain all of the complexities associated with this process. These models can broadly be classified into two types, those occurring by vertical gene transfer (Darwinian) and those involving horizontal or lateral DNA transfer. Here, we describe an experimental system to study the metastatic process involving the horizontal transfer of circulating DNA.}, } @article {pmid24818264, year = {2014}, author = {Dibrova, DV and Galperin, MY and Mulkidjanian, AY}, title = {Phylogenomic reconstruction of archaeal fatty acid metabolism.}, journal = {Environmental microbiology}, volume = {16}, number = {4}, pages = {907-918}, pmid = {24818264}, issn = {1462-2920}, support = {Z99 LM999999/NULL/Intramural NIH HHS/United States ; ZIA LM000073-14/NULL/Intramural NIH HHS/United States ; }, mesh = {3-Hydroxyacyl CoA Dehydrogenases/genetics/*metabolism ; Acyl-CoA Dehydrogenase/*metabolism ; Archaea/genetics/*metabolism ; Enoyl-CoA Hydratase/genetics/*metabolism ; Fatty Acids/*metabolism ; Gene Transfer, Horizontal ; Genomics ; Multienzyme Complexes/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {While certain archaea appear to synthesize and/or metabolize fatty acids, the respective pathways still remain obscure. By analysing the genomic distribution of the key lipid-related enzymes, we were able to identify the likely components of the archaeal pathway of fatty acid metabolism, namely, a combination of the enzymes of bacterial-type β-oxidation of fatty acids [acyl-coenzyme A (CoA) dehydrogenase, enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase] with paralogs of the archaeal acetyl-CoA C-acetyltransferase, an enzyme of the mevalonate biosynthesis pathway. These three β-oxidation enzymes working in the reverse direction could potentially catalyse biosynthesis of fatty acids, with paralogs of acetyl-CoA C-acetyltransferase performing addition of C2 fragments. The presence in archaea of the genes for energy-transducing membrane enzyme complexes, such as cytochrome bc complex, cytochrome c oxidase and diverse rhodopsins, was found to correlate with the presence of the proposed system of fatty acid biosynthesis. We speculate that because these membrane complexes functionally depend on fatty acid chains, their genes could have been acquired via lateral gene transfer from bacteria only by those archaea that already possessed a system of fatty acid biosynthesis. The proposed pathway of archaeal fatty acid metabolism operates in extreme conditions and therefore might be of interest in the context of biofuel production and other industrial applications.}, } @article {pmid24793159, year = {2014}, author = {Yu, D and Pi, B and Yu, M and Wang, Y and Ruan, Z and Feng, Y and Yu, Y}, title = {Diversity and evolution of oligopeptide permease systems in staphylococcal species.}, journal = {Genomics}, volume = {104}, number = {1}, pages = {8-13}, doi = {10.1016/j.ygeno.2014.04.003}, pmid = {24793159}, issn = {1089-8646}, mesh = {Bacterial Proteins/*genetics ; Coagulase/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Bacterial ; Hydrolases/genetics ; Interspersed Repetitive Sequences ; Membrane Transport Proteins/*genetics ; Operon ; Phylogeny ; Staphylococcus/classification/enzymology/*genetics ; }, abstract = {Several oligopeptide permease (Opp) systems have been found in staphylococcal species, including Opp1-4, Opp3' and the arginine catabolic mobile element (ACME)-encoded Opp system (ACME-Opp). They confer upon bacteria the increasing fitness, but their evolutionary histories remain unclear. In this work, we performed a genome-wide identification of Opp systems in staphylococcal species. Novel Opp systems were identified, including the duplicate of Opp4 in Staphylococcus pseudintermedius and the ACME-Opp-like systems in coagulase-negative staphylococci (CoNS). Phylogenetic analysis revealed that all of the identified Opp systems were derived from Opp3 system by operon duplication during species divergence, while lateral gene transfer might also confer to the dissemination of Opp in staphylococci. In addition, we proposed an improved theory on evolution of ACME: the Opp and arginine-deiminase systems were firstly transferred from Staphylococcus haemolyticus to Staphylococcus epidermidis independently; in S. epidermidis they were assembled together and then transferred to Staphylococcus aureus.}, } @article {pmid24747127, year = {2014}, author = {Parker, MA and Rousteau, A}, title = {Mosaic origins of Bradyrhizobium legume symbionts on the Caribbean island of Guadeloupe.}, journal = {Molecular phylogenetics and evolution}, volume = {77}, number = {}, pages = {110-115}, doi = {10.1016/j.ympev.2014.04.011}, pmid = {24747127}, issn = {1095-9513}, mesh = {Bayes Theorem ; Bradyrhizobium/classification/*genetics/isolation & purification ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; Guadeloupe ; *Phylogeny ; Sequence Analysis, DNA ; *Symbiosis/genetics ; }, abstract = {To analyze geographic affinities of Bradyrhizobium sp. symbionts associated with the diverse legume flora on the Caribbean island of Guadeloupe, 39 isolates from 18 legume genera were compared to a reference set of 269 Bradyrhizobium strains from North America, Central America, Puerto Rico and the Philippines. A multilocus sequence analysis (4192 bp) showed that nucleotide diversity in Guadeloupe equaled or exceeded that found in all other regional Bradyrhizobium populations examined. Bayesian phylogenetic tree analysis grouped the Guadeloupe Bradyrhizobium strains into clades with at least 20 distinct sets of non-Guadeloupe relatives, implying that the island was colonized numerous times from multiple source regions. However, for 18% of the Guadeloupe isolates, inferred geographic affinities for the nifD locus, in the symbiosis island region of the Bradyrhizobium chromosome, conflicted with the source region deduced from a tree based on six concatenated housekeeping genes. Geographic mosaic ancestry was therefore evident among Guadeloupe bradyrhizobia. Horizontal gene transfer subsequent to island colonization appears to have generated strains that carry combinations of genes from disparate source regions.}, } @article {pmid24736222, year = {2014}, author = {Pawluk, A and Bondy-Denomy, J and Cheung, VH and Maxwell, KL and Davidson, AR}, title = {A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa.}, journal = {mBio}, volume = {5}, number = {2}, pages = {e00896}, doi = {10.1128/mBio.00896-14}, pmid = {24736222}, issn = {2150-7511}, support = {MOP-130482//Canadian Institutes of Health Research/Canada ; MOP-62796//Canadian Institutes of Health Research/Canada ; }, mesh = {*CRISPR-Cas Systems ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Host-Parasite Interactions ; Pseudomonas Phages/*genetics/*growth & development ; Pseudomonas aeruginosa/*genetics/*virology ; Viral Proteins/*metabolism ; }, abstract = {CRISPR-Cas systems are one of the most widespread phage resistance mechanisms in prokaryotes. Our lab recently identified the first examples of phage-borne anti-CRISPR genes that encode protein inhibitors of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa. A key question arising from this work was whether there are other types of anti-CRISPR genes. In the current work, we address this question by demonstrating that some of the same phages carrying type I-F anti-CRISPR genes also possess genes that mediate inhibition of the type I-E CRISPR-Cas system of P. aeruginosa. We have discovered four distinct families of these type I-E anti-CRISPR genes. These genes do not inhibit the type I-F CRISPR-Cas system of P. aeruginosa or the type I-E system of Escherichia coli. Type I-E and I-F anti-CRISPR genes are located at the same position in the genomes of a large group of related P. aeruginosa phages, yet they are found in a variety of combinations and arrangements. We have also identified functional anti-CRISPR genes within nonprophage Pseudomonas genomic regions that are likely mobile genetic elements. This work emphasizes the potential importance of anti-CRISPR genes in phage evolution and lateral gene transfer and supports the hypothesis that more undiscovered families of anti-CRISPR genes exist. Finally, we provide the first demonstration that the type I-E CRISPR-Cas system of P. aeruginosa is naturally active without genetic manipulation, which contrasts with E. coli and other previously characterized I-E systems. IMPORTANCE The CRISPR-Cas system is an adaptive immune system possessed by the majority of prokaryotic organisms to combat potentially harmful foreign genetic elements. This study reports the discovery of bacteriophage-encoded anti-CRISPR genes that mediate inhibition of a well-studied subtype of CRISPR-Cas system. The four families of anti-CRISPR genes described here, which comprise only the second group of anti-CRISPR genes to be identified, encode small proteins that bear no sequence similarity to previously studied phage or bacterial proteins. Anti-CRISPR genes represent a newly discovered and intriguing facet of the ongoing evolutionary competition between phages and their bacterial hosts.}, } @article {pmid24371153, year = {2014}, author = {Jaron, KS and Moravec, JC and Martínková, N}, title = {SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {8}, pages = {1081-1086}, doi = {10.1093/bioinformatics/btt727}, pmid = {24371153}, issn = {1367-4811}, mesh = {Base Composition ; Computational Biology ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; *Genomic Islands ; Genomics/methods ; *Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.

RESULTS: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.

Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research-data-analysis-tools-sighunt are implemented in C and R and are platform-independent.

CONTACT: 376090@mail.muni.cz or martinkova@ivb.cz.}, } @article {pmid24695589, year = {2014}, author = {Whidden, C and Zeh, N and Beiko, RG}, title = {Supertrees Based on the Subtree Prune-and-Regraft Distance.}, journal = {Systematic biology}, volume = {63}, number = {4}, pages = {566-581}, doi = {10.1093/sysbio/syu023}, pmid = {24695589}, issn = {1076-836X}, mesh = {Algorithms ; Bacteria/*classification/genetics ; Classification/*methods ; *Computer Simulation ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; *Phylogeny ; Reproducibility of Results ; }, abstract = {Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Many supertree approaches use optimality criteria that do not reflect underlying processes, have known biases, and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and>50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of benchmark datasets simulated under plausible rates of LGT, we show that SPR supertrees are more similar to correct species histories than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera. A Small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT. [Lateral gene transfer; matrix representation with parsimony; phylogenomics; prokaryotic phylogeny; Robinson-Foulds; subtree prune-and-regraft; supertrees.].}, } @article {pmid24669202, year = {2014}, author = {Borrel, G and Gaci, N and Peyret, P and O'Toole, PW and Gribaldo, S and Brugère, JF}, title = {Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2014}, number = {}, pages = {374146}, doi = {10.1155/2014/374146}, pmid = {24669202}, issn = {1472-3654}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Bacteria/genetics ; Biosynthetic Pathways/*genetics ; Euryarchaeota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Code ; Lysine/*analogs & derivatives/biosynthesis ; Phylogeny ; RNA, Transfer/genetics ; Sequence Homology ; }, abstract = {Pyrrolysine (Pyl), the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber tRNA(Pyl) with an imperfect anticodon stem and a shortened tRNA(Pyl) synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.}, } @article {pmid24634779, year = {2014}, author = {Castagnola, A and Stock, SP}, title = {Common Virulence Factors and Tissue Targets of Entomopathogenic Bacteria for Biological Control of Lepidopteran Pests.}, journal = {Insects}, volume = {5}, number = {1}, pages = {139-166}, doi = {10.3390/insects5010139}, pmid = {24634779}, issn = {2075-4450}, support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; }, abstract = {This review focuses on common insecticidal virulence factors from entomopathogenic bacteria with special emphasis on two insect pathogenic bacteria Photorhabdus (Proteobacteria: Enterobacteriaceae) and Bacillus (Firmicutes: Bacillaceae). Insect pathogenic bacteria of diverse taxonomic groups and phylogenetic origin have been shown to have striking similarities in the virulence factors they produce. It has been suggested that the detection of phage elements surrounding toxin genes, horizontal and lateral gene transfer events, and plasmid shuffling occurrences may be some of the reasons that virulence factor genes have so many analogs throughout the bacterial kingdom. Comparison of virulence factors of Photorhabdus, and Bacillus, two bacteria with dissimilar life styles opens the possibility of re-examining newly discovered toxins for novel tissue targets. For example, nematodes residing in the hemolymph may release bacteria with virulence factors targeting neurons or neuromuscular junctions. The first section of this review focuses on toxins and their context in agriculture. The second describes the mode of action of toxins from common entomopathogens and the third draws comparisons between Gram positive and Gram negative bacteria. The fourth section reviews the implications of the nervous system in biocontrol.}, } @article {pmid24625962, year = {2014}, author = {Richards, VP and Palmer, SR and Pavinski Bitar, PD and Qin, X and Weinstock, GM and Highlander, SK and Town, CD and Burne, RA and Stanhope, MJ}, title = {Phylogenomics and the dynamic genome evolution of the genus Streptococcus.}, journal = {Genome biology and evolution}, volume = {6}, number = {4}, pages = {741-753}, doi = {10.1093/gbe/evu048}, pmid = {24625962}, issn = {1759-6653}, support = {T90 DE021990/DE/NIDCR NIH HHS/United States ; R01 AI073368/AI/NIAID NIH HHS/United States ; AI073368/AI/NIAID NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; 272200900007C//PHS HHS/United States ; }, mesh = {Base Sequence ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Genome, Bacterial/*physiology ; Humans ; Molecular Sequence Data ; *Phylogeny ; Streptococcus/*genetics ; }, abstract = {The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.}, } @article {pmid24625961, year = {2014}, author = {Meehan, CJ and Beiko, RG}, title = {A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.}, journal = {Genome biology and evolution}, volume = {6}, number = {3}, pages = {703-713}, doi = {10.1093/gbe/evu050}, pmid = {24625961}, issn = {1759-6653}, support = {CMF-108026//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Bacteria/*genetics/isolation & purification ; Butyric Acid/metabolism ; Ecosystem ; Evolution, Molecular ; Gastrointestinal Tract/*microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Mammals/microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Several bacterial families are known to be highly abundant within the human microbiome, but their ecological roles and evolutionary histories have yet to be investigated in depth. One such family, Lachnospiraceae (phylum Firmicutes, class Clostridia) is abundant in the digestive tracts of many mammals and relatively rare elsewhere. Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association of many species within the group with the production of butyric acid, a substance that is important for both microbial and host epithelial cell growth. We examined the genomes of 30 Lachnospiraceae isolates to better understand the origin of butyric acid capabilities and other ecological adaptations within this group. Butyric acid production-related genes were detected in fewer than half of the examined genomes with the distribution of this function likely arising in part from lateral gene transfer (LGT). An investigation of environment-specific functional signatures indicated that human gut-associated Lachnospiraceae possess genes for endospore formation, whereas other members of this family lack key sporulation-associated genes, an observation supported by analysis of metagenomes from the human gut, oral cavity, and bovine rumen. Our analysis demonstrates that adaptation to an ecological niche and acquisition of defining functional roles within a microbiome can arise through a combination of both habitat-specific gene loss and LGT.}, } @article {pmid24564205, year = {2013}, author = {Patterson, M and Szöllősi, G and Daubin, V and Tannier, E}, title = {Lateral gene transfer, rearrangement, reconciliation.}, journal = {BMC bioinformatics}, volume = {14 Suppl 15}, number = {}, pages = {S4}, doi = {10.1186/1471-2105-14-S15-S4}, pmid = {24564205}, issn = {1471-2105}, mesh = {Algorithms ; Cyanobacteria/genetics ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genome ; Software ; }, abstract = {BACKGROUND: Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. These models have so far ignored lateral gene transfer, even though in unicellular organisms it can have an important confounding effect, and can be a rich source of information on the function of genes through the detection of transfers of clusters of genes.

RESULT: We report an algorithm together with its implementation, DeCoLT, that reconstructs ancestral genome organization based on reconciled gene trees which summarize information on sequence evolution, gene origination, duplication, loss, and lateral transfer. DeCoLT optimizes in polynomial time on the number of rearrangements, computed as the number of gains and breakages of adjacencies between pairs of genes. We apply DeCoLT to 1099 gene families from 36 cyanobacteria genomes.

CONCLUSION: DeCoLT is able to reconstruct adjacencies in 35 ancestral bacterial genomes with a thousand gene families in a few hours, and detects clusters of co-transferred genes. DeCoLT may also be used with any relationship between genes instead of adjacencies, to reconstruct ancestral interactions, functions or complexes.

AVAILABILITY: http://pbil.univ-lyon1.fr/software/DeCoLT/}, } @article {pmid24562812, year = {2014}, author = {Sjöstrand, J and Tofigh, A and Daubin, V and Arvestad, L and Sennblad, B and Lagergren, J}, title = {A Bayesian method for analyzing lateral gene transfer.}, journal = {Systematic biology}, volume = {63}, number = {3}, pages = {409-420}, doi = {10.1093/sysbio/syu007}, pmid = {24562812}, issn = {1076-836X}, mesh = {Bayes Theorem ; Classification/*methods ; Cyanobacteria/classification/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Models, Theoretical ; Phylogeny ; Tenericutes/classification/genetics ; }, abstract = {Lateral gene transfer (LGT)--which transfers DNA between two non-vertically related individuals belonging to the same or different species--is recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications (GDs). Consequently, proposed LGT among specific gene families, and the rate of LGT in general, remain debated. We present a Bayesian Markov-chain Monte Carlo-based method that integrates GD, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close-species LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events.}, } @article {pmid24536043, year = {2014}, author = {Knöppel, A and Lind, PA and Lustig, U and Näsvall, J and Andersson, DI}, title = {Minor fitness costs in an experimental model of horizontal gene transfer in bacteria.}, journal = {Molecular biology and evolution}, volume = {31}, number = {5}, pages = {1220-1227}, doi = {10.1093/molbev/msu076}, pmid = {24536043}, issn = {1537-1719}, mesh = {Bacteria/*genetics/metabolism ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Fitness ; Humans ; *Models, Genetic ; Mutagenesis, Insertional ; Salmonella typhimurium/genetics/metabolism ; Selection, Genetic ; }, abstract = {Genes introduced by horizontal gene transfer (HGT) from other species constitute a significant portion of many bacterial genomes, and the evolutionary dynamics of HGTs are important for understanding the spread of antibiotic resistance and the emergence of new pathogenic strains of bacteria. The fitness effects of the transferred genes largely determine the fixation rates and the amount of neutral diversity of newly acquired genes in bacterial populations. Comparative analysis of bacterial genomes provides insight into what genes are commonly transferred, but direct experimental tests of the fitness constraints on HGT are scarce. Here, we address this paucity of experimental studies by introducing 98 random DNA fragments varying in size from 0.45 to 5 kb from Bacteroides, Proteus, and human intestinal phage into a defined position in the Salmonella chromosome and measuring the effects on fitness. Using highly sensitive competition assays, we found that eight inserts were deleterious with selection coefficients (s) ranging from ≈ -0.007 to -0.02 and 90 did not have significant fitness effects. When inducing transcription from a PBAD promoter located at one end of the insert, 16 transfers were deleterious and 82 were not significantly different from the control. In conclusion, a major fraction of the inserts had minor effects on fitness implying that extra DNA transferred by HGT, even though it does not confer an immediate selective advantage, could be maintained at selection-transfer balance and serve as raw material for the evolution of novel beneficial functions.}, } @article {pmid24502835, year = {2014}, author = {Sharma, P and Gupta, SK and Rolain, JM}, title = {Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution.}, journal = {Expert review of anti-infective therapy}, volume = {12}, number = {3}, pages = {343-355}, doi = {10.1586/14787210.2014.887441}, pmid = {24502835}, issn = {1744-8336}, mesh = {Burkholderia cepacia complex/genetics ; Cystic Fibrosis/*microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Humans ; Pseudomonas aeruginosa/genetics ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics ; }, abstract = {Cystic fibrosis (CF) airways harbor a wide variety of new and/or emerging multidrug resistant bacteria which impose a heavy burden on patients. These bacteria live in close proximity with one another, which increases the frequency of lateral gene transfer. The exchange and movement of mobile genetic elements and genomic islands facilitate the spread of genes between genetically diverse bacteria, which seem to be advantageous to the bacterium as it allows adaptation to the new niches of the CF lungs. Niche adaptation is one of the major evolutionary forces shaping bacterial genome composition and in CF the chronic strains adapt and become less virulent. The purpose of this review is to shed light on CF bacterial genome alterations. Next-generation sequencing technology is an exciting tool that may help us to decipher the genome architecture and the evolution of bacteria colonizing CF lungs.}, } @article {pmid24476498, year = {2014}, author = {Gona, F and Barbera, F and Pasquariello, AC and Grossi, P and Gridelli, B and Mezzatesta, ML and Caio, C and Stefani, S and Conaldi, PG}, title = {In vivo multiclonal transfer of bla(KPC-3) from Klebsiella pneumoniae to Escherichia coli in surgery patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {20}, number = {10}, pages = {O633-5}, doi = {10.1111/1469-0691.12577}, pmid = {24476498}, issn = {1469-0691}, mesh = {Bacterial Proteins/*genetics/metabolism ; Cross Infection/microbiology ; Enterobacteriaceae Infections/classification/*microbiology ; Escherichia coli/enzymology/genetics/*isolation & purification ; Gene Transfer, Horizontal ; Humans ; Italy ; Klebsiella pneumoniae/enzymology/genetics/*isolation & purification ; Multilocus Sequence Typing ; beta-Lactamases/*genetics/metabolism ; }, abstract = {During active surveillance at the Mediterranean Institute for Transplantation and Advanced Specialized Therapies (ISMETT, Palermo, Italy) with the CARBA screening medium, five pairs of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae and Escherichia coli strains were isolated in each of five colonized patients. In each patient, lateral gene transfer was demonstrated by comparing K. pneumoniae and E. coli strains, both possessing KPC-3, Tn4401a and pKpQIL-IT elements. The isolates were found to be multiclonal by multilocus sequence typing (sequence type (ST) 512 related to ST258, and ST307 belonging to a clonal complex different from the habitual sequence clone ST258 isolated in Italy) and pulsed-field gel electrophoresis. The results of our study highlight the easy transfer of KPC among Enterobacteriaceae colonizing the human intestine, and the active and careful surveillance required to identify and prevent the spread of these multidrug-resistant microorganisms.}, } @article {pmid24461455, year = {2014}, author = {Le, PT and Pontarotti, P and Raoult, D}, title = {Alphaproteobacteria species as a source and target of lateral sequence transfers.}, journal = {Trends in microbiology}, volume = {22}, number = {3}, pages = {147-156}, doi = {10.1016/j.tim.2013.12.006}, pmid = {24461455}, issn = {1878-4380}, mesh = {Alphaproteobacteria/*genetics ; Bacterial Secretion Systems ; Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {Alphaproteobacterial genomes show a remarkable genome plasticity linked with different lifestyles (intracellular, facultative, and free-living). They represent the major source of the genome repertoire of mitochondria, and their genes (specifically those of Wolbachia) have been massively transferred into their modern eukaryotic hosts, such as arthropods and nematodes. Conversely, other organisms (bacteria, viruses, archaea, and eukaryotes) and selfish DNA have contributed to their genomes. This bidirectional lateral sequence transfer explains the mosaic nature of their genomes. In contrast to those living in allopatry, alphaproteobacteria living in sympatry (in protist cells such as in the environment) favor lateral sequence transfer. Evidence shows that intracellular transfer of the type IV secretion system might have played a critical role in the evolution of these alphaproteobacteria.}, } @article {pmid24451210, year = {2014}, author = {Yabuki, A and Toyofuku, T and Takishita, K}, title = {Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1544-1547}, doi = {10.1038/ismej.2013.252}, pmid = {24451210}, issn = {1751-7370}, mesh = {Alveolata/classification/genetics ; Ecosystem ; *Gene Transfer, Horizontal ; *Genes, rRNA ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Stramenopiles/classification/*genetics ; }, abstract = {Ribosomal RNA (rRNA) genes are widely utilized in depicting organismal diversity and distribution in a wide range of environments. Although a few cases of lateral transfer of rRNA genes between closely related prokaryotes have been reported, it remains to be reported from eukaryotes. Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genome-walking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two protein-coding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.}, } @article {pmid24432015, year = {2014}, author = {Nielsen, KM and Bøhn, T and Townsend, JP}, title = {Detecting rare gene transfer events in bacterial populations.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {415}, doi = {10.3389/fmicb.2013.00415}, pmid = {24432015}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.}, } @article {pmid24398322, year = {2014}, author = {Sloan, DB and Nakabachi, A and Richards, S and Qu, J and Murali, SC and Gibbs, RA and Moran, NA}, title = {Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {857-871}, doi = {10.1093/molbev/msu004}, pmid = {24398322}, issn = {1537-1719}, support = {S10 RR029676/RR/NCRR NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; F32 GM099334/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; S10 RR019895/RR/NCRR NIH HHS/United States ; 1F32GM099334/GM/NIGMS NIH HHS/United States ; RR029676-01/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, Insect ; Genome, Bacterial ; Hemiptera/*genetics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; RNA, Messenger/genetics ; Sequence Analysis, RNA ; Symbiosis/*genetics ; }, abstract = {Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid Pachypsylla venusta, a sap-feeding insect that harbors an ancient endosymbiont (Carsonella) with one of the most reduced bacterial genomes ever identified. Carsonella retains many genes required for synthesis of essential amino acids that are scarce in plant sap, but most of these biosynthetic pathways have been disrupted by gene loss. Host genes that are upregulated in psyllid cells housing Carsonella appear to compensate for endosymbiont gene losses, resulting in highly integrated metabolic pathways that mirror those observed in other sap-feeding insects. The host contribution to these pathways is mediated by a combination of native eukaryotic genes and bacterial genes that were horizontally transferred from multiple donor lineages early in the evolution of psyllids, including one gene that appears to have been directly acquired from Carsonella. By comparing the psyllid genome to a recent analysis of mealybugs, we found that a remarkably similar set of functional pathways have been shaped by independent transfers of bacterial genes to the two hosts. These results show that horizontal gene transfer is an important and recurring mechanism driving coevolution between insects and their bacterial endosymbionts and highlight interesting similarities and contrasts with the evolutionary history of mitochondria and plastids.}, } @article {pmid24382125, year = {2014}, author = {Flood, BE and Bailey, JV and Biddle, JF}, title = {Horizontal gene transfer and the rock record: comparative genomics of phylogenetically distant bacteria that induce wrinkle structure formation in modern sediments.}, journal = {Geobiology}, volume = {12}, number = {2}, pages = {119-132}, doi = {10.1111/gbi.12072}, pmid = {24382125}, issn = {1472-4669}, mesh = {Beggiatoa/*genetics ; Cyanobacteria/*genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {Wrinkle structures are sedimentary features that are produced primarily through the trapping and binding of siliciclastic sediments by mat-forming micro-organisms. Wrinkle structures and related sedimentary structures in the rock record are commonly interpreted to represent the stabilizing influence of cyanobacteria on sediments because cyanobacteria are known to produce similar textures and structures in modern tidal flat settings. However, other extant bacteria such as filamentous representatives of the family Beggiatoaceae can also interact with sediments to produce sedimentary features that morphologically resemble many of those associated with cyanobacteria-dominated mats. While Beggiatoa spp. and cyanobacteria are metabolically and phylogenetically distant, genomic analyses show that the two groups share hundreds of homologous genes, likely as the result of horizontal gene transfer. The comparative genomics results described here suggest that some horizontally transferred genes may code for phenotypic traits such as filament formation, chemotaxis, and the production of extracellular polymeric substances that potentially underlie the similar biostabilizing influences of these organisms on sediments. We suggest that the ecological utility of certain basic life modes such as the construction of mats and biofilms, coupled with the lateral mobility of genes in the microbial world, introduces an element of uncertainty into the inference of specific phylogenetic origins from gross morphological features preserved in the ancient rock record.}, } @article {pmid24375688, year = {2014}, author = {List, JM and Nelson-Sathi, S and Geisler, H and Martin, W}, title = {Networks of lexical borrowing and lateral gene transfer in language and genome evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {2}, pages = {141-150}, doi = {10.1002/bies.201300096}, pmid = {24375688}, issn = {1521-1878}, mesh = {Biological Evolution ; Gene Transfer, Horizontal/*genetics ; Prokaryotic Cells/metabolism ; }, abstract = {Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution.}, } @article {pmid24369756, year = {2013}, author = {Richards, VP and Choi, SC and Pavinski Bitar, PD and Gurjar, AA and Stanhope, MJ}, title = {Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {920}, doi = {10.1186/1471-2164-14-920}, pmid = {24369756}, issn = {1471-2164}, support = {AI073368/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Cattle/microbiology ; *Ecotype ; Female ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Lactose/metabolism ; Mammary Glands, Animal/microbiology ; Mastitis, Bovine/microbiology ; Milk/microbiology ; Operon ; Phylogeny ; Streptococcus agalactiae/*genetics ; Transcriptome ; }, abstract = {BACKGROUND: Streptococcus agalactiae is a major cause of bovine mastitis, which is the dominant health disorder affecting milk production within the dairy industry and is responsible for substantial financial losses to the industry worldwide. However, there is considerable evidence for host adaptation (ecotypes) within S. agalactiae, with both bovine and human sourced isolates showing a high degree of distinctiveness, suggesting differing ability to cause mastitis. Here, we (i) generate RNAseq data from three S. agalactiae isolates (two putative bovine adapted and one human) and (ii) compare publicly available whole genome shotgun sequence data from an additional 202 isolates, obtained from six host species, to elucidate possible genetic factors/adaptations likely important for S. agalactiae growth and survival in the bovine mammary gland.

RESULTS: Tests for differential expression showed distinct expression profiles for the three isolates when grown in bovine milk. A key finding for the two putatively bovine adapted isolates was the up regulation of a lactose metabolism operon (Lac.2) that was strongly correlated with the bovine environment (all 36 bovine sourced isolates on GenBank possessed the operon, in contrast to only 8/151 human sourced isolates). Multi locus sequence typing of all genome sequences and phylogenetic analysis using conserved operon genes from 44 S. agalactiae isolates and 16 additional Streptococcus species provided strong evidence for acquisition of the operon via multiple lateral gene transfer events, with all Streptococcus species known to be major causes of mastitis, identified as possible donors. Furthermore, lactose fermentation tests were only positive for isolates possessing Lac.2. Combined, these findings suggest that lactose metabolism is likely an important adaptation to the bovine environment. Additional up regulation in the bovine adapted isolates included genes involved in copper homeostasis, metabolism of purine, pyrimidine, glycerol and glucose, and possibly aminoglycoside antibiotic resistance.

CONCLUSION: We detected several genetic factors likely important in S. agalactiae's adaptation to the bovine environment, in particular lactose metabolism. Of concern is the up regulation of a putative antibiotic resistance gene (GCN5-related N-acetyltransferase) that might reflect an adaptation to the use of aminoglycoside antibiotics within this environment.}, } @article {pmid24335826, year = {2014}, author = {Sato, T and Kuwahara, H and Fujita, K and Noda, S and Kihara, K and Yamada, A and Ohkuma, M and Hongoh, Y}, title = {Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut.}, journal = {The ISME journal}, volume = {8}, number = {5}, pages = {1008-1019}, doi = {10.1038/ismej.2013.222}, pmid = {24335826}, issn = {1751-7370}, mesh = {Animals ; Biological Evolution ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; In Situ Hybridization, Fluorescence ; Isoptera/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Verrucomicrobia/*physiology ; }, abstract = {In 1944, Harold Kirby described microorganisms living within nuclei of the protists Trichonympha in guts of termites; however, their taxonomic assignment remains to be accomplished. Here, we identified intranuclear symbionts of Trichonympha agilis in the gut of the termite Reticulitermes speratus. We isolated single nuclei of T. agilis, performed whole-genome amplification, and obtained bacterial 16S rRNA genes by PCR. Unexpectedly, however, all of the analyzed clones were from pseudogenes of 16S rRNA with large deletions and numerous sequence variations even within a single-nucleus sample. Authentic 16S rRNA gene sequences were finally recovered by digesting the nuclear DNA; these pseudogenes were present on the host Trichonympha genome. The authentic sequences represented two distinct bacterial species belonging to the phylum Verrucomicrobia, and the pseudogenes have originated from each of the two species. Fluorescence in situ hybridization confirmed that both species are specifically localized, and occasionally co-localized, within nuclei of T. agilis. Transmission electron microscopy revealed that they are distorted cocci with characteristic electron-dense and lucent regions, which resemble the intranuclear symbionts illustrated by Kirby. For these symbionts, we propose a novel genus and species, 'Candidatus Nucleococcus trichonymphae' and 'Candidatus Nucleococcus kirbyi'. These formed a termite-specific cluster with database sequences, other members of which were also detected within nuclei of various gut protists, including both parabasalids and oxymonads. We suggest that this group is widely distributed as intranuclear symbionts of diverse protists in termite guts and that they might have affected the evolution of the host genome through lateral gene transfer.}, } @article {pmid24323918, year = {2014}, author = {Schönknecht, G and Weber, AP and Lercher, MJ}, title = {Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {1}, pages = {9-20}, doi = {10.1002/bies.201300095}, pmid = {24323918}, issn = {1521-1878}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biological Evolution ; Eukaryota/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Phylogeny ; }, abstract = {In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga Galdieria sulphuraria to its hot, acid, toxic-metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice-binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism. Editor's suggested further reading in BioEssays Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution Abstract.}, } @article {pmid24317084, year = {2014}, author = {Guo, HJ and Wang, ET and Zhang, XX and Li, QQ and Zhang, YM and Tian, CF and Chen, WX}, title = {Replicon-dependent differentiation of symbiosis-related genes in Sinorhizobium strains nodulating Glycine max.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {4}, pages = {1245-1255}, doi = {10.1128/AEM.03037-13}, pmid = {24317084}, issn = {1098-5336}, mesh = {Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; *Plant Root Nodulation ; Recombination, Genetic ; Sequence Analysis, DNA ; Sinorhizobium/*genetics/*physiology ; Soybeans/*microbiology ; *Symbiosis ; }, abstract = {In order to investigate the genetic differentiation of Sinorhizobium strains nodulating Glycine max and related microevolutionary mechanisms, three housekeeping genes (SMc00019, truA, and thrA) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) of SMc00019-truA-thrA: Sinorhizobium fredii, Sinorhizobium sojae, Sinorhizobium sp. I, Sinorhizobium sp. II, and Sinorhizobium sp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons. S. sojae was the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.}, } @article {pmid24314259, year = {2013}, author = {Peeters, N and Carrère, S and Anisimova, M and Plener, L and Cazalé, AC and Genin, S}, title = {Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {859}, doi = {10.1186/1471-2164-14-859}, pmid = {24314259}, issn = {1471-2164}, mesh = {Bacterial Proteins/*genetics/metabolism ; Computational Biology/methods ; Databases, Genetic ; *Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Genomics ; Open Reading Frames ; Phylogeny ; Ralstonia solanacearum/classification/*genetics ; Recombination, Genetic ; Selection, Genetic ; *Terminology as Topic ; }, abstract = {BACKGROUND: Ralstonia solanacearum is a soil-borne beta-proteobacterium that causes bacterial wilt disease in many food crops and is a major problem for agriculture in intertropical regions. R. solanacearum is a heterogeneous species, both phenotypically and genetically, and is considered as a species complex. Pathogenicity of R. solanacearum relies on the Type III secretion system that injects Type III effector (T3E) proteins into plant cells. T3E collectively perturb host cell processes and modulate plant immunity to enable bacterial infection.

RESULTS: We provide the catalogue of T3E in the R. solanacearum species complex, as well as candidates in newly sequenced strains. 94 T3E orthologous groups were defined on phylogenetic bases and ordered using a uniform nomenclature. This curated T3E catalog is available on a public website and a bioinformatic pipeline has been designed to rapidly predict T3E genes in newly sequenced strains. Systematical analyses were performed to detect lateral T3E gene transfer events and identify T3E genes under positive selection. Our analyses also pinpoint the RipF translocon proteins as major discriminating determinants among the phylogenetic lineages.

CONCLUSIONS: Establishment of T3E repertoires in strains representatives of the R. solanacearum biodiversity allowed determining a set of 22 T3E present in all the strains but provided no clues on host specificity determinants. The definition of a standardized nomenclature and the optimization of predictive tools will pave the way to understanding how variation of these repertoires is correlated to the diversification of this species complex and how they contribute to the different strain pathotypes.}, } @article {pmid24296570, year = {2013}, author = {Sapp, J and Fox, GE}, title = {The singular quest for a universal tree of life.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {77}, number = {4}, pages = {541-550}, doi = {10.1128/MMBR.00038-13}, pmid = {24296570}, issn = {1098-5557}, mesh = {*Biological Evolution ; Gene Transfer, Horizontal/genetics ; RNA, Ribosomal/*genetics ; }, abstract = {Carl Woese developed a unique research program, based on rRNA, for discerning bacterial relationships and constructing a universal tree of life. Woese's interest in the evolution of the genetic code led to him to investigate the deep roots of evolution, develop the concept of the progenote, and conceive of the Archaea. In so doing, he and his colleagues at the University of Illinois in Urbana revolutionized microbiology and brought the classification of microbes into an evolutionary framework. Woese also provided definitive evidence for the role of symbiosis in the evolution of the eukaryotic cell while underscoring the importance of lateral gene transfer in microbial evolution. Woese and colleagues' proposal of three fundamental domains of life was brought forward in direct conflict with the prokaryote-eukaryote dichotomy. Together with several colleagues and associates, he brought together diverse evidence to support the rRNA evidence for the fundamentally tripartite nature of life. This paper aims to provide insight into his accomplishments, how he achieved them, and his place in the history of biology.}, } @article {pmid24281050, year = {2013}, author = {Eveleigh, RJ and Meehan, CJ and Archibald, JM and Beiko, RG}, title = {Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2478-2497}, doi = {10.1093/gbe/evt195}, pmid = {24281050}, issn = {1759-6653}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Archaea/genetics ; Bacteria/*classification/*genetics ; Base Sequence ; Cell Wall/genetics ; Clostridium/genetics ; Deltaproteobacteria/genetics ; Energy Metabolism/genetics/physiology ; Epsilonproteobacteria/genetics ; *Evolution, Molecular ; Flagella/genetics ; Flagellin/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Lipopolysaccharides/genetics ; Oxidative Phosphorylation ; Peptidoglycan/genetics ; Phylogeny ; Ribosomes/genetics ; }, abstract = {Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. Depending on which sets of genes are privileged, either Thermotogae or Epsilonproteobacteria is the most plausible adjacent lineage to the Aquificae. Both scenarios require massive sharing of genes to explain the history of this enigmatic group, whose history is further complicated by specific affinities of different members of Aquificae to different partner lineages.}, } @article {pmid24278351, year = {2013}, author = {Hossain, MJ and Waldbieser, GC and Sun, D and Capps, NK and Hemstreet, WB and Carlisle, K and Griffin, MJ and Khoo, L and Goodwin, AE and Sonstegard, TS and Schroeder, S and Hayden, K and Newton, JC and Terhune, JS and Liles, MR}, title = {Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80943}, doi = {10.1371/journal.pone.0080943}, pmid = {24278351}, issn = {1932-6203}, mesh = {Aeromonas hydrophila/classification/*genetics/isolation & purification/metabolism/virology ; Animals ; Computational Biology ; *Disease Outbreaks ; Fish Diseases/*epidemiology/microbiology/transmission ; Gene Order ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Genotype ; Ictaluridae/*microbiology ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Multigene Family ; O Antigens/genetics ; Phenotype ; Phylogeny ; Prophages/genetics ; Virulence Factors/genetics ; }, abstract = {To investigate the molecular basis of the emergence of Aeromonas hydrophila responsible for an epidemic outbreak of motile aeromonad septicemia of catfish in the Southeastern United States, we sequenced 11 A. hydrophila isolates that includes five reference and six recent epidemic isolates. Comparative genomics revealed that recent epidemic A. hydrophila isolates are highly clonal, whereas reference isolates are greatly diverse. We identified 55 epidemic-associated genetic regions with 313 predicted genes that are present in epidemic isolates but absent from reference isolates and 35% of these regions are located within genomic islands, suggesting their acquisition through lateral gene transfer. The epidemic-associated regions encode predicted prophage elements, pathogenicity islands, metabolic islands, fitness islands and genes of unknown functions, and 34 of the genes encoded in these regions were predicted as virulence factors. We found two pilus biogenesis gene clusters encoded within predicted pathogenicity islands. A functional metabolic island that encodes a complete pathway for myo-inositol catabolism was evident by the ability of epidemic A. hydrophila isolates to use myo-inositol as a sole carbon source. Testing of A. hydrophila field isolates found a consistent correlation between myo-inositol utilization as a sole carbon source and the presence of an epidemic-specific genetic marker. All epidemic isolates and one reference isolate shared a novel O-antigen cluster. Altogether we identified four different O-antigen biosynthesis gene clusters within the 11 sequenced A. hydrophila genomes. Our study reveals new insights into the evolutionary changes that have resulted in the emergence of recent epidemic A. hydrophila strains.}, } @article {pmid24263112, year = {2014}, author = {Velineni, S and Breathnach, CC and Timoney, JF}, title = {Evidence of lateral gene transfer among strains of Streptococcus zooepidemicus in weanling horses with respiratory disease.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {21}, number = {}, pages = {157-160}, doi = {10.1016/j.meegid.2013.11.006}, pmid = {24263112}, issn = {1567-7257}, mesh = {Animals ; Bacterial Proteins/*genetics ; Dogs ; Gene Transfer, Horizontal ; Herpesviridae Infections/*veterinary/virology ; Herpesvirus 1, Equid/physiology ; Horse Diseases/*microbiology/virology ; Horses ; Multilocus Sequence Typing ; Recombination, Genetic ; Respiratory Tract Infections/microbiology/*veterinary/virology ; Streptococcal Infections/complications/microbiology/*veterinary ; Streptococcus equi/classification/*genetics ; }, abstract = {Streptococcus zooepidemicus (Sz) is a tonsillar commensal of healthy horses but with potential to opportunistically invade the lower respiratory tract. Sz is genetically variable and recombinogenic based on analysis of gene sequences including szp, szm and MLST data. Although a variety of serovars of the protective SzP are commonly harbored in the tonsils of the same horse, lower respiratory infections usually involve a single clone. Nevertheless, isolation of specific clones from epizootics of respiratory disease has been recently reported in horses and dogs in N. America, Europe and Asia. In this report, we provide evidence suggestive of lateral gene exchange and recombination between strains of Sz from cases of respiratory disease secondary to experimental equine herpes 1 virus infection in an isolated group of weanling horses and ponies. Nasal swabs of 13 of 18 weanlings with respiratory disease yielded mucoid colonies of Sz following culture. Comparison of arcC, nrdE, proS, spi, tdk, tpi and yqiL of these Sz revealed 3 Clades. Clade-1 (ST-212) and 2 (ST-24) were composed of 7 and 3 isolates, respectively. ST-24 and 212 differed in all 7 housekeeping as well as szp and szm alleles. Two isolates of Clade-1 were assigned to ST-308, a single locus variant of ST-212 that contained the proS-16 allele sequenced in ST-24. One isolate of ST-308 contained szm-2, the same allele sequenced in Clade 2 isolates; the other was positive for the szp-N2HV2 allele of Clade 2. These observations are consistent with gene transfer between Sz in the natural host and may explain formation of novel clones that invade the lower respiratory tract or cause epizootics of respiratory disease in dogs and horses.}, } @article {pmid24262067, year = {2013}, author = {Wiesner, M and Fernández-Mora, M and Cevallos, MA and Zavala-Alvarado, C and Zaidi, MB and Calva, E and Silva, C}, title = {Conjugative transfer of an IncA/C plasmid-borne blaCMY-2 gene through genetic re-arrangements with an IncX1 plasmid.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {264}, doi = {10.1186/1471-2180-13-264}, pmid = {24262067}, issn = {1471-2180}, mesh = {Animals ; *Conjugation, Genetic ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/genetics ; Gene Rearrangement ; *Gene Transfer, Horizontal ; Humans ; Mexico ; Molecular Sequence Data ; *Plasmids ; Recombination, Genetic ; Salmonella Infections/microbiology ; Salmonella Infections, Animal/microbiology ; Salmonella typhimurium/*enzymology/*genetics/isolation & purification ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {BACKGROUND: Our observation that in the Mexican Salmonella Typhimurium population none of the ST19 and ST213 strains harbored both the Salmonella virulence plasmid (pSTV) and the prevalent IncA/C plasmid (pA/C) led us to hypothesize that restriction to horizontal transfer of these plasmids existed. We designed a conjugation scheme using ST213 strain YU39 as donor of the blaCMY-2 gene (conferring resistance to ceftriaxone; CRO) carried by pA/C, and two E. coli lab strains (DH5α and HB101) and two Typhimurium ST19 strains (SO1 and LT2) carrying pSTV as recipients. The aim of this study was to determine if the genetic background of the different recipient strains affected the transfer frequencies of pA/C.

RESULTS: YU39 was able to transfer CRO resistance, via a novel conjugative mechanism, to all the recipient strains although at low frequencies (10-7 to 10-10). The presence of pSTV in the recipients had little effect on the conjugation frequency. The analysis of the transconjugants showed that three different phenomena were occurring associated to the transfer of blaCMY-2: 1) the co-integration of pA/C and pX1; 2) the transposition of the CMY region from pA/C to pX1; or 3) the rearrangement of pA/C. In addition, the co-lateral mobilization of a small (5 kb) ColE1-like plasmid was observed. The transconjugant plasmids involving pX1 re-arrangements (either via co-integration or ISEcp1-mediated transposition) obtained the capacity to conjugate at very high levels, similar to those found for pX1 (10-1). Two versions of the region containing blaCMY-2 were found to transpose to pX1: the large version was inserted into an intergenic region located where the "genetic load" operons are frequently inserted into pX1, while the short version was inserted into the stbDE operon involved in plasmid addiction system. This is the first study to report the acquisition of an extended spectrum cephalosporin (ESC)-resistance gene by an IncX1 plasmid.

CONCLUSIONS: We showed that the transfer of the YU39 blaCMY-2 gene harbored on a non- conjugative pA/C requires the machinery of a highly conjugative pX1 plasmid. Our experiments demonstrate the complex interactions a single strain can exploit to contend with the challenge of horizontal transfer and antibiotic selective pressure.}, } @article {pmid24260361, year = {2013}, author = {Maj, A and Dziewit, L and Czarnecki, J and Wlodarczyk, M and Baj, J and Skrzypczyk, G and Giersz, D and Bartosik, D}, title = {Plasmids of carotenoid-producing Paracoccus spp. (Alphaproteobacteria) - structure, diversity and evolution.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80258}, doi = {10.1371/journal.pone.0080258}, pmid = {24260361}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*genetics/*metabolism ; Biological Evolution ; Carotenoids/*genetics/*metabolism ; Conjugation, Genetic/genetics ; DNA Replication/genetics ; Gene Transfer, Horizontal/genetics ; Genetic Variation/genetics ; Genetic Vectors/genetics ; Genome, Bacterial/genetics ; Paracoccus/*genetics/*metabolism ; Plasmids/*genetics ; }, abstract = {Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22. Comparative analyses revealed mosaic structures of the plasmids and recombinational shuffling of diverse genetic modules involved in (i) plasmid replication, (ii) stabilization (including toxin-antitoxin systems of the relBE/parDE, tad-ata, higBA, mazEF and toxBA families) and (iii) mobilization for conjugal transfer (encoding relaxases of the MobQ, MobP or MobV families). A common feature of the majority of the plasmids is the presence of AT-rich sequence islets (located downstream of exc1-like genes) containing genes, whose homologs are conserved in the chromosomes of many bacteria (encoding e.g. RelA/SpoT, SMC-like proteins and a retron-type reverse transcriptase). The results of this study have provided insight into the diversity and plasticity of plasmids of Paracoccus spp., and of the entire Alphaproteobacteria. Some of the identified plasmids contain replication systems not described previously in this class of bacteria. The composition of the plasmid genomes revealed frequent transfer of chromosomal genes into plasmids, which significantly enriches the pool of mobile DNA that can participate in lateral transfer. Many strains of Paracoccus spp. have great biotechnological potential, and the plasmid vectors constructed in this study will facilitate genetic studies of these bacteria.}, } @article {pmid24157054, year = {2014}, author = {Laranjo, M and Alexandre, A and Oliveira, S}, title = {Legume growth-promoting rhizobia: an overview on the Mesorhizobium genus.}, journal = {Microbiological research}, volume = {169}, number = {1}, pages = {2-17}, doi = {10.1016/j.micres.2013.09.012}, pmid = {24157054}, issn = {1618-0623}, mesh = {Evolution, Molecular ; Fabaceae/*growth & development/*microbiology/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Mesorhizobium/*physiology ; *Plant Development ; Plant Root Nodulation ; *Symbiosis ; }, abstract = {The need for sustainable agricultural practices is revitalizing the interest in biological nitrogen fixation and rhizobia-legumes symbioses, particularly those involving economically important legume crops in terms of food and forage. The genus Mesorhizobium includes species with high geographical dispersion and able to nodulate a wide variety of legumes, including important crop species, like chickpea or biserrula. Some cases of legume-mesorhizobia inoculant introduction represent exceptional opportunities to study the rhizobia genomes evolution and the evolutionary relationships among species. Complete genome sequences revealed that mesorhizobia typically harbour chromosomal symbiosis islands. The phylogenies of symbiosis genes, such as nodC, are not congruent with the phylogenies based on core genes, reflecting rhizobial host range, rather than species affiliation. This agrees with studies showing that Mesorhizobium species are able to exchange symbiosis genes through lateral transfer of chromosomal symbiosis islands, thus acquiring the ability to nodulate new hosts. Phylogenetic analyses of the Mesorhizobium genus based on core and accessory genes reveal complex evolutionary relationships and a high genomic plasticity, rendering the Mesorhizobium genus as a good model to investigate rhizobia genome evolution and adaptation to different host plants. Further investigation of symbiosis genes as well as stress response genes will certainly contribute to understand mesorhizobia-legume symbiosis and to develop more effective mesorhizobia inoculants.}, } @article {pmid24149625, year = {2014}, author = {Gherardi, G and Imperi, M and Palmieri, C and Magi, G and Facinelli, B and Baldassarri, L and Pataracchia, M and Creti, R}, title = {Genetic diversity and virulence properties of Streptococcus dysgalactiae subsp. equisimilis from different sources.}, journal = {Journal of medical microbiology}, volume = {63}, number = {Pt 1}, pages = {90-98}, doi = {10.1099/jmm.0.062109-0}, pmid = {24149625}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/pharmacology ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Carrier Proteins/genetics ; Carrier State/*microbiology ; Cell Line ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Endocytosis ; Epithelial Cells/microbiology ; *Genetic Variation ; Genotype ; Humans ; Italy/epidemiology ; Molecular Epidemiology ; Molecular Typing ; Polymerase Chain Reaction ; Streptococcal Infections/epidemiology/*microbiology ; Streptococcus/*classification/*genetics/isolation & purification/pathogenicity ; Virulence Factors/genetics ; }, abstract = {A recent increase in virulence of pathogenic Streptococcus dysgalactiae subsp. equisimilis (SDSE) has been widely proposed. Such an increase may be partly explained by the acquisition of new virulence traits by horizontal gene transfer from related streptococci such as Streptococcus pyogenes (GAS) and Streptococcus agalactiae (GBS). A collection of 54 SDSE strains isolated in Italy in the years 2000-2010 from different sources (paediatric throat carriage, invasive and non-invasive diseases) was characterized by emm typing and pulsed-field gel electrophoresis (PFGE) analysis. The virulence repertoire was evaluated by PCR for the presence of GAS superantigen (spe) genes, the streptolysin S (sagA) gene, the group G fibronectin-binding protein (gfbA) gene and GAS-GBS alpha-like protein family (alp) genes; moreover, the ability to invade human epithelial cells was investigated. Resistance to tetracycline, erythromycin and clindamycin was assessed. The combined use of emm typing and PFGE proved to be a reliable strategy for the epidemiological analysis of SDSE isolates. The most frequent emm types were the same as those more frequently reported in other studies, thus indicating the diffusion of a limited number of a few successful emm types fit to disseminate in humans. The speG gene was detected in SDSE strains of different genetic backgrounds. Erythromycin resistance determined by the erm(T) gene, and the unusual, foggy MLSB phenotype, observed in one and seven strains, respectively, have never previously, to our knowledge, been reported in SDSE. Moreover, a new member of the alp family was identified. The identification of new antibiotic and virulence determinants, despite the small size of the sample analysed, shows the importance of constant attention to monitoring the extent of lateral gene transfer in this emerging pathogen.}, } @article {pmid24146634, year = {2013}, author = {Robinson, KM and Sieber, KB and Dunning Hotopp, JC}, title = {A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer.}, journal = {PLoS genetics}, volume = {9}, number = {10}, pages = {e1003877}, doi = {10.1371/journal.pgen.1003877}, pmid = {24146634}, issn = {1553-7404}, support = {DP2 OD007372/OD/NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Chromosomes/genetics/microbiology ; DNA, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Interspersed Repetitive Sequences ; Neoplasms/*genetics/microbiology/virology ; Phylogeny ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {Lateral gene transfer (LGT) from bacteria to animals occurs more frequently than was appreciated prior to the advent of genome sequencing. In 2007, LGT from bacterial Wolbachia endosymbionts was detected in ~33% of the sequenced arthropod genomes using a bioinformatic approach. Today, Wolbachia/host LGT is thought to be widespread and many other cases of bacteria-animal LGT have been described. In insects, LGT may be more frequently associated with endosymbionts that colonize germ cells and germ stem cells, like Wolbachia endosymbionts. We speculate that LGT may occur from bacteria to a wide variety of eukaryotes, but only becomes vertically inherited when it occurs in germ cells. As such, LGT may happen routinely in somatic cells but never become inherited or fixed in the population. Lack of inheritance of such mutations greatly decreases our ability to detect them. In this review, we propose that such noninherited bacterial DNA integration into chromosomes in human somatic cells could induce mutations leading to cancer or autoimmune diseases in a manner analogous to mobile elements and viral integrations.}, } @article {pmid24118435, year = {2013}, author = {Gerth, M and Röthe, J and Bleidorn, C}, title = {Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny.}, journal = {Molecular ecology}, volume = {22}, number = {24}, pages = {6149-6162}, doi = {10.1111/mec.12549}, pmid = {24118435}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; Bees/genetics/*microbiology ; *Biological Evolution ; *Gene Transfer, Horizontal ; Models, Genetic ; Molecular Sequence Data ; Multilocus Sequence Typing ; *Phylogeny ; Symbiosis/genetics ; Wolbachia/classification/*genetics ; }, abstract = {The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite-host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.}, } @article {pmid24108212, year = {2013}, author = {Uhrig, RG and Kerk, D and Moorhead, GB}, title = {Evolution of bacterial-like phosphoprotein phosphatases in photosynthetic eukaryotes features ancestral mitochondrial or archaeal origin and possible lateral gene transfer.}, journal = {Plant physiology}, volume = {163}, number = {4}, pages = {1829-1843}, doi = {10.1104/pp.113.224378}, pmid = {24108212}, issn = {1532-2548}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea/*metabolism ; Bacteria/*enzymology ; Eukaryota/*enzymology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphoprotein Phosphatases/chemistry/*genetics ; Photosynthesis ; *Phylogeny ; Protein Transport ; Subcellular Fractions/enzymology ; }, abstract = {Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell. Dysfunction of members in either the protein kinase or phosphatase family can have wide-ranging deleterious effects in both metazoans and plants alike. Previously, three bacterial-like phosphoprotein phosphatase classes were uncovered in eukaryotes and named according to the bacterial sequences with which they have the greatest similarity: Shewanella-like (SLP), Rhizobiales-like (RLPH), and ApaH-like (ALPH) phosphatases. Utilizing the wealth of data resulting from recently sequenced complete eukaryotic genomes, we conducted database searching by hidden Markov models, multiple sequence alignment, and phylogenetic tree inference with Bayesian and maximum likelihood methods to elucidate the pattern of evolution of eukaryotic bacterial-like phosphoprotein phosphatase sequences, which are predominantly distributed in photosynthetic eukaryotes. We uncovered a pattern of ancestral mitochondrial (SLP and RLPH) or archaeal (ALPH) gene entry into eukaryotes, supplemented by possible instances of lateral gene transfer between bacteria and eukaryotes. In addition to the previously known green algal and plant SLP1 and SLP2 protein forms, a more ancestral third form (SLP3) was found in green algae. Data from in silico subcellular localization predictions revealed class-specific differences in plants likely to result in distinct functions, and for SLP sequences, distinctive and possibly functionally significant differences between plants and nonphotosynthetic eukaryotes. Conserved carboxyl-terminal sequence motifs with class-specific patterns of residue substitutions, most prominent in photosynthetic organisms, raise the possibility of complex interactions with regulatory proteins.}, } @article {pmid24107487, year = {2014}, author = {Piacente, F and Bernardi, C and Marin, M and Blanc, G and Abergel, C and Tonetti, MG}, title = {Characterization of a UDP-N-acetylglucosamine biosynthetic pathway encoded by the giant DNA virus Mimivirus.}, journal = {Glycobiology}, volume = {24}, number = {1}, pages = {51-61}, doi = {10.1093/glycob/cwt089}, pmid = {24107487}, issn = {1460-2423}, mesh = {Acanthamoeba/virology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mimiviridae/*enzymology/genetics ; *Phylogeny ; Uridine Diphosphate N-Acetylmuramic Acid/*biosynthesis/genetics ; Viral Proteins/genetics/*metabolism ; }, abstract = {Mimivirus is a giant DNA virus belonging to the Megaviridae family and infecting unicellular Eukaryotes of the genus Acanthamoeba. The viral particles are characterized by heavily glycosylated surface fibers. Several experiments suggest that Mimivirus and other related viruses encode an autonomous glycosylation system, forming viral glycoproteins independently of their host. In this study, we have characterized three Mimivirus proteins involved in the de novo uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) production: a glutamine-fructose-6-phosphate transaminase (CDS L619), a glucosamine-6-phosphate N-acetyltransferase (CDS L316) and a UDP-GlcNAc pyrophosphorylase (CDS R689). Sequence and enzymatic analyses have revealed some unique features of the viral pathway. While it follows the eukaryotic-like strategy, it also shares some properties of the prokaryotic pathway. Phylogenetic analyses revealed that the Megaviridae enzymes cluster in monophyletic groups, indicating that they share common ancestors, but did not support the hypothesis of recent acquisitions from one of the known hosts. Rather, viral clades branched at deep nodes in phylogenetic trees, forming independent clades outside sequenced cellular organisms. The intermediate properties between the eukaryotic and prokaryotic pathways, the phylogenetic analyses and the fact that these enzymes are shared between most of the known members of the Megaviridae family altogether suggest that the viral pathway has an ancient origin, resulting from lateral transfers of cellular genes early in the Megaviridae evolution, or from vertical inheritance from a more complex cellular ancestor (reductive evolution hypothesis). The identification of a virus-encoded UDP-GlcNAc pathway reinforces the concept that GlcNAc is a ubiquitous sugar representing a universal and fundamental process in all organisms.}, } @article {pmid24055388, year = {2013}, author = {Brown Kav, A and Benhar, I and Mizrahi, I}, title = {A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches.}, journal = {Journal of microbiological methods}, volume = {95}, number = {2}, pages = {272-279}, doi = {10.1016/j.mimet.2013.09.008}, pmid = {24055388}, issn = {1872-8359}, mesh = {Animals ; Cattle ; DNA, Bacterial/genetics/*isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Plasmids/genetics/*isolation & purification ; Polymerase Chain Reaction ; Rumen/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Deep sequencing techniques used in metagenomic approaches have greatly advanced the study of microbial communities in various environments. However, one microbial segment that has remained largely unexplored is the natural plasmids residing within microbial environments. Plasmids are perceived as mobile genetic elements that exist extra-chromosomally and occasionally carry accessory genes that confer an advantage to their host in its ecological niche. They are thus thought to play an important evolutionary role in microbial communities by laterally introducing genes and traits into microbial genomes. Despite their importance, technical obstacles still limit the metagenomic study of natural plasmids using deep sequencing techniques. These include low copy number of the plasmids and heterogeneity of microbes in environmental samples, reflected in the low abundance of each individual plasmid. Furthermore, the extracted plasmids usually contain remnants of chromosomal DNA that can potentially interfere with the analysis of unique plasmid traits. We have recently studied the rumen metagenomic plasmid population using a newly developed procedure that successfully overcomes these obstacles. This procedure enables extraction of pure plasmid DNA suited for deep sequencing studies. Here we present a detailed description and characterization of this procedure which could potentially allow the study of plasmids in other environmental niches.}, } @article {pmid24053607, year = {2013}, author = {Ioannidis, P and Johnston, KL and Riley, DR and Kumar, N and White, JR and Olarte, KT and Ott, S and Tallon, LJ and Foster, JM and Taylor, MJ and Dunning Hotopp, JC}, title = {Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {639}, doi = {10.1186/1471-2164-14-639}, pmid = {24053607}, issn = {1471-2164}, support = {DP2 OD007372/OD/NIH HHS/United States ; 1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Animals ; Brugia malayi/*genetics ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Helminth ; Open Reading Frames ; Sequence Analysis, DNA ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Lymphatic filariasis is a neglected tropical disease afflicting more than 120 million people, while another 1.3 billion people are at risk of infection. The nematode worm Brugia malayi is one of the causative agents of the disease and exists in a mutualistic symbiosis with Wolbachia bacteria. Since extensive lateral gene transfer occurs frequently between Wolbachia and its hosts, we sought to measure the extent of such LGT in B. malayi by whole genome sequencing of Wolbachia-depleted worms.

RESULTS: A considerable fraction (at least 115.4-kbp, or 10.6%) of the 1.08-Mbp Wolbachia wBm genome has been transferred to its nematode host and retains high levels of similarity, including 227 wBm genes and gene fragments. Complete open reading frames were transferred for 32 of these genes, meaning they have the potential to produce functional proteins. Moreover, four transfers have evidence of life stage-specific regulation of transcription at levels similar to other nematode transcripts, strengthening the possibility that they are functional.

CONCLUSIONS: There is extensive and ongoing transfer of Wolbachia DNA to the worm genome and some transfers are transcribed in a stage-specific manner at biologically relevant levels.}, } @article {pmid24030592, year = {2014}, author = {Sangwan, N and Verma, H and Kumar, R and Negi, V and Lax, S and Khurana, P and Khurana, JP and Gilbert, JA and Lal, R}, title = {Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {398-408}, doi = {10.1038/ismej.2013.153}, pmid = {24030592}, issn = {1751-7370}, mesh = {Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Gene Transfer, Horizontal ; Genotype ; India ; Japan ; Lindane/metabolism ; *Metagenomics ; Molecular Sequence Data ; Plasmids/genetics ; Sphingomonadaceae/*classification/*genetics/metabolism ; }, abstract = {Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.}, } @article {pmid24003001, year = {2013}, author = {Ivancevic, AM and Walsh, AM and Kortschak, RD and Adelson, DL}, title = {Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {12}, pages = {1071-1082}, doi = {10.1002/bies.201300072}, pmid = {24003001}, issn = {1521-1878}, mesh = {Animals ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Retroelements/*genetics ; }, abstract = {Horizontal transfer (HT) is the transmission of genetic material between non-mating species, a phenomenon thought to occur rarely in multicellular eukaryotes. However, many transposable elements (TEs) are not only capable of HT, but have frequently jumped between widely divergent species. Here we review and integrate reported cases of HT in retrotransposons of the BovB family, and DNA transposons, over a broad range of animals spanning all continents. Our conclusions challenge the paradigm that HT in vertebrates is restricted to infective long terminal repeat (LTR) retrotransposons or retroviruses. This raises the possibility that other non-LTR retrotransposons, such as L1 or CR1 elements, believed to be only vertically transmitted, can horizontally transfer between species. Growing evidence indicates that the process of HT is much more general across different TEs and species than previously believed, and that it likely shapes eukaryotic genomes and catalyses genome evolution.}, } @article {pmid23985741, year = {2014}, author = {Tamas, I and Smirnova, AV and He, Z and Dunfield, PF}, title = {The (d)evolution of methanotrophy in the Beijerinckiaceae--a comparative genomics analysis.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {369-382}, doi = {10.1038/ismej.2013.145}, pmid = {23985741}, issn = {1751-7370}, mesh = {Beijerinckiaceae/*classification/enzymology/*genetics ; Gene Transfer, Horizontal/genetics ; Genome ; Genome, Bacterial/*genetics ; *Genomics ; Membrane Transport Proteins/genetics ; Metabolic Networks and Pathways ; Methane/metabolism ; Oxygenases/genetics ; *Phylogeny ; }, abstract = {The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.}, } @article {pmid23977007, year = {2013}, author = {Svartström, O and Mushtaq, M and Pringle, M and Segerman, B}, title = {Genome-wide relatedness of Treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen Treponema denticola.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71281}, doi = {10.1371/journal.pone.0071281}, pmid = {23977007}, issn = {1932-6203}, mesh = {Animals ; Base Composition ; Gene Transfer, Horizontal ; Genetic Variation ; Genome Size ; *Genome, Bacterial ; Gingiva/*microbiology ; Humans ; *Phylogeny ; Sequence Homology, Nucleic Acid ; Swine/microbiology ; Treponema/*classification/genetics/isolation & purification ; Treponema denticola/*classification/genetics/isolation & purification ; }, abstract = {Treponema pedis and T. denticola are two genetically related species with different origins of isolation. Treponema denticola is part of the human oral microbiota and is associated with periodontitis while T. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. Although multiple Treponema phylotypes may exist in ulcerative lesions in pigs, T. pedis appears to be a predominant spirochete in these lesions. Treponema pedis can also be present in pig gingiva. In this study, we determined the complete genome sequence of T. pedis strain T A4, isolated from a porcine necrotic ear lesion, and compared its genome with that of T. denticola. Most genes in T. pedis were homologous to those in T. denticola and the two species were similar in general genomic features such as size, G+C content, and number of genes. In addition, many homologues of specific virulence-related genes in T. denticola were found in T. pedis. Comparing a selected pair of strains will usually not give a complete picture of the relatedness between two species. We therefore complemented the analysis with draft genomes from six T. pedis isolates, originating from gingiva and necrotic ulcers in pigs, and from twelve T. denticola strains. Each strain carried a considerable amount of accessory genetic material, of which a large part was strain specific. There was also extensive sequence variability in putative virulence-related genes between strains belonging to the same species. Signs of lateral gene-transfer events from bacteria known to colonize oral environments were found. This suggests that the oral cavity is an important habitat for T. pedis. In summary, we found extensive genomic similarities between T. pedis and T. denticola but also large variability within each species.}, } @article {pmid23932912, year = {2013}, author = {Friães, A and Lopes, JP and Melo-Cristino, J and Ramirez, M and , }, title = {Changes in Streptococcus pyogenes causing invasive disease in Portugal: evidence for superantigen gene loss and acquisition.}, journal = {International journal of medical microbiology : IJMM}, volume = {303}, number = {8}, pages = {505-513}, doi = {10.1016/j.ijmm.2013.07.004}, pmid = {23932912}, issn = {1618-0607}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Carrier Proteins/genetics ; Child ; Child, Preschool ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Deletion ; Gene Transfer, Horizontal ; Genetic Variation ; Genotype ; Humans ; Infant ; Male ; Middle Aged ; Molecular Epidemiology ; Molecular Typing ; Portugal/epidemiology ; Prevalence ; Streptococcal Infections/*epidemiology/*microbiology ; Streptococcus pyogenes/*genetics/*isolation & purification ; Superantigens/*genetics ; Young Adult ; }, abstract = {The emergence of highly virulent and successful Streptococcus pyogenes (group A streptococci - GAS) clones has been attributed to the exchange of virulence factors by lateral gene transfer mechanisms, which strongly contribute to genomic diversity. We characterized a collection of 191 GAS isolates recovered from normally sterile sites in Portugal during 2006-2009 and compared them to invasive isolates obtained during 2000-2005. Antimicrobial resistance rates did not change significantly between the two periods and were generally low. In 2006-2009, emm1, emm89, emm3, and emm6 represented 60% of the isolates. The chromosomally encoded superantigen (SAg) genes speG and smeZ were present in the majority (>90%) of the isolates, while speJ was found in only 45%. The phage encoded SAgs varied greatly in prevalence (2-53%). The distribution of emm types, pulsed-field gel electrophoresis profiling (PFGE) clusters, and SAg profiles changed significantly between the periods, although there were no statistically supported changes in the prevalence of individual types. While the macrolide susceptible clone emm1-T1-ST28 remained dominant (28%), there was a significant decrease in clonal diversity as indicated by both PFGE profiling and emm typing. This was accompanied by intra-clonal divergence of SAg profiles, which was statistically confirmed for isolates representing emm1, emm28, and emm44. This diversification was associated with the loss and acquisition of SAg genes, carried by phages and of chromosomal origin. These data suggest an ongoing genomic diversification of GAS invasive isolates in Portugal that may contribute to the persistence of clones with improved fitness or virulence.}, } @article {pmid23859822, year = {2013}, author = {Sand, A and Steel, M}, title = {The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees.}, journal = {Journal of theoretical biology}, volume = {335}, number = {}, pages = {295-298}, doi = {10.1016/j.jtbi.2013.07.002}, pmid = {23859822}, issn = {1095-8541}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; *Models, Genetic ; *Phylogeny ; }, abstract = {Evolutionary events such as incomplete lineage sorting and lateral gene transfers constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species tree. One particularly simple and efficient way to infer species trees from gene trees under such conditions is to combine three-taxon analyses for several genes using a majority vote approach. For incomplete lineage sorting this method is known to be statistically consistent; however, for lateral gene transfers it was recently shown that a zone of inconsistency exists for a specific four-taxon tree topology, and it was posed as an open question whether inconsistencies could exist for other four-taxon tree topologies? In this letter we analyze all remaining four-taxon topologies and show that no other inconsistencies exist.}, } @article {pmid23849122, year = {2013}, author = {Gardiner, DM and Kazan, K and Manners, JM}, title = {Cross-kingdom gene transfer facilitates the evolution of virulence in fungal pathogens.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {210}, number = {}, pages = {151-158}, doi = {10.1016/j.plantsci.2013.06.002}, pmid = {23849122}, issn = {1873-2259}, mesh = {Biological Evolution ; Fungal Proteins/*genetics ; Fungi/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Plant Diseases/*microbiology ; Plants/*microbiology ; Virulence/genetics ; }, abstract = {The constant interaction between plants and their pathogens has resulted in the evolution of a diverse array of microbial infection strategies. It is increasingly evident that horizontal acquisition of new virulence functions in fungi is one of the evolutionary processes that maintain pathogens' competitive edge over host plants. Genome analyses of fungi are pointing towards this phenomenon being particularly prevalent in the subphylum Pezizomycota. While the extent of cross-kingdom gene transfer can be determined with existing genomic tools and databases, so far very few horizontally transmitted genes have been functionally characterised, and an understanding of their physiological roles in virulence has been determined for even fewer genes. Understanding the evolutionary selection pressures that drive the retention of acquired genes in particular fungal lineages is important, as it will undoubtedly reveal new insights into both fungal virulence mechanisms and corresponding plant defence processes in the future.}, } @article {pmid23841456, year = {2013}, author = {Halary, S and McInerney, JO and Lopez, P and Bapteste, E}, title = {EGN: a wizard for construction of gene and genome similarity networks.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {146}, doi = {10.1186/1471-2148-13-146}, pmid = {23841456}, issn = {1471-2148}, mesh = {Borrelia/*genetics ; Evolution, Molecular ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Plasmids/genetics ; *Software ; }, abstract = {BACKGROUND: Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for the detection of distant homologs. Currently, such analyses require some computer programming skills due to the limited availability of user-friendly freely distributed software. Consequently, although appealing, the construction and analyses of these networks remain less familiar to biologists than do phylogenetic approaches.

RESULTS: In order to ease the use of similarity networks in the community of evolutionary biologists, we introduce a software program, EGN, that runs under Linux or MacOSX. EGN automates the reconstruction of gene and genome networks from nucleic and proteic sequences. EGN also implements statistics describing genetic diversity in these samples, for various user-defined thresholds of similarities. In the interest of studying the complexity of evolutionary processes affecting microbial evolution, we applied EGN to a dataset of 571,044 proteic sequences from the three domains of life and from mobile elements. We observed that, in Borrelia, plasmids play a different role than in most other eubacteria. Rather than being genetic couriers involved in lateral gene transfer, Borrelia's plasmids and their genes act as private genetic goods, that contribute to the creation of genetic diversity within their parasitic hosts.

CONCLUSION: EGN can be used for constructing, analyzing, and mining molecular datasets in evolutionary studies. The program can help increase our knowledge of the processes through which genes from distinct sources and/or from multiple genomes co-evolve in lineages of cellular organisms.}, } @article {pmid23840181, year = {2013}, author = {Riley, DR and Sieber, KB and Robinson, KM and White, JR and Ganesan, A and Nourbakhsh, S and Dunning Hotopp, JC}, title = {Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples.}, journal = {PLoS computational biology}, volume = {9}, number = {6}, pages = {e1003107}, doi = {10.1371/journal.pcbi.1003107}, pmid = {23840181}, issn = {1553-7358}, support = {1-DP2-OD007372/OD/NIH HHS/United States ; }, mesh = {Bacteria/genetics/*isolation & purification ; Base Sequence ; DNA, Bacterial/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Human ; Humans ; Molecular Sequence Data ; Neoplasms/*genetics/metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {There are 10× more bacterial cells in our bodies from the microbiome than human cells. Viral DNA is known to integrate in the human genome, but the integration of bacterial DNA has not been described. Using publicly available sequence data from the human genome project, the 1000 Genomes Project, and The Cancer Genome Atlas (TCGA), we examined bacterial DNA integration into the human somatic genome. Here we present evidence that bacterial DNA integrates into the human somatic genome through an RNA intermediate, and that such integrations are detected more frequently in (a) tumors than normal samples, (b) RNA than DNA samples, and (c) the mitochondrial genome than the nuclear genome. Hundreds of thousands of paired reads support random integration of Acinetobacter-like DNA in the human mitochondrial genome in acute myeloid leukemia samples. Numerous read pairs across multiple stomach adenocarcinoma samples support specific integration of Pseudomonas-like DNA in the 5'-UTR and 3'-UTR of four proto-oncogenes that are up-regulated in their transcription, consistent with conversion to an oncogene. These data support our hypothesis that bacterial integrations occur in the human somatic genome and may play a role in carcinogenesis. We anticipate that the application of our approach to additional cancer genome projects will lead to the more frequent detection of bacterial DNA integrations in tumors that are in close proximity to the human microbiome.}, } @article {pmid23763770, year = {2013}, author = {Dehghan, S and Seto, J and Liu, EB and Walsh, MP and Dyer, DW and Chodosh, J and Seto, D}, title = {Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events.}, journal = {Virology}, volume = {443}, number = {2}, pages = {197-207}, doi = {10.1016/j.virol.2013.05.014}, pmid = {23763770}, issn = {1096-0341}, support = {R01 EY013124/EY/NEI NIH HHS/United States ; EY013124/EY/NEI NIH HHS/United States ; }, mesh = {Adenovirus Infections, Human/virology ; Adenoviruses, Human/*genetics ; Adenoviruses, Simian/*genetics ; Animals ; Base Sequence ; Computational Biology/*methods ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Viral/*genetics ; Humans ; Molecular Sequence Data ; Pan troglodytes/virology ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Viral Proteins/genetics ; Zoonoses ; }, abstract = {Computational analysis of human adenovirus type 4 (HAdV-E4), a pathogen that is the only HAdV member of species E, provides insights into its zoonotic origin and molecular adaptation. Its genome encodes a domain of the major capsid protein, hexon, from HAdV-B16 recombined into the genome chassis of a simian adenovirus. Genomes of two recent field strains provide a clue to its adaptation to the new host: recombination of a NF-I binding site motif, which is required for efficient viral replication, from another HAdV genome. This motif is absent in the chimpanzee adenoviruses and the HAdV-E4 prototype, but is conserved amongst other HAdVs. This is the first report of an interspecies recombination event for HAdVs, and the first documentation of a lateral partial gene transfer from a chimpanzee AdV. The potential for such recombination events are important when considering chimpanzee adenoviruses as candidate gene delivery vectors for human patients.}, } @article {pmid23759724, year = {2013}, author = {Duron, O}, title = {Lateral transfers of insertion sequences between Wolbachia, Cardinium and Rickettsia bacterial endosymbionts.}, journal = {Heredity}, volume = {111}, number = {4}, pages = {330-337}, doi = {10.1038/hdy.2013.56}, pmid = {23759724}, issn = {1365-2540}, mesh = {Animals ; Arthropods/genetics/microbiology ; Bacteria/genetics ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Phylogeny ; Rickettsia/*genetics ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {Various bacteria live exclusively within arthropod cells and collectively act as an important driver of arthropod evolutionary ecology. Whereas rampant intra-generic DNA transfers were recently shown to have a pivotal role in the evolution of the most common of these endosymbionts, Wolbachia, the present study show that inter-generic DNA transfers also commonly take place, constituting a potent source of rapid genomic change. Bioinformatic, molecular and phylogenetic data provide evidence that a selfish genetic element, the insertion sequence ISRpe1, is widespread in the Wolbachia, Cardinium and Rickettsia endosymbionts and experiences recent (and likely ongoing) transfers over long evolutionary distances. Although many ISRpe1 copies were clearly expanding and leading to rapid endosymbiont diversification, degraded copies are also frequently found, constituting an unusual genomic fossil record suggestive of ancient ISRpe1 expansions. Overall, the present data highlight how ecological connections within the arthropod intracellular environment facilitate lateral DNA transfers between distantly related bacterial lineages.}, } @article {pmid23641238, year = {2013}, author = {Djordjevic, SP and Stokes, HW and Roy Chowdhury, P}, title = {Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {86}, doi = {10.3389/fmicb.2013.00086}, pmid = {23641238}, issn = {1664-302X}, abstract = {Multiple antibiotic resistant pathogens represent a major clinical challenge in both human and veterinary context. It is now well-understood that the genes that encode resistance are context independent. That is, the same gene is commonly present in otherwise very disparate pathogens in both humans and production and companion animals, and among bacteria that proliferate in an agricultural context. This can be true even for pathogenic species or clonal types that are otherwise confined to a single host or ecological niche. It therefore follows that mechanisms of gene flow must exist to move genes from one part of the microbial biosphere to another. It is widely accepted that lateral (or horizontal) gene transfer (L(H)GT) drives this gene flow. LGT is relatively well-understood mechanistically but much of this knowledge is derived from a reductionist perspective. We believe that this is impeding our ability to deal with the medical ramifications of LGT. Resistance genes and the genetic scaffolds that mobilize them in multiply drug resistant bacteria of clinical significance are likely to have their origins in completely unrelated parts of the microbial biosphere. Resistance genes are increasingly polluting the microbial biosphere by contaminating environmental niches where previously they were not detected. More attention needs to be paid to the way that humans have, through the widespread application of antibiotics, selected for combinations of mobile elements that enhance the flow of resistance genes between remotely linked parts of the microbial biosphere. Attention also needs to be paid to those bacteria that link human and animal ecosystems. We argue that multiply antibiotic resistant commensal bacteria are especially important in this regard. More generally, the post genomics era offers the opportunity for understanding how resistance genes are mobilized from a one health perspective. In the long term, this holistic approach offers the best opportunity to better manage what is an enormous problem to humans both in terms of health and food security.}, } @article {pmid23610429, year = {2013}, author = {Wu, B and Novelli, J and Jiang, D and Dailey, HA and Landmann, F and Ford, L and Taylor, MJ and Carlow, CK and Kumar, S and Foster, JM and Slatko, BE}, title = {Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {19}, pages = {7748-7753}, doi = {10.1073/pnas.1304049110}, pmid = {23610429}, issn = {1091-6490}, support = {L30 DK096501/DK/NIDDK NIH HHS/United States ; DK96501/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Bayes Theorem ; Brugia malayi/*enzymology/genetics ; Caenorhabditis elegans/genetics ; Cloning, Molecular ; Escherichia coli/metabolism ; Exons ; Female ; Ferrochelatase/*genetics ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; Genome ; Green Fluorescent Proteins/metabolism ; In Situ Hybridization ; Male ; Microscopy, Confocal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; }, abstract = {Lateral gene transfer events between bacteria and animals highlight an avenue for evolutionary genomic loss/gain of function. Herein, we report functional lateral gene transfer in animal parasitic nematodes. Members of the Nematoda are heme auxotrophs, lacking the ability to synthesize heme; however, the human filarial parasite Brugia malayi has acquired a bacterial gene encoding ferrochelatase (BmFeCH), the terminal step in heme biosynthesis. BmFeCH, encoded by a 9-exon gene, is a mitochondrial-targeted, functional ferrochelatase based on enzyme assays, complementation, and inhibitor studies. Homologs have been identified in several filariae and a nonfilarial nematode. RNAi and ex vivo inhibitor experiments indicate that BmFeCH is essential for viability, validating it as a potential target for filariasis control.}, } @article {pmid23608703, year = {2013}, author = {Schoenfeld, TW and Murugapiran, SK and Dodsworth, JA and Floyd, S and Lodes, M and Mead, DA and Hedlund, BP}, title = {Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa.}, journal = {Molecular biology and evolution}, volume = {30}, number = {7}, pages = {1653-1664}, doi = {10.1093/molbev/mst078}, pmid = {23608703}, issn = {1537-1719}, support = {R43HG002714/HG/NHGRI NIH HHS/United States ; R44 HG002714/HG/NHGRI NIH HHS/United States ; R43 HG006078/HG/NHGRI NIH HHS/United States ; R44HG002714/HG/NHGRI NIH HHS/United States ; R43HG006078/HG/NHGRI NIH HHS/United States ; R43 HG002714/HG/NHGRI NIH HHS/United States ; }, mesh = {Alveolata/enzymology/genetics ; Amino Acid Sequence ; Animals ; Bacteria/*enzymology/genetics ; Computational Biology ; DNA-Directed DNA Polymerase/*genetics ; Gene Transfer, Horizontal/*genetics ; Hot Springs/virology ; Phylogeny ; Sequence Homology, Amino Acid ; Viruses/*enzymology/genetics ; }, abstract = {Bioinformatics and functional screens identified a group of Family A-type DNA Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline hot springs in Yellowstone National Park and the US Great Basin. The proteins encoded by these viral polA genes (PolAs) shared no significant sequence similarity with any known viral proteins but were remarkably similar to PolAs encoded by two of three families of the bacterial phylum Aquificae and by several apicoplast-targeted PolA-like proteins found in the eukaryotic phylum Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and Toxoplasma. The viral gene products share signature elements previously associated only with Aquificae and Apicomplexa PolA-like proteins and were similar to proteins encoded by prophage elements of a variety of otherwise unrelated Bacteria, each of which additionally encoded a prototypical bacterial PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this study share with the Apicomplexa proteins large amino-terminal domains with putative helicase/primase elements but low primary sequence similarity. The genomic context and distribution, phylogeny, and biochemistry of these PolA proteins suggest that thermophilic viruses transferred polA genes to the Apicomplexa, likely through secondary endosymbiosis of a virus-infected proto-apicoplast, and to the common ancestor of two of three Aquificae families, where they displaced the orthologous cellular polA gene. On the basis of biochemical activity, gene structure, and sequence similarity, we speculate that the xenologous viral-type polA genes may have functions associated with diversity-generating recombination in both Bacteria and Apicomplexa.}, } @article {pmid23588684, year = {2013}, author = {Bouzat, JL and Hoostal, MJ}, title = {Evolutionary analysis and lateral gene transfer of two-component regulatory systems associated with heavy-metal tolerance in bacteria.}, journal = {Journal of molecular evolution}, volume = {76}, number = {5}, pages = {267-279}, doi = {10.1007/s00239-013-9558-z}, pmid = {23588684}, issn = {1432-1432}, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Composition ; Biological Evolution ; Cadmium/*metabolism ; Copper/*metabolism ; Escherichia coli/genetics/metabolism ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Gram-Negative Bacteria/*genetics/metabolism ; Models, Molecular ; Operon ; Phylogeny ; Plasmids ; Pseudomonas syringae/genetics/metabolism ; Ralstonia/genetics/metabolism ; Salmonella typhimurium/genetics/metabolism ; Structural Homology, Protein ; Zinc/*metabolism ; }, abstract = {Microorganisms have adapted intricate signal transduction mechanisms to coordinate tolerance to toxic levels of metals, including two-component regulatory systems (TCRS). In particular, both cop and czc operons are regulated by TCRS; the cop operon plays a key role in bacterial tolerance to copper, whereas the czc operon is involved in the efflux of cadmium, zinc, and cobalt from the cell. Although the molecular physiology of heavy metal tolerance genes has been extensively studied, their evolutionary relationships are not well-understood. Phylogenetic relationships among heavy-metal efflux proteins and their corresponding two-component regulatory proteins revealed orthologous and paralogous relationships from species divergences and ancient gene duplications. The presence of heavy metal tolerance genes on bacterial plasmids suggests these genes may be prone to spread through horizontal gene transfer. Phylogenetic inferences revealed nine potential examples of lateral gene transfer associated with metal efflux proteins and two examples for regulatory proteins. Notably, four of the examples suggest lateral transfer across major evolutionary domains. In most cases, differences in GC content in metal tolerance genes and their corresponding host genomes confirmed lateral gene transfer events. Three-dimensional protein structures predicted for the response regulators encoded by cop and czc operons showed a high degree of structural similarity with other known proteins involved in TCRS signal transduction, which suggests common evolutionary origins of functional phenotypes and similar mechanisms of action for these response regulators.}, } @article {pmid23575371, year = {2013}, author = {Hingamp, P and Grimsley, N and Acinas, SG and Clerissi, C and Subirana, L and Poulain, J and Ferrera, I and Sarmento, H and Villar, E and Lima-Mendez, G and Faust, K and Sunagawa, S and Claverie, JM and Moreau, H and Desdevises, Y and Bork, P and Raes, J and de Vargas, C and Karsenti, E and Kandels-Lewis, S and Jaillon, O and Not, F and Pesant, S and Wincker, P and Ogata, H}, title = {Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.}, journal = {The ISME journal}, volume = {7}, number = {9}, pages = {1678-1695}, doi = {10.1038/ismej.2013.59}, pmid = {23575371}, issn = {1751-7370}, mesh = {Animals ; *Biodiversity ; Cell Nucleus/virology ; Cytoplasm/virology ; DNA Viruses/*classification/genetics/*physiology ; Eukaryota/virology ; Gene Transfer, Horizontal ; Genes, Viral/genetics ; Genome, Viral/genetics ; Indian Ocean ; *Metagenome ; Oceans and Seas ; Oomycetes/virology ; Phycodnaviridae/classification/genetics/physiology ; Phylogeny ; Population Density ; Prokaryotic Cells/physiology ; }, abstract = {Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.}, } @article {pmid23567024, year = {2013}, author = {Kaminski, L and Lurie-Weinberger, MN and Allers, T and Gophna, U and Eichler, J}, title = {Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea.}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {2}, pages = {327-339}, doi = {10.1016/j.ympev.2013.03.024}, pmid = {23567024}, issn = {1095-9513}, mesh = {Archaea/enzymology/genetics ; Archaeal Proteins/*genetics/metabolism ; Codon ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Glycoproteins/*genetics/metabolism ; Glycosylation ; Haloferax/enzymology/*genetics ; Hexosyltransferases/genetics ; Membrane Proteins/genetics ; Multigene Family ; Phylogeny ; Protein Processing, Post-Translational/*genetics ; }, abstract = {N-glycosylation, the covalent attachment of oligosaccharides to target protein Asn residues, is a post-translational modification that occurs in all three domains of life. In Archaea, the N-linked glycans that decorate experimentally characterized glycoproteins reveal a diversity in composition and content unequaled by their bacterial or eukaryal counterparts. At the same time, relatively little is known of archaeal N-glycosylation pathways outside of a handful of model strains. To gain insight into the distribution and evolutionary history of the archaeal version of this universal protein-processing event, 168 archaeal genome sequences were scanned for the presence of aglB, encoding the known archaeal oligosaccharyltransferase, an enzyme key to N-glycosylation. Such analysis predicts the presence of AglB in 166 species, with some species seemingly containing multiple versions of the protein. Phylogenetic analysis reveals that the events leading to aglB duplication occurred at various points during archaeal evolution. In many cases, aglB is found as part of a cluster of putative N-glycosylation genes. The presence, arrangement and nucleotide composition of genes in aglB-based clusters in five species of the halophilic archaeon Haloferax points to lateral gene transfer as contributing to the evolution of archaeal N-glycosylation.}, } @article {pmid23550063, year = {2012}, author = {Domingues, S and da Silva, GJ and Nielsen, KM}, title = {Integrons: Vehicles and pathways for horizontal dissemination in bacteria.}, journal = {Mobile genetic elements}, volume = {2}, number = {5}, pages = {211-223}, doi = {10.4161/mge.22967}, pmid = {23550063}, issn = {2159-2543}, abstract = {Integrons are genetic elements first described at the end of the 1980s. Although most integrons were initially described in human clinical isolates, they have now been identified in many non-clinical environments, such as water and soil. Integrons are present in ≈10% of the sequenced bacterial genomes and are frequently linked to mobile genetic elements (MGEs); particularly the class 1 integrons. Genetic linkage to a diverse set of MGEs facilitates horizontal transfer of class 1 integrons within and between bacterial populations and species. The mechanistic aspects limiting transfer of MGEs will therefore limit the transfer of class 1 integrons. However, horizontal movement due to genes provided in trans and homologous recombination can result in class 1 integron dynamics independent of MGEs. A key determinant for continued dissemination of class 1 integrons is the probability that transferred MGEs will be vertically inherited in the recipient bacterial population. Heritability depends both on genetic stability as well as the fitness costs conferred to the host. Here we review the factors known to govern the dissemination of class 1 integrons in bacteria.}, } @article {pmid23542649, year = {2013}, author = {Cobbs, C and Heath, J and Stireman, JO and Abbot, P}, title = {Carotenoids in unexpected places: gall midges, lateral gene transfer, and carotenoid biosynthesis in animals.}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {2}, pages = {221-228}, doi = {10.1016/j.ympev.2013.03.012}, pmid = {23542649}, issn = {1095-9513}, mesh = {Animals ; Carotenoids/*biosynthesis/genetics ; Diptera/enzymology/*genetics ; Evolution, Molecular ; Gene Dosage ; *Gene Transfer, Horizontal ; Genes, Fungal ; Geranylgeranyl-Diphosphate Geranylgeranyltransferase/genetics ; Insect Proteins/*genetics ; Intramolecular Lyases/genetics ; Likelihood Functions ; Molecular Sequence Annotation ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Carotenoids are conjugated isoprenoid molecules with many important physiological functions in organisms, including roles in photosynthesis, oxidative stress reduction, vision, diapause, photoperiodism, and immunity. Until recently, it was believed that only plants, microorganisms, and fungi were capable of synthesizing carotenoids and that animals acquired them from their diet, but recent studies have demonstrated that two arthropods (pea aphid and spider mite) possess a pair of genes homologous to those required for the first step of carotenoid biosynthesis. Absent in all other known animal genomes, these genes appear to have been acquired by aphids and spider mites in one or several lateral gene transfer events from a fungal donor. We report the third case of fungal carotenoid biosynthesis gene homologs in an arthropod: flies from the family Cecidomyiidae, commonly known as gall midges. Using phylogenetic analyses we show that it is unlikely that lycopene cyclase/phytoene synthase and phytoene desaturase homologs were transferred singly to an ancient arthropod ancestor; instead we propose that genes were transferred independently from related fungal donors after divergence of the major arthropod lineages. We also examine variation in intron placement and copy number of the carotenoid genes that may underlie function in the midges. This trans-kingdom transfer of carotenoid genes may represent a key innovation, underlying the evolution of phytophagy and plant-galling in gall midges and facilitating their extensive diversification across plant lineages.}, } @article {pmid23541366, year = {2013}, author = {Huddleston, JR and Brokaw, JM and Zak, JC and Jeter, RM}, title = {Natural transformation as a mechanism of horizontal gene transfer among environmental Aeromonas species.}, journal = {Systematic and applied microbiology}, volume = {36}, number = {4}, pages = {224-234}, doi = {10.1016/j.syapm.2013.01.004}, pmid = {23541366}, issn = {1618-0984}, mesh = {Aeromonas/*genetics/physiology ; Culture Media/chemistry ; DNA Transformation Competence ; *Environmental Microbiology ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Transformation, Bacterial ; }, abstract = {Aeromonas species are common inhabitants of aquatic environments and relevant as human pathogens. Their potential as pathogens may be related in part to lateral transfer of genes associated with toxin production, biofilm formation, antibiotic resistance, and other virulence determinants. Natural transformation has not been characterized in aeromonads. DNA from wild-type, prototrophic strains that had been isolated from environmental sources was used as donor DNA in transformation assays with auxotrophs as the recipients. Competence was induced in 20% nutrient broth during the stationary phase of growth. Optimal transformation assay conditions for one chosen isolate were in Tris buffer with magnesium or calcium, pH 5-8, and a saturating concentration of 0.5 μg of DNA per assay (3.3 ng of DNA μl⁻¹) at 30°C. Sodium was also required and could not be replaced with ammonium, potassium, or lithium. The maximal transformation frequency observed was 1.95 × 10⁻³ transformants (recipient cell)⁻¹. A survey of environmental Aeromonas auxotrophic recipients (n=37), assayed with donor DNA from other wild-type environmental aeromonads under optimal assay conditions, demonstrated that 73% were able to act as recipients, and 100% were able to act as donors to at least some other aeromonads. Three different transformation groups were identified based on each isolates' ability to transform other strains with its DNA. The transformation groups roughly corresponded to phylogenetic groups. These results demonstrate that natural transformation is a general property of Aeromonas environmental isolates with implications for the genetic structures of coincident Aeromonas populations.}, } @article {pmid23533610, year = {2013}, author = {Wheeler, D and Redding, AJ and Werren, JH}, title = {Characterization of an ancient lepidopteran lateral gene transfer.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59262}, doi = {10.1371/journal.pone.0059262}, pmid = {23533610}, issn = {1932-6203}, support = {GM084917/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Enterococcus/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Lepidoptera/*genetics ; }, abstract = {Bacteria to eukaryote lateral gene transfers (LGT) are an important potential source of material for the evolution of novel genetic traits. The explosion in the number of newly sequenced genomes provides opportunities to identify and characterize examples of these lateral gene transfer events, and to assess their role in the evolution of new genes. In this paper, we describe an ancient lepidopteran LGT of a glycosyl hydrolase family 31 gene (GH31) from an Enterococcus bacteria. PCR amplification between the LGT and a flanking insect gene confirmed that the GH31 was integrated into the Bombyx mori genome and was not a result of an assembly error. Database searches in combination with degenerate PCR on a panel of 7 lepidopteran families confirmed that the GH31 LGT event occurred deep within the Order approximately 65-145 million years ago. The most basal species in which the LGT was found is Plutella xylostella (superfamily: Yponomeutoidea). Array data from Bombyx mori shows that GH31 is expressed, and low dN/dS ratios indicates the LGT coding sequence is under strong stabilizing selection. These findings provide further support for the proposition that bacterial LGTs are relatively common in insects and likely to be an underappreciated source of adaptive genetic material.}, } @article {pmid23526944, year = {2013}, author = {Riedel, T and Gómez-Consarnau, L and Tomasch, J and Martin, M and Jarek, M and González, JM and Spring, S and Rohlfs, M and Brinkhoff, T and Cypionka, H and Göker, M and Fiebig, A and Klein, J and Goesmann, A and Fuhrman, JA and Wagner-Döbler, I}, title = {Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e57487}, doi = {10.1371/journal.pone.0057487}, pmid = {23526944}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; Carotenoids/biosynthesis/genetics ; Flavobacteriaceae/classification/*genetics/*physiology ; Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Retinaldehyde/biosynthesis/genetics ; Rhodopsin/*genetics ; Rhodopsins, Microbial/*genetics ; Seawater/microbiology ; Species Specificity ; }, abstract = {Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.}, } @article {pmid23475938, year = {2013}, author = {Driscoll, T and Gillespie, JJ and Nordberg, EK and Azad, AF and Sobral, BW}, title = {Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont.}, journal = {Genome biology and evolution}, volume = {5}, number = {4}, pages = {621-645}, doi = {10.1093/gbe/evt036}, pmid = {23475938}, issn = {1759-6653}, support = {R01 AI017828/AI/NIAID NIH HHS/United States ; R01 AI059118/AI/NIAID NIH HHS/United States ; HHSN272200900040C/AI/NIAID NIH HHS/United States ; HHSN272200900040C//PHS HHS/United States ; R01AI017828/AI/NIAID NIH HHS/United States ; R01AI59118/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Genome ; Gram-Negative Bacteria/classification/genetics/isolation & purification/physiology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Placozoa/*genetics/*microbiology/physiology ; Rickettsiaceae/classification/*genetics/isolation & purification/physiology ; *Symbiosis ; }, abstract = {Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote-microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan's aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host-microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.}, } @article {pmid23451112, year = {2013}, author = {Dalquen, DA and Altenhoff, AM and Gonnet, GH and Dessimoz, C}, title = {The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56925}, doi = {10.1371/journal.pone.0056925}, pmid = {23451112}, issn = {1932-6203}, mesh = {Gene Duplication/*genetics ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Mutagenesis, Insertional/*genetics ; }, abstract = {The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studies. Yet, while dependent on model assumptions, simulation-based benchmarking offers unique advantages: contrary to empirical data, all aspects of simulated data are known with certainty. Furthermore, the flexibility of simulation makes it possible to investigate performance factors in isolation of one another.Here, we use simulated data to dissect the performance of six methods for orthology inference available as standalone software packages (Inparanoid, OMA, OrthoInspector, OrthoMCL, QuartetS, SPIMAP) as well as two generic approaches (bidirectional best hit and reciprocal smallest distance). We investigate the impact of various evolutionary forces (gene duplication, insertion, deletion, and lateral gene transfer) and technological artefacts (ambiguous sequences) on orthology inference. We show that while gene duplication/loss and insertion/deletion are well handled by most methods (albeit for different trade-offs of precision and recall), lateral gene transfer disrupts all methods. As for ambiguous sequences, which might result from poor sequencing, assembly, or genome annotation, we show that they affect alignment score-based orthology methods more strongly than their distance-based counterparts.}, } @article {pmid23442822, year = {2013}, author = {Alsmark, C and Foster, PG and Sicheritz-Ponten, T and Nakjang, S and Martin Embley, T and Hirt, RP}, title = {Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes.}, journal = {Genome biology}, volume = {14}, number = {2}, pages = {R19}, doi = {10.1186/gb-2013-14-2-r19}, pmid = {23442822}, issn = {1474-760X}, support = {268701//European Research Council/International ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; *Genome, Protozoan ; Molecular Sequence Annotation ; Parasites/*genetics ; }, abstract = {BACKGROUND: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution.

RESULTS: We used a phylogenomic approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers, dramatically affecting the enzymes of core pathways, particularly amino acid and sugar metabolism, but also providing new genes of potential adaptive significance in the life of parasites. A broad range of prokaryotic donors is involved in such transfers, but there is clear and significant enrichment for bacterial groups that share the same habitats, including the human microbiota, as the parasites investigated.

CONCLUSIONS: Our data show that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, although the outlines of the core eukaryotic metabolism are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric.}, } @article {pmid23407828, year = {2013}, author = {Marron, AO and Alston, MJ and Heavens, D and Akam, M and Caccamo, M and Holland, PW and Walker, G}, title = {A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1756}, pages = {20122543}, doi = {10.1098/rspb.2012.2543}, pmid = {23407828}, issn = {1471-2954}, support = {BB/E527604/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; CCC-1-10//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Biological Transport/genetics ; Carrier Proteins/*genetics/*metabolism ; Choanoflagellata/genetics/*metabolism ; Conserved Sequence ; Diatoms/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Silicon/*metabolism ; }, abstract = {Biosilicification is widespread across the eukaryotes and requires concentration of silicon in intracellular vesicles. Knowledge of the molecular mechanisms underlying this process remains limited, with unrelated silicon-transporting proteins found in the eukaryotic clades previously studied. Here, we report the identification of silicon transporter (SIT)-type genes from the siliceous loricate choanoflagellates Stephanoeca diplocostata and Diaphanoeca grandis. Until now, the SIT gene family has been identified only in diatoms and other siliceous stramenopiles, which are distantly related to choanoflagellates among the eukaryotes. This is the first evidence of similarity between SITs from different eukaryotic supergroups. Phylogenetic analysis indicates that choanoflagellate and stramenopile SITs form distinct monophyletic groups. The absence of putative SIT genes in any other eukaryotic groups, including non-siliceous choanoflagellates, leads us to propose that SIT genes underwent a lateral gene transfer event between stramenopiles and loricate choanoflagellates. We suggest that the incorporation of a foreign SIT gene into the stramenopile or choanoflagellate genome resulted in a major metabolic change: the acquisition of biomineralized silica structures. This hypothesis implies that biosilicification has evolved multiple times independently in the eukaryotes, and paves the way for a better understanding of the biochemical basis of silicon transport through identification of conserved sequence motifs.}, } @article {pmid23383996, year = {2013}, author = {Roch, S and Snir, S}, title = {Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {20}, number = {2}, pages = {93-112}, doi = {10.1089/cmb.2012.0234}, pmid = {23383996}, issn = {1557-8666}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Models, Genetic ; *Models, Statistical ; *Phylogeny ; }, abstract = {Lateral gene transfer (LGT) is a common mechanism of nonvertical evolution, during which genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive evolution with important medical implications. In evolutionary studies, LGT has been shown to create widespread discordance between gene trees as genomes become mosaics of gene histories. In particular, the Tree of Life has been questioned as an appropriate representation of bacterial evolutionary history. Nevertheless a common hypothesis is that prokaryotic evolution is primarily treelike, but that the underlying trend is obscured by LGT. Extensive empirical work has sought to extract a common treelike signal from conflicting gene trees. Here we give a probabilistic perspective on the problem of recovering the treelike trend despite LGT. Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree. Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods. Finally, we show that our results have implications for the discovery of highways of gene sharing.}, } @article {pmid23382812, year = {2013}, author = {Kim, BJ and Hong, SH and Kook, YH and Kim, BJ}, title = {Molecular evidence of lateral gene transfer in rpoB gene of Mycobacterium yongonense strains via multilocus sequence analysis.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e51846}, doi = {10.1371/journal.pone.0051846}, pmid = {23382812}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; DNA-Directed RNA Polymerases ; *Gene Transfer, Horizontal ; Humans ; Multilocus Sequence Typing ; Mycobacterium avium Complex/*genetics ; Nontuberculous Mycobacteria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; }, abstract = {Recently, a novel species, Mycobacterium yongonense (DSM 45126(T)), was introduced and while it is phylogenetically related to Mycobacterium intracellulare, it has a distinct RNA polymerase β-subunit gene (rpoB) sequence that is identical to that of Mycobacterium parascrofulaceum, which is a distantly related scotochromogen, which suggests the acquisition of the rpoB gene via a potential lateral gene transfer (LGT) event. The aims of this study are to prove the presence of the LGT event in the rpoB gene of the M. yongonense strains via multilocus sequence analysis (MLSA). In order to determine the potential of an LGT event in the rpoB gene of the M. yongonense, the MLSA based on full rpoB sequences (3447 or 3450 bp) and on partial sequences of five other targets [16S rRNA (1383 or 1395 bp), hsp65 (603 bp), dnaJ (192 bp), recA (1053 bp), and sodA (501 bp)] were conducted. Incongruences between the phylogenetic analysis of the full rpoB and the five other genes in a total of three M. yongonense strains [two clinical strains (MOTT-12 and MOTT-27) and one type strain (DSM 45126(T))] were observed, suggesting that rpoB gene of three M. yongonense strains may have been acquired very recently via an LGT event from M. parascrofulaceum, which is a distantly related scotochromogen.}, } @article {pmid23375108, year = {2013}, author = {Clarke, M and Lohan, AJ and Liu, B and Lagkouvardos, I and Roy, S and Zafar, N and Bertelli, C and Schilde, C and Kianianmomeni, A and Bürglin, TR and Frech, C and Turcotte, B and Kopec, KO and Synnott, JM and Choo, C and Paponov, I and Finkler, A and Heng Tan, CS and Hutchins, AP and Weinmeier, T and Rattei, T and Chu, JS and Gimenez, G and Irimia, M and Rigden, DJ and Fitzpatrick, DA and Lorenzo-Morales, J and Bateman, A and Chiu, CH and Tang, P and Hegemann, P and Fromm, H and Raoult, D and Greub, G and Miranda-Saavedra, D and Chen, N and Nash, P and Ginger, ML and Horn, M and Schaap, P and Caler, L and Loftus, BJ}, title = {Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.}, journal = {Genome biology}, volume = {14}, number = {2}, pages = {R11}, doi = {10.1186/gb-2013-14-2-r11}, pmid = {23375108}, issn = {1474-760X}, support = {281633//European Research Council/International ; BB/E016308/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acanthamoeba castellanii/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome, Protozoan ; Introns ; Protein-Tyrosine Kinases/*genetics/metabolism ; Protozoan Proteins/*genetics/metabolism ; *Signal Transduction ; }, abstract = {BACKGROUND: The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.

RESULTS: Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms.

CONCLUSIONS: Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.}, } @article {pmid23355531, year = {2013}, author = {Szöllosi, GJ and Tannier, E and Lartillot, N and Daubin, V}, title = {Lateral gene transfer from the dead.}, journal = {Systematic biology}, volume = {62}, number = {3}, pages = {386-397}, doi = {10.1093/sysbio/syt003}, pmid = {23355531}, issn = {1076-836X}, mesh = {Algorithms ; Biodiversity ; Biological Evolution ; Cyanobacteria/*genetics ; DNA, Bacterial/*analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Speciation ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria.}, } @article {pmid23349695, year = {2013}, author = {Sureshan, V and Deshpande, CN and Boucher, Y and Koenig, JE and , and Stokes, HW and Harrop, SJ and Curmi, PM and Mabbutt, BC}, title = {Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e52934}, doi = {10.1371/journal.pone.0052934}, pmid = {23349695}, issn = {1932-6203}, support = {U54 GM094585/GM/NIGMS NIH HHS/United States ; GM074942/GM/NIGMS NIH HHS/United States ; GM094568/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Integrons/*genetics ; Metagenome/genetics ; Models, Molecular ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Protein Binding ; Protein Structure, Secondary ; Vibrio cholerae/genetics/metabolism ; }, abstract = {Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions.}, } @article {pmid23340439, year = {2013}, author = {Steel, M and Linz, S and Huson, DH and Sanderson, MJ}, title = {Identifying a species tree subject to random lateral gene transfer.}, journal = {Journal of theoretical biology}, volume = {322}, number = {}, pages = {81-93}, doi = {10.1016/j.jtbi.2013.01.009}, pmid = {23340439}, issn = {1095-8541}, mesh = {Animals ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Models, Genetic ; Phylogeny ; Poisson Distribution ; }, abstract = {A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favor gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon has recently been well-studied, and some elegant solutions for species tree reconstruction have been proposed. One particularly simple and statistically consistent estimator of the species tree under incomplete lineage sorting is to combine three-taxon analyses, which are phylogenetically robust to incomplete lineage sorting. In this paper, we consider whether such an approach will also work under lateral gene transfer (LGT). By providing an exact analysis of some cases of this model, we show that there is a zone of inconsistency when majority-rule three-taxon gene trees are used to reconstruct species trees under LGT. However, a triplet-based approach will consistently reconstruct a species tree under models of LGT, provided that the expected number of LGT transfers is not too high. Our analysis involves a novel connection between the LGT problem and random walks on cyclic graphs. We have implemented a procedure for reconstructing trees subject to LGT or lineage sorting in settings where taxon coverage may be patchy and illustrate its use on two sample data sets.}, } @article {pmid23333318, year = {2013}, author = {Reinhard, F and Miyazaki, R and Pradervand, N and van der Meer, JR}, title = {Cell differentiation to "mating bodies" induced by an integrating and conjugative element in free-living bacteria.}, journal = {Current biology : CB}, volume = {23}, number = {3}, pages = {255-259}, doi = {10.1016/j.cub.2012.12.025}, pmid = {23333318}, issn = {1879-0445}, mesh = {Conjugation, Genetic ; DNA, Bacterial/*physiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Pseudomonas aeruginosa/*physiology ; }, abstract = {Lateral gene transfer (LGT) is one of the most important processes leading to prokaryotic genome innovation. LGT is typically associated with conjugative plasmids and bacteriophages, but recently, a new class of mobile DNA known as integrating and conjugative elements (ICE) was discovered, which is abundant and widespread among bacterial genomes. By studying at the single-cell level the behavior of a prevalent ICE type in the genus Pseudomonas, we uncover the remarkable way in which the ICE orchestrates host cell differentiation to ensure horizontal transmission. We find that the ICE induces a state of transfer competence (tc) in 3%-5% of cells in a population under nongrowing conditions. ICE factors control the development of tc cells into specific assemblies that we name "mating bodies." Interestingly, cells in mating bodies undergo fewer and slower division than non-tc cells and eventually lyse. Mutations in ICE genes disrupting mating-body formation lead to 5-fold decreased ICE transfer rates. Hence, by confining the tc state to a small proportion of the population, ICE horizontal transmission is achieved with little cost in terms of vertical transmission. Given the low transfer frequencies of most ICE, we anticipate regulation by subpopulation differentiation to be widespread.}, } @article {pmid23289559, year = {2013}, author = {Clerissi, C and Grimsley, N and Desdevises, Y}, title = {Genetic exchanges of inteins between prasinoviruses (phycodnaviridae).}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {1}, pages = {18-33}, doi = {10.1111/j.1558-5646.2012.01738.x}, pmid = {23289559}, issn = {1558-5646}, mesh = {Chlorophyta/virology ; DNA, Viral ; Evolution, Molecular ; Gene Transfer, Horizontal ; Inteins/*genetics ; Phycodnaviridae/*genetics ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic diversity in the Phycodnaviridae (double-stranded DNA viruses infecting photosynthetic eukaryotes) is most often studied using their DNA polymerase gene (PolB). This gene and its translated protein product can harbor a selfish genetic element called an "intein" that disrupts the sequence of the host gene without affecting its activity. After translation, the intein peptide sequence self-excises precisely, producing a functional ligated host protein. In addition, inteins can encode homing endonuclease (HEN) domains that permit the possibility of lateral transfers to intein-free alleles. However, no clear evidence for their transfer between viruses has previously been shown. The objective of this paper was to determine whether recent transfers of inteins have occurred between prasinoviruses (Phycodnaviridae) that infect the Mamiellophyceae, an abundant and widespread class of unicellular green algae, by using DNA sequence analyses and cophylogenetic methods. Our results suggest that transfer among prasinoviruses is a dynamic ongoing process and, for the first time in the Phycodnaviridae family, we showed a recombination event within an intein.}, } @article {pmid23281896, year = {2013}, author = {McNulty, SN and Fischer, K and Curtis, KC and Weil, GJ and Brattig, NW and Fischer, PU}, title = {Localization of Wolbachia-like gene transcripts and peptides in adult Onchocerca flexuosa worms indicates tissue specific expression.}, journal = {Parasites & vectors}, volume = {6}, number = {}, pages = {2}, doi = {10.1186/1756-3305-6-2}, pmid = {23281896}, issn = {1756-3305}, mesh = {Animals ; Bacterial Proteins/*biosynthesis ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Immunohistochemistry ; In Situ Hybridization ; Onchocerca/*microbiology ; *Transcription, Genetic ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Most filarial species in the genus Onchocerca depend on Wolbachia endobacteria to successfully carry out their life cycle. O. flexuosa is a Wolbachia-free species, but its genome contains Wolbachia-like sequences presumably obtained from Wolbachia via horizontal gene transfer. Proteogenomic studies have shown that many of these Wolbachia-like sequences are expressed in adult worms.

METHODS: Six Wolbachia-like sequences in O. flexuosa were chosen for further study based on their sequence conservation with Wolbachia genes, length of predicted open reading frames, and expression at the RNA and/or protein levels. In situ hybridization and immunohistochemical labeling were used to localize Wolbachia-like transcripts and peptides in adult worm tissues.

RESULTS: RNA probes representing three of the six target sequences produced hybridization signals in worm tissues. These probes bound to transcripts in the intestine and lateral chords of both sexes, in the hypodermis, median chords and uteri in females, and in sperm precursor cells in males. Antibodies raised to three peptides corresponding to these transcripts bound to specific bands in a soluble extract of adult O. flexuosa by Western blot that were not labeled by control antibodies in pre-immune serum. Two of the three antibodies produced labeling patterns in adult worm sections that were similar to those of the RNA probes, while the third produced a different pattern.

CONCLUSIONS: A subset of the Wolbachia-like sequences present in the genome of the Wolbachia-free filarial species O. flexuosa are transcribed in tissues where Wolbachia reside in infected filarial species. Some of the peptides and/or proteins derived from these transcripts appear to be concentrated in the same tissues while others may be exported to other regions of the worm. These results suggest that horizontally transferred Wolbachia genes and gene products may replicate important Wolbachia functions in uninfected filarial worms.}, } @article {pmid23277587, year = {2013}, author = {Walsh, AM and Kortschak, RD and Gardner, MG and Bertozzi, T and Adelson, DL}, title = {Widespread horizontal transfer of retrotransposons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {3}, pages = {1012-1016}, doi = {10.1073/pnas.1205856110}, pmid = {23277587}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Long Interspersed Nucleotide Elements ; Molecular Sequence Data ; Phylogeny ; *Retroelements ; Sequence Alignment ; Vertebrates/classification/genetics ; }, abstract = {In higher organisms such as vertebrates, it is generally believed that lateral transfer of genetic information does not readily occur, with the exception of retroviral infection. However, horizontal transfer (HT) of protein coding repetitive elements is the simplest way to explain the patchy distribution of BovB, a long interspersed element (LINE) about 3.2 kb long, that has been found in ruminants, marsupials, squamates, monotremes, and African mammals. BovB sequences are a major component of some of these genomes. Here we show that HT of BovB is significantly more widespread than believed, and we demonstrate the existence of two plausible arthropod vectors, specifically reptile ticks. A phylogenetic tree built from BovB sequences from species in all of these groups does not conform to expected evolutionary relationships of the species, and our analysis indicates that at least nine HT events are required to explain the observed topology. Our results provide compelling evidence for HT of genetic material that has transformed vertebrate genomes.}, } @article {pmid23275877, year = {2012}, author = {Pandeeti, EV and Longkumer, T and Chakka, D and Muthyala, VR and Parthasarathy, S and Madugundu, AK and Ghanta, S and Medipally, SR and Pantula, SC and Yekkala, H and Siddavattam, D}, title = {Multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in Sphingobium fuliginis ATCC 27551.}, journal = {G3 (Bethesda, Md.)}, volume = {2}, number = {12}, pages = {1541-1554}, doi = {10.1534/g3.112.004051}, pmid = {23275877}, issn = {2160-1836}, mesh = {Attachment Sites, Microbiological ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Cloning, Molecular ; Escherichia coli/metabolism ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Integrases/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Organophosphates/chemistry/*metabolism ; Plasmids/genetics/metabolism ; Recombination, Genetic ; Replication Origin/genetics ; Serine-tRNA Ligase/genetics ; Sphingomonadaceae/*genetics ; }, abstract = {The complete sequence of pPDL2 (37,317 bp), an indigenous plasmid of Sphingobium fuliginis ATCC 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attP, typically seen in integrative mobilizable elements (IME). In agreement with this sequence information, site-specific recombination was observed between pPDL2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attB site at the 3' end of the seryl tRNA gene of Sphingobium japonicum. The opd gene cluster on pPDL2 was found to be part of an active catabolic transposon with mobile elements y4qE and Tn3 at its flanking ends. Besides the previously reported opd cluster, this transposon contains genes coding for protocatechuate dioxygenase and for two transport proteins from the major facilitator family that are predicted to be involved in transport and metabolism of aromatic compounds. A pPDL2 derivative, pPDL2-K, was horizontally transferred into Escherichia coli and Acinetobacter strains, suggesting that the oriT identified in pPDL2 is functional. A well-defined replicative origin (oriV), repA was identified along with a plasmid addiction module relB/relE that would support stable maintenance of pPDL2 in Sphingobium fuliginis ATCC 27551. However, if pPDL2 is laterally transferred into hosts that do not support its replication, the opd cluster appears to integrate into the host chromosome, either through transposition or through site-specific integration. The data presented in this study help to explain the existence of identical opd genes among soil bacteria.}, } @article {pmid23247295, year = {2013}, author = {Farkas, A and Butiuc-Keul, A and Ciatarâş, D and Neamţu, C and Crăciunaş, C and Podar, D and Drăgan-Bularda, M}, title = {Microbiological contamination and resistance genes in biofilms occurring during the drinking water treatment process.}, journal = {The Science of the total environment}, volume = {443}, number = {}, pages = {932-938}, doi = {10.1016/j.scitotenv.2012.11.068}, pmid = {23247295}, issn = {1879-1026}, mesh = {Bacteria/genetics ; *Biofilms ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Integrons ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Biofilms are the predominant mode of microbial growth in drinking water systems. A dynamic exchange of individuals occurs between the attached and planktonic populations, while lateral gene transfer mediates genetic exchange in these bacterial communities. Integrons are important vectors for the spread of antimicrobial resistance. The presence of class 1 integrons (intI1, qac and sul genes) was assessed in biofilms occurring throughout the drinking water treatment process. Isolates from general and specific culture media, covering a wide range of environmental bacteria, fecal indicators and opportunistic pathogens were tested. From 96 isolates tested, 9.37% were found to possess genetic determinants of putative antimicrobial resistance, and these occurred in both Gram-positive and Gram-negative bacteria. Class 1 integron integrase gene was present in 8.33% of bacteria, all positive for the qacEΔ1 gene. The sul1 gene was present in 3.12% of total isolates, representing 37.5% of the class 1 integron positive cells. The present study shows that biofilm communities in a drinking water treatment plant are a reservoir of class 1 integrons, mainly in bacteria that may be associated with microbiological contamination. Eight out of nine integron bearing strains (88.8%) were identified based on 16S rRNA gene sequencing as either enteric bacteria or species that may be connected to animal and anthropogenic disturbance.}, } @article {pmid23226971, year = {2012}, author = {Blank, CE}, title = {Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2012}, number = {}, pages = {843539}, doi = {10.1155/2012/843539}, pmid = {23226971}, issn = {1472-3654}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Cluster Analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; Sequence Homology ; }, abstract = {Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the stable core of the genome. Surprisingly, such lateral transfer events were readily identified and quantifiable, occurring only a relatively small number of times in the archaeal domain of life. By placing gene acquisition events into a temporal framework, the rates by which new metabolic genes were acquired can be quantified. The highest lateral transfer rates were among cytochrome oxidase genes that use oxygen as a terminal electron acceptor (with a total of 12-14 lateral transfer events, or 3.4-4.0 events per billion years, across the entire archaeal domain). Genes involved in sulfur or nitrogen metabolism had much lower rates, on the order of one lateral transfer event per billion years. This suggests that lateral transfer rates of key metabolic proteins are rare and not rampant.}, } @article {pmid23226415, year = {2012}, author = {Paganini, J and Campan-Fournier, A and Da Rocha, M and Gouret, P and Pontarotti, P and Wajnberg, E and Abad, P and Danchin, EG}, title = {Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e50875}, doi = {10.1371/journal.pone.0050875}, pmid = {23226415}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; Base Composition/genetics ; Codon/genetics ; DNA Transposable Elements/genetics ; Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Genes, Protozoan/genetics ; Genetic Association Studies ; Genome/*genetics ; Open Reading Frames/genetics ; Parasites/*genetics ; Phylogeny ; Plant Diseases/*parasitology ; Plant Roots/*parasitology ; Plasmids/genetics ; Protozoan Proteins/genetics ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; Tylenchoidea/*genetics ; }, abstract = {Lateral gene transfers (LGT), species to species transmission of genes by means other than direct inheritance from a common ancestor, have played significant role in shaping prokaryotic genomes and are involved in gain or transfer of important biological processes. Whether LGT significantly contributed to the composition of an animal genome is currently unclear. In nematodes, multiple LGT are suspected to have favored emergence of plant-parasitism. With the availability of whole genome sequences it is now possible to assess whether LGT have significantly contributed to the composition of an animal genome and to establish a comprehensive list of these events. We generated clusters of homologous genes and automated phylogenetic inference, to detect LGT in the genomes of root-knot nematodes and found that up to 3.34% of the genes originate from LGT of non-metazoan origin. After their acquisition, the majority of genes underwent series of duplications. Compared to the rest of the genes in these species, several predicted functional categories showed a skewed distribution in the set of genes acquired via LGT. Interestingly, functions related to metabolism, degradation or modification of carbohydrates or proteins were substantially more frequent. This suggests that genes involved in these processes, related to a parasitic lifestyle, have been more frequently fixed in these parasites after their acquisition. Genes from soil bacteria, including plant-pathogens were the most frequent closest relatives, suggesting donors were preferentially bacteria from the rhizosphere. Several of these bacterial genes are plasmid-borne, pointing to a possible role of these mobile genetic elements in the transfer mechanism. Our analysis provides the first comprehensive description of the ensemble of genes of non-metazoan origin in an animal genome. Besides being involved in important processes regarding plant-parasitism, genes acquired via LGT now constitute a substantial proportion of protein-coding genes in these nematode genomes.}, } @article {pmid23221676, year = {2013}, author = {Dagan, T and Roettger, M and Stucken, K and Landan, G and Koch, R and Major, P and Gould, SB and Goremykin, VV and Rippka, R and Tandeau de Marsac, N and Gugger, M and Lockhart, PJ and Allen, JF and Brune, I and Maus, I and Pühler, A and Martin, WF}, title = {Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids.}, journal = {Genome biology and evolution}, volume = {5}, number = {1}, pages = {31-44}, doi = {10.1093/gbe/evs117}, pmid = {23221676}, issn = {1759-6653}, support = {232975//European Research Council/International ; 281357//European Research Council/International ; }, mesh = {Cyanobacteria/*genetics/metabolism ; Ecosystem ; *Evolution, Molecular ; Fresh Water ; Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genome, Plastid ; Multigene Family ; Photosynthesis/*genetics ; Phylogeny ; Plants/genetics ; Symbiosis/genetics ; Water/metabolism ; }, abstract = {Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.}, } @article {pmid23189077, year = {2012}, author = {Budd, A and Devos, DP}, title = {Evaluating the Evolutionary Origins of Unexpected Character Distributions within the Bacterial Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {401}, doi = {10.3389/fmicb.2012.00401}, pmid = {23189077}, issn = {1664-302X}, abstract = {Recently, several characters that are absent from most bacteria, but which are found in many eukaryotes or archaea, have been identified within the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum. Hypotheses of the evolutionary history of such characters are commonly based on the inference of phylogenies of gene or protein families associated with the traits, estimated from multiple sequence alignments (MSAs). So far, studies of this kind have focused on the distribution of (i) two genes involved in the synthesis of sterol, (ii) tubulin genes, and (iii) c1 transfer genes. In many cases, these analyses have concluded that horizontal gene transfer (HGT) is likely to have played a role in shaping the taxonomic distribution of these gene families. In this article, we describe several issues with the inference of HGT from such analyses, in particular concerning the considerable uncertainty associated with our estimation of both gene family phylogenies (especially those containing ancient lineage divergences) and the Tree of Life (ToL), and the need for wider use and further development of explicit probabilistic models to compare hypotheses of vertical and horizontal genetic transmission. We suggest that data which is often taken as evidence for the occurrence of ancient HGT events may not be as convincing as is commonly described, and consideration of alternative theories is recommended. While focusing on analyses including PVCs, this discussion is also relevant for inferences of HGT involving other groups of organisms.}, } @article {pmid23184964, year = {2012}, author = {Nelson-Sathi, S and Dagan, T and Landan, G and Janssen, A and Steel, M and McInerney, JO and Deppenmeier, U and Martin, WF}, title = {Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {50}, pages = {20537-20542}, doi = {10.1073/pnas.1209119109}, pmid = {23184964}, issn = {1091-6490}, mesh = {Archaeal Proteins/genetics ; Bacteria/*genetics ; Euryarchaeota/classification/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; }, abstract = {Archaebacterial halophiles (Haloarchaea) are oxygen-respiring heterotrophs that derive from methanogens--strictly anaerobic, hydrogen-dependent autotrophs. Haloarchaeal genomes are known to have acquired, via lateral gene transfer (LGT), several genes from eubacteria, but it is yet unknown how many genes the Haloarchaea acquired in total and, more importantly, whether independent haloarchaeal lineages acquired their genes in parallel, or as a single acquisition at the origin of the group. Here we have studied 10 haloarchaeal and 1,143 reference genomes and have identified 1,089 haloarchaeal gene families that were acquired by a methanogenic recipient from eubacteria. The data suggest that these genes were acquired in the haloarchaeal common ancestor, not in parallel in independent haloarchaeal lineages, nor in the common ancestor of haloarchaeans and methanosarcinales. The 1,089 acquisitions include genes for catabolic carbon metabolism, membrane transporters, menaquinone biosynthesis, and complexes I-IV of the eubacterial respiratory chain that functions in the haloarchaeal membrane consisting of diphytanyl isoprene ether lipids. LGT on a massive scale transformed a strictly anaerobic, chemolithoautotrophic methanogen into the heterotrophic, oxygen-respiring, and bacteriorhodopsin-photosynthetic haloarchaeal common ancestor.}, } @article {pmid23183983, year = {2013}, author = {Solheim, HT and Sekse, C and Urdahl, AM and Wasteson, Y and Nesse, LL}, title = {Biofilm as an environment for dissemination of stx genes by transduction.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {3}, pages = {896-900}, doi = {10.1128/AEM.03512-12}, pmid = {23183983}, issn = {1098-5336}, mesh = {Bacteriophages/*genetics/*growth & development ; Biofilms/*growth & development ; Escherichia coli/genetics/*physiology/virology ; Gene Transfer, Horizontal ; Shiga Toxin/*genetics ; Temperature ; *Transduction, Genetic ; }, abstract = {Dissemination of Shiga toxin (Stx)-encoding bacteriophages is the most likely mechanism for the spread of Stx-encoding genes and the emergence of new Stx-producing Escherichia coli (STEC). Biofilm has been reported to be a place where horizontal gene transfer by plasmid conjugation and DNA transformation may occur, and in this study, horizontal gene transfer by transduction has been demonstrated. Transfer of Stx-encoding bacteriophages to potentially pathogenic E. coli in biofilm was observed at both 20°C and 37°C. The infection rates were higher at 37°C than at 20°C. To our knowledge, this study is the first to show lateral gene transfer in biofilm mediated by a temperate bacteriophage. The study shows that the biofilm environment can be suitable for transduction events and can thereby be an environment for the emergence of new pathogenic E. coli.}, } @article {pmid23181807, year = {2012}, author = {Hobley, L and Lerner, TR and Williams, LE and Lambert, C and Till, R and Milner, DS and Basford, SM and Capeness, MJ and Fenton, AK and Atterbury, RJ and Harris, MA and Sockett, RE}, title = {Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {670}, doi = {10.1186/1471-2164-13-670}, pmid = {23181807}, issn = {1471-2164}, support = {BB/G003092/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G013632/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; G003092/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; G01362/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Antibiosis ; Bacterial Proteins/*genetics ; Bdellovibrio/*genetics/*growth & development/pathogenicity ; Escherichia coli/*genetics/growth & development ; *Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mutation ; Rivers/microbiology ; Symbiosis ; Synteny ; }, abstract = {BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.}, } @article {pmid23172108, year = {2013}, author = {Cui, Z and Gerfen, CR and Young, WS}, title = {Hypothalamic and other connections with dorsal CA2 area of the mouse hippocampus.}, journal = {The Journal of comparative neurology}, volume = {521}, number = {8}, pages = {1844-1866}, doi = {10.1002/cne.23263}, pmid = {23172108}, issn = {1096-9861}, support = {Z01 MH002498/MH/NIMH NIH HHS/United States ; ZIA MH002498-23/NULL/Intramural NIH HHS/United States ; Z01-MH-002498-23/MH/NIMH NIH HHS/United States ; Z01-MH-002947-23/MH/NIMH NIH HHS/United States ; }, mesh = {Adenoviridae/genetics/metabolism ; Animals ; Brain/anatomy & histology/cytology ; CA2 Region, Hippocampal/*physiology ; Entorhinal Cortex/cytology/physiology ; Functional Laterality ; Gene Transfer Techniques ; Green Fluorescent Proteins/genetics/metabolism ; Hypothalamus/*physiology ; Indoles/metabolism ; Male ; Mice ; Neural Pathways/*physiology ; Neurons/*physiology ; Plant Lectins/genetics/metabolism ; Stilbamidines/metabolism ; }, abstract = {The CA2 area is an important, although relatively unexplored, component of the hippocampus. We used various tracers to provide a comprehensive analysis of CA2 connections in C57BL/6J mice. Using various adeno-associated viruses that express fluorescent proteins, we found a vasopressinergic projection from the paraventricular nuclei of the hypothalamus (PVN) to the CA2 as well as a projection from pyramidal neurons of the CA2 to the supramammillary nuclei. These projections were confirmed by retrograde tracing. As expected, we observed CA2 afferent projections from neurons in ipsilateral entorhinal cortical layer II as well as from bilateral dorsal CA2 and CA3 using retrograde tracers. Additionally, we saw CA2 neuronal input from bilateral medial septal nuclei, vertical and horizontal limbs of the nucleus of diagonal band of Broca, supramammillary nuclei (SUM), and median raphe nucleus. Dorsal CA2 injections of adeno-associated virus expressing green fluorescent protein revealed axonal projections primarily to dorsal CA1, CA2, and CA3 bilaterally. No projection was detected to the entorhinal cortex from the dorsal CA2. These results are consistent with recent observations that the dorsal CA2 forms disynaptic connections with the entorhinal cortex to influence dynamic memory processing. Mouse dorsal CA2 neurons send bilateral projections to the medial and lateral septal nuclei, vertical and horizontal limbs of the diagonal band of Broca, and SUM. Novel connections from the PVN and to the SUM suggest important regulatory roles for CA2 in mediating social and emotional input for memory processing.}, } @article {pmid23171084, year = {2012}, author = {Rybarczyk-Mydłowska, K and Maboreke, HR and van Megen, H and van den Elsen, S and Mooyman, P and Smant, G and Bakker, J and Helder, J}, title = {Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {221}, doi = {10.1186/1471-2148-12-221}, pmid = {23171084}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Bayes Theorem ; Cellulases/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Introns ; Likelihood Functions ; Phylogeny ; Plant Roots/parasitology ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Sequence Analysis, DNA ; Tylenchida/enzymology/*genetics ; }, abstract = {BACKGROUND: Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed.

RESULTS: Single nematodes were used to obtain (partial) genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of ≈ 100 cellulase sequences revealed three types of catalytic domains (A, B, and C). Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated) small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns.

CONCLUSIONS: All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root-knot and cyst nematodes did not acquire this gene directly by lateral genes transfer. More likely, these genes were passed on by ancestors of a family nowadays known as the Pratylenchidae.}, } @article {pmid23145189, year = {2012}, author = {Ricaldi, JN and Fouts, DE and Selengut, JD and Harkins, DM and Patra, KP and Moreno, A and Lehmann, JS and Purushe, J and Sanka, R and Torres, M and Webster, NJ and Vinetz, JM and Matthias, MA}, title = {Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.}, journal = {PLoS neglected tropical diseases}, volume = {6}, number = {10}, pages = {e1853}, doi = {10.1371/journal.pntd.0001853}, pmid = {23145189}, issn = {1935-2735}, support = {D43TW007120/TW/FIC NIH HHS/United States ; R01TW05860/TW/FIC NIH HHS/United States ; HHSN272200900007C//PHS HHS/United States ; K24AI068903/AI/NIAID NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; R01 TW005860/TW/FIC NIH HHS/United States ; T32 GM008666/GM/NIGMS NIH HHS/United States ; D43 TW007120/TW/FIC NIH HHS/United States ; K24 AI068903/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Humans ; Leptospira/*genetics/*pathogenicity ; Molecular Sequence Data ; Multigene Family ; Prophages/genetics ; Sequence Analysis, DNA ; Virulence Factors/*genetics ; }, abstract = {The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.}, } @article {pmid23131563, year = {2012}, author = {Matsuda, A and Kurono, N and Kawano, C and Shirota, K and Hirabayashi, A and Horino, M and Etchuya, R and Sobue, R and Sasaki, Y and Miyaue, S and Sekoguchi, A and Sugiura, C and Shibata, Y and Ito, M and Ando, T and Maeda, S}, title = {Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids.}, journal = {Biochemical and biophysical research communications}, volume = {428}, number = {4}, pages = {445-450}, doi = {10.1016/j.bbrc.2012.10.098}, pmid = {23131563}, issn = {1090-2104}, mesh = {Conjugation, Genetic/*genetics ; Escherichia coli/*genetics ; Gene Knockout Techniques ; Gene Transfer, Horizontal/*genetics ; Mutation ; Plasmids/*genetics ; Sequence Analysis, DNA ; Transformation, Genetic ; }, abstract = {Acquiring new genetic traits by lateral gene transfer is a bacterial strategy for environment adaptation. We previously showed that Escherichia coli could laterally transmit non-conjugative plasmids in co-cultures containing strains with and without the plasmid. In this study, using the Keio collection, a comprehensive library of E. coli knock-out mutants for non-essential genes, we screened for genes responsible for repressing cell-to-cell plasmid transfer in recipient cells. By stepwise screening, we identified 55 'transfer-up' mutants that exhibited approximately 2- to 30-fold increased activities. We confirmed plasmid acquisition by these 'up' mutants and revealed that there were no significant changes in antibiotic resistance in the original Keio strains. The presumed functions of these gene products covered a wide range of activities, including metabolism and synthesis, transport, transcription or translation and others. Two competence-gene homologues (ybaV and yhiR) were identified from among these genes. The presumed localizations of these 55 gene products were estimated to be 34 cytoplasmic proteins, 20 in or around the cell surface and 1 unknown location. Our results suggest that these 55 genes may be involved in repressing plasmid uptake during cell-to-cell plasmid transfer.}, } @article {pmid23116195, year = {2012}, author = {Meehan, CJ and Beiko, RG}, title = {Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {248}, doi = {10.1186/1471-2180-12-248}, pmid = {23116195}, issn = {1471-2180}, support = {CMF-108026//Canadian Institutes of Health Research/Canada ; }, mesh = {ATP-Binding Cassette Transporters/*genetics ; Bacterial Proteins/*genetics ; Cluster Analysis ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Humans ; Metagenome ; Nickel/metabolism ; Phylogeny ; Sequence Homology ; }, abstract = {BACKGROUND: Several links have been established between the human gut microbiome and conditions such as obesity and inflammatory bowel syndrome. This highlights the importance of understanding what properties of the gut microbiome can affect the health of the human host. Studies have been undertaken to determine the species composition of this microbiome and infer functional profiles associated with such host properties. However, lateral gene transfer (LGT) between community members may result in misleading taxonomic attributions for the recipient organisms, thus making species-function links difficult to establish.

RESULTS: We identified a peptides/nickel transport complex whose components differed in abundance based upon levels of host obesity, and assigned the encoded proteins to members of the microbial community. Each protein was assigned to several distinct taxonomic groups, with moderate levels of agreement observed among different proteins in the complex. Phylogenetic trees of these proteins produced clusters that differed greatly from taxonomic attributions and indicated that habitat-directed LGT of this complex is likely to have occurred, though not always between the same partners.

CONCLUSIONS: These findings demonstrate that certain membrane transport systems may be an important factor within an obese-associated gut microbiome and that such complexes may be acquired several times by different strains of the same species. Additionally, an example of individual proteins from different organisms being transferred into one operon was observed, potentially demonstrating a functional complex despite the donors of the subunits being taxonomically disparate. Our results also highlight the potential impact of habitat-directed LGT on the resident microbiota.}, } @article {pmid23091700, year = {2012}, author = {Skippington, E and Ragan, MA}, title = {Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.}, journal = {Open biology}, volume = {2}, number = {9}, pages = {120112}, doi = {10.1098/rsob.120112}, pmid = {23091700}, issn = {2046-2441}, mesh = {Computer Simulation ; Ecosystem ; Escherichia coli/*classification/*genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; Shigella/*classification/*genetics ; }, abstract = {Genetic material can be transmitted not only vertically from parent to offspring, but also laterally (horizontally) from one bacterial lineage to another. Lateral genetic transfer is non-uniform; biases in its nature or frequency construct communities of genetic exchange. These biases have been proposed to arise from phylogenetic relatedness, shared ecology and/or common lifestyle. Here, we test these hypotheses using a graph-based abstraction of inferred genetic-exchange relationships among 27 Escherichia coli and Shigella genomes. We show that although barriers to inter-phylogenetic group lateral transfer are low, E. coli and Shigella are more likely to have exchanged genetic material with close relatives. We find little evidence of bias arising from shared environment or lifestyle. More than one-third of donor-recipient pairs in our analysis show some level of fragmentary gene transfer. Thus, within the E. coli-Shigella clade, intact genes and gene fragments have been disseminated non-uniformly and at appreciable frequency, constructing communities that transgress environmental and lifestyle boundaries.}, } @article {pmid23077201, year = {2012}, author = {Christin, PA and Wallace, MJ and Clayton, H and Edwards, EJ and Furbank, RT and Hattersley, PW and Sage, RF and Macfarlane, TD and Ludwig, M}, title = {Multiple photosynthetic transitions, polyploidy, and lateral gene transfer in the grass subtribe Neurachninae.}, journal = {Journal of experimental botany}, volume = {63}, number = {17}, pages = {6297-6308}, doi = {10.1093/jxb/ers282}, pmid = {23077201}, issn = {1460-2431}, mesh = {*Biological Evolution ; Carbon Isotopes/analysis ; Cell Nucleus/genetics ; *Gene Transfer, Horizontal ; Genetic Markers ; Genome Size ; Photosynthesis/*genetics ; Phylogeny ; Plant Leaves/classification/genetics/physiology ; Plastids/genetics ; Poaceae/classification/*genetics/physiology ; *Polyploidy ; }, abstract = {The Neurachninae is the only grass lineage known to contain C(3), C(4), and C(3)-C(4) intermediate species, and as such has been suggested as a model system for studies of photosynthetic pathway evolution in the Poaceae; however, a lack of a robust phylogenetic framework has hindered this possibility. In this study, plastid and nuclear markers were used to reconstruct evolutionary relationships among Neurachninae species. In addition, photosynthetic types were determined with carbon isotope ratios, and genome sizes with flow cytometry. A high frequency of autopolyploidy was found in the Neurachninae, including in Neurachne munroi F.Muell. and Paraneurachne muelleri S.T.Blake, which independently evolved C(4) photosynthesis. Phylogenetic analyses also showed that following their separate C(4) origins, these two taxa exchanged a gene encoding the C(4) form of phosphoenolpyruvate carboxylase. The C(3)-C(4) intermediate Neurachne minor S.T.Blake is phylogenetically distinct from the two C(4) lineages, indicating that intermediacy in this species evolved separately from transitional stages preceding C(4) origins. The Neurachninae shows a substantial capacity to evolve new photosynthetic pathways repeatedly. Enablers of these transitions might include anatomical pre-conditions in the C(3) ancestor, and frequent autopolyploidization. Transfer of key C(4) genetic elements between independently evolved C(4) taxa may have also facilitated a rapid adaptation of photosynthesis in these grasses that had to survive in the harsh climate appearing during the late Pliocene in Australia.}, } @article {pmid23070174, year = {2013}, author = {Del Castillo, CS and Hikima, J and Jang, HB and Nho, SW and Jung, TS and Wongtavatchai, J and Kondo, H and Hirono, I and Takeyama, H and Aoki, T}, title = {Comparative sequence analysis of a multidrug-resistant plasmid from Aeromonas hydrophila.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {1}, pages = {120-129}, doi = {10.1128/AAC.01239-12}, pmid = {23070174}, issn = {1098-6596}, mesh = {Acinetobacter baumannii/genetics ; Aeromonas hydrophila/drug effects/*genetics/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Fisheries ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Humans ; Integrons ; Phylogeny ; Phylogeography ; Plasmids/*chemistry/isolation & purification ; Sequence Analysis, DNA ; Tilapia/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Aeromonas hydrophila is a pathogenic bacterium that has been implicated in fish, animal, and human disease. Recently, a multidrug resistance (MDR) plasmid, pR148, was isolated from A. hydrophila obtained from a tilapia (Oreochromis niloticus) farm in Thailand. pR148 is a 165,906-bp circular plasmid containing 147 coding regions showing highest similarity to pNDM-1_Dok1, an MDR plasmid isolated from a human pathogen. pR148 was also very similar to other IncA/C plasmids isolated from humans, animals, food, and fish. pR148 contains a mercuric resistance operon and encodes the complete set of genes for the type 4 secretion system. pR148 encodes a Tn21 type transposon. This transposon contains the drug resistance genes qacH, bla(OXA-10), aadA1, and sul1 in a class 1 integron; tetA and tetR in transposon Tn1721; and catA2 and a duplicate sul1 in a locus showing 100% similarity to IncU plasmids isolated from fish. The bla(OXA-10) and aadA1 genes showed 100% similarity to those from the Acinetobacter baumannii AYE genome. The similarity of pR148 to a human pathogen-derived plasmid indicates that the plasmids were either transferred between different genera or that they are derived from a common origin. Previous studies have shown that IncA/C plasmids retain a conserved backbone, while the accessory region points to lateral gene transfer. These observations point out the dangers of indiscriminate use of antibiotics in humans and in animals and the necessity of understanding how drug resistance determinants are disseminated and transferred.}, } @article {pmid23049536, year = {2012}, author = {Lurie-Weinberger, MN and Peeri, M and Tuller, T and Gophna, U}, title = {Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae.}, journal = {Frontiers in genetics}, volume = {3}, number = {}, pages = {182}, doi = {10.3389/fgene.2012.00182}, pmid = {23049536}, issn = {1664-8021}, abstract = {Methanosphaera stadtmanae is a commensal methanogenic archaeon found in the human gut. As most of its niche-neighbors are bacteria, it is expected that lateral gene transfer (LGT) from bacteria might have contributed to the evolutionary history of this organism. We performed a phylogenomic survey of putative LGT events in M. stadtmanae, using a phylogenetic pipeline. Our analysis indicates that a substantial fraction of the proteins of M. stadtmanae are inferred to have been involved in inter-domain LGT. Laterally acquired genes have had a large contribution to surface functions, by providing novel glycosyltransferase functions. In addition, several ABC transporters seem to be of bacterial origin, including the molybdate transporter. Thus, bacterial genes contributed to the adaptation of M. stadtmanae to a host-dependent lifestyle by allowing a larger variation in surface structures and increasing transport efficiency in the gut niche which is diverse and competitive.}, } @article {pmid23043116, year = {2012}, author = {Szöllosi, GJ and Boussau, B and Abby, SS and Tannier, E and Daubin, V}, title = {Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {43}, pages = {17513-17518}, doi = {10.1073/pnas.1202997109}, pmid = {23043116}, issn = {1091-6490}, mesh = {*Gene Transfer, Horizontal ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; *Species Specificity ; }, abstract = {The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.}, } @article {pmid23030400, year = {2012}, author = {Azmuda, N and Rahman, MZ and Sultana, M and Jenssen, EL and Khan, SI and Birkeland, NK}, title = {Evidence of interspecies O antigen gene cluster transfer between Shigella boydii 15 and Escherichia fergusonii.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {120}, number = {12}, pages = {959-966}, doi = {10.1111/j.1600-0463.2012.02926.x}, pmid = {23030400}, issn = {1600-0463}, mesh = {Antigens, Bacterial/genetics/immunology ; Antigens, Surface/genetics/immunology ; DNA, Bacterial/genetics ; Escherichia/drug effects/*genetics/immunology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Microbial Sensitivity Tests ; O Antigens/chemistry/*genetics/immunology ; Phylogeny ; Shigella boydii/*genetics/immunology ; }, abstract = {An environmental bacterial isolate, Iso10, previously found to show serological cross-reactivity with type-specific Shigella boydii 15 antisera was subjected to further molecular and serological analyses that revealed interspecies transfer of the O antigen gene cluster. Western blot analysis of Iso10 cell surface extracts and purified lipopolysaccharides demonstrated strong cross-reactivity with S. boydii 15-specific monovalent antisera and a lipopolysaccharide gel banding profile similar to that of S. boydii 15. Biochemical and phylogenetic analyses identified the Iso10 isolate as Escherichia fergusonii. O antigen gene cluster analyses of Iso10, carried out by restriction fragment length analysis of the amplified ~10-kb O antigen-encoding gene cluster, revealed a profile highly similar to that of S. boydii 15, confirming the presence of the S. boydii 15 somatic antigen in Iso10. To the best of our knowledge, this is the first report of interspecies transfer of O antigen-encoding genes between S. boydii and E. fergusonii, and it has implications for our understanding of the role of lateral gene transfer in the emergence of novel Shigella serotypes.}, } @article {pmid23022563, year = {2012}, author = {Naumoff, DG and Dedysh, SN}, title = {Lateral gene transfer between the Bacteroidetes and Acidobacteria: the case of α-L-rhamnosidases.}, journal = {FEBS letters}, volume = {586}, number = {21}, pages = {3843-3851}, doi = {10.1016/j.febslet.2012.09.005}, pmid = {23022563}, issn = {1873-3468}, mesh = {Acidobacteria/classification/enzymology/*genetics ; Amino Acid Sequence ; Bacterial Proteins/classification/*genetics/metabolism ; Bacteroidetes/classification/enzymology/*genetics ; *Gene Transfer, Horizontal ; Glycoside Hydrolases/classification/*genetics/metabolism ; Hydrolysis ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Rhamnose/metabolism ; Sequence Alignment ; }, abstract = {α-L-Rhamnosidases catalyze the hydrolysis of the terminal α-L-rhamnose residues in various carbohydrates. The catalytic domains in most of these enzymes belong to the families GH78 and GH106 of glycoside hydrolases. In this study, we show that almost all genes encoding the GH78- and GH106-containing proteins from members of the poorly characterized bacterial phylum Acidobacteria originated from precursors belonging to the phylum Bacteroidetes. Members of the Acidobacteria and Bacteroidetes display similar functional capabilities and specialize on degradation of plant-derived organic matter. Several proposed lateral gene transfers between the Acidobacteria and Bacteroidetes occurred presumably during specialization of these bacteria for their environments.}, } @article {pmid23009612, year = {2012}, author = {Graham, LA and Li, J and Davidson, WS and Davies, PL}, title = {Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {190}, doi = {10.1186/1471-2148-12-190}, pmid = {23009612}, issn = {1471-2148}, support = {106612//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Antifreeze Proteins, Type II/*genetics ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Evolution, Molecular ; Expressed Sequence Tags ; Fish Proteins/*genetics ; *Gene Transfer, Horizontal ; Lectins, C-Type/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Osmeriformes/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Type II antifreeze protein (AFP) from the rainbow smelt, Osmerus mordax, is a calcium-dependent C-type lectin homolog, similar to the AFPs from herring and sea raven. While C-type lectins are ubiquitous, type II AFPs are only found in a few species in three widely separated branches of teleost fishes. Furthermore, several other non-homologous AFPs are found in intervening species. We have previously postulated that this sporadic distribution has resulted from lateral gene transfer. The alternative hypothesis, that the AFP evolved from a lectin present in a shared ancestor and that this gene was lost in most species, is not favored because both the exon and intron sequences are highly conserved.

RESULTS: Here we have sequenced and annotated a 160 kb smelt BAC clone containing a centrally-located AFP gene along with 14 other genes. Quantitative PCR indicates that there is but a single copy of this gene within the smelt genome, which is atypical for fish AFP genes. The corresponding syntenic region has been identified and searched in a number of other species and found to be devoid of lectin or AFP sequences. Unlike the introns of the AFP gene, the intronic sequences of the flanking genes are not conserved between species. As well, the rate and pattern of mutation in the AFP gene are radically different from those seen in other smelt and herring genes.

CONCLUSIONS: These results provide stand-alone support for an example of lateral gene transfer between vertebrate species. They should further inform the debate about genetically modified organisms by showing that gene transfer between 'higher' eukaryotes can occur naturally. Analysis of the syntenic regions from several fishes strongly suggests that the smelt acquired the AFP gene from the herring.}, } @article {pmid22997182, year = {2013}, author = {Tucker, RP}, title = {Horizontal gene transfer in choanoflagellates.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {320}, number = {1}, pages = {1-9}, doi = {10.1002/jez.b.22480}, pmid = {22997182}, issn = {1552-5015}, mesh = {*Biological Evolution ; Choanoflagellata/*genetics ; Gene Transfer, Horizontal/*genetics ; Genes, Protozoan/*genetics ; Nerve Tissue Proteins/genetics ; Phosphofructokinases/genetics ; *Phylogeny ; Species Specificity ; Tenascin/genetics ; }, abstract = {Horizontal gene transfer (HGT), also known as lateral gene transfer, results in the rapid acquisition of genes from another organism. HGT has long been known to be a driving force in speciation in prokaryotes, and there is evidence for HGT from symbiotic and infectious bacteria to metazoans, as well as from protists to bacteria. Recently, it has become clear that as many as a 1,000 genes in the genome of the choanoflagellate Monosiga brevicollis may have been acquired by HGT. Interestingly, these genes reportedly come from algae, bacteria, and other choanoflagellate prey. Some of these genes appear to have allowed an ancestral choanoflagellate to exploit nutrient-poor environments and were not passed on to metazoan descendents. However, some of these genes are also found in animal genomes, suggesting that HGT into a common ancestor of choanozoans and animals may have contributed to metazoan evolution.}, } @article {pmid22973561, year = {2012}, author = {Segerman, B}, title = {The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {116}, doi = {10.3389/fcimb.2012.00116}, pmid = {22973561}, issn = {2235-2988}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; }, abstract = {Strains within a bacterial species typically have a set of conserved core genes and a variable set of accessory genes. The accessory genes often appear to move laterally between strains, thereby forming new trait combinations. Sometimes, genetic material also moves laterally between species, thereby resulting in diffuse borders between them. The growing number of genome sequences offers new possibilities to study these processes. Ten species for which abundant genomic data exists were here selected for analysis of the species border integrity. The average core genome similarities and relative core genome sizes (RCGSs) were determined for strain pairs within the species and for strain pairs crossing the species border. The variability within the species as well as the border integrity varies for different bacterial species. Some have very distinct borders while others are more or less indefinable. From the growing amount of genomic data, it becomes even clearer that the concept of bacterial species is, in many cases, far from absolute.}, } @article {pmid22967797, year = {2012}, author = {Konrad, A and Piškur, J and Liberles, DA}, title = {The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1.}, journal = {Gene}, volume = {510}, number = {2}, pages = {154-161}, doi = {10.1016/j.gene.2012.08.046}, pmid = {22967797}, issn = {1879-0038}, mesh = {Bacteria/*enzymology/*genetics ; Catalytic Domain ; Escherichia coli/enzymology/genetics ; *Evolution, Molecular ; Pentosyltransferases/chemistry/classification/*genetics/*metabolism ; Phylogeny ; Purine-Nucleoside Phosphorylase/chemistry/genetics/metabolism ; Streptococcus pyogenes/enzymology/genetics ; Uridine Phosphorylase/chemistry/classification/genetics/metabolism ; }, abstract = {Nucleoside phosphorylases are essential for the salvage and catabolism of nucleotides in bacteria and other organisms, and members of this enzyme superfamily have been of interest for the development of antimicrobial and cancer therapies. The nucleotide phosphorylase superfamily 1 encompasses a number of different enzymes which share a general superfold and catalytic mechanism, while they differ in the nature of the nucleophiles used and in the nature of characteristic active site residues. Recently, one subfamily, the uridine phosphorylases, has been subdivided into two types which differ with respect to the mechanism of transition state stabilization, as dictated by differences in critical amino acid residues. Little is known about the phylogenetic distribution and relationship of the two different types, as well as the relationship to other NP-1 superfamily members. Here comparative genomic analysis illustrates that UP-1s and UP-2s fall into monophyletic groups and are biased with respect to species representation. UP-1 evolved in Gram negative bacteria, while Gram positive species tend to predominantly contain UP-2. PNP (a sister clade to all UPs) contains both Gram positive and Gram negative species. The findings imply that the nucleoside phosphorylase superfamily 1 evolved through a series of three important duplications, leading to the separate, monophyletic enzyme families, coupled to individual lateral transfer events. Extensive horizontal transfer explains the occurrence of unexpected uridine phosphorylases in some genomes. This study provides a basis for understanding the evolution of uridine and purine nucleoside phosphorylases with respect to DNA/RNA metabolism and with potential utility in the design of antimicrobial and anti-tumor drugs.}, } @article {pmid22920867, year = {2012}, author = {Daubin, V and Abby, S}, title = {[Healing the tree of life with lateral gene transfers].}, journal = {Medecine sciences : M/S}, volume = {28}, number = {8-9}, pages = {695-698}, doi = {10.1051/medsci/2012288007}, pmid = {22920867}, issn = {0767-0974}, mesh = {Bacteria/genetics ; *Evolution, Molecular ; Extinction, Biological ; *Gene Transfer, Horizontal ; Genetic Speciation ; Microbial Viability/genetics ; *Phylogeny ; Selection, Genetic ; }, } @article {pmid22919697, year = {2012}, author = {Bertelli, C and Greub, G}, title = {Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {110}, doi = {10.3389/fcimb.2012.00110}, pmid = {22919697}, issn = {2235-2988}, mesh = {Amoeba/*microbiology ; Bacteria/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Selection, Genetic ; }, abstract = {Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).}, } @article {pmid22919687, year = {2012}, author = {Bhandari, V and Naushad, HS and Gupta, RS}, title = {Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {98}, doi = {10.3389/fcimb.2012.00098}, pmid = {22919687}, issn = {2235-2988}, mesh = {Archaea/*genetics ; Archaeal Proteins/*genetics ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Phylogeny ; }, abstract = {The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.}, } @article {pmid22919680, year = {2012}, author = {Aravind, L and Anantharaman, V and Zhang, D and de Souza, RF and Iyer, LM}, title = {Gene flow and biological conflict systems in the origin and evolution of eukaryotes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {89}, doi = {10.3389/fcimb.2012.00089}, pmid = {22919680}, issn = {2235-2988}, mesh = {Adaptation, Biological ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; *Symbiosis ; }, abstract = {The endosymbiotic origin of eukaryotes brought together two disparate genomes in the cell. Additionally, eukaryotic natural history has included other endosymbiotic events, phagotrophic consumption of organisms, and intimate interactions with viruses and endoparasites. These phenomena facilitated large-scale lateral gene transfer and biological conflicts. We synthesize information from nearly two decades of genomics to illustrate how the interplay between lateral gene transfer and biological conflicts has impacted the emergence of new adaptations in eukaryotes. Using apicomplexans as example, we illustrate how lateral transfer from animals has contributed to unique parasite-host interfaces comprised of adhesion- and O-linked glycosylation-related domains. Adaptations, emerging due to intense selection for diversity in the molecular participants in organismal and genomic conflicts, being dispersed by lateral transfer, were subsequently exapted for eukaryote-specific innovations. We illustrate this using examples relating to eukaryotic chromatin, RNAi and RNA-processing systems, signaling pathways, apoptosis and immunity. We highlight the major contributions from catalytic domains of bacterial toxin systems to the origin of signaling enzymes (e.g., ADP-ribosylation and small molecule messenger synthesis), mutagenic enzymes for immune receptor diversification and RNA-processing. Similarly, we discuss contributions of bacterial antibiotic/siderophore synthesis systems and intra-genomic and intra-cellular selfish elements (e.g., restriction-modification, mobile elements and lysogenic phages) in the emergence of chromatin remodeling/modifying enzymes and RNA-based regulation. We develop the concept that biological conflict systems served as evolutionary "nurseries" for innovations in the protein world, which were delivered to eukaryotes via lateral gene flow to spur key evolutionary innovations all the way from nucleogenesis to lineage-specific adaptations.}, } @article {pmid22919651, year = {2012}, author = {Georgiades, K and Raoult, D}, title = {How microbiology helps define the rhizome of life.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {60}, doi = {10.3389/fcimb.2012.00060}, pmid = {22919651}, issn = {2235-2988}, mesh = {*Evolution, Molecular ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; *Selection, Genetic ; }, abstract = {In contrast to the tree of life (TOF) theory, species are mosaics of gene sequences with different origins. Observations of the extensive lateral sequence transfers in all organisms have demonstrated that the genomes of all life forms are collections of genes with different evolutionary histories that cannot be represented by a single TOF. Moreover, genes themselves commonly have several origins due to recombination. The human genome is not free from recombination events, so it is a mosaic like other organisms' genomes. Recent studies have demonstrated evidence for the integration of parasitic DNA into the human genome. Lateral transfer events have been accepted as major contributors of genome evolution in free-living bacteria. Furthermore, the accumulation of genomic sequence data provides evidence for extended genetic exchanges in intracellular bacteria and suggests that such events constitute an agent that promotes and maintains all bacterial species. Archaea and viruses also form chimeras containing primarily bacterial but also eukaryotic sequences. In addition to lateral transfers, orphan genes are indicative of the fact that gene creation is a permanent and unsettled phenomenon. Currently, a rhizome may more adequately represent the multiplicity and de novo creation of a genome. We wanted to confirm that the term "rhizome" in evolutionary biology applies to the entire cellular life history. This view of evolution should resemble a clump of roots representing the multiple origins of the repertoires of the genes of each species.}, } @article {pmid22919619, year = {2012}, author = {Danchin, EG and Rosso, MN}, title = {Lateral gene transfers have polished animal genomes: lessons from nematodes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {27}, doi = {10.3389/fcimb.2012.00027}, pmid = {22919619}, issn = {2235-2988}, mesh = {Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Nematoda/*genetics/physiology ; Plants/parasitology ; }, abstract = {It is now accepted that lateral gene transfers (LGT), have significantly contributed to the composition of bacterial genomes. The amplitude of the phenomenon is considered so high in prokaryotes that it challenges the traditional view of a binary hierarchical tree of life to correctly represent the evolutionary history of species. Given the plethora of transfers between prokaryotes, it is currently impossible to infer the last common ancestral gene set for any extant species. For this ensemble of reasons, it has been proposed that the Darwinian binary tree of life may be inappropriate to correctly reflect the actual relations between species, at least in prokaryotes. In contrast, the contribution of LGT to the composition of animal genomes is less documented. In the light of recent analyses that reported series of LGT events in nematodes, we discuss the importance of this phenomenon in the evolutionary history and in the current composition of an animal genome. Far from being neutral, it appears that besides having contributed to nematode genome contents, LGT have favored the emergence of important traits such as plant-parasitism.}, } @article {pmid22798451, year = {2012}, author = {Zhaxybayeva, O and Swithers, KS and Foght, J and Green, AG and Bruce, D and Detter, C and Han, S and Teshima, H and Han, J and Woyke, T and Pitluck, S and Nolan, M and Ivanova, N and Pati, A and Land, ML and Dlutek, M and Doolittle, WF and Noll, KM and Nesbø, CL}, title = {Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date.}, journal = {Genome biology and evolution}, volume = {4}, number = {8}, pages = {700-708}, doi = {10.1093/gbe/evs059}, pmid = {22798451}, issn = {1759-6653}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Gram-Negative Bacteria/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Here we describe the genome of Mesotoga prima MesG1.Ag4.2, the first genome of a mesophilic Thermotogales bacterium. Mesotoga prima was isolated from a polychlorinated biphenyl (PCB)-dechlorinating enrichment culture from Baltimore Harbor sediments. Its 2.97 Mb genome is considerably larger than any previously sequenced Thermotogales genomes, which range between 1.86 and 2.30 Mb. This larger size is due to both higher numbers of protein-coding genes and larger intergenic regions. In particular, the M. prima genome contains more genes for proteins involved in regulatory functions, for instance those involved in regulation of transcription. Together with its closest relative, Kosmotoga olearia, it also encodes different types of proteins involved in environmental and cell-cell interactions as compared with other Thermotogales bacteria. Amino acid composition analysis of M. prima proteins implies that this lineage has inhabited low-temperature environments for a long time. A large fraction of the M. prima genome has been acquired by lateral gene transfer (LGT): a DarkHorse analysis suggests that 766 (32%) of predicted protein-coding genes have been involved in LGT after Mesotoga diverged from the other Thermotogales lineages. A notable example of a lineage-specific LGT event is a reductive dehalogenase gene-a key enzyme in dehalorespiration, indicating M. prima may have a more active role in PCB dechlorination than was previously assumed.}, } @article {pmid22759432, year = {2012}, author = {Zhou, Z and Gu, J and Li, YQ and Wang, Y}, title = {Genome plasticity and systems evolution in Streptomyces.}, journal = {BMC bioinformatics}, volume = {13 Suppl 10}, number = {}, pages = {S8}, doi = {10.1186/1471-2105-13-S10-S8}, pmid = {22759432}, issn = {1471-2105}, support = {SC1 GM081068/GM/NIGMS NIH HHS/United States ; AI067543/AI/NIAID NIH HHS/United States ; G12 MD007591/MD/NIMHD NIH HHS/United States ; G12 RR013646/RR/NCRR NIH HHS/United States ; GM081068/GM/NIGMS NIH HHS/United States ; RR013646/RR/NCRR NIH HHS/United States ; SC1 GM100806/GM/NIGMS NIH HHS/United States ; AI080579/AI/NIAID NIH HHS/United States ; SC1 AI080579/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA/*methods ; Streptomyces/*genetics ; }, abstract = {BACKGROUND: Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.

RESULTS: We present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.

CONCLUSIONS: Our results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.}, } @article {pmid22763649, year = {2012}, author = {Sorokin, DY and Lücker, S and Vejmelkova, D and Kostrikina, NA and Kleerebezem, R and Rijpstra, WI and Damsté, JS and Le Paslier, D and Muyzer, G and Wagner, M and van Loosdrecht, MC and Daims, H}, title = {Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi.}, journal = {The ISME journal}, volume = {6}, number = {12}, pages = {2245-2256}, doi = {10.1038/ismej.2012.70}, pmid = {22763649}, issn = {1751-7370}, support = {P 24101//Austrian Science Fund FWF/Austria ; }, mesh = {Bioreactors/*microbiology ; Chemoautotrophic Growth ; Chloroflexi/*classification/genetics/isolation & purification/physiology ; Genome, Bacterial ; Genomics ; *Nitrification ; Nitrites/*metabolism ; Phylogeny ; Sewage/microbiology ; }, abstract = {Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25-63 °C) and low affinity for nitrite (K(s)=1 mM), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO(2), and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO(2) fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems.}, } @article {pmid22706053, year = {2012}, author = {Wei, H and Håvarstein, LS}, title = {Fratricide is essential for efficient gene transfer between pneumococci in biofilms.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {16}, pages = {5897-5905}, doi = {10.1128/AEM.01343-12}, pmid = {22706053}, issn = {1098-5336}, mesh = {Amidohydrolases/*metabolism ; Bacterial Proteins/*metabolism ; Bacteriolysis ; Biofilms/*growth & development ; *DNA Transformation Competence ; *Gene Transfer, Horizontal ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Streptococcus pneumoniae/genetics/*physiology ; }, abstract = {Streptococcus pneumoniae and a number of commensal streptococcal species are competent for natural genetic transformation. The natural habitat of these bacteria is multispecies biofilms in the human oral cavity and nasopharynx. Studies investigating lateral transfer of virulence and antibiotic resistance determinants among streptococci have shown that interspecies as well as intraspecies gene exchange takes place in these environments. We have previously shown that the action of a competence-specific murein hydrolase termed CbpD strongly increases the rate of gene transfer between pneumococci grown in liquid cultures. CbpD is the key component of a bacteriolytic mechanism termed the fratricide mechanism. It is secreted by competent pneumococci and mediates the release of donor DNA from sensitive streptococci present in the same environment. However, in nature, gene exchange between streptococci takes place in biofilms and not in liquid cultures. In the present study, we therefore investigated whether CbpD affects the rate of gene transfer in laboratory-grown biofilms. Our results show that the fratricide mechanism has a strong positive impact on intrabiofilm gene exchange, indicating that it is important for active acquisition of homologous donor DNA under natural conditions. Furthermore, we found that competent biofilm cells of S. pneumoniae acquire a Nov(r) marker much more efficiently from neighboring cells than from the growth medium. Efficient lysis of target cells requires that CbpD act in conjunction with the murein hydrolase LytC. In contrast, the major autolysin LytA does not seem to be important for fratricide-mediated gene exchange in a biofilm environment.}, } @article {pmid22641711, year = {2012}, author = {Chen, ZZ and Deng, F and Wang, L}, title = {Simultaneous identification of duplications, losses, and lateral gene transfers.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {9}, number = {5}, pages = {1515-1528}, doi = {10.1109/TCBB.2012.79}, pmid = {22641711}, issn = {1557-9964}, mesh = {*Algorithms ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; }, abstract = {We give a fixed-parameter algorithm for the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications, gene losses, and lateral gene transfers (LGTs) for a given species tree S and a given gene tree G. Our algorithm can work for the weighted version of the problem, where the costs of a gene duplication, a gene loss, and an LGT are left to the user's discretion. The algorithm runs in O(m + 3(k/c)n) time, where m is the number of vertices in S, n is the number of vertices in G, c is the smaller between a gene duplication cost and an LGT cost, and k is the minimum cost of an LCA-reconciliation between S and G. The time complexity is indeed better if the cost of a gene loss is greater than 0. In particular, when the cost of a gene loss is at least 0.614c, the running time of the algorithm is O(m + 2.78(k/c)n).}, } @article {pmid22583543, year = {2012}, author = {Kumar, N and Creasy, T and Sun, Y and Flowers, M and Tallon, LJ and Dunning Hotopp, JC}, title = {Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {230}, doi = {10.1186/1756-0500-5-230}, pmid = {22583543}, issn = {1756-0500}, mesh = {Actins/genetics ; Animals ; Drosophila/*genetics/*microbiology ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal/*genetics ; Genes, Insect/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 18S/genetics/*isolation & purification ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Numerous methods exist for enriching bacterial or mammalian mRNA prior to transcriptome experiments. Yet there persists a need for methods to enrich for mRNA in non-mammalian animal systems. For example, insects contain many important and interesting obligate intracellular bacteria, including endosymbionts and vector-borne pathogens. Such obligate intracellular bacteria are difficult to study by traditional methods. Therefore, genomics has greatly increased our understanding of these bacteria. Efficient subtraction methods are needed for removing both bacteria and insect rRNA in these systems to enable transcriptome-based studies.

FINDINGS: A method is described that efficiently removes >95% of insect rRNA from total RNA samples, as determined by microfluidics and transcriptome sequencing. This subtraction yielded a 6.2-fold increase in mRNA abundance. Such a host rRNA-depletion strategy, in combination with bacterial rRNA depletion, is necessary to analyze transcription of obligate intracellular bacteria. Here, transcripts were identified that arise from a lateral gene transfer of an entire Wolbachia bacterial genome into a Drosophila ananassae chromosome. In this case, an rRNA depletion strategy is preferred over polyA-based enrichment since transcripts arising from bacteria-to-animal lateral gene transfer may not be poly-adenylated.

CONCLUSIONS: This enrichment method yields a significant increase in mRNA abundance when poly-A selection is not suitable. It can be used in combination with bacterial rRNA subtraction to enable experiments to simultaneously measure bacteria and insect mRNA in vector and endosymbiont biology experiments.}, } @article {pmid22569756, year = {2011}, author = {César, CE and Álvarez, L and Bricio, C and van Heerden, E and Littauer, D and Berenguer, J}, title = {Unconventional lateral gene transfer in extreme thermophilic bacteria.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {14}, number = {4}, pages = {187-199}, doi = {10.2436/20.1501.01.148}, pmid = {22569756}, issn = {1618-1905}, mesh = {Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Conserved Sequence ; DNA Transformation Competence ; *Gene Transfer, Horizontal ; Thermus/*genetics ; }, abstract = {Conjugation and natural competence are two major mechanisms that explain the acquisition of foreign genes throughout bacterial evolution. In recent decades, several studies in model organisms have revealed in great detail the steps involved in such processes. The findings support the idea that the major basis of these mechanisms is essentially similar in all bacteria. However, recent work has pinpointed the existence of new, evolutionarily different processes underlying lateral gene transfer. In Thermus thermophilus HB27, at least 16 proteins are required for the activity of one of the most efficient natural competence systems known so far. Many of those proteins have no similarities to proteins involved in natural competence in other well-known models. This unusual competence system is conserved, in association with the chromosome, in all other Thermus spp. genomes so far available, it being functional even in strains from isolated environments, such as deep mines. Conjugation is also possible among Thermus spp. Homologues to proteins implicated in conjugation in model bacteria are encoded in the genome of a recently sequenced strain of Thermus thermophilus and shared by other members of the genus. Nevertheless, processive DNA transfer in the absence of a functional natural competence system in strains in which no conjugation homologous genes can be found hints at the existence of an additional and unconventional conjugation mechanism in these bacteria.}, } @article {pmid22507450, year = {2012}, author = {Singh, SP and Häder, DP and Sinha, RP}, title = {Bioinformatics evidence for the transfer of mycosporine-like amino acid core (4-deoxygadusol) synthesizing gene from cyanobacteria to dinoflagellates and an attempt to mutate the same gene (YP_324358) in Anabaena variabilis PCC 7937.}, journal = {Gene}, volume = {500}, number = {2}, pages = {155-163}, doi = {10.1016/j.gene.2012.03.063}, pmid = {22507450}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Amino Acids/biosynthesis/*genetics ; Anabaena variabilis/classification/*genetics ; Cluster Analysis ; Computational Biology ; Conjugation, Genetic ; Cyclohexanols/metabolism ; DNA, Bacterial/genetics ; Dinoflagellida/classification/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/*genetics ; Genetic Vectors ; Homologous Recombination ; Molecular Sequence Data ; Mutation ; Phosphorus-Oxygen Lyases/biosynthesis/genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Synechococcus/classification/*genetics ; }, abstract = {We have identified a homologue of 4-deoxygadusol (core of mycosporine-like amino acids) synthesizing gene (ZP_05036788) from Synechococcus sp. PCC 7335 that was found to have additional functionally unknown N-terminal domain similar to homologues from dinoflagellates based on the ClustalW analysis. Phylogenetic analysis revealed that Synechococcus sp. (ZP_05036788) makes a clade together with dinoflagellates and was closest to the Oxyrrhis marina. This study shows for the first time that N-terminal additional sequences that possess upstream plastid targeting sequence in Heterocapsa triquetra and Karlodinium micrum were already evolved in cyanobacteria, and plastid targeting sequence were evolved later in dinoflagellates after divergence from chloroplast lacking Oxyrrhis marina. Thus, MAAs synthesizing genes were transferred from cyanobacteria to dinoflagellates and possibly Synechococcus sp. PCC 7335 acted as a donor during lateral gene transfer event. In addition, we also tried to mutate 4-deoxygadusol synthesizing gene (YP_324358) of Anabaena variabilis PCC 7937 by homologous recombination, however, all approaches to get complete segregation of the mutants from the wild-type were unsuccessful, showing the essentiality of YP_324358 for A. variabilis PCC 7937.}, } @article {pmid22505998, year = {2012}, author = {Marron, AO and Akam, M and Walker, G}, title = {Nitrile hydratase genes are present in multiple eukaryotic supergroups.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e32867}, doi = {10.1371/journal.pone.0032867}, pmid = {22505998}, issn = {1932-6203}, support = {BB/E527604/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; CCC-1-10//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {DNA Barcoding, Taxonomic/methods ; Eukaryota/*enzymology/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hydro-Lyases/*genetics ; Introns ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {BACKGROUND: Nitrile hydratases are enzymes involved in the conversion of nitrile-containing compounds into ammonia and organic acids. Although they are widespread in prokaryotes, nitrile hydratases have only been reported in two eukaryotes: the choanoflagellate Monosiga brevicollis and the stramenopile Aureococcus anophagefferens. The nitrile hydratase gene in M. brevicollis was believed to have arisen by lateral gene transfer from a prokaryote, and is a fusion of beta and alpha nitrile hydratase subunits. Only the alpha subunit has been reported in A. anophagefferens.

Here we report the detection of nitrile hydratase genes in five eukaryotic supergroups: opisthokonts, amoebozoa, archaeplastids, CCTH and SAR. Beta-alpha subunit fusion genes are found in the choanoflagellates, ichthyosporeans, apusozoans, haptophytes, rhizarians and stramenopiles, and potentially also in the amoebozoans. An individual alpha subunit is found in a dinoflagellate and an individual beta subunit is found in a haptophyte. Phylogenetic analyses recover a clade of eukaryotic-type nitrile hydratases in the Opisthokonta, Amoebozoa, SAR and CCTH; this is supported by analyses of introns and gene architecture. Two nitrile hydratase sequences from an animal and a plant resolve in the prokaryotic nitrile hydratase clade.

CONCLUSIONS/SIGNIFICANCE: The evidence presented here demonstrates that nitrile hydratase genes are present in multiple eukaryotic supergroups, suggesting that a subunit fusion gene was present in the last common ancestor of all eukaryotes. The absence of nitrile hydratase from several sequenced species indicates that subunits were lost in multiple eukaryotic taxa. The presence of nitrile hydratases in many other eukaryotic groups is unresolved due to insufficient data and taxon sampling. The retention and expression of the gene in distantly related eukaryotic species suggests that it plays an important metabolic role. The novel family of eukaryotic nitrile hydratases presented in this paper represents a promising candidate for research into their molecular biology and possible biotechnological applications.}, } @article {pmid22487988, year = {2012}, author = {Willson, SJ}, title = {CSD homomorphisms between phylogenetic networks.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {9}, number = {4}, pages = {1128-1138}, doi = {10.1109/TCBB.2012.52}, pmid = {22487988}, issn = {1557-9964}, mesh = {Computational Biology/*methods ; Gene Transfer, Horizontal ; Hybridization, Genetic ; *Models, Genetic ; *Phylogeny ; }, abstract = {Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network N of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are situations where trees are inadequate. Consequently it is important to determine properties that characterize networks closely related to N and possibly more complicated than trees but lacking the full complexity of N. A connected surjective digraph map (CSD) is a map f from one network N to another network M such that every arc is either collapsed to a single vertex or is taken to an arc, such that f is surjective, and such that the inverse image of a vertex is always connected. CSD maps are shown to behave well under composition. It is proved that if there is a CSD map from N to M, then there is a way to lift an undirected version of M into N, often with added resolution. A CSD map from N to M puts strong constraints on N. In general, it may be useful to study classes of networks such that, for any N, there exists a CSD map from N to some standard member of that class.}, } @article {pmid22459247, year = {2012}, author = {Gillings, MR and Stokes, HW}, title = {Are humans increasing bacterial evolvability?.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {6}, pages = {346-352}, doi = {10.1016/j.tree.2012.02.006}, pmid = {22459247}, issn = {1872-8383}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*genetics/*pathogenicity ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Environmental Pollution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome ; Humans ; Mutation ; Phenotype ; Selection, Genetic ; }, abstract = {Attempts to control bacterial pathogens have led to an increase in antibiotic-resistant cells and the genetic elements that confer resistance phenotypes. These cells and genes are disseminated simultaneously with the original selective agents via human waste streams. This might lead to a second, unintended consequence of antimicrobial therapy; an increase in the evolvability of all bacterial cells. The genetic variation upon which natural selection acts is a consequence of mutation, recombination and lateral gene transfer (LGT). These processes are under selection, balancing genomic integrity against the advantages accrued by genetic innovation. Saturation of the environment with selective agents might cause directional selection for higher rates of mutation, recombination and LGT, producing unpredictable consequences for humans and the biosphere.}, } @article {pmid22452844, year = {2012}, author = {Okubo, T and Tsukui, T and Maita, H and Okamoto, S and Oshima, K and Fujisawa, T and Saito, A and Futamata, H and Hattori, R and Shimomura, Y and Haruta, S and Morimoto, S and Wang, Y and Sakai, Y and Hattori, M and Aizawa, S and Nagashima, KV and Masuda, S and Hattori, T and Yamashita, A and Bao, Z and Hayatsu, M and Kajiya-Kanegae, H and Yoshinaga, I and Sakamoto, K and Toyota, K and Nakao, M and Kohara, M and Anda, M and Niwa, R and Jung-Hwan, P and Sameshima-Saito, R and Tokuda, S and Yamamoto, S and Yamamoto, S and Yokoyama, T and Akutsu, T and Nakamura, Y and Nakahira-Yanaka, Y and Takada Hoshino, Y and Hirakawa, H and Mitsui, H and Terasawa, K and Itakura, M and Sato, S and Ikeda-Ohtsubo, W and Sakakura, N and Kaminuma, E and Minamisawa, K}, title = {Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs.}, journal = {Microbes and environments}, volume = {27}, number = {3}, pages = {306-315}, pmid = {22452844}, issn = {1347-4405}, mesh = {Bacterial Proteins/genetics ; Base Composition ; Bradyrhizobium/*genetics/isolation & purification/physiology ; DNA, Bacterial/*chemistry/*genetics ; *Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Open Reading Frames ; RNA, Untranslated/genetics ; *Sequence Analysis, DNA ; Soil Microbiology ; Symbiosis ; Synteny ; }, abstract = {Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.}, } @article {pmid22443110, year = {2012}, author = {Rodriguez-R, LM and Grajales, A and Arrieta-Ortiz, ML and Salazar, C and Restrepo, S and Bernal, A}, title = {Genomes-based phylogeny of the genus Xanthomonas.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {43}, doi = {10.1186/1471-2180-12-43}, pmid = {22443110}, issn = {1471-2180}, mesh = {Computational Biology ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Multigene Family ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Xanthomonas/*classification/genetics ; }, abstract = {BACKGROUND: The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus.

RESULTS: Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines.

CONCLUSIONS: Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.}, } @article {pmid22416123, year = {2012}, author = {Abby, SS and Tannier, E and Gouy, M and Daubin, V}, title = {Lateral gene transfer as a support for the tree of life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {13}, pages = {4962-4967}, doi = {10.1073/pnas.1116871109}, pmid = {22416123}, issn = {1091-6490}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {Lateral gene transfer (LGT), the acquisition of genes from other species, is a major evolutionary force. However, its success as an adaptive process makes the reconstruction of the history of life an intricate puzzle: If no gene has remained unaffected during the course of life's evolution, how can one rely on molecular markers to reconstruct the relationships among species? Here, we take a completely different look at LGT and its impact for the reconstruction of the history of life. Rather than trying to remove the effect of LGT in phylogenies, and ignoring as a result most of the information of gene histories, we use an explicit phylogenetic model of gene transfer to reconcile gene histories with the tree of species. We studied 16 bacterial and archaeal phyla, representing a dataset of 12,000 gene families distributed in 336 genomes. Our results show that, in most phyla, LGT provides an abundant phylogenetic signal on the pattern of species diversification and that this signal is robust to the choice of gene families under study. We also find that LGT brings an abundant signal on the location of the root of species trees, which has been previously overlooked. Our results quantify the great variety of gene transfer rates among lineages of the tree of life and provide strong support for the "complexity hypothesis," which states that genes whose products participate to macromolecular protein complexes are relatively resistant to transfer.}, } @article {pmid22411854, year = {2012}, author = {Moran, Y and Fredman, D and Szczesny, P and Grynberg, M and Technau, U}, title = {Recurrent horizontal transfer of bacterial toxin genes to eukaryotes.}, journal = {Molecular biology and evolution}, volume = {29}, number = {9}, pages = {2223-2230}, doi = {10.1093/molbev/mss089}, pmid = {22411854}, issn = {1537-1719}, support = {P 24858//Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Toxins/chemistry/*genetics/metabolism ; Cnidaria/genetics/metabolism ; Eukaryota/*genetics/metabolism ; Evolution, Molecular ; Gene Expression ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Pore Forming Cytotoxic Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; }, abstract = {In this work, we report likely recurrent horizontal (lateral) gene transfer events of genes encoding pore-forming toxins of the aerolysin family between species belonging to different kingdoms of life. Clustering based on pairwise similarity and phylogenetic analysis revealed several distinct aerolysin sequence groups, each containing proteins from multiple kingdoms of life. These results strongly support at least six independent transfer events between distantly related phyla in the evolutionary history of one protein family and discount selective retention of ancestral genes as a plausible explanation for this patchy phylogenetic distribution. We discuss the possible roles of these proteins and show evidence for a convergent new function in two extant species. We hypothesize that certain gene families are more likely to be maintained following horizontal gene transfer from commensal or pathogenic organism to its host if they 1) can function alone; and 2) are immediately beneficial for the ecology of the organism, as in the case of pore-forming toxins which can be utilized in multicellular organisms for defense and predation.}, } @article {pmid22392282, year = {2012}, author = {Lasek, R and Dziewit, L and Bartosik, D}, title = {Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon.}, journal = {Extremophiles : life under extreme conditions}, volume = {16}, number = {3}, pages = {363-376}, doi = {10.1007/s00792-012-0435-2}, pmid = {22392282}, issn = {1433-4909}, mesh = {DNA Restriction-Modification Enzymes/*genetics/metabolism ; Gene Transfer, Horizontal/*physiology ; Genes, Bacterial/*physiology ; Plasmids ; Psychrobacter/*genetics/metabolism ; Sequence Analysis, DNA/methods ; Sulfuric Acid Esters/*metabolism ; }, abstract = {The complete nucleotide sequence of plasmid pP62BP1 (34,467 bp), isolated from Arctic Psychrobacter sp. DAB_AL62B, was determined and annotated. The conserved plasmid backbone is composed of several genetic modules, including a replication system (REP) with similarities to the REP region of the iteron-containing plasmid pPS10 of Pseudomonas syringae. The additional genetic load of pP62BP1 includes two highly related type II restriction-modification systems and a set of genes (slfRCHSL) encoding enzymes engaged in the metabolism of organic sulfates, plus a putative transcriptional regulator (SlfR) of the AraC family. The pP62BP1 slf locus has a compact and unique structure. It is predicted that the enzymes SlfC, SlfH, SlfS and SlfL carry out a chain of reactions leading to the transformation of alkyl sulfates into acyl-CoA, with dodecyl sulfate (SDS) as a possible starting substrate. Comparative analysis of the nucleotide sequences of pP62BP1 and other Psychrobacter spp. plasmids revealed their structural diversity. However, the presence of a few highly conserved DNA segments in pP62BP1, plasmid 1 of P. cryohalolentis K5 and pRWF-101 of Psychrobacter sp. PRwf-1 is indicative of recombinational shuffling of genetic information, and is evidence of lateral gene transfer in the Arctic environment.}, } @article {pmid22380427, year = {2012}, author = {Gillings, MR}, title = {How evolution generates complexity without design: language as an instructional metaphor.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {3}, pages = {617-622}, doi = {10.1111/j.1558-5646.2011.01511.x}, pmid = {22380427}, issn = {1558-5646}, mesh = {*Biological Evolution ; Biology/*education ; Gene Transfer, Horizontal ; Genetic Variation ; *Language ; Mutation ; Recombination, Genetic ; Religious Philosophies ; Selection, Genetic ; }, abstract = {One of the major stumbling blocks to understanding evolution is the difficulty in reconciling the emergence of complexity with the apparently undirected forces that drive evolutionary processes. This difficulty was originally framed as the "Watch and Watchmaker" argument and more recently revived by proponents of "intelligent design." Undergraduates in particular often attribute purpose and forethought as the driving force behind biological phenomena, and have difficulty understanding evolutionary processes. To demonstrate that complexity can arise solely through mutations that fix in populations via natural selection or drift, we can use analogies where processes can be observed across short time frames and where the key data are accessible to those without specialized biological knowledge. The evolution of language provides such an example. Processes of natural selection, mutation, genetic drift, acquisition of new functions, punctuated equilibria, and lateral gene transfer can be illustrated using examples of changing spellings, neologism, and acquisition of words from other languages. The examples presented in this article are readily accessible, and demonstrate to students that languages have dynamically increased in complexity, simply driven by the usage patterns of their speakers.}, } @article {pmid22375811, year = {2012}, author = {Mouton, L and Thierry, M and Henri, H and Baudin, R and Gnankine, O and Reynaud, B and Zchori-Fein, E and Becker, N and Fleury, F and Delatte, H}, title = {Evidence of diversity and recombination in Arsenophonus symbionts of the Bemisia tabaci species complex.}, journal = {BMC microbiology}, volume = {12 Suppl 1}, number = {}, pages = {S10}, doi = {10.1186/1471-2180-12-S1-S10}, pmid = {22375811}, issn = {1471-2180}, mesh = {Animals ; Codon, Terminator ; DNA, Bacterial/analysis ; Enterobacteriaceae/*classification/genetics/*isolation & purification/physiology ; Gene Transfer, Horizontal ; Genetic Variation ; Hemiptera/classification/*microbiology/physiology ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Maternally inherited bacterial symbionts infecting arthropods have major implications on host ecology and evolution. Among them, the genus Arsenophonus is particularly characterized by a large host spectrum and a wide range of symbiotic relationships (from mutualism to parasitism), making it a good model to study the evolution of host-symbiont associations. However, few data are available on the diversity and distribution of Arsenophonus within host lineages. Here, we propose a survey on Arsenophonus diversity in whitefly species (Hemiptera), in particular the Bemisia tabaci species complex. This polyphagous insect pest is composed of genetic groups that differ in many ecological aspects. They harbor specific bacterial communities, among them several lineages of Arsenophonus, enabling a study of the evolutionary history of these bacteria at a fine host taxonomic level, in association to host geographical range and ecology.

RESULTS: Among 152 individuals, our analysis identified 19 allelic profiles and 6 phylogenetic groups, demonstrating this bacterium's high diversity. These groups, based on Arsenophonus phylogeny, correlated with B. tabaci genetic groups with two exceptions reflecting horizontal transfers. None of three genes analyzed provided evidence of intragenic recombination, but intergenic recombination events were detected. A mutation inducing a STOP codon on one gene in a strain infecting one B. tabaci genetic group was also found. Phylogenetic analyses of the three concatenated loci revealed the existence of two clades of Arsenophonus. One, composed of strains found in other Hemiptera, could be the ancestral clade in whiteflies. The other, which regroups strains found in Hymenoptera and Diptera, may have been acquired more recently by whiteflies through lateral transfers.

CONCLUSIONS: This analysis of the genus Arsenophonus revealed a diversity within the B. tabaci species complex which resembles that reported on the larger scale of insect taxonomy. We also provide evidence for recombination events within the Arsenophonus genome and horizontal transmission of strains among insect taxa. This work provides further insight into the evolution of the Arsenophonus genome, the infection dynamics of this bacterium and its influence on its insect host's ecology.}, } @article {pmid22369247, year = {2012}, author = {Parker, MA}, title = {Legumes select symbiosis island sequence variants in Bradyrhizobium.}, journal = {Molecular ecology}, volume = {21}, number = {7}, pages = {1769-1778}, doi = {10.1111/j.1365-294X.2012.05497.x}, pmid = {22369247}, issn = {1365-294X}, mesh = {Bradyrhizobium/*genetics ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; *Genomic Islands ; Linkage Disequilibrium ; Phylogeny ; *Selection, Genetic ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Bradyrhizobium strains sampled from 14 legume genera native to eastern North America showed substantial host-related phylogenetic clustering at three loci in the symbiotic island (SI) region (nodC, nifD, nifH), indicating selection of distinct suites of SI lineages by different legumes. Bacteria assorted consistently with particular legumes across two regions separated by 800 km, implying recurrent assembly of the same symbiotic combinations. High genetic polymorphism of all three SI loci relative to four nonsymbiotic loci supported the inference that a form of multiple-niche balancing selection has acted on the SI region, arising from differential symbiont utilization by different legume taxa. Extensive discordance between the tree for SI variants and a phylogenetic tree inferred for four housekeeping loci implied that lateral transfer of the symbiosis island region has been common (at least 26 transfer events among 85 Bradyrhizobium strains analysed). Patterns of linkage disequilibrium also supported the conclusion that recombination has impacted symbiotic and nonsymbiotic regions unequally. The high prevalence of lateral transfer suggests that acquisition of a novel SI variant may often confer a strong selective advantage for recipient cells.}, } @article {pmid22363321, year = {2012}, author = {Townsend, JP and Bøhn, T and Nielsen, KM}, title = {Assessing the probability of detection of horizontal gene transfer events in bacterial populations.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {27}, doi = {10.3389/fmicb.2012.00027}, pmid = {22363321}, issn = {1664-302X}, abstract = {Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings.}, } @article {pmid22348436, year = {2012}, author = {Ignacio-Espinoza, JC and Sullivan, MB}, title = {Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes.}, journal = {Environmental microbiology}, volume = {14}, number = {8}, pages = {2113-2126}, doi = {10.1111/j.1462-2920.2012.02704.x}, pmid = {22348436}, issn = {1462-2920}, mesh = {Bacteriophage T4/*classification/*genetics ; Biological Evolution ; Cyanobacteria/virology ; *Gene Transfer, Horizontal ; *Genome, Viral ; Oceans and Seas ; *Phylogeny ; Prochlorococcus/genetics/virology ; Recombination, Genetic ; }, abstract = {The last two decades have revealed that phages (viruses that infect bacteria) are abundant and play fundamental roles in the Earth System, with the T4-like myoviruses (herein T4-like phages) emerging as a dominant 'signal' in wild populations. Here we examine 27 T4-like phage genomes, with a focus on 17 that infect ocean picocyanobacteria (cyanophages), to evaluate lateral gene transfer (LGT) in this group. First, we establish a reference tree by evaluating concatenated core gene supertrees and whole genome gene content trees. Next, we evaluate what fraction of these 'core genes' shared by all 17 cyanophages appear prone to LGT. Most (47 out of 57 core genes) were vertically transferred as inferred from tree tests and genomic synteny. Of those 10 core genes that failed the tree tests, the bulk (8 of 10) remain syntenic in the genomes with only a few (3 of the 10) having identifiable signatures of mobile elements. Notably, only one of these 10 is shared not only by the 17 cyanophages, but also by all 27 T4-like phages (thymidylate synthase); its evolutionary history suggests cyanophages may be the origin of these genes to Prochlorococcus. Next, we examined intragenic recombination among the core genes and found that it did occur, even among these core genes, but that the rate was significantly higher between closely related phages, perhaps reducing any detectable LGT signal and leading to taxon cohesion. Finally, among 18 auxiliary metabolic genes (AMGs, a.k.a. 'host' genes), we found that half originated from their immediate hosts, in some cases multiple times (e.g. psbA, psbD, pstS), while the remaining have less clear evolutionary origins ranging from cyanobacteria (4 genes) or microbes (5 genes), with particular diversity among viral TalC and Hsp20 sequences. Together, these findings highlight the patterns and limits of vertical evolution, as well as the ecological and evolutionary roles of LGT in shaping T4-like phage genomes.}, } @article {pmid22342748, year = {2012}, author = {Christin, PA and Edwards, EJ and Besnard, G and Boxall, SF and Gregory, R and Kellogg, EA and Hartwell, J and Osborne, CP}, title = {Adaptive evolution of C(4) photosynthesis through recurrent lateral gene transfer.}, journal = {Current biology : CB}, volume = {22}, number = {5}, pages = {445-449}, doi = {10.1016/j.cub.2012.01.054}, pmid = {22342748}, issn = {1879-0445}, support = {BB/F009313/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Plant Leaves/genetics ; Plant Proteins/genetics/metabolism ; Poaceae/classification/cytology/*genetics ; Sequence Alignment ; Sequence Analysis, Protein ; Transcriptome ; }, abstract = {C(4) photosynthesis is a complex trait that confers higher productivity under warm and arid conditions. It has evolved more than 60 times via the co-option of genes present in C(3) ancestors followed by alteration of the patterns and levels of expression and adaptive changes in the coding sequences, but the evolutionary path to C(4) photosynthesis is still poorly understood. The grass lineage Alloteropsis offers unparalleled opportunities for studying C(4) evolution, because it includes a C(3) taxon and five C(4) species that vary significantly in C(4) anatomy and biochemistry. Using phylogenetic analyses of nuclear genes and leaf transcriptomes, we show that fundamental elements of the C(4) pathway in the grass lineage Alloteropsis were acquired via a minimum of four independent lateral gene transfers from C(4) taxa that diverged from this group more than 20 million years ago. The transfer of genes that were already fully adapted for C(4) function has occurred periodically over at least the last 10 million years and has been a recurrent source for the optimization of the C(4) pathway. This report shows that plant-plant lateral nuclear gene transfers can be a potent source of genetic novelty and adaptation in flowering plants.}, } @article {pmid22296756, year = {2012}, author = {Takishita, K and Chikaraishi, Y and Leger, MM and Kim, E and Yabuki, A and Ohkouchi, N and Roger, AJ}, title = {Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen.}, journal = {Biology direct}, volume = {7}, number = {}, pages = {5}, doi = {10.1186/1745-6150-7-5}, pmid = {22296756}, issn = {1745-6150}, support = {MOP-62809//Canadian Institutes of Health Research/Canada ; }, mesh = {*Adaptation, Biological ; Amino Acid Sequence ; Anaerobiosis ; Cell Membrane/chemistry ; Eukaryota/chemistry/classification/*genetics ; Gas Chromatography-Mass Spectrometry ; *Gene Transfer, Horizontal ; Lipids/analysis/chemistry/genetics ; Lyases/genetics ; Oxygen/chemistry ; Phagocytosis ; Phylogeny ; Sequence Alignment ; Species Specificity ; Triterpenes/*chemistry ; }, abstract = {Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. Here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments. Genes encoding the tetrahymanol synthesizing enzyme squalene-tetrahymanol cyclase were found from several phylogenetically diverged eukaryotes that live in oxygen-poor environments and appear to have been laterally transferred among such eukaryotes.}, } @article {pmid22240474, year = {2012}, author = {Langille, MG and Meehan, CJ and Beiko, RG}, title = {Human microbiome: a genetic bazaar for microbes?.}, journal = {Current biology : CB}, volume = {22}, number = {1}, pages = {R20-2}, doi = {10.1016/j.cub.2011.11.023}, pmid = {22240474}, issn = {1879-0445}, mesh = {DNA Transposable Elements ; *Gene Transfer, Horizontal ; Humans ; *Metagenome ; }, abstract = {A recent study suggests that lateral gene transfer has been particularly intense among human-associated microbes. What can this tell us about our relationship with our internal microbial world?}, } @article {pmid22223756, year = {2012}, author = {Skippington, E and Ragan, MA}, title = {Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes.}, journal = {Genome biology and evolution}, volume = {4}, number = {3}, pages = {330-345}, doi = {10.1093/gbe/evs001}, pmid = {22223756}, issn = {1759-6653}, mesh = {Escherichia coli/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Phylogeny ; RNA, Bacterial/*genetics ; Shigella/*genetics ; }, abstract = {Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. Most sRNAs act by base pairing with a target mRNA, modulating its translation and/or stability; many of these RNAs share only limited complementarity to their mRNA target, and require the chaperone Hfq to facilitate base pairing. Little is known about the evolutionary dynamics of bacterial sRNAs. Here, we apply phylogenetic and network analyses to investigate the evolutionary processes and principles that govern sRNA gene distribution in 27 E. coli and Shigella genomes. We identify core (encoded in all 27 genomes) and variable sRNAs; more than two-thirds of the E. coli K-12 MG1655 sRNAs are core, whereas the others show patterns of presence and absence that are principally due to genetic loss, not duplication or lateral genetic transfer. We present evidence that variable sRNAs are less tightly integrated into cellular genetic regulatory networks than are the core sRNAs, and that Hfq facilitates posttranscriptional cross talk between the E. coli-Shigella core and variable genomes. Finally, we present evidence that more than 80% of genes targeted by Hfq-associated core sRNAs have been transferred within the E. coli-Shigella clade, and that most of these genes have been transferred intact. These results suggest that Hfq and sRNAs help integrate laterally acquired genes into established regulatory networks.}, } @article {pmid25114551, year = {2012}, author = {Jin, H and Squier, TC and Long, PE}, title = {Dying for Good: Virus-Bacterium Biofilm Co-evolution Enhances Environmental Fitness.}, journal = {Biochemistry insights}, volume = {5}, number = {}, pages = {1-9}, doi = {10.4137/BCI.S9553}, pmid = {25114551}, issn = {1178-6264}, abstract = {Commonly used in biotechnology applications, filamentous M13 phage are non-lytic viruses that infect E. coli and other bacteria, with the potential to promote horizontal gene transfer in natural populations with synthetic biology implications for engineering community systems. Using the E. coli strain TG1, we have investigated how a selective pressure involving elevated levels of toxic chromate, mimicking that found in some superfund sites, alters population dynamics following infection with either wild-type M13 phage or an M13-phage encoding a chromate reductase (Gh-ChrR) capable of the reductive immobilization of chromate (ie, M13-phageGh-ChrR). In the absence of a selective pressure, M13-phage infection results in a reduction in bacterial growth rate; in comparison, in the presence of chromate there are substantial increases in both cellular killing and biomass formation following infection of E. coli strain TG1with M13-phageGh-ChrR that is dependent on chromate-reductase activity. These results are discussed in terms of community structures that facilitate lateral gene transfer of beneficial traits that enhance phage replication, infectivity, and stability against environmental change.}, } @article {pmid22160766, year = {2012}, author = {Dalquen, DA and Anisimova, M and Gonnet, GH and Dessimoz, C}, title = {ALF--a simulation framework for genome evolution.}, journal = {Molecular biology and evolution}, volume = {29}, number = {4}, pages = {1115-1123}, doi = {10.1093/molbev/msr268}, pmid = {22160766}, issn = {1537-1719}, mesh = {Algorithms ; Base Composition ; Computational Biology/*methods ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; *Genome ; *Models, Genetic ; Mutagenesis ; *Software ; }, abstract = {In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known. Computer programs for simulating sequence evolution in silico have shown to be viable test beds for the verification of newly developed methods and to compare different algorithms. However, current simulation packages tend to focus either on gene-level aspects of genome evolution such as character substitutions and insertions and deletions (indels) or on genome-level aspects such as genome rearrangement and speciation events. Here, we introduce Artificial Life Framework (ALF), which aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under simple or mixture models), indels, GC-content amelioration, gene duplication, gene loss, gene fusion, gene fission, genome rearrangement, lateral gene transfer (LGT), or speciation. The other distinctive feature of ALF is its user-friendly yet powerful web interface. We illustrate the utility of ALF with two possible applications: 1) we reanalyze data from a study of selection after globin gene duplication and test the statistical significance of the original conclusions and 2) we demonstrate that LGT can dramatically decrease the accuracy of two well-established orthology inference methods. ALF is available as a stand-alone application or via a web interface at http://www.cbrg.ethz.ch/alf.}, } @article {pmid22144149, year = {2012}, author = {Lima-Mendez, G}, title = {Reticulate classification of mosaic microbial genomes using NeAT website.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {804}, number = {}, pages = {81-91}, doi = {10.1007/978-1-61779-361-5_5}, pmid = {22144149}, issn = {1940-6029}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Bacteriophages/genetics ; Classification/*methods ; Cluster Analysis ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Models, Genetic ; *Phylogeny ; *Software ; }, abstract = {The tree of life is the classical representation of the evolutionary relationships between existent species. A tree is appropriate to display the divergence of species through mutation, i.e., by vertical descent. However, lateral gene transfer (LGT) is excluded from such representations. When LGT contribution to genome evolution cannot be neglected (e.g., for prokaryotes and mobile genetic elements), the tree becomes misleading. Networks appear as an intuitive way to represent both vertical and horizontal relationships, while overlapping groups within such graphs are more suitable for their classification. Here, we describe a method to represent both vertical and horizontal relationships. We start with a set of genomes whose coded proteins have been grouped into families based on sequence similarity. Next, all pairs of genomes are compared, counting the number of proteins classified into the same family. From this comparison, we derive a weighted graph where genomes with a significant number of similar proteins are linked. Finally, we apply a two-step clustering of this graph to produce a classification where nodes can be assigned to multiple clusters. The procedure can be performed using the Network Analysis Tools (NeAT) website.}, } @article {pmid22144148, year = {2012}, author = {Toussaint, A and Chandler, M}, title = {Prokaryote genome fluidity: toward a system approach of the mobilome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {804}, number = {}, pages = {57-80}, doi = {10.1007/978-1-61779-361-5_4}, pmid = {22144148}, issn = {1940-6029}, mesh = {Bacteriophages/classification/genetics ; Conjugation, Genetic/physiology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Homologous Recombination/physiology ; Interspersed Repetitive Sequences/*genetics ; Molecular Sequence Annotation/methods ; Systems Biology/*methods ; Transformation, Bacterial/physiology ; }, abstract = {The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of the increasing number of available genome sequences. LGT is largely due to the transfer and recombination activities of mobile genetic elements (MGEs). Bacterial and archaeal genomes are mosaics of vertically and horizontally transmitted DNA segments. This generates reticulate relationships between members of the prokaryotic world that are better represented by networks than by "classical" phylogenetic trees. In this review we summarize the nature and activities of MGEs, and the problems that presently limit their analysis on a large scale. We propose routes to improve their annotation in the flow of genomic and metagenomic sequences that currently exist and those that become available. We describe network analysis of evolutionary relationships among some MGE categories and sketch out possible developments of this type of approach to get more insight into the role of the mobilome in bacterial adaptation and evolution.}, } @article {pmid22113690, year = {2011}, author = {Grbić, M and Van Leeuwen, T and Clark, RM and Rombauts, S and Rouzé, P and Grbić, V and Osborne, EJ and Dermauw, W and Ngoc, PC and Ortego, F and Hernández-Crespo, P and Diaz, I and Martinez, M and Navajas, M and Sucena, É and Magalhães, S and Nagy, L and Pace, RM and Djuranović, S and Smagghe, G and Iga, M and Christiaens, O and Veenstra, JA and Ewer, J and Villalobos, RM and Hutter, JL and Hudson, SD and Velez, M and Yi, SV and Zeng, J and Pires-daSilva, A and Roch, F and Cazaux, M and Navarro, M and Zhurov, V and Acevedo, G and Bjelica, A and Fawcett, JA and Bonnet, E and Martens, C and Baele, G and Wissler, L and Sanchez-Rodriguez, A and Tirry, L and Blais, C and Demeestere, K and Henz, SR and Gregory, TR and Mathieu, J and Verdon, L and Farinelli, L and Schmutz, J and Lindquist, E and Feyereisen, R and Van de Peer, Y}, title = {The genome of Tetranychus urticae reveals herbivorous pest adaptations.}, journal = {Nature}, volume = {479}, number = {7374}, pages = {487-492}, doi = {10.1038/nature10640}, pmid = {22113690}, issn = {1476-4687}, support = {T32 GM007464/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics/physiology ; Animals ; Ecdysterone/analogs & derivatives/genetics ; Evolution, Molecular ; Fibroins/genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; Herbivory/*genetics/physiology ; Molecular Sequence Data ; Molting/genetics ; Multigene Family/genetics ; Nanostructures/chemistry ; Plants/parasitology ; Silk/biosynthesis/chemistry ; Tetranychidae/*genetics/*physiology ; Transcriptome/genetics ; }, abstract = {The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.}, } @article {pmid22107596, year = {2011}, author = {Cefalo, AD and Broadbent, JR and Welker, DL}, title = {Intraspecific and interspecific interactions among proteins regulating exopolysaccharide synthesis in Streptococcus thermophilus, Streptococcus iniae, and Lactococcus lactis subsp. cremoris and the assessment of potential lateral gene transfer.}, journal = {Canadian journal of microbiology}, volume = {57}, number = {12}, pages = {1002-1015}, doi = {10.1139/w11-090}, pmid = {22107596}, issn = {1480-3275}, mesh = {Amino Acid Sequence ; Bacterial Capsules/biosynthesis/genetics/metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Enzymes/chemistry/metabolism ; *Gene Transfer, Horizontal ; *Lactococcus lactis/genetics/metabolism ; Molecular Sequence Data ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; *Streptococcus/genetics/metabolism ; *Streptococcus thermophilus/genetics/metabolism ; Two-Hybrid System Techniques ; }, abstract = {Using the yeast two-hybrid system, intraspecific protein interactions were detected in Streptococcus iniae and Lactococcus lactis subsp. cremoris between the transmembrane activation protein (CpsC and EpsA, respectively) and the protein tyrosine kinase (CpsD and EpsB, respectively), between two protein tyrosine kinases, and between the protein tyrosine kinase and the phosphotyrosine phosphatase (CpsB and EpsC, respectively). For each of these intraspecific interactions, interspecific interactions were also detected when one protein was from S. iniae and the other was from Streptococcus thermophilus . Interactions were also observed between two protein tyrosine kinases when one protein was from either of the Streptococcus species and the other from L. lactis subsp. cremoris. The results and sequence comparisons performed in this study support the conclusion that interactions among the components of the tyrosine kinase - phosphatase regulatory system are conserved in the order Lactobacillales and that interspecific genetic exchanges of the genes that encode these proteins have the potential to form functional recombinants. A better understanding of intraspecific and interspecific protein interactions involved in regulating exopolysaccharide biosynthesis may facilitate construction of improved strains for industrial uses as well as identification of factors needed to form functional regulatory complexes in naturally occurring recombinants.}, } @article {pmid22093957, year = {2011}, author = {Labbate, M and Boucher, Y and Chowdhury, PR and Stokes, HW}, title = {Integration of a laterally acquired gene into a cell network important for growth in a strain of Vibrio rotiferianus.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {253}, doi = {10.1186/1471-2180-11-253}, pmid = {22093957}, issn = {1471-2180}, mesh = {Adaptation, Biological/*genetics ; Animals ; Evolution, Molecular ; Gene Expression ; Gene Transfer, Horizontal/*physiology ; Integrons/*genetics ; Porins/*genetics/metabolism ; Vibrio/*genetics/growth & development ; }, abstract = {BACKGROUND: Lateral Gene Transfer (LGT) is a major contributor to bacterial evolution and up to 25% of a bacterium's genome may have been acquired by this process over evolutionary periods of time. Successful LGT requires both the physical transfer of DNA and its successful incorporation into the host cell. One system that contributes to this latter step by site-specific recombination is the integron. Integrons are found in many diverse bacterial Genera and is a genetic system ubiquitous in vibrios that captures mobile DNA at a dedicated site. The presence of integron-associated genes, contained within units of mobile DNA called gene cassettes makes up a substantial component of the vibrio genome (1-3%). Little is known about the role of this system since the vast majority of genes in vibrio arrays are highly novel and functions cannot be ascribed. It is generally regarded that strain-specific mobile genes cannot be readily integrated into the cellular machinery since any perturbation of core metabolism is likely to result in a loss of fitness.

RESULTS: In this study, at least one mobile gene contained within the Vibrio rotiferianus strain DAT722, but lacking close relatives elsewhere, is shown to greatly reduce host fitness when deleted and tested in growth assays. The precise role of the mobile gene product is unknown but impacts on the regulation of outermembrane porins. This demonstrates that strain specific laterally acquired mobile DNA can be integrated rapidly into bacterial networks such that it becomes advantageous for survival and adaptation in changing environments.

CONCLUSIONS: Mobile genes that are highly strain specific are generally believed to act in isolation. This is because perturbation of existing cell machinery by the acquisition of a new gene by LGT is highly likely to lower fitness. In contrast, we show here that at least one mobile gene, apparently unique to a strain, encodes a product that has integrated into central cellular metabolic processes such that it greatly lowers fitness when lost under those conditions likely to be commonly encountered for the free living cell. This has ramifications for our understanding of the role mobile gene encoded products play in the cell from a systems biology perspective.}, } @article {pmid22093578, year = {2011}, author = {Puri, V and Goyal, A and Sankaranarayanan, R and Enright, AJ and Vaidya, T}, title = {Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {334}, doi = {10.1186/1471-2148-11-334}, pmid = {22093578}, issn = {1471-2148}, support = {079643/Z/06/Z//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Composition ; DNA, Protozoan/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Leishmania/*genetics/metabolism/pathogenicity ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Structure, Tertiary ; Protozoan Proteins/*genetics/secretion ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {BACKGROUND: Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear. We sought insights into the possible functions of META1 by studying its evolutionary origins.

RESULTS: Using multiple criteria including sequence similarity, nucleotide composition, phylogenetic analysis and selection pressure on gene sequence, we present evidence that META1 originated in trypanosomatids as a result of a lateral gene transfer of a bacterial heat-inducible protein, HslJ. Furthermore, within the Leishmania genome, META1 sequence is under negative selection pressure against change/substitution. Using homology modeling of Leishmania META1 based on solved NMR structure of HslJ, we show that META1 and HslJ share a similar structural fold. The best hit for other proteins with similar fold is MxiM, a protein involved in the type III secretion system in Shigella. The striking structural similarity shared by META1, HslJ and MxiM suggests a possibility of shared functions. Upon structural superposition with MxiM, we have observed a putative hydrophobic cavity in META1. Mutagenesis of select hydrophobic residues in this cavity affects the secretion of the secreted acid phosphatase (SAP), indicating META1's involvement in secretory processes in Leishmania.

CONCLUSIONS: Overall, this work uses an evolutionary biology approach, 3D-modeling and site-directed mutagenesis to arrive at new insights into functions of Leishmania META1.}, } @article {pmid22074255, year = {2011}, author = {Case, RJ and Boucher, Y}, title = {Molecular musings in microbial ecology and evolution.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {58}, doi = {10.1186/1745-6150-6-58}, pmid = {22074255}, issn = {1745-6150}, mesh = {Archaea/classification/genetics ; Bacteria/classification/*genetics ; Biota ; *Ecology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genes, rRNA ; Genetic Markers ; Genetic Variation ; Microbiological Phenomena ; Phylogeny ; Ribosomes/genetics ; }, abstract = {A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level.The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice.}, } @article {pmid22056789, year = {2012}, author = {Lurie-Weinberger, MN and Peeri, M and Gophna, U}, title = {Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen.}, journal = {Genomics}, volume = {99}, number = {1}, pages = {52-58}, doi = {10.1016/j.ygeno.2011.10.005}, pmid = {22056789}, issn = {1089-8646}, mesh = {ATP-Binding Cassette Transporters/genetics ; Adaptation, Physiological ; Adhesins, Bacterial/genetics ; Biological Evolution ; DNA Transposable Elements ; Gastrointestinal Tract/microbiology ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Glycosyltransferases/genetics ; Humans ; Methanobrevibacter/*genetics ; Phylogeny ; }, abstract = {Methanobrevibacter smithii is the most abundant archaeon in the human colon. As most of its neighbors are bacterial species, it is expected that lateral gene acquisition from bacteria might have contributed to the evolution and adaptation of this archaeon. We performed a tree-based genome-wide survey of putative lateral gene transfer products in M. smithii, using a phylogenetic pipeline. Over 15% of the coding genes of M. smithii are inferred to be bacterial in origin, based on this analysis. Laterally acquired genes have had the largest contribution to surface functions, and encode glycosyl-transferases and adhesin-like proteins. In addition, several important ABC transporters, especially metal transporters are of bacterial origin. Thus, bacterial genes contributed to the host-adaptation by allowing a larger variety of surface structures and increasing the efficiency of metal ion uptake in the competitive gut niche.}, } @article {pmid22037611, year = {2012}, author = {Wu, B and Gong, J and Liu, L and Li, T and Wei, T and Bai, Z}, title = {Evolution of prokaryotic homologues of the eukaryotic SEFIR protein domain.}, journal = {Gene}, volume = {492}, number = {1}, pages = {160-166}, doi = {10.1016/j.gene.2011.10.033}, pmid = {22037611}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Cluster Analysis ; Eukaryota/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; *Prokaryotic Cells ; Protein Structure, Tertiary/genetics ; Receptors, Interleukin-17/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {SEF/IL17 receptor (SEFIR) domains are mainly found in IL17 receptors (IL17Rs) and their adaptor proteins CIKS (connection to IKK and SAPK/JNK), which exert a host defense role in numbers of infectious diseases and promote inflammatory pathology in autoimmunity. Exploring the evolutionary pathway of SEFIR domains will provide further insight into their functions. Here, we have identified 84 SEFIR domain-containing proteins from more than 1400 prokaryotic genomes. As most SEFIR domain-containing bacterial genomes possess a single SEFIR encoding gene and the SEFIR protein domain forms homodimeric complexes like the Toll/IL1 receptor (TIR) domain, the single bacterial SEFIR proteins may receive binding partners from other organisms. Through comparative and phylogenetic sequence analyses, we show that bacterial SEFIR domain is more similar to that of vertebrate CIKS than IL17R, and it possibly emerges via a lateral gene transfer (LGT) from animals. In addition, our secondary and three-dimensional structural predictions of SEFIR domains reveal that human and pathogenic bacterial SEFIR domains share similar structural and electrostatic features. Our findings provide important clues for further experimental researches on determining the functions of SEFIR proteins in pathogenic prokaryotes.}, } @article {pmid22035052, year = {2011}, author = {Skippington, E and Ragan, MA}, title = {Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {532}, doi = {10.1186/1471-2164-12-532}, pmid = {22035052}, issn = {1471-2164}, mesh = {*Biological Evolution ; Escherichia coli/classification/*genetics ; Gene Regulatory Networks ; *Gene Transfer, Horizontal ; Phylogeny ; Shigella/classification/*genetics ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Changes in transcriptional regulation underlie many of the phenotypic differences observed within and between species of bacteria. Lateral genetic transfer (LGT) can significantly impact the transcription factor (TF) genes which drive these transcriptional changes. Although much emphasis has been placed on LGT of intact genes, the units of transfer and recombination do not necessarily correspond to regions delineated by exact gene boundaries. Here we apply phylogenetic and network-based methods to investigate the relationship between units of lateral transfer and recombination within the Escherichia coli - Shigella clade and the topological properties of genes in the E. coli transcriptional regulatory network (TRN).

RESULTS: We carried out a systematic phylogenetic study of genetic transfer among 5282 sets of putatively orthologous genes from 27 strains belonging to the E. coli - Shigella clade. We then used these results to examine the evolutionary histories of TF genes, as well as the transcriptional regulation of lateral genes. We found evidence of LGT in 2655 (50.3%) gene sets: 678 (12.8%) show evidence of recombination breakpoints within the gene boundaries. Thus, within- and whole- gene lateral transfer is widespread among strains of E. coli and Shigella. We found that unlike global regulators, which have mostly evolved vertically, neighbour regulators (genes which regulate adjacent genes on the chromosome) have frequently been subject to transfer within the E. coli - Shigella clade. At least 56 (62%) of the 90 neighbour regulator gene sets examined show evidence of LGT, 19 (34%) of which have internal recombination breakpoints. Neighbour regulators show no evidence of co-transfer with their nearby target genes. Rather, the frequency of recombination breakpoints, and conflicting evolutionary histories among neighbour regulators and their target genes, suggest that the genomic regions encoding these genes have been constructed through successive layering of LGT events within the clade. We find no difference in the relative complexity of regulation (i.e. the number of regulators) of lateral versus vertical genes.

CONCLUSIONS: Neighbour regulators show higher frequencies of transfer than other types of regulatory genes. This implicates the topological properties of regulatory genes in the TRN, and their physical proximity to targets on the chromosome, as contributing to successful LGT. The prevalence of recombination breakpoints within regulatory and target gene sets indicates that within-gene transfer has had a significant cumulative effect on the evolution of regulatory interactions in E. coli and Shigella.}, } @article {pmid21975191, year = {2011}, author = {Akiyama, Y and Goel, S and Conner, JA and Hanna, WW and Yamada-Akiyama, H and Ozias-Akins, P}, title = {Evolution of the apomixis transmitting chromosome in Pennisetum.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {289}, doi = {10.1186/1471-2148-11-289}, pmid = {21975191}, issn = {1471-2148}, mesh = {Apomixis/*genetics ; Base Sequence ; Bayes Theorem ; Chromosomes, Plant/*genetics ; DNA Primers/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Models, Genetic ; Molecular Sequence Data ; Pennisetum/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Apomixis is an intriguing trait in plants that results in maternal clones through seed reproduction. Apomixis is an elusive, but potentially revolutionary, trait for plant breeding and hybrid seed production. Recent studies arguing that apomicts are not evolutionary dead ends have generated further interest in the evolution of asexual flowering plants.

RESULTS: In the present study, we investigate karyotypic variation in a single chromosome responsible for transmitting apomixis, the Apospory-Specific Genomic Region carrier chromosome, in relation to species phylogeny in the genera Pennisetum and Cenchrus. A 1 kb region from the 3' end of the ndhF gene and a 900 bp region from trnL-F were sequenced from 12 apomictic and eight sexual species in the genus Pennisetum and allied genus Cenchrus. An 800 bp region from the Apospory-Specific Genomic Region also was sequenced from the 12 apomicts. Molecular cytological analysis was conducted in sixteen Pennisetum and two Cenchrus species. Our results indicate that the Apospory-Specific Genomic Region is shared by all apomictic species while it is absent from all sexual species or cytotypes. Contrary to our previous observations in Pennisetum squamulatum and Cenchrus ciliaris, retrotransposon sequences of the Opie-2-like family were not closely associated with the Apospory-Specific Genomic Region in all apomictic species, suggesting that they may have been accumulated after the Apospory-Specific Genomic Region originated.

CONCLUSIONS: Given that phylogenetic analysis merged Cenchrus and newly investigated Pennisetum species into a single clade containing a terminal cluster of Cenchrus apomicts, the presumed monophyletic origin of Cenchrus is supported. The Apospory-Specific Genomic Region likely preceded speciation in Cenchrus and its lateral transfer through hybridization and subsequent chromosome repatterning may have contributed to further speciation in the two genera.}, } @article {pmid21949820, year = {2011}, author = {Kent, BN and Funkhouser, LJ and Setia, S and Bordenstein, SR}, title = {Evolutionary genomics of a temperate bacteriophage in an obligate intracellular bacteria (Wolbachia).}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24984}, doi = {10.1371/journal.pone.0024984}, pmid = {21949820}, issn = {1932-6203}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01 GM085163-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; *Evolution, Molecular ; Genes, Bacterial ; Genome, Bacterial ; *Genomics ; Lysogeny ; Phylogeny ; Recombination, Genetic ; Selection, Genetic ; Wolbachia/*genetics ; }, abstract = {Genome evolution of bacteria is usually influenced by ecology, such that bacteria with a free-living stage have large genomes and high rates of horizontal gene transfer, while obligate intracellular bacteria have small genomes with typically low amounts of gene exchange. However, recent studies indicate that obligate intracellular species that host-switch frequently harbor agents of horizontal transfer such as mobile elements. For example, the temperate double-stranded DNA bacteriophage WO in Wolbachia persistently transfers between bacterial coinfections in the same host. Here we show that despite the phage's rampant mobility between coinfections, the prophage's genome displays features of constraint related to its intracellular niche. First, there is always at least one intact prophage WO and usually several degenerate, independently-acquired WO prophages in each Wolbachia genome. Second, while the prophage genomes are modular in composition with genes of similar function grouping together, the modules are generally not interchangeable with other unrelated phages and thus do not evolve by the Modular Theory. Third, there is an unusual core genome that strictly consists of head and baseplate genes; other gene modules are frequently deleted. Fourth, the prophage recombinases are diverse and there is no conserved integration sequence. Finally, the molecular evolutionary forces acting on prophage WO are point mutation, intragenic recombination, deletion, and purifying selection. Taken together, these analyses indicate that while lateral transfer of phage WO is pervasive between Wolbachia with occasional new gene uptake, constraints of the intracellular niche obstruct extensive mixture between WO and the global phage population. Although the Modular Theory has long been considered the paradigm of temperate bacteriophage evolution in free-living bacteria, it appears irrelevant in phages of obligate intracellular bacteria.}, } @article {pmid21899737, year = {2011}, author = {Yoshida, T and Claverie, JM and Ogata, H}, title = {Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.}, journal = {Virology journal}, volume = {8}, number = {}, pages = {427}, doi = {10.1186/1743-422X-8-427}, pmid = {21899737}, issn = {1743-422X}, mesh = {Animals ; Aquatic Organisms/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; Computational Biology ; DNA Breaks, Double-Stranded ; DNA Repair ; DNA Repair Enzymes/chemistry/*genetics ; DNA-Binding Proteins/chemistry/*genetics ; Databases, Genetic ; Deoxyribonucleases/genetics ; Endodeoxyribonucleases/chemistry/*genetics ; Escherichia coli Proteins/genetics ; Exodeoxyribonucleases/chemistry/*genetics ; Exonucleases/genetics ; Gene Transfer, Horizontal ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics ; Mimiviridae/chemistry/*genetics ; Phylogeny ; Plasmids/chemistry/genetics ; Saccharomyces cerevisiae Proteins/chemistry/*genetics ; Viral Fusion Proteins/chemistry/*genetics ; Viral Proteins/chemistry/*genetics ; }, abstract = {BACKGROUND: The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.

RESULTS: Our bioinformatics analysis revealed that R555 protein sequence is constituted from the fusion of an N-terminal Mre11-like domain with a C-terminal Rad50-like domain. A systematic database search revealed twelve additional cases of Mre11/Rad50 (or SbcD/SbcC) fusions in a wide variety of unrelated organisms including unicellular and multicellular eukaryotes, the megaplasmid of a bacterium associated to deep-sea hydrothermal vents (Deferribacter desulfuricans) and the plasmid of Clostridium kluyveri. We also showed that R555 homologs are abundant in the metagenomes from different aquatic environments and that they most likely belong to aquatic viruses. The observed phyletic distribution of these fusion proteins suggests their recurrent creation and lateral gene transfers across organisms.

CONCLUSIONS: The existence of the fused version of protein sequences is consistent with known functional interactions between Mre11 and Rad50, and the gene fusion probably enhanced the opportunity for lateral transfer. The abundance of the Mre11/Rad50 fusion genes in viral metagenomes and their sporadic phyletic distribution in cellular organisms suggest that viruses, plasmids and transposons played a crucial role in the formation of the fusion proteins and their propagation into cellular genomes.}, } @article {pmid21856213, year = {2011}, author = {Popa, O and Dagan, T}, title = {Trends and barriers to lateral gene transfer in prokaryotes.}, journal = {Current opinion in microbiology}, volume = {14}, number = {5}, pages = {615-623}, doi = {10.1016/j.mib.2011.07.027}, pmid = {21856213}, issn = {1879-0364}, mesh = {Evolution, Molecular ; *Gene Transfer, Horizontal ; Prokaryotic Cells/*physiology ; }, abstract = {Gene acquisition by lateral gene transfer (LGT) is an important mechanism for natural variation among prokaryotes. Laboratory experiments show that protein-coding genes can be laterally transferred extremely fast among microbial cells, inherited to most of their descendants, and adapt to a new regulatory regime within a short time. Recent advance in the phylogenetic analysis of microbial genomes using networks approach reveals a substantial impact of LGT during microbial genome evolution. Phylogenomic networks of LGT among prokaryotes reconstructed from completely sequenced genomes uncover barriers to LGT in multiple levels. Here we discuss the kinds of barriers to gene acquisition in nature including physical barriers for gene transfer between cells, genomic barriers for the integration of acquired DNA, and functional barriers for the acquisition of new genes.}, } @article {pmid21824414, year = {2011}, author = {Hinse, D and Vollmer, T and Rückert, C and Blom, J and Kalinowski, J and Knabbe, C and Dreier, J}, title = {Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {400}, doi = {10.1186/1471-2164-12-400}, pmid = {21824414}, issn = {1471-2164}, mesh = {Bacterial Proteins/genetics ; Chromosomes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Endocarditis, Bacterial/*microbiology ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; *Genomics ; Humans ; Plasmids/genetics ; Streptococcus/drug effects/*genetics/pathogenicity ; Tetracycline/pharmacology ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Streptococcus gallolyticus subsp. gallolyticus is an important causative agent of infectious endocarditis, while the pathogenicity of this species is widely unclear. To gain insight into the pathomechanisms and the underlying genetic elements for lateral gene transfer, we sequenced the entire genome of this pathogen.

RESULTS: We sequenced the whole genome of S. gallolyticus subsp. gallolyticus strain ATCC BAA-2069, consisting of a 2,356,444 bp circular DNA molecule with a G+C-content of 37.65% and a novel 20,765 bp plasmid designated as pSGG1. Bioinformatic analysis predicted 2,309 ORFs and the presence of 80 tRNAs and 21 rRNAs in the chromosome. Furthermore, 21 ORFs were detected on the plasmid pSGG1, including tetracycline resistance genes telL and tet(O/W/32/O). Screening of 41 S. gallolyticus subsp. gallolyticus isolates revealed one plasmid (pSGG2) homologous to pSGG1. We further predicted 21 surface proteins containing the cell wall-sorting motif LPxTG, which were shown to play a functional role in the adhesion of bacteria to host cells. In addition, we performed a whole genome comparison to the recently sequenced S. gallolyticus subsp. gallolyticus strain UCN34, revealing significant differences.

CONCLUSIONS: The analysis of the whole genome sequence of S. gallolyticus subsp. gallolyticus promotes understanding of genetic factors concerning the pathogenesis and adhesion to ECM of this pathogen. For the first time we detected the presence of the mobilizable pSGG1 plasmid, which may play a functional role in lateral gene transfer and promote a selective advantage due to a tetracycline resistance.}, } @article {pmid21820313, year = {2011}, author = {Dagan, T}, title = {Phylogenomic networks.}, journal = {Trends in microbiology}, volume = {19}, number = {10}, pages = {483-491}, doi = {10.1016/j.tim.2011.07.001}, pmid = {21820313}, issn = {1878-4380}, mesh = {Bacteria/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; *Genome, Bacterial ; Models, Genetic ; *Phylogeny ; Recombination, Genetic ; }, abstract = {Phylogenomics is aimed at studying functional and evolutionary aspects of genome biology using phylogenetic analysis of whole genomes. Current approaches to genome phylogenies are commonly founded in terms of phylogenetic trees. However, several evolutionary processes are non tree-like in nature, including recombination and lateral gene transfer (LGT). Phylogenomic networks are a special type of phylogenetic network reconstructed from fully sequenced genomes. The network model, comprising genomes connected by pairwise evolutionary relations, enables the reconstruction of both vertical and LGT events. Modeling genome evolution in the form of a network enables the use of an extensive toolbox developed for network research. The structural properties of phylogenomic networks open up fundamentally new insights into genome evolution.}, } @article {pmid21818306, year = {2011}, author = {Tarrío, R and Ayala, FJ and Rodríguez-Trelles, F}, title = {The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22279}, doi = {10.1371/journal.pone.0022279}, pmid = {21818306}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Catalytic Domain ; *Ecosystem ; Eukaryota/*genetics ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Prokaryotic Cells/*metabolism ; Proteins/chemistry/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Lateral gene transfer (LGT) is a major evolutionary mechanism in prokaryotes. Knowledge about LGT--particularly, multicellular--eukaryotes has only recently started to accumulate. A widespread assumption sees the gene as the unit of LGT, largely because little is yet known about how LGT chances are affected by structural/functional features at the subgenic level. Here we trace the evolutionary trajectory of VEin Patterning 1, a novel gene family known to be essential for plant development and defense. At the subgenic level VEP1 encodes a dinucleotide-binding Rossmann-fold domain, in common with members of the short-chain dehydrogenase/reductase (SDR) protein family. We found: i) VEP1 likely originated in an aerobic, mesophilic and chemoorganotrophic α-proteobacterium, and was laterally propagated through nets of ecological interactions, including multiple LGTs between phylogenetically distant green plant/fungi-associated bacteria, and five independent LGTs to eukaryotes. Of these latest five transfers, three are ancient LGTs, implicating an ancestral fungus, the last common ancestor of land plants and an ancestral trebouxiophyte green alga, and two are recent LGTs to modern embryophytes. ii) VEP1's rampant LGT behavior was enabled by the robustness and broad utility of the dinucleotide-binding Rossmann-fold, which provided a platform for the evolution of two unprecedented departures from the canonical SDR catalytic triad. iii) The fate of VEP1 in eukaryotes has been different in different lineages, being ubiquitous and highly conserved in land plants, whereas fungi underwent multiple losses. And iv) VEP1-harboring bacteria include non-phytopathogenic and phytopathogenic symbionts which are non-randomly distributed with respect to the type of harbored VEP1 gene. Our findings suggest that VEP1 may have been instrumental for the evolutionary transition of green plants to land, and point to a LGT-mediated 'Trojan Horse' mechanism for the evolution of bacterial pathogenesis against plants. VEP1 may serve as tool for revealing microbial interactions in plant/fungi-associated environments.}, } @article {pmid21816767, year = {2011}, author = {Fancello, L and Desnues, C and Raoult, D and Rolain, JM}, title = {Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {66}, number = {11}, pages = {2448-2454}, doi = {10.1093/jac/dkr315}, pmid = {21816767}, issn = {1460-2091}, support = {242729//European Research Council/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteriophages/*genetics ; Bacteroidetes/drug effects/genetics ; Cyanobacteria/drug effects/genetics ; Cystic Fibrosis/*microbiology/*virology ; DNA, Ribosomal/isolation & purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia/drug effects/genetics ; Fluoroquinolones/pharmacology ; Gene Transfer, Horizontal ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/isolation & purification ; Sputum/microbiology/virology ; beta-Lactamases/pharmacology ; }, abstract = {OBJECTIVES: The cystic fibrosis (CF) airway is now considered the site of a complex microbiota, where cross-talking between microbes and lateral gene transfer are believed to contribute to the adaptation of bacteria to this specific environment and to the emergence of multidrug-resistant bacteria. The objective of this study was to retrieve and analyse specific sequences associated with antimicrobial resistance from the CF viromes database.

METHODS: Specific sequences from CF metagenomic studies related to the 'antibiotic and toxic compound resistance' dataset were retrieved from the MG-RAST web site, assembled and functionally annotated for identification of the genes. Phylogenetic trees were constructed using a minimum parsimony starting tree topology search strategy.

RESULTS: Overall, we found 1031 short sequences in the CF virome putatively encoding resistance to antimicrobials versus only 3 reads in the non-CF virome dataset (P = 0.001). Among them, we could confidently identify 66 efflux pump genes, 15 fluoroquinolone resistance genes and 9 β-lactamase genes. Evolutionary relatedness determined using phylogenetic information demonstrates the different origins of these genes among the CF microbiota. Interestingly, among annotated sequences within CF viromes, we also found matching 16S rDNA sequences from Escherichia, Cyanobacteria and Bacteroidetes.

CONCLUSIONS: Our results suggest that phages in the CF sputum microbiota represent a reservoir of mobilizable genes associated with antimicrobial resistance that may spread in this specific niche. This phenomenon could explain the fantastic adaptation of CF strains to their niche and may represent a new potential therapeutic target to prevent the emergence of multidrug-resistant bacteria, which are responsible for most of the deaths in CF.}, } @article {pmid21816665, year = {2011}, author = {Bidle, KD and Vardi, A}, title = {A chemical arms race at sea mediates algal host-virus interactions.}, journal = {Current opinion in microbiology}, volume = {14}, number = {4}, pages = {449-457}, doi = {10.1016/j.mib.2011.07.013}, pmid = {21816665}, issn = {1879-0364}, mesh = {Biomarkers ; Caspases/metabolism ; Cell Death ; Enzyme Activation ; Eutrophication ; Gene Transfer, Horizontal ; *Genes, Viral ; Glycosphingolipids/chemistry ; Haptophyta/chemistry/genetics/virology ; *Host-Pathogen Interactions ; Oceans and Seas ; Phycodnaviridae/*chemistry/genetics/pathogenicity/physiology ; Phytoplankton/chemistry/genetics/*virology ; Virus Replication ; Water Microbiology ; }, abstract = {Despite the critical importance of viruses in shaping marine microbial ecosystems and lubricating upper ocean biogeochemical cycles, relatively little is known about the molecular mechanisms mediating phytoplankton host-virus interactions. Recent work in algal host-virus systems has begun to shed novel insight into the elegant strategies of viral infection and subcellular regulation of cell fate, which not only reveal tantalizing aspects of viral replication and host resistance strategies but also provide new diagnostic tools toward elucidating the impact of virus-mediated processes in the ocean. Widespread lateral gene transfer between viruses and their hosts plays a prominent role in host-virus diversification and in the regulation of host-virus infection mechanisms by allowing viruses to manipulate and 'rewire' host metabolic pathways to facilitate infection.}, } @article {pmid21784912, year = {2011}, author = {Zhang, YM and Li, Y and Chen, WF and Wang, ET and Tian, CF and Li, QQ and Zhang, YZ and Sui, XH and Chen, WX}, title = {Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {18}, pages = {6331-6342}, doi = {10.1128/AEM.00542-11}, pmid = {21784912}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics ; *Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Oxidoreductases/genetics ; *Phylogeography ; Rhizobiaceae/*classification/genetics/*isolation & purification ; Sequence Analysis, DNA ; Soybeans/*microbiology ; }, abstract = {As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera Sinorhizobium and Bradyrhizobium, including four novel groups, with S. fredii (68.28%) as the dominant group. The phylogeny of symbiotic genes nodC and nifH defined four lineages among the isolates associated with Sinorhizobium fredii, Bradyrhizobium elkanii, B. japonicum, and B. yuanmingense, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns: Sinorhizobium spp. were superdominant in sampling sites with alkaline-saline soils, while Bradyrhizobium spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.}, } @article {pmid21776603, year = {2011}, author = {Thuillard, M and Moulton, V}, title = {Identifying and reconstructing lateral transfers from distance matrices by combining the minimum contradiction method and neighbor-net.}, journal = {Journal of bioinformatics and computational biology}, volume = {9}, number = {4}, pages = {453-470}, pmid = {21776603}, issn = {1757-6334}, mesh = {Algorithms ; Bacteria/classification/genetics ; Biological Evolution ; Computational Biology/*methods/statistics & numerical data ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Models, Statistical ; Phylogeny ; }, abstract = {Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota.}, } @article {pmid21776602, year = {2011}, author = {Wong, L}, title = {Brief introduction to some new papers on lateral transfer reconstruction, drug candidate screening, disease gene identification, and other results.}, journal = {Journal of bioinformatics and computational biology}, volume = {9}, number = {4}, pages = {v-vii}, pmid = {21776602}, issn = {1757-6334}, mesh = {Biological Evolution ; *Computational Biology ; Disease/genetics ; Drug Evaluation, Preclinical/statistics & numerical data ; Gene Expression Profiling/statistics & numerical data ; Gene Transfer, Horizontal ; Humans ; Systems Biology ; }, } @article {pmid21774799, year = {2011}, author = {Beauregard-Racine, J and Bicep, C and Schliep, K and Lopez, P and Lapointe, FJ and Bapteste, E}, title = {Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {39; discussion 39}, doi = {10.1186/1745-6150-6-39}, pmid = {21774799}, issn = {1745-6150}, mesh = {DNA, Bacterial/genetics ; Escherichia coli/*genetics ; *Evolution, Molecular ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches.

RESULTS: We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements.

CONCLUSIONS: Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.}, } @article {pmid21769188, year = {2011}, author = {Bokhari, H and Anwar, M and Mirza, HB and Gillevet, PM}, title = {Evidences of lateral gene transfer between archaea and pathogenic bacteria.}, journal = {Bioinformation}, volume = {6}, number = {8}, pages = {293-296}, pmid = {21769188}, issn = {0973-2063}, abstract = {Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism's biology and may play a role in pathogenesis.}, } @article {pmid21741306, year = {2012}, author = {Danne, JC and Gornik, SG and Waller, RF}, title = {An assessment of vertical inheritance versus endosymbiont transfer of nucleus-encoded genes for mitochondrial proteins following tertiary endosymbiosis in Karlodinium micrum.}, journal = {Protist}, volume = {163}, number = {1}, pages = {76-90}, doi = {10.1016/j.protis.2011.03.002}, pmid = {21741306}, issn = {1618-0941}, mesh = {Cell Nucleus/*genetics ; Dinoflagellida/classification/*genetics/physiology ; Gene Transfer, Horizontal ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; Protozoan Proteins/*genetics ; Rhodophyta/*genetics/physiology ; *Symbiosis ; }, abstract = {Most photosynthetic dinoflagellates harbour a red alga-derived secondary plastid. In the dinoflagellate Karlodinium micrum, this plastid was replaced by a subsequent endosymbiosis, resulting in a tertiary plastid derived from a haptophyte. Evolution of endosymbionts entails substantial relocation of endosymbiont genes to the host nucleus: a process called endosymbiotic gene transfer (EGT). In K. micrum, numerous plastid genes from the haptophyte nucleus are found in the host nucleus, providing evidence for EGT in this system. In other cases of endosymbiosis, notably ancient primary endosymbiotic events, EGT has been inferred to contribute to remodeling of other cell functions by expression of proteins in compartments other than the endosymbiont from which they derived. K. micrum provides a more recently derived endosymbiotic system to test for evidence of EGT and gain of function in non-plastid compartments. In this study, we test for gain of haptophyte-derived proteins for mitochondrial function in K. micrum. Using molecular phylogenies we have analysed whether nucleus-encoded mitochondrial proteins were inherited by EGT from the haptophyte endosymbiont, or vertically inherited from the dinoflagellate host lineage. From this dataset we found no evidence of haptophyte-derived mitochondrial genes, and the only cases of non-vertical inheritance were genes derived from lateral gene transfer events.}, } @article {pmid21740576, year = {2011}, author = {Rhodes, ME and Spear, JR and Oren, A and House, CH}, title = {Differences in lateral gene transfer in hypersaline versus thermal environments.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {199}, doi = {10.1186/1471-2148-11-199}, pmid = {21740576}, issn = {1471-2148}, mesh = {Archaea/classification/*genetics/metabolism ; *Ecosystem ; *Gene Transfer, Horizontal ; Hot Temperature ; Molecular Sequence Data ; Phylogeny ; Sodium Chloride/metabolism ; Transformation, Genetic ; Water/analysis ; Water Microbiology ; }, abstract = {BACKGROUND: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles.

RESULTS: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles.

CONCLUSIONS: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. Furthermore, most hypersaline environments, as topographical minima, are natural collectors of cellular debris. Thus halophiles would in theory be exposed to a greater diversity and quantity of extracellular DNA than thermophiles.}, } @article {pmid21731639, year = {2011}, author = {Li, Y and Zheng, H and Liu, Y and Jiang, Y and Xin, J and Chen, W and Song, Z}, title = {The complete genome sequence of Mycoplasma bovis strain Hubei-1.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e20999}, doi = {10.1371/journal.pone.0020999}, pmid = {21731639}, issn = {1932-6203}, mesh = {Base Sequence ; Chromosomes, Bacterial/genetics ; DNA Repair/genetics ; DNA Replication/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Mycoplasma bovis/*genetics/metabolism/pathogenicity ; Phylogeny ; Protein Biosynthesis/genetics ; Pseudogenes/genetics ; Replication Origin/genetics ; Sequence Homology, Nucleic Acid ; Tandem Repeat Sequences/genetics ; Transcription, Genetic ; Virulence/genetics ; }, abstract = {Infection by Mycoplasma bovis (M. bovis) can induce diseases, such as pneumonia and otitis media in young calves and mastitis and arthritis in older animals. Here, we report the finished and annotated genome sequence of M. bovis strain Hubei-1, a strain isolated in 2008 that caused calf pneumonia on a Chinese farm. The genome of M. bovis strain Hubei-1 contains a single circular chromosome of 953,114 bp with a 29.37% GC content. We identified 803 open reading frames (ORFs) that occupy 89.5% of the genome. While 34 ORFs were Hubei-1 specific, 662 ORFs had orthologs in the M. bovis type strain PG45 genome. Genome analysis validated lateral gene transfer between M. bovis and the Mycoplasma mycoides subspecies mycoides, while phylogenetic analysis found that the closest M. bovis neighbor is Mycoplasma agalactiae. Glycerol may be the main carbon and energy source of M. bovis, and most of the biosynthesis pathways were incomplete. We report that 47 lipoproteins, 12 extracellular proteins and 18 transmembrane proteins are phase-variable and may help M. bovis escape the immune response. Besides lipoproteins and phase-variable proteins, genomic analysis found two possible pathogenicity islands, which consist of four genes and 11 genes each, and several other virulence factors including hemolysin, lipoate protein ligase, dihydrolipoamide dehydrogenase, extracellular cysteine protease and 5'-nucleotidase.}, } @article {pmid21714939, year = {2011}, author = {Beiko, RG}, title = {Telling the whole story in a 10,000-genome world.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {34}, doi = {10.1186/1745-6150-6-34}, pmid = {21714939}, issn = {1745-6150}, mesh = {Algorithms ; Archaea/classification/genetics ; Bacteria/classification/*genetics ; Bacterial Proteins/chemistry/genetics ; *Biological Evolution ; Computer Graphics ; Databases, Protein ; Gene Transfer, Horizontal ; Genomics/methods ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct purported trees of microbial life. Although such trees are easily interpreted and allow the use of a subset of genomes as "proxies" for the full set, LGT and other phenomena impact the positioning of different groups in genome trees, confounding and potentially invalidating attempts to construct a phylogeny-based taxonomy of microorganisms. Network and graph approaches can reveal complex sets of relationships, but applying these techniques to large data sets is a significant challenge. Notwithstanding the question of what exactly it might represent, generating and interpreting a Tree or Network of All Genomes will only be feasible if current algorithms can be improved upon.

RESULTS: Complex relationships among even the most-similar genomes demonstrate that proxy-based approaches to simplifying large sets of genomes are not alone sufficient to solve the analysis problem. A phylogenomic analysis of 1173 sequenced bacterial and archaeal genomes generated phylogenetic trees for 159,905 distinct homologous gene sets. The relationships inferred from this set can be heavily dependent on the inclusion of other taxa: for example, phyla such as Spirochaetes, Proteobacteria and Firmicutes are recovered as cohesive groups or split depending on the presence of other specific lineages. Furthermore, named groups such as Acidithiobacillus, Coprothermobacter and Brachyspira show a multitude of affiliations that are more consistent with their ecology than with small subunit ribosomal DNA-based taxonomy. Network and graph representations can illustrate the multitude of conflicting affinities, but all methods impose constraints on the input data and create challenges of construction and interpretation.

CONCLUSIONS: These complex relationships highlight the need for an inclusive approach to genomic data, and current methods with minor alterations will likely scale to allow the analysis of data sets with 10,000 or more genomes. The main challenges lie in the visualization and interpretation of genomic relationships, and the redefinition of microbial taxonomy when subsets of genomic data are so evidently in conflict with one another, and with the "canonical" molecular taxonomy.}, } @article {pmid21712432, year = {2011}, author = {Leigh, JW and Lapointe, FJ and Lopez, P and Bapteste, E}, title = {Evaluating phylogenetic congruence in the post-genomic era.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {571-587}, doi = {10.1093/gbe/evr050}, pmid = {21712432}, issn = {1759-6653}, mesh = {Algorithms ; Computational Biology ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; *Genomics ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; Prokaryotic Cells ; Viruses/genetics ; }, abstract = {Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures.}, } @article {pmid21682644, year = {2011}, author = {Wisecaver, JH and Hackett, JD}, title = {Dinoflagellate genome evolution.}, journal = {Annual review of microbiology}, volume = {65}, number = {}, pages = {369-387}, doi = {10.1146/annurev-micro-090110-102841}, pmid = {21682644}, issn = {1545-3251}, mesh = {Bacteria/genetics ; Cell Nucleus/genetics ; Dinoflagellida/classification/*genetics/microbiology ; *Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; *Genome, Protozoan ; Phylogeny ; Plastids/genetics ; }, abstract = {The dinoflagellates are an ecologically important group of microbial eukaryotes that have evolved many novel genomic characteristics. They possess some of the largest nuclear genomes among eukaryotes arranged on permanently condensed liquid-crystalline chromosomes. Recent advances have revealed the presence of genes arranged in tandem arrays, trans-splicing of messenger RNAs, and a reduced role for transcriptional regulation compared to other eukaryotes. In contrast, the mitochondrial and plastid genomes have the smallest gene content among functional eukaryotic organelles. Dinoflagellate biology and genome evolution have been dramatically influenced by lateral transfer of individual genes and large-scale transfer of genes through endosymbiosis. Next-generation sequencing technologies have only recently made genome-scale analyses of these organisms possible, and these new methods are helping researchers better understand the biology and evolution of this enigmatic group of eukaryotes.}, } @article {pmid21666019, year = {2011}, author = {Nelson, WC and Wollerman, L and Bhaya, D and Heidelberg, JF}, title = {Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {15}, pages = {5458-5466}, doi = {10.1128/AEM.05090-11}, pmid = {21666019}, issn = {1098-5336}, mesh = {Base Sequence ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Genome ; Genome, Bacterial ; Hot Springs/microbiology ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA ; Synechococcus/*genetics/isolation & purification/metabolism ; }, abstract = {Insertion sequences (ISs) are simple mobile genetic elements capable of relocating within a genome. Through this transposition activity, they are known to create mutations which are mostly deleterious to the cell, although occasionally they are beneficial. Two closely related isolates of thermophilic Synechococcus species from hot spring microbial mats are known to harbor a large number of diverse ISs. To explore the mechanism of IS acquisition within natural populations and survival in the face of high IS abundance, we examined IS content and location in natural populations of Synechococcus by comparing metagenomic data to the genomes of fully sequenced cultured isolates. The observed IS distribution in the metagenome was equivalent to the distribution in the isolates, indicating that the cultured isolates are appropriate models for the environmental population. High sequence conservation between IS families shared between the two isolates suggests that ISs are able to move between individuals within populations and between species via lateral gene transfer, consistent with models for IS family accumulation. Most IS families show evidence of recent activity, and interruption of critical genes in some individuals was observed, demonstrating that transposition is an ongoing mutational force in the populations.}, } @article {pmid21651684, year = {2012}, author = {Mazard, S and Ostrowski, M and Partensky, F and Scanlan, DJ}, title = {Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {372-386}, doi = {10.1111/j.1462-2920.2011.02514.x}, pmid = {21651684}, issn = {1462-2920}, support = {G0900740//Medical Research Council/United Kingdom ; }, mesh = {Aquatic Organisms ; Base Sequence ; Biological Evolution ; Cyanobacteria/classification/genetics ; Ecotype ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Synechococcus/classification/*genetics ; Water Microbiology ; }, abstract = {Conserved markers such as the 16S rRNA gene do not provide sufficient molecular resolution to identify spatially structured populations of marine Synechococcus, or 'ecotypes' adapted to distinct ecological niches. Multi-locus sequence analysis targeting seven 'core' genes was employed to taxonomically resolve Synechococcus isolates and correlate previous phylogenetic analyses encompassing a range of markers. Despite the recognized importance of lateral gene transfer in shaping the genomes of marine cyanobacteria, multi-locus sequence analysis of more than 120 isolates reflects a clonal population structure of major lineages and subgroups. A single core genome locus, petB, encoding the cytochrome b(6) subunit of the cytochrome b(6) f complex, was selected to expand our understanding of the diversity and ecology of marine Synechococcus populations. Environmental petB sequences cloned from contrasting sites highlight numerous genetically and ecologically distinct clusters, some of which represent novel, environmentally abundant clades without cultured representatives. With a view to scaling ecological analyses, the short sequence, taxonomic resolution and accurate automated alignment of petB is ideally suited to high-throughput and high-resolution sequencing projects to explore links between the ecology, evolution and biology of marine Synechococcus.}, } @article {pmid21625519, year = {2011}, author = {Gal-Mor, O and Elhadad, D and Deng, W and Rahav, G and Finlay, BB}, title = {The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL and is functionally different from a S. bongori ortholog.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20024}, doi = {10.1371/journal.pone.0020024}, pmid = {21625519}, issn = {1932-6203}, support = {//Canadian Institutes of Health Research/Canada ; //Howard Hughes Medical Institute/United States ; }, mesh = {Bacterial Proteins/*metabolism ; Base Sequence ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Promoter Regions, Genetic ; Salmonella enterica/genetics/*metabolism ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {To establish a successful infection within the host, a pathogen must closely regulate multiple virulence traits to ensure their accurate temporal and spatial expression. As a highly adapted intracellular pathogen, Salmonella enterica has acquired during its evolution various virulence genes via numerous lateral transfer events, including the acquisition of the Salmonella Pathogenicity Island 2 (SPI-2) and its associated effectors. Beneficial use of horizontally acquired genes requires that their expression is effectively coordinated with the already existing virulence programs and the regulatory set-up in the bacterium. As an example for such a mechanism, we show here that the ancestral PhoPQ system of Salmonella enterica is able to regulate directly the SPI-2 effector gene sseL (encoding a secreted deubiquitinase) in an SsrB-independent manner and that PhoP plays a part in a feed-forward regulatory loop, which fine-tunes the cellular level of SseL. Additionally, we demonstrate the presence of conserved cis regulatory elements in the promoter region of sseL and show direct binding of purified PhoP to this region. Interestingly, in contrast to the S. enterica PhoP, an ortholog regulator from a S. bongori SARC 12 strain was found to be impaired in promoting transcription of sseL and other genes from the PhoP regulon. These findings have led to the identification of a previously uncharacterized residue in the DNA-binding domain of PhoP, which is required for the transcriptional activation of PhoP regulated genes in Salmonella spp. Collectively our data demonstrate an interesting interface between the acquired SsrB regulon and the ancestral PhoPQ regulatory circuit, provide novel insights into the function of PhoP, and highlight a mechanism of regulatory integration of horizontally acquired genes into the virulence network of Salmonella enterica.}, } @article {pmid21622749, year = {2011}, author = {Chan, CX and Beiko, RG and Ragan, MA}, title = {Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements.}, journal = {Journal of bacteriology}, volume = {193}, number = {15}, pages = {3964-3977}, doi = {10.1128/JB.01524-10}, pmid = {21622749}, issn = {1098-5530}, mesh = {*Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; *Interspersed Repetitive Sequences ; Phylogeny ; Staphylococcal Infections/microbiology ; Staphylococcus/classification/*genetics ; }, abstract = {The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13 Staphylococcus genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within S. aureus appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.}, } @article {pmid21616910, year = {2011}, author = {de Mendoza, A and Ruiz-Trillo, I}, title = {The mysterious evolutionary origin for the GNE gene and the root of bilateria.}, journal = {Molecular biology and evolution}, volume = {28}, number = {11}, pages = {2987-2991}, doi = {10.1093/molbev/msr142}, pmid = {21616910}, issn = {1537-1719}, support = {206883//European Research Council/International ; }, mesh = {Animals ; Carbohydrate Epimerases/biosynthesis/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Invertebrates/*genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic changes" seem ideal to independently test previous phylogenetic hypotheses. We here describe a rare genomic change, the presence of the gene UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase (GNE). We show that GNE is encoded in the genomes of deuterostomes, acoelomorphs and Xenoturbella, whereas it is absent in protostomes and nonbilaterians. Moreover, the GNE has a complex evolutionary origin involving unique lateral gene transfer events and/or extensive hidden paralogy for each protein domain. However, rather than using GNE as a phylogenetic character, we argue that rare genomic changes such as the one presented here should be used with caution.}, } @article {pmid21536150, year = {2011}, author = {Richards, VP and Lang, P and Bitar, PD and Lefébure, T and Schukken, YH and Zadoks, RN and Stanhope, MJ}, title = {Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {6}, pages = {1263-1275}, doi = {10.1016/j.meegid.2011.04.019}, pmid = {21536150}, issn = {1567-7257}, support = {R01 AI073368/AI/NIAID NIH HHS/United States ; R01 AI073368-04/AI/NIAID NIH HHS/United States ; AI073368-01A2/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics ; Cattle ; DNA Transposable Elements ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Female ; Fructose/metabolism ; Gene Order ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Mastitis, Bovine/*microbiology ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Mutagenesis, Insertional ; Prophages/genetics ; Recombinases/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Streptococcus agalactiae/*genetics/pathogenicity ; Virulence Factors ; }, abstract = {In addition to causing severe invasive infections in humans, Streptococcus agalactiae, or group B Streptococcus (GBS), is also a major cause of bovine mastitis. Here we provide the first genome sequence for S. agalactiae isolated from a cow diagnosed with clinical mastitis (strain FSL S3-026). Comparison to eight S. agalactiae genomes obtained from human disease isolates revealed 183 genes specific to the bovine strain. Subsequent polymerase chain reaction (PCR) screening for the presence/absence of a subset of these loci in additional bovine and human strains revealed strong differentiation between the two groups (Fisher exact test: p<0.0001). The majority of the bovine strain-specific genes (∼ 85%) clustered tightly into eight genomic islands, suggesting these genes were acquired through lateral gene transfer (LGT). This bovine GBS also contained an unusually high proportion of insertion sequences (4.3% of the total genome), suggesting frequent genomic rearrangement. Comparison to other mastitis-causing species of bacteria provided strong evidence for two cases of interspecies LGT within the shared bovine environment: bovine S. agalactiae with Streptococcus uberis (nisin U operon) and Streptococcus dysgalactiae subsp. dysgalactiae (lactose operon). We also found evidence for LGT, involving the salivaricin operon, between the bovine S. agalactiae strain and either Streptococcus pyogenes or Streptococcus salivarius. Our findings provide insight into mechanisms facilitating environmental adaptation and acquisition of potential virulence factors, while highlighting both the key role LGT has played in the recent evolution of the bovine S. agalactiae strain, and the importance of LGT among pathogens within a shared environment.}, } @article {pmid21533164, year = {2011}, author = {Ruiz, JC and D'Afonseca, V and Silva, A and Ali, A and Pinto, AC and Santos, AR and Rocha, AA and Lopes, DO and Dorella, FA and Pacheco, LG and Costa, MP and Turk, MZ and Seyffert, N and Moraes, PM and Soares, SC and Almeida, SS and Castro, TL and Abreu, VA and Trost, E and Baumbach, J and Tauch, A and Schneider, MP and McCulloch, J and Cerdeira, LT and Ramos, RT and Zerlotini, A and Dominitini, A and Resende, DM and Coser, EM and Oliveira, LM and Pedrosa, AL and Vieira, CU and Guimarães, CT and Bartholomeu, DC and Oliveira, DM and Santos, FR and Rabelo, ÉM and Lobo, FP and Franco, GR and Costa, AF and Castro, IM and Dias, SR and Ferro, JA and Ortega, JM and Paiva, LV and Goulart, LR and Almeida, JF and Ferro, MI and Carneiro, NP and Falcão, PR and Grynberg, P and Teixeira, SM and Brommonschenkel, S and Oliveira, SC and Meyer, R and Moore, RJ and Miyoshi, A and Oliveira, GC and Azevedo, V}, title = {Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e18551}, doi = {10.1371/journal.pone.0018551}, pmid = {21533164}, issn = {1932-6203}, support = {D43 TW007012/TW/FIC NIH HHS/United States ; TW007012/TW/FIC NIH HHS/United States ; }, mesh = {Corynebacterium pseudotuberculosis/genetics/*pathogenicity ; *Evolution, Molecular ; *Genome, Bacterial ; Virulence/*genetics ; }, abstract = {BACKGROUND: Corynebacterium pseudotuberculosis, a gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity.

METHODOLOGY AND FINDINGS: We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer.

CONCLUSIONS: These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829.}, } @article {pmid21517914, year = {2011}, author = {Stokes, HW and Gillings, MR}, title = {Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {790-819}, doi = {10.1111/j.1574-6976.2011.00273.x}, pmid = {21517914}, issn = {1574-6976}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Gram-Negative Bacteria/*drug effects/*genetics ; Humans ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.}, } @article {pmid21501489, year = {2011}, author = {Maruyama, S and Suzaki, T and Weber, AP and Archibald, JM and Nozaki, H}, title = {Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {105}, doi = {10.1186/1471-2148-11-105}, pmid = {21501489}, issn = {1471-2148}, mesh = {Chlorophyta/*genetics/physiology ; Euglenida/classification/*genetics/physiology ; *Gene Transfer, Horizontal ; *Genome ; Molecular Sequence Data ; *Mosaicism ; Phylogeny ; Plastids/genetics ; Rhodophyta/*genetics/physiology ; Symbiosis ; }, abstract = {BACKGROUND: Euglenophytes are a group of photosynthetic flagellates possessing a plastid derived from a green algal endosymbiont, which was incorporated into an ancestral host cell via secondary endosymbiosis. However, the impact of endosymbiosis on the euglenophyte nuclear genome is not fully understood due to its complex nature as a 'hybrid' of a non-photosynthetic host cell and a secondary endosymbiont.

RESULTS: We analyzed an EST dataset of the model euglenophyte Euglena gracilis using a gene mining program designed to detect laterally transferred genes. We found E. gracilis genes showing affinity not only with green algae, from which the secondary plastid in euglenophytes evolved, but also red algae and/or secondary algae containing red algal-derived plastids. Phylogenetic analyses of these 'red lineage' genes suggest that E. gracilis acquired at least 14 genes via eukaryote-to-eukaryote lateral gene transfer from algal sources other than the green algal endosymbiont that gave rise to its current plastid. We constructed an EST library of the aplastidic euglenid Peranema trichophorum, which is a eukaryovorous relative of euglenophytes, and also identified 'red lineage' genes in its genome.

CONCLUSIONS: Our data show genome mosaicism in E. gracilis and P. trichophorum. One possible explanation for the presence of these genes in these organisms is that some or all of them were independently acquired by lateral gene transfer and contributed to the successful integration and functioning of the green algal endosymbiont as a secondary plastid. Alternative hypotheses include the presence of a phagocytosed alga as the single source of those genes, or a cryptic tertiary endosymbiont harboring secondary plastid of red algal origin, which the eukaryovorous ancestor of euglenophytes had acquired prior to the secondary endosymbiosis of a green alga.}, } @article {pmid21481756, year = {2011}, author = {Zhaxybayeva, O and Doolittle, WF}, title = {Lateral gene transfer.}, journal = {Current biology : CB}, volume = {21}, number = {7}, pages = {R242-6}, doi = {10.1016/j.cub.2011.01.045}, pmid = {21481756}, issn = {1879-0445}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; }, } @article {pmid21457552, year = {2011}, author = {Sitkiewicz, I and Green, NM and Guo, N and Mereghetti, L and Musser, JM}, title = {Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2) encoding secreted proteins.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {65}, doi = {10.1186/1471-2180-11-65}, pmid = {21457552}, issn = {1471-2180}, mesh = {Bacterial Proteins/*genetics/secretion ; Female ; *Gene Transfer, Horizontal ; Humans ; Interspersed Repetitive Sequences ; Sequence Homology ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/genetics/isolation & purification ; Streptococcus pyogenes/*genetics/isolation & purification ; Streptococcus thermophilus/genetics ; Synteny ; }, abstract = {BACKGROUND: The genome of serotype M28 group A Streptococcus (GAS) strain MGAS6180 contains a novel genetic element named Region of Difference 2 (RD2) that encodes seven putative secreted extracellular proteins. RD2 is present in all serotype M28 strains and strains of several other GAS serotypes associated with female urogenital infections. We show here that the GAS RD2 element is present in strain MGAS6180 both as an integrative chromosomal form and a circular extrachromosomal element. RD2-like regions were identified in publicly available genome sequences of strains representing three of the five major group B streptococcal serotypes causing human disease. Ten RD2-encoded proteins have significant similarity to proteins involved in conjugative transfer of Streptococcus thermophilus integrative chromosomal elements (ICEs).

RESULTS: We transferred RD2 from GAS strain MGAS6180 (serotype M28) to serotype M1 and M4 GAS strains by filter mating. The copy number of the RD2 element was rapidly and significantly increased following treatment of strain MGAS6180 with mitomycin C, a DNA damaging agent. Using a PCR-based method, we also identified RD2-like regions in multiple group C and G strains of Streptococcus dysgalactiae subsp.equisimilis cultured from invasive human infections.

CONCLUSIONS: Taken together, the data indicate that the RD2 element has disseminated by lateral gene transfer to genetically diverse strains of human-pathogenic streptococci.}, } @article {pmid21430389, year = {2011}, author = {Andersson, JO}, title = {Evolution of patchily distributed proteins shared between eukaryotes and prokaryotes: Dictyostelium as a case study.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {20}, number = {2}, pages = {83-95}, doi = {10.1159/000324505}, pmid = {21430389}, issn = {1660-2412}, mesh = {Bacteria/genetics ; Dictyostelium/*genetics ; Entamoeba/genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; Naegleria/genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Protein families are often patchily distributed in the tree of life; they are present in distantly related organisms, but absent in more closely related lineages. This could either be the result of lateral gene transfer between ancestors of organisms that encode them, or losses in the lineages that lack them. Here a novel approach is developed to study the evolution of patchily distributed proteins shared between prokaryotes and eukaryotes. Proteins encoded in the genome of cellular slime mold Dictyostelium discoideum and a restricted number of other lineages, including at least one prokaryote, were identified. Analyses of the phylogenetic distribution of 49 such patchily distributed protein families showed conflicts with organismal phylogenies; 25 are shared with the distantly related amoeboflagellate Naegleria (Excavata), whereas only two are present in the more closely related Entamoeba. Most protein families show unexpected topologies in phylogenetic analyses; eukaryotes are polyphyletic in 85% of the trees. These observations suggest that gene transfers have been an important mechanism for the distribution of patchily distributed proteins across all domains of life. Further studies of this exchangeable gene fraction are needed for a better understanding of the origin and evolution of eukaryotic genes and the diversification process of eukaryotes.}, } @article {pmid21406598, year = {2011}, author = {Babic, A and Berkmen, MB and Lee, CA and Grossman, AD}, title = {Efficient gene transfer in bacterial cell chains.}, journal = {mBio}, volume = {2}, number = {2}, pages = {}, doi = {10.1128/mBio.00027-11}, pmid = {21406598}, issn = {2150-7511}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; GM50895/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*genetics ; Conjugation, Genetic ; DNA, Bacterial/*genetics/*metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Microscopy, Fluorescence ; }, abstract = {Horizontal gene transfer contributes to evolution and the acquisition of new traits. In bacteria, horizontal gene transfer is often mediated by conjugative genetic elements that transfer directly from cell to cell. Integrative and conjugative elements (ICEs; also known as conjugative transposons) are mobile genetic elements that reside within a host genome but can excise to form a circle and transfer by conjugation to recipient cells. ICEs contribute to the spread of genes involved in pathogenesis, symbiosis, metabolism, and antibiotic resistance. Despite its importance, little is known about the mechanisms of conjugation in Gram-positive bacteria or how quickly or frequently transconjugants become donors. We visualized the transfer of the integrative and conjugative element ICEBs1 from a Bacillus subtilis donor to recipient cells in real time using fluorescence microscopy. We found that transfer of DNA from a donor to a recipient appeared to occur at a cell pole or along the lateral cell surface of either cell. Most importantly, we found that when acquired by 1 cell in a chain, ICEBs1 spread rapidly from cell to cell within the chain by additional sequential conjugation events. This intrachain conjugation is inherently more efficient than conjugation that is due to chance encounters between individual cells. Many bacterial species, including pathogenic, commensal, symbiotic, and nitrogen-fixing organisms, harbor ICEs and grow in chains, often as parts of microbial communities. It is likely that efficient intrachain spreading is a general feature of conjugative DNA transfer and serves to amplify the number of cells that acquire conjugative mobile genetic elements. IMPORTANCE Conjugative elements contribute to horizontal gene transfer and the acquisition of new traits. They are largely responsible for spreading antibiotic resistance in bacterial communities. To study the cell biology of conjugation, we visualized conjugative DNA transfer between Bacillus subtilis cells in real time using fluorescence microscopy. In contrast to previous predictions that transfer would occur preferentially from the donor cell pole, we found that transfer of DNA from a donor to a recipient appeared to occur at a cell pole or along the lateral cell surface of either cell. Most importantly, we found that when acquired by 1 cell in a chain, the conjugative DNA spread rapidly from cell to cell within the chain through sequential conjugation events. Since many bacterial species grow naturally in chains, this intrachain transfer is likely a common mechanism for accelerating the spread of conjugative elements within microbial communities.}, } @article {pmid21390549, year = {2011}, author = {Shigenobu, S and Wilson, AC}, title = {Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {68}, number = {8}, pages = {1297-1309}, doi = {10.1007/s00018-011-0645-2}, pmid = {21390549}, issn = {1420-9071}, mesh = {Animals ; Aphids/*genetics/*microbiology ; Buchnera/genetics/*physiology ; *Gene Transfer, Horizontal ; *Symbiosis ; }, abstract = {The symbiosis of the pea aphid Acyrthosphion pisum with the bacterium Buchnera aphidicola APS represents the best-studied insect obligate symbiosis. Here we present a refined picture of this symbiosis by linking pre-genomic observations to new genomic data that includes the complete genomes of the eukaryotic and prokaryotic symbiotic partners. In doing so, we address four issues central to understanding the patterns and processes operating at the A. pisum/Buchnera APS interface. These four issues include: (1) lateral gene transfer, (2) host immunity, (3) symbiotic metabolism, and (4) regulation.}, } @article {pmid21379317, year = {2011}, author = {Diao, Y and Qi, Y and Ma, Y and Xia, A and Sharakhov, I and Chen, X and Biedler, J and Ling, E and Tu, ZJ}, title = {Next-generation sequencing reveals recent horizontal transfer of a DNA transposon between divergent mosquitoes.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e16743}, doi = {10.1371/journal.pone.0016743}, pmid = {21379317}, issn = {1932-6203}, support = {R29 AI042121/AI/NIAID NIH HHS/United States ; R21 AI081023/AI/NIAID NIH HHS/United States ; AI042121/AI/NIAID NIH HHS/United States ; R21AI081023/AI/NIAID NIH HHS/United States ; R01 AI042121/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Culicidae/*classification/*genetics ; DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal/*physiology ; *Genetic Speciation ; High-Throughput Nucleotide Sequencing/methods ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {Horizontal transfer of genetic material between complex organisms often involves transposable elements (TEs). For example, a DNA transposon mariner has been shown to undergo horizontal transfer between different orders of insects and between different phyla of animals. Here we report the discovery and characterization of an ITmD37D transposon, MJ1, in Anopheles sinensis. We show that some MJ1 elements in Aedes aegypti and An. sinensis contain intact open reading frames and share nearly 99% nucleotide identity over the entire transposon, which is unexpectedly high given that these two genera had diverged 145-200 million years ago. Chromosomal hybridization and TE-display showed that MJ1 copy number is low in An. sinensis. Among 24 mosquito species surveyed, MJ1 is only found in Ae. aegypti and the hyrcanus group of anopheline mosquitoes to which An. sinensis belongs. Phylogenetic analysis is consistent with horizontal transfer and provides the basis for inference of its timing and direction. Although report of horizontal transfer of DNA transposons between higher eukaryotes is accumulating, our analysis is one of a small number of cases in which horizontal transfer of nearly identical TEs among highly divergent species has been thoroughly investigated and strongly supported. Horizontal transfer involving mosquitoes is of particular interest because there are ongoing investigations of the possibility of spreading pathogen-resistant genes into mosquito populations to control malaria and other infectious diseases. The initial indication of horizontal transfer of MJ1 came from comparisons between a 0.4x coverage An. sinensis 454 sequence database and available TEs in mosquito genomes. Therefore we have shown that it is feasible to use low coverage sequencing to systematically uncover horizontal transfer events. Expanding such efforts across a wide range of species will generate novel insights into the relative frequency of horizontal transfer of different TEs and provide the evolutionary context of these lateral transfer events.}, } @article {pmid21304512, year = {2011}, author = {Slamovits, CH and Okamoto, N and Burri, L and James, ER and Keeling, PJ}, title = {A bacterial proteorhodopsin proton pump in marine eukaryotes.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {183}, doi = {10.1038/ncomms1188}, pmid = {21304512}, issn = {2041-1723}, support = {MOP 84265//Canadian Institutes of Health Research/Canada ; }, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Blotting, Western ; Dinoflagellida/*genetics/metabolism ; Expressed Sequence Tags ; Fluorescent Antibody Technique ; Gene Transfer, Horizontal/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Protein Structure, Secondary ; Proton Pumps/genetics/*metabolism ; Rhodopsin/genetics/*metabolism ; Rhodopsins, Microbial ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Proteorhodopsins are light-driven proton pumps involved in widespread phototrophy. Discovered in marine proteobacteria just 10 years ago, proteorhodopsins are now known to have been spread by lateral gene transfer across diverse prokaryotes, but are curiously absent from eukaryotes. In this study, we show that proteorhodopsins have been acquired by horizontal gene transfer from bacteria at least twice independently in dinoflagellate protists. We find that in the marine predator Oxyrrhis marina, proteorhodopsin is indeed the most abundantly expressed nuclear gene and its product localizes to discrete cytoplasmic structures suggestive of the endomembrane system. To date, photosystems I and II have been the only known mechanism for transducing solar energy in eukaryotes; however, it now appears that some abundant zooplankton use this alternative pathway to harness light to power biological functions.}, } @article {pmid21293046, year = {2011}, author = {Stairs, CW and Roger, AJ and Hampl, V}, title = {Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a Firmicute.}, journal = {Molecular biology and evolution}, volume = {28}, number = {7}, pages = {2087-2099}, doi = {10.1093/molbev/msr032}, pmid = {21293046}, issn = {1537-1719}, support = {MOP 62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Acetyltransferases/*genetics ; Archamoebae/enzymology/genetics ; Bacterial Proteins/genetics ; Bayes Theorem ; Computer Simulation ; Enzymes/*genetics ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/enzymology/*genetics ; Phylogeny ; }, abstract = {Most of the major groups of eukaryotes have microbial representatives that thrive in low oxygen conditions. Those that have been studied in detail generate ATP via pathways involving anaerobically functioning enzymes of pyruvate catabolism that are typically absent in aerobic eukaryotes and whose origins remain controversial. These enzymes include pyruvate:ferredoxin oxidoreductase, pyruvate:NADP(+) oxidoreductase, and pyruvate formate lyase (Pfl). Pfl catalyzes the nonoxidative generation of formate and acetyl-Coenzyme A (CoA) from pyruvate and CoA and is activated by Pfl activating enzyme (Pfla). Within eukaryotes, this extremely oxygen-sensitive pathway was first described in the hydrogenosomes of anaerobic chytrid fungi and has more recently been characterized in the mitochondria and chloroplasts of the chlorophyte alga Chlamydomonas reinhardtii. To clarify the origins of this pathway, we have comprehensively searched for homologs of Pfl and Pfla in publicly available large-scale eukaryotic genomic and cDNA sequencing data, including our own from the anaerobic amoebozoan Mastigamoeba balamuthi. Surprisingly, we find that these enzymes are widely distributed and are present in diverse facultative or obligate anaerobic eukaryotic representatives of the archaeplastidan, metazoan, amoebozoan, and haptophyte lineages. Using maximum likelihood and Bayesian phylogenetic methods, we show that the eukaryotic Pfl and Pfla sequences each form monophyletic groups that are most closely related to homologs in firmicute gram-positive bacteria. Topology tests exclude both α-proteobacterial and cyanobacterial affinities for these genes suggesting that neither originated from the endosymbiotic ancestors of mitochondria or chloroplasts. Furthermore, the topologies of the eukaryote portion of the Pfl and Pfla trees significantly differ from well-accepted eukaryote relationships. Collectively, these results indicate that the Pfl pathway was first acquired by lateral gene transfer into a eukaryotic lineage most probably from a firmicute bacterial lineage and that it has since been spread across diverse eukaryotic groups by more recent eukaryote-to-eukaryote transfer events.}, } @article {pmid21290260, year = {2011}, author = {Tanaka, T and Fukuda, Y and Yoshino, T and Maeda, Y and Muto, M and Matsumoto, M and Mayama, S and Matsunaga, T}, title = {High-throughput pyrosequencing of the chloroplast genome of a highly neutral-lipid-producing marine pennate diatom, Fistulifera sp. strain JPCC DA0580.}, journal = {Photosynthesis research}, volume = {109}, number = {1-3}, pages = {223-229}, doi = {10.1007/s11120-011-9622-8}, pmid = {21290260}, issn = {1573-5079}, mesh = {Aquatic Organisms/genetics ; Base Sequence ; Biological Evolution ; Chloroplasts/*genetics ; DNA/chemistry/genetics ; Diatoms/*genetics ; Gene Transfer, Horizontal ; Genome, Chloroplast/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Molecular Sequence Data ; Open Reading Frames/*genetics ; Photosystem II Protein Complex/genetics ; Sequence Analysis, DNA ; }, abstract = {The chloroplast genome of the highly neutral-lipid-producing marine pennate diatom Fistulifera sp. strain JPCC DA0580 was fully sequenced using high-throughput pyrosequencing. The general features and gene content were compared with three other complete diatom chloroplast genomes. The chloroplast genome is 134,918 bp with an inverted repeat of 13,330 bp and is slightly larger than the other diatom chloroplast genomes due to several low gene-density regions lacking similarity to the other diatom chloroplast genomes. Protein-coding genes were nearly identical to those from Phaeodactylum tricornutum. On the other hand, we found unique sequence variations in genes of photosystem II which differ from the consensus in other diatom chloroplasts. Furthermore, five functional unknown ORFs and a putative serine recombinase gene, serC2, are located in the low gene-density regions. SerC2 was also identified in the plasmids of another pennate diatom, Cylindrotheca fusiformis, and in the plastid genome of the diatom endosymbiont of Kryptoperidinium foliaceum. Exogenous plasmids might have been incorporated into the chloroplast genome of Fistulifera sp. by lateral gene transfer. Chloroplast genome sequencing analysis of this novel diatom provides many important insights into diatom evolution.}, } @article {pmid21270172, year = {2011}, author = {Popa, O and Hazkani-Covo, E and Landan, G and Martin, W and Dagan, T}, title = {Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes.}, journal = {Genome research}, volume = {21}, number = {4}, pages = {599-609}, doi = {10.1101/gr.115592.110}, pmid = {21270172}, issn = {1549-5469}, support = {R01 LM010009/LM/NLM NIH HHS/United States ; LM010009-01/LM/NLM NIH HHS/United States ; }, mesh = {Base Composition/genetics ; Computational Biology ; DNA Repair/*genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; Prokaryotic Cells/*metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. Here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. For 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. Among these, donor-recipient relationships could be specified through phylogenetic reconstruction for 7% of the pairs, yielding 32,028 polarized recent gene acquisition events, which constitute the edges of our directed networks. We find that the frequency of recent LGT is linearly correlated both with genome sequence similarity and with proteome similarity of donor-recipient pairs. Genome sequence similarity accounts for 25% of the variation in gene-transfer frequency, with proteome similarity adding only 1% to the variability explained. The range of donor-recipient GC content similarity within the network is extremely narrow, with 86% of the LGTs occurring between donor-recipient pairs having ≤5% difference in GC content. Hence, genome sequence similarity and GC content similarity are strong barriers to LGT in prokaryotes. But they are not insurmountable, as we detected 1530 recent transfers between distantly related genomes. The directed network revealed that recipient genomes of distant transfers encode proteins of nonhomologous end-joining (NHEJ; a DNA repair mechanism) far more frequently than the recipient lacking that mechanism. This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier.}, } @article {pmid21252347, year = {2011}, author = {Khomyakova, M and Bükmez, Ö and Thomas, LK and Erb, TJ and Berg, IA}, title = {A methylaspartate cycle in haloarchaea.}, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6015}, pages = {334-337}, doi = {10.1126/science.1196544}, pmid = {21252347}, issn = {1095-9203}, mesh = {Acetates/*metabolism ; Acetyl Coenzyme A/metabolism ; Archaeal Proteins/metabolism ; Fumarates/metabolism ; Gene Transfer, Horizontal ; Genes, Archaeal ; Glutamic Acid/metabolism ; Glyoxylates/metabolism ; Haloarcula marismortui/enzymology/genetics/*metabolism ; Malates/metabolism ; Maleates/metabolism ; *Metabolic Networks and Pathways ; N-Methylaspartate/*metabolism ; Oxidation-Reduction ; Proteome ; Succinic Acid/metabolism ; }, abstract = {Access to novel ecological niches often requires adaptation of metabolic pathways to cope with new environments. For conversion to cellular building blocks, many substrates enter central carbon metabolism via acetyl-coenzyme A (acetyl-CoA). Until now, only two such pathways have been identified: the glyoxylate cycle and the ethylmalonyl-CoA pathway. Prokaryotes in the haloarchaea use a third pathway by which acetyl-CoA is oxidized to glyoxylate via the key intermediate methylaspartate. Glyoxylate condensation with another acetyl-CoA molecule yields malate, the final assimilation product. This cycle combines reactions that originally belonged to different metabolic processes in different groups of prokaryotes, which suggests lateral gene transfer and evolutionary tinkering of acetate assimilation. Moreover, it requires elevated intracellular glutamate concentrations, as well as coupling carbon assimilation with nitrogen metabolism.}, } @article {pmid21244532, year = {2011}, author = {Li, M and Shen, X and Yan, J and Han, H and Zheng, B and Liu, D and Cheng, H and Zhao, Y and Rao, X and Wang, C and Tang, J and Hu, F and Gao, GF}, title = {GI-type T4SS-mediated horizontal transfer of the 89K pathogenicity island in epidemic Streptococcus suis serotype 2.}, journal = {Molecular microbiology}, volume = {79}, number = {6}, pages = {1670-1683}, doi = {10.1111/j.1365-2958.2011.07553.x}, pmid = {21244532}, issn = {1365-2958}, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Conjugation, Genetic ; Epidemics ; *Gene Transfer, Horizontal ; *Genomic Islands ; Humans ; Molecular Sequence Data ; Streptococcal Infections/epidemiology/*microbiology ; Streptococcus suis/*genetics/metabolism ; }, abstract = {Pathogenicity islands (PAIs), a distinct type of genomic island (GI), play important roles in the rapid adaptation and increased virulence of pathogens. 89K is a newly identified PAI in epidemic Streptococcus suis isolates that are related to the two recent large-scale outbreaks of human infection in China. However, its mechanism of evolution and contribution to the epidemic spread of S. suis 2 remain unknown. In this study, the potential for mobilization of 89K was evaluated, and its putative transfer mechanism was investigated. We report that 89K can spontaneously excise to form an extrachromosomal circular product. The precise excision is mediated by an 89K-borne integrase through site-specific recombination, with help from an excisionase. The 89K excision intermediate acts as a substrate for lateral transfer to non-89K S. suis 2 recipients, where it reintegrates site-specifically into the target site. The conjugal transfer of 89K occurred via a GI type IV secretion system (T4SS) encoded in 89K, at a frequency of 10(-6) transconjugants per donor. This is the first demonstration of horizontal transfer of a Gram-positive PAI mediated by a GI-type T4SS. We propose that these genetic events are important in the emergence, pathogenesis and persistence of epidemic S. suis 2 strains.}, } @article {pmid21233529, year = {2011}, author = {Tofigh, A and Hallett, M and Lagergren, J}, title = {Simultaneous identification of duplications and lateral gene transfers.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {8}, number = {2}, pages = {517-535}, doi = {10.1109/TCBB.2010.14}, pmid = {21233529}, issn = {1557-9964}, mesh = {*Algorithms ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Models, Genetic ; }, abstract = {The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers). The reasonable biological constraint that a lateral gene transfer may only occur between contemporary species leads to the notion of acyclic DTL-scenarios. Parsimony methods are introduced by defining appropriate optimization problems. We show that finding most parsimonious acyclic DTL-scenarios is NP-hard. However, by dropping the condition of acyclicity, the problem becomes tractable, and we provide a dynamic programming algorithm as well as a fixed-parameter tractable algorithm for finding most parsimonious DTL-scenarios.}, } @article {pmid21232122, year = {2011}, author = {Mayer, WE and Schuster, LN and Bartelmes, G and Dieterich, C and Sommer, RJ}, title = {Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {13}, doi = {10.1186/1471-2148-11-13}, pmid = {21232122}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Cellulase/chemistry/*genetics/*metabolism ; *Gene Transfer, Horizontal ; *Genome, Helminth ; Helminth Proteins/chemistry/*genetics/*metabolism ; Molecular Sequence Data ; Nematoda/classification/*enzymology/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: Natural acquisition of novel genes from other organisms by horizontal or lateral gene transfer is well established for microorganisms. There is now growing evidence that horizontal gene transfer also plays important roles in the evolution of eukaryotes. Genome-sequencing and EST projects of plant and animal associated nematodes such as Brugia, Meloidogyne, Bursaphelenchus and Pristionchus indicate horizontal gene transfer as a key adaptation towards parasitism and pathogenicity. However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes.

RESULTS: We examine the transfer of cellulase genes to the free-living and beetle-associated nematode Pristionchus pacificus, for which detailed phylogenetic knowledge is available, to address predictions by evolutionary theory for successful gene transfer. We used transcriptomics in seven Pristionchus species and three other related diplogastrid nematodes with a well-defined phylogenetic framework to study the evolution of ancestral cellulase genes acquired by horizontal gene transfer. We performed intra-species, inter-species and inter-genic analysis by comparing the transcriptomes of these ten species and tested for cellulase activity in each species. Species with cellulase genes in their transcriptome always exhibited cellulase activity indicating functional integration into the host's genome and biology. The phylogenetic profile of cellulase genes was congruent with the species phylogeny demonstrating gene longevity. Cellulase genes show notable turnover with elevated birth and death rates. Comparison by sequencing of three selected cellulase genes in 24 natural isolates of Pristionchus pacificus suggests these high evolutionary dynamics to be associated with copy number variations and positive selection.

CONCLUSION: We could demonstrate functional integration of acquired cellulase genes into the nematode's biology as predicted by theory. Thus, functional assimilation, remarkable gene turnover and selection might represent key features of horizontal gene transfer events in nematodes.}, } @article {pmid21223321, year = {2011}, author = {Skippington, E and Ragan, MA}, title = {Lateral genetic transfer and the construction of genetic exchange communities.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {5}, pages = {707-735}, doi = {10.1111/j.1574-6976.2010.00261.x}, pmid = {21223321}, issn = {1574-6976}, mesh = {*Adaptation, Biological ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics ; Bacterial Infections/microbiology ; Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; Humans ; Recombination, Genetic ; *Selection, Genetic ; }, abstract = {Lateral genetic transfer (LGT) is a major source of phenotypic innovation among bacteria. Determinants for antibiotic resistance and other adaptive traits can spread rapidly, particularly by conjugative plasmids, but also phages and natural transformation. Each successive step from the uptake of foreign DNA, its genetic recombination and regulatory integration, to its establishment in the host population presents differential barriers and opportunities. The emergence of successive multidrug-resistant strains of Staphylococcus aureus illustrates the ongoing role of LGT in the combinatorial assembly of pathogens. The dynamic interplay among hosts, vectors, DNA elements, combinations of genetic determinants and environments constructs communities of genetic exchange. These relations can be abstracted as a graph, within which an exchange community might correspond to a path, transitively closed set, clique or near-clique. We provide a set-based definition, and review the features of actual genetic exchange communities (GECs), adopting first a knowledge-driven approach based on literature, and then a synoptic data-centric bioinformatic approach. GECs are diverse, but share some common features. Differential opportunity and barriers to lateral genetic transfer create bacterial communities of exchange.}, } @article {pmid21212120, year = {2011}, author = {Sheppard, SK and McCarthy, ND and Jolley, KA and Maiden, MC}, title = {Introgression in the genus Campylobacter: generation and spread of mosaic alleles.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 4}, pages = {1066-1074}, doi = {10.1099/mic.0.045153-0}, pmid = {21212120}, issn = {1465-2080}, support = {087622//Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Bacterial Proteins/*genetics ; Campylobacter coli/classification/*genetics ; Campylobacter jejuni/classification/*genetics ; *Polymorphism, Genetic ; *Recombination, Genetic ; Sequence Homology ; }, abstract = {Horizontal genetic exchange strongly influences the evolution of many bacteria, substantially contributing to difficulties in defining their position in taxonomic groups. In particular, how clusters of related bacterial genotypes - currently classified as microbiological species - evolve and are maintained remains controversial. The nature and magnitude of gene exchange between two closely related (approx. 15 % nucleotide divergence) microbiologically defined species, Campylobacter jejuni and Campylobacter coli, was investigated by the examination of mosaic alleles, those with some ancestry from each population. A total of 1738 alleles from 2953 seven-locus housekeeping gene sequence types (STs) were probabilistically assigned to each species group with the model-based clustering algorithm structure. Alleles with less than 75 % assignment probability to one of the populations were confirmed as mosaics using the structure linkage model. For each of these, the putative source of the recombinant region was determined and the allele was mapped onto a clonalframe genealogy derived from concatenated ST sequences. This enabled the direction and frequency of introgression between the two populations to be established, with 8.3 % of C. coli clade 1 alleles having acquired C. jejuni sequence, compared to 0.5 % for the reciprocal process. Once generated, mosaic genes spread within C. coli clade 1 by a combination of clonal expansion and lateral gene transfer, with some evidence of erosion of the mosaics by reacquisition of C. coli sequence. These observations confirm previous analyses of the exchange of complete housekeeping alleles and extend this work by describing the processes of horizontal gene transfer and subsequent spread within recipient species.}, } @article {pmid21187861, year = {2010}, author = {Foster, JM and Davis, PJ and Raverdy, S and Sibley, MH and Raleigh, EA and Kumar, S and Carlow, CK}, title = {Evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers.}, journal = {PloS one}, volume = {5}, number = {10}, pages = {e13576}, doi = {10.1371/journal.pone.0013576}, pmid = {21187861}, issn = {1932-6203}, support = {2R44 A1061865-02//PHS HHS/United States ; }, mesh = {Bacteria/*enzymology/genetics/growth & development ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; Genome, Archaeal ; Genome, Bacterial ; Phosphoglycerate Kinase/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: The glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (NISE) having independent evolutionary origins and no similarity in primary sequence, 3D structure, or catalytic mechanism. Cofactor-dependent PGM (dPGM) requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM) does not. The PGM profile of any given bacterium is unpredictable and some organisms such as Escherichia coli encode both forms.

METHODS/PRINCIPAL FINDINGS: To examine the distribution of PGM NISE throughout the Bacteria, and gain insight into the evolutionary processes that shape their phyletic profiles, we searched bacterial genome sequences for the presence of dPGM and iPGM. Both forms exhibited patchy distributions throughout the bacterial domain. Species within the same genus, or even strains of the same species, frequently differ in their PGM repertoire. The distribution is further complicated by the common occurrence of dPGM paralogs, while iPGM paralogs are rare. Larger genomes are more likely to accommodate PGM paralogs or both NISE forms. Lateral gene transfers have shaped the PGM profiles with intradomain and interdomain transfers apparent. Archaeal-type iPGM was identified in many bacteria, often as the sole PGM. To address the function of PGM NISE in an organism encoding both forms, we analyzed recombinant enzymes from E. coli. Both NISE were active mutases, but the specific activity of dPGM greatly exceeded that of iPGM, which showed highest activity in the presence of manganese. We created PGM null mutants in E. coli and discovered the ΔdPGM mutant grew slowly due to a delay in exiting stationary phase. Overexpression of dPGM or iPGM overcame this defect.

CONCLUSIONS/SIGNIFICANCE: Our biochemical and genetic analyses in E. coli firmly establish dPGM and iPGM as NISE. Metabolic redundancy is indicated since only larger genomes encode both forms. Non-orthologous gene displacement can fully account for the non-uniform PGM distribution we report across the bacterial domain.}, } @article {pmid21169443, year = {2011}, author = {Alvarez, L and Bricio, C and Gómez, MJ and Berenguer, J}, title = {Lateral transfer of the denitrification pathway genes among Thermus thermophilus strains.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1352-1358}, doi = {10.1128/AEM.02048-10}, pmid = {21169443}, issn = {1098-5336}, mesh = {Base Sequence ; Denitrification/genetics ; Gene Expression ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; Genetic Linkage ; Multigene Family ; Nitrate Reductase/chemistry/metabolism ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites/metabolism ; *Plasmids ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Thermus thermophilus/enzymology/*genetics/*metabolism ; }, abstract = {Nitrate respiration is a common and strain-specific property in Thermus thermophilus encoded by the nitrate respiration conjugative element (NCE) that can be laterally transferred by conjugation. In contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. These later steps of the denitrification pathway are under the regulatory control of an NCE-encoded transcription factor, but nothing is known about their coding sequences or its putative genetic linkage to the NCE. In this study we examine the genetic linkage between nitrate and nitrite respiration through lateral gene transfer (LGT) assays and describe a cluster of genes encoding the nitrite-nitric oxide respiration in T. thermophilus PRQ25. We show that the whole denitrification pathway can be transferred from the denitrificant strain PRQ25 to an aerobic strain, HB27, and that the genes coding for nitrite and nitric oxide respiration are encoded near the NCE. Sequence data from the draft genome of PRQ25 confirmed these results and allowed us to describe the most compact nor-nir cluster known thus far and to demonstrate the expression and activities of the encoded enzymes in the HB27 denitrificant derivatives obtained by LGT. We conclude that this NCE nor-nir supercluster constitutes a whole denitrification island that can be spread by lateral transfer among Thermus thermophilus strains.}, } @article {pmid21149709, year = {2011}, author = {Gophna, U and Ofran, Y}, title = {Lateral acquisition of genes is affected by the friendliness of their products.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {1}, pages = {343-348}, doi = {10.1073/pnas.1009775108}, pmid = {21149709}, issn = {1091-6490}, mesh = {Adaptation, Biological/*genetics ; Amino Acid Sequence ; Computational Biology ; Databases, Protein ; Escherichia coli K12 ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genomics/methods ; Protein Interaction Domains and Motifs/*genetics ; Sequence Alignment ; Statistics, Nonparametric ; Systems Biology/methods ; }, abstract = {A major factor in the evolution of microbial genomes is the lateral acquisition of genes that evolved under the functional constraints of other species. Integration of foreign genes into a genome that has different components and circuits poses an evolutionary challenge. Moreover, genes belonging to complex modules in the pretransfer species are unlikely to maintain their functionality when transferred alone to new species. Thus, it is widely accepted that lateral gene transfer favors proteins with only a few protein-protein interactions. The propensity of proteins to participate in protein-protein interactions can be assessed using computational methods that identify putative interaction sites on the protein. Here we report that laterally acquired proteins contain significantly more putative interaction sites than native proteins. Thus, genes encoding proteins with multiple protein-protein interactions may in fact be more prone to transfer than genes with fewer interactions. We suggest that these proteins have a greater chance of forming new interactions in new species, thus integrating into existing modules. These results reveal basic principles for the incorporation of novel genes into existing systems.}, } @article {pmid21124976, year = {2010}, author = {Férandon, C and Moukha, S and Callac, P and Benedetto, JP and Castroviejo, M and Barroso, G}, title = {The Agaricus bisporus cox1 gene: the longest mitochondrial gene and the largest reservoir of mitochondrial group i introns.}, journal = {PloS one}, volume = {5}, number = {11}, pages = {e14048}, doi = {10.1371/journal.pone.0014048}, pmid = {21124976}, issn = {1932-6203}, mesh = {Agaricus/enzymology/*genetics ; Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Fungal Proteins/*genetics ; Fungi/classification/genetics ; Gene Transfer, Horizontal ; Genome, Mitochondrial/*genetics ; Introns/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms. Large introns (up to 5 kbp) are frequent in mitochondrial genomes of plant and fungi but scarce in Metazoa, even if these organisms are grouped with fungi among the Opisthokonts. Mitochondrial introns are classified in two groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism. Most of these mitochondrial group I introns carry a "Homing Endonuclease Gene" (heg) encoding a DNA endonuclease acting in transfer and site-specific integration ("homing") and allowing intron spreading and gain after lateral transfer even between species from different kingdoms. Opposed to this gain mechanism, is another which implies that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss. The importance of both mechanisms (loss and gain) is matter of debate. Here we report the sequence of the cox1 gene of the button mushroom Agaricus bisporus, the most widely cultivated mushroom in the world. This gene is both the longest mitochondrial gene (29,902 nt) and the largest group I intron reservoir reported to date with 18 group I and 1 group II. An exhaustive analysis of the group I introns available in cox1 genes shows that they are mobile genetic elements whose numerous events of loss and gain by lateral transfer combine to explain their wide and patchy distribution extending over several kingdoms. An overview of intron distribution, together with the high frequency of eroded heg, suggests that they are evolving towards loss. In this landscape of eroded and lost intron sequences, the A. bisporus cox1 gene exhibits a peculiar dynamics of intron keeping and catching, leading to the largest collection of mitochondrial group I introns reported to date in a Eukaryote.}, } @article {pmid21110998, year = {2011}, author = {Zhang, Q and Zmasek, CM and Cai, X and Godzik, A}, title = {TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog.}, journal = {Developmental and comparative immunology}, volume = {35}, number = {4}, pages = {461-468}, doi = {10.1016/j.dci.2010.11.013}, pmid = {21110998}, issn = {1879-0089}, support = {P20 GM076221-01/GM/NIGMS NIH HHS/United States ; P20 GM076221/GM/NIGMS NIH HHS/United States ; GM076221/GM/NIGMS NIH HHS/United States ; R01 GM087218/GM/NIGMS NIH HHS/United States ; R01 GM087218-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cytoskeletal Proteins/chemistry/*genetics/*immunology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; Humans ; Metagenomics ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary ; Receptors, Interleukin-1/chemistry/genetics/immunology ; Signal Transduction ; }, abstract = {Toll/interleukin-1 receptor (TIR) domain-containing proteins play important roles in defense against pathogens in both animals and plants, connecting the immunity signaling pathways via a chain of specific protein-protein interactions. Among them is SARM, the only TIR domain-containing adaptor that can negatively regulate TLR signaling. By extensive phylogenetic analysis, we show here that SARM is closely related to bacterial proteins with TIR domains, suggesting that this family has a different evolutionary history from other animal TIR-containing adaptors, possibly emerging via a lateral gene transfer from bacteria to animals. We also show evidence of several similar, independent transfer events, none of which, however, survived in vertebrates. An evolutionary relationship between the animal SARM adaptor and bacterial proteins with TIR domains illustrates the possible role that bacterial TIR-containing proteins play in regulating eukaryotic immune responses and how this mechanism was possibly adapted by the eukaryotes themselves.}, } @article {pmid21106786, year = {2011}, author = {Macheras, E and Roux, AL and Bastian, S and Leão, SC and Palaci, M and Sivadon-Tardy, V and Gutierrez, C and Richter, E and Rüsch-Gerdes, S and Pfyffer, G and Bodmer, T and Cambau, E and Gaillard, JL and Heym, B}, title = {Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.}, journal = {Journal of clinical microbiology}, volume = {49}, number = {2}, pages = {491-499}, doi = {10.1128/JCM.01274-10}, pmid = {21106786}, issn = {1098-660X}, mesh = {Bacterial Proteins/genetics ; *Bacterial Typing Techniques ; Brazil ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA-Directed RNA Polymerases/*genetics ; France ; Germany ; Humans ; Molecular Sequence Data ; *Multilocus Sequence Typing ; Mycobacterium/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Switzerland ; }, abstract = {Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies.}, } @article {pmid21103900, year = {2011}, author = {Kittang, BR and Skrede, S and Langeland, N and Haanshuus, CG and Mylvaganam, H}, title = {emm gene diversity, superantigen gene profiles and presence of SlaA among clinical isolates of group A, C and G streptococci from western Norway.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {30}, number = {3}, pages = {423-433}, doi = {10.1007/s10096-010-1105-x}, pmid = {21103900}, issn = {1435-4373}, mesh = {Amino Acid Sequence ; Antigens, Bacterial/chemistry/*genetics ; Bacterial Outer Membrane Proteins/chemistry/*genetics/immunology ; Carrier Proteins/chemistry/*genetics ; Frameshift Mutation ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Molecular Sequence Data ; Norway ; Phospholipases A2/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic ; Sequence Analysis, Protein ; Streptococcal Infections/microbiology ; Streptococcus/*genetics/immunology/pathogenicity ; Streptococcus pyogenes/*genetics/immunology/isolation & purification/pathogenicity ; Superantigens/*genetics/immunology ; }, abstract = {In order to investigate molecular characteristics of beta-hemolytic streptococcal isolates from western Norway, we analysed the entire emm gene sequences, obtained superantigen gene profiles and determined the prevalence of the gene encoding streptococcal phospholipase A2 (SlaA) of 165 non-invasive and 34 contemporary invasive group A, C and G streptococci (GAS, GCS and GGS). Among the 25 GAS and 26 GCS/GGS emm subtypes identified, only emm3.1 was significantly associated with invasive disease. M protein size variation within GAS and GCS/GGS emm types was frequently identified. Two non-invasive and one invasive GGS possessed emm genes that translated to truncated M proteins as a result of frameshift mutations. Results suggestive of recombinations between emm or emm-like gene segments were found in isolates of emm4 and stG485 types. One non-invasive GGS possessed speC, speG, speH, speI and smeZ, and another non-invasive GGS harboured SlaA. speA and SlaA were over-represented among invasive GAS, probably because they were associated with emm3. speG(dys) was identified in 83% of invasive and 63% of non-invasive GCS/GGS and correlated with certain emm subtypes. Our results indicate the invasive potential of isolates belonging to emm3, and show substantial emm gene diversity and possible lateral gene transfers in our streptococcal population.}, } @article {pmid21081560, year = {2011}, author = {Palmeira, L and Penel, S and Lotteau, V and Rabourdin-Combe, C and Gautier, C}, title = {PhEVER: a database for the global exploration of virus-host evolutionary relationships.}, journal = {Nucleic acids research}, volume = {39}, number = {Database issue}, pages = {D569-75}, doi = {10.1093/nar/gkq1013}, pmid = {21081560}, issn = {1362-4962}, mesh = {Cluster Analysis ; *Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; Genomics ; Host-Pathogen Interactions/*genetics ; Phylogeny ; Sequence Homology ; User-Computer Interface ; Viral Proteins/chemistry/classification/genetics ; Viruses/classification/*genetics ; }, abstract = {Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains. Indeed, viruses are involved in the development of a wide range of pathologies and understanding how viruses and host cells interact in the context of adaptation remains an open question. In order to provide insights into the complex interactions between viruses and their host organisms and namely in the acquisition of novel functions through exchanges of genetic material, we developed the PhEVER database. This database aims at providing accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. PhEVER (http://pbil.univ-lyon1.fr/databases/phever) is a unique database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. PhEVER integrates extensive data from up-to-date completely sequenced genomes (2426 non-redundant viral genomes, 1007 non-redundant prokaryotic genomes, 43 eukaryotic genomes ranging from plants to vertebrates) and offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families. Public access to PhEVER is available through its webpage and through all dedicated ACNUC retrieval systems.}, } @article {pmid21071191, year = {2011}, author = {Kamikawa, R and Yabuki, A and Nakayama, T and Ishida, K and Hashimoto, T and Inagaki, Y}, title = {Cercozoa comprises both EF-1α-containing and EFL-containing members.}, journal = {European journal of protistology}, volume = {47}, number = {1}, pages = {24-28}, doi = {10.1016/j.ejop.2010.08.002}, pmid = {21071191}, issn = {1618-0429}, mesh = {Cercozoa/*genetics ; Evolution, Molecular ; Gene Deletion ; Gene Transfer, Horizontal ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Elongation factor 1α (EF-1α) and elongation factor-like protein (EFL) are considered to be functionally equivalent proteins involved in peptide synthesis. Eukaryotes can be fundamentally divided into 'EF-1α-containing' and 'EFL-containing' types. Recently, EF-1α and EFL genes have been surveyed across the diversity of eukaryotes to explore the origin and evolution of EFL genes. Although the phylum Cercozoa is a diverse group, gene data for either EFL or EF-1α are absent from all cercozoans except chlorarachniophytes which were previously defined as EFL-containing members. Our survey revealed that two members of the cercozoan subphylum Filosa (Thaumatomastix sp. and strain YPF610) are EFL-containing members. Importantly, we identified EF-1α genes from two members of Filosa (Paracercomonas marina and Paulinella chromatophora) and a member of the other subphylum Endomyxa (Filoreta japonica). All cercozoan EFL homologues could not be recovered as a monophyletic group in maximum-likelihood and Bayesian analyses, suggesting that lateral gene transfer was involved in the EFL evolution in this protist assemblage. In contrast, EF-1α analysis successfully recovered a monophyly of three homologues sampled from the two cercozoan subphyla. Based on the results, we postulate that cercozoan EF-1α genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1α genes.}, } @article {pmid21059789, year = {2011}, author = {Kloesges, T and Popa, O and Martin, W and Dagan, T}, title = {Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths.}, journal = {Molecular biology and evolution}, volume = {28}, number = {2}, pages = {1057-1074}, doi = {10.1093/molbev/msq297}, pmid = {21059789}, issn = {1537-1719}, mesh = {Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Proteobacteria/*classification/*genetics ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism of natural variation among prokaryotes. Over the full course of evolution, most or all of the genes resident in a given prokaryotic genome have been affected by LGT, yet the frequency of LGT can vary greatly across genes and across prokaryotic groups. The proteobacteria are among the most diverse of prokaryotic taxa. The prevalence of LGT in their genome evolution calls for the application of network-based methods instead of tree-based methods to investigate the relationships among these species. Here, we report networks that capture both vertical and horizontal components of evolutionary history among 1,207,272 proteins distributed across 329 sequenced proteobacterial genomes. The network of shared proteins reveals modularity structure that does not correspond to current classification schemes. On the basis of shared protein-coding genes, the five classes of proteobacteria fall into two main modules, one including the alpha-, delta-, and epsilonproteobacteria and the other including beta- and gammaproteobacteria. The first module is stable over different protein identity thresholds. The second shows more plasticity with regard to the sequence conservation of proteins sampled, with the gammaproteobacteria showing the most chameleon-like evolutionary characteristics within the present sample. Using a minimal lateral network approach, we compared LGT rates at different phylogenetic depths. In general, gene evolution by LGT within proteobacteria is very common. At least one LGT event was inferred to have occurred in at least 75% of the protein families. The average LGT rate at the species and class depth is about one LGT event per protein family, the rate doubling at the phylum level to an average of two LGT events per protein family. Hence, our results indicate that the rate of gene acquisition per protein family is similar at the level of species (by recombination) and at the level of classes (by LGT). The frequency of LGT per genome strongly depends on the species lifestyle, with endosymbionts showing far lower LGT frequencies than free-living species. Moreover, the nature of the transferred genes suggests that gene transfer in proteobacteria is frequently mediated by conjugation.}, } @article {pmid22881207, year = {2010}, author = {De Leenheer, P and Dockery, J and Gedeon, T and Pilyugin, SS}, title = {The chemostat with lateral gene transfer.}, journal = {Journal of biological dynamics}, volume = {4}, number = {6}, pages = {607-620}, doi = {10.1080/17513750903540858}, pmid = {22881207}, issn = {1751-3766}, mesh = {Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal/*genetics ; *Models, Biological ; }, abstract = {We investigate the standard chemostat model when lateral gene transfer is taken into account. We will show that when the different genotypes have growth rate functions that are sufficiently close to a common growth rate function, and when the yields of the genotypes are sufficiently close to a common value, then the population evolves to a globally stable steady state, at which all genotypes coexist. These results can explain why the antibiotic-resistant strains persist in the pathogen population.}, } @article {pmid20980981, year = {2010}, author = {Grunau, C and Boissier, J}, title = {No evidence for lateral gene transfer between salmonids and schistosomes.}, journal = {Nature genetics}, volume = {42}, number = {11}, pages = {918-919}, doi = {10.1038/ng1110-918}, pmid = {20980981}, issn = {1546-1718}, mesh = {Animals ; Base Sequence ; DNA/genetics ; DNA Transposable Elements/genetics ; Female ; *Gene Transfer, Horizontal ; Male ; Polymerase Chain Reaction ; Reproducibility of Results ; Salmonidae/*genetics ; Schistosoma/*genetics ; Schistosoma japonicum/genetics ; Schistosoma mansoni/genetics ; }, } @article {pmid20880410, year = {2010}, author = {Bittar, F and Rolain, JM}, title = {Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {16}, number = {7}, pages = {809-820}, doi = {10.1111/j.1469-0691.2010.03236.x}, pmid = {20880410}, issn = {1469-0691}, mesh = {Bacteria/*classification/growth & development/*isolation & purification ; Base Sequence ; Biodiversity ; Cystic Fibrosis/*microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Gene Transfer, Horizontal ; Humans ; Lung/microbiology ; Microbial Consortia ; Molecular Diagnostic Techniques ; Respiratory Tract Infections/*microbiology ; Spectrometry, Mass, Fast Atom Bombardment/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Spectroscopy, Fourier Transform Infrared/methods ; }, abstract = {Respiratory infections remain a major threat to cystic fibrosis (CF) patients. The detection and correct identification of the bacteria implicated in these infections is critical for the therapeutic management of patients. The traditional methods of culture and phenotypic identification of bacteria lack both sensitivity and specificity because many bacteria can be missed and/or misidentified. Molecular analyses have recently emerged as useful means to resolve these problems, including molecular methods for accurate identification or detection of bacteria and molecular methods for evaluation of microbial diversity. These recent molecular technologies have increased the list of new and/or emerging pathogens and epidemic strains associated with CF patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells has also emerged recently as a powerful and rapid method for the routine identification of bacteria in clinical microbiology laboratories and will certainly represent the method of choice also for the routine identification of bacteria in the context of CF. Finally, recent data derived from molecular culture-independent analyses indicate the presence of a previously underestimated, complex microbial community in sputa from CF patients. Interestingly, full genome sequencing of some bacteria frequently recovered from CF patients has highlighted the fact that the lungs of CF patients are hotspots for lateral gene transfer and the adaptation of these ecosystems to a specific chronic condition.}, } @article {pmid20877579, year = {2010}, author = {Barbour, AG and Travinsky, B}, title = {Evolution and distribution of the ospC Gene, a transferable serotype determinant of Borrelia burgdorferi.}, journal = {mBio}, volume = {1}, number = {4}, pages = {}, doi = {10.1128/mBio.00153-10}, pmid = {20877579}, issn = {2150-7511}, support = {AI-065359/AI/NIAID NIH HHS/United States ; CI 00171-01/CI/NCPDCID CDC HHS/United States ; }, mesh = {Animals ; Antigens, Bacterial/*genetics/metabolism ; Bacterial Outer Membrane Proteins/*genetics/metabolism ; Borrelia burgdorferi/classification/*genetics/isolation & purification/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Lyme Disease/microbiology ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Ticks/microbiology ; United States ; }, abstract = {Borrelia burgdorferi, an emerging bacterial pathogen, is maintained in nature by transmission from one vertebrate host to another by ticks. One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. We accessed and supplemented collections of DNA sequences of ospC and other loci from ticks in three U.S. regions (the Northeast, the Midwest, and northern California); a total of 839 ospC sequences were analyzed. Three overlapping but distinct populations of B. burgdorferi corresponded to the geographic regions. In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. Besides recombinations with traces limited to the ospC gene itself, there was evidence of lateral gene transfers that involved (i) part of the ospC gene and one of the two flanks or (ii) the entire ospC gene and different lengths of both flanks. Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. By acquisition of the complete part or a large part of a novel ospC gene, an otherwise adapted strain would assume a new serotypic identity, thereby being comparatively fitter in an area with a high prevalence of immunity to existing OspC types.}, } @article {pmid20876108, year = {2010}, author = {Danchin, EG and Rosso, MN and Vieira, P and de Almeida-Engler, J and Coutinho, PM and Henrissat, B and Abad, P}, title = {Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {41}, pages = {17651-17656}, doi = {10.1073/pnas.1008486107}, pmid = {20876108}, issn = {1091-6490}, mesh = {Animals ; Base Composition ; Bayes Theorem ; *Biological Evolution ; Codon/genetics ; Computational Biology ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Glycoside Hydrolases/genetics ; Models, Genetic ; Nematoda/*genetics/physiology ; *Phylogeny ; Plants/*parasitology ; Polygalacturonase/genetics ; Polysaccharide-Lyases/genetics ; Ralstonia solanacearum/*enzymology/genetics ; }, abstract = {Lateral gene transfer from prokaryotes to animals is poorly understood, and the scarce documented examples generally concern genes of uncharacterized role in the receiver organism. In contrast, in plant-parasitic nematodes, several genes, usually not found in animals and similar to bacterial homologs, play essential roles for successful parasitism. Many of these encode plant cell wall-degrading enzymes that constitute an unprecedented arsenal in animals in terms of both abundance and diversity. Here we report that independent lateral gene transfers from different bacteria, followed by gene duplications and early gain of introns, have shaped this repertoire. We also show protein immunolocalization data that suggest additional roles for some of these cell wall-degrading enzymes in the late stages of these parasites' life cycle. Multiple functional acquisitions of exogenous genes that provide selective advantage were probably crucial for the emergence and proficiency of plant parasitism in nematodes.}, } @article {pmid20870714, year = {2010}, author = {Brew, K and Tumbale, P and Acharya, KR}, title = {Family 6 glycosyltransferases in vertebrates and bacteria: inactivation and horizontal gene transfer may enhance mutualism between vertebrates and bacteria.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {48}, pages = {37121-37127}, doi = {10.1074/jbc.R110.176248}, pmid = {20870714}, issn = {1083-351X}, mesh = {Animals ; Bacteria/chemistry/classification/*enzymology/genetics ; *Bacterial Physiological Phenomena ; Bacterial Proteins/chemistry/genetics/*metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Glycosyltransferases/chemistry/genetics/*metabolism ; Humans ; Molecular Sequence Data ; Phylogeny ; Vertebrates/classification/genetics/*physiology ; }, abstract = {Glycosyltransferases (GTs) control the synthesis and structures of glycans. Inactivation and intense allelic variation in members of the GT6 family generate species-specific and individual variations in carbohydrate structures, including histo-blood group oligosaccharides, resulting in anti-glycan antibodies that target glycan-decorated pathogens. GT6 genes are ubiquitous in vertebrates but are otherwise rare, existing in a few bacteria, one protozoan, and cyanophages, suggesting lateral gene transfer. Prokaryotic GT6 genes correspond to one exon of vertebrate genes, yet their translated protein sequences are strikingly similar. Bacterial and phage GT6 genes influence the surface chemistry of bacteria, affecting their interactions, including those with vertebrate hosts.}, } @article {pmid20861243, year = {2010}, author = {Moreau, H and Piganeau, G and Desdevises, Y and Cooke, R and Derelle, E and Grimsley, N}, title = {Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer.}, journal = {Journal of virology}, volume = {84}, number = {24}, pages = {12555-12563}, doi = {10.1128/JVI.01123-10}, pmid = {20861243}, issn = {1098-5514}, mesh = {*Biological Evolution ; DNA Virus Infections/*genetics/virology ; DNA Viruses/*genetics/*pathogenicity ; DNA, Viral/physiology ; *Gene Transfer, Horizontal ; Genes, Viral/physiology ; Genetic Variation ; *Genome, Viral ; *Marine Biology ; Microalgae/*virology ; Phylogeny ; }, abstract = {Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.}, } @article {pmid20856925, year = {2010}, author = {Saisongkorh, W and Robert, C and La Scola, B and Raoult, D and Rolain, JM}, title = {Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {e12666}, doi = {10.1371/journal.pone.0012666}, pmid = {20856925}, issn = {1932-6203}, mesh = {Agrobacterium tumefaciens/classification/*genetics ; Bacterial Proteins/*genetics ; Bartonella/classification/*genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; }, abstract = {BACKGROUND: Bartonella species cospeciate with mammals and live within erythrocytes. Even in these specific niches, it has been recently suggested by bioinformatic analysis of full genome sequences that Lateral Gene Transfer (LGT) may occur but this has never been demonstrated biologically. Here we describe the sequence of the B. rattaustraliani (AUST/NH4(T)) circular plasmid (pNH4) that encodes the tra cluster of the Type IV secretion system (T4SS) and we eventually provide evidence that Bartonella species may conjugate and exchange this plasmid inside amoeba.

PRINCIPAL FINDINGS: The T4SS of pNH4 is critical for intracellular viability of bacterial pathogens, exhibits bioinformatic evidence of LGT among bacteria living in phagocytic protists. For instance, 3 out of 4 T4SS encoding genes from pNH4 appear to be closely related to Rhizobiales, suggesting that gene exchange occurs between intracellular bacteria from mammals (bartonellae) and plants (Rhizobiales). We show that B. rattaustraliani and Rhizobium radiobacter both survived within the amoeba Acanthamoeba polyphaga and can conjugate together. Our findings further support the hypothesis that tra genes might also move into and out of bacterial communities by conjugation, which might be the primary means of genomic evolution for intracellular adaptation by cross-talk of interchangeable genes between Bartonella species and plant pathogens.

CONCLUSIONS: Based on this, we speculate that amoeba favor the transfer of genes as phagocytic protists, which allows for intraphagocytic survival and, as a consequence, promotes the creation of potential pathogenic organisms.}, } @article {pmid20851041, year = {2010}, author = {Cho, YJ and Yi, H and Lee, JH and Kim, DW and Chun, J}, title = {Genomic evolution of Vibrio cholerae.}, journal = {Current opinion in microbiology}, volume = {13}, number = {5}, pages = {646-651}, doi = {10.1016/j.mib.2010.08.007}, pmid = {20851041}, issn = {1879-0364}, mesh = {Africa ; Asia ; Bacterial Typing Techniques ; Cholera/epidemiology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomic Islands ; Genotype ; Humans ; Pandemics ; Vibrio cholerae/*classification/*genetics ; }, abstract = {Vibrio cholera, the causal agent of cholera, also occupies an autochthonous aquatic inhabitant. The current, seventh cholera pandemic is linked to O1 El Tor biotype and O139 serogroups. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones in Asia and Africa. Recent comparative genomic studies have identified a large 'mobilome', or composed of mobile genomic islands in V. cholerae. All seventh pandemic isolates have highly related genome sequences, but they can be differentiated by set of these genomic islands. A consequence of the extensive lateral gene transfer is that classically important diagnostic markers, such as serotype and biotype, are not reliable and new methods based on genomic sequences are required.}, } @article {pmid20829345, year = {2011}, author = {Wägele, H and Deusch, O and Händeler, K and Martin, R and Schmitt, V and Christa, G and Pinzger, B and Gould, SB and Dagan, T and Klussmann-Kolb, A and Martin, W}, title = {Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobranchus ocellatus does not entail lateral transfer of algal nuclear genes.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {699-706}, doi = {10.1093/molbev/msq239}, pmid = {20829345}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Chlorophyta/cytology/*genetics ; Expressed Sequence Tags ; Gastropoda/classification/*genetics/*physiology/ultrastructure ; Gene Expression Profiling ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Plastids/*genetics/ultrastructure ; }, abstract = {Sacoglossan sea slugs are unique in the animal kingdom in that they sequester and maintain active plastids that they acquire from the siphonaceous algae upon which they feed, making the animals photosynthetic. Although most sacoglossan species digest their freshly ingested plastids within hours, four species from the family Plakobranchidae retain their stolen plastids (kleptoplasts) in a photosynthetically active state on timescales of weeks to months. The molecular basis of plastid maintenance within the cytosol of digestive gland cells in these photosynthetic metazoans is yet unknown but is widely thought to involve gene transfer from the algal food source to the slugs based upon previous investigations of single genes. Indeed, normal plastid development requires hundreds of nuclear-encoded proteins, with protein turnover in photosystem II in particular known to be rapid under various conditions. Moreover, only algal plastids, not the algal nuclei, are sequestered by the animals during feeding. If algal nuclear genes are transferred to the animal either during feeding or in the germ line, and if they are expressed, then they should be readily detectable with deep-sequencing methods. We have sequenced expressed mRNAs from actively photosynthesizing, starved individuals of two photosynthetic sea slug species, Plakobranchus ocellatus Van Hasselt, 1824 and Elysia timida Risso, 1818. We find that nuclear-encoded, algal-derived genes specific to photosynthetic function are expressed neither in P. ocellatus nor in E. timida. Despite their dramatic plastid longevity, these photosynthetic sacoglossan slugs do not express genes acquired from algal nuclei in order to maintain plastid function.}, } @article {pmid20802057, year = {2011}, author = {Chi Fru, E}, title = {Microbial evolution of sulphate reduction when lateral gene transfer is geographically restricted.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {61}, number = {Pt 7}, pages = {1725-1735}, doi = {10.1099/ijs.0.026914-0}, pmid = {20802057}, issn = {1466-5034}, mesh = {*Biological Evolution ; DNA, Bacterial/genetics ; Gene Flow ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Hot Springs/microbiology ; Hydrogensulfite Reductase/*genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; Sulfur-Reducing Bacteria/*classification/genetics ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.}, } @article {pmid20716256, year = {2011}, author = {Merhej, V and Raoult, D}, title = {Rickettsial evolution in the light of comparative genomics.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {86}, number = {2}, pages = {379-405}, doi = {10.1111/j.1469-185X.2010.00151.x}, pmid = {20716256}, issn = {1469-185X}, mesh = {Animals ; *Biological Evolution ; *Genome, Bacterial ; *Genomics ; Host-Pathogen Interactions ; Humans ; Rickettsia/*genetics ; }, abstract = {Rickettsia are best known as strictly intracellular vector-borne bacteria that cause mild to severe diseases in humans and other animals. Recent advances in molecular tools and biological experiments have unveiled a wide diversity of Rickettsia spp. that include species with a broad host range and some species that act as endosymbiotic associates. Molecular phylogenies of Rickettsia spp. contain some ambiguities, such as the position of R. canadensis and relationships within the spotted fever group. In the modern era of genomics, with an ever-increasing number of sequenced genomes, there is enhanced interest in the use of whole-genome sequences to understand pathogenesis and assess evolutionary relationships among rickettsial species. Rickettsia have small genomes (1.1-1.5 Mb) as a result of reductive evolution. These genomes contain split genes, gene remnants and pseudogenes that, owing to the colinearity of some rickettsial genomes, may represent different steps of the genome degradation process. Genomics reveal extreme genome reduction and massive gene loss in highly vertebrate-pathogenic Rickettsia compared to less virulent or endosymbiotic species. Information gleaned from rickettsial genomics challenges traditional concepts of pathogenesis that focused primarily on the acquisition of virulence factors. Another intriguing phenomenon about the reduced rickettsial genomes concerns the large fraction of non-coding DNA and possible functionality of these "non-coding" sequences, because of the high conservation of these regions. Despite genome streamlining, Rickettsia spp. contain gene families, selfish DNA, repeat palindromic elements and genes encoding eukaryotic-like motifs. These features participate in sequence and functional diversity and may play a crucial role in adaptation to the host cell and pathogenesis. Genome analyses have identified a large fraction of mobile genetic elements, including plasmids, suggesting the possibility of lateral gene transfer in these intracellular bacteria. Phylogenetic analyses have identified several candidates for horizontal gene acquisition among Rickettsia spp. including tra, pat2, and genes encoding for the type IV secretion system and ATP/ADP translocase that may have been acquired from bacteria living in amoebae. Gene loss, gene duplication, DNA repeats and lateral gene transfer all have shaped rickettsial genome evolution. A comprehensive analysis of the entire genome, including genes and non-coding DNA, will help to unlock the mysteries of rickettsial evolution and pathogenesis.}, } @article {pmid20688752, year = {2010}, author = {Lefébure, T and Bitar, PD and Suzuki, H and Stanhope, MJ}, title = {Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {646-655}, doi = {10.1093/gbe/evq048}, pmid = {20688752}, issn = {1759-6653}, support = {N01AI30054/AI/NIAID NIH HHS/United States ; }, mesh = {Campylobacter coli/*genetics ; Campylobacter jejuni/*genetics ; Chromosome Mapping ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species.}, } @article {pmid20632805, year = {2010}, author = {Frost, LS and Koraimann, G}, title = {Regulation of bacterial conjugation: balancing opportunity with adversity.}, journal = {Future microbiology}, volume = {5}, number = {7}, pages = {1057-1071}, doi = {10.2217/fmb.10.70}, pmid = {20632805}, issn = {1746-0921}, support = {MT 11249//Canadian Institutes of Health Research/Canada ; }, mesh = {*Adaptation, Biological ; *Bacteriophages ; Conjugation, Genetic/genetics/*physiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; *Plasmids ; *Recombination, Genetic ; }, abstract = {Conjugative plasmids are involved in the dissemination of important traits such as antibiotic resistance, virulence determinants and metabolic pathways involved in adapting to environmental niches, a process termed horizontal or lateral gene transfer. Conjugation is the process of transferring DNA from a donor to a recipient cell with the establishment of the incoming DNA and its cargo of genetic traits within the transconjugant. Conjugation is mediated by self-transmissible plasmids as well as phage-like sequences that have been integrated into the bacterial chromosome, such as integrative and conjugative elements (ICEs) that now include conjugative transposons. Both conjugative plasmids and ICEs can mediate the transfer of mobilizable elements by sharing their conjugative machinery. Conjugation can either be induced, usually by small molecules or peptides or by excision of the ICE from the host chromosome, or it can be tightly regulated by plasmid- and host-encoded factors. The transfer potential of these transfer regions depends on the integration of many signals in response to environmental and physiological cues. This review will focus on the mechanisms that influence transfer potential in these systems, particularly those of the IncF incompatibility group.}, } @article {pmid20629700, year = {2010}, author = {Wildschutte, H and Preheim, SP and Hernandez, Y and Polz, MF}, title = {O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates.}, journal = {Environmental microbiology}, volume = {12}, number = {11}, pages = {2977-2987}, doi = {10.1111/j.1462-2920.2010.02274.x}, pmid = {20629700}, issn = {1462-2920}, support = {F32GM084640/GM/NIGMS NIH HHS/United States ; }, mesh = {Antigenic Variation ; Base Sequence ; *Gene Transfer, Horizontal ; Genetic Loci ; *Genetic Variation ; Genome, Bacterial ; Massachusetts ; Molecular Sequence Data ; Multilocus Sequence Typing ; *O Antigens/analysis/classification/genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Serotyping ; Vibrio/*genetics/*immunology ; Water Microbiology ; }, abstract = {The O-antigen is a highly diverse structure expressed on the outer surface of Gram-negative bacteria. The products responsible for O-antigen synthesis are encoded in the wbe region, which exhibits extensive genetic diversity. While heterogeneous O-antigens are observed within Vibrio species, characterization of these structures has been devoted almost exclusively to pathogens. Here, we investigate O-antigen diversity among coastal marine Vibrio splendidus-like isolates. The wbe region was first identified and characterized using the sequenced genomes of strains LGP32, 12B01 and Med222. These regions were genetically diverse, reflective of their expressed O-antigen. Additional isolates from physically distinct habitats in Plum Island Estuary (MA, USA), including within animal hosts and on suspended particles, were further characterized based on multilocus sequence analysis (MLSA) and O-antigen profiles. Results showed serotype diversity within an ecological setting. Among 48 isolates which were identical in three MLSA genes, 41 showed gpm genetic diversity, a gene closely linked to the wbe locus, and at least 12 expressed different O-antigen profiles further suggesting wbe genetic diversity. Our results demonstrate O-antigen hyper-variability among these environmental strains and suggest that frequent lateral gene transfer generates wbe extensive diversity among V. splendidus and its close relatives.}, } @article {pmid20601965, year = {2010}, author = {Wozniak, RA and Waldor, MK}, title = {Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow.}, journal = {Nature reviews. Microbiology}, volume = {8}, number = {8}, pages = {552-563}, doi = {10.1038/nrmicro2382}, pmid = {20601965}, issn = {1740-1534}, support = {R37 AI042347/AI/NIAID NIH HHS/United States ; R37 AI-42347/AI/NIAID NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*genetics ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; Evolution, Molecular ; *Gene Flow ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Recombination, Genetic ; }, abstract = {Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in both Gram-positive and Gram-negative bacteria. These elements primarily reside in a host chromosome but retain the ability to excise and to transfer by conjugation. Although ICEs use a range of mechanisms to promote their core functions of integration, excision, transfer and regulation, there are common features that unify the group. This Review compares and contrasts the core functions for some of the well-studied ICEs and discusses them in the broader context of mobile-element and genome evolution.}, } @article {pmid20551687, year = {2010}, author = {Filée, J and Chandler, M}, title = {Gene exchange and the origin of giant viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {354-361}, doi = {10.1159/000312920}, pmid = {20551687}, issn = {1423-0100}, mesh = {Amoeba/virology ; DNA, Viral/*genetics ; Eukaryota/virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; *Recombination, Genetic ; Viruses/*genetics ; }, abstract = {Giant viruses or nucleocytoplasmic large DNA viruses (NCLDVs) infect a wide range of eukaryotic hosts (including, algae, amoebae and metazoans) and show a very large range in genome size (between 100 kb and 1.2 Mb). Here we review some recent results concerning the extensive lateral gene transfer which appears to have occurred during NCLDV evolution. Current data suggest that giant viruses probably originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins. A large array of lateral gene transfers from diverse cellular sources, including several families of mobile genetic elements, is probably responsible for the huge diversity of genome size and composition found in extant giant viruses.}, } @article {pmid20551685, year = {2010}, author = {Colson, P and Raoult, D}, title = {Gene repertoire of amoeba-associated giant viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {330-343}, doi = {10.1159/000312918}, pmid = {20551685}, issn = {1423-0100}, mesh = {Amoeba/*virology ; Archaea/genetics ; Bacteria/genetics ; DNA Viruses/*genetics ; Eukaryota/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Viral ; *Genome, Viral ; Open Reading Frames ; Recombination, Genetic ; Sequence Homology ; Viral Proteins/*genetics ; }, abstract = {Acanthamoeba polyphaga mimivirus, Marseillevirus, and Sputnik, a virophage, are intra-amoebal viruses that have been isolated from water collected in cooling towers. They have provided fascinating data and have raised exciting questions about viruses definition and evolution. Mimivirus and Marseillevirus have been classified in the nucleo-cytoplasmic large DNA viruses (NCLDVs) class. Their genomes are the largest and fifth largest viral genomes sequenced so far. The gene repertoire of these amoeba-associated viruses can be divided into four groups: the core genome, genes acquired by lateral gene transfer, duplicated genes, and ORFans. Open reading frames (ORFs) that have homologs in the NCLDVs core gene set represent 2.9 and 6.1% of the Mimivirus and Marseillevirus gene contents, respectively. A substantial proportion of the Mimivirus, Marseillevirus and Sputnik ORFs exhibit sequence similarities to homologs found in bacteria, archaea, eukaryotes or viruses. The large amount of chimeric genes in these viral genomes might have resulted from acquisitions by lateral gene transfers, implicating sympatric bacteria and viruses with an intra-amoebal lifestyle. In addition, lineage-specific gene expansion may have played a major role in the genome shaping. Altogether, the data so far accumulated on amoeba-associated giant viruses are a powerful incentive to isolate and study additional strains to gain better understanding of their pangenome.}, } @article {pmid20551684, year = {2010}, author = {Raoult, D and Boyer, M}, title = {Amoebae as genitors and reservoirs of giant viruses.}, journal = {Intervirology}, volume = {53}, number = {5}, pages = {321-329}, doi = {10.1159/000312917}, pmid = {20551684}, issn = {1423-0100}, mesh = {Amoeba/microbiology/*virology ; Bacteria/genetics/isolation & purification ; DNA Viruses/genetics/*isolation & purification ; Evolution, Molecular ; Fungi/genetics/isolation & purification ; Gene Transfer, Horizontal ; Recombination, Genetic ; }, abstract = {Amoebae are unicellular phagocytes that feed on microorganisms in their environment. Some amoebae have the largest genome size currently known on earth. They phagocytose any inert particle larger than 0.5 microm. Phagocytic amoebae can harbor different bacteria, fungi and giant viruses within the same cell. There is evidence of lateral gene transfer between the amoeba and its microbiological hosts. There is also evidence of gene exchange between viruses and bacteria hosted in amoebae. Moreover, there is evidence of gene transfer between viruses, such as Mimivirus and the virophage. As a consequence, viruses and intracellular bacteria living in amoebae have a sympatric lifestyle and large chimeric genome repertoires. We conclude that phagocytic protists continuously generate new species with chimeric repertoires that may succeed later if adapted to the environmental conditions and selected in a specific niche.}, } @article {pmid20550700, year = {2010}, author = {Abby, SS and Tannier, E and Gouy, M and Daubin, V}, title = {Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {324}, doi = {10.1186/1471-2105-11-324}, pmid = {20550700}, issn = {1471-2105}, mesh = {*Algorithms ; Archaea/genetics ; Bacteria/genetics ; *Gene Transfer, Horizontal ; *Phylogeny ; Software ; }, abstract = {BACKGROUND: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.

RESULTS: We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.

CONCLUSIONS: The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univ-lyon1.fr/software/prunier.}, } @article {pmid20537944, year = {2010}, author = {Lurie-Weinberger, MN and Gomez-Valero, L and Merault, N and Glöckner, G and Buchrieser, C and Gophna, U}, title = {The origins of eukaryotic-like proteins in Legionella pneumophila.}, journal = {International journal of medical microbiology : IJMM}, volume = {300}, number = {7}, pages = {470-481}, doi = {10.1016/j.ijmm.2010.04.016}, pmid = {20537944}, issn = {1618-0607}, mesh = {Adaptation, Biological ; Bacterial Proteins/*genetics ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Legionella pneumophila/*genetics ; Mimiviridae/genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Viral Proteins/genetics ; }, abstract = {Legionella pneumophila, the causative agent of Legionnaires' disease, is known to be an intracellular pathogen of multiple species of protozoa and is assumed to have co-evolved with these organisms for millions of years. Genome sequencing of L. pneumophila strains has revealed an abundance of eukaryotic-like proteins (ELPs). Here, we study the evolution of these ELPs, in order to investigate their origin. Thirty-four new ELPs were identified, based on a higher similarity to eukaryotic proteins than to bacterial ones. Phylogenetic analyses demonstrated that both lateral gene transfer from eukaryotic hosts and bacterial genes that became eukaryotic-like by gradual adaptation to the intracellular milieu or gene fragment acquisition, contributed to the existing repertoire of ELPs, which comprise over 3% of the putative proteome of L. pneumophila strains. A PCR survey of 72 L. pneumophila strains showed that most ELPs were conserved in nearly all of these strains, indicating that they are likely to play important roles in this species. Genes of different evolutionary origin have distinct patterns of selection, as reflected by their ratio of a synonymous vs. synonymous mutations. One ELP is common to several strains of Legionella, but outside this genus has homologs only in Acanthamoeba polyphaga mimivirus, indicating that gene exchange involving eukaryotic viruses and intracellular bacterial pathogens may also contribute to the evolution of virulence in either or both of these groups of organisms. Information on selection patterns and eukaryotic-like status was combined as a novel approach to predict type IV secretion system effectors of Legionella, which represent promising targets for future study.}, } @article {pmid20535601, year = {2010}, author = {Sapp, J}, title = {Saltational symbiosis.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {129}, number = {2-3}, pages = {125-133}, doi = {10.1007/s12064-010-0089-5}, pmid = {20535601}, issn = {1611-7530}, mesh = {Animals ; Archaea/physiology ; Bacterial Physiological Phenomena/genetics ; Bacteriophages/physiology ; *Biological Evolution ; Chloroplasts/physiology ; Fungi/physiology ; Gene Transfer, Horizontal ; Humans ; Mitochondria/pathology ; Organelles/physiology ; Phylogeny ; Plant Physiological Phenomena/genetics ; Selection, Genetic/physiology ; Symbiosis/*physiology ; Virus Physiological Phenomena/genetics ; }, abstract = {Symbiosis has long been associated with saltational evolutionary change in contradistinction to gradual Darwinian evolution based on gene mutations and recombination between individuals of a species, as well as with super-organismal views of the individual in contrast to the classical one-genome: one organism conception. Though they have often been dismissed, and overshadowed by Darwinian theory, suggestions that symbiosis and lateral gene transfer are fundamental mechanisms of evolutionary innovation are borne out today by molecular phylogenetic research. It is time to treat these processes as central principles of evolution.}, } @article {pmid20533948, year = {2010}, author = {Tian, CF and Young, JP and Wang, ET and Tamimi, SM and Chen, WX}, title = {Population mixing of Rhizobium leguminosarum bv. viciae nodulating Vicia faba: the role of recombination and lateral gene transfer.}, journal = {FEMS microbiology ecology}, volume = {73}, number = {3}, pages = {563-576}, doi = {10.1111/j.1574-6941.2010.00909.x}, pmid = {20533948}, issn = {1574-6941}, mesh = {China ; DNA, Bacterial/genetics ; Europe ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Variation ; Genetics, Population ; Genotype ; Geography ; *Phylogeny ; Rhizobium leguminosarum/*genetics ; Sequence Analysis, DNA ; Symbiosis ; Vicia faba/*microbiology ; }, abstract = {The level and mechanisms of population mixing among faba bean (Vicia faba) rhizobia of different geographic origins (three ecoregions of China and several Western countries) were analysed by sequencing three chromosomal housekeeping loci (atpD, recA and glnII) and one nodulation gene (nodD). Eight distinct sublineages of Rhizobium leguminosarum bv. viciae (Rlv) were identified by concatenated sequences of chromosomal loci. structure analysis revealed admixture patterns of Rlv populations of different geographic origins. Recombination, particularly among these chromosomal loci, was revealed to be an important microevolutionary force in shaping the observed genetic diversity and the phylogeny of Rlv. The phylogeny of nodD is largely independent of that of the chromosomal loci, reflecting multiple gene transfers between sublineages and possibly selection imposed by different faba bean gene pools. The dominant nodulation genotype of faba bean rhizobia in the spring growing region of China is identical to the prevalent type of Europe, while the winter growing region of China has another related, but distinct, dominant nodulation genotype. Although several geographically specific sublineages of Rlv were observed, recombination and lateral gene transfer have driven the process of population mixing among different ecoregions of China or between China and countries to the west.}, } @article {pmid20525631, year = {2010}, author = {Stern, A and Mayrose, I and Penn, O and Shaul, S and Gophna, U and Pupko, T}, title = {An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes.}, journal = {Systematic biology}, volume = {59}, number = {2}, pages = {212-225}, doi = {10.1093/sysbio/syp104}, pmid = {20525631}, issn = {1076-836X}, mesh = {Base Composition ; Base Sequence ; Classification/methods ; Computational Biology ; Computer Simulation ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; Thymidylate Synthase/*genetics ; }, abstract = {Thymidylate synthases (Thy) are key enzymes in the synthesis of deoxythymidylate, 1 of the 4 building blocks of DNA. As such, they are essential for all DNA-based forms of life and therefore implicated in the hypothesized transition from RNA genomes to DNA genomes. Two evolutionally unrelated Thy enzymes, ThyA and ThyX, are known to catalyze the same biochemical reaction. Both enzymes are sporadically distributed within each of the 3 domains of life in a pattern that suggests multiple nonhomologous lateral gene transfer (LGT) events. We present a phylogenetic analysis of the evolution of the 2 enzymes, aimed at unraveling their entangled evolutionary history and tracing their origin back to early life. A novel probabilistic evolutionary model was developed, which allowed us to compute the posterior probabilities and the posterior expectation of the number of LGT events. Simulation studies were performed to validate the model's ability to accurately detect LGT events, which have occurred throughout a large phylogeny. Applying the model to the Thy data revealed widespread nonhomologous LGT between and within all 3 domains of life. By reconstructing the ThyA and ThyX gene trees, the most likely donor of each LGT event was inferred. The role of viruses in LGT of Thy is finally discussed.}, } @article {pmid20520734, year = {2010}, author = {Nelson, DM and Cann, IK and Altermann, E and Mackie, RI}, title = {Phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10785}, doi = {10.1371/journal.pone.0010785}, pmid = {20520734}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Gene Transfer, Horizontal/*genetics ; Iguanas/*genetics ; Intestines/*metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood.

We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52% of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT.

CONCLUSION: Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members of the phylum Firmicutes inhabiting the intestinal tract of marine iguanas.}, } @article {pmid20494129, year = {2010}, author = {Holmgren, L}, title = {Horizontal gene transfer: you are what you eat.}, journal = {Biochemical and biophysical research communications}, volume = {396}, number = {1}, pages = {147-151}, doi = {10.1016/j.bbrc.2010.04.026}, pmid = {20494129}, issn = {1090-2104}, mesh = {Aneuploidy ; Animals ; *Apoptosis ; Endodeoxyribonucleases/genetics/metabolism ; Endothelial Cells/metabolism/pathology ; *Gene Transfer, Horizontal ; *Genomic Instability ; Humans ; Mice ; Neoplasms/*genetics/pathology ; Tumor Suppressor Protein p53/metabolism ; Viruses/genetics ; }, abstract = {Horizontal or lateral gene transfer is an effective mechanism for the exchange of genetic information in bacteria allowing bacterial diversification and facilitating adaptation to new environments. Recent data demonstrate that DNA may also be transferred between somatic cells via the uptake of apoptotic bodies. This process allows transfer of viral genes that have been incorporated into the genome in a receptor-independent fashion. Transferred DNA is replicated and propagated in daughter cells in cell that have an inactivated DNA response which may impact tumor progression.}, } @article {pmid20471307, year = {2010}, author = {Rep, M and Kistler, HC}, title = {The genomic organization of plant pathogenicity in Fusarium species.}, journal = {Current opinion in plant biology}, volume = {13}, number = {4}, pages = {420-426}, doi = {10.1016/j.pbi.2010.04.004}, pmid = {20471307}, issn = {1879-0356}, mesh = {Chromosomes, Fungal ; DNA Transposable Elements ; Evolution, Molecular ; Fusarium/*genetics ; Gene Transfer, Horizontal ; *Genome, Fungal ; Humans ; }, abstract = {Comparative genomics is a powerful tool to infer the molecular basis of fungal pathogenicity and its evolution by identifying differences in gene content and genomic organization between fungi with different hosts or modes of infection. Through comparative analysis, pathogenicity-related chromosomes have been identified in Fusarium oxysporum and Fusarium solani that contain genes for host-specific virulence. Lateral transfer of pathogenicity chromosomes, inferred from genomic data, now has been experimentally confirmed. Likewise, comparative genomics reveals the evolutionary relationships among toxin gene clusters whereby the loss and gain of genes from the cluster may be understood in an evolutionary context of toxin diversification. The genomic milieu of effector genes, encoding small secreted proteins, also suggests mechanisms that promote genetic diversification for the benefit of the pathogen.}, } @article {pmid20450979, year = {2010}, author = {Kamikawa, R and Sakaguchi, M and Matsumoto, T and Hashimoto, T and Inagaki, Y}, title = {Rooting for the root of elongation factor-like protein phylogeny.}, journal = {Molecular phylogenetics and evolution}, volume = {56}, number = {3}, pages = {1082-1088}, doi = {10.1016/j.ympev.2010.04.040}, pmid = {20450979}, issn = {1095-9513}, mesh = {Bayes Theorem ; Eukaryota/classification/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Likelihood Functions ; Peptide Elongation Factors/classification/*genetics ; *Phylogeny ; }, abstract = {Lateral gene transfer (LGT) may play a pivotal role in the evolution of elongation factor-like (EFL) genes in eukaryotes. To date, numbers of putative cases for lateral transfer of EFL genes have been postulated based on unrooted EFL phylogenies. Nevertheless, the root position in EFL phylogeny is important to validate lateral EFL gene transfer: for instance, a clade of two EFL homologs from distantly related organisms in an unrooted EFL tree does not necessarily confirm the LGT, since the possibility that the root may locate in this clade cannot be excluded. Cocquyt et al. (2009, p. 39) recently demonstrated that a putative case of lateral EFL gene transfer, which was originally proposed based on an unrooted phylogeny, could not be endorsed by the corresponding rooted analysis. Although rooting EFL phylogeny is indispensable to elucidate various aspects in EFL gene evolution, we suspected that the outgroup clade comprised of EF-1alpha and eukaryote-specific EF-1alpha paralogs erroneously attached to long EFL branches in Cocquyt et al. (2009) - a typical long branch attraction (LBA) artifact. Here, we systematically assessed the putative LBA artifact between the branch leading to the outgroup clade and long ingroup branches by analyzing the original dataset used in Cocquyt et al. (2009) with and without modifying ingroup-sequence sampling. A series of the rooted EFL analyses indicated that the root inference was highly susceptible to presence and absence of long-branched ingroup-sequences, suggesting that the rooted EFL phylogenies cannot be free from severe LBA artifact. We also discussed a new aspect in EFL gene evolution in stramenopiles identified in the course of the EFL analyses described above. Finally, the relative timing of the first emergence of EFL gene in eukaryotes was contemplated based on the current EF-1alpha/EFL distribution.}, } @article {pmid20431015, year = {2010}, author = {Moran, NA and Jarvik, T}, title = {Lateral transfer of genes from fungi underlies carotenoid production in aphids.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5978}, pages = {624-627}, doi = {10.1126/science.1187113}, pmid = {20431015}, issn = {1095-9203}, mesh = {Animals ; Aphids/*genetics/*metabolism/microbiology ; Carotenoids/analysis/*biosynthesis/genetics ; Crosses, Genetic ; Fungi/genetics ; Gene Duplication ; *Gene Transfer, Horizontal ; *Genes, Fungal ; *Genes, Insect ; Genome, Insect ; Heterozygote ; Molecular Sequence Data ; Mutation ; Oxidoreductases/genetics ; Phylogeny ; Pigmentation/genetics ; Pigments, Biological/chemistry ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {Carotenoids are colored compounds produced by plants, fungi, and microorganisms and are required in the diet of most animals for oxidation control or light detection. Pea aphids display a red-green color polymorphism, which influences their susceptibility to natural enemies, and the carotenoid torulene occurs only in red individuals. Unexpectedly, we found that the aphid genome itself encodes multiple enzymes for carotenoid biosynthesis. Phylogenetic analyses show that these aphid genes are derived from fungal genes, which have been integrated into the genome and duplicated. Red individuals have a 30-kilobase region, encoding a single carotenoid desaturase that is absent from green individuals. A mutation causing an amino acid replacement in this desaturase results in loss of torulene and of red body color. Thus, aphids are animals that make their own carotenoids.}, } @article {pmid20401627, year = {2010}, author = {Khan, AA and Shrivastava, A}, title = {Bacterial infections associated with cancer: possible implication in etiology with special reference to lateral gene transfer.}, journal = {Cancer metastasis reviews}, volume = {29}, number = {2}, pages = {331-337}, doi = {10.1007/s10555-010-9217-4}, pmid = {20401627}, issn = {1573-7233}, mesh = {Animals ; Bacteria/*genetics ; Bacterial Infections/*complications/genetics ; *Gene Transfer, Horizontal ; Humans ; Neoplasms/*genetics/*microbiology ; }, abstract = {Bacteria are capable of exchanging DNA between each other and even from other organisms including human, but what will be the fate of such exchange? Enigmatic association between bacterial infections and cancer is also demonstrated recently with unknown exact cause and effect mechanism. This enigma may be resolved not in all but in few cases with the view of horizontal DNA transfer. The present article tries to examine this association in the frame of new idea. This article concludes that knowledge of this association may aid in management of cancer in clinical settings.}, } @article {pmid20335363, year = {2010}, author = {Sagane, Y and Zech, K and Bouquet, JM and Schmid, M and Bal, U and Thompson, EM}, title = {Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans.}, journal = {Development (Cambridge, England)}, volume = {137}, number = {9}, pages = {1483-1492}, doi = {10.1242/dev.044503}, pmid = {20335363}, issn = {1477-9129}, mesh = {Animals ; Cellulose/metabolism ; Chordata/classification/*embryology/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Glucosyltransferases/*genetics/*metabolism ; In Situ Hybridization ; Phylogeny ; Prokaryotic Cells/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Extracellular matrices play important, but poorly investigated, roles in morphogenesis. Extracellular cellulose is central to regulation of pattern formation in plants, but among metazoans only tunicates are capable of cellulose biosynthesis. Cellulose synthase (CesA) gene products are present in filter-feeding structures of all tunicates and also regulate metamorphosis in the ascidian Ciona. Ciona CesA is proposed to have been acquired by lateral gene transfer from a prokaryote. We identified two CesA genes in the sister-class larvacean Oikopleura dioica. Each has a mosaic structure of a glycoslyltransferase 2 domain upstream of a glycosyl hydrolase family 6 cellulase-like domain, a signature thus far unique to tunicates. Spatial-temporal expression analysis revealed that Od-CesA1 produces long cellulose fibrils along the larval tail, whereas Od-CesA2 is responsible for the cellulose scaffold of the post-metamorphic filter-feeding house. Knockdown of Od-CesA1 inhibited cellulose production in the extracellular matrix of the larval tail. Notochord cells either failed to align or were misaligned, the tail did not elongate properly and tailbud embryos also exhibited a failure to hatch. Knockdown of Od-CesA2 did not elicit any of these phenotypes and instead caused a mild delay in pre-house formation. Phylogenetic analyses including Od-CesAs indicate that a single lateral gene transfer event from a prokaryote at the base of the lineage conferred biosynthetic capacity in all tunicates. Ascidians possess one CesA gene, whereas duplicated larvacean genes have evolved distinct temporal and functional specializations. Extracellular cellulose microfibrils produced by the pre-metamorphic Od-CesA1 duplicate have a role in notochord and tail morphogenesis.}, } @article {pmid20180279, year = {2009}, author = {Ragan, MA}, title = {Thinking laterally about genomes.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {23}, number = {1}, pages = {221-222}, pmid = {20180279}, issn = {0919-9454}, mesh = {*Gene Transfer, Horizontal ; *Genome ; }, abstract = {Perhaps the most-surprising discovery of the genome era has been the extent to which prokaryotic and many eukaryotic genomes incorporate genetic material from sources other than their parent(s). Lateral genetic transfer (LGT) among bacteria was first observed about 100 years ago, and is now accepted to underlie important phenomena including the spread of antibiotic resistance and ability to degrade xenobiotics. LGT is invoked, perhaps too readily, to explain a breadth of awkward data including compositional heterogeneity of genomes, disagreement among gene-sequence trees, and mismatch between physiology and systematics. At the same time many details of LGT remain unknown or controversial, and some key questions have scarcely been asked. Here I critically review what we think we know about the existence, extent, mechanism and impact of LGT; identify important open questions; and point to research directions that hold particular promise for elucidating the role of LGT in genome evolution. Evidence for LGT in nature is not only inferential but also direct, and potential vectors are ubiquitous. Genetic material can pass between diverse habitats and be significantly altered during residency in viruses, complicating the inference of donors, In prokaryotes about twice as many genes are interrupted by LGT as are transferred intact, and about 5Short protein domains can be privileged units of transfer. Unresolved phylogenetic issues include the correct null hypothesis, and genes as units of analysis. Themes are beginning to emerge regarding the effect of LGT on cellular networks, but I show why generalization is premature. LGT can associate with radical changes in physiology and ecological niche. Better quantitative models of genome evolution are needed, and theoretical frameworks remain to be developed for some observations including chromosome assembly by LGT.}, } @article {pmid20170524, year = {2010}, author = {Rozhon, W and Petutschnig, E and Khan, M and Summers, DK and Poppenberger, B}, title = {Frequency and diversity of small cryptic plasmids in the genus Rahnella.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {56}, doi = {10.1186/1471-2180-10-56}, pmid = {20170524}, issn = {1471-2180}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Cloning, Molecular ; Gene Transfer, Horizontal ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plasmids/chemistry/genetics/*isolation & purification ; Rahnella/*genetics ; Sequence Alignment ; Vegetables/microbiology ; }, abstract = {BACKGROUND: Rahnella is a widely distributed genus belonging to the Enterobacteriaceae and frequently present on vegetables. Although Rahnella has interesting agro-economical and industrial properties and several strains possess antibiotic resistances and toxin genes which might spread within microbial communities, little is known about plasmids of this genus. Thus, we isolated a number of Rahnella strains and investigated their complements of small plasmids.

RESULTS: In total 53 strains were investigated and 11 plasmids observed. Seven belonged to the ColE1 family; one was ColE2-like and three shared homology to rolling circle plasmids. One of them belonged to the pC194/pUB110 family and two showed similarity to poorly characterised plasmid groups. The G+C content of two rolling circle plasmids deviated considerably from that of Rahnella, indicating that their usual hosts might belong to other genera. Most ColE1-like plasmids formed a subgroup within the ColE1 family that seems to be fairly specific for Rahnella. Intriguingly, the multimer resolution sites of all ColE1-like plasmids had the same orientation with respect to the origin of replication. This arrangement might be necessary to prevent inappropriate synthesis of a small regulatory RNA that regulates cell division. Although the ColE1-like plasmids did not possess any mobilisation system, they shared large parts with high sequence identity in coding and non-coding regions. In addition, highly homologous regions of plasmids isolated from Rahnella and the chromosomes of Erwinia tasmaniensis and Photorhabdus luminescens could be identified.

CONCLUSIONS: For the genus Rahnella we observed plasmid-containing isolates at a frequency of 19%, which is in the average range for Enterobacteriaceae. These plasmids belonged to different groups with members of the ColE1-family most frequently found. Regions of striking sequence homology of plasmids and bacterial chromosomes highlight the importance of plasmids for lateral gene transfer (including chromosomal sequences) to distinct genera.}, } @article {pmid20169193, year = {2010}, author = {Hecht, MM and Nitz, N and Araujo, PF and Sousa, AO and Rosa, Ade C and Gomes, DA and Leonardecz, E and Teixeira, AR}, title = {Inheritance of DNA transferred from American trypanosomes to human hosts.}, journal = {PloS one}, volume = {5}, number = {2}, pages = {e9181}, doi = {10.1371/journal.pone.0009181}, pmid = {20169193}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Animals ; Brazil ; Chagas Disease/*genetics/parasitology ; Child ; DNA, Protozoan/*genetics ; Female ; *Gene Transfer, Horizontal ; Genome, Human/genetics ; Geography ; Host-Parasite Interactions/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Long Interspersed Nucleotide Elements/genetics ; Male ; Middle Aged ; Molecular Sequence Data ; Pedigree ; Recombination, Genetic ; Sequence Analysis, DNA ; Trypanosoma cruzi/*genetics/physiology ; U937 Cells ; Young Adult ; }, abstract = {Interspecies DNA transfer is a major biological process leading to the accumulation of mutations inherited by sexual reproduction among eukaryotes. Lateral DNA transfer events and their inheritance has been challenging to document. In this study we modified a thermal asymmetric interlaced PCR by using additional targeted primers, along with Southern blots, fluorescence techniques, and bioinformatics, to identify lateral DNA transfer events from parasite to host. Instances of naturally occurring human infections by Trypanosoma cruzi are documented, where mitochondrial minicircles integrated mainly into retrotransposable LINE-1 of various chromosomes. The founders of five families show minicircle integrations that were transferred vertically to their progeny. Microhomology end-joining of 6 to 22 AC-rich nucleotide repeats in the minicircles and host DNA mediates foreign DNA integration. Heterogeneous minicircle sequences were distributed randomly among families, with diversity increasing due to subsequent rearrangement of inserted fragments. Mosaic recombination and hitchhiking on retrotransposition events to different loci were more prevalent in germ line as compared to somatic cells. Potential new genes, pseudogenes, and knockouts were identified. A pathway of minicircle integration and maintenance in the host genome is suggested. Thus, infection by T. cruzi has the unexpected consequence of increasing human genetic diversity, and Chagas disease may be a fortuitous share of negative selection. This demonstration of contemporary transfer of eukaryotic DNA to the human genome and its subsequent inheritance by descendants introduces a significant change in the scientific concept of evolutionary biology and medicine.}, } @article {pmid20163713, year = {2010}, author = {Baldo, L and Desjardins, CA and Russell, JA and Stahlhut, JK and Werren, JH}, title = {Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {48}, doi = {10.1186/1471-2148-10-48}, pmid = {20163713}, issn = {1471-2148}, mesh = {Animals ; Arthropods/immunology/microbiology/physiology ; Bacterial Outer Membrane Proteins/chemistry/*genetics/immunology ; *Evolution, Molecular ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {BACKGROUND: Outer membrane proteins (OMPs) of Gram-negative bacteria are key players in the biology of bacterial-host interactions. However, while considerable attention has been given to OMPs of vertebrate pathogens, relatively little is known about the role of these proteins in bacteria that primarily infect invertebrates. One such OMP is found in the intracellular bacteria Wolbachia, which are widespread symbionts of arthropods and filarial nematodes. Recent experimental studies have shown that the Wolbachia surface protein (WSP) can trigger host immune responses and control cell death programming in humans, suggesting a key role of WSP for establishment and persistence of the symbiosis in arthropods.

RESULTS: Here we performed an analysis of 515 unique alleles found in 831 Wolbachia isolates, to investigate WSP structure, microevolution and population genetics. WSP shows an eight-strand transmembrane beta-barrel structure with four extracellular loops containing hypervariable regions (HVRs). A clustering approach based upon patterns of HVR haplotype diversity was used to group similar WSP sequences and to estimate the relative contribution of mutation and recombination during early stages of protein divergence. Results indicate that although point mutations generate most of the new protein haplotypes, recombination is a predominant force triggering diversity since the very first steps of protein evolution, causing at least 50% of the total amino acid variation observed in recently diverged proteins. Analysis of synonymous variants indicates that individual WSP protein types are subject to a very rapid turnover and that HVRs can accommodate a virtually unlimited repertoire of peptides. Overall distribution of WSP across hosts supports a non-random association of WSP with the host genus, although extensive horizontal transfer has occurred also in recent times.

CONCLUSIONS: In OMPs of vertebrate pathogens, large recombination impact, positive selection, reduced structural and compositional constraints, and extensive lateral gene transfer are considered hallmarks of evolution in response to the adaptive immune system. However, Wolbachia do not infect vertebrates. Here we predict that the rapid turnover of WSP loop motifs could aid in evading or inhibiting the invertebrate innate immune response. Overall, these features identify WSP as a strong candidate for future studies of host-Wolbachia interactions that affect establishment and persistence of this widespread endosymbiosis.}, } @article {pmid20132306, year = {2010}, author = {Rosewarne, CP and Pettigrove, V and Stokes, HW and Parsons, YM}, title = {Class 1 integrons in benthic bacterial communities: abundance, association with Tn402-like transposition modules and evidence for coselection with heavy-metal resistance.}, journal = {FEMS microbiology ecology}, volume = {72}, number = {1}, pages = {35-46}, doi = {10.1111/j.1574-6941.2009.00823.x}, pmid = {20132306}, issn = {1574-6941}, mesh = {Aeromonas/drug effects/genetics ; Bacteria/drug effects/*genetics ; Comamonas testosteroni/drug effects/genetics ; *DNA Transposable Elements ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Fresh Water ; Gene Transfer, Horizontal ; Geologic Sediments/chemistry/*microbiology ; Integrases/genetics ; *Integrons ; Metals, Heavy/analysis/*pharmacology ; Polymerase Chain Reaction ; Pseudomonas/drug effects/genetics ; *Selection, Genetic ; Sewage ; Victoria ; Water Pollution ; }, abstract = {The integron/gene cassette system contributes to lateral gene transfer of genetic information in bacterial communities, with gene cassette-encoded proteins potentially playing an important role in adaptation to stress. Class 1 integrons are a particularly important class as they themselves seem to be broadly disseminated among the Proteobacteria and have an established role in the spread of antibiotic resistance genes. The abundance and structure of class 1 integrons in freshwater sediment bacterial communities was assessed through sampling of 30 spatially distinct sites encompassing different substrate and catchment types from the Greater Melbourne Area of Victoria, Australia. Real-time PCR was used to demonstrate that the abundance of intI1 was increased as a result of ecosystem perturbation, indicated by classification of sample locations based on the catchment type and a strong positive correlation with the first principal component factor score, comprised primarily of the heavy metals zinc, mercury, lead and copper. Additionally, the abundance of intI1 at sites located downstream from treated sewage outputs was associated with the percentage contribution of the discharge to the basal flow rate. Characterization of class 1 integrons in bacteria cultured from selected sediment samples identified an association with complete Tn402-like transposition modules, and the potential for coselection of heavy-metal and antibiotic resistance mechanisms in benthic environments.}, } @article {pmid20124348, year = {2010}, author = {Ginger, ML and McFadden, GI and Michels, PA}, title = {Rewiring and regulation of cross-compartmentalized metabolism in protists.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {831-845}, doi = {10.1098/rstb.2009.0259}, pmid = {20124348}, issn = {1471-2970}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {*Biological Evolution ; Eukaryota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Glycolysis ; *Metabolic Networks and Pathways ; Models, Biological ; Organelles/genetics/metabolism ; Plastids/genetics/metabolism ; Symbiosis ; Systems Biology ; Terpenes/metabolism ; Trypanosomatina/genetics/metabolism ; }, abstract = {Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.}, } @article {pmid20090786, year = {2010}, author = {Kenzaka, T and Tani, K and Nasu, M}, title = {High-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level.}, journal = {The ISME journal}, volume = {4}, number = {5}, pages = {648-659}, doi = {10.1038/ismej.2009.145}, pmid = {20090786}, issn = {1751-7370}, mesh = {Bacteriophage P1/genetics ; Bacteriophage T4/genetics ; Bacteriophages/*genetics ; Enterobacteriaceae/*genetics/*virology ; Fresh Water/*microbiology/*virology ; *Gene Transfer, Horizontal ; In Situ Hybridization, Fluorescence ; Japan ; Nucleic Acid Amplification Techniques ; }, abstract = {Lateral gene transfer by phages has contributed significantly to the genetic diversity of bacteria. To accurately determine the frequency and range of phage-mediated gene transfer, it is important to understand the movement of DNA among microbes. Using an in situ DNA amplification technique (cycling primed in situ amplification-fluorescent in situ hybridization; CPRINS-FISH), we examined the propensity for phage-mediated gene transfer in freshwater environments at the single-cell level. Phage P1, T4 and isolated Escherichia coli phage EC10 were used as vectors. All E. coli phages mediated gene transfer from E. coli to both plaque-forming and non-plaque-forming Enterobacteriaceae strains at frequencies of 0.3-8 x 10(-3) per plaque-forming unit (PFU), whereas culture methods using selective agar media could not detect transductants in non-plaque-forming strains. The DNA transfer frequencies through phage EC10 ranged from undetectable to 9 x 10(-2) per PFU (undetectable to 2 x 10(-3) per total direct count) when natural bacterial communities were recipients. Direct viable counting combined with CPRINS-FISH revealed that more than 20% of the cells carrying the transferred gene retained their viability in most cases. These results indicate that the exchange of DNA sequences among bacteria occurs frequently and in a wide range of bacteria, and may promote rapid evolution of the prokaryotic genome in freshwater environments.}, } @article {pmid20087669, year = {2010}, author = {van Iersel, L and Semple, C and Steel, M}, title = {Quantifying the extent of lateral gene transfer required to Avert a 'genome of Eden'.}, journal = {Bulletin of mathematical biology}, volume = {72}, number = {7}, pages = {1783-1798}, doi = {10.1007/s11538-010-9506-7}, pmid = {20087669}, issn = {1522-9602}, mesh = {Algorithms ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; *Models, Genetic ; Prokaryotic Cells/*physiology ; }, abstract = {The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss, and lateral gene transfer (LGT). The extent of LGT, particularly in prokaryotes, and its implications for creating a 'network of life' rather than a 'tree of life' is controversial. In this paper, we formally model the problem of quantifying LGT, and provide exact mathematical bounds, and new computational results. In particular, we investigate the computational complexity of quantifying the extent of LGT under the simple models of gene genesis, loss, and transfer on which a recent heuristic analysis of biological data relied. Our approach takes advantage of a relationship between LGT optimization and graph-theoretical concepts such as tree width and network flow.}, } @article {pmid20075255, year = {2010}, author = {Werren, JH and Richards, S and Desjardins, CA and Niehuis, O and Gadau, J and Colbourne, JK and , and Werren, JH and Richards, S and Desjardins, CA and Niehuis, O and Gadau, J and Colbourne, JK and Beukeboom, LW and Desplan, C and Elsik, CG and Grimmelikhuijzen, CJ and Kitts, P and Lynch, JA and Murphy, T and Oliveira, DC and Smith, CD and van de Zande, L and Worley, KC and Zdobnov, EM and Aerts, M and Albert, S and Anaya, VH and Anzola, JM and Barchuk, AR and Behura, SK and Bera, AN and Berenbaum, MR and Bertossa, RC and Bitondi, MM and Bordenstein, SR and Bork, P and Bornberg-Bauer, E and Brunain, M and Cazzamali, G and Chaboub, L and Chacko, J and Chavez, D and Childers, CP and Choi, JH and Clark, ME and Claudianos, C and Clinton, RA and Cree, AG and Cristino, AS and Dang, PM and Darby, AC and de Graaf, DC and Devreese, B and Dinh, HH and Edwards, R and Elango, N and Elhaik, E and Ermolaeva, O and Evans, JD and Foret, S and Fowler, GR and Gerlach, D and Gibson, JD and Gilbert, DG and Graur, D and Gründer, S and Hagen, DE and Han, Y and Hauser, F and Hultmark, D and Hunter, HC and Hurst, GD and Jhangian, SN and Jiang, H and Johnson, RM and Jones, AK and Junier, T and Kadowaki, T and Kamping, A and Kapustin, Y and Kechavarzi, B and Kim, J and Kim, J and Kiryutin, B and Koevoets, T and Kovar, CL and Kriventseva, EV and Kucharski, R and Lee, H and Lee, SL and Lees, K and Lewis, LR and Loehlin, DW and Logsdon, JM and Lopez, JA and Lozado, RJ and Maglott, D and Maleszka, R and Mayampurath, A and Mazur, DJ and McClure, MA and Moore, AD and Morgan, MB and Muller, J and Munoz-Torres, MC and Muzny, DM and Nazareth, LV and Neupert, S and Nguyen, NB and Nunes, FM and Oakeshott, JG and Okwuonu, GO and Pannebakker, BA and Pejaver, VR and Peng, Z and Pratt, SC and Predel, R and Pu, LL and Ranson, H and Raychoudhury, R and Rechtsteiner, A and Reese, JT and Reid, JG and Riddle, M and Robertson, HM and Romero-Severson, J and Rosenberg, M and Sackton, TB and Sattelle, DB and Schlüns, H and Schmitt, T and Schneider, M and Schüler, A and Schurko, AM and Shuker, DM and Simões, ZL and Sinha, S and Smith, Z and Solovyev, V and Souvorov, A and Springauf, A and Stafflinger, E and Stage, DE and Stanke, M and Tanaka, Y and Telschow, A and Trent, C and Vattathil, S and Verhulst, EC and Viljakainen, L and Wanner, KW and Waterhouse, RM and Whitfield, JB and Wilkes, TE and Williamson, M and Willis, JH and Wolschin, F and Wyder, S and Yamada, T and Yi, SV and Zecher, CN and Zhang, L and Gibbs, RA}, title = {Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.}, journal = {Science (New York, N.Y.)}, volume = {327}, number = {5963}, pages = {343-348}, doi = {10.1126/science.1178028}, pmid = {20075255}, issn = {1095-9203}, support = {R01 GM064864/GM/NIGMS NIH HHS/United States ; R01 GM085163-01/GM/NIGMS NIH HHS/United States ; 5R24GM084917-02/GM/NIGMS NIH HHS/United States ; R01 GM070026-04S1/GM/NIGMS NIH HHS/United States ; R24 GM084917/GM/NIGMS NIH HHS/United States ; R01GM064864/GM/NIGMS NIH HHS/United States ; R01 GM085233/GM/NIGMS NIH HHS/United States ; R01 GM064864-05A2/GM/NIGMS NIH HHS/United States ; R01 AI055624/AI/NIAID NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; R01 GM070026/GM/NIGMS NIH HHS/United States ; //Intramural NIH HHS/United States ; R01 HG000747-14/HG/NHGRI NIH HHS/United States ; R24 GM084917-02/GM/NIGMS NIH HHS/United States ; 5R01HG000747-14/HG/NHGRI NIH HHS/United States ; R01 GM064864-04/GM/NIGMS NIH HHS/United States ; R01 GM085163/GM/NIGMS NIH HHS/United States ; R01 GM079484/GM/NIGMS NIH HHS/United States ; 5R01GM070026-04/GM/NIGMS NIH HHS/United States ; AI028309-13A2/AI/NIAID NIH HHS/United States ; R24 GM084917-01/GM/NIGMS NIH HHS/United States ; U54 HG003273-03/HG/NHGRI NIH HHS/United States ; R01 HG000747/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Arthropods/parasitology ; *Biological Evolution ; DNA Methylation ; DNA Transposable Elements ; Female ; Gene Transfer, Horizontal ; Genes, Insect ; Genetic Speciation ; Genetic Variation ; *Genome, Insect ; Host-Parasite Interactions ; Insect Proteins/genetics/metabolism ; Insect Viruses/genetics ; Insecta/genetics ; Male ; Molecular Sequence Data ; Quantitative Trait Loci ; Recombination, Genetic ; Sequence Analysis, DNA ; Wasp Venoms/chemistry/toxicity ; Wasps/*genetics/physiology ; Wolbachia/genetics ; }, abstract = {We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.}, } @article {pmid20049599, year = {2010}, author = {Farajzadeh, D and Aliasgharzad, N and Sokhandan Bashir, N and Yakhchali, B}, title = {Cloning and characterization of a plasmid encoded ACC deaminase from an indigenous Pseudomonas fluorescens FY32.}, journal = {Current microbiology}, volume = {61}, number = {1}, pages = {37-43}, doi = {10.1007/s00284-009-9573-x}, pmid = {20049599}, issn = {1432-0991}, mesh = {Amino Acids, Cyclic/*metabolism ; Anti-Bacterial Agents/pharmacology ; Carbon-Carbon Lyases/*genetics/*metabolism ; Cloning, Molecular ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/genetics ; Ethylenes/metabolism ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Polymerase Chain Reaction ; Pseudomonas fluorescens/drug effects/*enzymology/*genetics ; Recombinant Fusion Proteins/metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {In addition to the characterized mechanisms responsible for many direct effects of plant growth promoting bacteria (PGPB) on plants, it has been suggested that a number of PGPB contain the enzyme ACC deaminase that catalyzes degradation of 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, into alpha-ketobutyrate and ammonia. As part of an effort to obtain an ACC deaminase encoding gene from a collection of soil samples, only one bacterial isolate, Pseudomonas fluorescens FY32 was capable of growing on ACC as a sole source of nitrogen. The ACC deaminase gene was amplified from the above isolate by polymerase chain reaction (PCR) giving an expected DNA fragment, 1017 bp. Sequence analysis of the fragment showed that it was highly homologous (94% and 98% identities at nucleotide and amino acid levels, respectively) to the previously characterized acdS gene from Pseudomonas sp. 6G5. Furthermore, fusion of the ACC deaminase ORF with lacZ gene resulted in the expression of active enzyme in Escherichia coli. In addition, further analyses revealed that the acdS gene was plasmid-encoded so that a large plasmid (pFY32) with almost 50 kb in size was identified from this bacterium. Furthermore, transfer of pFY32 into E. coli DH5alpha proved its ACC deaminase activity. This result was in accordance with previous reports suggesting horizontal transfer of the acdS gene. However, it needs more investigation to identify whether this pFY32 plasmid has undergone lateral gene transfer during the evolutionary process.}, } @article {pmid19922616, year = {2009}, author = {Pearson, T and Giffard, P and Beckstrom-Sternberg, S and Auerbach, R and Hornstra, H and Tuanyok, A and Price, EP and Glass, MB and Leadem, B and Beckstrom-Sternberg, JS and Allan, GJ and Foster, JT and Wagner, DM and Okinaka, RT and Sim, SH and Pearson, O and Wu, Z and Chang, J and Kaul, R and Hoffmaster, AR and Brettin, TS and Robison, RA and Mayo, M and Gee, JE and Tan, P and Currie, BJ and Keim, P}, title = {Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {78}, doi = {10.1186/1741-7007-7-78}, pmid = {19922616}, issn = {1741-7007}, support = {U54 AI065359/AI/NIAID NIH HHS/United States ; U01AI-075568/AI/NIAID NIH HHS/United States ; U54AI-56359/AI/NIAID NIH HHS/United States ; }, mesh = {Australia ; Burkholderia pseudomallei/*genetics ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal/*physiology ; *Genes, Bacterial ; *Genetics, Population ; Genome, Bacterial ; Humans ; Molecular Epidemiology ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {BACKGROUND: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction.

RESULTS: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia.

CONCLUSION: We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.}, } @article {pmid19915034, year = {2010}, author = {Delorme, C and Bartholini, C and Bolotine, A and Ehrlich, SD and Renault, P}, title = {Emergence of a cell wall protease in the Streptococcus thermophilus population.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {2}, pages = {451-460}, doi = {10.1128/AEM.01018-09}, pmid = {19915034}, issn = {1098-5336}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; Cell Wall/enzymology ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Serine Endopeptidases/*genetics ; Streptococcus thermophilus/classification/*enzymology/genetics ; }, abstract = {Streptococcus thermophilus is perceived as a recently emerged food bacterium that evolved from a commensal ancestor by loss and gain of functions. Here, we provide data allowing a better understanding of this evolutionary scheme. A multilocus sequence typing approach that we developed showed that S. thermophilus diverges significantly from its potential ancestors of the salivarius group and displays a low level of allelic variability, confirming its likely recent emergence. An analysis of the origin and dissemination of the prtS gene was carried out within this evolutionary scheme. This gene encodes a protease that allows better growth in milk by facilitating casein breakdown to supply amino acids. The S. thermophilus protease exhibits 95% identity to the animal Streptococcus suis protein PrtS. Genomic analysis showed that prtS is part of an island flanked by two tandem insertion sequence elements and containing three other genes which present the best identities and synteny with the S. suis genome. These data indicate a potential origin for this "ecological" island in a species closely related to S. suis. The analysis of the distribution of the prtS gene in S. thermophilus showed that the gene is infrequent in historical collections but frequent in recent industrial ones. Moreover, this "ecological" island conferring an important metabolic trait for milk adaptation appears to have disseminated by lateral transfer in the S. thermophilus population. Taken together, these data support an evolutionary scheme of S. thermophilus where gene acquisition and selection by food producers are determining factors. The source and impact of genes acquired by horizontal gene transfer on the physiology and safety of strains should be addressed.}, } @article {pmid19906794, year = {2010}, author = {Chafee, ME and Funk, DJ and Harrison, RG and Bordenstein, SR}, title = {Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations.}, journal = {Molecular biology and evolution}, volume = {27}, number = {3}, pages = {501-505}, doi = {10.1093/molbev/msp275}, pmid = {19906794}, issn = {1537-1719}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01 GM085163-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/*genetics ; Bayes Theorem ; Coleoptera/genetics/*microbiology/virology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Gryllidae/genetics/*microbiology/virology ; Interspersed Repetitive Sequences ; Phylogeny ; Wolbachia/*genetics/virology ; }, abstract = {Lateral transfer of mobile DNA is a hallmark of bacteria with a free-living replicative stage; however, its significance in obligate intracellular bacteria and other heritable endosymbionts remains controversial. Comparative sequence analyses from laboratory stocks infected with Wolbachia pipientis provide some of the most compelling evidence that bacteriophage WO-B transfers laterally between infections of the same insect host. Lateral transfer between coinfections, however, has been evaluated neither in natural populations nor between closely related Wolbachia strains. Here, we analyze bacterial and phage genes from two pairs of natural sympatric field isolates, of Gryllus pennsylvanicus field crickets and of Neochlamisus bebbianae leaf beetles, to demonstrate WO-B transfers between supergroup B Wolbachia. N. bebbianae revealed the highest number of phage haplotypes yet recorded, hinting that lab lines could underestimate phage haplotype variation and lateral transfer. Finally, using the approximate age of insect host species as the maximum available time for phage transfer between host-associated bacteria, we very conservatively estimate phage WO-B transfer to occur at least once every 0-5.4 My within a host species. Increasing discoveries of mobile elements, intragenic recombination, and bacterial coinfections in host-switching obligate intracellular bacteria specify that mobile element transfer is common in these species.}, } @article {pmid19889369, year = {2009}, author = {Lawrence, JG}, title = {Microbial evolution: enforcing cooperation by partial kin selection.}, journal = {Current biology : CB}, volume = {19}, number = {20}, pages = {R943-5}, doi = {10.1016/j.cub.2009.09.045}, pmid = {19889369}, issn = {1879-0445}, mesh = {*Biological Evolution ; Escherichia coli/genetics/metabolism/*physiology ; Escherichia coli Proteins/metabolism/physiology ; Gene Transfer, Horizontal ; *Microbial Interactions ; }, abstract = {How do bacterial cells mediate effective cooperation? A new paper suggests two routes: converting the uninitiated to their cause by lateral gene transfer, and enforcing cooperative behavior by killing revertants.}, } @article {pmid19865522, year = {2009}, author = {Arnold, ML and Fogarty, ND}, title = {Reticulate evolution and marine organisms: the final frontier?.}, journal = {International journal of molecular sciences}, volume = {10}, number = {9}, pages = {3836-3860}, doi = {10.3390/ijms10093836}, pmid = {19865522}, issn = {1422-0067}, mesh = {Animals ; Aquatic Organisms/*genetics ; DNA Transposable Elements ; Diatoms/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Plant ; Genetic Loci ; Genetic Markers ; }, abstract = {The role that reticulate evolution (i.e., via lateral transfer, viral recombination and/or introgressive hybridization) has played in the origin and adaptation of individual taxa and even entire clades continues to be tested for all domains of life. Though falsified for some groups, the hypothesis of divergence in the face of gene flow is becoming accepted as a major facilitator of evolutionary change for many microorganisms, plants and animals. Yet, the effect of reticulate evolutionary change in certain assemblages has been doubted, either due to an actual dearth of genetic exchange among the lineages belonging to these clades or because of a lack of appropriate data to test alternative hypotheses. Marine organisms represent such an assemblage. In the past half-century, some evolutionary biologists interested in the origin and trajectory of marine organisms, particularly animals, have posited that horizontal transfer, introgression and hybrid speciation have been rare. In this review, we provide examples of such genetic exchange that have come to light largely as a result of analyses of molecular markers. Comparisons among these markers and between these loci and morphological characters have provided numerous examples of marine microorganisms, plants and animals that possess the signature of mosaic genomes.}, } @article {pmid19798411, year = {2009}, author = {Nan, J and Brostromer, E and Liu, XY and Kristensen, O and Su, XD}, title = {Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7245}, doi = {10.1371/journal.pone.0007245}, pmid = {19798411}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Computational Biology/*methods ; Crystallography, X-Ray/methods ; Databases, Protein ; Dental Caries/microbiology ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Streptococcus mutans/*metabolism ; }, abstract = {As an oral bacterial pathogen, Streptococcus mutans has been known as the aetiologic agent of human dental caries. Among a total of 1960 identified proteins within the genome of this organism, there are about 500 without any known functions. One of these proteins, SMU.440, has very few homologs in the current protein databases and it does not fall into any protein functional families. Phylogenetic studies showed that SMU.440 is related to a particular ecological niche and conserved specifically in some oral pathogens, due to lateral gene transfer. The co-occurrence of a MarR protein within the same operon among these oral pathogens suggests that SMU.440 may be associated with antibiotic resistance. The structure determination of SMU.440 revealed that it shares the same fold and a similar pocket as polyketide cyclases, which indicated that it is very likely to bind some polyketide-like molecules. From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general approach for functional studies of a protein with unknown function.}, } @article {pmid19780824, year = {2009}, author = {Hu, X and Swiecicka, I and Timmery, S and Mahillon, J}, title = {Sympatric soil communities of Bacillus cereus sensu lato: population structure and potential plasmid dynamics of pXO1- and pXO2-like elements.}, journal = {FEMS microbiology ecology}, volume = {70}, number = {3}, pages = {344-355}, doi = {10.1111/j.1574-6941.2009.00771.x}, pmid = {19780824}, issn = {1574-6941}, mesh = {Bacillus cereus/classification/*genetics/*isolation & purification ; Bacterial Typing Techniques ; Belgium ; Computational Biology ; Conjugation, Genetic ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Genetic Variation ; Plasmids/*genetics ; Replicon ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Eighty soil-borne Bacillus cereus group isolates were collected from two neighbouring geographical sites in Belgium. Their genetic relationships and population structure were assessed using Multilocus sequence typing analysis of five chromosomal genes, while the contribution of extrachromosomal elements to the population dynamics was gauged by the presence, diversity and transfer capacity of pXO1- and pXO2-like plasmids. Globally, the bacterial population displayed a broad diversity, including an important subpopulation of psychrotolerant isolates related to Bacillus weihenstephanensis. pXO1- and pXO2-like replicons were present in 12% and 21% of the isolates, but no Bacillus anthracis-related toxin genes were found. Furthermore, only one of the isolates containing a pXO2-related plasmid was shown to be able to mobilize small non-self-conjugative plasmids. Interestingly, several B. cereus sensu lato isolates displaying the same sequence type were observed to have different plasmid contents, suggesting the occurrence of horizontal gene exchange. Similarly, a number of pXO2-like replicons with identical sequences were found in distinct bacterial isolates, therefore strongly arguing for lateral transfers among sympatric bacteria.}, } @article {pmid19747963, year = {2010}, author = {Novick, P and Smith, J and Ray, D and Boissinot, S}, title = {Independent and parallel lateral transfer of DNA transposons in tetrapod genomes.}, journal = {Gene}, volume = {449}, number = {1-2}, pages = {85-94}, doi = {10.1016/j.gene.2009.08.017}, pmid = {19747963}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; DNA/*genetics ; DNA Primers ; *DNA Transposable Elements ; Gene Transfer, Horizontal ; *Genome ; }, abstract = {In animals, the mode of transmission of transposable elements is generally vertical. However, recent studies have suggested that lateral transfer has occurred repeatedly in several distantly related tetrapod lineages, including mammals. Using transposons extracted from the genome of the lizard Anolis carolinensis as probes, we identified four novel families of hAT transposons that share extremely high similarity with elements in other genomes including several mammalian lineages (primates, chiropters, marsupials), one amphibian and one flatworm, the planarian Schmidtea mediterranea. The discontinuous phylogenetic distribution of these hAT families, coupled with very low synonymous divergence between species, strongly suggests that these elements were laterally transferred to these different species. This indicates that the horizontal transfer of DNA transposons in vertebrates might be more common than previously thought. Yet, it appears that the transfer of DNA transposons did not occur randomly as the same genomes have been invaded independently by different, unrelated transposon families whereas others seem to be immune to lateral transfer. This suggests that some organisms might be intrinsically more vulnerable to DNA transposon lateral transfer, possibly because of a weakened defense against transposons or because they have developed mechanisms to tolerate their impact.}, } @article {pmid19720995, year = {2009}, author = {Chun, J and Grim, CJ and Hasan, NA and Lee, JH and Choi, SY and Haley, BJ and Taviani, E and Jeon, YS and Kim, DW and Lee, JH and Brettin, TS and Bruce, DC and Challacombe, JF and Detter, JC and Han, CS and Munk, AC and Chertkov, O and Meincke, L and Saunders, E and Walters, RA and Huq, A and Nair, GB and Colwell, RR}, title = {Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {36}, pages = {15442-15447}, doi = {10.1073/pnas.0907787106}, pmid = {19720995}, issn = {1091-6490}, support = {N01AI40001/AI/NIAID NIH HHS/United States ; 1R01A139129-01//PHS HHS/United States ; N01-AI-30001/AI/NIAID NIH HHS/United States ; N01-AI-40001/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; Cholera Toxin/genetics ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genomic Islands/genetics ; Genomics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Vibrio cholerae O1/*genetics ; }, abstract = {Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a "shift" between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a "drift" between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.}, } @article {pmid19664294, year = {2009}, author = {Maruyama, S and Matsuzaki, M and Misawa, K and Nozaki, H}, title = {Cyanobacterial contribution to the genomes of the plastid-lacking protists.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {197}, doi = {10.1186/1471-2148-9-197}, pmid = {19664294}, issn = {1471-2148}, mesh = {Animals ; Cyanobacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Fungi/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Fungal ; Genome, Protozoan ; Genomics/methods ; Multigene Family ; Phylogeny ; Plastids/genetics ; }, abstract = {BACKGROUND: Eukaryotic genes with cyanobacterial ancestry in plastid-lacking protists have been regarded as important evolutionary markers implicating the presence of plastids in the early evolution of eukaryotes. Although recent genomic surveys demonstrated the presence of cyanobacterial and algal ancestry genes in the genomes of plastid-lacking protists, comparative analyses on the origin and distribution of those genes are still limited.

RESULTS: We identified 12 gene families with cyanobacterial ancestry in the genomes of a taxonomically wide range of plastid-lacking eukaryotes (Phytophthora [Chromalveolata], Naegleria [Excavata], Dictyostelium [Amoebozoa], Saccharomyces and Monosiga [Opisthokonta]) using a novel phylogenetic pipeline. The eukaryotic gene clades with cyanobacterial ancestry were mostly composed of genes from bikonts (Archaeplastida, Chromalveolata, Rhizaria and Excavata). We failed to find genes with cyanobacterial ancestry in Saccharomyces and Dictyostelium, except for a photorespiratory enzyme conserved among fungi. Meanwhile, we found several Monosiga genes with cyanobacterial ancestry, which were unrelated to other Opisthokonta genes.

CONCLUSION: Our data demonstrate that a considerable number of genes with cyanobacterial ancestry have contributed to the genome composition of the plastid-lacking protists, especially bikonts. The origins of those genes might be due to lateral gene transfer events, or an ancient primary or secondary endosymbiosis before the diversification of bikonts. Our data also show that all genes identified in this study constitute multi-gene families with punctate distribution among eukaryotes, suggesting that the transferred genes could have survived through rounds of gene family expansion and differential reduction.}, } @article {pmid19643761, year = {2009}, author = {Naum, M and Brown, EW and Mason-Gamer, RJ}, title = {Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 10}, pages = {3187-3199}, doi = {10.1099/mic.0.029892-0}, pmid = {19643761}, issn = {1350-0872}, mesh = {Bacterial Proteins/*genetics ; Cluster Analysis ; Conserved Sequence ; DNA, Bacterial/chemistry/genetics ; Enterobacteriaceae/*genetics/isolation & purification ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Membrane Transport Proteins/*genetics ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; Sequence Homology ; Virulence Factors/genetics ; }, abstract = {This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic gamma and beta proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic gamma and beta proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.}, } @article {pmid19639166, year = {2009}, author = {Sinkovics, JG}, title = {Horizontal gene transfers and cell fusions in microbiology, immunology and oncology (Review).}, journal = {International journal of oncology}, volume = {35}, number = {3}, pages = {441-465}, pmid = {19639166}, issn = {1019-6439}, mesh = {Allergy and Immunology ; Animals ; *Cell Fusion ; Cell Transformation, Neoplastic/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Microbiology ; }, abstract = {Evolving young genomes of archaea, prokaryota and unicellular eukaryota were wide open for the acceptance of alien genomic sequences, which they often preserved and vertically transferred to their descendants throughout three billion years of evolution. Established complex large genomes, although seeded with ancestral retroelements, have come to regulate strictly their integrity. However, intruding retroelements, especially the descendents of Ty3/Gypsy, the chromoviruses, continue to find their ways into even the most established genomes. The simian and hominoid-Homo genomes preserved and accommodated a large number of endogenous retroviral genomic segments. These retroelements may mature into exogenous retroviruses, or into functional new genes. Phages and viruses have been instrumental in incorporating and transferring host cell genes. These events profoundly influenced and altered the course of evolution. Horizontal (lateral) gene transfers (HGT) overwhelmed the genomes of the ancient protocells and the evolving unicellular microorganisms, actually leading to their Cambrian explosion. While the rigidly organized genomes of multicellular organisms increasingly resist H/LGT, de-differentiated cells assuming the metabolism of their onto- or phylogenetic ancestors, open up widely to the practice of H/LGT by direct transfer, or to transfers mediated by viruses, or by cell fusions. This activity is intensified in malignantly transformed cells, thus rendering these subjects receptive to therapy with oncolytic viruses and with viral vectors of tumor-suppressive or immunogenic genetic materials. Naturally formed hybrids of dendritic and tumor cells are often tolerogenic, whereas laboratory products of these unisons may be immunogenic in the hosts of origin. As human breast cancer stem cells are induced by a treacherous class of CD8+ T cells to undergo epithelial to mesenchymal (ETM) transition and to yield to malignant transformation by the omnipresent proto-ocogenes (for example, the ras oncogenes), they become defenseless toward oncolytic viruses. Cell fusions and horizontal exchanges of genes are fundamental attributes and inherent characteristics of the living matter.}, } @article {pmid19619164, year = {2009}, author = {Nedelcu, AM and Blakney, AJ and Logue, KD}, title = {Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention.}, journal = {Journal of evolutionary biology}, volume = {22}, number = {9}, pages = {1882-1894}, doi = {10.1111/j.1420-9101.2009.01797.x}, pmid = {19619164}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Cation Transport Proteins/genetics ; Choanoflagellata/*genetics ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; Glutamate Synthase/genetics ; Glutamate-Ammonia Ligase/genetics ; Metabolic Networks and Pathways/*genetics ; }, abstract = {Although lateral gene transfer (LGT) is now recognized as a major force in the evolution of prokaryotes, the contribution of LGT to the evolution and diversification of eukaryotes is less understood. Notably, transfers of complete pathways are believed to be less likely between eukaryotes, because the successful transfer of a pathway requires the physical clustering of functionally related genes. Here, we report that in one of the closest unicellular relatives of animals, the choanoflagellate, Monosiga, three genes whose products work together in the glutamate synthase cycle are of algal origin. The concerted retention of these three independently acquired genes is best explained as the consequence of a series of adaptive replacement events. More generally, this study argues that (i) eukaryote-to-eukaryote transfers of entire metabolic pathways are possible, (ii) adaptive functional replacements of primary pathways can occur, and (iii) functional replacements involving eukaryotic genes are likely to have also contributed to the evolution of eukaryotes. Lastly, these data underscore the potential contribution of algal genes to the evolution of nonphotosynthetic lineages.}, } @article {pmid19614592, year = {2009}, author = {Zámocký, M and Furtmüller, PG and Obinger, C}, title = {Two distinct groups of fungal catalase/peroxidases.}, journal = {Biochemical Society transactions}, volume = {37}, number = {Pt 4}, pages = {772-777}, doi = {10.1042/BST0370772}, pmid = {19614592}, issn = {1470-8752}, support = {P 20996//Austrian Science Fund FWF/Austria ; }, mesh = {Catalase/*classification/genetics ; Computational Biology ; Evolution, Molecular ; Fungal Proteins/*classification/genetics ; Fungi/*enzymology ; Gene Transfer, Horizontal ; Peroxidases/*classification/genetics ; *Phylogeny ; }, abstract = {Catalase/peroxidases (KatGs) are bifunctional haem b-containing (Class I) peroxidases with overwhelming catalase activity and substantial peroxidase activity with various one-electron donors. These unique oxidoreductases evolved in ancestral bacteria revealing a complex gene-duplicated structure. Besides being found in numerous bacteria of all phyla, katG genes were also detected in genomes of lower eukaryotes, most prominently of sac and club fungi. Phylogenetic analysis demonstrates the occurrence of two distinct groups of fungal KatGs that differ in localization, structural and functional properties. Analysis of lateral gene transfer of bacterial katGs into fungal genomes reveals that the most probable progenitor was a katG from a bacteroidetes predecessor. The putative physiological role(s) of both fungal KatG groups is discussed with respect to known structure-function relationships in bacterial KatGs and is related with the acquisition of (phyto)pathogenicity in fungi.}, } @article {pmid19585148, year = {2009}, author = {Vidal, NM and Ludwig, A and Loreto, EL}, title = {Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species.}, journal = {Molecular genetics and genomics : MGG}, volume = {282}, number = {4}, pages = {351-362}, doi = {10.1007/s00438-009-0468-0}, pmid = {19585148}, issn = {1617-4623}, mesh = {Animals ; Drosophilidae/*genetics ; *Evolution, Molecular ; Genetic Variation/physiology ; Phylogeny ; Retroelements/*genetics ; Selection, Genetic ; Species Specificity ; Terminal Repeat Sequences/genetics ; }, abstract = {LTR retrotransposons are the most abundant transposable elements in Drosophila and are believed to have contributed significantly to genome evolution. Different reports have shown that many LTR retrotransposon families in Drosophila melanogaster emerged from recent evolutionary episodes of transpositional activity. To contribute to the knowledge of the evolutionary history of Drosophila LTR retrotransposons and the mechanisms that control their abundance, distribution and diversity, we conducted analyses of four related families of LTR retrotransposons, 297, 17.6, rover and Tom. Our results show that these elements seem to be restricted to species from the D. melanogaster group, except for 17.6, which is also present in D. virilis and D. mojavensis. Genetic divergences and phylogenetic analyses of a 1-kb fragment region of the pol gene illustrate that the evolutionary dynamics of Tom, 297, 17.6 and rover retrotransposons are similar in several aspects, such as low codon bias, the action of purifying selection and phylogenies that are incongruent with those of the host species. We found an extremely complex association among the retrotransposon sequences, indicating that different processes shaped the evolutionary history of these elements, and we detected a very high number of possible horizontal transfer events, corroborating the importance of lateral transmission in the evolution and maintenance of LTR retrotransposons.}, } @article {pmid19577655, year = {2009}, author = {Kamikawa, R and Sanchez-Perez, GF and Sako, Y and Roger, AJ and Inagaki, Y}, title = {Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {53}, number = {2}, pages = {565-570}, doi = {10.1016/j.ympev.2009.06.016}, pmid = {19577655}, issn = {1095-9513}, mesh = {DNA, Algal/genetics ; Diatoms/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Methionine Adenosyltransferase/*genetics ; Models, Genetic ; Multigene Family ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Most eukaryotes possess the highly-conserved enzyme methionine adenosyltransferase (MAT) that produces S-adenosyl-l-methionine, a molecule essential to a variety of cellular processes. However, a recent study revealed that genomes of a very few eukaryote lineages encode a highly divergent type of MAT (called MATX), instead of the canonical MAT enzyme. Since MATX-containing eukaryotes are phylogenetically interspersed with MAT-containing organisms, it is likely that the MATX gene was spread into the MAT-containing groups via multiple eukaryote-to-eukaryote lateral gene transfer events. Here, we further investigate the evolutionary history of these gene families by vastly increasing the sampling of species containing MAT (22 new taxa) and MATX (8 new taxa). Our expanded analyses reveal the first example of lateral transfer of a MAT gene between the pelagophycean alga Aureococcusanophagefferens and a cryptomonad. The increased MATX sampling also provided new insights into the evolution of MATX. Specifically, our MATX phylogeny robustly grouped the haptophyte homologues with the Aureococcus homologue to the exclusion of the diatom homologues, suggesting a transfer of the MATX gene between haptophytes and pelagophytes. Various scenarios of MAT and MATX gene family evolution in diatoms are re-evaluated in light of the new data.}, } @article {pmid19575565, year = {2009}, author = {Andersson, JO}, title = {Gene transfer and diversification of microbial eukaryotes.}, journal = {Annual review of microbiology}, volume = {63}, number = {}, pages = {177-193}, doi = {10.1146/annurev.micro.091208.073203}, pmid = {19575565}, issn = {1545-3251}, mesh = {*Biodiversity ; Cluster Analysis ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {The importance of lateral gene transfer in genome evolution of microbial eukaryotes is slowly being appreciated. Acquisitions of genes have led to metabolic adaptation in diverse eukaryotic lineages. In most cases the metabolic genes have originated from prokaryotes, often followed by sequential transfers between eukaryotes. However, the knowledge of gene transfer in eukaryotes is still mainly based on anecdotal evidence. Some of the observed patterns may be biases in experimental approaches and sequence databases rather than evolutionary trends. Rigorous systematic studies of gene acquisitions that allow for the possibility of exchanges of all categories of genes from all sources are needed to get a more objective view of gene transfer in eukaryote evolution. It may be that the role of gene transfer in the diversification process of microbial eukaryotes currently is underestimated.}, } @article {pmid19571895, year = {2009}, author = {Brazelton, WJ and Baross, JA}, title = {Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm.}, journal = {The ISME journal}, volume = {3}, number = {12}, pages = {1420-1424}, doi = {10.1038/ismej.2009.79}, pmid = {19571895}, issn = {1751-7370}, mesh = {Atlantic Ocean ; *Biodiversity ; *Biofilms ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; *Hot Springs ; *Metagenome ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Transposases/*genetics ; }, abstract = {The carbonate chimneys of the Lost City Hydrothermal Field on the Mid-Atlantic Ridge are coated in thick microbial biofilms consisting of just a few dominant species. We report a preliminary analysis of a biofilm metagenome that revealed a remarkable abundance and diversity of genes potentially involved in lateral gene transfer (LGT). More than 8% of all metagenomic reads showed significant sequence similarity to transposases; all available metagenomic data sets from other environments contained at least an order of magnitude fewer transposases. Furthermore, the sequence diversity of transposase genes in the biofilm was much greater than that of 16S rRNA genes. The small size and high sequencing coverage of contigs containing transposases indicate that they are located on small but abundant extragenomic molecules. These results suggest that rampant LGT among members of the Lost City biofilm may serve as a generator of phenotypic diversity in a community with very low organismal diversity.}, } @article {pmid19571244, year = {2009}, author = {Ragan, MA and Beiko, RG}, title = {Lateral genetic transfer: open issues.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2241-2251}, doi = {10.1098/rstb.2009.0031}, pmid = {19571244}, issn = {1471-2970}, mesh = {*Environment ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.}, } @article {pmid19571242, year = {2009}, author = {Doolittle, WF}, title = {The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2221-2228}, doi = {10.1098/rstb.2009.0032}, pmid = {19571242}, issn = {1471-2970}, mesh = {*Biological Evolution ; Classification/*methods ; Gene Transfer, Horizontal/*genetics ; *Models, Theoretical ; *Phylogeny ; }, abstract = {Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.}, } @article {pmid19571239, year = {2009}, author = {Dagan, T and Martin, W}, title = {Getting a better picture of microbial evolution en route to a network of genomes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {364}, number = {1527}, pages = {2187-2196}, doi = {10.1098/rstb.2009.0040}, pmid = {19571239}, issn = {1471-2970}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Classification/*methods ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; *Phylogeny ; }, abstract = {Most current thinking about evolution is couched in the concept of trees. The notion of a tree with recursively bifurcating branches representing recurrent divergence events is a plausible metaphor to describe the evolution of multicellular organisms like vertebrates or land plants. But if we try to force the tree metaphor onto the whole of the evolutionary process, things go badly awry, because the more closely we inspect microbial genomes through the looking glass of gene and genome sequence comparisons, the smaller the amount of the data that fits the concept of a bifurcating tree becomes. That is mainly because among microbes, endosymbiosis and lateral gene transfer are important, two mechanisms of natural variation that differ from the kind of natural variation that Darwin had in mind. For such reasons, when it comes to discussing the relationships among all living things, that is, including the microbes and all of their genes rather than just one or a select few, many biologists are now beginning to talk about networks rather than trees in the context of evolutionary relationships among microbial chromosomes. But talk is not enough. If we were to actually construct networks instead of trees to describe the evolutionary process, what would they look like? Here we consider endosymbiosis and an example of a network of genomes involving 181 sequenced prokaryotes and how that squares off with some ideas about early cell evolution.}, } @article {pmid19557346, year = {2009}, author = {Han, LL and Wang, ET and Lu, YL and Zhang, YF and Sui, XH and Chen, WF and Chen, WX}, title = {Bradyrhizobium spp. and Sinorhizobium fredii are predominant in root nodules of Vigna angularis, a native legume crop in the subtropical region of China.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {47}, number = {3}, pages = {287-296}, doi = {10.1007/s12275-009-0001-5}, pmid = {19557346}, issn = {1976-3794}, mesh = {Bacterial Proteins/genetics ; Bradyrhizobium/*isolation & purification ; China ; Cluster Analysis ; DNA Fingerprinting/methods ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Evolution, Molecular ; Fabaceae/*microbiology ; Gene Transfer, Horizontal ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Phylogeny ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sinorhizobium fredii/*isolation & purification ; }, abstract = {Adzuki bean (Vigna angularis) is an important legume crop native to China, but its rhizobia have not been well characterized. In the present study, a total of 60 rhizobial strains isolated from eight provinces of China were analyzed with amplified 16S rRNA gene RFLP, IGS-RFLP, and sequencing analyses of 16S rRNA, atpD, recA, and nodC genes. These strains were identified as genomic species within Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, and Ochrobactrum. The most abundant groups were Bradyrhizobium species and Sinorhizobium fredii. Diverse nodC genes were found in these strains, which were mainly co-evolved with the housekeeping genes, but a possible lateral transfer of nodC from Sinorhizobium to Rhizobium was found. Analyses of the genomic and symbiotic gene backgrounds showed that adzuki bean shared the same rhizobial gene pool with soybean (legume native to China) and the exotic Vigna species. All of these data demonstrated that nodule formation is the interaction of rhizobia, host plants, and environment characters.}, } @article {pmid19525398, year = {2009}, author = {Ratmann, O and Andrieu, C and Wiuf, C and Richardson, S}, title = {Model criticism based on likelihood-free inference, with an application to protein network evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {26}, pages = {10576-10581}, doi = {10.1073/pnas.0807882106}, pmid = {19525398}, issn = {1091-6490}, support = {BB/C519670/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Algorithms ; Bacterial Proteins/*genetics/metabolism ; Bayes Theorem ; Computational Biology/methods ; Databases, Protein ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Helicobacter pylori/genetics/metabolism ; Likelihood Functions ; *Models, Biological ; Monte Carlo Method ; Protein Interaction Mapping ; Treponema pallidum/genetics/metabolism ; }, abstract = {Mathematical models are an important tool to explain and comprehend complex phenomena, and unparalleled computational advances enable us to easily explore them without any or little understanding of their global properties. In fact, the likelihood of the data under complex stochastic models is often analytically or numerically intractable in many areas of sciences. This makes it even more important to simultaneously investigate the adequacy of these models-in absolute terms, against the data, rather than relative to the performance of other models-but no such procedure has been formally discussed when the likelihood is intractable. We provide a statistical interpretation to current developments in likelihood-free Bayesian inference that explicitly accounts for discrepancies between the model and the data, termed Approximate Bayesian Computation under model uncertainty (ABCmicro). We augment the likelihood of the data with unknown error terms that correspond to freely chosen checking functions, and provide Monte Carlo strategies for sampling from the associated joint posterior distribution without the need of evaluating the likelihood. We discuss the benefit of incorporating model diagnostics within an ABC framework, and demonstrate how this method diagnoses model mismatch and guides model refinement by contrasting three qualitative models of protein network evolution to the protein interaction datasets of Helicobacter pylori and Treponema pallidum. Our results make a number of model deficiencies explicit, and suggest that the T. pallidum network topology is inconsistent with evolution dominated by link turnover or lateral gene transfer alone.}, } @article {pmid19523153, year = {2009}, author = {Spallek, T and Robatzek, S and Göhre, V}, title = {How microbes utilize host ubiquitination.}, journal = {Cellular microbiology}, volume = {11}, number = {10}, pages = {1425-1434}, doi = {10.1111/j.1462-5822.2009.01346.x}, pmid = {19523153}, issn = {1462-5822}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Host-Pathogen Interactions ; Models, Biological ; *Ubiquitination ; }, abstract = {Activity, abundance and localization of eukaryotic proteins can be regulated through covalent attachment of ubiquitin and ubiquitin-like moieties. Ubiquitination is important in various aspects of immunity. Pathogens utilize host ubiquitination for the suppression of immune signalling and reprogramming host processes to promote microbial life. They deliver so-called effector molecules into host cells, which functionally or structurally resemble components of the host ubiquitination machinery utilizing this enzymatic process or they secrete molecules to inhibit ubiquitin-mediated degradation. Since prokaryotic pathogens lack a classical ubiquitination system, effector mimicry of components of the ubiquitin machinery could be achieved through gene flow. Horizontal gene transfer allows pathogenic bacteria to access ubiquitination enzymes from a potential host, while lateral gene transfer recruits components from another pathogen providing spread within the microbial community. Additionally, convergent evolution can shape bacterial proteins to acquire ubiquitination functions.}, } @article {pmid19485766, year = {2009}, author = {Martínez-Romero, E}, title = {Coevolution in Rhizobium-legume symbiosis?.}, journal = {DNA and cell biology}, volume = {28}, number = {8}, pages = {361-370}, doi = {10.1089/dna.2009.0863}, pmid = {19485766}, issn = {1557-7430}, mesh = {Evolution, Molecular ; Fabaceae/classification/*genetics/microbiology ; Gene Transfer, Horizontal ; Genetic Variation ; Host-Pathogen Interactions ; Rhizobium/classification/*genetics/physiology ; Root Nodules, Plant/genetics/microbiology ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {Legume nodules, specialized structures for nitrogen fixation, are probably the result of coevolution of plants and ancestral rhizobia. Among the evolutionary processes leading to legume radiation and divergence, coevolution with rhizobia might have occurred. Alternatively, bacteria could have been constantly selected by plants, with bacteria slightly influencing plant evolution (required to fulfill the criteria for a coevolutionary hypothesis). Evidence of bacterial effects on plant evolution is scarce but being searched for. Bacterial genetic plasticity may be indicative of the large capacity of Rhizobium to adapt to legumes. Events such as symbiotic replacement, easy recruitment of symbiotic bacteria by legume plants, and lateral transfer of symbiotic genes seem to erase the coevolutionary or selected relationships in rhizobial-legume symbiosis. In particular, the hypotheses proposed are (1) Rhizobium replaced Bradyrhizobium in a few hosts of the Phaseoleae tribe, Phaseolus vulgaris and P. coccineus; (2) Rhizobium etli as a species did not coevolve with bean; and (3) beta-Proteobacteria replaced alpha-Proteobacteria in South American mimosas. Novel results on symbiosis suggest a more complex evolutionary process for nodulation that may include multiple organisms, such as mycorrhiza, nematodes, and other bacteria in addition to rhizobia.}, } @article {pmid19457437, year = {2009}, author = {Filée, J}, title = {Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses.}, journal = {Journal of invertebrate pathology}, volume = {101}, number = {3}, pages = {169-171}, doi = {10.1016/j.jip.2009.03.010}, pmid = {19457437}, issn = {1096-0805}, mesh = {Cytoplasm/*virology ; DNA Viruses/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; }, abstract = {Nucleo Cytoplasmic Large DNA viruses (NCLDVs) are a diverse group that infects a wide range of eukaryotic hosts (for example, vertebrates, insects, protists,...) and also show a huge range in genome size (between 100kb and 1.2Mb). Here I review some recent results that shed light on the origin and genome evolution of these viruses. Current data suggests that NCLDVs could have originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins. Subsequent lateral gene transfer of both cellular genes and diverse families of Mobile Genetic Elements, followed by massive lineage-specific gene duplications is probably responsible for the huge diversity of genome size and composition found in extant NCLDVs.}, } @article {pmid19443855, year = {2009}, author = {Roettger, M and Martin, W and Dagan, T}, title = {A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies.}, journal = {Molecular biology and evolution}, volume = {26}, number = {9}, pages = {1931-1939}, doi = {10.1093/molbev/msp105}, pmid = {19443855}, issn = {1537-1719}, mesh = {*Artificial Intelligence ; *Gene Transfer, Horizontal ; Genome/genetics ; *Phylogeny ; Principal Component Analysis ; Proteins/chemistry ; Sequence Alignment/*methods ; }, abstract = {Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.}, } @article {pmid19416510, year = {2009}, author = {Ros, VI and Hurst, GD}, title = {Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant?.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {20}, doi = {10.1186/1741-7007-7-20}, pmid = {19416510}, issn = {1741-7007}, mesh = {Animals ; Eukaryotic Cells/*cytology/*metabolism ; Gene Transfer, Horizontal/*genetics ; Prokaryotic Cells/*metabolism ; Symbiosis/genetics ; }, abstract = {The expansion of genome sequencing projects has produced accumulating evidence for lateral transfer of genes between prokaryotic and eukaryotic genomes. However, it remains controversial whether these genes are of functional importance in their recipient host. Nikoh and Nakabachi, in a recent paper in BMC Biology, take a first step and show that two genes of bacterial origin are highly expressed in the pea aphid Acyrthosiphon pisum. Active gene expression of transferred genes is supported by three other recent studies. Future studies should reveal whether functional proteins are produced and whether and how these are targeted to the appropriate compartment. We argue that the transfer of genes between host and symbiont may occasionally be of great evolutionary importance, particularly in the evolution of the symbiotic interaction itself.}, } @article {pmid19393086, year = {2009}, author = {Hooper, SD and Mavromatis, K and Kyrpides, NC}, title = {Microbial co-habitation and lateral gene transfer: what transposases can tell us.}, journal = {Genome biology}, volume = {10}, number = {4}, pages = {R45}, doi = {10.1186/gb-2009-10-4-r45}, pmid = {19393086}, issn = {1474-760X}, mesh = {Bacillus cereus/genetics/growth & development ; Bacteria/classification/*genetics/growth & development ; Bacterial Proteins/genetics ; Databases, Genetic ; *Ecosystem ; Escherichia coli/genetics/growth & development ; Fresh Water/microbiology ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Proteobacteria/genetics/growth & development ; Salmonella enterica/genetics/growth & development ; Seawater/microbiology ; Soil Microbiology ; Transposases/genetics ; Water Microbiology ; }, abstract = {BACKGROUND: Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?

RESULTS: All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections.

CONCLUSIONS: We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.}, } @article {pmid19390587, year = {2009}, author = {Koenig, JE and Sharp, C and Dlutek, M and Curtis, B and Joss, M and Boucher, Y and Doolittle, WF}, title = {Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney tar ponds.}, journal = {PloS one}, volume = {4}, number = {4}, pages = {e5276}, doi = {10.1371/journal.pone.0005276}, pmid = {19390587}, issn = {1932-6203}, mesh = {Algorithms ; Bacterial Proteins/*genetics ; Biodegradation, Environmental ; DNA, Bacterial/chemistry ; Gene Transfer, Horizontal ; Genetic Variation ; *Industrial Waste ; Integrons/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; Transcription Factors/*genetics ; Water Microbiology ; }, abstract = {Integrons are genetic platforms that accelerate lateral gene transfer (LGT) among bacteria. They were first detected on plasmids bearing single and multiple drug resistance determinants in human pathogens, and it is abundantly clear that integrons have played a major role in the evolution of this public health menace. Similar genetic elements can be found in nonpathogenic environmental bacteria and in metagenomic environmental DNA samples, and it is reasonable to suppose that integrons have facilitated microbial adaptation through LGT in niches outside infectious disease wards. Here we show that a heavily impacted estuary, exposed for almost a century to products of coal and steel industries, has developed a rich and unique cassette metagenome, containing genes likely to aid in the catabolism of compounds associated with industrial waste found there. In addition, we report that the most abundant cassette recovered in this study is one that encodes a putative LysR protein. This autoregulatory transcriptional regulator is known to activate transcription of linked target genes or unlinked regulons encoding diverse functions including chlorocatechol and dichlorophenol catabolism. Finally, only class 1 integrase genes were amplified in this study despite using different primer sets, and it may be that the cassettes present in the Tar Ponds will prove to be associated with class 1 integrase genes. Nevertheless, our cassette library provides a snapshot of a complex evolutionary process involving integron-meditated LGT likely to be important in natural bioremediation.}, } @article {pmid19389774, year = {2009}, author = {Ishmael, N and Dunning Hotopp, JC and Ioannidis, P and Biber, S and Sakamoto, J and Siozios, S and Nene, V and Werren, J and Bourtzis, K and Bordenstein, SR and Tettelin, H}, title = {Extensive genomic diversity of closely related Wolbachia strains.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 7}, pages = {2211-2222}, doi = {10.1099/mic.0.027581-0}, pmid = {19389774}, issn = {1350-0872}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01-GM085163-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ankyrins/genetics ; Comparative Genomic Hybridization ; DNA, Bacterial/analysis/genetics ; Drosophila melanogaster/*microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Variation ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Species Specificity ; Wolbachia/*genetics ; }, abstract = {Using microarray-based comparative genome hybridization (mCGH), the genomic content of Wolbachia pipientis wMel from Drosophila melanogaster was compared to the closely related Wolbachia from D. innubila (wInn), D. santomea (wSan), and three strains from D. simulans (wAu, wRi, wSim). A large number of auxiliary genes are identified in these five strains, with most absent/divergent genes being unique to a given strain. Each strain caused an average of approximately 60 genes to be removed from the core genome. As such, these organisms do not appear to have the streamlined genomes expected of obligate intracellular bacteria. Prophage, hypothetical and ankyrin repeat genes are over-represented in the absent/divergent genes, with 21-87% of absent/divergent genes coming from prophage regions. The only wMel region absent/divergent in all five query strains is that containing WD_0509 to WD_0511, including a DNA mismatch repair protein MutL-2, a degenerate RNase, and a conserved hypothetical protein. A region flanked by the two portions of the WO-B prophage in wMel is found in four of the five Wolbachia strains as well as on a plasmid of a rickettsial endosymbiont of Ixodes scapularis, suggesting lateral gene transfer between these two obligate intracellular species. Overall, these insect-associated Wolbachia have highly mosaic genomes, with lateral gene transfer playing an important role in their diversity and evolution.}, } @article {pmid19346162, year = {2009}, author = {Kamikawa, R and Masuda, I and Demura, M and Oyama, K and Yoshimatsu, S and Kawachi, M and Sako, Y}, title = {Mitochondrial group II introns in the raphidophycean flagellate Chattonella spp. suggest a diatom-to-Chattonella lateral group II intron transfer.}, journal = {Protist}, volume = {160}, number = {3}, pages = {364-375}, doi = {10.1016/j.protis.2009.02.003}, pmid = {19346162}, issn = {1618-0941}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Protozoan/chemistry/genetics ; Diatoms/*genetics ; Electron Transport Complex IV/*genetics ; Eukaryota/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Protein Structure, Tertiary ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {In the cytochrome c oxidase subunit I (cox1) gene of four raphidophycean flagellates Chattonella antiqua, C. marina, C. ovata, and C. minima we found two group II introns described here as Chattonella cox1-i1 and Chattonella cox1-i2 encoding an open reading frame (ORF) comprised of three domains: reverse transcriptase (RT), RNA maturase (Ma) and zinc finger (H-N-H) endonuclease domains. The secondary structures show both Chattonella cox1-i1 and Chattonella cox1-i2 belong to group IIA1, albeit the former possesses a group IIB-like secondary structural character in the epsilon' region of arm I. Our phylogenetic analysis inferred from RT domain sequences of the intronic ORF, comparison of the insertion sites, and the secondary structures of the introns suggests that Chattonella cox1-i1 likely shares an evolutionary origin with the group II introns inserted in cox1 genes of five phylogenetically diverged eukaryotes. In contrast, Chattonella cox1-i2 was suggested to bear a close evolutionary affinity to the group II introns found in diatom cox1 genes. The RT domain-based phylogeny shows a tree topology in which Chattonella cox1-i2 is nested in the diatom sequences suggesting that a diatom-to-Chattonella intron transfer has taken place. Finally, we found no intron in cox1 genes from deeper-branching raphidophyceans. Based on parsimonious discussion, Chattonella cox1-i1 and Chattonella cox1-i2 have invaded into the cox1 gene of an ancestral Chattonella cell after diverging from C. subsalsa.}, } @article {pmid19331657, year = {2009}, author = {Mihali, TK and Kellmann, R and Neilan, BA}, title = {Characterisation of the paralytic shellfish toxin biosynthesis gene clusters in Anabaena circinalis AWQC131C and Aphanizomenon sp. NH-5.}, journal = {BMC biochemistry}, volume = {10}, number = {}, pages = {8}, doi = {10.1186/1471-2091-10-8}, pmid = {19331657}, issn = {1471-2091}, mesh = {Anabaena/classification/*genetics/metabolism ; Aphanizomenon/classification/*genetics/metabolism ; Australia ; Base Sequence ; Biosynthetic Pathways ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Genes, Bacterial/genetics ; Inverted Repeat Sequences ; Molecular Sequence Data ; Molecular Structure ; *Multigene Family ; Neurotoxins/*biosynthesis/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saxitoxin/*analogs & derivatives/*biosynthesis/chemistry ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Saxitoxin and its analogues collectively known as the paralytic shellfish toxins (PSTs) are neurotoxic alkaloids and are the cause of the syndrome named paralytic shellfish poisoning. PSTs are produced by a unique biosynthetic pathway, which involves reactions that are rare in microbial metabolic pathways. Nevertheless, distantly related organisms such as dinoflagellates and cyanobacteria appear to produce these toxins using the same pathway. Hypothesised explanations for such an unusual phylogenetic distribution of this shared uncommon metabolic pathway, include a polyphyletic origin, an involvement of symbiotic bacteria, and horizontal gene transfer.

RESULTS: We describe the identification, annotation and bioinformatic characterisation of the putative paralytic shellfish toxin biosynthesis clusters in an Australian isolate of Anabaena circinalis and an American isolate of Aphanizomenon sp., both members of the Nostocales. These putative PST gene clusters span approximately 28 kb and contain genes coding for the biosynthesis and export of the toxin. A putative insertion/excision site in the Australian Anabaena circinalis AWQC131C was identified, and the organization and evolution of the gene clusters are discussed. A biosynthetic pathway leading to the formation of saxitoxin and its analogues in these organisms is proposed.

CONCLUSION: The PST biosynthesis gene cluster presents a mosaic structure, whereby genes have apparently transposed in segments of varying size, resulting in different gene arrangements in all three sxt clusters sequenced so far. The gene cluster organizational structure and sequence similarity seems to reflect the phylogeny of the producer organisms, indicating that the gene clusters have an ancient origin, or that their lateral transfer was also an ancient event. The knowledge we gain from the characterisation of the PST biosynthesis gene clusters, including the identity and sequence of the genes involved in the biosynthesis, may also afford the identification of these gene clusters in dinoflagellates, the cause of human mortalities and significant financial loss to the tourism and shellfish industries.}, } @article {pmid19319912, year = {2009}, author = {Boucher, Y and Bapteste, E}, title = {Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {5}, pages = {526-536}, doi = {10.1002/bies.200800216}, pmid = {19319912}, issn = {1521-1878}, mesh = {Gene Transfer, Horizontal/genetics/physiology ; Genetic Variation/genetics ; Models, Theoretical ; Mutation/genetics/physiology ; *Phylogeny ; Prokaryotic Cells/*classification/*metabolism ; }, abstract = {Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of "open lineages" to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with "closed lineages," in which most of the changes are caused by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed.}, } @article {pmid19284579, year = {2009}, author = {Butler, JE and Young, ND and Lovley, DR}, title = {Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {103}, doi = {10.1186/1471-2164-10-103}, pmid = {19284579}, issn = {1471-2164}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/*genetics/metabolism ; *Biological Evolution ; Cluster Analysis ; DNA, Bacterial/genetics ; Deltaproteobacteria/*genetics/metabolism ; Fermentation/*genetics ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration.

RESULTS: In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern Geobacter and Desulfuromonas species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in Pelobacter carbinolicus and Pelobacter propionicus. Furthermore, P. carbinolicus gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the Pelobacter species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the c-type cytochromes required for extracellular electron transfer.

CONCLUSION: The results suggest that Pelobacter species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.}, } @article {pmid19284544, year = {2009}, author = {Nikoh, N and Nakabachi, A}, title = {Aphids acquired symbiotic genes via lateral gene transfer.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {12}, doi = {10.1186/1741-7007-7-12}, pmid = {19284544}, issn = {1741-7007}, mesh = {Amino Acid Sequence ; Animal Structures/metabolism/microbiology ; Animals ; Aphids/cytology/*microbiology ; Buchnera/genetics/*physiology ; Carboxypeptidases/chemistry/genetics ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Order ; Gene Transfer, Horizontal/*genetics ; Lipoprotein(a)/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: Aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist Buchnera aphidicola (gamma-Proteobacteria). Buchnera has lost many of the genes that appear to be essential for bacterial life. From the bacteriocyte of the pea aphid Acyrthosiphon pisum, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. Southern blot analysis demonstrated that they are encoded in the aphid genome. In this study, in order to assess the possibility of lateral gene transfer, we determined the full-length sequences of these transcripts, and performed detailed structural and phylogenetic analyses. We further examined their expression levels in the bacteriocyte using real-time quantitative RT-PCR.

RESULTS: Sequence similarity searches demonstrated that these fully sequenced transcripts are significantly similar to the bacterial genes ldcA (product, LD-carboxypeptidase) and rlpA (product, rare lipoprotein A), respectively. Buchnera lacks these genes, whereas many other bacteria, including Escherichia coli, a close relative of Buchnera, possess both ldcA and rlpA. Molecular phylogenetic analysis clearly demonstrated that the aphid ldcA was derived from a rickettsial bacterium closely related to the extant Wolbachia spp. (alpha-Proteobacteria, Rickettsiales), which are intracellular symbionts of various lineages of arthropods. The evolutionary origin of rlpA was not fully resolved, but it was clearly demonstrated that its double-psi beta-barrel domain is of bacterial origin. Real-time quantitative RT-PCR demonstrated that ldcA and rlpA are expressed 11.6 and 154-fold higher in the bacteriocyte than in the whole body, respectively. LdcA is an enzyme required for recycling murein (peptidoglycan), which is a component of the bacterial cell wall. As Buchnera possesses a cell wall composed of murein but lacks ldcA, a high level of expression of the aphid ldcA in the bacteriocyte may be essential to maintain Buchnera. Although the function of RlpA is not well known, conspicuous up-regulation of the aphid rlpA in the bacteriocyte implies that this gene is also essential for Buchnera.

CONCLUSION: In this study, we obtained several lines of evidence indicating that aphids acquired genes from bacteria via lateral gene transfer and that these genes are used to maintain the obligately mutualistic bacterium, Buchnera.}, } @article {pmid19281950, year = {2009}, author = {Lopez, P and Bapteste, E}, title = {Molecular phylogeny: reconstructing the forest.}, journal = {Comptes rendus biologies}, volume = {332}, number = {2-3}, pages = {171-182}, doi = {10.1016/j.crvi.2008.07.003}, pmid = {19281950}, issn = {1768-3238}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Trees/*physiology ; }, abstract = {Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come.}, } @article {pmid19271186, year = {2009}, author = {Zhaxybayeva, O}, title = {Detection and quantitative assessment of horizontal gene transfer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {195-213}, doi = {10.1007/978-1-60327-853-9_11}, pmid = {19271186}, issn = {1064-3745}, mesh = {Computational Biology ; Databases, Genetic/statistics & numerical data ; *Gene Transfer, Horizontal ; Genomics/*methods/statistics & numerical data ; Models, Genetic ; Phylogeny ; }, abstract = {This chapter discusses the pros and cons of the existing computational methods for the detection of horizontal (or lateral) gene transfer and highlights the genome-wide studies utilizing these methods. The impact of horizontal gene transfer (HGT) on prokaryote genome evolution is discussed.}, } @article {pmid19270122, year = {2009}, author = {Andeer, PF and Stahl, DA and Bruce, NC and Strand, SE}, title = {Lateral transfer of genes for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3258-3262}, doi = {10.1128/AEM.02396-08}, pmid = {19270122}, issn = {1098-5336}, mesh = {Actinomycetales/*genetics/metabolism ; Cytochrome P-450 Enzyme System/*genetics/metabolism ; DNA, Bacterial/chemistry/*genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/*genetics/metabolism ; Phylogeny ; Plasmids ; Rhodococcus/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Triazines/*metabolism ; }, abstract = {Recent studies demonstrated that degradation of the military explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by species of Rhodococcus, Gordonia, and Williamsia is mediated by a novel cytochrome P450 with a fused flavodoxin reductase domain (XplA) in conjunction with a flavodoxin reductase (XplB). Pulse field gel analysis was used to localize xplA to extrachromosomal elements in a Rhodococcus sp. and distantly related Microbacterium sp. strain MA1. Comparison of Rhodococcus rhodochrous 11Y and Microbacterium plasmid sequences in the vicinity of xplB and xplA showed near identity (6,710 of 6,721 bp). Sequencing of the associated 52.2-kb region of the Microbacterium plasmid pMA1 revealed flanking insertion sequence elements and additional genes implicated in RDX uptake and degradation.}, } @article {pmid19229333, year = {2009}, author = {Chan, CX and Darling, AE and Beiko, RG and Ragan, MA}, title = {Are protein domains modules of lateral genetic transfer?.}, journal = {PloS one}, volume = {4}, number = {2}, pages = {e4524}, doi = {10.1371/journal.pone.0004524}, pmid = {19229333}, issn = {1932-6203}, mesh = {Computational Biology/*methods ; Eukaryotic Cells ; Gene Transfer, Horizontal/*genetics ; Genome ; Protein Structure, Tertiary/genetics ; Proteins/*genetics ; Recombination, Genetic ; }, abstract = {BACKGROUND: In prokaryotes and some eukaryotes, genetic material can be transferred laterally among unrelated lineages and recombined into new host genomes, providing metabolic and physiological novelty. Although the process is usually framed in terms of gene sharing (e.g. lateral gene transfer, LGT), there is little reason to imagine that the units of transfer and recombination correspond to entire, intact genes. Proteins often consist of one or more spatially compact structural regions (domains) which may fold autonomously and which, singly or in combination, confer the protein's specific functions. As LGT is frequent in strongly selective environments and natural selection is based on function, we hypothesized that domains might also serve as modules of genetic transfer, i.e. that regions of DNA that are transferred and recombined between lineages might encode intact structural domains of proteins.

We selected 1,462 orthologous gene sets representing 144 prokaryotic genomes, and applied a rigorous two-stage approach to identify recombination breakpoints within these sequences. Recombination breakpoints are very significantly over-represented in gene sets within which protein domain-encoding regions have been annotated. Within these gene sets, breakpoints significantly avoid the domain-encoding regions (domons), except where these regions constitute most of the sequence length. Recombination breakpoints that fall within longer domons are distributed uniformly at random, but those that fall within shorter domons may show a slight tendency to avoid the domon midpoint. As we find no evidence for differential selection against nucleotide substitutions following the recombination event, any bias against disruption of domains must be a consequence of the recombination event per se.

CONCLUSIONS/SIGNIFICANCE: This is the first systematic study relating the units of LGT to structural features at the protein level. Many genes have been interrupted by recombination following inter-lineage genetic transfer, during which the regions within these genes that encode protein domains have not been preferentially preserved intact. Protein domains are units of function, but domons are not modules of transfer and recombination. Our results demonstrate that LGT can remodel even the most functionally conservative modules within genomes.}, } @article {pmid19207744, year = {2009}, author = {Averhoff, B}, title = {Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilus.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {3}, pages = {611-626}, doi = {10.1111/j.1574-6976.2008.00160.x}, pmid = {19207744}, issn = {1574-6976}, mesh = {Bacterial Proteins/metabolism ; DNA, Bacterial/genetics/*metabolism ; Membrane Transport Proteins/metabolism ; Thermus thermophilus/genetics/*physiology ; *Transformation, Bacterial ; }, abstract = {Natural transformation permits the transport of DNA through bacterial membranes and represents a dominant mode for the transfer of genetic information between bacteria and between microorganisms of distant evolutionary lineages and even between members of different domains. This phenomenon, known as horizontal, or lateral, gene transfer, has been a major force for genome plasticity over evolutionary history, and is largely responsible for the spread of fitness-enhancing traits, including antibiotic resistance and virulence factors. In particular, for adaptation of prokaryotes to extreme environments, lateral gene transfer seems to have played a crucial role. Here, we present a survey of the natural transformation machinery of the thermophile Thermus thermophilus HB27. A tentative model of the transformation machinery comprising of components similar to proteins of type IV pili and type II secretion systems is presented. A comparative discussion of the subunits and the structure of the DNA translocator and the underlying mechanism of transfer of free DNA in T. thermophilus highlights conserved and unique features of the DNA translocator in T. thermophilus. We hypothesize that the extraordinary broad substrate specificity and the high efficiency of the T. thermophilus DNA uptake system is of major importance for thermoadaptation and interdomain DNA transfer in hot environments.}, } @article {pmid19207739, year = {2009}, author = {Dorman, CJ and Kane, KA}, title = {DNA bridging and antibridging: a role for bacterial nucleoid-associated proteins in regulating the expression of laterally acquired genes.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {3}, pages = {587-592}, doi = {10.1111/j.1574-6976.2008.00155.x}, pmid = {19207739}, issn = {1574-6976}, mesh = {*Bacterial Physiological Phenomena ; Bacterial Proteins/*metabolism ; Chromosomes, Bacterial/*metabolism ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/*metabolism ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Horizontal DNA transfer plays a major role in the evolution of bacteria. It allows them to acquire new traits rapidly and these may confer fitness advantages as the bacteria compete with others in the environment. Historically, the mechanisms of horizontal DNA transfer, chiefly conjugation, transformation and transduction, have received a great deal of attention. Less attention has been focused on the regulatory problems that may accompany the acquisition of new genes by lateral routes. How are these genes integrated into the existing regulatory circuits of the cell? Does a process of 'plug-and-play' operate, or are the new genes silenced pending the evolution of regulatory mechanisms that make their expression not only safe but also beneficial to both the gene and its new host? Recent research shows that bacterial nucleoid-associated proteins such as H-NS, HU and Fis are important contributors to the processes of regulatory integration that accompany horizontal gene transfer. A key emerging theme is the antagonism that exists between the DNA-protein-DNA bridging activity of the H-NS repressor and the DNA-bending and DNA-wrapping activities of regulatory proteins that oppose H-NS.}, } @article {pmid19207562, year = {2009}, author = {Frickey, T and Kannenberg, E}, title = {Phylogenetic analysis of the triterpene cyclase protein family in prokaryotes and eukaryotes suggests bidirectional lateral gene transfer.}, journal = {Environmental microbiology}, volume = {11}, number = {5}, pages = {1224-1241}, doi = {10.1111/j.1462-2920.2008.01851.x}, pmid = {19207562}, issn = {1462-2920}, support = {AI059577/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*enzymology ; Cluster Analysis ; Eukaryotic Cells/*enzymology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Intramolecular Transferases/*genetics ; Models, Molecular ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Functional constraints to modifications in triterpene cyclase amino acid sequences make them good candidates for evolutionary studies on the phylogenetic relatedness of these enzymes in prokaryotes as well as in eukaryotes. In this study, we used a set of identified triterpene cyclases, a group of mainly bacterial squalene cyclases and a group of predominantly eukaryotic oxidosqualene cyclases, as seed sequences to identify 5288 putative triterpene cyclase homologues in publicly available databases. The Cluster Analysis of Sequences software was used to detect groups of sequences with increased pairwise sequence similarity. The sequences fall into two main clusters, a bacterial and a eukaryotic. The conserved, informative regions of a multiple sequence alignment of the family were used to construct a neighbour-joining phylogenetic tree using the AsaturA and maximum likelihood phylogenetic tree using the PhyML software. Both analyses showed that most of the triterpene cyclase sequences were similarly grouped to the accepted taxonomic relationships of the organism the sequences originated from, supporting the idea of vertical transfer of cyclase genes from parent to offspring as the main evolutionary driving force in this protein family. However, a small group of sequences from three bacterial species (Stigmatella, Gemmata and Methylococcus) grouped with an otherwise purely eukaryotic cluster of oxidosqualene cyclases, while a small group of sequences from seven fungal species and a sequence from the fern Adiantum grouped consistently with a cluster of otherwise purely bacterial squalene cyclases. This suggests that lateral gene transfer may have taken place, entailing a transfer of oxidosqualene cyclases from eukaryotes to bacteria and a transfer of squalene cyclase from bacteria to an ancestor of the group of Pezizomycotina fungi.}, } @article {pmid19195810, year = {2009}, author = {Lu, YL and Chen, WF and Wang, ET and Guan, SH and Yan, XR and Chen, WX}, title = {Genetic diversity and biogeography of rhizobia associated with Caragana species in three ecological regions of China.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {5}, pages = {351-361}, doi = {10.1016/j.syapm.2008.10.004}, pmid = {19195810}, issn = {1618-0984}, mesh = {Bacterial Proteins/analysis/genetics ; Caragana/*microbiology ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Gene Transfer, Horizontal ; *Genetic Variation ; Geography ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Phylogeny ; Proteome/analysis ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/chemistry/*classification/genetics/*isolation & purification ; Sequence Analysis, DNA ; }, abstract = {Twenty-two genospecies belonging mainly to Mesorhizobium, and occasionally to Rhizobium and Bradyrhizobium, were defined among the 174 rhizobia strains isolated from Caragana species. Highly similar nodC genes were found in the sole Bradyrhizobium strain and among all the detected Mesorhizobium strains. A clear correlation between rhizobial genospecies and the eco-regions where they were isolated was found using homogeneity analysis. All these results demonstrated that Caragana species had stringently selected the rhizobia symbiotic genotype, but not the genomic background; lateral transfer of symbiotic genes from Mesorhizobium to Bradyrhizobium and among the Mesorhizobium species has happened in the Caragana rhizobia; and biogeography of Caragana rhizobia exists. Furthermore, a combined cluster analysis, based upon the patterns obtained from amplified 16S rRNA gene and 16S-23S intergenic spacer restriction analyses, BOX PCR and SDS-PAGE of proteins, was reported to be an efficient method to define the genospecies.}, } @article {pmid19168609, year = {2009}, author = {Davies, MR and Shera, J and Van Domselaar, GH and Sriprakash, KS and McMillan, DJ}, title = {A novel integrative conjugative element mediates genetic transfer from group G Streptococcus to other {beta} -hemolytic Streptococci.}, journal = {Journal of bacteriology}, volume = {191}, number = {7}, pages = {2257-2265}, doi = {10.1128/JB.01624-08}, pmid = {19168609}, issn = {1098-5530}, mesh = {Arsenates/pharmacology ; Cadmium/pharmacology ; *Conjugation, Genetic ; Drug Resistance ; *Gene Transfer, Horizontal ; Hemolysis ; *Interspersed Repetitive Sequences ; Molecular Sequence Data ; Multigene Family ; Streptococcal Infections ; Streptococcus/drug effects/*genetics ; }, abstract = {Lateral gene transfer is a significant contributor to the ongoing evolution of many bacterial pathogens, including beta-hemolytic streptococci. Here we provide the first characterization of a novel integrative conjugative element (ICE), ICESde3396, from Streptococcus dysgalactiae subsp. equisimilis (group G streptococcus [GGS]), a bacterium commonly found in the throat and skin of humans. ICESde3396 is 64 kb in size and encodes 66 putative open reading frames. ICESde3396 shares 38 open reading frames with a putative ICE from Streptococcus agalactiae (group B streptococcus [GBS]), ICESa2603. In addition to genes involves in conjugal processes, ICESde3396 also carries genes predicted to be involved in virulence and resistance to various metals. A major feature of ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb internal recombinogenic region containing four unique gene clusters, which appear to have been acquired from streptococcal and nonstreptococcal bacterial species. The four clusters include two cadmium resistance operons, an arsenic resistance operon, and genes with orthologues in a group A streptococcus (GAS) prophage. Streptococci that naturally harbor ICESde3396 have increased resistance to cadmium and arsenate, indicating the functionality of genes present in the 18-kb recombinogenic region. By marking ICESde3396 with a kanamycin resistance gene, we demonstrate that the ICE is transferable to other GGS isolates as well as GBS and GAS. To investigate the presence of the ICE in clinical streptococcal isolates, we screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the presence of three separate regions of ICESde3396. Eleven isolates possessed all three regions, suggesting they harbored ICESde3396-like elements. Another four isolates possessed ICESa2603-like elements. We propose that ICESde3396 is a mobile genetic element that is capable of acquiring DNA from multiple bacterial sources and is a vehicle for dissemination of this DNA through the wider beta-hemolytic streptococcal population.}, } @article {pmid19161360, year = {2009}, author = {Kado, CI}, title = {Horizontal gene transfer: sustaining pathogenicity and optimizing host-pathogen interactions.}, journal = {Molecular plant pathology}, volume = {10}, number = {1}, pages = {143-150}, doi = {10.1111/j.1364-3703.2008.00518.x}, pmid = {19161360}, issn = {1364-3703}, mesh = {Bacteria/*genetics/pathogenicity ; *Gene Transfer, Horizontal ; Genes, Plant ; Plants/*microbiology ; Virulence ; }, abstract = {Successful host-pathogen interactions require the presence, maintenance and expression of gene cassettes called 'pathogenicity islands' (PAIs) and 'metabolic islands' (MAIs) in the respective pathogen. The products of these genes confer on the pathogen the means to recognize their host(s) and to efficiently evade host defences in order to colonize, propagate within the host and eventually disseminate from the host. Virulence effectors secreted by type III and type IV secretion systems, among others, play vital roles in sustaining pathogenicity and optimizing host-pathogen interactions. Complete genome sequences of plant pathogenic bacteria have revealed the presence of PAIs and MAIs. The genes of these islands possess mosaic structures with regions displaying differences in nucleotide composition and codon usage in relation to adjacent genome structures, features that are highly suggestive of their acquisition from a foreign donor. These donors can be other bacteria, as well as lower members of the Archaea and Eukarya. Genes that have moved from the domains Archaea and Eukarya to the domain Bacteria are true cases of horizontal gene transfer. They represent interdomain genetic transfer. Genetic exchange between distinct members of the domain Bacteria, however, represents lateral gene transfer, an intradomain event. Both horizontal and lateral gene transfer events have been used to facilitate survival fitness of the pathogen.}, } @article {pmid19138386, year = {2009}, author = {Hinderhofer, M and Walker, CA and Friemel, A and Stuermer, CA and Möller, HM and Reuter, A}, title = {Evolution of prokaryotic SPFH proteins.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {10}, doi = {10.1186/1471-2148-9-10}, pmid = {19138386}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; Conserved Sequence ; Databases, Protein ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Membrane Proteins/chemistry/*genetics ; Molecular Sequence Data ; Operon ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: The SPFH protein superfamily is a diverse family of proteins whose eukaryotic members are involved in the scaffolding of detergent-resistant microdomains. Recently the origin of the SPFH proteins has been questioned. Instead, convergent evolution has been proposed. However, an independent, convergent evolution of three large prokaryotic and three eukaryotic families is highly unlikely, especially when other mechanisms such as lateral gene transfer which could also explain their distribution pattern have not yet been considered.To gain better insight into this very diverse protein family, we have analyzed the genomes of 497 microorganisms and investigated the pattern of occurrence as well as the genomic vicinity of the prokaryotic SPFH members.

RESULTS: According to sequence and operon structure, a clear division into 12 subfamilies was evident. Three subfamilies (SPFH1, SPFH2 and SPFH5) show a conserved operon structure and two additional subfamilies are linked to those three through functional aspects (SPFH1, SPFH3, SPFH4: interaction with FtsH protease). Therefore these subgroups most likely share common ancestry. The complex pattern of occurrence among the different phyla is indicative of lateral gene transfer. Organisms that do not possess a single SPFH protein are almost exclusively endosymbionts or endoparasites.

CONCLUSION: The conserved operon structure and functional similarities suggest that at least 5 subfamilies that encompass almost 75% of all prokaryotic SPFH members share a common origin. Their similarity to the different eukaryotic SPFH families, as well as functional similarities, suggests that the eukaryotic SPFH families originated from different prokaryotic SPFH families rather than one. This explains the difficulties in obtaining a consistent phylogenetic tree of the eukaryotic SPFH members. Phylogenetic evidence points towards lateral gene transfer as one source of the very diverse patterns of occurrence in bacterial species.}, } @article {pmid19136009, year = {2009}, author = {Guogas, LM and Kennedy, SA and Lee, JH and Redinbo, MR}, title = {A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer.}, journal = {Journal of molecular biology}, volume = {386}, number = {2}, pages = {554-568}, doi = {10.1016/j.jmb.2008.12.057}, pmid = {19136009}, issn = {1089-8638}, support = {R01 AI078924/AI/NIAID NIH HHS/United States ; R01 AI078924-01/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Conjugation, Genetic ; Crystallography, X-Ray ; DNA Helicases/*chemistry/*metabolism ; DNA, Bacterial/*metabolism ; Escherichia coli/*physiology ; Escherichia coli Proteins/*chemistry/*metabolism ; Gene Transfer, Horizontal ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {TraI relaxase-helicase is the central catalytic component of the multiprotein relaxosome complex responsible for conjugative DNA transfer (CDT) between bacterial cells. CDT is a primary mechanism for the lateral propagation of microbial genetic material, including the spread of antibiotic resistance genes. The 2.4-A resolution crystal structure of the C-terminal domain of the multifunctional Escherichia coli F (fertility) plasmid TraI protein is presented, and specific structural regions essential for CDT are identified. The crystal structure reveals a novel fold composed of a 28-residue N-terminal alpha-domain connected by a proline-rich loop to a compact alpha/beta-domain. Both the globular nature of the alpha/beta-domain and the presence as well as rigidity of the proline-rich loop are required for DNA transfer and single-stranded DNA binding. Taken together, these data establish the specific structural features of this noncatalytic domain that are essential to DNA conjugation.}, } @article {pmid19130745, year = {2008}, author = {Sinkovics, JG}, title = {"Up-dating the monograph." [corrected] Cytolytic immune lymphocytes in the armamentarium of the human host.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {55}, number = {4}, pages = {371-382}, doi = {10.1556/AMicr.55.2008.4.2}, pmid = {19130745}, issn = {1217-8950}, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; Herpesviridae/genetics/immunology/physiology ; Host-Pathogen Interactions/*immunology ; Humans ; Immunity, Cellular/genetics ; Immunotherapy, Adoptive ; Interleukin-2 Receptor alpha Subunit/metabolism ; Killer Cells, Natural/*immunology/radiation effects/transplantation ; Lymphocyte Activation ; Membrane Fusion ; Neoplasms/*immunology/therapy/*virology ; Oncolytic Virotherapy ; Oncolytic Viruses/physiology ; Sea Urchins/genetics/virology ; Sharks/genetics/virology ; T-Lymphocytes, Regulatory/immunology/metabolism ; VDJ Recombinases/genetics ; *Virus Physiological Phenomena ; }, abstract = {The author of the monograph "Cytolytic Immune Lymphocytes..." (published in 2008 by Schenk Buchverlag Campus Dialog, Budapest, Passau, Pécs) proposed several research projects and described certain clinical events that require further elaboration and documentation. In this article the author provides what is required and has since become available. The first subject matter in question concerns the fusogenic viruses. The ancient fusogenic viruses might have created the first eukaryotic cell(s) by uniting archaeabacterial and prokaryotic/protobacterial protospheroplasts. Extant fusogenic viruses either produce tumor cell syncytia and lyse them, thus practicing viral oncolysis. Or, create chimaeric fusion products, the so-called "natural hybridomas", of lymphoma cells exhibiting transmembrane budding of retrovirus particles or envelope proteins, and anti-viral specific antibody-producing plasma cells. The second topic concerns the horizontal-lateral mode of acquisition of those genes, which were "present in the waiting" in the amphioxus, sea urchin, and the agnathans, and met in the primitive gnatostomata sharks to encode in unison the entire adaptive immune system. The consensus of opinion is such that these genes derived from newly acquired transposons/retrotransposons. The author points out that the extant Epstein-Barr virus harbors genes displaying sequence homology with those genes from the sharks up to mammals that regulate the somatic hypermutation of specific antibody production. The author proposes that an ancient herpesvirus might have propagated the V(D)J and RAG genes from sea urchins to sharks. The third area is that of lymphocytes cytotoxic/cytolytic to virally infected or malignantly transformed host cells. This discovery led to the adoptive immune lymphocyte therapy of tumors. Installed in the adaptive immune system are regulatory T cells and myeloid-derived suppressor cells for he protection of "self". Tumor cells masquerading as "self" are protected by these cells from attacks launched by immune T cells. The author supports the replacement of IL-2 by IL-15, inasmuch as IL-2 stimulates not only immune T cells, but also regulatory T cells expressing the CD25 IL-2 receptor. The administration of low dose whole body radiotherapy prior to immune lymphocyte therapy increases the efficacy of immune lymphocyte therapy. The author observed this phenomenon in the mid-1960s. The explanation of this phenomenon revealed itself just recently. In pre-irradiated hosts the intestinal wall becomes permeable to the gut flora; the intestinal bacteria activate the entire innate immune system in the mesenteric lymph nodes and a rapid activation of the adaptive immune faculties follows.}, } @article {pmid19124572, year = {2009}, author = {Nesbø, CL and Bapteste, E and Curtis, B and Dahle, H and Lopez, P and Macleod, D and Dlutek, M and Bowman, S and Zhaxybayeva, O and Birkeland, NK and Doolittle, WF}, title = {The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.}, journal = {Journal of bacteriology}, volume = {191}, number = {6}, pages = {1974-1978}, doi = {10.1128/JB.01448-08}, pmid = {19124572}, issn = {1098-5530}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics/isolation & purification ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Lateral gene transfers (LGT) (also called horizontal gene transfers) have been a major force shaping the Thermosipho africanus TCF52B genome, whose sequence we describe here. Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea.}, } @article {pmid19118969, year = {2009}, author = {Stucken, K and Murillo, AA and Soto-Liebe, K and Fuentes-Valdés, JJ and Méndez, MA and Vásquez, M}, title = {Toxicity phenotype does not correlate with phylogeny of Cylindrospermopsis raciborskii strains.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {1}, pages = {37-48}, doi = {10.1016/j.syapm.2008.10.002}, pmid = {19118969}, issn = {0723-2020}, mesh = {Bacterial Toxins ; Cylindrospermopsis/*classification/genetics/*pathogenicity/physiology ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Peptide Synthases/genetics/metabolism ; Phenotype ; *Phylogeny ; Polyketide Synthases/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics/*metabolism ; Sequence Analysis, DNA ; Species Specificity ; Uracil/*analogs & derivatives/metabolism ; }, abstract = {Cylindrospermopsis raciborskii is a species of freshwater, bloom-forming cyanobacterium. C. raciborskii produces toxins, including cylindrospermopsin (hepatotoxin) and saxitoxin (neurotoxin), although non toxin-producing strains are also observed. In spite of differences in toxicity, C. raciborskii strains comprise a monophyletic group, based upon 16S rRNA gene sequence identities (greater than 99%). We performed phylogenetic analyses; 16S rRNA gene and 16S-23S rRNA gene internally transcribed spacer (ITS-1) sequence comparisons, and genomic DNA restriction fragment length polymorphism (RFLP), resolved by pulsed-field gel electrophoresis (PFGE), of strains of C. raciborskii, obtained mainly from the Australian phylogeographic cluster. Our results showed no correlation between toxic phenotype and phylogenetic association in the Australian strains. Analyses of the 16S rRNA gene and the respective ITS-1 sequences (long L, and short S) showed an independent evolution of each ribosomal operon. The genes putatively involved in the cylindrospermopsin biosynthetic pathway were present in one locus and only in the hepatotoxic strains, demonstrating a common genomic organization for these genes and the absence of mutated or inactivated biosynthetic genes in the non toxic strains. In summary, our results support the hypothesis that the genes involved in toxicity may have been transferred as an island by processes of gene lateral transfer, rather than convergent evolution.}, } @article {pmid20333212, year = {2009}, author = {Chan, CX and Beiko, RG and Darling, AE and Ragan, MA}, title = {Lateral transfer of genes and gene fragments in prokaryotes.}, journal = {Genome biology and evolution}, volume = {1}, number = {}, pages = {429-438}, doi = {10.1093/gbe/evp044}, pmid = {20333212}, issn = {1759-6653}, abstract = {Lateral genetic transfer (LGT) involves the movement of genetic material from one lineage into another and its subsequent incorporation into the new host genome via genetic recombination. Studies in individual taxa have indicated lateral origins for stretches of DNA of greatly varying length, from a few nucleotides to chromosome size. Here we analyze 1,462 sets of single-copy, putatively orthologous genes from 144 fully sequenced prokaryote genomes, asking to what extent complete genes and fragments of genes have been transferred and recombined in LGT. Using a rigorous phylogenetic approach, we find evidence for LGT in at least 476 (32.6%) of these 1,462 gene sets: 286 (19.6%) clearly show one or more "observable recombination breakpoints" within the boundaries of the open reading frame, while a further 190 (13.0%) yield trees that are topologically incongruent with the reference tree but do not contain a recombination breakpoint within the open reading frame. We refer to these gene sets as observable recombination breakpoint positive (ORB(+)) and negative (ORB(-)) respectively. The latter are prima facie instances of lateral transfer of an entire gene or beyond. We observe little functional bias between ORB(+) and ORB(-) gene sets, but find that incorporation of entire genes is potentially more frequent in pathogens than in nonpathogens. As ORB(+) gene sets are about 50% more common than ORB(-) sets in our data, the transfer of gene fragments has been relatively frequent, and the frequency of LGT may have been systematically underestimated in phylogenetic studies.}, } @article {pmid19085328, year = {2008}, author = {Beiko, RG and Doolittle, WF and Charlebois, RL}, title = {The impact of reticulate evolution on genome phylogeny.}, journal = {Systematic biology}, volume = {57}, number = {6}, pages = {844-856}, doi = {10.1080/10635150802559265}, pmid = {19085328}, issn = {1076-836X}, mesh = {Classification/*methods ; Computer Simulation ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genetic Variation ; *Genome ; *Phylogeny ; }, abstract = {Genome phylogenies are used to build tree-like representations of evolutionary relationships among genomes. However, in condensing the phylogenetic signals within a set of genomes down to a single tree, these methods generally do not explicitly take into account discordant signals arising due to lateral genetic transfer. Because conflicting vertical and horizontal signals can produce compromise trees that do not reflect either type of history, it is essential to understand the sensitivity of inferred genome phylogenies to these confounding effects. Using replicated simulations of genome evolution, we show that different scenarios of lateral genetic transfer have significant impacts on the ability to recover the "true" tree of genomes, even when corrections for phylogenetically discordant signals are used.}, } @article {pmid19077301, year = {2008}, author = {Cardona, G and Rosselló, F and Valiente, G}, title = {Extended Newick: it is time for a standard representation of phylogenetic networks.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {532}, doi = {10.1186/1471-2105-9-532}, pmid = {19077301}, issn = {1471-2105}, mesh = {Computer Graphics/*standards ; Databases, Genetic ; *Gene Transfer, Horizontal ; *Hybridization, Genetic ; *Phylogeny ; *Software ; }, abstract = {BACKGROUND: Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network).

RESULTS: The standard we advocate as extended Newick format describes a whole phylogenetic network with k hybrid nodes as a single Newick string with k repeated nodes, and this representation is unique once the phylogenetic network is drawn or the ordering among children nodes is fixed. The extended Newick format facilitates phylogenetic data sharing and exchange, and also allows for the practical use of phylogenetic networks in computer programs and scripts. This standard has been recently agreed upon by a number of computational biologists, is already supported by several phylogenetic tools, and avoids the different drawbacks of using an a priori unknown number of Newick strings without any additional mark-up to represent a phylogenetic network.

CONCLUSION: The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetic networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.}, } @article {pmid19047393, year = {2009}, author = {Leikoski, N and Fewer, DP and Sivonen, K}, title = {Widespread occurrence and lateral transfer of the cyanobactin biosynthesis gene cluster in cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {3}, pages = {853-857}, doi = {10.1128/AEM.02134-08}, pmid = {19047393}, issn = {1098-5336}, mesh = {Cyanobacteria/*genetics/*metabolism ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Metabolic Networks and Pathways/*genetics ; *Multigene Family ; Peptides, Cyclic/*biosynthesis ; }, abstract = {Cyanobactins are small cyclic peptides produced by cyanobacteria. Here we demonstrate the widespread but sporadic occurrence of the cyanobactin biosynthetic pathway. We detected a cyanobactin biosynthetic gene in 48 of the 132 strains included in this study. Our results suggest that cyanobactin biosynthetic genes have a complex evolutionary history in cyanobacteria punctuated by a series of ancient horizontal gene transfer events.}, } @article {pmid19037243, year = {2009}, author = {Marchetti, A and Parker, MS and Moccia, LP and Lin, EO and Arrieta, AL and Ribalet, F and Murphy, ME and Maldonado, MT and Armbrust, EV}, title = {Ferritin is used for iron storage in bloom-forming marine pennate diatoms.}, journal = {Nature}, volume = {457}, number = {7228}, pages = {467-470}, doi = {10.1038/nature07539}, pmid = {19037243}, issn = {1476-4687}, mesh = {Binding Sites ; Ceruloplasmin/metabolism ; Crystallography, X-Ray ; Diatoms/chemistry/genetics/growth & development/*metabolism ; *Eutrophication ; Ferritins/*chemistry/genetics/*metabolism ; Gene Transfer, Horizontal ; Iron/deficiency/*metabolism ; Marine Biology ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/analysis/genetics ; Seawater ; }, abstract = {Primary productivity in 30-40% of the world's oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO(2) over geological timescales.}, } @article {pmid19036122, year = {2008}, author = {Filée, J and Pouget, N and Chandler, M}, title = {Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {320}, doi = {10.1186/1471-2148-8-320}, pmid = {19036122}, issn = {1471-2148}, mesh = {Animals ; DNA/metabolism ; DNA Viruses/*classification/*genetics ; Eukaryota/virology ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Phycodnaviridae/genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Nucleo-Cytoplasmic Large DNA viruses (NCLDV), a diverse group that infects a wide range of eukaryotic hosts, exhibit a large heterogeneity in genome size (between 100 kb and 1.2 Mb) but have been suggested to form a monophyletic group on the basis of a small subset of approximately 30 conserved genes. NCLDV were proposed to have evolved by simplification from cellular organism although some of the giant NCLDV have clearly grown by gene accretion from a bacterial origin.

RESULTS: We demonstrate here that many NCLDV lineages appear to have undergone frequent gene exchange in two different ways. Viruses which infect protists directly (Mimivirus) or algae which exist as intracellular protists symbionts (Phycodnaviruses) acquire genes from a bacterial source. Metazoan viruses such as the Poxviruses show a predominant acquisition of host genes. In both cases, the laterally acquired genes show a strong tendency to be positioned at the tip of the genome. Surprisingly, several core genes believed to be ancestral in the family appear to have undergone lateral gene transfers, suggesting that the NCLDV ancestor might have had a smaller genome than previously believed. Moreover, our data show that the larger the genome, the higher is the number of laterally acquired genes. This pattern is incompatible with a genome reduction from a cellular ancestor.

CONCLUSION: We propose that the NCLDV viruses have evolved by significant growth of a simple DNA virus by gene acquisition from cellular sources.}, } @article {pmid19019219, year = {2008}, author = {Tripathi, LP and Sowdhamini, R}, title = {Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {549}, doi = {10.1186/1471-2164-9-549}, pmid = {19019219}, issn = {1471-2164}, mesh = {Carboxypeptidases/genetics ; Cluster Analysis ; Endopeptidase Clp/genetics ; Gene Transfer, Horizontal ; *Genome ; Genomics ; Phylogeny ; Prokaryotic Cells ; Protease La/genetics ; Serine Endopeptidases/*genetics ; Subtilisin/genetics ; Trypsin/genetics ; }, abstract = {BACKGROUND: Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms.

RESULTS: A total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques. Phylogenetic analysis reveals several species-specific clusters of serine proteases suggesting their possible involvement in organism-specific functions. Atypical phylogenetic associations suggest an important role for lateral gene transfer events in facilitating the widespread distribution of the serine proteases in the prokaryotes. Domain organisations of the gene products were analysed, employing sensitive sequence search methods, to infer their probable biological functions. Trypsin, subtilisin and Lon protease families account for a significant proportion of the multi-domain representatives, while the D-Ala-D-Ala carboxypeptidase and the Clp protease families are mostly single-domain polypeptides in prokaryotes. Regulatory domains for protein interaction, signalling, pathogenesis, cell adhesion etc. were found tethered to the serine protease domains. Some domain combinations (such as S1-PDZ; LON-AAA-S16 etc.) were found to be widespread in the prokaryotic lineages suggesting a critical role in prokaryotes.

CONCLUSION: Domain architectures of many serine proteases and their homologues identified in prokaryotes are very different from those observed in eukaryotes, suggesting distinct roles for serine proteases in prokaryotes.