@article {pmid3390124,
year = {1988},
author = {Fasolo, A and Panzica, GC and Viglietti-Panzica, C and Renda, T and D'Este, L},
title = {Comparative chemical anatomy of the brain: concepts and methods.},
journal = {Basic and applied histochemistry},
volume = {32},
number = {1},
pages = {15-30},
pmid = {3390124},
issn = {0391-7258},
mesh = {Anatomy, Comparative/*methods ; Animals ; Brain Chemistry ; Humans ; Immunohistochemistry/methods ; Neuropeptides/analysis/genetics/physiology ; Phylogeny ; },
abstract = {The study of neuropeptides represents an appropriate playground for comparative and evolutionary research. Comparative analysis can give insight into the conservative pattern of intercellular transmission molecules, possibly bound both to some evolutionary antiquity and to cellular constraints. In the same time it can teach us how modulation has occurred at molecular, cellular, multicellular levels in order to give the species-specific functional organization. Using some examples from vertebrate central neurons system (CNS) immunocytochemical analyses, the results so far obtained suggest the rise of a new comparative chemical neuroanatomy. The rationale of "what" and "why" we are comparing is, however, needed in order to understand constancy, heterogeneity or else trends toward complexity in the distribution of neuropeptides.},
}

Anatomy, Comparative/*methods
Animals
Brain Chemistry
Humans
Immunohistochemistry/methods
Neuropeptides/analysis/genetics/physiology
Phylogeny

@article {pmid3902346,
year = {1985},
author = {Vinogradov, SN},
title = {The structure of invertebrate extracellular hemoglobins (erythrocruorins and chlorocruorins).},
journal = {Comparative biochemistry and physiology. B, Comparative biochemistry},
volume = {82},
number = {1},
pages = {1-15},
doi = {10.1016/0305-0491(85)90120-8},
pmid = {3902346},
issn = {0305-0491},
support = {HL 25952/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Erythrocruorins/genetics/*metabolism ; Extracellular Space/metabolism ; Hemeproteins/genetics/*metabolism ; Hemoglobins/*metabolism ; Invertebrates/*metabolism ; Macromolecular Substances ; Oxygen/metabolism ; *Phylogeny ; Protein Binding ; Species Specificity ; Structure-Activity Relationship ; },
abstract = {The knowledge accumulated over the last 30 years concerning the subunit structures of the invertebrate extracellular hemoglobins permits us to classify them into four distinct groups. Single-domain, single-subunit hemoglobins consisting of single, heme-binding polypeptide chains which have a molecular mass of ca. 16 KDa. These molecules are found in multicellular parasitic organisms such as the trematodes Dicrocoelium and Fasciolopsis and in a few insects, namely in the adult Anisops and in the larvae of Chironomus and of Buenoa. Two-domain, multi-subunit hemoglobins consisting of 30-37 KDa polypeptide chains each containing two, linearly connected heme-binding domains, which form polymeric aggregates with molecular masses ranging from 250 to 800 KDa. These hemoglobins are found extensively among the carapaced branchiopod crustaceans: Caenestheria, Daphnia and Lepidurus hemoglobins have been found to consist of 10, 16 and 24 two-domain chains, respectively. Judging from their electron microscopic appearances, some of the hemoglobins may possess different molecular symmetries. Multi-domain, multi-subunit hemoglobins consisting of two or more polypeptide chains, each comprising many heme-binding domains of ca. 15-20 KDa each. Examples of this class are found among the carapaceless branchiopod crustaceans, the planorbid snails and the clams from the families Astartidae and Carditidae. Artemia hemoglobin consists of two chains of ca. 125 KDa, each containing 8 heme-binding domains. Planorbis and Helisoma hemoglobins possess a molecular mass of ca. 1700 KDa and consist of 10 chains of 170-200 KDa. Astarte and Cardita hemoglobins appear in electron micrographs as rod-like polymers of variable dimensions, 20-30 nm in diameter and 20-100 nm in length and consist of polypeptide chains of ca. 300 KDa. The crustacean and gastropod hemoglobins vary in their electron microscopic appearance and may possess different molecular symmetries. Single-domain, multi-subunit hemoglobins consisting of aggregates of several small subunits, some of which are disulfide-bonded and not all of which contain heme. These molecules are widely distributed among the annelids and possibly also among the pogonophores. They are characterized by a two-tiered, hexagonal electron microscopic appearance, with a vertex-to-vertex diameter of 30 nm and a height of 20 nm, an acidic isoelectric point, a sedimentation coefficient of 50-60 S and a low iron content of 0.24 +/- 0.03%.(ABSTRACT TRUNCATED AT 400 WORDS)},
}

Animals
Erythrocruorins/genetics/*metabolism
Extracellular Space/metabolism
Hemeproteins/genetics/*metabolism
Hemoglobins/*metabolism
Invertebrates/*metabolism
Macromolecular Substances
Oxygen/metabolism
*Phylogeny
Protein Binding
Species Specificity
Structure-Activity Relationship

@article {pmid7565716,
year = {1995},
author = {Zhou, K and Takegawa, K and Emr, SD and Firtel, RA},
title = {A phosphatidylinositol (PI) kinase gene family in Dictyostelium discoideum: biological roles of putative mammalian p110 and yeast Vps34p PI 3-kinase homologs during growth and development.},
journal = {Molecular and cellular biology},
volume = {15},
number = {10},
pages = {5645-5656},
pmid = {7565716},
issn = {0270-7306},
support = {CA60559/CA/NCI NIH HHS/United States ; },
mesh = {1-Phosphatidylinositol 4-Kinase ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; Dictyostelium/*enzymology/genetics/growth & development ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Fungal ; Genes, Fungal/*genetics ; Mammals/genetics ; Molecular Sequence Data ; Multigene Family/*genetics ; Phosphatidylinositol 3-Kinases ; Phosphotransferases (Alcohol Group Acceptor)/genetics/*physiology ; Phylogeny ; RNA, Antisense/genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Three groups of phosphatidylinositol (PI) kinases convert PI into PI(3)phosphate, PI(4)phosphate, PI(4,5) bisphosphate, and PI(3,4,5)trisphosphate. These phosphoinositides have been shown to function in vesicle-mediated protein sorting, and they serve as second-messenger signaling molecules for regulating cell growth. To further elucidate the mechanism of regulation and function of phosphoinositides, we cloned genes encoding five putative PI kinases from Dictyostelium discoideum. Database analysis indicates that D. discoideum PIK1 (DdPIK1), -2, and -3 are most closely related to the mammalian p110 PI 3-kinase, DdPIK5 is closest to the yeast Vps34p PI 3-kinase, and DdPIK4 is most homologous to PI 4-kinases. Together with other known PI kinases, a superfamily of PI kinase genes has been defined, with all of the encoded proteins sharing a common highly conserved catalytic core domain. DdPIK1, -2, and -3 may have redundant functions because disruption of any single gene had no effect on D. discoideum growth or development. However, strains in which both of the two most highly related genes, DdPIK1 and DdPIK2, were disrupted showed both growth and developmental defects, while double knockouts of DdPIK1 and DdPIK3 and DdPIK2 and DdPIK3 appear to be lethal. The delta Ddpik1 delta Ddpik2 null cells were smaller than wild-type cells and grew slowly both in association with bacteria and in axenic medium when attached to petri plates but were unable to grow in suspension in axenic medium. When delta Ddpik1 delta Ddpik2 null cells were plated for multicellular development, they formed aggregates having multiple tips and produced abnormal fruiting bodies. Antisense expression of DdPIK5 (a putative homolog of the Saccharomyces cerevisiae VPS34) led to a defect in the growth of D. discoideum cells on bacterial lawns and abnormal development. DdPIK5 complemented the temperature-sensitive growth defect of a Schizosaccharomyces pombe delta Svps34 mutant strain, suggesting DdPIK5 encodes a functional homolog of yeast Vps34p. These observations indicate that in D. discoideum, different PI kinases regulate distinct cellular processes, including cell growth, development, and protein trafficking.},
}

1-Phosphatidylinositol 4-Kinase
Amino Acid Sequence
Animals
Base Sequence
Cloning, Molecular
Conserved Sequence
Dictyostelium/*enzymology/genetics/growth & development
Gene Expression Regulation, Developmental
Gene Expression Regulation, Fungal
Genes, Fungal/*genetics
Mammals/genetics
Molecular Sequence Data
Multigene Family/*genetics
Phosphatidylinositol 3-Kinases
Phosphotransferases (Alcohol Group Acceptor)/genetics/*physiology
Phylogeny
RNA, Antisense/genetics
*Saccharomyces cerevisiae Proteins
Sequence Analysis, DNA
Sequence Homology, Amino Acid

@article {pmid7906442,
year = {1993},
author = {Shenk, MA and Steele, RE},
title = {A molecular snapshot of the metazoan 'Eve'.},
journal = {Trends in biochemical sciences},
volume = {18},
number = {12},
pages = {459-463},
doi = {10.1016/0968-0004(93)90003-6},
pmid = {7906442},
issn = {0968-0004},
mesh = {Animals ; Cell Communication/genetics/physiology ; Cnidaria/*genetics ; Drosophila ; Extracellular Matrix Proteins/genetics/physiology ; Molecular Biology ; *Phylogeny ; Signal Transduction/genetics/physiology ; Transcription Factors/genetics/physiology ; },
abstract = {A description of the molecular make-up of the ancestral multicellular animal is emerging from the growing availability of molecular biological and biochemical data gleaned from the study of modern members of ancient groups of animals. We use the distributions of classes of transcription factors, signal transduction systems and other molecular innovations among metazoan phyla to infer some of the characteristics of the first animals.},
}

Animals
Cell Communication/genetics/physiology
Cnidaria/*genetics
Drosophila
Extracellular Matrix Proteins/genetics/physiology
Molecular Biology
*Phylogeny
Signal Transduction/genetics/physiology
Transcription Factors/genetics/physiology

@article {pmid8078481,
year = {1994},
author = {Prade, RA and Timberlake, WE},
title = {The Penicillium chrysogenum and Aspergillus nidulans wetA developmental regulatory genes are functionally equivalent.},
journal = {Molecular & general genetics : MGG},
volume = {244},
number = {5},
pages = {539-547},
pmid = {8078481},
issn = {0026-8925},
support = {GM37886/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Aspergillus nidulans/*genetics/physiology ; Base Sequence ; Conserved Sequence ; DNA Mutational Analysis ; DNA Primers ; DNA, Fungal/genetics ; Fungal Proteins/chemistry/genetics ; *Gene Expression Regulation, Fungal ; *Genes, Fungal ; Genes, Regulator ; Molecular Sequence Data ; Morphogenesis ; Penicillium chrysogenum/*genetics/physiology ; Phylogeny ; Promoter Regions, Genetic ; Spores, Fungal/cytology/*growth & development ; },
abstract = {Aspergillus nidulans and Penicillium chrysogenum are related fungi that reproduce asexually by forming multicellular conidiophores and uninucleate conidia. In A. nidulans, spore maturation is controlled by the wetA (AwetA) regulatory gene. We cloned a homologous gene (PwetA) from P. chrysogenum to determine if spore maturation is regulated by a similar mechanism in this species. The PwetA and AwetA genes are similar in structure and functional organization. The inferred polypeptides share 77% overall amino acid sequence similarity, with several regions having > 85% similarity. The genes also had significant, local sequence similarities in their 5' flanking regions, including conserved binding sites for the product of the regulatory gene abaA. PwetA fully complemented an A. nidulans wetA deletion mutation, demonstrating that PwetA and its 5' regulatory sequences function normally in A. nidulans. These results indicate that the mechanisms controlling sporulation in A. nidulans and P. chrysogenum are evolutionarily conserved.},
}

Amino Acid Sequence
Aspergillus nidulans/*genetics/physiology
Base Sequence
Conserved Sequence
DNA Mutational Analysis
DNA Primers
DNA, Fungal/genetics
Fungal Proteins/chemistry/genetics
*Gene Expression Regulation, Fungal
*Genes, Fungal
Genes, Regulator
Molecular Sequence Data
Morphogenesis
Penicillium chrysogenum/*genetics/physiology
Phylogeny
Promoter Regions, Genetic
Spores, Fungal/cytology/*growth & development

@article {pmid8364691,
year = {1993},
author = {West, L and Powers, D},
title = {Molecular phylogenetic position of hexactinellid sponges in relation to the Protista and Demospongiae.},
journal = {Molecular marine biology and biotechnology},
volume = {2},
number = {2},
pages = {71-75},
pmid = {8364691},
issn = {1053-6426},
mesh = {Animals ; Base Sequence ; DNA, Ribosomal/chemistry/isolation & purification ; Eukaryota/*classification/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Porifera/*classification/genetics ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Although it is generally accepted that the first multicellular organisms arose from unicellular ancestors, the phylogenetic relationships linking these groups remain unclear. Anatomical, physiological, and molecular studies of current multicellular organisms with relatively simple body organization suggest key characteristics of the earliest multicellular lineages. Glass sponges, the Hexactinellida, possess cellular characteristics that resemble some unicellular protistan organisms. These unique sponges were abundant in shallow seas of the early Cambrian, but they are currently restricted to polar habitats or very deep regions of the world oceans. Due in part to their relative inaccessibility, their potential significance to the early phylogeny of the eukaryotic kingdoms has been largely overlooked. We used sequences of the 18s ribosomal RNA gene of Farrea occa, a representative of the deep-water hexactinellid sponges, and Coelocarteria singaporense, a representative of the more common demosponges, and compared them with selected ribosomal RNA gene sequences available within the Protista. Using four computational methods for phylogenetic analysis of ribosomal DNA sequences, we found that the hexactinellid sponge-demosponge cluster is most closely related to Volvox and Acanthamoeba.},
}

Animals
Base Sequence
DNA, Ribosomal/chemistry/isolation & purification
Eukaryota/*classification/genetics
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
Porifera/*classification/genetics
RNA, Ribosomal, 18S/genetics

@article {pmid8541419,
year = {1995},
author = {Katayama, T and Wada, H and Furuya, H and Satoh, N and Yamamoto, M},
title = {Phylogenetic position of the dicyemid mesozoa inferred from 18S rDNA sequences.},
journal = {The Biological bulletin},
volume = {189},
number = {2},
pages = {81-90},
doi = {10.2307/1542458},
pmid = {8541419},
issn = {0006-3185},
mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Ribosomal/*genetics ; Invertebrates/*classification/genetics ; Molecular Sequence Data ; Mollusca/parasitology ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Homology, Nucleic Acid ; Symbiosis ; },
abstract = {The dicyemid mesozoa, obligate symbionts in the cephalopod kidney, are simply organized multicellular animals. They have long been the subject of phylogenetic debates. Some authors have suggested that dicyemids represent an offshoot from an early metazoan ancestor. Other workers considered them to be degenerated progeny of higher metazoa, possibly parasitic trematodes. We determined the almost complete nucleotide sequences of 18S rDNA in two species of dicyemid, Dicyema orientale and Dicyema acuticephalum, isolated purely from cephalopod urine. We compared these sequences with sequences determined in the present study from three flatworm species, as well as with a variety of eukaryote sequences obtained from databases. The phylogenetic trees reconstructed with the use of the neighbor-joining, maximum-parsimony, and maximum-likelihood methods indicated that the dicyemids belong among the triploblastic animals (Bilateria). However, we cannot firmly establish the position of the dicyemids within the Bilateria because we cannot ignore the problem of long branch attraction between the myxozoans, dicyemids, nematodes, and acoel flatworms. The present results favor the hypothesis that the dicyemids do not represent an early divergent metazoan group, but rather a group degenerated from a triploblastic ancestor.},
}

Animals
Base Sequence
DNA Primers
DNA, Ribosomal/*genetics
Invertebrates/*classification/genetics
Molecular Sequence Data
Mollusca/parasitology
Phylogeny
RNA, Ribosomal, 18S/*genetics
Sequence Homology, Nucleic Acid
Symbiosis

@article {pmid8590468,
year = {1995},
author = {Bouget, FY and Kerbourc'h, C and Liaud, MF and Loiseaux de Goër, S and Quatrano, RS and Cerff, R and Kloareg, B},
title = {Structural features and phylogeny of the actin gene of Chondrus crispus (Gigartinales, Rhodophyta).},
journal = {Current genetics},
volume = {28},
number = {2},
pages = {164-172},
pmid = {8590468},
issn = {0172-8083},
mesh = {Actins/*genetics ; Amino Acid Sequence ; Base Sequence ; Blotting, Southern ; DNA, Complementary ; Molecular Sequence Data ; *Phylogeny ; Rhodophyta/*genetics ; Sequence Homology, Amino Acid ; },
abstract = {We have characterized the cDNA and genomic sequences that encode actin from the multicellular red alga Chondrus crispus. Southern-blot analysis indicates that the C. crispus actin gene (ChAc) is present as a single copy. Northern analysis shows that, like the GapA gene, the actin gene is well expressed in gametophytes but weakly in protoplasts. Compared to actin genes of animals, fungi, green plants and oomycetes, that of C. crispus displays a higher evolutionary rate and does not show any of the amino-acid signatures characteristic of the other lineages. As previously described for GapA, ChAc is interrupted by a single intron at the beginning of the coding region. The site of initiation of transcription was characterized by RNAse protection. The promoter region displays a CAAT box but lacks a canonical TATA motif. Other noticeable features, such as a high content of pyrimidines as well as a 14-nt motif found in both the 5'-untranslated region and the intron, were observed.},
}

Actins/*genetics
Amino Acid Sequence
Base Sequence
Blotting, Southern
DNA, Complementary
Molecular Sequence Data
*Phylogeny
Rhodophyta/*genetics
Sequence Homology, Amino Acid

@article {pmid8995053,
year = {1996},
author = {Marinets, A and Müller, M and Johnson, PJ and Kulda, J and Scheiner, O and Wiedermann, G and Duchêne, M},
title = {The sequence and organization of the core histone H3 and H4 genes in the early branching amitochondriate protist Trichomonas vaginalis.},
journal = {Journal of molecular evolution},
volume = {43},
number = {6},
pages = {563-571},
pmid = {8995053},
issn = {0022-2844},
support = {AI11942/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Complementary/genetics ; Genome ; Histones/*genetics/physiology ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/*genetics/physiology ; },
abstract = {Among the unicellular protists, several of which are parasitic, some of the most divergent eukaryotic species are found. The evolutionary distances between protists are so large that even slowly evolving proteins like histones are strongly divergent. In this study we isolated cDNA and genomic histone H3 and H4 clones from Trichomonas vaginalis. Two histone H3 and three histone H4 genes were detected on three genomic clones with one complete H3 and two complete H4 sequences. H3 and H4 genes were divergently transcribed with very short intergenic regions of only 194 bp, which contained T. vaginalis-specific as well as histone-specific putative promoter elements. Southern blot analysis showed that there may be several more histone gene pairs. The two complete histone H4 genes were different on the nucleotide level but encoded the same amino acid sequence. Comparison of the amino acid sequences of the T. vaginalis H3 and H4 histones with sequences from animals, fungi, and plants as well as other protists revealed a significant divergence not only from the sequences in multicellular organisms but especially from the sequences in other protists like Entamoeba histolytica, Trypanosoma cruzi, and Leishmania infantum.},
}

Amino Acid Sequence
Animals
Base Sequence
Blotting, Southern
Cloning, Molecular
DNA, Complementary/genetics
Genome
Histones/*genetics/physiology
Molecular Sequence Data
*Phylogeny
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Trichomonas vaginalis/*genetics/physiology

@article {pmid9175266,
year = {1996},
author = {Boute, N and Exposito, JY and Boury-Esnault, N and Vacelet, J and Noro, N and Miyazaki, K and Yoshizato, K and Garrone, R},
title = {Type IV collagen in sponges, the missing link in basement membrane ubiquity.},
journal = {Biology of the cell},
volume = {88},
number = {1-2},
pages = {37-44},
doi = {10.1016/s0248-4900(97)86829-3},
pmid = {9175266},
issn = {0248-4900},
mesh = {Amino Acid Sequence ; Animals ; Basement Membrane/chemistry ; Cloning, Molecular ; Collagen/*analysis ; DNA, Complementary/isolation & purification ; Genome ; Humans ; Molecular Sequence Data ; Oligonucleotide Probes ; Phylogeny ; Porifera/*chemistry ; Species Specificity ; },
abstract = {Basement membrane structures, or their main component, type IV collagen, have been detected in all multicellular animal species, except sponges. We cancel this exception by the demonstration of type IV collagenous sequences in a new marine sponge species by cDNA and genomic DNA studies. One of these sequences is long enough to demonstrate the specific characteristics of type IV collagen chains. The 12 cysteines are at conserved positions in the carboxyl-terminal non-helical NCl domain, as are the interruptions in the carboxyl-terminal end of the triple helical domain. The gene organization of the region coding for the NCl domain is similar to that of the human genes COL4A2, COL4A4 and COL4A6. An additional, shorter sequence suggests the presence of a second chain. The expected tissue localization of this collagen has been confirmed using polyclonal antibodies raised against a sponge recombinant protein. These results demonstrate that type IV collagen is representated in all animal phyla. It is actually the only known ubiquitous collagen and it has at least two different alpha chains in all the species where it has been characterized.},
}

Amino Acid Sequence
Animals
Basement Membrane/chemistry
Cloning, Molecular
Collagen/*analysis
DNA, Complementary/isolation & purification
Genome
Humans
Molecular Sequence Data
Oligonucleotide Probes
Phylogeny
Porifera/*chemistry
Species Specificity

@article {pmid9406022,
year = {1997},
author = {Cassone, VM and Natesan, AK},
title = {Time and time again: the phylogeny of melatonin as a transducer of biological time.},
journal = {Journal of biological rhythms},
volume = {12},
number = {6},
pages = {489-497},
doi = {10.1177/074873049701200602},
pmid = {9406022},
issn = {0748-7304},
mesh = {Amino Acid Sequence ; Animals ; Circadian Rhythm/*physiology ; Humans ; Melatonin/*physiology ; Molecular Sequence Data ; Phylogeny ; Signal Transduction/*physiology ; },
abstract = {The circadian secretion of melatonin is a critical component in circadian and seasonal rhythms in many vertebrate species. This hormone is produced by photoreceptors and cell types derived from photoreceptors in vertebrate retinas and pineal complexes via circadian regulation of the biosynthetic enzymes arylalkylamine N-acetyltransferase and hydroxyindole-O-methyltransferase at both transcriptional and posttranscriptional levels. The question of whether other multicellular animals and organisms from other taxa produce melatonin in a homologously regulated pathway is at this point unclear, but preliminary evidence suggests that vertebrate and insect melatonin are produced by convergent or parallel phylogenies. The existence and function of algal and plant melatonin is worthy of further study but is unresolved at this point. In vertebrates, the role of melatonin in behavioral and systems physiology follows two phylogenetic patterns. First, the circadian regulation of visual system structures, including the hypothalamic suprachiasmatic area, the inner retina, and retinorecipient and integrative visual structures, is a primitive characteristic among vertebrate species. Second, the relative loss of visual regulation and the presence of melatonin binding in the pars tuberalis of the adenohypophysis among mammals is a derived characteristic because these characteristics are present in this group only.},
}

Amino Acid Sequence
Animals
Circadian Rhythm/*physiology
Humans
Melatonin/*physiology
Molecular Sequence Data
Phylogeny
Signal Transduction/*physiology

@article {pmid9562423,
year = {1998},
author = {Gomez-Escobar, N and Lewis, E and Maizels, RM},
title = {A novel member of the transforming growth factor-beta (TGF-beta) superfamily from the filarial nematodes Brugia malayi and B. pahangi.},
journal = {Experimental parasitology},
volume = {88},
number = {3},
pages = {200-209},
doi = {10.1006/expr.1998.4248},
pmid = {9562423},
issn = {0014-4894},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Brugia malayi/*chemistry/genetics ; Brugia pahangi/*chemistry/genetics ; DNA, Helminth/chemistry/isolation & purification ; Exons ; Female ; Gene Expression ; Male ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Messenger/analysis ; Sequence Alignment ; Transforming Growth Factor beta/chemistry/*genetics ; },
abstract = {Transforming growth factor-beta (TGF-beta) superfamily genes encode products controlling pattern formation, cell differentiation, and immune-mediated inflammation. Members of this superfamily are known in multicellular organisms from mammals to the model nematode Caenorhabditis elegans. Using PCR with oligonucleotides complementary to highly conserved motifs in the TGF-beta superfamily, we first isolated a genomic clone from the filarial nematode Brugia malayi. This gene, termed Bm-tgh-1 (TGF-beta homolog-1), spans 2.5 kb of genomic DNA and contains seven exons. Transcripts of this gene are poorly represented in cDNA libraries, but a full-length cDNA was isolated by RACE from B. pahangi (Bp-tgh-1). The tgh-1 genes from the two species are >98% identical at the nucleotide and amino acid levels, differing at 18/1576 base pairs and 5/428 amino acids; all nonsynonymous substitutions are in the long N-terminal propeptide. They show a high level of similarity throughout all seven exons to a C. elegans gene on cosmid T25F10. Homology to other members of the TGF-beta superfamily is restricted to the C-terminal domain which contains the mature active protein. Key features shared with other members of the superfamily include the tetrabasic proteolytic cleavage site to release an active C-terminal peptide, seven cysteines arrayed in identical fashion, and conserved sequence motifs. tgh-1 is most similar to the BMP-1 subfamily involved in developmental signaling in nematodes, insects, and vertebrates. RT-PCR on first-strand cDNA from both Brugia species, with primers specific to the 3' end, showed that tgh-1 is not expressed in the microfilarial stage, but is detectable in the mosquito-derived infective larvae and is maximal in maturing parasites around the time of molting in the mammalian host. Adult parasites show a relatively low level of expression. The identification of tgh-1, and its preferential expression in developing parasites, suggests that it may be involved in key developmental events in the complex filarial life cycle.},
}

Amino Acid Sequence
Animals
Base Sequence
Brugia malayi/*chemistry/genetics
Brugia pahangi/*chemistry/genetics
DNA, Helminth/chemistry/isolation & purification
Exons
Female
Gene Expression
Male
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
RNA, Messenger/analysis
Sequence Alignment
Transforming Growth Factor beta/chemistry/*genetics

@article {pmid9714748,
year = {1998},
author = {Cetkovic, H and Müller, IM and Müller, WE and Gamulin, V},
title = {Characterization and phylogenetic analysis of a cDNA encoding the Fes/FER related, non-receptor protein-tyrosine kinase in the marine sponge sycon raphanus.},
journal = {Gene},
volume = {216},
number = {1},
pages = {77-84},
doi = {10.1016/s0378-1119(98)00320-5},
pmid = {9714748},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Animals ; DNA, Complementary/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Porifera/chemistry/*enzymology/*genetics ; Protein-Tyrosine Kinases/genetics ; Proto-Oncogene Proteins/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {In search of ancient versions of phylogenetically conserved genes/proteins, which are typical for multicellular animals, we have decided to analyse marine sponges (Porifera), the most ancient and most primitive metazoan organisms. We report here the complete nucleotide sequence of Sycon raphanus cDNA coding for a 879 aa long protein, which displays high overall similarity in primary structure and organization of domains with non-receptor tyrosine kinases (TKs) from the Fes/FER family. The encoded protein, which we named Fes/FER_SR, has a highly conserved, 260 aa long tyrosine kinase domain at the C-terminus. Amino-terminal to the catalytic domain is an 85 aa long SH2 domain. The N-terminus is over 500 aa long and displays homology only with N-terminal domains of protein-tyrosine kinases (PTKs) from the Fes/FER family. Mammalian Fes/FER proteins show around 58% overall homology with Fes/FER_SR (identity and similarity) and lower homology was found with Drosophila melanogaster Fps (FER) protein (49%). Homologies in TK, SH2 and N-terminal domains are on average 78%, 65% and 49%, respectively. Fes/FER_SR shows next to best homology with the Abl family of non-receptor PTKs, while Src-related PTKs from the fresh-water sponge Spongilla lacustris are related only distantly to Fes/FER_SR. Phylogenetic analysis shows that the S. raphanus TK is indeed the most ancient known member of the Fes/FER family of non-receptor PTKs. The role of these PTKs in signal transduction in higher animals is still enigmatic; they are present in the nucleus as well as in the cytoplasm and FER is found in all cell types examined. The function of Fes/FER_SR in sponge, the most primitive multicellular animal which lacks specialized organ systems, remains to be elucidated.},
}

Amino Acid Sequence
Animals
DNA, Complementary/chemistry/*genetics
Molecular Sequence Data
Phylogeny
Porifera/chemistry/*enzymology/*genetics
Protein-Tyrosine Kinases/genetics
Proto-Oncogene Proteins/*genetics
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Amino Acid

@article {pmid9797404,
year = {1998},
author = {Bhattacharya, D and Weber, K and An, SS and Berning-Koch, W},
title = {Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants.},
journal = {Journal of molecular evolution},
volume = {47},
number = {5},
pages = {544-550},
doi = {10.1007/pl00006410},
pmid = {9797404},
issn = {0022-2844},
mesh = {Actins/*genetics ; Base Sequence ; Chlorophyta/*genetics ; DNA Primers ; DNA, Complementary ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {Green algae and land plants trace their evolutionary history to a unique common ancestor. This "green lineage" is phylogenetically subdivided into two distinct assemblages, the Chlorophyta and the Streptophyta. The Chlorophyta includes the Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Prasinopohyceae, whereas the Streptophyta includes the Charophyceae plus the bryophytes, ferns, and all other multicellular land plants (Embryophyta). The Prasinophyceae is believed to contain the earliest divergences within the green lineage. Phylogenetic analyses using rDNA sequences identify the prasinophytes as a paraphyletic taxon that diverges at the base of the Chlorophyta. rDNA analyses, however, provide ambiguous results regarding the identity of the flagellate ancestor of the Streptophyta. We have sequenced the actin-encoding cDNAs from Scherffelia dubia (Prasinophyceae), Coleochaete scutata, Spirogyra sp. (Charophyceae), and the single-copy actin gene from Mesostigma viride (Prasinophyceae). Phylogenetic analyses show Mesostigma to be the earliest divergence within the Streptophyta and provide direct evidence for a scaly, biflagellate, unicellular ancestor for this lineage. This result is supported by the existence of two conserved actin-coding region introns (positions 20-3, 152-1), and one intron in the 5'-untranslated region of the actin gene shared by Mesostigma and the embryophytes.},
}

Actins/*genetics
Base Sequence
Chlorophyta/*genetics
DNA Primers
DNA, Complementary
Molecular Sequence Data
*Phylogeny

@article {pmid9818725,
year = {1998},
author = {Rayner, TF and Stark, MJ},
title = {Identification and characterization of the KlCMD1 gene encoding Kluyveromyces lactis calmodulin.},
journal = {Yeast (Chichester, England)},
volume = {14},
number = {9},
pages = {869-875},
doi = {10.1002/(SICI)1097-0061(19980630)14:9<869::AID-YEA278>3.0.CO;2-U},
pmid = {9818725},
issn = {0749-503X},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Base Sequence ; Calmodulin/chemistry/*genetics ; Genes, Fungal ; Humans ; Kluyveromyces/*genetics ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The KlCMD1 gene was isolated from a Kluyveromyces lactis genomic library as a suppressor of the Saccharomyces cerevisiae temperature-sensitive mutant spc110-124, an allele previously shown to be suppressed by elevated copy number of the S. cerevisiae calmodulin gene CMD1. The KlCMD1 gene encodes a polypeptide which is 95% identical to S. cerevisiae calmodulin and 55% identical to calmodulin from Schizosaccharomyces pombe. Complementation of a S. cerevisiae cdm1 deletion mutant by KlCMD1 demonstrates that this gene encodes a functional calmodulin homologue. Multiple sequence alignment of calmodulins from yeast and multicellular eukaryotes shows that the K. lactis and S. cerevisiae calmodulins are considerably more closely related to each other than to other calmodulins, most of which have four functional Ca2+-binding EF hand domains. Thus like its S. cerevisiae counterpart Cmd1p, the KlCMD1 product is predicted to form only three Ca2+-binding motifs.},
}

Amino Acid Sequence
Base Sequence
Calmodulin/chemistry/*genetics
Genes, Fungal
Humans
Kluyveromyces/*genetics
Molecular Sequence Data
Phylogeny
Saccharomyces cerevisiae/genetics
Sequence Alignment
Sequence Analysis, DNA

@article {pmid10092866,
year = {1999},
author = {Bof, M and Brandolin, G and Satre, M and Klein, G},
title = {The mitochondrial adenine nucleotide translocator from Dictyostelium discoideum. Functional characterization and DNA sequencing.},
journal = {European journal of biochemistry},
volume = {259},
number = {3},
pages = {795-800},
doi = {10.1046/j.1432-1327.1999.00088.x},
pmid = {10092866},
issn = {0014-2956},
mesh = {Animals ; Atractyloside/analogs & derivatives/pharmacology ; Cell Differentiation/genetics ; Cell Division/drug effects ; Cloning, Molecular ; Dictyostelium/*genetics ; Enzyme Inhibitors/pharmacology ; Gene Expression Regulation, Developmental/genetics ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/*genetics ; Phylogeny ; Protozoan Proteins/chemistry/*genetics ; RNA, Messenger/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial adenine nucleotide translocator (ANT) catalyses the exchange of ATP and ADP between the mitochondria and the cytosol. We have cloned and sequenced the gene encoding the Dictyostelium discoideum ANT (DdANT) and analysed its transcriptional regulation. The single copy D. discoideum ant gene encodes a protein of 309 amino acid residues with a predicted molecular mass of 33,469 Da and a pI of 9.85. These values are comparable to those of ANTs from mammals, insects and fungi. The long N-terminal extension characteristic of plant ANT is absent in DdANT. The protein coding region of the D. discoideum ant gene is interrupted by three introns. Polyclonal antibodies directed against the beef heart mitochondrial ANT or its C-terminal peptide recognized the D. discoideum protein. Northern blot analysis revealed that the expression of the D. discoideum ant gene decreased rapidly during the first hours of multicellular development but the amount of protein remained stable throughout differentiation.},
}

Animals
Atractyloside/analogs & derivatives/pharmacology
Cell Differentiation/genetics
Cell Division/drug effects
Cloning, Molecular
Dictyostelium/*genetics
Enzyme Inhibitors/pharmacology
Gene Expression Regulation, Developmental/genetics
Mitochondria/*metabolism
Mitochondrial ADP, ATP Translocases/chemistry/*genetics
Phylogeny
Protozoan Proteins/chemistry/*genetics
RNA, Messenger/metabolism
Sequence Alignment
Sequence Analysis, DNA

@article {pmid10361098,
year = {1999},
author = {Copley, RR and Schultz, J and Ponting, CP and Bork, P},
title = {Protein families in multicellular organisms.},
journal = {Current opinion in structural biology},
volume = {9},
number = {3},
pages = {408-415},
doi = {10.1016/S0959-440X(99)80055-4},
pmid = {10361098},
issn = {0959-440X},
mesh = {Animals ; Conserved Sequence ; Genome ; Humans ; Intracellular Fluid/physiology ; *Multigene Family ; Phylogeny ; Proteins/*chemistry/*genetics/physiology ; Signal Transduction/genetics ; },
abstract = {The complete sequence of the nematode worm Caenorhabditis elegans contains the genetic machinery that is required to undertake the core biological processes of single cells. However, the genome also encodes proteins that are associated with multicellularity, as well as others that are lineage-specific expansions of phylogenetically widespread families and yet more that are absent in non-nematodes. Ongoing analysis is beginning to illuminate the similarities and differences among human proteins and proteins that are encoded by the genomes of the multicellular worm and the unicellular yeast, and will be essential in determining the reliability of transferring experimental data among phylogenetically distant species.},
}

Animals
Conserved Sequence
Genome
Humans
Intracellular Fluid/physiology
*Multigene Family
Phylogeny
Proteins/*chemistry/*genetics/physiology
Signal Transduction/genetics

@article {pmid10403058,
year = {1999},
author = {Soldati, T and Geissler, H and Schwarz, EC},
title = {How many is enough? Exploring the myosin repertoire in the model eukaryote Dictyostelium discoideum.},
journal = {Cell biochemistry and biophysics},
volume = {30},
number = {3},
pages = {389-411},
doi = {10.1007/BF02738121},
pmid = {10403058},
issn = {1085-9195},
mesh = {Actins/physiology ; Animals ; Cytoplasm/metabolism ; Cytoskeleton/physiology ; Dictyostelium/*metabolism ; Models, Biological ; Myosins/classification/*physiology ; Phagocytosis ; Phylogeny ; Protein Binding ; Signal Transduction ; Structure-Activity Relationship ; },
abstract = {The cytoplasm of eukaryotic cells is a very complex milieu and unraveling how its unique cytoarchitecture is achieved and maintained is a central theme in modern cell biology. It is crucial to understand how organelles and macro-complexes of RNA and/or proteins are transported to and/or maintained at their specific cellular locations. The importance of filamentous-actin-directed myosin-powered cargo transport was only recently realized, and after an initial explosion in the identification of new molecules, the field is now concentrating on their functional dissection. Direct connections of myosins to a variety of cellular tasks are now slowly emerging, such as in cytokinesis, phagocytosis, endocytosis, polarized secretion and exocytosis, axonal transport, etc. Unconventional myosins have been identified in a wide variety of organisms, making the presence of actin and myosins a hallmark of eukaryotism. The genome of S. cerevisiae encodes only five myosins, whereas a mammalian cell has the capacity to express between two and three dozen myosins. Why is it so crucial to arrive at this final census? The main questions that we would like to discuss are the following. How many distinct myosin-powered functions are carried out in a typical higher eukaryote? Or, in other words, what is the minimal set of myosins essential to accomplish the multitude of tasks related to motility and intracellular dynamics in a multicellular organism? And also, as a corollary, what is the degree of functional redundancy inside a given myosin class? In that respect, the choice of a model organism suitable for such an investigation is more crucial than ever. Here we argue that Dictyostelium discoideum is affirming its position as an ideal system of intermediate complexity to study myosin-powered trafficking and is or will soon become the second eukaryote for which complete knowledge of the whole repertoire of myosins is available.},
}

Actins/physiology
Animals
Cytoplasm/metabolism
Cytoskeleton/physiology
Dictyostelium/*metabolism
Models, Biological
Myosins/classification/*physiology
Phagocytosis
Phylogeny
Protein Binding
Signal Transduction
Structure-Activity Relationship

@article {pmid10521526,
year = {1999},
author = {Serino, G and Tsuge, T and Kwok, S and Matsui, M and Wei, N and Deng, XW},
title = {Arabidopsis cop8 and fus4 mutations define the same gene that encodes subunit 4 of the COP9 signalosome.},
journal = {The Plant cell},
volume = {11},
number = {10},
pages = {1967-1980},
pmid = {10521526},
issn = {1040-4651},
mesh = {Alleles ; Animals ; Arabidopsis/*genetics ; *Arabidopsis Proteins ; COP9 Signalosome Complex ; Chromatography, Affinity ; Chromosome Mapping ; Cloning, Molecular ; *Genes, Plant ; Humans ; Molecular Sequence Data ; Multiprotein Complexes ; *Mutation ; Peptide Hydrolases ; Phenotype ; Phylogeny ; Plant Proteins/*genetics/isolation & purification/metabolism ; *Proteins ; Sequence Homology, Amino Acid ; *Signal Transduction ; },
abstract = {The pleiotropic constitutive photomorphogenic/deetiolated/fusca (cop/det/fus) mutants of Arabidopsis exhibit features of light-grown seedlings when grown in the dark. Cloning and biochemical analysis of COP9 have revealed that it is a component of a multiprotein complex, the COP9 signalosome (previously known as the COP9 complex). Here, we compare the immunoaffinity and the biochemical purification of the COP9 signalosome from cauliflower and confirm its eight-subunit composition. Molecular cloning of subunit 4 of the complex revealed that it is a proteasome-COP9 complex-eIF3 domain protein encoded by a gene that maps to chromosome 5, near the chromosomal location of the cop8 and fus4 mutations. Genetic complementation tests showed that the cop8 and fus4 mutations define the same locus, now designated as COP8. Molecular analysis of the subunit 4-encoding gene in both cop8 and fus4 mutants identified specific molecular lesions, and overexpression of the subunit 4 cDNA in a cop8 mutant background resulted in complete rescue of the mutant phenotype. Thus, we conclude that COP8 encodes subunit 4 of the COP9 signalosome. Examination of possible molecular interactions by using the yeast two-hybrid assay indicated that COP8 is capable of strong self-association as well as interaction with COP9, FUS6/COP11, FUS5, and Arabidopsis JAB1 homolog 1, the latter four proteins being previously defined subunits of the Arabidopsis COP9 signalosome. A comparative sequence analysis indicated that COP8 is highly conserved among multicellular eukaryotes and is also similar to a subunit of the 19S regulatory particle of the 26S proteasome.},
}

Alleles
Animals
Arabidopsis/*genetics
*Arabidopsis Proteins
COP9 Signalosome Complex
Chromatography, Affinity
Chromosome Mapping
Cloning, Molecular
*Genes, Plant
Humans
Molecular Sequence Data
Multiprotein Complexes
*Mutation
Peptide Hydrolases
Phenotype
Phylogeny
Plant Proteins/*genetics/isolation & purification/metabolism
*Proteins
Sequence Homology, Amino Acid
*Signal Transduction

@article {pmid10542368,
year = {1999},
author = {Mohri, H and Inaba, K and Kubo-Irie, M and Takai, H and Yano-Toyoshima, Y},
title = {Characterization of outer arm dynein in sea anemone, Anthopleura midori.},
journal = {Cell motility and the cytoskeleton},
volume = {44},
number = {3},
pages = {202-208},
doi = {10.1002/(SICI)1097-0169(199911)44:3<202::AID-CM5>3.0.CO;2-E},
pmid = {10542368},
issn = {0886-1544},
mesh = {Animals ; Dyneins/*chemistry/isolation & purification/physiology/ultrastructure ; Male ; Phylogeny ; Sea Anemones/classification/*enzymology ; Sperm Tail/ultrastructure ; },
abstract = {Outer arm dynein was purified from sperm flagella of a sea anemone, Anthopleura midori, and its biochemical and biophysical properties were characterized. The dynein, obtained at a 20S ATPase peak by sucrose density gradient centrifugation, consisted of two heavy chains, three intermediate chains, and seven light chains. The specific ATPase activity of dynein was 1.3 micromol Pi/mg/min. Four polypeptides (296, 296, 225, and 206 kDa) were formed by UV cleavage at 365 nm of dynein in the presence of vanadate and ATP. In addition, negatively stained images of dynein molecules and the hook-shaped image of the outer arm of the flagella indicated that sea anemone outer arm dynein is two-headed. In contrast to protist dyneins, which are three-headed, outer arm dyneins of flagella and cilia in multicellular animals are two-headed molecules corresponding to the two heavy chains. Phylogenetic considerations were made concerning the diversity of outer arm dyneins.},
}

Animals
Dyneins/*chemistry/isolation & purification/physiology/ultrastructure
Male
Phylogeny
Sea Anemones/classification/*enzymology
Sperm Tail/ultrastructure

@article {pmid10561504,
year = {1999},
author = {Quesada, V and Ponce, MR and Micol, JL},
title = {OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana.},
journal = {FEBS letters},
volume = {461},
number = {1-2},
pages = {101-106},
doi = {10.1016/s0014-5793(99)01426-x},
pmid = {10561504},
issn = {0014-5793},
mesh = {Adaptor Proteins, Vesicular Transport ; Amino Acid Sequence ; Arabidopsis/*genetics ; *Arabidopsis Proteins ; Base Sequence ; Cell Nucleus/*genetics ; DNA, Bacterial/genetics/metabolism ; DNA, Complementary/metabolism ; Genes, Overlapping ; Genome, Plant ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis ; Nerve Tissue Proteins/*genetics ; Ornithine Carbamoyltransferase/*genetics ; Phenotype ; Phosphoproteins/*genetics ; Phylogeny ; Plant Proteins/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; },
abstract = {In contrast to bacterial, fungal and vertebrate ornithine transcarbamylases (OTCs; EC 2.1.3.3), very little is known about the enzyme in plants. We report here the isolation of a T-DNA-tagged mutant displaying sensitivity to ornithine, whose characterization has allowed for the identification of several complementary and genomic DNA clones encoding the OTC and auxilin-like 1 (AUL1) proteins of the crucifer Arabidopsis thaliana. Transcript mapping revealed that at least 22 bp within the OTC-AUL1 intercoding region are transcribed from both strands, which makes this one of the rarely described cases of convergent and overlapping transcription units in the nuclear genome of a multicellular eukaryote. Transcription of the OTC gene was shown to be ubiquitous in aerial organs of adult plants, whereas that of AUL1 was obscured by the existence of a putative second copy of the gene. The OTC-AUL1 locus maps at the bottom of chromosome 1.},
}

Adaptor Proteins, Vesicular Transport
Amino Acid Sequence
Arabidopsis/*genetics
*Arabidopsis Proteins
Base Sequence
Cell Nucleus/*genetics
DNA, Bacterial/genetics/metabolism
DNA, Complementary/metabolism
Genes, Overlapping
Genome, Plant
Models, Genetic
Molecular Sequence Data
Mutagenesis
Nerve Tissue Proteins/*genetics
Ornithine Carbamoyltransferase/*genetics
Phenotype
Phosphoproteins/*genetics
Phylogeny
Plant Proteins/*genetics
Reverse Transcriptase Polymerase Chain Reaction
Transcription, Genetic

@article {pmid10673278,
year = {2000},
author = {McCue, LA and McDonough, KA and Lawrence, CE},
title = {Functional classification of cNMP-binding proteins and nucleotide cyclases with implications for novel regulatory pathways in Mycobacterium tuberculosis.},
journal = {Genome research},
volume = {10},
number = {2},
pages = {204-219},
doi = {10.1101/gr.10.2.204},
pmid = {10673278},
issn = {1088-9051},
support = {5RO1-HG0125703/HG/NHGRI NIH HHS/United States ; },
mesh = {Adenylyl Cyclases/metabolism ; Amino Acid Sequence ; Carrier Proteins/*classification/*metabolism ; Computational Biology ; Guanylate Cyclase/metabolism ; Molecular Sequence Data ; Mycobacterium tuberculosis/*enzymology/metabolism ; Nucleotides, Cyclic/*metabolism ; Phosphorus-Oxygen Lyases/*classification/*metabolism ; Phylogeny ; Sequence Alignment ; },
abstract = {We have analyzed the cyclic nucleotide (cNMP)-binding protein and nucleotide cyclase superfamilies using Bayesian computational methods of protein family identification and classification. In addition to the known cNMP-binding proteins (cNMP-dependent kinases, cNMP-gated channels, cAMP-guanine nucleotide exchange factors, and bacterial cAMP-dependent transcription factors), new functional groups of cNMP-binding proteins were identified, including putative ABC-transporter subunits, translocases, and esterases. Classification of the nucleotide cyclases revealed subtle differences in sequence conservation of the active site that distinguish the five classes of cyclases: the multicellular eukaryotic adenylyl cyclases, the eukaryotic receptor-type guanylyl cyclases, the eukaryotic soluble guanylyl cyclases, the unicellular eukaryotic and prokaryotic adenylyl cyclases, and the putative prokaryotic guanylyl cyclases. Phylogenetic distribution of the cNMP-binding proteins and cyclases was analyzed, with particular attention to the 22 complete archaeal and eubacterial genome sequences. Mycobacterium tuberculosis H37Rv and Synechocystis PCC6803 were each found to encode several more putative cNMP-binding proteins than other prokaryotes; many of these proteins are of unknown function. M. tuberculosis also encodes several more putative nucleotide cyclases than other prokaryotic species.},
}

Adenylyl Cyclases/metabolism
Amino Acid Sequence
Carrier Proteins/*classification/*metabolism
Computational Biology
Guanylate Cyclase/metabolism
Molecular Sequence Data
Mycobacterium tuberculosis/*enzymology/metabolism
Nucleotides, Cyclic/*metabolism
Phosphorus-Oxygen Lyases/*classification/*metabolism
Phylogeny
Sequence Alignment

@article {pmid10760743,
year = {2000},
author = {Czaker, R},
title = {Extracellular matrix (ECM) components in a very primitive multicellular animal, the dicyemid mesozoan Kantharella antarctica.},
journal = {The Anatomical record},
volume = {259},
number = {1},
pages = {52-59},
doi = {10.1002/(SICI)1097-0185(20000501)259:1<52::AID-AR6>3.0.CO;2-J},
pmid = {10760743},
issn = {0003-276X},
mesh = {Animals ; Antarctic Regions ; Collagen/metabolism ; Extracellular Matrix/*metabolism/ultrastructure ; Fibronectins/metabolism ; Invertebrates/*metabolism/*ultrastructure ; Laminin/metabolism ; Phylogeny ; },
abstract = {One of the most vital synapomorphic properties of metazoans is the presence of an extracellular matrix (ECM), i.e., a complex of proteoglycans, adhesive glycoproteins, and collagens. The genetically controlled ECM mediates between the respective receptors morphogenesis and cell differentiation and is central to gastrulation, i.e., the process which generates the embryonic germ layers, upon which all metazoan body structures are based. However, the primitive metazoans include a phylum, viz. the Dicyemida, which lacks any kind of typical metazoan ECM structures including a basement membrane, and hence does not develop through gastrulation. Since the ECM components fibronectin, laminin, and type IV collagen, all of which are essential constituents of each basement membrane, have been proved to be evolutionary ancient molecules from the lowest metazoans up to vertebrates, antibodies against the respective vertebrate ECM components were employed by electron microscopy to look for these molecules also in the dicyemid mesozoan Kantharella antarctica. As a result, all three protein families showed an immunolabel which was localized intracellularly and intimately associated with the cell membranes as well as with the submembranously arranged delicate filamentous network. The immunolabel was most intense in the fibronectin-like protein, followed by the type IV collagen-like protein and weakest in the laminin-like protein. From an evolutionary point of view, this kind of distribution of ECM components, primarily found in intracellular regions, seems to reflect a very primitive situation of the structures of the respective ECM molecules having not yet reached their definitive position outside the cell, thus generating the complete biological function of typical ECM. Moreover, these results confirm the long-standing presumption that the dicyemid mesozoan body structure might be the missing link between the Protozoa and Metazoa.},
}

Animals
Antarctic Regions
Collagen/metabolism
Extracellular Matrix/*metabolism/ultrastructure
Fibronectins/metabolism
Invertebrates/*metabolism/*ultrastructure
Laminin/metabolism
Phylogeny

@article {pmid10842308,
year = {2000},
author = {Thacker, C and Rose, AM},
title = {A look at the Caenorhabditis elegans Kex2/Subtilisin-like proprotein convertase family.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {22},
number = {6},
pages = {545-553},
doi = {10.1002/(SICI)1521-1878(200006)22:6<545::AID-BIES7>3.0.CO;2-F},
pmid = {10842308},
issn = {0265-9247},
mesh = {Animals ; Caenorhabditis elegans/*enzymology/genetics ; Genes, Helminth ; Humans ; Multigene Family ; Mutation ; Phylogeny ; *Proprotein Convertases ; *Saccharomyces cerevisiae Proteins ; Subtilisins/chemistry/genetics/*metabolism ; },
abstract = {Significant advances have recently been made in our understanding of the mechanisms of activation of proteins that require processing. Often this involves endoproteolytic cleavage of precursor forms at basic residues, and is carried out by a group of serine endoproteinases, termed the proprotein convertases. In mammals, seven different convertases have been identified to date. These act in both the regulated secretory pathway for the processing of prohormones and proneuropeptides and in the constitutive secretory pathway, in which a variety of proproteins are activated endoproteolytically. The recently completed sequence of the nematode Caenorhabditis elegans genome affords a unique opportunity to examine the entire proprotein convertase family in a multicellular organism. Here we review the nature of the family, emphasising the structural features, characteristic of the four nematode genes, that supply all of the necessary functions unique to this group of serine endoproteinases. Studies of the C. elegans genes not only provide important information about the evaluation of this gene family but should help to illuminate the roles of these proteins in mammalian systems. BioEssays 22:545-553, 2000.},
}

Animals
Caenorhabditis elegans/*enzymology/genetics
Genes, Helminth
Humans
Multigene Family
Mutation
Phylogeny
*Proprotein Convertases
*Saccharomyces cerevisiae Proteins
Subtilisins/chemistry/genetics/*metabolism

@article {pmid10879630,
year = {2000},
author = {Böhm, M and Schröder, HC and Müller, IM and Müller, WE and Gamulin, V},
title = {The mitogen-activated protein kinase p38 pathway is conserved in metazoans: cloning and activation of p38 of the SAPK2 subfamily from the sponge Suberites domuncula.},
journal = {Biology of the cell},
volume = {92},
number = {2},
pages = {95-104},
doi = {10.1016/s0248-4900(00)89017-6},
pmid = {10879630},
issn = {0248-4900},
mesh = {Amino Acid Sequence ; Animals ; *Conserved Sequence ; Enzyme Activation ; Gene Library ; Genes, Immediate-Early ; Hot Temperature ; Hydrogen Peroxide/pharmacology ; Marine Biology ; Mitogen-Activated Protein Kinases/classification/*genetics ; Models, Genetic ; Molecular Sequence Data ; Osmotic Pressure ; Phylogeny ; Porifera/classification/drug effects/*genetics/radiation effects ; Sequence Analysis ; Sequence Homology, Amino Acid ; Signal Transduction ; Ultraviolet Rays ; p38 Mitogen-Activated Protein Kinases ; },
abstract = {Our recent data suggest that during auto- and allograft recognition in sponges (Porifera), cytokines are differentially expressed. Since the mitogen-activated protein kinase (MAPK) signal transduction modulates the synthesis and release of cytokines, we intended to identify one key molecule of this pathway. Therefore, a cDNA from the marine sponge Suberites domuncula encoding the MAPK was isolated and analyzed. Its encoded protein is 366 amino acids long (calculated Mr 42 209), has a TGY dual phosphorylation motif in protein kinase subdomain VIII and displays highest overall similarity to the mammalian p38 stress activated protein kinase (SAPK2), one subfamily of MAPKs. The sponge protein was therefore termed p38_SD. The overall homology (identity and similarity) between p38_SD and human p38alpha (CSBP2) kinase is 82%. One feature of the sponge kinase is the absence of threonine at position 106. In human p38alpha MAPK this residue is involved in the interaction with the specific pyridinyl-imidazole inhibitor; T106 is replaced in p38_SD by methionine. Inhibition studies with the respective inhibitor SB 203580 showed that it had no effect on the phosphorylation of the p38 substrate myelin basic protein. A stress responsive kinase Krs_SD similar to mammalian Ste20 kinases, upstream regulators of p38, had already previously been found in S. domuncula. The S. domuncula p38 MAPK is phosphorylated after treatment of the animal in hypertonic medium. In contrast, exposure of cells to hydrogen peroxide, heat shock and ultraviolet light does not cause any phosphorylation of p38. It is concluded that sponges, the oldest and most simple multicellular animals, utilize the conserved p38 MAPK signaling pathway, known to be involved in stress and immune (inflammatory) responses in higher animals.},
}

Amino Acid Sequence
Animals
*Conserved Sequence
Enzyme Activation
Gene Library
Genes, Immediate-Early
Hot Temperature
Hydrogen Peroxide/pharmacology
Marine Biology
Mitogen-Activated Protein Kinases/classification/*genetics
Models, Genetic
Molecular Sequence Data
Osmotic Pressure
Phylogeny
Porifera/classification/drug effects/*genetics/radiation effects
Sequence Analysis
Sequence Homology, Amino Acid
Signal Transduction
Ultraviolet Rays
p38 Mitogen-Activated Protein Kinases

@article {pmid11125040,
year = {2001},
author = {Tatusov, RL and Natale, DA and Garkavtsev, IV and Tatusova, TA and Shankavaram, UT and Rao, BS and Kiryutin, B and Galperin, MY and Fedorova, ND and Koonin, EV},
title = {The COG database: new developments in phylogenetic classification of proteins from complete genomes.},
journal = {Nucleic acids research},
volume = {29},
number = {1},
pages = {22-28},
pmid = {11125040},
issn = {1362-4962},
mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Caenorhabditis elegans/genetics ; *Databases, Factual ; Drosophila melanogaster/genetics ; Genome ; Information Storage and Retrieval ; Internet ; Phylogeny ; *Proteins/classification/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; },
abstract = {The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih. gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.},
}

Animals
Archaea/genetics
Bacteria/genetics
Caenorhabditis elegans/genetics
*Databases, Factual
Drosophila melanogaster/genetics
Genome
Information Storage and Retrieval
Internet
Phylogeny
*Proteins/classification/genetics
Saccharomyces cerevisiae/genetics
Sequence Alignment

@article {pmid11158292,
year = {2001},
author = {Wu, J and Glass, NL},
title = {Identification of specificity determinants and generation of alleles with novel specificity at the het-c heterokaryon incompatibility locus of Neurospora crassa.},
journal = {Molecular and cellular biology},
volume = {21},
number = {4},
pages = {1045-1057},
pmid = {11158292},
issn = {0270-7306},
support = {R01 GM060468/GM/NIGMS NIH HHS/United States ; GM60468/GM/NIGMS NIH HHS/United States ; },
mesh = {Alleles ; Amino Acid Sequence ; Base Sequence ; Chimera/genetics ; DNA Primers/genetics ; Fungal Proteins/chemistry/*genetics ; Genes, Fungal ; Genetic Variation ; Models, Biological ; Molecular Sequence Data ; Neurospora crassa/*genetics/growth & development ; Phenotype ; Phylogeny ; Protein Structure, Tertiary ; Transformation, Genetic ; },
abstract = {The capacity for nonself recognition is a ubiquitous and essential aspect of biology. In filamentous fungi, nonself recognition during vegetative growth is believed to be mediated by genetic differences at heterokaryon incompatibility (het) loci. Filamentous fungi are capable of undergoing hyphal fusion to form mycelial networks and with other individuals to form vegetative heterokaryons, in which genetically distinct nuclei occupy a common cytoplasm. In Neurospora crassa, 11 het loci have been identified that affect the viability of such vegetative heterokaryons. The het-c locus has at least three mutually incompatible alleles, termed het-c(OR), het-c(PA), and het-c(GR). Hyphal fusion between strains that are of alternative het-c specificity results in vegetative heterokaryons that are aconidial and which show growth inhibition and hyphal compartmentation and death. A 34- to 48-amino-acid variable domain, which is dissimilar in HET-C(OR), HET-C(PA), and HET-C(GR), confers allelic specificity. To assess requirements for allelic specificity, we constructed chimeras between the het-c variable domain from 24 different isolates that displayed amino acid and insertion or deletion variations and determined their het-c specificity by introduction into N. crassa. We also constructed a number of artificial alleles that contained novel het-c specificity domains. By this method, we identified four additional and novel het-c specificities. Our results indicate that amino acid and length variations within the insertion or deletion motif are the primary determinants for conferring het-c allelic specificity. These results provide a molecular model for nonself recognition in multicellular eucaryotes.},
}

Alleles
Amino Acid Sequence
Base Sequence
Chimera/genetics
DNA Primers/genetics
Fungal Proteins/chemistry/*genetics
Genes, Fungal
Genetic Variation
Models, Biological
Molecular Sequence Data
Neurospora crassa/*genetics/growth & development
Phenotype
Phylogeny
Protein Structure, Tertiary
Transformation, Genetic

@article {pmid11250079,
year = {2001},
author = {Huizing, M and Didier, A and Walenta, J and Anikster, Y and Gahl, WA and Krämer, H},
title = {Molecular cloning and characterization of human VPS18, VPS 11, VPS16, and VPS33.},
journal = {Gene},
volume = {264},
number = {2},
pages = {241-247},
doi = {10.1016/s0378-1119(01)00333-x},
pmid = {11250079},
issn = {0378-1119},
support = {R01 EY010199/EY/NEI NIH HHS/United States ; EY10199/EY/NEI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Blotting, Northern ; Carrier Proteins/*genetics ; DNA, Complementary/chemistry/genetics ; Female ; Humans ; Membrane Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, DNA ; Tissue Distribution ; *Vesicular Transport Proteins ; },
abstract = {In multicellular organisms, the delivery of proteins to lysosomes is essential. Many of the genes necessary for this process have first been identified by their requirement for vacuolar delivery in yeast. A subset of these genes, the four class C vps genes, is necessary for the delivery of endocytic and biosynthetic cargo in yeast, and also in Drosophila. Here, we describe the sequence and expression pattern of four human homologs of these genes. This initial molecular description of these four genes is an important step towards their evaluation as candidate genes that may be involved in the pathogenesis of Hermansky-Pudlak syndrome-related diseases.},
}

Amino Acid Sequence
Blotting, Northern
Carrier Proteins/*genetics
DNA, Complementary/chemistry/genetics
Female
Humans
Membrane Proteins/*genetics
Molecular Sequence Data
Phylogeny
Proteins/*genetics
RNA, Messenger/genetics/metabolism
Sequence Analysis, DNA
Tissue Distribution
*Vesicular Transport Proteins

@article {pmid11321585,
year = {2001},
author = {Ueki, T and Inouye, S},
title = {SigB, SigC, and SigE from Myxococcus xanthus homologous to sigma32 are not required for heat shock response but for multicellular differentiation.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {3},
number = {2},
pages = {287-293},
pmid = {11321585},
issn = {1464-1801},
support = {GM26843/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Bacterial Proteins/biosynthesis/chemistry/*genetics ; Base Sequence ; Conserved Sequence ; *DNA-Binding Proteins ; Gene Deletion ; *Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Developmental ; Heat-Shock Proteins/chemistry/*genetics ; Hot Temperature ; Molecular Sequence Data ; Myxococcus xanthus/genetics/growth & development/*physiology ; Open Reading Frames ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sigma Factor/biosynthesis/chemistry/*genetics ; Transcription Factors/chemistry/*genetics ; },
abstract = {Myxococcus xanthus has been known to have multiple sigma factors which are considered to play important roles in regulation of gene expression in development. A new gene encoding a putative sigma factor, sigE, was cloned by using a degenerate oligonucleotide corresponding to the conserved region 2.2 of M. xanthus SigA. In the 2.0-kb nucleotide sequence, an open reading frame consisting of 280 amino acid residues was identified. The amino acid sequence of SigE shows high similarity to heat shock sigma factors in bacteria. However, the sigE gene is not induced by heat shock and deletion of sigE does not affect production of heat shock proteins. SigE is expressed during both vegetative growth and fruiting body development. In the deletion mutant of the sigE gene fruiting body formation is initiated earlier and fewer spores are produced than in the parent strain. Interestingly, the deltasigE mutant shows defects in fruiting body formation at 37 degrees C. In addition to SigE, SigB and SigC show high sequence similarity to heat shock sigma factors. However, even if all three sigma factor genes are disrupted, heat shock proteins are still normally induced. A deltasigBdeltasigCdeltasigE triple deletion strain forms fruiting bodies earlier, but sporulats later than the parent strain. Spores from the triple deletion mutant are aberrant and their viability is less than 0.001% compared with that of the parent strain, suggesting that these sigma factors may have redundant functions in multicellular differentiation of M. xanthus.},
}

Amino Acid Sequence
Bacterial Proteins/biosynthesis/chemistry/*genetics
Base Sequence
Conserved Sequence
*DNA-Binding Proteins
Gene Deletion
*Gene Expression Regulation, Bacterial
Gene Expression Regulation, Developmental
Heat-Shock Proteins/chemistry/*genetics
Hot Temperature
Molecular Sequence Data
Myxococcus xanthus/genetics/growth & development/*physiology
Open Reading Frames
Phylogeny
Sequence Alignment
Sequence Homology, Amino Acid
Sigma Factor/biosynthesis/chemistry/*genetics
Transcription Factors/chemistry/*genetics

@article {pmid11346655,
year = {2001},
author = {Sánchez-Fernández, R and Davies, TG and Coleman, JO and Rea, PA},
title = {The Arabidopsis thaliana ABC protein superfamily, a complete inventory.},
journal = {The Journal of biological chemistry},
volume = {276},
number = {32},
pages = {30231-30244},
doi = {10.1074/jbc.M103104200},
pmid = {11346655},
issn = {0021-9258},
mesh = {ATP-Binding Cassette Transporters/*chemistry/metabolism ; Algorithms ; Arabidopsis/*chemistry/*genetics ; Binding Sites ; DNA, Complementary/metabolism ; Databases, Factual ; Expressed Sequence Tags ; Models, Genetic ; Multigene Family ; Mutation ; Open Reading Frames ; Phylogeny ; Plant Proteins/*chemistry ; Protein Binding ; Protein Structure, Tertiary ; },
abstract = {We describe the first complete inventory of ATP-binding cassette (ABC) proteins from a multicellular organism, the model plant Arabidopsis thaliana. By the application of several search criteria, Arabidopsis was found to contain a total of 129 open reading frames (ORFs) capable of encoding ABC proteins, of which 103 possessed contiguous transmembrane spans and were identified as putative intrinsic membrane proteins. Fifty-two of the putative intrinsic membrane proteins contained at least two transmembrane domains (TMDs) and two nucleotide-binding folds (NBFs) and could be classified as belonging to one of five subfamilies of full-molecule transporters. The other 51 putative membrane proteins, all of which were half-molecule transporters, fell into five subfamilies. Of the remaining ORFs identified, all of which encoded proteins lacking TMDs, 11 could be classified into three subfamilies. There were no obvious homologs in other organisms for 15 of the ORFs which encoded a heterogeneous group of non-intrinsic ABC proteins (NAPs). Unrooted phylogenetic analyses substantiated the subfamily designations. Notable features of the Arabidopsis ABC superfamily was the presence of a large yeast-like PDR subfamily, and the absence of genes encoding bona fide cystic fibrosis transmembrane conductance regulator (CFTR), sulfonylurea receptor (SUR), and heavy metal tolerance factor 1 (HMT1) homologs. Arabidopsis was unusual in its large allocation of ORFs (a minimum of 0.5%) to members of the ABC protein superfamily.},
}

ATP-Binding Cassette Transporters/*chemistry/metabolism
Algorithms
Arabidopsis/*chemistry/*genetics
Binding Sites
DNA, Complementary/metabolism
Databases, Factual
Expressed Sequence Tags
Models, Genetic
Multigene Family
Mutation
Open Reading Frames
Phylogeny
Plant Proteins/*chemistry
Protein Binding
Protein Structure, Tertiary

@article {pmid11438670,
year = {2001},
author = {Krause, SA and Loupart, ML and Vass, S and Schoenfelder, S and Harrison, S and Heck, MM},
title = {Loss of cell cycle checkpoint control in Drosophila Rfc4 mutants.},
journal = {Molecular and cellular biology},
volume = {21},
number = {15},
pages = {5156-5168},
pmid = {11438670},
issn = {0270-7306},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Alleles ; Amino Acid Sequence ; Animals ; Bromodeoxyuridine/metabolism ; Cell Cycle ; Cell Nucleus/metabolism ; Cells, Cultured ; Chromosome Aberrations ; Chromosome Disorders ; Chromosomes/metabolism/ultrastructure ; Cloning, Molecular ; DNA/metabolism ; DNA-Binding Proteins/*genetics ; Drosophila/metabolism ; Indoles/metabolism ; Larva/metabolism ; Microscopy, Fluorescence ; Mitosis ; Molecular Sequence Data ; *Mutation ; Phylogeny ; Polymerase Chain Reaction ; Replication Protein C ; Salivary Glands/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Two alleles of the Drosophila melanogaster Rfc4 (DmRfc4) gene, which encodes subunit 4 of the replication factor C (RFC) complex, cause striking defects in mitotic chromosome cohesion and condensation. These mutations produce larval phenotypes consistent with a role in DNA replication but also result in mitotic chromosomal defects appearing either as premature chromosome condensation-like or precocious sister chromatid separation figures. Though the DmRFC4 protein localizes to all replicating nuclei, it is dispersed from chromatin in mitosis. Thus the mitotic defects appear not to be the result of a direct role for RFC4 in chromosome structure. We also show that the mitotic defects in these two DmRfc4 alleles are the result of aberrant checkpoint control in response to DNA replication inhibition or damage to chromosomes. Not all surveillance function is compromised in these mutants, as the kinetochore attachment checkpoint is operative. Intriguingly, metaphase delay is frequently observed with the more severe of the two alleles, indicating that subsequent chromosome segregation may be inhibited. This is the first demonstration that subunit 4 of RFC functions in checkpoint control in any organism, and our findings additionally emphasize the conserved nature of RFC's involvement in checkpoint control in multicellular eukaryotes.},
}

Alleles
Amino Acid Sequence
Animals
Bromodeoxyuridine/metabolism
Cell Cycle
Cell Nucleus/metabolism
Cells, Cultured
Chromosome Aberrations
Chromosome Disorders
Chromosomes/metabolism/ultrastructure
Cloning, Molecular
DNA/metabolism
DNA-Binding Proteins/*genetics
Drosophila/metabolism
Indoles/metabolism
Larva/metabolism
Microscopy, Fluorescence
Mitosis
Molecular Sequence Data
*Mutation
Phylogeny
Polymerase Chain Reaction
Replication Protein C
Salivary Glands/metabolism
Sequence Homology, Amino Acid

@article {pmid11481037,
year = {2001},
author = {Ohkouchi, S and Nishio, K and Maeda, M and Hitomi, K and Adachi, H and Maki, M},
title = {Identification and characterization of two penta-EF-hand Ca(2+)-binding proteins in Dictyostelium discoideum.},
journal = {Journal of biochemistry},
volume = {130},
number = {2},
pages = {207-215},
doi = {10.1093/oxfordjournals.jbchem.a002974},
pmid = {11481037},
issn = {0021-924X},
mesh = {Amino Acid Sequence ; Animals ; Calcium/metabolism ; Calcium-Binding Proteins/*chemistry/classification/genetics/*metabolism ; Cell Fractionation ; Dictyostelium/*chemistry/genetics ; *EF Hand Motifs ; Gene Expression Regulation, Developmental ; In Situ Hybridization ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/chemistry/classification/genetics/metabolism ; Sequence Alignment ; },
abstract = {Penta-EF-hand (PEF) proteins such as ALG-2 (apoptosis-linked gene 2 product) and the calpain small subunit are a newly classified family of Ca(2+)-binding proteins that possess five EF-hand-like motifs. We identified two mutually homologous PEF proteins, designated DdPEF-1 and DdPEF-2 (64% amino acid residue identities), in the cellular slime mold Dictyostelium discoideum. Both PEF proteins showed a higher similarity to mammalian ALG-2 and peflin (Group I PEF proteins) than to calpain and sorcin subfamily (Group II PEF proteins) in the first EF-hand (EF-1) regions. Northern blot analyses revealed that DdPEF-1 and DdPEF-2 were constitutively expressed throughout development of Dictyostelium, but their levels of expression were developmentally regulated. In situ hybridization analyses demonstrated that DdPEF-1 was expressed in both the anterior prestalk and the posterior prespore regions of the tipped aggregate, slugs and early culminants. On the other hand, DdPEF-2 was dominantly expressed in the anterior tip region of these multicellular structures. Both PEF proteins were detected as 22-23-kDa proteins in soluble fractions in the presence of EGTA but in particulate fractions in the presence of Ca(2+) by Western blotting using specific monoclonal antibodies. Together with the finding of PEF-like sequences in DNA databases of plants, fungi and protists, our results strongly suggest that Group I PEF proteins are ubiquitously present in all eukaryotes and play important roles in basic cellular functions.},
}

Amino Acid Sequence
Animals
Calcium/metabolism
Calcium-Binding Proteins/*chemistry/classification/genetics/*metabolism
Cell Fractionation
Dictyostelium/*chemistry/genetics
*EF Hand Motifs
Gene Expression Regulation, Developmental
In Situ Hybridization
Molecular Sequence Data
Phylogeny
Protozoan Proteins/chemistry/classification/genetics/metabolism
Sequence Alignment

@article {pmid11498045,
year = {2001},
author = {Breakefield, XO and Kamm, C and Hanson, PI},
title = {TorsinA: movement at many levels.},
journal = {Neuron},
volume = {31},
number = {1},
pages = {9-12},
doi = {10.1016/s0896-6273(01)00350-6},
pmid = {11498045},
issn = {0896-6273},
mesh = {Animals ; Carrier Proteins/chemistry/*genetics/metabolism ; Dystonia Musculorum Deformans/*genetics/physiopathology ; Humans ; Models, Molecular ; *Molecular Chaperones ; Multigene Family ; Phylogeny ; Protein Conformation ; Sequence Deletion ; },
abstract = {TorsinA is the causative protein in the human neurologic disease early onset torsin dystonia, a movement disorder involving dysfunction in the basal ganglia without apparent neurodegeneration. Most cases result from a dominantly acting three-base pair deletion in the TOR1A gene causing loss of a glutamic acid near the carboxyl terminus of torsinA. Torsins are members of the AAA(+) superfamily of ATPases and are present in all multicellular organisms. Initial studies suggest that torsinA is an ER protein involved in chaperone functions and/or membrane movement.},
}

Animals
Carrier Proteins/chemistry/*genetics/metabolism
Dystonia Musculorum Deformans/*genetics/physiopathology
Humans
Models, Molecular
*Molecular Chaperones
Multigene Family
Phylogeny
Protein Conformation
Sequence Deletion

@article {pmid11516343,
year = {2001},
author = {Verhagen, AM and Coulson, EJ and Vaux, DL},
title = {Inhibitor of apoptosis proteins and their relatives: IAPs and other BIRPs.},
journal = {Genome biology},
volume = {2},
number = {7},
pages = {REVIEWS3009},
pmid = {11516343},
issn = {1474-760X},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis/genetics/physiology ; Caspase Inhibitors ; Caspases/metabolism ; Chromosomal Proteins, Non-Histone/genetics/physiology ; Humans ; Inhibitor of Apoptosis Proteins ; Insect Proteins/*genetics/physiology ; *Microtubule-Associated Proteins ; Molecular Sequence Data ; Neoplasm Proteins ; Phylogeny ; Proteins/*genetics/physiology ; Sequence Homology, Amino Acid ; Survivin ; X-Linked Inhibitor of Apoptosis Protein ; },
abstract = {Apoptosis is a physiological cell death process important for development, homeostasis and the immune defence of multicellular animals. The key effectors of apoptosis are caspases, cysteine proteases that cleave after aspartate residues. The inhibitor of apoptosis (IAP) family of proteins prevent cell death by binding to and inhibiting active caspases and are negatively regulated by IAP-binding proteins, such as the mammalian protein DIABLO/Smac. IAPs are characterized by the presence of one to three domains known as baculoviral IAP repeat (BIR) domains and many also have a RING-finger domain at their carboxyl terminus. More recently, a second group of BIR-domain-containing proteins (BIRPs) have been identified that includes the mammalian proteins Bruce and Survivin as well as BIR-containing proteins in yeasts and Caenorhabditis elegans. These Survivin-like BIRPs regulate cytokinesis and mitotic spindle formation. In this review, we describe the IAPs and other BIRPs, their evolutionary relationships and their subcellular and tissue localizations.},
}

Amino Acid Sequence
Animals
Apoptosis/genetics/physiology
Caspase Inhibitors
Caspases/metabolism
Chromosomal Proteins, Non-Histone/genetics/physiology
Humans
Inhibitor of Apoptosis Proteins
Insect Proteins/*genetics/physiology
*Microtubule-Associated Proteins
Molecular Sequence Data
Neoplasm Proteins
Phylogeny
Proteins/*genetics/physiology
Sequence Homology, Amino Acid
Survivin
X-Linked Inhibitor of Apoptosis Protein

@article {pmid11595174,
year = {2001},
author = {Li, QZ and Wang, CY and Shi, JD and Ruan, QG and Eckenrode, S and Davoodi-Semiromi, A and Kukar, T and Gu, Y and Lian, W and Wu, D and She, JX},
title = {Molecular cloning and characterization of the mouse and human TUSP gene, a novel member of the tubby superfamily.},
journal = {Gene},
volume = {273},
number = {2},
pages = {275-284},
doi = {10.1016/s0378-1119(01)00582-0},
pmid = {11595174},
issn = {0378-1119},
support = {P01 AI-42288/AI/NIAID NIH HHS/United States ; },
mesh = {Adaptor Proteins, Signal Transducing ; Alternative Splicing ; Amino Acid Sequence ; Animals ; Blotting, Northern ; Cell Line ; Chromosome Mapping ; Chromosomes, Human, Pair 6/genetics ; Cloning, Molecular ; Cytoplasm/metabolism ; DNA, Complementary/chemistry/genetics ; Diabetes Mellitus/genetics ; Dinucleotide Repeats/genetics ; Female ; Gene Expression ; Genes/genetics ; Green Fluorescent Proteins ; Humans ; Intracellular Signaling Peptides and Proteins ; Luminescent Proteins/genetics/metabolism ; Male ; Mice ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Proteins/*genetics ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tissue Distribution ; },
abstract = {We report here the cloning and characterization of a novel gene belonging to the tubby superfamily proteins (TUSP) in mouse and human. The mouse Tusp cDNA is 9120 bp in length and encodes a deduced protein of 1547 amino acids, while the human TUSP gene is 11,127 bp and encodes a deduced protein of 1544 amino acids. The human and mouse genes are 87% identical for their nucleotide sequences and 85% identical for their amino acid sequences. The protein sequences of these genes are 40-48% identical to other tubby family proteins at the C-terminal conserved 'tubby domain'. In addition, the TUSP proteins contain a tubby signature motif (FXGRVTQ), two bipartite nuclear localization signals (NLSs) at the C-terminal, two proline-rich regions, one WD40 repeat region and one suppressor of cytokines signaling domain. Transfection assay with green fluorescent protein-tagged TUSP expression constructs showed that the complete TUSP protein and the N-terminal portion of TUSP are localized in the cytoplasm but the C-terminal portion with the two NLSs produced distinct dots or spots localized in the cytoplasm. Northern blotting analysis showed that the major transcript with the complete coding sequence is expressed mainly in the brain, skeletal muscle, testis and kidney. Radiation hybrid mapping localized the mouse gene to chromosome 17q13 and the human TUSP gene to chromosome 6q25-q26 near the type 1 diabetes gene IDDM5. However, association analysis in diabetic families with a polymorphic microsatellite marker did not show any evidence for association between TUSP and type 1 diabetes. The precise biological function of the tubby superfamily genes is still unknown; the highly conserved tubby domain in different species, however, suggests that these proteins must have fundamental biological functions in a wide range of multi-cellular organisms.},
}

Adaptor Proteins, Signal Transducing
Alternative Splicing
Amino Acid Sequence
Animals
Blotting, Northern
Cell Line
Chromosome Mapping
Chromosomes, Human, Pair 6/genetics
Cloning, Molecular
Cytoplasm/metabolism
DNA, Complementary/chemistry/genetics
Diabetes Mellitus/genetics
Dinucleotide Repeats/genetics
Female
Gene Expression
Genes/genetics
Green Fluorescent Proteins
Humans
Intracellular Signaling Peptides and Proteins
Luminescent Proteins/genetics/metabolism
Male
Mice
Molecular Sequence Data
Phylogeny
Polymorphism, Genetic
Proteins/*genetics
RNA, Messenger/genetics/metabolism
Recombinant Fusion Proteins/genetics/metabolism
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Tissue Distribution

@article {pmid11596926,
year = {2001},
author = {Lasek-Nesselquist, E and Katz, LA},
title = {Phylogenetic position of Sorogena stoianovitchae and relationships within the class Colpodea (Ciliophora) based on SSU rDNA sequences.},
journal = {The Journal of eukaryotic microbiology},
volume = {48},
number = {5},
pages = {604-607},
doi = {10.1111/j.1550-7408.2001.tb00197.x},
pmid = {11596926},
issn = {1066-5234},
mesh = {Animals ; Ciliophora/*classification/*genetics ; DNA, Protozoan/analysis ; DNA, Ribosomal/*analysis ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; *Sequence Analysis, DNA ; },
abstract = {The ciliate Sorogena stoianovitchae, which can form a multicellular fruiting body, has been classified based upon its ultrastructure and morphology: the oral and somatic infraciliature of S. stoianovitchae most closely resemble those of members of the order Cyrtolophosidida in the class Colpodea. We characterized the small subunit ribosomal DNA (SSU rDNA) gene sequence from S. stoianovitchae and compared this sequence with those from representatives of all ciliate classes. These analyses placed S. stoianovitchae as either sister to members of the class Nassophorea or Colpodea. In an in-group analysis, including all SSU rDNA sequences from members of the classes Nassophorea and Colpodea and representatives of appropriate outgroups, S. stoianovitchae was always sister to Platyophrya vorax (class Colpodea, order Cyrtolophosidida). However, our analyses failed to support the monophyly of the class Colpodea. Instead, our data suggest that there are essentially three unresolved clades: (1) the class Nassophorea; (2) Bresslaua vorax, Colpoda inflata, Pseudoplatyophrya nana, and Bursaria truncatella (class Colpodea); and (3) P. vorax and S. stoianovitchae (class Colpodea).},
}

Animals
Ciliophora/*classification/*genetics
DNA, Protozoan/analysis
DNA, Ribosomal/*analysis
Molecular Sequence Data
*Phylogeny
RNA, Ribosomal/*genetics
*Sequence Analysis, DNA

@article {pmid11800396,
year = {2001},
author = {Horling, F and Baier, M and Dietz, KJ},
title = {Redox-regulation of the expression of the peroxide-detoxifying chloroplast 2-cys peroxiredoxin in the liverwort Riccia fluitans.},
journal = {Planta},
volume = {214},
number = {2},
pages = {304-313},
doi = {10.1007/s004250100623},
pmid = {11800396},
issn = {0032-0935},
mesh = {Amino Acid Sequence ; Arabidopsis Proteins ; Ascorbic Acid/pharmacology ; Blotting, Western ; Chloroplasts/metabolism ; Cloning, Molecular ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Glutathione/pharmacology ; Molecular Sequence Data ; Oxidation-Reduction ; Peroxidases/genetics/*metabolism ; Peroxiredoxins ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plants/drug effects/genetics/*metabolism ; Sequence Homology, Amino Acid ; Signal Transduction ; },
abstract = {2-Cys peroxiredoxins (2-CPs) are H2O2- and alkyl hydroperoxide-detoxifying enzymes, and occur in animals, fungi, bacteria and higher plants. Here, the cDNA encoding a peroxiredoxin of a multicellular cryptogamic plant was first cloned from the liverwort Riccia fluitans L., and the dependence of its expression on the cellular redox state was analysed. The presence of an N-terminal targeting signal indicates that, like 2-CPs from higher plants, Riccia 2-CP is posttranslationally imported into chloroplasts. Addition of ascorbate and other reductants suppressed 2-CP gene expression and decreased 2-CP protein levels. With ascorbate, the decrease in 2-CP transcript level was fast, concentration dependent, and correlated with the amounts of ascorbate taken up by the tissue. In an approach to identify signaling components, staurosporine was proved to be a highly potent inhibitor of ascorbate-dependent repression of 2-CP-expression. The staurosporine effect indicates that a serine/threonine-kinase is involved in ascorbate-modulated redox regulation of 2-CP expression.},
}

Amino Acid Sequence
Arabidopsis Proteins
Ascorbic Acid/pharmacology
Blotting, Western
Chloroplasts/metabolism
Cloning, Molecular
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Glutathione/pharmacology
Molecular Sequence Data
Oxidation-Reduction
Peroxidases/genetics/*metabolism
Peroxiredoxins
Phylogeny
Plant Proteins/genetics/metabolism
Plants/drug effects/genetics/*metabolism
Sequence Homology, Amino Acid
Signal Transduction

@article {pmid11837302,
year = {2002},
author = {Hanada, S and Takaichi, S and Matsuura, K and Nakamura, K},
title = {Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {52},
number = {Pt 1},
pages = {187-193},
doi = {10.1099/00207713-52-1-187},
pmid = {11837302},
issn = {1466-5026},
mesh = {Bacteriochlorophylls/metabolism ; Carotenoids/metabolism ; Chlorobi/*classification/genetics/*physiology/ultrastructure ; DNA, Ribosomal/analysis ; Fresh Water/microbiology ; Light-Harvesting Protein Complexes ; Molecular Sequence Data ; *Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; },
abstract = {A novel thermophilic, photosynthetic bacterium, designated strain HLO8T, was isolated from a bacterial mat in a Japanese hot spring. Morphologically, the isolate was an unbranched multicellular filament with a cell diameter of 0.8-1.0 microm. The bacterium was red to reddish-brown in colour and formed a distinct red bacterial mat in the natural environment. It was able to grow photoheterotrophically under anaerobic light conditions and also chemoheterotrophically under aerobic dark conditions. Optimal growth occurred at 50 degrees C and pH 7.5-8.0. The cells contained bacteriochlorophyll (Bchl) a and gamma-carotene derivatives as photosynthetic pigments, but lacked Bchl c and chlorosomes. Cellular fatty acids in the isolate were mainly C16:0, C14:0 and C15:0. The major quinone was menaquinone-11. The DNA G+C content was 62.0 mol% (by HPLC). Phylogenetic analysis based on 16S rDNA sequencing suggested that the isolate belonged to the anoxygenic filamentous phototrophic bacteria represented by Chloroflexus aurantiacus, but was clearly distant from all members in this group (the sequence similarities between the isolate and its relatives were less than 83.8%). Based on genotypic and phenotypic data, the name Roseiflexus castenholzii gen. nov., sp. nov. is proposed for this isolate; the type strain is HLO8T (= DSM 13941T = JCM 11240T).},
}

Bacteriochlorophylls/metabolism
Carotenoids/metabolism
Chlorobi/*classification/genetics/*physiology/ultrastructure
DNA, Ribosomal/analysis
Fresh Water/microbiology
Light-Harvesting Protein Complexes
Molecular Sequence Data
*Photosynthesis
Photosynthetic Reaction Center Complex Proteins/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Temperature

@article {pmid11854508,
year = {2002},
author = {Schutte, BC and Mitros, JP and Bartlett, JA and Walters, JD and Jia, HP and Welsh, MJ and Casavant, TL and McCray, PB},
title = {Discovery of five conserved beta -defensin gene clusters using a computational search strategy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {99},
number = {4},
pages = {2129-2133},
pmid = {11854508},
issn = {0027-8424},
support = {P30-HD27748/HD/NICHD NIH HHS/United States ; CA-85188/CA/NCI NIH HHS/United States ; HL-61234/HL/NHLBI NIH HHS/United States ; K12 HD027748/HD/NICHD NIH HHS/United States ; P50 HL061234/HL/NHLBI NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Computers ; Conserved Sequence ; Contig Mapping ; Cysteine/chemistry ; Exons ; Humans ; Markov Chains ; Mice ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Sequence Homology, Amino Acid ; Software ; beta-Defensins/*chemistry/*genetics ; },
abstract = {The innate immune system includes antimicrobial peptides that protect multicellular organisms from a diverse spectrum of microorganisms. beta-Defensins comprise one important family of mammalian antimicrobial peptides. The annotation of the human genome fails to reveal the expected diversity, and a recent query of the draft sequence with the blast search engine found only one new beta-defensin gene (DEFB3). To define better the beta-defensin gene family, we adopted a genomics approach that uses hmmer, a computational search tool based on hidden Markov models, in combination with blast. This strategy identified 28 new human and 43 new mouse beta-defensin genes in five syntenic chromosomal regions. Within each syntenic cluster, the gene sequences and organization were similar, suggesting each cluster pair arose from a common ancestor and was retained because of conserved functions. Preliminary analysis indicates that at least 26 of the predicted genes are transcribed. These results demonstrate the value of a genomewide search strategy to identify genes with conserved structural motifs. Discovery of these genes represents a new starting point for exploring the role of beta-defensins in innate immunity.},
}

Amino Acid Motifs
Amino Acid Sequence
Animals
Computers
Conserved Sequence
Contig Mapping
Cysteine/chemistry
Exons
Humans
Markov Chains
Mice
Models, Genetic
Molecular Sequence Data
Multigene Family
Phylogeny
Sequence Homology, Amino Acid
Software
beta-Defensins/*chemistry/*genetics

@article {pmid11867702,
year = {2002},
author = {Schröder, J and Kautz, K and Wernicke, W},
title = {Gamma-tubulin in barley and tobacco: sequence relationship and RNA expression patterns in developing leaves during mitosis and post-mitotic growth.},
journal = {Plant & cell physiology},
volume = {43},
number = {2},
pages = {224-229},
doi = {10.1093/pcp/pcf030},
pmid = {11867702},
issn = {0032-0781},
mesh = {Amino Acid Sequence ; Blotting, Northern ; DNA, Complementary/genetics/isolation & purification ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Hordeum/*genetics/growth & development ; Mitosis/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/*genetics/growth & development ; RNA, Plant/genetics/metabolism ; Sequence Homology, Amino Acid ; Nicotiana/*genetics/growth & development ; Tubulin/biosynthesis/*genetics ; },
abstract = {gamma-Tubulin is typically associated with microtubule organising centres, such as the centrosome, and appears to mediate microtubule nucleation. Centrosomes are usually not found in higher plants, but active genes homologous to gamma-tubulin have been identified in the plant kingdom, including the angiosperms Arabidopsis, maize and rice. We have isolated and characterised gamma-tubulin cDNA sequences of two further angiosperm species, barley and tobacco. Sequence comparison revealed a phylogenetic tree with distinct clusters corresponding to the systematic position of the species. Furthermore, domains, thought to be exposed in the folded protein and to be candidates for interaction with associated, nucleation-site related proteins, exhibited motifs highly specific of multicellular plants. Strong expression of the gamma-tubulin genes, as determined by Northern blotting, correlated with mitotic activity. Expression dropped distinctly when mitotic activity ceased. Thus, in post-mitotic tissues that showed intricate reshuffling of cortical microtubule arrays related to cell shaping only very low gamma-tubulin steady-state RNA levels were found, contrasting with the situation for alpha-tubulin. The findings indicate that gamma-tubulin expression in plants may be more tightly linked to mitosis, although there is some gamma-tubulin expression at the RNA level even after mitosis. It follows that the post-mitotic changes in microtubular arrays may be less dependent on concurrent gamma-tubulin RNA expression than mitotic cells.},
}

Amino Acid Sequence
Blotting, Northern
DNA, Complementary/genetics/isolation & purification
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Hordeum/*genetics/growth & development
Mitosis/genetics
Molecular Sequence Data
Phylogeny
Plant Leaves/*genetics/growth & development
RNA, Plant/genetics/metabolism
Sequence Homology, Amino Acid
Nicotiana/*genetics/growth & development
Tubulin/biosynthesis/*genetics

@article {pmid11925432,
year = {2002},
author = {Bouché, N and Scharlat, A and Snedden, W and Bouchez, D and Fromm, H},
title = {A novel family of calmodulin-binding transcription activators in multicellular organisms.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {24},
pages = {21851-21861},
doi = {10.1074/jbc.M200268200},
pmid = {11925432},
issn = {0021-9258},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Arabidopsis ; Caenorhabditis elegans ; Calmodulin/*chemistry/*metabolism ; Cell Line ; Cell Nucleus/metabolism ; Chromatography, Affinity ; Cloning, Molecular ; Conserved Sequence ; DNA/metabolism ; DNA, Complementary/metabolism ; Databases as Topic ; Dose-Response Relationship, Drug ; Drosophila ; Gene Library ; Glutathione Transferase/metabolism ; Humans ; Insecta ; Kinetics ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Peptides/chemistry ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Signal Transduction ; *Transcription, Genetic ; Transcriptional Activation ; Two-Hybrid System Techniques ; beta-Galactosidase/metabolism ; },
abstract = {Screening of cDNA expression libraries derived from plants exposed to stress, with 35S-labeled recombinant calmodulin as a probe, revealed a new family of proteins containing a transcription activation domain and two types of DNA-binding domains designated the CG-1 domain and the transcription factor immunoglobulin domain, ankyrin repeats, and a varying number of IQ calmodulin-binding motifs. Based on domain organization and amino acid sequence comparisons, similar proteins, with the same domain organization, were identified in the genomes of other multicellular organisms including human, Drosophila, and Caenorhabditis, whereas none were found in the complete genomes of single cell eukaryotes and prokaryotes. This family of proteins was designated calmodulin-binding transcription activators (CAMTAs). Arabidopsis thaliana contains six CAMTA genes (AtCAMTA1-AtCAMTA6). The transcription activation domain of AtCAMTA1 was mapped by testing a series of protein fusions with the DNA-binding domain of the bacterial LexA transcription factor and two reporter genes fused to LexA recognition sequences in yeast cells. Two human proteins designated HsCAMTA1 and HsCAMTA2 were also shown to activate transcription in yeast using the same reporter system. Subcellular fractionation of Arabidopsis tissues revealed the presence of CAMTAs predominantly in the nucleus. Calmodulin binding assays identified a region of 25 amino acids capable of binding calmodulin with high affinity (K(d) = 1.2 nm) in the presence of calcium. We suggest that CAMTAs comprise a conserved family of transcription factors in a wide range of multicellular eukaryotes, which possibly respond to calcium signaling by direct binding of calmodulin.},
}

Amino Acid Motifs
Amino Acid Sequence
Animals
Arabidopsis
Caenorhabditis elegans
Calmodulin/*chemistry/*metabolism
Cell Line
Cell Nucleus/metabolism
Chromatography, Affinity
Cloning, Molecular
Conserved Sequence
DNA/metabolism
DNA, Complementary/metabolism
Databases as Topic
Dose-Response Relationship, Drug
Drosophila
Gene Library
Glutathione Transferase/metabolism
Humans
Insecta
Kinetics
Models, Genetic
Molecular Sequence Data
Multigene Family
Peptides/chemistry
Phylogeny
Protein Binding
Protein Structure, Tertiary
Sequence Homology, Amino Acid
Signal Transduction
*Transcription, Genetic
Transcriptional Activation
Two-Hybrid System Techniques
beta-Galactosidase/metabolism

@article {pmid11956206,
year = {2002},
author = {Sugiura, M and Kono, K and Liu, H and Shimizugawa, T and Minekura, H and Spiegel, S and Kohama, T},
title = {Ceramide kinase, a novel lipid kinase. Molecular cloning and functional characterization.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {26},
pages = {23294-23300},
doi = {10.1074/jbc.M201535200},
pmid = {11956206},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Blotting, Northern ; Cloning, Molecular ; Humans ; Mice ; Molecular Sequence Data ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/*genetics/physiology ; Phylogeny ; Recombinant Proteins/biosynthesis/chemistry ; },
abstract = {Ceramide-1-phosphate is a sphingolipid metabolite that has been implicated in membrane fusion of brain synaptic vesicles and neutrophil phagolysosome formation. Ceramide-1-phosphate can be produced by ATP-dependent ceramide kinase activity, although little is known of this enzyme because it has not yet been highly purified or cloned. Based on sequence homology to sphingosine kinase type 1, we have now cloned a related lipid kinase, human ceramide kinase (hCERK). hCERK encodes a protein of 537 amino acids that has a catalytic region with a high degree of similarity to the diacylglycerol kinase catalytic domain. hCERK also has a putative N-myristoylation site on its NH(2) terminus followed by a pleckstrin homology domain. Membrane but not cytosolic fractions from HEK293 cells transiently transfected with a hCERK expression vector readily phosphorylated ceramide but not sphingosine or other sphingoid bases, diacylglycerol or phosphatidylinositol. This activity was clearly distinguished from those of bacterial or human diacylglycerol kinases. With natural ceramide as a substrate, the enzyme had a pH optimum of 6.0-7.5 and showed Michaelis-Menten kinetics, with K(m) values of 187 and 32 microm for ceramide and ATP, respectively. Northern blot analysis revealed that hCERK mRNA expression was high in the brain, heart, skeletal muscle, kidney, and liver. A BLAST search analysis using the hCERK sequence revealed that putative ceramide kinases (CERKs) exist widely in diverse multicellular organisms including plants, nematodes, insects, and vertebrates. Phylogenetic analysis revealed that CERKs are a new class of lipid kinases that are clearly distinct from sphingosine and diacylglycerol kinases. Cloning of CERK should provide new molecular tools to investigate the physiological functions of ceramide-1-phosphate.},
}

Amino Acid Sequence
Animals
Blotting, Northern
Cloning, Molecular
Humans
Mice
Molecular Sequence Data
Phosphotransferases (Alcohol Group Acceptor)/chemistry/*genetics/physiology
Phylogeny
Recombinant Proteins/biosynthesis/chemistry

@article {pmid11976967,
year = {2002},
author = {Meiri, E and Levitan, A and Guo, F and Christopher, DA and Schaefer, D and Zrÿd, JP and Danon, A},
title = {Characterization of three PDI-like genes in Physcomitrella patens and construction of knock-out mutants.},
journal = {Molecular genetics and genomics : MGG},
volume = {267},
number = {2},
pages = {231-240},
doi = {10.1007/s00438-002-0658-5},
pmid = {11976967},
issn = {1617-4615},
mesh = {Amino Acid Sequence ; Base Sequence ; Bryopsida/enzymology/*genetics ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Gene Targeting ; *Genes, Plant ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phylogeny ; Protein Disulfide-Isomerases/*genetics ; Sequence Homology, Amino Acid ; },
abstract = {Plant genomes typically contain several sequences homologous to protein disulfide isomerase (PDI). PDI was first identified as an abundant enzyme in the endoplasmic reticulum, where it catalyzes the formation, reduction, and isomerization of disulfide bonds during protein folding. PDI-like proteins have also been implicated in a variety of other functions, such as the regulation of cell adhesion, and may act as elicitors of the autoimmune response in mammals. A PDI-like protein (RB60) was recently shown to be imported into chloroplasts in the unicellular green alga Chlamydomonas reinhardtii and a higher plant, Pisum sativum, where it associates with thylakoid membranes. This suggests that the different PDI-like proteins in plant and animals may have diverse biological roles. To begin to elucidate the roles of PDI-like proteins, we have cloned, characterized, and generated knock-out mutants for three PDI-like genes that have high, medium, and low levels of expression, respectively, in the moss Physcomitrella patens. Phylogenetic analysis indicates that the three PDI-like proteins cluster with RB60 and four proteins from Arabidopsis thaliana. They are typified by an N-terminal domain rich in negatively charged residues. The knock-out mutants, which are the first knock-outs available for PDI-like proteins in a multicellular organism, were found to be viable, indicating that the function of each single gene is dispensable, and suggesting that they may be functionally complementary.},
}

Amino Acid Sequence
Base Sequence
Bryopsida/enzymology/*genetics
DNA, Complementary/genetics
DNA, Plant/genetics
Gene Targeting
*Genes, Plant
Molecular Sequence Data
Mutagenesis, Insertional
Phylogeny
Protein Disulfide-Isomerases/*genetics
Sequence Homology, Amino Acid

@article {pmid11985014,
year = {2002},
author = {Enmark, E and Gustafsson, JA},
title = {[Nuclear receptors in man, fly and worm provide greater understanding of disease].},
journal = {Lakartidningen},
volume = {99},
number = {11},
pages = {1186-1190},
pmid = {11985014},
issn = {0023-7205},
mesh = {Animals ; *Base Sequence ; Caenorhabditis elegans/genetics ; Drosophila melanogaster/genetics ; *Genetics, Medical ; Genomic Library ; Hominidae/genetics ; Humans ; Phylogeny ; Receptors, Cytoplasmic and Nuclear/*genetics ; Transcription Factors/*genetics ; },
abstract = {Recently the complete genomic sequences for three very different multicellular organisms have been published, from one nematode (Caenorhabditis elegans), one fly (Drosophila melanogaster) and human (Homo sapiens). Of course, this means a breakthrough in many ways for biological research. Summarised in this article are the findings made using these genomic sequences regarding the protein family of nuclear receptors. This is a group of transcription factors involved in many important biological processes, i.e. regulation of cholesterol homeostasis and fertility; classical members of this protein family are, amongst others, the receptors for estradiol and progesterone.},
}

Animals
*Base Sequence
Caenorhabditis elegans/genetics
Drosophila melanogaster/genetics
*Genetics, Medical
Genomic Library
Hominidae/genetics
Humans
Phylogeny
Receptors, Cytoplasmic and Nuclear/*genetics
Transcription Factors/*genetics

@article {pmid12019231,
year = {2002},
author = {Mason, DA and Fleming, RJ and Goldfarb, DS},
title = {Drosophila melanogaster importin alpha1 and alpha3 can replace importin alpha2 during spermatogenesis but not oogenesis.},
journal = {Genetics},
volume = {161},
number = {1},
pages = {157-170},
pmid = {12019231},
issn = {0016-6731},
support = {GM40362/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Animals, Genetically Modified ; *Drosophila Proteins ; Drosophila melanogaster/*physiology ; Female ; Fertility/physiology ; Gene Dosage ; Male ; Oogenesis/*physiology ; Ovary/metabolism ; Phosphorylation ; Phylogeny ; Spermatogenesis/*physiology ; Testis/metabolism/ultrastructure ; alpha Karyopherins/*physiology ; },
abstract = {Importin alpha's mediate the nuclear transport of many classical nuclear localization signal (cNLS)-containing proteins. Multicellular animals contain multiple importin alpha genes, most of which fall into three conventional phylogenetic clades, here designated alpha1, alpha2, and alpha3. Using degenerate PCR we cloned Drosophila melanogaster importin alpha1, alpha2, and alpha3 genes, demonstrating that the complete conventional importin alpha gene family arose prior to the split between invertebrates and vertebrates. We have begun to analyze the genetic interactions among conventional importin alpha genes by studying their capacity to rescue the male and female sterility of importin alpha2 null flies. The sterility of alpha2 null males was rescued to similar extents by importin alpha1, alpha2, and alpha3 transgenes, suggesting that all three conventional importin alpha's are capable of performing the important role of importin alpha2 during spermatogenesis. In contrast, sterility of alpha2 null females was rescued only by importin alpha2 transgenes, suggesting that it plays a paralog-specific role in oogenesis. Female infertility was also rescued by a mutant importin alpha2 transgene lacking a site that is normally phosphorylated in ovaries. These rescue experiments suggest that male and female gametogenesis have distinct requirements for importin alpha2.},
}

Animals
Animals, Genetically Modified
*Drosophila Proteins
Drosophila melanogaster/*physiology
Female
Fertility/physiology
Gene Dosage
Male
Oogenesis/*physiology
Ovary/metabolism
Phosphorylation
Phylogeny
Spermatogenesis/*physiology
Testis/metabolism/ultrastructure
alpha Karyopherins/*physiology

@article {pmid12176051,
year = {2002},
author = {Thorpe, C and Hoober, KL and Raje, S and Glynn, NM and Burnside, J and Turi, GK and Coppock, DL},
title = {Sulfhydryl oxidases: emerging catalysts of protein disulfide bond formation in eukaryotes.},
journal = {Archives of biochemistry and biophysics},
volume = {405},
number = {1},
pages = {1-12},
doi = {10.1016/s0003-9861(02)00337-5},
pmid = {12176051},
issn = {0003-9861},
support = {GM26643/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Birds ; Disulfides ; Endoplasmic Reticulum/metabolism ; Extracellular Matrix/metabolism ; Humans ; Immunohistochemistry ; Models, Biological ; Models, Genetic ; Models, Molecular ; Molecular Sequence Data ; Multigene Family ; Oxidoreductases/*metabolism/*physiology ; Phylogeny ; Saponins ; Sequence Homology, Amino Acid ; Thioredoxins/metabolism ; Trypanosoma ; Oxidoreductases Acting on Sulfur Group Donors ; },
abstract = {Members of the Quiescin-sulfhydryl oxidase (QSOX) family utilize a thioredoxin domain and a small FAD-binding domain homologous to the yeast ERV1p protein to oxidize sulfhydryl groups to disulfides with the reduction of oxygen to hydrogen peroxide. QSOX enzymes are found in all multicellular organisms for which complete genomes exist and in Trypanosoma brucei, but are not found in yeast. The avian QSOX is the best understood enzymatically: its preferred substrates are peptides and proteins, not monothiols such as glutathione. Mixtures of avian QSOX and protein disulfide isomerase catalyze the rapid insertion of the correct disulfide pairings in reduced RNase. Immunohistochemical studies of human tissues show a marked and highly localized concentration of QSOX in cell types associated with heavy secretory loads. Consistent with this role in the formation of disulfide bonds, QSOX is typically found in the cell in the endoplasmic reticulum and Golgi and outside the cell. In sum, this review suggests that QSOX enzymes play a significant role in oxidative folding of a large variety of proteins in a wide range of multicellular organisms.},
}

Amino Acid Sequence
Animals
Birds
Disulfides
Endoplasmic Reticulum/metabolism
Extracellular Matrix/metabolism
Humans
Immunohistochemistry
Models, Biological
Models, Genetic
Models, Molecular
Molecular Sequence Data
Multigene Family
Oxidoreductases/*metabolism/*physiology
Phylogeny
Saponins
Sequence Homology, Amino Acid
Thioredoxins/metabolism
Trypanosoma
Oxidoreductases Acting on Sulfur Group Donors

@article {pmid12242490,
year = {2002},
author = {Anctil, M and Hurtubise, P and Gillis, MA},
title = {Tyrosine hydroxylase and dopamine-beta-hydroxylase immunoreactivities in the cnidarian Renilla koellikeri.},
journal = {Cell and tissue research},
volume = {310},
number = {1},
pages = {109-117},
doi = {10.1007/s00441-002-0601-4},
pmid = {12242490},
issn = {0302-766X},
mesh = {Adrenal Glands/enzymology ; Animals ; Anthozoa/cytology/*enzymology ; Antibody Specificity/immunology ; Catecholamines/*biosynthesis ; Cell Size/physiology ; Cross Reactions/immunology ; Dopamine beta-Hydroxylase/metabolism ; Ectoderm/cytology ; Endoderm/cytology ; Immunohistochemistry ; Mice ; Nerve Net/cytology/*enzymology ; Nervous System/cytology/*enzymology ; Neurites/enzymology/ultrastructure ; Neurons, Afferent/cytology/*enzymology ; Phylogeny ; Species Specificity ; Tyrosine 3-Monooxygenase/metabolism ; },
abstract = {Western Blot and immunohistochemical studies were conducted in the sea pansy Renilla koellikeri, a representative of the earliest multicellular animals with a nervous system, using various antibodies raised against enzymes of the catecholamine biosynthetic pathway. Western blots of sea pansy extracts revealed a protein band that co-migrated with dopamine-beta-hydroxylase (DBH) from mouse adrenal glands. Similar experiments with antisera against tyrosine hydroxylase (TH) revealed several immunoreactive protein bands, all of larger molecular weight than mammalian tyrosine hydroxylase. DBH-like and, to a lesser extent, TH-like and phenylethanolamine N-methyltransferase-like immunoreactivities were detected in ectodermal sensory neurons and associated subectodermal neurites, in neurons of the mesogleal nerve-net and associated amoebocytes, and in some endodermal neurons. While it is still not clear whether the detected TH-immunoreactive proteins represent some form of TH, the presence in sea pansies of a DBH-like protein is in agreement with previously detected norepinephrine-like immunoreactivity in the same species. The widespread distribution of these immunoreactivities in various sea pansy neurons suggests important roles for catecholamines in nerve net activity.},
}

Adrenal Glands/enzymology
Animals
Anthozoa/cytology/*enzymology
Antibody Specificity/immunology
Catecholamines/*biosynthesis
Cell Size/physiology
Cross Reactions/immunology
Dopamine beta-Hydroxylase/metabolism
Ectoderm/cytology
Endoderm/cytology
Immunohistochemistry
Mice
Nerve Net/cytology/*enzymology
Nervous System/cytology/*enzymology
Neurites/enzymology/ultrastructure
Neurons, Afferent/cytology/*enzymology
Phylogeny
Species Specificity
Tyrosine 3-Monooxygenase/metabolism

@article {pmid12325127,
year = {2002},
author = {Money, NP},
title = {Mushroom stem cells.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {24},
number = {10},
pages = {949-952},
doi = {10.1002/bies.10160},
pmid = {12325127},
issn = {0265-9247},
mesh = {Agaricales/*cytology/physiology ; Cell Differentiation ; Cell Division ; Cell Lineage ; Fungi/*cytology/*physiology ; Phylogeny ; },
abstract = {Contrary to the rarity of totipotent cells in animals, almost every cell formed by a fungus can function as a "stem cell". The multicellular fruiting bodies of basidiomycete fungi consist of the same kind of filamentous hyphae that form the feeding phase, or mycelium, of the organism, and visible cellular differentiation is almost nonexistent. Mushroom primordia develop from masses of converging hyphae, and the stipe (or stem), cap, and gills are clearly demarcated within the embryonic fruiting body long before the organ expands and unfolds through water uptake and cell wall loosening. Though frequent references are made to gilled mushrooms in this article, the totipotent nature of fruiting body cells and lack of meristems is also applicable to basidiomycetes that spread their spore-producing tissues inside tubes (e.g., boletes), over spines and rippled surfaces, or form spores in cavities within the fruiting body. Even in the mature mushroom, every hypha retains its totipotency. Among animals, only sponges exhibit a similar degree of developmental flexibility, which is interesting, because these simple metazoans may be relatively close relatives of fungi.},
}

Agaricales/*cytology/physiology
Cell Differentiation
Cell Division
Cell Lineage
Fungi/*cytology/*physiology
Phylogeny

@article {pmid12421749,
year = {2002},
author = {Müller, A and MacCallum, RM and Sternberg, MJ},
title = {Structural characterization of the human proteome.},
journal = {Genome research},
volume = {12},
number = {11},
pages = {1625-1641},
pmid = {12421749},
issn = {1088-9051},
mesh = {Algorithms ; Animals ; Archaeal Proteins/chemistry/classification/genetics/physiology ; Bacterial Proteins/chemistry/classification/genetics/physiology ; Caenorhabditis elegans Proteins/chemistry/classification/genetics/physiology ; Databases, Genetic/statistics & numerical data ; Drosophila Proteins/chemistry/classification/genetics/physiology ; Escherichia coli Proteins/chemistry/classification/genetics/physiology ; Gene Duplication ; Genetic Diseases, Inborn/genetics ; Humans ; Markov Chains ; Membrane Proteins/chemistry/classification/genetics/physiology ; Online Systems/statistics & numerical data ; Phylogeny ; Protein Structure, Quaternary/genetics/physiology ; Proteome/*chemistry/classification/physiology ; Saccharomyces cerevisiae Proteins/chemistry/classification/genetics/physiology ; },
abstract = {This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.},
}

Algorithms
Animals
Archaeal Proteins/chemistry/classification/genetics/physiology
Bacterial Proteins/chemistry/classification/genetics/physiology
Caenorhabditis elegans Proteins/chemistry/classification/genetics/physiology
Databases, Genetic/statistics & numerical data
Drosophila Proteins/chemistry/classification/genetics/physiology
Escherichia coli Proteins/chemistry/classification/genetics/physiology
Gene Duplication
Genetic Diseases, Inborn/genetics
Humans
Markov Chains
Membrane Proteins/chemistry/classification/genetics/physiology
Online Systems/statistics & numerical data
Phylogeny
Protein Structure, Quaternary/genetics/physiology
Proteome/*chemistry/classification/physiology
Saccharomyces cerevisiae Proteins/chemistry/classification/genetics/physiology

@article {pmid12426481,
year = {2002},
author = {Okuyama, M and Saito, Y and Ogawa, M and Takeuchi, A and Jing, Z and Naganuma, T and Hirose, E},
title = {Morphological studies on the bathyal ascidian, Megalodicopia hians Oka 1918 (Octacnemidae, Phlebobranchia), with remarks on feeding and tunic morphology.},
journal = {Zoological science},
volume = {19},
number = {10},
pages = {1181-1189},
doi = {10.2108/zsj.19.1181},
pmid = {12426481},
issn = {0289-0003},
mesh = {Animals ; Environment ; *Feeding Behavior ; Gonads/anatomy & histology ; Integumentary System/anatomy & histology/microbiology ; Intestines/anatomy & histology ; Japan ; Oceans and Seas ; Phylogeny ; Species Specificity ; Urochordata/*anatomy & histology/classification/*physiology ; },
abstract = {Megalodicopia hians Oka is a solitary ascidian belonging to the family Octacnemidae inhabiting the bathyal /abyssal zone as well as other octacnemid ascidians. The phylogenetic relationship of octacnemids is open to argument because of its extraordinary morphological features due to habitat adaptation, e.g., a pharynx lacking ciliated stigmata. Aggregations of M. hians were discovered by the manned submersible Shinkai 2000 in the bathyal seafloor of Toyama Bay, Japan Sea, in 2000; this was the first in situ observation of M. hians in the Japanese coastal waters. In 2001, a total of 36 M. hians specimens were collected from the bay (592 to approximately 978 m deep). In situ observation indicated that M. hians usually opens its large oral apertures to engulf the drifting food particles in the water current. Microscopical observation of the gut contents also showed that M. hians is a non selective macrophagous feeding on small crustaceans, diatoms, detritus, and so on. Along with the position of the intestinal loop and gonad, the morphological characteristics of the tunic (integument of ascidians) suggest that M. hians is closely related to Cionidae and/or Corellidae. Some symbiotic/parasitic organisms were occasionally found in the tunic, including rod-shaped bacteria, fungi-like multicellular structure, and spawns of unknown animals.},
}

Animals
Environment
*Feeding Behavior
Gonads/anatomy & histology
Integumentary System/anatomy & histology/microbiology
Intestines/anatomy & histology
Japan
Oceans and Seas
Phylogeny
Species Specificity
Urochordata/*anatomy & histology/classification/*physiology

@article {pmid12443689,
year = {2002},
author = {Yatsuda, AP and Eysker, M and Vieira-Bressan, MC and De Vries, E},
title = {A family of activation associated secreted protein (ASP) homologues of Cooperia punctata.},
journal = {Research in veterinary science},
volume = {73},
number = {3},
pages = {297-306},
doi = {10.1016/s0034-5288(02)00125-x},
pmid = {12443689},
issn = {0034-5288},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Western ; Cattle ; Cattle Diseases/*parasitology ; DNA, Complementary/genetics ; Enzyme-Linked Immunosorbent Assay ; Escherichia coli/genetics ; Helminth Proteins/*genetics/metabolism/physiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Helminth/genetics/metabolism ; Random Amplified Polymorphic DNA Technique ; Recombinant Proteins/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Trichostrongyloidea/*genetics/metabolism/physiology ; Trichostrongyloidiasis/parasitology/*veterinary ; },
abstract = {Activation-associated secreted proteins (ASP) of nematodes have been studied as potential vaccine components. In this study we report the cloning and analysis of cDNA and genomic sequences of Cooperia punctata and establish the presence of two 75% identical ASP-1 genes in C. punctata. Additional C. punctata ASP paralogues were shown to be present. Analysis of PCR products amplified from genomic DNA from a pool of worms revealed extensive sequence diversity within this family of proteins, reflecting the presence of different ASP paralogues in a single worm as well as extensive polymorphisms between different worms. ASP proteins contain a conserved region called the sperm-coating protein (SCP) domain of unknown function, which is present as a single copy in proteins from yeast and a wide range of multi-cellular organisms. Only in three nematodes has a protein composed of duplicated SCP-domains been identified. C. punctata is the first organism in which at least two such genes are found. Database searches identified similarity of the C-terminal cysteine-rich domain of ASP proteins to a nematode metallothionein motif. Cp-asp-1b was expressed in Escherichia coli and both the N-terminal and C-terminal domain were shown to be recognized by sera of C. punctata infected bovines. The description of the asp gene family of C. punctata provides the basis for more detailed studies into the extent of variation and immunological recognition of this family that may assist in rational vaccine design.},
}

Amino Acid Sequence
Animals
Base Sequence
Blotting, Western
Cattle
Cattle Diseases/*parasitology
DNA, Complementary/genetics
Enzyme-Linked Immunosorbent Assay
Escherichia coli/genetics
Helminth Proteins/*genetics/metabolism/physiology
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
RNA, Helminth/genetics/metabolism
Random Amplified Polymorphic DNA Technique
Recombinant Proteins/genetics/metabolism
Reverse Transcriptase Polymerase Chain Reaction
Sequence Homology, Nucleic Acid
Trichostrongyloidea/*genetics/metabolism/physiology
Trichostrongyloidiasis/parasitology/*veterinary

@article {pmid12452280,
year = {2002},
author = {Andrianopoulos, A},
title = {Control of morphogenesis in the human fungal pathogen Penicillium marneffei.},
journal = {International journal of medical microbiology : IJMM},
volume = {292},
number = {5-6},
pages = {331-347},
doi = {10.1078/1438-4221-00217},
pmid = {12452280},
issn = {1438-4221},
mesh = {Cell Division/genetics ; Gene Expression Regulation, Fungal ; Humans ; Hyphae/genetics/*growth & development ; Penicillium/genetics/*growth & development ; Phylogeny ; Signal Transduction/genetics ; Spores, Fungal/genetics/*growth & development ; Yeasts/genetics/*growth & development ; },
abstract = {Fungal pathogens are an increasing threat to human health due to the increasing population of immunocompromised individuals and the increased incidence of treatment-derived infections. Penicillium marneffei is an emerging fungal pathogen endemic to South-east Asia, where it is AIDS defining. Like many other fungal pathogens, P. marneffei is capable of alternating between a filamentous and a yeast growth form, known as dimorphic switching, in response to environmental stimuli. P. marneffei grows in the filamentous form at 25 degrees C and in the yeast form at 37 degrees C. During filamentous growth and in response to environmental cues, P. marneffei undergoes asexual development to form complex multicellular structures from which the infectious agents, the conidia, are produced. At 37 degrees C, P. marneffei undergoes the dimorphic switching program to produce the pathogenic yeast cells. These yeast cells are found intracellularly in the mononuclear phagocyte system of the host and divide by fission, in contrast to the budding mode of division exhibited by most other fungal pathogens. In addition, P. marneffei is evolutionarily distinct from most other dimorphic fungal pathogens and is the only known Penicillium species which exhibits dimorphic growth. The unique evolutionary history of P. marneffei and the rapidly increasing incidence of infection, coupled with the presence of both complex asexual development and dimorphic switching programs in one organism, makes this system a valuable one for the study of morphogenesis and pathogenicity. Recent development of molecular genetic techniques for P. marneffei, including DNA-mediated transformation, have greatly facilitated the study of these two important morphogenetic programs, asexual development and dimorphic switching, and we are beginning to uncover important determinants which control these events. Understand these programs is providing insights into the biology of P. marneffei and its pathogenic capacity.},
}

Cell Division/genetics
Gene Expression Regulation, Fungal
Humans
Hyphae/genetics/*growth & development
Penicillium/genetics/*growth & development
Phylogeny
Signal Transduction/genetics
Spores, Fungal/genetics/*growth & development
Yeasts/genetics/*growth & development

@article {pmid12552117,
year = {2003},
author = {Burger, G and Forget, L and Zhu, Y and Gray, MW and Lang, BF},
title = {Unique mitochondrial genome architecture in unicellular relatives of animals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {100},
number = {3},
pages = {892-897},
pmid = {12552117},
issn = {0027-8424},
mesh = {Amino Acid Motifs ; Animals ; Base Sequence ; Chromosomes/ultrastructure ; DNA, Mitochondrial/*genetics ; Electrophoresis, Agar Gel ; *Genome ; Genome, Bacterial ; Genome, Fungal ; Genome, Plant ; Humans ; Introns ; Models, Genetic ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; },
abstract = {Animal mtDNAs are typically small (approximately 16 kbp), circular-mapping molecules that encode 37 or fewer tightly packed genes. Here we investigate whether similarly compact mitochondrial genomes are also present in the closest unicellular relatives of animals, i.e., choanoflagellate and ichthyosporean protists. We find that the gene content and architecture of the mitochondrial genomes of the choanoflagellate Monosiga brevicollis, the ichthyosporean Amoebidium parasiticum, and Metazoa are radically different from one another. The circular-mapping choanoflagellate mtDNA with its long intergenic regions is four times as large and contains two times as many protein genes as do animal mtDNAs, whereas the ichthyosporean mitochondrial genome totals >200 kbp and consists of several hundred linear chromosomes that share elaborate terminal-specific sequence patterns. The highly peculiar organization of the ichthyosporean mtDNA raises questions about the mechanism of mitochondrial genome replication and chromosome segregation during cell division in this organism. Considering that the closest unicellular relatives of animals possess large, spacious, gene-rich mtDNAs, we posit that the distinct compaction characteristic of metazoan mitochondrial genomes occurred simultaneously with the emergence of a multicellular body plan in the animal lineage.},
}

Amino Acid Motifs
Animals
Base Sequence
Chromosomes/ultrastructure
DNA, Mitochondrial/*genetics
Electrophoresis, Agar Gel
*Genome
Genome, Bacterial
Genome, Fungal
Genome, Plant
Humans
Introns
Models, Genetic
Molecular Sequence Data
Open Reading Frames
Phylogeny

@article {pmid12568336,
year = {2002},
author = {Winckler, T and Dingermann, T and Glöckner, G},
title = {Dictyostelium mobile elements: strategies to amplify in a compact genome.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {59},
number = {12},
pages = {2097-2111},
doi = {10.1007/s000180200010},
pmid = {12568336},
issn = {1420-682X},
mesh = {Animals ; *DNA Transposable Elements ; Dictyostelium/*genetics ; Genes, Protozoan ; Genome, Protozoan ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; *Retroelements ; },
abstract = {Dictyostelium discoideum is a eukaryotic microorganism that is attractive for the study of fundamental biological phenomena such as cell-cell communication, formation of multicellularity, cell differentiation and morphogenesis. Large-scale sequencing of the D. discoideum genome has provided new insights into evolutionary strategies evolved by transposable elements (TEs) to settle in compact microbial genomes and to maintain active populations over evolutionary time. The high gene density (about 1 gene/2.6 kb) of the D. discoideum genome leaves limited space for selfish molecular invaders to move and amplify without causing deleterious mutations that eradicate their host. Targeting of transfer RNA (tRNA) gene loci appears to be a generally successful strategy for TEs residing in compact genomes to insert away from coding regions. In D. discoideum, tRNA gene-targeted retrotransposition has evolved independently at least three times by both non-long terminal repeat (LTR) retrotransposons and retrovirus-like LTR retrotransposons. Unlike the nonspecifically inserting D. discoideum TEs, which have a strong tendency to insert into preexisting TE copies and form large and complex clusters near the ends of chromosomes, the tRNA gene-targeted retrotransposons have managed to occupy 75% of the tRNA gene loci spread on chromosome 2 and represent 80% of the TEs recognized on the assembled central 6.5-Mb part of chromosome 2. In this review we update the available information about D. discoideum TEs which emerges both from previous work and current large-scale genome sequencing, with special emphasis on the fact that tRNA genes are principal determinants of retrotransposon insertions into the D. discoideum genome.},
}

Animals
*DNA Transposable Elements
Dictyostelium/*genetics
Genes, Protozoan
Genome, Protozoan
Open Reading Frames
Phylogeny
RNA, Transfer/genetics
*Retroelements

@article {pmid12672462,
year = {2003},
author = {Maytal-Kivity, V and Pick, E and Piran, R and Hofmann, K and Glickman, MH},
title = {The COP9 signalosome-like complex in S. cerevisiae and links to other PCI complexes.},
journal = {The international journal of biochemistry & cell biology},
volume = {35},
number = {5},
pages = {706-715},
doi = {10.1016/s1357-2725(02)00378-3},
pmid = {12672462},
issn = {1357-2725},
mesh = {Amino Acid Sequence ; COP9 Signalosome Complex ; Cysteine Endopeptidases/genetics ; DNA-Binding Proteins/*chemistry/genetics ; Humans ; Intracellular Signaling Peptides and Proteins ; Microscopy, Fluorescence ; Molecular Sequence Data ; Multienzyme Complexes/genetics ; Multiprotein Complexes ; Peptide Hydrolases ; Phylogeny ; Proteasome Endopeptidase Complex ; Proteins/*chemistry/genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics ; Saccharomycetales/*genetics ; Sequence Alignment ; Sequence Homology ; Transcription Factors/*chemistry/genetics ; Ubiquitin/genetics ; },
abstract = {The COP9 signalosome (CSN), the lid subcomplex of the proteasome and translational initiation factor 3 (eIF3) share structural similarities and are often referred to as the PCI family of complexes. In multicellular eukaryotes, the CSN is highly conserved as an 8-subunit complex but in Saccharomyces cerevisiae the complex is rather divergent. We further characterize the composition and properties of the CSN in budding yeast and its interactions with these related complexes. Using the generalized profile method we identified CSN candidates, four with PCI domains: Csn9, Csn10, Pci8/Csn11, and Csn12, and one with an MPN domain, Csn5/Rri1. These proteins and an additional interactor, Csi1, were tested for pairwise interactions by yeast two-hybrid and were found to form a cluster surrounding Csn12. Csn5 and Csn12 cofractionate in a complexed form with an apparent molecular weight of roughly 250kDa. However, Csn5 migrates as a monomer in Deltacsn12 supporting the pivotal role of Csn12 in stabilizing the complex. Confocal fluorescence microscopy detects GFP-tagged Csn5 preferentially in the nucleus, whereas in absence of Csn12, Csn10, Pci8/Csn11, or Csi1, Csn5 is delocalized throughout the cell, indicating that multiple subunits are required for nuclear localization of Csn5. Two CSN subunits, Csn9 and Csi1, interact with the proteasome lid subunit Rpn5. Pci8/Csn11 has previously been shown to interact with eIF3. Together, these results point to a network of interactions between these three structurally similar, yet functionally diverse, complexes.},
}

Amino Acid Sequence
COP9 Signalosome Complex
Cysteine Endopeptidases/genetics
DNA-Binding Proteins/*chemistry/genetics
Humans
Intracellular Signaling Peptides and Proteins
Microscopy, Fluorescence
Molecular Sequence Data
Multienzyme Complexes/genetics
Multiprotein Complexes
Peptide Hydrolases
Phylogeny
Proteasome Endopeptidase Complex
Proteins/*chemistry/genetics
Saccharomyces cerevisiae/*genetics
Saccharomyces cerevisiae Proteins/*chemistry/genetics
Saccharomycetales/*genetics
Sequence Alignment
Sequence Homology
Transcription Factors/*chemistry/genetics
Ubiquitin/genetics

@article {pmid12718397,
year = {2003},
author = {Furusawa, G and Yoshikawa, T and Yasuda, A and Sakata, T},
title = {Algicidal activity and gliding motility of Saprospira sp. SS98-5.},
journal = {Canadian journal of microbiology},
volume = {49},
number = {2},
pages = {92-100},
doi = {10.1139/w03-017},
pmid = {12718397},
issn = {0008-4166},
mesh = {Base Sequence ; Culture Media ; Diatoms/*cytology/drug effects/ultrastructure ; Gram-Negative Anaerobic Straight, Curved, and Helical Rods/cytology/*physiology/ultrastructure ; Microtubules/ultrastructure ; Movement ; Peptones/pharmacology ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Alignment ; },
abstract = {A marine bacterium, Saprospira sp. SS98-5, which was isolated from Kagoshima Bay, Japan, was able to kill and lyse the cells of the diatom Chaetoceros ceratosporum. The multicellular filamentous cells of this bacterium captured the diatom cells, formed cell aggregates, and lysed them in an enriched sea water (ESS) liquid medium. Strain SS98-5 also formed plaques on double layer agar plates incorporating diatom cells. The diatom cell walls were partially degraded at the contact sites with the bacteria, the bacteria invaded from there into the diatom cells, and then the diatom cells were completely lysed. The strain possessed gliding motility and grew as spreading colonies on ESS agar plates containing lower concentrations of polypeptone (below 0.1%) while forming nonspreading colonies on ESS agar plates containing 0.5% polypeptone. Electron micrographs of ultrathin sections demonstrated that microtubule-like structures were observable only in gliding motile cells. Both the gliding motility and the microtubule-like structures were diminished by the addition of podophyllotoxin, an inhibitor of microtubule assembly, suggesting that the microtubule-like structures observed in these bacterial cells are related to their gliding motility.},
}

Base Sequence
Culture Media
Diatoms/*cytology/drug effects/ultrastructure
Gram-Negative Anaerobic Straight, Curved, and Helical Rods/cytology/*physiology/ultrastructure
Microtubules/ultrastructure
Movement
Peptones/pharmacology
Phylogeny
RNA, Ribosomal, 16S/analysis
Sequence Alignment

@article {pmid12724425,
year = {2003},
author = {Jedrusik, MA and Schulze, E},
title = {Telomeric position effect variegation in Saccharomyces cerevisiae by Caenorhabditis elegans linker histones suggests a mechanistic connection between germ line and telomeric silencing.},
journal = {Molecular and cellular biology},
volume = {23},
number = {10},
pages = {3681-3691},
pmid = {12724425},
issn = {0270-7306},
mesh = {Animals ; Caenorhabditis elegans/*metabolism ; Cell Nucleus/metabolism ; Chromatin/metabolism ; DNA/metabolism ; Flow Cytometry ; Fluorescent Antibody Technique, Indirect ; *Gene Silencing ; Green Fluorescent Proteins ; Histones/metabolism ; Hydroxamic Acids/pharmacology ; Luminescent Proteins/metabolism ; Peptides/chemistry ; Phylogeny ; Precipitin Tests ; Protein Structure, Tertiary ; Protein Synthesis Inhibitors/pharmacology ; Protein Transport ; RNA Interference ; Saccharomyces cerevisiae/*metabolism ; Software ; *Telomere ; },
abstract = {Linker histones are nonessential for the life of single-celled eukaryotes. Linker histones, however, can be important components of specific developmental programs in multicellular animals and plants. For Caenorhabditis elegans a single linker histone variant (H1.1) is essential in a chromatin silencing process which is crucial for the proliferation and differentiation of the hermaphrodite germ line. In this study we analyzed the whole linker histone complement of C. elegans by telomeric position effect variegation in budding yeast. In this assay an indicator gene (URA3) placed close to the repressive telomeric chromatin structure is subject to epigenetically inherited gene inactivation. Just one out of seven C. elegans linker histones (H1.1) was able to enhance the telomeric position effect in budding yeast. Since these results reflect the biological function of H1.1 in C. elegans, we suggest that chromatin silencing in C. elegans is governed by molecular mechanisms related to the telomere-dependent silencing in budding yeast. We confirmed this hypothesis by testing C. elegans homologs of three yeast genes which are established modifiers of the yeast telomeric chromatin structure (SIR2, SET1, and RAD17) for their influence on repeat-dependent transgene silencing for C. elegans.},
}

Animals
Caenorhabditis elegans/*metabolism
Cell Nucleus/metabolism
Chromatin/metabolism
DNA/metabolism
Flow Cytometry
Fluorescent Antibody Technique, Indirect
*Gene Silencing
Green Fluorescent Proteins
Histones/metabolism
Hydroxamic Acids/pharmacology
Luminescent Proteins/metabolism
Peptides/chemistry
Phylogeny
Precipitin Tests
Protein Structure, Tertiary
Protein Synthesis Inhibitors/pharmacology
Protein Transport
RNA Interference
Saccharomyces cerevisiae/*metabolism
Software
*Telomere

@article {pmid12736201,
year = {2003},
author = {Hennig, L and Taranto, P and Walser, M and Schönrock, N and Gruissem, W},
title = {Arabidopsis MSI1 is required for epigenetic maintenance of reproductive development.},
journal = {Development (Cambridge, England)},
volume = {130},
number = {12},
pages = {2555-2565},
doi = {10.1242/dev.00470},
pmid = {12736201},
issn = {0950-1991},
mesh = {Arabidopsis/*embryology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Computational Biology ; Flowering Tops/growth & development ; Gene Expression Regulation, Plant/physiology ; Heterochromatin/physiology ; Phylogeny ; Plant Leaves/growth & development ; RNA Interference/physiology ; RNA, Messenger/metabolism ; },
abstract = {WD40 repeat proteins similar to yeast MSI1 are conserved in animals and plants, in which they participate in complexes involved in chromatin metabolism. Although MSI1-like proteins are well characterised biochemically, their function in the development of multicellular eukaryotes is not well understood. We constructed Arabidopsis plants in which the AtMSI1 protein level was altered. Strong ectopic expression of AtMSI1 produced no visible altered phenotype, but reduction of AtMSI1 dramatically affected development. The primary shoot apical meristem was unable to develop organs after the transition to flowering. Flowers that developed on floral shoots from axillary meristems experienced a progressive loss of floral morphology, including a reduction in size of the petals and stamens and the development of carpel-like sepals. Ovule development was disrupted in all flowers, resulting in complete female sterility. Molecular analysis of the mutant plants revealed that AtMSI1 is required to maintain the correct temporal and organ-specific expression of homeotic genes, including AGAMOUS and APETALA2. In contrast, FAS1 and FAS2, which together with AtMSI1 form the chromatin assembly complex CAF-1, are not required for repression of these genes. Therefore, AtMSI1 has specific functions in addition to CAF-1-mediated chromatin assembly. Efficient formation of heterochromatin, but not methylation of centromeric DNA repeats, depends on AtMSI1 presence demonstrating a key role of AtMSI1 in maintenance of chromatin structure.},
}

Arabidopsis/*embryology/genetics
Arabidopsis Proteins/genetics/*metabolism
Computational Biology
Flowering Tops/growth & development
Gene Expression Regulation, Plant/physiology
Heterochromatin/physiology
Phylogeny
Plant Leaves/growth & development
RNA Interference/physiology
RNA, Messenger/metabolism

@article {pmid12752763,
year = {2003},
author = {Perović, S and Schröder, HC and Sudek, S and Grebenjuk, VA and Batel, R and Stifanić, M and Müller, IM and Müller, WE},
title = {Expression of one sponge Iroquois homeobox gene in primmorphs from Suberites domuncula during canal formation.},
journal = {Evolution & development},
volume = {5},
number = {3},
pages = {240-250},
doi = {10.1046/j.1525-142x.2003.03023.x},
pmid = {12752763},
issn = {1520-541X},
mesh = {Animals ; Base Sequence ; Blotting, Northern ; Cluster Analysis ; DNA Primers ; Ferric Compounds/metabolism ; *Gene Expression Profiling ; Genes, Homeobox/*genetics ; In Situ Hybridization ; Molecular Sequence Data ; *Phylogeny ; Porifera/*anatomy & histology/*genetics ; Sequence Analysis, DNA ; },
abstract = {Sponges (Porifera) represent the evolutionary oldest multicellular animals. They are provided with the basic molecules involved in cell-cell and cell-matrix interactions. We report here the isolation and characterization of a complementary DNA from the sponge Suberites domuncula coding for the sponge homeobox gene, SUBDOIRX-a. The deduced polypeptide with a predicted Mr of 44,375 possesses the highly conserved Iroquois-homeodomain. We applied in situ hybridization to localize Iroquois in the sponge. The expression of this gene is highest in cells adjacent to the canals of the sponge in the medulla region. To study the expression of Iroquois during development, the in vitro primmorph system from S. domuncula was used. During the formation of these three-dimensional aggregates composed of proliferating cells, the expression of Iroquois depends on ferric iron and water current. An increased expression in response to water current is paralleled with the formation of canal-like pores in the primmorphs. It is suggested that Iroquois expression is involved in the formation of the aquiferous system, the canals in sponges and the canal-like structures in primmorphs.},
}

Animals
Base Sequence
Blotting, Northern
Cluster Analysis
DNA Primers
Ferric Compounds/metabolism
*Gene Expression Profiling
Genes, Homeobox/*genetics
In Situ Hybridization
Molecular Sequence Data
*Phylogeny
Porifera/*anatomy & histology/*genetics
Sequence Analysis, DNA

@article {pmid12911623,
year = {2003},
author = {Bouchard, C and Ribeiro, P and Dubé, F and Anctil, M},
title = {A new G protein-coupled receptor from a primitive metazoan shows homology with vertebrate aminergic receptors and displays constitutive activity in mammalian cells.},
journal = {Journal of neurochemistry},
volume = {86},
number = {5},
pages = {1149-1161},
doi = {10.1046/j.1471-4159.2003.01924.x},
pmid = {12911623},
issn = {0022-3042},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biogenic Amines/metabolism ; Calcium Signaling ; Cell Line ; Cloning, Molecular ; Cnidaria/*metabolism ; GTP-Binding Proteins/metabolism ; Gene Expression ; Genes, Reporter ; Humans ; Kidney/cytology/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Receptors, Cell Surface/*genetics/*metabolism ; Sequence Homology, Amino Acid ; Signal Transduction/physiology ; Transfection ; Vertebrates ; },
abstract = {Biogenic amine receptors mediate wide-ranging hormonal and modulatory functions in vertebrates, but are largely unknown in primitive invertebrates. In a representative of the most basal multicellular animals possessing a nervous system, the cnidarian Renilla koellikeri, aminergic-like receptors were previously characterized pharmacologically and found to engender control of the animal's bioluminescent and peristaltic reactions. Using degenerate oligonucleotides in a RT-PCR strategy, we obtained a full-length cDNA encoding a polypeptide with typical G protein-coupled receptor (GPCR) characteristics and which displayed a significant degree of sequence similarity (up to 45%) to biogenic amine receptors, particularly dopamine and adrenergic receptors. The new receptor, named Ren1, did not resemble any one specific type of amine GPCR and thus could not be identified on the basis of sequence. Ren1 was expressed transiently and stably in cultured mammalian cells, as demonstrated by immunocytochemistry and western blotting. Functional analysis of transfected HEK293, LTK- and COS-7 cells, based on both cAMP and Ca2+ signalling assays, revealed that Ren1 was not activated by any of the known biogenic amines tested and several related metabolites. The results indicated, however, that cells stably expressing Ren1 contained, on average, an 11-fold higher level of cAMP than the controls, in the absence of agonist stimulation. The high basal cAMP levels were shown to be specific for Ren1 and to vary proportionally with the level of Ren1 expressed in the transfected cells. Taken together, the data suggested that Ren1 was expressed as a constitutively active receptor. Its identification provides a basis for examination of the early evolutionary emergence of GPCRs and their functional properties.},
}

Amino Acid Sequence
Animals
Base Sequence
Biogenic Amines/metabolism
Calcium Signaling
Cell Line
Cloning, Molecular
Cnidaria/*metabolism
GTP-Binding Proteins/metabolism
Gene Expression
Genes, Reporter
Humans
Kidney/cytology/metabolism
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
Receptors, Cell Surface/*genetics/*metabolism
Sequence Homology, Amino Acid
Signal Transduction/physiology
Transfection
Vertebrates

@article {pmid12915181,
year = {2003},
author = {Hernandez, VP and Higgins, L and Schwientek, MS and Fallon, AM},
title = {The histone-like C-terminal extension in ribosomal protein S6 in Aedes and Anopheles mosquitoes is encoded within the distal portion of exon 3.},
journal = {Insect biochemistry and molecular biology},
volume = {33},
number = {9},
pages = {901-910},
doi = {10.1016/s0965-1748(03)00095-x},
pmid = {12915181},
issn = {0965-1748},
support = {AI 20385/AI/NIAID NIH HHS/United States ; },
mesh = {Aedes/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Anopheles/chemistry/*genetics ; Base Sequence ; Cell Line ; DNA, Complementary/chemistry/genetics ; Drosophila/genetics ; Exons/*genetics ; Histones/*chemistry/genetics ; Introns/genetics ; Molecular Sequence Data ; Phylogeny ; Ribosomal Protein S6/chemistry/*genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Ubiquitin/genetics ; },
abstract = {In eukaryotic cells, ribosomal protein S6 (RPS6) is the major phosphorylated protein on the small ribosomal subunit. In the mosquitoes Aedes aegypti and Aedes albopictus, the cDNA encoding RPS6 contains 300 additional nucleotides, relative to the Drosophila homolog. The additional sequence encodes a 100-amino acid, lysine-rich C-terminal extension of the RPS6 protein with 42-49% identity to histone H1 proteins from the chicken and other multicellular organisms. Using mass spectrometry we now show that the C-terminal extension predicted by the cDNA is present on RPS6 protein isolated from ribosomal subunits purified from Ae. albopictus cells. To expand our analysis beyond the genus Aedes, we cloned the rpS6 cDNA from an Anopheles stephensi mosquito cell line. The cDNA also encoded a lysine-rich C-terminal extension. However, in An. stephensi rpS6 the extension was approximately 70 amino acids longer than that in Ae. albopictus, and at the nucleotide level, it most closely resembled histone H1 proteins from the unicellular eukaryotes Leishmania and Chlamydomonas, and the bacterium Bordetella pertussis. To examine how the histone-like C-terminal extension is encoded in the genome, we used PCR-based approaches to obtain the genomic DNA sequence encoding Ae. aegypti and Ae. albopictus rpS6. The sequence encoding the histone-like C-terminal extension was contiguous with upstream coding sequence within a single open reading frame in Exon 3, indicating that the lysine-rich extension in mosquito RPS6 is not the result of an aberrant splicing event. An in silico investigation of the Anopheles gambiae genome based on the cDNA sequence from An. stephensi allowed us to map the An. gambiae gene to chromosome 2R, to deduce its exon-intron organization, and to confirm that Exon 3 encodes a C-terminal histone-like extension. Because the C-terminal extension is absent from Drosophila melanogaster, we examined a partial cDNA clone from a Psychodid fly, which shares a relatively recent common ancestor with the mosquitoes. The absence of the C-terminal extension in the Psychodid rpS6 cDNA suggests that the unusual RPS6 structure is restricted to a relatively small group of flies in the Nematocera.},
}

Aedes/chemistry/*genetics
Amino Acid Sequence
Animals
Anopheles/chemistry/*genetics
Base Sequence
Cell Line
DNA, Complementary/chemistry/genetics
Drosophila/genetics
Exons/*genetics
Histones/*chemistry/genetics
Introns/genetics
Molecular Sequence Data
Phylogeny
Ribosomal Protein S6/chemistry/*genetics
Sequence Homology, Amino Acid
Sequence Homology, Nucleic Acid
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Ubiquitin/genetics

@article {pmid13678526,
year = {2003},
author = {Dixon, DP and Van Lith, M and Edwards, R and Benham, A},
title = {Cloning and initial characterization of the Arabidopsis thaliana endoplasmic reticulum oxidoreductins.},
journal = {Antioxidants & redox signaling},
volume = {5},
number = {4},
pages = {389-396},
doi = {10.1089/152308603768295122},
pmid = {13678526},
issn = {1523-0864},
mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Base Sequence ; Cell Line ; Cloning, Molecular ; Exons/genetics ; Genes, Plant/genetics ; Glycoproteins/chemistry/*genetics/*metabolism ; Glycosylation ; Humans ; Introns/genetics ; Membrane Glycoproteins/*genetics/metabolism ; Molecular Sequence Data ; Oxidoreductases ; Oxidoreductases Acting on Sulfur Group Donors ; Phylogeny ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; },
abstract = {The oxidation and isomerization of disulfide bonds is necessary for the growth of all organisms. In yeast, the oxidative folding of secretory pathway proteins is catalyzed by protein disulfide isomerase (PDI), which requires Ero1p (endoplasmic reticulum oxidoreductin) for its own oxidation. In Homo sapiens, two homologues of Ero1p, Ero1-Lalpha and Ero1-Lbeta, have been cloned. Both Ero1-Lalpha and Ero1-Lbeta interact via disulfide bonds with PDI and support the oxidation of immunoglobulin light chains. However, the function of Ero proteins in plants has not yet been analyzed. In this article, we report the cloning of the two Ero1p homologues present in Arabidopsis thaliana, demonstrating that one of the cDNAs has a shorter terminal exon than predicted and differs from the annotated sequence found in the genome database. Sequence analysis of the Arabidopsis endoplasmic reticulum oxidoreductins (AEROs) reveals that both AERO1 and AERO2 are more closely related to each other than to either of the human Eros. Both in vitro translated AERO proteins are targeted to the endoplasmic reticulum and glycosylated. The ability to use a genetically tractable multicellular organism in combination with biochemical approaches should further our understanding of redox networks and Ero function in both plants and animals.},
}

Arabidopsis/*genetics
Arabidopsis Proteins/*genetics/metabolism
Base Sequence
Cell Line
Cloning, Molecular
Exons/genetics
Genes, Plant/genetics
Glycoproteins/chemistry/*genetics/*metabolism
Glycosylation
Humans
Introns/genetics
Membrane Glycoproteins/*genetics/metabolism
Molecular Sequence Data
Oxidoreductases
Oxidoreductases Acting on Sulfur Group Donors
Phylogeny
*Saccharomyces cerevisiae Proteins
Sequence Alignment

@article {pmid14604590,
year = {2003},
author = {Michor, F and Frank, SA and May, RM and Iwasa, Y and Nowak, MA},
title = {Somatic selection for and against cancer.},
journal = {Journal of theoretical biology},
volume = {225},
number = {3},
pages = {377-382},
doi = {10.1016/s0022-5193(03)00267-4},
pmid = {14604590},
issn = {0022-5193},
mesh = {Animals ; Apoptosis ; Cell Division/genetics ; *Genes, Tumor Suppressor ; Genetic Drift ; Models, Biological ; Mutation ; Neoplasms/*genetics/pathology ; *Oncogenes ; },
abstract = {In multicellular organisms, cells cooperate within a well-defined developmental program. Cancer is a breakdown of such cooperation: cells mutate to phenotypes of uncoordinated proliferation. We study basic principles of the architecture of solid tissues that influence the rate of cancer initiation. In particular, we explore how somatic selection acts to prevent or to promote cancer. Cells with mutations in oncogenes or tumor suppressor genes often have increased proliferation rates. Somatic selection increases their abundance and thus enhances the risk of cancer. Many potentially harmful mutations, however, increase the probability of triggering apoptosis and, hence, initially lead to cells with reduced net proliferation rates. Such cells are eliminated by somatic selection, which therefore also works to reduce the risk of cancer. We show that a tissue organization into small compartments avoids the rapid spread of mutations in oncogenes and tumor suppressor genes, but promotes genetic instability. In small compartments, genetic instability, which confers a selective disadvantage for the cell, can spread by random drift. If both deleterious and advantageous mutations participate in tumor initiation, then we find an intermediate optimum for the compartment size.},
}

Animals
Apoptosis
Cell Division/genetics
*Genes, Tumor Suppressor
Genetic Drift
Models, Biological
Mutation
Neoplasms/*genetics/pathology
*Oncogenes

@article {pmid14657113,
year = {2003},
author = {Sekiguchi, Y and Yamada, T and Hanada, S and Ohashi, A and Harada, H and Kamagata, Y},
title = {Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {53},
number = {Pt 6},
pages = {1843-1851},
doi = {10.1099/ijs.0.02699-0},
pmid = {14657113},
issn = {1466-5026},
mesh = {Bacteria/classification ; Chloroflexi/*classification/*genetics/growth & development/ultrastructure ; Microscopy, Electron ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {Two thermophilic, Gram-negative, non-spore-forming, multicellular filamentous micro-organisms were isolated from thermophilic granular sludge in an upflow anaerobic sludge blanket reactor treating fried soybean-curd manufacturing waste water (strain UNI-1(T)) and from a hot spring sulfur-turf in Japan (strain STL-6-O1(T)). The filaments were longer than 100 microm and of 0.2-0.3 microm (strain UNI-1(T)) or 0.7-0.8 microm (strain STL-6-O1(T)) in width. Strain UNI-1(T) was a strictly anaerobic organism. The optimum temperature for growth was around 55 degrees C; growth occurred in the range 50-60 degrees C. The optimum pH for growth was around 7.0; growth occurred in the range pH 6.0-8.0. Strain STL-6-O1(T) was a facultatively aerobic bacterium. The optimum temperature for growth was around 55 degrees C; growth occurred in the range 37-65 degrees C. The optimum pH for growth was around 7.5-8.0; growth occurred in the range pH 7.0-9.0. The two organisms grew chemo-organotrophically on a number of carbohydrates and amino acids in the presence of yeast extract. The G+C content of the DNA of strains UNI-1(T) and STL-6-O1(T) was 54.5 and 59.0 mol%, respectively. Major cellular fatty acids for strain UNI-1(T) were C(16 : 0), C(15 : 0), C(14 : 0) and C(18 : 0), whereas those for strain STL-6-O1(T) were C(18 : 0), C(16 : 0), C(17 : 0) and iso-C(17 : 0). MK-10 was the major quinone from aerobically grown STL-6-O1(T) cells. Phylogenetic analyses based on 16S rDNA sequences revealed that both strains belong to an uncultured, previously recognized clone lineage of the phylum Chloroflexi (formerly known as green non-sulfur bacteria). These phenotypic and genetic properties suggested that each strain should be classified into a new independent genus; hence, the names Anaerolinea thermophila and Caldilinea aerophila are proposed for strains UNI-1(T) (=JCM 11387(T)=DSM 14523(T)) and STL-6-O1(T)(=JCM 11388(T)=DSM 14525(T)), respectively. These strains represent the type and sole species of the genera Anaerolinea and Caldilinea, respectively.},
}

Bacteria/classification
Chloroflexi/*classification/*genetics/growth & development/ultrastructure
Microscopy, Electron
Molecular Sequence Data
*Phylogeny

@article {pmid14660383,
year = {2003},
author = {Borucki, MK and Peppin, JD and White, D and Loge, F and Call, DR},
title = {Variation in biofilm formation among strains of Listeria monocytogenes.},
journal = {Applied and environmental microbiology},
volume = {69},
number = {12},
pages = {7336-7342},
pmid = {14660383},
issn = {0099-2240},
mesh = {Animals ; Bacteriological Techniques ; Biofilms/*growth & development ; Culture Media ; Humans ; Listeria monocytogenes/*classification/genetics/*growth & development/pathogenicity ; Microscopy, Electron, Scanning ; Milk/microbiology ; Phylogeny ; Polysaccharides, Bacterial/biosynthesis ; Polyvinyl Chloride ; Serotyping ; Stainless Steel ; },
abstract = {Contamination of food by Listeria monocytogenes is thought to occur most frequently in food-processing environments where cells persist due to their ability to attach to stainless steel and other surfaces. Once attached these cells may produce multicellular biofilms that are resistant to disinfection and from which cells can become detached and contaminate food products. Because there is a correlation between virulence and serotype (and thus phylogenetic division) of L. monocytogenes, it is important to determine if there is a link between biofilm formation and disease incidence for L. monocytogenes. Eighty L. monocytogenes isolates were screened for biofilm formation to determine if there is a robust relationship between biofilm formation, phylogenic division, and persistence in the environment. Statistically significant differences were detected between phylogenetic divisions. Increased biofilm formation was observed in Division II strains (serotypes 1/2a and 1/2c), which are not normally associated with food-borne outbreaks. Differences in biofilm formation were also detected between persistent and nonpersistent strains isolated from bulk milk samples, with persistent strains showing increased biofilm formation relative to nonpersistent strains. There were no significant differences detected among serotypes. Exopolysaccharide production correlated with cell adherence for high-biofilm-producing strains. Scanning electron microscopy showed that a high-biofilm-forming strain produced a dense, three-dimensional structure, whereas a low-biofilm-forming strain produced a thin, patchy biofilm. These data are consistent with data on persistent strains forming biofilms but do not support a consistent relationship between enhanced biofilm formation and disease incidence.},
}

Animals
Bacteriological Techniques
Biofilms/*growth & development
Culture Media
Humans
Listeria monocytogenes/*classification/genetics/*growth & development/pathogenicity
Microscopy, Electron, Scanning
Milk/microbiology
Phylogeny
Polysaccharides, Bacterial/biosynthesis
Polyvinyl Chloride
Serotyping
Stainless Steel

@article {pmid14693369,
year = {2004},
author = {Xu, R and Ye, X and Quinn Li, Q},
title = {AtCPSF73-II gene encoding an Arabidopsis homolog of CPSF 73 kDa subunit is critical for early embryo development.},
journal = {Gene},
volume = {324},
number = {},
pages = {35-45},
doi = {10.1016/j.gene.2003.09.025},
pmid = {14693369},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth & development ; Arabidopsis Proteins/*genetics ; Base Sequence ; Cleavage And Polyadenylation Specificity Factor ; Cloning, Molecular ; DNA, Bacterial/genetics ; DNA, Complementary/chemistry/genetics ; Fertility/genetics ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Genes, Lethal/genetics ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phenotype ; Phylogeny ; Seeds/*genetics/growth & development ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {We have identified and genetically characterized an Arabidopsis thaliana gene encoding a homolog of the Cleavage and Polyadenylation Specificity Factor (CPSF). This gene, named AtCPSF73-II, has been found to have a critical role in development by loss-of-function analysis using a Dissociation (Ds) insertion line SGT1922. The homozygous SGT1922 plants were lethal, but the heterozygous plants, while retaining their normal vegetative growth, displayed empty seed spaces as well as aborted seeds with embryos arrested at the globular stage. Genetic analysis indicated that the disruption of the AtCPSF73-II gene in SGT1922 plants caused severe reduction in genetic transmission of female gametes due to a loss of fertility, while the transmission of male gametes was normal. Two independent heterozygous lines with T-DNA insertion on the AtCPSF73-II gene also showed the similar phenotype. Gene expression analysis demonstrated that AtCPSF73-II was preferentially expressed in flowers. Protein sequence analysis revealed a group of AtCPSF73-II homologs with unknown function in animals, but not in yeast, which suggested a potential important function of this group of genes in the development of multicellular organisms.},
}

Amino Acid Sequence
Arabidopsis/*genetics/growth & development
Arabidopsis Proteins/*genetics
Base Sequence
Cleavage And Polyadenylation Specificity Factor
Cloning, Molecular
DNA, Bacterial/genetics
DNA, Complementary/chemistry/genetics
Fertility/genetics
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Genes, Lethal/genetics
Molecular Sequence Data
Mutagenesis, Insertional
Phenotype
Phylogeny
Seeds/*genetics/growth & development
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Amino Acid

@article {pmid15005568,
year = {2004},
author = {Seipel, K and Yanze, N and Schmid, V},
title = {The germ line and somatic stem cell gene Cniwi in the jellyfish Podocoryne carnea.},
journal = {The International journal of developmental biology},
volume = {48},
number = {1},
pages = {1-7},
doi = {10.1387/ijdb.15005568},
pmid = {15005568},
issn = {0214-6282},
mesh = {Aging/genetics ; Amino Acid Sequence ; Animals ; Cell Differentiation ; Cell Division ; Cloning, Molecular ; Gene Expression Regulation, Developmental ; Germ Cells/*metabolism ; Hydrozoa/*cytology/*genetics/growth & development ; Larva/genetics ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Stem Cells/*metabolism ; },
abstract = {In most animal phyla from insects to mammals, there is a clear division of somatic and germ line cells. This is however not the case in plants and some animal phyla including tunicates, flatworms and the basal phylum Cnidaria, where germ stem cells arise de novo from somatic cells. Piwi-like genes represent essential stem cell genes in diverse multicellular organisms. The cnidarian Piwihomolog Cniwiwas cloned from Podocoryne carnea, a hydrozoan with a full life cycle. CniwiRNA is present in all developmental stages with highest levels in the egg and the medusa. In the adult medusa, Cniwi expression is prominent in the gonads where it likely functions as a germ stem cell gene. The gene is also expressed, albeit at low levels, in differentiated somatic cells like the striated muscle of the medusa. Isolated striated muscle cells can be induced to transdifferentiate into smooth muscle cells which proliferate and differentiate into nerve cells. Cniwi expression is upregulated transiently after induction of transdifferentiation and again when the emerging smooth muscle cells proliferate and differentiate. The continuous low-level expression of an inducible stem cell gene in differentiated somatic cells may underlie the ability to form medusa buds from polyp cells and explain the extraordinary transdifferentation and regeneration potential of Podocoryne carnea.},
}

Aging/genetics
Amino Acid Sequence
Animals
Cell Differentiation
Cell Division
Cloning, Molecular
Gene Expression Regulation, Developmental
Germ Cells/*metabolism
Hydrozoa/*cytology/*genetics/growth & development
Larva/genetics
Molecular Sequence Data
Phylogeny
Proteins/*genetics
RNA, Messenger/genetics/metabolism
Sequence Alignment
Stem Cells/*metabolism

@article {pmid15031265,
year = {2004},
author = {Mouchel, CF and Briggs, GC and Hardtke, CS},
title = {Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root.},
journal = {Genes & development},
volume = {18},
number = {6},
pages = {700-714},
pmid = {15031265},
issn = {0890-9369},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*growth & development ; Arabidopsis Proteins/*genetics/metabolism ; Cell Division/*physiology ; *Gene Expression Regulation, Plant ; Molecular Sequence Data ; Phylogeny ; Plant Roots/*growth & development ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/*genetics/metabolism ; Yeasts/genetics/physiology ; },
abstract = {Mutant analysis has been tremendously successful in deciphering the genetics of plant development. However, less is known about the molecular basis of morphological variation within species, which is caused by naturally occurring alleles. In this study, we succeeded in isolating a novel regulator of root growth by exploiting natural genetic variation in the model plant Arabidopsis. Quantitative trait locus analysis of a cross between isogenized accessions revealed that a single locus is responsible for approximately 80% of the variance of the observed difference in root length. This gene, named BREVIS RADIX (BRX), controls the extent of cell proliferation and elongation in the growth zone of the root tip. We isolated BRX by positional cloning. BRX is a member of a small group of highly conserved genes, the BRX gene family, which is only found in multicellular plants. Analyses of Arabidopsis single and double mutants suggest that BRX is the only gene of this family with a role in root development. The BRX protein is nuclear localized and activates transcription in a heterologous yeast system, indicating that BRX family proteins represent a novel class of transcription factors. Thus, we have identified a novel regulatory factor controlling quantitative aspects of root growth.},
}

Amino Acid Sequence
Arabidopsis/genetics/*growth & development
Arabidopsis Proteins/*genetics/metabolism
Cell Division/*physiology
*Gene Expression Regulation, Plant
Molecular Sequence Data
Phylogeny
Plant Roots/*growth & development
Sequence Alignment
Sequence Analysis, DNA
Transcription Factors/*genetics/metabolism
Yeasts/genetics/physiology

@article {pmid15170403,
year = {2004},
author = {Nudleman, E and Kaiser, D},
title = {Pulling together with type IV pili.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {7},
number = {1-2},
pages = {52-62},
doi = {10.1159/000077869},
pmid = {15170403},
issn = {1464-1801},
mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; Bacterial Proteins/chemistry/*physiology ; Fimbriae, Bacterial/*physiology/*ultrastructure ; Models, Molecular ; Movement ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; },
abstract = {Type IV pili are an efficient and versatile device for bacterial surface motility. They are widespread among the beta-, gamma-, and delta-proteobacteria and the cyanobacteria. Within that diversity, there is a core of conserved proteins that includes the pilin (PilA), the motors PilB and PilT, and various components of pilus biogenesis and assembly, PilC, PilD, PilM, PilN, PilO, PilP, and PilQ. Progress has been made in understanding the motor and the secretory functions. PilT is a motor protein that catalyzes pilus retraction; PilB may play a similar role in pilus extension. Type IV pili are multifunctional complexes that can act as bacterial virulence factors because pilus-based motility is used to spread pathogens over the surface of a tissue, or to build multicellular structures such as biofilms and fruiting bodies.},
}

Bacteria/classification
*Bacterial Physiological Phenomena
Bacterial Proteins/chemistry/*physiology
Fimbriae, Bacterial/*physiology/*ultrastructure
Models, Molecular
Movement
Phylogeny
Protein Conformation
Protein Structure, Secondary

@article {pmid15186489,
year = {2004},
author = {Budd, A and Blandin, S and Levashina, EA and Gibson, TJ},
title = {Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?.},
journal = {Genome biology},
volume = {5},
number = {6},
pages = {R38},
pmid = {15186489},
issn = {1474-760X},
mesh = {Alphaproteobacteria/genetics ; Amino Acid Sequence/genetics ; Bacterial Proteins/genetics ; Bacteroidetes/genetics ; Betaproteobacteria/genetics ; Computational Biology/methods ; Cyanobacteria/genetics ; Databases, Protein ; Fusobacteria/genetics ; Gene Expression Profiling/methods ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Humans ; Magnetospirillum/genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/methods ; Phylogeny ; Spirochaetales/genetics ; alpha-Macroglobulins/*genetics ; },
abstract = {BACKGROUND: Invasive bacteria are known to have captured and adapted eukaryotic host genes. They also readily acquire colonizing genes from other bacteria by horizontal gene transfer. Closely related species such as Helicobacter pylori and Helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. The protease inhibitor alpha2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion.

RESULTS: Database searches with metazoan alpha2-macroglobulin sequences revealed homologous sequences in bacterial proteomes. The bacterial alpha2-macroglobulin phylogenetic distribution is patchy and violates the vertical descent model. Bacterial alpha2-macroglobulin genes are found in diverse clades, including purple bacteria (proteobacteria), fusobacteria, spirochetes, bacteroidetes, deinococcids, cyanobacteria, planctomycetes and thermotogae. Most bacterial species with bacterial alpha2-macroglobulin genes exploit higher eukaryotes (multicellular plants and animals) as hosts. Both pathogenically invasive and saprophytically colonizing species possess bacterial alpha2-macroglobulins, indicating that bacterial alpha2-macroglobulin is a colonization rather than a virulence factor.

CONCLUSIONS: Metazoan alpha2-macroglobulins inhibit proteases of pathogens. The bacterial homologs may function in reverse to block host antimicrobial defenses. Alpha2-macroglobulin was probably acquired one or more times from metazoan hosts and has then spread widely through other colonizing bacterial species by more than 10 independent horizontal gene transfers. yfhM-like bacterial alpha2-macroglobulin genes are often found tightly linked with pbpC, encoding an atypical peptidoglycan transglycosylase, PBP1C, that does not function in vegetative peptidoglycan synthesis. We suggest that YfhM and PBP1C are coupled together as a periplasmic defense and repair system. Bacterial alpha2-macroglobulins might provide useful targets for enhancing vaccine efficacy in combating infections.},
}

Alphaproteobacteria/genetics
Amino Acid Sequence/genetics
Bacterial Proteins/genetics
Bacteroidetes/genetics
Betaproteobacteria/genetics
Computational Biology/methods
Cyanobacteria/genetics
Databases, Protein
Fusobacteria/genetics
Gene Expression Profiling/methods
Gene Transfer, Horizontal/*genetics
Genes, Bacterial/genetics
*Genome, Bacterial
Humans
Magnetospirillum/genetics
Molecular Sequence Data
Oligonucleotide Array Sequence Analysis/methods
Phylogeny
Spirochaetales/genetics
alpha-Macroglobulins/*genetics

@article {pmid15221385,
year = {2004},
author = {Geldner, N},
title = {The plant endosomal system--its structure and role in signal transduction and plant development.},
journal = {Planta},
volume = {219},
number = {4},
pages = {547-560},
pmid = {15221385},
issn = {0032-0935},
mesh = {Animals ; Arabidopsis/growth & development/metabolism ; Drosophila/growth & development/metabolism ; Endosomes/*metabolism/physiology ; Models, Molecular ; Phylogeny ; Plant Development ; Plants/*metabolism ; *Signal Transduction ; },
abstract = {Endosomes are highly dynamic membrane systems that receive endocytosed plasma membrane proteins and sort them for either degradation or recycling back to the cell surface. In addition, they receive newly synthesised proteins destined for vacuolar/lysosomal compartments. Sorting in the endosomes is necessary for the establishment and maintenance of cell polarity and it is needed to control levels and function of receptors and transporters at the cellular surface. Both processes are crucial for correct cell behaviour during tissue and organ development and for intercellular communication in general. It has therefore become an imperative to investigate structure and function of the endosomal system if we want to obtain a deeper mechanistic understanding of signal transduction and development. This review will compare our current understanding of endosomal trafficking in animals and yeast with what is known in plants, and will highlight some important breakthroughs in our understanding of the role of endosomes in signal transduction and multicellular development in Drosophila, as well as in Arabidopsis.},
}

Animals
Arabidopsis/growth & development/metabolism
Drosophila/growth & development/metabolism
Endosomes/*metabolism/physiology
Models, Molecular
Phylogeny
Plant Development
Plants/*metabolism
*Signal Transduction

@article {pmid15226389,
year = {2004},
author = {Kessels, MM and Qualmann, B},
title = {The syndapin protein family: linking membrane trafficking with the cytoskeleton.},
journal = {Journal of cell science},
volume = {117},
number = {Pt 15},
pages = {3077-3086},
doi = {10.1242/jcs.01290},
pmid = {15226389},
issn = {0021-9533},
mesh = {Actin-Related Protein 2 ; Actin-Related Protein 3 ; Actins/metabolism ; Adaptor Proteins, Signal Transducing ; Animals ; Carrier Proteins/metabolism/*physiology ; Cell Membrane/*metabolism ; Chickens ; Cytoskeletal Proteins/metabolism ; Cytoskeleton/*metabolism ; Endocytosis ; Golgi Apparatus/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins ; Mice ; Models, Biological ; Nerve Tissue Proteins/chemistry ; Neuropeptides/metabolism/*physiology ; Phosphoproteins/physiology ; Phylogeny ; Protein Binding ; Protein Transport ; Proteins/physiology ; Rats ; Signal Transduction ; Wiskott-Aldrich Syndrome Protein, Neuronal ; },
abstract = {Syndapins--also called PACSINs--are highly conserved Src-homology 3 (SH3)-domain-containing proteins that seem to exist in all multicellular eukaryotes. They interact with the large GTPase dynamin and several other proteins implicated in vesicle trafficking. Syndapin-dynamin complexes appear to play an important role in vesicle fission at different donor membranes, including the plasma membrane (endocytosis) and Golgi membranes. In addition, syndapins are implicated in later steps of vesicle cycling in neuronal and non-neuronal cells. Syndapins also interact with N-WASP, a potent activator of the Arp2/3 complex that forms a critical part of the actin polymerization machinery. Syndapin oligomers can thereby couple bursts of actin polymerization with the vesicle fission step involving dynamins. This allows newly formed vesicles to move away from the donor membrane driven by actin polymerization. Syndapins also engage in additional interactions with molecules involved in several signal transduction pathways, producing crosstalk at the interface between membrane trafficking and the cytoskeleton. Given the distinct expression patterns of the different syndapins and their splice forms, these proteins could have isoform-specific functions.},
}

Actin-Related Protein 2
Actin-Related Protein 3
Actins/metabolism
Adaptor Proteins, Signal Transducing
Animals
Carrier Proteins/metabolism/*physiology
Cell Membrane/*metabolism
Chickens
Cytoskeletal Proteins/metabolism
Cytoskeleton/*metabolism
Endocytosis
Golgi Apparatus/metabolism
Humans
Intracellular Signaling Peptides and Proteins
Mice
Models, Biological
Nerve Tissue Proteins/chemistry
Neuropeptides/metabolism/*physiology
Phosphoproteins/physiology
Phylogeny
Protein Binding
Protein Transport
Proteins/physiology
Rats
Signal Transduction
Wiskott-Aldrich Syndrome Protein, Neuronal

@article {pmid15246533,
year = {2004},
author = {Bhatt, AM and Zhang, Q and Harris, SA and White-Cooper, H and Dickinson, H},
title = {Gene structure and molecular analysis of Arabidopsis thaliana ALWAYS EARLY homologs.},
journal = {Gene},
volume = {336},
number = {2},
pages = {219-229},
doi = {10.1016/j.gene.2004.03.033},
pmid = {15246533},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Base Sequence ; Binding Sites/genetics ; Cell Nucleus/metabolism ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Microscopy, Confocal ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic/genetics ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; TATA Box/genetics ; Nicotiana/cytology ; },
abstract = {Drosophila always early (aly) is essential for spermatogenesis, and is related to the LIN-9 protein of Caenorhabditis elegans; lin-9 is a class B Synthetic Multivulva gene (synMuvB) required for gonadal sheath development. Aly/LIN-9 have two conserved regions, called domains 1 and 2, which have been identified in homologous proteins from several multicellular eukaryotes, including the model plant Arabidopsis thaliana. We cloned and sequenced cDNAs of three different A. thaliana ALWAYS EARLY homologs (AtALY1, AtALY2 and AtALY3), analysed the expression pattern of these three genes and show that AtALY1, like Aly, is nuclear localised. We also demonstrate that the plant homologs of aly/lin-9 contain an additional N-terminal myb domain not present in the animal Aly/LIN-9 proteins, and that part of the ALY/LIN-9 conserved domain 1 in the predicted plant proteins is related to the TUDOR domain.},
}

Amino Acid Sequence
Arabidopsis/*genetics
Arabidopsis Proteins/*genetics/metabolism
Base Sequence
Binding Sites/genetics
Cell Nucleus/metabolism
Cloning, Molecular
DNA, Complementary/chemistry/genetics
Gene Expression Regulation, Plant
Genes, Plant/genetics
Microscopy, Confocal
Molecular Sequence Data
Phylogeny
Promoter Regions, Genetic/genetics
Recombinant Fusion Proteins/genetics/metabolism
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Amino Acid
TATA Box/genetics
Nicotiana/cytology

@article {pmid15280020,
year = {2004},
author = {Zeng, LC and Liu, F and Zhang, X and Zhu, ZD and Wang, ZQ and Han, ZG and Ma, WJ},
title = {hOLF44, a secreted glycoprotein with distinct expression pattern, belongs to an uncharacterized olfactomedin-like subfamily newly identified by phylogenetic analysis.},
journal = {FEBS letters},
volume = {571},
number = {1-3},
pages = {74-80},
doi = {10.1016/j.febslet.2004.06.059},
pmid = {15280020},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Animals ; Chickens ; Cloning, Molecular ; Conserved Sequence ; Embryo, Mammalian/physiology ; Embryo, Nonmammalian ; Extracellular Matrix Proteins/*classification/genetics ; Female ; Glycoproteins/*classification/*genetics ; Humans ; Molecular Sequence Data ; *Phylogeny ; Placenta/physiology ; Pregnancy ; Protein Biosynthesis/genetics ; Recombinant Proteins/chemistry/classification ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transcription, Genetic/genetics ; Transfection ; Intercellular Signaling Peptides and Proteins ; },
abstract = {Secreted proteins are indispensable for the development and differentiation of multicellular organisms. Cloning and characterization of novel or hypothetical genes encoding these proteins are therefore inviting great incentives. Using bioinformatics tools and experimental approaches, we isolated and characterized a human secreted glycoprotein, hOLF44, which contains a highly conserved olfactomedin-like (OLF) domain in the C-terminal. However, phylogenetic analysis revealed that hOLF44 is not clustered into any of the OLF subfamilies containing characterized members, and obviously falls into a newly identified uncharacterized OLF subfamily. Western blot analysis showed that hOLF44 protein is robustly secreted from the transfected COS-7 cells. Expression levels of hOLF44 mRNA are abundant in placenta, moderate in liver and heart, whereas fairly weak in other tissues examined. Immunohistochemical study on human term placenta demonstrated that hOLF44 is mainly localized extracellularly surrounding the syncytiotrophoblastic cells and very rarely expressed in the maternal decidua layer. These results suggest that hOLF44 may have matrix-related function involved in human placental and embryonic development, or play a similar role in other physiological processes. The further functional characterization of hOLF44 may provide insights into a better understanding of the newly identified OLF subfamily.},
}

Amino Acid Sequence
Animals
Chickens
Cloning, Molecular
Conserved Sequence
Embryo, Mammalian/physiology
Embryo, Nonmammalian
Extracellular Matrix Proteins/*classification/genetics
Female
Glycoproteins/*classification/*genetics
Humans
Molecular Sequence Data
*Phylogeny
Placenta/physiology
Pregnancy
Protein Biosynthesis/genetics
Recombinant Proteins/chemistry/classification
Sequence Alignment
Sequence Homology, Amino Acid
Transcription, Genetic/genetics
Transfection
Intercellular Signaling Peptides and Proteins

@article {pmid15308755,
year = {2004},
author = {Ramirez-Parra, E and López-Matas, MA and Fründt, C and Gutierrez, C},
title = {Role of an atypical E2F transcription factor in the control of Arabidopsis cell growth and differentiation.},
journal = {The Plant cell},
volume = {16},
number = {9},
pages = {2350-2363},
pmid = {15308755},
issn = {1040-4651},
mesh = {Arabidopsis/genetics/*growth & development/*metabolism ; Arabidopsis Proteins/*genetics/isolation & purification/*metabolism ; Cell Cycle Proteins/genetics/isolation & purification/*metabolism ; Cell Differentiation/*genetics ; Cell Division/genetics ; Cell Wall/genetics/metabolism ; DNA, Complementary/analysis/genetics ; DNA-Binding Proteins/*genetics/isolation & purification/*metabolism ; E2F Transcription Factors ; Gene Expression Regulation, Plant/*genetics ; Genes, cdc ; Growth Inhibitors/metabolism ; Hypocotyl/genetics/growth & development/metabolism ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Plant Roots/genetics/growth & development/metabolism ; Ploidies ; Promoter Regions, Genetic/genetics ; RNA, Messenger/metabolism ; Repressor Proteins/*genetics/metabolism ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics/isolation & purification/*metabolism ; },
abstract = {The balance between cell proliferation and differentiation is crucial in multicellular organisms, where it is regulated by complex gene expression networks. This is particularly relevant in plants because organogenesis is a continuous postembryonic process. Here, we investigate the function of Arabidopsis thaliana E2Ff, an atypical member of the E2F family of transcription factors, which acts independently of a dimerization partner. We have focused our analysis on roots and hypocotyls, organs where (1) cell proliferation and differentiation are spatially and/or temporally separated, (2) growth depends on cell expansion in the longitudinal axis, and (3) the AtE2Ff promoter is active. AtE2Ff overexpression produced a reduction in the size of differentiated cells of these organs. Cells of mutant e2ff-1 plants with reduced levels of AtE2Ff mRNA were larger, especially in the hypocotyl, suggesting a role as a growth regulator. These effects of AtE2Ff are not associated with changes in nuclear ploidy levels or in the expression of cell cycle marker genes. However, expression of a subset of cell wall biogenesis genes is misregulated in an AtE2Ff-dependent manner, and based on chromatin immunoprecipitation experiments, they seem to be direct E2F targets. Our results highlight the complex regulatory function exerted by E2F and suggest a possible role of AtE2Ff in repressing cell wall biosynthesis genes during cell elongation in differentiated cells.},
}

Arabidopsis/genetics/*growth & development/*metabolism
Arabidopsis Proteins/*genetics/isolation & purification/*metabolism
Cell Cycle Proteins/genetics/isolation & purification/*metabolism
Cell Differentiation/*genetics
Cell Division/genetics
Cell Wall/genetics/metabolism
DNA, Complementary/analysis/genetics
DNA-Binding Proteins/*genetics/isolation & purification/*metabolism
E2F Transcription Factors
Gene Expression Regulation, Plant/*genetics
Genes, cdc
Growth Inhibitors/metabolism
Hypocotyl/genetics/growth & development/metabolism
Molecular Sequence Data
Mutation/genetics
Phylogeny
Plant Roots/genetics/growth & development/metabolism
Ploidies
Promoter Regions, Genetic/genetics
RNA, Messenger/metabolism
Repressor Proteins/*genetics/metabolism
Sequence Homology, Amino Acid
Sequence Homology, Nucleic Acid
Transcription Factors/genetics/isolation & purification/*metabolism

@article {pmid15331635,
year = {2004},
author = {Okai, T and Araki, Y and Tada, M and Tateno, T and Kontani, K and Katada, T},
title = {Novel small GTPase subfamily capable of associating with tubulin is required for chromosome segregation.},
journal = {Journal of cell science},
volume = {117},
number = {Pt 20},
pages = {4705-4715},
doi = {10.1242/jcs.01347},
pmid = {15331635},
issn = {0021-9533},
mesh = {ADP-Ribosylation Factors/classification/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Cell Cycle/physiology ; Cell Line ; Chromosome Aberrations ; *Chromosome Segregation ; Drosophila melanogaster ; GTP Phosphohydrolases/classification/genetics/*metabolism ; Humans ; Microtubule-Associated Proteins/classification/genetics/*metabolism ; Microtubules/metabolism ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Isoforms/classification/genetics/*metabolism ; RNA Interference ; Sequence Alignment ; Tissue Distribution ; Tubulin/*metabolism ; },
abstract = {The small GTPase superfamily, which includes the Ras, Rho/Rac, Rab, Arf and Ran subfamilies, serves as a signal transducer to regulate cell proliferation and differentiation, actin cytoskeleton, membrane trafficking, and nuclear transport. Here, we identify novel GTPases (human Gie1 and Gie2) that form a distinct subfamily of the small GTPases in terms of their sequences and intracellular function. Gie stands for 'novel GTPase indispensable for equal segregation of chromosomes', and this subfamily is conserved in multicellular organisms. Expression of dominant-negative Gie mutants in mammalian cells or knockdown of Gie transcripts using RNA interference in Drosophila S2 cells induced abnormal morphology in the chromosome segregation. Gie protein has ability to bind to tubulin and localizes with microtubules on the spindle mid-zone in late mitosis. Furthermore, overexpression of Gie mutants that lack putative effector domains but have tubulin-binding ability induced micronucleus formation. Thus, this is the first report showing that a small GTPase subfamily capable of associating with microtubules might be involved in chromosome segregation.},
}

ADP-Ribosylation Factors/classification/genetics/*metabolism
Amino Acid Sequence
Animals
Cell Cycle/physiology
Cell Line
Chromosome Aberrations
*Chromosome Segregation
Drosophila melanogaster
GTP Phosphohydrolases/classification/genetics/*metabolism
Humans
Microtubule-Associated Proteins/classification/genetics/*metabolism
Microtubules/metabolism
Molecular Sequence Data
Multigene Family
Phylogeny
Protein Isoforms/classification/genetics/*metabolism
RNA Interference
Sequence Alignment
Tissue Distribution
Tubulin/*metabolism

@article {pmid15465387,
year = {2004},
author = {Malagnac, F and Lalucque, H and Lepère, G and Silar, P},
title = {Two NADPH oxidase isoforms are required for sexual reproduction and ascospore germination in the filamentous fungus Podospora anserina.},
journal = {Fungal genetics and biology : FG & B},
volume = {41},
number = {11},
pages = {982-997},
doi = {10.1016/j.fgb.2004.07.008},
pmid = {15465387},
issn = {1087-1845},
mesh = {Amino Acid Sequence ; Base Sequence ; Consensus Sequence ; DNA Primers ; Molecular Sequence Data ; NADPH Oxidases/antagonists & inhibitors/genetics/*metabolism ; Phylogeny ; Podospora/enzymology/genetics/*physiology ; Polymerase Chain Reaction ; Reproduction/physiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {NADPH oxidases are enzymes that produce reactive oxygen species (ROS) using electrons derived from intracellular NADPH. In plants and mammals, ROS have been proposed to be second messengers that signal defence responses or cell proliferation. By inactivating PaNox1 and PaNox2, two genes encoding NADPH oxidases, we demonstrate the crucial role of these enzymes in the control of two key steps of the filamentous fungus Podospora anserina life cycle. PaNox1 mutants are impaired in the differentiation of fruiting bodies from their progenitor cells, and the deletion of the PaNox2 gene specifically blocks ascospore germination. Furthermore, we show that PaNox1 likely acts upstream of PaASK1, a MAPKKK previously implicated in stationary phase differentiation and cell degeneration. Using nitro blue tetrazolium (NBT) and diaminobenzidine (DAB) assays, we detect a regulated secretion of both superoxide and peroxide during P. anserina vegetative growth. In addition, two oxidative bursts are shown to occur during fruiting body development and ascospore germination. Analysis of mutants establishes that PaNox1, PaNox2, and PaASK1, as well as a still unknown additional source of ROS, modulate these secretions. Altogether, our data point toward a role for NADPH oxidases in signalling fungal developmental transitions with respect to nutrient availability. These enzymes are conserved in other multicellular eukaryotes, suggesting that early eukaryotes were endowed with a redox network used for signalling purposes.},
}

Amino Acid Sequence
Base Sequence
Consensus Sequence
DNA Primers
Molecular Sequence Data
NADPH Oxidases/antagonists & inhibitors/genetics/*metabolism
Phylogeny
Podospora/enzymology/genetics/*physiology
Polymerase Chain Reaction
Reproduction/physiology
Sequence Alignment
Sequence Homology, Amino Acid

@article {pmid15467096,
year = {2004},
author = {Yu, FH and Catterall, WA},
title = {The VGL-chanome: a protein superfamily specialized for electrical signaling and ionic homeostasis.},
journal = {Science's STKE : signal transduction knowledge environment},
volume = {2004},
number = {253},
pages = {re15},
doi = {10.1126/stke.2532004re15},
pmid = {15467096},
issn = {1525-8882},
mesh = {Animals ; Calcium Signaling/*physiology ; Cations/*metabolism ; Homeostasis/*physiology ; Humans ; Membrane Potentials/physiology ; Models, Biological ; Phylogeny ; Potassium Channels, Calcium-Activated/*physiology ; Potassium Channels, Voltage-Gated/*physiology ; },
abstract = {Complex multicellular organisms require rapid and accurate transmission of information among cells and tissues and tight coordination of distant functions. Electrical signals and resulting intracellular calcium transients, in vertebrates, control contraction of muscle, secretion of hormones, sensation of the environment, processing of information in the brain, and output from the brain to peripheral tissues. In nonexcitable cells, calcium transients signal many key cellular events, including secretion, gene expression, and cell division. In epithelial cells, huge ion fluxes are conducted across tissue boundaries. All of these physiological processes are mediated in part by members of the voltage-gated ion channel protein superfamily. This protein superfamily of 143 members is one of the largest groups of signal transduction proteins, ranking third after the G protein-coupled receptors and the protein kinases in number. Each member of this superfamily contains a similar pore structure, usually covalently attached to regulatory domains that respond to changes in membrane voltage, intracellular signaling molecules, or both. Eight families are included in this protein superfamily-voltage-gated sodium, calcium, and potassium channels; calcium-activated potassium channels; cyclic nucleotide-modulated ion channels; transient receptor potential (TRP) channels; inwardly rectifying potassium channels; and two-pore potassium channels. This article identifies all of the members of this protein superfamily in the human genome, reviews the molecular and evolutionary relations among these ion channels, and describes their functional roles in cell physiology.},
}

Animals
Calcium Signaling/*physiology
Cations/*metabolism
Homeostasis/*physiology
Humans
Membrane Potentials/physiology
Models, Biological
Phylogeny
Potassium Channels, Calcium-Activated/*physiology
Potassium Channels, Voltage-Gated/*physiology

@article {pmid15522508,
year = {2004},
author = {Keim, CN and Martins, JL and Abreu, F and Rosado, AS and de Barros, HL and Borojevic, R and Lins, U and Farina, M},
title = {Multicellular life cycle of magnetotactic prokaryotes.},
journal = {FEMS microbiology letters},
volume = {240},
number = {2},
pages = {203-208},
doi = {10.1016/j.femsle.2004.09.035},
pmid = {15522508},
issn = {0378-1097},
mesh = {Brazil ; Cell Division ; DNA, Bacterial/chemistry/isolation & purification ; DNA, Ribosomal/chemistry/isolation & purification ; Deltaproteobacteria/classification/*cytology/isolation & purification/*physiology ; Genes, rRNA ; Geologic Sediments/microbiology ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {Most multicellular organisms, prokaryotes as well as animals, plants, and algae have a unicellular stage in their life cycle. Here, we describe an uncultured prokaryotic magnetotactic multicellular organism that reproduces by binary fission. It is multicellular in all the stages of its life cycle, and during most of the life cycle the cells organize into a hollow sphere formed by a functionally coordinated and polarized single-cell layer that grows by increasing the cell size. Subsequently, all the cells divide synchronously; the organism becomes elliptical, and separates into two equal spheres with a torsional movement in the equatorial plane. Unicellular bacteria similar to the cells that compose these organisms have not been found. Molecular biology analysis showed that all the organisms studied belong to a single genetic population phylogenetically related to many-celled magnetotactic prokaryotes in the delta sub-group of the proteobacteria. This appears to be the first report of a multicellular prokaryotic organism that proliferates by dividing into two equal multicellular organisms each similar to the parent one.},
}

Brazil
Cell Division
DNA, Bacterial/chemistry/isolation & purification
DNA, Ribosomal/chemistry/isolation & purification
Deltaproteobacteria/classification/*cytology/isolation & purification/*physiology
Genes, rRNA
Geologic Sediments/microbiology
Microscopy, Electron
Molecular Sequence Data
Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Seawater/microbiology
Sequence Analysis, DNA
*Water Microbiology

@article {pmid15596456,
year = {2005},
author = {Kapraun, DF},
title = {Nuclear DNA content estimates in multicellular green, red and brown algae: phylogenetic considerations.},
journal = {Annals of botany},
volume = {95},
number = {1},
pages = {7-44},
pmid = {15596456},
issn = {0305-7364},
mesh = {Cell Nucleus/genetics ; Chlorophyta/*genetics ; DNA/*genetics ; *Genome ; Microspectrophotometry ; Phaeophyceae/*genetics ; Phylogeny ; Rhodophyta/*genetics ; },
abstract = {BACKGROUND AND AIMS: Multicellular eukaryotic algae are phylogenetically disparate. Nuclear DNA content estimates have been published for fewer than 1 % of the described species of Chlorophyta, Phaeophyta and Rhodophyta. The present investigation aims to summarize the state of our knowledge and to add substantially to our database of C-values for theses algae.

METHODS: The DNA-localizing fluorochrome DAPI (4', 6-diamidino-2-phenylindole) and RBC (chicken erythrocyte) standard were used to estimate 2C values with static microspectrophotometry.

KEY RESULTS: 2C DNA contents for 85 species of Chlorophyta range from 0.2-6.1 pg, excluding the highly polyploidy Charales and Desmidiales with DNA contents of up to 39.2 and 20.7 pg, respectively. 2C DNA contents for 111 species of Rhodophyta range from 0.1-2.8 pg, and for 44 species of Phaeophyta range from 0.2-1.8 pg.

CONCLUSIONS: New availability of consensus higher-level molecular phylogenies provides a framework for viewing C-value data in a phylogenetic context. Both DNA content ranges and mean values are greater in taxa considered to be basal. It is proposed that the basal, ancestral genome in each algal group was quite small. Both mechanistic and ecological processes are discussed that could have produced the observed C-value ranges.},
}

Cell Nucleus/genetics
Chlorophyta/*genetics
DNA/*genetics
*Genome
Microspectrophotometry
Phaeophyceae/*genetics
Phylogeny
Rhodophyta/*genetics

@article {pmid15642091,
year = {2005},
author = {Sano, R and Juárez, CM and Hass, B and Sakakibara, K and Ito, M and Banks, JA and Hasebe, M},
title = {KNOX homeobox genes potentially have similar function in both diploid unicellular and multicellular meristems, but not in haploid meristems.},
journal = {Evolution & development},
volume = {7},
number = {1},
pages = {69-78},
doi = {10.1111/j.1525-142X.2005.05008.x},
pmid = {15642091},
issn = {1520-541X},
mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/chemistry ; Cell Lineage ; Cloning, Molecular ; DNA, Complementary/metabolism ; *Diploidy ; *Gene Expression Regulation, Plant ; *Genes, Homeobox ; Genes, Plant ; *Haploidy ; Homeodomain Proteins/genetics ; In Situ Hybridization ; Meristem/*physiology ; Models, Genetic ; Phenotype ; Phylogeny ; Plant Proteins/chemistry ; RNA/metabolism ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {Members of the class 1 knotted-like homeobox (KNOX) gene family are important regulators of shoot apical meristem development in angiosperms. To determine whether they function similarly in seedless plants, three KNOX genes (two class 1 genes and one class 2 gene) from the fern Ceratopteris richardii were characterized. Expression of both class 1 genes was detected in the shoot apical cell, leaf primordia, marginal part of the leaves, and vascular bundles by in situ hybridization, a pattern that closely resembles that of class 1 KNOX genes in angiosperms with compound leaves. The fern class 2 gene was expressed in all sporophyte tissues examined, which is characteristic of class 2 gene expression in angiosperms. All three CRKNOX genes were not detected in gametophyte tissues by RNA gel blot analysis. Arabidopsis plants overexpressing the fern class 1 genes resembled plants that overexpress seed plant class 1 KNOX genes in leaf morphology. Ectopic expression of the class 2 gene in Arabidopsis did not result in any unusual phenotypes. Taken together with phylogenetic analysis, our results suggest that (a) the class 1 and 2 KNOX genes diverged prior to the divergence of fern and seed plant lineages, (b) the class 1 KNOX genes function similarly in seed plant and fern sporophyte meristem development despite their differences in structure, (c) KNOX gene expression is not required for the development of the fern gametophyte, and (d) the sporophyte and gametophyte meristems of ferns are not regulated by the same developmental mechanisms at the molecular level.},
}

Arabidopsis/*genetics
Arabidopsis Proteins/chemistry
Cell Lineage
Cloning, Molecular
DNA, Complementary/metabolism
*Diploidy
*Gene Expression Regulation, Plant
*Genes, Homeobox
Genes, Plant
*Haploidy
Homeodomain Proteins/genetics
In Situ Hybridization
Meristem/*physiology
Models, Genetic
Phenotype
Phylogeny
Plant Proteins/chemistry
RNA/metabolism
RNA, Messenger/metabolism
Reverse Transcriptase Polymerase Chain Reaction

@article {pmid15740615,
year = {2005},
author = {Rivero, F and Muramoto, T and Meyer, AK and Urushihara, H and Uyeda, TQ and Kitayama, C},
title = {A comparative sequence analysis reveals a common GBD/FH3-FH1-FH2-DAD architecture in formins from Dictyostelium, fungi and metazoa.},
journal = {BMC genomics},
volume = {6},
number = {},
pages = {28},
pmid = {15740615},
issn = {1471-2164},
mesh = {Actin Cytoskeleton ; Actins/chemistry ; Amino Acid Sequence ; Animals ; Caenorhabditis elegans ; Carrier Proteins/chemistry ; DNA, Complementary/metabolism ; Databases, Protein ; Dictyostelium/*metabolism ; Drosophila ; Fungal Proteins/*chemistry ; Gene Expression Regulation ; Humans ; Microfilament Proteins/chemistry ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms ; Protein Structure, Tertiary ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/metabolism ; Schizosaccharomyces/metabolism ; Sequence Analysis, DNA/*methods ; Sequence Homology, Amino Acid ; },
abstract = {BACKGROUND: Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 (formin homology 1) domain. Formins act as profilin-modulated processive actin nucleators conserved throughout a wide range of eukaryotes.

RESULTS: We present a detailed sequence analysis of the 10 formins (ForA to J) identified in the genome of the social amoeba Dictyostelium discoideum. With the exception of ForI and ForC all other formins conform to the domain structure GBD/FH3-FH1-FH2-DAD, where DAD is the Diaphanous autoinhibition domain and GBD/FH3 is the Rho GTPase-binding domain/formin homology 3 domain that we propose to represent a single domain. ForC lacks a FH1 domain, ForI lacks recognizable GBD/FH3 and DAD domains and ForA, E and J have additional unique domains. To establish the relationship between formins of Dictyostelium and other organisms we constructed a phylogenetic tree based on the alignment of FH2 domains. Real-time PCR was used to study the expression pattern of formin genes. Expression of forC, D, I and J increased during transition to multi-cellular stages, while the rest of genes displayed less marked developmental variations. During sexual development, expression of forH and forI displayed a significant increase in fusion competent cells.

CONCLUSION: Our analysis allows some preliminary insight into the functionality of Dictyostelium formins: all isoforms might display actin nucleation activity and, with the exception of ForI, might also be susceptible to autoinhibition and to regulation by Rho GTPases. The architecture GBD/FH3-FH1-FH2-DAD appears common to almost all Dictyostelium, fungal and metazoan formins, for which we propose the denomination of conventional formins, and implies a common regulatory mechanism.},
}

Actin Cytoskeleton
Actins/chemistry
Amino Acid Sequence
Animals
Caenorhabditis elegans
Carrier Proteins/chemistry
DNA, Complementary/metabolism
Databases, Protein
Dictyostelium/*metabolism
Drosophila
Fungal Proteins/*chemistry
Gene Expression Regulation
Humans
Microfilament Proteins/chemistry
Molecular Sequence Data
Phylogeny
Protein Isoforms
Protein Structure, Tertiary
Reverse Transcriptase Polymerase Chain Reaction
Saccharomyces cerevisiae/metabolism
Schizosaccharomyces/metabolism
Sequence Analysis, DNA/*methods
Sequence Homology, Amino Acid

@article {pmid15795378,
year = {2005},
author = {Koide, T and Hayata, T and Cho, KW},
title = {Xenopus as a model system to study transcriptional regulatory networks.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {102},
number = {14},
pages = {4943-4948},
pmid = {15795378},
issn = {0027-8424},
support = {R01 HD029507/HD/NICHD NIH HHS/United States ; HD29507/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; DNA/genetics ; Endoderm/cytology ; Gene Expression Regulation, Developmental ; Genes, Regulator ; Genomics ; Intercellular Signaling Peptides and Proteins ; Mesoderm/cytology ; Models, Genetic ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Promoter Regions, Genetic ; Proteins/genetics ; Signal Transduction ; Transcription, Genetic ; Transcriptional Activation ; Xenopus/*embryology/*genetics ; Xenopus Proteins ; },
abstract = {Development is controlled by a complex series of events requiring sequential gene activation. Understanding the logic of gene networks during development is necessary for a complete understanding of how genes contribute to phenotype. Pioneering work initiated in the sea urchin and Drosophila has demonstrated that reasonable transcriptional regulatory network diagrams representing early development in multicellular animals can be generated through use of appropriate genomic, genetic, and biochemical tools. Establishment of similar regulatory network diagrams for vertebrate development is a necessary step. The amphibian Xenopus has long been used as a model for vertebrate early development and has contributed greatly to the elucidation of gene regulation. Because the best and most extensively studied transcriptional regulatory network in Xenopus is that underlying the formation and function of Spemann's organizer, we describe the current status of our understanding of this gene regulatory network and its relationship to mesodermal patterning. Seventy-four transcription factors currently known to be expressed in the mesoendoderm of Xenopus gastrula were characterized according to their modes of action, DNA binding consensus sequences, and target genes. Among them, nineteen transcription factors were characterized sufficiently in detail, allowing us to generate a gene regulatory network diagram. Additionally, we discuss recent amphibian work using a combined DNA microarray and bioinformatics approach that promises to accelerate regulatory network studies.},
}

Animals
Base Sequence
DNA/genetics
Endoderm/cytology
Gene Expression Regulation, Developmental
Genes, Regulator
Genomics
Intercellular Signaling Peptides and Proteins
Mesoderm/cytology
Models, Genetic
Oligonucleotide Array Sequence Analysis
Phylogeny
Promoter Regions, Genetic
Proteins/genetics
Signal Transduction
Transcription, Genetic
Transcriptional Activation
Xenopus/*embryology/*genetics
Xenopus Proteins

@article {pmid15818467,
year = {2005},
author = {Römling, U},
title = {Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {62},
number = {11},
pages = {1234-1246},
pmid = {15818467},
issn = {1420-682X},
mesh = {Animals ; Biofilms/growth & development ; Cellulose/biosynthesis ; Cyclic GMP/*analogs & derivatives/metabolism ; *Enterobacteriaceae/cytology/growth & development/metabolism ; Escherichia coli Proteins ; Humans ; Models, Biological ; Phylogeny ; Trans-Activators/metabolism ; },
abstract = {The rdar morphotype, a multicellular behaviour of Salmonella enterica and Escherichia coli is characterized by the expression of the adhesive extracellular matrix components cellulose and curli fimbriae. The response regulator CsgD, which transcriptionally activates the biosynthesis of the exopolysaccharide cellulose and curli, also transforms cell physiology to the multicellular state. However, the only role of CsgD in cellulose biosynthesis is the activation of AdrA, a GGDEF domain protein that mediates production of the allosteric activator cyclic-di-(3'-5')guanylic acid (c-di-GMP). In S. enterica serovar Typhimurium a regulatory network consisting of 19 GGDEF/EAL domain-containing proteins tightly controls the concentration of c-di-GMP. c-di-GMP not only regulates the expression of cellulose, but also stimulates expression of adhesive curli and represses various modes of motility. Functions of characterized GGDEF and EAL domain proteins, as well as database searches, point to a global role for c-di-GMP as a novel secondary messenger that regulates a variety of cellular functions in response to diverse environmental stimuli already in the deepest roots of the prokaryotes.},
}

Animals
Biofilms/growth & development
Cellulose/biosynthesis
Cyclic GMP/*analogs & derivatives/metabolism
*Enterobacteriaceae/cytology/growth & development/metabolism
Escherichia coli Proteins
Humans
Models, Biological
Phylogeny
Trans-Activators/metabolism

@article {pmid15875012,
year = {2005},
author = {Eichinger, L and Pachebat, JA and Glöckner, G and Rajandream, MA and Sucgang, R and Berriman, M and Song, J and Olsen, R and Szafranski, K and Xu, Q and Tunggal, B and Kummerfeld, S and Madera, M and Konfortov, BA and Rivero, F and Bankier, AT and Lehmann, R and Hamlin, N and Davies, R and Gaudet, P and Fey, P and Pilcher, K and Chen, G and Saunders, D and Sodergren, E and Davis, P and Kerhornou, A and Nie, X and Hall, N and Anjard, C and Hemphill, L and Bason, N and Farbrother, P and Desany, B and Just, E and Morio, T and Rost, R and Churcher, C and Cooper, J and Haydock, S and van Driessche, N and Cronin, A and Goodhead, I and Muzny, D and Mourier, T and Pain, A and Lu, M and Harper, D and Lindsay, R and Hauser, H and James, K and Quiles, M and Madan Babu, M and Saito, T and Buchrieser, C and Wardroper, A and Felder, M and Thangavelu, M and Johnson, D and Knights, A and Loulseged, H and Mungall, K and Oliver, K and Price, C and Quail, MA and Urushihara, H and Hernandez, J and Rabbinowitsch, E and Steffen, D and Sanders, M and Ma, J and Kohara, Y and Sharp, S and Simmonds, M and Spiegler, S and Tivey, A and Sugano, S and White, B and Walker, D and Woodward, J and Winckler, T and Tanaka, Y and Shaulsky, G and Schleicher, M and Weinstock, G and Rosenthal, A and Cox, EC and Chisholm, RL and Gibbs, R and Loomis, WF and Platzer, M and Kay, RR and Williams, J and Dear, PH and Noegel, AA and Barrell, B and Kuspa, A},
title = {The genome of the social amoeba Dictyostelium discoideum.},
journal = {Nature},
volume = {435},
number = {7038},
pages = {43-57},
pmid = {15875012},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_U105115237/MRC_/Medical Research Council/United Kingdom ; R01 HD035925/HD/NICHD NIH HHS/United States ; },
mesh = {ATP-Binding Cassette Transporters/genetics ; Animals ; Base Composition ; Cell Adhesion/genetics ; Cell Movement/genetics ; Centromere/genetics ; Conserved Sequence/genetics ; DNA Transposable Elements/genetics ; DNA, Ribosomal/genetics ; Dictyostelium/cytology/enzymology/*genetics/metabolism ; Eukaryotic Cells/metabolism ; Gene Duplication ; Gene Transfer, Horizontal/genetics ; *Genome ; *Genomics ; Humans ; Molecular Sequence Data ; Phylogeny ; Proteome ; Protozoan Proteins/chemistry/genetics ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Signal Transduction/genetics ; *Social Behavior ; Telomere/genetics ; },
abstract = {The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.},
}

ATP-Binding Cassette Transporters/genetics
Animals
Base Composition
Cell Adhesion/genetics
Cell Movement/genetics
Centromere/genetics
Conserved Sequence/genetics
DNA Transposable Elements/genetics
DNA, Ribosomal/genetics
Dictyostelium/cytology/enzymology/*genetics/metabolism
Eukaryotic Cells/metabolism
Gene Duplication
Gene Transfer, Horizontal/genetics
*Genome
*Genomics
Humans
Molecular Sequence Data
Phylogeny
Proteome
Protozoan Proteins/chemistry/genetics
RNA, Transfer/genetics
Repetitive Sequences, Nucleic Acid/genetics
Sequence Analysis, DNA
Signal Transduction/genetics
*Social Behavior
Telomere/genetics