@article {pmid37156858,
year = {2023},
author = {Smirnova, J and Loerke, J and Kleinau, G and Schmidt, A and Bürger, J and Meyer, EH and Mielke, T and Scheerer, P and Bock, R and Spahn, CMT and Zoschke, R},
title = {Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.},
journal = {Nature plants},
volume = {9},
number = {6},
pages = {987-1000},
pmid = {37156858},
issn = {2055-0278},
support = {416210002//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 221545957//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 394046635//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 421152132//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ZO 302/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TRR 175 (A4)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 956314//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Cytosol ; *RNA, Ribosomal/chemistry ; Cryoelectron Microscopy ; Phylogeny ; Models, Molecular ; *Ribosomes/chemistry ; Plants/genetics ; Nicotiana/genetics ; },
abstract = {In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.},
}

Cytosol
*RNA, Ribosomal/chemistry
Cryoelectron Microscopy
Phylogeny
Models, Molecular
*Ribosomes/chemistry
Plants/genetics
Nicotiana/genetics

@article {pmid37158879,
year = {2023},
author = {Shamanskiy, V and Mikhailova, AA and Tretiakov, EO and Ushakova, K and Mikhailova, AG and Oreshkov, S and Knorre, DA and Ree, N and Overdevest, JB and Lukowski, SW and Gostimskaya, I and Yurov, V and Liou, CW and Lin, TK and Kunz, WS and Reymond, A and Mazunin, I and Bazykin, GA and Fellay, J and Tanaka, M and Khrapko, K and Gunbin, K and Popadin, K},
title = {Secondary structure of the human mitochondrial genome affects formation of deletions.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {103},
pmid = {37158879},
issn = {1741-7007},
support = {DOC 33/FWF_/Austrian Science Fund FWF/Austria ; UL1 TR001873/TR/NCATS NIH HHS/United States ; K23 DC019678/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Genome, Mitochondrial ; Mitochondria ; DNA, Mitochondrial/genetics ; Genome, Human ; Protein Structure, Secondary ; DNA, Single-Stranded ; Mammals ; },
abstract = {BACKGROUND: Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions.

RESULTS: By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9 kb and another within 13-16 kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11 kb and contacting regions between 6-9 kb and 13-16 kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482 bp (base pair) and a second arm at 13,447-13,459 bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging.

CONCLUSIONS: Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.},
}

Animals
Humans
*Genome, Mitochondrial
Mitochondria
DNA, Mitochondrial/genetics
Genome, Human
Protein Structure, Secondary
DNA, Single-Stranded
Mammals

@article {pmid37162347,
year = {2023},
author = {Ezawa, T and Silvestri, A and Maruyama, H and Tawaraya, K and Suzuki, M and Duan, Y and Turina, M and Lanfranco, L},
title = {Structurally distinct mitoviruses: are they an ancestral lineage of the Mitoviridae exclusive to arbuscular mycorrhizal fungi (Glomeromycotina)?.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0024023},
pmid = {37162347},
issn = {2150-7511},
mesh = {*Mycorrhizae/genetics ; Symbiosis ; Phylogeny ; Ecosystem ; *Glomeromycota/genetics ; Plants/microbiology ; *RNA Viruses/genetics ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {Mitoviruses in the family Mitoviridae are the mitochondria-replicating "naked RNA viruses" with genomes encoding only the replicase RNA-dependent RNA polymerase (RdRp) and prevalent across fungi, plants, and invertebrates. Arbuscular mycorrhizal fungi in the subphylum Glomeromycotina are obligate plant symbionts that deliver water and nutrients to the host. We discovered distinct mitoviruses in glomeromycotinian fungi, namely "large duamitovirus," encoding unusually large RdRp with a unique N-terminal motif that is endogenized in some host genomes. More than 400 viral sequences similar to the large duamitoviruses are present in metatranscriptome databases. They are globally distributed in soil ecosystems, consistent with the cosmopolitan distribution of glomeromycotinian fungi, and formed the most basal clade of the Mitoviridae in phylogenetic analysis. Given that glomeromycotinian fungi are the only confirmed hosts of these viruses, we propose the hypothesis that large duamitoviruses are the most ancestral lineage of the Mitoviridae that have been maintained exclusively in glomeromycotinian fungi.},
}

*Mycorrhizae/genetics
Symbiosis
Phylogeny
Ecosystem
*Glomeromycota/genetics
Plants/microbiology
*RNA Viruses/genetics
RNA-Dependent RNA Polymerase/genetics

@article {pmid37166629,
year = {2023},
author = {Agrawal, RK and Majumdar, S},
title = {Evolution: Mitochondrial Ribosomes Across Species.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2661},
number = {},
pages = {7-21},
pmid = {37166629},
issn = {1940-6029},
support = {R01 GM061576/GM/NIGMS NIH HHS/United States ; R01 GM139277/GM/NIGMS NIH HHS/United States ; R01 AI132422/AI/NIAID NIH HHS/United States ; R01 AI155473/AI/NIAID NIH HHS/United States ; },
mesh = {*Mitochondrial Ribosomes/metabolism ; *Mitochondria/genetics/metabolism ; Ribosomes/metabolism ; Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Mitochondrial Proteins/metabolism ; Cryoelectron Microscopy ; Ribosomal Proteins/metabolism ; },
abstract = {The ribosome is among the most complex and ancient cellular macromolecular assemblies that plays a central role in protein biosynthesis in all living cells. Its function of translation of genetic information encoded in messenger RNA into protein molecules also extends to subcellular compartments in eukaryotic cells such as apicoplasts, chloroplasts, and mitochondria. The origin of mitochondria is primarily attributed to an early endosymbiotic event between an alpha-proteobacterium and a primitive (archaeal) eukaryotic cell. The timeline of mitochondrial acquisition, the nature of the host, and their diversification have been studied in great detail and are continually being revised as more genomic and structural data emerge. Recent advancements in high-resolution cryo-EM structure determination have provided architectural details of mitochondrial ribosomes (mitoribosomes) from various species, revealing unprecedented diversifications among them. These structures provide novel insights into the evolution of mitoribosomal structure and function. Here, we present a brief overview of the existing mitoribosomal structures in the context of the eukaryotic evolution tree showing their diversification from their last common ancestor.},
}

*Mitochondrial Ribosomes/metabolism
*Mitochondria/genetics/metabolism
Ribosomes/metabolism
Eukaryota/genetics/metabolism
Eukaryotic Cells/metabolism
Mitochondrial Proteins/metabolism
Cryoelectron Microscopy
Ribosomal Proteins/metabolism

@article {pmid37166631,
year = {2023},
author = {Chrzanowska-Lightowlers, ZM and Lightowlers, RN},
title = {Translation in Mitochondrial Ribosomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2661},
number = {},
pages = {53-72},
pmid = {37166631},
issn = {1940-6029},
support = {203105/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Mitochondrial Ribosomes/metabolism ; Cryoelectron Microscopy ; *Mitochondria/genetics/metabolism ; Protein Biosynthesis ; Oxidative Phosphorylation ; Mitochondrial Proteins/genetics/metabolism ; },
abstract = {Mitochondrial protein synthesis is essential for the life of aerobic eukaryotes. Without it, oxidative phosphorylation cannot be coupled. Evolution has shaped a battery of factors and machinery that are key to production of just a handful of critical proteins. In this general concept chapter, we attempt to briefly summarize our current knowledge of the overall process in mitochondria from a variety of species, breaking this down to the four parts of translation: initiation, elongation, termination, and recycling. Where appropriate, we highlight differences between species and emphasize gaps in our understanding. Excitingly, with the current revolution in cryoelectron microscopy and mitochondrial genome editing, it is highly likely that many of these gaps will be resolved in the near future. However, the absence of a faithful in vitro reconstituted system to study mitochondrial translation is still problematic.},
}

*Mitochondrial Ribosomes/metabolism
Cryoelectron Microscopy
*Mitochondria/genetics/metabolism
Protein Biosynthesis
Oxidative Phosphorylation
Mitochondrial Proteins/genetics/metabolism

@article {pmid37166639,
year = {2023},
author = {Maiti, P and Fontanesi, F},
title = {Metabolic Labeling of Mitochondrial Translation Products in Whole Cells and Isolated Organelles.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2661},
number = {},
pages = {193-215},
pmid = {37166639},
issn = {1940-6029},
mesh = {Animals ; *Protein Biosynthesis ; *Mitochondria/metabolism ; Methionine/metabolism ; Amino Acids/metabolism ; Mitochondrial Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Mammals/genetics ; },
abstract = {Mitochondria retain their own genome and translational apparatus that is highly specialized in the synthesis of a handful of proteins, essential components of the oxidative phosphorylation system. During evolution, the players and mechanisms involved in mitochondrial translation have acquired some unique features, which we have only partially disclosed. The study of the mitochondrial translation process has been historically hampered by the lack of an in vitro translational system and has largely relied on the analysis of the incorporation rate of radiolabeled amino acids into mitochondrial proteins in cellulo or in organello. In this chapter, we describe methods to monitor mitochondrial translation by labeling newly synthesized mitochondrial polypeptides with [S[35]]-methionine in either yeast or mammalian whole cells or isolated mitochondria.},
}

Animals
*Protein Biosynthesis
*Mitochondria/metabolism
Methionine/metabolism
Amino Acids/metabolism
Mitochondrial Proteins/metabolism
Saccharomyces cerevisiae/genetics
Mammals/genetics

@article {pmid37171259,
year = {2023},
author = {Dowling, DK and Wolff, JN},
title = {Evolutionary genetics of the mitochondrial genome: insights from Drosophila.},
journal = {Genetics},
volume = {224},
number = {3},
pages = {},
pmid = {37171259},
issn = {1943-2631},
mesh = {Animals ; *Drosophila/genetics ; *Genome, Mitochondrial ; Eukaryota/genetics ; Mitochondria/genetics ; Oxidative Phosphorylation ; DNA, Mitochondrial ; },
abstract = {Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.},
}

Animals
*Drosophila/genetics
*Genome, Mitochondrial
Eukaryota/genetics
Mitochondria/genetics
Oxidative Phosphorylation
DNA, Mitochondrial

@article {pmid37175542,
year = {2023},
author = {Ke, SJ and Liu, DK and Tu, XD and He, X and Zhang, MM and Zhu, MJ and Zhang, DY and Zhang, CL and Lan, SR and Liu, ZJ},
title = {Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics.},
journal = {International journal of molecular sciences},
volume = {24},
number = {9},
pages = {},
pmid = {37175542},
issn = {1422-0067},
support = {72202200205//Fujian Agriculture and Forestry University/ ; },
mesh = {Phylogeny ; *Genome, Mitochondrial ; Mitochondria/genetics ; RNA, Ribosomal/genetics ; *Orchidaceae/genetics ; },
abstract = {Apostasia shenzhenica belongs to the subfamily Apostasioideae and is a primitive group located at the base of the Orchidaceae phylogenetic tree. However, the A. shenzhenica mitochondrial genome (mitogenome) is still unexplored, and the phylogenetic relationships between monocots mitogenomes remain unexplored. In this study, we discussed the genetic diversity of A. shenzhenica and the phylogenetic relationships within its monocotyledon mitogenome. We sequenced and assembled the complete mitogenome of A. shenzhenica, resulting in a circular mitochondrial draft of 672,872 bp, with an average read coverage of 122× and a GC content of 44.4%. A. shenzhenica mitogenome contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis revealed a large number of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high mitogenome conservation in related species. RNA editing identified 416 sites in the protein-coding region. Furthermore, we found 44 chloroplast genomic DNA fragments that were transferred from the chloroplast to the mitogenome of A. shenzhenica, with five plastid-derived genes remaining intact in the mitogenome. Finally, the phylogenetic analysis of the mitogenomes from A. shenzhenica and 28 other monocots showed that the evolution and classification of most monocots were well determined. These findings enrich the genetic resources of orchids and provide valuable information on the taxonomic classification and molecular evolution of monocots.},
}

Phylogeny
*Genome, Mitochondrial
Mitochondria/genetics
RNA, Ribosomal/genetics
*Orchidaceae/genetics

@article {pmid37179826,
year = {2023},
author = {Casanova, A and Wevers, A and Navarro-Ledesma, S and Pruimboom, L},
title = {Mitochondria: It is all about energy.},
journal = {Frontiers in physiology},
volume = {14},
number = {},
pages = {1114231},
pmid = {37179826},
issn = {1664-042X},
abstract = {Mitochondria play a key role in both health and disease. Their function is not limited to energy production but serves multiple mechanisms varying from iron and calcium homeostasis to the production of hormones and neurotransmitters, such as melatonin. They enable and influence communication at all physical levels through interaction with other organelles, the nucleus, and the outside environment. The literature suggests crosstalk mechanisms between mitochondria and circadian clocks, the gut microbiota, and the immune system. They might even be the hub supporting and integrating activity across all these domains. Hence, they might be the (missing) link in both health and disease. Mitochondrial dysfunction is related to metabolic syndrome, neuronal diseases, cancer, cardiovascular and infectious diseases, and inflammatory disorders. In this regard, diseases such as cancer, Alzheimer's, Parkinson's, amyotrophic lateral sclerosis (ALS), chronic fatigue syndrome (CFS), and chronic pain are discussed. This review focuses on understanding the mitochondrial mechanisms of action that allow for the maintenance of mitochondrial health and the pathways toward dysregulated mechanisms. Although mitochondria have allowed us to adapt to changes over the course of evolution, in turn, evolution has shaped mitochondria. Each evolution-based intervention influences mitochondria in its own way. The use of physiological stress triggers tolerance to the stressor, achieving adaptability and resistance. This review describes strategies that could recover mitochondrial functioning in multiple diseases, providing a comprehensive, root-cause-focused, integrative approach to recovering health and treating people suffering from chronic diseases.},
}

@article {pmid37188954,
year = {2023},
author = {Lee, SY and Cheah, JS and Zhao, B and Xu, C and Roh, H and Kim, CK and Cho, KF and Udeshi, ND and Carr, SA and Ting, AY},
title = {Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells.},
journal = {Nature methods},
volume = {20},
number = {6},
pages = {908-917},
pmid = {37188954},
issn = {1548-7105},
support = {R01 DK121409/DK/NIDDK NIH HHS/United States ; RC2 DK129964/DK/NIDDK NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; R01 DA026223/DA/NIDA NIH HHS/United States ; },
mesh = {*Proteomics ; *Mitochondria ; Endoplasmic Reticulum ; Biotin ; },
abstract = {The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeling, a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the proximity labeling enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. 'LOV-Turbo' works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffic between endoplasmic reticulum, nuclear and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling. Overall, LOV-Turbo increases the spatial and temporal precision of proximity labeling, expanding the scope of experimental questions that can be addressed with proximity labeling.},
}

*Proteomics
*Mitochondria
Endoplasmic Reticulum
Biotin

@article {pmid37198654,
year = {2023},
author = {Kienzle, L and Bettinazzi, S and Choquette, T and Brunet, M and Khorami, HH and Jacques, JF and Moreau, M and Roucou, X and Landry, CR and Angers, A and Breton, S},
title = {A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {111},
pmid = {37198654},
issn = {1741-7007},
mesh = {Humans ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; HeLa Cells ; Mitochondria/genetics ; Open Reading Frames ; Peptides ; *NADH Dehydrogenase/genetics ; },
abstract = {BACKGROUND: Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed.

RESULTS: We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology.

CONCLUSIONS: Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.},
}

Humans
DNA, Mitochondrial/genetics
*Genome, Mitochondrial
HeLa Cells
Mitochondria/genetics
Open Reading Frames
Peptides
*NADH Dehydrogenase/genetics

@article {pmid37199915,
year = {2023},
author = {Begeman, A and Babaian, A and Lewis, SC},
title = {Metatranscriptomic analysis uncovers prevalent viral ORFs compatible with mitochondrial translation.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0100222},
pmid = {37199915},
issn = {2379-5077},
support = {R00 GM129456/GM/NIGMS NIH HHS/United States ; R35 GM147218/GM/NIGMS NIH HHS/United States ; T32 GM007232/GM/NIGMS NIH HHS/United States ; R00GM129456/NH/NIH HHS/United States ; },
mesh = {Open Reading Frames ; *RNA Viruses/genetics ; *Viruses/genetics ; Codon ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {RNA viruses are ubiquitous components of the global virosphere, yet relatively little is known about their genetic diversity or the cellular mechanisms by which they exploit the biology of their diverse eukaryotic hosts. A hallmark of (+)ssRNA (positive single-stranded RNA) viruses is the ability to remodel host endomembranes for their own replication. However, the subcellular interplay between RNA viruses and host organelles that harbor gene expression systems, such as mitochondria, is complex and poorly understood. Here we report the discovery of 763 new virus sequences belonging to the family Mitoviridae by metatranscriptomic analysis, the identification of previously uncharacterized mitovirus clades, and a putative new viral class. With this expanded understanding of the diversity of mitovirus and encoded RNA-dependent RNA polymerases (RdRps), we annotate mitovirus-specific protein motifs and identify hallmarks of mitochondrial translation, including mitochondrion-specific codons. This study expands the known diversity of mitochondrial viruses and provides additional evidence that they co-opt mitochondrial biology for their survival. IMPORTANCE Metatranscriptomic studies have rapidly expanded the cadre of known RNA viruses, yet our understanding of how these viruses navigate the cytoplasmic milieu of their hosts to survive remains poorly characterized. In this study, we identify and assemble 763 new viral sequences belonging to the Mitoviridae, a family of (+)ssRNA viruses thought to interact with and remodel host mitochondria. We exploit this genetic diversity to identify new clades of Mitoviridae, annotate clade-specific sequence motifs that distinguish the mitoviral RdRp, and reveal patterns of RdRp codon usage consistent with translation on host cell mitoribosomes. These results serve as a foundation for understanding how mitoviruses co-opt mitochondrial biology for their proliferation.},
}

Open Reading Frames
*RNA Viruses/genetics
*Viruses/genetics
Codon
RNA-Dependent RNA Polymerase/genetics

@article {pmid37208299,
year = {2023},
author = {Dapper, AL and Diegel, AE and Wade, MJ},
title = {Relative rates of evolution of male-beneficial nuclear compensatory mutations and male-harming Mother's Curse mitochondrial alleles.},
journal = {Evolution; international journal of organic evolution},
volume = {77},
number = {9},
pages = {1945-1955},
doi = {10.1093/evolut/qpad087},
pmid = {37208299},
issn = {1558-5646},
mesh = {Female ; Animals ; Male ; Humans ; *Mothers ; Alleles ; *Mitochondria/genetics ; Cell Nucleus/genetics ; Mutation ; },
abstract = {Mother's Curse alleles represent a significant source of potential male fitness defects. The maternal inheritance of mutations with the pattern of sex-specific fitness effects, s♀>0>s♂, allows Mother's Curse alleles to spread through a population even though they reduce male fitness. Although the mitochondrial genomes of animals contain only a handful of protein-coding genes, mutations in many of these genes have been shown to have a direct effect on male fertility. The evolutionary process of nuclear compensation is hypothesized to counteract the male-limited mitochondrial defects that spread via Mother's Curse. Here we use population genetic models to investigate the evolution of compensatory autosomal nuclear mutations that act to restore the loss of fitness caused by mitochondrial mutation pressures. We derive the rate of male fitness deterioration by Mother's Curse and the rate of restoration by nuclear compensatory evolution. We find that the rate of nuclear gene compensation is many times slower than that of its deterioration by cytoplasmic mutation pressure, resulting in a significant lag in the recovery of male fitness. Thus, the numbers of nuclear genes capable of restoring male mitochondrial fitness defects must be large in order to sustain male fitness in the face of mutation pressures.},
}

Female
Animals
Male
Humans
*Mothers
Alleles
*Mitochondria/genetics
Cell Nucleus/genetics
Mutation

@article {pmid37212044,
year = {2023},
author = {Postel, Z and Sloan, DB and Gallina, S and Godé, C and Schmitt, E and Mangenot, S and Drouard, L and Varré, JS and Touzet, P},
title = {The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process.},
journal = {The New phytologist},
volume = {239},
number = {2},
pages = {766-777},
doi = {10.1111/nph.18966},
pmid = {37212044},
issn = {1469-8137},
mesh = {*Silene/genetics ; Plant Breeding ; Cell Nucleus/genetics ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {There is growing evidence that cytonuclear incompatibilities (i.e. disruption of cytonuclear coadaptation) might contribute to the speciation process. In a former study, we described the possible involvement of plastid-nuclear incompatibilities in the reproductive isolation between four lineages of Silene nutans (Caryophyllaceae). Because organellar genomes are usually cotransmitted, we assessed whether the mitochondrial genome could also be involved in the speciation process, knowing that the gynodioecious breeding system of S. nutans is expected to impact the evolutionary dynamics of this genome. Using hybrid capture and high-throughput DNA sequencing, we analyzed diversity patterns in the genic content of the organellar genomes in the four S. nutans lineages. Contrary to the plastid genome, which exhibited a large number of fixed substitutions between lineages, extensive sharing of polymorphisms between lineages was found in the mitochondrial genome. In addition, numerous recombination-like events were detected in the mitochondrial genome, loosening the linkage disequilibrium between the organellar genomes and leading to decoupled evolution. These results suggest that gynodioecy shaped mitochondrial diversity through balancing selection, maintaining ancestral polymorphism and, thus, limiting the involvement of the mitochondrial genome in evolution of hybrid inviability between S. nutans lineages.},
}

*Silene/genetics
Plant Breeding
Cell Nucleus/genetics
Mitochondria/genetics
*Genome, Mitochondrial/genetics
Evolution, Molecular
Phylogeny

@article {pmid37214873,
year = {2023},
author = {Cronin, SJF and Yu, W and Hale, A and Licht-Mayer, S and Crabtree, MJ and Korecka, JA and Tretiakov, EO and Sealey-Cardona, M and Somlyay, M and Onji, M and An, M and Fox, JD and Turnes, BL and Gomez-Diaz, C and da Luz Scheffer, D and Cikes, D and Nagy, V and Weidinger, A and Wolf, A and Reither, H and Chabloz, A and Kavirayani, A and Rao, S and Andrews, N and Latremoliere, A and Costigan, M and Douglas, G and Freitas, FC and Pifl, C and Walz, R and Konrat, R and Mahad, DJ and Koslov, AV and Latini, A and Isacson, O and Harkany, T and Hallett, PJ and Bagby, S and Woolf, CJ and Channon, KM and Je, HS and Penninger, JM},
title = {Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37214873},
issn = {2692-8205},
support = {DOC 33/FWF_/Austrian Science Fund FWF/Austria ; R01 NS112266/NS/NINDS NIH HHS/United States ; R35 NS105076/NS/NINDS NIH HHS/United States ; RG/F/22/110085/BHF_/British Heart Foundation/United Kingdom ; },
abstract = {Dopa-responsive dystonia (DRD) and Parkinson's disease (PD) are movement disorders caused by the dysfunction of nigrostriatal dopaminergic neurons. Identifying druggable pathways and biomarkers for guiding therapies is crucial due to the debilitating nature of these disorders. Recent genetic studies have identified variants of GTP cyclohydrolase-1 (GCH1), the rate-limiting enzyme in tetrahydrobiopterin (BH4) synthesis, as causative for these movement disorders. Here, we show that genetic and pharmacological inhibition of BH4 synthesis in mice and human midbrain-like organoids accurately recapitulates motor, behavioral and biochemical characteristics of these human diseases, with severity of the phenotype correlating with extent of BH4 deficiency. We also show that BH4 deficiency increases sensitivities to several PD-related stressors in mice and PD human cells, resulting in worse behavioral and physiological outcomes. Conversely, genetic and pharmacological augmentation of BH4 protects mice from genetically- and chemically induced PD-related stressors. Importantly, increasing BH4 levels also protects primary cells from PD-affected individuals and human midbrain-like organoids (hMLOs) from these stressors. Mechanistically, BH4 not only serves as an essential cofactor for dopamine synthesis, but also independently regulates tyrosine hydroxylase levels, protects against ferroptosis, scavenges mitochondrial ROS, maintains neuronal excitability and promotes mitochondrial ATP production, thereby enhancing mitochondrial fitness and cellular respiration in multiple preclinical PD animal models, human dopaminergic midbrain-like organoids and primary cells from PD-affected individuals. Our findings pinpoint the BH4 pathway as a key metabolic program at the intersection of multiple protective mechanisms for the health and function of midbrain dopaminergic neurons, identifying it as a potential therapeutic target for PD.},
}

@article {pmid37221210,
year = {2023},
author = {Paukszto, Ł and Górski, P and Krawczyk, K and Maździarz, M and Szczecińska, M and Ślipiko, M and Sawicki, J},
title = {The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8303},
pmid = {37221210},
issn = {2045-2322},
mesh = {*Hepatophyta ; *Genome, Mitochondrial ; Phylogeny ; Mitochondria ; *Genome, Plastid ; *Anemone ; },
abstract = {Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts-109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.},
}

*Hepatophyta
*Genome, Mitochondrial
Phylogeny
Mitochondria
*Genome, Plastid
*Anemone

@article {pmid37221926,
year = {2023},
author = {Dong, X and Zhang, H and Zhu, X and Wang, K and Xue, H and Ye, Z and Zheng, C and Bu, W},
title = {Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae).},
journal = {Molecular phylogenetics and evolution},
volume = {184},
number = {},
pages = {107802},
doi = {10.1016/j.ympev.2023.107802},
pmid = {37221926},
issn = {1095-9513},
mesh = {Animals ; *Heteroptera ; Phylogeny ; China ; *Genome, Mitochondrial ; Mitochondria ; Mitomycin ; },
abstract = {Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.},
}

Animals
*Heteroptera
Phylogeny
China
*Genome, Mitochondrial
Mitochondria
Mitomycin

@article {pmid37231782,
year = {2023},
author = {Shi, J and Yan, S and Li, W and Yang, X and Cui, Z and Li, J and Li, G and Li, Y and Hu, Y and Gao, S},
title = {PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes.},
journal = {RNA biology},
volume = {20},
number = {1},
pages = {248-256},
pmid = {37231782},
issn = {1555-8584},
mesh = {Animals ; *Genome, Chloroplast ; Gene Expression Profiling ; Molecular Sequence Annotation ; Transcriptome ; DNA, Mitochondrial/genetics ; Chloroplasts/genetics ; *Arabidopsis/genetics ; },
abstract = {Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.},
}

Animals
*Genome, Chloroplast
Gene Expression Profiling
Molecular Sequence Annotation
Transcriptome
DNA, Mitochondrial/genetics
Chloroplasts/genetics
*Arabidopsis/genetics

@article {pmid37239339,
year = {2023},
author = {Wu, Z and Yang, T and Qin, R and Liu, H},
title = {Complete Mitogenome and Phylogenetic Analysis of the Carthamus tinctorius L.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239339},
issn = {2073-4425},
mesh = {Phylogeny ; *Carthamus tinctorius/genetics ; *Genome, Mitochondrial/genetics ; Repetitive Sequences, Nucleic Acid ; },
abstract = {Carthamus tinctorius L. 1753 (Asteraceae), also called safflower, is a cash crop with both edible and medical properties. We analyzed and reported the safflower mitogenome based on combined short and long reads obtained from Illumina and Pacbio platforms, respectively. This safflower mitogenome mainly contained two circular chromosomes, with a total length of 321,872 bp, and encoded 55 unique genes, including 34 protein-coding genes (PCGs), 3 rRNA genes, and 18 tRNA genes. The total length of repeat sequences greater than 30 bp was 24,953 bp, accounting for 7.75% of the whole mitogenome. Furthermore, we characterized the RNA editing sites of protein-coding genes located in the safflower mitogenome, and the total number of RNA editing sites was 504. Then, we revealed partial sequence transfer events between plastid and mitochondria, in which one plastid-derived gene (psaB) remained intact in the mitogenome. Despite extensive arrangement events among the three mitogenomes of C. tinctorius, Arctium lappa, and Saussurea costus, the constructed phylogenetic tree based on mitogenome PCGs showed that C. tinctorius has a closer relationship with three Cardueae species, A. lappa, A. tomentosum, and S. costus, which is similar to the phylogeny constructed from the PCGs of plastid genomes. This mitogenome not only enriches the genetic information of safflower but also will be useful in the phylogeny and evolution study of the Asteraceae.},
}

Phylogeny
*Carthamus tinctorius/genetics
*Genome, Mitochondrial/genetics
Repetitive Sequences, Nucleic Acid

@article {pmid37239358,
year = {2023},
author = {Ran, B and Zhu, W and Zhao, X and Li, L and Yi, Z and Li, M and Wang, T and Li, D},
title = {Studying Genetic Diversity and Relationships between Mountainous Meihua Chickens Using Mitochondrial DNA Control Region.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239358},
issn = {2073-4425},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Chickens/genetics ; Genetic Variation/genetics ; Phylogeny ; Mitochondria/genetics ; },
abstract = {The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics.},
}

Animals
*DNA, Mitochondrial/genetics
*Chickens/genetics
Genetic Variation/genetics
Phylogeny
Mitochondria/genetics

@article {pmid37239904,
year = {2023},
author = {Rossi, F and Picone, G and Cappadone, C and Sorrentino, A and Columbaro, M and Farruggia, G and Catelli, E and Sciutto, G and Prati, S and Oliete, R and Pasini, A and Pereiro, E and Iotti, S and Malucelli, E},
title = {Shedding Light on Osteosarcoma Cell Differentiation: Impact on Biomineralization and Mitochondria Morphology.},
journal = {International journal of molecular sciences},
volume = {24},
number = {10},
pages = {},
pmid = {37239904},
issn = {1422-0067},
mesh = {Humans ; Osteogenesis ; Biomineralization ; Cell Line, Tumor ; *Osteosarcoma/metabolism ; Cell Differentiation/physiology ; Mitochondria/metabolism ; *Bone Neoplasms/metabolism ; Cell Proliferation/physiology ; },
abstract = {Osteosarcoma (OS) is the most common primary malignant bone tumor and its etiology has recently been associated with osteogenic differentiation dysfunctions. OS cells keep a capacity for uncontrolled proliferation showing a phenotype similar to undifferentiated osteoprogenitors with abnormal biomineralization. Within this context, both conventional and X-ray synchrotron-based techniques have been exploited to deeply characterize the genesis and evolution of mineral depositions in a human OS cell line (SaOS-2) exposed to an osteogenic cocktail for 4 and 10 days. A partial restoration of the physiological biomineralization, culminating with the formation of hydroxyapatite, was observed at 10 days after treatment together with a mitochondria-driven mechanism for calcium transportation within the cell. Interestingly, during differentiation, mitochondria showed a change in morphology from elongated to rounded, indicating a metabolic reprogramming of OS cells possibly linked to an increase in glycolysis contribution to energy metabolism. These findings add a dowel to the genesis of OS giving new insights on the development of therapeutic strategies able to restore the physiological mineralization in OS cells.},
}

Humans
Osteogenesis
Biomineralization
Cell Line, Tumor
*Osteosarcoma/metabolism
Cell Differentiation/physiology
Mitochondria/metabolism
*Bone Neoplasms/metabolism
Cell Proliferation/physiology

@article {pmid37249052,
year = {2023},
author = {Chen, Y and Guo, Y and Xie, X and Wang, Z and Miao, L and Yang, Z and Jiao, Y and Xie, C and Liu, J and Hu, Z and Xin, M and Yao, Y and Ni, Z and Sun, Q and Peng, H and Guo, W},
title = {Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae.},
journal = {Plant physiology},
volume = {193},
number = {1},
pages = {578-594},
pmid = {37249052},
issn = {1532-2548},
mesh = {*Poaceae/genetics ; Triticum/genetics ; Genome, Plant/genetics ; *Oryza/genetics ; Zea mays/genetics ; Evolution, Molecular ; },
abstract = {Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.},
}

*Poaceae/genetics
Triticum/genetics
Genome, Plant/genetics
*Oryza/genetics
Zea mays/genetics
Evolution, Molecular

@article {pmid37254790,
year = {2023},
author = {López-García, P and Moreira, D},
title = {The symbiotic origin of the eukaryotic cell.},
journal = {Comptes rendus biologies},
volume = {346},
number = {},
pages = {55-73},
doi = {10.5802/crbiol.118},
pmid = {37254790},
issn = {1768-3238},
mesh = {*Eukaryotic Cells ; *Symbiosis ; Phylogeny ; Archaea/genetics ; Eukaryota/genetics ; Biological Evolution ; },
abstract = {Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.},
}

*Eukaryotic Cells
*Symbiosis
Phylogeny
Archaea/genetics
Eukaryota/genetics
Biological Evolution

@article {pmid37262983,
year = {2023},
author = {Camus, MF and Dhawanjewar, AS},
title = {Multilevel selection on mitochondrial genomes.},
journal = {Current opinion in genetics & development},
volume = {80},
number = {},
pages = {102050},
doi = {10.1016/j.gde.2023.102050},
pmid = {37262983},
issn = {1879-0380},
mesh = {*Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Biological Evolution ; Eukaryota/genetics ; Evolution, Molecular ; },
abstract = {Mitochondria are vital organelles for life in eukaryotes, taking centre stage in the process of cellular respiration. This process is regulated via a series of finely coordinated obligate interactions of molecules encoded by two genomes: nuclear DNA and mitochondrial DNA. Both genomes are required to work harmoniously to provide cellular energy, with detrimental consequences occurring when there is miscommunication between them. Whilst the need for cooperation is strong, vast differences between genomes (ploidy, size, and inheritance) create an arena for conflict. Here, we examine the varying levels of selection operating on the mitochondrial genome and the consequences they have on all these levels. We conclude by highlighting the potential for conflict when selection at different levels is driven by different evolutionary forces.},
}

*Genome, Mitochondrial/genetics
DNA, Mitochondrial/genetics
Mitochondria/genetics
Biological Evolution
Eukaryota/genetics
Evolution, Molecular

@article {pmid37267944,
year = {2023},
author = {Záhonová, K and Low, RS and Warren, CJ and Cantoni, D and Herman, EK and Yiangou, L and Ribeiro, CA and Phanprasert, Y and Brown, IR and Rueckert, S and Baker, NL and Tachezy, J and Betts, EL and Gentekaki, E and van der Giezen, M and Clark, CG and Jackson, AP and Dacks, JB and Tsaousis, AD},
title = {Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis.},
journal = {Current biology : CB},
volume = {33},
number = {12},
pages = {2449-2464.e8},
doi = {10.1016/j.cub.2023.05.025},
pmid = {37267944},
issn = {1879-0445},
mesh = {Animals ; Humans ; *Blastocystis/genetics ; *Gastrointestinal Microbiome/genetics ; Mitochondria/genetics/metabolism ; Organelles/metabolism ; Eukaryota ; },
abstract = {Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.},
}

Animals
Humans
*Blastocystis/genetics
*Gastrointestinal Microbiome/genetics
Mitochondria/genetics/metabolism
Organelles/metabolism
Eukaryota

@article {pmid37268349,
year = {2023},
author = {Pellielo, G and Agyapong, ED and Pinton, P and Rimessi, A},
title = {Control of mitochondrial functions by Pseudomonas aeruginosa in cystic fibrosis.},
journal = {International review of cell and molecular biology},
volume = {377},
number = {},
pages = {19-43},
doi = {10.1016/bs.ircmb.2023.03.008},
pmid = {37268349},
issn = {1937-6448},
mesh = {Humans ; *Cystic Fibrosis ; Pseudomonas aeruginosa/physiology ; Persistent Infection ; Inflammation/genetics ; Mitochondria ; },
abstract = {Cystic fibrosis (CF) is a genetic disease characterized by mutations of cystic fibrosis transmembrane conductance regulator (CFTR) gene, which lead to a dysfunctional chloride and bicarbonate channel. Abnormal mucus viscosity, persistent infections and hyperinflammation that preferentially affect the airways, referred to the pathogenesis of CF lung disease. It has largely demonstrated that Pseudomonas aeruginosa (P. aeruginosa) represents the most important pathogen that affect CF patients, leading to worsen inflammation by stimulating pro-inflammatory mediators release and tissue destruction. The conversion to mucoid phenotype and formation of biofilms, together with the increased frequency of mutations, are only few changes that characterize the P. aeruginosa's evolution during CF lung chronic infection. Recently, mitochondria received increasing attention due to their involvement in inflammatory-related diseases, including in CF. Alteration of mitochondrial homeostasis is sufficient to stimulate immune response. Exogenous or endogenous stimuli that perturb mitochondrial activity are used by cells, which, through the mitochondrial stress, potentiate immunity programs. Studies show the relationship between mitochondria and CF, supporting the idea that mitochondrial dysfunction endorses the exacerbation of inflammatory responses in CF lung. In particular, evidences suggest that mitochondria in CF airway cells are more susceptible to P. aeruginosa infection, with consequent detrimental effects that lead to amplify the inflammatory signals. This review discusses the evolution of P. aeruginosa in relationship with the pathogenesis of CF, a fundamental step to establish chronic infection in CF lung disease. Specifically, we focus on the role of P. aeruginosa in the exacerbation of inflammatory response, by triggering mitochondria in CF.},
}

Humans
*Cystic Fibrosis
Pseudomonas aeruginosa/physiology
Persistent Infection
Inflammation/genetics
Mitochondria

@article {pmid37269314,
year = {2023},
author = {Patriarcheas, D and Momtareen, T and Gallagher, JEG},
title = {Yeast of Eden: microbial resistance to glyphosate from a yeast perspective.},
journal = {Current genetics},
volume = {69},
number = {4-6},
pages = {203-212},
pmid = {37269314},
issn = {1432-0983},
support = {R03 ES034881/ES/NIEHS NIH HHS/United States ; NIH NIEHS R03 ES034881/NH/NIH HHS/United States ; NIH NIEHS R03 ES034881/NH/NIH HHS/United States ; },
mesh = {Saccharomyces cerevisiae/genetics/metabolism ; *Herbicides/pharmacology ; Glycine/pharmacology/metabolism ; Plants ; Amino Acids, Aromatic ; },
abstract = {First marketed as RoundUp, glyphosate is history's most popular herbicide because of its low acute toxicity to metazoans and broad-spectrum effectiveness across plant species. The development of glyphosate-resistant crops has led to increased glyphosate use and consequences from the use of glyphosate-based herbicides (GBH). Glyphosate has entered the food supply, spurred glyphosate-resistant weeds, and exposed non-target organisms to glyphosate. Glyphosate targets EPSPS/AroA/Aro1 (orthologs across plants, bacteria, and fungi), the rate-limiting step in the production of aromatic amino acids from the shikimate pathway. Metazoans lacking this pathway are spared from acute toxicity and acquire their aromatic amino acids from their diet. However, glyphosate resistance is increasing in non-target organisms. Mutations and natural genetic variation discovered in Saccharomyces cerevisiae illustrate similar types of glyphosate resistance mechanisms in fungi, plants, and bacteria, in addition to known resistance mechanisms such as mutations in Aro1 that block glyphosate binding (target-site resistance (TSR)) and mutations in efflux drug transporters non-target-site resistance (NTSR). Recently, genetic variation and mutations in an amino transporter affecting glyphosate resistance have uncovered potential off-target effects of glyphosate in fungi and bacteria. While glyphosate is a glycine analog, it is transported into cells using an aspartic/glutamic acid (D/E) transporter. The size, shape, and charge distribution of glyphosate closely resembles D/E, and, therefore, glyphosate is a D/E amino acid mimic. The mitochondria use D/E in several pathways and mRNA-encoding mitochondrial proteins are differentially expressed during glyphosate exposure. Mutants downstream of Aro1 are not only sensitive to glyphosate but also a broad range of other chemicals that cannot be rescued by exogenous supplementation of aromatic amino acids. Glyphosate also decreases the pH when unbuffered and many studies do not consider the differences in pH that affect toxicity and resistance mechanisms.},
}

Saccharomyces cerevisiae/genetics/metabolism
*Herbicides/pharmacology
Glycine/pharmacology/metabolism
Plants
Amino Acids, Aromatic

@article {pmid37275157,
year = {2023},
author = {Himmelstrand, K and Brandström Durling, M and Karlsson, M and Stenlid, J and Olson, Å},
title = {Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1159811},
pmid = {37275157},
issn = {1664-302X},
abstract = {INTRODUCTION: Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species.

METHODS: In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers.

RESULTS AND DISCUSSION: Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.},
}

@article {pmid37276405,
year = {2023},
author = {Kumar, P and Babu, KSD and Singh, AK and Singh, DK and Nalli, A and Mukul, SJ and Roy, A and Mazeed, M and Raman, B and Kruparani, SP and Siddiqi, I and Sankaranarayanan, R},
title = {Distinct localization of chiral proofreaders resolves organellar translation conflict in plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {24},
pages = {e2219292120},
pmid = {37276405},
issn = {1091-6490},
mesh = {*Organelles/metabolism ; Mitochondria/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Chloroplasts/metabolism ; RNA, Transfer/metabolism ; *Arabidopsis/genetics ; },
abstract = {Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.},
}

*Organelles/metabolism
Mitochondria/metabolism
RNA, Transfer, Amino Acyl/metabolism
Chloroplasts/metabolism
RNA, Transfer/metabolism
*Arabidopsis/genetics

@article {pmid37277654,
year = {2023},
author = {Devant, P and Kagan, JC},
title = {Molecular mechanisms of gasdermin D pore-forming activity.},
journal = {Nature immunology},
volume = {24},
number = {7},
pages = {1064-1075},
pmid = {37277654},
issn = {1529-2916},
support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI116550/AI/NIAID NIH HHS/United States ; R01 AI167993/AI/NIAID NIH HHS/United States ; R37 AI116550/AI/NIAID NIH HHS/United States ; },
mesh = {*Intracellular Signaling Peptides and Proteins/genetics/metabolism ; *Gasdermins ; Pyroptosis ; Interleukin-1/metabolism ; Cell Membrane/metabolism ; Inflammasomes/metabolism ; },
abstract = {The regulated disruption of the plasma membrane, which can promote cell death, cytokine secretion or both is central to organismal health. The protein gasdermin D (GSDMD) is a key player in this process. GSDMD forms membrane pores that can promote cytolysis and the release of interleukin-1 family cytokines into the extracellular space. Recent discoveries have revealed biochemical and cell biological mechanisms that control GSDMD pore-forming activity and its diverse downstream immunological effects. Here, we review these multifaceted regulatory activities, including mechanisms of GSDMD activation by proteolytic cleavage, dynamics of pore assembly, regulation of GSDMD activities by posttranslational modifications, membrane repair and the interplay of GSDMD and mitochondria. We also address recent insights into the evolution of the gasdermin family and their activities in species across the kingdoms of life. In doing so, we hope to condense recent progress and inform future studies in this rapidly moving field in immunology.},
}

*Intracellular Signaling Peptides and Proteins/genetics/metabolism
*Gasdermins
Pyroptosis
Interleukin-1/metabolism
Cell Membrane/metabolism
Inflammasomes/metabolism

@article {pmid37278219,
year = {2023},
author = {Markaki, M and Tsagkari, D and Tavernarakis, N},
title = {Mitophagy and long-term neuronal homeostasis.},
journal = {Journal of cell science},
volume = {136},
number = {11},
pages = {},
doi = {10.1242/jcs.260638},
pmid = {37278219},
issn = {1477-9137},
support = {ERC-GA695190-MANNA/ERC_/European Research Council/International ; },
mesh = {Humans ; *Mitophagy/physiology ; Autophagy/physiology ; Neurons/metabolism ; *Neurodegenerative Diseases/metabolism ; Homeostasis ; },
abstract = {Neurons are highly polarized, post-mitotic cells that are characterized by unique morphological diversity and complexity. As highly differentiated cells that need to survive throughout organismal lifespan, neurons face exceptional energy challenges in time and space. Therefore, neurons are heavily dependent on a healthy mitochondrial network for their proper function and maintenance under both physiological and stress conditions. Multiple quality control systems have evolved to fine-tune mitochondrial number and quality, thus preserving neuronal energy homeostasis. Here, we review the contribution of mitophagy, a selective form of autophagy that targets dysfunctional or superfluous mitochondria for degradation, in maintaining nervous system homeostasis. In addition, we discuss recent evidence implicating defective or dysregulated mitophagy in the pathogenesis of neurodegenerative diseases.},
}

Humans
*Mitophagy/physiology
Autophagy/physiology
Neurons/metabolism
*Neurodegenerative Diseases/metabolism
Homeostasis

@article {pmid37279941,
year = {2023},
author = {Sheikh, S and Pánek, T and Gahura, O and Týč, J and Záhonová, K and Lukeš, J and Eliáš, M and Hashimi, H},
title = {A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37279941},
issn = {1537-1719},
mesh = {*Giant Viruses/genetics/metabolism ; Phylogeny ; Mitochondrial Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Dynamins/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; },
abstract = {The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases, we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister group to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.},
}

*Giant Viruses/genetics/metabolism
Phylogeny
Mitochondrial Proteins/genetics/metabolism
Mitochondria/genetics/metabolism
Dynamins/genetics/metabolism
Saccharomyces cerevisiae/genetics

@article {pmid37282330,
year = {1989},
author = {Andreuccetti, P},
title = {Ultrastructural Observations on the Germ Plasm in the Lizard Podarcis sicula: (germ plasm/germ cells/ultrastructure/reptiles).},
journal = {Development, growth & differentiation},
volume = {31},
number = {3},
pages = {269-273},
doi = {10.1111/j.1440-169X.1989.00269.x},
pmid = {37282330},
issn = {1440-169X},
abstract = {Ultrastructural studies on embryos and adult females of Podarcis sicula revealed fibrogranular electron-dense aggregates in the cytoplasm of primordial germ cells, oogonia, and oocytes. The ultrastructural similarities of these aggregates to fibrogranular aggregates in germ cells of some animal species and their relationship with mitochondria, free ribosomes, as well as cisternae of the rough endoplasmic reticulum strongly suggest that they correspond to the germ plasm.},
}

@article {pmid37286063,
year = {2023},
author = {Abalde, S and Crocetta, F and Tenorio, MJ and D'Aniello, S and Fassio, G and Rodríguez-Flores, PC and Uribe, JE and Afonso, CML and Oliverio, M and Zardoya, R},
title = {Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus.},
journal = {Molecular phylogenetics and evolution},
volume = {186},
number = {},
pages = {107838},
doi = {10.1016/j.ympev.2023.107838},
pmid = {37286063},
issn = {1095-9513},
mesh = {Humans ; Animals ; Phylogeny ; *Mitochondria/genetics ; Genetic Speciation ; *Genome, Mitochondrial ; Snails/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.},
}

Humans
Animals
Phylogeny
*Mitochondria/genetics
Genetic Speciation
*Genome, Mitochondrial
Snails/genetics
DNA, Mitochondrial/genetics

@article {pmid37289794,
year = {2023},
author = {Hebert, PDN and Bock, DG and Prosser, SWJ},
title = {Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286620},
pmid = {37289794},
issn = {1932-6203},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genome, Insect ; Mitochondria/genetics ; Insecta/genetics ; Risk Assessment ; Cell Nucleus/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.},
}

Animals
*DNA, Mitochondrial/genetics
*Genome, Insect
Mitochondria/genetics
Insecta/genetics
Risk Assessment
Cell Nucleus/genetics
Phylogeny
Sequence Analysis, DNA

@article {pmid37291154,
year = {2023},
author = {Lee, Y and Cho, CH and Noh, C and Yang, JH and Park, SI and Lee, YM and West, JA and Bhattacharya, D and Jo, K and Yoon, HS},
title = {Origin of minicircular mitochondrial genomes in red algae.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3363},
pmid = {37291154},
issn = {2041-1723},
mesh = {Phylogeny ; *Genome, Mitochondrial/genetics ; Eukaryotic Cells ; Mitochondria/genetics ; *Rhodophyta/genetics ; Evolution, Molecular ; },
abstract = {Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.},
}

Phylogeny
*Genome, Mitochondrial/genetics
Eukaryotic Cells
Mitochondria/genetics
*Rhodophyta/genetics
Evolution, Molecular

@article {pmid37295735,
year = {2023},
author = {Gul, I and Abbas, MN and Kausar, S and Luo, J and Gao, X and Mu, Y and Fan, W and Cui, H},
title = {Insight into crustacean cathepsins: Structure-evolutionary relationships and functional roles in physiological processes.},
journal = {Fish & shellfish immunology},
volume = {139},
number = {},
pages = {108852},
doi = {10.1016/j.fsi.2023.108852},
pmid = {37295735},
issn = {1095-9947},
mesh = {Animals ; *Cathepsins/genetics/chemistry ; Proteins ; Biological Evolution ; *Physiological Phenomena ; },
abstract = {Cathepsins belong to a group of proteins that are present in both prokaryotic and eukaryotic organisms and have an extremely high degree of evolutionary conservation. These proteins are functionally active in extracellular environments as soluble enzymatic proteins or attached to plasma membrane receptors. In addition, they occur in cellular secretory vesicles, mitochondria, the cytosol, and within the nuclei of eukaryotic cells. Cathepsins are classified into various groups based on their sequence variations, leading to their structural and functional diversification. The molecular understanding of the physiology of crustaceans has shown that proteases, including cathepsins, are expressed ubiquitously. They also contain one of the central regulatory systems for crustacean reproduction, growth, and immune responses. This review focuses on various aspects of the crustaceans cathepsins and emphasizes their biological roles in different physiological processes such as reproduction, growth, development, and immune responses. We also describe the bioactivity of crustaceans cathepsins. Because of the vital biological roles that cathepsins play as cellular proteases in physiological processes, they have been proposed as potential novel targets for the development of management strategies for the aquaculture industries.},
}

Animals
*Cathepsins/genetics/chemistry
Proteins
Biological Evolution
*Physiological Phenomena

@article {pmid37299482,
year = {2023},
author = {Manilla, V and Santopaolo, F and Gasbarrini, A and Ponziani, FR},
title = {Type 2 Diabetes Mellitus and Liver Disease: Across the Gut-Liver Axis from Fibrosis to Cancer.},
journal = {Nutrients},
volume = {15},
number = {11},
pages = {},
pmid = {37299482},
issn = {2072-6643},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Diabetes Mellitus, Type 2/complications/pathology ; *Carcinoma, Hepatocellular/metabolism ; Dysbiosis/complications/pathology ; *Liver Neoplasms/metabolism ; Liver/metabolism ; Liver Cirrhosis ; Fibrosis ; },
abstract = {Type 2 diabetes mellitus is a widespread disease worldwide, and is one of the cornerstones of metabolic syndrome. The existence of a strong relationship between diabetes and the progression of liver fibrosis has been demonstrated by several studies, using invasive and noninvasive techniques. Patients with type 2 diabetes mellitus (T2DM) and nonalcoholic fatty liver disease (NAFLD) show faster progression of fibrosis than patients without diabetes. Many confounding factors make it difficult to determine the exact mechanisms involved. What we know so far is that both liver fibrosis and T2DM are expressions of metabolic dysfunction, and we recognize similar risk factors. Interestingly, both are promoted by metabolic endotoxemia, a low-grade inflammatory condition caused by increased endotoxin levels and linked to intestinal dysbiosis and increased intestinal permeability. There is broad evidence on the role of the gut microbiota in the progression of liver disease, through both metabolic and inflammatory mechanisms. Therefore, dysbiosis that is associated with diabetes can act as a modifier of the natural evolution of NAFLD. In addition to diet, hypoglycemic drugs play an important role in this scenario, and their benefit is also the result of effects exerted in the gut. Here, we provide an overview of the mechanisms that explain why diabetic patients show a more rapid progression of liver disease up to hepatocellular carcinoma (HCC), focusing especially on those involving the gut-liver axis.},
}

Humans
*Non-alcoholic Fatty Liver Disease/metabolism
*Diabetes Mellitus, Type 2/complications/pathology
*Carcinoma, Hepatocellular/metabolism
Dysbiosis/complications/pathology
*Liver Neoplasms/metabolism
Liver/metabolism
Liver Cirrhosis
Fibrosis

@article {pmid37303610,
year = {2023},
author = {Liang, Y and Fang, X and Zheng, L and Wu, H and He, Z and Xiong, Z and Hong, J and Ai, X and Liang, G},
title = {The complete mitochondrial genome of Choristoneura metasequoiacola Liu,1983 (Lepidoptera: Tortricidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {8},
number = {6},
pages = {653-657},
pmid = {37303610},
issn = {2380-2359},
abstract = {Choristoneura metasequoiacola Liu, 1983 is an important caterpillar species that specifically infests the leaves and branches of Metasequoia glyptostroboides Hu & W. C. Cheng 1948 with short larval infestations, long-term dormancy, and has a limited distribution in Lichuan, Hubei, China. The complete mitochondria genome of C. metasequoiacola was determined by using Illumina NovaSeq, and analyzed based on previously annotated sibling species. In total, we obtained mitochondria genome with 15,128 bp in length, circular in shape with a double-stranded closed ring structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and an AT-rich region. Of which the nucleotide composition was highly A + T biased, accounting for 81.98% of the whole mitogenome. Thirteen protein-coding genes (PCGs) were 11,142 bp; Twenty-two tRNA genes and AT-rich region were 1,472 and 199 bp, respectively. Phylogenetically, the relationship between Choristoneura spp. (containing C. metasequoiacola) and Adoxophyes spp. was closer than any other two genera from Tortricidae, and the relationship between C. metasequoiacola and C.murinana was the closest among nine sibling species from that genus, which helps to explain species evolution within the family Tortricidae.},
}

@article {pmid37305924,
year = {2023},
author = {Floriano, AM and Batisti Biffignandi, G and Castelli, M and Olivieri, E and Clementi, E and Comandatore, F and Rinaldi, L and Opara, M and Plantard, O and Palomar, AM and Noël, V and Vijay, A and Lo, N and Makepeace, BL and Duron, O and Jex, A and Guy, L and Sassera, D},
title = {The evolution of intramitochondriality in Midichloria bacteria.},
journal = {Environmental microbiology},
volume = {25},
number = {11},
pages = {2102-2117},
doi = {10.1111/1462-2920.16446},
pmid = {37305924},
issn = {1462-2920},
mesh = {Animals ; *Ixodes/microbiology ; Bacteria/genetics ; Mitochondria/genetics ; Phylogeny ; Symbiosis ; },
abstract = {Midichloria spp. are intracellular bacterial symbionts of ticks. Representatives of this genus colonise mitochondria in the cells of their hosts. To shed light on this unique interaction we evaluated the presence of an intramitochondrial localization for three Midichloria in the respective tick host species and generated eight high-quality draft genomes and one closed genome, showing that this trait is non-monophyletic, either due to losses or multiple acquisitions. Comparative genomics supports the first hypothesis, as the genomes of non-mitochondrial symbionts are reduced subsets of those capable of colonising the organelles. We detect genomic signatures of mitochondrial tropism, including the differential presence of type IV secretion system and flagellum, which could allow the secretion of unique effectors and/or direct interaction with mitochondria. Other genes, including adhesion molecules, proteins involved in actin polymerisation, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, to fuse with the organelles or manipulate the mitochondrial network.},
}

Animals
*Ixodes/microbiology
Bacteria/genetics
Mitochondria/genetics
Phylogeny
Symbiosis

@article {pmid37309528,
year = {2021},
author = {Yang, W and Zou, J and Yu, Y and Long, W and Li, S},
title = {Repeats in mitochondrial and chloroplast genomes characterize the ecotypes of the Oryza.},
journal = {Molecular breeding : new strategies in plant improvement},
volume = {41},
number = {1},
pages = {7},
pmid = {37309528},
issn = {1572-9788},
abstract = {UNLABELLED: Mitochondria and chloroplast are very important organelles for organism, participating in basic life activity. Their genomes contain many repeats which can lead to a variation of genome structure. Oryza is an important genus for human beings' nutrition. Several mitochondrial and chloroplast genomes of Oryza have been sequenced, which help us to insight the distribution and evolution of the repeats in Oryza species. In this paper, we compared six mitochondrial and 13 chloroplast genomes of Oryza and found that the structures of mitochondrial genomes were more diverse than chloroplast genomes. Since repeats can change the structure of the genome, resulting in the structural diversity of the genome, we analyzed all repeats and found 31 repeats in mitochondrial and 13 repeats in chloroplast genomes. Further, we developed 21 pairs of MRS molecular markers and 12 pairs of CRS molecular markers based on mitochondrial repeats and chloroplast repeats, respectively. These molecular markers can be used to detect the repeat-mediated recombination in Oryza mitochondrial and chloroplast genomes by PCR or fluorescence quantification.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-020-01198-6.},
}

@article {pmid37311262,
year = {2023},
author = {Annes, K and Ferreira, CR and Valente, RS and Marsico, TV and Tannura, JH and da Silveira, JC and Silva, FH and Landim-Alvarenga, FDC and Mesquista, FS and Sudano, MJ},
title = {Contribution of lipids to the organelle differential profile of in vitro-produced bovine embryos.},
journal = {Theriogenology},
volume = {208},
number = {},
pages = {109-118},
doi = {10.1016/j.theriogenology.2023.06.005},
pmid = {37311262},
issn = {1879-3231},
mesh = {Female ; Pregnancy ; Cattle ; Animals ; *Endoplasmic Reticulum ; *Mitochondria ; Lipid Droplets ; Blastocyst ; Ceramides ; },
abstract = {Each living organism is unique because of the lipid identity of its organelles. The diverse distribution of these molecules also contributes to the role of each organelle in cellular activity. The lipid profiles of whole embryos are well documented in the literature. However, this approach can often lead to the loss of relevant information at the subcellular and consequently, metabolic levels, hindering a deeper understanding of key physiological processes during preimplantation development. Therefore, we aimed to characterize four organelles in vitro-produced bovine embryos: lipid droplets (LD), endoplasmic reticulum (ER), mitochondria (MIT), and nuclear membrane (NUC), and evaluate the contribution of the lipid species to each organelle evaluated. Expanded blastocysts were subjected to cell organelle isolation. Thereafter, lipid extraction from cell organelles and lipid analysis using the Multiple Reaction Monitoring (MRM) profiling method were performed. The LD and ER displayed a greater number of lipids (Phosphatidylcholine - PC, Ceramide - Cer, and Sphingomielin - SM) with high signal-to-noise intensities. This result is due to the high rate of biosynthesis, lipid distribution, and ability to store and recycle lipid species of these organelles. The NUC had a more distinct lipid profile than the other three organelles, with high relative intensities of PC, SM, and triacylglycerols (TG), which is consistent with its high nuclear activity. MIT had an intermediate profile that was close to that of LD and ER, which aligns with its autonomous metabolism for some classes of phospholipids (PL). Our study revealed the lipid composition of each organelle studied, and the roles of these lipids could be associated with the characteristic organellar activity. Our findings highlight the lipid species and classes that are relevant for the homeostasis and function of each associated organelle and provide tentative biomarkers for the determination of in vitro embryonic development and quality.},
}

Female
Pregnancy
Cattle
Animals
*Endoplasmic Reticulum
*Mitochondria
Lipid Droplets
Blastocyst
Ceramides

@article {pmid37325898,
year = {2023},
author = {Sabbah, HN and Taylor, C and Vernon, HJ},
title = {Temporal evolution of the heart failure phenotype in Barth syndrome and treatment with elamipretide.},
journal = {Future cardiology},
volume = {19},
number = {4},
pages = {211-225},
doi = {10.2217/fca-2023-0008},
pmid = {37325898},
issn = {1744-8298},
mesh = {Humans ; *Barth Syndrome/genetics/pathology ; *Heart Failure/drug therapy ; Stroke Volume ; Phenotype ; Cardiolipins ; Oligopeptides ; },
abstract = {Barth syndrome (BTHS) is a rare genetic disorder caused by pathogenic variants in TAFAZZIN leading to reduced remodeled cardiolipin (CL), a phospholipid essential to mitochondrial function and structure. Cardiomyopathy presents in most patients with BTHS, typically appearing as dilated cardiomyopathy (DCM) in infancy and evolving to hypertrophic cardiomyopathy (HCM) resembling heart failure (HF) with preserved ejection fraction (HFpEF) in some patients ≥12 years. Elamipretide localizes to the inner mitochondrial membrane where it associates with CL, improving mitochondrial function, structure and bioenergetics, including ATP synthesis. Numerous preclinical and clinical studies in BTHS and other forms of HF have demonstrated that elamipretide improves left ventricular relaxation by ameliorating mitochondrial dysfunction, making it well suited for therapeutic use in adolescent and adult patients with BTHS.},
}

Humans
*Barth Syndrome/genetics/pathology
*Heart Failure/drug therapy
Stroke Volume
Phenotype
Cardiolipins
Oligopeptides

@article {pmid37327832,
year = {2023},
author = {Thacker, CE and Tyler McCraney, W and Harrington, RC and Near, TJ and Shelley, JJ and Adams, M and Hammer, MP and Unmack, PJ},
title = {Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families.},
journal = {Molecular phylogenetics and evolution},
volume = {186},
number = {},
pages = {107841},
doi = {10.1016/j.ympev.2023.107841},
pmid = {37327832},
issn = {1095-9513},
mesh = {Humans ; Animals ; Phylogeny ; *Fishes/genetics ; *Perciformes/genetics ; Mitochondria ; Fossils ; },
abstract = {Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a timescale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.},
}

Humans
Animals
Phylogeny
*Fishes/genetics
*Perciformes/genetics
Mitochondria
Fossils

@article {pmid37330026,
year = {2023},
author = {Nguyen, TP and Nguyen, BT and Dao, TNL and Ho, TH and Lee, PT},
title = {Investigation of the functional role of UNC93B1 in Nile tilapia (Oreochromis niloticus): mRNA expression, subcellular localization, and physical interaction with fish-specific TLRs.},
journal = {Fish & shellfish immunology},
volume = {139},
number = {},
pages = {108902},
doi = {10.1016/j.fsi.2023.108902},
pmid = {37330026},
issn = {1095-9947},
mesh = {Humans ; Animals ; Mice ; *Cichlids ; Phylogeny ; Fish Proteins/chemistry ; Toll-Like Receptors/genetics/metabolism ; Phagocytosis ; Streptococcus agalactiae/physiology ; *Fish Diseases ; *Streptococcal Infections/veterinary ; Gene Expression Regulation ; Immunity, Innate/genetics ; Membrane Transport Proteins/genetics ; },
abstract = {Nile tilapia (Oreochromis niloticus) is one of the major food fish worldwide. The farming business, on the other hand, has faced considerable obstacles, such as disease infestations. Toll-like receptors (TLRs) play an important function in the activation of the innate immune system in response to infections. Unc-93 homolog B1 (UNC93B1) is a key regulator of nucleic acid (NA)-sensing TLRs. Here the UNC93B1 gene, which was cloned from Nile tilapia tissue for this investigation, had the same genetic structure as a homologous gene in humans and mice. Phylogenetic analysis revealed that Nile tilapia UNC93B1 clustered with UNC93B1 from other species and separately from the UNC93A clade. The gene structure of the Nile tilapia UNC93B1 was found to be identical to that of human UNC93B1. Our gene expression studies revealed that Nile tilapia UNC93B1 was highly expressed in the spleen, followed by other immune-related tissues such as the head kidney, gills, and intestine. Moreover, Nile tilapia UNC93B1 mRNA transcripts were up-regulated in vivo in the head kidney and spleen tissues from poly I:C and Streptococcus agalactiae injected Nile tilapia, as well as in vitro in LPS stimulated Tilapia head kidney (THK) cells. The Nile tilapia UNC93B1-GFP protein signal was detected in the cytosol of THK cells and was co-localized with endoplasmic reticulum and lysosome but not with mitochondria. Moreover, the results of a co-immunoprecipitation and immunostaining analysis showed that Nile tilapia UNC93B1 can be pulled down with fish-specific TLRs such as TLR18 and TLR25 from Nile tilapia, and was found to be co-localized with these fish-specific TLRs in the THK cells. Overall, our findings highlight the potential role of UNC93B1 as an accessory protein in fish-specific TLR signaling.},
}

Humans
Animals
Mice
*Cichlids
Phylogeny
Fish Proteins/chemistry
Toll-Like Receptors/genetics/metabolism
Phagocytosis
Streptococcus agalactiae/physiology
*Fish Diseases
*Streptococcal Infections/veterinary
Gene Expression Regulation
Immunity, Innate/genetics
Membrane Transport Proteins/genetics

@article {pmid37333265,
year = {2023},
author = {Hanson, SE and Doyle, MT and Bernstein, HD},
title = {The patatin-like protein PlpD forms novel structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37333265},
issn = {2692-8205},
abstract = {Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we found that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.},
}

@article {pmid37336341,
year = {2023},
author = {Liu, S and Xu, S and Liu, S and Chen, H},
title = {Importance of DJ-1 in autophagy regulation and disease.},
journal = {Archives of biochemistry and biophysics},
volume = {743},
number = {},
pages = {109672},
doi = {10.1016/j.abb.2023.109672},
pmid = {37336341},
issn = {1096-0384},
mesh = {Humans ; Reactive Oxygen Species/metabolism ; *Oxidative Stress/physiology ; Hypoxia/metabolism ; *Neoplasms ; Autophagy/physiology ; Protein Deglycase DJ-1/metabolism ; },
abstract = {Autophagy is a highly conserved biological process that has evolved across evolution. It can be activated by various external stimuli including oxidative stress, amino acid starvation, infection, and hypoxia. Autophagy is the primary mechanism for preserving cellular homeostasis and is implicated in the regulation of metabolism, cell differentiation, tolerance to starvation conditions, and resistance to aging. As a multifunctional protein, DJ-1 is commonly expressed in vivo and is associated with a variety of biological processes. Its most widely studied role is its function as an oxidative stress sensor that inhibits the production of excessive reactive oxygen species (ROS) in the mitochondria and subsequently the cellular damage caused by oxidative stress. In recent years, many studies have identified DJ-1 as another important factor regulating autophagy; it regulates autophagy in various ways, most commonly by regulating the oxidative stress response. In particular, DJ-1-regulated autophagy is involved in cancer progression and plays a key role in alleviating neurodegenerative diseases(NDS) and defective reperfusion diseases. It could serve as a potential target for the regulation of autophagy and participate in disease treatment as a meaningful modality. Therefore, exploring DJ-1-regulated autophagy could provide new avenues for future disease treatment.},
}

Humans
Reactive Oxygen Species/metabolism
*Oxidative Stress/physiology
Hypoxia/metabolism
*Neoplasms
Autophagy/physiology
Protein Deglycase DJ-1/metabolism

@article {pmid37338543,
year = {2023},
author = {Wong, JE and Zíková, A and Gahura, O},
title = {The Ancestral Shape of the Access Proton Path of Mitochondrial ATP Synthases Revealed by a Split Subunit-a.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37338543},
issn = {1537-1719},
mesh = {*Mitochondrial Proton-Translocating ATPases/genetics/chemistry/metabolism ; *Proton-Translocating ATPases/metabolism ; Protons ; Eukaryota/metabolism ; Escherichia coli/genetics/metabolism ; Adenosine Triphosphate/metabolism ; },
abstract = {The passage of protons across membranes through F1Fo-ATP synthases spins their rotors and drives the synthesis of ATP. While the principle of torque generation by proton transfer is known, the mechanisms and routes of proton access and release and their evolution are not fully understood. Here, we show that the entry site and path of protons in the lumenal half channel of mitochondrial ATP synthases are largely defined by a short N-terminal α-helix of subunit-a. In Trypanosoma brucei and other Euglenozoa, the α-helix is part of another polypeptide chain that is a product of subunit-a gene fragmentation. This α-helix and other elements forming the proton pathway are widely conserved across eukaryotes and in Alphaproteobacteria, the closest extant relatives of mitochondria, but not in other bacteria. The α-helix blocks one of two proton routes found in Escherichia coli, resulting in a single proton entry site in mitochondrial and alphaproteobacterial ATP synthases. Thus, the shape of the access half channel predates eukaryotes and originated in the lineage from which mitochondria evolved by endosymbiosis.},
}

*Mitochondrial Proton-Translocating ATPases/genetics/chemistry/metabolism
*Proton-Translocating ATPases/metabolism
Protons
Eukaryota/metabolism
Escherichia coli/genetics/metabolism
Adenosine Triphosphate/metabolism

@article {pmid37364099,
year = {2023},
author = {Lynch, M},
title = {Mutation pressure, drift, and the pace of molecular coevolution.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {27},
pages = {e2306741120},
pmid = {37364099},
issn = {1091-6490},
support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; R35-GM122566-01/NH/NIH HHS/United States ; },
mesh = {*Evolution, Molecular ; Mutation ; *Mutation Rate ; Genome ; Genetic Drift ; },
abstract = {Most aspects of the molecular biology of cells involve tightly coordinated intermolecular interactions requiring specific recognition at the nucleotide and/or amino acid levels. This has led to long-standing interest in the degree to which constraints on interacting molecules result in conserved vs. accelerated rates of sequence evolution, with arguments commonly being made that molecular coevolution can proceed at rates exceeding the neutral expectation. Here, a fairly general model is introduced to evaluate the degree to which the rate of evolution at functionally interacting sites is influenced by effective population sizes (Ne), mutation rates, strength of selection, and the magnitude of recombination between sites. This theory is of particular relevance to matters associated with interactions between organelle- and nuclear-encoded proteins, as the two genomic environments often exhibit dramatic differences in the power of mutation and drift. Although genes within low Ne environments can drive the rate of evolution of partner genes experiencing higher Ne, rates exceeding the neutral expectation require that the former also have an elevated mutation rate. Testable predictions, some counterintuitive, are presented on how patterns of coevolutionary rates should depend on the relative intensities of drift, selection, and mutation.},
}

*Evolution, Molecular
Mutation
*Mutation Rate
Genome
Genetic Drift

@article {pmid37364695,
year = {2023},
author = {Barrera, CA and Ortega, J and Gutierrez-Guerrero, YT and Baeza, JA},
title = {Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae.},
journal = {Gene},
volume = {879},
number = {},
pages = {147588},
doi = {10.1016/j.gene.2023.147588},
pmid = {37364695},
issn = {1879-0038},
mesh = {Animals ; Phylogeny ; *Chiroptera/genetics ; Plant Nectar ; Genomics ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; },
abstract = {Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.},
}

Animals
Phylogeny
*Chiroptera/genetics
Plant Nectar
Genomics
Mitochondria/genetics
*Genome, Mitochondrial/genetics
RNA, Transfer/genetics

@article {pmid37367622,
year = {2023},
author = {van der Walt, D and Steenkamp, ET and Wingfield, BD and Wilken, PM},
title = {Evidence of Biparental Mitochondrial Inheritance from Self-Fertile Crosses between Closely Related Species of Ceratocystis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {6},
pages = {},
pmid = {37367622},
issn = {2309-608X},
abstract = {Hybridization is recognized as a notable driver of evolution and adaptation, which closely related species may exploit in the form of incomplete reproductive barriers. Three closely related species of Ceratocystis (i.e., C. fimbriata, C. manginecans and C. eucalypticola) have previously been shown to hybridize. In such studies, naturally occurring self-sterile strains were mated with an unusual laboratory-generated sterile isolate type, which could have impacted conclusions regarding the prevalence of hybridization and inheritance of mitochondria. In the current study, we investigated whether interspecific crosses between fertile isolates of these three species are possible and, if so, how mitochondria are inherited by the progeny. For this purpose, a PCR-RFLP method and a mitochondrial DNA-specific PCR technique were custom-made. These were applied in a novel approach of typing complete ascospore drops collected from the fruiting bodies in each cross to distinguish between self-fertilizations and potential hybridization. These markers showed hybridization between C. fimbriata and C. eucalypticola and between C. fimbriata and C. manginecans, while no hybridization was detected in the crosses involving C. manginecans and C. eucalypticola. In both sets of hybrid progeny, we detected biparental inheritance of mitochondria. This study was the first to successfully produce hybrids from a cross involving self-fertile isolates of Ceratocystis and also provided the first direct evidence of biparental mitochondrial inheritance in the Ceratocystidaceae. This work lays the foundation for further research focused on investigating the role of hybridization in the speciation of Ceratocystis species and if mitochondrial conflict could have influenced the process.},
}

@article {pmid37368881,
year = {2023},
author = {Tanabe, TS and Grosser, M and Hahn, L and Kümpel, C and Hartenfels, H and Vtulkin, E and Flegler, W and Dahl, C},
title = {Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.},
journal = {PLoS biology},
volume = {21},
number = {6},
pages = {e3002177},
pmid = {37368881},
issn = {1545-7885},
mesh = {*Thioctic Acid/genetics/metabolism ; Peptide Synthases/genetics/metabolism ; Phylogeny ; Bacterial Proteins/metabolism ; Sulfur ; },
abstract = {Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.},
}

*Thioctic Acid/genetics/metabolism
Peptide Synthases/genetics/metabolism
Phylogeny
Bacterial Proteins/metabolism
Sulfur

@article {pmid37371486,
year = {2023},
author = {Ding, Y and Zhang, S and Guo, Q and Leng, J},
title = {Mitochondrial Diabetes Is Associated with the ND4 G11696A Mutation.},
journal = {Biomolecules},
volume = {13},
number = {6},
pages = {},
pmid = {37371486},
issn = {2218-273X},
mesh = {Adult ; Phylogeny ; *NADH Dehydrogenase/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; East Asian People ; Mutation ; Humans ; Aged ; *Diabetes Mellitus, Type 2/genetics ; Middle Aged ; },
abstract = {Type 2 diabetes mellitus (T2DM) is a common endocrine disorder which remains a large challenge for clinicians. Previous studies have suggested that mitochondrial dysfunction plays an active role in T2DM progression, but a detailed mechanism is still elusive. In the current study, two Han Chinese families with maternally inherited T2DM were evaluated using clinical, genetic, molecular, and biochemical analyses. The mitochondrial genomes were PCR amplified and sequenced. Phylogenetic and bioinformatic analyses were used to assess the potential pathogenicity of mitochondrial DNA (mtDNA) mutations. Interestingly, the matrilineal relatives of these pedigrees exhibited variable severity of T2DM, in particular, the age at onset of T2DM varied from 26 to 65 years, with an average of 49 years. Sequence analysis revealed the presence of ND4 G11696A mutation, which resulted in the substitution of an isoleucine for valine at amino acid (AA) position 312. Indeed, this mutation was present in homoplasmy only in the maternal lineage, not in other members of these families, as well as 200 controls. Furthermore, the m.C5601T in the tRNA[Ala] and novel m.T5813C in the tRNA[Cys], showing high evolutional conservation, may contribute to the phenotypic expression of ND4 G11696A mutation. In addition, biochemical analysis revealed that cells with ND4 G11696A mutation exhibited higher levels of reactive oxygen species (ROS) productions than the controls. In contrast, the levels of mitochondrial membrane potential (MMP), ATP, mtDNA copy number (mtDNA-CN), Complex I activity, and NAD[+]/NADH ratio significantly decreased in cell lines carrying the m.G11696A and tRNA mutations, suggesting that these mutations affected the respiratory chain function and led to mitochondrial dysfunction that was involved in T2DM. Thus, our study broadened the clinical phenotypes of m.G11696A mutation.},
}

Adult
Phylogeny
*NADH Dehydrogenase/genetics
*DNA, Mitochondrial/genetics
*Mitochondria/genetics
East Asian People
Mutation
Humans
Aged
*Diabetes Mellitus, Type 2/genetics
Middle Aged

@article {pmid37381996,
year = {2023},
author = {Zhao, JH and Chen, YC and Hua, ZY and Liu, TR and Zhao, YY and Huang, LQ and Yuan, Y},
title = {[Cloning and gene function of dicarboxylate-tricarboxylate carrier protein in Gastrodia elata].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {12},
pages = {3140-3148},
doi = {10.19540/j.cnki.cjcmm.20230310.102},
pmid = {37381996},
issn = {1001-5302},
mesh = {*Gastrodia/genetics ; Phylogeny ; Amino Acids ; Cloning, Molecular ; Carrier Proteins ; },
abstract = {The gene GeDTC encoding the dicarboxylate-tricarboxylate carrier protein in Gastrodia elata was cloned by specific primers which were designed based on the transcriptome data of G. elata. Bioinformatics analysis on GeDTC gene was carried out by using ExPASY, ClustalW, MEGA, etc. Positive transgenic plants and potato minituber were obtained by virtue of the potato genetic transformation system. Agronomic characters, such as size, weight, organic acid content, and starch content, of potato minituber were tested and analyzed and GeDTC gene function was preliminarily investigated. The results showed that the open reading frame of GeDTC gene was 981 bp in length and 326 amino acid residues were encoded, with a relative molecular weight of 35.01 kDa. It was predicted that the theoretical isoelectric point of GeDTC protein was 9.83, the instability coefficient was 27.88, and the average index of hydrophilicity was 0.104, which was indicative of a stable hydrophilic protein. GeDTC protein had a transmembrane structure and no signal peptide and was located in the inner membrane of mitochondria. The phylogenetic tree showed that GeDTC was highly homologous with DTC proteins of other plant species, among which GeDTC had the highest homology with DcDTC(XP＿020675804.1) in Dendrobium candidum, reaching 85.89%. GeDTC overexpression vector pCambia1300-35Spro-GeDTC was constructed by double digests, and transgenic potato plants were obtained by Agrobacterium-mediated gene transformation. Compared with the wild-type plants, transgenic potato minituber harvested by transplanting had smaller size, lighter weight, lower organic acid content, and no significant difference in starch content. It is preliminarily induced that GeDTC is the efflux channel of tricarboxylate and related to the tuber development, which lays a foundation for further elucidating the molecular mechanism of G. elata tuber development.},
}

*Gastrodia/genetics
Phylogeny
Amino Acids
Cloning, Molecular
Carrier Proteins

@article {pmid37386734,
year = {2023},
author = {Arnqvist, G and Rowe, L},
title = {Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes.},
journal = {Molecular ecology},
volume = {32},
number = {17},
pages = {4713-4724},
doi = {10.1111/mec.17062},
pmid = {37386734},
issn = {1365-294X},
mesh = {*Polymorphism, Genetic ; Selection, Genetic ; Biological Evolution ; Alleles ; *Life History Traits ; Models, Genetic ; Genetic Variation ; Epistasis, Genetic ; },
abstract = {Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.},
}

*Polymorphism, Genetic
Selection, Genetic
Biological Evolution
Alleles
*Life History Traits
Models, Genetic
Genetic Variation
Epistasis, Genetic

@article {pmid37389212,
year = {2023},
author = {Stefano, GB and Büttiker, P and Weissenberger, S and Esch, T and Anders, M and Raboch, J and Kream, RM and Ptacek, R},
title = {Independent and sensory human mitochondrial functions reflecting symbiotic evolution.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1130197},
pmid = {37389212},
issn = {2235-2988},
mesh = {Humans ; *Mitochondria ; *Genes, Bacterial ; Quorum Sensing ; Virion ; },
abstract = {The bacterial origin of mitochondria has been a widely accepted as an event that occurred about 1.45 billion years ago and endowed cells with internal energy producing organelle. Thus, mitochondria have traditionally been viewed as subcellular organelle as any other - fully functionally dependent on the cell it is a part of. However, recent studies have given us evidence that mitochondria are more functionally independent than other organelles, as they can function outside the cells, engage in complex "social" interactions, and communicate with each other as well as other cellular components, bacteria and viruses. Furthermore, mitochondria move, assemble and organize upon sensing different environmental cues, using a process akin to bacterial quorum sensing. Therefore, taking all these lines of evidence into account we hypothesize that mitochondria need to be viewed and studied from a perspective of a more functionally independent entity. This view of mitochondria may lead to new insights into their biological function, and inform new strategies for treatment of disease associated with mitochondrial dysfunction.},
}

Humans
*Mitochondria
*Genes, Bacterial
Quorum Sensing
Virion

@article {pmid37406344,
year = {2023},
author = {Lamb, IM and Okoye, IC and Mather, MW and Vaidya, AB},
title = {Unique Properties of Apicomplexan Mitochondria.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {541-560},
pmid = {37406344},
issn = {1545-3251},
support = {R01 AI028398/AI/NIAID NIH HHS/United States ; R01 AI100569/AI/NIAID NIH HHS/United States ; R01 AI132508/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mitochondria/genetics/metabolism ; *Toxoplasma/metabolism ; Biological Evolution ; *Malaria ; },
abstract = {Apicomplexan parasites constitute more than 6,000 species infecting a wide range of hosts. These include important pathogens such as those causing malaria and toxoplasmosis. Their evolutionary emergence coincided with the dawn of animals. Mitochondrial genomes of apicomplexan parasites have undergone dramatic reduction in their coding capacity, with genes for only three proteins and ribosomal RNA genes present in scrambled fragments originating from both strands. Different branches of the apicomplexans have undergone rearrangements of these genes, with Toxoplasma having massive variations in gene arrangements spread over multiple copies. The vast evolutionary distance between the parasite and the host mitochondria has been exploited for the development of antiparasitic drugs, especially those used to treat malaria, wherein inhibition of the parasite mitochondrial respiratory chain is selectively targeted with little toxicity to the host mitochondria. We describe additional unique characteristics of the parasite mitochondria that are being investigated and provide greater insights into these deep-branching eukaryotic pathogens.},
}

Animals
Mitochondria/genetics/metabolism
*Toxoplasma/metabolism
Biological Evolution
*Malaria

@article {pmid37407024,
year = {2023},
author = {Healy, TM and Burton, RS},
title = {Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence.},
journal = {Evolution; international journal of organic evolution},
volume = {77},
number = {9},
pages = {2100-2108},
doi = {10.1093/evolut/qpad122},
pmid = {37407024},
issn = {1558-5646},
mesh = {Animals ; *Copepoda/genetics ; Mitochondria/genetics/metabolism ; Chromosomes ; Genome ; Genotype ; DNA, Mitochondrial/genetics ; },
abstract = {All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.},
}

Animals
*Copepoda/genetics
Mitochondria/genetics/metabolism
Chromosomes
Genome
Genotype
DNA, Mitochondrial/genetics

@article {pmid37408243,
year = {2023},
author = {Frigo, E and Tommasin, L and Lippe, G and Carraro, M and Bernardi, P},
title = {The Haves and Have-Nots: The Mitochondrial Permeability Transition Pore across Species.},
journal = {Cells},
volume = {12},
number = {10},
pages = {},
pmid = {37408243},
issn = {2073-4409},
mesh = {Animals ; *Mitochondrial Permeability Transition Pore/metabolism ; *Mitochondrial Membrane Transport Proteins/metabolism ; Drosophila melanogaster/metabolism ; Mitochondria/metabolism ; Saccharomyces cerevisiae/metabolism ; Adenosine Triphosphate/metabolism ; Mammals/metabolism ; },
abstract = {The demonstration that F1FO (F)-ATP synthase and adenine nucleotide translocase (ANT) can form Ca[2+]-activated, high-conductance channels in the inner membrane of mitochondria from a variety of eukaryotes led to renewed interest in the permeability transition (PT), a permeability increase mediated by the PT pore (PTP). The PT is a Ca[2+]-dependent permeability increase in the inner mitochondrial membrane whose function and underlying molecular mechanisms have challenged scientists for the last 70 years. Although most of our knowledge about the PTP comes from studies in mammals, recent data obtained in other species highlighted substantial differences that could be perhaps attributed to specific features of F-ATP synthase and/or ANT. Strikingly, the anoxia and salt-tolerant brine shrimp Artemia franciscana does not undergo a PT in spite of its ability to take up and store Ca[2+] in mitochondria, and the anoxia-resistant Drosophila melanogaster displays a low-conductance, selective Ca[2+]-induced Ca[2+] release channel rather than a PTP. In mammals, the PT provides a mechanism for the release of cytochrome c and other proapoptotic proteins and mediates various forms of cell death. In this review, we cover the features of the PT (or lack thereof) in mammals, yeast, Drosophila melanogaster, Artemia franciscana and Caenorhabditis elegans, and we discuss the presence of the intrinsic pathway of apoptosis and of other forms of cell death. We hope that this exercise may help elucidate the function(s) of the PT and its possible role in evolution and inspire further tests to define its molecular nature.},
}

Animals
*Mitochondrial Permeability Transition Pore/metabolism
*Mitochondrial Membrane Transport Proteins/metabolism
Drosophila melanogaster/metabolism
Mitochondria/metabolism
Saccharomyces cerevisiae/metabolism
Adenosine Triphosphate/metabolism
Mammals/metabolism

@article {pmid37408307,
year = {2023},
author = {Yang, C and Li, X and Yang, L and Chen, S and Liao, J and Li, K and Zhou, J and Shen, W and Zhuang, X and Bai, M and Bassham, DC and Gao, C},
title = {A positive feedback regulation of SnRK1 signaling by autophagy in plants.},
journal = {Molecular plant},
volume = {16},
number = {7},
pages = {1192-1211},
doi = {10.1016/j.molp.2023.07.001},
pmid = {37408307},
issn = {1752-9867},
mesh = {Protein Serine-Threonine Kinases/genetics/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; *Arabidopsis/metabolism ; Feedback ; Autophagy/genetics ; Gene Expression Regulation, Plant ; },
abstract = {SnRK1, an evolutionarily conserved heterotrimeric kinase complex that acts as a key metabolic sensor in maintaining energy homeostasis in plants, is an important upstream activator of autophagy that serves as a cellular degradation mechanism for the healthy growth of plants. However, whether and how the autophagy pathway is involved in regulating SnRK1 activity remains unknown. In this study, we identified a clade of plant-specific and mitochondria-localized FCS-like zinc finger (FLZ) proteins as currently unknown ATG8-interacting partners that actively inhibit SnRK1 signaling by repressing the T-loop phosphorylation of the catalytic α subunits of SnRK1, thereby negatively modulating autophagy and plant tolerance to energy deprivation caused by long-term carbon starvation. Interestingly, these AtFLZs are transcriptionally repressed by low-energy stress, and AtFLZ proteins undergo a selective autophagy-dependent pathway to be delivered to the vacuole for degradation, thereby constituting a positive feedback regulation to relieve their repression of SnRK1 signaling. Bioinformatic analyses show that the ATG8-FLZ-SnRK1 regulatory axis first appears in gymnosperms and seems to be highly conserved during the evolution of seed plants. Consistent with this, depletion of ATG8-interacting ZmFLZ14 confers enhanced tolerance, whereas overexpression of ZmFLZ14 leads to reduced tolerance to energy deprivation in maize. Collectively, our study reveals a previously unknown mechanism by which autophagy contributes to the positive feedback regulation of SnRK1 signaling, thereby enabling plants to better adapt to stressful environments.},
}

Protein Serine-Threonine Kinases/genetics/metabolism
*Arabidopsis Proteins/genetics/metabolism
*Arabidopsis/metabolism
Feedback
Autophagy/genetics
Gene Expression Regulation, Plant

@article {pmid37419430,
year = {2023},
author = {Françoso, E and Zuntini, AR and Ricardo, PC and Araujo, NS and Silva, JPN and Brown, MJF and Arias, MC},
title = {The complete mitochondrial genome of Trigonisca nataliae (Hymenoptera, Apidae) assemblage reveals heteroplasmy in the control region.},
journal = {Gene},
volume = {881},
number = {},
pages = {147621},
doi = {10.1016/j.gene.2023.147621},
pmid = {37419430},
issn = {1879-0038},
mesh = {Bees/genetics ; Animals ; *Hymenoptera/genetics ; *Genome, Mitochondrial ; Heteroplasmy ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The evolution of mitochondrial genomes in the stingless bees is surprisingly dynamic, making them a model system to understand mitogenome structure, function, and evolution. Out of the seven mitogenomes available in this group, five exhibit atypical characteristics, including extreme rearrangements, rapid evolution and complete mitogenome duplication. To further explore the mitogenome diversity in these bees, we utilized isolated mtDNA and Illumina sequencing to assemble the complete mitogenome of Trigonisca nataliae, a species found in Northern Brazil. The mitogenome of T. nataliae was highly conserved in gene content and structure when compared to Melipona species but diverged in the control region (CR). Using PCR amplification, cloning and Sanger sequencing, six different CR haplotypes, varying in size and content, were recovery. These findings indicate that heteroplasmy, where different mitochondrial haplotypes coexist within individuals, occurs in T. nataliae. Consequently, we argue that heteroplasmy might indeed be a common phenomenon in bees that could be associated with variations in mitogenome size and challenges encountered during the assembly process.},
}

Bees/genetics
Animals
*Hymenoptera/genetics
*Genome, Mitochondrial
Heteroplasmy
DNA, Mitochondrial/genetics
Mitochondria/genetics
Phylogeny

@article {pmid37424728,
year = {2023},
author = {Gospodaryov, DV and Ballard, JWO and Camus, MF and DeSalle, R and Garvin, MR and Richter, U},
title = {Editorial: Energy-producing organelles and the nucleus: a phenomenal genomic friendship.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1230032},
pmid = {37424728},
issn = {1664-8021},
}

@article {pmid37424790,
year = {2023},
author = {Margenat, M and Betancour, G and Irving, V and Costábile, A and García-Cedrés, T and Portela, MM and Carrión, F and Herrera, FE and Villarino, A},
title = {Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1095060},
pmid = {37424790},
issn = {2235-2988},
mesh = {Humans ; Lipid Metabolism ; *Mycobacterium tuberculosis ; Phylogeny ; Ubiquitins ; *Mitochondrial Trifunctional Protein/metabolism ; *Bacterial Proteins/metabolism ; },
abstract = {During Mycobacterium tuberculosis (Mtb) infection, the virulence factor PtpA belonging to the protein tyrosine phosphatase family is delivered into the cytosol of the macrophage. PtpA interacts with numerous eukaryotic proteins modulating phagosome maturation, innate immune response, apoptosis, and potentially host-lipid metabolism, as previously reported by our group. In vitro, the human trifunctional protein enzyme (hTFP) is a bona fide PtpA substrate, a key enzyme of mitochondrial β-oxidation of long-chain fatty acids, containing two alpha and two beta subunits arranged in a tetramer structure. Interestingly, it has been described that the alpha subunit of hTFP (ECHA, hTFPα) is no longer detected in mitochondria during macrophage infection with the virulent Mtb H37Rv. To better understand if PtpA could be the bacterial factor responsible for this effect, in the present work, we studied in-depth the PtpA activity and interaction with hTFPα. With this aim, we performed docking and in vitro dephosphorylation assays defining the P-Tyr-271 as the potential target of mycobacterial PtpA, a residue located in the helix-10 of hTFPα, previously described as relevant for its mitochondrial membrane localization and activity. Phylogenetic analysis showed that Tyr-271 is absent in TFPα of bacteria and is present in more complex eukaryotic organisms. These results suggest that this residue is a specific PtpA target, and its phosphorylation state is a way of regulating its subcellular localization. We also showed that phosphorylation of Tyr-271 can be catalyzed by Jak kinase. In addition, we found by molecular dynamics that PtpA and hTFPα form a stable protein complex through the PtpA active site, and we determined the dissociation equilibrium constant. Finally, a detailed study of PtpA interaction with ubiquitin, a reported PtpA activator, showed that additional factors are required to explain a ubiquitin-mediated activation of PtpA. Altogether, our results provide further evidence supporting that PtpA could be the bacterial factor that dephosphorylates hTFPα during infection, potentially affecting its mitochondrial localization or β-oxidation activity.},
}

Humans
Lipid Metabolism
*Mycobacterium tuberculosis
Phylogeny
Ubiquitins
*Mitochondrial Trifunctional Protein/metabolism
*Bacterial Proteins/metabolism

@article {pmid37429000,
year = {2023},
author = {Wan, H and Zhang, Y and Wu, L and Zhou, G and Pan, L and Fernie, AR and Ruan, YL},
title = {Evolution of cytosolic and organellar invertases empowered the colonization and thriving of land plants.},
journal = {Plant physiology},
volume = {193},
number = {2},
pages = {1227-1243},
pmid = {37429000},
issn = {1532-2548},
mesh = {Humans ; Cytosol/metabolism ; *beta-Fructofuranosidase/metabolism ; Plants/genetics/metabolism ; *Embryophyta/metabolism ; Carbon/metabolism ; Evolution, Molecular ; },
abstract = {The molecular innovation underpinning efficient carbon and energy metabolism during evolution of land plants remains largely unknown. Invertase-mediated sucrose cleavage into hexoses is central to fuel growth. Why some cytoplasmic invertases (CINs) function in the cytosol, whereas others operate in chloroplasts and mitochondria, is puzzling. We attempted to shed light on this question from an evolutionary perspective. Our analyses indicated that plant CINs originated from a putatively orthologous ancestral gene in cyanobacteria and formed the plastidic CIN (α1 clade) through endosymbiotic gene transfer, while its duplication in algae with a loss of its signal peptide produced the β clade CINs in the cytosol. The mitochondrial CINs (α2) were derived from duplication of the plastidic CINs and coevolved with vascular plants. Importantly, the copy number of mitochondrial and plastidic CINs increased upon the emergence of seed plants, corresponding with the rise of respiratory, photosynthetic, and growth rates. The cytosolic CIN (β subfamily) kept expanding from algae to gymnosperm, indicating its role in supporting the increase in carbon use efficiency during evolution. Affinity purification mass spectrometry identified a cohort of proteins interacting with α1 and 2 CINs, which points to their roles in plastid and mitochondrial glycolysis, oxidative stress tolerance, and the maintenance of subcellular sugar homeostasis. Collectively, the findings indicate evolutionary roles of α1 and α2 CINs in chloroplasts and mitochondria for achieving high photosynthetic and respiratory rates, respectively, which, together with the expanding of cytosolic CINs, likely underpin the colonization of land plants through fueling rapid growth and biomass production.},
}

Humans
Cytosol/metabolism
*beta-Fructofuranosidase/metabolism
Plants/genetics/metabolism
*Embryophyta/metabolism
Carbon/metabolism
Evolution, Molecular

@article {pmid37429369,
year = {2023},
author = {Ahlawat, S and Sharma, U and Arora, R and Sharma, R and Chhabra, P and Veer Singh, K and Vijh, RK},
title = {Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys.},
journal = {Gene},
volume = {880},
number = {},
pages = {147627},
doi = {10.1016/j.gene.2023.147627},
pmid = {37429369},
issn = {1879-0038},
mesh = {Animals ; Humans ; *Equidae/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Africa ; Domestication ; Haplotypes ; Genetic Variation ; },
abstract = {To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.},
}

Animals
Humans
*Equidae/genetics
Phylogeny
*DNA, Mitochondrial/genetics
Africa
Domestication
Haplotypes
Genetic Variation

@article {pmid37437976,
year = {2023},
author = {Atayik, MC and Çakatay, U},
title = {Mitochondria-associated cellular senescence mechanisms: Biochemical and pharmacological perspectives.},
journal = {Advances in protein chemistry and structural biology},
volume = {136},
number = {},
pages = {117-155},
doi = {10.1016/bs.apcsb.2023.03.003},
pmid = {37437976},
issn = {1876-1631},
mesh = {*Mitochondria ; *Cellular Senescence ; Signal Transduction ; },
abstract = {Initially, endosymbiotic relation of mitochondria and other cellular compartments had been continued mutually. However, that evolutionary adaptation impaired because of the deterioration of endosymbiotic crosstalk due to aging and several pathological consequences in cellular redox status are seen, such as deterioration in redox integrity of mitochondria, interfered inter-organelle redox signaling and inefficient antioxidant response element mediated gene expression. Although the dysfunction of mitochondria is known to be a classical pattern of senescence, it is unresolved that why dysfunctional mitochondria is the core of senescence-associated secretory phenotype (SASP). Redox impairment and SASP-related disease development are generally together with weaken immunity. Impaired mitochondrial redox integrity and its ineffectiveness in immunity control render elders to be more prone to age-related diseases. As senotherapeutic agents, senolytics remove senescent cells whilst senomorphics/senostatics inhibits the secretion of SASP. Senotherapeutics and the novel approaches for ameliorating SASP-related unfavorable effects are recently thought to be promising ways as mitochondria-targeted gerotherapeutic options.},
}

*Mitochondria
*Cellular Senescence
Signal Transduction

@article {pmid37451476,
year = {2023},
author = {Záhonová, K and Valach, M and Tripathi, P and Benz, C and Opperdoes, FR and Barath, P and Lukáčová, V and Danchenko, M and Faktorová, D and Horváth, A and Burger, G and Lukeš, J and Škodová-Sveráková, I},
title = {Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1867},
number = {9},
pages = {130419},
doi = {10.1016/j.bbagen.2023.130419},
pmid = {37451476},
issn = {1872-8006},
mesh = {*Mitochondria/metabolism ; *Pyruvate Dehydrogenase Complex/metabolism ; Multienzyme Complexes/metabolism ; Ketoglutarate Dehydrogenase Complex/metabolism ; Pyruvates/metabolism ; },
abstract = {In eukaryotes, pyruvate, a key metabolite produced by glycolysis, is converted by a tripartite mitochondrial pyruvate dehydrogenase (PDH) complex to acetyl-coenzyme A, which is fed into the tricarboxylic acid cycle. Two additional enzyme complexes with analogous composition catalyze similar oxidative decarboxylation reactions albeit using different substrates, the branched-chain ketoacid dehydrogenase (BCKDH) complex and the 2-oxoglutarate dehydrogenase (OGDH) complex. Comparative transcriptome analyses of diplonemids, one of the most abundant and diverse groups of oceanic protists, indicate that the conventional E1, E2, and E3 subunits of the PDH complex are lacking. E1 was apparently replaced in the euglenozoan ancestor of diplonemids by an AceE protein of archaeal type, a substitution that we also document in dinoflagellates. Here, we demonstrate that the mitochondrion of the model diplonemid Paradiplonema papillatum displays pyruvate and 2-oxoglutarate dehydrogenase activities. Protein mass spectrometry of mitochondria reveal that the AceE protein is as abundant as the E1 subunit of BCKDH. This corroborates the view that the AceE subunit is a functional component of the PDH complex. We hypothesize that by acquiring AceE, the diplonemid ancestor not only lost the eukaryotic-type E1, but also the E2 and E3 subunits of the PDH complex, which are present in other euglenozoans. We posit that the PDH activity in diplonemids seems to be carried out by a complex, in which the AceE protein partners with the E2 and E3 subunits from BCKDH and/or OGDH.},
}

*Mitochondria/metabolism
*Pyruvate Dehydrogenase Complex/metabolism
Multienzyme Complexes/metabolism
Ketoglutarate Dehydrogenase Complex/metabolism
Pyruvates/metabolism

@article {pmid37453661,
year = {2023},
author = {Dreishpoon, MB and Bick, NR and Petrova, B and Warui, DM and Cameron, A and Booker, SJ and Kanarek, N and Golub, TR and Tsvetkov, P},
title = {FDX1 regulates cellular protein lipoylation through direct binding to LIAS.},
journal = {The Journal of biological chemistry},
volume = {299},
number = {9},
pages = {105046},
pmid = {37453661},
issn = {1083-351X},
support = {R01 CA279550/CA/NCI NIH HHS/United States ; R35 CA242457/CA/NCI NIH HHS/United States ; R35 GM122595/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Humans ; Cell Proliferation/genetics ; Cell Respiration/genetics ; *Ferredoxins/genetics/metabolism ; *Lipoylation/genetics ; Metabolome ; Protein Binding ; *Sulfurtransferases/metabolism ; },
abstract = {Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D, and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore-induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post-translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss of function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling established that FDX1 loss-of-function results in the induction of both compensatory metabolism-related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-function is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting its role in cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.},
}

Humans
Cell Proliferation/genetics
Cell Respiration/genetics
*Ferredoxins/genetics/metabolism
*Lipoylation/genetics
Metabolome
Protein Binding
*Sulfurtransferases/metabolism

@article {pmid37453725,
year = {2023},
author = {Shively, CA and Frye, BM and Negrey, JD and Johnson, CSC and Sutphen, CL and Molina, AJA and Yadav, H and Snyder-Mackler, N and Register, TC},
title = {The interactive effects of psychosocial stress and diet composition on health in primates.},
journal = {Neuroscience and biobehavioral reviews},
volume = {152},
number = {},
pages = {105320},
pmid = {37453725},
issn = {1873-7528},
support = {R01 AG054523/AG/NIA NIH HHS/United States ; R01 AG061805/AG/NIA NIH HHS/United States ; R01 HL122393/HL/NHLBI NIH HHS/United States ; T32 AG033534/AG/NIA NIH HHS/United States ; RF1 AG058829/AG/NIA NIH HHS/United States ; T32 AG052354/AG/NIA NIH HHS/United States ; R01 HL087103/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Primates ; Stress, Psychological ; Anxiety ; *Diet, Mediterranean ; Social Isolation ; },
abstract = {Social disadvantage and diet composition independently impact myriad dimensions of health. They are closely entwined, as social disadvantage often yields poor diet quality, and may interact to fuel differential health outcomes. This paper reviews effects of psychosocial stress and diet composition on health in nonhuman primates and their implications for aging and human health. We examined the effects of social subordination stress and Mediterranean versus Western diet on multiple systems. We report that psychosocial stress and Western diet have independent and additive adverse effects on hypothalamic-pituitary-adrenal and autonomic nervous system reactivity to psychological stressors, brain structure, and ovarian function. Compared to the Mediterranean diet, the Western diet resulted in accelerated aging, nonalcoholic fatty liver disease, insulin resistance, gut microbial changes associated with increased disease risk, neuroinflammation, neuroanatomical perturbations, anxiety, and social isolation. This comprehensive, multisystem investigation lays the foundation for future investigations of the mechanistic underpinnings of psychosocial stress and diet effects on health, and advances the promise of the Mediterranean diet as a therapeutic intervention on psychosocial stress.},
}

Animals
Humans
*Primates
Stress, Psychological
Anxiety
*Diet, Mediterranean
Social Isolation

@article {pmid37463427,
year = {2023},
author = {Warren, JM and Broz, AK and Martinez-Hottovy, A and Elowsky, C and Christensen, AC and Sloan, DB},
title = {Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss.},
journal = {Molecular biology and evolution},
volume = {40},
number = {7},
pages = {},
pmid = {37463427},
issn = {1537-1719},
mesh = {*Amino Acyl-tRNA Synthetases/genetics ; RNA, Transfer/genetics ; Cell Nucleus/genetics ; Mitochondria/genetics ; Genome, Plant ; },
abstract = {The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or nuclear-encoded (cytosolic) tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement in Sileneae mitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells.},
}

*Amino Acyl-tRNA Synthetases/genetics
RNA, Transfer/genetics
Cell Nucleus/genetics
Mitochondria/genetics
Genome, Plant

@article {pmid37464732,
year = {2023},
author = {Wang, F and Zhang, N and Zhao, C and Song, Z and Caiyan, X},
title = {Codon usage bias analysis of mitochondrial protein-coding genes in 12 species of Candida.},
journal = {Journal of genetics},
volume = {102},
number = {},
pages = {},
pmid = {37464732},
issn = {0973-7731},
mesh = {Humans ; *Codon Usage ; *Candida/genetics ; Codon/genetics ; Mitochondrial Proteins/genetics ; Mitochondria/genetics ; Nucleotides/genetics ; },
abstract = {The incidence of diseases that are caused by fungal infection is gradually increasing, together with antibiotic abuse and the number of patients with hypoimmunity. The many challenges in clinical anti-fungi treatment include serious adverse effects and drug resistance. The mitochondria of fungi have been found to be closely associated with pathopoiesia and drug resistance. Hence, we investigated patterns in Candida mitochondrial genes codon usage bias to provide new information to guide anti-fungal research. According to the nucleotide composition results, most mitochondrial genes of the analysed Candida tended to use A/T bases rather than G/C bases. The relative synonymous codon usage values demonstrated that UUA, AGU, CCU, GCU, UGA, AGA and GGU were the common preferential codons of mitochondrial genes in 12 Candida species. Codon adaptation index (CAI) analysis indicated that the ATP9 of Candida parapsilosis had the highest value, and the ND6 of C. auris had the lowest value. The CAI clearly correlated with the codon bias index, except in C. maltose and C. viswanathii, and was significantly positively correlated with the average GC content. Together, our results suggested that the codon usage pattern is affected by multiple factors, among which GC content is critical. Nucleotide composition, selection pressure and mutation pressure influence codon bias in Candida mitochondrial genes, with dominant status to mutation pressure. Codon usage bias analyses of Candida mitochondrial genes may provide new insight into its evolution.},
}

Humans
*Codon Usage
*Candida/genetics
Codon/genetics
Mitochondrial Proteins/genetics
Mitochondria/genetics
Nucleotides/genetics

@article {pmid37479023,
year = {2023},
author = {Boël, M and Voituron, Y and Roussel, D},
title = {Body mass dependence of oxidative phosphorylation efficiency in liver mitochondria from mammals.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {284},
number = {},
pages = {111490},
doi = {10.1016/j.cbpa.2023.111490},
pmid = {37479023},
issn = {1531-4332},
mesh = {Animals ; *Oxidative Phosphorylation ; *Mitochondria, Liver/metabolism ; Adenosine Triphosphate/metabolism ; Mitochondria/metabolism ; Mammals/metabolism ; Oxygen Consumption/physiology ; },
abstract = {In eukaryotes, the performances of an organism are dependent on body mass and chemically supported by the mitochondrial production of ATP. Although the relationship between body mass and mitochondrial oxygen consumption is well described, the allometry of the transduction efficiency from oxygen to ATP production (ATP/O) is still poorly understood. Using a comparative approach, we investigated the oxygen consumption and ATP production of liver mitochondria from twelve species of mammals ranging from 5 g to 600 kg. We found that both oxygen consumption and ATP production are mass dependent but not the ATP/O at the maximal phosphorylating state. The results also showed that for sub-maximal phosphorylating states the ATP/O value positively correlated with body mass, irrespective of the metabolic intensity. This result contrasts with previous data obtained in mammalian muscles, suggesting a tissue-dependence of the body mass effect on mitochondrial efficiency.},
}

Animals
*Oxidative Phosphorylation
*Mitochondria, Liver/metabolism
Adenosine Triphosphate/metabolism
Mitochondria/metabolism
Mammals/metabolism
Oxygen Consumption/physiology

@article {pmid37479726,
year = {2023},
author = {Falchi, FA and Forti, F and Carnelli, C and Genco, A and Pizzoccheri, R and Manzari, C and Pavesi, G and Briani, F},
title = {Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {11771},
pmid = {37479726},
issn = {2045-2322},
mesh = {Humans ; *Escherichia coli/genetics ; *R-Loop Structures ; Causality ; Gene Expression Regulation ; RNA/genetics ; },
abstract = {Polyribonucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. In Escherichia coli, PNPase controls complex phenotypic traits like biofilm formation and growth at low temperature. In human cells, PNPase is located in mitochondria, where it is implicated in the RNA import from the cytoplasm, the mitochondrial RNA degradation and the processing of R-loops, namely stable RNA-DNA hybrids displacing a DNA strand. In this work, we show that the human PNPase (hPNPase) expressed in E. coli causes oxidative stress, SOS response activation and R-loops accumulation. Hundreds of E. coli RNAs are stabilized in presence of hPNPase, whereas only few transcripts are destabilized. Moreover, phenotypic traits typical of E. coli strains lacking PNPase are strengthened in presence of the human enzyme. We discuss the hypothesis that hPNPase expressed in E. coli may bind, but not degrade, the RNA, in agreement with previous in vitro data showing that phosphate concentrations in the range of those found in the bacterial cytoplasm and, more relevant, in the mitochondria, inhibit its activity.},
}

Humans
*Escherichia coli/genetics
*R-Loop Structures
Causality
Gene Expression Regulation
RNA/genetics

@article {pmid37481145,
year = {2023},
author = {DeCicco, LH and DeRaad, DA and Ostrow, EN and Moyle, RG},
title = {A complete species-level phylogeny of the Erythrura parrotfinches (Aves: Estrildidae).},
journal = {Molecular phylogenetics and evolution},
volume = {187},
number = {},
pages = {107883},
doi = {10.1016/j.ympev.2023.107883},
pmid = {37481145},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Passeriformes/genetics ; DNA ; Genes, Mitochondrial ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; },
abstract = {Identifying species boundaries and phylogenetic relationships among groups of closely related species provides a necessary framework for understanding how biodiversity evolves in natural systems. Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. We included intra-species geographic sampling that allowed us to comment on species limits in some taxa. We recovered the Gouldian Finch (Chloebia gouldiae) of Australia which has often been placed in the monotypic genus Chloebia, as being sister to a clade comprising all Erythrura species. In addition, we recovered a well-supported clade comprising eight species distributed throughout the Pacific Island eco-region, whereas those species occurring in continental southeast Asia, the Greater Sundas, and the Philippines, were recovered as earlier branching lineages. Of note was the early branching of the Fiji-endemic E. kleinschmidti which corroborates its unique phenotype. We also found a deep phylogenetic split (8.59% corrected, 7.89% uncorrected divergence in the mitochondrial gene ND2) between the Java and Philippine populations of E. hyperythra, indicating unrecognized species-level diversity within this taxon. In contrast, genome-wide nuclear data suggested that the New Guinea endemic species E. papuana is embedded within the widespread species E. trichroa in all phylogenetic reconstructions, corroborating previously published mitochondrial data that suggested a similar pattern. By generating a phylogenetic hypothesis for the relationships among all species of Erythrura parrotfinches, we provide a framework for better understanding the extant diversity and evolutionary history of this group.},
}

Animals
Phylogeny
*Passeriformes/genetics
DNA
Genes, Mitochondrial
Mitochondria/genetics
DNA, Mitochondrial/genetics
Sequence Analysis, DNA

@article {pmid37481257,
year = {2023},
author = {Collington, E and Lobb, B and Mazen, NA and Doxey, AC and Glerum, DM},
title = {Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity.},
journal = {Genome biology and evolution},
volume = {15},
number = {8},
pages = {},
pmid = {37481257},
issn = {1759-6653},
mesh = {Animals ; Phylogeny ; Reactive Oxygen Species/metabolism ; *Parasites ; Electron Transport Complex IV/genetics ; Caenorhabditis elegans/genetics/metabolism ; Oxygen/metabolism ; },
abstract = {The terminal electron acceptor of most aerobic respiratory chains, cytochrome c oxidase (COX), has been highly conserved throughout evolution, from aerobic prokaryotes to complex eukaryotes. Oxygen metabolism in parasitic helminths differs significantly from that of most aerobic eukaryotes, as these organisms can switch between aerobic and anaerobic metabolisms throughout their life cycles. Early studies suggested a lack of COX activity in certain parasitic helminths, and the role of COX in helminth mitochondria remains unclear. To determine whether a functional COX is widely present in helminths, we analyzed the phylogenetic distribution of oxygen metabolism systems across 155 helminth genomes, investigating three distinct sets of protein-coding genes involved in different aspects of oxygen metabolism: COX and its assembly factors, peroxisomes, and the most abundant reactive oxygen species (ROS)-metabolizing proteins. While glycolytic and citric acid cycle enzymes are highly conserved in helminthic species, we observed an apparent widespread absence of essential COX genes across 52% of helminth species investigated. While the most common proteins involved in the defense against ROS are highly maintained across virtually all lineages, we also observed an apparent absence of essential peroxisomal protein-coding genes in 42% of species investigated. Our results suggest that a subset of parasitic helminths utilize oxygen differently from related, nonparasitic species such as Caenorhabditis elegans, with significant differences in their mitochondrial electron transport chains and peroxisomes. The identification of substantive differences between parasite and host metabolism offers a new avenue for the development of anthelmintic agents that could target these divergent pathways.},
}

Animals
Phylogeny
Reactive Oxygen Species/metabolism
*Parasites
Electron Transport Complex IV/genetics
Caenorhabditis elegans/genetics/metabolism
Oxygen/metabolism

@article {pmid37489100,
year = {2023},
author = {Yordanov, G and Palova, N and Mehandjyiski, I and Hristov, P},
title = {Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives - Danubian horse and Serbian Nonius.},
journal = {Animal biotechnology},
volume = {34},
number = {8},
pages = {3897-3907},
doi = {10.1080/10495398.2023.2237533},
pmid = {37489100},
issn = {1532-2378},
mesh = {Animals ; Horses/genetics ; Female ; *DNA, Mitochondrial/genetics ; Serbia ; *Genetic Variation/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; Haplotypes/genetics ; Phylogeny ; },
abstract = {From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O'P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O'P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations.In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.},
}

Animals
Horses/genetics
Female
*DNA, Mitochondrial/genetics
Serbia
*Genetic Variation/genetics
Mitochondria/genetics
Sequence Analysis, DNA
Haplotypes/genetics
Phylogeny

@article {pmid37491310,
year = {2023},
author = {Costa, RD and Thomaz Neto, FJ and Moustafa, MT and Atilano, SR and Chwa, M and Cáceres-Del-Carpi, J and Mohamed, MH and Kenney, MC and Kuppermann, BD},
title = {The role of mitochondrial genes on nuclear gene expression in neovascular age related macular degeneration: analysis of nuclear VEGF gene expression after ranibizumab treatment in cytoplasmic hybrid retinal pigment epithelial cell lines correlated with clinical evolution.},
journal = {International journal of retina and vitreous},
volume = {9},
number = {1},
pages = {44},
pmid = {37491310},
issn = {2056-9920},
support = {P30 EY034070/EY/NEI NIH HHS/United States ; },
abstract = {PURPOSE: The present study tests the hypothesis that mitochondrial genes have retrograde signaling capacity that influences the expression of nuclear genes related to angiogenesis pathways. Cytoplasmic hybrid (cybrid) in vitro cell lines with patient specific mitochondria inserted into an immortalized retinal pigment epithelial cell line (ARPE-19) were used to test this hypothesis. This type of analysis can provide important information to identify the optimal regimen of anti-VEGF treatment, personalizing age-related macular degeneration (AMD) therapies.

METHODS: Mitochondria deficient ARPE-19 cells (Rho0) were fused with AMD donor's platelets to create individual cybrid cell lines containing mitochondria from patients with phenotypic AMD disease and nuclear DNA from the immortalized RPE cell line. The cybrids were treated with Ranibizumab (Lucentis, Genentech, San Francisco, CA), at 4 different concentrations for 24 h, and subsequently the levels of reactive oxygen species (ROS), gene expression for VEGF-A, hypoxia-inducible factor 1-alpha (HIF1-a) and manganese superoxide dismutase (SOD2) were measured. The clinical evolution of the two AMD-donors were correlated with the molecular findings found in their 'personalized' cybrids.

RESULTS: Cybrids from Patient-01 showed down-regulation of gene expression of VEGF-A and HIF-1a at both 1X and 4X Ranibizumab concentrations. Patient-01 AMD cybrid cultures had an increase in the ROS levels at 1X (P = 0.0317), no changes at 2X (P = 0.8350) and a decrease at 4X (P = 0.0015) and 10X (P = 0.0011) of Ranibizumab. Clinically, Patient-01 responded to anti-VEGF therapy but eventually developed geographic atrophy. Patient-02 cybrids demonstrated up-regulation of gene expression of VEGF-A and HIF-1a at Ranibizumab 1X and 4X concentrations. There was decreased ROS levels with Ranibizumab 1X (P = 0.1606), 2X (P = 0.0388), 4X (P = 0.0010) and 10X (P =  < 0.0001). Clinically, Patient-02 presented with a neovascular lesion associated with a prominent production of intraretinal fluid in clinical follow-up requiring regular and repeated intravitreal injections of Ranibizumab with recurrent subretinal fluid.

CONCLUSIONS: Our cybrid model has the potential to help personalize the treatment regimen with anti-VEGF drugs in patients with neovascular AMD. Further investigation is needed to better understand the role that the mitochondria play in the cellular response to anti-VEGF drugs. Future studies that focus on this model have the potential to help personalize anti-VEGF treatment.},
}

@article {pmid37491455,
year = {2023},
author = {von der Dunk, SHA and Hogeweg, P and Snel, B},
title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {777},
pmid = {37491455},
issn = {2399-3642},
mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; },
abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.},
}

Phylogeny
*Eukaryotic Cells/metabolism
*Symbiosis/genetics
Biological Evolution
Mitochondria/genetics

@article {pmid37493549,
year = {2023},
author = {Jagielska, M and Hałakuc, P and Płecha, M and Milanowski, R},
title = {[Mitochondrial genomes – unity and diversity].},
journal = {Postepy biochemii},
volume = {69},
number = {2},
pages = {113-121},
doi = {10.18388/pb.2021_486},
pmid = {37493549},
issn = {0032-5422},
mesh = {*Genome, Mitochondrial ; Evolution, Molecular ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Cell Nucleus ; Phylogeny ; },
abstract = {The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene transfers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.},
}

*Genome, Mitochondrial
Evolution, Molecular
Mitochondria/genetics
DNA, Mitochondrial/genetics
Cell Nucleus
Phylogeny

@article {pmid37497665,
year = {2023},
author = {Millet, AMC and Coustham, C and Champigny, C and Botella, M and Demeilliers, C and Devin, A and Galinier, A and Belenguer, P and Bordeneuve-Guibé, J and Davezac, N and Merabet, N},
title = {OPA1 deficiency impairs oxidative metabolism in cycling cells, underlining a translational approach for degenerative diseases.},
journal = {Disease models & mechanisms},
volume = {16},
number = {9},
pages = {},
pmid = {37497665},
issn = {1754-8411},
mesh = {Humans ; *Optic Atrophy, Autosomal Dominant/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Mitochondria/metabolism ; Cell Respiration ; Oxidative Stress ; GTP Phosphohydrolases/genetics/metabolism ; },
abstract = {Dominant optic atrophy is an optic neuropathy with varying clinical symptoms and progression. A severe disorder is associated with certain OPA1 mutations and includes additional symptoms for >20% of patients. This underscores the consequences of OPA1 mutations in different cellular populations, not only retinal ganglionic cells. We assessed the effects of OPA1 loss of function on oxidative metabolism and antioxidant defences using an RNA-silencing strategy in a human epithelial cell line. We observed a decrease in the mitochondrial respiratory chain complexes, associated with a reduction in aconitase activity related to an increase in reactive oxygen species (ROS) production. In response, the NRF2 (also known as NFE2L2) transcription factor was translocated into the nucleus and upregulated SOD1 and GSTP1. This study highlights the effects of OPA1 deficiency on oxidative metabolism in replicative cells, as already shown in neurons. It underlines a translational process to use cycling cells to circumvent and describe oxidative metabolism. Moreover, it paves the way to predict the evolution of dominant optic atrophy using mathematical models that consider mitochondrial ROS production and their detoxifying pathways.},
}

Humans
*Optic Atrophy, Autosomal Dominant/genetics/metabolism
Reactive Oxygen Species/metabolism
Mitochondria/metabolism
Cell Respiration
Oxidative Stress
GTP Phosphohydrolases/genetics/metabolism

@article {pmid37498958,
year = {2024},
author = {Schmid, LM and Manavski, N and Chi, W and Meurer, J},
title = {Chloroplast Ribosome Biogenesis Factors.},
journal = {Plant & cell physiology},
volume = {65},
number = {4},
pages = {516-536},
doi = {10.1093/pcp/pcad082},
pmid = {37498958},
issn = {1471-9053},
support = {ME 1794/10 TRR 175 A03//Deutsche Forschungsgemeinschaft/ ; 2022YFF1001700//National Key Research and Development Program of China/ ; },
mesh = {*Ribosomes/metabolism ; *Chloroplasts/metabolism ; RNA, Ribosomal/genetics/metabolism ; Plants/metabolism/genetics ; },
abstract = {The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.},
}

*Ribosomes/metabolism
*Chloroplasts/metabolism
RNA, Ribosomal/genetics/metabolism
Plants/metabolism/genetics

@article {pmid37502859,
year = {2023},
author = {Cal, K and Leyva, A and Rodríguez-Duarte, J and Ruiz, S and Santos, L and Colella, L and Ingold, M and Vilaseca, C and Galliussi, G and Ziegler, L and Peclat, TR and Bresque, M and Handy, RM and King, R and Dos Reis, LM and Espasandin, C and Breining, P and Dapueto, R and Lopez, A and Thompson, KL and Agorrody, G and DeVallance, E and Meadows, E and Lewis, SE and Barbosa, GCS and de Souza, LOL and Chichierchio, MS and Valez, V and Aicardo, A and Contreras, P and Vendelbo, MH and Jakobsen, S and Kamaid, A and Porcal, W and Calliari, A and Verdes, JM and Du, J and Wang, Y and Hollander, JM and White, TA and Radi, R and Moyna, G and Quijano, C and O'Doherty, R and Moraes-Vieira, P and Holloway, GP and Leonardi, R and Mori, MA and Camacho-Pereira, J and Kelley, EE and Duran, R and Lopez, GV and Batthyány, C and Chini, EN and Escande, C},
title = {A nitroalkene derivative of salicylate alleviates diet-induced obesity by activating creatine metabolism and non-shivering thermogenesis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37502859},
issn = {2693-5015},
support = {R01 HL128485/HL/NHLBI NIH HHS/United States ; R01 HL153532/HL/NHLBI NIH HHS/United States ; R35 GM119528/GM/NIGMS NIH HHS/United States ; R01 HL168290/HL/NHLBI NIH HHS/United States ; R01 DK124510/DK/NIDDK NIH HHS/United States ; },
abstract = {Obesity-related type II diabetes (diabesity) has increased global morbidity and mortality dramatically. Previously, the ancient drug salicylate demonstrated promise for the treatment of type II diabetes, but its clinical use was precluded due to high dose requirements. In this study, we present a nitroalkene derivative of salicylate, 5-(2-nitroethenyl)salicylic acid (SANA), a molecule with unprecedented beneficial effects in diet-induced obesity (DIO). SANA reduces DIO, liver steatosis and insulin resistance at doses up to 40 times lower than salicylate. Mechanistically, SANA stimulated mitochondrial respiration and increased creatine-dependent energy expenditure in adipose tissue. Indeed, depletion of creatine resulted in the loss of SANA action. Moreover, we found that SANA binds to creatine kinases CKMT1/2, and downregulation CKMT1 interferes with the effect of SANA in vivo. Together, these data demonstrate that SANA is a first-in-class activator of creatine-dependent energy expenditure and thermogenesis in adipose tissue and emerges as a candidate for the treatment of diabesity.},
}

@article {pmid37503831,
year = {2023},
author = {Sanchez-Puerta, MV and Ceriotti, LF and Gatica-Soria, LM and Roulet, ME and Garcia, LE and Sato, HA},
title = {Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites.},
journal = {Annals of botany},
volume = {132},
number = {5},
pages = {909-928},
pmid = {37503831},
issn = {1095-8290},
support = {PICT2020-01018//Fondo para la Investigación Científica y Tecnológica/ ; 06/A092-T1//Universidad Nacional de Cuyo/ ; },
mesh = {*Magnoliopsida/genetics ; Plants/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Plastids ; Phylogeny ; },
abstract = {BACKGROUND: The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments.

SCOPE: This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles.

CONCLUSIONS: Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.},
}

*Magnoliopsida/genetics
Plants/genetics
*Genome, Mitochondrial/genetics
Evolution, Molecular
Plastids
Phylogeny

@article {pmid37507225,
year = {2023},
author = {Esposti, MD},
title = {Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis.},
journal = {FEBS letters},
volume = {597},
number = {19},
pages = {2484-2496},
doi = {10.1002/1873-3468.14708},
pmid = {37507225},
issn = {1873-3468},
mesh = {*Bacteria/metabolism ; *Inositol/metabolism ; *Models, Biological ; Archaea/metabolism ; *Eukaryotic Cells/metabolism ; *Eukaryota/metabolism ; },
abstract = {The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.},
}

*Bacteria/metabolism
*Inositol/metabolism
*Models, Biological
Archaea/metabolism
*Eukaryotic Cells/metabolism
*Eukaryota/metabolism

@article {pmid37508434,
year = {2023},
author = {Preziuso, A and Piccirillo, S and Cerqueni, G and Serfilippi, T and Terenzi, V and Vinciguerra, A and Orciani, M and Amoroso, S and Magi, S and Lariccia, V},
title = {Exploring the Role of NCX1 and NCX3 in an In Vitro Model of Metabolism Impairment: Potential Neuroprotective Targets for Alzheimer's Disease.},
journal = {Biology},
volume = {12},
number = {7},
pages = {},
pmid = {37508434},
issn = {2079-7737},
support = {2017YH3SXK//Ministry of Education, Universities and Research/ ; },
abstract = {Alzheimer's disease (AD) is a widespread neurodegenerative disorder, affecting a large number of elderly individuals worldwide. Mitochondrial dysfunction, metabolic alterations, and oxidative stress are regarded as cooperating drivers of the progression of AD. In particular, metabolic impairment amplifies the production of reactive oxygen species (ROS), resulting in detrimental alterations to intracellular Ca[2+] regulatory processes. The Na[+]/Ca[2+] exchanger (NCX) proteins are key pathophysiological determinants of Ca[2+] and Na[+] homeostasis, operating at both the plasma membrane and mitochondria levels. Our study aimed to explore the role of NCX1 and NCX3 in retinoic acid (RA) differentiated SH-SY5Y cells treated with glyceraldehyde (GA), to induce impairment of the default glucose metabolism that typically precedes Aβ deposition or Tau protein phosphorylation in AD. By using an RNA interference-mediated approach to silence either NCX1 or NCX3 expression, we found that, in GA-treated cells, the knocking-down of NCX3 ameliorated cell viability, increased the intracellular ATP production, and reduced the oxidative damage. Remarkably, NCX3 silencing also prevented the enhancement of Aβ and pTau levels and normalized the GA-induced decrease in NCX reverse-mode activity. By contrast, the knocking-down of NCX1 was totally ineffective in preventing GA-induced cytotoxicity except for the increase in ATP synthesis. These findings indicate that NCX3 and NCX1 may differently influence the evolution of AD pathology fostered by glucose metabolic dysfunction, thus providing a potential target for preventing AD.},
}

@article {pmid37511042,
year = {2023},
author = {Luo, L and Xu, Y and Wang, S and Zhang, R and Guo, K and Xu, W and Zhao, Z},
title = {Complete Mitochondrial Genome Sequence and Phylogenetic Analysis of Procambarus clarkii and Cambaroides dauricus from China.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511042},
issn = {1422-0067},
support = {2020YFD0900402//the National Key Research and Development Project/ ; 2020TD56//the Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Astacoidea/genetics ; Phylogeny ; NAD/genetics ; Sequence Analysis, DNA ; },
abstract = {To enhance the management and protection of crayfish genetic diversity and germplasm resources in Cambaroides dauricus (C. dauricus), a common species of Procambarus clarkii (P. clarkii) was used as a control group to compare the whole mitochondrial genome sequence using Illumina sequencing technology. This study found that the mitochondrial genome of C. dauricus is 15580 bp in length, with a base composition of A (31.84%), G (17.66%), C (9.42%), and T (41.08%) and a C + G content of 27.08%. The C + G in the D-loop is rich in 17.06%, indicating a significant preference. The mitochondrial genome of C. dauricus contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with most of the genes labeled in the negative direction, except for a few genes that are labeled in the positive direction. The start codons of the ten coding sequences are ATG, and the quintessential TAA and TAG are the stop codons. This study also found that the Ka/Ks ratios of most protein-coding genes in the mitochondria of both shrimps are lower than 1, indicating weak natural selection, except for nad 2, nad 5, and cox 1. The Ka/Ks ratio of cox 3 is the lowest (less than 0.1), indicating that this protein-coding gene bears strong natural selection pressure and functional constraint in the process of mitochondrial genetic evolution of both shrimps. Furthermore, we constructed phylogenetic analyses based on the entire sequence, which effectively distinguishes the high body from other shrimp species of the genus based on the mitochondrial genome. This study provides molecular genetic data for the diversity investigation and protection of fishery resources with Chinese characteristics and a scientific reference for the evolutionary study of Procambarus.},
}

Animals
*Genome, Mitochondrial/genetics
Astacoidea/genetics
Phylogeny
NAD/genetics
Sequence Analysis, DNA

@article {pmid37512520,
year = {2023},
author = {Hu, M and Jiang, Y and Xu, JJ},
title = {Characterization of Arabidopsis thaliana Coq9 in the CoQ Biosynthetic Pathway.},
journal = {Metabolites},
volume = {13},
number = {7},
pages = {},
pmid = {37512520},
issn = {2218-1989},
support = {no//Yunnan Revitalization Talent Support Program "Top Team" Project/ ; PFGR202201//Open Fund of Shanghai Key Laboratory of Plant Functional Genomics and Resources under Grant/ ; 222414//Special Fund for Shanghai Landscaping Administration Bureau Program/ ; YDZX20223100001003//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {Coenzyme Q, also known as ubiquinone, is a fat-soluble isoprene quinone that serves as a cofactor for numerous enzymes across all domains of life. However, the biosynthetic pathway for this important molecule in plants has been examined in only a limited number of studies. In yeast and mammals, Coq9, an isoprenoid-lipid-binding protein, is essential for CoQ biosynthesis. Previous studies showed that Arabidopsis thaliana Coq9 failed to complement the fission yeast Schizosaccharomyces pombe coq9 null mutant, and its function in plants remains unknown. In this study, we demonstrated that expression of Arabidopsis Coq9 rescued the growth of a yeast temperature-sensitive coq9 mutant and increased CoQ content. Phylogenetic analysis revealed that Coq9 is widely present in green plants. Green fluorescent protein (GFP) fusion experiments showed that Arabidopsis Coq9 is targeted to mitochondria. Disruption of the Coq9 gene in Arabidopsis results in lower amounts of CoQ. Our work suggests that plant Coq9 is required for efficient CoQ biosynthesis. These findings provide new insights into the evolution of CoQ biosynthesis in plants. The identification of Coq9 as a key player in CoQ biosynthesis in plants opens up new avenues for understanding the regulation of this important metabolic pathway.},
}

@article {pmid37515372,
year = {2024},
author = {Fernández-Moncada, I and Rodrigues, RS and Fundazuri, UB and Bellocchio, L and Marsicano, G},
title = {Type-1 cannabinoid receptors and their ever-expanding roles in brain energy processes.},
journal = {Journal of neurochemistry},
volume = {168},
number = {5},
pages = {693-703},
doi = {10.1111/jnc.15922},
pmid = {37515372},
issn = {1471-4159},
support = {//INSERM/ ; Micabra, ERC-2017-AdG-786467//the European Research Council/ ; DRM20101220445//Fondation pour la Recherche Medicale/ ; ALTF87-2018//EMBO/ ; //the Human Frontiers Science Program/ ; 17219710//Region Aquitaine/ ; CanBrain, AAP2022A-2021-16763610//Region Aquitaine/ ; ANR-19-CE14-0039//French State/Agence Nationale de la Recherche/ ; ERA-Net Neuron CanShank, ANR-21-NEU2-0001-04//French State/Agence Nationale de la Recherche/ ; MitObesity, ANR 18-CE14-0029-01//French State/Agence Nationale de la Recherche/ ; CaCoVi, ANR 18-CE16-0001-02//French State/Agence Nationale de la Recherche/ ; GPR BRAIN_2030//University of Bordeaux's IdEx "Investments for the Future" program/ ; },
mesh = {*Receptor, Cannabinoid, CB1/metabolism ; Humans ; Animals ; *Brain/metabolism ; *Energy Metabolism/physiology ; Mitochondria/metabolism ; Neurons/metabolism ; },
abstract = {The brain requires large quantities of energy to sustain its functions. At the same time, the brain is isolated from the rest of the body, forcing this organ to develop strategies to control and fulfill its own energy needs. Likely based on these constraints, several brain-specific mechanisms emerged during evolution. For example, metabolically specialized cells are present in the brain, where intercellular metabolic cycles are organized to separate workload and optimize the use of energy. To orchestrate these strategies across time and space, several signaling pathways control the metabolism of brain cells. One of such controlling systems is the endocannabinoid system, whose main signaling hub in the brain is the type-1 cannabinoid (CB1) receptor. CB1 receptors govern a plethora of different processes in the brain, including cognitive function, emotional responses, or feeding behaviors. Classically, the mechanisms of action of CB1 receptors on brain function had been explained by its direct targeting of neuronal synaptic function. However, new discoveries have challenged this view. In this review, we will present and discuss recent data about how a small fraction of CB1 receptors associated to mitochondrial membranes (mtCB1), are able to exert a powerful control on brain functions and behavior. mtCB1 receptors impair mitochondrial functions both in neurons and astrocytes. In the latter cells, this effect is linked to an impairment of astrocyte glycolytic function, resulting in specific behavioral outputs. Finally, we will discuss the potential implications of (mt)CB1 expression on oligodendrocytes and microglia metabolic functions, with the aim to encourage interdisciplinary approaches to better understand the role of (mt)CB1 receptors in brain function and behavior.},
}

*Receptor, Cannabinoid, CB1/metabolism
Humans
Animals
*Brain/metabolism
*Energy Metabolism/physiology
Mitochondria/metabolism
Neurons/metabolism

@article {pmid37518286,
year = {2023},
author = {Zhang, G and Gao, JJ and Takano, KT and Yafuso, M and Suwito, A and Meleng, PA and Toda, MJ},
title = {Phylogenetic classification and palm-inflorescence anthophily of the Colocasiomyia zeylanica species group (Diptera: Drosophilidae), with descriptions of five new species.},
journal = {Zootaxa},
volume = {5278},
number = {2},
pages = {201-238},
doi = {10.11646/zootaxa.5278.2.1},
pmid = {37518286},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Drosophilidae/genetics ; Phylogeny ; Inflorescence ; Mitochondria ; },
abstract = {The zeylanica group is one of the six species groups of the anthophilic genus Colocasiomyia de Meijere in the family Drosophilidae. In addition to two known species, five morphospecies have been recognized as members of this species group but left undescribed formally. In this study, species delimitation of these putatively new species was determined by barcoding of the mitochondrial COI (cytochrome c oxydase subunit I) gene and morphological comparison. Phylogenetic relationships within the genus Colocasiomyia were inferred by a cladistic analysis of 89 morphological characters. Based on the results of these analyses, we redefined the zeylanica species group and established two subgroups within it: the zeylanica subgroup comprised of C. zeylanica, C. nepalensis, C. pinangae sp. nov., C. besaris sp. nov. and C. luciphila sp. nov., and the oligochaeta subgroup of C. oligochaeta sp. nov. and C. grimaldii sp. nov. In addition, we briefly address the anthophilic habits of drosophilid flies using palm (Arecaceae) inflorescences, especially of the zeylanica group, compiling scattered collection records from the Oriental and Papuan regions.},
}

Animals
*Diptera
*Drosophilidae/genetics
Phylogeny
Inflorescence
Mitochondria

@article {pmid37518493,
year = {2023},
author = {Tomimori, Y and Matsui, M and Okawa, H and Nishikawa, K and Tanabe, S and Kamasaka, R},
title = {Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae).},
journal = {Zootaxa},
volume = {5293},
number = {1},
pages = {145-160},
doi = {10.11646/zootaxa.5293.1.6},
pmid = {37518493},
issn = {1175-5334},
mesh = {Animals ; *Caudata/genetics ; Phylogeny ; Japan ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recently reported (H. sumidai and H. geiyoensis), and the use of these names has been previously advocated. However, their sympatric distribution was rejected based on nuclear DNA data, which we consider is more reliable than mtDNA. We thus clarify geographic boundary of these two species and revise the species delimitations.},
}

Animals
*Caudata/genetics
Phylogeny
Japan
*DNA, Mitochondrial/genetics
Mitochondria/genetics

@article {pmid37518527,
year = {2023},
author = {Kuhara, N and Nozaki, T and Zhang, AO and Zhou, X},
title = {DNA barcoding facilitates discovery and description of two new species of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) in Japan.},
journal = {Zootaxa},
volume = {5306},
number = {2},
pages = {215-231},
doi = {10.11646/zootaxa.5306.2.3},
pmid = {37518527},
issn = {1175-5334},
mesh = {Female ; Animals ; Male ; Japan ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Holometabola ; Mitochondria ; },
abstract = {We examined adult specimens of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) collected in Japan and confirm three species including M. azureus Linnaeus 1761 and two new species, M. rivularis and M. moritai. Males and females of the new species are described. Mystacides azureus in Japan is shown to have a considerable variation in morphology of the male tergum X. We analyzed mitochondrial COI barcodes of the genus Mystacides including these three species to confirm their species status. A maximum likelihood phylogeny based on COI barcodes shows monophyly of the new species. It also supports the hypothesis that morphological variation of the male tergum X in Japanese populations is intraspecific in only M. azureus.},
}

Female
Animals
Male
Japan
*DNA Barcoding, Taxonomic
Phylogeny
*Holometabola
Mitochondria

@article {pmid37518710,
year = {2023},
author = {Russell, PJC and Pateman, JE and Gagarina, AV and Lukhtanov, VA},
title = {Investigations into the Melitaea ornata species complex in the Levant: M. telona and the newly erected species Melitaea klili Benyamini, 2021 (Lepidoptera: Nymphalidae).},
journal = {Zootaxa},
volume = {5285},
number = {1},
pages = {187-195},
doi = {10.11646/zootaxa.5285.1.9},
pmid = {37518710},
issn = {1175-5334},
mesh = {Male ; Animals ; *Butterflies/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; DNA Barcoding, Taxonomic ; },
abstract = {Melitaea klili Benyamini, 2021 was recently described from Israel as a species closely related to M. telona Fruhstorfer, 1908, but different in phenology, ecological preferences and with an allopatric distribution. Here, based on comparative examinations of mitochondrial DNA-barcodes, male genitalia and larval behaviour under laboratory conditions, we synonymize M. klili with M. telona. The COI barcodes of M. klili were found to be identical to those of M. telona. Analysis of 658 bp fragment of the mitochondrial gene COI demonstrated that the minimum uncorrected p-distance between M. ornata and M. telona was 1.98%. This value is remarkably less than the 3% threshold traditionally accepted as a species boundary in DNA barcoding studies. The morphological differences between these taxa are minimal. In fact, M. ornata and M. telona represent two phylogenetic lineages, the taxonomic status of which (separate species or subspecies of the same species) is intermediate and debatable.},
}

Male
Animals
*Butterflies/genetics
Phylogeny
DNA, Mitochondrial/genetics
Mitochondria/genetics
Genes, Mitochondrial
DNA Barcoding, Taxonomic

@article {pmid37522604,
year = {2023},
author = {Chukaew, T and Isomura, N and Mezaki, T and Matsumoto, H and Kitano, YF and Nozawa, Y and Tachikawa, H and Fukami, H},
title = {Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species.},
journal = {Zoological science},
volume = {40},
number = {4},
pages = {326-340},
doi = {10.2108/zs230009},
pmid = {37522604},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Japan ; DNA, Ribosomal/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; },
abstract = {The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.},
}

Animals
Phylogeny
*Anthozoa/genetics
Japan
DNA, Ribosomal/genetics
Mitochondria/genetics
Sequence Analysis, DNA

@article {pmid37538245,
year = {2023},
author = {Zhang, H and Li, X and Fan, W and Pandovski, S and Tian, Y and Dillin, A},
title = {Inter-tissue communication of mitochondrial stress and metabolic health.},
journal = {Life metabolism},
volume = {2},
number = {1},
pages = {},
pmid = {37538245},
issn = {2755-0230},
support = {R01 AG059566/AG/NIA NIH HHS/United States ; R01 ES021667/ES/NIEHS NIH HHS/United States ; },
abstract = {Mitochondria function as a hub of the cellular metabolic network. Mitochondrial stress is closely associated with aging and a variety of diseases, including neurodegeneration and cancer. Cells autonomously elicit specific stress responses to cope with mitochondrial stress to maintain mitochondrial homeostasis. Interestingly, mitochondrial stress responses may also be induced in a non-autonomous manner in cells or tissues that are not directly experiencing such stress. Such non-autonomous mitochondrial stress responses are mediated by secreted molecules called mitokines. Due to their significant translational potential in improving human metabolic health, there has been a surge in mitokine-focused research. In this review, we summarize the findings regarding inter-tissue communication of mitochondrial stress in animal models. In addition, we discuss the possibility of mitokine-mediated intercellular mitochondrial communication originating from bacterial quorum sensing.},
}

@article {pmid37548336,
year = {2023},
author = {Ryan, K and Greenway, R and Landers, J and Arias-Rodriguez, L and Tobler, M and Kelley, JL},
title = {Selection on standing genetic variation mediates convergent evolution in extremophile fish.},
journal = {Molecular ecology},
volume = {32},
number = {18},
pages = {5042-5054},
doi = {10.1111/mec.17081},
pmid = {37548336},
issn = {1365-294X},
mesh = {Animals ; *Hydrogen Sulfide/toxicity ; *Extremophiles ; Ecosystem ; Sulfides ; *Poecilia/genetics ; Genetic Variation/genetics ; Selection, Genetic ; },
abstract = {Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.},
}

Animals
*Hydrogen Sulfide/toxicity
*Extremophiles
Ecosystem
Sulfides
*Poecilia/genetics
Genetic Variation/genetics
Selection, Genetic

@article {pmid37551058,
year = {2023},
author = {Huynh, SD and Melonek, J and Colas des Francs-Small, C and Bond, CS and Small, I},
title = {A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria.},
journal = {The New phytologist},
volume = {240},
number = {2},
pages = {830-845},
doi = {10.1111/nph.19166},
pmid = {37551058},
issn = {1469-8137},
mesh = {*Genes, Plant ; Mitochondria/metabolism ; Cytoplasm/metabolism ; Plant Proteins/metabolism ; *Arabidopsis/genetics/metabolism ; Fertility/genetics ; Plant Infertility/genetics ; },
abstract = {Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.},
}

*Genes, Plant
Mitochondria/metabolism
Cytoplasm/metabolism
Plant Proteins/metabolism
*Arabidopsis/genetics/metabolism
Fertility/genetics
Plant Infertility/genetics

@article {pmid37556561,
year = {2023},
author = {Raval, PK and Martin, WF and Gould, SB},
title = {Mitochondrial evolution: Gene shuffling, endosymbiosis, and signaling.},
journal = {Science advances},
volume = {9},
number = {32},
pages = {eadj4493},
pmid = {37556561},
issn = {2375-2548},
mesh = {*Symbiosis/genetics ; *Mitochondria/genetics ; Eukaryotic Cells/metabolism ; Genes, Mitochondrial ; Phylogeny ; Biological Evolution ; Evolution, Molecular ; },
abstract = {Genes for cardiolipin and ceramide synthesis occur in some alphaproteobacterial genomes. They shed light on mitochondrial origin and signaling in the first eukaryotic cells.},
}

*Symbiosis/genetics
*Mitochondria/genetics
Eukaryotic Cells/metabolism
Genes, Mitochondrial
Phylogeny
Biological Evolution
Evolution, Molecular

@article {pmid37557975,
year = {2023},
author = {Weaver, RJ and McDonald, AE},
title = {Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1864},
number = {4},
pages = {149003},
doi = {10.1016/j.bbabio.2023.149003},
pmid = {37557975},
issn = {1879-2650},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Plant Proteins/genetics ; Oxidoreductases/genetics ; Mitochondria/genetics ; Plants ; Eukaryota/genetics ; Alternative Oxidase ; },
abstract = {The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.},
}

Animals
*Gene Transfer, Horizontal
*Plant Proteins/genetics
Oxidoreductases/genetics
Mitochondria/genetics
Plants
Eukaryota/genetics
Alternative Oxidase

@article {pmid37558671,
year = {2023},
author = {Kuhle, B and Hirschi, M and Doerfel, LK and Lander, GC and Schimmel, P},
title = {Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4794},
pmid = {37558671},
issn = {2041-1723},
support = {R01 NS095892/NS/NINDS NIH HHS/United States ; R01 NS092829/NS/NINDS NIH HHS/United States ; S10 OD021634/OD/NIH HHS/United States ; R01 GM125908/GM/NIGMS NIH HHS/United States ; R21 GM142196/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; RNA, Mitochondrial ; *RNA, Transfer/genetics/metabolism ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Mitochondria/genetics/metabolism ; },
abstract = {Animal mitochondrial gene expression relies on specific interactions between nuclear-encoded aminoacyl-tRNA synthetases and mitochondria-encoded tRNAs. Their evolution involves an antagonistic interplay between strong mutation pressure on mtRNAs and selection pressure to maintain their essential function. To understand the molecular consequences of this interplay, we analyze the human mitochondrial serylation system, in which one synthetase charges two highly divergent mtRNA[Ser] isoacceptors. We present the cryo-EM structure of human mSerRS in complex with mtRNA[Ser(UGA)], and perform a structural and functional comparison with the mSerRS-mtRNA[Ser(GCU)] complex. We find that despite their common function, mtRNA[Ser(UGA)] and mtRNA[Ser(GCU)] show no constrain to converge on shared structural or sequence identity motifs for recognition by mSerRS. Instead, mSerRS evolved a bimodal readout mechanism, whereby a single protein surface recognizes degenerate identity features specific to each mtRNA[Ser]. Our results show how the mutational erosion of mtRNAs drove a remarkable innovation of intermolecular specificity rules, with multiple evolutionary pathways leading to functionally equivalent outcomes.},
}

Animals
Humans
RNA, Mitochondrial
*RNA, Transfer/genetics/metabolism
*Amino Acyl-tRNA Synthetases/genetics/metabolism
Mitochondria/genetics/metabolism

@article {pmid37565789,
year = {2023},
author = {Yang, Y and Oldenkott, B and Ramanathan, S and Lesch, E and Takenaka, M and Schallenberg-Rüdinger, M and Knoop, V},
title = {DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection.},
journal = {The Plant journal : for cell and molecular biology},
volume = {116},
number = {3},
pages = {840-854},
doi = {10.1111/tpj.16412},
pmid = {37565789},
issn = {1365-313X},
mesh = {RNA, Plant/metabolism ; *Plant Proteins/metabolism ; *RNA Editing/genetics ; Cytidine Deaminase/chemistry/genetics/metabolism ; Chloroplasts/metabolism ; },
abstract = {The protein factors for the specific C-to-U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA-binding pentatricopeptide repeats (PPRs) linked to carboxy-terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein-protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C-terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off-targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long-range impact on the nucleotide selectivity of the upstream PPRs.},
}

RNA, Plant/metabolism
*Plant Proteins/metabolism
*RNA Editing/genetics
Cytidine Deaminase/chemistry/genetics/metabolism
Chloroplasts/metabolism