@article {pmid39016375,
year = {2024},
author = {Martini, D and De Cesari, C and Digregorio, M and Muscò, A and Giudetti, G and Giannaccini, M and Andreazzoli, M},
title = {Expression analysis of thg1l during Xenopus laevis development.},
journal = {The International journal of developmental biology},
volume = {68},
number = {2},
pages = {85-91},
doi = {10.1387/ijdb.240033ma},
pmid = {39016375},
issn = {1696-3547},
mesh = {Animals ; *Xenopus laevis/metabolism/embryology/genetics ; *Gene Expression Regulation, Developmental ; *Xenopus Proteins/genetics/metabolism ; Nucleotidyltransferases/genetics/metabolism ; Embryo, Nonmammalian/metabolism/embryology ; Embryonic Development/genetics ; RNA, Messenger/genetics/metabolism ; },
abstract = {The tRNA-histidine guanylyltransferase 1-like (THG1L), also known as induced in high glucose-1 (IHG-1), encodes for an essential mitochondria-associated protein highly conserved throughout evolution, that catalyses the 3'-5' addition of a guanine to the 5'-end of tRNA-histidine (tRNA[His]). Previous data indicated that THG1L plays a crucial role in the regulation of mitochondrial biogenesis and dynamics, in ATP production, and is critically involved in the modulation of apoptosis, cell-cycle progression and survival, as well as in cellular stress responses and redox homeostasis. Dysregulations of THG1L expression play a central role in various pathologies, including nephropathies, and neurodevelopmental disorders often characterized by developmental delay and cerebellar ataxia. Despite the essential role of THG1L, little is known about its expression during vertebrate development. Herein, we examined the detailed spatio-temporal expression of this gene in the developing Xenopus laevis. Our results show that thg1l is maternally inherited and its temporal expression suggests a role during the earliest stages of embryogenesis. Spatially, thg1l mRNA localizes in the ectoderm and marginal zone mesoderm during early stages of development. Then, at tadpole stages, thg1l transcripts mostly localise in neural crests and their derivatives, somites, developing kidney and central nervous system, therefore largely coinciding with territories displaying intense energy metabolism during organogenesis in Xenopus.},
}

Animals
*Xenopus laevis/metabolism/embryology/genetics
*Gene Expression Regulation, Developmental
*Xenopus Proteins/genetics/metabolism
Nucleotidyltransferases/genetics/metabolism
Embryo, Nonmammalian/metabolism/embryology
Embryonic Development/genetics
RNA, Messenger/genetics/metabolism

@article {pmid39009246,
year = {2024},
author = {Guttipatti, P and Saadallah, N and Ji, R and Avula, UMR and Goulbourne, CN and Wan, EY},
title = {Quantitative 3D electron microscopy characterization of mitochondrial structure, mitophagy, and organelle interactions in murine atrial fibrillation.},
journal = {Journal of structural biology},
volume = {216},
number = {3},
pages = {108110},
doi = {10.1016/j.jsb.2024.108110},
pmid = {39009246},
issn = {1095-8657},
abstract = {Atrial fibrillation (AF) is the most common clinical arrhythmia, however there is limited understanding of its pathophysiology including the cellular and ultrastructural changes rendered by the irregular rhythm, which limits pharmacological therapy development. Prior work has demonstrated the importance of reactive oxygen species (ROS) and mitochondrial dysfunction in the development of AF. Mitochondrial structure, interactions with other organelles such as sarcoplasmic reticulum (SR) and T-tubules (TT), and degradation of dysfunctional mitochondria via mitophagy are important processes to understand ultrastructural changes due to AF. However, most analysis of mitochondrial structure and interactome in AF has been limited to two-dimensional (2D) modalities such as transmission electron microscopy (EM), which does not fully visualize the morphological evolution of the mitochondria during mitophagy. Herein, we utilize focused ion beam-scanning electron microscopy (FIB-SEM) and perform reconstruction of three-dimensional (3D) EM from murine left atrial samples and measure the interactions of mitochondria with SR and TT. We developed a novel 3D quantitative analysis of FIB-SEM in a murine model of AF to quantify mitophagy stage, mitophagosome size in cardiomyocytes, and mitochondrial structural remodeling when compared with control mice. We show that in our murine model of spontaneous and continuous AF due to persistent late sodium current, left atrial cardiomyocytes have heterogenous mitochondria, with a significant number which are enlarged with increased elongation and structural complexity. Mitophagosomes in AF cardiomyocytes are located at Z-lines where they neighbor large, elongated mitochondria. Mitochondria in AF cardiomyocytes show increased organelle interaction, with 5X greater contact area with SR and are 4X as likely to interact with TT when compared to control. We show that mitophagy in AF cardiomyocytes involves 2.5X larger mitophagosomes that carry increased organelle contents. In conclusion, when oxidative stress overcomes compensatory mechanisms, mitophagy in AF faces a challenge of degrading bulky complex mitochondria, which may result in increased SR and TT contacts, perhaps allowing for mitochondrial Ca[2+] maintenance and antioxidant production.},
}

@article {pmid38995516,
year = {2024},
author = {Lin, YE and Chiu, HL and Wu, CS and Chaw, SM},
title = {Phylogenomics identifies parents of naturally occurring tetraploid bananas.},
journal = {Botanical studies},
volume = {65},
number = {1},
pages = {19},
pmid = {38995516},
issn = {1817-406X},
support = {23-23//Academia Sinica/ ; },
abstract = {BACKGROUND: Triploid bananas are almost sterile. However, we succeeded in harvesting seeds from two edible triploid banana individuals (Genotype: ABB) in our conservation repository where various wild diploid bananas were also grown. The resulting rare offspring survived to seedling stages. DNA content analyses reveal that they are tetraploid. Since bananas contain maternally inherited plastids and paternally inherited mitochondria, we sequenced and assembled plastomes and mitogenomes of these seedlings to trace their hybridization history.

RESULTS: The coding sequences of both organellar genomic scaffolds were extracted, aligned, and concatenated for constructing phylogenetic trees. Our results suggest that these tetraploid seedlings be derived from hybridization between edible triploid bananas and wild diploid Musa balbisiana (BB) individuals. We propose that generating female triploid gametes via apomeiosis may allow the triploid maternal bananas to produce viable seeds.

CONCLUSIONS: Our study suggests a practical avenue towards expanding genetic recombination and increasing genetic diversity of banana breeding programs. Further cellular studies are needed to understand the fusion and developmental processes that lead to formation of hybrid embryos in banana reproduction, polyploidization, and evolution.},
}

@article {pmid38995057,
year = {2024},
author = {Smith, CH and Mejia-Trujillo, R and Havird, JC},
title = {Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpae108},
pmid = {38995057},
issn = {1558-5646},
abstract = {Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males transmit a different mtDNA (M mtDNA) solely to their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded in M mtDNA evolve under relaxed selection due to their function being limited to sperm only (vs. all other tissues for F mtDNA). This has led to the hypothesis that mitonuclear coevolution is less important for M mtDNA. Here, we use comparative phylogenetics, transcriptomics, and proteomics to understand mitonuclear interactions in DUI bivalves. We found nuclear OXPHOS proteins coevolve and maintain compatibility similarly with both F and M mtDNA OXPHOS proteins. Mitochondrial recombination did not influence mitonuclear compatibility and nuclear-encoded OXPHOS genes were not upregulated in tissues with M mtDNA to offset dysfunction. Our results support that selection maintains mitonuclear compatibility with F and M mtDNA despite relaxed selection on M mtDNA. Strict sperm transmission, lower effective population size, and higher mutation rates may explain the evolution of M mtDNA. Our study highlights that mitonuclear coevolution and compatibility may be broad features of eukaryotes.},
}

@article {pmid38980999,
year = {2024},
author = {Gammuto, L and Serra, V and Petroni, G and Todaro, MA},
title = {Molecular phylogenetic position and description of a new genus and species of freshwater Chaetonotidae (Gastrotricha: Chaetonotida: Paucitubulatina), and the annotation of its mitochondrial genome.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS23059},
pmid = {38980999},
issn = {1447-2600},
mesh = {*Phylogeny ; *Genome, Mitochondrial/genetics ; Animals ; Species Specificity ; Fresh Water ; },
abstract = {Chaetonotidae is the most diversified family of the entire phylum Gastrotricha; it comprises ~430 species distributed across 16 genera. The current classification, established mainly on morphological traits, has been challenged in recent years by phylogenetic studies, indicating that the cuticular ornamentations used to discriminate among species may be misleading when used to identify groupings, which has been the practice until now. Therefore, a consensus is developing toward implementing novel approaches to better define species identity and affiliation at a higher taxonomic ranking. Using an integrative morphological and molecular approach, including annotation of the mitogenome, we report on some freshwater gastrotrichs characterised by a mixture of two types of cuticular scales diagnostic of the genera Aspidiophorus and Heterolepidoderma . Our specimens' overall anatomical characteristics find no correspondence in the taxa of these two genera, calling for their affiliation to a new species. Phylogenetic analyses based on the sequence of the ribosomal RNA genes of 96 taxa consistently found the new species unrelated to Aspidiophorus or Heterolepidoderma but allied with Chaetonotus aff. subtilis, as a subset of a larger clade, including mostly planktonic species. Morphological uniqueness and position along the non-monophyletic Chaetonotidae branch advocate erecting a new genus to accommodate the current specimens; consequently, the name Litigonotus ghinii gen. nov., sp. nov. is proposed. The complete mitochondrial genome of the new taxon resulted in a single circular molecule 14,384 bp long, including 13 protein-coding genes, 17 tRNA genes and 2 rRNAs genes, showing a perfect synteny and collinearity with the only other gastrotrich mitogenome available, a possible hint of a high level of conservation in the mitochondria of Chaetonotidae. ZooBank: urn:lsid:zoobank.org:pub:9803F659-306F-4EC3-A73B-8C704069F24A.},
}

*Phylogeny
*Genome, Mitochondrial/genetics
Animals
Species Specificity
Fresh Water

@article {pmid38970720,
year = {2024},
author = {Shannan, PZT and Suganya, SG and Ramesh, M and Jemima, EA},
title = {Molecular based identification and phylogenetic relationship of the leech Hirudinaria manillensis from India by using mitochondrial cytochrome c oxidase subunit I gene.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {787},
pmid = {38970720},
issn = {1573-4978},
mesh = {Animals ; *Phylogeny ; *Leeches/genetics/enzymology/classification ; *Electron Transport Complex IV/genetics ; India ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA/methods ; Mitochondria/genetics/enzymology ; Base Sequence ; },
abstract = {BACKGROUND: A molecular approach for the identification of unknown species by the using mitochondrial cox1 gene is an effective and reliable as compared with morphological-based identification. Hirudinaria manillensis referred to as Asian Buffalo Leech, is found in South Asia and traditionally used as medicine owing to its medicinal properties.

METHODS AND RESULTS: The study aimed to isolate and identify the leech species using cox1 gene sequencing and their phylogenetic relationships. The nucleotide sequences of cytochrome c oxidase subunit I (cox1) mitochondrial genes were analyzed for species identification and the phylogenetic relationship of crucial therapeutic leech Hirudinaria manillensis. The isolated DNA from the leech sample was amplified with cox1 gene-specific primers. BLAST results with the H. manillensis sequence showed 89.24% homology with H. manillensis and phylogenetic tree analysis revealed the genetic relationship with other GenBank submitted sequences.

CONCLUSION: The present study concluded that the cox1 gene could be an effective way to identify the leech H. manillensis and provided sufficient phylogenetic information to distinguish H. manillensis indicating a significant mtDNA-based approach to species identification.},
}

Animals
*Phylogeny
*Leeches/genetics/enzymology/classification
*Electron Transport Complex IV/genetics
India
DNA, Mitochondrial/genetics
Sequence Analysis, DNA/methods
Mitochondria/genetics/enzymology
Base Sequence

@article {pmid38946300,
year = {2024},
author = {Elnegris, HM and Abdelrahman, AA and El-Roghy, ES},
title = {The potential therapeutic effects of exosomes derived from bone marrow mesenchymal stem cells on ileum injury of a rat sepsis model (histological and immunohistochemical study).},
journal = {Ultrastructural pathology},
volume = {48},
number = {4},
pages = {274-296},
doi = {10.1080/01913123.2024.2368011},
pmid = {38946300},
issn = {1521-0758},
mesh = {Animals ; *Sepsis/complications ; Rats ; *Ileum/pathology ; *Mesenchymal Stem Cells ; *Disease Models, Animal ; *Exosomes/metabolism ; Male ; Immunohistochemistry ; Rats, Wistar ; Nitric Oxide Synthase Type II/metabolism ; },
abstract = {Sepsis denotes a serious high mortality concern. The study was designed to evaluate the effect of mesenchymal stem cell exosomes (MSC-exosomes) on the evolution of the animal model of sepsis. In this study, 36 rats were distributed into three groups, (I) controls, (II) LPS-treated, and (III) LPS+MSC-EVs. Sepsis was simulated by administering E. coli-LPS to the laboratory animals. Group III was given MSC-exosomes four hours after the LPS injection. Forty-eight hours later rats were sacrificed. Ileum samples were excised, and processed for the histological assessment, immunohistochemical identification of CD44, and inducible nitric oxide synthase (iNOS). Ileum homogenate was used to estimate tumor necrosis factor α (TNF α) besides Cyclooxygenase-2 (COX 2). PCR was used for the detection of interleukin 1α (IL‑1α), and interleukin 17 (IL‑17). Statistical and morphometrical analysis was done. The LPS-treated group showed increased TNF-α, IL‑1α, IL‑17, and decreased COX 2. LPS administration led to cytoplasmic vacuolization of enterocytes, an increase in the vasculature, and cellular infiltrations invaded the lamina propria. There was a significant rise in goblet cells and the proportion of collagen fibers. Ultrastructurally, the enterocytes displayed nuclear irregularity, rough endoplasmic reticulum (rER) dilatation, and increased mitochondria number. Sepsis induces a significant increase in iNOS and a decrease in CD44 immune expressions. LPS+MSC-EVs group restored normal ileum structure and revealed a significant elevation in CD44 and a reduction in iNOS immunoreactions. LPS-sepsis induced an obvious ileum inflammatory deterioration ameliorated by MSC-exosomes, mostly through their antioxidant, anti-inflammatory, and anti-apoptotic properties.},
}

Animals
*Sepsis/complications
Rats
*Ileum/pathology
*Mesenchymal Stem Cells
*Disease Models, Animal
*Exosomes/metabolism
Male
Immunohistochemistry
Rats, Wistar
Nitric Oxide Synthase Type II/metabolism

@article {pmid38940122,
year = {2024},
author = {Sashittal, P and Chen, V and Pasarkar, A and Raphael, BJ},
title = {Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Supplement_1},
pages = {i218-i227},
pmid = {38940122},
issn = {1367-4811},
support = {U24 CA264027/CA/NCI NIH HHS/United States ; //NIH/ ; U24CA248453/BC/NCI NIH HHS/United States ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Cell Lineage/genetics ; *Mitochondria/genetics ; Mutation ; Genome, Mitochondrial ; Algorithms ; Evolution, Molecular ; },
abstract = {MOTIVATION: Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even in nondividing cells, by means of a relatively error-prone process resulting in somatic mutations in their genome. Because of the higher mutation rate compared to the nuclear genome, mitochondrial mutations have been used to track cellular lineage, particularly using single-cell sequencing that measures mitochondrial mutations in individual cells. However, existing methods to infer the cell lineage tree from mitochondrial mutations do not model "heteroplasmy," which is the presence of multiple mitochondrial clones with distinct sets of mutations in an individual cell. Single-cell sequencing data thus provide a mixture of the mitochondrial clones in individual cells, with the ancestral relationships between these clones described by a mitochondrial clone tree. While deconvolution of somatic mutations from a mixture of evolutionarily related genomes has been extensively studied in the context of bulk sequencing of cancer tumor samples, the problem of mitochondrial deconvolution has the additional constraint that the mitochondrial clone tree must be concordant with the cell lineage tree.

RESULTS: We formalize the problem of inferring a concordant pair of a mitochondrial clone tree and a cell lineage tree from single-cell sequencing data as the Nested Perfect Phylogeny Mixture (NPPM) problem. We derive a combinatorial characterization of the solutions to the NPPM problem, and formulate an algorithm, MERLIN, to solve this problem exactly using a mixed integer linear program. We show on simulated data that MERLIN outperforms existing methods that do not model mitochondrial heteroplasmy nor the concordance between the mitochondrial clone tree and the cell lineage tree. We use MERLIN to analyze single-cell whole-genome sequencing data of 5220 cells of a gastric cancer cell line and show that MERLIN infers a more biologically plausible cell lineage tree and mitochondrial clone tree compared to existing methods.

https://github.com/raphael-group/MERLIN.},
}

*Single-Cell Analysis/methods
Humans
*Cell Lineage/genetics
*Mitochondria/genetics
Mutation
Genome, Mitochondrial
Algorithms
Evolution, Molecular

@article {pmid38936100,
year = {2024},
author = {Montoliu Nebot, J and Iradi Casal, A and Cepeda Madrigal, S and Rissi, G and Sanz Saz, S and Molés Gimeno, JD and Miravet Sorribes, LM},
title = {[Physiological assessment and management of post-COVID patients with normal cardiopulmonary imaging and functional tests].},
journal = {Semergen},
volume = {50},
number = {8},
pages = {102282},
doi = {10.1016/j.semerg.2024.102282},
pmid = {38936100},
issn = {1578-8865},
abstract = {OBJECTIVE: Contributing to elucidate the pathophysiology of dyspnoea and exertion intolerance in post-COVID syndrome patients with normal cardiopulmonary imaging and functional tests at rest, while determining their fitness and level of endurance in order to individualize working parameters for physical rehabilitation.

MATERIAL AND METHODS: After an anamnesis and clinical examination at rest, 27 subjects (50±11.9 years) (14 women) with post-COVID syndrome of more than 6 months of evolution performed a continuous maximal-incremental graded cardiopulmonary exercise test (CPET) with breath-by-breath gas-exchange monitoring and continuous ECG registration, on an electromagnetically braked cycle ergometer. The values obtained were compared with those of reference, gender or controls, using the Chi-square, t-Student or ANOVA test.

RESULTS: The clinical examination at rest and the CPET were clinically normal and without adverse events. Reasons for stopping exercise were leg discomfort. It is only worth noting a BMI=29.9±5.8kg/m[2] and a basal lactate concentration of 2.1±0.7mmol/L. The physiological assessment of endurance showed the following results relative to predicted VO2máx: 1)peakVO2=80.5±18.6%; 2)VO2 at ventilatory threshold1 (VO2VT1): 46.0±12.9%; 3)VO2VT2: 57.2±16.4%; 4)working time in acidosis: 5.6±3,0minutes; and 5)maximum lactate concentration: 5.1±2.2mmol/L.

CONCLUSIONS: The CPET identified limited aerobic metabolism and early increase in glycolytic metabolism as causes of dyspnoea and exercise intolerance, determined fitness for physical rehabilitation, and individualized it based on the level of endurance.},
}

@article {pmid38934796,
year = {2024},
author = {Khachaturyan, M and Santer, M and Reusch, TBH and Dagan, T},
title = {Heteroplasmy Is Rare in Plant Mitochondria Compared with Plastids despite Similar Mutation Rates.},
journal = {Molecular biology and evolution},
volume = {41},
number = {7},
pages = {},
pmid = {38934796},
issn = {1537-1719},
support = {HIDSS-0005)//Helmholtz School for Marine Data Science/ ; RGP0011/2022//HFSP/ ; 101043835//ERC/ ; },
mesh = {*Plastids/genetics ; *Mitochondria/genetics/metabolism ; *Mutation Rate ; *Heteroplasmy ; Alleles ; },
abstract = {Plant cells harbor two membrane-bound organelles containing their own genetic material-plastids and mitochondria. Although the two organelles coexist and coevolve within the same plant cells, they differ in genome copy number, intracellular organization, and mode of segregation. How these attributes affect the time to fixation or, conversely, loss of neutral alleles is currently unresolved. Here, we show that mitochondria and plastids share the same mutation rate, yet plastid alleles remain in a heteroplasmic state significantly longer compared with mitochondrial alleles. By analyzing genetic variants across populations of the marine flowering plant Zostera marina and simulating organelle allele dynamics, we examine the determinants of allele segregation and allele fixation. Our results suggest that the bottlenecks on the cell population, e.g. during branching or seeding, and stratification of the meristematic tissue are important determinants of mitochondrial allele dynamics. Furthermore, we suggest that the prolonged plastid allele dynamics are due to a yet unknown active plastid partition mechanism. The dissimilarity between plastid and mitochondrial novel allele fixation at different levels of organization may manifest in differences in adaptation processes. Our study uncovers fundamental principles of organelle population genetics that are essential for further investigations of long-term evolution and molecular dating of divergence events.},
}

*Plastids/genetics
*Mitochondria/genetics/metabolism
*Mutation Rate
*Heteroplasmy
Alleles

@article {pmid38915079,
year = {2024},
author = {Wu, CS and Wang, RJ and Chaw, SM},
title = {Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {140},
pmid = {38915079},
issn = {1741-7007},
support = {No. 2022B1111040003//Guangdong Provincial Key R&D Programme/ ; },
mesh = {*Phylogeny ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Gnetum/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Magnoliopsida/genetics ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.

RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.

CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.},
}

*Phylogeny
*Gene Transfer, Horizontal
*Genome, Mitochondrial
*Gnetum/genetics
DNA, Plant/genetics
Evolution, Molecular
Magnoliopsida/genetics

@article {pmid38906137,
year = {2024},
author = {Iwata, R and Vanderhaeghen, P},
title = {Metabolic mechanisms of species-specific developmental tempo.},
journal = {Developmental cell},
volume = {59},
number = {13},
pages = {1628-1639},
doi = {10.1016/j.devcel.2024.05.027},
pmid = {38906137},
issn = {1878-1551},
mesh = {Animals ; *Species Specificity ; Humans ; Mitochondria/metabolism ; Biological Evolution ; Metabolic Networks and Pathways ; Gene Expression Regulation, Developmental ; },
abstract = {Development consists of a highly ordered suite of steps and transitions, like choreography. Although these sequences are often evolutionarily conserved, they can display species variations in duration and speed, thereby modifying final organ size or function. Despite their evolutionary significance, the mechanisms underlying species-specific scaling of developmental tempo have remained unclear. Here, we will review recent findings that implicate global cellular mechanisms, particularly intermediary and protein metabolism, as species-specific modifiers of developmental tempo. In various systems, from somitic cell oscillations to neuronal development, metabolic pathways display species differences. These have been linked to mitochondrial metabolism, which can influence the species-specific speed of developmental transitions. Thus, intermediary metabolic pathways regulate developmental tempo together with other global processes, including proteostasis and chromatin remodeling. By linking metabolism and the evolution of developmental trajectories, these findings provide opportunities to decipher how species-specific cellular timing can influence organism fitness.},
}

Animals
*Species Specificity
Humans
Mitochondria/metabolism
Biological Evolution
Metabolic Networks and Pathways
Gene Expression Regulation, Developmental

@article {pmid38900713,
year = {2024},
author = {Molinet, J and Navarrete, JP and Villarroel, CA and Villarreal, P and Sandoval, FI and Nespolo, RF and Stelkens, R and Cubillos, FA},
title = {Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing.},
journal = {PLoS genetics},
volume = {20},
number = {6},
pages = {e1011154},
pmid = {38900713},
issn = {1553-7404},
mesh = {*Beer/microbiology ; *Fermentation/genetics ; *Saccharomyces cerevisiae/genetics/metabolism ; *Hybridization, Genetic ; Saccharomyces/genetics/metabolism ; Ethanol/metabolism ; Mitochondria/genetics/metabolism ; Genome, Fungal ; Evolution, Molecular ; Genetic Variation ; Maltose/metabolism ; Mutation ; },
abstract = {Lager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity and hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding of diverse S. eubayanus lineages from Patagonia offers potential for generating new lager yeasts with different flavour profiles. Here, we leverage the natural genetic diversity of S. eubayanus and expand the lager yeast repertoire by including three distinct Patagonian S. eubayanus lineages. We used experimental evolution and selection on desirable traits to enhance the fermentation profiles of novel S. cerevisiae x S. eubayanus hybrids. Our analyses reveal an intricate interplay of pre-existing diversity, selection on species-specific mitochondria, de-novo mutations, and gene copy variations in sugar metabolism genes, resulting in high ethanol production and unique aroma profiles. Hybrids with S. eubayanus mitochondria exhibited greater evolutionary potential and superior fitness post-evolution, analogous to commercial lager hybrids. Using genome-wide screens of the parental subgenomes, we identified genetic changes in IRA2, IMA1, and MALX genes that influence maltose metabolism, and increase glycolytic flux and sugar consumption in the evolved hybrids. Functional validation and transcriptome analyses confirmed increased maltose-related gene expression, influencing greater maltotriose consumption in evolved hybrids. This study demonstrates the potential for generating industrially viable lager yeast hybrids from wild Patagonian strains. Our hybridization, evolution, and mitochondrial selection approach produced hybrids with high fermentation capacity and expands lager beer brewing options.},
}

*Beer/microbiology
*Fermentation/genetics
*Saccharomyces cerevisiae/genetics/metabolism
*Hybridization, Genetic
Saccharomyces/genetics/metabolism
Ethanol/metabolism
Mitochondria/genetics/metabolism
Genome, Fungal
Evolution, Molecular
Genetic Variation
Maltose/metabolism
Mutation

@article {pmid38892163,
year = {2024},
author = {Hong, YH and Yuan, YN and Li, K and Storey, KB and Zhang, JY and Zhang, SS and Yu, DN},
title = {Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38892163},
issn = {1422-0067},
support = {31801963//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; *Anura/genetics/physiology ; *Phylogeny ; Cold-Shock Response/genetics ; Cold Temperature ; Adaptation, Physiological/genetics ; Gene Expression Regulation ; },
abstract = {Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: Dryophytes japonicus, D. immaculata, Hyla annectans, H. chinensis and H. zhaopingensis. It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in D. immaculata, transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure (p < 0.05); hence, we put forward the conjecture that D. immaculata adapts by entering a hibernation state at low temperature. In H. annectans, the transcripts of 10 genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2 and ATP8) were significantly reduced in response to cold exposure, and five mitochondrial genes in H. chinensis (ND1, ND2, ND3, ND4L and ATP6) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of ND2 and ATP6 in H. zhaopingensis were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, H. zhaopingensis has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.},
}

Animals
*Genome, Mitochondrial
*Anura/genetics/physiology
*Phylogeny
Cold-Shock Response/genetics
Cold Temperature
Adaptation, Physiological/genetics
Gene Expression Regulation

@article {pmid38890582,
year = {2024},
author = {Gendron, EMS and Qing, X and Sevigny, JL and Li, H and Liu, Z and Blaxter, M and Powers, TO and Thomas, WK and Porazinska, DL},
title = {Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {615},
pmid = {38890582},
issn = {1471-2164},
mesh = {Animals ; *Genome, Mitochondrial ; *Nematoda/genetics ; *Selection, Genetic ; *Genomics/methods ; *Phylogeny ; Base Composition ; Evolution, Molecular ; Codon/genetics ; },
abstract = {BACKGROUND: Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures.

RESULTS: Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection.

CONCLUSIONS: Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.},
}

Animals
*Genome, Mitochondrial
*Nematoda/genetics
*Selection, Genetic
*Genomics/methods
*Phylogeny
Base Composition
Evolution, Molecular
Codon/genetics

@article {pmid38882704,
year = {2024},
author = {Tomizawa, Y and Aizawa, M and Jouraku, A and Sonoda, S},
title = {Field survey of reproductive modes and sodium channel mutations associated with pyrethroid resistance in Thrips tabaci.},
journal = {Journal of pesticide science},
volume = {49},
number = {2},
pages = {122-129},
pmid = {38882704},
issn = {1348-589X},
abstract = {Using PCR-Restriction Fragment Length Polymorphism (RFLP) with mitochondrial cytochrome c oxidase subunit I sequences, we examined the reproductive modes of female adults of Thrips tabaci collected at 54 sites across Japan. Results showed the presence of heteroplasmic insects harboring mitochondria associated with arrhenotoky and thelytoky. Using the insects, we also applied PCR-RFLP to examine the genotypes for the amino acid mutation (T929I) site involved in pyrethroid resistance. Findings showed the presence of thelytokous heterozygotes under the circumstance that most arrhenotokous insects are resistant homozygotes, and many thelytokous insects are susceptible homozygotes. These results suggest that, in the field, genetic exchange occurs between insects through of both reproductive modes. A survey of the genotypes for the other amino acid mutations using nucleotide sequencing showed a decline of insects with an M918T and L1014F pair and an increase of insects with M918L. These results suggest the evolutional progression of amino acid mutations associated with pyrethroid resistance in T. tabaci.},
}

@article {pmid38877225,
year = {2024},
author = {Hu, X and Hoffmann, DS and Wang, M and Schuhmacher, L and Stroe, MC and Schreckenberger, B and Elstner, M and Fischer, R},
title = {GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting.},
journal = {Nature microbiology},
volume = {9},
number = {7},
pages = {1752-1763},
pmid = {38877225},
issn = {2058-5276},
support = {FI 459/26-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STR1784/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Caenorhabditis elegans/microbiology/metabolism ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Mitochondria/metabolism ; *Ascomycota/metabolism/genetics ; *Fungal Proteins/metabolism/genetics ; Pheromones/metabolism ; Humans ; Gene Expression Regulation, Fungal ; },
abstract = {Initiation of development requires differential gene expression and metabolic adaptations. Here we show in the nematode-trapping fungus, Arthrobotrys flagrans, that both are achieved through a dual-function G-protein-coupled receptor (GPCR). A. flagrans develops adhesive traps and recognizes its prey, Caenorhabditis elegans, through nematode-specific pheromones (ascarosides). Gene-expression analyses revealed that ascarosides activate the fungal GPCR, GprC, at the plasma membrane and together with the G-protein alpha subunit GasA, reprograms the cell. However, GprC and GasA also reside in mitochondria and boost respiration. This dual localization of GprC in A. flagrans resembles the localization of the cannabinoid receptor CB1 in humans. The C. elegans ascaroside-sensing GPCR, SRBC66 and GPCRs of many fungi are also predicted for dual localization, suggesting broad evolutionary conservation. An SRBC64/66-GprC chimaeric protein was functional in A. flagrans, and C. elegans SRBC64/66 and DAF38 share ascaroside-binding sites with the fungal GprC receptor, suggesting 400-million-year convergent evolution.},
}

Animals
*Caenorhabditis elegans/microbiology/metabolism
*Receptors, G-Protein-Coupled/metabolism/genetics
*Mitochondria/metabolism
*Ascomycota/metabolism/genetics
*Fungal Proteins/metabolism/genetics
Pheromones/metabolism
Humans
Gene Expression Regulation, Fungal

@article {pmid38869631,
year = {2024},
author = {de Jong, TJ and Shmida, A},
title = {Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers.},
journal = {Acta biotheoretica},
volume = {72},
number = {2},
pages = {7},
pmid = {38869631},
issn = {1572-8358},
mesh = {*DNA, Mitochondrial/genetics ; *Tracheophyta/genetics ; *Paternal Inheritance ; Reproduction/genetics ; Pollen/genetics ; DNA, Plant/genetics ; },
abstract = {In angiosperms cytoplasmic DNA is typically passed on maternally through ovules. Genes in the mtDNA may cause male sterility. When male-sterile (female) cytotypes produce more seeds than cosexuals, they pass on more copies of their mtDNA and will co-occur with cosexuals with a neutral cytotype. Cytoplasmic gynodioecy is a well-known phenomenon in angiosperms, both in wild and crop plants. In some conifer families (e.g. Pinaceae) mitochondria are also maternally inherited. However in some other families (e.g. Taxaceae and Cupressaceae) mtDNA is paternally inherited through the pollen. With paternal mtDNA inheritance, male cytotypes that produce more pollen than cosexuals are expected to co-occur with cosexuals. This is uncharted territory. An ESS model shows that the presence of male cytotypes selects for more female allocation in the cosexual, i.e. for sexual specialisation. An allele that switches sex from male to female can then invade. This leads to rapid loss of the neutral cytotype of the cosexual, fixation of the male cytotype and dioecy with 50% males and 50% females. The models suggest that paternal inheritance of mtDNA facilitates the evolution dioecy. Consistent with this hypothesis the Pinaceae are 100% monoecious, while dioecy is common in the Taxaceae family and in the genus Juniperus (Cupressaceae). However, no reliable data are yet available on both mode of inheritance of mtDNA and gender variation of the same species. When cosexuals benefit from reproductive assurance (high selfing rate, low inbreeding depression, low fertilisation) they maintain themselves next to males and females. This predicted pattern with three sex types present in the same population is observed in conifers in nature.},
}

*DNA, Mitochondrial/genetics
*Tracheophyta/genetics
*Paternal Inheritance
Reproduction/genetics
Pollen/genetics
DNA, Plant/genetics

@article {pmid38868915,
year = {2024},
author = {Baird, LM and Berndsen, CE and Monroe, JD},
title = {Malate dehydrogenase in plants: evolution, structure, and a myriad of functions.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20230089},
pmid = {38868915},
issn = {1744-1358},
support = {MCB-2322867//National Science Foundation (NSF)/ ; },
abstract = {Malate dehydrogenase (MDH) catalyzes the interconversion of oxaloacetate and malate coupled to the oxidation/reduction of coenzymes NAD(P)H/NAD(P)+. While most animals have two isoforms of MDH located in the cytosol and mitochondria, all major groups of land plants have at least six MDHs localized to the cytosol, mitochondria, plastids, and peroxisomes. This family of enzymes participates in important reactions in plant cells including photosynthesis, photorespiration, lipid metabolism, and NH4+ metabolism. MDH also helps to regulate the energy balance in the cell and may help the plant cope with various environmental stresses. Despite their functional diversity, all of the plant MDH enzymes share a similar structural fold and act as dimers. In this review, we will introduce readers to our current understanding of the plant MDHs, including their evolution, structure, and function. The focus will be on the MDH enzymes of the model plant Arabidopsis thaliana.},
}

@article {pmid38866808,
year = {2024},
author = {Faustino, M and Lourenço, T and Strobbe, S and Cao, D and Fonseca, A and Rocha, I and Van Der Straeten, D and Oliveira, MM},
title = {OsTH1 is a key player in thiamin biosynthesis in rice.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {13591},
pmid = {38866808},
issn = {2045-2322},
mesh = {*Oryza/genetics/metabolism ; *Thiamine/biosynthesis/metabolism ; *Plant Proteins/metabolism/genetics ; Phylogeny ; Gene Expression Regulation, Plant ; },
abstract = {Thiamin is a vital nutrient that acts as a cofactor for several enzymes primarily localized in the mitochondria. These thiamin-dependent enzymes are involved in energy metabolism, nucleic acid biosynthesis, and antioxidant machinery. The enzyme HMP-P kinase/thiamin monophosphate synthase (TH1) holds a key position in thiamin biosynthesis, being responsible for the phosphorylation of HMP-P into HMP-PP and for the condensation of HMP-PP and HET-P to form TMP. Through mathematical kinetic model, we have identified TH1 as a critical player for thiamin biofortification in rice. We further focused on the functional characterization of OsTH1. Sequence and gene expression analysis, along with phylogenetic studies, provided insights into OsTH1 bifunctional features and evolution. The indispensable role of OsTH1 in thiamin biosynthesis was validated by heterologous expression of OsTH1 and successful complementation of yeast knock-out mutants impaired in thiamin production. We also proved that the sole OsTH1 overexpression in rice callus significantly improves B1 concentration, resulting in 50% increase in thiamin accumulation. Our study underscores the critical role of OsTH1 in thiamin biosynthesis, shedding light on its bifunctional nature and evolutionary significance. The significant enhancement of thiamin accumulation in rice callus upon OsTH1 overexpression constitutes evidence of its potential application in biofortification strategies.},
}

*Oryza/genetics/metabolism
*Thiamine/biosynthesis/metabolism
*Plant Proteins/metabolism/genetics
Phylogeny
Gene Expression Regulation, Plant

@article {pmid38864935,
year = {2024},
author = {Mochizuki, H},
title = {Pathological mechanisms and treatment of sporadic Parkinson's disease: past, present, and future.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {131},
number = {6},
pages = {597-607},
pmid = {38864935},
issn = {1435-1463},
support = {JPMJCR18H4//Core Research for Evolutional Science and Technology/ ; JP18dm0207020//Japan Agency for Medical Research and Development/ ; JP22dm0207070//Japan Agency for Medical Research and Development/ ; 22H02951//Japan Society for the Promotion of Science London/ ; 23K18255//Japan Society for the Promotion of Science London/ ; },
mesh = {Humans ; *Parkinson Disease/therapy/pathology/metabolism ; Animals ; Substantia Nigra/pathology/metabolism ; alpha-Synuclein/metabolism ; },
abstract = {For a special issue, we review studies on the pathogenesis of nigral cell death and the treatment of sporadic Parkinson's disease (sPD) over the past few decades, with a focus on the studies performed by Prof. Mizuno and our group. Prof. Mizuno proposed the initial concept that mitochondrial function may be impaired in sPD. When working at Jichi Medical School, he found a decrease in complex I of the mitochondrial electron transfer complex in the substantia nigra of patients with Parkinson's disease (PD) and MPTP models. After moving to Juntendo University as a professor and chairman, he continued to study the mechanisms of cell death in the substantia nigra of patients with sPD. Under his supervision, I studied the relationships between PD and apoptosis, PD and iron involvement, mitochondrial dysfunction and apoptosis, and PD and neuroinflammation. Moving to Kitasato University, we focused on PD and the cytotoxicity of alpha synuclein (αSyn) as well as brain neuropathology. Eventually, I moved to Osaka University, where I continued working on PD and αSyn projects to promote therapeutic research. In this paper, we present the details of these studies in the following order: past, present, and future.},
}

Humans
*Parkinson Disease/therapy/pathology/metabolism
Animals
Substantia Nigra/pathology/metabolism
alpha-Synuclein/metabolism

@article {pmid38853081,
year = {2024},
author = {Rackham, O and Saurer, M and Ban, N and Filipovska, A},
title = {Unique architectural features of mammalian mitochondrial protein synthesis.},
journal = {Trends in cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tcb.2024.05.001},
pmid = {38853081},
issn = {1879-3088},
abstract = {Mitochondria rely on coordinated expression of their own mitochondrial DNA (mtDNA) with that of the nuclear genome for their biogenesis. The bacterial ancestry of mitochondria has given rise to unique and idiosyncratic features of the mtDNA and its expression machinery that can be specific to different organisms. In animals, the mitochondrial protein synthesis machinery has acquired many new components and mechanisms over evolution. These include several new ribosomal proteins, new stop codons and ways to recognise them, and new mechanisms to deliver nascent proteins into the mitochondrial inner membrane. Here we describe the mitochondrial protein synthesis machinery in mammals and its unique mechanisms of action elucidated to date and highlight the technologies poised to reveal the next generation of discoveries in mitochondrial translation.},
}

@article {pmid38851366,
year = {2024},
author = {Tapanainen, R and Aasumets, K and Fekete, Z and Goffart, S and Dufour, E and L O Pohjoismäki, J},
title = {Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution.},
journal = {Gene},
volume = {926},
number = {},
pages = {148644},
doi = {10.1016/j.gene.2024.148644},
pmid = {38851366},
issn = {1879-0038},
mesh = {Animals ; *Hares/genetics ; *Genome, Mitochondrial ; *Tandem Repeat Sequences/genetics ; *DNA, Mitochondrial/genetics ; *Polymorphism, Genetic ; *Evolution, Molecular ; *Species Specificity ; Phylogeny ; },
abstract = {The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130-160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.},
}

Animals
*Hares/genetics
*Genome, Mitochondrial
*Tandem Repeat Sequences/genetics
*DNA, Mitochondrial/genetics
*Polymorphism, Genetic
*Evolution, Molecular
*Species Specificity
Phylogeny

@article {pmid38842420,
year = {2024},
author = {Dorrell, RG and Zhang, Y and Liang, Y and Gueguen, N and Nonoyama, T and Croteau, D and Penot, M and Adiba, S and Bailleul, B and Gros, V and Pierella Karlusich, JJ and Zweig, N and Fernie, AR and Jouhet, J and Maréchal, E and Bowler, C},
title = {Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koae168},
pmid = {38842420},
issn = {1532-298X},
abstract = {Organic carbon fixed in chloroplasts through the Calvin-Benson-Bassham Cycle can be diverted towards different metabolic fates, including cyoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis-gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis-gluconeogenesis, Enolase and bis-phospho-glycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.},
}

@article {pmid38835243,
year = {2024},
author = {Zwahlen, SM and Hayward, JA and Maguire, CS and Qin, AR and van Dooren, GG},
title = {A myzozoan-specific protein is an essential membrane-anchoring component of the succinate dehydrogenase complex in Toxoplasma parasites.},
journal = {Open biology},
volume = {14},
number = {6},
pages = {230463},
doi = {10.1098/rsob.230463},
pmid = {38835243},
issn = {2046-2441},
support = {//National Health and Medical Research Council/ ; },
mesh = {*Toxoplasma/metabolism/genetics/enzymology ; *Succinate Dehydrogenase/metabolism/genetics ; *Protozoan Proteins/metabolism/genetics/chemistry ; Humans ; Mitochondrial Proteins/metabolism/genetics ; Mitochondria/metabolism ; Phylogeny ; Animals ; },
abstract = {Succinate dehydrogenase (SDH) is a protein complex that functions in the tricarboxylic acid cycle and the electron transport chain of mitochondria. In most eukaryotes, SDH is highly conserved and comprises the following four subunits: SdhA and SdhB form the catalytic core of the complex, while SdhC and SdhD anchor the complex in the membrane. Toxoplasma gondii is an apicomplexan parasite that infects one-third of humans worldwide. The genome of T. gondii encodes homologues of the catalytic subunits SdhA and SdhB, although the physiological role of the SDH complex in the parasite and the identity of the membrane-anchoring subunits are poorly understood. Here, we show that the SDH complex contributes to optimal proliferation and O2 consumption in the disease-causing tachyzoite stage of the T. gondii life cycle. We characterize a small membrane-bound subunit of the SDH complex called mitochondrial protein ookinete developmental defect (MPODD), which is conserved among myzozoans, a phylogenetic grouping that incorporates apicomplexan parasites and their closest free-living relatives. We demonstrate that TgMPODD is essential for SDH activity and plays a key role in attaching the TgSdhA and TgSdhB proteins to the membrane anchor of the complex. Our findings highlight a unique and important feature of mitochondrial energy metabolism in apicomplexan parasites and their relatives.},
}

*Toxoplasma/metabolism/genetics/enzymology
*Succinate Dehydrogenase/metabolism/genetics
*Protozoan Proteins/metabolism/genetics/chemistry
Humans
Mitochondrial Proteins/metabolism/genetics
Mitochondria/metabolism
Phylogeny
Animals

@article {pmid38827288,
year = {2024},
author = {Liu, Y and Fu, X and Wang, Y and Liu, J and Liu, Y and Li, C and Dong, J},
title = {Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida).},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17480},
pmid = {38827288},
issn = {2167-8359},
mesh = {Animals ; *Phylogeny ; Genome, Mitochondrial/genetics ; Leeches/genetics/classification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 28S/genetics ; },
abstract = {BACKGROUND: Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae.

METHODS: Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method.

RESULTS: The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.},
}

Animals
*Phylogeny
Genome, Mitochondrial/genetics
Leeches/genetics/classification
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 28S/genetics

@article {pmid38825738,
year = {2024},
author = {Boscaro, V and James, ER and Fiorito, R and Del Campo, J and Scheffrahn, RH and Keeling, PJ},
title = {Updated classification of the phylum Parabasalia.},
journal = {The Journal of eukaryotic microbiology},
volume = {71},
number = {4},
pages = {e13035},
doi = {10.1111/jeu.13035},
pmid = {38825738},
issn = {1550-7408},
support = {RGPIN-2014-03994//Natural Sciences and Engineering Research Council of Canada/ ; //Gordon and Betty Moore Foundation/ ; },
mesh = {*Phylogeny ; Animals ; Parabasalidea/classification/genetics ; Symbiosis ; },
abstract = {The phylum Parabasalia includes very diverse single-cell organisms that nevertheless share a distinctive set of morphological traits. Most are harmless or beneficial gut symbionts of animals, but some have turned into parasites in other body compartments, the most notorious example being Trichomonas vaginalis in humans. Parabasalians have garnered attention for their nutritional symbioses with termites, their modified anaerobic mitochondria (hydrogenosomes), their character evolution, and the wholly unique features of some species. The molecular revolution confirmed the monophyly of Parabasalia, but considerably changed our view of their internal relationships, prompting a comprehensive reclassification 14 years ago. This classification has remained authoritative for many subgroups despite a greatly expanded pool of available data, but the large number of species and sequences that have since come out allow for taxonomic refinements in certain lineages, which we undertake here. We aimed to introduce as little disruption as possible but at the same time ensure that most taxa are truly monophyletic, and that the larger clades are subdivided into meaningful units. In doing so, we also highlighted correlations between the phylogeny of parabasalians and that of their hosts.},
}

*Phylogeny
Animals
Parabasalidea/classification/genetics
Symbiosis

@article {pmid38818026,
year = {2024},
author = {Tower, J},
title = {Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging.},
journal = {Frontiers in aging},
volume = {5},
number = {},
pages = {1376060},
pmid = {38818026},
issn = {2673-6217},
abstract = {Rules of biology typically involve conservation of resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, and scaling laws involve conservation of energy. Here a relationship with the opposite theme is discussed, which is the selectively advantageous instability (SAI) of one or more components of a replicating system, such as the cell. By increasing the complexity of the system, SAI can have benefits in addition to the generation of energy or the mobilization of building blocks. SAI involves a potential cost to the replicating system for the materials and/or energy required to create the unstable component, and in some cases, the energy required for its active degradation. SAI is well-studied in cells. Short-lived transcription and signaling factors enable a rapid response to a changing environment, and turnover is critical for replacement of damaged macromolecules. The minimal gene set for a viable cell includes proteases and a nuclease, suggesting SAI is essential for life. SAI promotes genetic diversity in several ways. Toxin/antitoxin systems promote maintenance of genes, and SAI of mitochondria facilitates uniparental transmission. By creating two distinct states, subject to different selective pressures, SAI can maintain genetic diversity. SAI of components of synthetic replicators favors replicator cycling, promoting emergence of replicators with increased complexity. Both classical and recent computer modeling of replicators reveals SAI. SAI may be involved at additional levels of biological organization. In summary, SAI promotes replicator genetic diversity and reproductive fitness, and may promote aging through loss of resources and maintenance of deleterious alleles.},
}

@article {pmid38816808,
year = {2024},
author = {Xing, J and Zhang, Y and Song, W and Ali, NA and Su, K and Sun, X and Sun, Y and Jiang, Y and Zhao, X},
title = {Comprehensive identification, characterization, and expression analysis of the MORF gene family in Brassica napus.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {475},
pmid = {38816808},
issn = {1471-2229},
support = {32170556//National Natural Science Foundation of China/ ; the Hundred-Talent Program//Zhejiang University/ ; },
mesh = {*Brassica napus/genetics/metabolism ; *Multigene Family ; *Phylogeny ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Genes, Plant ; RNA Editing ; Gene Expression Profiling ; Chloroplasts/genetics/metabolism ; },
abstract = {BACKGROUND: RNA editing in chloroplast and mitochondrion transcripts of plants is an important type of post-transcriptional RNA modification in which members of the multiple organellar RNA editing factor gene family (MORF) play a crucial role. However, a systematic identification and characterization of MORF members in Brassica napus is still lacking.

RESULTS: In this study, a total of 43 MORF genes were identified from the genome of the Brassica napus cultivar "Zhongshuang 11". The Brassica napus MORF (BnMORF) family members were divided into three groups through phylogenetic analysis. BnMORF genes distributed on 14 chromosomes and expanded due to segmental duplication and whole genome duplication repetitions. The majority of BnMORF proteins were predicted to be localized to mitochondria and chloroplasts. The promoter cis-regulatory element analysis, spatial-temporal expression profiling, and co-expression network of BnMORF genes indicated the involvement of BnMORF genes in stress and phytohormone responses, as well as growth and development.

CONCLUSION: This study provides a comprehensive analysis of BnMORF genes and lays a foundation for further exploring their physiological functions in Brassica napus.},
}

*Brassica napus/genetics/metabolism
*Multigene Family
*Phylogeny
*Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant
Genes, Plant
RNA Editing
Gene Expression Profiling
Chloroplasts/genetics/metabolism

@article {pmid38813885,
year = {2024},
author = {Bennett, GM and Kwak, Y and Maynard, R},
title = {Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again.},
journal = {Genome biology and evolution},
volume = {16},
number = {6},
pages = {},
pmid = {38813885},
issn = {1759-6653},
support = {NSF-1347116//National Science Foundation/ ; GT15982/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Symbiosis ; *Biological Evolution ; Animals ; Bacteria/genetics ; Biodiversity ; Evolution, Molecular ; },
abstract = {Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.},
}

*Symbiosis
*Biological Evolution
Animals
Bacteria/genetics
Biodiversity
Evolution, Molecular

@article {pmid38813783,
year = {2024},
author = {Wolyniak, MJ and Frazier, RH and Gemborys, PK and Loehr, HE},
title = {Malate dehydrogenase: a story of diverse evolutionary radiation.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20230076},
pmid = {38813783},
issn = {1744-1358},
support = {//Hampden-Sydney College Office of Undergraduate Research/ ; },
abstract = {Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.},
}

@article {pmid38812744,
year = {2024},
author = {Marques, E and Kramer, R and Ryan, DG},
title = {Multifaceted mitochondria in innate immunity.},
journal = {NPJ metabolic health and disease},
volume = {2},
number = {1},
pages = {6},
pmid = {38812744},
issn = {2948-2828},
abstract = {The ability of mitochondria to transform the energy we obtain from food into cell phosphorylation potential has long been appreciated. However, recent decades have seen an evolution in our understanding of mitochondria, highlighting their significance as key signal-transducing organelles with essential roles in immunity that extend beyond their bioenergetic function. Importantly, mitochondria retain bacterial motifs as a remnant of their endosymbiotic origin that are recognised by innate immune cells to trigger inflammation and participate in anti-microbial defence. This review aims to explore how mitochondrial physiology, spanning from oxidative phosphorylation (OxPhos) to signalling of mitochondrial nucleic acids, metabolites, and lipids, influences the effector functions of phagocytes. These myriad effector functions include macrophage polarisation, efferocytosis, anti-bactericidal activity, antigen presentation, immune signalling, and cytokine regulation. Strict regulation of these processes is critical for organismal homeostasis that when disrupted may cause injury or contribute to disease. Thus, the expanding body of literature, which continues to highlight the central role of mitochondria in the innate immune system, may provide insights for the development of the next generation of therapies for inflammatory diseases.},
}

@article {pmid38812151,
year = {2024},
author = {Zhang, XY and Yu, JC and Chen, WT and Zhou, DY and Yuan, Y and Liu, HG and Liang, YL},
title = {[Identification of HSP70 gene family members in Fritillaria cirrhosa and expression analysis in different tissues under high temperature stress].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {9},
pages = {2422-2433},
doi = {10.19540/j.cnki.cjcmm.20240214.101},
pmid = {38812151},
issn = {1001-5302},
mesh = {*HSP70 Heat-Shock Proteins/genetics/metabolism/chemistry ; *Plant Proteins/genetics/metabolism/chemistry ; *Fritillaria/genetics/chemistry ; *Phylogeny ; *Gene Expression Regulation, Plant ; Hot Temperature ; Stress, Physiological/genetics ; Gene Expression Profiling ; Multigene Family ; },
abstract = {The heat shock protein 70 family contains the stress proteins ubiquitous in plants. These proteins are involved in the responses to different abiotic stress conditions and have highly conserved gene sequences. However, little is known about the molecular mechanisms of Fritillaria cirrhosa in response to high-temperature stress. Here, 26 HSP70s, FcHSP70-1 to FcHSP70-26, were identified from the transcriptome data of root, bulb, stem, leaf, and fruit samples of F. cirrhosa. The proteins encoded by FcHSP70s had the lengths ranging from 560 aa to 944 aa, with the molecular weight of 61.64-100.01 kDa and the theoretical isoelectric point between 5.00 and 6.59. The secondary structural elements of HSP70s were mainly random coils and α-helixes. Subcellular localization prediction revealed that FcHSP70s were distributed in mitochondria, chloroplasts, nuclei, endoplasmic reticulum, and cytoplasm. The phylogenetic tree showed that 7 members of the HSP70 family belonged to the Dnak subfamily and 19 members belonged to the HSP110/SSE subfamily. In addition, the qRT-PCR results showed that the expression of FcHSP70-5, FcHSP70-8, FcHSP70-17, FcHSP70-18, and FcHSP70-23 in F. cirrhosa was significantly up-regulated at 35 ℃, which indicated that these genes might play a role in the response to high temperature stress. In addition, compared with other tissues, stems and leaves were sensitive to high temperature stress, with the expression of 18 genes up-regulated by 18.18 and 8.03 folds on average, respectively. These findings provide valuable information about the molecular mechanism of HSP70s of F. cirrhosa in response to high temperature stress.},
}

*HSP70 Heat-Shock Proteins/genetics/metabolism/chemistry
*Plant Proteins/genetics/metabolism/chemistry
*Fritillaria/genetics/chemistry
*Phylogeny
*Gene Expression Regulation, Plant
Hot Temperature
Stress, Physiological/genetics
Gene Expression Profiling
Multigene Family

@article {pmid38809522,
year = {2024},
author = {Li, W and Cai, Z and Schindler, F and Afjehi-Sadat, L and Montsch, B and Heffeter, P and Heiss, EH and Weckwerth, W},
title = {Elevated PINK1/Parkin-Dependent Mitophagy and Boosted Mitochondrial Function Mediate Protection of HepG2 Cells from Excess Palmitic Acid by Hesperetin.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {23},
pages = {13039-13053},
pmid = {38809522},
issn = {1520-5118},
mesh = {Humans ; Hep G2 Cells ; *Palmitic Acid/pharmacology ; *Hesperidin/pharmacology ; *Mitophagy/drug effects ; *Ubiquitin-Protein Ligases/metabolism/genetics ; *Mitochondria/drug effects/metabolism ; *Protein Kinases/metabolism/genetics ; Reactive Oxygen Species/metabolism ; Hepatocytes/drug effects/metabolism ; Membrane Potential, Mitochondrial/drug effects ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; Non-alcoholic Fatty Liver Disease/metabolism/drug therapy ; Protective Agents/pharmacology ; },
abstract = {Deregulation of mitochondrial functions in hepatocytes contributes to many liver diseases, such as nonalcoholic fatty liver disease (NAFLD). Lately, it was referred to as MAFLD (metabolism-associated fatty liver disease). Hesperetin (Hst), a bioactive flavonoid constituent of citrus fruit, has been proven to attenuate NAFLD. However, a potential connection between its preventive activities and the modulation of mitochondrial functions remains unclear. Here, our results showed that Hst alleviates palmitic acid (PA)-triggered NLRP3 inflammasome activation and cell death by inhibition of mitochondrial impairment in HepG2 cells. Hst reinstates fatty acid oxidation (FAO) rates measured by seahorse extracellular flux analyzer and intracellular acetyl-CoA levels as well as intracellular tricarboxylic acid cycle metabolites levels including NADH and FADH2 reduced by PA exposure. In addition, Hst protects HepG2 cells against PA-induced abnormal energetic profile, ATP generation reduction, overproduction of mitochondrial reactive oxygen species, and collapsed mitochondrial membrane potential. Furthermore, Hst improves the protein expression involved in PINK1/Parkin-mediated mitophagy. Our results demonstrate that it restores PA-impaired mitochondrial function and sustains cellular homeostasis due to the elevation of PINK1/Parkin-mediated mitophagy and the subsequent disposal of dysfunctional mitochondria. These results provide therapeutic potential for Hst utilization as an effective intervention against fatty liver disease.},
}

Humans
Hep G2 Cells
*Palmitic Acid/pharmacology
*Hesperidin/pharmacology
*Mitophagy/drug effects
*Ubiquitin-Protein Ligases/metabolism/genetics
*Mitochondria/drug effects/metabolism
*Protein Kinases/metabolism/genetics
Reactive Oxygen Species/metabolism
Hepatocytes/drug effects/metabolism
Membrane Potential, Mitochondrial/drug effects
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics
Non-alcoholic Fatty Liver Disease/metabolism/drug therapy
Protective Agents/pharmacology

@article {pmid38805695,
year = {2024},
author = {McElroy, KE and Masonbrink, R and Chudalayandi, S and Severin, AJ and Serb, JM},
title = {A chromosome-level genome assembly of the disco clam, Ctenoides ales.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae115},
pmid = {38805695},
issn = {2160-1836},
abstract = {The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales, which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and report a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, will be valuable resources for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.},
}

@article {pmid38804831,
year = {2024},
author = {Wang, J and Taki, M and Ohba, Y and Arita, M and Yamaguchi, S},
title = {Fluorescence Lifetime Imaging of Lipid Heterogeneity in the Inner Mitochondrial Membrane with a Super-photostable Environment-Sensitive Probe.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {63},
number = {28},
pages = {e202404328},
doi = {10.1002/anie.202404328},
pmid = {38804831},
issn = {1521-3773},
support = {19H02849//Japan Society for the Promotion of Science/ ; 23K06101//Japan Society for the Promotion of Science/ ; JP22H04926//Japan Society for the Promotion of Science/ ; JPMJCR21O5//Core Research for Evolutional Science and Technology/ ; JPMJER2101//Exploratory Research for Advanced Technology/ ; },
mesh = {*Fluorescent Dyes/chemistry ; *Mitochondrial Membranes/metabolism/chemistry ; *Optical Imaging ; Humans ; Lipids/chemistry ; Microscopy, Fluorescence ; Reactive Oxygen Species/metabolism/analysis ; HeLa Cells ; Mitochondria/metabolism/chemistry ; },
abstract = {The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red-emissive IMM-labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super-resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.},
}

*Fluorescent Dyes/chemistry
*Mitochondrial Membranes/metabolism/chemistry
*Optical Imaging
Humans
Lipids/chemistry
Microscopy, Fluorescence
Reactive Oxygen Species/metabolism/analysis
HeLa Cells
Mitochondria/metabolism/chemistry

@article {pmid38791655,
year = {2024},
author = {Zhou, S and Wang, X and Wang, L and Gao, X and Lyu, T and Xia, T and Shi, L and Dong, Y and Mei, X and Zhang, Z and Zhang, H},
title = {Different Evolutionary Trends of Galloanseres: Mitogenomics Analysis.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {10},
pages = {},
pmid = {38791655},
issn = {2076-2615},
support = {32200407//National Natural Science Foundation of China/ ; 32270444//National Natural Science Foundation of China/ ; ZR2023ZD47//Natural Science Foundation of Shandong Province/ ; GZC20231394//Postdoctoral Fellowship Program of CPSF/ ; GZC20231395//Postdoctoral Fellowship Program of CPSF/ ; GZC20231396//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {The two existing clades of Galloanseres, orders Galliformes (landfowl) and Anseriformes (waterfowl), exhibit dramatically different evolutionary trends. Mitochondria serve as primary sites for energy production in organisms, and numerous studies have revealed their role in biological evolution and ecological adaptation. We assembled the complete mitogenome sequences of two species of the genus Aythya within Anseriformes: Aythya baeri and Aythya marila. A phylogenetic tree was constructed for 142 species within Galloanseres, and their divergence times were inferred. The divergence between Galliformes and Anseriformes occurred ~79.62 million years ago (Mya), followed by rapid evolution and diversification after the Middle Miocene (~13.82 Mya). The analysis of selective pressure indicated that the mitochondrial protein-coding genes (PCGs) of Galloanseres species have predominantly undergone purifying selection. The free-ratio model revealed that the evolutionary rates of COX1 and COX3 were lower than those of the other PCGs, whereas ND2 and ND6 had faster evolutionary rates. The CmC model also indicated that most PCGs in Anseriformes exhibited stronger selective constraints. Our study suggests that the distinct evolutionary trends and energy requirements of Galliformes and Anseriformes drive different evolutionary patterns in the mitogenome.},
}

@article {pmid38791521,
year = {2024},
author = {Singh, MK and Shin, Y and Han, S and Ha, J and Tiwari, PK and Kim, SS and Kang, I},
title = {Molecular Chaperonin HSP60: Current Understanding and Future Prospects.},
journal = {International journal of molecular sciences},
volume = {25},
number = {10},
pages = {},
pmid = {38791521},
issn = {1422-0067},
support = {NRF-2018R1A6A1A03025124//National Research Foundation/ ; },
mesh = {*Chaperonin 60/metabolism/genetics ; Humans ; Animals ; *Oxidative Stress ; *Mitochondria/metabolism ; Neoplasms/metabolism/genetics/pathology ; Apoptosis ; Neurodegenerative Diseases/metabolism ; Protein Folding ; Reactive Oxygen Species/metabolism ; },
abstract = {Molecular chaperones are highly conserved across evolution and play a crucial role in preserving protein homeostasis. The 60 kDa heat shock protein (HSP60), also referred to as chaperonin 60 (Cpn60), resides within mitochondria and is involved in maintaining the organelle's proteome integrity and homeostasis. The HSP60 family, encompassing Cpn60, plays diverse roles in cellular processes, including protein folding, cell signaling, and managing high-temperature stress. In prokaryotes, HSP60 is well understood as a GroEL/GroES complex, which forms a double-ring cavity and aids in protein folding. In eukaryotes, HSP60 is implicated in numerous biological functions, like facilitating the folding of native proteins and influencing disease and development processes. Notably, research highlights its critical involvement in sustaining oxidative stress and preserving mitochondrial integrity. HSP60 perturbation results in the loss of the mitochondria integrity and activates apoptosis. Currently, numerous clinical investigations are in progress to explore targeting HSP60 both in vivo and in vitro across various disease models. These studies aim to enhance our comprehension of disease mechanisms and potentially harness HSP60 as a therapeutic target for various conditions, including cancer, inflammatory disorders, and neurodegenerative diseases. This review delves into the diverse functions of HSP60 in regulating proteo-homeostasis, oxidative stress, ROS, apoptosis, and its implications in diseases like cancer and neurodegeneration.},
}

*Chaperonin 60/metabolism/genetics
Humans
Animals
*Oxidative Stress
*Mitochondria/metabolism
Neoplasms/metabolism/genetics/pathology
Apoptosis
Neurodegenerative Diseases/metabolism
Protein Folding
Reactive Oxygen Species/metabolism

@article {pmid38789593,
year = {2024},
author = {Qu, K and Chen, Y and Liu, D and Guo, H and Xu, T and Jing, Q and Ge, L and Shu, X and Xin, X and Xie, X and Tong, B},
title = {Comprehensive analysis of the complete mitochondrial genome of Lilium tsingtauense reveals a novel multichromosome structure.},
journal = {Plant cell reports},
volume = {43},
number = {6},
pages = {150},
pmid = {38789593},
issn = {1432-203X},
support = {2020070316//National Forestry and Grassland Administration/ ; 2021070307//National Forestry and Grassland Administration/ ; Lu Financial Preliminary Guide [2021] No. 1//Shandong provincial department of finance/ ; 2021LZGC023//Department of Science and Technology of Shandong Province/ ; 2005-DKA21003//Chinese Academy of Forestry/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Lilium/genetics ; *Chromosomes, Plant/genetics ; *Phylogeny ; RNA, Transfer/genetics ; Genome, Plant/genetics ; Base Composition/genetics ; },
abstract = {Lilium tsingtauense mitogenome comprises 27 independent chromosome molecules, it undergoes frequent genomic recombination, and the rate of recombination and mutation between different repetitive sequences affects the formation of multichromosomal structures. Given the extremely large genome of Lily, which likely harbors additional genetic resources, it serves as an ideal material for studying the phylogenetic evolution of organisms. Although the Lilium chloroplast genome has been documented, the sequence of its mitochondrial genome (mitogenome) remains uncharted. Using BGI short reads and Nanopore long reads, we sequenced, assembled, and annotated the mitogenome of Lilium tsingtauense. This effort culminated in the characterization of Lilium's first complete mitogenome. Comparative analysis with other angiosperms revealed the unique multichromosomal structure of the L. tsingtauense mitogenome, spanning 1,125,108 bp and comprising 27 independent circular chromosomes. It contains 36 protein-coding genes, 12 tRNA genes, and 3 rRNA genes, with a GC content of 44.90%. Notably, three chromosomes in the L. tsingtauense mitogenome lack identifiable genes, hinting at the potential existence of novel genes and noncoding elements. The high degree of observed genome fragmentation implies frequent reorganization, with recombination and mutation rates among diverse repetitive sequences likely driving the formation of multichromosomal structures. Our comprehensive analysis, covering genome size, coding genes, structure, RNA editing, repetitive sequences, and sequence migration, sheds light on the evolutionary and molecular biology of multichromosomal mitochondria in Lilium. This high-quality mitogenome of L. tsingtauense not only enriches our understanding of multichromosomal mitogenomes but also establishes a solid foundation for future genome breeding and germplasm innovation in Lilium.},
}

*Genome, Mitochondrial/genetics
*Lilium/genetics
*Chromosomes, Plant/genetics
*Phylogeny
RNA, Transfer/genetics
Genome, Plant/genetics
Base Composition/genetics

@article {pmid38782915,
year = {2024},
author = {Hanson, SE and Dowdy, T and Larion, M and Doyle, MT and Bernstein, HD},
title = {The patatin-like protein PlpD forms structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4389},
pmid = {38782915},
issn = {2041-1723},
support = {Intramural Program//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Intramural Program//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; Intramural Program//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Pseudomonas aeruginosa/metabolism/genetics ; *Bacterial Outer Membrane Proteins/metabolism/chemistry/genetics ; *Protein Multimerization ; Periplasm/metabolism ; Protein Domains ; Bacterial Outer Membrane/metabolism ; Models, Molecular ; Bacterial Proteins/metabolism/chemistry/genetics ; },
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 find 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.},
}

*Pseudomonas aeruginosa/metabolism/genetics
*Bacterial Outer Membrane Proteins/metabolism/chemistry/genetics
*Protein Multimerization
Periplasm/metabolism
Protein Domains
Bacterial Outer Membrane/metabolism
Models, Molecular
Bacterial Proteins/metabolism/chemistry/genetics

@article {pmid38776415,
year = {2024},
author = {Liao, T and Wang, S and Zhang, H and Stüeken, EE and Luo, H},
title = {Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils.},
journal = {Molecular biology and evolution},
volume = {41},
number = {5},
pages = {},
pmid = {38776415},
issn = {1537-1719},
support = {14107823//Hong Kong Research Grants Council (RGC) General Research Fund/ ; 42293294//Natural Science Foundation of China/ ; AoE/M-403/16//Hong Kong Research Grants Council Area of Excellence Scheme/ ; 2022A1515010844//Guangdong Basic and Applied Basic Research Foundation/ ; 2021M702296//China Postdoctoral Science Foundation/ ; },
mesh = {*Ammonia/metabolism ; *Oxidation-Reduction ; *Fossils ; Gammaproteobacteria/metabolism/genetics ; Bacteria/metabolism/genetics ; Biological Evolution ; Phylogeny ; Symbiosis ; Eukaryota/metabolism/genetics ; Nitrogen Cycle ; },
abstract = {Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.},
}

*Ammonia/metabolism
*Oxidation-Reduction
*Fossils
Gammaproteobacteria/metabolism/genetics
Bacteria/metabolism/genetics
Biological Evolution
Phylogeny
Symbiosis
Eukaryota/metabolism/genetics
Nitrogen Cycle

@article {pmid38773202,
year = {2024},
author = {Pfingstl, T and Hiruta, SF and Shimano, S},
title = {Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11634},
pmid = {38773202},
issn = {2045-2322},
support = {I 3815//Austrian Science Fund/ ; },
mesh = {Animals ; *Mites/genetics/classification ; *Phylogeny ; *Metagenomics/methods ; Genome, Mitochondrial ; Mitochondria/genetics ; Metagenome ; Evolution, Molecular ; Ecosystem ; },
abstract = {Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.},
}

Animals
*Mites/genetics/classification
*Phylogeny
*Metagenomics/methods
Genome, Mitochondrial
Mitochondria/genetics
Metagenome
Evolution, Molecular
Ecosystem

@article {pmid38772414,
year = {2024},
author = {Dohnálek, V and Doležal, P},
title = {Installation of LYRM proteins in early eukaryotes to regulate the metabolic capacity of the emerging mitochondrion.},
journal = {Open biology},
volume = {14},
number = {5},
pages = {240021},
doi = {10.1098/rsob.240021},
pmid = {38772414},
issn = {2046-2441},
support = {//Gordon and Betty Moore Foundation and Simons Foundation/ ; //Czech Science Foundation/ ; },
mesh = {*Mitochondria/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; Animals ; Evolution, Molecular ; Eukaryota/metabolism ; Acyl Carrier Protein/metabolism/genetics ; Phylogeny ; Models, Molecular ; Humans ; Amino Acid Sequence ; },
abstract = {Core mitochondrial processes such as the electron transport chain, protein translation and the formation of Fe-S clusters (ISC) are of prokaryotic origin and were present in the bacterial ancestor of mitochondria. In animal and fungal models, a family of small Leu-Tyr-Arg motif-containing proteins (LYRMs) uniformly regulates the function of mitochondrial complexes involved in these processes. The action of LYRMs is contingent upon their binding to the acylated form of acyl carrier protein (ACP). This study demonstrates that LYRMs are structurally and evolutionarily related proteins characterized by a core triplet of α-helices. Their widespread distribution across eukaryotes suggests that 12 specialized LYRMs were likely present in the last eukaryotic common ancestor to regulate the assembly and folding of the subunits that are conserved in bacteria but that lack LYRM homologues. The secondary reduction of mitochondria to anoxic environments has rendered the function of LYRMs and their interaction with acylated ACP dispensable. Consequently, these findings strongly suggest that early eukaryotes installed LYRMs in aerobic mitochondria as orchestrated switches, essential for regulating core metabolism and ATP production.},
}

*Mitochondria/metabolism
*Mitochondrial Proteins/metabolism/genetics
Animals
Evolution, Molecular
Eukaryota/metabolism
Acyl Carrier Protein/metabolism/genetics
Phylogeny
Models, Molecular
Humans
Amino Acid Sequence

@article {pmid38758976,
year = {2024},
author = {Giannakis, K and Richards, L and Dauda, KA and Johnston, IG},
title = {Connecting Species-Specific Extents of Genome Reduction in Mitochondria and Plastids.},
journal = {Molecular biology and evolution},
volume = {41},
number = {6},
pages = {},
pmid = {38758976},
issn = {1537-1719},
support = {//BBSRC/ ; //MIBTP Doctoral Training Scheme/ ; /ERC_/European Research Council/International ; 805046//European Union's Horizon 2020/ ; //EvoConBiO/ ; TMS2021TMT09//Trond Mohn Foundation/ ; //Centre for Antimicrobial Resistance in Western Norway/ ; TMS2020TMT11//CAMRIA/ ; },
mesh = {*Genome, Mitochondrial ; *Genome, Plastid ; *Plastids/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Mitochondria/genetics ; Species Specificity ; Biological Evolution ; Eukaryota/genetics ; },
abstract = {Mitochondria and plastids have both dramatically reduced their genomes since the endosymbiotic events that created them. The similarities and differences in the evolution of the two organelle genome types have been the target of discussion and investigation for decades. Ongoing work has suggested that similar mechanisms may modulate the reductive evolution of the two organelles in a given species, but quantitative data and statistical analyses exploring this picture remain limited outside of some specific cases like parasitism. Here, we use cross-eukaryote organelle genome data to explore evidence for coevolution of mitochondrial and plastid genome reduction. Controlling for differences between clades and pseudoreplication due to relatedness, we find that extents of mtDNA and ptDNA gene retention are related to each other across taxa, in a generally positive correlation that appears to differ quantitatively across eukaryotes, for example, between algal and nonalgal species. We find limited evidence for coevolution of specific mtDNA and ptDNA gene pairs, suggesting that the similarities between the two organelle types may be due mainly to independent responses to consistent evolutionary drivers.},
}

*Genome, Mitochondrial
*Genome, Plastid
*Plastids/genetics
DNA, Mitochondrial/genetics
Evolution, Molecular
Mitochondria/genetics
Species Specificity
Biological Evolution
Eukaryota/genetics

@article {pmid38753873,
year = {2024},
author = {Thielen, M and Gärtner, B and Knoop, V and Schallenberg-Rüdinger, M and Lesch, E},
title = {Conquering new grounds: plant organellar C-to-U RNA editing factors can be functional in the plant cytosol.},
journal = {The Plant journal : for cell and molecular biology},
volume = {119},
number = {2},
pages = {895-915},
doi = {10.1111/tpj.16804},
pmid = {38753873},
issn = {1365-313X},
support = {SCHA 1952 2-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*RNA Editing ; *Chloroplasts/metabolism/genetics ; *Cytosol/metabolism ; *Bryopsida/genetics/metabolism ; *Mitochondria/metabolism/genetics ; *RNA, Plant/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Cytidine/metabolism/genetics ; RNA-Binding Proteins/metabolism/genetics ; Gene Expression Regulation, Plant ; Uridine/metabolism/genetics ; },
abstract = {Plant mitochondrial and chloroplast transcripts are subject to numerous events of specific cytidine-to-uridine (C-to-U) RNA editing to correct genetic information. Key protein factors for this process are specific RNA-binding pentatricopeptide repeat (PPR) proteins, which are encoded in the nucleus and post-translationally imported into the two endosymbiotic organelles. Despite hundreds of C-to-U editing sites in the plant organelles, no comparable editing has been found for nucleo-cytosolic mRNAs raising the question why plant RNA editing is restricted to chloroplasts and mitochondria. Here, we addressed this issue in the model moss Physcomitrium patens, where all PPR-type RNA editing factors comprise specific RNA-binding and cytidine deamination functionalities in single proteins. To explore whether organelle-type RNA editing can principally also take place in the plant cytosol, we expressed PPR56, PPR65 and PPR78, three editing factors recently shown to also function in a bacterial setup, together with cytosolic co-transcribed native targets in Physcomitrium. While we obtained unsatisfying results upon their constitutive expression, we found strong cytosolic RNA editing under hormone-inducible expression. Moreover, RNA-Seq analyses revealed varying numbers of up to more than 900 off-targets in other cytosolic transcripts. We conclude that PPR-mediated C-to-U RNA editing is not per se incompatible with the plant cytosol but that its limited target specificity has restricted its occurrence to the much less complex transcriptomes of mitochondria and chloroplast in the course of evolution.},
}

*RNA Editing
*Chloroplasts/metabolism/genetics
*Cytosol/metabolism
*Bryopsida/genetics/metabolism
*Mitochondria/metabolism/genetics
*RNA, Plant/genetics/metabolism
Plant Proteins/genetics/metabolism
Cytidine/metabolism/genetics
RNA-Binding Proteins/metabolism/genetics
Gene Expression Regulation, Plant
Uridine/metabolism/genetics

@article {pmid38750703,
year = {2024},
author = {Gong, Y and Luo, X and Zhang, T and Zhou, G and Li, J and Zhang, B and Li, P and Huang, H},
title = {Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica).},
journal = {Genomics},
volume = {116},
number = {3},
pages = {110859},
doi = {10.1016/j.ygeno.2024.110859},
pmid = {38750703},
issn = {1089-8646},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Luffa/genetics ; RNA, Transfer/genetics ; Genome, Plant ; Plant Proteins/genetics/metabolism ; },
abstract = {Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate the functions of the mitochondrial (mt) genome of Luffa cylindrica. The mt genome of L. cylindrica contained two chromosomes with lengths of 380,879 bp and 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 pseudogene, were identified. About 90.63% of the codons ended with A or U bases, and 98.63% of monomers contained A/T, which contributed to the high A/T content (55.91%) of the complete mt genome. Six genes (ATP8, CCMFC, NAD4, RPL10, RPL5 and RPS4) showed positive selection. Phylogenetic analysis indicates that L. cylindrica is closely related to L. acutangula. The present results provide the mt genome of L. cylindrica, which may facilitate possible genetic variation, evolutionary, and molecular breeding studies of L. cylindrica.},
}

*Genome, Mitochondrial
*Phylogeny
*Luffa/genetics
RNA, Transfer/genetics
Genome, Plant
Plant Proteins/genetics/metabolism

@article {pmid38750421,
year = {2024},
author = {Wang, X and Pei, J and Xiong, L and Bao, P and Chu, M and Ma, X and La, Y and Liang, C and Yan, P and Guo, X},
title = {Genetic diversity, phylogeography, and maternal origin of yak (Bos grunniens).},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {481},
pmid = {38750421},
issn = {1471-2164},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; 25-LZIHPS-01//the Innovation Project of Chinese Academy of Agricultural Sciences/ ; },
mesh = {Animals ; Cattle/genetics ; *Phylogeography ; *Genetic Variation ; *Haplotypes ; *Phylogeny ; *Genome, Mitochondrial ; Maternal Inheritance ; Female ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND: There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity.

RESULTS: A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks.

CONCLUSIONS: Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.},
}

Animals
Cattle/genetics
*Phylogeography
*Genetic Variation
*Haplotypes
*Phylogeny
*Genome, Mitochondrial
Maternal Inheritance
Female
DNA, Mitochondrial/genetics

@article {pmid38741523,
year = {2024},
author = {Hervas, LS and do Amaral-Silva, L and Sartori, MR and Guadalupe-Silva, A and Gargaglioni, LH and Lerchner, J and Oliveira, MT and Bícego, KC},
title = {Mitochondrial function in skeletal muscle contributes to reproductive endothermy in tegu lizards (Salvator merianae).},
journal = {Acta physiologica (Oxford, England)},
volume = {240},
number = {7},
pages = {e14162},
doi = {10.1111/apha.14162},
pmid = {38741523},
issn = {1748-1716},
support = {2021/10910-0//São Paulo State Research Foundation-FAPESP/ ; 2021/06711-2//São Paulo State Research Foundation-FAPESP/ ; 2020/10961-1//São Paulo State Research Foundation-FAPESP/ ; 2020/07520-3//São Paulo State Research Foundation-FAPESP/ ; 309899/2022-2//CNPq/ ; 148915/2019-1//CNPq/ ; 147536/2018-9//CNPq/ ; 88887.194785/2018-00//CAPES PrInt/ ; },
mesh = {Animals ; *Lizards/physiology/metabolism ; *Muscle, Skeletal/metabolism/physiology ; *Reproduction/physiology ; Thermogenesis/physiology ; Female ; Male ; Seasons ; Mitochondria, Muscle/metabolism ; Energy Metabolism/physiology ; },
abstract = {AIM: In cyclic climate variations, including seasonal changes, many animals regulate their energy demands to overcome critical transitory moments, restricting their high-demand activities to phases of resource abundance, enabling rapid growth and reproduction. Tegu lizards (Salvator merianae) are ectotherms with a robust annual cycle, being active during summer, hibernating during winter, and presenting a remarkable endothermy during reproduction in spring. Here, we evaluated whether changes in mitochondrial respiratory physiology in skeletal muscle could serve as a mechanism for the increased thermogenesis observed during the tegu's reproductive endothermy.

METHODS: We performed high-resolution respirometry and calorimetry in permeabilized red and white muscle fibers, sampled during summer (activity) and spring (high activity and reproduction), in association with citrate synthase measurements.

RESULTS: During spring, the muscle fibers exhibited increased oxidative phosphorylation. They also enhanced uncoupled respiration and heat production via adenine nucleotide translocase (ANT), but not via uncoupling proteins (UCP). Citrate synthase activity was higher during the spring, suggesting greater mitochondrial density compared to the summer. These findings were consistent across both sexes and muscle types (red and white).

CONCLUSION: The current results highlight potential cellular thermogenic mechanisms in an ectothermic reptile that contribute to transient endothermy. Our study indicates that the unique feature of transitioning to endothermy through nonshivering thermogenesis during the reproductive phase may be facilitated by higher mitochondrial density, function, and uncoupling within the skeletal muscle. This knowledge contributes significant elements to the broader picture of models for the evolution of endothermy, particularly in relation to the enhancement of aerobic capacity.},
}

Animals
*Lizards/physiology/metabolism
*Muscle, Skeletal/metabolism/physiology
*Reproduction/physiology
Thermogenesis/physiology
Female
Male
Seasons
Mitochondria, Muscle/metabolism
Energy Metabolism/physiology

@article {pmid38740928,
year = {2024},
author = {Rakotonirina, A and Dauga, C and Pol, M and Hide, M and Vuth, L and Ballan, V and Kilama, S and Russet, S and Marcombe, S and Boyer, S and Pocquet, N},
title = {Speciation patterns of Aedes mosquitoes in the Scutellaris Group: a mitochondrial perspective.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10930},
pmid = {38740928},
issn = {2045-2322},
mesh = {Animals ; *Aedes/genetics/classification ; *Genetic Speciation ; *Phylogeny ; *Electron Transport Complex IV/genetics ; *Mitochondria/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Asia ; },
abstract = {The Scutellaris Group of Aedes comprises 47 mosquito species, including Aedes albopictus. While Ae. albopictus is widely distributed, the other species are mostly found in the Asia-Pacific region. Evolutionary history researches of Aedes species within the Scutellaris Group have mainly focused on Ae. albopictus, a species that raises significant public health concerns, neglecting the other species. In this study, we aimed to assess genetic diversity and estimate speciation times of several species within the Scutellaris Group. Mosquitoes were therefore collected from various Asia-Pacific countries. Their mitochondrial cytochrome c oxidase subunit 1 (cox1) and subunit 3 (cox3) sequences were analyzed alongside those of other Scutellaris Group species available in the GenBank database. To estimate the divergence time, we analyzed 1849 cox1 gene sequences from 21 species, using three species (Aedes aegypti, Aedes notoscriptus and Aedes vigilax) as outgroups. We found that most of the speciation dates occurred during the Paleogene and the Neogene periods. A separation between the Scutellaris Subgroup and the Albopictus Subgroup occurred approximately 64-61 million years ago (MYA). We also identified a split between species found in Asia/Micronesia and those collected in Melanesia/Polynesia approximately 36-35 MYA. Our findings suggest that the speciation of Aedes species within the Scutellaris Group may be driven by diversity in mammalian hosts, climate and environmental changes, and geological dynamics rather than human migration.},
}

Animals
*Aedes/genetics/classification
*Genetic Speciation
*Phylogeny
*Electron Transport Complex IV/genetics
*Mitochondria/genetics
Genetic Variation
DNA, Mitochondrial/genetics
Evolution, Molecular
Asia

@article {pmid38740227,
year = {2024},
author = {Zhang, M and Li, W and Zhang, X and Bi, M and Wang, X and Sun, F and Lu, J and Chi, Y and Han, Y and Li, Q and Li, T},
title = {Lamprey VDAC2: Suppressing hydrogen peroxide-induced 293T cell apoptosis by downregulating BAK expression.},
journal = {Fish & shellfish immunology},
volume = {150},
number = {},
pages = {109622},
doi = {10.1016/j.fsi.2024.109622},
pmid = {38740227},
issn = {1095-9947},
mesh = {Animals ; Humans ; Amino Acid Sequence ; *Apoptosis ; bcl-2 Homologous Antagonist-Killer Protein/metabolism ; Down-Regulation/drug effects ; *Fish Proteins/genetics/immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation ; HEK293 Cells ; Hydrogen Peroxide ; *Lampreys/genetics/immunology ; Phylogeny ; Sequence Alignment/veterinary ; *Voltage-Dependent Anion Channel 2/metabolism ; },
abstract = {The voltage-dependent anion channel 2 (VDAC2) is the abundant protein in the outer mitochondrial membrane. Opening VDAC2 pores leads to the induction of mitochondrial energy and material transport, facilitating interaction with various mitochondrial proteins implicated in essential processes such as cell apoptosis and proliferation. To investigate the VDAC2 in lower vertebrates, we identified Lr-VDAC2, a homologue of VDAC2 found in lamprey (Lethenteron reissneri), sharing a sequence identity of greater than 50 % with its counterparts. Phylogenetic analysis revealed that the position of Lr-VDAC2 aligns with the lamprey phylogeny, indicating its evolutionary relationship within the species. The Lr-VDAC2 protein was primarily located in the mitochondria of lamprey cells. The expression of the Lr-VDAC2 protein was elevated in high energy-demanding tissues, such as the gills, muscles, and myocardial tissue in normal lampreys. Lr-VDAC2 suppressed H2O2 (hydrogen peroxide)-induced 293 T cell apoptosis by reducing the expression levels of Caspase 3, Caspase 9, and Cyt C (cytochrome c). Further research into the mechanism indicated that the Lr-VDAC2 protein inhibited the pro-apoptotic activity of BAK (Bcl-2 antagonist/killer) protein by downregulating its expression at the protein translational level, thus exerting an anti-apoptotic function similar to the role of VDAC2 in humans.},
}

Animals
Humans
Amino Acid Sequence
*Apoptosis
bcl-2 Homologous Antagonist-Killer Protein/metabolism
Down-Regulation/drug effects
*Fish Proteins/genetics/immunology
Gene Expression Profiling/veterinary
Gene Expression Regulation
HEK293 Cells
Hydrogen Peroxide
*Lampreys/genetics/immunology
Phylogeny
Sequence Alignment/veterinary
*Voltage-Dependent Anion Channel 2/metabolism

@article {pmid38735623,
year = {2024},
author = {Strücker, GK and Jaramillo, ML and de Quadros, T and Nazari, EM},
title = {UVB radiation exposure modulates mitophagy in embryonic cells of freshwater prawn Macrobrachium olfersii: Exploring a protective organelle quality control mechanism.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {295},
number = {},
pages = {111664},
doi = {10.1016/j.cbpa.2024.111664},
pmid = {38735623},
issn = {1531-4332},
mesh = {Animals ; *Ultraviolet Rays/adverse effects ; *Mitophagy/radiation effects ; *Palaemonidae/radiation effects/embryology/genetics ; Mitochondria/metabolism/radiation effects ; Embryo, Nonmammalian/radiation effects/metabolism ; Arthropod Proteins/metabolism/genetics ; Phylogeny ; Organelles/metabolism/radiation effects ; },
abstract = {Aquatic environments are subject to ultraviolet B (UVB) radiation incidence, and its effects on organisms are dose-dependent. Besides DNA, mitochondria are an important target of this radiation that causes structural damage and impairs its functional dynamics. Here, we hypothesize that mitophagy acts as an organelle quality control mechanism to mitigate UVB impacts in embryonic cells. Then, freshwater prawn Macrobrachium olfersii embryos was used as a model to investigate the effects of UVB on genes (Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3) and proteins (TOM20, PINK1, p62 and LC3B) involved in mitophagy modulation. The choice of genes and proteins was based on the identification of mitochondrial membrane (Tomm20, Opa1 and TOM20), mediation of mitophagy (Pink1, Prkn and PINK1), and recognition of mitochondria by the autophagosome membrane (Sqstm1, Map1lc3, p62 and LC3B). First, the phylogeny of all genes presented bootstrap values >80 and conserved domains among crustacean species. Gene expression was inherently modulated during development, with transcripts (Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3) overexpressed in the initial and final stages of development. Moreover, UVB radiation induced upregulation of Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3 genes at 6 h after exposure. Interestingly, after 12 h, the protein content of PINK1, p62, and LC3B increased, while TOM20 was not responsive. Despite UVB radiation's harmful effects on embryonic cells, the chronology of gene expression and protein content indicates rapid activation of mitophagy, serving as an organelle quality control mechanism, given the analyzed cells' integrity.},
}

Animals
*Ultraviolet Rays/adverse effects
*Mitophagy/radiation effects
*Palaemonidae/radiation effects/embryology/genetics
Mitochondria/metabolism/radiation effects
Embryo, Nonmammalian/radiation effects/metabolism
Arthropod Proteins/metabolism/genetics
Phylogeny
Organelles/metabolism/radiation effects

@article {pmid38733988,
year = {2024},
author = {Sangineto, M and Ciarnelli, M and Colangelo, T and Moola, A and Bukke, VN and Duda, L and Villani, R and Romano, A and Giandomenico, S and Kanwal, H and Serviddio, G},
title = {Monocyte bioenergetics: An immunometabolic perspective in metabolic dysfunction-associated steatohepatitis.},
journal = {Cell reports. Medicine},
volume = {5},
number = {5},
pages = {101564},
pmid = {38733988},
issn = {2666-3791},
mesh = {Humans ; *Energy Metabolism ; Animals ; *Monocytes/metabolism/immunology ; Mice ; *Mitochondria/metabolism ; Fatty Liver/metabolism/pathology/immunology ; Male ; Glycolysis ; Reactive Oxygen Species/metabolism ; Mice, Inbred C57BL ; Macrophages/metabolism/immunology ; Female ; Liver/metabolism/pathology ; },
abstract = {Monocytes (Mos) are crucial in the evolution of metabolic dysfunction-associated steatotic liver disease (MASLD) to metabolic dysfunction-associated steatohepatitis (MASH), and immunometabolism studies have recently suggested targeting leukocyte bioenergetics in inflammatory diseases. Here, we reveal a peculiar bioenergetic phenotype in circulating Mos of patients with MASH, characterized by high levels of glycolysis and mitochondrial (mt) respiration. The enhancement of mt respiratory chain activity, especially complex II (succinate dehydrogenase [SDH]), is unbalanced toward the production of reactive oxygen species (ROS) and is sustained at the transcriptional level with the involvement of the AMPK-mTOR-PGC-1α axis. The modulation of mt activity with dimethyl malonate (DMM), an SDH inhibitor, restores the metabolic profile and almost abrogates cytokine production. Analysis of a public single-cell RNA sequencing (scRNA-seq) dataset confirms that in murine models of MASH, liver Mo-derived macrophages exhibit an upregulation of mt and glycolytic energy pathways. Accordingly, the DMM injection in MASH mice contrasts Mo infiltration and macrophagic enrichment, suggesting immunometabolism as a potential target in MASH.},
}

Humans
*Energy Metabolism
Animals
*Monocytes/metabolism/immunology
Mice
*Mitochondria/metabolism
Fatty Liver/metabolism/pathology/immunology
Male
Glycolysis
Reactive Oxygen Species/metabolism
Mice, Inbred C57BL
Macrophages/metabolism/immunology
Female
Liver/metabolism/pathology

@article {pmid38731291,
year = {2024},
author = {Zhang, J and Xu, C and Wang, S and Wang, S and Li, Y},
title = {Variations in Genetic Diversity of Invasive Species Lithobates catesbeianus in China.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {9},
pages = {},
pmid = {38731291},
issn = {2076-2615},
support = {32030070//National Science Foundation of China/ ; 2019QZKK0501//Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; 050001-521100222045//the High-Level Talents Research Start-Up Project of Hebei University/ ; C2022201042//Hebei Natural Science Foundation/ ; Sino-BON//China's Biodiversity Observation Network/ ; },
abstract = {The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk.},
}

@article {pmid38713727,
year = {2024},
author = {K Raval, P and MacLeod, AI and Gould, SB},
title = {A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms.},
journal = {PLoS biology},
volume = {22},
number = {5},
pages = {e3002608},
pmid = {38713727},
issn = {1545-7885},
mesh = {*Plastids/metabolism/genetics ; *Magnoliopsida/genetics/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; *Phylogeny ; Evolution, Molecular ; Biological Evolution ; Mitochondria/metabolism/genetics ; Plant Proteins/metabolism/genetics ; Proteome/metabolism ; Symbiosis/genetics ; Organelles/metabolism/genetics ; },
abstract = {Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.},
}

*Plastids/metabolism/genetics
*Magnoliopsida/genetics/metabolism
*Mitochondrial Proteins/metabolism/genetics
*Phylogeny
Evolution, Molecular
Biological Evolution
Mitochondria/metabolism/genetics
Plant Proteins/metabolism/genetics
Proteome/metabolism
Symbiosis/genetics
Organelles/metabolism/genetics

@article {pmid38692277,
year = {2024},
author = {Kumar, A and Gok, MO and Nguyen, KN and Connor, OM and Reese, ML and Wideman, JG and Muñoz-Gómez, SA and Friedman, JR},
title = {A dynamin superfamily-like pseudoenzyme coordinates with MICOS to promote cristae architecture.},
journal = {Current biology : CB},
volume = {34},
number = {12},
pages = {2606-2622.e9},
pmid = {38692277},
issn = {1879-0445},
support = {S10 OD021685/OD/NIH HHS/United States ; S10 OD028630/OD/NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; R01 AI150715/AI/NIAID NIH HHS/United States ; R21 AI171227/AI/NIAID NIH HHS/United States ; R35 GM137894/GM/NIGMS NIH HHS/United States ; },
mesh = {*Schizosaccharomyces/metabolism/genetics ; *Schizosaccharomyces pombe Proteins/metabolism/genetics ; *Mitochondrial Membranes/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; Dynamins/metabolism/genetics ; Mitochondria/metabolism ; Mitochondria Associated Membranes ; },
abstract = {Mitochondrial cristae architecture is crucial for optimal respiratory function of the organelle. Cristae shape is maintained in part by the mitochondrial contact site and cristae organizing system (MICOS) complex. While MICOS is required for normal cristae morphology, the precise mechanistic role of each of the seven human MICOS subunits, and how the complex coordinates with other cristae-shaping factors, has not been fully determined. Here, we examine the MICOS complex in Schizosaccharomyces pombe, a minimal model whose genome only encodes for four core subunits. Using an unbiased proteomics approach, we identify a poorly characterized inner mitochondrial membrane protein that interacts with MICOS and is required to maintain cristae morphology, which we name Mmc1. We demonstrate that Mmc1 works in concert with MICOS to promote normal mitochondrial morphology and respiratory function. Mmc1 is a distant relative of the dynamin superfamily of proteins (DSPs), GTPases, which are well established to shape and remodel membranes. Similar to DSPs, Mmc1 self-associates and forms high-molecular-weight assemblies. Interestingly, however, Mmc1 is a pseudoenzyme that lacks key residues required for GTP binding and hydrolysis, suggesting that it does not dynamically remodel membranes. These data are consistent with the model that Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane. Our study reveals a new class of proteins that evolved early in fungal phylogeny and is required for the maintenance of cristae architecture. This highlights the possibility that functionally analogous proteins work with MICOS to establish cristae morphology in metazoans.},
}

*Schizosaccharomyces/metabolism/genetics
*Schizosaccharomyces pombe Proteins/metabolism/genetics
*Mitochondrial Membranes/metabolism
*Mitochondrial Proteins/metabolism/genetics
Dynamins/metabolism/genetics
Mitochondria/metabolism
Mitochondria Associated Membranes

@article {pmid38673928,
year = {2024},
author = {Aleshina, YA and Aleshin, VA},
title = {Evolutionary Changes in Primate Glutamate Dehydrogenases 1 and 2 Influence the Protein Regulation by Ligands, Targeting and Posttranslational Modifications.},
journal = {International journal of molecular sciences},
volume = {25},
number = {8},
pages = {},
pmid = {38673928},
issn = {1422-0067},
support = {23-74-10036//Russian Science Foundation/ ; },
mesh = {Animals ; Humans ; *Evolution, Molecular ; *Glutamate Dehydrogenase/metabolism/genetics/chemistry ; Ligands ; Mutation ; Primates/genetics ; *Protein Processing, Post-Translational ; },
abstract = {There are two paralogs of glutamate dehydrogenase (GDH) in humans encoded by the GLUD1 and GLUD2 genes as a result of a recent retroposition during the evolution of primates. The two human GDHs possess significantly different regulation by allosteric ligands, which is not fully characterized at the structural level. Recent advances in identification of the GDH ligand binding sites provide a deeper perspective on the significance of the accumulated substitutions within the two GDH paralogs. In this review, we describe the evolution of GLUD1 and GLUD2 after the duplication event in primates using the accumulated sequencing and structural data. A new gibbon GLUD2 sequence questions the indispensability of ancestral R496S and G509A mutations for GLUD2 irresponsiveness to GTP, providing an alternative with potentially similar regulatory features. The data of both GLUD1 and GLUD2 evolution not only confirm substitutions enhancing GLUD2 mitochondrial targeting, but also reveal a conserved mutation in ape GLUD1 mitochondrial targeting sequence that likely reduces its transport to mitochondria. Moreover, the information of GDH interactors, posttranslational modification and subcellular localization are provided for better understanding of the GDH mutations. Medically significant point mutations causing deregulation of GDH are considered from the structural and regulatory point of view.},
}

Animals
Humans
*Evolution, Molecular
*Glutamate Dehydrogenase/metabolism/genetics/chemistry
Ligands
Mutation
Primates/genetics
*Protein Processing, Post-Translational

@article {pmid38668970,
year = {2024},
author = {Muthye, V and Lavrov, DV},
title = {Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2757},
number = {},
pages = {239-257},
pmid = {38668970},
issn = {1940-6029},
mesh = {Animals ; *Ctenophora/metabolism/genetics ; *Proteome ; *Mitochondrial Proteins/metabolism/genetics ; Computational Biology/methods ; Mitochondria/metabolism ; Proteomics/methods ; Software ; },
abstract = {Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.},
}

Animals
*Ctenophora/metabolism/genetics
*Proteome
*Mitochondrial Proteins/metabolism/genetics
Computational Biology/methods
Mitochondria/metabolism
Proteomics/methods
Software

@article {pmid38668357,
year = {2024},
author = {Martinez, P and Baghli, I and Gourjon, G and Seyfried, TN},
title = {Mitochondrial-Stem Cell Connection: Providing Additional Explanations for Understanding Cancer.},
journal = {Metabolites},
volume = {14},
number = {4},
pages = {},
pmid = {38668357},
issn = {2218-1989},
abstract = {The cancer paradigm is generally based on the somatic mutation model, asserting that cancer is a disease of genetic origin. The mitochondrial-stem cell connection (MSCC) proposes that tumorigenesis may result from an alteration of the mitochondria, specifically a chronic oxidative phosphorylation (OxPhos) insufficiency in stem cells, which forms cancer stem cells (CSCs) and leads to malignancy. Reviewed evidence suggests that the MSCC could provide a comprehensive understanding of all the different stages of cancer. The metabolism of cancer cells is altered (OxPhos insufficiency) and must be compensated by using the glycolysis and the glutaminolysis pathways, which are essential to their growth. The altered mitochondria regulate the tumor microenvironment, which is also necessary for cancer evolution. Therefore, the MSCC could help improve our understanding of tumorigenesis, metastases, the efficiency of standard treatments, and relapses.},
}

@article {pmid38658571,
year = {2024},
author = {Xing, L and Gkini, V and Nieminen, AI and Zhou, HC and Aquilino, M and Naumann, R and Reppe, K and Tanaka, K and Carmeliet, P and Heikinheimo, O and Pääbo, S and Huttner, WB and Namba, T},
title = {Functional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3468},
pmid = {38658571},
issn = {2041-1723},
support = {340179, 351966, 336234//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Neocortex/metabolism/embryology/growth & development/cytology ; Humans ; Animals ; *Glutamate Dehydrogenase/metabolism/genetics ; *GTPase-Activating Proteins/metabolism/genetics ; Ketoglutaric Acids/metabolism ; Neuroglia/metabolism ; Glutamic Acid/metabolism ; Mitochondria/metabolism/genetics ; Mice ; Citric Acid Cycle/genetics ; Female ; },
abstract = {Metabolism has recently emerged as a major target of genes implicated in the evolutionary expansion of human neocortex. One such gene is the human-specific gene ARHGAP11B. During human neocortex development, ARHGAP11B increases the abundance of basal radial glia, key progenitors for neocortex expansion, by stimulating glutaminolysis (glutamine-to-glutamate-to-alpha-ketoglutarate) in mitochondria. Here we show that the ape-specific protein GLUD2 (glutamate dehydrogenase 2), which also operates in mitochondria and converts glutamate-to-αKG, enhances ARHGAP11B's ability to increase basal radial glia abundance. ARHGAP11B + GLUD2 double-transgenic bRG show increased production of aspartate, a metabolite essential for cell proliferation, from glutamate via alpha-ketoglutarate and the TCA cycle. Hence, during human evolution, a human-specific gene exploited the existence of another gene that emerged during ape evolution, to increase, via concerted changes in metabolism, progenitor abundance and neocortex size.},
}

*Neocortex/metabolism/embryology/growth & development/cytology
Humans
Animals
*Glutamate Dehydrogenase/metabolism/genetics
*GTPase-Activating Proteins/metabolism/genetics
Ketoglutaric Acids/metabolism
Neuroglia/metabolism
Glutamic Acid/metabolism
Mitochondria/metabolism/genetics
Mice
Citric Acid Cycle/genetics
Female

@article {pmid38658152,
year = {2024},
author = {Fan, C and Yang, J and Chen, R and Liu, W and Xiang, X},
title = {[Identification and expression analysis of the HSP70 gene family under abiotic stresses in Litchi chinensis].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {40},
number = {4},
pages = {1102-1119},
doi = {10.13345/j.cjb.230450},
pmid = {38658152},
issn = {1872-2075},
mesh = {*Litchi/genetics/metabolism ; *HSP70 Heat-Shock Proteins/genetics/metabolism ; *Stress, Physiological/genetics ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism/biosynthesis ; *Phylogeny ; *Droughts ; Multigene Family ; Salt Stress/genetics ; },
abstract = {HSP70 protein, as an important member of the heat shock protein (HSP) family, plays an important role in plant growth, development, and response to biotic and abiotic stresses. In order to explore the role of HSP70 gene family members in Litchi chinensis under low temperature, high temperature, drought, and salt stress, bioinformatics methods were used to identify the HSP70 gene family members within the entire L. chinensis genome. The expression of these genes under various abiotic stresses was then detected using quantitative real-time PCR (qRT-PCR). The results showed that the LcHSP70 gene family consisted of 18 members, which were unevenly distributed across ten L. chinensis chromosomes. The LcHSP70 protein contained 479-851 amino acids, with isoelectric points ranging from 5.07 to 6.95, and molecular weights from 52.44 kDa to 94.07 kDa. The predicted subcellular localization showed that LcHSP70 protein was present in the nucleus, cytoplasm, endoplasmic reticulum, mitochondria, and chloroplast. Phylogenetic analysis divided the LcHSP70 proteins into five subgroups, namely Ⅰ, Ⅱ, Ⅲ, Ⅳ, and Ⅵ. The promoter regions of the LcHSP70 genes contained various cis-acting elements related to plant growth, development, hormone response, and stress response. Moreover, the expression of LcHSP70 genes displayed distint tissue-specific expression level, categorized into universal expression and specific expression. From the selected 6 LcHSP70 genes (i.e., LcHSP70-1, LcHSP70-5, LcHSP70-10, LcHSP70-14, LcHSP70-16, and LcHSP70-18), their relative expression levels were assessed under different abiotic stresses using qRT-PCR. The results indicated that the gene family members exhibited diverse responses to low temperature, high temperature, drought, and salt stress, with significant variations in their expression levels across different time periods. These results provide a foundation for further exploration of the function of the LcHSP70 gene family.},
}

*Litchi/genetics/metabolism
*HSP70 Heat-Shock Proteins/genetics/metabolism
*Stress, Physiological/genetics
*Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism/biosynthesis
*Phylogeny
*Droughts
Multigene Family
Salt Stress/genetics

@article {pmid38652016,
year = {2024},
author = {Kwok van der Giezen, FM and Viljoen, A and Campbell-Clause, L and Dao, NT and Colas des Francs-Small, C and Small, I},
title = {Insights into U-to-C RNA editing from the lycophyte Phylloglossum drummondii.},
journal = {The Plant journal : for cell and molecular biology},
volume = {119},
number = {1},
pages = {445-459},
doi = {10.1111/tpj.16775},
pmid = {38652016},
issn = {1365-313X},
support = {DP200102981//Australian Research Council/ ; },
mesh = {*RNA Editing/genetics ; *RNA, Plant/genetics ; Genome, Mitochondrial/genetics ; Transcriptome ; Uridine/metabolism/genetics ; Genome, Chloroplast ; Phylogeny ; Mitochondria/genetics/metabolism ; },
abstract = {The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U-to-C RNA editing enzymes. Four putative U-to-C editing factors could be matched to the four mitochondrial U-to-C editing sites. Due to the unusually few numbers of U-to-C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.},
}

*RNA Editing/genetics
*RNA, Plant/genetics
Genome, Mitochondrial/genetics
Transcriptome
Uridine/metabolism/genetics
Genome, Chloroplast
Phylogeny
Mitochondria/genetics/metabolism

@article {pmid38630841,
year = {2024},
author = {Gonzalez, RC and Bezerra de Lima, LC and Passos, P and Silva, MJJ},
title = {The good, the bad and the boa: An unexpected new species of a true boa revealed by morphological and molecular evidence.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0298159},
pmid = {38630841},
issn = {1932-6203},
mesh = {Animals ; Male ; Phylogeny ; *Boidae/genetics ; Mitochondria/genetics ; Brazil ; *Lepidoptera ; },
abstract = {Snakes of the genus Boa are outstanding elements of the New World biota with a broad sociological influence on pop culture. Historically, several taxa have been recognized in the past 300 years, being mostly described in the early days of binomial nomenclature. As a rule, these taxa were recognized based on a suite of phenotypic characters mainly those from the external morphology. However, there is a huge disagreement with respect to the current taxonomy and available molecular phylogenies. In order to reconcile both lines of evidence, we investigate the phylogenetic reconstruction (using mitochondrial and nuclear genes) of the genus in parallel to the detailed study of some phenotypic systems from a geographically representative sample of the cis-Andean mainland Boa constrictor. We used cyt-b only (744bp) from 73 samples, and cyt-b, ND4, NTF3, and ODC partial sequences (in a total of 2305 bp) from 35 samples, comprising nine currently recognized taxa (species or subspecies), to infer phylogenetic relationships of boas. Topologies recovered along all the analyses and genetic distances obtained allied to a unique combination of morphological traits (colouration, pholidosis, meristic, morphometric, and male genitalia features) allowed us to recognize B. constrictor lato sensu, B. nebulosa, B. occidentalis, B. orophias and a distinct lineage from the eastern coast of Brazil, which we describe here as a new species, diagnosing it from the previously recognized taxa. Finally, we discuss the minimally necessary changes in the taxonomy of Boa constrictor complex; the value of some usually disregarded phenotypic character system; and we highlight the urgency of continuing environmental policy to preserve one of the most impacted Brazilian hotspots, the Atlantic Forest, which represents an ecoregion full of endemism.},
}

Animals
Male
Phylogeny
*Boidae/genetics
Mitochondria/genetics
Brazil
*Lepidoptera

@article {pmid38611479,
year = {2024},
author = {Qian, F and Zuo, D and Zeng, T and Gu, L and Wang, H and Du, X and Zhu, B and Ou, J},
title = {Identification, Evolutionary Dynamics, and Gene Expression Patterns of the ACP Gene Family in Responding to Salt Stress in Brassica Genus.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611479},
issn = {2223-7747},
support = {32060463//National Natural Science Foundation of China/ ; 32260460//National Natural Science Foundation of China/ ; Qian Kehe Support [2022] key 026//Guizhou Provincial Science and Technology Plan Project/ ; Qiankehezhicheng【2022】Key 031//The Scientific and Technological Key Program of Guizhou province/ ; },
abstract = {Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes.},
}

@article {pmid38603509,
year = {2024},
author = {Coale, TH and Loconte, V and Turk-Kubo, KA and Vanslembrouck, B and Mak, WKE and Cheung, S and Ekman, A and Chen, JH and Hagino, K and Takano, Y and Nishimura, T and Adachi, M and Le Gros, M and Larabell, C and Zehr, JP},
title = {Nitrogen-fixing organelle in a marine alga.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6692},
pages = {217-222},
doi = {10.1126/science.adk1075},
pmid = {38603509},
issn = {1095-9203},
mesh = {*Cyanobacteria/genetics/metabolism ; *Haptophyta/microbiology ; *Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Seawater/microbiology ; Symbiosis ; *Mitochondria/metabolism ; Chloroplasts/metabolism ; },
abstract = {Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N2) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N2-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle, or "nitroplast."},
}

*Cyanobacteria/genetics/metabolism
*Haptophyta/microbiology
*Nitrogen/metabolism
*Nitrogen Fixation/genetics
Seawater/microbiology
Symbiosis
*Mitochondria/metabolism
Chloroplasts/metabolism

@article {pmid38601302,
year = {2024},
author = {Fukasawa, Y and Driguez, P and Bougouffa, S and Carty, K and Putra, A and Cheung, MS and Ermini, L},
title = {Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1339594},
pmid = {38601302},
issn = {1664-462X},
abstract = {The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.},
}

@article {pmid38597829,
year = {2024},
author = {Regina-Ferreira, L and Valdivieso-Rivera, F and Angelim, MKSC and Menezes Dos Reis, L and Furino, VO and Morari, J and Maia de Sousa, L and Consonni, SR and Sponton, CH and Moraes-Vieira, PM and Velloso, LA},
title = {Inhibition of Crif1 protects fatty acid-induced POMC neuron-like cell-line damage by increasing CPT-1 function.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {326},
number = {5},
pages = {E681-E695},
doi = {10.1152/ajpendo.00420.2023},
pmid = {38597829},
issn = {1522-1555},
support = {2013/07607-8//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; },
mesh = {Animals ; Mice ; *Carnitine O-Palmitoyltransferase/metabolism/genetics ; Cell Line ; *Fatty Acids/metabolism ; Hypothalamus/metabolism/drug effects ; *Mitochondria/metabolism/drug effects ; Neurons/drug effects/metabolism ; Pro-Opiomelanocortin/metabolism/genetics ; Reactive Oxygen Species/metabolism ; *Cell Cycle Proteins/antagonists & inhibitors/metabolism ; },
abstract = {Hypothalamic proopiomelanocortin (POMC) neurons are sensors of signals that reflect the energy stored in the body. Inducing mild stress in proopiomelanocortin neurons protects them from the damage promoted by the consumption of a high-fat diet, mitigating the development of obesity; however, the cellular mechanisms behind these effects are unknown. Here, we induced mild stress in a proopiomelanocortin neuron cell line by inhibiting Crif1. In proopiomelanocortin neurons exposed to high levels of palmitate, the partial inhibition of Crif1 reverted the defects in mitochondrial respiration and ATP production; this was accompanied by improved mitochondrial fusion/fission cycling. Furthermore, the partial inhibition of Crif1 resulted in increased reactive oxygen species production, increased fatty acid oxidation, and reduced dependency on glucose for mitochondrial respiration. These changes were dependent on the activity of CPT-1. Thus, we identified a CPT-1-dependent metabolic shift toward greater utilization of fatty acids as substrates for respiration as the mechanism behind the protective effect of mild stress against palmitate-induced damage of proopiomelanocortin neurons.NEW & NOTEWORTHY Saturated fats can damage hypothalamic neurons resulting in positive energy balance, and this is mitigated by mild cellular stress; however, the mechanisms behind this protective effect are unknown. Using a proopiomelanocortin cell line, we show that under exposure to a high concentration of palmitate, the partial inhibition of the mitochondrial protein Crif1 results in protection due to a metabolic shift warranted by the increased expression and activity of the mitochondrial fatty acid transporter CPT-1.},
}

Animals
Mice
*Carnitine O-Palmitoyltransferase/metabolism/genetics
Cell Line
*Fatty Acids/metabolism
Hypothalamus/metabolism/drug effects
*Mitochondria/metabolism/drug effects
Neurons/drug effects/metabolism
Pro-Opiomelanocortin/metabolism/genetics
Reactive Oxygen Species/metabolism
*Cell Cycle Proteins/antagonists & inhibitors/metabolism

@article {pmid38594641,
year = {2024},
author = {Shen, B and Shen, A and Liu, L and Tan, Y and Li, S and Tan, Z},
title = {Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {255},
pmid = {38594641},
issn = {1471-2229},
support = {Xiangzi Caihuan Zhi (2022) No. 64; Xiangzi Caihuan Zhi (2022) No. 67; Xiangzi Caihuan Zhi (2023) No. 26; Xiangzi Caihuan Zhi (2023) No. 72//the Hunan Provincial Forestry Ecological Protection, Restoration and Development Special Fund Project/ ; 2023JJ50073//the Hunan Provincial Natural Science Foundation/ ; },
mesh = {*Genome, Mitochondrial/genetics ; Phylogeny ; Mitochondria/genetics ; DNA ; *Orchidaceae/genetics ; },
abstract = {BACKGROUND: Orchidaceae is one of the largest groups of angiosperms, and most species have high economic value and scientific research value due to their ornamental and medicinal properties. In China, Chinese Cymbidium is a popular ornamental orchid with high economic value and a long history. However, to date, no detailed information on the mitochondrial genome of any species of Chinese Cymbidium has been published.

RESULTS: Here, we present the complete assembly and annotation of the mitochondrial genome of Cymbidium ensifolium (L.) Sw. The mitogenome of C. ensifolium was 560,647 bp in length and consisted of 19 circular subgenomes ranging in size from 21,995 bp to 48,212 bp. The genome encoded 35 protein-coding genes, 36 tRNAs, 3 rRNAs, and 3405 ORFs. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 915 dispersed repeats, 162 simple repeats, 45 tandem repeats, and 530 RNA editing sites. Analysis of codon usage showed a preference for codons ending in A/T. Interorganellar DNA transfer was identified in 13 of the 19 chromosomes, with plastid-derived DNA fragments representing 6.81% of the C. ensifolium mitochondrial genome. The homologous fragments of the mitochondrial genome and nuclear genome were also analysed. Comparative analysis showed that the GC content was conserved, but the size, structure, and gene content of the mitogenomes varied greatly among plants with multichromosomal mitogenome structure. Phylogenetic analysis based on the mitogenomes reflected the evolutionary and taxonomic statuses of C. ensifolium. Interestingly, compared with the mitogenomes of Cymbidium lancifolium Hook. and Cymbidium macrorhizon Lindl., the mitogenome of C. ensifolium lost 8 ribosomal protein-coding genes.

CONCLUSION: In this study, we assembled and annotated the mitogenome of C. ensifolium and compared it with the mitogenomes of other Liliidae and plants with multichromosomal mitogenome structures. Our findings enrich the mitochondrial genome database of orchid plants and reveal the rapid structural evolution of Cymbidium mitochondrial genomes, highlighting the potential for mitochondrial genes to help decipher plant evolutionary history.},
}

*Genome, Mitochondrial/genetics
Phylogeny
Mitochondria/genetics
DNA
*Orchidaceae/genetics

@article {pmid38592734,
year = {2024},
author = {Kwasniak-Owczarek, M and Janska, H},
title = {Experimental approaches to studying translation in plant semi-autonomous organelles.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erae151},
pmid = {38592734},
issn = {1460-2431},
abstract = {Plant mitochondria and chloroplasts are semi-autonomous organelles originated from free-living bacteria and retaining respective reduced genomes during evolution. As a consequence, relatively few of the mitochondrial and chloroplast proteins are encoded in the organellar genomes and synthesized by the organellar ribosomes. Since the both organellar genomes encode mainly components of the energy transduction systems, oxidative phosphorylation in mitochondria and photosynthetic apparatus in chloroplasts, understanding the organellar translation is critical to a thorough comprehension of the key aspects of mitochondrial and chloroplast activity affecting plant growth and development. Recent studies have clearly shown that translation is a key regulatory node in the expression of plant organellar genes, underscoring the need for an adequate methodology to study this unique stage of gene expression. The organellar translatome can be analysed by studying newly synthesized proteins or the mRNA pool recruited to the organellar ribosomes. In this review, we present in some detail the experimental approaches used to date for studying translation in the plant bioenergetic organelles. Their benefits and limitations, as well as the critical steps are discussed. Additionally, we briefly mention several recently developed strategies to study organellar translation that have not yet been applied to plants.},
}

@article {pmid38587065,
year = {2024},
author = {Shen, C and Xu, H and Huang, WZ and Zhao, Q and Zhu, RL},
title = {Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum.},
journal = {The New phytologist},
volume = {242},
number = {6},
pages = {2817-2831},
doi = {10.1111/nph.19750},
pmid = {38587065},
issn = {1469-8137},
support = {//East China Normal University/ ; 31970215//National Natural Science Foundation of China/ ; 32370218//National Natural Science Foundation of China/ ; },
mesh = {*RNA Editing/genetics ; *Hepatophyta/genetics ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Mitochondria/genetics/metabolism ; Genes, Plant ; Amino Acid Sequence ; },
abstract = {RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.},
}

*RNA Editing/genetics
*Hepatophyta/genetics
*Phylogeny
Plant Proteins/genetics/metabolism
Chloroplasts/genetics/metabolism
Mitochondria/genetics/metabolism
Genes, Plant
Amino Acid Sequence

@article {pmid38568891,
year = {2024},
author = {D'Ercole, J and Dapporto, L and Opler, P and Schmidt, CB and Ho, C and Menchetti, M and Zakharov, EV and Burns, JM and Hebert, PDN},
title = {A genetic atlas for the butterflies of continental Canada and United States.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0300811},
pmid = {38568891},
issn = {1932-6203},
mesh = {Animals ; United States ; *Butterflies/genetics ; Phylogeography ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; Haplotypes ; Genetic Variation ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.},
}

Animals
United States
*Butterflies/genetics
Phylogeography
DNA, Mitochondrial/genetics/chemistry
Mitochondria/genetics
Haplotypes
Genetic Variation
DNA Barcoding, Taxonomic
Phylogeny

@article {pmid38561677,
year = {2024},
author = {Chen, L and Dong, X and Huang, H and Xu, H and Rono, PC and Cai, X and Hu, G},
title = {Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {322},
pmid = {38561677},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; Phylogeny ; DNA, Mitochondrial/genetics ; *Lamiales/genetics ; Mitochondria/genetics ; *Genome, Chloroplast ; },
abstract = {BACKGROUND: Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported.

RESULTS: In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted.

CONCLUSIONS: This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.},
}

*Genome, Mitochondrial
Phylogeny
DNA, Mitochondrial/genetics
*Lamiales/genetics
Mitochondria/genetics
*Genome, Chloroplast

@article {pmid38555796,
year = {2024},
author = {Casimir, P and Iwata, R and Vanderhaeghen, P},
title = {Linking mitochondria metabolism, developmental timing, and human brain evolution.},
journal = {Current opinion in genetics & development},
volume = {86},
number = {},
pages = {102182},
pmid = {38555796},
issn = {1879-0380},
mesh = {Humans ; *Mitochondria/metabolism/genetics ; *Brain/growth & development/metabolism ; Animals ; *Biological Evolution ; *Neurons/metabolism/cytology ; Species Specificity ; Neurogenesis/genetics ; Mice ; },
abstract = {Changes in developmental timing are an important factor of evolution in organ shape and function. This is particularly striking for human brain development, which, compared with other mammals, is considerably prolonged at the level of the cerebral cortex, resulting in brain neoteny. Here, we review recent findings that indicate that mitochondria and metabolism contribute to species differences in the tempo of cortical neuron development. Mitochondria display species-specific developmental timeline and metabolic activity patterns that are highly correlated with the speed of neuron maturation. Enhancing mitochondrial activity in human cortical neurons results in their accelerated maturation, while its reduction leads to decreased maturation rates in mouse neurons. Together with other global and gene-specific mechanisms, mitochondria thus act as a cellular hourglass of neuronal developmental tempo and may thereby contribute to species-specific features of human brain ontogeny.},
}

Humans
*Mitochondria/metabolism/genetics
*Brain/growth & development/metabolism
Animals
*Biological Evolution
*Neurons/metabolism/cytology
Species Specificity
Neurogenesis/genetics
Mice

@article {pmid38554118,
year = {2024},
author = {Laugier, F and Saclier, N and Béthune, K and Braun, A and Konecny, L and Lefébure, T and Luquet, E and Plénet, S and Romiguier, J and David, P},
title = {Both nuclear and cytoplasmic polymorphisms are involved in genetic conflicts over male fertility in the gynodioecious snail, Physa acuta.},
journal = {Evolution; international journal of organic evolution},
volume = {78},
number = {7},
pages = {1227-1236},
doi = {10.1093/evolut/qpae053},
pmid = {38554118},
issn = {1558-5646},
support = {ANR-19-CE02-0017//MINIGAN/ ; //French National Research Agency/ ; },
mesh = {Animals ; *Polymorphism, Genetic ; Male ; *Snails/genetics/physiology ; *Genome, Mitochondrial ; Cell Nucleus/genetics ; Fertility/genetics ; Hermaphroditic Organisms/genetics ; Evolution, Molecular ; Female ; Cytoplasm/genetics ; Infertility, Male/genetics ; },
abstract = {Gynodioecy, the coexistence of hermaphrodites with females, often reflects conflicts between cytoplasmic male sterility (CMS) genes and nuclear genes restoring male fertility. CMS is frequent in plants and has been recently discovered in one animal: the freshwater snail, Physa acuta. In this system, CMS was linked to a single divergent mitochondrial genome (D), devoid of apparent nuclear restoration. Our study uncovers a second, novel CMS-associated mitogenome (K) in Physa acuta, demonstrating an extraordinary acceleration of molecular evolution throughout the entire K mitochondrial genome, akin to the previously observed pattern in D. This suggests a pervasive occurrence of accelerated evolution in both CMS-associated lineages. Through a 17-generation introgression experiment, we further show that nuclear polymorphisms in K-mitogenome individuals contribute to the restoration of male function in natural populations. Our results underscore shared characteristics in gynodioecy between plants and animals, emphasizing the presence of multiple CMS mitotypes and cytonuclear conflicts. This reaffirms the pivotal role of mitochondria in influencing male function and in generating genomic conflicts that impact reproductive processes in animals.},
}

Animals
*Polymorphism, Genetic
Male
*Snails/genetics/physiology
*Genome, Mitochondrial
Cell Nucleus/genetics
Fertility/genetics
Hermaphroditic Organisms/genetics
Evolution, Molecular
Female
Cytoplasm/genetics
Infertility, Male/genetics

@article {pmid38548188,
year = {2024},
author = {He, X and Qian, Z and Gichira, AW and Chen, J and Li, Z},
title = {Assembly and comparative analysis of the first complete mitochondrial genome of the invasive water hyacinth, Eichhornia crassipes.},
journal = {Gene},
volume = {914},
number = {},
pages = {148416},
doi = {10.1016/j.gene.2024.148416},
pmid = {38548188},
issn = {1879-0038},
mesh = {*Genome, Mitochondrial ; *Eichhornia/genetics ; *Phylogeny ; Introduced Species ; RNA, Transfer/genetics ; Base Composition ; RNA Editing ; Genome, Plant ; },
abstract = {Eichhornia crassipes is an aquatic plant in tropical and subtropical regions, renowned for its notorious invasive tendencies. In this study, we assembled the complete mitogenome of E. crassipes into a single circle molecule of 397,361 bp. The mitogenome has 58 unique genes, including 37 protein-coding genes (PCGs), 18 tRNA genes, three rRNA genes, and 47 % GC content. Sixteen (6.93 %) homologous fragments, ranging from 31 bp to 8548 bp, were identified, indicating the transfer of genetic material from chloroplasts to mitochondria. In addition, we detected positive selection in six PCGs (ccmB, ccmC, ccmFC, nad3, nad4 and sdh4), along with the identification of 782 RNA editing sites across 37 mt-PCGs. These findings suggest a potential contribution to the robust adaptation of this invasive plant to the stressful environment. Lastly, we inferred that phylogenetic conflicts of E. crassipes between the plastome and mitogenome may be attributed to the difference in nucleotide substitution rates between the two organelle genomes. In conclusion, our study provided vital genomic resources for further understanding the invasive mechanism of this species and exploring the dynamic evolution of mitogenomes within the monocot clade.},
}

*Genome, Mitochondrial
*Eichhornia/genetics
*Phylogeny
Introduced Species
RNA, Transfer/genetics
Base Composition
RNA Editing
Genome, Plant

@article {pmid38547729,
year = {2024},
author = {Queiroz, MIC and Lazaro, CM and Dos Santos, LMB and Rentz, T and Virgilio-da-Silva, JV and Moraes-Vieira, PMM and Cunha, FAS and Santos, JCC and Vercesi, AE and Leite, ACR and Oliveira, HCF},
title = {In vivo chronic exposure to inorganic mercury worsens hypercholesterolemia, oxidative stress and atherosclerosis in the LDL receptor knockout mice.},
journal = {Ecotoxicology and environmental safety},
volume = {275},
number = {},
pages = {116254},
doi = {10.1016/j.ecoenv.2024.116254},
pmid = {38547729},
issn = {1090-2414},
mesh = {Animals ; Mice ; *Atherosclerosis/chemically induced ; Hydrogen Peroxide ; *Hypercholesterolemia ; Kidney Diseases ; *Mercury/toxicity ; Mice, Knockout ; Oxidative Stress/physiology ; Receptors, LDL/genetics ; },
abstract = {Heavy metal exposure leads to multiple system dysfunctions. The mechanisms are likely multifactorial and involve inflammation and oxidative stress. The aim of this study was to evaluate markers and risk factors for atherosclerosis in the LDL receptor knockout mouse model chronically exposed to inorganic mercury (Hg) in the drinking water. Results revealed that Hg exposed mice present increased plasma levels of cholesterol, without alterations in glucose. As a major source and target of oxidants, we evaluated mitochondrial function. We found that liver mitochondria from Hg treated mice show worse respiratory control, lower oxidative phosphorylation efficiency and increased H2O2 release. In addition, Hg induced mitochondrial membrane permeability transition. Erythrocytes from Hg treated mice showed a 50% reduction in their ability to take up oxygen, lower levels of reduced glutathione (GSH) and of antioxidant enzymes (SOD, catalase and GPx). The Hg treatment disturbed immune system cells counting and function. While lymphocytes were reduced, monocytes, eosinophils and neutrophils were increased. Peritoneal macrophages from Hg treated mice showed increased phagocytic activity. Hg exposed mice tissues present metal impregnation and parenchymal architecture alterations. In agreement, increased systemic markers of liver and kidney dysfunction were observed. Plasma, liver and kidney oxidative damage indicators (MDA and carbonyl) were increased while GSH and thiol groups were diminished by Hg exposure. Importantly, atherosclerotic lesion size in the aorta root of Hg exposed mice were larger than in controls. In conclusion, in vivo chronic exposure to Hg worsens the hypercholesterolemia, impairs mitochondrial bioenergetics and redox function, alters immune cells profile and function, causes several tissues oxidative damage and accelerates atherosclerosis development.},
}

Animals
Mice
*Atherosclerosis/chemically induced
Hydrogen Peroxide
*Hypercholesterolemia
Kidney Diseases
*Mercury/toxicity
Mice, Knockout
Oxidative Stress/physiology
Receptors, LDL/genetics

@article {pmid38547143,
year = {2024},
author = {Charrasse, S and Racine, V and Saint-Omer, C and Poquillon, T and Lionnard, L and Ledru, M and Gonindard, C and Delaunois, S and Kissa, K and Frye, RE and Pastore, M and Reynes, C and Frechet, M and Chajra, H and Aouacheria, A},
title = {Quantitative imaging and semiotic phenotyping of mitochondrial network morphology in live human cells.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0301372},
pmid = {38547143},
issn = {1932-6203},
mesh = {Humans ; *Hydrogen Peroxide/pharmacology/metabolism ; *Mitochondria/metabolism ; Software ; Image Processing, Computer-Assisted/methods ; Algorithms ; },
abstract = {The importance of mitochondria in tissue homeostasis, stress responses and human diseases, combined to their ability to transition between various structural and functional states, makes them excellent organelles for monitoring cell health. There is therefore a need for technologies to accurately analyze and quantify changes in mitochondrial organization in a variety of cells and cellular contexts. Here we present an innovative computerized method that enables accurate, multiscale, fast and cost-effective analysis of mitochondrial shape and network architecture from confocal fluorescence images by providing more than thirty features. In order to facilitate interpretation of the quantitative results, we introduced two innovations: the use of Kiviat-graphs (herein named MitoSpider plots) to present highly multidimensional data and visualization of the various mito-cellular configurations in the form of morphospace diagrams (called MitoSigils). We tested our fully automated image analysis tool on rich datasets gathered from live normal human skin cells cultured under basal conditions or exposed to specific stress including UVB irradiation and pesticide exposure. We demonstrated the ability of our proprietary software (named MitoTouch) to sensitively discriminate between control and stressed dermal fibroblasts, and between normal fibroblasts and other cell types (including cancer tissue-derived fibroblasts and primary keratinocytes), showing that our automated analysis captures subtle differences in morphology. Based on this novel algorithm, we report the identification of a protective natural ingredient that mitigates the deleterious impact of hydrogen peroxide (H2O2) on mitochondrial organization. Hence we conceived a novel wet-plus-dry pipeline combining cell cultures, quantitative imaging and semiotic analysis for exhaustive analysis of mitochondrial morphology in living adherent cells. Our tool has potential for broader applications in other research areas such as cell biology and medicine, high-throughput drug screening as well as predictive and environmental toxicology.},
}

Humans
*Hydrogen Peroxide/pharmacology/metabolism
*Mitochondria/metabolism
Software
Image Processing, Computer-Assisted/methods
Algorithms

@article {pmid38543688,
year = {2024},
author = {Ramos-González, PL and Alexandre, MAV and Potsclam-Barro, M and Duarte, LML and Michea Gonzalez, GL and Chabi-Jesus, C and Ramos, AF and Harakava, R and Lorenzi, H and Freitas-Astúa, J and Kitajima, EW},
title = {Two Novel Betarhabdovirins Infecting Ornamental Plants and the Peculiar Intracellular Behavior of the Cytorhabdovirus in the Liana Aristolochia gibertii.},
journal = {Viruses},
volume = {16},
number = {3},
pages = {},
pmid = {38543688},
issn = {1999-4915},
support = {PNPD20132154 - 33141010001P4 - PNPD - IBSP, 88882.157041/2017-01//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 17/50334-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/25078-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/02179-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {*Aristolochia/genetics ; *Mirabilis/genetics ; Genome, Viral ; *Rhabdoviridae ; Plants/genetics ; Phylogeny ; Plant Diseases ; },
abstract = {Two novel members of the subfamily Betarhabdovirinae, family Rhabdoviridae, were identified in Brazil. Overall, their genomes have the typical organization 3'-N-P-P3-M-G-L-5' observed in mono-segmented plant-infecting rhabdoviruses. In aristolochia-associated cytorhabdovirus (AaCV), found in the liana aristolochia (Aristolochia gibertii Hook), an additional short orphan ORF encoding a transmembrane helix was detected between P3 and M. The AaCV genome and inferred encoded proteins share the highest identity values, consistently < 60%, with their counterparts of the yerba mate chlorosis-associated virus (Cytorhabdovirus flaviyerbamate). The second virus, false jalap virus (FaJV), was detected in the herbaceous plant false jalap (Mirabilis jalapa L.) and represents together with tomato betanucleorhabdovirus 2, originally found in tomato plants in Slovenia, a tentative new species of the genus Betanucleorhabdovirus. FaJV particles accumulate in the perinuclear space, and electron-lucent viroplasms were observed in the nuclei of the infected cells. Notably, distinct from typical rhabdoviruses, most virions of AaCV were observed to be non-enclosed within membrane-bounded cavities. Instead, they were frequently seen in close association with surfaces of mitochondria or peroxisomes. Unlike FaJV, AaCV was successfully graft-transmitted to healthy plants of three species of the genus Aristolochia, while mechanical and seed transmission proved unsuccessful for both viruses. Data suggest that these viruses belong to two new tentative species within the subfamily Betarhabdovirinae.},
}

*Aristolochia/genetics
*Mirabilis/genetics
Genome, Viral
*Rhabdoviridae
Plants/genetics
Phylogeny
Plant Diseases

@article {pmid38540407,
year = {2024},
author = {Zhang, G and Jiao, Y and Zhao, Z and Chen, Q and Wang, Z and Zhu, J and Lv, N and Sun, G},
title = {Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum.},
journal = {Genes},
volume = {15},
number = {3},
pages = {},
pmid = {38540407},
issn = {2073-4425},
mesh = {*Gossypium/metabolism ; *Verticillium/genetics ; Phylogeny ; Disease Resistance/genetics ; Chromosome Mapping ; },
abstract = {Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton.},
}

*Gossypium/metabolism
*Verticillium/genetics
Phylogeny
Disease Resistance/genetics
Chromosome Mapping

@article {pmid38534456,
year = {2024},
author = {Casey, W and Kumaran, T and Massey, SE and Mishra, B},
title = {How Mitochondrial Signaling Games May Shape and Stabilize the Nuclear-Mitochondrial Symbiosis.},
journal = {Biology},
volume = {13},
number = {3},
pages = {},
pmid = {38534456},
issn = {2079-7737},
abstract = {The eukaryotic lineage has enjoyed a long-term "stable" mutualism between nucleus and mitochondrion, since mitochondrial endosymbiosis began about 2 billion years ago. This mostly cooperative interaction has provided the basis for eukaryotic expansion and diversification, which has profoundly altered the forms of life on Earth. While we ignore the exact biochemical details of how the alpha-proteobacterial ancestor of mitochondria entered into endosymbiosis with a proto-eukaryote, in more general terms, we present a signaling games perspective of how the cooperative relationship became established, and has been maintained. While games are used to understand organismal evolution, information-asymmetric games at the molecular level promise novel insights into endosymbiosis. Using a previously devised biomolecular signaling games approach, we model a sender-receiver information asymmetric game, in which the informed mitochondrial sender signals and the uninformed nuclear receiver may take actions (involving for example apoptosis, senescence, regeneration and autophagy/mitophagy). The simulation shows that cellularization is a stabilizing mechanism for Pareto efficient sender/receiver strategic interaction. In stark contrast, the extracellular environment struggles to maintain efficient outcomes, as senders are indifferent to the effects of their signals upon the receiver. Our hypothesis has translational implications, such as in cellular therapy, as mitochondrial medicine matures. It also inspires speculative conjectures about how an analogous human-AI endosymbiosis may be engineered.},
}

@article {pmid38531492,
year = {2024},
author = {López-Hervas, K and Santos, JC and Ron, SR and Betancourth-Cundar, M and Cannatella, DC and Tarvin, RD},
title = {Deep divergences among inconspicuously colored clades of Epipedobates poison frogs.},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108065},
doi = {10.1016/j.ympev.2024.108065},
pmid = {38531492},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Poison Frogs ; *Anura/genetics ; Mitochondria ; Ecuador ; },
abstract = {Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is ∼11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador. A Spanish translation of this text is available in the supplementary materials.},
}

Animals
Phylogeny
*Poison Frogs
*Anura/genetics
Mitochondria
Ecuador

@article {pmid38525035,
year = {2024},
author = {Krasovec, G and Horkan, HR and Quéinnec, É and Chambon, JP},
title = {Intrinsic apoptosis is evolutionarily divergent among metazoans.},
journal = {Evolution letters},
volume = {8},
number = {2},
pages = {267-282},
pmid = {38525035},
issn = {2056-3744},
abstract = {Apoptosis is regulated cell death that depends on caspases. A specific initiator caspase is involved upstream of each apoptotic signaling pathway. Characterized in nematode, fly, and mammals, intrinsic apoptosis is considered to be ancestral, conserved among animals, and depends on shared initiators: caspase-9, Apaf-1 and Bcl-2. However, the biochemical role of mitochondria, the pivotal function of cytochrome c and the modality of caspase activation remain highly heterogeneous and hide profound molecular divergence among apoptotic pathways in animals. Uncovering the phylogenetic history of apoptotic actors, especially caspases, is crucial to shed light on the evolutionary history of intrinsic apoptosis. Here, we demonstrate with phylogenetic analyses that caspase-9, the fundamental key of intrinsic apoptosis, is deuterostome-specific, while caspase-2 is ancestral to bilaterians. Our analysis of Bcl-2 and Apaf-1 confirms heterogeneity in functional organization of apoptotic pathways in animals. Our results support emergence of distinct intrinsic apoptotic pathways during metazoan evolution.},
}

@article {pmid38503840,
year = {2024},
author = {Duran, DP and Laroche, RA and Roman, SJ and Godwin, W and Herrmann, DP and Bull, E and Egan, SP},
title = {Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6617},
pmid = {38503840},
issn = {2045-2322},
mesh = {Animals ; Phylogeny ; *DNA, Mitochondrial/genetics ; Mitochondria ; Biodiversity ; *Coleoptera/genetics ; Species Specificity ; },
abstract = {In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.},
}

Animals
Phylogeny
*DNA, Mitochondrial/genetics
Mitochondria
Biodiversity
*Coleoptera/genetics
Species Specificity

@article {pmid38503345,
year = {2024},
author = {Nuryadi, H and Mandagi, IF and Masengi, KWA and Kusumi, J and Inomata, N and Yamahira, K},
title = {Evidence for hybridization-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake.},
journal = {Biology letters},
volume = {20},
number = {3},
pages = {20230385},
pmid = {38503345},
issn = {1744-957X},
mesh = {Humans ; Animals ; *Heteroplasmy ; Lakes ; Phylogeny ; *Oryzias/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridization. The extra haplotype was unique and contained two non-synonymous substitutions. These findings demonstrate that this hybridization-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.},
}

Humans
Animals
*Heteroplasmy
Lakes
Phylogeny
*Oryzias/genetics
DNA, Mitochondrial/genetics

@article {pmid38502499,
year = {2024},
author = {Kuntz, M and Dimnet, L and Pullara, S and Moyet, L and Rolland, N},
title = {The Main Functions of Plastids.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2776},
number = {},
pages = {89-106},
pmid = {38502499},
issn = {1940-6029},
mesh = {*Plastids/metabolism ; *Mitochondria/genetics ; },
abstract = {Plastids are semi-autonomous organelles like mitochondria and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.},
}

*Plastids/metabolism
*Mitochondria/genetics

@article {pmid38502495,
year = {2024},
author = {Maréchal, E},
title = {How Did Thylakoids Emerge in Cyanobacteria, and How Were the Primary Chloroplast and Chromatophore Acquired?.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2776},
number = {},
pages = {3-20},
pmid = {38502495},
issn = {1940-6029},
mesh = {Thylakoids/metabolism ; Chloroplasts/genetics/metabolism ; Photosynthesis/genetics ; *Cyanobacteria/genetics/metabolism ; Eukaryota ; *Chromatophores ; Symbiosis/genetics ; },
abstract = {The emergence of thylakoid membranes in cyanobacteria is a key event in the evolution of all oxygenic photosynthetic cells, from prokaryotes to eukaryotes. Recent analyses show that they could originate from a unique lipid phase transition rather than from a supposed vesicular budding mechanism. Emergence of thylakoids coincided with the great oxygenation event, more than two billion years ago. The acquisition of semi-autonomous organelles, such as the mitochondrion, the chloroplast, and, more recently, the chromatophore, is a critical step in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and, finally, the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter further details our current understanding of primary endosymbiosis, focusing on primary chloroplasts, thought to have appeared over a billion years ago, and the chromatophore, which appeared around a hundred years ago.},
}

Thylakoids/metabolism
Chloroplasts/genetics/metabolism
Photosynthesis/genetics
*Cyanobacteria/genetics/metabolism
Eukaryota
*Chromatophores
Symbiosis/genetics

@article {pmid38500026,
year = {2024},
author = {Yang, Y and Duan, C},
title = {Mitochondrial genome features and systematic evolution of diospyros kaki thunb 'Taishuu'.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {285},
pmid = {38500026},
issn = {1471-2164},
support = {YCKJ-2021021//Modern Agriculture Project of Yuncheng/ ; YCKJ-2021021//Modern Agriculture Project of Yuncheng/ ; },
mesh = {*Diospyros/genetics ; *Genome, Mitochondrial ; Repetitive Sequences, Nucleic Acid ; Codon, Terminator ; RNA, Transfer/genetics ; Phylogeny ; },
abstract = {BACKGROUND: 'Taishuu' has a crisp texture, abundant juice, and sweet flavor with hints of cantaloupe. The availability of mitochondrial genome data of Diospyros species is far from the known number of species.

RESULTS: The sequencing data were assembled into a closed circular mitochondrial chromosome with a 421,308 bp length and a 45.79% GC content. The mitochondrial genome comprised 40 protein-coding, 24 tRNA, and three rRNA genes. The most common codons for arginine (Arg), proline (Pro), glycine (Gly), tryptophan (Trp), valine (Val), alanine (Ala), and leucine (Leu) were AGA, CCA, GGA, UGG, GUA, GCA, and CUA, respectively. The start codon for cox1 and nad4L protein-coding genes was ACG (ATG), whereas the remaining protein-coding genes started with ATG. There are four types of stop codons: CGA, TAA, TAG, and TGA, with TAA being the most frequently used stop codon (45.24%). In the D. kaki Thunb. 'Taishuu' mitochondrial genome, a total of 645 repeat sequences were identified, including 125 SSRs, 7 tandem repeats, and 513 dispersed repeats. Collinearity analysis revealed a close relationship between D. kaki Thunb. 'Taishuu' and Diospyros oleifera, with conserved homologous gene fragments shared among these species in large regions of the mitochondrial genome. The protein-coding genes ccmB and nad4L were observed to undergo positive selection. Analysis of homologous sequences between chloroplasts and mitochondria identified 28 homologous segments, with a total length of 24,075 bp, accounting for 5.71% of the mitochondrial genome. These homologous segments contain 8 annotated genes, including 6 tRNA genes and 2 protein-coding genes (rrn18 and ccmC). There are 23 homologous genes between chloroplasts and nuclei. Mitochondria, chloroplasts, and nuclei share two homologous genes, which are trnV-GAC and trnW-CCA.

CONCLUSION: In conclusion, a high-quality chromosome-level draft genome for D. kaki was generated in this study, which will contribute to further studies of major economic traits in the genus Diospyros.},
}

*Diospyros/genetics
*Genome, Mitochondrial
Repetitive Sequences, Nucleic Acid
Codon, Terminator
RNA, Transfer/genetics
Phylogeny

@article {pmid38493987,
year = {2024},
author = {Wang, S and Li, Y and Jiang, K and Zhou, J and Chen, J and Liang, J and Ndoni, A and Xue, H and Ye, Z and Bu, W},
title = {Identifying a potentially invasive population in the native range of a species: The enlightenment from the phylogeography of the yellow spotted stink bug, Erthesina fullo (Hemiptera: Pentatomidae).},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108056},
doi = {10.1016/j.ympev.2024.108056},
pmid = {38493987},
issn = {1095-9513},
mesh = {Animals ; Phylogeography ; Phylogeny ; *Heteroptera/genetics ; Biological Evolution ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; },
abstract = {The yellow spotted stink bug (YSSB), Erthesina fullo (Thunberg, 1783) is an important Asian pest that has recently successfully invaded Europe and an excellent material for research on the initial stage of biological invasion. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of YSSB for the first time based on population genetic methods [using double digest restriction-site associated DNA (ddRAD) data and mitochondrial COI and CYTB] and ecological niche modelling. The results showed that four lineages (east, west, southwest, and Hainan Island) were established in the native range with a strong east-west differentiation phylogeographical structure, and the violent climate fluctuation might cause population divergence during the Middle and Upper Pleistocene. In addition, land bridges and monsoon promote dispersal and directional genetic exchanging between island populations and neighboring continental populations. The east lineage (EA) was identified as the source of invasion in Albania. EA had the widest geographical distribution among all other lineages, with a star-like haplotype network with the main haplotype as the core. It also had a rapid population expansion history, indicating that the source lineage might have stronger diffusion ability and adaptability. Our findings provided a significant biological basis for fine tracking of invasive source at the lineage or population level and promote early invasion warning of potential invasive species on a much subtler lineage level.},
}

Animals
Phylogeography
Phylogeny
*Heteroptera/genetics
Biological Evolution
Mitochondria/genetics
DNA, Mitochondrial/genetics
Genetic Variation

@article {pmid38492251,
year = {2024},
author = {Keeling, PJ and Mtawali, M and Trznadel, M and Livingston, SJ and Wakeman, KC},
title = {Parallel functional reduction in the mitochondria of apicomplexan parasites.},
journal = {European journal of protistology},
volume = {94},
number = {},
pages = {126065},
doi = {10.1016/j.ejop.2024.126065},
pmid = {38492251},
issn = {1618-0429},
mesh = {*Apicomplexa/genetics/physiology/classification ; *Mitochondria/genetics ; Biological Evolution ; },
abstract = {Extreme functional reduction of mitochondria has taken place in parallel in many distantly related lineages of eukaryotes, leading to a number of recurring metabolic states with variously lost electron transport chain (ETC) complexes, loss of the tricarboxylic acid (TCA) cycle, and/or loss of the mitochondrial genome. The resulting mitochondria-related organelles (MROs) are generally structurally reduced and in the most extreme cases barely recognizable features of the cell with no role in energy metabolism whatsoever (e.g., mitosomes, which generally only make iron-sulfur clusters). Recently, a wide diversity of MROs were discovered to be hiding in plain sight: in gregarine apicomplexans. This diverse group of invertebrate parasites has been known and observed for centuries, but until recent applications of culture-free genomics, their mitochondria were unremarkable. The genomics, however, showed that mitochondrial function has reduced in parallel in multiple gregarine lineages to several different endpoints, including the most reduced mitosomes. Here we review this remarkable case of parallel evolution of MROs, and some of the interesting questions this work raises.},
}

*Apicomplexa/genetics/physiology/classification
*Mitochondria/genetics
Biological Evolution

@article {pmid38485499,
year = {2024},
author = {Li, CY and Liu, XC and Li, YZ and Wang, Y and Nie, YH and Xu, YT and Zhang, XT and Lu, Y and Sun, Q},
title = {Generation of mitochondrial replacement monkeys by female pronucleus transfer.},
journal = {Zoological research},
volume = {45},
number = {2},
pages = {292-298},
pmid = {38485499},
issn = {2095-8137},
mesh = {Mice ; Humans ; Female ; Animals ; *Mitochondrial Diseases/genetics/prevention & control/veterinary ; Haplorhini/genetics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Primates/genetics ; *Rodent Diseases ; },
abstract = {Mutations in mitochondrial DNA (mtDNA) are maternally inherited and have the potential to cause severe disorders. Mitochondrial replacement therapies, including spindle, polar body, and pronuclear transfers, are promising strategies for preventing the hereditary transmission of mtDNA diseases. While pronuclear transfer has been used to generate mitochondrial replacement mouse models and human embryos, its application in non-human primates has not been previously reported. In this study, we successfully generated four healthy cynomolgus monkeys (Macaca fascicularis) via female pronuclear transfer. These individuals all survived for more than two years and exhibited minimal mtDNA carryover (3.8%-6.7%), as well as relatively stable mtDNA heteroplasmy dynamics during development. The successful establishment of this non-human primate model highlights the considerable potential of pronuclear transfer in reducing the risk of inherited mtDNA diseases and provides a valuable preclinical research model for advancing mitochondrial replacement therapies in humans.},
}

Mice
Humans
Female
Animals
*Mitochondrial Diseases/genetics/prevention & control/veterinary
Haplorhini/genetics
Mitochondria/genetics
DNA, Mitochondrial/genetics
Primates/genetics
*Rodent Diseases

@article {pmid38485105,
year = {2024},
author = {Na, I and Campos, C and Lax, G and Kwong, WK and Keeling, PJ},
title = {Phylogenomics reveals Adeleorina are an ancient and distinct subgroup of Apicomplexa.},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108060},
doi = {10.1016/j.ympev.2024.108060},
pmid = {38485105},
issn = {1095-9513},
mesh = {Animals ; Humans ; Phylogeny ; Plastids/genetics ; Genome ; *Apicomplexa/genetics ; *Genome, Plastid ; },
abstract = {Apicomplexans are a diverse phylum of unicellular eukaryotes that share obligate relationships with terrestrial and aquatic animal hosts. Many well-studied apicomplexans are responsible for several deadly zoonotic and human diseases, most notably malaria caused by Plasmodium. Interest in the evolutionary origin of apicomplexans has also spurred recent work on other more deeply-branching lineages, especially gregarines and sister groups like squirmids and chrompodellids. But a full picture of apicomplexan evolution is still lacking several lineages, and one major, diverse lineage that is notably absent is the adeleorinids. Adeleorina apicomplexans comprises hundreds of described species that infect invertebrate and vertebrate hosts across the globe. Although historically considered coccidians, phylogenetic trees based on limited data have shown conflicting branch positions for this subgroup, leaving this question unresolved. Phylogenomic trees and large-scale analyses comparing cellular functions and metabolism between major subgroups of apicomplexans have not incorporated Adeleorina because only a handful of molecular markers and a couple organellar genomes are available, ultimately excluding this group from contributing to our understanding of apicomplexan evolution and biology. To address this gap, we have generated complete genomes from mitochondria and plastids, as well as multiple deep-coverage single-cell transcriptomes of nuclear genes from two Adeleorina species, Klossia helicina and Legerella nova, and inferred a 206-protein phylogenomic tree of Apicomplexa. We observed distinct structures reported in species descriptions as remnant host structures surrounding adeleorinid oocysts. Klossia helicina and L. nova branched, as expected, with monoxenous adeleorinids within the Adeleorina and their mitochondrial and plastid genomes exhibited similarity to published organellar adeleorinid genomes. We show with a phylogeneomic tree and subsequent phylogenomic analyses that Adeleorina are not closely related to any of the currently sampled apicomplexan subgroups, and instead fall as a sister to a large clade encompassing Coccidia, Protococcidia, Hematozoa, and Nephromycida, collectively. This resolves Adeleorina as a key independently-branching group, separate from coccidians, on the tree of Apicomplexa, which now has all known major lineages sampled.},
}

Animals
Humans
Phylogeny
Plastids/genetics
Genome
*Apicomplexa/genetics
*Genome, Plastid

@article {pmid38480360,
year = {2024},
author = {Ghamizi, M and Falniowski, A and Boudellah, A and Hofman, S and Rharras, AE and Assad, N and Moutaouakil, S and Jaszczyska, A},
title = {Two new genera and species of the valvatiform hydrobiid snails (Caenogastropoda: Truncatelloidea: Hydrobiidae) from Morocco.},
journal = {Zootaxa},
volume = {5418},
number = {3},
pages = {223-239},
doi = {10.11646/zootaxa.5418.3.2},
pmid = {38480360},
issn = {1175-5334},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; Morocco ; *Snails/genetics ; Phylogeny ; *Mitochondria/genetics ; },
abstract = {Stygobiont and crenobiont minute gastropods representing the family Hydrobiidae (Caenogastropoda: Truncatelloidea), characterized by the valvatoid low-spired shell, were collected from one spring and four wells in Bouregreg region, NW Morocco. The shells were photographed and measured; shell biometry is illustrated with principal component analysis. Penes were illustrated and described. Mitochondrial cytochrome oxidase subunit 1 (COI) and 16S rRNA, as well as nuclear 18S rRNA sequences were used to infer the phylogeny. The snails represented two genera, both new to science. Their closest relatives were taxa from the Iberian Peninsula, the rough molecular estimate of the time of divergence between these Moroccan and Iberian genera coincided with the Pliocene Flooding, which restored the Strait of Gibraltar to connect the Mediterranean Basin with Atlantic Ocean.},
}

Animals
RNA, Ribosomal, 16S/genetics
Morocco
*Snails/genetics
Phylogeny
*Mitochondria/genetics

@article {pmid38480282,
year = {2024},
author = {Gordon, DP and Quek, ZBR and Huang, D},
title = {Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa.},
journal = {Zootaxa},
volume = {5424},
number = {3},
pages = {323-357},
doi = {10.11646/zootaxa.5424.3.3},
pmid = {38480282},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; New Zealand ; RNA, Ribosomal, 18S/genetics ; Base Sequence ; *Mitochondria/genetics ; },
abstract = {All eight extant species ofRhabdopleuradescribed between 1869 and 2018 are provisionally accepted as valid based on a review of the literature and new data on two little-known species from the Azores. Additionally, four new species are described from the New Zealand region, increasing global diversity by 50%, and a dichotomous key to all 12 described species is provided based on morphological criteria. The distinction between colony morphologies based on erect-tube inception is regarded as particularly helpful in initial characterization of species. Erect ringed tubes are either produced directly from the surface of creeping-tubes or indirectly, i.e. a short adherent side branch from a creeping tube is interpolated between the creeping tube and an erect tube; such side branches are blind-ending. These two modes of erect-tube origination are here respectively termeddirectandindirect. Species with indirect erect-tube budding are predominant in the North Atlantic whereas species with direct erect-tube budding dominate in New Zealand waters. The only indirect-erect species from New Zealand, Rhabdopleura chathamica n. sp., was discovered on deepwater coral from 10081075 m, constituting the deepest record of the genus to date. Rhabdopleura emancipata n. sp., collected only in a detached state, constitutes a three-dimensional tangled growth that grew freely into the water columna unique morphology hitherto unknown among extant species. Owing to this growth mode, it provided a substratum for epibionts from several phyla. Rhabdopleura francesca n. sp. and Rhabdopleura decipula n. sp. are morphologically very similar but are distinguishable by their distinct placements in a phylogeny based on 16S mitochondrial and 18S nuclear rRNA genes. Phylogenetic reconstructions based on rRNA and mitochondrial genome data contribute to an updated phylogeny of all Rhabdopleura species sequenced thus far, some of which require more molecular sequences and morphological analyses for taxonomic determination.},
}

Animals
Phylogeny
New Zealand
RNA, Ribosomal, 18S/genetics
Base Sequence
*Mitochondria/genetics

@article {pmid38480132,
year = {2024},
author = {Methou, P and Chen, C and Komai, T},
title = {Revision of the alvinocaridid shrimp genus Rimicaris Williams & Rona, 1986 (Decapoda: Caridea) with description of a new species from the Mariana Arc hydrothermal vents.},
journal = {Zootaxa},
volume = {5406},
number = {4},
pages = {501-518},
doi = {10.11646/zootaxa.5406.4.1},
pmid = {38480132},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; *Hydrothermal Vents ; *Decapoda ; Mitochondria ; },
abstract = {A new species of alvinocaridid shrimp is reported, from the Northwest Eifuku hydrothermal vent field at 16191667 m depth on the Mariana Arc. A comprehensive phylogenetic reconstruction of Alvinocarididae based on the mitochondrial cytochrome c oxidase subunit I (COI) gene including this new species reveals the paraphyly of the genus Rimicaris Williams & Rona, 1986 with four other generaAlvinocaridinides, Manuscaris, Opaepele, and Shinkaicarisnested within it. We re-examine material of these four problematic genera, and synonymise them under Rimicaris whose diagnosis has been amended, in order to maintain a monophyletic Rimicaris. Our new species, Rimicaris cambonae sp. nov. is genetically close to Rimicaris loihi (Williams & Dobbs, 1995) comb. nov. (previously Opaepele loihi) with which it co-occurs, but can be morphologically distinguished by the less elevated dorsal surface of the rostrum, this being devoid of a median carina, a stronger pterygostomial tooth on the carapace, and a blunt rather than acuminate proximolateral process on the antennular stylocerite. Species previously assigned to the above listed, synonymized genera are also discussed, with new material examined for three key species: R. loihi, R. acuminata, and R. leurokolos. Further, Alvinocaridinides formosa Komai & Chan, 2010 and Manuscaris liui Wang & Sha, 2016 are synonymized under Rimicaris leurokolos (Kikuchi & Hashimoto, 2000) comb. nov. and R. acuminata (Komai & Tsuchida, 2015) comb. nov., respectively. Revised diagnoses are presented for R. loihi, R. acuminata, and R. leurokolos. After the present revision revision, Rimicaris now consists of 15 species.},
}

Animals
Phylogeny
*Hydrothermal Vents
*Decapoda
Mitochondria

@article {pmid38475850,
year = {2024},
author = {Vesala, L and Basikhina, Y and Tuomela, T and Nurminen, A and Siukola, E and Vale, PF and Salminen, TS},
title = {Mitochondrial perturbation in immune cells enhances cell-mediated innate immunity in Drosophila.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {60},
pmid = {38475850},
issn = {1741-7007},
support = {RPG-2018-369//Leverhulme Trust/ ; 322732//Academy of Finland/ ; 328979//Academy of Finland/ ; 353367//Academy of Finland/ ; 3122800849//Sigrid Juséliuksen Säätiö/ ; },
mesh = {Animals ; Humans ; *Drosophila ; Drosophila melanogaster/metabolism ; *Wasps/genetics ; Mitochondria ; Immunity, Innate ; Hemocytes/metabolism ; },
abstract = {BACKGROUND: Mitochondria participate in various cellular processes including energy metabolism, apoptosis, autophagy, production of reactive oxygen species, stress responses, inflammation and immunity. However, the role of mitochondrial metabolism in immune cells and tissues shaping the innate immune responses are not yet fully understood. We investigated the effects of tissue-specific mitochondrial perturbation on the immune responses at the organismal level. Genes for oxidative phosphorylation (OXPHOS) complexes cI-cV were knocked down in the fruit fly Drosophila melanogaster, targeting the two main immune tissues, the fat body and the immune cells (hemocytes).

RESULTS: While OXPHOS perturbation in the fat body was detrimental, hemocyte-specific perturbation led to an enhanced immunocompetence. This was accompanied by the formation of melanized hemocyte aggregates (melanotic nodules), a sign of activation of cell-mediated innate immunity. Furthermore, the hemocyte-specific OXPHOS perturbation induced immune activation of hemocytes, resulting in an infection-like hemocyte profile and an enhanced immune response against parasitoid wasp infection. In addition, OXPHOS perturbation in hemocytes resulted in mitochondrial membrane depolarization and upregulation of genes associated with the mitochondrial unfolded protein response.

CONCLUSIONS: Overall, we show that while the effects of mitochondrial perturbation on immune responses are highly tissue-specific, mild mitochondrial dysfunction can be beneficial in immune-challenged individuals and contributes to variation in infection outcomes among individuals.},
}

Animals
Humans
*Drosophila
Drosophila melanogaster/metabolism
*Wasps/genetics
Mitochondria
Immunity, Innate
Hemocytes/metabolism

@article {pmid38474079,
year = {2024},
author = {Mourokh, L and Friedman, J},
title = {Mitochondria at the Nanoscale: Physics Meets Biology-What Does It Mean for Medicine?.},
journal = {International journal of molecular sciences},
volume = {25},
number = {5},
pages = {},
pmid = {38474079},
issn = {1422-0067},
support = {Award # 66061-00 54//PSC-CUNY/ ; },
mesh = {Humans ; *Mitochondria/physiology ; *Mitochondrial Membranes/metabolism ; Proton Pumps/metabolism ; Physics ; Biology ; },
abstract = {Mitochondria are commonly perceived as "cellular power plants". Intriguingly, power conversion is not their only function. In the first part of this paper, we review the role of mitochondria in the evolution of eukaryotic organisms and in the regulation of the human body, specifically focusing on cancer and autism in relation to mitochondrial dysfunction. In the second part, we overview our previous works, revealing the physical principles of operation for proton-pumping complexes in the inner mitochondrial membrane. Our proposed simple models reveal the physical mechanisms of energy exchange. They can be further expanded to answer open questions about mitochondrial functions and the medical treatment of diseases associated with mitochondrial disorders.},
}

Humans
*Mitochondria/physiology
*Mitochondrial Membranes/metabolism
Proton Pumps/metabolism
Physics
Biology

@article {pmid38468713,
year = {2024},
author = {Iverson, ENK},
title = {Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world.},
journal = {Evolutionary applications},
volume = {17},
number = {3},
pages = {e13642},
pmid = {38468713},
issn = {1752-4571},
abstract = {Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.},
}

@article {pmid38461774,
year = {2024},
author = {Diaz-Cuadros, M},
title = {Mitochondrial metabolism and the continuing search for ultimate regulators of developmental rate.},
journal = {Current opinion in genetics & development},
volume = {86},
number = {},
pages = {102178},
doi = {10.1016/j.gde.2024.102178},
pmid = {38461774},
issn = {1879-0380},
mesh = {*Mitochondria/metabolism/genetics ; Animals ; *Embryonic Development/genetics ; *Gene Expression Regulation, Developmental/genetics ; Species Specificity ; Humans ; Protein Biosynthesis ; },
abstract = {The rate of embryonic development is a species-specific trait that depends on the properties of the intracellular environment, namely, the rate at which gene products flow through the central dogma of molecular biology. Although any given step in the production and degradation of gene products could theoretically be co-opted by evolution to modulate developmental speed, species are observed to accelerate or slow down all steps simultaneously. This suggests the rate of these molecular processes is jointly regulated by an upstream, ultimate factor. Mitochondrial metabolism was recently proposed to act as an ultimate regulator by controlling the pace of protein synthesis upstream of developmental tempo. Alternative candidates for ultimate regulators include species-specific gene expression levels of factors involved in the central dogma, as well as species-specific cell size. Overall, much work remains to be done before we can confidently identify the ultimate causes of species-specific developmental rates.},
}

*Mitochondria/metabolism/genetics
Animals
*Embryonic Development/genetics
*Gene Expression Regulation, Developmental/genetics
Species Specificity
Humans
Protein Biosynthesis

@article {pmid38456969,
year = {2024},
author = {Ovciarikova, J and Shikha, S and Lacombe, A and Courjol, F and McCrone, R and Hussain, W and Maclean, A and Lemgruber, L and Martins-Duarte, ES and Gissot, M and Sheiner, L},
title = {Two ancient membrane pores mediate mitochondrial-nucleus membrane contact sites.},
journal = {The Journal of cell biology},
volume = {223},
number = {4},
pages = {},
pmid = {38456969},
issn = {1540-8140},
support = {/WT_/Wellcome Trust/United Kingdom ; 217173/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/N003675/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Eukaryotic Cells ; *Mitochondria/genetics/metabolism ; Mitochondria Associated Membranes ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/metabolism ; *Toxoplasma/cytology ; *Cell Nucleus/metabolism ; Nuclear Envelope/metabolism ; Nuclear Pore/metabolism ; Protozoan Proteins/metabolism ; },
abstract = {Coordination between nucleus and mitochondria is essential for cell survival, and thus numerous communication routes have been established between these two organelles over eukaryotic cell evolution. One route for organelle communication is via membrane contact sites, functional appositions formed by molecular tethers. We describe a novel nuclear-mitochondrial membrane contact site in the protozoan Toxoplasma gondii. We have identified specific contacts occurring at the nuclear pore and demonstrated an interaction between components of the nuclear pore and the mitochondrial protein translocon, highlighting them as molecular tethers. Genetic disruption of the nuclear pore or the TOM translocon components, TgNup503 or TgTom40, respectively, result in contact site reduction, supporting their potential involvement in this tether. TgNup503 depletion further leads to specific mitochondrial morphology and functional defects, supporting a role for nuclear-mitochondrial contacts in mediating their communication. The discovery of a contact formed through interaction between two ancient mitochondrial and nuclear complexes sets the ground for better understanding of mitochondrial-nuclear crosstalk in eukaryotes.},
}

Eukaryotic Cells
*Mitochondria/genetics/metabolism
Mitochondria Associated Membranes
Mitochondrial Membranes/metabolism
Mitochondrial Proteins/genetics/metabolism
*Toxoplasma/cytology
*Cell Nucleus/metabolism
Nuclear Envelope/metabolism
Nuclear Pore/metabolism
Protozoan Proteins/metabolism

@article {pmid38456649,
year = {2024},
author = {Kutzer, MAM and Cornish, B and Jamieson, M and Zawistowska, O and Monteith, KM and Vale, PF},
title = {Mitochondrial background can explain variable costs of immune deployment.},
journal = {Journal of evolutionary biology},
volume = {37},
number = {4},
pages = {442-450},
doi = {10.1093/jeb/voae027},
pmid = {38456649},
issn = {1420-9101},
support = {RPG-2018-369//Leverhulme Trust Research Project/ ; },
mesh = {Animals ; Female ; *Drosophila melanogaster/physiology ; *Mitochondria/genetics ; Longevity/genetics ; Genotype ; Fertility/genetics ; },
abstract = {Organismal health and survival depend on the ability to mount an effective immune response against infection. Yet immune defence may be energy-demanding, resulting in fitness costs if investment in immune function deprives other physiological processes of resources. While evidence of costly immunity resulting in reduced longevity and reproduction is common, the role of energy-producing mitochondria on the magnitude of these costs is unknown. Here we employed Drosophila melanogaster cybrid lines, where several mitochondrial genotypes (mitotypes) were introgressed onto a single nuclear genetic background, to explicitly test the role of mitochondrial variation on the costs of immune stimulation. We exposed female flies carrying one of nine distinct mitotypes to either a benign, heat-killed bacterial pathogen (stimulating immune deployment while avoiding pathology) or a sterile control and measured lifespan, fecundity, and locomotor activity. We observed mitotype-specific costs of immune stimulation and identified a positive genetic correlation between life span and the proportion of time cybrids spent moving while alive. Our results suggest that costs of immunity are highly variable depending on the mitochondrial genome, adding to a growing body of work highlighting the important role of mitochondrial variation in host-pathogen interactions.},
}

Animals
Female
*Drosophila melanogaster/physiology
*Mitochondria/genetics
Longevity/genetics
Genotype
Fertility/genetics

@article {pmid38449346,
year = {2024},
author = {Speijer, D},
title = {How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {46},
number = {5},
pages = {e2300193},
doi = {10.1002/bies.202300193},
pmid = {38449346},
issn = {1521-1878},
mesh = {*Oxygen/metabolism ; *Mitochondria/metabolism/genetics ; *Mitochondrial Membranes/metabolism ; Animals ; Eukaryota/metabolism/genetics ; Adenosine Triphosphate/metabolism ; Biological Evolution ; Eukaryotic Cells/metabolism ; },
abstract = {Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.},
}

*Oxygen/metabolism
*Mitochondria/metabolism/genetics
*Mitochondrial Membranes/metabolism
Animals
Eukaryota/metabolism/genetics
Adenosine Triphosphate/metabolism
Biological Evolution
Eukaryotic Cells/metabolism