Molecular biology and evolution最新文献_第2页

Evolutionary novelty of Apolipoprotein D facilitates metabolic plasticity in lepidopteran wings.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-12 DOI: 10.1093/molbev/msae252

Shunze Jia, Rongqiao Li, Yinghui Li, Yuxin Huang, Minmin Liu, Yanyan Zhou, Yanting Liang, Zhihua Hao, Yusong Xu, Huabing Wang

{"title":"Evolutionary novelty of Apolipoprotein D facilitates metabolic plasticity in lepidopteran wings.","authors":"Shunze Jia, Rongqiao Li, Yinghui Li, Yuxin Huang, Minmin Liu, Yanyan Zhou, Yanting Liang, Zhihua Hao, Yusong Xu, Huabing Wang","doi":"10.1093/molbev/msae252","DOIUrl":"https://doi.org/10.1093/molbev/msae252","url":null,"abstract":"Understanding metabolic plasticity of animal evolution is a fundamental challenge in evolutionary biology. Owing to the diversification of insect wing morphology and dynamic energy requirements, the molecular adaptation mechanisms underlying the metabolic pathways in wing evolution remain largely unknown. This study reveals the pivotal role of the duplicated Apolipoprotein D (ApoD) gene in lipid and energy homeostasis in the lepidopteran wing. ApoD underwent significant expansion in insects, with gene duplication and consistent retention observed in Lepidoptera. Notably, duplicated ApoD2 was highly expressed in lepidopteran wings and encoded a unique C-terminal tail, conferring distinct ligand-binding properties. Using Bombyx mori as a model organism, we integrated evolutionary analysis, multiomics, and in vivo functional experiments to elucidate the way duplicated ApoD2 mediates lipid trafficking and homeostasis via the AMP-activated protein kinase pathway in wings. Moreover, we revealed the specific expression and functional divergence of duplicated ApoD as a key mechanism regulating lipid homeostasis in the lepidopteran wing. These findings highlight an evolutionary scenario in which neofunctionalization conferred a novel role of ApoD in shaping adaptive lipid metabolic regulatory networks during wing phenotypic evolution. Overall, we provide in vivo evidence for the functional differentiation of duplicate genes in shaping adaptive metabolic regulatory networks during phenotypic evolution.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary Dynamics of Proinflammatory Caspases in Primates and Rodents. 灵长类和啮齿类动物中促炎 Caspases 的进化动态。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae220

Mische Holland, Rachel Rutkowski, Tera C Levin

{"title":"Evolutionary Dynamics of Proinflammatory Caspases in Primates and Rodents.","authors":"Mische Holland, Rachel Rutkowski, Tera C Levin","doi":"10.1093/molbev/msae220","DOIUrl":"10.1093/molbev/msae220","url":null,"abstract":"Caspase-1 and related proteases are key players in inflammation and innate immunity. Here, we characterize the evolutionary history of caspase-1 and its close relatives across 19 primates and 21 rodents, focusing on differences that may cause discrepancies between humans and animal studies. While caspase-1 has been retained in all these taxa, other members of the caspase-1 subfamily (caspase-4, caspase-5, caspase-11, and caspase-12 and CARD16, 17, and 18) each have unique evolutionary trajectories. Caspase-4 is found across simian primates, whereas we identified multiple pseudogenization and gene loss events in caspase-5, caspase-11, and the CARDs. Because caspase-4 and caspase-11 are both key players in the noncanonical inflammasome pathway, we expected that these proteins would be likely to evolve rapidly. Instead, we found that these two proteins are largely conserved, whereas caspase-4's close paralog, caspase-5, showed significant indications of positive selection, as did primate caspase-1. Caspase-12 is a nonfunctional pseudogene in humans. We find this extends across most primates, although many rodents and some primates retain an intact, and likely functional, caspase-12. In mouse laboratory lines, we found that 50% of common strains carry nonsynonymous variants that may impact the functions of caspase-11 and caspase-12 and therefore recommend specific strains to be used (and avoided). Finally, unlike rodents, primate caspases have undergone repeated rounds of gene conversion, duplication, and loss leading to a highly dynamic proinflammatory caspase repertoire. Thus, we uncovered many differences in the evolution of primate and rodent proinflammatory caspases and discuss the potential implications of this history for caspase gene functions.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multiple-Wave Admixture and Adaptive Evolution of the Pamirian Wakhi People. 帕米尔瓦希人的多波混血和适应性进化。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae237

Wanxing Xu, Jiaojiao Liu, Xiaoxi Zhang, Jia Wen, Qidi Feng, Yang Gao, Yuwen Pan, Yan Lu, Asifullah Khan, Shuhua Xu

{"title":"Multiple-Wave Admixture and Adaptive Evolution of the Pamirian Wakhi People.","authors":"Wanxing Xu, Jiaojiao Liu, Xiaoxi Zhang, Jia Wen, Qidi Feng, Yang Gao, Yuwen Pan, Yan Lu, Asifullah Khan, Shuhua Xu","doi":"10.1093/molbev/msae237","DOIUrl":"10.1093/molbev/msae237","url":null,"abstract":"While whole-genome sequencing has been applied extensively to investigate the genetic diversity of global populations, ethnic minority groups in Pakistan are generally underrepresented. In particular, little is known about the genetic origin and highland adaptation of the Pamirian Wakhi people. According to Chinese historical records, the geographical location and language usage of Wakhi may be closely related to Xinjiang Tajiks. In this study, based on high-coverage (∼30×) whole-genome sequencing of eight Wakhi and 25 Xinjiang Tajik individuals, we performed data analyses together with worldwide populations to gain insights into their genetic composition, demography, and adaptive evolution to the highland environment. The Wakhi derived more than 85% of their ancestry from West Eurasian populations (European ∼44.5%, South Asian ∼42.2%) and 10% from East Eurasian populations (Siberian ∼6.0%, East Asian ∼4.3%). Modeling the admixture history of the Wakhi indicated that the early West-East admixture occurred ∼3,875 to 2,250 years ago and that the recent admixture occurred ∼750 to 375 years ago. We identified selection signatures across EGLN3, in particular, a distinctive evolutionary signature was observed, and a certain underlying selected haplotype showed higher frequency (87.5%) in the Wakhi than in nearby Xinjiang Tajiks and other highlanders. Interestingly, we found high-frequency archaic sequences in the Wakhi genome, which overlapped with several genes related to cellular signaling transduction, including MAGI2, previously associated with high-altitude adaptation. Our analysis indicates that the Wakhi are distinct from the Xinjiang Tajiks and Tajikistan Tajiks and sheds light on the Wakhi's ancestral origin and genetic basis of high-altitude adaptation.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative Genomics Provides Insights into Adaptive Evolution and Demographics of Bats. 比较基因组学为蝙蝠的适应性进化和人口统计提供了洞察力。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae208

Gaoming Liu, Qi Pan, Pingfen Zhu, Xinyu Guo, Zhan Zhang, Zihao Li, Yaolei Zhang, Xiaoxiao Zhang, Jiahao Wang, Weiqiang Liu, Chunyan Hu, Yang Yu, Xiao Wang, Weixiao Chen, Meng Li, Wenhua Yu, Xin Liu, Inge Seim, Guangyi Fan, Xuming Zhou

{"title":"Comparative Genomics Provides Insights into Adaptive Evolution and Demographics of Bats.","authors":"Gaoming Liu, Qi Pan, Pingfen Zhu, Xinyu Guo, Zhan Zhang, Zihao Li, Yaolei Zhang, Xiaoxiao Zhang, Jiahao Wang, Weiqiang Liu, Chunyan Hu, Yang Yu, Xiao Wang, Weixiao Chen, Meng Li, Wenhua Yu, Xin Liu, Inge Seim, Guangyi Fan, Xuming Zhou","doi":"10.1093/molbev/msae208","DOIUrl":"10.1093/molbev/msae208","url":null,"abstract":"Bats possess a range of distinctive characteristics, including flight, echolocation, impressive longevity, and the ability to harbor various zoonotic pathogens. Additionally, they account for the second-highest species diversity among mammalian orders, yet their phylogenetic relationships and demographic history remain underexplored. Here, we generated de novo assembled genomes for 17 bat species and 2 of their mammalian relatives (the Amur hedgehog and Chinese mole shrew), with 12 genomes reaching chromosome-level assembly. Comparative genomics and ChIP-seq assays identified newly gained genomic regions in bats potentially linked to the regulation of gene activity and expression. Notably, some antiviral infection-related gene under positive selection exhibited the activity of suppressing cancer, evidencing the linkage between virus tolerance and cancer resistance in bats. By integrating published bat genome assemblies, phylogenetic reconstruction established the proximity of noctilionoid bats to vesper bats. Interestingly, we found 2 distinct patterns of ancient population dynamics in bats and population changes since the last glacial maximum does not reflect species phylogenetic relationships. These findings enriched our understanding of adaptive mechanisms and demographic history of bats.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Elevated Rates of Molecular Evolution Genome-wide in Mutualist Legumes and Rhizobia. 互生豆科植物和根瘤菌全基因组的分子进化速度加快。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae245

Tia L Harrison, John R Stinchcombe, Megan E Frederickson

{"title":"Elevated Rates of Molecular Evolution Genome-wide in Mutualist Legumes and Rhizobia.","authors":"Tia L Harrison, John R Stinchcombe, Megan E Frederickson","doi":"10.1093/molbev/msae245","DOIUrl":"10.1093/molbev/msae245","url":null,"abstract":"Rates of molecular evolution vary greatly among even closely related species. Although theory predicts that antagonistic interactions between species increase rates of molecular evolution, predictions for how mutualism affects evolutionary rates are mixed. We compared rates of molecular evolution between (i) mutualistic and non-mutualistic legumes, (ii) an independent set of symbiotic rhizobia and their non-symbiotic close relatives, and (iii) symbiotic and non-symbiotic clades within Ensifer, a diverse genus of bacteria with various lifestyles. We assembled transcriptomes de novo for 12 legume species and calculated dN/dS ratios at orthologous genes in all species to determine if genes in mutualistic plants evolve faster or slower than in their non-mutualistic relatives. We also calculated dN/dS ratios in genes known to be important for symbiosis. We found that mutualists have higher rates of molecular evolution genome-wide compared to non-mutualistic legumes, but this pattern did not hold in symbiosis genes. We next calculated dN/dS ratios in 14 bacteria species across the proteobacteria phylogeny that differ in whether they associate mutualistically with plants, using published data. In most pairs, symbiotic rhizobia show higher dN/dS values compared to their non-symbiotic relatives. Within a bacterial genus with many well-characterized mutualist species (Ensifer), we calculated dN/dS ratios in symbiotic and non-symbiotic clades and found that symbiotic lineages have higher rates of molecular evolution genome-wide, but not at genes on the symbiotic plasmid pSymB. Our results suggest that although mutualism between legumes and rhizobia is associated with elevated rates of molecular evolution genome-wide, symbiosis genes may be evolutionarily stagnant.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae251

Peipei Bian, Jiaxin Li, Shishuo Zhou, Xingquan Wang, Mian Gong, Xi Guo, Yudong Cai, Qimeng Yang, Jiaqi Fu, Rongrong Li, Shuhong Huang, Funong Luo, Ali Mujtaba Shah, Johannes A Lenstra, Joram M Mwacharo, Ran Li, Gang Ren, Xiaolong Wang, Cong Li, Wenxin Zheng, Yu Jiang, Xihong Wang

{"title":"A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation.","authors":"Peipei Bian, Jiaxin Li, Shishuo Zhou, Xingquan Wang, Mian Gong, Xi Guo, Yudong Cai, Qimeng Yang, Jiaqi Fu, Rongrong Li, Shuhong Huang, Funong Luo, Ali Mujtaba Shah, Johannes A Lenstra, Joram M Mwacharo, Ran Li, Gang Ren, Xiaolong Wang, Cong Li, Wenxin Zheng, Yu Jiang, Xihong Wang","doi":"10.1093/molbev/msae251","DOIUrl":"10.1093/molbev/msae251","url":null,"abstract":"Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113-Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions, and 24,954 other complex SV alleles. This resource allowed reliable graph-based genotyping from short reads of 79 wild and 1,148 worldwide domestic goats. Selection signal analysis of SV captured a novel immune-related domestication locus containing the galectin-9 gene and extra copies of the ruminant-specific galectin-9-like genes (LGALS9L), which have high tissue specificity. A segmental duplication in domestic goats generates three additional LGALS9L copies. Ancient goat genome sequences show a gradual increase in frequency of this duplication from the Neolithic to the present. Two other newly detected SVs also have higher selection signals than adjacent SNPs, a truncated-LINE1 deletion in EDAR2 associated with cashmere production and a VNTR-related insertion in PAPSS2 linked to high-altitude adaptation. In summary, the multi-assembly goat pangenome and long-read SV database facilitates detecting complex variations that are important in evolution and selection.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae250

Carolina Prediger, Erina A Ferreira, Samara Videira Zorzato, Aurélie Hua-Van, Lisa Klasson, Wolfgang J Miller, Amir Yassin, Lilian Madi-Ravazzi

{"title":"Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group.","authors":"Carolina Prediger, Erina A Ferreira, Samara Videira Zorzato, Aurélie Hua-Van, Lisa Klasson, Wolfgang J Miller, Amir Yassin, Lilian Madi-Ravazzi","doi":"10.1093/molbev/msae250","DOIUrl":"10.1093/molbev/msae250","url":null,"abstract":"Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no \"true\" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two based on our new assemblies using either conserved genes or ≥50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora, and two consisted of windows from pseudo-reference genomes aligned to either an ingroup or outgroup species. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed ∼7% of the blocks in the most conflicting species quartets. High incidences of reticulation were restricted to three nodes on the tree that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inferring Long-Term and Short-Term Determinants of Genetic Diversity in Honey Bees: Beekeeping Impact and Conservation Strategies.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae249

Thibault Leroy, Pierre Faux, Benjamin Basso, Sonia Eynard, David Wragg, Alain Vignal

{"title":"Inferring Long-Term and Short-Term Determinants of Genetic Diversity in Honey Bees: Beekeeping Impact and Conservation Strategies.","authors":"Thibault Leroy, Pierre Faux, Benjamin Basso, Sonia Eynard, David Wragg, Alain Vignal","doi":"10.1093/molbev/msae249","DOIUrl":"https://doi.org/10.1093/molbev/msae249","url":null,"abstract":"Bees are vital pollinators in natural and agricultural landscapes around the globe, playing a key role in maintaining flowering plant biodiversity and ensuring food security. Among the honey bee species, the Western honey bee (Apis mellifera) is particularly significant, not only for its extensive crop pollination services but also for producing economically valuable products such as honey. Here, we analyzed whole-genome sequence data from four Apis species to explore how honey bee evolution has shaped current diversity patterns. Using Approximate Bayesian Computation, we first reconstructed the demographic history of A. mellifera in Europe, finding support for postglacial secondary contacts, therefore predating human-mediated transfers linked to modern beekeeping. However, our analysis of recent demographic changes reveals significant bottlenecks due to beekeeping practices, which have notably affected genetic diversity. Black honey bee populations from conservatories, particularly those on islands, exhibit considerable genetic loss, highlighting the need to evaluate the long-term effectiveness of current conservation strategies. Additionally, we observed a high degree of conservation in the genomic landscapes of nucleotide diversity across the four species, despite a divergence gradient spanning over 15 million years, consistent with a long-term conservation of the recombination landscapes. Taken together, our results provide the most comprehensive assessment of diversity patterns in honey bees to date and offer insights into the optimal management of resources to ensure the long-term persistence of honey bees and their invaluable pollination services.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"41 12","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense γ-Irradiation. 对古老的 Methanococcales 苹果酸脱氢酶进行表征后发现，其强大的热稳定性可防止其在强γ-辐照下解折。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae231

Dominique Madern, Frédéric Halgand, Chantal Houée-Levin, Anne-Béatrice Dufour, Sandrine Coquille, Salomé Ansanay-Alex, Sophie Sacquin-Mora, Céline Brochier-Armanet

{"title":"The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense γ-Irradiation.","authors":"Dominique Madern, Frédéric Halgand, Chantal Houée-Levin, Anne-Béatrice Dufour, Sandrine Coquille, Salomé Ansanay-Alex, Sophie Sacquin-Mora, Céline Brochier-Armanet","doi":"10.1093/molbev/msae231","DOIUrl":"10.1093/molbev/msae231","url":null,"abstract":"Malate dehydrogenases (MalDHs) (EC.1.1.1.37), which are involved in the conversion of oxaloacetate to pyruvate in the tricarboxylic acid cycle, are a relevant model for the study of enzyme evolution and adaptation. Likewise, a recent study showed that Methanococcales, a major lineage of Archaea, is a good model to study the molecular processes of proteome thermoadaptation in prokaryotes. Here, we use ancestral sequence reconstruction and paleoenzymology to characterize both ancient and extant MalDHs. We observe a good correlation between inferred optimal growth temperatures and experimental optimal temperatures for activity (A-Topt). In particular, we show that the MalDH present in the ancestor of Methanococcales was hyperthermostable and had an A-Topt of 80 °C, consistent with a hyperthermophilic lifestyle. This ancestor gave rise to two lineages with different thermal constraints: one remained hyperthermophilic, while the other underwent several independent adaptations to colder environments. Surprisingly, the enzymes of the first lineage have retained a thermoresistant behavior (i.e. strong thermostability and high A-Topt), whereas the ancestor of the second lineage shows a strong thermostability, but a reduced A-Topt. Using mutants, we mimic the adaptation trajectory toward mesophily and show that it is possible to significantly reduce the A-Topt without altering the thermostability of the enzyme by introducing a few mutations. Finally, we reveal an unexpected link between thermostability and the ability to resist γ-irradiation-induced unfolding.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Digital Image Processing to Detect Adaptive Evolution. 检测适应性进化的数字图像处理

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2024-12-06 DOI: 10.1093/molbev/msae242

Md Ruhul Amin, Mahmudul Hasan, Michael DeGiorgio

{"title":"Digital Image Processing to Detect Adaptive Evolution.","authors":"Md Ruhul Amin, Mahmudul Hasan, Michael DeGiorgio","doi":"10.1093/molbev/msae242","DOIUrl":"10.1093/molbev/msae242","url":null,"abstract":"In recent years, advances in image processing and machine learning have fueled a paradigm shift in detecting genomic regions under natural selection. Early machine learning techniques employed population-genetic summary statistics as features, which focus on specific genomic patterns expected by adaptive and neutral processes. Though such engineered features are important when training data are limited, the ease at which simulated data can now be generated has led to the recent development of approaches that take in image representations of haplotype alignments and automatically extract important features using convolutional neural networks. Digital image processing methods termed α-molecules are a class of techniques for multiscale representation of objects that can extract a diverse set of features from images. One such α-molecule method, termed wavelet decomposition, lends greater control over high-frequency components of images. Another α-molecule method, termed curvelet decomposition, is an extension of the wavelet concept that considers events occurring along curves within images. We show that application of these α-molecule techniques to extract features from image representations of haplotype alignments yield high true positive rate and accuracy to detect hard and soft selective sweep signatures from genomic data with both linear and nonlinear machine learning classifiers. Moreover, we find that such models are easy to visualize and interpret, with performance rivaling those of contemporary deep learning approaches for detecting sweeps.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0