Molecular biology and evolution最新文献

Accelerated pseudogenization in the ancient endosymbionts of giant scale insects. 巨型蚧虫古代内共生体的加速假原化。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-30 DOI: 10.1093/molbev/msaf125

Jinyeong Choi, Pradeep Palanichamy, Hirotaka Tanaka, Takumasa Kondo, Matthew E Gruwell, Filip Husnik

{"title":"Accelerated pseudogenization in the ancient endosymbionts of giant scale insects.","authors":"Jinyeong Choi, Pradeep Palanichamy, Hirotaka Tanaka, Takumasa Kondo, Matthew E Gruwell, Filip Husnik","doi":"10.1093/molbev/msaf125","DOIUrl":"https://doi.org/10.1093/molbev/msaf125","url":null,"abstract":"Symbiotic microorganisms are subject to a complex interplay of environmental and population-genetic pressures that drive their gene loss. Despite the widely held perception that ancient symbionts have stable genomes, even tiny genomes experience ongoing pseudogenization. Whether these tiny genomes also experience bursts of rapid gene loss is, however, less understood. Giant scale insects (Monophlebidae) feed on plant sap and rely on the symbiotic bacterium Walczuchella, which provides them with essential nutrients. When compared to other ancient symbionts with similar genome sizes, such as Karelsulcia, Walczuchella's genome was previously reported as unusually pseudogene-rich (10 % of coding sequences). However, this result was based on only one genome assembly, raising questions about the assembly quality or a recent ecological shift such as co-symbiont acquisition driving the gene loss. Here, we generated six complete genomes of Walczuchella from three genera of giant scales, each with distinct co-symbiotic partners. We show that all the genomes are highly degraded, and particularly genes related to the cellular envelope and energy metabolism seem to be undergoing pseudogenization. Apart from general mechanisms driving genome reduction, such as the long-term intracellular lifestyle with transmission bottlenecks, we hypothesize that a more profound loss of DNA replication and repair genes, together with recent co-obligate symbiont acquisitions, likely contribute to the accelerated degradation of Walczuchella genomes. Our results highlight that even ancient symbionts with small genomes can experience significant bursts of gene loss when stochastic processes erase a gene that accelerates gene loss or when the selection pressure changes such as after co-symbiont acquisition.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182859","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

Conservation evolutionary biology: a unified framework connecting the past, present, and future of biodiversity conservation. 保护进化生物学：连接生物多样性保护的过去、现在和未来的统一框架。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-30 DOI: 10.1093/molbev/msaf122

Yisi Hu, Wenliang Zhou, Yibo Hu, Fuwen Wei

{"title":"Conservation evolutionary biology: a unified framework connecting the past, present, and future of biodiversity conservation.","authors":"Yisi Hu, Wenliang Zhou, Yibo Hu, Fuwen Wei","doi":"10.1093/molbev/msaf122","DOIUrl":"https://doi.org/10.1093/molbev/msaf122","url":null,"abstract":"Evolutionary insights are fundamental to biodiversity conservation, as they reveal the ultimate causes that drive adaptation and persistence of populations, species, and ecosystems over time. In recent decades, the field of conservation biology has expanded to incorporate species' evolutionary histories, adaptive mechanisms, rapid evolution, and interactions with ecosystems to better understand the complexities of species' persistence in the long run. To address this growing recognition that conservation is inherently an evolutionary question, we propose \"conservation evolutionary biology\" as a new subdiscipline of conservation biology. It aims to explore the past, present, and future of biodiversity from an evolutionary viewpoint, revealing how species and ecosystems respond and adapt to changing environments, thereby to inform science-based, future-oriented conservation strategies to sustain biodiversity in a rapidly changing world. This article highlights the principles, research focus, methodologies, and practices of this emerging field, encouraging further exploration to address the conservation challenges of our time within a unified framework.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181131","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

Accounting for chimerism in demographic inference: reconstructing the history of common marmosets (Callithrix jacchus) from high-quality, whole-genome, population-level data. 人口统计学推断中的嵌合现象：利用高质量、全基因组、种群水平的数据重建普通狨猴（Callithrix jacchus）的历史。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-26 DOI: 10.1093/molbev/msaf119

Vivak Soni, Cyril J Versoza, Eric J Vallender, Jeffrey D Jensen, Susanne P Pfeifer

{"title":"Accounting for chimerism in demographic inference: reconstructing the history of common marmosets (Callithrix jacchus) from high-quality, whole-genome, population-level data.","authors":"Vivak Soni, Cyril J Versoza, Eric J Vallender, Jeffrey D Jensen, Susanne P Pfeifer","doi":"10.1093/molbev/msaf119","DOIUrl":"https://doi.org/10.1093/molbev/msaf119","url":null,"abstract":"As a species of considerable biomedical importance, characterizing the evolutionary genomics of the common marmoset (Callithrix jacchus) is of significance across multiple fields of research. However, at least two peculiarities of this species potentially preclude commonly utilized population genetic modeling and inference approaches: a high frequency of twin births and hematopoietic chimerism. We here investigate these effects within the context of demographic inference, demonstrating via simulation that neglecting these biological features results in significant mis-inference of the underlying population history. Based upon this result, we develop a novel approximate Bayesian inference approach accounting for both common twin-births as well as chimeric sampling. In addition, we newly present population genomic data from 15 individuals sequenced to high-coverage, and utilize gene-level annotations to identify neutrally evolving intergenic regions appropriate for demographic inference. Applying our developed methodology, we estimate a well-fitting population history for this species, which suggests robust ancestral and current population sizes, as well as a size reduction roughly 7,000 years ago likely associated with a shift from arboreal to savanna vegetation in north-eastern Brazil during this period.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151199","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 Genomics Unravels the Responses and Adaptation to Climate Change in a Key Alpine Forest Tree Species. 进化基因组学揭示了一种重要高山森林树种对气候变化的响应和适应。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-26 DOI: 10.1093/molbev/msaf116

Zhiqin Long, Yupeng Sang, Jiajun Feng, Xinxin Zhang, Tingting Shi, Lushui Zhang, Kangshan Mao, Loren H Rieseberg, Jianquan Liu, Jing Wang

{"title":"Evolutionary Genomics Unravels the Responses and Adaptation to Climate Change in a Key Alpine Forest Tree Species.","authors":"Zhiqin Long, Yupeng Sang, Jiajun Feng, Xinxin Zhang, Tingting Shi, Lushui Zhang, Kangshan Mao, Loren H Rieseberg, Jianquan Liu, Jing Wang","doi":"10.1093/molbev/msaf116","DOIUrl":"https://doi.org/10.1093/molbev/msaf116","url":null,"abstract":"Despite widespread biodiversity loss, our understanding of how species and populations will respond to accelerated climate change remains limited. In this study, we integrate population genomics, experimental evolution, and environmental modeling to elucidate the evolutionary responses to climate change in Populus lasiocarpa, a key alpine forest tree species primarily distributed in the mountainous regions of a global biodiversity hotspot. Over historical timescales, our findings demonstrate that demographic dynamics, divergent selection, and long-term balancing selection have shaped and maintained genetic variation within and between populations. In examining genomic signatures of contemporary climate adaptation, we found that haplotype blocks, potentially caused by inversion polymorphisms that suppress recombination, are linked to enriched combinations of locally adaptive environmental variations. We further assessed the relative contributions of environmentally induced plastic responses, constitutive expression divergence between genetic clusters, and their interactions in driving gene expression variation and divergence. Notably, we observed a strong correlation between sequence divergence and constitutive differential expression among genetic clusters. Finally, by incorporating genetic adaptation, migration, and genetic load into our predictions of population-level climate change risks, we identified western populations-primarily distributed in the Hengduan Mountains, a region known for its environmental heterogeneity and significant biodiversity-as the most vulnerable to climate change. These populations should be prioritized for conservation and management. Overall, our study advances the understanding of the relative roles of long-term natural selection, local environmental adaptation, and immediate plastic expression changes in shaping the responses of natural populations of keystone species to climate change.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143013","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

Relaxed purifying selection is associated with an accumulation of transposable elements in flies. 放松的净化选择与果蝇转座因子的积累有关。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-26 DOI: 10.1093/molbev/msaf111

Vincent Mérel, Théo Tricou, Nelly Burlet, Annabelle Haudry

{"title":"Relaxed purifying selection is associated with an accumulation of transposable elements in flies.","authors":"Vincent Mérel, Théo Tricou, Nelly Burlet, Annabelle Haudry","doi":"10.1093/molbev/msaf111","DOIUrl":"https://doi.org/10.1093/molbev/msaf111","url":null,"abstract":"Although the mechanisms driving genome size evolution are not yet fully understood, one potentially important factor is the dynamics of the accumulation of transposable elements (TEs). Since most TEs are neutral or slightly deleterious, a negative correlation between genome size and the efficacy of selection is expected. However, previous empirical studies on closely related species with distinct life history traits (thought to undergo different selective regimes) have yielded inconsistent results. Here, we perform the first large-scale analysis of the effect of genetic drift on genome size evolution, without any prior assumption on the amount of genetic drift. We reconstructed a phylogeny based on whole-genome data (2,242 genes) for 77 Drosophilid species to examine correlations between genome size, TE content, and the efficacy of selection (using dN/dS ratios of non-synonymous to synonymous divergence). Using an integrative approach that controls for shared evolutionary history, we reveal that genome-wide dN/dS are strongly positively correlated with genome size and TE content, particularly in GC-poor genes. This study suggests the critical importance of controlling for heterogeneity in base composition when estimating dN/dS. Furthermore, we emphasize that the lack of evidence for TE accumulation due to increased genetic drift in several previous studies may be due to a secondary effect of changes in life history traits (i.e. asexuality) on TE dynamics. In conclusion, this work provides evidence for TE proliferation in fly genomes when purifying selection is reduced, shedding new light on the role of TEs and genetic drift in the evolution of genome architecture.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143016","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

ShiNyP: Unlocking SNP-Based Population Genetics-An AI-Assisted Platform for Rapid and Interactive Visual Exploration. 解锁基于snp的群体遗传学——一个人工智能辅助的快速互动视觉探索平台。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-26 DOI: 10.1093/molbev/msaf117

Yen-Hsiang Huang, Ling-Yu Chen, Endang M Septiningsih, Pei-Hsiu Kao, Chung-Feng Kao

{"title":"ShiNyP: Unlocking SNP-Based Population Genetics-An AI-Assisted Platform for Rapid and Interactive Visual Exploration.","authors":"Yen-Hsiang Huang, Ling-Yu Chen, Endang M Septiningsih, Pei-Hsiu Kao, Chung-Feng Kao","doi":"10.1093/molbev/msaf117","DOIUrl":"https://doi.org/10.1093/molbev/msaf117","url":null,"abstract":"Efficient and accessible analysis of genome-wide single nucleotide polymorphism (SNP) data is vital for advancing molecular biology, evolutionary genetics, and breeding research. However, current analytical pipelines are often fragmented and require command-line expertise, limiting accessibility for many researchers. Here, we present ShiNyP, an interactive R/Shiny platform that integrates all popular SNP analysis modules within a single and intuitive user interface, supporting the entire workflow from data import and quality control to population structure inference, diversity analysis, selective scan, and core collection. ShiNyP accommodates datasets from haploid, diploid, and polyploid species and automates the generation of over 70 publication-ready visualizations and summary tables. A distinctive feature is its automated report module, which employs generative AI to deliver structured, interpretable narratives of complex statistical results. Performance benchmarks demonstrate that ShiNyP efficiently processes large-scale datasets on standard hardware. The ShiNyP platform is freely available at https://github.com/TeddYenn/ShiNyP, providing an efficient, reproducible, and user-friendly solution for population genomics research.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151203","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 fire ant social chromosome exerts a major influence on genome regulation. 火蚁的社会性染色体对基因组调控有重要影响。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-24 DOI: 10.1093/molbev/msaf112

Beryl M Jones, Alex H Waugh, Michael A Catto, Sasha Kay, Karl M Glastad, Michael A D Goodisman, Sarah D Kocher, Brendan G Hunt

{"title":"The fire ant social chromosome exerts a major influence on genome regulation.","authors":"Beryl M Jones, Alex H Waugh, Michael A Catto, Sasha Kay, Karl M Glastad, Michael A D Goodisman, Sarah D Kocher, Brendan G Hunt","doi":"10.1093/molbev/msaf112","DOIUrl":"https://doi.org/10.1093/molbev/msaf112","url":null,"abstract":"Supergenes underlying complex trait polymorphisms ensure sets of coadapted alleles remain genetically linked. Despite their prevalence in nature, the mechanisms of supergene effects on genome regulation are poorly understood. In the fire ant Solenopsis invicta, a supergene containing over 500 individual genes influences trait variation in multiple castes to collectively underpin a colony level social polymorphism. Here, we present results of an integrative investigation of supergene effects on gene regulation. We present analyses of ATAC-seq data to investigate variation in chromatin accessibility by supergene genotype and STARR-seq data to characterize enhancer activity by supergene haplotype. Integration with gene co-expression analyses, newly mapped intact transposable elements (TEs), and previously identified copy number variants (CNVs), collectively reveal widespread effects of the supergene on chromatin structure, gene transcription, and regulatory element activity, with a genome-wide bias for open chromatin and increased expression in the presence of the derived supergene haplotype, particularly in regions that harbor intact TEs. Integrated consideration of CNVs and regulatory element divergence suggests each evolved in concert to shape the expression of supergene encoded factors, including several transcription factors that may directly contribute to the trans-regulatory footprint of a heteromorphic social chromosome. Overall, we show how genome structure in the form of a supergene has wide-reaching effects on gene regulation and gene expression.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136084","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

GBRAP: A Comprehensive Database and Tool for Exploring Genomic Diversity Across All Domains of Life. GBRAP：一个探索生命所有领域基因组多样性的综合数据库和工具。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-05-24 DOI: 10.1093/molbev/msaf114

Sachithra Kalhari Yaddehige, Chiara Vischioni, Michele Berselli, Leonardo Alberghini, Massimo Mezzavilla, Tania Bobbo, Cristian Taccioli

{"title":"GBRAP: A Comprehensive Database and Tool for Exploring Genomic Diversity Across All Domains of Life.","authors":"Sachithra Kalhari Yaddehige, Chiara Vischioni, Michele Berselli, Leonardo Alberghini, Massimo Mezzavilla, Tania Bobbo, Cristian Taccioli","doi":"10.1093/molbev/msaf114","DOIUrl":"https://doi.org/10.1093/molbev/msaf114","url":null,"abstract":"Evolutionary studies require extensive examination of genomic information across all domains of life. Despite the availability of a large number of genomes through GenBank, the effective visualisation or comparison of the information they contain is challenging due to many reasons, including their size. We introduce GBRAP, a comprehensive software tool to analyse genome files, and an online database housing an extensive collection of carefully curated, high-quality genome statistics for all the organisms available in the RefSeq database of NCBI. Users can either directly search, or select from pre-categorized groups, the organisms of their choice and retrieve data, the output is generated as tables containing more than 200 columns of useful genomic information (Base counts, GC content, Shannon Entropy, Codon Usage etc.) separately calculated for different genomic elements (eg. CDS, Introns, tRNA, rRNA, ncRNA, etc.). The data are independently displayed (if applicable) for each chromosomal, mitochondrial, plastid, or plasmid sequence. All the data can be visualised on the database or downloaded as CSV or Excel files. The GBRAP database is free to access without any registration and is publicly available at http://tacclab.org/gbrap/.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136082","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

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species. 泛基因组分析揭示了橡树物种对气候渗入的局部适应。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf088

Yi-Ye Liang, Hui Liu, Qiong-Qiong Lin, Yong Shi, Biao-Feng Zhou, Jing-Shu Wang, Xue-Yan Chen, Zhao Shen, Liang-Jing Qiao, Jing-Wei Niu, Shao-Jun Ling, Wen-Ji Luo, Wei Zhao, Jian-Feng Liu, Yuan-Wen Kuang, Pär K Ingvarsson, Ya-Long Guo, Baosheng Wang

{"title":"Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species.","authors":"Yi-Ye Liang, Hui Liu, Qiong-Qiong Lin, Yong Shi, Biao-Feng Zhou, Jing-Shu Wang, Xue-Yan Chen, Zhao Shen, Liang-Jing Qiao, Jing-Wei Niu, Shao-Jun Ling, Wen-Ji Luo, Wei Zhao, Jian-Feng Liu, Yuan-Wen Kuang, Pär K Ingvarsson, Ya-Long Guo, Baosheng Wang","doi":"10.1093/molbev/msaf088","DOIUrl":"https://doi.org/10.1093/molbev/msaf088","url":null,"abstract":"The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 5","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023801","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

Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis. Caspase-8和ASC相互作用驱动裂解细胞死亡的进化和功能分析。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf096

Sivakumar Prasanth Kumar, Eswar Kumar Nadendla, R K Subbarao Malireddi, Syed Asfarul Haque, Raghvendra Mall, Andrew F Neuwald, Thirumala-Devi Kanneganti

{"title":"Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis.","authors":"Sivakumar Prasanth Kumar, Eswar Kumar Nadendla, R K Subbarao Malireddi, Syed Asfarul Haque, Raghvendra Mall, Andrew F Neuwald, Thirumala-Devi Kanneganti","doi":"10.1093/molbev/msaf096","DOIUrl":"https://doi.org/10.1093/molbev/msaf096","url":null,"abstract":"Caspases are evolutionarily conserved proteins essential for driving cell death in development and host defense. Caspase-8, a key member of the caspase family, is implicated in nonlytic apoptosis, as well as lytic forms of cell death. Recently, caspase-8 has been identified as an integral component of PANoptosomes, multiprotein complexes formed in response to innate immune sensor activation. Several innate immune sensors can nucleate caspase-8-containing PANoptosome complexes to drive inflammatory lytic cell death, PANoptosis. However, how the evolutionarily conserved and diverse functions of caspase-8 drive PANoptosis remains unclear. To address this, we performed evolutionary, sequence, structural, and functional analyses to decode caspase-8's complex-forming abilities and its interaction with the PANoptosome adaptor ASC. Our study distinguished distinct subgroups within the death domain superfamily based on their evolutionary and functional relationships, identified homotypic traits among subfamily members, and captured key events in caspase evolution. We also identified critical residues defining the heterotypic interaction between caspase-8's death effector domain and ASC's pyrin domain, validated through cross-species analyses, dynamic simulations, and in vitro experiments. Overall, our study elucidated recent evolutionary adaptations of caspase-8 that allowed it to interact with ASC, improving our understanding of critical molecular associations in PANoptosome complex formation and the underlying PANoptotic responses in host defense and inflammation. These findings have implications for understanding mammalian immune responses and developing new therapeutic strategies for inflammatory diseases.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 5","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029778","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