Journal of Molecular Evolution最新文献_第4页

Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases. 更正：G:U-independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Syntheases.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 DOI: 10.1007/s00239-024-10203-x

Misa Arutaki, Ryodai Kurihara, Toru Matsuoka, Ayako Inami, Kei Tokunaga, Tomomasa Ohno, Hiroki Takahashi, Haruka Takano, Tadashi Ando, Hiromi Mutsuro-Aoki, Takuya Umehara, Koji Tamura

引用次数: 0

In Silico Investigation of the Interactions Between Cotton Leaf Curl Multan Virus Proteins and the Transcriptional Gene Silencing Factors of Gossypium hirsutum L. 棉花卷叶 Multan 病毒蛋白质与 Gossypium hirsutum L.转录基因沉默因子之间相互作用的硅学研究

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-14 DOI: 10.1007/s00239-024-10216-6

Heena Jain, Ekta Rawal, Prabhat Kumar, Satish Kumar Sain, Priyanka Siwach

{"title":"In Silico Investigation of the Interactions Between Cotton Leaf Curl Multan Virus Proteins and the Transcriptional Gene Silencing Factors of Gossypium hirsutum L.","authors":"Heena Jain, Ekta Rawal, Prabhat Kumar, Satish Kumar Sain, Priyanka Siwach","doi":"10.1007/s00239-024-10216-6","DOIUrl":"10.1007/s00239-024-10216-6","url":null,"abstract":"The highly dynamic nature of the Cotton leaf curl virus (CLCuV) complex (causing Cotton leaf curl disease, a significant global threat to cotton) presents a formidable challenge in unraveling precise molecular mechanisms governing viral-host interactions. To address this challenge, the present study investigated the molecular interactions of 6 viral proteins (Rep, TrAP, C4, C5, V2, and βC1) with 18 cotton Transcriptional Gene Silencing (TGS) proteins. Protein-protein dockings conducted for different viral-host protein pairs using Clustered Protein Docking (ClusPro) and Global RAnge Molecular Matching (GRAMM) (216 docking runs), revealed variable binding energies. The interacting pairs with the highest binding affinities were further scrutinized using bioCOmplexes COntact MAPS (COCOMAPS) server, which revealed robust binding of three viral proteins- TrAP, C4, and C5 with 14 TGS proteins, identifying several novel interactions (not reported yet by earlier studies), such as TrAP targeting DCL3, HDA6, and SUVH6; C4 targeting RAV2, CMT2, and DMT1; and C5 targeting CLSY1, RDR1, RDR2, AGO4, SAMS, and SAHH. Visualizing these interactions in PyMol provided a detailed insight into interacting regions. Further assessment of the impact of 18 variants of the C4 protein on interaction with CMT2 revealed no correlation between sequence variation and docking energies. However, conserved residues in the C4 binding regions emerged as potential targets for disrupting viral integrity. Hence, this study provides valuable insights into the viral-host interplay, advancing our understanding of Cotton leaf curl Multan virus pathogenicity and opening novel avenues for devising various antiviral strategies by targeting the host-viral interacting regions after experimental validation.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"891-911"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality. 进化蛋白质多功能性的内在紊乱和其他可塑武库

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-08-30 DOI: 10.1007/s00239-024-10196-7

Asifa Aftab, Souradeep Sil, Seema Nath, Anirneya Basu, Sankar Basu

{"title":"Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality.","authors":"Asifa Aftab, Souradeep Sil, Seema Nath, Anirneya Basu, Sankar Basu","doi":"10.1007/s00239-024-10196-7","DOIUrl":"10.1007/s00239-024-10196-7","url":null,"abstract":"Microscopic evolution at the functional biomolecular level is an ongoing process. Leveraging functional and high-throughput assays, along with computational data mining, has led to a remarkable expansion of our understanding of multifunctional protein (and gene) families over the past few decades. Various molecular and intermolecular mechanisms are now known that collectively meet the cumulative multifunctional demands in higher organisms along an evolutionary path. This multitasking ability is attributed to a certain degree of intrinsic or adapted flexibility at the structure-function level. Evolutionary diversification of structure-function relationships in proteins highlights the functional importance of intrinsically disordered proteins/regions (IDPs/IDRs) which are highly dynamic biological soft matter. Multifunctionality is favorably supported by the fluid-like shapes of IDPs/IDRs, enabling them to undergo disorder-to-order transitions upon binding to different molecular partners. Other new malleable members of the protein superfamily, such as those involved in fold-switching, also undergo structural transitions. This new insight diverges from all traditional notions of functional singularity in enzyme classes and emphasizes a far more complex, multi-layered diversification of protein functionality. However, a thorough review in this line, focusing on flexibility and function-driven structural transitions related to evolved multifunctionality in proteins, is currently missing. This review attempts to address this gap while broadening the scope of multifunctionality beyond single protein sequences. It argues that protein intrinsic disorder is likely the most striking mechanism for expressing multifunctionality in proteins. A phenomenological analogy has also been drawn to illustrate the increasingly complex nature of modern digital life, driven by the need for multitasking, particularly involving media.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"669-684"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates. 脊椎动物性别决定的随机表观遗传修饰与进化

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-20 DOI: 10.1007/s00239-024-10213-9

Sergio Branciamore, Andrei S Rodin, Arthur D Riggs

{"title":"Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates.","authors":"Sergio Branciamore, Andrei S Rodin, Arthur D Riggs","doi":"10.1007/s00239-024-10213-9","DOIUrl":"10.1007/s00239-024-10213-9","url":null,"abstract":"In this report, we propose a novel mathematical model of the origin and evolution of sex determination in vertebrates that is based on the stochastic epigenetic modification (SEM) mechanism. We have previously shown that SEM, with rates consistent with experimental observation, can both increase the rate of gene fixation and decrease pseudogenization, thus dramatically improving the efficacy of evolution. Here, we present a conjectural model of the origin and evolution of sex determination wherein the SEM mechanism alone is sufficient to parsimoniously trigger and guide the evolution of heteromorphic sex chromosomes from the initial homomorphic chromosome configuration, without presupposing any allele frequency differences. Under this theoretical model, the SEM mechanism (i) predated vertebrate sex determination origins and evolution, (ii) has been conveniently and parsimoniously co-opted by the vertebrate sex determination systems during the evolutionary transitioning to the extant vertebrate sex determination, likely acting \"on top\" of these systems, and (iii) continues existing, alongside all known vertebrate sex determination systems, as a universal pan-vertebrate sex determination modulation mechanism.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"861-873"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology. 更正：野生动物抗癌进化适应性分析及在人类肿瘤学中的应用。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 DOI: 10.1007/s00239-024-10209-5

Bokai K Zhang, Leoned Gines

引用次数: 0

A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans. 了解鲸目动物嗅觉进化的比较基因组学方法。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-25 DOI: 10.1007/s00239-024-10217-5

April A Jauhal, Rochelle Constantine, Richard D Newcomb

{"title":"A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans.","authors":"April A Jauhal, Rochelle Constantine, Richard D Newcomb","doi":"10.1007/s00239-024-10217-5","DOIUrl":"10.1007/s00239-024-10217-5","url":null,"abstract":"Major evolutionary transitions, such as the shift of cetaceans from terrestrial to marine life, can put pressure on sensory systems to adapt to a new set of relevant stimuli. Relatively little is known about the role of smell in the evolution of mysticetes (baleen whales). While their toothed cousins, the odontocetes, lack the anatomical features to smell, it is less clear whether baleen whales have retained this sense, and if so, when the pressure on olfaction diverged in the cetacean evolutionary lineage. We examined eight genes encoding olfactory signal transduction pathway components and key chaperones for signs of inactivating mutations and selective pressures. All of the genes we examined were intact in all eight mysticete genomes examined, despite inactivating mutations in odontocete homologs in multiple genes. We also tested several models representing various hypotheses regarding the evolutionary history of olfaction in cetaceans. Our results support a model where olfactory ability is specifically reduced in the odontocete lineage following their split from stem cetaceans and serve to clarify the evolutionary history of olfaction in cetaceans.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"912-929"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Survey for Activating Oncogenic Mutation Variants in Metazoan Germline Genes. 调查元古宙种系基因中的激活性致癌突变变异。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-12-01 Epub Date: 2024-11-26 DOI: 10.1007/s00239-024-10218-4

Karl E Krueger

{"title":"Survey for Activating Oncogenic Mutation Variants in Metazoan Germline Genes.","authors":"Karl E Krueger","doi":"10.1007/s00239-024-10218-4","DOIUrl":"10.1007/s00239-024-10218-4","url":null,"abstract":"Most cancers present with mutations or amplifications in distinctive tumor promoter genes that activate principal cell-signaling cascades promoting cell proliferation, dedifferentiation, cell survival, and replicative immortality. Somatic mutations found in this these driver proto-oncogenes invariably result in constitutive activation of the encoded protein. A salient feature of the activating mutations observed throughout many thousands of clinical tumor specimens reveals these driver missense mutations are recurrent and restricted to just one or very few codons of the entire gene, suggesting they have been positively selected during the course of tumor development. The purpose of this study is to investigate whether these characteristic oncogenic driver mutations are observed in the germline genes of any metazoan species. Six well-known tumor promoter genes were chosen for this survey including BRAF, KRAS, JAK2, PIK3CA, EGFR, and IDH1/2. The sites of all driver mutations were found to occur in highly conserved regions of each gene comparing protein sequences throughout diverse phyla of metazoan species. None of the oncogenic missense mutations were found in germlines of any species of current genome and protein databases. Despite many tumors readily selecting these somatic mutations, the conclusion drawn from this study is that these variants are negatively rejected if encountered as a germline mutation. While cancer expansion ensues from dysregulated growth elicited by these mutations, this effect is likely detrimental to embryonic development and/or survival of multicellular organisms. Although all oncogenic mutations considered here are gain-of-function where five of the six increase activity of the encoded proteins, clonal advancement promotes tumor growth by these genomic changes without conferring selection advantages benefiting the organism or species.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"930-943"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Volatile Organic Compound Metabolism on Early Earth. 早期地球上的挥发性有机化合物代谢。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-07-17 DOI: 10.1007/s00239-024-10184-x

S Marshall Ledford, Laura K Meredith

引用次数: 0

The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA. 核糖体编码生物的最后一个普遍共同祖先：LUCA 的肖像

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-08-19 DOI: 10.1007/s00239-024-10186-9

Patrick Forterre

{"title":"The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA.","authors":"Patrick Forterre","doi":"10.1007/s00239-024-10186-9","DOIUrl":"10.1007/s00239-024-10186-9","url":null,"abstract":"The existence of LUCA in the distant past is the logical consequence of the binary mechanism of cell division. The biosphere in which LUCA and contemporaries were living was the product of a long cellular evolution from the origin of life to the second age of the RNA world. A parsimonious scenario suggests that the molecular fabric of LUCA was much simpler than those of modern organisms, explaining why the evolutionary tempo was faster at the time of LUCA than it was during the diversification of the three domains. Although LUCA was possibly equipped with a RNA genome and most likely lacked an ATP synthase, it was already able to perform basic metabolic functions and to produce efficient proteins. However, the proteome of LUCA and its inferred metabolism remains to be correctly explored by in-depth phylogenomic analyses and updated datasets. LUCA was probably a mesophile or a moderate thermophile since phylogenetic analyses indicate that it lacked reverse gyrase, an enzyme systematically present in all hyperthermophiles. The debate about the position of Eukarya in the tree of life, either sister group to Archaea or descendants of Archaea, has important implications to draw the portrait of LUCA. In the second alternative, one can a priori exclude the presence of specific eukaryotic features in LUCA. In contrast, if Archaea and Eukarya are sister group, some eukaryotic features, such as the spliceosome, might have been present in LUCA and later lost in Archaea and Bacteria. The nature of the LUCA virome is another matter of debate. I suggest here that DNA viruses only originated during the diversification of the three domains from an RNA-based LUCA to explain the odd distribution pattern of DNA viruses in the tree of life.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"550-583"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Introduction to the Special Issue on Early Evolution and the Last Common Ancestor. 早期进化与最后的共同祖先》特刊导言。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-09-20 DOI: 10.1007/s00239-024-10208-6

Arturo Becerra, Aaron D Goldman

引用次数: 0