Journal of Molecular Evolution最新文献_第6页

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

Evolution of Cellular Organization Along the First Branches of the Tree of Life. 生命之树最初枝条上的细胞组织进化。

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/s00239-024-10188-7

Freya Kailing, Jules Lieberman, Joshua Wang, Joshua L Turner, Aaron D Goldman

{"title":"Evolution of Cellular Organization Along the First Branches of the Tree of Life.","authors":"Freya Kailing, Jules Lieberman, Joshua Wang, Joshua L Turner, Aaron D Goldman","doi":"10.1007/s00239-024-10188-7","DOIUrl":"10.1007/s00239-024-10188-7","url":null,"abstract":"Current evidence suggests that some form of cellular organization arose well before the time of the last universal common ancestor (LUCA). Standard phylogenetic analyses have shown that several protein families associated with membrane translocation, membrane transport, and membrane bioenergetics were very likely present in the proteome of the LUCA. Despite these cellular systems emerging prior to the LUCA, extant archaea, bacteria, and eukaryotes have significant differences in cellular infrastructure and the molecular functions that support it, leading some researchers to argue that true cellularity did not evolve until after the LUCA. Here, we use recently reconstructed minimal proteomes of the LUCA as well as the last archaeal common ancestor (LACA) and the last bacterial common ancestor (LBCA) to characterize the evolution of cellular systems along the first branches of the tree of life. We find that a broad set of functions associated with cellular organization were already present by the time of the LUCA. The functional repertoires of the LACA and LBCA related to cellular organization nearly doubled along each branch following the divergence of the LUCA. These evolutionary trends created the foundation for similarities and differences in cellular organization between the taxonomic domains that are still observed today.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"618-623"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141633757","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

Perspective: Protocells and the Path to Minimal Life. 透视：原电池和极简生活之路。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-09-04 DOI: 10.1007/s00239-024-10197-6

David Deamer

引用次数: 0

The Unfinished Reconstructed Nature of the Last Universal Common Ancestor. 未完成的最后一个世界共同祖先的性质重建。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-07-18 DOI: 10.1007/s00239-024-10187-8

Luis Delaye

{"title":"The Unfinished Reconstructed Nature of the Last Universal Common Ancestor.","authors":"Luis Delaye","doi":"10.1007/s00239-024-10187-8","DOIUrl":"10.1007/s00239-024-10187-8","url":null,"abstract":"The ultimate consequence of Darwin's theory of common descent implies that all life on earth descends ultimately from a common ancestor. Biochemistry and molecular biology now provide sufficient evidence of shared ancestry of all extant life forms. However, the nature of the Last Universal Common Ancestor (LUCA) has been a topic of much debate over the years. This review offers a historical perspective on different attempts to infer LUCA's nature, exploring the debate surrounding its complexity. We further examine how different methodologies identify sets of ancient protein that exhibit only partial overlap. For example, different bioinformatic approaches have identified distinct protein subunits from the ATP synthetase identified as potentially inherited from LUCA. Additionally, we discuss how detailed molecular evolutionary analysis of reverse gyrase has modified previous inferences about an hyperthermophilic LUCA based mainly on automatic bioinformatic pipelines. We conclude by emphasizing the importance of developing a database dedicated to studying genes and proteins traceable back to LUCA and earlier stages of cellular evolution. Such a database would house the most ancient genes on earth.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"584-592"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723741","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

Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition. 干生命：理解前生物-生物过渡的框架》（A Framework for Understanding the Prebiotic-Biotic Transition）。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-09-08 DOI: 10.1007/s00239-024-10201-z

Gregory P Fournier

引用次数: 0

A New View of the Last Universal Common Ancestor. 最后一个世界共同祖先的新观点。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-08-09 DOI: 10.1007/s00239-024-10193-w

Aaron D Goldman, Arturo Becerra

引用次数: 0

RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome. RNA还是DNA？重新审视先天基因组的化学本质