Journal of Molecular Evolution最新文献

Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli. 压力对大肠杆菌重要基因表达噪音的限制

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-11 DOI: 10.1007/s00239-024-10211-x

Perry A LaBoone, Raquel Assis

{"title":"Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli.","authors":"Perry A LaBoone, Raquel Assis","doi":"10.1007/s00239-024-10211-x","DOIUrl":"https://doi.org/10.1007/s00239-024-10211-x","url":null,"abstract":"Gene expression is an inherently noisy process that is constrained by natural selection. Yet the condition dependence of constraint on expression noise remains unclear. Here, we address this problem by studying constraint on expression noise of E. coli genes in eight diverse growth conditions. In particular, we use variation in expression noise as an analog for constraint, examining its relationships to expression level and to the number of regulatory inputs from transcription factors across and within conditions. We show that variation in expression noise is negatively associated with expression level, implicating constraint to minimize expression noise of highly expressed genes. However, this relationship is condition dependent, with the strongest constraint observed when E. coli are grown in the presence of glycerol or ciprofloxacin, which result in carbon or antibiotic stress, respectively. In contrast, we do not observe evidence of constraint on expression noise of highly regulated genes, suggesting that highly expressed and highly regulated genes represent distinct classes of genes. Indeed, we find that essential genes are often highly expressed but not highly regulated, with elevated expression noise in glycerol and ciprofloxacin conditions. Thus, our findings support the hypothesis that selective constraint on expression noise is condition dependent in E. coli, illustrating how it may play a critical role in ensuring expression stability of essential genes in unstable environments.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406432","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

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 : 2024-10-07 DOI: 10.1007/s00239-024-10209-5

Bokai K Zhang, Leoned Gines

引用次数: 0

Putative MutS2 Homologs in Algae: More Goods in Shopping Bag? 藻类中的推定 MutS2 同源物：购物袋里还有更多商品？

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-10-04 DOI: 10.1007/s00239-024-10210-y

Mariia Berdieva, Vera Kalinina, Olga Palii, Sergei Skarlato

{"title":"Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?","authors":"Mariia Berdieva, Vera Kalinina, Olga Palii, Sergei Skarlato","doi":"10.1007/s00239-024-10210-y","DOIUrl":"https://doi.org/10.1007/s00239-024-10210-y","url":null,"abstract":"MutS2 proteins are presumably involved in either control of recombination or translation quality control in bacteria. MutS2 homologs have been found in plants and some algae; however, their actual diversity in eukaryotes remains unknown. We found putative MutS2 homologs in various species of photosynthetic eukaryotes and performed a detailed analysis of the revealed amino acid sequences. Three groups of homologs were distinguished depending on their domain composition: MutS2 homologs with full set of specific domains, MutS2-like sequences without endonuclease Smr domain, and MutS2-like homologs lacking Smr and clamp in domain IV, the extreme form of which are proteins with only a complete ATPase domain. We clarified the information about amino acid composition and set of specific motifs in the conserved domains in MutS2 and MutS2-like sequences. The models of the predicted tertiary structure were obtained for each group of homologs. The phylogenetic analysis demonstrated that all eukaryotic sequences split into two large groups. The first group included homologs belonging to species of Archaeplastida and a subset of haptophyte homologs, while the second-sequences of organisms from CASH groups (cryptophytes, alveolates, stramenopiles, haptophytes) and chlorarachniophytes. The cyanobacterial MutS2 clustered together with the first group, and proteins belonging to Deltaproteobacteria (orders Myxococcales and Bradymonadales) showed phylogenetic affinity to the CASH-including group with strong support. The observed tree pattern did not support a clear differentiation of eukaryotes into lineages with red and green algae-derived plastids. The results are discussed in the context of current conceptions of serial endosymbioses and genetic mosaicism in algae with complex plastids.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372076","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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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

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