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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":"<p><p>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.</p>","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
{"title":"Introduction to the Special Issue on Early Evolution and the Last Common Ancestor.","authors":"Arturo Becerra, Aaron D Goldman","doi":"10.1007/s00239-024-10208-6","DOIUrl":"10.1007/s00239-024-10208-6","url":null,"abstract":"<p><p>The early evolution of life spans an extensive period preceding the emergence of the first eukaryotic cell. This epoch, which transpired from 4.5 to 2.5 billion years ago, marked the advent of many fundamental cellular attributes and witnessed the existence of the Last Common Ancestor (LCA) of all life forms. Uncovering and reconstructing this elusive LCA's characteristics and genetic makeup represents a formidable challenge and a pivotal pursuit in early evolution. While most scientific accounts concur that the LCA resembles contemporary prokaryotes, its precise definition, genome composition, metabolic capabilities, and ecological niche remain subjects of contentious debate.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"527-529"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142289379","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
{"title":"Perspective: Protocells and the Path to Minimal Life.","authors":"David Deamer","doi":"10.1007/s00239-024-10197-6","DOIUrl":"10.1007/s00239-024-10197-6","url":null,"abstract":"<p><p>The path to minimal life involves a series of stages that can be understood in terms of incremental, stepwise additions of complexity ranging from simple solutions of organic compounds to systems of encapsulated polymers capable of capturing nutrients and energy to grow and reproduce. This brief review will describe the initial stages that lead to populations of protocells capable of undergoing selection and evolution. The stages incorporate knowledge of chemical and physical properties of organic compounds, self-assembly of membranous compartments, non-enzymatic polymerization of amino acids and nucleotides followed by encapsulation of polymers to produce protocell populations. The results are based on laboratory simulations related to cyclic hydrothermal conditions on the prebiotic Earth. The final portion of the review looks ahead to what remains to be discovered about this process in order to understand the evolutionary path to minimal life.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"530-538"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125896","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
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":"<p><p>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.</p>","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
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":"<p><p>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.</p>","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
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
{"title":"A New View of the Last Universal Common Ancestor.","authors":"Aaron D Goldman, Arturo Becerra","doi":"10.1007/s00239-024-10193-w","DOIUrl":"10.1007/s00239-024-10193-w","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"659-661"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141912997","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
{"title":"Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition.","authors":"Gregory P Fournier","doi":"10.1007/s00239-024-10201-z","DOIUrl":"10.1007/s00239-024-10201-z","url":null,"abstract":"<p><p>Abiogenesis is frequently envisioned as a linear, ladder-like progression of increasingly complex chemical systems, eventually leading to the ancestors of extant cellular life. This \"pre-cladistics\" view is in stark contrast to the well-accepted principles of organismal evolutionary biology, as informed by paleontology and phylogenetics. Applying this perspective to origins, I explore the paradigm of \"Stem Life,\" which embeds abiogenesis within a broader continuity of diversification and extinction of both hereditary lineages and chemical systems. In this new paradigm, extant life's ancestral lineage emerged alongside and was dependent upon many other complex prebiotic chemical systems, as part of a diverse and fecund prebiosphere. Drawing from several natural history analogies, I show how this shift in perspective enriches our understanding of Origins and directly informs debates on defining Life, the emergence of the Last Universal Common Ancestor (LUCA), and the implications of prebiotic chemical experiments.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"539-549"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154370","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
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
IF 2.1 3区 生物学
Journal of Molecular Evolution Pub Date : 2024-10-01 Epub Date: 2024-08-15 DOI: 10.1007/s00239-024-10194-9
Wolfgang Cottom-Salas, Arturo Becerra, Antonio Lazcano
{"title":"RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome.","authors":"Wolfgang Cottom-Salas, Arturo Becerra, Antonio Lazcano","doi":"10.1007/s00239-024-10194-9","DOIUrl":"10.1007/s00239-024-10194-9","url":null,"abstract":"<p><p>One of the central issues in the understanding of early cellular evolution is the characterisation of the cenancestor. This includes the description of the chemical nature of its genome. The disagreements on this question comprise several proposals, including the possibility that AlkB-mediated methylation repair of alkylated RNA molecules may be interpreted as evidence of a cenancestral RNA genome. We present here an evolutionary analysis of the cupin-like protein superfamily based on tertiary structure-based phylogenies that includes the oxygen-dependent AlkB and its homologs. Our results suggest that the repair of methylated RNA molecules is the outcome of the enzyme substrate ambiguity, and doesn´t necessarily indicates that the last common ancestor was endowed with an RNA genome.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"647-658"},"PeriodicalIF":2.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141982491","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: Perspectives on the Origin of Biological Homochirality on Earth. 更正：地球上生物同性起源的视角》（Perspectives on the Origin of Biological Homochirality on Earth）。
IF 2.1 3区 生物学
Journal of Molecular Evolution Pub Date : 2024-09-26 DOI: 10.1007/s00239-024-10206-8
Koji Tamura
{"title":"Correction: Perspectives on the Origin of Biological Homochirality on Earth.","authors":"Koji Tamura","doi":"10.1007/s00239-024-10206-8","DOIUrl":"https://doi.org/10.1007/s00239-024-10206-8","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142348405","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
High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity. 高核苷酸偏斜 Palindromic DNA 序列因其解压缩倾向而成为潜在的复制起源。
IF 2.1 3区 生物学
Journal of Molecular Evolution Pub Date : 2024-09-23 DOI: 10.1007/s00239-024-10202-y
Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian
{"title":"High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.","authors":"Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian","doi":"10.1007/s00239-024-10202-y","DOIUrl":"https://doi.org/10.1007/s00239-024-10202-y","url":null,"abstract":"<p><p>Locations of DNA replication initiation in prokaryotes, called \"origins of replication\", are well-characterized. However, a mechanistic understanding of the sequence dependence of the local unzipping of double-stranded DNA, the first step towards replication initiation, is lacking. Here, utilizing a Markov chain model that was created to address the directional nature of DNA unzipping and replication, we model the sequence dependence of local melting of double-stranded linear DNA segments. We show that generalized palindromic sequences with high nucleotide skews have a low kinetic barrier for local melting near melting temperatures. This allows for such sequences to function as potential replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307910","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
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