Journal of Molecular Evolution最新文献

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 : 2024-11-20 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":"https://doi.org/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":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation. 冷活性脂肪酶（Glaciozyma antarctica PI12）的结构洞察：Alphafold2 预测与分子动力学模拟。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-11-16 DOI: 10.1007/s00239-024-10219-3

Adamu Idris Matinja, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Siti Nurbaya Oslan, Mohd Shukuri Mohamad Ali

{"title":"Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation.","authors":"Adamu Idris Matinja, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Siti Nurbaya Oslan, Mohd Shukuri Mohamad Ali","doi":"10.1007/s00239-024-10219-3","DOIUrl":"https://doi.org/10.1007/s00239-024-10219-3","url":null,"abstract":"Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644389","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

Models of Fluctuating Selection Between Generations: A Solution for the Theoretical Inconsistency. 代间波动选择模型：理论不一致性的解决方案》。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-11-16 DOI: 10.1007/s00239-024-10214-8

Xun Gu

{"title":"Models of Fluctuating Selection Between Generations: A Solution for the Theoretical Inconsistency.","authors":"Xun Gu","doi":"10.1007/s00239-024-10214-8","DOIUrl":"https://doi.org/10.1007/s00239-024-10214-8","url":null,"abstract":"The theory of selection fluctuation between generations has been a topic with much activities in population genetics and molecular evolution in 1970's. Most studies suggested that, as the result of fluctuating selection between generations, the frequency of an (on average) neutral mutation may fluctuate around 0.5 during the long-term evolution before it was ultimately fixed or lost. However, this pattern can only be derived from a specific type Wright-Fisher additive model, coined by the Nei-Yokoyama puzzle. In this commentary, I revisited this issue and figured out a theoretical assumption that has never been claimed explicitly, the notion of reference phenotype. Consider one locus with two-alleles: A is the wildtype allele and A' is the mutation. The fluctuating selection model actually requires a constraint that one of three genotypes (AA, AA', or A'A') must maintain a constant fitness without fluctuating between generations. It appears that the balancing selection at a frequency of 0.5 emerges only when the heterozygote (AA') is the reference genotype. Because it is difficult to determine which genotype could be the reference genotype in a real population, a desirable population genetics model should take all three possibilities into account. To this end, I propose a mixture model, where each genotype has a certain chance to be the reference genotype. My analysis showed that the emergence of balancing selection depends on the relative proportions of three different reference genotypes.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644317","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

Cryptic Diversity in Scorpaenodes xyris (Jordan & Gilbert 1882) (Scorpaeniformes: Scorpaenidae) Throughout the Tropical Eastern Pacific. Scorpaenodes xyris (Jordan & Gilbert 1882) (Scorpaeniformes: Scorpaenidae) 在整个东太平洋热带地区的隐秘多样性。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-11-16 DOI: 10.1007/s00239-024-10212-w

Moises Emanuel Bernal-Hernández, Rosa Gabriela Beltrán-López, D Ross Robertson, Carole C Baldwin, Eduardo Espinoza, Juan Esteban Martínez-Gómez, Enrique Barraza, Arturo Angulo, Jonathan Valdiviezo-Rivera, Adrian F González Acosta, Omar Domínguez-Domínguez

{"title":"Cryptic Diversity in Scorpaenodes xyris (Jordan & Gilbert 1882) (Scorpaeniformes: Scorpaenidae) Throughout the Tropical Eastern Pacific.","authors":"Moises Emanuel Bernal-Hernández, Rosa Gabriela Beltrán-López, D Ross Robertson, Carole C Baldwin, Eduardo Espinoza, Juan Esteban Martínez-Gómez, Enrique Barraza, Arturo Angulo, Jonathan Valdiviezo-Rivera, Adrian F González Acosta, Omar Domínguez-Domínguez","doi":"10.1007/s00239-024-10212-w","DOIUrl":"https://doi.org/10.1007/s00239-024-10212-w","url":null,"abstract":"The tropical eastern Pacific (TEP) is a biogeographic region with a substantial set of isolated oceanic islands and mainland shoreline habitat barriers, as well as complex oceanographic dynamics due to major ocean currents, upwelling areas, eddies, and thermal instabilities. These characteristics have shaped spatial patterns of biodiversity between and within species of reef and shore fishes of the region, which has a very high rate of endemism. Scorpaenodes xyris, a small ecologically cryptic reef-dwelling scorpionfish, is widely distributed throughout the TEP, including all the mainland reef areas and all the oceanic islands. This wide distribution and its ecological characteristics make this species a good model to study the evolutionary history of this type of reef fish across the breadth of a tropical biogeographical region. Our evaluation of geographic patterns of genetic (mitochondrial and nuclear) variation shows that S. xyris comprises two highly differentiated clades (A and B), one of which contains four independent evolutionary subunits. Clade A includes four sub-clades: 1. The Cortez mainland Province; 2. The Revillagigedo Islands; 3. Clipperton Atoll; and 4. The Galapagos Islands. Clade B, in contrast, comprises a single unit that includes the Mexican and Panamic mainland provinces, plus Cocos Island. This geographical arrangement largely corresponds to previously indicated regionalization of the TEP. Oceanic distances isolating the islands have produced much of that evolutionary pattern, although oceanographic processes likely have also contributed.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644289","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

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 : 2024-11-14 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":"https://doi.org/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":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-14","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

Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Thermodynamic Properties of Formation and Biosynthesis. 血红蛋白和红细胞的生物热力学：基于分子和经验公式、生物合成反应以及形成和生物合成的热力学性质，分析血红蛋白和红细胞的结构和演变。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-11-08 DOI: 10.1007/s00239-024-10205-9

Marko E Popović, Maja Stevanović, Marijana Pantović Pavlović

{"title":"Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Thermodynamic Properties of Formation and Biosynthesis.","authors":"Marko E Popović, Maja Stevanović, Marijana Pantović Pavlović","doi":"10.1007/s00239-024-10205-9","DOIUrl":"https://doi.org/10.1007/s00239-024-10205-9","url":null,"abstract":"Hemoglobin and red blood cells (erythrocytes) have been studied extensively from the perspective of life and biomedical sciences. However, no analysis of hemoglobin and red blood cells from the perspective of chemical thermodynamics has been reported in the literature. Such an analysis would provide an insight into their structure and turnover from the aspect of biothermodynamics and bioenergetics. In this paper, a biothermodynamic analysis was made of hemoglobin and red blood cells. Molecular formulas, empirical formulas, biosynthesis reactions, and thermodynamic properties of formation and biosynthesis were determined for the alpha chain, beta chain, heme B, hemoglobin and red blood cells. Empirical formulas and thermodynamic properties of hemoglobin were compared to those of other biological macromolecules, which include proteins and nucleic acids. Moreover, the energetic requirements of biosynthesis of hemoglobin and red blood cells were analyzed. Based on this, a discussion was made of the specific structure of red blood cells (i.e. no nuclei nor organelles) and its role as an evolutionary adaptation for more energetically efficient biosynthesis needed for the turnover of red blood cells.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622144","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

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":" ","pages":""},"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":" ","pages":""},"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