Journal of Molecular Evolution最新文献

{"title":"Integrative Structural Bioinformatics and Molecular Dynamics Analyses of Synaptic Vesicle Proteins and Their Water-Soluble QTY-Variants Reveal Membrane Constraints and Evolutionary Coupling of T ⇔ V.","authors":"Taner Karagöl, Alper Karagöl, Shuguang Zhang","doi":"10.1007/s00239-026-10315-6","DOIUrl":"https://doi.org/10.1007/s00239-026-10315-6","url":null,"abstract":"<p><p>Synaptic vesicle proteins, including the synaptophysin, synaptogyrins, and synaptic vesicle glycoprotein 2 family are fundamental for neurotransmitter release and synaptic function, influencing numerous physiological processes. Although these proteins hold promise as therapeutic targets, their study has remained complicated due to their location within the cell membrane. To tackle this, we performed comparative analyses on these proteins and their water-soluble variants, which were designed using the QTY code. This approach involves systematically replacing hydrophobic amino acids L (leucine), V/I (valine/isoleucine), and F (phenylalanine) with hydrophilic amino acids Q (glutamine), T (threonine), and Y (tyrosine). The water-soluble QTY variants generated in our study, despite having significant differences in their transmembrane sequences up to 55%, maintained structural similarity, with RMSD values below 1.9 Å. We performed 100 ns molecular dynamics simulations to evaluate the structural stability and conformational dynamics of native and QTY variants. The analysis revealed that QTY substitutions preserved overall fold integrity while inducing localized flexibility, with lipid interactions contributing nonlinear effects that modulate residue-specific dynamics and evolutionary constraints. Our study further identified 155 single nucleotide variants (SNVs) in human genomic databases, and we examined their phenotypic and topological properties. By integrating evolutionary statistics, we provided insights into the substitutional dynamics of hydrophilic and hydrophobic alpha-helices. Notably, we found a strong evolutionary relationship between threonine and valine frequencies in homologous sequences. This coupling persists despite the high mutational barrier requiring a double-nucleotide change, suggesting a functional evolutionary necessity. Our data suggest that QTY variants of synaptic vesicle proteins could be valuable for research in structural biology, evolutionary studies, and medicine, potentially leading to innovative therapeutic strategies for a range of conditions.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839046","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}

{"title":"Prebiotic β-Strand Peptides May Be a Plausible Solution to the Protocell Permeability Problem.","authors":"Arda Şems","doi":"10.1007/s00239-026-10314-7","DOIUrl":"https://doi.org/10.1007/s00239-026-10314-7","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147816299","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}

{"title":"The GFI1 Gene Family: Evolution, Structure, and Its Role in Immune Responses.","authors":"Piotr Religa, Norwin Kubick, Marzena Łazarczyk, Biniyam Tsegaye, Michał Ławiński, Justyna Paszkiewicz, Atanas Atanasov, Jarosław Horbańczuk, Mariusz Sacharczuk, Michel Mickael","doi":"10.1007/s00239-026-10313-8","DOIUrl":"https://doi.org/10.1007/s00239-026-10313-8","url":null,"abstract":"<p><p>The immune system's evolution is crucial for its role in fighting pathogens and involvement in autoimmune and neurodegenerative diseases. The GFI1 gene family plays a role in the regulation of the function of immune cells, including neutrophils and CD4 + T cells. GFI1 consists of two members, GFI1A and GFI1B. GFI1A is vital for myeloid and lymphoid differentiation, while GFI1B is crucial for generating red blood cells and platelets. Both genes share a repressor SNAG domain and C2H2 zinc finger domains. However, the full relationship between their structure and function remains unclear. We aimed to decipher the relationship between structural evolution and novel functionalization in the GFI1 gene family. We employed a comprehensive phylogenetic approach that integrated tree construction, ancestral state reconstruction, positive selection analysis, motif mining, and non-homology-based functional prediction to trace GFI1 family evolutionary history over 700 million years. Our analysis revealed that the GFI1 gene family originated from a single ancestral gene in early metazoans and underwent multiple lineage-specific duplication events in invertebrates, jawless vertebrates, and jawed vertebrates, indicating adaptive diversification across evolutionary lineages, albeit without evidence of significant positive selection. We identified new motifs in the less-characterized middle regions, such as the SPOP-binding motif in GFI1A, potentially regulating cytokine production in CD4 + T cells, and the FEDFW motif, possibly involved in neutrophil recruitment. These motifs are unique to GFI1A in higher vertebrates. In GFI1B, we discovered a unique EPLRP motif, a separase cleavage site linked to sister chromatid separation. Our results indicate that GFI1 has evolved new functions to adapt to the complexity of the vertebrate immune system.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147773842","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}

{"title":"A Bayesian Framework for the Network Analysis of Transmission Dynamics in Infectious Disease.","authors":"Jianing Xu, Jihyun Kim, Pengsheng Ji, Lili Yu, Christopher C Whalen, Liang Liu","doi":"10.1007/s00239-026-10303-w","DOIUrl":"10.1007/s00239-026-10303-w","url":null,"abstract":"<p><p>Understanding the transmission dynamics of infectious diseases is critical for effective public health intervention. Traditional models often rely on simplifying assumptions that overlook the complexity of real-world contact patterns. In this study, we present an extended Bayesian framework that integrates genomic, temporal, and network data to reconstruct transmission networks with greater accuracy. By incorporating network structure as a prior, the model accounts for social and spatial proximity, allowing transmission probabilities to vary with contact or social distance. We further enhance inference sensitivity through a hypothesis testing procedure optimized via constrained likelihood estimation. Simulation results demonstrate that network-informed models outperform non-network-informed models, particularly under limited genetic resolution. Application to a tuberculosis dataset from Kampala, Uganda reveals that the network-informed model resolves transmission ambiguities more effectively than models based solely on genetic and temporal data. Additionally, Exponential Random Graph Model (ERGM) analysis indicates that transmission is more likely to occur through weak social ties than within tightly connected clusters, aligning with sociological theories of information flow. While the framework shows strong performance, limitations such as data sparsity and computational demands remain. Future work will focus on integrating mobility data to further refine transmission inference. This integrative approach offers a robust tool for epidemiological analysis and supports more targeted public health decision-making.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"316-327"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13076497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146220060","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}

{"title":"Genetic Exchanges Shape the Evolutionary Diversification Among Shigella phages.","authors":"Joyeeta Chatterjee, Pratanu Kayet, Manisha Ghosh, Shanta Dutta, Surajit Basak","doi":"10.1007/s00239-026-10304-9","DOIUrl":"10.1007/s00239-026-10304-9","url":null,"abstract":"<p><p>Shigella is a genus of bacteria that is a prevalent cause of bacterial diarrhoea (i.e., shigellosis). Shigella bacteriophages are shaping bacterial fitness. Bacteriophages can carry genes that contribute to Shigella virulence and antibiotic resistance, and these genes are frequently found on mobile genetic elements (MGEs). Horizontal gene transfer (HGT) of these components is a major driver of bacterial evolution. A comprehensive genomic analysis of these bacteriophages is required to deepen understanding of candidate genes for MGEs and HGTs. Through genetic exchange, phages acquire novel genetic features that confer selective advantages. In this study, we identified the weighted gene repertoire relatedness (wGRR) metric. We associated it with the infecting host species andgenetic exchanges among Shigella phages using the weighted gene repertoire relatedness (wGRR) metric. We associated them with the infecting host species and phage lifestyles to examine evolutionary constraints among phages. We observed that HGTs can affect genes' GC content, which, in turn, influences amino acid usage, thereby shaping the amino acid usage of the resulting proteins. Host-range expansion is also observed among Shigella phages. However, we also noted that Shigella phages do not have the propensity for genetic transfer with dissimilar lifestyles. The gene pool of bacteriophages, due to horizontal transfer, can broaden their host range, making them more suitable for applications in phage therapy against antibiotic-resistant bacteria. Horizontal gene transfer can expand the bacteriophage gene pool, thereby increasing host range and making them more suitable for phage therapy against antibiotic-resistant bacteria. Overall, this study provides deeper insight into MGEs and HGTs among Shigella phages and their evolutionary significance for infectivity.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"328-339"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146213169","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}

{"title":"Conservation of NLRP3 Inflammasome Pathway in Monotremes and Large-Scale Restructuring of the Caspase-1 Gene Cluster Region in Mammals.","authors":"David Stevens, Tasman Daish, Frank Grützner","doi":"10.1007/s00239-026-10307-6","DOIUrl":"10.1007/s00239-026-10307-6","url":null,"abstract":"<p><p>Activation of the NLRP3 inflammasome can be triggered by components of fungi, bacteria and viruses, as well as cellular stress and environmental irritants. The NLRP3 inflammasome has been well characterised in mouse and humans but limited information is available from other mammalian species. To gain a better understanding of the evolution of genes involved in the NLRP3 inflammasome pathway, we examined them in mammalian species representing the three major lineages (eutheria, metatheria and prototheria) and in chicken as an outgroup. Our results show that the inflammasome pathway machinery is generally well conserved in the species examined. We identified four NLRP members in echidna and seven in platypus as well as confirming Nlrp3 is present in marsupials and monotremes. Monotremes feature eleven Dectin family genes that are split across two chromosomes. Only three family members were found in opossum, Tasmanian devil and koala. Of the four Dectin family members known to be involved in the NLRP3 inflammasome pathway only Clec4e (Mincle) was identified in all species examined. Echidna possesses a single copy of Caspase-1 which, alongside previous results reported in the platypus, supports the conclusion that this is the only proinflammatory caspase in the monotremes. Our analysis suggests that Caspase-1 moved to a new chromosomal region in early mammalian evolution. This was followed by expansion of the cluster and accumulation of additional genes. The expansion of key gene families flanking Caspase-1 may have led to an expansion of inflammasome pathways and a more regulated immune system through the CARD genes.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"353-368"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13076529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147443811","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}

{"title":"How Binding Affinity and Binding Specificity Map to Sequence Space.","authors":"David A Liberles, Michelle M Meyer","doi":"10.1007/s00239-026-10308-5","DOIUrl":"10.1007/s00239-026-10308-5","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"279-285"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13076558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574356","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}

{"title":"Type II LDH/MDH Oxidoreductases in Pacific Oyster Magallana gigas (Thunberg, 1793): Gene Organization and Expression Patterns During Development and Across Tissues.","authors":"Mikhail V Puzakov, Ludmila V Puzakova, Polina M Puzakova, Igor O Babenko","doi":"10.1007/s00239-026-10301-y","DOIUrl":"10.1007/s00239-026-10301-y","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"304-315"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145998395","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}

{"title":"Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.","authors":"Ujwal Dahal, Rupendra Shakya, Bhumandeep Kour, Binju Khanal, Bhupinder Singh","doi":"10.1007/s00239-026-10305-8","DOIUrl":"10.1007/s00239-026-10305-8","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"286-303"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147355485","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}

{"title":"The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny.","authors":"Yang Li, Xiaomei Huang, Yuanhao Li, Ting Wang, Yuhui Xing, Jingjing Guo, Xiaoya Ma, Bojian Zhong","doi":"10.1007/s00239-026-10306-7","DOIUrl":"10.1007/s00239-026-10306-7","url":null,"abstract":"","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"340-352"},"PeriodicalIF":1.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147443833","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}