Journal of Molecular Evolution最新文献

De Novo Creation of Two Novel Spliceosomal Introns of RECG1 by Intronization of Formerly Exonic Sequences in Orchidaceae.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-04-09 DOI: 10.1007/s00239-025-10242-y

Yuan-Yuan Xie, Bin Wen, Ming-Zhu Bai, Yan-Yan Guo

{"title":"De Novo Creation of Two Novel Spliceosomal Introns of RECG1 by Intronization of Formerly Exonic Sequences in Orchidaceae.","authors":"Yuan-Yuan Xie, Bin Wen, Ming-Zhu Bai, Yan-Yan Guo","doi":"10.1007/s00239-025-10242-y","DOIUrl":"https://doi.org/10.1007/s00239-025-10242-y","url":null,"abstract":"Spliceosomal introns are a key characteristic of eukaryotic genes. However, the origins and mechanisms of new spliceosomal introns remain elusive, and definitive case studies documenting intron creation are still limited. This study examined the RECG1 genes of 49 land plants, including 21 orchids and 28 non-orchid species. Sequence comparison revealed that the fourth intron of Gastrodia and Platanthera (Orchidaceae) is a newly gained spliceosomal intron, originating from the intronization of former exonic sequences. This intronization event was accompanied by the creation of novel recognizable GT/AG splice sites. In contrast, other orchid species lack the corresponding splice sites in the counterpart regions. Moreover, the secondary and tertiary protein structures implied that the intronization events do not affect the protein function. Given the diverse trophic modes of the two genera, we infer that relaxed selection may have contributed to the fluidity of gene structures. This study provides a typical example of de novo lineage-specific intron creation via intronization in orchids supported by multiple lines of evidence, and the two intronization events occurred independently in the same gene. This research enhances our understanding of gene evolution in orchids and provides valuable insights that may assist the annotation of structurally complex genes.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810923","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

EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-04-05 DOI: 10.1007/s00239-025-10244-w

Celia Blanco, Allison Tee, Pramesh Sharma, Matilda S Newton, Kun-Hwa Lee, Samuel E Erickson, Burckhard Seelig, Irene A Chen

{"title":"EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids.","authors":"Celia Blanco, Allison Tee, Pramesh Sharma, Matilda S Newton, Kun-Hwa Lee, Samuel E Erickson, Burckhard Seelig, Irene A Chen","doi":"10.1007/s00239-025-10244-w","DOIUrl":"https://doi.org/10.1007/s00239-025-10244-w","url":null,"abstract":"In vitro evolution is a powerful technique for identifying functional nucleic acids and peptides, but the analysis of the resulting high-throughput sequencing data poses significant challenges, particularly in peptide selections. Existing bioinformatics tools often lack the specificity needed for this task, leaving researchers to navigate complex datasets with inadequate resources. To address these challenges, we present EasyDIVER + , an enhanced pipeline building on the foundation of the original EasyDIVER tool, which was designed for pre-processing sequencing data. EasyDIVER + not only processes raw, paired-end, demultiplexed Illumina read files but also introduces advanced analytical capabilities, including the calculation of enrichment values for each unique sequence across consecutive selection rounds. Furthermore, EasyDIVER + offers a highly flexible and customizable visualization platform, enabling detailed graphical representations of sequence metrics. These new features mark a significant advance in bioinformatics for peptide and protein data, providing researchers with intuitive tools for comprehensive data analysis and interpretation.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788530","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

Comparative Analysis of Drosophila Bam and Bgcn Sequences and Predicted Protein Structural Evolution.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-04-03 DOI: 10.1007/s00239-025-10245-9

Luke R Arnce, Jaclyn E Bubnell, Charles F Aquadro

{"title":"Comparative Analysis of Drosophila Bam and Bgcn Sequences and Predicted Protein Structural Evolution.","authors":"Luke R Arnce, Jaclyn E Bubnell, Charles F Aquadro","doi":"10.1007/s00239-025-10245-9","DOIUrl":"https://doi.org/10.1007/s00239-025-10245-9","url":null,"abstract":"The protein encoded by the Drosophila melanogaster gene bag of marbles (bam) plays an essential role in early gametogenesis by complexing with the gene product of benign gonial cell neoplasm (bgcn) to promote germline stem cell daughter differentiation in males and females. Here, we compared the AlphaFold2 and AlphaFold Multimer predicted structures of Bam protein and the Bam:Bgcn protein complex between D. melanogaster, D. simulans, and D. yakuba, where bam is necessary in gametogenesis to that in D. teissieri, where it is not. Despite significant sequence divergence, we find very little evidence of significant structural differences in high confidence regions of the structures across the four species. This suggests that Bam structure is unlikely to be a direct cause of its functional differences between species and that Bam may simply not be integrated in an essential manner for GSC differentiation in D. teissieri. Patterns of positive selection and significant amino acid diversification across species is consistent with the Selection, Pleiotropy, and Compensation (SPC) model, where detected selection at bam is consistent with adaptive change in one major trait followed by positively selected compensatory changes for pleiotropic effects (in this case perhaps preserving structure). In the case of bam, we suggest that the major trait could be genetic interaction with the endosymbiotic bacteria Wolbachia pipientis. Following up on detected signals of positive selection and comparative structural analysis could provide insight into the distribution of a primary adaptive change versus compensatory changes following a primary change.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772511","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

Mutations Inactivating Biosynthesis of Dispensable Carbohydrate-Antigens Prevented Extinctions in Primate/Human Lineage Evolution.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-03-30 DOI: 10.1007/s00239-025-10243-x

Uri Galili

{"title":"Mutations Inactivating Biosynthesis of Dispensable Carbohydrate-Antigens Prevented Extinctions in Primate/Human Lineage Evolution.","authors":"Uri Galili","doi":"10.1007/s00239-025-10243-x","DOIUrl":"https://doi.org/10.1007/s00239-025-10243-x","url":null,"abstract":"The human natural anti-carbohydrate antibodies anti-Gal, anti-Neu5Gc, and anti-Forssman are \"living-fossils\" that appeared in ancestral apes, monkeys and hominins millions of years ago. These antibodies appeared at various evolutionary periods in few mutated-offspring that lost the ability to synthesize the corresponding dispensable (i.e., nonessential) carbohydrate-antigens, α-gal epitope, Neu5Gc (N-glycolyl neuraminic acid) and Forssman-antigen, respectively. Production of these antibodies is stimulated by environmental antigens such as those of the human microbiota. Elimination of carbohydrate-antigens in the few mutated-offspring was caused by accidental nonsense or missense mutations that inactivated genes encoding enzymes involved in their biosynthesis, while most individuals in parental-populations continued synthesizing these carbohydrate-antigens. It has been suggested that dispensable carbohydrate-antigens which are absent in some mammalian species were evolutionary eliminated due to selective pressure by lethal viruses using these carbohydrate-antigens as \"docking\" receptors. An alternative selective mechanism which is based on the distribution of anti-Gal, anti-Neu5Gc and anti-Forssman in mammals, is presented in this review and is associated with the protective effects of these natural antibodies. It is suggested that epidemics of lethal enveloped-viruses caused the extinction of parental-populations synthesizing the corresponding carbohydrate-antigens of these antibodies, independent of the cell adhesion mechanisms of such viruses. However, the few mutated offspring were protected by these natural antibodies which bound to carbohydrate-antigens synthesized on viruses as a result of their replication in individuals of the parental-populations. Recent studies suggest that these antibodies continue to contribute to the immune protection of humans against zoonotic infections by viruses presenting α-gal, Neu5Gc or Forssman antigens.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753022","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 to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms. Correction to：扁形虫体内福克斯基因家族多次独立扩展的证据

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-03-28 DOI: 10.1007/s00239-025-10241-z

Ludwik Gąsiorowski

引用次数: 0

Correction: Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-03-04 DOI: 10.1007/s00239-025-10239-7

Ramses Alejandro Rosales-Garcia, Rhett M Rautsaw, Erich P Hofmann, Christoph I Grünwald, Hector Franz-Chavez, Ivan T Ahumada-Carrillo, Ricardo Ramirez-Chaparro, Miguel Angel de la Torre-Loranca, Jason L Strickland, Andrew J Mason, Matthew L Holding, Miguel Borja, Gamaliel Castaneda-Gaytan, Edward A Myers, Mahmood Sasa, Darin R Rokyta, Christopher L Parkinson

引用次数: 0

Prebiotic Peptide Synthesis: How Did Longest Peptide Appear?

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-24 DOI: 10.1007/s00239-025-10237-9

Yuling Yang, Zhibiao Wang, Jin Bai, Hai Qiao

{"title":"Prebiotic Peptide Synthesis: How Did Longest Peptide Appear?","authors":"Yuling Yang, Zhibiao Wang, Jin Bai, Hai Qiao","doi":"10.1007/s00239-025-10237-9","DOIUrl":"https://doi.org/10.1007/s00239-025-10237-9","url":null,"abstract":"The origin of proteins is a fundamental question in the study of the origin of life. Peptides, as the building blocks of proteins, necessarily preceded the first proteins in prebiotic chemical evolution. Prebiotic peptides may have also played crucial roles in early life's evolution, contributing to self-catalysis, interacting with nucleic acids, and stabilizing primitive cell compartments. Longer and more complicated prebiotic peptides often have greater structural flexibility and functional potential to support the emergence and evolution of early life. Since the Miller-Urey experiment demonstrated that amino acids can be synthesized in a prebiotic manner, the prebiotic synthesis route of peptides has garnered increasing attention from researchers. However, it is difficult for amino acids to condense into peptides in aqueous solutions spontaneously. Over the past few decades, researchers have explored various routes of prebiotic peptide synthesis in the plausible prebiotic Earth environment, such as thermal polymerization, clay mineral catalysis, wet-dry cycles, condensing agents, and lipid-mediated. This paper reviews advancements in prebiotic peptide synthesis research and discusses the conditions that may have facilitated the emergence of longer peptides.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482087","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

An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-18 DOI: 10.1007/s00239-025-10238-8

Qiuhua Xie, Yuange Duan

引用次数: 0

Detection of an Alphacoronavirus in a Brazilian Bat (Molossus sp.).

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-17 DOI: 10.1007/s00239-025-10236-w

C L Molina, M M Magalhães, A C Rodrigues, S A Taniwaki, S O de Souza Silva, G A König, P E Brandão

{"title":"Detection of an Alphacoronavirus in a Brazilian Bat (Molossus sp.).","authors":"C L Molina, M M Magalhães, A C Rodrigues, S A Taniwaki, S O de Souza Silva, G A König, P E Brandão","doi":"10.1007/s00239-025-10236-w","DOIUrl":"https://doi.org/10.1007/s00239-025-10236-w","url":null,"abstract":"Due to the COVID-19 pandemic and the uncertainty about aspects of its origin, in recent years there has been an increased interest in investigating coronaviruses in wild animals. Bats are hosts of the greatest diversity of coronaviruses to date, including the ancestors of viruses that have caused outbreaks in humans. Although in Brazil, information on coronaviruses in bats has expanded, still they remain unrepresentative. To help shed some light on this matter, we collected 175 samples from bats of different species from two Brazilian states. Here, we report the previously unknown presence of an alphacoronavirus in a bat (Molossus sp.) from Ceará. The phylogenetic analysis showed close relationships with alphacoronaviruses from Brazil and Argentina, but it was not possible to determine the subgenus or species of this virus using RNA-dependent RNA-polymerase (RdRp) domain of the nsp12 protein-coding sequence as it was distant from the specimens considered by the International Committee on Taxonomy of Viruses (ICTV). Finally, by performing High-Throughput Sequencing, we were able to find contigs mostly belonging to domains of the replicase of bat coronaviruses related to American bats of the Molossidae and Vespertilionidae families.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441168","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

Selection Pressure Regulates the Evolution-Structure-Function Paradigm of Monocyte Chemoattractant Protein Family.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-05 DOI: 10.1007/s00239-025-10235-x

Nupur Nagar, Khushboo Gulati, Krishna Mohan Poluri

{"title":"Selection Pressure Regulates the Evolution-Structure-Function Paradigm of Monocyte Chemoattractant Protein Family.","authors":"Nupur Nagar, Khushboo Gulati, Krishna Mohan Poluri","doi":"10.1007/s00239-025-10235-x","DOIUrl":"https://doi.org/10.1007/s00239-025-10235-x","url":null,"abstract":"Monocyte chemoattractant proteins (MCPs) are involved in monocyte trafficking during severe inflammation by modulating the chemokine-glycosaminoglycan-receptor signaling axis. MCPs comprise a family of four chemokines (CCL2, CCL7, CCL8, and CCL13/12) that exhibit differential expression patterns in mammals, functional diversity, and receptor/glycosaminoglycan (GAG) binding promiscuity. In this context, the evolution-structure-function paradigm of MCP chemokines in mammals was established by assessing phylogeny, functional divergence, selection pressure, and coevolution in correlation with structural and surface characteristics. Comprehensive analyses were performed using an array of evolutionary and structural bioinformatic methods including molecular dynamics simulations. Our findings demonstrate that substitutions in receptor/GAG-interacting residues mediate episodic diversification and functional diversity in MCP chemokines. Additionally, a balanced interplay of selection pressures has driven the functional changes observed among MCP paralogs, with positive selection at various receptor/GAG-binding sites contributing to their promiscuous receptor/GAG interactions. Meanwhile, processes like purifying selection and coevolution maintain the classical chemokine structure and preserve the ancestral functions of MCP chemokines. Overall, this study suggests that selection pressure on sites within the N-terminal region [N-loop and 310-helix] and 40S loop of MCP chemokines alters surface properties to fine-tune the molecular interactions and functional characteristics without altering the overall chemokine structure.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189430","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