Journal of Molecular Evolution最新文献_第3页

Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology 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 3.9 3区生物学

Journal of Molecular Evolution Pub Date : 2024-09-11 DOI: 10.1007/s00239-024-10204-w

Bokai K. Zhang, Leonard Gines

{"title":"Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology","authors":"Bokai K. Zhang, Leonard Gines","doi":"10.1007/s00239-024-10204-w","DOIUrl":"https://doi.org/10.1007/s00239-024-10204-w","url":null,"abstract":"This literature review is to present a new direction in developing better treatment or preventive measures. The larger the body of an organism, the more numerous the cells, which theoretically lead to a higher risk of cancer. However, observational studies suggest the lack of correlation between body size and cancer risk, which is known as Peto’s paradox. The corollary of Peto’s paradox is that large organisms must be cancer-resistant. Further investigation of the anti-cancer mechanisms in each species could be potentially rewarding, and how the anti-cancer mechanisms found in wild animals can help influence and develop more effective cancer treatment in humans is the main focus of this literature review. Due to a lack of research and understanding of the exact molecular mechanisms of the researched species, only a few (Elephants and rodents) that have been extensively researched have made substantive contributions to human oncology. A new research direction is to investigate the positively selective genes that are related to cancer resistance and see if homologous genes are presented in humans. Despite the great obstacle of applying anti-cancer mechanisms to the human body from phylogenetically distant species, this research direction of gaining insights through investigating cancer-resisting evolutionary adaptations in wild animals has great potential in human oncology research.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142194313","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

Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality. 进化蛋白质多功能性的内在紊乱和其他可塑武库

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-30 DOI: 10.1007/s00239-024-10196-7

Asifa Aftab, Souradeep Sil, Seema Nath, Anirneya Basu, Sankar Basu

{"title":"Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality.","authors":"Asifa Aftab, Souradeep Sil, Seema Nath, Anirneya Basu, Sankar Basu","doi":"10.1007/s00239-024-10196-7","DOIUrl":"https://doi.org/10.1007/s00239-024-10196-7","url":null,"abstract":"Microscopic evolution at the functional biomolecular level is an ongoing process. Leveraging functional and high-throughput assays, along with computational data mining, has led to a remarkable expansion of our understanding of multifunctional protein (and gene) families over the past few decades. Various molecular and intermolecular mechanisms are now known that collectively meet the cumulative multifunctional demands in higher organisms along an evolutionary path. This multitasking ability is attributed to a certain degree of intrinsic or adapted flexibility at the structure-function level. Evolutionary diversification of structure-function relationships in proteins highlights the functional importance of intrinsically disordered proteins/regions (IDPs/IDRs) which are highly dynamic biological soft matter. Multifunctionality is favorably supported by the fluid-like shapes of IDPs/IDRs, enabling them to undergo disorder-to-order transitions upon binding to different molecular partners. Other new malleable members of the protein superfamily, such as those involved in fold-switching, also undergo structural transitions. This new insight diverges from all traditional notions of functional singularity in enzyme classes and emphasizes a far more complex, multi-layered diversification of protein functionality. However, a thorough review in this line, focusing on flexibility and function-driven structural transitions related to evolved multifunctionality in proteins, is currently missing. This review attempts to address this gap while broadening the scope of multifunctionality beyond single protein sequences. It argues that protein intrinsic disorder is likely the most striking mechanism for expressing multifunctionality in proteins. A phenomenological analogy has also been drawn to illustrate the increasingly complex nature of modern digital life, driven by the need for multitasking, particularly involving media.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108231","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

Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning. 分子进化原理：多层次学习理论的非平衡热力学概念》。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-29 DOI: 10.1007/s00239-024-10195-8

Jens Smiatek

引用次数: 0

Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks. 软体动物中 Pif/BMSP 中 von Willebrand Factor A 和几丁质结合域的多样化。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-01 Epub Date: 2024-06-12 DOI: 10.1007/s00239-024-10180-1

Keisuke Shimizu, Lumi Negishi, Hitoshi Kurumizaka, Michio Suzuki

{"title":"Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks.","authors":"Keisuke Shimizu, Lumi Negishi, Hitoshi Kurumizaka, Michio Suzuki","doi":"10.1007/s00239-024-10180-1","DOIUrl":"10.1007/s00239-024-10180-1","url":null,"abstract":"Pif is a shell matrix protein (SMP) identified in the nacreous layer of Pinctada fucata (Pfu) comprised two proteins, Pif97 and Pif 80. Pif97 contains a von Willebrand factor A (VWA) and chitin-binding domains, whereas Pif80 can bind calcium carbonate crystals. The VWA domain is conserved in the SMPs of various mollusk species; however, their phylogenetic relationship remains obscure. Furthermore, although the VWA domain participates in protein-protein interactions, its role in shell formation has not been established. Accordingly, in the current study, we investigate the phylogenetic relationship between PfuPif and other VWA domain-containing proteins in major mollusk species. The shell-related proteins containing VWA domains formed a large clade (the Pif/BMSP family) and were classified into eight subfamilies with unique sequential features, expression patterns, and taxa diversity. Furthermore, a pull-down assay using recombinant proteins containing the VWA domain of PfuPif 97 revealed that the VWA domain interacts with five nacreous layer-related SMPs of P. fucata, including Pif 80 and nacrein. Collectively, these results suggest that the VWA domain is important in the formation of organic complexes and participates in shell mineralisation.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306068","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

Sampling Strategies for Experimentally Mapping Molecular Fitness Landscapes Using High-Throughput Methods. 使用高通量方法实验绘制分子健壮性景观的取样策略

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-01 Epub Date: 2024-06-17 DOI: 10.1007/s00239-024-10179-8

Steven K Chen, Jing Liu, Alexander Van Nynatten, Benjamin M Tudor-Price, Belinda S W Chang

{"title":"Sampling Strategies for Experimentally Mapping Molecular Fitness Landscapes Using High-Throughput Methods.","authors":"Steven K Chen, Jing Liu, Alexander Van Nynatten, Benjamin M Tudor-Price, Belinda S W Chang","doi":"10.1007/s00239-024-10179-8","DOIUrl":"10.1007/s00239-024-10179-8","url":null,"abstract":"Empirical studies of genotype-phenotype-fitness maps of proteins are fundamental to understanding the evolutionary process, in elucidating the space of possible genotypes accessible through mutations in a landscape of phenotypes and fitness effects. Yet, comprehensively mapping molecular fitness landscapes remains challenging since all possible combinations of amino acid substitutions for even a few protein sites are encoded by an enormous genotype space. High-throughput mapping of genotype space can be achieved using large-scale screening experiments known as multiplexed assays of variant effect (MAVEs). However, to accommodate such multi-mutational studies, the size of MAVEs has grown to the point where a priori determination of sampling requirements is needed. To address this problem, we propose calculations and simulation methods to approximate minimum sampling requirements for multi-mutational MAVEs, which we combine with a new library construction protocol to experimentally validate our approximation approaches. Analysis of our simulated data reveals how sampling trajectories differ between simulations of nucleotide versus amino acid variants and among mutagenesis schemes. For this, we show quantitatively that marginal gains in sampling efficiency demand increasingly greater sampling effort when sampling for nucleotide sequences over their encoded amino acid equivalents. We present a new library construction protocol that efficiently maximizes sequence variation, and demonstrate using ultradeep sequencing that the library encodes virtually all possible combinations of mutations within the experimental design. Insights learned from our analyses together with the methodological advances reported herein are immediately applicable toward pooled experimental screens of arbitrary design, enabling further assay upscaling and expanded testing of genotype space.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419508","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: Untangling the Evolution of the Receptor-Binding Motif of SARS-CoV-2. 更正：解开 SARS-CoV-2 的受体结合基团的演变。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-01 DOI: 10.1007/s00239-024-10183-y

Luis Delaye, Lizbeth Román-Padilla

引用次数: 0

Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes. 无颌鱼类中长波长敏感光蛋白的扩展和功能多样化

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-01 Epub Date: 2024-06-11 DOI: 10.1007/s00239-024-10181-0

Jan Gerwin, Julián Torres-Dowdall, Thomas F Brown, Axel Meyer

{"title":"Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes.","authors":"Jan Gerwin, Julián Torres-Dowdall, Thomas F Brown, Axel Meyer","doi":"10.1007/s00239-024-10181-0","DOIUrl":"10.1007/s00239-024-10181-0","url":null,"abstract":"Gene duplication is one of the most important sources of novel genotypic diversity and the subsequent evolution of phenotypic diversity. Determining the evolutionary history and functional changes of duplicated genes is crucial for a comprehensive understanding of adaptive evolution. The evolutionary history of visual opsin genes is very dynamic, with repeated duplication events followed by sub- or neofunctionalization. While duplication of the green-sensitive opsins rh2 is common in teleost fish, fewer cases of multiple duplication events of the red-sensitive opsin lws are known. In this study, we investigate the visual opsin gene repertoire of the anabantoid fishes, focusing on the five lws opsin genes found in the genus Betta. We determine the evolutionary history of the lws opsin gene by taking advantage of whole-genome sequences of nine anabantoid species, including the newly assembled genome of Betta imbellis. Our results show that at least two independent duplications of lws occurred in the Betta lineage. The analysis of amino acid sequences of the lws paralogs of Betta revealed high levels of diversification in four of the seven transmembrane regions of the lws protein. Amino acid substitutions at two key-tuning sites are predicted to lead to differentiation of absorption maxima (λmax) between the paralogs within Betta. Finally, eye transcriptomics of B. splendens at different developmental stages revealed expression shifts between paralogs for all cone opsin classes. The lws genes are expressed according to their relative position in the lws opsin cluster throughout ontogeny. We conclude that temporal collinearity of lws expression might have facilitated subfunctionalization of lws in Betta and teleost opsins in general.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300795","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 Role of Selection and Migration in the Evolution of (Auto)Immunity Genes. 选择和迁移在（自身）免疫基因进化中的作用》（The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes.

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-01 Epub Date: 2024-06-26 DOI: 10.1007/s00239-024-10182-z

Konstantinos Voskarides

引用次数: 0

Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing. 从密码表中学习：趋同重编码为 A 到 I RNA 编辑的进化提供了新的理解。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-01 Epub Date: 2024-07-16 DOI: 10.1007/s00239-024-10190-z

Ling Ma, Caiqing Zheng, Jiyao Liu, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Yuange Duan

{"title":"Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing.","authors":"Ling Ma, Caiqing Zheng, Jiyao Liu, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Yuange Duan","doi":"10.1007/s00239-024-10190-z","DOIUrl":"10.1007/s00239-024-10190-z","url":null,"abstract":"Adenosine-to-inosine (A-to-I) RNA editing recodes the genetic information. Apart from diversifying the proteome, another tempting advantage of RNA recoding is to correct deleterious DNA mutation and restore ancestral allele. Solid evidences for beneficial restorative editing are very rare in animals. By searching for \"convergent recoding\" under a phylogenetic context, we proposed this term for judging the potential restorative functions of particular editing site. For the well-known mammalian Gln>Arg (Q>R) recoding site, its ancestral state in vertebrate genomes was the pre-editing Gln, and all 470 available mammalian genomes strictly avoid other three equivalent ways to achieve Arg in protein. The absence of convergent recoding from His>Arg, or synonymous mutations on Gln codons, could be attributed to the strong maintenance on editing motif and structure, but the absence of direct A-to-G mutation is extremely unexpected. With similar ideas, we found cases of convergent recoding in Drosophila genus, reducing the possibility of their restorative function. In summary, we defined an interesting scenario of convergent recoding, the occurrence of which could be used as preliminary judgements for whether a recoding site has a sole restorative role. Our work provides novel insights to the natural selection and evolution of RNA editing.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620133","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

Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders. 基因组巨型化与新热带蝾螈选择效率降低无关

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2024-08-01 Epub Date: 2024-06-06 DOI: 10.1007/s00239-024-10177-w

Hairo Rios-Carlos, María Guadalupe Segovia-Ramírez, Matthew K Fujita, Sean M Rovito

{"title":"Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders.","authors":"Hairo Rios-Carlos, María Guadalupe Segovia-Ramírez, Matthew K Fujita, Sean M Rovito","doi":"10.1007/s00239-024-10177-w","DOIUrl":"10.1007/s00239-024-10177-w","url":null,"abstract":"Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141283892","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