Mobile genetic elements最新文献_第4页

Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome. 微生物群落中的基因流动可以解释大肠杆菌核心基因组中意想不到的同义变异模式。

Mobile genetic elements Pub Date : 2016-01-25 eCollection Date: 2016-01-01 DOI: 10.1080/2159256X.2015.1137380

Rohan Maddamsetti

{"title":"Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome.","authors":"Rohan Maddamsetti","doi":"10.1080/2159256X.2015.1137380","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1137380","url":null,"abstract":"Researchers contest the importance of gene flow in bacterial core genomes, as traditionalists view microbes as predominantly clonal, asexually reproducing organisms. Contrary to the traditional perspective, Escherichia coli core genes vary greatly in their levels of synonymous genetic diversity. This observation indicates that the relative importance of evolutionary forces such as mutation, selection, and recombination varies from gene to gene. In this paper, I highlight why the synonymous diversity observation is broadly relevant to researchers interested in the evolutionary dynamics of microbial populations and communities. I explain how a model of evolution called the coalescent relates neutral diversity (i.e. mutations with negligible fitness effects) to mutation rates, evolutionary time, and a parameter called effective population size. I then describe the possible ways in which mutation, selection, and recombination can explain observed patterns of synonymous diversity in E. coli. Finally, I describe a model for E. coli genome evolution in which different loci are subject to varying levels of gene flow among co-occurring microbes and viruses in the environment. Researchers can falsify the gene flow hypothesis by sequencing genes and strains isolated from stable microbiomes or by carrying out evolution experiments that trace gene genealogies in real-time.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":"e1137380"},"PeriodicalIF":0.0,"publicationDate":"2016-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1137380","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34755233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

MIX and match: mobile T6SS MIX-effectors enhance bacterial fitness. 混合搭配:移动T6SS混合效应器增强细菌适应度。

Mobile genetic elements Pub Date : 2016-01-13 eCollection Date: 2016-01-01 DOI: 10.1080/2159256X.2015.1123796

Dor Salomon

引用次数: 10

The role of mobile genetic elements in evolutionary longevity of heritable endobacteria. 活动遗传因子在可遗传内细菌进化寿命中的作用。

Mobile genetic elements Pub Date : 2015-12-30 eCollection Date: 2016-01-01 DOI: 10.1080/2159256X.2015.1136375

Mizue Naito, Teresa E Pawlowska

{"title":"The role of mobile genetic elements in evolutionary longevity of heritable endobacteria.","authors":"Mizue Naito, Teresa E Pawlowska","doi":"10.1080/2159256X.2015.1136375","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1136375","url":null,"abstract":"The movement of mobile genetic elements (MGEs), including bacteriophages, insertion sequence (IS) elements, and integrative and conjugative elements (ICEs) can have profound effects on bacterial evolution by introducing novel genes, or disrupting the existing ones. Obligate endobacteria are a distinctive group of bacteria that reside within the intracellular compartments of their eukaryotic hosts. Many obligate endobacteria are reproductively dependent on their hosts. Vertical transmission, in addition to degenerative genome contraction and loss of MGEs, makes heritable endobacteria vulnerable to Muller's ratchet, a process that jeopardizes evolutionary longevity of small populations. Mycoplasma-related endobacteria (MRE) are ancient heritable endosymbionts of arbuscular mycorrhizal fungi. Their genomes harbour numerous MGEs. To explore the significance of MGEs in the evolution of MRE and other obligate endobacteria, we analyze the impact of transmission mode, recombination, and evolutionary age on the maintenance of MGEs. Furthermore, we discuss the ability of MGEs to act as sites of gene conversion and recombination in endobacterial genomes. We propose that MGEs are important instruments of genome shuffling, contributing to population heterogeneity and evolutionary longevity in heritable obligate endobacteria.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":"e1136375"},"PeriodicalIF":0.0,"publicationDate":"2015-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1136375","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34741722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Stress out the LINEs. 强调台词。

Mobile genetic elements Pub Date : 2015-12-29 eCollection Date: 2016-01-01 DOI: 10.1080/2159256X.2015.1133267

Siqi Hu, Chen Liang, Fei Guo

引用次数: 0

The challenge of ORF1p phosphorylation: Effects on L1 activity and its host. ORF1p磷酸化的挑战:对L1活性及其宿主的影响。

Mobile genetic elements Pub Date : 2015-12-04 eCollection Date: 2016-01-01 DOI: 10.1080/2159256X.2015.1119927

Anthony V Furano, Pamela R Cook

引用次数: 9

The devil is in the details: Transposable element analysis of the Tasmanian devil genome. 细节决定成败:袋獾基因组的转座因子分析。

Mobile genetic elements Pub Date : 2015-12-04 eCollection Date: 2016-01-01 DOI: 10.1080/2159256X.2015.1119926

Maria A Nilsson

引用次数: 5

New clues on the regulation of the CRISPR-Cas immune system CRISPR-Cas免疫系统调控的新线索

Mobile genetic elements Pub Date : 2015-11-02 DOI: 10.1080/2159256X.2015.1117169

Magnus Lundgren

引用次数: 1

Alu elements and DNA double-strand break repair Alu元件与DNA双链断裂修复

Mobile genetic elements Pub Date : 2015-11-02 DOI: 10.1080/2159256X.2015.1093067

T. White, M. E. Morales, P. Deininger

{"title":"Alu elements and DNA double-strand break repair","authors":"T. White, M. E. Morales, P. Deininger","doi":"10.1080/2159256X.2015.1093067","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1093067","url":null,"abstract":"Alu elements represent one of the most common sources of homology and homeology in the human genome. Homeologous recombination between Alu elements represents a major form of genetic instability leading to deletions and duplications. Although these types of events have been studied extensively through genomic sequencing to assess the impact of Alu elements on disease mutations and genome evolution, the overall abundance of Alu elements in the genome often makes it difficult to assess the relevance of the Alu elements to specific recombination events. We recently reported a powerful new reporter gene system that allows the assessment of various cis and trans factors on the contribution of Alu elements to various forms of genetic instability. This allowed a quantitative measurement of the influence of mismatches on Alu elements and instability. It also confirmed that homeologous Alu elements are able to stimulate non-homologous end joining events in their vicinity. This appears to be dependent on portions of the mismatch repair pathway. We are now in a position to begin to unravel the complex influences of Alu density, mismatch and location with alterations of DNA repair processes in various tissues and tumors.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"81 - 85"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1093067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 18

The dualistic nature of integrative and conjugative elements 整体和共轭元素的二元性

Mobile genetic elements Pub Date : 2015-10-21 DOI: 10.1080/2159256X.2015.1102796

Nicolas Carraro, Vincent Burrus

{"title":"The dualistic nature of integrative and conjugative elements","authors":"Nicolas Carraro, Vincent Burrus","doi":"10.1080/2159256X.2015.1102796","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1102796","url":null,"abstract":"Integrative and conjugative elements (ICEs) are mobile genetic elements that play a key role in bacterial adaptation. Such elements are found in almost every bacterial genera and species, and often code for adaptive traits conferring selective advantages to their host. ICEs maintain by integrating into and replicating along with a replicon of the host genome. ICEs can propagate by conjugative transfer toward a recipient cell following excision from the replicon as a circular covalently-closed molecule. For a long time, the excised form of ICEs was assumed to be non-replicative. This assumption predicts that excised ICEs are sensitive to loss during cell division, unless they carry stabilization systems such as addiction modules or antibiotic resistance genes. Over the past few years, growing evidence have been presented that support conditional replication of the circular intermediate as an intrinsic feature of ICEs. We recently confirmed this feature in the large family of SXT/R391 ICEs, which thrive in several species of Enterobacteriaceae and Vibrionaceae. Furthermore, we demonstrated that SXT/R391 ICEs encode a functional plasmid-like type II partition system that enhances their stability, such systems being probably encoded by other ICEs. The lifecycle of ICEs is therefore much more complex than initially thought as many ICEs may use plasmid-like features to improve their stability and dissemination.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"98 - 102"},"PeriodicalIF":0.0,"publicationDate":"2015-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1102796","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 38

LINE retrotransposition and host DNA repair machinery. LINE逆转录和宿主DNA修复机制

Mobile genetic elements Pub Date : 2015-10-20 eCollection Date: 2015-11-01 DOI: 10.1080/2159256X.2015.1096998

Katsumi Yamaguchi, Masaki Kajikawa, Norihiro Okada

{"title":"LINE retrotransposition and host DNA repair machinery.","authors":"Katsumi Yamaguchi, Masaki Kajikawa, Norihiro Okada","doi":"10.1080/2159256X.2015.1096998","DOIUrl":"10.1080/2159256X.2015.1096998","url":null,"abstract":"Long interspersed elements (LINEs), or non-long-terminal repeat (LTR) retrotransposons, are mobile genetic elements that exist in the genomic DNA of most eukaryotes, comprising a considerable portion of the host chromosomes. LINEs constitute endogenous mutagens that cause insertional mutations in host chromosomes and have a large impact on host genome evolution. Despite their importance, however, the molecular mechanism of LINE retrotransposition is not fully understood. Several studies suggest that host proteins that participate in the repair of DNA breaks modulate LINE retrotransposition. Recently, we provided evidence that there are 2 distinct pathways-annealing and direct-that join the 5'-end of LINEs to host chromosomal DNA. These pathways appear to be used distinctively by zebrafish LINEs and the human L1 in DT40 cells. In HeLa cells, only the annealing pathway appears to be used. This implies that different characteristics of the 2 LINEs and also host factors dictate which pathway is selected. Here, we discuss the 5'-end-joining pathways of LINE retrotransposition and propose that the pathways of LINE integration adopt certain host repair factors.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"92-97"},"PeriodicalIF":0.0,"publicationDate":"2015-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0