Mobile genetic elements最新文献_第6页

Unraveling the regulatory network of IncA/C plasmid mobilization: When genomic islands hijack conjugative elements. 解开印加/C质粒动员的调控网络:当基因组岛劫持共轭元件。

Mobile genetic elements Pub Date : 2015-05-21 eCollection Date: 2015-05-01 DOI: 10.1080/2159256X.2015.1045116

Nicolas Carraro, Dominick Matteau, Vincent Burrus, Sébastien Rodrigue

{"title":"Unraveling the regulatory network of IncA/C plasmid mobilization: When genomic islands hijack conjugative elements.","authors":"Nicolas Carraro, Dominick Matteau, Vincent Burrus, Sébastien Rodrigue","doi":"10.1080/2159256X.2015.1045116","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1045116","url":null,"abstract":"Conjugative plasmids of the A/C incompatibility group (IncA/C) have become substantial players in the dissemination of multidrug resistance. These large conjugative plasmids are characterized by their broad host-range, extended spectrum of antimicrobials resistance, and prevalence in enteric bacteria recovered from both environmental and clinical settings. Until recently, relatively little was known about the basic biology of IncA/C plasmids, mostly because of the hindrance of multidrug resistance for molecular biology experiments. To circumvent this issue, we previously developed pVCR94ΔX, a convenient prototype that codes for a reduced set of antibiotic resistances. Using pVCR94ΔX, we then characterized the regulatory pathway governing IncA/C plasmid dissemination. We found that the expression of roughly 2 thirds of the genes encoded by this plasmid, including large operons involved in the conjugation process, depends on an FlhCD-like master activator called AcaCD. Beyond the mobility of IncA/C plasmids, AcaCD was also shown to play a key role in the mobilization of different classes of genomic islands (GIs) identified in various pathogenic bacteria. By doing so, IncA/C plasmids can have a considerable impact on bacterial genomes plasticity and evolution.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 3","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2015-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1045116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34134152","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: 22

LINE-1 activity as molecular basis for genomic instability associated with light exposure at night. LINE-1活性作为夜间光照下基因组不稳定性的分子基础。

Mobile genetic elements Pub Date : 2015-04-07 eCollection Date: 2015-05-01 DOI: 10.1080/2159256X.2015.1037416

Victoria P Belancio

引用次数: 16

Stable persistence of the yeast plasmid by hitchhiking on chromosomes during vegetative and germ-line divisions of host cells. 寄主细胞营养分裂和种系分裂期间，酵母质粒在染色体上搭便车的稳定持久性。

Mobile genetic elements Pub Date : 2015-04-07 eCollection Date: 2015-03-01 DOI: 10.1080/2159256X.2015.1031359

Soumitra Sau, Yen-Ting Liu, Chien-Hui Ma, Makkuni Jayaram

{"title":"Stable persistence of the yeast plasmid by hitchhiking on chromosomes during vegetative and germ-line divisions of host cells.","authors":"Soumitra Sau, Yen-Ting Liu, Chien-Hui Ma, Makkuni Jayaram","doi":"10.1080/2159256X.2015.1031359","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1031359","url":null,"abstract":"The chromosome-like stability of the Saccharomyces cerevisiae plasmid 2 micron circle likely stems from its ability to tether to chromosomes and segregate by a hitchhiking mechanism. The plasmid partitioning system, responsible for chromosome-coupled segregation, is comprised of 2 plasmid coded proteins Rep1 and Rep2 and a partitioning locus STB. The evidence for the hitchhiking model for mitotic plasmid segregation, although compelling, is almost entirely circumstantial. Direct tests for plasmid-chromosome association are hampered by the limited resolving power of current cell biological tools for analyzing yeast chromosomes. Recent investigations, exploiting the improved resolution of yeast meiotic chromosomes, have revealed the plasmid's propensity to be present at or near chromosome tips. This localization is consistent with the rapid plasmid movements during meiosis I prophase, closely resembling telomere dynamics driven by a meiosis-specific nuclear envelope motor. Current evidence is consistent with the plasmid utilizing the motor as a platform for gaining access to telomeres. Episomes of viruses of the papilloma family and the gammaherpes subfamily persist in latently infected cells by tethering to chromosomes. Selfish genetic elements from fungi to mammals appear to have, by convergent evolution, arrived at the common strategy of chromosome association as a means for stable propagation.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 2","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2015-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1031359","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34134147","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: 5

The "complex" RNA post-transcriptional element of a "simple" retrovirus. “简单”逆转录病毒的“复杂”RNA转录后元件。

Mobile genetic elements Pub Date : 2015-03-16 eCollection Date: 2015-03-01 DOI: 10.1080/2159256X.2015.1017085

Katarzyna J Purzycka, Guy R Pilkington, Barbara K Felber, Stuart F J Le Grice

{"title":"The \"complex\" RNA post-transcriptional element of a \"simple\" retrovirus.","authors":"Katarzyna J Purzycka, Guy R Pilkington, Barbara K Felber, Stuart F J Le Grice","doi":"10.1080/2159256X.2015.1017085","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1017085","url":null,"abstract":"Replication of retroviruses and transposition of endogenous retroelements exploits a unique mechanism of post-transcriptional regulation as a means of exporting their incompletely-spliced mRNAs (which serve as both the genomic RNA and the template for protein synthesis). Following discovery of the Rev response element (RRE) that mediates nucleocytoplasmic export of the full-length and singly-spliced human immunodeficiency virus type 1 (HIV-1) genome, equivalent cis-acting regulatory elements have been characterized for both complex and simple retroviruses and retroelements, together with the obligate viral and host proteins with which they interact. The exception to this is the gammaretrovirus family of simple retroviruses, exemplified by reticuloendotheliosis virus (REV), murine leukemia virus (MLV) and xenotropic MLV-related retrovirus (XMRV). In this commentary, we discuss our recent data that reported structural and functional data on the MLV/XMRV post-transcriptional regulatory element (designated the PTE). The PTE was characterized by a highly-structured region of multiple stem-loops (SL1 - SL7) overlapping the pro and 5' portion of the pol open reading frames, comprising a bipartite export signal whose structures are separated by ∼1400 nt. In addition, structural probing suggested that SL3 nucleotides were involved in pseudoknot formation. These data, when compared with RNA transport elements of complex retroviruses (HIV) and simple murine retrotransposons (musD), collectively present an emerging picture that long-range tertiary interactions are critical mediators of their biological function.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 2","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2015-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1017085","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34134148","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: 1

Applications of DNA integrating elements: Facing the bias bully. DNA整合元素的应用:面对偏见欺凌者。

Mobile genetic elements Pub Date : 2015-03-09 eCollection Date: 2014-11-01 DOI: 10.4161/2159256X.2014.992694

Johann de Jong, Lodewyk F A Wessels, Maarten van Lohuizen, Jeroen de Ridder, Waseem Akhtar

引用次数: 4

Rebooting the genome: The role of negative feedback in horizontal gene transfer. 重新启动基因组:负反馈在水平基因转移中的作用。

Mobile genetic elements Pub Date : 2015-02-23 eCollection Date: 2014-11-01 DOI: 10.4161/2159256X.2014.988069

Raul Fernandez-Lopez, Fernando de la Cruz

{"title":"Rebooting the genome: The role of negative feedback in horizontal gene transfer.","authors":"Raul Fernandez-Lopez, Fernando de la Cruz","doi":"10.4161/2159256X.2014.988069","DOIUrl":"https://doi.org/10.4161/2159256X.2014.988069","url":null,"abstract":"Horizontal Gene Transfer (HGT) is one of the key mechanisms driving bacterial evolution. Conjugative plasmids are fundamental vehicles for HGT in bacteria, playing an essential role in the spread of antibiotic resistances. Although the classical view has stressed the instrumental role of these mobile genetic elements in the dissemination of antibiotic resistance genes, plasmids contain a rich physiology devoted to horizontal and vertical reproduction. This particular lifestyle imposes specific constrains and trade-offs on plasmid physiology, and plasmids have evolved dedicated circuits to balance the opposing demands of vertical and horizontal reproduction. Recent studies on the transcriptional networks of IncW plasmids and other incompatibility groups have unveiled common architectures in the regulatory networks of different plasmid groups. Comparative studies show that negative feedback loops (NFLs) with strong gains are preferred, opening the question of a possible convergent evolution dictated by certain adaptive properties of this particular network motif. System analysis of NFLs with strong feedback gains indicate that this architecture exhibits transient overshooting after horizontal gene transfer. Since plasmid burden is dependent on the expression of plasmid functions, transcriptional overshooting results in a transient increase of the burden immediately after conjugation. We discuss the possible implications of this phenomenon on plasmid propagation, and the regulatory networks that plasmids have evolved to counteract the detrimental side effects of transient overshooting.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 6","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2015-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/2159256X.2014.988069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34236999","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: 11

Mobile genetic elements are involved in bacterial sociality. 移动遗传因子参与了细菌的社会性。

Mobile genetic elements Pub Date : 2015-02-04 eCollection Date: 2015-01-01 DOI: 10.1080/2159256X.2015.1006110

Tatiana Dimitriu, Dusan Misevic, Ariel B Lindner, François Taddei

{"title":"Mobile genetic elements are involved in bacterial sociality.","authors":"Tatiana Dimitriu, Dusan Misevic, Ariel B Lindner, François Taddei","doi":"10.1080/2159256X.2015.1006110","DOIUrl":"10.1080/2159256X.2015.1006110","url":null,"abstract":"Mobile genetic elements in bacteria are enriched in genes participating in social behaviors, suggesting an evolutionary link between gene mobility and social evolution. Cooperative behaviors, like the production of secreted public good molecules, are susceptible to the invasion of non-cooperative individuals, and their evolutionary maintenance requires mechanisms ensuring that benefits are directed preferentially to cooperators. In order to investigate the reasons for the mobility of public good genes, we designed a synthetic bacterial system where we control and quantify the transfer of public good production genes. In our recent study, we have experimentally shown that horizontal transfer helps maintain public good production in the face of both non-producer organisms and non-producer plasmids. Transfer spreads genes to neighboring cells, thus increasing relatedness and directing a higher proportion of public good benefits to producers. The effect is the strongest when public good genes undergo epidemics dynamics, making horizontal transfer especially relevant for pathogenic bacteria that repeatedly infect new hosts and base their virulence on costly public goods. The promotion of cooperation may be a general consequence of horizontal gene transfer in prokaryotes. Our work has an intriguing parallel, cultural transmission, where horizontal transfer, such as teaching, may preferentially promote cooperative behaviors.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"7-11"},"PeriodicalIF":0.0,"publicationDate":"2015-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f0/3d/kmge-05-01-1006110.PMC4588217.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34128794","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

Drawing a fine line on endogenous retroelement activity. 在内源性逆转录因子活性上划清界限。

Mobile genetic elements Pub Date : 2015-02-03 eCollection Date: 2015-01-01 DOI: 10.1080/2159256X.2015.1006109

Nathaly Castro-Diaz, Marc Friedli, Didier Trono

{"title":"Drawing a fine line on endogenous retroelement activity.","authors":"Nathaly Castro-Diaz, Marc Friedli, Didier Trono","doi":"10.1080/2159256X.2015.1006109","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1006109","url":null,"abstract":"Endogenous retroelements (EREs) are essential motors of evolution yet require careful control to prevent genomic catastrophes, notably during the vulnerable phases of epigenetic reprogramming that occur immediately after fertilization and in germ cells. Accordingly, a variety of mechanisms restrict these mobile genetic units. Previous studies have revealed the importance of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor, KAP1, in the early embryonic silencing of endogenous retroviruses and so-called SVAs, but the implication of this transcriptional repression system in the control of LINE-1, the only known active autonomous retrotransposon in the human genome, was thought to be marginal. Two recent studies straighten the record by revealing that the KRAB/KAP system is key to the control of L1 in embryonic stem (ES) cells, and go further in demonstrating that DNA methylation and KRAB/KAP1-induced repression contribute to this process in an evolutionally dynamic fashion. These results shed light on the delicate equilibrium between higher vertebrates and endogenous retroelements, which are not just genetic invaders calling for strict control but rather a constantly renewed and nicely exploitable source of evolutionary potential.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2015-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1006109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34237002","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: 24

Endogenous retrovirus-mediated genomic variations in chimpanzees. 内源性逆转录病毒介导的黑猩猩基因组变异。

Mobile genetic elements Pub Date : 2015-02-03 eCollection Date: 2014-11-01 DOI: 10.4161/2159256X.2014.990792

Yun-Ji Kim, Kyudong Han

{"title":"Endogenous retrovirus-mediated genomic variations in chimpanzees.","authors":"Yun-Ji Kim, Kyudong Han","doi":"10.4161/2159256X.2014.990792","DOIUrl":"10.4161/2159256X.2014.990792","url":null,"abstract":"Transposable elements (TEs) have played a significant role in the evolution of host genome by triggering genomic rearrangements. TEs have been studied in various research fields, ranging from population genomics to personalized medicines. Human-specific TEs and TEs existing in the human genome have been well studied. Unlike them, non-human primate-specific TEs remain shrouded in mystery. However, the study of TE-mediated genomic or genetic variations through comparative genomics is essential to understand mechanisms which TEs utilize to modify species-specific genome architecture and to cause species-specific diseases, Therefore, we have studied chimpanzee-specific TEs as well as human-specific TEs. At first, we identified human-specific HERV-K integrated into the human genome after the divergence of human and chimpanzee. Then, for a comparative study of HERV-Ks and non-human ERVs, we extracted chimpanzee-specific endogenous retroviruses (PtERVs) from the chimpanzee genome. We identified 256 chimpanzee-specific PtERVs and characterized them, focusing on their estimated evolutionary age, polymorphism level in chimpanzee populations, and potential impact on the difference between the human and chimpanzee genomes.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 6","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2015-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588550/pdf/kmge-04-06-990792.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34134145","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

Autonomous and non-autonomous Tn3-family transposons and their role in the evolution of mobile genetic elements. 自主和非自主tn3家族转座子及其在移动遗传元件进化中的作用。

Mobile genetic elements Pub Date : 2015-02-03 eCollection Date: 2014-11-01 DOI: 10.1080/2159256X.2014.998537

Magdalena Szuplewska, Jakub Czarnecki, Dariusz Bartosik

引用次数: 17