IF 2.6 4区生物学

Plasmid Pub Date : 2023-07-01 DOI: 10.1016/j.plasmid.2023.102696

Patricia Siguier , Philippe Rousseau , François Cornet , Michael Chandler

{"title":"A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites","authors":"Patricia Siguier , Philippe Rousseau , François Cornet , Michael Chandler","doi":"10.1016/j.plasmid.2023.102696","DOIUrl":"10.1016/j.plasmid.2023.102696","url":null,"abstract":"<div>We describe here a new family of IS which are related to IS1202, originally isolated from Streptococcus pneumoniae in the mid-1990s and previously tagged as an emerging IS family in the ISfinder database. Members of this family have impacted some important properties of their hosts. We describe here another potentially important property of certain family members: specific targeting of xrs recombination sites.The family could be divided into three subgroups based on their transposase sequences and the length on the target repeats (DR) they generate on insertion: subgroup IS1202 (24–29 bp); ISTde1 (15–18 bp); and ISAba32 (5–6 bp). Members of the ISAba32 subgroup were repeatedly found abutting Xer recombinase recombination sites (xrs), separated by an intervening copy of a DR. These xrs sites, present in multiple copies in a number of Acinetobacter plasmids flanking antibiotic resistance genes, were proposed to form a new type of mobile genetic element using the chromosomally-encoded XerCD recombinase for mobility. Transposase alignments identified subgroup-specific indels which may be responsible for the differences in the transposition properties of the three subgroups (i.e. DR length and target specificity). We propose that this collection of IS be classed as a new insertion sequence family: the IS1202 family composed of three subgroups, only one of which specifically targets plasmid-borne xrs. We discuss the implications of xrs targeting for gene mobility.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10079716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Effect of the S008-sgaCD operon on IncC plasmid stability in the presence of SGI1-K or absence of an SGI1 variant 在存在SGI1-K或不存在SGI1变体的情况下，S008 sgaCD操纵子对IncC质粒稳定性的影响。

IF 2.6 4区生物学

Plasmid Pub Date : 2023-07-01 DOI: 10.1016/j.plasmid.2023.102698

Stephanie J. Ambrose, Ruth M. Hall

{"title":"Effect of the S008-sgaCD operon on IncC plasmid stability in the presence of SGI1-K or absence of an SGI1 variant","authors":"Stephanie J. Ambrose, Ruth M. Hall","doi":"10.1016/j.plasmid.2023.102698","DOIUrl":"10.1016/j.plasmid.2023.102698","url":null,"abstract":"<div>An IncC or IncA plasmid is needed to enable transfer of SGI1 type integrative mobilisable elements but an IncC plasmid does not stably co-exist with SGI1. However, the plasmid is stably maintained with SGI1-K, a natural SGI1 deletion variant that lacks the sgaDC genes (S007 and S006) and the upstream open reading frame (S008) found in the SGI1 backbone. Here, the effect of the sgaDC genes and S008 on the stability of an IncC plasmid in an Escherichia coli strain with or without SGI1-K was examined. Co-transcription of the S008 open reading frame with the downstream sgaDC genes was established. When a strain containing SGI1-K complemented with a pK18 plasmid that included S008-sgaDC or sgaDC expressed from the constitutive pUC promoter was grown without antibiotic selection, the resident IncC plasmid was rapidly lost but loss was slower when S008 was present. In contrast, SGI1-K and the S008-sgaDC or sgaDC plasmid were quite stably maintained for >100 generations. However, the high copy number plasmids carrying the SGI1-derived S008-sgaDC or sgaDC genes constitutively expressed could not be introduced into an E. coli strain carrying the IncC plasmid but without SGI1-K. Using equivalent plasmids with S008-sgaDC or sgaDC genes controlled by an arabinose-inducible promoter, under inducing conditions the IncC plasmid was stable but the plasmid containing the SGI1-derived genes was rapidly lost. This unexpected observation indicates that there are multiple interactions between the IncC plasmid and SGI1 in which the transcriptional activator genes sgaDC play a role. These interactions will require further investigation.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10069671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 overview of plasmid transfer in the plant microbiome 植物微生物组中质粒转移的综述。

IF 2.6 4区生物学

Plasmid Pub Date : 2023-07-01 DOI: 10.1016/j.plasmid.2023.102695

Angela M. Sánchez-Salazar , Tanvi Taparia , Asmus K. Olesen , Jacquelinne J. Acuña , Søren J. Sørensen , Milko A. Jorquera

{"title":"An overview of plasmid transfer in the plant microbiome","authors":"Angela M. Sánchez-Salazar , Tanvi Taparia , Asmus K. Olesen , Jacquelinne J. Acuña , Søren J. Sørensen , Milko A. Jorquera","doi":"10.1016/j.plasmid.2023.102695","DOIUrl":"10.1016/j.plasmid.2023.102695","url":null,"abstract":"<div>Plant microbiomes are pivotal for healthy plant physiological development. Microbes live in complex co-association with plant hosts, and interactions within these microbial communities vary with plant genotype, plant compartment, phenological stage, and soil properties, among others. Plant microbiomes also harbor a substantial and diverse pool of mobile genes encoded on plasmids. Several plasmid functions attributed to plant-associated bacteria are relatively poorly understood. Additionally, the role of plasmids in disseminating genetic traits within plant compartments is not well known. Here, we present the current knowledge on the occurrence, diversity, function, and transfer of plasmids in plant microbiomes, emphasizing the factors that could modulate gene transfer in-planta. We also describe the role of the plant microbiome as a plasmid reservoir and the dissemination of its genetic material. We include a brief discussion on the current methodological limitations in studying plasmid transfer within plant microbiomes. This information could be useful to elucidate the dynamics of the bacterial gene pools, the adaptations different organisms have made, and variations in bacterial populations that might have never been described before, particularly in complex microbial communities associated with plants in natural and anthropogenic impacted environments.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10453055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 2

CFTR and dystrophin encoding plasmids carrying both luciferase reporter gene, nuclear import specific sequences and triple helix sites CFTR和肌营养不良蛋白编码质粒携带荧光素酶报告基因、核导入特异性序列和三螺旋位点。

IF 2.6 4区生物学

Plasmid Pub Date : 2023-07-01 DOI: 10.1016/j.plasmid.2023.102686

Delphine Maze , Caroline Girardin , Nathalie Benz , Tristan Montier , Chantal Pichon , Patrick Midoux

{"title":"CFTR and dystrophin encoding plasmids carrying both luciferase reporter gene, nuclear import specific sequences and triple helix sites","authors":"Delphine Maze , Caroline Girardin , Nathalie Benz , Tristan Montier , Chantal Pichon , Patrick Midoux","doi":"10.1016/j.plasmid.2023.102686","DOIUrl":"10.1016/j.plasmid.2023.102686","url":null,"abstract":"<div>Duchenne Muscular Dystrophy and Cystic Fibrosis are two major monogenetic diseases which could be treated by non-viral gene therapy. For this purpose, plasmid DNA (pDNA) coding for the functional genes requires its equipment with signal molecules favouring its intracellular trafficking and delivery in the nucleus of the target cells. Here, two novel constructions of large pDNAs encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and full-length dystrophin (DYS) genes are reported. The expression of CFTR and DYS genes are driven respectively by the hCEF1 airway epithelial cells and spc5–12 muscle cells specific promoter. Those pDNAs encode also the luciferase reporter gene driven by the CMV promoter to evaluate gene delivery in animals by bioluminescence. In addition, oligopurine • oligopyrimidine sequences are inserted to enable equipment of pDNAs with peptides conjugated with a triple helix forming oligonucleotide (TFO). Furthermore, specific κB sequences are also inserted to promote their NFκB-mediated nuclear import. pDNA constructions are reported; transfection efficiency, tissue specific expression of CFTR and dystrophin in target cells, and triple helix formation are demonstrated. These plasmids are tools of interest to develop non-viral gene therapy of Cystic Fibrosis and Duchenne Muscular Dystrophy.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10090361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Plasmids on the move: Latest advances in Plasmid Biology from ISPB2022 移动中的质粒：来自ISPB2022的质粒生物学最新进展。

IF 2.6 4区生物学

Plasmid Pub Date : 2023-07-01 DOI: 10.1016/j.plasmid.2023.102697

Jean-Yves Bouet , François Cornet , Eva Top

引用次数: 0

Guidelines for the estimation and reporting of plasmid conjugation rates 质粒偶联率的估计和报告指南

IF 2.6 4区生物学

Plasmid Pub Date : 2023-05-01 DOI: 10.1016/j.plasmid.2023.102685

Olivia Kosterlitz , Jana S. Huisman

引用次数: 2

Reprogramming Targeted-Antibacterial-Plasmids (TAPs) to achieve broad-host range antibacterial activity 重编程靶向抗菌质粒(TAPs)以实现广泛的宿主抗菌活性

IF 2.6 4区生物学

Plasmid Pub Date : 2023-05-01 DOI: 10.1016/j.plasmid.2023.102680

Sarah Djermoun, Audrey Reuter, Elisabeth Derollez, Christian Lesterlin, Sarah Bigot

{"title":"Reprogramming Targeted-Antibacterial-Plasmids (TAPs) to achieve broad-host range antibacterial activity","authors":"Sarah Djermoun, Audrey Reuter, Elisabeth Derollez, Christian Lesterlin, Sarah Bigot","doi":"10.1016/j.plasmid.2023.102680","DOIUrl":"10.1016/j.plasmid.2023.102680","url":null,"abstract":"<div>The emergence and spread of antimicrobial resistance results in antibiotic inefficiency against multidrug resistant bacterial strains. Alternative treatment to antibiotics must be investigated to fight bacterial infections and limit this global public health problem. We recently developed an innovative strategy based on mobilizable Targeted-Antibacterial-Plasmids (TAPs) that deliver CRISPR/Cas systems with strain-specific antibacterial activity, using the F plasmid conjugation machinery for transfer into the targeted strains. These TAPs were shown to specifically kill a variety of Enterobacteriaceae strains, including E. coli K12 and the pathogen strains EPEC, Enterobacter cloacae and Citrobacter rodentium. Here, we extend the host-range of TAPs using the RP4 plasmid conjugation system for their mobilization, thus allowing the targeting of E. coli but also phylogenetically distant species, including Salmonella enterica Thyphimurium, Klebsiella pneumoniae, Vibrio cholerae, and Pseudomonas aeruginosa. This work demonstrates the versatility of the TAP strategy and represents a significant step toward the development of non-antibiotic strain-specific antimicrobial treatments.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9522047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 4

Calcium-responsive plasmid copy number regulation is dependent on discrete YopD domains in Yersinia pseudotuberculosis 假结核耶尔森菌中钙响应性质粒拷贝数调控依赖于离散的YopD结构域

IF 2.6 4区生物学

Plasmid Pub Date : 2023-05-01 DOI: 10.1016/j.plasmid.2023.102683

Pit Engling , Tifaine Héchard , Tomas Edgren , Matthew Francis , Petra Dersch , Helen Wang

{"title":"Calcium-responsive plasmid copy number regulation is dependent on discrete YopD domains in Yersinia pseudotuberculosis","authors":"Pit Engling , Tifaine Héchard , Tomas Edgren , Matthew Francis , Petra Dersch , Helen Wang","doi":"10.1016/j.plasmid.2023.102683","DOIUrl":"10.1016/j.plasmid.2023.102683","url":null,"abstract":"<div>Yersinia pathogenicity depends mainly on a Type III Secretion System (T3SS) responsible for translocating effector proteins into the eukaryotic target cell cytosol. The T3SS is encoded on a 70 kb, low copy number virulence plasmid, pYV. A key T3SS regulator, YopD, is a multifunctional protein and consists of discrete modular domains that are essential for pore formation and translocation of Yop effectors. In Y. pseudotuberculosis, the temperature-dependent plasmid copy number increase that is essential for elevated T3SS gene dosage and virulence is also affected by YopD. Here, we found that the presence of intracellular YopD results in increased levels of the CopA-RNA and CopB, two inhibitors of plasmid replication. Secretion of YopD leads to decreased expression of copA and copB, resulting in increased plasmid copy number. Moreover, using a systematic mutagenesis of YopD mutants, we demonstrated that the same discrete modular domains important for YopD translocation are also necessary for both the regulation of plasmid copy number as well as copA and copB expression. Hence, Yersinia has evolved a mechanism coupling active secretion of a plasmid-encoded component of the T3SS, YopD, to the regulation of plasmid replication. Our work provides evidence for the cross-talk between plasmid-encoded functions with the IncFII replicon.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9891223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Iteron control of oriV function in IncP-1 plasmid RK2 IncP-1质粒RK2中oriV功能的Iteron调控

IF 2.6 4区生物学

Plasmid Pub Date : 2023-05-01 DOI: 10.1016/j.plasmid.2023.102681

Anand P. Maurya , Alessandro Lazdins, Helen Wilson , Georgina S. Lloyd, Elton R. Stephens, Anthony S. Haines, Christopher M. Thomas

{"title":"Iteron control of oriV function in IncP-1 plasmid RK2","authors":"Anand P. Maurya , Alessandro Lazdins, Helen Wilson , Georgina S. Lloyd, Elton R. Stephens, Anthony S. Haines, Christopher M. Thomas","doi":"10.1016/j.plasmid.2023.102681","DOIUrl":"10.1016/j.plasmid.2023.102681","url":null,"abstract":"<div>Replication control of many plasmids is mediated by the balance between the positive and negative effects of Rep protein binding repeated sequences (iterons) associated with the replication origin, oriV. Negative control is thought to be mediated by dimeric Rep protein linking iterons in a process termed “handcuffing”. The well-studied oriV region of RK2 contains 9 iterons arranged as a singleton (iteron 1), a group of 3 (iterons 2–4) and a group of 5 (iterons 5–9), but only iterons 5 to 9 are essential for replication. An additional iteron (iteron 10), oriented in the opposite direction, is also involved and reduces copy-number nearly two-fold. Since iterons 1 and 10 share an identical upstream hexamer (5’ TTTCAT 3′) it has been hypothesised that they form a TrfA-mediated loop facilitated by their inverted orientation. Here we report that contrary to the hypothesis, flipping one or other so they are in direct orientation results in marginally lower rather than higher copy-number. In addition, following mutagenesis of the hexamer upstream of iteron 10, we report that the Logo for the hexamer “upstream” of the regulatory iterons (1 to 4 and 10) differs from that of the essential iterons, suggesting functional differences in their interaction with TrfA.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Plasmid classifications 质粒的分类

IF 2.6 4区生物学

Plasmid Pub Date : 2023-05-01 DOI: 10.1016/j.plasmid.2023.102684

M. Pilar Garcillán-Barcia , Santiago Redondo-Salvo , Fernando de la Cruz

引用次数: 5

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