IF 2.6 4区生物学

Plasmid Pub Date : 2023-09-01 DOI: 10.1016/j.plasmid.2023.102707

Stephanie J. Ambrose , Mehrad Hamidian , Ruth M. Hall

{"title":"The extensively antibiotic resistant ST111 Acinetobacter baumannii isolate RBH2 carries an extensive mobile element complement of plasmids, transposons and insertion sequences","authors":"Stephanie J. Ambrose , Mehrad Hamidian , Ruth M. Hall","doi":"10.1016/j.plasmid.2023.102707","DOIUrl":"10.1016/j.plasmid.2023.102707","url":null,"abstract":"<div>The complete genome of RBH2, a sporadic, carbapenem resistant ST111 Acinetobacter baumannii isolate from Brisbane, Australia was determined and analysed. RBH2 is extensively resistant and the chromosome includes two transposons carrying antibiotic resistance genes, AbaR4 (oxa23 in Tn2006) and Tn7::Tn2006 (dfrA1, sat2, aadA1, oxa23). The chromosome also includes two copies of Tn6175, a transposon carrying putative copper resistance genes, and 1–17 copies of six different insertion sequences. RBH2 has six plasmids ranging in size from 6 kb – 141 kb, four carrying antibiotic resistance genes. Plasmids pRBH2–1 (aadB) and pRBH2–2 (aphA6 in TnaphA6) were found to be essentially identical to known plasmids pRAY*-v1 and pS21–1, respectively. The largest plasmids, pRBH2–5 (oxa23 in AbaR4) and pRBH2–6 (oxa23 in AbaR4::ISAba11 and sul2, tet(B), strA and strB in Tn6172) have known transfer-proficient relatives. pRBH2–5, an RP-T1 (RepAci6) plasmid, also carries a different putative copper resistance transposon related to Tn6177 found in pS21–2. The backbone of pRBH2–5 is related to those of previously described RepAci6 plasmids pAb-G7–2 and pA85–3 but has some distinctive features. Three different RepAci6 backbone types were distinguished, Type 1 (pAb-G7–2), Type 2 (pA85–3) and Type 3 (pRBH2–5 and pS21–2). pRBH2–6 is closely related to pAB3 and their backbones differ by only 5 SNPs. Plasmids pRBH2–3 and pRBH2–4 do not carry antibiotic resistance genes. pRBH2–3 does not include an identifiable rep gene and is a novel plasmid type. pRBH2–4 is of the R3-T3 type and includes segments of the larger pABTJ2 that heads this group. Other ST111 genomes carry different plasmids.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"128 ","pages":"Article 102707"},"PeriodicalIF":2.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10268015","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

pSK41/pGO1-family conjugative plasmids of Staphylococcus aureus encode a cryptic repressor of replication 金黄色葡萄球菌pSK41/ pgo1家族结合质粒编码一个隐性复制抑制因子。

IF 2.6 4区生物学

Plasmid Pub Date : 2023-09-01 DOI: 10.1016/j.plasmid.2023.102708

Alvina Sarosh , Stephen M. Kwong , Slade O. Jensen , Faith Northern , William G. Walton , Thomas C. Eakes , Matthew R. Redinbo , Neville Firth , Krystle J. McLaughlin

{"title":"pSK41/pGO1-family conjugative plasmids of Staphylococcus aureus encode a cryptic repressor of replication","authors":"Alvina Sarosh , Stephen M. Kwong , Slade O. Jensen , Faith Northern , William G. Walton , Thomas C. Eakes , Matthew R. Redinbo , Neville Firth , Krystle J. McLaughlin","doi":"10.1016/j.plasmid.2023.102708","DOIUrl":"10.1016/j.plasmid.2023.102708","url":null,"abstract":"<div>The majority of large multiresistance plasmids of Staphylococcus aureus utilise a RepA_N-type replication initiation protein, the expression of which is regulated by a small antisense RNA (RNAI) that overlaps the rep mRNA leader. The pSK41/pGO1-family of conjugative plasmids additionally possess a small (86 codon) divergently transcribed ORF (orf86) located upstream of the rep locus. The product of pSK41 orf86 was predicted to have a helix-turn-helix motif suggestive of a likely function in transcriptional repression. In this study, we investigated the effect of Orf86 on transcription of thirteen pSK41 backbone promoters. We found that Orf86 only repressed transcription from the rep promoter, and hence now redesignate the product as Cop. Over-expression of Cop in trans reduced the copy number of pSK41 mini-replicons, both in the presence and absence of rnaI. in vitro protein-DNA binding experiments with purified 6 × His-Cop demonstrated specific DNA binding, adjacent to, and partially overlapping the −35 hexamer of the rep promoter. The crystal structure of Cop revealed a dimeric structure similar to other known transcriptional regulators. Cop mRNA was found to result from “read-through” transcription from the strong RNAI promoter that escapes the rnaI terminator. Thus, PrnaI is responsible for transcription of two distinct negative regulators of plasmid copy number; the antisense RNAI that primarily represses Rep translation, and Cop protein that can repress rep transcription. Deletion of cop in a native plasmid did not appear to impact copy number, indicating a cryptic auxiliary role.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"128 ","pages":"Article 102708"},"PeriodicalIF":2.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134650275","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

Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro 临床抗生素耐药质粒对体外培养的大肠杆菌生物膜形成和种群生长影响不大

IF 2.6 4区生物学

Plasmid Pub Date : 2023-09-01 DOI: 10.1016/j.plasmid.2023.102706

Laura Brülisauer , Ricardo León-Sampedro , Alex R. Hall

{"title":"Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro","authors":"Laura Brülisauer , Ricardo León-Sampedro , Alex R. Hall","doi":"10.1016/j.plasmid.2023.102706","DOIUrl":"10.1016/j.plasmid.2023.102706","url":null,"abstract":"<div>Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain-dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"128 ","pages":"Article 102706"},"PeriodicalIF":2.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10532255","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

In-silico functional analysis of hypothetical proteins from Lactiplantibacillus plantarum plasmids reveals enrichment of cell envelope proteins 对来自植物乳杆菌质粒的假定蛋白质的计算机功能分析揭示了细胞包膜蛋白质的富集。

IF 2.6 4区生物学

Plasmid Pub Date : 2023-07-01 DOI: 10.1016/j.plasmid.2023.102693

Dimple Davray, Ram Kulkarni

{"title":"In-silico functional analysis of hypothetical proteins from Lactiplantibacillus plantarum plasmids reveals enrichment of cell envelope proteins","authors":"Dimple Davray, Ram Kulkarni","doi":"10.1016/j.plasmid.2023.102693","DOIUrl":"10.1016/j.plasmid.2023.102693","url":null,"abstract":"<div>Lactiplantibacillus plantarum is one of the important species of lactic acid bacterium (LAB) found in diverse environments, with many strains exhibiting probiotic properties. In our previous study, 41.6% of protein families (PFs) encoded by 395 plasmids from several L. plantarum strains were found to be hypothetical proteins with no predicted function. This study aimed at predicting the functions of these 647 hypothetical proteins using 21 different bioinformatics methods. As a result, 160 PFs could be newly annotated. A lower proportion of plasmid-specific functions was annotated as compared to the functions shared between plasmids and chromosomes. Also, hypothetical proteins were less conserved than the annotated proteins across L. plantarum plasmids. Based on the subcellular localization, cell envelope proteins represented the biggest category in the newly annotated proteins. Transporters (112 PFs) which was a part of cell envelop proteins represented the largest functional group. Additionally, 40 and 25 other PFs were predicted to contain signal peptides and transmembrane helices, respectively. We speculate that such hypothetical proteins might be involved in the transport of various chemicals and environmental interactions in L. plantarum. In the future, functional characterization of these proteins through wet-lab experimental approach can provide novel insights into their contribution to the physiology, probiotic properties, and industrial utility of these bacteria.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"127 ","pages":"Article 102693"},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10432780","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: 1

Atypical low-copy number plasmid segregation systems, all in one? 非典型低拷贝数质粒分离系统，集于一体？

IF 2.6 4区生物学

Plasmid Pub Date : 2023-07-01 DOI: 10.1016/j.plasmid.2023.102694

Patricia Siguier, Manuel Campos, François Cornet, Jean-Yves Bouet, Catherine Guynet

引用次数: 0

A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites 细菌插入序列IS1202家族的一个亚类靶向XerCD重组位点。

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":"127 ","pages":"Article 102696"},"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":"127 ","pages":"Article 102698"},"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":"127 ","pages":"Article 102695"},"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":"127 ","pages":"Article 102686"},"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

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