Plasmid最新文献 - Book学术

A Tribute to Manolo Espinosa 致敬马诺洛·埃斯皮诺萨

IF 2.2 4区生物学

Plasmid Pub Date : 2025-09-01 DOI: 10.1016/j.plasmid.2025.102758

Gloria del Solar , Christopher M. Thomas , Elisabeth Grohmann

引用次数: 0

Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs. 单菌株移动组测序量化细菌对应激的遗传反应，包括IS元件、前噬菌体、rna和REPINs的活性。

IF 2.2 4区生物学

Plasmid Pub Date : 2025-09-01 DOI: 10.1016/j.plasmid.2025.102759

Tue Kjærgaard Nielsen, Lars Hestbjerg Hansen

{"title":"Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs.","authors":"Tue Kjærgaard Nielsen, Lars Hestbjerg Hansen","doi":"10.1016/j.plasmid.2025.102759","DOIUrl":"10.1016/j.plasmid.2025.102759","url":null,"abstract":"<div><div>Microbial genomes are continuously being rearranged by mobile genetic elements (MGEs), leading to configurations that may confer novel phenotypic traits such as antibiotic resistance, degradation of compounds, or metabolic features. Standard genomic sequencing provides a snapshot of a genome in one configuration, but this static image does not give insight into the dynamics of genomic evolution and whether MGEs are actively changing a genome. We applied single-strain mobilome sequencing to <em>Escherichia coli</em> K-12 MG1655 under various stress conditions: UV, SDS, nalidixic acid, tetracycline, cetrimide, and copper. Under these conditions, we quantified the activity of a range of genetic elements, including extrachromosomal circular DNA (eccDNA) from IS elements, RNA genes, the UV-inducible e14 prophage, and intergenic repetitive sites (REP). Of the stressors, copper and SDS are among the largest inducers of eccDNA formation from some IS elements, while elevated levels of hypothetical RNA/DNA heteroduplexes of ribosomal and transfer RNAs, and Rhs-nuclease proteins are induced under various stressors, especially copper and SDS. This approach holds promise for quantifying the genetic response to environmental stress and implications for genome plasticity. The mobilization of IS elements upon copper and other stressors helps to explain co-selection of heavy metals with antibiotic resistance genes and MGEs.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102759"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151801","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

Insights from public database sequences related to the replication initiation protein TrfA of the IncP-1 plasmid RK2 来自IncP-1质粒RK2复制起始蛋白TrfA的公共数据库序列的见解。

IF 2.2 4区生物学

Plasmid Pub Date : 2025-08-16 DOI: 10.1016/j.plasmid.2025.102756

Haruo Suzuki , Kazuki Moriguchi , Masaki Shintani , Masato Suzuki , Hideaki Nojiri

{"title":"Insights from public database sequences related to the replication initiation protein TrfA of the IncP-1 plasmid RK2","authors":"Haruo Suzuki , Kazuki Moriguchi , Masaki Shintani , Masato Suzuki , Hideaki Nojiri","doi":"10.1016/j.plasmid.2025.102756","DOIUrl":"10.1016/j.plasmid.2025.102756","url":null,"abstract":"<div><div>Replicon typing identifies sequences similar to known DNA replication initiators and is widely used to detect specific plasmid groups (e.g., IncP-1) in genome and metagenome sequencing data. However, the characteristics of these homologous sequences in public databases have not been systematically assessed, making it difficult to determine whether detecting a specific replicon type reliably indicates the presence of a particular plasmid group. Here, we conducted amino acid sequence alignments to identify sequences similar to the replication initiation protein TrfA of the IncP-1 plasmid RK2 in the NCBI non-redundant (nr) database. In the nr nucleotide database, TrfA-matched nucleotide sequences were found across diverse taxonomic groups and replicons, including complete and partial plasmids and chromosomes. In total, 76 protein sequences from the reference plasmid RK2 were screened against the nucleotide sequences of the <em>trfA</em>-harboring plasmids to identify candidate IncP-1 plasmids. TrfA-related proteins, originating from bacterial chromosomes, plasmids, and phages, were selected from the nr amino acid database and used to infer phylogenetic trees. Our phylogenetic analyses reveal that TrfA homologs have diverged through vertical inheritance within IncP-1 and horizontal gene transfer across replicons and taxa. These findings caution against overreliance on single-gene replicon typing to infer plasmid group identity from sequence data.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102756"},"PeriodicalIF":2.2,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876492","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

Prevention of RK2 plasmid replication initiation in starved Escherichia coli cells 饥饿大肠杆菌细胞中RK2质粒复制起始的预防

IF 1.8 4区生物学

Plasmid Pub Date : 2025-07-20 DOI: 10.1016/j.plasmid.2025.102755

Ewelina Boguszewska , Igor Konieczny

{"title":"Prevention of RK2 plasmid replication initiation in starved Escherichia coli cells","authors":"Ewelina Boguszewska , Igor Konieczny","doi":"10.1016/j.plasmid.2025.102755","DOIUrl":"10.1016/j.plasmid.2025.102755","url":null,"abstract":"<div><div>Bacterial adaptation to environmental stress involves stringent regulation of DNA replication. While the mechanisms controlling chromosomal replication under adverse conditions, such as amino acid starvation, are relatively well characterized, the molecular basis for stress-induced inhibition of plasmid replication remains largely unknown. In this study, we investigated how amino acid starvation affects the replication of the broad-host-range RK2 plasmid in <em>Escherichia coli</em>, focusing on the plasmid-encoded replication initiator TrfA and host-encoded initiator DnaA. We found that the RK2 plasmid origin of replication (<em>oriV</em>) occupation by TrfA and DnaA is prevented in stress conditions. We also did not detect increase of plasmid DNA level showing that new rounds of RK2 replication are not initiated. The replication-inactive state persisted even in cells expressing a hyperactive monomeric TrfA variant that is incapable of handcuffing, indicating that other regulatory mechanisms, beyond handcuffing, contribute to the prevention of the plasmid replication. The reduction of initiators binding to the plasmid origin during stress coincided with a substantial decrease in the intracellular levels of TrfA, as shown in this study, and of DnaA, as reported previously. Given that cell division is arrested during stress, the only explanation for the observed gradual decrease of TrfA levels is proteolysis. Our findings demonstrate that during amino acids starvation, RK2 plasmid replication in <em>E. coli</em> is likely prevented by a significant drop in initiator proteins concentrations. This uncovers a previously underappreciated layer of plasmid replication control under stress conditions.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102755"},"PeriodicalIF":1.8,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680624","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

Strategies for zygotic gene expression during plasmid establishment 质粒建立过程中合子基因表达策略。

IF 1.8 4区生物学

Plasmid Pub Date : 2025-06-26 DOI: 10.1016/j.plasmid.2025.102754

Nathan Fraikin , Bruria Samuel , David Burstein , Christian Lesterlin

引用次数: 0

Discovery and assembly of plasmids in the fish pathogen Tenacibaculum 鱼病原体腱藻质粒的发现与组装。

IF 1.8 4区生物学

Plasmid Pub Date : 2025-06-18 DOI: 10.1016/j.plasmid.2025.102753

Ashton N. Sies , Joseph P. Nowlan , Laura J. Schnell , John S. Lumsden , Spencer Russell , Andrew D.S. Cameron

{"title":"Discovery and assembly of plasmids in the fish pathogen Tenacibaculum","authors":"Ashton N. Sies , Joseph P. Nowlan , Laura J. Schnell , John S. Lumsden , Spencer Russell , Andrew D.S. Cameron","doi":"10.1016/j.plasmid.2025.102753","DOIUrl":"10.1016/j.plasmid.2025.102753","url":null,"abstract":"<div><div>Members of the marine bacterial genus <em>Tenacibaculum</em> cause disease in finfish and outbreaks result in significant animal harm and losses in aquaculture around the globe. Plasmids have not been previously identified in <em>Tenacibaculum</em>, but long-read DNA sequencing of genomes from disease-associated <em>Tenacibaculum</em> isolates collected between 2017 and 2020 in British Columbia, Canada, revealed circular putative plasmids in three <em>Tenacibaculum</em> species. In addition to high-quality circular assembly, the putative plasmids contained genes encoding plasmid replication, mobility, and partitioning proteins. Genes for type B conjugation machinery and type 6<sub>iii</sub> secretion system components were also identified on each of the two largest plasmid sequences. Several protocols were tested to visualize and enrich <em>Tenacibaculum</em> plasmid DNA. Rolling-circle replication with Phi29 DNA polymerase amplified putative plasmids smaller than 100 kb. Alkaline lysis extraction provided weak enrichment of putative plasmid DNA, but plasmids could not be confidently resolved by Eckhardt extraction and electrophoresis in agarose gels. The newly assembled plasmids matched previously sequenced <em>Tenacibaculum</em> contigs, suggesting that publicly available <em>Tenacibaculum</em> genomes contain unrecognized plasmids. The discovery of putative plasmids in <em>Tenacibaculum</em> is significant because plasmids often confer important functions to host cells and serve as vehicles for horizontal gene transfer within and beyond the host bacterial species.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102753"},"PeriodicalIF":1.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337179","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

Rep_3 plasmids found in Acinetobacter species that include orfX also harbour dif modules 在含有orfX的不动杆菌中发现的Rep_3质粒也含有dif模块

IF 1.8 4区生物学

Plasmid Pub Date : 2025-01-01 DOI: 10.1016/j.plasmid.2025.102745

Stephanie J. Ambrose, Carol H. Pong, Ruth M. Hall

{"title":"Rep_3 plasmids found in Acinetobacter species that include orfX also harbour dif modules","authors":"Stephanie J. Ambrose, Carol H. Pong, Ruth M. Hall","doi":"10.1016/j.plasmid.2025.102745","DOIUrl":"10.1016/j.plasmid.2025.102745","url":null,"abstract":"<div><div>Plasmids found in <em>Acinetobacter</em> species are not found in other Gram-negative species. There are many distinct plasmid types and the majority encode a Rep_3 family RepA replication initiation protein. Among these, a number were known to carry <em>dif</em> modules. Here, the representative plasmid for each of the 78 reported R3 types was examined to identity features of the plasmid backbone that are associated with the carriage of <em>dif</em> modules. A conserved open reading frame designated orfX (IPR047783) was found downstream of <em>repA</em> in 35 of them, and the backbones of those 35 plasmids were bounded by recombination sites recognised by XerC and XerD, known as p<em>dif</em> sites. These plasmid backbones are all equivalent to a C-type <em>dif</em> module as the p<em>dif</em> sites are in the orientation D/C at one end and C/D at the other end, i.e. the XerC binding sites are internal. Hence, to provide the XerD binding sites and generate a complete plasmid at least one D-type <em>dif</em> module is needed. Phylogenies of the RepA and OrfX proteins revealed that plasmids with closely-related RepA proteins are not always associated with closely-related OrfX proteins and vice-versa indicating extensive backbone recombination. Folded structures of diverse OrfX proteins predicted using AlphaFold 3 revealed an N-terminal HTH domain followed by a long α-helix that is predicted to promote dimerization and a disordered C-terminus. Given the correlation between the presence of orfX and one or more <em>dif</em> modules, the possibility that OrfX is involved in <em>dif</em> module movement deserves to be investigated.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"133 ","pages":"Article 102745"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891122","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

SGI1 excludes IncA and IncC plasmids SGI1不包括IncA和IncC质粒。

IF 1.8 4区生物学

Plasmid Pub Date : 2025-01-01 DOI: 10.1016/j.plasmid.2025.102743

Stephanie J. Ambrose, Ruth M. Hall

{"title":"SGI1 excludes IncA and IncC plasmids","authors":"Stephanie J. Ambrose, Ruth M. Hall","doi":"10.1016/j.plasmid.2025.102743","DOIUrl":"10.1016/j.plasmid.2025.102743","url":null,"abstract":"<div><div>SGI1 and its many variant forms are integrative mobilizable elements that rely on IncA or IncC plasmids for transfer functions. However, the coexistence of SGI1 with the plasmid is unstable in the longer term. Here, we have investigated the effect of SGI1 type integrative elements on the initial entry of these plasmids. Using two transfer proficient IncC plasmids and the IncA plasmid RA1, exclusion indices were 40–100-fold for SGI1-I or SGI1-D which have a complete backbone. Using the SGI1-K and SGI1-LK1 variants that lack backbone segments, loss of a region of 5793 bp that includes the <em>traHG</em> transfer genes and the downstream open reading frame S010 was found to abolish exclusion. S010 was shown to be co-transcribed with <em>traHG</em> and hence also under the control of an AcaDC inducible promoter. However, complementation with a 5.2 kbp fragment that included the <em>traHG</em>-S010 operon did not restore exclusion activity to SGI1-LK1. Part of S013 that encodes a small polypeptide of unknown function, was also lost from SGI1-LK1. S013 and the adjacent S014 gene were also co-transcribed. However complementation with S013-S014 did not restore exclusion activity to SGI1-LK1. Hence, the precise cause of the SGI1-mediated plasmid exclusion remains elusive.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"133 ","pages":"Article 102743"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Our friend and colleague Laura Frost: A brief tribute 我们的朋友和同事劳拉·弗罗斯特：简短的致敬。

IF 1.8 4区生物学

Plasmid Pub Date : 2025-01-01 DOI: 10.1016/j.plasmid.2025.102744

Beth Traxler , Eva Top

引用次数: 0

Characterization and functional insights of the novel RC-type plasmid pAnox1 from Anoxybacillus gonensis 05S15 来自冈氏无氧杆菌 05S15 的新型 RC 型质粒 pAnox1 的特征和功能研究

IF 1.8 4区生物学

Plasmid Pub Date : 2024-09-01 DOI: 10.1016/j.plasmid.2024.102732

Gamze Cubukci , Hatice Ayyildiz , Kadriye Inan Bektas , Ali Osman Belduz , Halil Ibrahim Guler

{"title":"Characterization and functional insights of the novel RC-type plasmid pAnox1 from Anoxybacillus gonensis 05S15","authors":"Gamze Cubukci , Hatice Ayyildiz , Kadriye Inan Bektas , Ali Osman Belduz , Halil Ibrahim Guler","doi":"10.1016/j.plasmid.2024.102732","DOIUrl":"10.1016/j.plasmid.2024.102732","url":null,"abstract":"<div><div>The plasmid pAnox1, isolated from <em>Anoxybacillus gonensis</em> 05S15, was sequenced and characterized as a circular, double-stranded DNA molecule of 1592 base pairs with a GC content of 40.01 %. Despite its cryptic nature and small genome, bioinformatic analyses identified conserved motifs associated with replication-related proteins, though BLAST searches revealed no significant homology with other plasmids. The plasmid genome contains five putative Open Reading Frames (ORFs), four palindromic sequences, and two direct repeats on both strands, suggesting regulatory roles. Electron microscopy and Southern hybridization studies confirmed that pAnox1 follows a Rolling Circle (RC) replication mode. The study further demonstrated that the plasmid encodes three distinct transcripts: ORF-1 and ORF-3 are oriented in the same direction, while ORF-5 is on the opposite strand. RACE and LACE analyses revealed transcript lengths of 903 bp for ORF1, 499 bp for ORF3, and 211 bp for ORF5. Quantitative real-time PCR estimated the relative copy number of pAnox1 at 127 ± 2 copies per chromosomal equivalent. This novel RC-type plasmid in the Anoxybacillus genome holds promise as a cloning and expression vector for biotechnological applications and in vivo protein engineering.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"131 ","pages":"Article 102732"},"PeriodicalIF":1.8,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142444650","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