Plasmid最新文献

{"title":"Megaplasmids of the enteropathogenic species Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus represent a group of novel genetic elements unrelated to other plasmids of Vibrionaceae","authors":"Maria Borowiak,&nbsp;Jens A. Hammerl,&nbsp;Eckhard Strauch","doi":"10.1016/j.plasmid.2025.102770","DOIUrl":"10.1016/j.plasmid.2025.102770","url":null,"abstract":"<div><div><em>Vibrio</em> (<em>V.</em>) <em>parahaemolyticus</em> is a marine-associated bacterium that has previously been linked to foodborne illness associated with seafood consumption. Various plasmids harbouring antimicrobial resistance and virulence genes have been described for <em>V. parahaemolyticus</em>. By whole genome sequencing, we found two <em>V. parahaemolyticus</em> strains harbouring a large additional circular genomic element of 0.882 Mbp. NCBI database search revealed that this element represents a rare but globally distributed megaplasmid detected in four additional <em>Vibrio</em> strains spanning distinct species (<em>V. parahaemolyticus</em>, <em>V. cholerae</em> and <em>V. vulnificus</em>), geographical origins, and hosts. In addition to the two megaplasmid-harbouring <em>V. parahaemolyticus</em> strains from our study, we also identified two megaplasmid-free isogenic strains in our strain collection, confirming that the megaplasmid is indeed a plasmid encoding non-obligatory functional traits. The divergent GC content and codon usage of the megaplasmid suggest a non-<em>Vibrio</em> origin. The genetic diversity found in the six investigated megaplasmid sequences indicates adaptation within the different <em>Vibrio</em> hosts. Although many of the megaplasmid genes could not be categorised through Cluster of Orthologous Genes (COG) classification, genes coding for partitioning systems, type IV secretion systems, defence systems, and toxin-antitoxin modules were identified. These contribute to a high plasmid stability, as we demonstrated by the curing experiments performed with our strains. Consequently, the megaplasmid described here represents a highly stable but adaptive genetic element that is characterised by as yet unexplored genetic traits.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"135 ","pages":"Article 102770"},"PeriodicalIF":2.2,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145705681","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}

{"title":"Comparative genomics of diverse Escherichia coli O157:H7 strains to characterize plasmids, prophages, virulence and antimicrobial resistance genes","authors":"Sydney Menzeko Gambushe ,&nbsp;Peter Ayodeji Idowu ,&nbsp;Oliver Tendayi Zishiri","doi":"10.1016/j.plasmid.2025.102771","DOIUrl":"10.1016/j.plasmid.2025.102771","url":null,"abstract":"<div><div>Plasmids play a critical role in bacterial evolution and represent major drivers of the emergence and dissemination of antimicrobial resistance. As primary mobile genetic elements (MGEs), plasmids facilitate the horizontal transfer of resistance determinants alongside genes associated with virulence, metabolic functions, and broader adaptive advantages. Recent studies have further highlighted the importance of conjugative plasmids, such as IncI1-like elements, in mediating the spread of extended-spectrum β-lactamase (ESBL) genes and other clinically relevant traits across diverse bacterial populations. Whether the recurrent detection of these plasmids is coincidental or reflects unique genetic features that enhance their capacity for transmission remains an important question in microbial genomics. In this context, the present study analyses complete genome sequences and whole-genome maps of <em>Escherichia coli</em> O157:H7 strains to characterize their antimicrobial resistance genes, virulence-associated loci, prophage content, and plasmid profiles. Publicly available sequences from the NCBI GenBank repository were examined using comparative genomic tools, including BRIG, VirulenceFinder, ResFinder, PlasmidFinder, and PHASTEST. This work also underscores the limited availability of whole-genome data for <em>E. coli</em> O157:H7 and O157:H7NM in developing regions, particularly within African countries, highlighting the need for expanded genomic surveillance. Comparative analyses revealed that most strains displayed high genomic similarity to the reference Sakai strain, with relatively few missing regions, although a subset exhibited reduced homology marked by numerous gaps. Prophages, bacteriophages integrated into the bacterial genome, were found to contribute substantially to genomic diversity, influencing virulence potential, antimicrobial resistance, and patterns of horizontal gene transfer. These findings emphasize the complex role of mobile genetic elements in shaping the evolution of <em>E. coli</em> O157:H7 and reinforce the importance of continued genomic sequencing to further elucidate the pathogen's diversity and adaptive mechanisms.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"135 ","pages":"Article 102771"},"PeriodicalIF":2.2,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145726945","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}

{"title":"Insights from public database sequences related to the replication initiation protein TrfA of the IncP-1 plasmid RK2","authors":"Haruo Suzuki ,&nbsp;Kazuki Moriguchi ,&nbsp;Masaki Shintani ,&nbsp;Masato Suzuki ,&nbsp;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":"2025-09-01","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}

{"title":"Prevention of RK2 plasmid replication initiation in starved Escherichia coli cells","authors":"Ewelina Boguszewska ,&nbsp;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":"2025-09-01","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}

{"title":"Discovery and assembly of plasmids in the fish pathogen Tenacibaculum","authors":"Ashton N. Sies ,&nbsp;Joseph P. Nowlan ,&nbsp;Laura J. Schnell ,&nbsp;John S. Lumsden ,&nbsp;Spencer Russell ,&nbsp;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_iii 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":"2025-09-01","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}

{"title":"A Tribute to Manolo Espinosa","authors":"Gloria del Solar ,&nbsp;Christopher M. Thomas ,&nbsp;Elisabeth Grohmann","doi":"10.1016/j.plasmid.2025.102758","DOIUrl":"10.1016/j.plasmid.2025.102758","url":null,"abstract":"","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102758"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145049353","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}

{"title":"Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids","authors":"Hanna Theodora Noordzij ,&nbsp;Meike T. Wortel ,&nbsp;Anna Heintz-Buschart ,&nbsp;Patricija Petrikonyte ,&nbsp;Eric J. de Muinck ,&nbsp;Pål Trosvik","doi":"10.1016/j.plasmid.2025.102761","DOIUrl":"10.1016/j.plasmid.2025.102761","url":null,"abstract":"<div><div>Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant <em>Bacteroides</em> plasmid pBI143. Overall, the genus <em>Bacteroides</em> had the highest plasmid carriage, while the highest plasmid diversity was observed in <em>Clostridium</em>, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102761"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145304067","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}

{"title":"Expression, purification, and refolding of an optimized SARS-CoV-2 receptor binding domain in E. coli","authors":"Anamika Biswas,&nbsp;Arighna Sarkar,&nbsp;Sreejith Raran-Kurussi,&nbsp;Kalyaneswar Mandal","doi":"10.1016/j.plasmid.2025.102760","DOIUrl":"10.1016/j.plasmid.2025.102760","url":null,"abstract":"<div><div>The outbreak of Coronavirus Disease 2019 (COVID-19) has posed a significant risk to global health, warranting the formulation of efficient preventive and therapeutic measures to tackle its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of coronaviruses plays a pivotal role in viral attachment and entry into host cells. The receptor-binding domain (RBD) of the SARS-CoV-2 S protein has demonstrated a robust binding affinity to ACE2 receptors in humans. Consequently, it has become a prime target for therapeutic interventions using antibodies, vaccines, or other designed inhibitors. We engineered an RBD sequence with refined ORF boundaries guided by structural insights, which enabled efficient in vitro refolding. This highlights the critical role of precise expression cassette design in a plasmid, extending beyond conventional parameters such as promoter or fusion tag selection. Using customized refolding procedures, we obtained 10–12 mg of active protein from a one-liter LB culture. The biological activity of the refolded RBD was confirmed by monitoring its interaction with the designed LCB1 miniprotein ligand by surface plasmon resonance, wherein they exhibited significant affinity levels as reflected by their dissociation constants (K_D values &lt;10 nM). The resulting RBD could be an ideal target for designing potent COVID-19 antivirals.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102760"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145264981","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}

{"title":"Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs.","authors":"Tue Kjærgaard Nielsen,&nbsp;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}

{"title":"Strategies for zygotic gene expression during plasmid establishment","authors":"Nathan Fraikin ,&nbsp;Bruria Samuel ,&nbsp;David Burstein ,&nbsp;Christian Lesterlin","doi":"10.1016/j.plasmid.2025.102754","DOIUrl":"10.1016/j.plasmid.2025.102754","url":null,"abstract":"<div><div>Conjugative plasmids are key drivers of horizontal gene transfer and the spread of antimicrobial resistance. Their successful establishment in new hosts requires overcoming diverse bacterial defence mechanisms, such as restriction-modification systems, CRISPR-Cas systems, and the SOS response. Plasmids achieve this through a leading region-encoded zygotic program of anti-defence genes expressed early in conjugation. This program employs diverse strategies, including single-stranded promoters, repressed double-stranded promoters, and protein translocation. This review explores the diversity of these zygotic programs, the mechanisms underlying their timely regulation, and the array of anti-defence functions they encode. Further investigation of leading region genes is crucial for discovering novel counter-defence strategies and understanding their tailored regulation across diverse plasmid and bacterial species, ultimately enabling us to better understand and potentially manipulate plasmid transfer.</div></div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":"134 ","pages":"Article 102754"},"PeriodicalIF":1.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144530724","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}