Plasmid最新文献 - Book学术

miRNA heterologous production in bacteria: A systematic review focusing on the choice of plasmid features and bacterial/prokaryotic microfactory. 细菌中的 miRNA 异源生产：系统综述，重点关注质粒特征选择和细菌/原核生物微工厂。

IF 1.8 4区生物学

Plasmid Pub Date : 2024-09-28 DOI: 10.1016/j.plasmid.2024.102731

Nyelson da Silva Nonato, Leandro Silva Nunes, Amanda Weege da Silveira Martins, Danillo Pinhal, William Borges Domingues, Dionet Keny Bellido-Quispe, Mariana Härter Remião, Vinicius Farias Campos

{"title":"miRNA heterologous production in bacteria: A systematic review focusing on the choice of plasmid features and bacterial/prokaryotic microfactory.","authors":"Nyelson da Silva Nonato, Leandro Silva Nunes, Amanda Weege da Silveira Martins, Danillo Pinhal, William Borges Domingues, Dionet Keny Bellido-Quispe, Mariana Härter Remião, Vinicius Farias Campos","doi":"10.1016/j.plasmid.2024.102731","DOIUrl":"10.1016/j.plasmid.2024.102731","url":null,"abstract":"Bacteria, the primary microorganisms used for industrial molecule production, do not naturally generate miRNAs. This study aims to systematically review current literature on miRNA expression systems in bacteria and address three key questions: (1) Which microorganism is most efficient for heterologous miRNA production? (2) What essential elements should be included in a plasmid construction to optimize miRNA expression? (3) Which commercial plasmid is most used for miRNA expression? Initially, 832 studies were identified across three databases, with fifteen included in this review. Three species-Escherichia coli, Salmonella typhimurium, and Rhodovulum sulfidophilum-were found as host organisms for recombinant miRNA expression. A total of 78 miRNAs were identified, out of which 75 were produced in E. coli, one in R. sulfidophilum (miR-29b), and two in S. typhimurium (mi-INHA and miRNA CCL22). Among gram-negative bacteria, R. sulfidophilum emerged as an efficient platform for heterologous production, thanks to features like nucleic acid secretion, RNase non-secretion, and seawater cultivation capability. However, E. coli remains the widely recognized model for large-scale miRNA production in biotechnology market. Regarding plasmids for miRNA expression in bacteria, those with an lpp promoter and multiple cloning sites appear to be the most suitable due to their robust expression cassette. The reengineering of recombinant constructs holds potential, as improvements in construct characteristics maximize the expression of desired molecules. The utilization of recombinant bacteria as platforms for producing new molecules is a widely used approach, with a focus on miRNAs expression for therapeutic contexts.","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330998","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

Development of a thermostable Cre/lox-based gene disruption system and in vivo manipulations of the megaplasmid pTT27 in Thermus thermophilus HB27 开发基于恒温 Cre/lox 的基因破坏系统并在嗜热菌 HB27 中对巨型质粒 pTT27 进行体内操作。

IF 1.8 4区生物学

Plasmid Pub Date : 2024-07-30 DOI: 10.1016/j.plasmid.2024.102730

{"title":"Development of a thermostable Cre/lox-based gene disruption system and in vivo manipulations of the megaplasmid pTT27 in Thermus thermophilus HB27","authors":"","doi":"10.1016/j.plasmid.2024.102730","DOIUrl":"10.1016/j.plasmid.2024.102730","url":null,"abstract":"<div>We previously reported the development of a Cre/lox-based gene disruption system for multiple markerless gene disruption in Thermus thermophilus; however, it was a time-consuming method because it functioned at 50 °C, the minimum growth temperature of T. thermophilus HB27. In the present study, we improved this system by introducing random mutations into the cre-expressing plasmid, pSH-Cre. One of the resulting mutant plasmids, pSH-CreFM allowed us to remove selection marker genes by Cre-mediated recombination at temperatures up to 70 °C. By using the thermostable Cre/lox system with pSH-CreFM, we successfully constructed two valuable pTT27 megaplasmid mutant strains, a plasmid-free strain and β-galactosidase gene deletion strain, which were produced by different methods. The thermostable Cre/lox system improved the time-consuming nature of the original Cre/lox system, but it was not suitable for multiple markerless gene disruption in T. thermophilus because of its highly efficient induction of Cre-mediated recombination even at 70 °C. However, in vivo megaplasmid manipulations performed at 65 °C were faster and easier than with the original Cre/lox system. Collectively, these results indicate that this system is a powerful tool for engineering T. thermophilus megaplasmids.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876503","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

Intercellular transfer of plasmid DNA between in vitro cultured HEK293 cells following transient transfection 瞬时转染后质粒 DNA 在体外培养的 HEK293 细胞之间的细胞间转移。

IF 1.8 4区生物学

Plasmid Pub Date : 2024-06-12 DOI: 10.1016/j.plasmid.2024.102729

Christoph Gerdes , F. Buket Basmanav

{"title":"Intercellular transfer of plasmid DNA between in vitro cultured HEK293 cells following transient transfection","authors":"Christoph Gerdes , F. Buket Basmanav","doi":"10.1016/j.plasmid.2024.102729","DOIUrl":"10.1016/j.plasmid.2024.102729","url":null,"abstract":"<div>Gene overexpression by transient transfection of in vitro cultured model cell lines with plasmid DNA is a commonly used method for studying molecular aspects of human biology and pathobiology. However, there is accumulating evidence suggesting that human cells may actively secrete fragments of DNA and the implications of this phenomenon for in vitro cultured cells transiently transfected with foreign nucleic acids has been overlooked. Therefore, in the current study we investigated whether a cell-to-cell transmission of acquired plasmid DNA takes place in a commonly used human cell line model.We transiently transfected HEK293 cells with EGFP encoding plasmids to serve as donor cells and either co-cultured these with stably mCherry expressing recipient cells in different set-ups or transferred their culture medium to the recipient cells. We found that recipient cells produced EGFP after being co-cultured with donor cells but not when they were exposed to their culture medium. The employment of different co-culture set-ups excluded that the observed effect stemmed from technical artefacts and provided evidence that an intercellular plasmid transfer takes place requiring physical proximity between living cells. This phenomenon could represent a significant biological artefact for certain studies such as those addressing protein transmissions in prion diseases.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0147619X2400009X/pdfft?md5=1390f4a6b988cc8a6b4f238ee9b2aaf7&pid=1-s2.0-S0147619X2400009X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321934","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

Variation in the plasmid backbone and dif module content of R3-T33 Acinetobacter plasmids R3-T33 阴沟杆菌质粒骨架和 dif 模块含量的变化

IF 2.6 4区生物学

Plasmid Pub Date : 2024-04-16 DOI: 10.1016/j.plasmid.2024.102722

Stephanie J. Ambrose, Ruth M. Hall

{"title":"Variation in the plasmid backbone and dif module content of R3-T33 Acinetobacter plasmids","authors":"Stephanie J. Ambrose, Ruth M. Hall","doi":"10.1016/j.plasmid.2024.102722","DOIUrl":"https://doi.org/10.1016/j.plasmid.2024.102722","url":null,"abstract":"<div>The predominant type of plasmids found in Acinetobacter species encode a Rep_3 initiation protein and many of these carry their accessory genes in dif modules. Here, available sequences of the 14 members of the group of Rep_3 plasmids typed as R3-T33, using a threshold of 95% identity in the repA gene, were compiled and compared. These plasmids were from various Acinetobacter species. The pdif sites were identified allowing the backbone and dif modules to be defined. As for other Rep_3 plasmids carrying dif modules, orfX encoding a protein of unknown function was found downstream of repA followed by a pdif site in the orientation XerC binding site–spacer–XerD binding site. Most backbones (n = 12) also included mobA and mobC genes but the two plasmids with the most diverged repA and orfX genes had different backbone contents. Although the gene content of the plasmid backbone was largely conserved, extensive recombinational exchange was detected and only two small groups carried identical or nearly identical backbones. Individual plasmids were associated with 1 to 13 dif modules. Many different dif modules were identified, including ones containing antibiotic or chromate resistance genes and several toxin/antitoxin gene pairs. In some cases, modules carrying the same genes were significantly diverged. Generally, the orientation of the pdif sites alternated such that C modules (XerC binding sites internal) alternated with D modules (XerD binding sites internal). However, fusions of two dif modules via mutational inactivation or loss of a pdif site were also detected.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0147619X24000027/pdfft?md5=e5d925dcad79fa60e75605f3964b2f92&pid=1-s2.0-S0147619X24000027-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140619425","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

Is the distribution of plasmid lengths bimodal? 质粒长度的分布是双峰的吗？

IF 2.6 4区生物学

Plasmid Pub Date : 2024-01-01 DOI: 10.1016/j.plasmid.2024.102721

Ian Dewan, Hildegard Uecker

引用次数: 0

The extensively antibiotic resistant ST111 Acinetobacter baumannii isolate RBH2 carries an extensive mobile element complement of plasmids, transposons and insertion sequences 广泛耐药的ST111鲍曼不动杆菌分离物RBH2携带广泛的质粒、转座子和插入序列的可移动元件补体

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":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":"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