IF 2.6 4区生物学

Plasmid Pub Date : 2022-01-01 DOI: 10.1016/j.plasmid.2021.102616

Semiramis Castro-Jaimes , Gabriela Guerrero , Elena Bello-López , Miguel A. Cevallos

{"title":"Replication initiator proteins of Acinetobacter baumannii plasmids: An update note","authors":"Semiramis Castro-Jaimes , Gabriela Guerrero , Elena Bello-López , Miguel A. Cevallos","doi":"10.1016/j.plasmid.2021.102616","DOIUrl":"10.1016/j.plasmid.2021.102616","url":null,"abstract":"<div>The bioinformatic analysis that we made of 492 Acinetobacter baumannii plasmid sequences identified 418 genes encoding Replication Initiator (Rep) proteins that fell into at least fourteen groups according to the protein domains that they contained. The most abundant group of Rep proteins contained a Rep_3 superfamily domain, followed by Rep proteins containing Replicase/PriCT_1 superfamily domains, and then by Reps possessing only an HTH_MerR-SF superfamily domain. The remaining eleven groups contain only a few members. To evaluate the diversity of these Rep proteins, we classify them using the current scheme of GR homology groups, which contains 34 groups. However, we needed to create 22 additional GR homology groups to capture all the Rep protein diversity of the plasmid collection. Finally, our bioinformatic analysis suggests that a large fraction of the plasmids seem to have a restricted host range limited to Acinetobacter species, except for those belonging to GR38 that have a very wide host range. To facilitate the future analysis of the Rep proteins, we included a list of the DNA and protein sequences, in fasta format, of the representatives of each one of the GR homology groups.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39874655","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

Complete sequence of classic F-type plasmid pRK100 shows unique conservation over time and geographic location 经典f型质粒pRK100的完整序列在时间和地理位置上具有独特的保守性

IF 2.6 4区生物学

Plasmid Pub Date : 2022-01-01 DOI: 10.1016/j.plasmid.2022.102618

Marjanca Starčič Erjavec , Karmen Jeseničnik , Lauren P. Elam , Andrej Kastrin , Luka Predojević , Tatyana A. Sysoeva

{"title":"Complete sequence of classic F-type plasmid pRK100 shows unique conservation over time and geographic location","authors":"Marjanca Starčič Erjavec , Karmen Jeseničnik , Lauren P. Elam , Andrej Kastrin , Luka Predojević , Tatyana A. Sysoeva","doi":"10.1016/j.plasmid.2022.102618","DOIUrl":"10.1016/j.plasmid.2022.102618","url":null,"abstract":"<div>Plasmids exhibit great diversity of gene content and host ranges and are famous for quick adaptation to the genetic background of the bacterial host cell. In addition to observing ever evolving plasmids, some plasmids have conserved backbones: a stable core composition and arrangement of genes in addition to variable regions. There are a few reports of extremely conserved plasmids. Here we report the complete sequence of pRK100 plasmid – a large, well-characterized conjugative F-like plasmid found in an Escherichia coli strain isolated from a urinary tract infection patient in 1990. The sequence shows that the 142 kb-long pRK100 plasmid is nearly identical to plasmids circulating in distant geographical locations and found in different host E. coli strains between 2007 and 2017. We also performed additional functional characterization of pRK100. Our results showed that pRK100 does not have a strong pathogenicity phenotype in porcine primary bladder epithelial cell culture. Moreover, the conjugation of pRK100 seems to strongly depend on recipient characteristics. These observations and identification of the pRK100 plasmid in different strain genotypes leave the extreme sequence conservation and broad distribution of this plasmid unexplained.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ff/06/nihms-1777151.PMC8978152.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39858639","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

A role for the last C-terminal helix of the F plasmid segregating protein SopA in nucleoid binding and plasmid maintenance F质粒分离蛋白SopA的最后c端螺旋在类核结合和质粒维持中的作用

IF 2.6 4区生物学

Plasmid Pub Date : 2022-01-01 DOI: 10.1016/j.plasmid.2022.102617

Dipika Mishra, Anirudh Jakhmola, Ramanujam Srinivasan

{"title":"A role for the last C-terminal helix of the F plasmid segregating protein SopA in nucleoid binding and plasmid maintenance","authors":"Dipika Mishra, Anirudh Jakhmola, Ramanujam Srinivasan","doi":"10.1016/j.plasmid.2022.102617","DOIUrl":"10.1016/j.plasmid.2022.102617","url":null,"abstract":"<div>The rapid emergence and spread of antibiotic resistance is a growing global burden. Antibiotic resistance is often associated with large single or low copy number plasmids, which rely upon cytoskeletal proteins for their stable maintenance. While the mechanism of plasmid partitioning has been well established for the R plasmids, the molecular details by which the F plasmid is maintained is only beginning to emerge. The partitioning function of the F plasmid depends upon a ParA/ MinD family of proteins known as SopA. SopA, by virtue of its ATP-dependent non-specific DNA binding activity and association with the bacterial nucleoid, drives the segregation of the F plasmid into the daughter cells. This function further depends upon the stimulation of the ATPase activity of SopA by the SopBC complex. Here, we report that several residues in the last C-terminal helix in SopA play a crucial but distinct role in SopA function and plasmid maintenance. While the deletion of the last five residues in SopA does not affect its ability to bind the nucleoid or SopB, they severely affect the plasmid partitioning function. Further, we show that while mutations in certain polar residues in the C-terminal helix only mildly affect its localisation to the nucleoid, others cause defects in nsDNA binding and disrupt plasmid maintenance functions.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39919897","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

A single step three-strain in vivo Gateway reaction 单步三菌株体内Gateway反应

IF 2.6 4区生物学

Plasmid Pub Date : 2021-11-01 DOI: 10.1016/j.plasmid.2021.102608

Aaron Nicholas Gillman , Alexandra Helleux , Sören Abel

引用次数: 0

Frequency and diversity of small plasmids in mesophilic Aeromonas isolates from fish, water and sediment 鱼、水和沉积物中嗜中温气单胞菌分离株小质粒的频率和多样性

IF 2.6 4区生物学

Plasmid Pub Date : 2021-11-01 DOI: 10.1016/j.plasmid.2021.102607

Daniel Pérez-García , Violeta Larios-Serrato , Rogelio Rojas-Rios , Jorge Erick Otero-Olarra , Itza Mendoza-Sanchez , Everardo Curiel-Quesada , Abigail Pérez-Valdespino

{"title":"Frequency and diversity of small plasmids in mesophilic Aeromonas isolates from fish, water and sediment","authors":"Daniel Pérez-García , Violeta Larios-Serrato , Rogelio Rojas-Rios , Jorge Erick Otero-Olarra , Itza Mendoza-Sanchez , Everardo Curiel-Quesada , Abigail Pérez-Valdespino","doi":"10.1016/j.plasmid.2021.102607","DOIUrl":"10.1016/j.plasmid.2021.102607","url":null,"abstract":"<div>Plasmids are autonomous genetic elements ubiquitously present in bacteria. In addition to containing genetic determinants responsible for their replication and stability, some plasmids may carry genes that help bacteria adapt to different environments, while others without a known function are classified as cryptic. In this work we identified and characterized plasmids from a collection of mesophilic Aeromonas spp. (N = 90) isolated from water, sediments and fish. A total of 15 small plasmids ranging from 2287 to 10,558 bp, with an incidence of 16.7% (15/90) was found. Plasmids were detected in A. hydrophila (6), A. veronii (4), A. taiwanensis (2), A. jandaei (1), A. media (1) and Aeromonas sp. (1). There were no large or megaplasmids in the strains studied in this work. Analysis of coding sequences identified proteins associated to replication, mobilization, antibiotic resistance, virulence and stability. A considerable number of hypothetical proteins with unknown functions were also found. Some strains shared identical plasmid profiles, however, only two of them were clones. Small plasmids could be acting as a gene repositories as suggested by the presence of a gene encoding for a putative zonula occludens toxin (Zot) that causes diarrhea and the qnrB gene involved in quinolone resistance harbored in plasmids pAerXII and pAerXIII respectively.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39641184","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: 6

Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae 当代IncI1质粒参与肠杆菌科抗菌素耐药性的传播和扩散

IF 2.6 4区生物学

Plasmid Pub Date : 2021-11-01 DOI: 10.1016/j.plasmid.2018.12.001

Alessandra Carattoli, Laura Villa, Daniela Fortini, Aurora García-Fernández

引用次数: 50

Sequence polarity between the promoter and the adjacent gene modulates promoter activity 启动子和相邻基因之间的序列极性调节启动子的活性

IF 2.6 4区生物学

Plasmid Pub Date : 2021-09-01 DOI: 10.1016/j.plasmid.2021.102598

Tam T. Tran, Trevor C. Charles

{"title":"Sequence polarity between the promoter and the adjacent gene modulates promoter activity","authors":"Tam T. Tran, Trevor C. Charles","doi":"10.1016/j.plasmid.2021.102598","DOIUrl":"10.1016/j.plasmid.2021.102598","url":null,"abstract":"<div>Promoter engineering has been employed as a strategy to enhance and optimize the production of bio-products. Availability of promoters with predictable activities is needed for downstream application. However, whether promoter activity remains the same in different gene contexts remains unknown. Six consecutive promoters that have previously been determined to have different activity levels were used to construct six different versions of plasmid backbone pTH1227, followed by inserted genes encoding two polymer-producing enzymes. In some cases, promoter activity in the presence of inserted genes did not correspond to the reported activity levels in a previous study. After removing the inserted genes, the activity of these promoters returned to their previously reported level. These changes were further confirmed to occur at the transcriptional level. Polymer production using our newly constructed plasmids showed polymer accumulation levels corresponding to the promoter activity reported in our study. Our study demonstrated the importance of re-assessing promoter activity levels with regard to gene context, which could influence promoter activity, leading to different outcomes in downstream applications.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.plasmid.2021.102598","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39398310","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

An expression system of channelrhodopsin-2 driven by a minimal Arc/Arg3.1 promoter and Tet system was developed in human neuroblastoma cells 建立了由Arc/Arg3.1最小启动子和Tet系统驱动的channelrhodopsin-2在人神经母细胞瘤细胞中的表达体系

IF 2.6 4区生物学

Plasmid Pub Date : 2021-09-01 DOI: 10.1016/j.plasmid.2021.102597

Akara Metasuk , Narisorn Kitiyanant , Banthit Chetsawang

{"title":"An expression system of channelrhodopsin-2 driven by a minimal Arc/Arg3.1 promoter and Tet system was developed in human neuroblastoma cells","authors":"Akara Metasuk , Narisorn Kitiyanant , Banthit Chetsawang","doi":"10.1016/j.plasmid.2021.102597","DOIUrl":"10.1016/j.plasmid.2021.102597","url":null,"abstract":"<div>Advances in neuroscience have relied on the development of techniques that examine neuronal cell activities. One major challenge involves the limitations in labeling and controlling neuronal activities relating to the cell's activation state. In this study, the modified human codon-optimized channelrhodopsin-2 photoreceptor hChR2(C128S) was integrated into function with inducible gene expression methods and materials: the Tet system and the highly efficient minimum promoter of Arc/Arg3.1. The system successfully expressed the target fusion gene exclusively in activated SH-SY5Y human neuroblastoma cells while maintaining the essential characteristics of ChR2. The expression of the channelrhodopsin construct was observed, while the expression duration was refined by treatment with doxycycline. The optogenetic construct here tested the application of the minimum Arc/Arg3.1 promoter, an advanced immediate-early gene promoter, for the expression of the channelrhodopsin gene. Along with its noninvasive nature, this expression system promises to serve dual functions as a cell activity indicator and cell actuator, creating the possibility for researchers to precisely label cells according to their activation state and control the activities of specific neuronal cell populations.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.plasmid.2021.102597","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39326469","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

Simultaneous transformation of five vectors in Gluconobacter oxydans 五种载体在氧化葡萄杆菌中的同时转化

IF 2.6 4区生物学

Plasmid Pub Date : 2021-09-01 DOI: 10.1016/j.plasmid.2021.102588

Li Liu , Yue Chen , Shiqin Yu , Jian Chen , Jingwen Zhou

{"title":"Simultaneous transformation of five vectors in Gluconobacter oxydans","authors":"Li Liu , Yue Chen , Shiqin Yu , Jian Chen , Jingwen Zhou","doi":"10.1016/j.plasmid.2021.102588","DOIUrl":"10.1016/j.plasmid.2021.102588","url":null,"abstract":"<div>Gluconobacter oxydans is an obligate Gram-negative bacterium that belongs to the family Acetobacteraceae. It is one of the most frequently used microorganisms in industrial biotechnology to produce chemicals related to incomplete oxidation. However, the fine-tuning of G. oxydans is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. Thus, a series of shuttle vectors for G. oxydans inspired by a series of wild-type plasmids in different G. oxydans strains were constructed. Fifteen shuttle vectors were employed to express mCherry in G. oxydans WSH-003 using the replication origin of these wild-type plasmids. Among them, the intensity of fluorescent proteins expressed by p15-K-mCherry was about 10 times that of fluorescent proteins expressed by p5-K-mCherry. Quantitative real-time polymerase chain reaction showed that the relative copy number of p15-K-mCherry reached 19 and had high stability. In contrast, some of the plasmids had a relative copy number of less than 10. The co-expression of multiple shuttle vectors revealed five shuttle vectors that could be transformed into G. oxydans WSH-003 and could express five different fluorescent proteins. The shuttle vectors will facilitate genetic operations for Gluconobacter strains to produce useful compounds more efficiently.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.plasmid.2021.102588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39179512","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: 6

One-step construction of a food-grade expression system based on the URA3 gene in Kluyveromyces lactis 乳酸菌URA3基因一步法食品级表达体系的构建

IF 2.6 4区生物学

Plasmid Pub Date : 2021-07-01 DOI: 10.1016/j.plasmid.2021.102577

Zhicheng Liang , Mulan Deng , Zhi Zhang , Meirong Li , SuJin Zhou , ZhengGang Zhao , YunPing Mu , LiNa Wang , Chengyun Ning , Allan Zijian Zhao , Fanghong Li

{"title":"One-step construction of a food-grade expression system based on the URA3 gene in Kluyveromyces lactis","authors":"Zhicheng Liang , Mulan Deng , Zhi Zhang , Meirong Li , SuJin Zhou , ZhengGang Zhao , YunPing Mu , LiNa Wang , Chengyun Ning , Allan Zijian Zhao , Fanghong Li","doi":"10.1016/j.plasmid.2021.102577","DOIUrl":"10.1016/j.plasmid.2021.102577","url":null,"abstract":"<div>Proteins from food-grade expression systems can be used in food products and medical applications. Herein, we describe a one-step method of constructing an expression vector in Kluyveromyces lactis by combining a URA3-deficient strain and a plasmid vector with no drug-resistant selection. Adjacent DNA elements of the vector were assembled in a targeted manner through a reaction with a special recombinase to form a plasmid vector using a one-step reaction. The unnecessary fragments containing the pUC origin and the ampicillin resistance gene were removed, and the vector was isolated and purified before transformation. A single transformation of the vector can produce a URA3-deficient strain. PCR assay, sequencing, and western blot analysis all indicated that the method of vector construction and target protein expression (mCherry and human serum albumin) were successful. This method may potentially be applied to any species containing the URA3 gene; this system has the potential to become a safe and powerful tool for promoting protein expression in food-safe species.</div>","PeriodicalId":49689,"journal":{"name":"Plasmid","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.plasmid.2021.102577","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39036567","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

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