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Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
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Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
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2
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Cerdán L, Álvarez B, Fernández LÁ. Massive integration of large gene libraries in the chromosome of Escherichia coli. Microb Biotechnol 2024; 17:e14367. [PMID: 37971317 PMCID: PMC10832519 DOI: 10.1111/1751-7915.14367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/21/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023] Open
Abstract
Large gene libraries are frequently created in Escherichia coli plasmids, which can induce cell toxicity and expression instability due to the high gene dosage. To address these limitations, gene libraries can be integrated in a single copy into the bacterial chromosome. Here, we describe an efficient system for the massive integration (MAIN) of large gene libraries in the E. coli chromosome that generates in-frame gene fusions that are expressed stably. MAIN uses a thermosensitive integrative plasmid that is linearized in vivo to promote extensive integration of the gene library via homologous recombination. Positive and negative selections efficiently remove bacteria lacking gene integration in the target site. We tested MAIN with a library of 107 VHH genes that encode nanobodies (Nbs). The integration of VHH genes into a custom target locus of the E. coli chromosome enabled stable expression and surface display of the Nbs. Next-generation DNA sequencing confirmed that MAIN preserved the diversity of the gene library after integration. Finally, we screened the integrated library to select Nbs that bind a specific antigen using magnetic and fluorescence-activated cell sorting. This allowed us to identify Nbs binding the epidermal growth factor receptor that were not previously isolated in a similar screening of a multicopy plasmid library. Our results demonstrate that MAIN enables large gene library integration into the E. coli chromosome, creating stably expressed in-frame fusions for functional screening.
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Affiliation(s)
- Lidia Cerdán
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Beatriz Álvarez
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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3
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Kaltenbrunner A, Reimann V, Hoffmann UA, Aoyagi T, Sakata M, Nimura-Matsune K, Watanabe S, Steglich C, Wilde A, Hess WR. Regulation of pSYSA defense plasmid copy number in Synechocystis through RNase E and a highly transcribed asRNA. Front Microbiol 2023; 14:1112307. [PMID: 36876071 PMCID: PMC9978351 DOI: 10.3389/fmicb.2023.1112307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Synthetic biology approaches toward the development of cyanobacterial producer strains require the availability of appropriate sets of plasmid vectors. A factor for the industrial usefulness of such strains is their robustness against pathogens, such as bacteriophages infecting cyanobacteria. Therefore, it is of great interest to understand the native plasmid replication systems and the CRISPR-Cas based defense mechanisms already present in cyanobacteria. In the model cyanobacterium Synechocystis sp. PCC 6803, four large and three smaller plasmids exist. The ~100 kb plasmid pSYSA is specialized in defense functions by encoding all three CRISPR-Cas systems and several toxin-antitoxin systems. The expression of genes located on pSYSA depends on the plasmid copy number in the cell. The pSYSA copy number is positively correlated with the expression level of the endoribonuclease E. As molecular basis for this correlation we identified the RNase E-mediated cleavage within the pSYSA-encoded ssr7036 transcript. Together with a cis-encoded abundant antisense RNA (asRNA1), this mechanism resembles the control of ColE1-type plasmid replication by two overlapping RNAs, RNA I and II. In the ColE1 mechanism, two non-coding RNAs interact, supported by the small protein Rop, which is encoded separately. In contrast, in pSYSA the similar-sized protein Ssr7036 is encoded within one of the interacting RNAs and it is this mRNA that likely primes pSYSA replication. Essential for plasmid replication is furthermore the downstream encoded protein Slr7037 featuring primase and helicase domains. Deletion of slr7037 led to the integration of pSYSA into the chromosome or the other large plasmid pSYSX. Moreover, the presence of slr7037 was required for successful replication of a pSYSA-derived vector in another model cyanobacterium, Synechococcus elongatus PCC 7942. Therefore, we annotated the protein encoded by slr7037 as Cyanobacterial Rep protein A1 (CyRepA1). Our findings open new perspectives on the development of shuttle vectors for genetic engineering of cyanobacteria and of modulating the activity of the entire CRISPR-Cas apparatus in Synechocystis sp. PCC 6803.
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Affiliation(s)
- Alena Kaltenbrunner
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Viktoria Reimann
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ute A Hoffmann
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Tomohiro Aoyagi
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Minori Sakata
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Chen PW, Lin CF. Characterization of a novel theta-type replicon of indigenous plasmid pTE15 from Lactobacillus reuteri N16. BMC Microbiol 2022; 22:298. [PMID: 36510154 PMCID: PMC9743546 DOI: 10.1186/s12866-022-02718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND pTE15 is a ~ 15-kb narrow-host-range indigenous plasmid from Lactobacillus reuteri N16 that does not replicate in selected Bacillus spp., Staphylococcus spp., and other Lactobacillus spp. METHODS Combined deletion analysis the minireplicon essential of pTE15 with replicon-probe vector pUE80 (-) to confirmed sufficient for replication and from the ssDNA intermediate detection, plasmid amplification tested by chloramphenicol treatment, and replication origin sequence analysis to delineated the novel theta-type replication of pTE15. RESULTS Single-stranded intermediate of pTE15 DNA was not detected in L. reuteri, indicating that this plasmid does not replicate via a rolling circle mechanism. The replicon of pTE15 did not display the structural organization typical of rolling-circle plasmids, nor were they similar to known rolling-circle plasmids. We further provided evidence that this plasmid applied a new mode of theta-type replication mechanism: (1) the size of this plasmid was > 10-kb; (2) the minireplicon consisted of AT-rich (directed repeat, iteron) and DnaA sequences; (3) the minireplicon did not contain double-strand origin (DSO) and essential rep genes, and it also showed no single-strand origin (SSO) structure; (4) the intermediate single-stranded DNA products were not observed for pTE15 replication; (5) the minireplicon did not contain a typical essential replication protein, Rep, (6) its copy number was decreased by chloramphenicol treatment, and (7) genes in pTE15 replication region encoded truncated RepA (TRepA), RepB and RepC, which were replication-associated proteins, but they were not essential for pTE15 replication. CONCLUSIONS Collectively, our results strongly suggested that the indigenous plasmid pTE15 of L. reuteri N16 belongs to a new class of theta replicons.
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Affiliation(s)
- Po-Wen Chen
- grid.260542.70000 0004 0532 3749Department of Veterinary Medicine, National Chung Hsing University, Taichung, 40249 Taiwan
| | - Chuen-Fu Lin
- grid.412083.c0000 0000 9767 1257Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201 Taiwan ,grid.412083.c0000 0000 9767 1257Animal disease diagnostic center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201 Taiwan
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Global Distribution and Diversity of Prevalent Sewage Water Plasmidomes. mSystems 2022; 7:e0019122. [PMID: 36069451 PMCID: PMC9600348 DOI: 10.1128/msystems.00191-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Sewage water from around the world contains an abundance of short plasmids, several of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions are only starting to be unveiled. Here, we utilized a previously created data set of 159,332 assumed small plasmids from 24 different global sewage samples. The detailed phylogeny, as well as the interplay between their protein domains, ARGs, and predicted bacterial host genera, were investigated to understand sewage plasmidome dynamics globally. A total of 58,429 circular elements carried genes encoding plasmid-related features, and MASH distance analyses showed a high degree of diversity. A single (yet diverse) cluster of 520 predicted Acinetobacter plasmids was predominant among the European sewage water. Our results suggested a prevalence of plasmid-backbone gene combinations over others. This could be related to selected bacterial genera that act as bacterial hosts. These combinations also mirrored the geographical locations of the sewage samples. Our functional domain network analysis identified three groups of plasmids. However, these backbone domains were not exclusive to any given group, and Acinetobacter was the dominant host genus among the theta-replicating plasmids, which contained a reservoir of the macrolide resistance gene pair msr(E) and mph(E). Macrolide resistance genes were the most common in the sewage plasmidomes and were found in the largest number of unique plasmids. While msr(E) and mph(E) were limited to Acinetobacter, erm(B) was disseminated among a range of Firmicutes plasmids, including Staphylococcus and Streptococcus, highlighting a potential reservoir of antibiotic resistance for these pathogens from around the globe. IMPORTANCE Antimicrobial resistance is a global threat to human health, as it inhibits our ability to treat infectious diseases. This study utilizes sewage water plasmidomes to identify plasmid-derived features and highlights antimicrobial resistance genes, particularly macrolide resistance genes, as abundant in sewage water plasmidomes in Firmicutes and Acinetobacter hosts. The emergence of macrolide resistance in these bacteria suggests that macrolide selective pressure exists in sewage water and that the resident bacteria can readily acquire macrolide resistance via small plasmids.
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Thomsen J, Schmitz RA. Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon. Int J Mol Sci 2022; 23:ijms231911910. [PMID: 36233214 PMCID: PMC9569500 DOI: 10.3390/ijms231911910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about its replication mechanism in methanoarchaea remain unknown. Here, we report on a significant optimisation of the rather large shuttle vector pWM321 (8.9 kbp) generated by Metcalf through a decrease in its size by about 35% by means of the deletion of several non-coding regions and the ssrA gene. The resulting plasmid (pRS1595) still stably replicates in M. mazei and—most likely due to its reduced size—shows a significantly higher transformation efficiency compared to pWM321. In addition, we investigate the essential gene repA, coding for a rep type protein. RepA was heterologously expressed in Escherichia coli, purified and characterised, demonstrating the significant binding and nicking activity of supercoiled plasmid DNA. Based on our findings we propose that the optimised shuttle vector replicates via a rolling circle mechanism with RepA as the initial replication protein in Methanosarcina. On the basis of bioinformatic comparisons, we propose the presence and location of a double-strand and a single-strand origin, which need to be further verified.
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Plasmid-Based Gene Expression Systems for Lactic Acid Bacteria: A Review. Microorganisms 2022; 10:microorganisms10061132. [PMID: 35744650 PMCID: PMC9229153 DOI: 10.3390/microorganisms10061132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 01/27/2023] Open
Abstract
Lactic acid bacteria (LAB) play a very vital role in food production, preservation, and as probiotic agents. Some of these species can colonize and survive longer in the gastrointestinal tract (GIT), where their presence is crucially helpful to promote human health. LAB has also been used as a safe and efficient incubator to produce proteins of interest. With the advent of genetic engineering, recombinant LAB have been effectively employed as vectors for delivering therapeutic molecules to mucosal tissues of the oral, nasal, and vaginal tracks and for shuttling therapeutics for diabetes, cancer, viral infections, and several gastrointestinal infections. The most important tool needed to develop genetically engineered LABs to produce proteins of interest is a plasmid-based gene expression system. To date, a handful of constitutive and inducible vectors for LAB have been developed, but their limited availability, host specificity, instability, and low carrying capacity have narrowed their spectrum of applications. The current review discusses the plasmid-based vectors that have been developed so far for LAB; their functionality, potency, and constraints; and further highlights the need for a new, more stable, and effective gene expression platform for LAB.
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Hubert B. SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids. Sci Data 2022; 9:92. [PMID: 35318332 PMCID: PMC8941118 DOI: 10.1038/s41597-022-01179-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
GC skew denotes the relative excess of G nucleotides over C nucleotides on the leading versus the lagging replication strand of eubacteria. While the effect is small, typically around 2.5%, it is robust and pervasive. GC skew and the analogous TA skew are a localized deviation from Chargaff’s second parity rule, which states that G and C, and T and A occur with (mostly) equal frequency even within a strand. Different bacterial phyla show different kinds of skew, and differing relations between TA and GC skew. This article introduces an open access database (https://skewdb.org) of GC and 10 other skews for over 30,000 chromosomes and plasmids. Further details like codon bias, strand bias, strand lengths and taxonomic data are also included. The SkewDB can be used to generate or verify hypotheses. Since the origins of both the second parity rule and GC skew itself are not yet satisfactorily explained, such a database may enhance our understanding of prokaryotic DNA. Measurement(s) | Imbalances in the use of DNA nucleotides | Technology Type(s) | Next Generation Sequencing | Factor Type(s) | Position within DNA sequence • Organism type | Sample Characteristic - Organism | bacterium • archaea | Sample Characteristic - Environment | Varying | Sample Characteristic - Location | World |
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Affiliation(s)
- Bert Hubert
- AHU Holding Research, Nootdorp, Netherlands.
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9
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Synchrotron Radiation Circular Dichroism, a New Tool to Probe Interactions between Nucleic Acids Involved in the Control of ColE1-Type Plasmid Replication. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Hfq is a bacterial master regulator which promotes the pairing of nucleic acids. Due to the high molecular weight of the complexes formed between nucleic acids and the amyloid form of the protein, it is difficult to analyze solely by a gel shift assay the complexes formed, as they all migrate at the same position in the gel. In addition, precise kinetics measurements are not possible using a gel shift assay. Here, we used a synchrotron-based biophysical approach, synchrotron radiation circular dichroism (SRCD), to probe the interaction of the Escherichia coli Hfq C-terminal amyloid region with nucleic acids involved in the control of ColE1-like plasmid replication. We observed that this C-terminal region of Hfq has an unexpected and significant effect on the annealing of nucleic acids involved in this process and, more importantly, on their alignment. Functional consequences of this newly discovered property of the Hfq amyloid region are discussed in terms of the biological significance of Hfq in the ColE1-type plasmid replication process and antibiotic resistance.
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IWAMOTO D, ISHIZAKI M, MIURA T, SASAKI Y. Novel shuttle vector pGMβ1 for conjugative chromosomal manipulation of <i>Lactobacillus delbrueckii</i> subsp. <i>bulgaricus</i>. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2022; 41:20-29. [PMID: 35036250 PMCID: PMC8727053 DOI: 10.12938/bmfh.2021-014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/22/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Daiki IWAMOTO
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Megumi ISHIZAKI
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Taiki MIURA
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Yasuko SASAKI
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
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Ares-Arroyo M, Rocha EPC, Gonzalez-Zorn B. Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance. PLoS Genet 2021; 17:e1009919. [PMID: 34847155 PMCID: PMC8683028 DOI: 10.1371/journal.pgen.1009919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 12/17/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
Antimicrobial resistance is one of the major threats to Public Health worldwide. Understanding the transfer and maintenance of antimicrobial resistance genes mediated by mobile genetic elements is thus urgent. In this work, we focus on the ColE1-like plasmid family, whose distinctive replication and multicopy nature has given rise to key discoveries and tools in molecular biology. Despite being massively used, the hosts, functions, and evolutionary history of these plasmids remain poorly known. Here, we built specific Hidden Markov Model (HMM) profiles to search ColE1 replicons within genomes. We identified 1,035 ColE1 plasmids in five Orders of γ-Proteobacteria, several of which are described here for the first time. The phylogenetic analysis of these replicons and their characteristic MOBP5/HEN relaxases suggest that ColE1 plasmids have diverged apart, with little transfer across orders, but frequent transfer across families. Additionally, ColE1 plasmids show a functional shift over the last decades, losing their characteristic bacteriocin production while gaining several antimicrobial resistance genes, mainly enzymatic determinants and including several extended-spectrum betalactamases and carbapenemases. Furthermore, ColE1 plasmids facilitate the intragenomic mobilization of these determinants, as various replicons were identified co-integrated with large non-ColE1 plasmids, mostly via transposases. These results illustrate how families of plasmids evolve and adapt their gene repertoires to bacterial adaptive requirements. The extraordinary adaptability of bacteria and the massive prevalence of mobile genetic elements within populations has turned antimicrobial resistance into a growing threat to Public Health. Among all the mobile genetic elements, plasmids have been the focus of attention as these extrachromosomal molecules of DNA are able to mobilize several antimicrobial resistance genes at once through conjugation. However, although small mobilizable and non-conjugative replicons have been traditionally overlooked when analyzing plasmid-mediated antimicrobial resistance, they have recently been described as important carriers of AMR genes. In this work, we have analyzed the ColE1-like plasmid family, whose study has been neglected even if they are one of the main groups of small plasmids in natural populations of Proteobacteria. We observed that these plasmids have evolved for a long time within γ-Proteobacteria acquiring different genetic features in specific hosts, being major players in the spread of antimicrobial resistance determinants.
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Affiliation(s)
- Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Faculty of Veterinary Medicine and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit (ARU), Faculty of Veterinary Medicine and VISAVET, Complutense University of Madrid, Madrid, Spain
- * E-mail:
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Smits WK, Roseboom AM, Corver J. Plasmids of Clostridioides difficile. Curr Opin Microbiol 2021; 65:87-94. [PMID: 34775173 DOI: 10.1016/j.mib.2021.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 12/16/2022]
Abstract
Plasmids are ubiquitous in the bacterial world. In many microorganisms, plasmids have been implicated in important aspects of bacterial physiology and contribute to horizontal gene transfer. In contrast, knowledge on plasmids of the enteropathogen Clostridioides difficile is limited, and there appears to be no phenotypic consequence to carriage of many of the identified plasmids. Emerging evidence suggests, however, that plasmids are common in C. difficile and may encode functions relevant to pathogenesis, such as antimicrobial resistance and toxin production. Here, we review our current knowledge about the abundance, functions and clinical relevance of plasmids in C. difficile.
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Affiliation(s)
- Wiep Klaas Smits
- Experimental Bacteriology Group, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden, The Netherlands; Leiden University Center for Infectious Diseases (LU-CID), Leiden, The Netherlands.
| | - Anna Maria Roseboom
- Experimental Bacteriology Group, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Corver
- Experimental Bacteriology Group, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden, The Netherlands; Leiden University Center for Infectious Diseases (LU-CID), Leiden, The Netherlands
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Hu W, Wang Y, Yang B, Lin C, Yu H, Liu G, Deng Z, Ou HY, He X. Bacterial YedK represses plasmid DNA replication and transformation through its DNA single-strand binding activity. Microbiol Res 2021; 252:126852. [PMID: 34454309 DOI: 10.1016/j.micres.2021.126852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/30/2021] [Accepted: 08/21/2021] [Indexed: 10/20/2022]
Abstract
The SOS response-associated peptidase (SRAP) is an ancient protein superfamily in all domains of life. The mammalian SRAP was recently reported to covalently bind to the abasic sites (AP) in single stranded (ss) DNA to shield the chromosome integrity. YedK, the Escherichia coli SRAP, is not functionally characterized. Here we report the fortuitous pull-down of YedK from bacterial cell lysates by short (<20 bp) double stranded (ds) DNAs, further enrichment of YedK was observed when single stranded (ss) DNA was added. YedK can bind multiple DNA substrates, particularly with a high affinity to DNA duplex with single strand segment. As a SRAP protein, the involvement of YedK in SOS response was extensively examined, however yedK mutant of Escherichia coli showed no difference from the wild type strain upon the treatments with UV and various DNA damaging reagents, indicating its non-essentiality or redundancy in E. coli. Surprisingly, yedK mutants derived from Escherichia coli and Samonella enterica both showed an increased plasmid DNA transformation efficiency compared to the wild types. In accordance with this, induction of YedK effectively decreased the copy number of plasmid DNA. Site-directed mutagenesis of YedK demonstrated that residues involved in single strand DNA binding and cysteine residue at position 2 from N-terminus can discharge the repression of the plasmid transformation efficiency.
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Affiliation(s)
- Wenyue Hu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Yuli Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Bingxu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Chen Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
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Differential Chromosome- and Plasmid-Borne Resistance of Escherichia coli hfq Mutants to High Concentrations of Various Antibiotics. Int J Mol Sci 2021; 22:ijms22168886. [PMID: 34445592 PMCID: PMC8396180 DOI: 10.3390/ijms22168886] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
The Hfq protein is a bacterial RNA chaperone, involved in many molecular interactions, including control of actions of various small RNA regulatory molecules. We found that the presence of Hfq was required for survival of plasmid-containing Escherichia coli cells against high concentrations of chloramphenicol (plasmid p27cmr), tetracycline (pSC101, pBR322) and ampicillin (pBR322), as hfq+ strains were more resistant to these antibiotics than the hfq-null mutant. In striking contrast, production of Hfq resulted in low resistance to high concentrations of kanamycin when the antibiotic-resistance marker was chromosome-borne, with deletion of hfq resulting in increasing bacterial survival. These results were observed both in solid and liquid medium, suggesting that antibiotic resistance is an intrinsic feature of these strains rather than a consequence of adaptation. Despite its major role as RNA chaperone, which also affects mRNA stability, Hfq was not found to significantly affect kan and tet mRNAs turnover. Nevertheless, kan mRNA steady-state levels were higher in the hfq-null mutant compared to the hfq+ strain, suggesting that Hfq can act as a repressor of kan expression.This observation does correlate with the enhanced resistance to high levels of kanamycin observed in the hfq-null mutant. Furthermore, dependency on Hfq for resistance to high doses of tetracycline was found to depend on plasmid copy number, which was only observed when the resistance marker was expressed from a low copy plasmid (pSC101) but not from a medium copy plasmid (pBR322). This suggests that Hfq may influence survival against high doses of antibiotics through mechanisms that remain to be determined. Studies with pBR322Δrom may also suggest an interplay between Hfq and Rom in the regulation of ColE1-like plasmid replication. Results of experiments with a mutant devoid of the part of the hfq gene coding for the C-terminal region of Hfq suggested that this region, as well as the N-terminal region, may be involved in the regulation of expression of antibiotic resistance in E. coli independently.
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15
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Morgado SM, Paulo Vicente AC. Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS. Microb Genom 2021; 6. [PMID: 32496186 PMCID: PMC7478629 DOI: 10.1099/mgen.0.000382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nevertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the Mycobacteriaceae family, focusing on strains from Brazilian Atlantic Forest soil. Novel Mycolicibacterium and Mycobacteroides strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type-VII secretion system (T7SS) and mobility-associated genes. In addition, we also identified a T4SS-mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the Mycobacteriaceae mobilome, providing the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS.
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16
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Kim JW, Bugata V, Cortés-Cortés G, Quevedo-Martínez G, Camps M. Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0026-2019. [PMID: 33210586 PMCID: PMC7724965 DOI: 10.1128/ecosalplus.esp-0026-2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 11/20/2022]
Abstract
Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at oriC, a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA-dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host's replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (ori). Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. The timing of plasmid replication and segregation are also critical for optimizing plasmid gene expression. Therefore, we propose that plasmid replication needs to be understood in its biological context, where complex origins of replication (redundant origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin systems are often present. Highlighting their tight functional integration with ori function, we show that both partition and toxin-antitoxin systems tend to be encoded in close physical proximity to the ori in a large collection of Escherichia coli plasmids. We also propose that adaptation of plasmids to their host optimizes their contribution to the host's fitness while restricting access to broad genetic diversity, and we argue that this trade-off between adaptation to host and access to genetic diversity is likely a determinant factor shaping the distribution of replicons in populations of enterobacteria.
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Affiliation(s)
- Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Vega Bugata
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Gerardo Cortés-Cortés
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Giselle Quevedo-Martínez
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
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17
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Wiegand T, Semenova E, Shiriaeva A, Fedorov I, Datsenko K, Severinov K, Wiedenheft B. Reproducible Antigen Recognition by the Type I-F CRISPR-Cas System. CRISPR J 2020; 3:378-387. [PMID: 33095052 PMCID: PMC7580607 DOI: 10.1089/crispr.2020.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CRISPR-associated proteins 1 and 2 (Cas1-2) are necessary and sufficient for new spacer acquisition in some CRISPR-Cas systems (e.g., type I-E), but adaptation in other systems (e.g., type II-A) involves the crRNA-guided surveillance complex. Here we show that the type I-F Cas1-2/3 proteins are necessary and sufficient to produce low levels of spacer acquisition, but the presence of the type I-F crRNA-guided surveillance complex (Csy) improves the efficiency of adaptation and significantly increases the fidelity of protospacer adjacent motif selection. Sequences selected for integration are preferentially derived from specific regions of extrachromosomal DNA, and patterns of spacer selection are highly reproducible between independent biological replicates. This work helps define the role of the Csy complex in I-F adaptation and reveals that actively replicating mobile genetic elements have antigenic signatures that facilitate their integration during CRISPR adaptation.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA; Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
| | - Anna Shiriaeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Microbiology, Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg, Russia; Russian Academy of Sciences, Moscow, Russia
| | - Ivan Fedorov
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
| | - Kirill Datsenko
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia; and Russian Academy of Sciences, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA; Russian Academy of Sciences, Moscow, Russia
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Abstract
The ancestral strain of Bacillus subtilis NCIB3610 (3610) bears a large, low-copy-number plasmid, called pBS32, that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been because it encodes a potent inhibitor of natural genetic competence (ComI), as laboratory strains were selected for high-frequency transformation. Previous studies have shown that pBS32 and its sibling, pLS32 in Bacillus subtilis subsp. natto, encode a replication initiation protein (RepN), a plasmid partitioning system (AlfAB), a biofilm inhibitor (RapP), and an alternative sigma factor (SigN) that can induce plasmid-mediated cell death in response to DNA damage. Here, we review the literature on pBS32/pLS32, the genes found on it, and their associated phenotypes.
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19
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Luo H, Gao F. DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Res 2020; 47:D74-D77. [PMID: 30364951 PMCID: PMC6323995 DOI: 10.1093/nar/gky1014] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007. DoriC 5.0, an updated database of oriC regions in both bacterial and archaeal genomes, was published in the 2013 Nucleic Acids Research database issue. Now, the latest release DoriC 10, a large-scale update of replication origins in prokaryotic genomes including chromosomes and plasmids, has been presented with a completely redesigned user interface, which is freely available at http://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/. In the current release, the database of DoriC has made significant improvements compared with version 5.0 as follows: (i) inclusion of oriCs on more bacterial chromosomes increased from 1633 to 7580; (ii) inclusion of oriCs on more archaeal chromosomes increased from 86 to 226; (iii) inclusion of 1209 plasmid replication origins retrieved from NCBI annotations or predicted by in silico analysis; (iv) inclusion of more replication origin elements on bacterial chromosomes including DnaA-trio motifs. Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication origin predictions.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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20
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Abdallah II, Xue D, Pramastya H, van Merkerk R, Setroikromo R, Quax WJ. A regulated synthetic operon facilitates stable overexpression of multigene terpenoid pathway in Bacillus subtilis. ACTA ACUST UNITED AC 2020; 47:243-249. [DOI: 10.1007/s10295-019-02257-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/14/2019] [Indexed: 01/17/2023]
Abstract
Abstract
The creation of microbial cell factories for sustainable production of natural products is important for medical and industrial applications. This requires stable expression of biosynthetic pathways in a host organism with favorable fermentation properties such as Bacillus subtilis. The aim of this study is to construct B. subtilis strains that produce valuable terpenoid compounds by overexpressing the innate methylerythritol phosphate (MEP) pathway. A synthetic operon allowing the concerted and regulated expression of multiple genes was developed. Up to 8 genes have been combined in this operon and a stably inherited plasmid-based vector was constructed resulting in a high production of C30 carotenoids. For this, two vectors were examined, one with rolling circle replication and another with theta replication. Theta-replication constructs were clearly superior in structural and segregational stability compared to rolling circle constructs. A strain overexpressing all eight genes of the MEP pathway on a theta-replicating plasmid clearly produced the highest level of carotenoids. The level of transcription for each gene in the operon was similar as RT-qPCR analysis indicated. Hence, that corresponding strain can be used as a stable cell factory for production of terpenoids. This is the first report of merging and stably expressing this large-size operon (eight genes) from a plasmid-based system in B. subtilis enabling high C30 carotenoid production.
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Affiliation(s)
- Ingy I Abdallah
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Dan Xue
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Hegar Pramastya
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
- grid.434933.a 0000 0004 1808 0563 Pharmaceutical Biology Research Group, School of Pharmacy Institut Teknologi Bandung 40132 Bandung Indonesia
| | - Ronald van Merkerk
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rita Setroikromo
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Wim J Quax
- grid.4830.f 0000 0004 0407 1981 Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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21
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Uelze L, Grützke J, Borowiak M, Hammerl JA, Juraschek K, Deneke C, Tausch SH, Malorny B. Typing methods based on whole genome sequencing data. ONE HEALTH OUTLOOK 2020; 2:3. [PMID: 33829127 PMCID: PMC7993478 DOI: 10.1186/s42522-020-0010-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/08/2020] [Indexed: 05/12/2023]
Abstract
Whole genome sequencing (WGS) of foodborne pathogens has become an effective method for investigating the information contained in the genome sequence of bacterial pathogens. In addition, its highly discriminative power enables the comparison of genetic relatedness between bacteria even on a sub-species level. For this reason, WGS is being implemented worldwide and across sectors (human, veterinary, food, and environment) for the investigation of disease outbreaks, source attribution, and improved risk characterization models. In order to extract relevant information from the large quantity and complex data produced by WGS, a host of bioinformatics tools has been developed, allowing users to analyze and interpret sequencing data, starting from simple gene-searches to complex phylogenetic studies. Depending on the research question, the complexity of the dataset and their bioinformatics skill set, users can choose between a great variety of tools for the analysis of WGS data. In this review, we describe the relevant approaches for phylogenomic studies for outbreak studies and give an overview of selected tools for the characterization of foodborne pathogens based on WGS data. Despite the efforts of the last years, harmonization and standardization of typing tools are still urgently needed to allow for an easy comparison of data between laboratories, moving towards a one health worldwide surveillance system for foodborne pathogens.
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Affiliation(s)
- Laura Uelze
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Josephine Grützke
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Katharina Juraschek
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Simon H. Tausch
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
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22
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Drolet M, Brochu J. R-loop-dependent replication and genomic instability in bacteria. DNA Repair (Amst) 2019; 84:102693. [DOI: 10.1016/j.dnarep.2019.102693] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022]
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23
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Wawrzyniak P, Sobolewska-Ruta A, Zaleski P, Łukasiewicz N, Kabaj P, Kierył P, Gościk A, Bierczyńska-Krzysik A, Baran P, Mazurkiewicz-Pisarek A, Płucienniczak A, Bartosik D. Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions. BMC Microbiol 2019; 19:254. [PMID: 31722681 PMCID: PMC6854812 DOI: 10.1186/s12866-019-1595-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 09/10/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gene overlapping is a frequent phenomenon in microbial genomes. Excluding so-called "trivial overlapping", there are significant implications of such genetic arrangements, including regulation of gene expression and modification of protein activity. It is also postulated that, besides gene duplication, the appearance of overlapping genes (OGs) is one of the most important factors promoting a genome's novelty and evolution. OGs coding for in-frame proteins with different functions are a particularly interesting case. In this study we identified and characterized two in-frame proteins encoded by OGs on plasmid pIGRK from Klebsiella pneumoniae, a representative of the newly distinguished pHW126 plasmid family. RESULTS A single repR locus located within the replication system of plasmid pIGRK encodes, in the same frame, two functional polypeptides: a full-length RepR protein and a RepR' protein (with N-terminal truncation) translated from an internal START codon. Both proteins form homodimers, and interact with diverse DNA regions within the plasmid replication origin and repR promoter operator. Interestingly, RepR and RepR' have opposing functions - RepR is crucial for initiation of pIGRK replication, while RepR' is a negative regulator of this process. Nevertheless, both proteins act cooperatively as negative transcriptional regulators of their own expression. CONCLUSIONS Regulation of the initiation of pIGRK replication is a complex process in which a major role is played by two in-frame proteins with antagonistic functions. In-frame encoded Rep proteins are uncommon, having been described in only a few plasmids. This is the first description of such proteins in a plasmid of the pHW126 family.
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Affiliation(s)
- Paweł Wawrzyniak
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Sobolewska-Ruta
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Piotr Zaleski
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Natalia Łukasiewicz
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Paulina Kabaj
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Piotr Kierył
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Agata Gościk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Bierczyńska-Krzysik
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Piotr Baran
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Anna Mazurkiewicz-Pisarek
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Andrzej Płucienniczak
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
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24
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Ramirez MS, Iriarte A, Reyes-Lamothe R, Sherratt DJ, Tolmasky ME. Small Klebsiella pneumoniae Plasmids: Neglected Contributors to Antibiotic Resistance. Front Microbiol 2019; 10:2182. [PMID: 31616398 PMCID: PMC6764390 DOI: 10.3389/fmicb.2019.02182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is the causative agent of community- and, more commonly, hospital-acquired infections. Infections caused by this bacterium have recently become more dangerous due to the acquisition of multiresistance to antibiotics and the rise of hypervirulent variants. Plasmids usually carry genes coding for resistance to antibiotics or virulence factors, and the recent sequence of complete K. pneumoniae genomes showed that most strains harbor many of them. Unlike large plasmids, small, usually high copy number plasmids, did not attract much attention. However, these plasmids may include genes coding for specialized functions, such as antibiotic resistance, that can be expressed at high levels due to gene dosage effect. These genes may be part of mobile elements that not only facilitate their dissemination but also participate in plasmid evolution. Furthermore, high copy number plasmids may also play a role in evolution by allowing coexistence of mutated and non-mutated versions of a gene, which helps to circumvent the constraints imposed by trade-offs after certain genes mutate. Most K. pneumoniae plasmids 25-kb or smaller replicate by the ColE1-type mechanism and many of them are mobilizable. The transposon Tn1331 and derivatives were found in a high percentage of these plasmids. Another transposon that was found in representatives of this group is the bla KPC-containing Tn4401. Common resistance determinants found in these plasmids were aac(6')-Ib and genes coding for β-lactamases including carbapenemases.
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Affiliation(s)
- Maria S. Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Universidad de la República de Uruguay, Montevideo, Uruguay
| | | | - David J. Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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25
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Abstract
Plasmids have a major role in the development of disease caused by enteric bacterial pathogens. Virulence plasmids are usually large (>40 kb) low copy elements and encode genes that promote host-pathogen interactions. Although virulence plasmids provide advantages to bacteria in specific conditions, they often impose fitness costs on their host. In this Review, we discuss virulence plasmids in Enterobacteriaceae that are important causes of diarrhoea in humans, Shigella spp., Salmonella spp., Yersinia spp and pathovars of Escherichia coli. We contrast these plasmids with those that are routinely used in the laboratory and outline the mechanisms by which virulence plasmids are maintained in bacterial populations. We highlight examples of virulence plasmids that encode multiple mechanisms for their maintenance (for example, toxin-antitoxin and partitioning systems) and speculate on how these might contribute to their propagation and success.
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26
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López-Ochoa AJ, Sánchez-Alonso P, Vázquez-Cruz C, Horta-Valerdi G, Negrete-Abascal E, Vaca-Pacheco S, Mejía R, Pérez-Márquez M. Molecular and genetic characterization of the pOV plasmid from Pasteurella multocida and construction of an integration vector for Gallibacterium anatis. Plasmid 2019; 103:45-52. [PMID: 31022414 DOI: 10.1016/j.plasmid.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/18/2019] [Accepted: 04/21/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND The pOV plasmid isolated from the Pasteurella multocida strain PMOV is a new plasmid, and its molecular characterization is important for determining its gene content and its replicative properties in Pasteurellaceae family bacteria. METHODS Antimicrobial resistance mediated by the pOV plasmid was tested in bacteria. Purified pOV plasmid DNA was used to transform E. coli DH5α and Gallibacterium anatis 12656-12, including the pBluescript II KS(-) plasmid DNA as a control for genetic transformation. The pOV plasmid was digested with EcoRI for cloning fragments into the pBluescript II KS(-) vector to obtain constructs and to determine the full DNA sequence of pOV. RESULTS The pOV plasmid is 13.5 kb in size; confers sulfonamide, streptomycin and ampicillin resistance to P. multocida PMOV; and can transform E. coli DH5α and G. anatis 12656-12. The pOV plasmid was digested for the preparation of chimeric constructs and used to transform E. coli DH5α, conferring resistance to streptomycin (plasmid pSEP3), ampicillin (pSEP4) and sulfonamide (pSEP5) on the bacteria; however, similar to pBluescript II KS(-), the chimeric plasmids did not transform G. anatis 12656-12. A 1.4 kb fragment of the streptomycin cassette from pSEP3 was amplified by PCR and used to construct pSEP7, which in turn was used to interrupt a chromosomal DNA locus of G. anatis by double homologous recombination, introducing strA-strB into the G. anatis chromosome. CONCLUSION The pOV plasmid is a wide-range, low-copy-number plasmid that is able to replicate in some gamma-proteobacteria. Part of this plasmid was integrated into the G. anatis 12656-12 chromosome. This construct may prove to be a useful tool for genetic studies of G. anatis.
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Affiliation(s)
- Ana Jaqueline López-Ochoa
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México
| | - Patricia Sánchez-Alonso
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México
| | - Candelario Vázquez-Cruz
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México.
| | - Guillermo Horta-Valerdi
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México
| | - Erasmo Negrete-Abascal
- Carrera de Biología, Facultad de Estudios Superiores de Iztacala UNAM, Tlalnepantla, Edo de México 54090, México
| | - Sergio Vaca-Pacheco
- Carrera de Biología, Facultad de Estudios Superiores de Iztacala UNAM, Tlalnepantla, Edo de México 54090, México
| | - Ricardo Mejía
- Carrera de Biología, Facultad de Estudios Superiores de Iztacala UNAM, Tlalnepantla, Edo de México 54090, México
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27
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Yano H, Shintani M, Tomita M, Suzuki H, Oshima T. Reconsidering plasmid maintenance factors for computational plasmid design. Comput Struct Biotechnol J 2018; 17:70-81. [PMID: 30619542 PMCID: PMC6312765 DOI: 10.1016/j.csbj.2018.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/08/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, 5180, Kurokawa, Imizu, Toyama 939-0398, Japan
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28
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Briggs E, Hamilton G, Crouch K, Lapsley C, McCulloch R. Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome. Nucleic Acids Res 2018; 46:11789-11805. [PMID: 30304482 PMCID: PMC6294496 DOI: 10.1093/nar/gky928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/25/2018] [Accepted: 10/05/2018] [Indexed: 01/09/2023] Open
Abstract
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localization was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the regions between coding sequences of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination the most widespread localization of R-loops in T. brucei suggests a novel correlation with pre-mRNA processing. Finally, we find little evidence for correlation between R-loop localization and mapped sites of DNA replication initiation.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Rd, Bearsden, G61 1QH, UK
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
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29
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Gillis A, Fayad N, Makart L, Bolotin A, Sorokin A, Kallassy M, Mahillon J. Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensis. FEMS Microbiol Rev 2018; 42:829-856. [PMID: 30203090 PMCID: PMC6199540 DOI: 10.1093/femsre/fuy034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Bacillus thuringiensis is a well-known biopesticide that has been used for more than 80 years. This spore-forming bacterium belongs to the group of Bacillus cereus that also includes, among others, emetic and diarrheic pathotypes of B. cereus, the animal pathogen Bacillus anthracis and the psychrotolerant Bacillus weihenstephanensis. Bacillus thuringiensis is rather unique since it has adapted its lifestyle as an efficient pathogen of specific insect larvae. One of the peculiarities of B. thuringiensis strains is the extent of their extrachromosomal pool, with strains harbouring more than 10 distinct plasmid molecules. Among the numerous serovars of B. thuringiensis, 'israelensis' is certainly emblematic since its host spectrum is apparently restricted to dipteran insects like mosquitoes and black flies, vectors of human and animal diseases such as malaria, yellow fever, or river blindness. In this review, the putative role of the mobile gene pool of B. thuringiensis serovar israelensis in its pathogenicity and dedicated lifestyle is reviewed, with specific emphasis on the nature, diversity, and potential mobility of its constituents. Variations among the few related strains of B. thuringiensis serovar israelensis will also be reported and discussed in the scope of this specialised insect pathogen, whose lifestyle in the environment remains largely unknown.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Nancy Fayad
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
- Laboratory of Biodiversity and Functional Genomics (BGF), Faculty of Sciences, Université Saint-Joseph, 1107 2050 Beirut, Lebanon
| | - Lionel Makart
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Alexander Bolotin
- UMR1319 Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Alexei Sorokin
- UMR1319 Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Mireille Kallassy
- Laboratory of Biodiversity and Functional Genomics (BGF), Faculty of Sciences, Université Saint-Joseph, 1107 2050 Beirut, Lebanon
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
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30
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Li Y, da Silva GC, Li Y, Rossi CC, Fernandez Crespo R, Williamson SM, Langford PR, Bazzolli DMS, Bossé JT. Evidence of Illegitimate Recombination Between Two Pasteurellaceae Plasmids Resulting in a Novel Multi-Resistance Replicon, pM3362MDR, in Actinobacillus pleuropneumoniae. Front Microbiol 2018; 9:2489. [PMID: 30405558 PMCID: PMC6206304 DOI: 10.3389/fmicb.2018.02489] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022] Open
Abstract
Evidence of plasmids carrying the tetracycline resistance gene, tet(B), was found in the previously reported whole genome sequences of 14 United Kingdom, and 4 Brazilian, isolates of Actinobacillus pleuropneumoniae. Isolation and sequencing of selected plasmids, combined with comparative sequence analysis, indicated that the four Brazilian isolates all harbor plasmids that are nearly identical to pB1001, a plasmid previously found in Pasteurella multocida isolates from Spain. Of the United Kingdom isolates, 13/14 harbor plasmids that are (almost) identical to pTetHS016 from Haemophilus parasuis. The remaining United Kingdom isolate, MIDG3362, harbors a 12666 bp plasmid that shares extensive regions of similarity with pOV from P. multocida (which carries blaROB-1 , sul2, and strAB genes), as well as with pTetHS016. The newly identified multi-resistance plasmid, pM3362MDR, appears to have arisen through illegitimate recombination of pTetHS016 into the stop codon of the truncated strB gene in a pOV-like plasmid. All of the tet(B)-carrying plasmids studied were capable of replicating in Escherichia coli, and predicted origins of replication were identified. A putative origin of transfer (oriT) sequence with similar secondary structure and a nic-site almost identical to that of RP4 was also identified in these plasmids, however, attempts to mobilize them from an RP4-encoding E. coli donor strain were not successful, indicating that specific conjugation machinery may be required.
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Affiliation(s)
- Yinghui Li
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom.,Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Giarlã Cunha da Silva
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Ciro C Rossi
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Denise Mara Soares Bazzolli
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
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31
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1130] [Impact Index Per Article: 188.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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32
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Miyano M, Tanaka K, Ishikawa S, Mori K, Miguel-Arribas A, Meijer WJJ, Yoshida KI. A novel method for transforming the thermophilic bacterium Geobacillus kaustophilus. Microb Cell Fact 2018; 17:127. [PMID: 30119674 PMCID: PMC6098629 DOI: 10.1186/s12934-018-0969-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial strains of the genus Geobacillus grow at high temperatures of 50-75 °C and could thus be useful for biotechnological applications. However, genetic manipulation of these species is difficult because the current techniques for transforming Geobacillus species are not efficient. In this study, we developed an easy and efficient method for transforming Geobacillus kaustophilus using the conjugative plasmid pLS20cat. RESULTS We constructed a transformation system comprising (i) a mobilizable Bacillus subtilis-G. kaustophilus shuttle plasmid named pGK1 that carries the elements for selection and replication in Geobacillus, and (ii) a pLS20cat-harboring B. subtilis donor strain expressing the dam methylase gene of Escherichia coli and the conjugation-stimulating rapLS20 gene of pLS20cat. This system can be used to efficiently introduce pGK1 into G. kaustophilus by mobilization in a pLS20cat-dependent way. Whereas the thermostable kanamycin marker and Geobacillus replication origin of pGK1 as well as expression of dam methylase in the donor were indispensable for mobilization, ectopic expression of rapLS20 increased its efficiency. In addition, the conditions of the recipient influenced mobilization efficiency: the highest mobilization efficiencies were obtained using recipient cells that were in the exponential growth phase. Furthermore, elimination of the origin of transfer from pLS20cat enhanced the mobilization. CONCLUSIONS We describe a novel method of plasmid mobilization into G. kaustophilus recipient from B. subtilis donor depending on the helper function of pLS20cat, which enables simple, rapid, and easy transformation of the thermophilic Gram-positive bacterium.
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Grants
- 17K19237 Ministry of Education, Culture, Sports, Science and Technology
- 18H02128 Ministry of Education, Culture, Sports, Science and Technology
- Bio2013-41489-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2016-77883-C2-1-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
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Affiliation(s)
- Megumi Miyano
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kosei Tanaka
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
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Hua M, Guo J, Li M, Chen C, Zhang Y, Song C, Jiang D, Du P, Zeng H. A Dual-Replicon Shuttle Vector System for Heterologous Gene Expression in a Broad Range of Gram-Positive and Gram-Negative Bacteria. Curr Microbiol 2018; 75:1391-1400. [PMID: 29987521 DOI: 10.1007/s00284-018-1535-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/26/2018] [Indexed: 11/27/2022]
Abstract
Origin of replication (ori in theta-replicating plasmids or dso in rolling circle replicating plasmids) initiates plasmid replication in a broad range of bacteria. These two kinds of plasmids were both identified in Streptococcus, a genus composed of both human commensal bacteria and pathogens with the ability to cause severe community-acquired infections, including meningitides, septicemia, and respiratory tract diseases. Given the important roles of Streptococcus in the exchange of genetic elements with other symbiotic microbes, the genotypes and phenotypes of both Streptococcus spp. and other symbiotic species could be changed during colonization of the host. Therefore, an improved plasmid system is required to study the functional, complicated, and changeable genomes of Streptococcus. In this study, a dual-replicon shuttle vector system named pDRE was constructed to achieve heterologous gene expression. The vector system contained theta replicon for Escherichia coli. The origin of rolling circle replicon was synthesized according to pMV158 in Gram-positive bacteria. By measuring the products of inserted genes at multiple cloning sites, the ability of this vector system in the replication and expression of heterologous genes was assessed in four Streptococcus and three other Gram-positive bacteria: Bacillus subtilis, Lactococcus lactis, and Staphylococcus aureus. The results showed that the newly constructed vector could simultaneously replicate and express heterologous genes in a broad range of Gram-positive and Gram-negative bacteria, thus providing a potentially powerful genetic tool for further functional analysis.
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Affiliation(s)
- Mingxi Hua
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Jingjing Guo
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Min Li
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Chen Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Chuan Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Dong Jiang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China.
| | - Hui Zeng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China.
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34
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Standley MS, Million-Weaver S, Alexander DL, Hu S, Camps M. Genetic control of ColE1 plasmid stability that is independent of plasmid copy number regulation. Curr Genet 2018; 65:179-192. [PMID: 29909438 DOI: 10.1007/s00294-018-0858-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 02/07/2023]
Abstract
ColE1-like plasmid vectors are widely used for expression of recombinant genes in E. coli. For these vectors, segregation of individual plasmids into daughter cells during cell division appears to be random, making them susceptible to loss over time when no mechanisms ensuring their maintenance are present. Here we use the plasmid pGFPuv in a recA relA strain as a sensitized model to study factors affecting plasmid stability in the context of recombinant gene expression. We find that in this model, plasmid stability can be restored by two types of genetic modifications to the plasmid origin of replication (ori) sequence: point mutations and a novel 269 nt duplication at the 5' end of the plasmid ori, which we named DAS (duplicated anti-sense) ori. Combinations of these modifications produce a range of copy numbers and of levels of recombinant expression. In direct contradiction with the classic random distribution model, we find no correlation between increased plasmid copy number and increased plasmid stability. Increased stability cannot be explained by reduced levels of recombinant gene expression either. Our observations would be more compatible with a hybrid clustered and free-distribution model, which has been recently proposed based on detection of individual plasmids in vivo using super-resolution fluorescence microscopy. This work suggests a role for the plasmid ori in the control of segregation of ColE1 plasmids that is distinct from replication initiation, opening the door for the genetic regulation of plasmid stability as a strategy aimed at enhancing large-scale recombinant gene expression or bioremediation.
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Affiliation(s)
- Melissa S Standley
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Samuel Million-Weaver
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- College of Engineering, University of Wisconsin-Madison, Madison, 53706, USA
| | - David L Alexander
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Biomolecular Engineering, UCSC, Santa Cruz, USA
| | - Shuai Hu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
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35
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Salto IP, Torres Tejerizo G, Wibberg D, Pühler A, Schlüter A, Pistorio M. Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats. Sci Rep 2018; 8:7783. [PMID: 29773850 PMCID: PMC5958079 DOI: 10.1038/s41598-018-26180-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.
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Affiliation(s)
- Ileana P Salto
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina.
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36
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Ares-Arroyo M, Bernabe-Balas C, Santos-Lopez A, Baquero MR, Prasad KN, Cid D, Martin-Espada C, San Millan A, Gonzalez-Zorn B. PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms. Front Microbiol 2018; 9:469. [PMID: 29615998 PMCID: PMC5864857 DOI: 10.3389/fmicb.2018.00469] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/28/2018] [Indexed: 02/04/2023] Open
Abstract
ColE1 plasmids are important vehicles for the spread of antibiotic resistance in the Enterobacteriaceae and Pasteurellaceae families of bacteria. Their monitoring is essential, as they harbor important resistant determinants in humans, animals and the environment. In this work, we have analyzed ColE1 replicons using bioinformatic and experimental approaches. First, we carried out a computational study examining the structure of different ColE1 plasmids deposited in databases. Bioinformatic analysis of these ColE1 replicons revealed a mosaic genetic structure consisting of a host-adapted conserved region responsible for the housekeeping functions of the plasmid, and a variable region encoding a wide variety of genes, including multiple antibiotic resistance determinants. From this exhaustive computational analysis we developed a new PCR-based technique, targeting a specific sequence in the conserved region, for the screening, capture and sequencing of these small plasmids, either specific for Enterobacteriaceae or specific for Pasteurellaceae. To validate this PCR-based system, we tested various collections of isolates from both bacterial families, finding that ColE1 replicons were not only highly prevalent in antibiotic-resistant isolates, but also present in susceptible bacteria. In Pasteurellaceae, ColE1 plasmids carried almost exclusively antibiotic resistance genes. In Enterobacteriaceae, these plasmids encoded a large range of traits, including not only antibiotic resistance determinants, but also a wide variety of genes, showing the huge genetic plasticity of these small replicons. Finally, we also used a metagenomic approach in order to validate this technique, performing this PCR system using total DNA extractions from fecal samples from poultry, turkeys, pigs and humans. Using Illumina sequencing of the PCR products we identified a great diversity of genes encoded by ColE1 replicons, including different antibiotic resistance determinants, supporting the previous results achieved with the collections of bacterial isolates. In addition, we detected cryptic ColE1 plasmids in both families with no known genes in their variable region, which we have named sentinel plasmids. In conclusion, in this work we present a useful genetic tool for the detection and analysis of ColE1 plasmids, and confirm their important role in the dissemination of antibiotic resistance, especially in the Pasteurellaceae family of bacteria.
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Affiliation(s)
- Manuel Ares-Arroyo
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Alfonso Santos-Lopez
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Maria R Baquero
- Departamento de Microbiología, Facultad de Veterinaria, Universidad Alfonso X el Sabio, Madrid, Spain
| | - Kashi N Prasad
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Dolores Cid
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Carmen Martin-Espada
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Alvaro San Millan
- Servicio de Microbiología Hospital Universitario Ramón y Cajal, Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Bruno Gonzalez-Zorn
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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Ceccarelli D, Garriss G, Choi SY, Hasan NA, Stepanauskas R, Pop M, Huq A, Colwell RR. Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139. Front Microbiol 2017; 8:2283. [PMID: 29218035 PMCID: PMC5703827 DOI: 10.3389/fmicb.2017.02283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022] Open
Abstract
We report the complete sequence of two novel plasmids, pSDH-1 and pSDH-2, isolated from clinical Vibrio cholerae non-O1/non-O139 during the early phase of the 2010 Haitian cholera epidemic. Plasmids were revealed by employing single-cell genomics and their genome content suggests self-mobilization and, for pSDH-2, a toxin-antitoxin (TA) system for plasmid stabilization was identified. The putative origin of replication of pSDH-2 was mapped suggesting it replicates following the ColE1 model of plasmid replication. pSDH-1 and pSDH-2 were widespread among environmental V. cholerae non-O1/non-O139 with variable prevalence in four Haitian Departments. pSDH-2 was the most common element, either alone or with pSDH-1. The two plasmids detection adds to the composite scenario of mobile genetic elements (MGEs) observed in V. cholerae in Haiti. The role these small cryptic plasmids circulating in Vibrio spp. play in bacterial fitness or pathogenicity merits further investigation.
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Affiliation(s)
- Daniela Ceccarelli
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Geneviève Garriss
- Department of Microbiology, Cell Biology and Tumor Biology, Karolinska Institutet, Stockholm, Sweden
| | - Seon Y Choi
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,CosmosID Inc., Rockville, MD, United States
| | - Nur A Hasan
- CosmosID Inc., Rockville, MD, United States.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | | | - Mihai Pop
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | - Anwar Huq
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,Maryland Institute of Applied Environmental Health, University of Maryland, College Park, MD, United States
| | - Rita R Colwell
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,CosmosID Inc., Rockville, MD, United States.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States.,Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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Bardaji L, Añorga M, Ruiz-Masó JA, Del Solar G, Murillo J. Plasmid Replicons from Pseudomonas Are Natural Chimeras of Functional, Exchangeable Modules. Front Microbiol 2017; 8:190. [PMID: 28243228 PMCID: PMC5304414 DOI: 10.3389/fmicb.2017.00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/25/2017] [Indexed: 01/05/2023] Open
Abstract
Plasmids are a main factor for the evolution of bacteria through horizontal gene exchange, including the dissemination of pathogenicity genes, resistance to antibiotics and degradation of pollutants. Their capacity to duplicate is dependent on their replication determinants (replicon), which also define their bacterial host range and the inability to coexist with related replicons. We characterize a second replicon from the virulence plasmid pPsv48C, from Pseudomonas syringae pv. savastanoi, which appears to be a natural chimera between the gene encoding a newly described replication protein and a putative replication control region present in the widespread family of PFP virulence plasmids. We present extensive evidence of this type of chimerism in structurally similar replicons from species of Pseudomonas, including environmental bacteria as well as plant, animal and human pathogens. We establish that these replicons consist of two functional modules corresponding to putative control (REx-C module) and replication (REx-R module) regions. These modules are functionally separable, do not show specificity for each other, and are dynamically exchanged among replicons of four distinct plasmid families. Only the REx-C module displays strong incompatibility, which is overcome by a few nucleotide changes clustered in a stem-and-loop structure of a putative antisense RNA. Additionally, a REx-C module from pPsv48C conferred replication ability to a non-replicative chromosomal DNA region containing features associated to replicons. Thus, the organization of plasmid replicons as independent and exchangeable functional modules is likely facilitating rapid replicon evolution, fostering their diversification and survival, besides allowing the potential co-option of appropriate genes into novel replicons and the artificial construction of new replicon specificities.
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Affiliation(s)
- Leire Bardaji
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra Pamplona, Spain
| | - Maite Añorga
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra Pamplona, Spain
| | - José A Ruiz-Masó
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
| | - Gloria Del Solar
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
| | - Jesús Murillo
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra Pamplona, Spain
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Hardee CL, Arévalo-Soliz LM, Hornstein BD, Zechiedrich L. Advances in Non-Viral DNA Vectors for Gene Therapy. Genes (Basel) 2017; 8:E65. [PMID: 28208635 PMCID: PMC5333054 DOI: 10.3390/genes8020065] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/01/2017] [Indexed: 01/08/2023] Open
Abstract
Uses of viral vectors have thus far eclipsed uses of non-viral vectors for gene therapy delivery in the clinic. Viral vectors, however, have certain issues involving genome integration, the inability to be delivered repeatedly, and possible host rejection. Fortunately, development of non-viral DNA vectors has progressed steadily, especially in plasmid vector length reduction, now allowing these tools to fill in specifically where viral or other non-viral vectors may not be the best options. In this review, we examine the improvements made to non-viral DNA gene therapy vectors, highlight opportunities for their further development, address therapeutic needs for which their use is the logical choice, and discuss their future expansion into the clinic.
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Affiliation(s)
- Cinnamon L. Hardee
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.A.-S.); (B.D.H.)
| | - Lirio Milenka Arévalo-Soliz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.A.-S.); (B.D.H.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Benjamin D. Hornstein
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.A.-S.); (B.D.H.)
| | - Lynn Zechiedrich
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (L.M.A.-S.); (B.D.H.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
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Zawilak-Pawlik A, Zakrzewska-Czerwińska J. Recent Advances in Helicobacter pylori Replication: Possible Implications in Adaptation to a Pathogenic Lifestyle and Perspectives for Drug Design. Curr Top Microbiol Immunol 2017; 400:73-103. [PMID: 28124150 DOI: 10.1007/978-3-319-50520-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA replication is an important step in the life cycle of every cell that ensures the continuous flow of genetic information from one generation to the next. In all organisms, chromosome replication must be coordinated with overall cell growth. Helicobacter pylori growth strongly depends on its interaction with the host, particularly with the gastric epithelium. Moreover, H. pylori actively searches for an optimal microniche within a stomach, and it has been shown that not every microniche equally supports growth of this bacterium. We postulate that besides nutrients, H. pylori senses different, unknown signals, which presumably also affect chromosome replication to maintain H. pylori propagation at optimal ratio allowing H. pylori to establish a chronic, lifelong infection. Thus, H. pylori chromosome replication and particularly the regulation of this process might be considered important for bacterial pathogenesis. Here, we summarize our current knowledge of chromosome and plasmid replication in H. pylori and discuss the mechanisms responsible for regulating this key cellular process. The results of extensive studies conducted thus far allow us to propose common and unique traits in H. pylori chromosome replication. Interestingly, the repertoire of proteins involved in replication in H. pylori is significantly different to that in E. coli, strongly suggesting that novel factors are engaged in H. pylori chromosome replication and could represent attractive drug targets.
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Affiliation(s)
- Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Ul. Weigla 12, 53-114, Wrocław, Poland.
| | - Jolanta Zakrzewska-Czerwińska
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Ul. Weigla 12, 53-114, Wrocław, Poland
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Ul. Joliot-Curie 14A, 50-383, Wrocław, Poland
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Hayes S, Wang W, Rajamanickam K, Chu A, Banerjee A, Hayes C. Lambda gpP-DnaB Helicase Sequestration and gpP-RpoB Associated Effects: On Screens for Auxotrophs, Selection for Rif(R), Toxicity, Mutagenicity, Plasmid Curing. Viruses 2016; 8:E172. [PMID: 27338450 PMCID: PMC4926192 DOI: 10.3390/v8060172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/25/2016] [Accepted: 06/09/2016] [Indexed: 12/03/2022] Open
Abstract
The bacteriophage lambda replication initiation protein P exhibits a toxic effect on its Escherichia coli (E. coli) host, likely due to the formation of a dead-end P-DnaB complex, sequestering the replicative DnaB helicase from further activity. Intracellular expression of P triggers SOS-independent cellular filamentation and rapidly cures resident ColE1 plasmids. The toxicity of P is suppressed by alleles of P or dnaB. We asked whether P buildup within a cell can influence E. coli replication fidelity. The influence of P expression from a defective prophage, or when cloned and expressed from a plasmid was examined by screening for auxotrophic mutants, or by selection for rifampicin resistant (Rif(R)) cells acquiring mutations within the rpoB gene encoding the β-subunit of RNA polymerase (RNAP), nine of which proved unique. Using fluctuation assays, we show that the intracellular expression of P evokes a mutator effect. Most of the Rif(R) mutants remained P(S) and localized to the Rif binding pocket in RNAP, but a subset acquired a P(R) phenotype, lost sensitivity to ColE1 plasmid curing, and localized outside of the pocket. One P(R) mutation was identical to rpo*Q148P, which alleviates the UV-sensitivity of ruv strains defective in the migration and resolution of Holliday junctions and destabilizes stalled RNAP elongation complexes. The results suggest that P-DnaB sequestration is mutagenic and supports an earlier observation that P can interact with RNAP.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Wen Wang
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Karthic Rajamanickam
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Audrey Chu
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Anirban Banerjee
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Connie Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
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Son YJ, Ryu AJ, Li L, Han NS, Jeong KJ. Development of a high-copy plasmid for enhanced production of recombinant proteins in Leuconostoc citreum. Microb Cell Fact 2016; 15:12. [PMID: 26767787 PMCID: PMC4714500 DOI: 10.1186/s12934-015-0400-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 12/16/2015] [Indexed: 11/17/2022] Open
Abstract
Background Leuconostoc is a hetero-fermentative lactic acid bacteria, and its importance is widely recognized in the dairy industry. However, due to limited genetic tools including plasmids for Leuconostoc, there has not been much extensive research on the genetics and engineering of Leuconostoc yet. Thus, there is a big demand for high-copy-number plasmids for useful gene manipulation and overproduction of recombinant proteins in Leuconostoc. Results Using an existing low-copy plasmid, the copy number of plasmid was increased by random mutagenesis followed by FACS-based high-throughput screening. First, a random library of plasmids was constructed by randomizing the region responsible for replication in Leuconostoc citreum; additionally, a superfolder green fluorescent protein (sfGFP) was used as a reporter protein. With a high-speed FACS sorter, highly fluorescent cells were enriched, and after two rounds of sorting, single clone exhibiting the highest level of sfGFP was isolated. The copy number of the isolated plasmid (pCB4270) was determined by quantitative PCR (qPCR). It was found that the isolated plasmid has approximately a 30-fold higher copy number (approx. 70 copies per cell) than that of the original plasmid. From the sequence analysis, a single mutation (C→T) at position 4690 was found, and we confirmed that this single mutation was responsible for the increased plasmid copy number. The effectiveness of the isolated high-copy-number plasmid for the overproduction of recombinant proteins was successfully demonstrated with two protein models Glutathione-S-transferase (GST) and α–amylase. Conclusions The high-copy number plasmid was successfully isolated by FACS-based high-throughput screening of a plasmid library in L. citreum. The isolated plasmid could be a useful genetic tool for high-level gene expression in Leuconostoc, and for extending the applications of this useful bacteria to various areas in the dairy and pharmaceutical industries.
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Affiliation(s)
- Yeon Jeong Son
- Department of Chemical and Biomolecular Engineering, BK21 Plus PROGRAM, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Ae Jin Ryu
- Department of Chemical and Biomolecular Engineering, BK21 Plus PROGRAM, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Ling Li
- Division of Animal, Horticultural and Food Sciences, Brain Korea 21 Center for Bio-Resource Development, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Nam Soo Han
- Division of Animal, Horticultural and Food Sciences, Brain Korea 21 Center for Bio-Resource Development, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, BK21 Plus PROGRAM, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Attéré SA, Vincent AT, Trudel MV, Chanut R, Charette SJ. Diversity and Homogeneity among Small Plasmids of Aeromonas salmonicida subsp. salmonicida Linked with Geographical Origin. Front Microbiol 2015; 6:1274. [PMID: 26635745 PMCID: PMC4655240 DOI: 10.3389/fmicb.2015.01274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/31/2015] [Indexed: 01/31/2023] Open
Abstract
Furunculosis, which is caused by Aeromonas salmonicida subsp. salmonicida, is a major salmonid disease in fish farms worldwide. Several plasmids found in this bacterium confer phenotypes such drug resistance and virulence. Small plasmids (pAsa1, pAsa2, pAsa3, and pAsal1) related to ColE1- and ColE2-type replicons are usually present in its normal plasmidome. In the present study, with the objective to investigate if these plasmids display particularities related to the origin of the isolates bearing them, a total of 153 isolates, including 78 new and 75 previously described, were analyzed for the presence of small plasmids by PCR and DNA restriction fragment profiling. A geographical dichotomy between Canadian and European isolates for their propensity to do not have pAsa3 or pAsal1 was found. In addition, the genotyping analysis led to the identification of two European isolates harboring an unusual pAsal1. An investigation by next-generation sequencing (NGS) of these two isolates shed light on two pAsal1 variants (pAsal1C and pAsal1D). As with pAsal1B, another pAsal1 variant previously described, these two new variants bore a second insertion sequence (ISAS5) in addition to the usual ISAS11. The characterization of these variants suggested that they could predominate over the wild-type pAsal1 in stressful conditions such as growth at temperatures of 25°C and above. To obtain a comprehensive portrait of the mutational pressure on small plasmids, 26 isolates whose DNA had been sequenced by NGS were investigated. pAsa3 and pAsal1 were more prone to mutations than pAsa1 and pAsa2, especially in the mobA gene, which encodes a relaxase and a primase. Lastly, the average copy number of each plasmid per cell was assessed using raw sequencing data. A clear trend with respect to the relative proportion per cell of each plasmid was identified. Our large-scale study revealed a geographical dichotomy in small plasmid repertoire in addition to a clear trend for pAsa3 and pAsal1 to be more frequently altered. Moreover, we present the discovery of two new variants of pAsal1: pAsal1C and pAsal1D.
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Affiliation(s)
- Sabrina A Attéré
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Antony T Vincent
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Mélanie V Trudel
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Romain Chanut
- Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Steve J Charette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
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