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Tsiklauri R, Gabashvili E, Kobakhidze S, Tabatadze L, Bobokhidze E, Dadiani K, Koulouris S, Kotetishvili M. In-silico analyses provide strong statistical evidence for intra-species recombination events of the gyrA and CmeABC operon loci contributing to the continued emergence of resistance to fluoroquinolones in natural populations of Campylobacter jejuni. J Glob Antimicrob Resist 2022; 31:22-31. [PMID: 35985623 DOI: 10.1016/j.jgar.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The continued emergence of Campylobacter jejuni strains resistant to fluoroquinolones (FQs) has posed a significant threat to global public health, leading frequently to undesirable outcomes of human campylobacteriosis treatment. The molecular genetic mechanisms contributing to the increased retention of resistance to FQs in natural populations of this species, especially in antibiotic-free environments, are not clearly understood. This study aimed to determine whether genetic recombination could be such a mechanism. METHODS We applied a large array of algorithms, imbedded in the SplitsTree and RDP4 software packages, to analyse the DNA sequences of the chromosomal loci, including the gyrA gene and the CmeABC operon, to identify events of their genetic recombination between C. jejuni strains. RESULTS The SplitsTree analyses of the above genetic loci resulted in several parallelograms with the bootstrap values being in a range of 94.7 to 100, with the high fit estimates being 99.3 to 100. These analyses were further strongly supported by the Phi test results (P ≤ 0.02715) and the RDP4-generated statistics (P ≤ 0.04005). The recombined chromosomal regions, along with the gyrA gene and CmeABC operon loci, were also found to contain the genetic loci that included, but were not limited to, the genes encoding for phosphoribosyltransferase, lipoprotein, outer membrane motility protein, and radical SAM domain protein. CONCLUSION These findings strongly suggest that the genetic recombination of the chromosomal regions involving gyrA, CmeABC, and their adjacent loci may be an additional mechanism underlying the constant emergence of epidemiologically successful FQ-resistant strains in natural populations of C. jejuni.
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Affiliation(s)
- Rusudan Tsiklauri
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Ekaterine Gabashvili
- Bioinformatics Core, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Saba Kobakhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Leila Tabatadze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Ekaterine Bobokhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Ketevan Dadiani
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, Tbilisi, Georgia; G. Natadze Scientific-Research Institute of Sanitation, Hygiene and Medical Ecology, Tbilisi, Georgia
| | - Stylianos Koulouris
- European Commission, Directorate General for Health and Food Safety, Bruxelles/Brussel, Belgium
| | - Mamuka Kotetishvili
- G. Natadze Scientific-Research Institute of Sanitation, Hygiene and Medical Ecology, Tbilisi, Georgia; School of Science and Technology, Scientific Research Institute of the University of Georgia, Tbilisi, Georgia.
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Ran Sapir S, Boichis E, Herskovits AA. Generation of Markerless Gene Deletion Mutants in Listeria monocytogenes Using a Mutated pheS for Counterselection. Methods Mol Biol 2022; 2427:3-10. [PMID: 35619020 DOI: 10.1007/978-1-0716-1971-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gene alteration/deletion by allelic exchange is the preferred strategy for gene manipulation in bacteria. Here we present the fundamentals for an efficient allelic exchange gene deletion method in the bacterial pathogen Listeria monocytogenes. Combining vector generation by Gibson assembly with a counterselection system based on the mutated phenylalanine synthetase (pheS*) makes the generation of gene deletion mutants straightforward and time efficient.
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Affiliation(s)
- Shai Ran Sapir
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Etai Boichis
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Anat A Herskovits
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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Campellone KG, Coulter AM. Lambda Red-Mediated Recombination in Shiga Toxin-Producing Escherichia coli. Methods Mol Biol 2021; 2291:145-62. [PMID: 33704752 DOI: 10.1007/978-1-0716-1339-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The bacteriophage Lambda (λ) "Red" recombination system has enabled the development of efficient methods for engineering bacterial chromosomes. This system has been particularly important to the field of bacterial pathogenesis, where it has advanced the study of virulence factors from Shiga toxin-producing and enteropathogenic Escherichia coli (STEC and EPEC). Transient plasmid-driven expression of Lambda Red allows homologous recombination between PCR-derived linear DNA substrates and target loci in the STEC/EPEC chromosomes. Red-associated techniques can be used to create individual gene knockouts, generate deletions of large pathogenicity islands, and make markerless allelic exchanges. This chapter describes specific strategies and procedures for performing Lambda Red-mediated genome engineering in STEC.
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Abstract
Genetic manipulation of Streptococcus pyogenes (Group A Streptococcus, GAS) has historically been a challenging process, with considerable variation in efficiency between different strains. Here, we outline an optimized, rapid method for creating markerless isogenic mutations that combines Gibson assembly cloning with a new temperature-sensitive plasmid, pLZts. This method is highly efficient and reduces the time needed to create GAS mutants to ~2-3 weeks, with the ability to prepare multiple mutants simultaneously.
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Affiliation(s)
- Timothy C Barnett
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia. .,Centre for Child Health Research, University of Western Australia, Nedlands, WA, Australia.
| | - Jessica N Daw
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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Luo L, De Buck J. Inducing cellular immune responses with a marked Mycobacterium avium subsp. paratuberculosis strain in dairy calves. Vet Microbiol 2020; 244:108665. [PMID: 32402345 DOI: 10.1016/j.vetmic.2020.108665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 10/24/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of Johne's disease, a chronic granulomatous enteritis with a high global prevalence in dairy cattle. This disease causes significant economic loss in the dairy industry and has been challenging to control, as current diagnostic assays are low in sensitivity and specificity, and previously developed vaccines do not prevent infection and face regulatory concerns due to interference with bovine tuberculosis diagnostics. To remediate this issue, positive and negative immune markers were created in a MAP strain as a step towards a vaccine capable of differentiating infected from vaccinated animals (DIVA). A gene coding for an immunogenic protein (MAP1693c) in the MAP genome was replaced with a library of epitope-tagged immunogenic genes (pepA) via a stable allelic exchange method. These markers were evaluated in a calf infection trial, where Holstein-Friesian dairy calves were inoculated at two weeks of age with either the marked strain or the parent strain, or remained uninfected controls. Cellular immune responses to the markers were measured using an interferon gamma release assay (IGRA). There were no MAP1693c marker-specific differences in cellular immune responses between infection groups. A scrambled version of the HA (human influenza hemagglutinin) epitope, but not the actual HA epitope, induced a significant IFN-γ response in marker-infected calves compared to WT-infected and uninfected groups at 4.5 months post-inoculation. This scrambled HA epitope thus holds potential as a diagnostic tool as part of a DIVA vaccine for Johne's disease.
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Affiliation(s)
- Lucy Luo
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
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Abstract
Performing genetic manipulation is often key to understanding bacterial gene function. In this chapter, we present the method of allelic exchange using temperature-sensitive plasmids to generate mutations in Staphylococcus, including single-nucleotide mutations, insertions, and gene deletions. In addition, this chapter summarizes other key genetic technologies used for the manipulation of S. aureus, including the CRISPR/Cas9 system and complementation.
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Affiliation(s)
- Crystal M Austin
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jeffrey L Bose
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.
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Abstract
Progress in understanding molecular mechanisms contributing to chlamydial pathogenesis has been greatly facilitated by recent advances in genetic manipulation of C. trachomatis. Valuable approaches such as random, chemically induced mutagenesis or targeted, insertion-based gene disruption have led to significant discoveries. We describe herein a technique for generating definitive null strains via complete deletion of chromosomal genes in C. trachomatis. Fluorescence-reported allelic exchange mutagenesis (FRAEM), using the suicide vector pSUmC, enables targeted deletion of desired chromosomal DNA. The protocol provided here describes steps required to produce transformation competent chlamydiae, generate a specific allelic exchange plasmid construct, carry out mutagenesis, and isolate clonal populations of resulting mutant strains.
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Abstract
Acinetobacter baumannii is characterized as a nosocomial, gram-negative, multidrug-resistant bacterium, which has gained increasing attention due to its prevalence in hospital settings and high mortality rates upon infection. Currently, a number of different protocols have been developed in attempts to genetically alter A. baumannii, including multidrug-resistant strains. Although the bacterium has an unusual ability to uptake exogenous DNA in the natural environments, within the laboratory setting, gene manipulation to study virulence properties can be challenging. In this chapter we describe a general protocol for modification of specific genes using homologous recombination and a counterselectable marker.
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Affiliation(s)
- Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - Joshua Mettlach
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
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Wang T, Wang D, Lyu Y, Feng E, Zhu L, Liu C, Wang Y, Liu X, Wang H. Construction of a high-efficiency cloning system using the Golden Gate method and I-SceI endonuclease for targeted gene replacement in Bacillus anthracis. J Biotechnol 2018; 271:8-16. [PMID: 29438783 DOI: 10.1016/j.jbiotec.2018.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 11/30/2022]
Abstract
To investigate gene function in Bacillus anthracis, a high-efficiency cloning system is required with an increased rate of allelic exchange. Golden Gate cloning is a molecular cloning strategy allowing researchers to simultaneously and directionally assemble multiple DNA fragments to construct target plasmids using type IIs restriction enzymes and T4 DNA ligase in the same reaction system. Here, a B. anthracis S-layer protein EA1 allelic exchange vector was successfully constructed using the Golden Gate method. No new restriction sites were introduced into this knockout vector, and seamless assembly of the DNA fragments was achieved. To elevate the efficiency of homologous recombination between the allelic exchange vector and chromosomal DNA, we introduced an I-SceI site into the allelic exchange vector. The eag gene was successfully knocked out in B. anthracis using this vector. Simultaneously, the allelic exchange vector construction method was developed into a system for generating B. anthracis allelic exchange vectors. To verify the effectiveness of this system, some other allelic exchange vectors were constructed and gene replacements were performed in B. anthracis. It is speculated that this gene knockout vector construction system and high-efficiency targeted gene replacement using I-SceI endonuclease can be applied to other Bacillus spp.
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Affiliation(s)
- Tiantian Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Dongshu Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Yufei Lyu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Erling Feng
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Li Zhu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Chunjie Liu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Yanchun Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Xiankai Liu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
| | - Hengliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijng 100071, China.
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Rudenko O, Barnes AC. Gibson Assembly facilitates bacterial allelic exchange mutagenesis. J Microbiol Methods 2018; 144:157-63. [PMID: 29196271 DOI: 10.1016/j.mimet.2017.11.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 02/01/2023]
Abstract
Allelic exchange mutagenesis that relies on RecA-mediated homologous recombination up- and downstream from the targeted gene is a generalizable method of site-specific bacterial gene knock-out and knock-in. However, generation of a mutagenic DNA construct (alternative allele flanked by regions surrounding the gene target) and subsequent mutant selection are laborious procedures. Here we demonstrate allelic exchange knock-out facilitated by Gibson Assembly in Streptococcus iniae. Gibson Assembly allows rapid construction of a large allelic exchange cassette simultaneous with cloning, as well as rapid reconstruction of complete recombinant vector sequence when required. Additionally, we show that during two-step mutant selection, absence of recombination at one of the homologous regions (single cross-over) might be rapidly detected by colony PCR of meroploid clones and resolved by extension/shifting of corresponding sequence in DNA construct. The combination of Gibson Assembly for mutagenic DNA construction/redesign with colony PCR screening of meroploids to detect recombination at both sides of the exchange target may significantly accelerate generation of chromosomal mutants in a wide range of bacterial taxa.
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Sheng L, Kovács K, Winzer K, Zhang Y, Minton NP. Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955. Biotechnol Biofuels 2017; 10:5. [PMID: 28066509 PMCID: PMC5210280 DOI: 10.1186/s13068-016-0692-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/17/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The thermophile Geobacillus thermoglucosidasius has considerable attraction as a chassis for the production of chemicals and fuels. It utilises a wide range of sugars and oligosaccharides typical of those derived from lignocellulose and grows at elevated temperatures. The latter improves the rate of feed conversion, reduces fermentation cooling costs and minimises the risks of contamination. Full exploitation of its potential has been hindered by a dearth of effective gene tools. RESULTS Here we designed and tested a collection of vectors (pMTL60000 series) in G. thermoglucosidasius NCIMB 11955 equivalent to the widely used clostridial pMTL80000 modular plasmid series. By combining a temperature-sensitive replicon and a heterologous pyrE gene from Geobacillus kaustophilus as a counter-selection marker, a highly effective and rapid gene knock-out/knock-in system was established. Its use required the initial creation of uracil auxotroph through deletion of pyrE using allele-coupled exchange (ACE) and selection for resistance to 5-fluoroorotic acid. The turnaround time for the construction of further mutants in this pyrE minus strain was typically 5 days. Following the creation of the desired mutant, the pyrE allele was restored to wild type, within 3 days, using ACE and selection for uracil prototrophy. Concomitant with this process, cargo DNA (pheB) could be readily integrated at the pyrE locus. The system's utility was demonstrated through the generation in just 30 days of three independently engineered strains equivalent to a previously constructed ethanol production strain, TM242. This involved the creation of two in-frame deletions (ldh and pfl) and the replacement of a promoter region of a third gene (pdh) with an up-regulated variant. In no case did the production of ethanol match that of TM242. Genome sequencing of the parental strain, TM242, and constructed mutant derivatives suggested that NCIMB 11955 is prone to the emergence of random mutations which can dramatically affect phenotype. CONCLUSIONS The procedures and principles developed for clostridia, based on the use of pyrE alleles and ACE, may be readily deployed in G. thermoglucosidasius. Marker-less, in-frame deletion mutants can be rapidly generated in 5 days. However, ancillary mutations frequently arise, which can influence phenotype. This observation emphasises the need for improved screening and selection procedures at each step of the engineering processes, based on the generation of multiple, independent strains and whole-genome sequencing.
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Affiliation(s)
- Lili Sheng
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Katalin Kovács
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Nigel Peter Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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Abstract
Sortase is a cysteine-transpeptidase that anchors LPXTG-containing proteins on the Gram-positive bacterial cell wall. Previously, sortase was considered to be an important factor for bacterial pathogenesis and fitness, but not cell growth. However, the Actinomyces oris sortase is essential for cell viability, due to its coupling to a glycosylation pathway. In this chapter, we describe the methods to generate conditional srtA deletion mutants and identify srtA suppressors by Tn5 transposon mutagenesis. We also provide procedures for analyzing cell morphology of this mutant by thin-section electron microscopy. These techniques can be applied for analyses of other essential genes in A. oris.
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Minton NP, Ehsaan M, Humphreys CM, Little GT, Baker J, Henstra AM, Liew F, Kelly ML, Sheng L, Schwarz K, Zhang Y. A roadmap for gene system development in Clostridium. Anaerobe 2016; 41:104-112. [PMID: 27234263 PMCID: PMC5058259 DOI: 10.1016/j.anaerobe.2016.05.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/19/2016] [Accepted: 05/21/2016] [Indexed: 01/18/2023]
Abstract
Clostridium species are both heroes and villains. Some cause serious human and animal diseases, those present in the gut microbiota generally contribute to health and wellbeing, while others represent useful industrial chassis for the production of chemicals and fuels. To understand, counter or exploit, there is a fundamental requirement for effective systems that may be used for directed or random genome modifications. We have formulated a simple roadmap whereby the necessary gene systems maybe developed and deployed. At its heart is the use of ‘pseudo-suicide’ vectors and the creation of a pyrE mutant (a uracil auxotroph), initially aided by ClosTron technology, but ultimately made using a special form of allelic exchange termed ACE (Allele-Coupled Exchange). All mutants, regardless of the mutagen employed, are made in this host. This is because through the use of ACE vectors, mutants can be rapidly complemented concomitant with correction of the pyrE allele and restoration of uracil prototrophy. This avoids the phenotypic effects frequently observed with high copy number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention. Once available, the pyrE host may be used to stably insert all manner of application specific modules. Examples include, a sigma factor to allow deployment of a mariner transposon, hydrolases involved in biomass deconstruction and therapeutic genes in cancer delivery vehicles. To date, provided DNA transfer is obtained, we have not encountered any clostridial species where this technology cannot be applied. These include, Clostridium difficile, Clostridium acetobutylicum, Clostridium beijerinckii, Clostridium botulinum, Clostridium perfringens, Clostridium sporogenes, Clostridium pasteurianum, Clostridium ljungdahlii, Clostridium autoethanogenum and even Geobacillus thermoglucosidasius. A simple roadmap for the development and deployment of gene systems in clostridia. Allelic exchange using pyrE alleles and pseudo-suicide vectors. Knock-out and knock-in using allele-coupled exchange (ACE). Complementation studies through genome insertion. Genome insertion of application specific modules.
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Affiliation(s)
- Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK; Nottingham Digestive Disease Centre, NIHR Biomedical Research Unit, The University of Nottingham, University Park, Nottingham, UK.
| | - Muhammad Ehsaan
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Christopher M Humphreys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Gareth T Little
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jonathan Baker
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anne M Henstra
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Fungmin Liew
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michelle L Kelly
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK; Nottingham Digestive Disease Centre, NIHR Biomedical Research Unit, The University of Nottingham, University Park, Nottingham, UK
| | - Lili Sheng
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Katrin Schwarz
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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Ehsaan M, Kuit W, Zhang Y, Cartman ST, Heap JT, Winzer K, Minton NP. Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824. Biotechnol Biofuels 2016; 9:4. [PMID: 26732067 PMCID: PMC4700727 DOI: 10.1186/s13068-015-0410-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/04/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND Clostridium acetobutylicum represents a paradigm chassis for the industrial production of the biofuel biobutanol and a focus for metabolic engineering. We have previously developed procedures for the creation of in-frame, marker-less deletion mutants in the pathogen Clostridium difficile based on the use of pyrE and codA genes as counter selection markers. In the current study we sought to test their suitability for use in C. acetobutylicum. RESULTS Both systems readily allowed the isolation of in-frame deletions of the C. acetobutylicum ATCC 824 spo0A and the cac824I genes, leading to a sporulation minus phenotype and improved transformation, respectively. The pyrE-based system was additionally used to inactivate a putative glycogen synthase (CA_C2239, glgA) and the pSOL1 amylase gene (CA_P0168, amyP), leading to lack of production of granulose and amylase, respectively. Their isolation provided the opportunity to make use of one of the key pyrE system advantages, the ability to rapidly complement mutations at appropriate gene dosages in the genome. In both cases, their phenotypes were restored in terms of production of granulose (glgA) and amylase (amyP). Genome re-sequencing of the ATCC 824 COSMIC consortium laboratory strain used revealed the presence of 177 SNVs and 49 Indels, including a 4916-bp deletion in the pSOL1 megaplasmid. A total of 175 SNVs and 48 Indels were subsequently shown to be present in an 824 strain re-acquired (Nov 2011) from the ATCC and are, therefore, most likely errors in the published genome sequence, NC_003030 (chromosome) and NC_001988 (pSOL1). CONCLUSIONS The codA or pyrE counter selection markers appear equally effective in isolating deletion mutants, but there is considerable merit in using a pyrE mutant as the host as, through the use of ACE (Allele-Coupled Exchange) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic effects frequently observed with high copy number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention. Our study also revealed a surprising number of errors in the ATCC 824 genome sequence, while at the same time emphasising the need to re-sequence commonly used laboratory strains.
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Affiliation(s)
- Muhammad Ehsaan
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Wouter Kuit
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />MicCell Bioservices B.V., Edisonstraat 101, 7006 RB Doetinchem, The Netherlands
| | - Ying Zhang
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Stephen T. Cartman
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />Intermediates Sustainability, INVISTA Intermediates, Wilton Centre, Redcar, TS10 4RF UK
| | - John T. Heap
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
- />Department of Life Sciences, Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
| | - Klaus Winzer
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Nigel P. Minton
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, University Park, Nottingham, NG7 2RD UK
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15
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Abstract
Precise manipulation (in-frame deletions and substitutions) of the Clostridium difficile genome is possible through a two-stage process of single-crossover integration and subsequent isolation of double-crossover excision events using replication-defective plasmids that carry a counterselection marker. Use of a codA (cytosine deaminase) or pyrE (orotate phosphoribosyltransferase) as counter selection markers appears equally effective, but there is considerable merit in using a pyrE mutant as the host as, through the use of allele-coupled exchange (ACE) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic effects frequently observed with high-copy-number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention.
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Affiliation(s)
- Muhammad Ehsaan
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Sarah A Kuehne
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,Nottingham Digestive Disease Centre, NIHR Biomedical Research Unit, The University of Nottingham, University Park, Nottingham, UK
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK. .,Nottingham Digestive Disease Centre, NIHR Biomedical Research Unit, The University of Nottingham, University Park, Nottingham, UK.
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16
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Gengler S, Batoko H, Wattiau P. Method for fluorescent marker swapping and its application in Steinernema nematode colonization studies. J Microbiol Methods 2015; 113:34-7. [PMID: 25835465 DOI: 10.1016/j.mimet.2015.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/27/2015] [Accepted: 03/29/2015] [Indexed: 10/23/2022]
Abstract
An allelic exchange vector was constructed to replace gfp by mCherry in bacteria previously tagged with mini-Tn5 derivatives. The method was successfully applied to a gfp-labeled Yersinia pseudotuberculosis strain and the re-engineered bacterium was used to study the colonization of Steinernema nematodes hosting their Xenorhabdus symbiont using dual-color confocal microscopy.
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Affiliation(s)
- Samuel Gengler
- Veterinary & Agrochemical Research Centre, Brussels, Belgium; Institute of life sciences (ISV), Catholic University of Louvain-la-Neuve (UCL), Belgium
| | - Henri Batoko
- Institute of life sciences (ISV), Catholic University of Louvain-la-Neuve (UCL), Belgium
| | - Pierre Wattiau
- Veterinary & Agrochemical Research Centre, Brussels, Belgium.
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17
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Chen J, Ram G, Yoong P, Penadés JR, Shopsin B, Novick RP. An rpsL-based allelic exchange vector for Staphylococcus aureus. Plasmid 2015; 79:8-14. [PMID: 25659529 DOI: 10.1016/j.plasmid.2015.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 01/23/2015] [Accepted: 02/02/2015] [Indexed: 11/17/2022]
Abstract
Staphylococcus aureus is one of the most successful bacterial pathogens, harboring a vast repertoire of virulence factors in its arsenal. As such, the genetic manipulation of S. aureus chromosomal DNA is an important tool for the study of genes involved in virulence and survival in the host. Previously reported allelic exchange vectors for S. aureus are shuttle vectors that can be propagated in Escherichia coli, so that standard genetic manipulations can be carried out. Most of the vectors currently in use carry the temperature-sensitive replicon (pE194ts) that was originally developed for use in Bacillus subtilis. Here we show that in S. aureus, the thermosensitivity of a pE194ts vector is incomplete at standard non-permissive temperatures (42 °C), and replication of the plasmid is impaired but not abolished. We report rpsL-based counterselection vectors, with an improved temperature-sensitive replicon (pT181 repC3) that is completely blocked for replication in S. aureus at non-permissive and standard growth temperature (37 °C). We also describe a set of temperature-sensitive vectors that can be cured at standard growth temperature. These vectors provide highly effective tools for rapidly generating allelic replacement mutations and curing expression plasmids, and expand the genetic tool set available for the study of S. aureus.
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Affiliation(s)
- John Chen
- Skirball Institute Program in Molecular Pathogenesis, Departments of Microbiology and Medicine, New York University Medical Center, New York, NY 10016, USA.
| | - Geeta Ram
- Skirball Institute Program in Molecular Pathogenesis, Departments of Microbiology and Medicine, New York University Medical Center, New York, NY 10016, USA
| | - Pauline Yoong
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Bo Shopsin
- Departments of Medicine and Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Richard P Novick
- Skirball Institute Program in Molecular Pathogenesis, Departments of Microbiology and Medicine, New York University Medical Center, New York, NY 10016, USA.
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18
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Abstract
Methods used to understand the function of a gene/protein are one of the hallmarks of modern molecular genetics. The ability to genetically manipulate bacteria has become a fundamental tool in studying these organisms and while basic cloning has become a routine task in molecular biology laboratories, generating directed mutations can be a daunting task. This chapter describes the method of allelic exchange in Staphylococcus aureus using temperature-sensitive plasmids that have successfully produced a variety of chromosomal mutations, including in-frame deletions, insertion of antibiotic-resistance cassettes, and even single-nucleotide point mutations.
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Affiliation(s)
- McKenzie K Lehman
- Department of Pathology and Microbiology, Center for Staphylococcal Research, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Jeffrey L Bose
- Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, MSN 3029, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Kenneth W Bayles
- Department of Pathology and Microbiology, Center for Staphylococcal Research, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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