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Gu Q, Zhu X, Yu Y, Jiang T, Pan Z, Ma J, Yao H. Type II and IV toxin-antitoxin systems coordinately stabilize the integrative and conjugative element of the ICESa2603 family conferring multiple drug resistance in Streptococcus suis. PLoS Pathog 2024; 20:e1012169. [PMID: 38640137 PMCID: PMC11062541 DOI: 10.1371/journal.ppat.1012169] [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: 01/17/2024] [Revised: 05/01/2024] [Accepted: 04/02/2024] [Indexed: 04/21/2024] Open
Abstract
Integrative and conjugative elements (ICEs) play a vital role in bacterial evolution by carrying essential genes that confer adaptive functions to the host. Despite their importance, the mechanism underlying the stable inheritance of ICEs, which is necessary for the acquisition of new traits in bacteria, remains poorly understood. Here, we identified SezAT, a type II toxin-antitoxin (TA) system, and AbiE, a type IV TA system encoded within the ICESsuHN105, coordinately promote ICE stabilization and mediate multidrug resistance in Streptococcus suis. Deletion of SezAT or AbiE did not affect the strain's antibiotic susceptibility, but their duple deletion increased susceptibility, mainly mediated by the antitoxins SezA and AbiEi. Further studies have revealed that SezA and AbiEi affect the genetic stability of ICESsuHN105 by moderating the excision and extrachromosomal copy number, consequently affecting the antibiotic resistance conferred by ICE. The DNA-binding proteins AbiEi and SezA, which bind palindromic sequences in the promoter, coordinately modulate ICE excision and extracellular copy number by binding to sequences in the origin-of-transfer (oriT) and the attL sites, respectively. Furthermore, AbiEi negatively regulates the transcription of SezAT by binding directly to its promoter, optimizing the coordinate network of SezAT and AbiE in maintaining ICESsuHN105 stability. Importantly, SezAT and AbiE are widespread and conserved in ICEs harbouring diverse drug-resistance genes, and their coordinated effects in promoting ICE stability and mediating drug resistance may be broadly applicable to other ICEs. Altogether, our study uncovers the TA system's role in maintaining the genetic stability of ICE and offers potential targets for overcoming the dissemination and evolution of drug resistance.
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Affiliation(s)
- Qibing Gu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Xiayu Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Yong Yu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Tao Jiang
- Department of Stomatology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Zihao Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Jiale Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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Boss L, Kędzierska B. Bacterial Toxin-Antitoxin Systems' Cross-Interactions-Implications for Practical Use in Medicine and Biotechnology. Toxins (Basel) 2023; 15:380. [PMID: 37368681 DOI: 10.3390/toxins15060380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Toxin-antitoxin (TA) systems are widely present in bacterial genomes. They consist of stable toxins and unstable antitoxins that are classified into distinct groups based on their structure and biological activity. TA systems are mostly related to mobile genetic elements and can be easily acquired through horizontal gene transfer. The ubiquity of different homologous and non-homologous TA systems within a single bacterial genome raises questions about their potential cross-interactions. Unspecific cross-talk between toxins and antitoxins of non-cognate modules may unbalance the ratio of the interacting partners and cause an increase in the free toxin level, which can be deleterious to the cell. Moreover, TA systems can be involved in broadly understood molecular networks as transcriptional regulators of other genes' expression or modulators of cellular mRNA stability. In nature, multiple copies of highly similar or identical TA systems are rather infrequent and probably represent a transition stage during evolution to complete insulation or decay of one of them. Nevertheless, several types of cross-interactions have been described in the literature to date. This implies a question of the possibility and consequences of the TA system cross-interactions, especially in the context of the practical application of the TA-based biotechnological and medical strategies, in which such TAs will be used outside their natural context, will be artificially introduced and induced in the new hosts. Thus, in this review, we discuss the prospective challenges of system cross-talks in the safety and effectiveness of TA system usage.
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Affiliation(s)
- Lidia Boss
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, 80-309 Gdańsk, Poland
| | - Barbara Kędzierska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, 80-309 Gdańsk, Poland
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Sato JL, Fonseca DLDH, Galhardo RS. rumAB genes from SXT/R391 ICEs confer UV-induced mutability to Proteus mirabilis hosts and improve conjugation after UV irradiation. DNA Repair (Amst) 2022; 112:103297. [DOI: 10.1016/j.dnarep.2022.103297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 01/08/2023]
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Guilloteau H, Pradalier C, Roman VL, Bellanger X, Billard P, Merlin C. Identification of antibiotics triggering the dissemination of antibiotic resistance genes by SXT/R391 elements using a dedicated high-throughput whole-cell biosensor assay. J Antimicrob Chemother 2021; 77:112-123. [PMID: 34673974 DOI: 10.1093/jac/dkab374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mobile genetic elements (MGEs) are widely involved in the dissemination of antibiotic resistance genes and some of them, such as the integrative and conjugative element SXT, are even induced by specific antibiotics at sub-lethal concentrations. OBJECTIVES This work explores collateral effects of a broad range of antibiotics on the mobility of the SXTMO10 element using a specifically designed high-throughput screening test. METHODS Twenty-five promoters involved in the mobility of SXT and six artificial constitutive promoters were transcriptionally fused to luxCDABE bioluminescent genes and introduced into Escherichia coli strains with or without SXT to build whole-cell biosensors for a large-scale screening involving 48 antibiotics. A bioluminescent assay implementing a classical agar diffusion approach was coupled to an automated data processing pipeline developed to extract and analyse luminescence data from over 2000 antibiotic/biosensor combination profiles. RESULTS In addition to quinolones previously reported as inducing the expression of SXT mobility genes, we found that specific antibiotics belonging to other classes, such as imipenem and azithromycin, also behave as inducers. The use of a control set of constitutive biosensors also revealed an unexpected intricate relationship between cell respiration and light production that allowed the identification of antibiotics interfering with the respiration process. CONCLUSIONS The effect of antibiotics goes beyond the interaction with their primary cell targets and may lead to adverse effects such as triggering the dissemination of resistance by MGEs, sometimes in unpredictable ways. Identifying such MGE-triggering antibiotics is of prime importance for better controlling collateral effects during therapy.
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Affiliation(s)
| | - Cédric Pradalier
- GeorgiaTech Lorraine, CNRS, UMI, 2958 GT-CNRS, F-57070, Metz, France
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Bhandari M, Jennison AV, Rathnayake IU, Huygens F. Evolution, distribution and genetics of atypical Vibrio cholerae - A review. INFECTION GENETICS AND EVOLUTION 2021; 89:104726. [PMID: 33482361 DOI: 10.1016/j.meegid.2021.104726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae is the etiological agent of cholera, a severe diarrheal disease, which can occur as either an epidemic or sporadic disease. Cholera pandemic-causing V. cholerae O1 and O139 serogroups originated from the Indian subcontinent and spread globally and millions of lives are lost each year, mainly in developing and underdeveloped countries due to this disease. V. cholerae O1 is further classified as classical and El Tor biotype which can produce biotype specific cholera toxin (CT). Since 1961, the current seventh pandemic El Tor strains replaced the sixth pandemic strains resulting in the classical biotype strain that produces classical CT. The ongoing evolution of Atypical El Tor V. cholerae srains encoding classical CT is of global concern. The severity in the pathophysiology of these Atypical El Tor strains is significantly higher than El Tor or classical strains. Pathogenesis of V. cholerae is a complex process that involves coordinated expression of different sets of virulence-associated genes to cause disease. We are yet to understand the complete virulence profile of V. cholerae, including direct and indirect expression of genes involved in its survival and stress adaptation in the host. In recent years, whole genome sequencing has paved the way for better understanding of the evolution and strain distribution, outbreak identification and pathogen surveillance for the implementation of direct infection control measures in the clinic against many infectious pathogens including V. cholerae. This review provides a synopsis of recent studies that have contributed to the understanding of the evolution, distribution and genetics of the seventh pandemic Atypical El Tor V. cholerae strains.
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Affiliation(s)
- Murari Bhandari
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia; Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Flavia Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.
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Carraro N, Richard X, Sulser S, Delavat F, Mazza C, van der Meer JR. An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element. eLife 2020; 9:57915. [PMID: 32720896 PMCID: PMC7423338 DOI: 10.7554/elife.57915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/24/2020] [Indexed: 01/08/2023] Open
Abstract
Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3–5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida, we uncovered an ‘upstream’ cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. One of the uncovered transcription factors (named BisR) is representative for a new regulator family. Initiation activates a feedback loop, controlled by a second hitherto unrecognized heteromeric transcription factor named BisDC. Stochastic modelling and experimental data demonstrated the feedback loop to act as a scalable converter of unimodal (population-wide or ‘analog’) input to bistable (subpopulation-specific or ‘digital’) output. The feedback loop further enables prolonged production of BisDC, which ensures expression of the ‘downstream’ functions mediating ICE transfer competence in activated cells. Phylogenetic analyses showed that the ICEclc regulatory constellation with BisR and BisDC is widespread among Gamma- and Beta-proteobacteria, including various pathogenic strains, highlighting its evolutionary conservation and prime importance to control the behaviour of this wide family of conjugative elements. Mobile DNA elements are pieces of genetic material that can jump from one bacterium to another, and even across species. They are often useful to their host, for example carrying genes that allow bacteria to resist antibiotics. One example of bacterial mobile DNA is the ICEclc element. Usually, ICEclc sits passively within the bacterium’s own DNA, but in a small number of cells, it takes over, hijacking its host to multiply and to get transferred to other bacteria. Cells that can pass on the elements cannot divide, and so this ability is ultimately harmful to individual bacteria. Carrying ICEclc can therefore be positive for a bacterium but passing it on is not in the cell’s best interest. On the other hand, mobile DNAs like ICEclc have evolved to be disseminated as efficiently as possible. To shed more light on this tense relationship, Carraro et al. set out to identify the molecular mechanisms ICEclc deploys to control its host. Experiments using mutant bacteria revealed that for ICEclc to successfully take over the cell, a number of proteins needed to be produced in the correct order. In particular, a protein called BisDC triggers a mechanism to make more of itself, creating a self-reinforcing ‘feedback loop’. Mathematical simulations of the feedback loop showed that it could result in two potential outcomes for the cell. In most of the ‘virtual cells’, ICEclc ultimately remained passive; however, in a few, ICEclc managed to take over its hosts. In this case, the feedback loop ensured that there was always enough BisDC to maintain ICEclc’s control over the cell. Further analyses suggested that this feedback mechanism is also common in many other mobile DNA elements, including some that help bacteria to resist drugs. These results are an important contribution to understand how mobile DNAs manipulate their bacterial host in order to propagate and disperse. In the future, this knowledge could help develop new strategies to combat the spread of antibiotic resistance.
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Affiliation(s)
- Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Xavier Richard
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Mathematics, University of Fribourg, Fribourg, Switzerland
| | - Sandra Sulser
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - François Delavat
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,UMR CNRS 6286 UFIP, University of Nantes, Nantes, France
| | - Christian Mazza
- Department of Mathematics, University of Fribourg, Fribourg, Switzerland
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9
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Gonzalez M, Huston D, McLenigan MP, McDonald JP, Garcia AM, Borden KS, Woodgate R. SetR ICE391, a negative transcriptional regulator of the integrating conjugative element 391 mutagenic response. DNA Repair (Amst) 2018; 73:99-109. [PMID: 30581075 DOI: 10.1016/j.dnarep.2018.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 11/16/2022]
Abstract
The integrating conjugative element ICE391 (formerly known as IncJ R391) harbors an error-prone DNA polymerase V ortholog, polVICE391, encoded by the ICE391 rumAB operon. polV and its orthologs have previously been shown to be major contributors to spontaneous and DNA damage-induced mutagenesis in vivo. As a result, multiple levels of regulation are imposed on the polymerases so as to avoid aberrant mutagenesis. We report here, that the mutagenesis-promoting activity of polVICE391 is additionally regulated by a transcriptional repressor encoded by SetRICE391, since Escherichia coli expressing SetRICE391 demonstrated reduced levels of polVICE391-mediated spontaneous mutagenesis relative to cells lacking SetRICE391. SetRICE391 regulation was shown to be specific for the rumAB operon and in vitro studies with highly purified SetRICE391 revealed that under alkaline conditions, as well as in the presence of activated RecA, SetRICE391 undergoes a self-mediated cleavage reaction that inactivates repressor functions. Conversely, a non-cleavable SetRICE391 mutant capable of maintaining repressor activity, even in the presence of activated RecA, exhibited low levels of polVICE391-dependent mutagenesis. Electrophoretic mobility shift assays revealed that SetRICE391 acts as a transcriptional repressor by binding to a site overlapping the -35 region of the rumAB operon promoter. Our study therefore provides evidence indicating that SetRICE391 acts as a transcriptional repressor of the ICE391-encoded mutagenic response.
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Affiliation(s)
- Martín Gonzalez
- Department of Biology, Southwestern University, Georgetown, TX 78626, USA.
| | - Donald Huston
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Mary P McLenigan
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Audrey M Garcia
- Department of Biology, Southwestern University, Georgetown, TX 78626, USA
| | - Kylie S Borden
- Department of Biology, Southwestern University, Georgetown, TX 78626, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR. The hidden life of integrative and conjugative elements. FEMS Microbiol Rev 2017; 41:512-537. [PMID: 28369623 PMCID: PMC5812530 DOI: 10.1093/femsre/fux008] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE 'fitness'). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells.
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Affiliation(s)
- François Delavat
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8566, Japan
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Nicolas Pradervand
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
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11
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Ryan MP, Armshaw P, Pembroke JT. SXT/R391 Integrative and Conjugative Elements (ICEs) Encode a Novel 'Trap-Door' Strategy for Mobile Element Escape. Front Microbiol 2016; 7:829. [PMID: 27303400 PMCID: PMC4885824 DOI: 10.3389/fmicb.2016.00829] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/17/2016] [Indexed: 11/18/2022] Open
Abstract
Integrative conjugative elements (ICEs) are a class of bacterial mobile elements that have the ability to mediate their own integration, excision, and transfer from one host genome to another by a mechanism of site-specific recombination, self-circularisation, and conjugative transfer. Members of the SXT/R391 ICE family of enterobacterial mobile genetic elements display an unusual UV-inducible sensitization function which results in stress induced killing of bacterial cells harboring the ICE. This sensitization has been shown to be associated with a stress induced overexpression of a mobile element encoded conjugative transfer gene, orf43, a traV homolog. This results in cell lysis and release of a circular form of the ICE. Induction of this novel system may allow transfer of an ICE, enhancing its survival potential under conditions not conducive to conjugative transfer.
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Affiliation(s)
- Michael P Ryan
- Molecular and Structural Biochemistry Group, Department of Chemical and Environmental Sciences, Materials and Surface Science Institute, University of Limerick Limerick, Ireland
| | - Patricia Armshaw
- Molecular and Structural Biochemistry Group, Department of Chemical and Environmental Sciences, Materials and Surface Science Institute, University of Limerick Limerick, Ireland
| | - J Tony Pembroke
- Molecular and Structural Biochemistry Group, Department of Chemical and Environmental Sciences, Materials and Surface Science Institute, University of Limerick Limerick, Ireland
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Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element. Proc Natl Acad Sci U S A 2016; 113:E3375-83. [PMID: 27247406 DOI: 10.1073/pnas.1604479113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using time-lapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer.
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Goodman MF, McDonald JP, Jaszczur MM, Woodgate R. Insights into the complex levels of regulation imposed on Escherichia coli DNA polymerase V. DNA Repair (Amst) 2016; 44:42-50. [PMID: 27236212 DOI: 10.1016/j.dnarep.2016.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
It is now close to 40 years since the isolation of non-mutable umu/uvm strains of Escherichia coli and the realization that damage induced mutagenesis in E.coli is not a passive process. Early models of mutagenesis envisioned the Umu proteins as accessory factors to the cell's replicase that not only reduced its normally high fidelity, but also allowed the enzyme to traverse otherwise replication-blocking lesions in the genome. However, these models underwent a radical revision approximately 15 years ago, with the discovery that the Umu proteins actually encode for a DNA polymerase, E.coli pol V. The polymerase lacks 3'→5' exonucleolytic proofreading activity and is inherently error-prone when replicating both undamaged and damage DNA. So as to limit any "gratuitous" mutagenesis, the activity of pol V is strictly regulated in the cell at multiple levels. This review will summarize our current understanding of the myriad levels of regulation imposed on pol V including transcriptional control, posttranslational modification, targeted proteolysis, activation of the catalytic activity of pol V through protein-protein interactions and the very recently described intracellular spatial regulation of pol V. Remarkably, despite the multiple levels at which pol V is regulated, the enzyme is nevertheless able to contribute to the genetic diversity and evolutionary fitness of E.coli.
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Affiliation(s)
- Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles, CA 90089-2910, USA.
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Malgorzata M Jaszczur
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, CA 90089-2910, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA.
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Abstract
Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.
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Huang J, Liang Y, Guo D, Shang K, Ge L, Kashif J, Wang L. Comparative Genomic Analysis of the ICESa2603 Family ICEs and Spread of erm(B)- and tet(O)-Carrying Transferable 89K-Subtype ICEs in Swine and Bovine Isolates in China. Front Microbiol 2016; 7:55. [PMID: 26870017 PMCID: PMC4735348 DOI: 10.3389/fmicb.2016.00055] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
Integrative and conjugative elements (ICEs) of the ICESa2603 family have been isolated from several species of Streptococcus spp.; however, the comparative genomic and evolutionary analyses of these particular ICEs are currently only at their initial stages. By investigating 13 ICEs of the ICESa2603 family and two ICESa2603 family-like ICEs derived from diverse hosts and locations, we have determined that ICEs comprised a backbone of 30 identical syntenic core genes and accessory genes that were restricted to the intergenic sites or the 3′-end of the non-conserved domain of core genes to maintain its function. ICESa2603 family integrase IntICESa2603 specifically recognized a 15-bp att sequence (TTATTTAAGAGTAAC) at the 3′-end of rplL, which was highly conserved in genus Streptococcus. Phylogenetic analyses suggest that extensive recombination/insertion and the occurrence of a hybrid/mosaic in the ICESa2603 family were responsible for the significant increase in ICE diversity, thereby broadening its host range. Approximately 42.5 and 38.1% of the tested Streptococcus suis and Streptococcus agalactiae clinical isolates respectively contained ICESa2603 family Type IV secretion system (T4SS) genes, and 80.5 and 62.5% of which also respectively carried intICESa2603, indicating that ICESa2603 family is widely distributed across these bacteria. Sequencing and conjugation transfer of a novel sequence type ST303 clinical S. suis isolate HB1011 demonstrated that the 89K-subtype ICESsuHB1011 retained its transferrable function, thereby conferring tetracycline and macrolide resistance.
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Affiliation(s)
- Jinhu Huang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Yuan Liang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Dawei Guo
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Kexin Shang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Lin Ge
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jam Kashif
- Department of Veterinary Pharmacology, Sindh Agricultural University Tandojam, Pakistan
| | - Liping Wang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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A λ Cro-Like Repressor Is Essential for the Induction of Conjugative Transfer of SXT/R391 Elements in Response to DNA Damage. J Bacteriol 2015; 197:3822-33. [PMID: 26438816 DOI: 10.1128/jb.00638-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/26/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Integrative and conjugative elements (ICEs) of the SXT/R391 family are the main contributors to acquired multidrug resistance in the seventh pandemic lineage of Vibrio cholerae, the etiological agent of the diarrheal disease cholera. Conjugative transfer of SXT/R391 ICEs is triggered by antibiotics and agents promoting DNA damage through RecA-dependent autoproteolysis of SetR, an ICE-encoded λ CI-like repressor. Here, we describe the role of CroS, a distant λ Cro homolog, as a key component contributing to the regulation of expression of the activator SetCD that orchestrates the expression of the conjugative transfer genes. We show that deletion of croS abolishes the SOS response-dependent induction of SXT despite the presence of a functional setR gene. Using quantitative reverse transcription-PCR and lacZ reporter assays, we also show that CroS represses setR and setCD expression by binding to operator sites shared with SetR. Furthermore, we provide evidence of an additional operator site bound by SetR and CroS. Finally, we show that SetCD expression generates a positive feedback loop due to SXT excision and replication in a fraction of the cell population. Together, these results refine our understanding of the genetic regulation governing the propagation of major vectors of multidrug resistance. IMPORTANCE Healthcare systems worldwide are challenged by an alarming drug resistance crisis caused by the massive and rapid propagation of antibiotic resistance genes and the associated emergence of multidrug-resistant pathogenic bacteria. SXT/R391 ICEs contribute to this phenomenon not only in clinical and environmental vibrios but also in several members of the family Enterobacteriaceae. We have identified and characterized here the regulator CroS as a key factor in the stimulation of conjugative transfer of these ICEs in response to DNA-damaging agents. We have also untangled conflicting evidence regarding autoactivation of transfer by the master activator of SXT/R391 ICEs, SetCD. Discovery of CroS provides a clearer and more complete understanding of the regulatory network that governs the dissemination of SXT/R391 ICEs in bacterial populations.
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Poulin-Laprade D, Carraro N, Burrus V. The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids. Front Microbiol 2015; 6:837. [PMID: 26347724 PMCID: PMC4542580 DOI: 10.3389/fmicb.2015.00837] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/31/2015] [Indexed: 12/14/2022] Open
Abstract
Nowadays, healthcare systems are challenged by a major worldwide drug resistance crisis caused by the massive and rapid dissemination of antibiotic resistance genes and associated emergence of multidrug resistant pathogenic bacteria, in both clinical and environmental settings. Conjugation is the main driving force of gene transfer among microorganisms. This mechanism of horizontal gene transfer mediates the translocation of large DNA fragments between two bacterial cells in direct contact. Integrative and conjugative elements (ICEs) of the SXT/R391 family (SRIs) and IncA/C conjugative plasmids (ACPs) are responsible for the dissemination of a broad spectrum of antibiotic resistance genes among diverse species of Enterobacteriaceae and Vibrionaceae. The biology, diversity, prevalence and distribution of these two families of conjugative elements have been the subject of extensive studies for the past 15 years. Recently, the transcriptional regulators that govern their dissemination through the expression of ICE- or plasmid-encoded transfer genes have been described. Unrelated repressors control the activation of conjugation by preventing the expression of two related master activator complexes in both types of elements, i.e., SetCD in SXT/R391 ICEs and AcaCD in IncA/C plasmids. Finally, in addition to activating ICE- or plasmid-borne genes, these master activators have been shown to specifically activate phylogenetically unrelated mobilizable genomic islands (MGIs) that also disseminate antibiotic resistance genes and other adaptive traits among a plethora of pathogens such as Vibrio cholerae and Salmonella enterica.
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Affiliation(s)
- Dominic Poulin-Laprade
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke , Sherbrooke, QC, Canada
| | - Nicolas Carraro
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke , Sherbrooke, QC, Canada
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke , Sherbrooke, QC, Canada
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Poulin-Laprade D, Matteau D, Jacques PÉ, Rodrigue S, Burrus V. Transfer activation of SXT/R391 integrative and conjugative elements: unraveling the SetCD regulon. Nucleic Acids Res 2015; 43:2045-56. [PMID: 25662215 PMCID: PMC4344509 DOI: 10.1093/nar/gkv071] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Integrative and conjugative elements (ICEs) of the SXT/R391 family have been recognized as key drivers of antibiotic resistance dissemination in the seventh-pandemic lineage of Vibrio cholerae. SXT/R391 ICEs propagate by conjugation and integrate site-specifically into the chromosome of a wide range of environmental and clinical Gammaproteobacteria. SXT/R391 ICEs bear setC and setD, two conserved genes coding for a transcriptional activator complex that is essential for activation of conjugative transfer. We used chromatin immunoprecipitation coupled with exonuclease digestion (ChIP-exo) and RNA sequencing (RNA-seq) to characterize the SetCD regulon of three representative members of the SXT/R391 family. We also identified the DNA sequences bound by SetCD in MGIVflInd1, a mobilizable genomic island phylogenetically unrelated to SXT/R391 ICEs that hijacks the conjugative machinery of these ICEs to drive its own transfer. SetCD was found to bind a 19-bp sequence that is consistently located near the promoter −35 element of SetCD-activated genes, a position typical of class II transcriptional activators. Furthermore, we refined our understanding of the regulation of excision from and integration into the chromosome for SXT/R391 ICEs and demonstrated that de novo expression of SetCD is crucial to allow integration of the incoming ICE DNA into a naive host following conjugative transfer.
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Affiliation(s)
- Dominic Poulin-Laprade
- Laboratory of Bacterial Molecular Genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Dominick Matteau
- Laboratory of Microbial Systems and Synthetic Biology, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Pierre-Étienne Jacques
- Laboratory of Bioinformatics and Genomics, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Sébastien Rodrigue
- Laboratory of Microbial Systems and Synthetic Biology, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
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Pradervand N, Sulser S, Delavat F, Miyazaki R, Lamas I, van der Meer JR. An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13. PLoS Genet 2014; 10:e1004441. [PMID: 24945944 PMCID: PMC4063739 DOI: 10.1371/journal.pgen.1004441] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/30/2014] [Indexed: 11/18/2022] Open
Abstract
The integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria. Integrative and conjugative elements (ICEs) are a relatively newly recognized class of mobile elements in bacteria, which integrate at one or more positions in a host chromosome, can be excised, circularized, and transfer by conjugation to a new recipient cell. Genome sequencing indicated that ICEs often carry genes with potential adaptive functions for the host. Various ICE-types have been described and ICEclc is a useful model for a wide class of elements found in Beta- and Gammaproteobacteria. Because ICEs normally remain “silent” in the host chromosome and often lack selectable markers, their lifestyle is difficult to study. One of the characteristics of ICEclc is that transfer is initiated in only 3-5% of donor cells in a population during stationary phase. Here, we describe an operon of three regulatory genes, two of which control the transfer initiation of ICEclc. Our findings suggest that the low transfer rate results from the repression of an activator and that this is essential to minimize the deleterious effect of hyper-activation of transfer initiation. While the individual regulatory genes are quite common on ICEs, they rarely occur in this configuration.
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Affiliation(s)
- Nicolas Pradervand
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sandra Sulser
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - François Delavat
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Ryo Miyazaki
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Iker Lamas
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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20
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Kim S, Yun Z, Ha UH, Lee S, Park H, Kwon EE, Cho Y, Choung S, Oh J, Medriano CA, Chandran K. Transfer of antibiotic resistance plasmids in pure and activated sludge cultures in the presence of environmentally representative micro-contaminant concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 468-469:813-820. [PMID: 24076502 DOI: 10.1016/j.scitotenv.2013.08.100] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 06/02/2023]
Abstract
The presence of antibiotics in the natural environment has been a growing issue. This presence could also account for the influence that affects microorganisms in such a way that they develop resistance against these antibiotics. The aim of this study was to evaluate whether the antibiotic resistant gene (ARG) plasmid transfer can be facilitated by the impact of 1) environmentally representative micro-contaminant concentrations in ppb (part per billion) levels and 2) donor-recipient microbial complexity (pure vs. mixed). For this purpose, the multidrug resistant plasmid, pB10, and Escherichia coli DH5α were used as a model plasmid and a model donor, respectively. Based on conjugation experiments with pure (Pseudomonas aeruginosa PAKexoT) and mixed (activated sludge) cultures as recipients, increased relative plasmid transfer frequencies were observed at ppb (μg/L) levels of tetracycline and sulfamethoxazole micro-contaminant exposure. When sludge, a more complex community, was used as a recipient, the increases of the plasmid transfer rate were always statistically significant but not always in P. aeruginosa. The low concentration (10 ppb) of tetracycline exposure led to the pB10 transfer to enteric bacteria, which are clinically important pathogens.
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Affiliation(s)
- Sungpyo Kim
- Department of Environmental Engineering, Korea University, Sejong 339-700, Republic of Korea.
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PAL BB, KHUNTIA HK, SAMAL SK, KERKETTA AS, KAR SK, KARMAKAR M, PATTNAIK B. Large outbreak of cholera caused by El Tor variant Vibrio cholerae O1 in the eastern coast of Odisha, India during 2009. Epidemiol Infect 2013; 141:2560-7. [PMID: 23461927 PMCID: PMC9151365 DOI: 10.1017/s0950268813000368] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 08/24/2012] [Accepted: 01/30/2013] [Indexed: 11/07/2022] Open
Abstract
A large outbreak of cholera reported during April-July 2009 in the Kendrapada district of Odisha, India was investigated. Forty-one rectal swabs and 41 water samples, collected from diarrhoeal patients and from different villages were bacteriologically analysed for the isolation of bacterial enteriopathogens, antibiogram profile and detection of various toxic genes. The bacteriological analysis of rectal swabs and environmental water samples revealed the presence of V. cholerae O1 Ogawa biotype El Tor. The V. cholerae strains were resistant to ciprofloxacin, co-trimoxazole, chloramphenicol, streptomycin, ampicillin, furazolidone and nalidixic acid. The multiplex polymerase chain reaction (PCR) assay on V. cholerae strains revealed the presence of ctxA and tcpA genes. The mismatch amplification of mutation assay (MAMA) PCR on clinical and environmental isolates of V. cholerae revealed that the strains were El Tor biotype, which harboured the ctxB gene of the classical strain. The random amplified polymorphic DNA PCR analysis and pulsed-field gel electrophoresis results indicated that the V. cholerae isolates belonged to the same clone. This investigation gives a warning that the El Tor variant of V. cholerae has spread to the coastal district causing a large outbreak that requires close monitoring and surveillance on diarrhoeal outbreaks in Odisha.
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Affiliation(s)
- B. B. PAL
- Microbiology Division, Regional Medical Research Centre, ICMR, Odisha, India
| | - H. K. KHUNTIA
- Microbiology Division, Regional Medical Research Centre, ICMR, Odisha, India
| | - S. K. SAMAL
- Microbiology Division, Regional Medical Research Centre, ICMR, Odisha, India
| | - A. S. KERKETTA
- Microbiology Division, Regional Medical Research Centre, ICMR, Odisha, India
| | - S. K. KAR
- Microbiology Division, Regional Medical Research Centre, ICMR, Odisha, India
| | - M. KARMAKAR
- National Rural Health Mission, Bhubaneswar, Odisha, India
| | - B. PATTNAIK
- Integrated Disease Surveillance Project, Directorate of Health Services, Government of Odisha, India
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DNA-damaging agents induce the RecA-independent homologous recombination functions of integrating conjugative elements of the SXT/R391 family. J Bacteriol 2013; 195:1991-2003. [PMID: 23435980 DOI: 10.1128/jb.02090-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Integrating conjugative elements (ICEs) of the SXT/R391 family are major contributors to the spread of antibiotic resistance genes. These elements also catalyze their own diversity by promoting inter-ICE recombination through the action of the RecA-independent homologous recombination system that they encode. Here, we report that expression of this recombination system, which consists of the single-stranded DNA annealing protein Bet and the exonuclease Exo, is induced by DNA-damaging agents via ICE-encoded transcriptional regulators. We show that the bet and exo genes are part of a large polycistronic transcript that contains many conserved ICE genes that are not involved in the main integration/excision and conjugative transfer processes. We show that although the recombination genes are highly transcribed, their translation is subject to additional strong regulatory mechanisms. We also show that an ICE-encoded putative single-stranded DNA binding protein (Ssb) limits hybrid ICE formation. Finally, a thorough in silico analysis reveals that orthologues of Bet and Exo are widely distributed in bacterial strains belonging to very distantly related bacterial species and are carried by various mobile genetic elements. Phylogenetic analyses suggest that the annealing proteins and exonucleases that compose these systems sometimes have different evolutionary origins, underscoring the strong selective pressure to maintain the functionality of these unrelated cooperating proteins.
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Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element. PLoS Genet 2012; 8:e1002818. [PMID: 22807690 PMCID: PMC3395598 DOI: 10.1371/journal.pgen.1002818] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 05/23/2012] [Indexed: 01/12/2023] Open
Abstract
Conjugative transfer of the integrative and conjugative element ICEclc in the bacterium Pseudomonas knackmussii is the consequence of a bistable decision taken in some 3% of cells in a population during stationary phase. Here we study the possible control exerted by the stationary phase sigma factor RpoS on the bistability decision. The gene for RpoS in P. knackmussii B13 was characterized, and a loss-of-function mutant was produced and complemented. We found that, in absence of RpoS, ICEclc transfer rates and activation of two key ICEclc promoters (Pint and PinR) decrease significantly in cells during stationary phase. Microarray and gene reporter analysis indicated that the most direct effect of RpoS is on PinR, whereas one of the gene products from the PinR-controlled operon (InrR) transmits activation to Pint and other ICEclc core genes. Addition of a second rpoS copy under control of its native promoter resulted in an increase of the proportion of cells expressing the Pint and PinR promoters to 18%. Strains in which rpoS was replaced by an rpoS-mcherry fusion showed high mCherry fluorescence of individual cells that had activated Pint and PinR, whereas a double-copy rpoS-mcherry–containing strain displayed twice as much mCherry fluorescence. This suggested that high RpoS levels are a prerequisite for an individual cell to activate PinR and thus ICEclc transfer. Double promoter–reporter fusions confirmed that expression of PinR is dominated by extrinsic noise, such as being the result of cellular variability in RpoS. In contrast, expression from Pint is dominated by intrinsic noise, indicating it is specific to the ICEclc transmission cascade. Our results demonstrate how stochastic noise levels of global transcription factors can be transduced to a precise signaling cascade in a subpopulation of cells leading to ICE activation. Horizontal gene transfer is one of the amazing phenomena in the prokaryotic world, by which DNA can be moved between species with means of a variety of specialized “elements” and/or specific host cell mechanisms. In particular the molecular decisions that have to be made in order to transfer DNA from one cell to another are fascinating, but very little is known about this at a cellular basis. Here we study a member of a widely distributed type of mobile DNA called “integrative and conjugative elements” or ICE. ICEclc normally resides in the chromosome of its bacterial host, but can excise from the chromosome and prepare for conjugation. Interestingly, the decision to excise ICEclc is made in only 3%–5% of cells in a clonal population in stationary phase. We focus specifically on the question of which mechanism may be responsible for setting this threshold level of ICEclc activation. We find that ICEclc activation is dependent on the individual cell level of the stationary phase sigma factor RpoS. The noise in RpoS expression across a population of cells thus sets the “threshold” for ICEclc to excise and prepare transfer.
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Lang KS, Danzeisen JL, Xu W, Johnson TJ. Transcriptome mapping of pAR060302, a blaCMY-2-positive broad-host-range IncA/C plasmid. Appl Environ Microbiol 2012; 78:3379-86. [PMID: 22344651 PMCID: PMC3346456 DOI: 10.1128/aem.07199-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 02/08/2012] [Indexed: 11/20/2022] Open
Abstract
The multidrug resistance-encoding plasmids belonging to the IncA/C incompatibility group have recently emerged among Escherichia coli and Salmonella enterica strains in the United States. These plasmids have a unique genetic structure compared to other enterobacterial plasmid types, a broad host range, and a propensity to acquire large numbers of antimicrobial resistance genes via their accessory regions. Using E. coli strain DH5α harboring the prototype IncA/C plasmid pAR060302, we sought to define the baseline transcriptome of IncA/C plasmids under laboratory growth and in the face of selective pressure. The effects of ampicillin, florfenicol, or streptomycin exposure were compared to those on cells left untreated at logarithmic phase using Illumina platform-based RNA sequencing (RNA-Seq). Under growth in Luria-Bertani broth lacking antibiotics, much of the backbone of pAR060302 was transcriptionally inactive, including its putative transfer regions. A few plasmid backbone genes of interest were highly transcribed, including genes of a putative toxin-antitoxin system and an H-NS-like transcriptional regulator. In contrast, numerous genes within the accessory regions of pAR060302 were highly transcribed, including the resistance genes floR, bla(CMY-2), aadA, and aacA. Treatment with ampicillin or streptomycin resulted in no genes being differentially expressed compared to controls lacking antibiotics, suggesting that many of the resistance-associated genes are not differentially expressed due to exposure to these antibiotics. In contrast, florfenicol treatment resulted in the upregulation of floR and numerous chromosomal genes. Overall, the transcriptome mapping of pAR060302 suggests that it mitigates the fitness costs of carrying resistance-associated genes through global regulation with its transcriptional regulators.
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Affiliation(s)
- Kevin S. Lang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Jessica L. Danzeisen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Wayne Xu
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
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Sanchez-Alberola N, Campoy S, Barbé J, Erill I. Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes. BMC Genomics 2012; 13:58. [PMID: 22305460 PMCID: PMC3323433 DOI: 10.1186/1471-2164-13-58] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 02/03/2012] [Indexed: 12/18/2022] Open
Abstract
Background The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to regulate the activity of integrases in the chromosomal superintegrons of the Vibrionaceae, which encompasses a wide range of pathogenic species harboring multiple chromosomes. Here we combine in silico and in vitro techniques to perform a comparative genomics analysis of the SOS regulon in the Vibrionaceae, and we extend the methodology to map this transcriptional network in other bacterial species harboring multiple chromosomes. Results Our analysis provides the first comprehensive description of the SOS response in a family (Vibrionaceae) that includes major human pathogens. It also identifies several previously unreported members of the SOS transcriptional network, including two proteins of unknown function. The analysis of the SOS response in other bacterial species with multiple chromosomes uncovers additional regulon members and reveals that there is a conserved core of SOS genes, and that specialized additions to this basic network take place in different phylogenetic groups. Our results also indicate that across all groups the main elements of the SOS response are always found in the large chromosome, whereas specialized additions are found in the smaller chromosomes and plasmids. Conclusions Our findings confirm that the SOS response of the Vibrionaceae is strongly linked with pathogenicity and dissemination of antibiotic resistance, and suggest that the characterization of the newly identified members of this regulon could provide key insights into the pathogenesis of Vibrio. The persistent location of key SOS genes in the large chromosome across several bacterial groups confirms that the SOS response plays an essential role in these organisms and sheds light into the mechanisms of evolution of global transcriptional networks involved in adaptability and rapid response to environmental changes, suggesting that small chromosomes may act as evolutionary test beds for the rewiring of transcriptional networks.
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Affiliation(s)
- Neus Sanchez-Alberola
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Cambray G, Sanchez-Alberola N, Campoy S, Guerin É, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I. Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons. Mob DNA 2011; 2:6. [PMID: 21529368 PMCID: PMC3108266 DOI: 10.1186/1759-8753-2-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 04/30/2011] [Indexed: 11/26/2022] Open
Abstract
Background Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain. Results Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes. Conclusions Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.
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Affiliation(s)
- Guillaume Cambray
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
| | - Neus Sanchez-Alberola
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
| | - Susana Campoy
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Émilie Guerin
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Sandra Da Re
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Bruno González-Zorn
- Departamento de Sanidad Animal, Facultad de Veterinaria, and VISAVET, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Marie-Cécile Ploy
- Université de Limoges, Faculté de Médecine, EA3175, INSERM, Equipe Avenir, Limoges 87000, France
| | - Jordi Barbé
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171, 75015 Paris, France
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA
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Abstract
Many bacterial chromosomes contain genomic islands, large DNA segments that became incorporated into the chromosome following their horizontal transmission. However, the mechanisms that mediate the lateral transfer of genomic islands are for the most part unknown. In this issue of Molecular Microbiology, Daccord et al. describe a new type of transmissible genomic island that can be mobilized by co-resident integrating conjugative elements (ICEs). These 'mobilizable genomic islands' (MGIs) require many ICE-encoded factors for their transmission, including transcription activators to induce MGI excision, the relaxase to initiate transfer at the MGI oriT and the conjugation machinery to transport MGI DNA to recipient cells. However, MGIs encode their own integrases, which enable their recombination with the chromosome of a new host, as well as a variety of other genes that do not have functions related to mobility. The MGI oriT, which resembles the ICE oriT, can also serve as a site for initiation of ICE-mediated conjugative transfer of large regions of chromosomal DNA. Overall, these findings raise the possibility that mobilization of chromosomal DNA from cyptic oriTs within genomic islands or elsewhere on the chromosome could be more common place than has been previously appreciated.
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Affiliation(s)
- Matthew K Waldor
- Channing Laboratory/Brigham and Women's Hospital, Boston, MA, USA.
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Jain M, Goel A, Bhattacharya P, Ghatole M, Kamboj D. Multidrug resistant Vibrio cholerae O1 El Tor carrying classical ctxB allele involved in a cholera outbreak in South Western India. Acta Trop 2011; 117:152-6. [PMID: 21147057 DOI: 10.1016/j.actatropica.2010.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 12/01/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022]
Abstract
Cholera is a fatal diarrheal disease characterized with enormous fluid loss through stools. A total of 41 Vibrio cholerae isolates collected from a recent cholera outbreak in Solapur, South Western India were found to belong to serogroup O1, biotype El Tor and serotype Ogawa. Molecular analysis revealed the prevalence of different toxigenic and pathogenic genes in the isolates. All the isolates harboured rstR(El)(Tor) allele indicating the presence of CTXΦ(El)(Tor). However, cholera toxin (ctxB) gene sequencing and a ctxB allele specific PCR of the isolates confirmed the presence of ctxB of classical biotype. The antibiogram profile revealed the resistance for several antibiotics including nalidixic acid, polymyxin B, streptomycin, sulfamethoxazole, trimethoprim, rifampicin and vibriostatic agent 2,4-diamino-6,7-diisopropylpteridine (O/129). All the isolates were PCR positive for class 1 integron and SXT elements also. Fingerprinting analysis revealed the clonal relationship among the outbreak isolates. The results suggested the involvement of multidrug resistant V. cholerae El Tor biotype isolates having ctxB gene of classical biotype in the cholera outbreak.
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Genetic determinants of virulence, antibiogram and altered biotype among the Vibrio cholerae O1 isolates from different cholera outbreaks in India. INFECTION GENETICS AND EVOLUTION 2010; 10:815-9. [DOI: 10.1016/j.meegid.2009.06.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 06/22/2009] [Accepted: 06/26/2009] [Indexed: 11/19/2022]
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Wozniak RAF, Waldor MK. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 2010; 8:552-63. [PMID: 20601965 DOI: 10.1038/nrmicro2382] [Citation(s) in RCA: 523] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in both Gram-positive and Gram-negative bacteria. These elements primarily reside in a host chromosome but retain the ability to excise and to transfer by conjugation. Although ICEs use a range of mechanisms to promote their core functions of integration, excision, transfer and regulation, there are common features that unify the group. This Review compares and contrasts the core functions for some of the well-studied ICEs and discusses them in the broader context of mobile-element and genome evolution.
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31
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Goel AK, Jain M, Kumar P, Jiang SC. Molecular characterization of Vibrio cholerae outbreak strains with altered El Tor biotype from southern India. World J Microbiol Biotechnol 2010; 26:281-287. [DOI: doi 10.1007/s11274-009-0171-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
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32
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Wozniak RAF, Fouts DE, Spagnoletti M, Colombo MM, Ceccarelli D, Garriss G, Déry C, Burrus V, Waldor MK. Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet 2009; 5:e1000786. [PMID: 20041216 PMCID: PMC2791158 DOI: 10.1371/journal.pgen.1000786] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 11/24/2009] [Indexed: 01/01/2023] Open
Abstract
Integrating and conjugative elements (ICEs) are one of the three principal types of self-transmissible mobile genetic elements in bacteria. ICEs, like plasmids, transfer via conjugation; but unlike plasmids and similar to many phages, these elements integrate into and replicate along with the host chromosome. Members of the SXT/R391 family of ICEs have been isolated from several species of gram-negative bacteria, including Vibrio cholerae, the cause of cholera, where they have been important vectors for disseminating genes conferring resistance to antibiotics. Here we developed a plasmid-based system to capture and isolate SXT/R391 ICEs for sequencing. Comparative analyses of the genomes of 13 SXT/R391 ICEs derived from diverse hosts and locations revealed that they contain 52 perfectly syntenic and nearly identical core genes that serve as a scaffold capable of mobilizing an array of variable DNA. Furthermore, selection pressure to maintain ICE mobility appears to have restricted insertions of variable DNA into intergenic sites that do not interrupt core functions. The variable genes confer diverse element-specific phenotypes, such as resistance to antibiotics. Functional analysis of a set of deletion mutants revealed that less than half of the conserved core genes are required for ICE mobility; the functions of most of the dispensable core genes are unknown. Several lines of evidence suggest that there has been extensive recombination between SXT/R391 ICEs, resulting in re-assortment of their respective variable gene content. Furthermore, our analyses suggest that there may be a network of phylogenetic relationships among sequences found in all types of mobile genetic elements.
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Affiliation(s)
- Rachel A. F. Wozniak
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Tufts Medical School, Boston, Massachusetts, United States of America
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Derrick E. Fouts
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Matteo Spagnoletti
- Dipartimento di Biologia Cellulare e dello Sviluppo, Universitá di Roma La Sapienza, Rome, Italy
| | - Mauro M. Colombo
- Dipartimento di Biologia Cellulare e dello Sviluppo, Universitá di Roma La Sapienza, Rome, Italy
| | - Daniela Ceccarelli
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Geneviève Garriss
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Christine Déry
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail: (VB); (MKW)
| | - Matthew K. Waldor
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Tufts Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail: (VB); (MKW)
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Molecular characterization of Vibrio cholerae outbreak strains with altered El Tor biotype from southern India. World J Microbiol Biotechnol 2009; 26:281-287. [PMID: 20495624 PMCID: PMC2872801 DOI: 10.1007/s11274-009-0171-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 08/26/2009] [Indexed: 11/03/2022]
Abstract
Forty-four Vibrio cholerae isolates collected over a 7-month period in Chennai, India in 2004 were characterized for gene traits, antimicrobial susceptibility and genomic fingerprints. All 44 isolates were identified as O1 El Tor Ogawa, positive for various toxigenic and pathogenic genes viz. ace, ctxB, hlyA, ompU, ompW, rfbO1, rtx, tcpA, toxR and zot. Nucleotide sequencing revealed the presence of cholera toxin B of classical biotype in all the El Tor isolates, suggesting infection of isolates by classical CTXPhi. Antibiogram analysis showed a broad-spectrum antibiotic resistance that was also confirmed by the presence of resistant genes in the genomes. All isolates contained a class 1 integron and an SXT constin. However, isolates were sensitive to chloramphenicol and tested negative for the chloramphenicol resistant gene suggesting a deletion in SXT constin. Fingerprinting analysis of isolates by ERIC- and Box PCR revealed similar DNA patterns indicating the clonal dissemination of a single predominant V. cholerae O1 strain throughout the 2004 outbreak in Chennai. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11274-009-0171-7) contains supplementary material, which is available to authorized users.
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Wozniak RAF, Waldor MK. A toxin-antitoxin system promotes the maintenance of an integrative conjugative element. PLoS Genet 2009; 5:e1000439. [PMID: 19325886 PMCID: PMC2654960 DOI: 10.1371/journal.pgen.1000439] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 02/25/2009] [Indexed: 11/18/2022] Open
Abstract
SXT is an integrative and conjugative element (ICE) that confers resistance to multiple antibiotics upon many clinical isolates of Vibrio cholerae. In most cells, this ∼100 Kb element is integrated into the host genome in a site-specific fashion; however, SXT can excise to form an extrachromosomal circle that is thought to be the substrate for conjugative transfer. Daughter cells lacking SXT can theoretically arise if cell division occurs prior to the element's reintegration. Even though ∼2% of SXT-bearing cells contain the excised form of the ICE, cells that have lost the element have not been detected. Here, using a positive selection-based system, SXT loss was detected rarely at a frequency of ∼1×10−7. As expected, excision appears necessary for loss, and factors influencing the frequency of excision altered the frequency of SXT loss. We screened the entire 100 kb SXT genome and identified two genes within SXT, now designated mosA and mosT (for maintenance of SXT Antitoxin and Toxin), that promote SXT stability. These two genes, which lack similarity to any previously characterized genes, encode a novel toxin-antitoxin pair; expression of mosT greatly impaired cell growth and mosA expression ameliorated MosT toxicity. Factors that promote SXT excision upregulate mosAT expression. Thus, when the element is extrachromosomal and vulnerable to loss, SXT activates a TA module to minimize the formation of SXT-free cells. Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in many bacteria. These elements integrate into the host chromosome as well as excise and transfer to other bacteria. SXT, an ICE that encodes resistances to multiple antibiotics, is currently present in most clinical isolates of V. cholerae, the cause of cholera. Cells in which SXT is excised can potentially lose the ICE if cell division occurs prior to its re-integration, but explorations of mechanisms that promote ICE maintenance have received almost no attention. Using a positive selection-based strategy to detect SXT loss, we found that loss of this ICE was very rare (1 in 107 cells). Two genes, mosAT, that lack similarity to genes of known function were found to promote SXT maintenance. We show that MosT blocks cell growth in the absence of SXT and its activity can be neutralized by MosA. Thus, these genes encode a functional toxin–antitoxin (TA) system. When SXT is extrachromosomal and vulnerable to loss, mosAT expression increases, minimizing the formation of SXT-free cells. The activity of mosAT may contribute to the maintenance of antibiotic resistance in bacterial populations.
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Affiliation(s)
- Rachel A. F. Wozniak
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Program in Genetics, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Matthew K. Waldor
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Program in Genetics, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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35
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Identification of a novel prophage-like gene cluster actively expressed in both virulent and avirulent strains of Leptospira interrogans serovar Lai. Infect Immun 2008; 76:2411-9. [PMID: 18362131 DOI: 10.1128/iai.01730-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA microarray analysis was used to compare the differential gene expression profiles between Leptospira interrogans serovar Lai type strain 56601 and its corresponding attenuated strain IPAV. A 22-kb genomic island covering a cluster of 34 genes (i.e., genes LA0186 to LA0219) was actively expressed in both strains but concomitantly upregulated in strain 56601 in contrast to that of IPAV. Reverse transcription-PCR assays proved that the gene cluster comprised five transcripts. Gene annotation of this cluster revealed characteristics of a putative prophage-like remnant with at least 8 of 34 sequences encoding prophage-like proteins, of which the LA0195 protein is probably a putative prophage CI-like regulator. The transcription initiation activities of putative promoter-regulatory sequences of transcripts I, II, and III, all proximal to the LA0195 gene, were further analyzed in the Escherichia coli promoter probe vector pKK232-8 by assaying the reporter chloramphenicol acetyltransferase (CAT) activities. The strong promoter activities of both transcripts I and II indicated by the E. coli CAT assay were well correlated with the in vitro sequence-specific binding of the recombinant LA0195 protein to the corresponding promoter probes detected by the electrophoresis mobility shift assay. On the other hand, the promoter activity of transcript III was very low in E. coli and failed to show active binding to the LA0195 protein in vitro. These results suggested that the LA0195 protein is likely involved in the transcription of transcripts I and II. However, the identical complete DNA sequences of this prophage remnant from these two strains strongly suggests that possible regulatory factors or signal transduction systems residing outside of this region within the genome may be responsible for the differential expression profiling in these two strains.
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Collateral effects of antibiotics: carbadox and metronidazole induce VSH-1 and facilitate gene transfer among Brachyspira hyodysenteriae strains. Appl Environ Microbiol 2008; 74:2950-6. [PMID: 18359835 DOI: 10.1128/aem.00189-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Brachyspira hyodysenteriae is an anaerobic spirochete and the etiologic agent of swine dysentery. The genome of this spirochete contains a mitomycin C-inducible, prophage-like gene transfer agent designated VSH-1. VSH-1 particles package random 7.5-kb fragments of the B. hyodysenteriae genome and transfer genes between B. hyodysenteriae cells. The chemicals and conditions inducing VSH-1 production are largely unknown. Antibiotics used in swine management and stressors inducing traditional prophages might induce VSH-1 and thereby stimulate lateral gene transfer between B. hyodysenteriae cells. In these studies, VSH-1 induction was initially detected by a quantitative real-time reverse transcriptase PCR assay evaluating increased transcription of hvp38 (VSH-1 head protein gene). VSH-1 induction was confirmed by detecting VSH-1-associated 7.5-kb DNA and VSH-1 particles in B. hyodysenteriae cultures. Nine antibiotics (chlortetracycline, lincomycin, tylosin, tiamulin, virginiamycin, ampicillin, ceftriaxone, vancomycin, and florfenicol) at concentrations affecting B. hyodysenteriae growth did not induce VSH-1 production. By contrast, VSH-1 was detected in B. hyodysenteriae cultures treated with mitomycin C (10 microg/ml), carbadox (0.5 microg/ml), metronidazole (0.5 microg/ml), and H(2)O(2) (300 microM). Carbadox- and metronidazole-induced VSH-1 particles transmitted tylosin and chloramphenicol resistance determinants between B. hyodysenteriae strains. The results of these studies suggest that certain antibiotics may induce the production of prophage or prophage-like elements by intestinal bacteria and thereby impact intestinal microbial ecology.
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Abstract
All organisms possess a diverse set of genetic programs that are used to alter cellular physiology in response to environmental cues. The gram-negative bacterium, Escherichia coli, mounts what is known as the "SOS response" following DNA damage, replication fork arrest, and a myriad of other environmental stresses. For over 50 years, E. coli has served as the paradigm for our understanding of the transcriptional, and physiological changes that occur following DNA damage (400). In this chapter, we summarize the current view of the SOS response and discuss how this genetic circuit is regulated. In addition to examining the E. coli SOS response, we also include a discussion of the SOS regulatory networks in other bacteria to provide a broader perspective on how prokaryotes respond to DNA damage.
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38
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Walsh TR. Combinatorial genetic evolution of multiresistance. Curr Opin Microbiol 2006; 9:476-82. [PMID: 16942901 DOI: 10.1016/j.mib.2006.08.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2006] [Accepted: 08/16/2006] [Indexed: 11/20/2022]
Abstract
The explosion in genetic information, whilst extending our knowledge, might not necessary increase our conceptual understanding on the complexities of bacterial genetics, or why some antibiotic resistant genotypes such as blaCTX-M-15 and blaVIM-2 appear to dominate. However, the information we have thus far suggests that clinical isolates have 'hijacked' plasmids, primarily built of backbone-DNA originating from environmental bacteria. Additionally, the combinatorial presence of other elements such as transposons, integrons, insertion sequence (IS) elements and the 'new' ISCR (IS common region) elements have also contributed to the increase in antibiotic resistance - an antibiotic resistant cluster composing four or five genes has become commonplace. In some instances, the presence of antibiotics themselves, such as fluoroquinolones, can mediate a bacterial SOS cell response, subsequently amplifying and/or augmenting the transfer of large genetic entities therefore, potentially promoting long-term detrimental effects.
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Affiliation(s)
- Timothy R Walsh
- Department of Molecular and Cellular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
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Burrus V, Marrero J, Waldor MK. The current ICE age: biology and evolution of SXT-related integrating conjugative elements. Plasmid 2006; 55:173-83. [PMID: 16530834 DOI: 10.1016/j.plasmid.2006.01.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 12/30/2005] [Accepted: 01/07/2006] [Indexed: 11/18/2022]
Abstract
SXT is an integrating conjugative element (ICE) that was initially isolated from a 1992 Vibrio cholerae O139 clinical isolate from India. This approximately 100-kb ICE encodes resistance to multiple antibiotics. SXT or closely related ICEs are now present in most clinical and some environmental V. cholerae isolates from Asia and Africa. SXT-related ICEs are not limited to V. cholerae. It is now clear that so-called IncJ elements such as R391 are closely related to SXT. More than 25 members of the SXT/R391 family of ICEs have now been identified in environmental and clinical isolates of diverse species of gamma-proteobacteria worldwide. In this review, we discuss the diversity, evolution and biology of this family of ICEs.
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Affiliation(s)
- Vincent Burrus
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Howard Hughes Medical Institute Boston, MA 02111, USA
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40
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Marrero J, Waldor MK. Interactions between Inner Membrane Proteins in Donor and Recipient Cells Limit Conjugal DNA Transfer. Dev Cell 2005; 8:963-70. [PMID: 15935784 DOI: 10.1016/j.devcel.2005.05.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Revised: 03/23/2005] [Accepted: 03/28/2005] [Indexed: 11/17/2022]
Abstract
Conjugation enables horizontal transmission of DNA among bacteria, thereby facilitating the rapid spread of genes such as those conferring resistance to antibiotics. Cell-cell contact is required for conjugative DNA transfer but does not ensure its success. The presence of certain plasmids in potential recipient cells inhibits redundant transfer of these plasmids from competent donors despite contact between donor and recipient cells. Here, we used two closely related integrating conjugative elements (ICEs), SXT and R391, to identify genes that inhibit redundant conjugative transfer. Cells containing SXT exclude transfer of a second copy of SXT but not R391 and vice versa. The specific exclusion of SXT and R391 is dependent upon variants of TraG and Eex, ICE-encoded inner membrane proteins in donor and recipient cells, respectively. We identified short sequences within each variant that determine the exquisite specificity of self-recognition; these data suggest that direct interactions between TraG and Eex mediate exclusion.
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Affiliation(s)
- Joeli Marrero
- Department of Molecular Microbiology, Tufts University School of Medicine, Howard Hughes Medical Institute, Boston, Massachusetts 02111, USA
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