1
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Nayar G, Terrizzano I, Seabolt E, Agarwal A, Boucher C, Ruiz J, Slizovskiy IB, Kaufman JH, Noyes NR. ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks. Front Genet 2022; 13:1024577. [PMID: 36568361 PMCID: PMC9779932 DOI: 10.3389/fgene.2022.1024577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.
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Affiliation(s)
- Gowri Nayar
- Department of Biomedical Informatics, Stanford University, Stanford, CA, United States
| | | | - Ed Seabolt
- IBM Research Almaden, San Jose, CA, United States
| | | | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States
| | - Jaime Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States
| | - Ilya B. Slizovskiy
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | | | - Noelle R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Noelle R. Noyes,
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2
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Bacterial Hosts and Genetic Characteristics of Antibiotic Resistance Genes in Wastewater Treatment Plants of Xinjiang (China) Revealed by Metagenomics. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063100] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibiotic resistance genes (ARGs) pose a widespread concern for human health and wastewater treatment plants (WWTPs) are considered to be a major source of ARG transmission. In this paper, the potential hosts and genetic characteristics of ARGs in the influent, activated sludge and effluent of WWTPs in Xinjiang were studied by metagenomics. Bacitracin resistance gene (bacA), beta-lactamase gene (class A beta-lactamase), multidrug resistance genes (mexD, qacEdelta1), and sulfonamide resistance genes (sul1, and sul2) are persistent antibiotic resistance genes (PARGs). The potential hosts of ARGs were mainly pathogens, with Escherichia coli (12.9%), Acinetobacter johnsonii (8.94%), and Klebsiella pneumoniae (5.30%) accounting for the highest proportions. Chromosomal sequences and plasmid sequences accounted for 42.0% and 22.6% of ARG-carrying contigs (ACCs) in the influent, respectively. Meanwhile, the effluent contained 58.3% of ACCs in plasmids and 8.30% in chromosomes. Bacitracin resistance genes and multidrug resistance genes were mainly carried by chromosomes, while resistance genes for macrolide–lincosamide–streptogramin (MLS), vancomycin, sulfonamide, beta-lactam, tetracycline, chloramphenicol, and aminoglycoside were mainly carried by plasmids. ICEPae690-sul1-qacEdelta1 and ICEPmiChn3-sul2 were stable coexistence structures and heighten the transfer potential of ARGs in the environment. This study provided a clearer picture of host bacterial sources and genetic context of ARGs in the environment.
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3
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Colistin- and tigecycline-resistant CTX-M-14-producing Salmonella enterica serovar Kentucky ST198 from retail chicken meat, China. Int J Antimicrob Agents 2021; 59:106504. [PMID: 34929292 DOI: 10.1016/j.ijantimicag.2021.106504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/03/2021] [Accepted: 12/11/2021] [Indexed: 11/21/2022]
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4
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Smyshlyaev G, Bateman A, Barabas O. Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. Mol Syst Biol 2021; 17:e9880. [PMID: 34018328 PMCID: PMC8138268 DOI: 10.15252/msb.20209880] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence‐based classification system that dissects the characteristics of MGE‐borne YRs. We revealed that MGE‐related YRs evolved from non‐mobile YRs by acquisition of a regulatory arm‐binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination.
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Affiliation(s)
- Georgy Smyshlyaev
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Orsolya Barabas
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Molecular Biology, University of Geneva, Geneva, Switzerland
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5
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
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6
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Adator EH, Walker M, Narvaez-Bravo C, Zaheer R, Goji N, Cook SR, Tymensen L, Hannon SJ, Church D, Booker CW, Amoako K, Nadon CA, Read R, McAllister TA. Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum. Microorganisms 2020; 8:microorganisms8030448. [PMID: 32235751 PMCID: PMC7143971 DOI: 10.3390/microorganisms8030448] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; blaEC, blaTEM-1, blaSHV, blaOXA, blaCTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32),blaCTX-M-1, blaCTX-M-14, blaOXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while blaTEM-150, blaSHV-11–12,dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources.
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Affiliation(s)
- Emelia H. Adator
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
| | - Matthew Walker
- National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada; (M.W.); (C.A.N.)
| | - Claudia Narvaez-Bravo
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
| | - Noriko Goji
- Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge Laboratory, Lethbridge, AB T1J 3Z4, Canada; (N.G.); (K.A.)
| | - Shaun R. Cook
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada; (S.R.C.); (L.T.)
| | - Lisa Tymensen
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada; (S.R.C.); (L.T.)
| | - Sherry J. Hannon
- Feedlot Health Management Services Ltd., Okotoks, AB T1S 2A2, Canada; (S.J.H.); (D.C.); (C.W.B.)
| | - Deirdre Church
- Feedlot Health Management Services Ltd., Okotoks, AB T1S 2A2, Canada; (S.J.H.); (D.C.); (C.W.B.)
| | - Calvin W. Booker
- Feedlot Health Management Services Ltd., Okotoks, AB T1S 2A2, Canada; (S.J.H.); (D.C.); (C.W.B.)
| | - Kingsley Amoako
- Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge Laboratory, Lethbridge, AB T1J 3Z4, Canada; (N.G.); (K.A.)
| | - Celine A. Nadon
- National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada; (M.W.); (C.A.N.)
| | - Ron Read
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada;
| | - Tim A. McAllister
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
- Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
- Correspondence:
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7
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ICEKp2: description of an integrative and conjugative element in Klebsiella pneumoniae, co-occurring and interacting with ICEKp1. Sci Rep 2019; 9:13892. [PMID: 31554924 PMCID: PMC6761156 DOI: 10.1038/s41598-019-50456-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
Klebsiella pneumoniae is a human pathogen, prominent in antimicrobial-resistant and nosocomial infection. The integrative and conjugative element ICEKp1 is present in a third of clinical isolates and more prevalent in invasive disease; it provides genetic diversity and enables the spread of virulence-associated genes. We report a second integrative conjugative element that can co-occur with ICEKp1 in K. pneumoniae. This element, ICEKp2, is similar to the Pseudomonas aeruginosa pathogenicity island PAPI. We identified ICEKp2 in K. pneumoniae sequence types ST11, ST258 and ST512, which are associated with carbapenem-resistant outbreaks in China and the US, including isolates with and without ICEKp1. ICEKp2 was competent for excision, but self-mobilisation to recipient Escherichia coli was not detected. In an isolate with both elements, ICEKp2 positively influenced the efficiency of plasmid mobilisation driven by ICEKp1. We propose a putative mechanism, in which a Mob2 ATPase of ICEKp2 may contribute to the ICEKp1 conjugation machinery. Supporting this mechanism, mob2, but not a variant with mutations in the ATPase motif, restored transfer efficiency to an ICEKp2 knockout. This is the first demonstration of the interaction between integrative and conjugative genetic elements in a single Gram-negative bacterium with implications for understanding evolution by horizontal gene transfer.
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8
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1139] [Impact Index Per Article: 189.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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9
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Zamarro MT, Martín-Moldes Z, Díaz E. The ICE XTD of Azoarcus sp. CIB, an integrative and conjugative element with aerobic and anaerobic catabolic properties. Environ Microbiol 2016; 18:5018-5031. [PMID: 27450529 DOI: 10.1111/1462-2920.13465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 11/28/2022]
Abstract
Integrative and conjugative elements (ICE) play a major role in aerobic degradation of aromatic compounds, but they have not yet been shown to be involved in anaerobic degradation. We have characterized here the ICEXTD element which endows to the beta-proteobacterium Azoarcus sp. CIB with the ability to utilize aromatic hydrocarbons. The core region of ICEXTD , which shows a remarkable synteny with that of ICEclc-like elements, allows its own intracellular and intercellular mobility. ICEXTD integrates at the tRNAGly of the host chromosome, but it can also excise to produce a ready to transfer circular form. The adaptation modules of ICEXTD represent a unique combination of gene clusters for aerobic (tod genes) and anaerobic (bss-bbs and mbd genes) degradation of certain aromatic hydrocarbons, e.g., toluene, m-xylene and cumene. Transfer of ICEXTD to other Azoarcus strains, e.g., A. evansii, confers them the ability to degrade aromatic hydrocarbons both aerobically and anaerobically. Interestingly, ICEXTD allows Cupriavidus pinatubonensis, a bacterium unable to degrade anaerobically aromatic compounds, to grow with m-xylene under anoxic conditions. Thus, ICEXTD constitutes the first mobile genetic element able to expand the catabolic abilities of certain bacteria for the removal of aromatic hydrocarbons either in the presence or absence of oxygen.
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Affiliation(s)
- María Teresa Zamarro
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Zaira Martín-Moldes
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
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10
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Shi Q, Straus MR, Caron JJ, Wang H, Chung YS, Guarné A, Peters JE. Conformational toggling controls target site choice for the heteromeric transposase element Tn7. Nucleic Acids Res 2015; 43:10734-45. [PMID: 26384427 PMCID: PMC4678854 DOI: 10.1093/nar/gkv913] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 08/29/2015] [Indexed: 01/07/2023] Open
Abstract
The bacterial transposon Tn7 facilitates horizontal transfer by directing transposition into actively replicating DNA with the element-encoded protein TnsE. Structural analysis of the C-terminal domain of wild-type TnsE identified a novel protein fold including a central V-shaped loop that toggles between two distinct conformations. The structure of a robust TnsE gain-of-activity variant has this loop locked in a single conformation, suggesting that conformational flexibility regulates TnsE activity. Structure-based analysis of a series of TnsE mutants relates transposition activity to DNA binding stability. Wild-type TnsE appears to naturally form an unstable complex with a target DNA, whereas mutant combinations required for large changes in transposition frequency and targeting stabilized this interaction. Collectively, our work unveils a unique structural proofreading mechanism where toggling between two conformations regulates target commitment by limiting the stability of target DNA engagement until an appropriate insertion site is identified.
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Affiliation(s)
- Qiaojuan Shi
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA,These authors contributed equally to the paper as the first authors
| | - Marco R. Straus
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA,These authors contributed equally to the paper as the first authors
| | - Jeremy J. Caron
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Huasheng Wang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Yu Seon Chung
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada,Correspondence may also be addressed to Alba Guarné. Tel: +1 905 525 9140 (ext. 26394); Fax: +1 905 522 9033;
| | - Joseph E. Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA,To whom correspondence should be addressed. Tel: +1 607 255 2271; Fax: +1 607 255 3904;
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11
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Abstract
Horizontal gene transfer plays a major role in microbial evolution, allowing microbes to acquire new genes and phenotypes. Integrative and conjugative elements (ICEs, a.k.a. conjugative transposons) are modular mobile genetic elements integrated into a host genome and are passively propagated during chromosomal replication and cell division. Induction of ICE gene expression leads to excision, production of the conserved conjugation machinery (a type IV secretion system), and the potential to transfer DNA to appropriate recipients. ICEs typically contain cargo genes that are not usually related to the ICE life cycle and that confer phenotypes to host cells. We summarize the life cycle and discovery of ICEs, some of the regulatory mechanisms, and how the types of cargo have influenced our view of ICEs. We discuss how ICEs can acquire new cargo genes and describe challenges to the field and various perspectives on ICE biology.
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Affiliation(s)
- Christopher M Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; ,
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12
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De Maayer P, Chan WY, Martin DAJ, Blom J, Venter SN, Duffy B, Cowan DA, Smits THM, Coutinho TA. Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis. Front Microbiol 2015; 6:576. [PMID: 26106378 PMCID: PMC4458695 DOI: 10.3389/fmicb.2015.00576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 12/31/2022] Open
Abstract
Pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. The ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. One such element is an Integrative and Conjugative Element (ICE). By means of in silico analyses the ICE elements belonging to a novel family, ICEPan, were identified in the genome sequences of five P. ananatis strains and characterized. PCR screening showed that ICEPan is prevalent among P. ananatis strains isolated from different environmental sources and geographic locations. Members of the ICEPan family share a common origin with ICEs of other enterobacteria, as well as conjugative plasmids of Erwinia spp. Aside from core modules for ICEPan integration, maintenance and dissemination, the ICEPan contain extensive non-conserved islands coding for proteins that may contribute toward various phenotypes such as stress response and antibiosis, and the highly diverse ICEPan thus plays a major role in the diversification of P. ananatis. An island is furthermore integrated within an ICEPan DNA repair-encoding locus umuDC and we postulate its role in stress-induced dissemination and/or expression of the genes on this island.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa ; Department of Microbiology, University of Pretoria Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Douglas A J Martin
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen Giessen, Germany
| | - Stephanus N Venter
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences Wädenswil, Switzerland
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa ; Department of Genetics, University of Pretoria Pretoria, South Africa
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences Wädenswil, Switzerland
| | - Teresa A Coutinho
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
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13
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Bellanger X, Payot S, Leblond-Bourget N, Guédon G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev 2014; 38:720-60. [DOI: 10.1111/1574-6976.12058] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 11/28/2022] Open
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14
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Abstract
ibeA is a virulence factor found in some extraintestinal pathogenic Escherichia coli (ExPEC) strains from the B2 phylogenetic group and particularly in newborn meningitic and avian pathogenic strains. It was shown to be involved in the invasion process of the newborn meningitic strain RS218. In a previous work, we showed that in the avian pathogenic E. coli (APEC) strain BEN2908, isolated from a colibacillosis case, ibeA was rather involved in adhesion to eukaryotic cells by modulating type 1 fimbria synthesis (M. A. Cortes et al., Infect. Immun. 76:4129-4136, 2008). In this study, we demonstrate a new role for ibeA in oxidative stress resistance. We showed that an ibeA mutant of E. coli BEN2908 was more sensitive than its wild-type counterpart to H(2)O(2) killing. This phenotype was also observed in a mutant deleted for the whole GimA genomic region carrying ibeA and might be linked to alterations in the expression of a subset of genes involved in the oxidative stress response. We also showed that RpoS expression was not altered by the ibeA deletion. Moreover, the transfer of an ibeA-expressing plasmid into an E. coli K-12 strain, expressing or not expressing type 1 fimbriae, rendered it more resistant to an H(2)O(2) challenge. Altogether, these results show that ibeA by itself is able to confer increased H(2)O(2) resistance to E. coli. This feature could partly explain the role played by ibeA in the virulence of pathogenic strains.
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Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. strain KKS102, which are located on an integrative and conjugative element. J Bacteriol 2012; 194:4237-48. [PMID: 22685277 DOI: 10.1128/jb.00352-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A polychlorinated biphenyl (PCB)/biphenyl degradation gene cluster in Acidovorax sp. strain KKS102, which is very similar to that in Tn4371 from Cupriavidus oxalaticus A5, was transferred to several proteobacterial strains by conjugation. The mobilized DNA fragment consisted of 61,807 bp and carried genes for mating-pair formation (mpf), DNA transfer (dtr), integrase (int), and replication-partition proteins (rep-parAB). In the transconjugants, transferred DNA was integrated at ATTGCATCAG or similar sequences. The circular-form integrative and conjugative element (ICE) was detected by PCR, and quantitative PCR analyses revealed that, in KKS102 cells, the ratio of the circular form to the integrated form was very low (approximately 10(-5)). The circular form was not detected in a mutant of the int gene, which was located at the extreme left and transcribed in the inward direction, and the level of int transcriptional activity was much higher in the circular form than in the integrated form. These findings clearly demonstrated that the genes for PCB/biphenyl degradation in KKS102 cells are located on an ICE, which was named ICE(KKS102)4677. Comparisons of similar ICE-like elements collected from the public database suggested that those of beta- and gammaproteobacteria were distinguishable from other ICE-like elements, including those in alphaproteobacteria, with respect to the gene composition and gene organization.
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Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae. J Bacteriol 2012; 194:1494-504. [PMID: 22247511 DOI: 10.1128/jb.06403-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae.
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Michael GB, Kadlec K, Sweeney MT, Brzuszkiewicz E, Liesegang H, Daniel R, Murray RW, Watts JL, Schwarz S. ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer. J Antimicrob Chemother 2011; 67:91-100. [DOI: 10.1093/jac/dkr411] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Schneider G, Dobrindt U, Middendorf B, Hochhut B, Szijártó V, Emody L, Hacker J. Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitro support the role of conjugation for horizontal transfer of genomic islands. BMC Microbiol 2011; 11:210. [PMID: 21943043 PMCID: PMC3202238 DOI: 10.1186/1471-2180-11-210] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Accepted: 09/24/2011] [Indexed: 12/14/2022] Open
Abstract
Background A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II536 was supplemented with the mobRP4 region, an origin of replication (oriVR6K), an origin of transfer (oriTRP4) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II536 construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II536 existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II536 in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II536 construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II536 deletion mutant of E. coli 536. Conclusions Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.
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Affiliation(s)
- György Schneider
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str, 2/Building D15, Würzburg, 97070, Germany
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Toleman MA, Walsh TR. Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 2011; 35:912-35. [DOI: 10.1111/j.1574-6976.2011.00294.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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