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Cai H, Zhu Y, Hu D, Li Y, Leptihn S, Loh B, Hua X, Yu Y. Co-harboring of Novel bla KPC-2 Plasmid and Integrative and Conjugative Element Carrying Tn 6203 in Multidrug-Resistant Pseudomonas aeruginosa. Front Microbiol 2021; 12:674974. [PMID: 34290680 PMCID: PMC8287167 DOI: 10.3389/fmicb.2021.674974] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/31/2021] [Indexed: 11/18/2022] Open
Abstract
Many strains of the opportunistic pathogen Pseudomonas aeruginosa have acquired resistance to multiple antibiotics. Carbapenem-resistant P. aeruginosa poses a global healthcare problem due to limited therapeutic options for the treatment of infections. Plasmids and integrative and conjugative elements (ICEs) are the major vectors of antibiotic-resistance gene transfer. In our study, four carbapenem-resistant strains of P. aeruginosa were isolated from the same patient in a tertiary referral hospital in China, one of these was resistant to gentamicin and tobramycin. In this strain P33, we observed a non-transferable plasmid, pP33-2, carrying a novel blaKPC−2 gene segment (ISKpn27-blaKPC−2-ISKpn6-korC-ORF-klcA-IS26), which we concluded to have been formed by IS26-mediated gene cluster translocation. In addition, by comparing the chromosomes of the P. aeruginosa strains that belong to the same sequence type, we identified an ICE, ICEP33, adjacent to a prophage. The attL site of ICEP33 is identical to the terminal part of the attR site of the prophage. The ICEP33 element contains the transposon Tn6203, which encodes antibiotic and metal resistance genes. The insertion of ICEP33 in the chromosome mediates resistance to multiple antibiotics. Our study contributes to the understanding of the acquisition of antibiotic resistance in P. aeruginosa facilitated by mobile genetic elements.
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Affiliation(s)
- Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiwei Zhu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dandan Hu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sebastian Leptihn
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
| | - Belinda Loh
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Blesa A, Baquedano I, González-de la Fuente S, Mencía M, Berenguer J. Integrative and Conjugative Element ICETh1 Functions as a Pangenomic DNA Capture Module in Thermus thermophilus. Microorganisms 2020; 8:microorganisms8122051. [PMID: 33371442 PMCID: PMC7767461 DOI: 10.3390/microorganisms8122051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/16/2022] Open
Abstract
Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within an integrative and conjugative element (ICETh1) in the strain Tth HB27, whereas the NCA is constitutively expressed in both mates. Previous experiments suggested the presence of multiple origins of transfer along the genome, which could generate genomic mosaicity among the progeny. Here, we designed transjugation experiments between two closely related strains of Tth with highly syntenic genomes, containing enough single nucleotide polymorphisms to allow precise parenthood analysis. Individual clones from the progeny were sequenced, revealing their origin as derivatives of our ICETh1-containing intended “donor” strain (HB27), which had acquired separate fragments from the genome of the ICETh1-free HB8 cells, which are our intended recipient. Due to the bidirectional nature of transjugation, only assays employing competence-defective HB27 derivatives as donors allowed the recovery of HB8-derived progeny. These results show a preference for a retrotransfer mechanism in transjugation in ICETh1-bearing strains, supporting an inter-strain gene-capture function for ICETh1. This function could benefit the donor-capable host by facilitating the acquisition of adaptive traits from external sources, ultimately increasing the open pangenome of Thermus, maximizing the potential repertoire of physiological and phenotypical traits related to adaptation and speciation.
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Affiliation(s)
- Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain
- Correspondence: (A.B.); (J.B.); Tel.: +34-91194498 (J.B.)
| | - Ignacio Baquedano
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
| | - Mario Mencía
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
- Correspondence: (A.B.); (J.B.); Tel.: +34-91194498 (J.B.)
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3
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Lao J, Guédon G, Lacroix T, Charron-Bourgoin F, Libante V, Loux V, Chiapello H, Payot S, Leblond-Bourget N. Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment. Genes (Basel) 2020; 11:genes11090999. [PMID: 32858915 PMCID: PMC7563491 DOI: 10.3390/genes11090999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 01/15/2023] Open
Abstract
Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.
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Affiliation(s)
- Julie Lao
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Gérard Guédon
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Thomas Lacroix
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Florence Charron-Bourgoin
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Hélène Chiapello
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Nathalie Leblond-Bourget
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Correspondence: ; Tel.: +33-3-72-74-51-46
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4
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Liu M, Li X, Xie Y, Bi D, Sun J, Li J, Tai C, Deng Z, Ou HY. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res 2020; 47:D660-D665. [PMID: 30407568 PMCID: PMC6323972 DOI: 10.1093/nar/gky1123] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022] Open
Abstract
ICEberg 2.0 (http://db-mml.sjtu.edu.cn/ICEberg/) is an updated database that provides comprehensive information about bacterial integrative and conjugative elements (ICEs). Compared with the previous version, three major improvements were made. First, with the aid of text mining and manual curation, it now recorded the details of 1032 ICEs, including 270 with experimental supports and 762 from bioinformatics prediction. Second, as increasing evidence has shown that ICEs frequently mobilize the so-called ‘hitchhikers’, such as integrative and mobilizable elements (IMEs) and cis-mobilizable elements (CIMEs), 83 known transfer interactions between 49 IMEs and 7 CIMEs with 19 ICEs taken from the literature were included and illustrated with visually intuitive directed graphs. An expanded collection of 260 chromosome-borne IMEs and 235 CIMEs was also added. At last, ICEberg 2.0 provides an online tool ICEfinder to predict ICEs or IMEs in bacterial genome sequences. It combines a similarity search for the integrase, relaxase and/or type IV secretion system and the co-localization of these corresponding homologous genes. With the recent updates, ICEberg 2.0 might provide better support for understanding the biological traits of ICEs, especially as their interaction with cognate mobilizable elements may further promote horizontal gene flow.
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Affiliation(s)
- Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaobin Li
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yingzhou Xie
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Dexi Bi
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Cury J, Abby SS, Doppelt-Azeroual O, Néron B, Rocha EPC. Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan. Methods Mol Biol 2020; 2075:265-283. [PMID: 31584169 DOI: 10.1007/978-1-4939-9877-7_19] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present a computational method to identify conjugative systems in plasmids and chromosomes using the CONJscan module of MacSyFinder. The method relies on the identification of the protein components of the system using hidden Markov model profiles and then checking that the composition and genetic organization of the system is consistent with that expected from a conjugative system. The method can be assessed online using the Galaxy workflow or locally using a standalone software. The latter version allows to modify the models of the module (i.e., to change the expected components, their number, and their organization).CONJscan identifies conjugative systems, but when the mobile genetic element is integrative (ICE), one often also wants to delimit it from the chromosome. We present a method, with a script, to use the results of CONJscan and comparative genomics to delimit ICE in chromosomes. The method provides a visual representation of the ICE location. Together, these methods facilitate the identification of conjugative elements in bacterial genomes.
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Affiliation(s)
- Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- CNRS, UMR3525, Paris, France
| | - Sophie S Abby
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Olivia Doppelt-Azeroual
- Bioinformatics and Biostatistics Hub-C3BI, Institut Pasteur, Paris, France
- CNRS, USR 3756, Paris, France
| | - Bertrand Néron
- Bioinformatics and Biostatistics Hub-C3BI, Institut Pasteur, Paris, France
- CNRS, USR 3756, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.
- CNRS, UMR3525, Paris, France.
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6
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The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems. Genes (Basel) 2017; 8:genes8110337. [PMID: 29165361 PMCID: PMC5704250 DOI: 10.3390/genes8110337] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.
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7
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Wang P, Zeng Z, Wang W, Wen Z, Li J, Wang X. Dissemination and loss of a biofilm-related genomic island in marine Pseudoalteromonas mediated by integrative and conjugative elements. Environ Microbiol 2017; 19:4620-4637. [PMID: 28892292 DOI: 10.1111/1462-2920.13925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 01/24/2023]
Abstract
Acquisition of genomic islands (GIs) plays a central role in the diversification and adaptation of bacteria. Some GIs can be mobilized in trans by integrative and conjugative elements (ICEs) or conjugative plasmids if the GIs carry specific transfer-related sequences. However, the transfer mechanism of GIs lacking such elements remains largely unexplored. Here, we investigated the transmissibility of a GI found in a coral-associated marine bacterium. This GI does not carry genes with transfer functions, but it carries four genes required for robust biofilm formation. Notably, this GI is inserted in the integration site for SXT/R391 ICEs. We demonstrated that acquisition of an SXT/R391 ICE results in either a tandem GI/ICE arrangement or the complete displacement of the GI. The GI displacement by the ICE greatly reduces biofilm formation. In contrast, the tandem integration of the ICE with the GI in cis allows the GI to hijack the transfer machinery of the ICE to excise, transfer and re-integrate into a new host. Collectively, our findings reveal that the integration of an ICE into a GI integration site enables rapid genome dynamics and a new mechanism by which SXT/R391 ICEs can augment genome plasticity.
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Affiliation(s)
- Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhenshun Zeng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongling Wen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Cury J, Touchon M, Rocha EPC. Integrative and conjugative elements and their hosts: composition, distribution and organization. Nucleic Acids Res 2017; 45:8943-8956. [PMID: 28911112 PMCID: PMC5587801 DOI: 10.1093/nar/gkx607] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/04/2017] [Indexed: 12/22/2022] Open
Abstract
Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species’ pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses revealed that ICEs are structured in functional modules. Integrases and conjugation systems have different evolutionary histories, even if the gene repertoires of ICEs can be grouped in function of conjugation types. Our characterization of the composition and organization of ICEs paves the way for future functional and evolutionary analyses of their cargo genes, composed of a majority of unknown function genes.
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Affiliation(s)
- Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue du Dr Roux, Paris 75015, France.,CNRS, UMR3525, 28, rue Dr Roux, Paris 75015, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue du Dr Roux, Paris 75015, France.,CNRS, UMR3525, 28, rue Dr Roux, Paris 75015, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue du Dr Roux, Paris 75015, France.,CNRS, UMR3525, 28, rue Dr Roux, Paris 75015, France
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9
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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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10
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Haskett TL, Ramsay JP, Bekuma AA, Sullivan JT, O'Hara GW, Terpolilli JJ. Evolutionary persistence of tripartite integrative and conjugative elements. Plasmid 2017; 92:30-36. [DOI: 10.1016/j.plasmid.2017.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
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11
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Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer. Appl Environ Microbiol 2017; 83:AEM.00337-17. [PMID: 28432093 DOI: 10.1128/aem.00337-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 01/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.
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Coluzzi C, Guédon G, Devignes MD, Ambroset C, Loux V, Lacroix T, Payot S, Leblond-Bourget N. A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins. Front Microbiol 2017; 8:443. [PMID: 28373865 PMCID: PMC5357655 DOI: 10.3389/fmicb.2017.00443] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.
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Affiliation(s)
- Charles Coluzzi
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Marie-Dominique Devignes
- UMR7503 Laboratoire Lorrain de Recherche en Informatique et ses Applications, Centre National de la Recherche Scientifique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Chloé Ambroset
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Valentin Loux
- UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thomas Lacroix
- UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sophie Payot
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Nathalie Leblond-Bourget
- UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France
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Zhang Y, Loria R. Emergence of Novel Pathogenic Streptomyces Species by Site-Specific Accretion and cis-Mobilization of Pathogenicity Islands. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:72-82. [PMID: 27977935 DOI: 10.1094/mpmi-09-16-0190-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The main pathogenicity factor of Streptomyces species associated with the potato common scab disease is a nitrated diketopiperazine called thaxtomin A (ThxA). In Streptomyces scabiei (syn. S. scabies), which is thought to be the most ancient pathogenic Streptomyces species, the ThxA biosynthetic cluster is located within a mobile genomic island called the toxicogenic region (TR). Three attachment (att) sites further separate TR into two subregions (TR1 and TR2). TR1 contains the ThxA biosynthetic cluster and is conserved among several pathogenic Streptomyces species. However, TR2, an integrative and conjugative element, is missing in most pathogenic species. In our previous study, we demonstrated the mobilization of the whole TR element or TR2 alone between S. scabiei and nonpathogenic Streptomyces species. TR1 alone did not mobilize in these experiments. These data suggest that TR2 is required for the mobilization of TR1. Here, we show that TR2 can self mobilize to pathogenic Streptomyces species harboring only TR1 and integrate into the att site of TR1, leading to the tandem accretion of resident TR1 and incoming TR2. The incoming TR2 can further mobilize resident TR1 in cis and transfer to a new recipient cell. Our study demonstrated that TR1 is a nonautonomous cis-mobilizable element and that it can hijack TR2 recombination and conjugation machinery to excise, transfer, and integrate, leading to the dissemination of pathogenicity genes and emergence of novel pathogenic species. Additionally, comparative genomic analysis of 23 pathogenic Streptomyces isolates from ten species revealed that the composite pathogenicity island (PAI) formed by TR1 and TR2 is dynamic and various compositions of the island exist within the population of newly emerged pathogenic species, indicating the structural instability of this composite PAI.
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Affiliation(s)
- Yucheng Zhang
- Department of Plant Pathology, University of Florida, Gainesville, U.S.A
| | - Rosemary Loria
- Department of Plant Pathology, University of Florida, Gainesville, U.S.A
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14
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Patel S. Drivers of bacterial genomes plasticity and roles they play in pathogen virulence, persistence and drug resistance. INFECTION GENETICS AND EVOLUTION 2016; 45:151-164. [DOI: 10.1016/j.meegid.2016.08.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 12/11/2022]
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15
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Chapleau M, Guertin JF, Farrokhi A, Lerat S, Burrus V, Beaulieu C. Identification of genetic and environmental factors stimulating excision from Streptomyces scabiei chromosome of the toxicogenic region responsible for pathogenicity. MOLECULAR PLANT PATHOLOGY 2016; 17:501-9. [PMID: 26177341 PMCID: PMC6638466 DOI: 10.1111/mpp.12296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The genes conferring pathogenicity in Streptomyces turgidiscabies, a pathogen causing common scab of potato, are grouped together on a pathogenicity island (PAI), which has been found to be mobile and appears to transfer and disseminate like an integrative and conjugative element (ICE). However, in Streptomyces scabiei, another common scab-inducing species, the pathogenicity genes are clustered in two regions: the toxicogenic region (TR) and the colonization region. The S. scabiei 87.22 genome was analysed to investigate the potential mobility of the TR. Attachment sites (att), short homologous sequences that delineate ICEs, were identified at both extremities of the TR. An internal att site was also found, suggesting that the TR has a composite structure (TR1 and TR2). Thaxtomin biosynthetic genes, essential for pathogenicity, were found in TR1, whereas candidate genes with known functions in recombination, replication and conjugal transfer were found in TR2. Excision of the TR1 or TR2 subregions alone, or of the entire TR region, was observed, although the excision frequency of TR was low. However, the excision frequency was considerably increased in the presence of either mitomycin C or Streptomyces coelicolor cells. A composite TR structure was not observed in all S. scabiei and Streptomyces acidiscabies strains tested. Of the ten strains analysed, seven lacked TR2 and no TR excision event could be detected in these strains, thus suggesting the implication of TR2 in the mobilization of S. scabiei TR.
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Affiliation(s)
- Mélanie Chapleau
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Julien F Guertin
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Ali Farrokhi
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Sylvain Lerat
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Vincent Burrus
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | - Carole Beaulieu
- Centre SÈVE, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
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16
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Carraro N, Libante V, Morel C, Charron-Bourgoin F, Leblond P, Guédon G. Plasmid-like replication of a minimal streptococcal integrative and conjugative element. MICROBIOLOGY-SGM 2016; 162:622-632. [PMID: 26825653 DOI: 10.1099/mic.0.000219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements encoding their own excision from a replicon of their bacterial host, transfer by conjugation to a recipient bacterium and reintegration for maintenance. The conjugation, recombination and regulation modules of ICEs of the ICESt3 family are grouped together in a region called the ICE 'core region'. In addition to this core region, elements belonging to this family carry a highly variable region including cargo genes that could be involved in bacterial adaptation or in the maintenance of the element. Although ICEs are a major class of mobile elements through bacterial genomes, the functionality of an element encoding only its excision, transfer, integration and regulation has never been demonstrated experimentally. We engineered MiniICESt3, an artificial ICE derived from ICESt3, devoid of its cargo genes and thus only harbouring the core region. The functionality of this minimal element was assessed. MiniICESt3 was found to be able to excise at a rate of 3.1 %, transfer with a frequency of 1.0 × 10- 5 transconjugants per donor cell and stably maintain by site-specific integration into the 3' end of the fda gene, the same as ICESt3. Furthermore, MiniICESt3 was found in ∼10 copies per chromosome, this multicopy state likely contributing to its stability for >100 generations even in the absence of selection. Therefore, although ICEs were primarily assumed to only replicate along with the chromosome, our results uncovered extrachromosomal rolling-circle replicating plasmid-like forms of MiniICESt3.
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Affiliation(s)
- Nicolas Carraro
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Virginie Libante
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Catherine Morel
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Florence Charron-Bourgoin
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Pierre Leblond
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Gérard Guédon
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
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17
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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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18
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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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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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20
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Puymège A, Bertin S, Guédon G, Payot S. Analysis of Streptococcus agalactiae pan-genome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNA(Lys CTT) gene. Mol Genet Genomics 2015; 290:1727-40. [PMID: 25832353 DOI: 10.1007/s00438-015-1031-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/17/2015] [Indexed: 11/27/2022]
Abstract
Streptococcus agalactiae is the first cause of invasive infections in human neonates and is also a major bovine and fish pathogen. High genomic diversity was observed in this species that hosts numerous mobile genetic elements, in particular elements transferable by conjugation. This works aims to evaluate the contribution of these elements to GBS genome diversity. Focusing on genomic islands integrated in the tRNA(Lys) (CTT) gene, a known hotspot of recombination, an extensive in silico search was performed on the sequenced genome of 303 strains of S. agalactiae isolated from different hosts. In all the isolates (except 9), whatever their origin (human, bovine, camel, dog, gray seal, dolphin, fish species or bullfrog), this locus carries highly diverse genomic islands transferable by conjugation such as integrative and conjugative elements (ICEs), integrative and mobilizable elements (IMEs), CIs-mobilizable elements (CIMEs) or composite elements. Transfer of an ICE from an ST67 bovine strain to a phylogenetically distant ST23 human isolate was obtained experimentally indicating that there was no barrier to ICE transfer between strains from different hosts. Interestingly, a novel family of putative IMEs that site-specifically integrate in the nic site of oriT of ICEs belonging to Tn916/ICESt3 superfamily was detected in silico. These elements carry an antibiotic resistance gene (lsa(C)) already described to confer cross-resistance to lincosamides, streptogramins A and pleuromutilins. Further work is needed to evaluate the impact of these IMEs on the transfer of targeted ICEs and the mobility and the dissemination of these IMEs.
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Affiliation(s)
- Aurore Puymège
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Stéphane Bertin
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Sophie Payot
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France. .,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.
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Abstract
Horizontal gene transfer (HGT) is a main driving force of bacterial evolution and innovation. This phenomenon was long thought to be marginal in mycoplasmas, a large group of self-replicating bacteria characterized by minute genomes as a result of successive gene losses during evolution. Recent comparative genomic analyses challenged this paradigm, but the occurrence of chromosomal exchanges had never been formally addressed in mycoplasmas. Here, we demonstrated the conjugal transfer of large chromosomal regions within and among ruminant mycoplasma species, with the incorporation of the incoming DNA occurring by homologous recombination into the recipient chromosome. By combining classical mating experiments with high-throughput next-generation sequencing, we documented the transfer of almost every position of the mycoplasma chromosome. Mycoplasma conjugation relies on the occurrence of an integrative conjugative element (ICE) in at least one parent cell. While ICE propagates horizontally from ICE-positive to ICE-negative cells, chromosomal transfers (CTs) occurred in the opposite direction, from ICE-negative to ICE-positive cells, independently of ICE movement. These findings challenged the classical mechanisms proposed for other bacteria in which conjugative CTs are driven by conjugative elements, bringing into the spotlight a new means for rapid mycoplasma innovation. Overall, they radically change our current views concerning the evolution of mycoplasmas, with particularly far-reaching implications given that over 50 species are human or animal pathogens. Horizontal gene transfers (HGT) shape bacterial genomes and are key contributors to microbial diversity and innovation. One main mechanism involves conjugation, a process that allows the simultaneous transfer of significant amounts of DNA upon cell-to-cell contact. Recognizing and deciphering conjugal mechanisms are thus essential in understanding the impact of gene flux on bacterial evolution. We addressed this issue in mycoplasmas, the smallest and simplest self-replicating bacteria. In these organisms, HGT was long thought to be marginal. We showed here that nearly every position of the Mycoplasma agalactiae chromosome could be transferred via conjugation, using an unconventional mechanism. The transfer involved DNA blocks containing up to 80 genes that were incorporated into the host chromosome by homologous recombination. These findings radically change our views concerning mycoplasma evolution and adaptation with particularly far-reaching implications given that over 50 species are human or animal pathogens.
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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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Conjugative transfer and cis-mobilization of a genomic island by an integrative and conjugative element of Streptococcus agalactiae. J Bacteriol 2012; 195:1142-51. [PMID: 23275243 DOI: 10.1128/jb.02199-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913-6917, 2008). We investigated here the mobility of the elements integrated into the 3' end of a tRNA(Lys) gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNA(Lys)) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3' end of the tRNA(Lys) gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.
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Differential regulation of two closely related integrative and conjugative elements from Streptococcus thermophilus. BMC Microbiol 2011; 11:238. [PMID: 22024428 PMCID: PMC3234194 DOI: 10.1186/1471-2180-11-238] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 10/24/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Two closely related ICEs, ICESt1 and ICESt3, have been identified in the lactic acid bacterium Streptococcus thermophilus. While their conjugation and recombination modules are almost identical (95% nucleotide identity) and their regulation modules related, previous work has demonstrated that transconjugants carrying ICESt3 were generated at rate exceeding by a 1000 factor that of ICESt1. RESULTS The functional regulation of ICESt1 and ICESt3 transcription, excision and replication were investigated under different conditions (exponential growth or stationary phase, DNA damage by exposition to mitomycin C). Analysis revealed an identical transcriptional organization of their recombination and conjugation modules (long unique transcript) whereas the transcriptional organization of their regulation modules were found to be different (two operons in ICESt1 but only one in ICESt3) and to depend on the conditions (promoter specific of stationary phase in ICESt3). For both elements, stationary phase and DNA damage lead to the rise of transcript levels of the conjugation-recombination and regulation modules. Whatever the growth culture conditions, excision of ICESt1 was found to be lower than that of ICESt3, which is consistent with weaker transfer frequencies. Furthermore, for both elements, excision increases in stationary phase (8.9-fold for ICESt1 and 1.31-fold for ICESt3) and is strongly enhanced by DNA damage (38-fold for ICESt1 and 18-fold for ICESt3). Although ICEs are generally not described as replicative elements, the copy number of ICESt3 exhibited a sharp increase (9.6-fold) after mitomycin C exposure of its harboring strain CNRZ385. This result was not observed when ICESt3 was introduced in a strain deriving ICESt1 host strain CNRZ368, deleted for this element. This finding suggests an impact of the host cell on ICE behavior. CONCLUSIONS All together, these results suggest a novel mechanism of regulation shared by ICESt1, ICESt3 and closely related ICEs, which we identified by analysis of recently sequenced genomes of firmicutes. This is the first report of a partial shutdown of the activity of an ICE executed by a strain belonging to its primary host species. The sharp increase of ICESt3 copy number suggests an induction of replication; such conditional intracellular replication may be common among ICEs.
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