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Han Y, Gao YF, Xu HT, Li JP, Li C, Song CL, Lei CW, Chen X, Wang Q, Ma BH, Wang HN. Characterization and risk assessment of novel SXT/R391 integrative and conjugative elements with multidrug resistance in Proteus mirabilis isolated from China, 2018-2020. Microbiol Spectr 2024; 12:e0120923. [PMID: 38197656 PMCID: PMC10871549 DOI: 10.1128/spectrum.01209-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 11/09/2023] [Indexed: 01/11/2024] Open
Abstract
Proteus mirabilis can transfer transposons, insertion sequences, and gene cassettes to the chromosomes of other hosts through SXT/R391 integrative and conjugative elements (ICEs), significantly increasing the possibility of antibiotic resistance gene (ARG) evolution and expanding the risk of ARGs transmission among bacteria. A total of 103 strains of P. mirabilis were isolated from 25 farms in China from 2018 to 2020. The positive detection rate of SXT/R391 ICEs was 25.2% (26/103). All SXT/R391 ICEs positive P. mirabilis exhibited a high level of overall drug resistance. Conjugation experiments showed that all 26 SXT/R391 ICEs could efficiently transfer to Escherichia coli EC600 with a frequency of 2.0 × 10-7 to 6.0 × 10-5. The acquired ARGs, genetic structures, homology relationships, and conservation sequences of 26 (19 different subtypes) SXT/R391 ICEs were investigated by high-throughput sequencing, whole-genome typing, and phylogenetic tree construction. ICEPmiChnHBRJC2 carries erm (42), which have never been found within an SXT/R391 ICE in P. mirabilis, and ICEPmiChnSC1111 carries 19 ARGs, including clinically important cfr, blaCTX-M-65, and aac(6')-Ib-cr, making it the ICE with the most ARGs reported to date. Through genetic stability, growth curve, and competition experiments, it was found that the transconjugant of ICEPmiChnSCNNC12 did not have a significant fitness cost on the recipient bacterium EC600 and may have a higher risk of transmission and dissemination. Although the transconjugant of ICEPmiChnSCSZC20 had a relatively obvious fitness cost on EC600, long-term resistance selection pressure may improve bacterial fitness through compensatory adaptation, providing scientific evidence for risk assessment of horizontal transfer and dissemination of SXT/R391 ICEs in P. mirabilis.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) is a major public health concern. The study investigated the prevalence and genetic diversity of integrative and conjugative elements (ICEs) in Proteus mirabilis, which can transfer ARGs to other hosts. The study found that all of the P. mirabilis strains carrying ICEs exhibited a high level of drug resistance and a higher risk of transmission and dissemination of ARGs. The analysis of novel multidrug-resistant ICEs highlighted the potential for the evolution and spread of novel resistance mechanisms. These findings emphasize the importance of monitoring the spread of ICEs carrying ARGs and the urgent need for effective strategies to combat antibiotic resistance. Understanding the genetic diversity and potential for transmission of ARGs among bacteria is crucial for developing targeted interventions to mitigate the threat of antibiotic resistance.
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Affiliation(s)
- Yun Han
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yu-Feng Gao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - He-ting Xu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jin-Peng Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cai-Liang Song
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chang-Wei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qin Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Bo-Heng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Ning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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2
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Samperio S, Guzmán-Herrador DL, May-Cuz R, Martín MC, Álvarez MA, Llosa M. Conjugative DNA Transfer From E. coli to Transformation-Resistant Lactobacilli. Front Microbiol 2021; 12:606629. [PMID: 33643236 PMCID: PMC7905204 DOI: 10.3389/fmicb.2021.606629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) belonging to the genus classically known as Lactobacillus, recently split into 25 different genera, include many relevant species for the food industry. The well-known properties of lactobacilli as probiotics make them an attractive model also for vaccines and therapeutic proteins delivery in humans. However, scarce tools are available to accomplish genetic modification of these organisms, and most are only suitable for laboratory strains. Here, we test bacterial conjugation as a new tool to introduce genetic modifications into many biotechnologically relevant laboratory and wild type lactobacilli. Using mobilizable shuttle plasmids from a donor Escherichia coli carrying either RP4 or R388 conjugative systems, we were able to get transconjugants to all tested Lactocaseibacillus casei strains, including many natural isolates, and to several other genera, including Lentilactobacillus parabuchneri, for which no transformation protocol has been reported. Transconjugants were confirmed by the presence of the oriT and 16S rRNA gene sequencing. Serendipitously, we also found transconjugants into researcher-contaminant Staphylococcus epidermidis. Conjugative DNA transfer from E. coli to S. aureus was previously described, but at very low frequencies. We have purified this recipient strain and used it in standard conjugation assays, confirming that both R388 and RP4 conjugative systems mediate mobilization of plasmids into S. epidermidis. This protocol could be assayed to introduce DNA into other Gram-positive microorganisms which are resistant to transformation.
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Affiliation(s)
- Sara Samperio
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Dolores L Guzmán-Herrador
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Rigoberto May-Cuz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | | | | | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
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3
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Guzmán-Herrador DL, Llosa M. The secret life of conjugative relaxases. Plasmid 2019; 104:102415. [PMID: 31103521 DOI: 10.1016/j.plasmid.2019.102415] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/17/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
Conjugative relaxases are well-characterized proteins responsible for the site- and strand-specific endonucleolytic cleavage and strand transfer reactions taking place at the start and end of the conjugative DNA transfer process. Most of the relaxases characterized biochemically and structurally belong to the HUH family of endonucleases. However, an increasing number of new families of relaxases are revealing a variety of protein folds and catalytic alternatives to accomplish conjugative DNA processing. Relaxases show high specificity for their cognate target DNA sequences, but several recent reports underscore the importance of their activity on secondary targets, leading to widespread mobilization of plasmids containing an oriT-like sequence. Some relaxases perform other functions associated with their nicking and strand transfer ability, such as catalyzing site-specific recombination or initiation of plasmid replication. They perform these roles in the absence of conjugation, and the validation of these functions in several systems strongly suggest that they are not mere artifactual laboratory observations. Other unexpected roles recently assigned to relaxases include controlling plasmid copy number and promoting retrotransposition. Their capacity to mediate promiscuous mobilization and genetic reorganizations can be exploited for a number of imaginative biotechnological applications. Overall, there is increasing evidence that conjugative relaxases are not only key enzymes for horizontal gene transfer, but may have been adapted to perform other roles which contribute to prokaryotic genetic plasticity. Relaxed target specificity may be key to this versatility.
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Affiliation(s)
- Dolores Lucía Guzmán-Herrador
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain.
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4
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Agúndez L, Zárate-Pérez F, Meier AF, Bardelli M, Llosa M, Escalante CR, Linden RM, Henckaerts E. Exchange of functional domains between a bacterial conjugative relaxase and the integrase of the human adeno-associated virus. PLoS One 2018; 13:e0200841. [PMID: 30016371 PMCID: PMC6049929 DOI: 10.1371/journal.pone.0200841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/02/2018] [Indexed: 12/21/2022] Open
Abstract
Endonucleases of the HUH family are specialized in processing single-stranded DNA in a variety of evolutionarily highly conserved biological processes related to mobile genetic elements. They share a structurally defined catalytic domain for site-specific nicking and strand-transfer reactions, which is often linked to the activities of additional functional domains, contributing to their overall versatility. To assess if these HUH domains could be interchanged, we created a chimeric protein from two distantly related HUH endonucleases, containing the N-terminal HUH domain of the bacterial conjugative relaxase TrwC and the C-terminal DNA helicase domain of the human adeno-associated virus (AAV) replicase and site-specific integrase. The purified chimeric protein retained oligomerization properties and DNA helicase activities similar to Rep68, while its DNA binding specificity and cleaving-joining activity at oriT was similar to TrwC. Interestingly, the chimeric protein could catalyse site-specific integration in bacteria with an efficiency comparable to that of TrwC, while the HUH domain of TrwC alone was unable to catalyze this reaction, implying that the Rep68 C-terminal helicase domain is complementing the TrwC HUH domain to achieve site-specific integration into TrwC targets in bacteria. Our results illustrate how HUH domains could have acquired through evolution other domains in order to attain new roles, contributing to the functional flexibility observed in this protein superfamily.
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Affiliation(s)
- Leticia Agúndez
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Francisco Zárate-Pérez
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
| | - Anita F. Meier
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Martino Bardelli
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
- * E-mail: (EH); (ML)
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
| | - R. Michael Linden
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Els Henckaerts
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
- * E-mail: (EH); (ML)
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5
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Wawrzyniak P, Płucienniczak G, Bartosik D. The Different Faces of Rolling-Circle Replication and Its Multifunctional Initiator Proteins. Front Microbiol 2017; 8:2353. [PMID: 29250047 PMCID: PMC5714925 DOI: 10.3389/fmicb.2017.02353] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR). RCR is one of the most well characterized models of DNA replication. Although many studies have focused on describing its mechanism, the role of replication initiator proteins has only recently been subject to in-depth analysis, which indicates their involvement in multiple biological process associated with RCR. In this review, we present a general overview of RCR and its impact in HGT. We focus on the molecular characteristics of RCR initiator proteins belonging to the HUH and Rep_trans protein families. Despite analogous mechanisms of action these are distinct groups of proteins with different catalytic domain structures. This is the first review describing the multifunctional character of various types of RCR initiator proteins, including the latest discoveries in the field. Recent reports provide evidence that (i) proteins initiating vegetative replication (Rep) or mobilization for conjugal transfer (Mob) may also have integrase (Int) activity, (ii) some Mob proteins are capable of initiating vegetative replication (Rep activity), and (iii) some Rep proteins can act like Mob proteins to mobilize plasmid DNA for conjugal transfer. These findings have significant consequences for our understanding of the role of RCR, not only in DNA metabolism but also in the biology of many MGEs.
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Affiliation(s)
- Paweł Wawrzyniak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland.,Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Grażyna Płucienniczak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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6
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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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Guzmán-Herrador DL, Steiner S, Alperi A, González-Prieto C, Roy CR, Llosa M. DNA Delivery and Genomic Integration into Mammalian Target Cells through Type IV A and B Secretion Systems of Human Pathogens. Front Microbiol 2017; 8:1503. [PMID: 28878740 PMCID: PMC5572225 DOI: 10.3389/fmicb.2017.01503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/26/2017] [Indexed: 12/20/2022] Open
Abstract
We explore the potential of bacterial secretion systems as tools for genomic modification of human cells. We previously showed that foreign DNA can be introduced into human cells through the Type IV A secretion system of the human pathogen Bartonella henselae. Moreover, the DNA is delivered covalently attached to the conjugative relaxase TrwC, which promotes its integration into the recipient genome. In this work, we report that this tool can be adapted to other target cells by using different relaxases and secretion systems. The promiscuous relaxase MobA from plasmid RSF1010 can be used to deliver DNA into human cells with higher efficiency than TrwC. MobA also promotes DNA integration, albeit at lower rates than TrwC. Notably, we report that DNA transfer to human cells can also take place through the Type IV secretion system of two intracellular human pathogens, Legionella pneumophila and Coxiella burnetii, which code for a distantly related Dot/Icm Type IV B secretion system. This suggests that DNA transfer could be an intrinsic ability of this family of secretion systems, expanding the range of target human cells. Further analysis of the DNA transfer process showed that recruitment of MobA by Dot/Icm was dependent on the IcmSW chaperone, which may explain the higher DNA transfer rates obtained. Finally, we observed that the presence of MobA negatively affected the intracellular replication of C. burnetii, suggesting an interference with Dot/Icm translocation of virulence factors.
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Affiliation(s)
- Dolores L Guzmán-Herrador
- Departamento de Biología Molecular, Universidad de Cantabria (UC), Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, UC-CSIC-SODERCAN)Santander, Spain
| | - Samuel Steiner
- Department of Microbial Pathogenesis, Boyer Center for Molecular Medicine, Yale University School of Medicine, New HavenCT, United States
| | - Anabel Alperi
- Departamento de Biología Molecular, Universidad de Cantabria (UC), Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, UC-CSIC-SODERCAN)Santander, Spain
| | - Coral González-Prieto
- Departamento de Biología Molecular, Universidad de Cantabria (UC), Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, UC-CSIC-SODERCAN)Santander, Spain
| | - Craig R Roy
- Department of Microbial Pathogenesis, Boyer Center for Molecular Medicine, Yale University School of Medicine, New HavenCT, United States
| | - Matxalen Llosa
- Departamento de Biología Molecular, Universidad de Cantabria (UC), Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, UC-CSIC-SODERCAN)Santander, Spain
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8
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The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome. Appl Environ Microbiol 2017; 83:AEM.00207-17. [PMID: 28411218 DOI: 10.1128/aem.00207-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT gene, covalently attaches to it, and leads the single-stranded DNA (ssDNA) into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the type IV secretion system of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes. Compared to Mob relaxase from plasmid pBGR1, we found that TrwC mediated a 10-fold increase in the rate of plasmid DNA transfer to human cells and a 100-fold increase in the rate of chromosomal integration of the transferred DNA. We used linear amplification-mediated PCR and plasmid rescue to characterize the integration pattern in the human genome. DNA sequence analysis revealed mostly reconstituted oriT sequences, indicating that TrwC is active and recircularizes transferred DNA in human cells. One TrwC-mediated site-specific integration event was detected, proving that TrwC is capable of mediating site-specific integration in the human genome, albeit with very low efficiency compared to the rate of random integration. Our results suggest that TrwC may stabilize the plasmid DNA molecules in the nucleus of the human cell, probably by recircularization of the transferred DNA strand. This stabilization would increase the opportunities for integration of the DNA by the host machinery.IMPORTANCE Different biotechnological applications, including gene therapy strategies, require permanent modification of target cells. Long-term expression is achieved either by extrachromosomal persistence or by integration of the introduced DNA. Here, we studied the utility of conjugative relaxase TrwC, a bacterial protein with site-specific integrase activity in bacteria, as an integrase in human cells. Although it is not efficient as a site-specific integrase, we found that TrwC is active in human cells and promotes random integration of the transferred DNA in the human genome, probably acting as a DNA chaperone until it is integrated by host mechanisms. TrwC-DNA complexes can be delivered to human cells through a type IV secretion system involved in pathogenesis. Thus, TrwC could be used in vivo to transfer the DNA of interest into the appropriate cell and promote its integration. If used in combination with a site-specific nuclease, it could lead to site-specific integration of the incoming DNA by homologous recombination.
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Fernández-González E, Bakioui S, Gomes MC, O'Callaghan D, Vergunst AC, Sangari FJ, Llosa M. A Functional oriT in the Ptw Plasmid of Burkholderia cenocepacia Can Be Recognized by the R388 Relaxase TrwC. Front Mol Biosci 2016; 3:16. [PMID: 27200362 PMCID: PMC4853378 DOI: 10.3389/fmolb.2016.00016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/14/2016] [Indexed: 12/14/2022] Open
Abstract
Burkholderia cenocepacia is both a plant pathogen and the cause of serious opportunistic infections, particularly in cystic fibrosis patients. B. cenocepacia K56-2 harbors a native plasmid named Ptw for its involvement in the Plant Tissue Watersoaking phenotype. Ptw has also been reported to be important for survival in human cells. Interestingly, the presence of PtwC, a homolog of the conjugative relaxase TrwC of plasmid R388, suggests a possible function for Ptw in conjugative DNA transfer. The ptw region includes Type IV Secretion System genes related to those of the F plasmid. However, genes in the adjacent region shared stronger homology with the R388 genes involved in conjugative DNA metabolism. This region included the putative relaxase ptwC, a putative coupling protein and accessory nicking protein, and a DNA segment with high number of inverted repeats and elevated AT content, suggesting a possible oriT. Although we were unable to detect conjugative transfer of the Ptw resident plasmid, we detected conjugal mobilization of a co-resident plasmid containing the ptw region homologous to R388, demonstrating the cloned ptw region contains an oriT. A similar plasmid lacking ptwC could not be mobilized, suggesting that the putative relaxase PtwC must act in cis on its oriT. Remarkably, we also detected mobilization of a plasmid containing the Ptw oriT by the R388 relaxase TrwC, yet we could not detect PtwC-mediated mobilization of an R388 oriT-containing plasmid. Our data unambiguously show that the Ptw plasmid harbors DNA transfer functions, and suggests the Ptw plasmid may play a dual role in horizontal DNA transfer and eukaryotic infection.
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Affiliation(s)
- Esther Fernández-González
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, UC-SODERCAN-Consejo Superior de Investigaciones Científicas Santander, Spain
| | - Sawsane Bakioui
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - Margarida C Gomes
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - David O'Callaghan
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - Annette C Vergunst
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - Félix J Sangari
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, UC-SODERCAN-Consejo Superior de Investigaciones Científicas Santander, Spain
| | - Matxalen Llosa
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, UC-SODERCAN-Consejo Superior de Investigaciones Científicas Santander, Spain
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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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González-Prieto C, Agúndez L, Llosa M. Chloramphenicol Selection of IS10 Transposition in the cat Promoter Region of Widely Used Cloning Vectors. PLoS One 2015; 10:e0138615. [PMID: 26375469 PMCID: PMC4574204 DOI: 10.1371/journal.pone.0138615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/01/2015] [Indexed: 11/19/2022] Open
Abstract
The widely used pSU8 family of cloning vectors is based on a p15A replicon and a chloramphenicol acetyltransferase (cat) gene conferring chloramphenicol resistance. We frequently observed an increase in the size of plasmids derived from these vectors. Analysis of the bigger molecular species shows that they have an IS10 copy inserted at a specific site between the promoter and the cat open reading frame. Promoter activity from both ends of IS10 has been reported, suggesting that the insertion events could lead to higher CAT production. Insertions were observed in certain constructions containing inserts that could lead to plasmid instability. To test the possibility that IS10 insertions were selected as a response to chloramphenicol selection, we have grown these constructs in the presence of different amounts of antibiotic and we observed that insertions arise promptly under higher chloramphenicol selective pressure. IS10 is present in many E. coli laboratory strains, so the possibility of insertion in constructions involving cat-containing vectors should be taken into account. Using lower chloramphenicol concentrations could solve this problem.
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Affiliation(s)
- Coral González-Prieto
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
| | - Leticia Agúndez
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
- Department of Genetics, University College London, Institute of Ophthalmology, London, United Kingdom
| | - Matxalen Llosa
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
- * E-mail:
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A translocation motif in relaxase TrwC specifically affects recruitment by its conjugative type IV secretion system. J Bacteriol 2013; 195:4999-5006. [PMID: 23995644 DOI: 10.1128/jb.00367-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Type IV secretion system (T4SS) substrates are recruited through a translocation signal that is poorly defined for conjugative relaxases. The relaxase TrwC of plasmid R388 is translocated by its cognate conjugative T4SS, and it can also be translocated by the VirB/D4 T4SS of Bartonella henselae, causing DNA transfer to human cells. In this work, we constructed a series of TrwC variants and assayed them for DNA transfer to bacteria and human cells to compare recruitment requirements by both T4SSs. Comparison with other reported relaxase translocation signals allowed us to determine two putative translocation sequence (TS) motifs, TS1 and TS2. Mutations affecting TS1 drastically affected conjugation frequencies, while mutations affecting either motif had only a mild effect on DNA transfer rates through the VirB/D4 T4SS of B. henselae. These results indicate that a single substrate can be recruited by two different T4SSs through different signals. The C terminus affected DNA transfer rates through both T4SSs tested, but no specific sequence requirement was detected. The addition of a Bartonella intracellular delivery (BID) domain, the translocation signal for the Bartonella VirB/D4 T4SS, increased DNA transfer up to 4% of infected human cells, providing an excellent tool for DNA delivery to specific cell types. We show that the R388 coupling protein TrwB is also required for this high-efficiency TrwC-BID translocation. Other elements apart from the coupling protein may also be involved in substrate recognition by T4SSs.
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Abstract
HUH endonucleases are numerous and widespread in all three domains of life. The major function of these enzymes is processing a range of mobile genetic elements by catalysing cleavage and rejoining of single-stranded DNA using an active-site Tyr residue to make a transient 5'-phosphotyrosine bond with the DNA substrate. These enzymes have a key role in rolling-circle replication of plasmids and bacteriophages, in plasmid transfer, in the replication of several eukaryotic viruses and in various types of transposition. They have also been appropriated for cellular processes such as intron homing and the processing of bacterial repeated extragenic palindromes. Here, we provide an overview of these fascinating enzymes and their functions, using well-characterized examples of Rep proteins, relaxases and transposases, and we explore the molecular mechanisms used in their diverse activities.
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González-Prieto C, Agúndez L, Linden RM, Llosa M. HUH site-specific recombinases for targeted modification of the human genome. Trends Biotechnol 2013; 31:305-12. [PMID: 23545167 DOI: 10.1016/j.tibtech.2013.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 11/16/2022]
Abstract
Site-specific recombinases (SSRs) have been crucial in the development of mammalian transgenesis. For gene therapy purposes, this approach remains challenging, because, for example, SSR delivery is largely unresolved and SSR DNA substrates must pre-exist in target cells. In this review, we discuss the potential of His-hydrophobic-His (HUH) recombinases to overcome some of the limitations of conventional SSRs. Members of the HUH protein family cleave single-stranded (ss)DNA, but can mediate site-specific integration with the aid of the host replication machinery. Adeno-associated virus (AAV) Rep remains the only known example to support site-specific integration in human cells, and AAV is an excellent gene delivery vector that can be targeted to specific cells and organelles. Bacterial protein TrwC catalyzes integration into human sequences and can be delivered to human cells covalently linked to DNA, offering attractive new features for targeted genome modification.
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Affiliation(s)
- Coral González-Prieto
- Departamento de Biología Molecular (Universidad de Cantabria) and IBBTEC (UC, CSIC, SODERCAN), Santander, Spain
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Llosa M, Schröder G, Dehio C. New perspectives into bacterial DNA transfer to human cells. Trends Microbiol 2012; 20:355-9. [PMID: 22748513 DOI: 10.1016/j.tim.2012.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 05/28/2012] [Accepted: 05/31/2012] [Indexed: 12/26/2022]
Abstract
The type IV secretion system (T4SS) VirB/D4 of the facultative intracellular pathogen Bartonella henselae is known to translocate bacterial effector proteins into human cells. Two recent reports on DNA transfer into human cells have demonstrated the versatility of this bacterial secretion system for macromolecular substrate transfer. Moreover, these findings have opened the possibility for developing new tools for DNA delivery into specific human cell types. DNA can be introduced into these cells covalently attached to a site-specific integrase with potential target sequences in the human genome. This novel DNA delivery system is discussed in the context of existing methods for genetic modification of human cells.
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Affiliation(s)
- Matxalen Llosa
- Departamento de Biología Molecular, Universidad de Cantabria-UC, and IBBTEC-UC-CSIC-SODERCAN, Santander, Spain
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