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Richard E, Darracq B, Littner E, Vit C, Whiteway C, Bos J, Fournes F, Garriss G, Conte V, Lapaillerie D, Parissi V, Rousset F, Skovgaard O, Bikard D, Rocha EPC, Mazel D, Loot C. Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems. SCIENCE ADVANCES 2024; 10:eadj3498. [PMID: 38215203 DOI: 10.1126/sciadv.adj3498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Integrons are adaptive bacterial devices that rearrange promoter-less gene cassettes into variable ordered arrays under stress conditions, thereby sampling combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent gene cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat to genome integrity. How this activity is regulated and controlled, particularly through selective pressures, to maintain such large cassette arrays is unknown. Here, we show a key role of promoter-containing toxin-antitoxin (TA) cassettes as systems that kill the cell when the overall cassette excision rate is too high. These results highlight the importance of TA cassettes regulating the cassette recombination dynamics and provide insight into the evolution and success of integrons in bacterial genomes.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, F-75005 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
- DGA CBRN Defence, 91710 Vert-le-Petit, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Clémence Whiteway
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Julia Bos
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Florian Fournes
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Geneviève Garriss
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Delphine Lapaillerie
- University of Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS, UMR 5234, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Vincent Parissi
- University of Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS, UMR 5234, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - François Rousset
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, 75015 Paris, France
| | - Ole Skovgaard
- Department of Science, Systems and Models, Roskilde University, Roskilde DK-4000, Denmark
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, 75015 Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
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Zhu Y, Wang T, Zhu W, Wei Q. Influence of class 2 integron integrase concentration on gene cassette insertion and excision in vivo. Braz J Microbiol 2023; 54:645-653. [PMID: 36808308 PMCID: PMC10235263 DOI: 10.1007/s42770-023-00926-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/07/2023] [Indexed: 02/23/2023] Open
Abstract
Integron can capture and express antimicrobial resistance gene cassettes and plays important roles in horizontal gene transfer. The establishment of a complete in vitro reaction system will help to reveal integron integrase mediated site-specific recombination process and regulation mechanism. As an enzymatic reaction, the concentration of integrase is assumed to have a great influence on the reaction rate. To determine the influence of different concentrations of integrase on the reaction rate and to find the best range of enzyme concentration were essential to optimizing the in vitro reaction system. In this study, plasmids with gradient transcription levels of class 2 integron integrase gene intI2 under different promoters were constructed. Among plasmids pI2W16, pINTI2N, pI2W, and pI2NW, intI2 transcription levels ranged from about 0.61-fold to 49.65-fold of that in pINTI2N. And the frequencies of gene cassette sat2 integration and excision catalyzed by IntI2 were positively correlated with the transcription levels of intI2 within this range. Western blotting results indicated high expression of IntI2 partly existed in the form of an inclusion body. When compared with Pc of class 1 integron, the spacer sequence of PintI2 can increase the strength of PcW but decrease the strength of PcS. In conclusion, the frequencies of gene cassette integration and excision were positively correlated with the concentration of IntI2. intI2 driving by PcW with PintI2 spacer sequence can obtain the optimum IntI2 concentration required to achieve the maximum recombination efficiency in vivo in this study.
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Affiliation(s)
- Yu Zhu
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Tong Wang
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Wenwen Zhu
- Department of Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Quhao Wei
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China.
- Department of Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China.
- Department of Laboratory Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 6600 Nanfeng Road, Shanghai, 201499, China.
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Zhao W, Zeng W, Pang B, Luo M, Peng Y, Xu J, Kan B, Li Z, Lu X. Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing. Front Microbiol 2023; 14:1179966. [PMID: 37256057 PMCID: PMC10225699 DOI: 10.3389/fmicb.2023.1179966] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/27/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction Genome-based analysis is crucial in monitoring antibiotic-resistant bacteria (ARB)and antibiotic-resistance genes (ARGs). Short-read sequencing is typically used to obtain incomplete draft genomes, while long-read sequencing can obtain genomes of multidrug resistance (MDR) plasmids and track the transmission of plasmid-borne antimicrobial resistance genes in bacteria. However, long-read sequencing suffers from low-accuracy base calling, and short-read sequencing is often required to improve genome accuracy. This increases costs and turnaround time. Methods In this study, a novel ONT sequencing method is described, which uses the latest ONT chemistry with improved accuracy to assemble genomes of MDR strains and plasmids from long-read sequencing data only. Three strains of Salmonella carrying MDR plasmids were sequenced using the ONT SQK-LSK114 kit with flow cell R10.4.1, and de novo genome assembly was performed with average read accuracy (Q > 10) of 98.9%. Results and Discussion For a 5-Mb-long bacterial genome, finished genome sequences with accuracy of >99.99% could be obtained at 75× sequencing coverage depth using Flye and Medaka software. Thus, this new ONT method greatly improves base-calling accuracy, allowing for the de novo assembly of high-quality finished bacterial or plasmid genomes without the need for short-read sequencing. This saves both money and time and supports the application of ONT data in critical genome-based epidemiological analyses. The novel ONT approach described in this study can take the place of traditional combination genome assembly based on short- and long-read sequencing, enabling pangenomic analyses based on high-quality complete bacterial and plasmid genomes to monitor the spread of antibiotic-resistant bacteria and antibiotic resistance genes.
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Affiliation(s)
- Wenxuan Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Jinzhong, Shanxi, China
| | - Wei Zeng
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Shandong University, Jinan, China
| | - Bo Pang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ming Luo
- Yulin Center for Disease Control and Prevention, Yulin, Shanxi, China
| | - Yao Peng
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jialiang Xu
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, China
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Shandong University, Jinan, China
| | - Zhenpeng Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Lu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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A Novel Phytogenic Formulation, EUBIO-BPSG, as a Promising One Health Approach to Replace Antibiotics and Promote Reproduction Performance in Laying Hens. Bioengineering (Basel) 2023; 10:bioengineering10030346. [PMID: 36978737 PMCID: PMC10045918 DOI: 10.3390/bioengineering10030346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Gut microbiota play a key role in health maintenance and disease pathogenesis in animals. Dietary phytochemicals are crucial factors shaping gut bacteria. Here, we investigated the function and mechanism of a phytogenic formulation, EUBIO-BPSG (BP), in laying hens. We found that BP dose-dependently improved health and egg production in 54-week-old hens. Furthermore, BP was correlated with increased fecal Lactobacillus, decreased Escherichia coli and Salmonella enterica, and reduced antibiotic resistance (AR) and antibiotic resistance genes (ARG) in chicken stools. The 16S rDNA data showed that BP increased seven genera of probiotics and reduced 13 genera of pathogens in chicken feces. In vitro co-culture experiments showed that BP at 4 µg/mL and above promoted growth of L. reuteri while large 100- and 200-fold higher doses suppressed growth of E. coli and S. enterica, respectively. Mechanistic studies indicated that L. reuteri and its supernatants antagonized growth of E. coli and S. enterica but not vice-versa. Five short-chain fatty acids and derivatives (SCFA) produced from L. reuteri directly killed both pathogens via membrane destruction. Furthermore, BP inhibited conjugation and recombination of ARG via interference with conjugation machinery and integrase activity in E. coli. Collectively, this work suggests that BP promotes host health and reproductive performance in laying hens through regulation of gut microbiota through increasing probiotics and decreasing pathogens and spreading ARG.
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Ghaly TM, Tetu SG, Penesyan A, Qi Q, Rajabal V, Gillings MR. Discovery of integrons in Archaea: Platforms for cross-domain gene transfer. SCIENCE ADVANCES 2022; 8:eabq6376. [PMID: 36383678 PMCID: PMC9668308 DOI: 10.1126/sciadv.abq6376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Qin Qi
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
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