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Zhang J, Zhao L, Wang W, Zhang Q, Wang XT, Xing DF, Ren NQ, Lee DJ, Chen C. Large language model for horizontal transfer of resistance gene: From resistance gene prevalence detection to plasmid conjugation rate evaluation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172466. [PMID: 38626826 DOI: 10.1016/j.scitotenv.2024.172466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
The burgeoning issue of plasmid-mediated resistance genes (ARGs) dissemination poses a significant threat to environmental integrity. However, the prediction of ARGs prevalence is overlooked, especially for emerging ARGs that are potentially evolving gene exchange hotspot. Here, we explored to classify plasmid or chromosome sequences and detect resistance gene prevalence by using DNABERT. Initially, the DNABERT fine-tuned in plasmid and chromosome sequences followed by multilayer perceptron (MLP) classifier could achieve 0.764 AUC (Area under curve) on external datasets across 23 genera, outperforming 0.02 AUC than traditional statistic-based model. Furthermore, Escherichia, Pseudomonas single genera based model were also be trained to explore its predict performance to ARGs prevalence detection. By integrating K-mer frequency attributes, our model could boost the performance to predict the prevalence of ARGs in an external dataset in Escherichia with 0.0281-0.0615 AUC and Pseudomonas with 0.0196-0.0928 AUC. Finally, we established a random forest model aimed at forecasting the relative conjugation transfer rate of plasmids with 0.7956 AUC, drawing on data from existing literature. It identifies the plasmid's repression status, cellular density, and temperature as the most important factors influencing transfer frequency. With these two models combined, they provide useful reference for quick and low-cost integrated evaluation of resistance gene transfer, accelerating the process of computer-assisted quantitative risk assessment of ARGs transfer in environmental field.
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Affiliation(s)
- Jiabin Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
| | - Quan Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Xue-Ting Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China; Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
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Vincent J, Tenore A, Mattei MR, Frunzo L. Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms. Bull Math Biol 2024; 86:63. [PMID: 38664322 DOI: 10.1007/s11538-024-01289-x] [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: 12/11/2023] [Accepted: 03/27/2024] [Indexed: 05/23/2024]
Abstract
In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.
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Affiliation(s)
- Julien Vincent
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
- Microbial Ecology Laboratory, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Alberto Tenore
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
| | - Maria Rosaria Mattei
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy.
| | - Luigi Frunzo
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
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Murata T, Gotoh Y, Hayashi T. A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis. DNA Res 2024; 31:dsae002. [PMID: 38300630 PMCID: PMC10838148 DOI: 10.1093/dnares/dsae002] [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: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024] Open
Abstract
While conjugation-related genes have been identified in many plasmids by genome sequencing, functional analyses have not yet been performed in most cases, and a full set of conjugation genes has been identified for only a few plasmids. Rts1, a prototype IncT plasmid, is a conjugative plasmid that was originally isolated from Proteus vulgaris. Here, we conducted a systematic deletion analysis of Rts1 to fully understand its conjugation system. Through this analysis along with complementation assays, we identified 32 genes that are required for the efficient conjugation of Rts1 from Escherichia coli to E. coli. In addition, the functions of the 28 genes were determined or predicted; 21 were involved in mating-pair formation, three were involved in DNA transfer and replication, including a relaxase gene belonging to the MOBH12 family, one was involved in coupling, and three were involved in transcriptional regulation. Among the functionally well-analysed conjugation systems, most of the 28 genes showed the highest similarity to those of the SXT element, which is an integrative conjugative element of Vibrio cholerae. The Rts1 conjugation gene set included all 23 genes required for the SXT system. Two groups of plasmids with conjugation systems nearly identical or very similar to that of Rts1 were also identified.
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Affiliation(s)
- Takahiro Murata
- Department of Pediatrics, Teikyo University School of Medicine, Mizonokuchi Hospital, Takatsu-ku, Kawasaki, Kanagawa 213-8507, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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Sun L, Chen Y, Qu T, Shi K, Han X, Wu W, Jiang Y, Yu Y. Characterisation of a Novel Hybrid IncFII pHN7A8:IncR:IncN Plasmid Co-Harboring blaNDM-5 and blaKPC-2 from a Clinical ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain. Infect Drug Resist 2023; 16:7621-7628. [PMID: 38107435 PMCID: PMC10725640 DOI: 10.2147/idr.s435195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Purpose We aimed to characterize a novel blaNDM-5 and blaKPC-2 co-carrying hybrid plasmid from a clinical carbapenem-resistant Klebsiella pneumoniae (CRKP) strain. Methods Antimicrobial susceptibility was determined by the broth microdilution method. Plasmid size and localization were estimated using S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting. Plasmid transfer ability was evaluated by conjugation experiments. Whole genome sequencing (WGS) was performed using Illumina NovaSeq6000 and Oxford Nanopore MinION platforms. Genomic characteristics were analyzed using bioinformatics methods. Results Strain ZY27320 was a multidrug-resistant (MDR) clinical ST11 K. pneumoniae strain that confers high-level resistance to carbapenems (meropenem, MIC 128 mg/L; imipenem, MIC 64 mg/L) and ceftazidime/avibactam (MIC >128/4 mg/L). Both S1-PFGE-Southern blotting and whole genome sequencing revealed that the carbapenemase genes blaKPC-2 and blaNDM-5 were carried by the same IncFIIpHN7A8:IncR:IncN hybrid plasmid (pKPC2_NDM5). Conjugation experiments indicated that pKPC2_NDM5 was a non-conjugative plasmid. Conclusion This is the first report of a hybrid plasmid carrying both carbapenemase genes blaNDM-5 and blaKPC-2 in a clinical K. pneumoniae ST11 isolate that confers resistance to both ceftazidime/avibactam and carbapenems, thereby presenting a serious threat to treatment in clinical practice.
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Affiliation(s)
- Lingyan Sun
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, People’s Republic of China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Infection Control Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Keren Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Xinhong Han
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Wenhao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Infection Control Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
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Allard N, Collette A, Paquette J, Rodrigue S, Côté JP. Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids. Commun Biol 2023; 6:1172. [PMID: 37973843 PMCID: PMC10654706 DOI: 10.1038/s42003-023-05534-2] [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: 03/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Arianne Collette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Josianne Paquette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| | - Jean-Philippe Côté
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
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6
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Li Y, Ni M. Regulation of biofilm formation in Klebsiella pneumoniae. Front Microbiol 2023; 14:1238482. [PMID: 37744914 PMCID: PMC10513181 DOI: 10.3389/fmicb.2023.1238482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Klebsiella pneumoniae is an important Gram-negative opportunistic pathogen that is responsible for a variety of nosocomial and community-acquired infections. Klebsiella pneumoniae has become a major public health issue owing to the rapid global spread of extensively-drug resistant (XDR) and hypervirulent strains. Biofilm formation is an important virulence trait of K. pneumoniae. A biofilm is an aggregate of microorganisms attached to an inert or living surface by a self-produced exo-polymeric matrix that includes proteins, polysaccharides and extracellular DNA. Bacteria within the biofilm are shielded from antibiotics treatments and host immune responses, making it more difficult to eradicate K. pneumoniae-induced infection. However, the detailed mechanisms of biofilm formation in K. pneumoniae are still not clear. Here, we review the factors involved in the biofilm formation of K. pneumoniae, which might provide new clues to address this clinical challenge.
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Affiliation(s)
| | - Ming Ni
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Disease, Huazhong University of Science and Technology, Wuhan, China
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7
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Li J, Zhao C, Li C, Xue B, Wang S, Zhang X, Yang X, Shen Z, Bo L, He X, Qiu Z, Wang J. Multidrug-resistant plasmid RP4 increases NO and N 2O yields via the electron transport system in Nitrosomonas europaea ammonia oxidation. WATER RESEARCH 2023; 242:120266. [PMID: 37421866 DOI: 10.1016/j.watres.2023.120266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
Antibiotic resistance genes (ARGs) have recently become an important public health problem and therefore several studies have characterized ARG composition and distribution. However, few studies have assessed their impact on important functional microorganisms in the environment. Therefore, our study sought to investigate the mechanisms through which multidrug-resistant plasmid RP4 affected the ammonia oxidation capacity of ammonia-oxidizing bacteria, which play a key role in the nitrogen cycle. The ammonia oxidation capacity of N. europaea ATCC25978 (RP4) was significantly inhibited, and NO and N2O were produced instead of nitrite. Our findings demonstrated that the decrease in electrons from NH2OH decreased the ammonia monooxygenase (AMO) activity, leading to a decrease in ammonia consumption. In the ammonia oxidation process, N. europaea ATCC25978 (RP4) exhibited ATP and NADH accumulation. The corresponding mechanism was the overactivation of Complex Ⅰ, ATPase, and the TCA cycle by the RP4 plasmid. The genes encoding TCA cycle enzymes related to energy generation, including gltA, icd, sucD, and NE0773, were upregulated in N. europaea ATCC25978 (RP4). These results demonstrate the ecological risks of ARGs, including the inhibition of the ammonia oxidation process and an increased production of greenhouse gases such as NO and N2O.
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Affiliation(s)
- Jia Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhiqiang Shen
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Lin Bo
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Tiangong University, Tianjin, China
| | - Xinxin He
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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9
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Xiao Y, Zhang Y, Xie F, Olsen RH, Shi L, Li L. Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System. Int J Mol Sci 2023; 24:10585. [PMID: 37445761 DOI: 10.3390/ijms241310585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.
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Affiliation(s)
- Yawen Xiao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Yan Zhang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Fengjun Xie
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
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10
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Piscon B, Pia Esposito E, Fichtman B, Samburski G, Efremushkin L, Amselem S, Harel A, Rahav G, Zarrilli R, Gal-Mor O. The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation. Microbiol Spectr 2023; 11:e0368822. [PMID: 36995224 PMCID: PMC10269834 DOI: 10.1128/spectrum.03688-22] [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: 09/12/2022] [Accepted: 03/11/2023] [Indexed: 03/31/2023] Open
Abstract
Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.
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Affiliation(s)
- Bar Piscon
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eliana Pia Esposito
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Guy Samburski
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Lihi Efremushkin
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Shimon Amselem
- SpacePharma R&D Israel LTD., Herzliya Pituach, Israel & SpacePharma SA, Courgenay, Switzerland
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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11
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Jo C, Bernstein DB, Vaisman N, Frydman HM, Segrè D. Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions. mSystems 2023; 8:e0001721. [PMID: 36802169 PMCID: PMC10134821 DOI: 10.1128/msystems.00017-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 01/24/2023] [Indexed: 02/23/2023] Open
Abstract
The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microorganisms. Quantitative measurements of these interactions are important for understanding and engineering ecosystem structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from the Drosophila melanogaster gut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by two Lactobacillus strains to an Acetobacter strain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair of Escherichia coli amino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells by demonstrating that, under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions. IMPORTANCE Microbial communities participate in many essential processes from biogeochemical cycles to the maintenance of human health. The structure and functions of these communities are dynamic properties that depend on poorly understood interactions among different species. Unraveling these interactions is therefore a crucial step toward understanding natural microbiota and engineering artificial ones. Microbial interactions have been difficult to measure directly, largely due to limitations of existing methods to disentangle the contribution of different organisms in mixed cocultures. To overcome these limitations, we developed the BioMe plate, a custom microplate-based device that enables direct measurement of microbial interactions, by detecting the abundance of segregated populations of microbes that can exchange small molecules through a membrane. We demonstrated the possible application of the BioMe plate for studying both natural and artificial consortia. BioMe is a scalable and accessible platform that can be used to broadly characterize microbial interactions mediated by diffusible molecules.
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Affiliation(s)
- Charles Jo
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - David B. Bernstein
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Natalie Vaisman
- Department of Biology, Boston University, Boston, Massachusetts, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | | | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
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12
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Wedel E, Bernabe-Balas C, Ares-Arroyo M, Montero N, Santos-Lopez A, Mazel D, Gonzalez-Zorn B. Insertion Sequences Determine Plasmid Adaptation to New Bacterial Hosts. mBio 2023:e0315822. [PMID: 37097157 DOI: 10.1128/mbio.03158-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Plasmids facilitate the vertical and horizontal spread of antimicrobial resistance genes between bacteria. The host range and adaptation of plasmids to new hosts determine their impact on the spread of resistance. In this work, we explore the mechanisms driving plasmid adaptation to novel hosts in experimental evolution. Using the small multicopy plasmid pB1000, usually found in Pasteurellaceae, we studied its adaptation to a host from a different bacterial family, Escherichia coli. We observed two different mechanisms of adaptation. One mechanism is single nucleotide polymorphisms (SNPs) in the origin of replication (oriV) of the plasmid, which increase the copy number in E. coli cells, elevating the stability, and resistance profile. The second mechanism consists of two insertion sequences (ISs), IS1 and IS10, which decrease the fitness cost of the plasmid by disrupting an uncharacterized gene on pB1000 that is harmful to E. coli. Both mechanisms increase the stability of pB1000 independently, but only their combination allows long-term maintenance. Crucially, we show that the mechanisms have a different impact on the host range of the plasmid. SNPs in oriV prevent the replication in the original host, resulting in a shift of the host range. In contrast, the introduction of ISs either shifts or expands the host range, depending on the IS. While IS1 leads to expansion, IS10 cannot be reintroduced into the original host. This study gives new insights into the relevance of ISs in plasmid-host adaptation to understand the success in spreading resistance. IMPORTANCE ColE1-like plasmids are small, mobilizable plasmids that can be found across at least four orders of Gammaproteobacteria and are strongly associated with antimicrobial resistance genes. Plasmid pB1000 carries the gene blaROB-1, conferring high-level resistance to penicillins and cefaclor. pB1000 has been described in various species of the family Pasteurellaceae, for example, in Haemophilus influenzae, which can cause diseases such as otitis media, meningitis, and pneumonia. To understand the resistance spread through horizontal transfer, it is essential to study the mechanisms of plasmid adaptation to novel hosts. In this work we identify that a gene from pB1000, which encodes a peptide that is toxic for E. coli, and the low plasmid copy number (PCN) of pB1000 in E. coli cells are essential targets in the described plasmid-host adaptation and therefore limit the spread of pB1000-encoded blaROB-1. Furthermore, we show how the interplay of two adaptation mechanisms leads to successful plasmid maintenance in a different bacterial family.
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Affiliation(s)
- Emilia Wedel
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Alfonso Santos-Lopez
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Didier Mazel
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
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13
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Ortiz Charneco G, Kelleher P, Buivydas A, Dashko S, de Waal PP, van Peij NNME, Roberts RJ, Mahony J, van Sinderen D. Delineation of a lactococcal conjugation system reveals a restriction-modification evasion system. Microb Biotechnol 2023; 16:1250-1263. [PMID: 36942662 DOI: 10.1111/1751-7915.14221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 03/23/2023] Open
Abstract
Plasmid pUC11B is a 49.3-kb plasmid harboured by the fermented meat isolate Lactococcus lactis subsp. lactis UC11. Among other features, pUC11B encodes a pMRC01-like conjugation system and tetracycline-resistance. In this study, we demonstrate that this plasmid can be conjugated at high frequencies to recipient strains. Mutational analysis of the 22 genes encompassing the presumed pUC11B conjugation cluster revealed the presence of several genes with essential conjugation functions, as well as a gene, trsR, encoding a putative transcriptional repressor of this conjugation cluster. Furthermore, plasmid pUC11B encodes an anti-restriction protein, TrsAR, which facilitates higher conjugation frequencies when pUC11B is transferred into recipient strains containing Type II or Type III RM systems. These findings demonstrate how RM mechanisms can be circumvented when they act as a biological barrier for conjugation events.
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Affiliation(s)
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Sofia Dashko
- DSM Food and Beverage, Center for Food Innovation, Delft, The Netherlands
| | - Paul P de Waal
- DSM Food and Beverage, Center for Food Innovation, Delft, The Netherlands
| | | | | | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
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14
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Apari P, Földvári G. Domestication and microbiome succession may drive pathogen spillover. Front Microbiol 2023; 14:1102337. [PMID: 37007505 PMCID: PMC10065160 DOI: 10.3389/fmicb.2023.1102337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.
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Affiliation(s)
- Péter Apari
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Gábor Földvári
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
- Centre for Eco-Epidemiology, National Laboratory for Health Security, Budapest, Hungary
- *Correspondence: Gábor Földvári,
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15
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Farghaly M, Hynes MF, Nazari M, Checkley S, Liljebjelke K. Examination of the horizontal gene transfer dynamics of an integrative and conjugative element encoding multidrug resistance in Histophilus somni. Can J Microbiol 2023; 69:123-135. [PMID: 36495587 DOI: 10.1139/cjm-2021-0349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Integrative and conjugative elements (ICEs) are self-transferable mobile genetic elements that play a significant role in disseminating antimicrobial resistance between bacteria via horizontal gene transfer. A recently identified ICE in a clinical isolate of Histophilus somni (ICEHs02) is 72 914 base pairs in length and harbours seven predicted antimicrobial resistance genes conferring resistance to tetracycline (tetR-tet(H)), florfenicol (floR), sulfonamide (Sul2), aminoglycosides (APH(3″)-Ib, APH(6)-Id, APH(3')-Ia), and copper (mco). This study investigated ICEHs02 host range, assessed effects of antimicrobial stressors on transfer frequency, and examined effects of ICEHs02 acquisition on hosts. Conjugation assays examined transfer frequency of ICEHs02 to H. somni and Pasteurella multocida strains. Polymerase chain reaction assays confirmed the presence of a circular intermediate, ICE-associated core genes, and cargo genes in recipient strains. Susceptibility testing examined ICEHs02-associated resistance phenotypes in recipient strains. Tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02 in vitro. The copy numbers of the circular intermediate of ICEHs02 per chromosome exhibited significant increases of ∼37-fold after tetracycline exposure and ∼4-fold after ciprofloxacin treatment. The acquisition of ICEHs02 reduced the relative fitness of H. somni transconjugants (TG) by 28% (w = 0.72 ± 0.04) and the relative fitness of P. multocida TG was decreased by 15% (w = 0.85 ± 0.01).
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Affiliation(s)
- Mai Farghaly
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael F Hynes
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Mohammad Nazari
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sylvia Checkley
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Karen Liljebjelke
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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16
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Thompson CMA, Hall JPJ, Chandra G, Martins C, Saalbach G, Panturat S, Bird SM, Ford S, Little RH, Piazza A, Harrison E, Jackson RW, Brockhurst MA, Malone JG. Plasmids manipulate bacterial behaviour through translational regulatory crosstalk. PLoS Biol 2023; 21:e3001988. [PMID: 36787297 PMCID: PMC9928087 DOI: 10.1371/journal.pbio.3001988] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/04/2023] [Indexed: 02/15/2023] Open
Abstract
Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.
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Affiliation(s)
- Catriona M. A. Thompson
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - James P. J. Hall
- Department of Evolution, Ecology and Behaviour Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Crown Street, Liverpool, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Carlo Martins
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Gerhard Saalbach
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Supakan Panturat
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Susannah M. Bird
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Samuel Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Richard H. Little
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ainelen Piazza
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Robert W. Jackson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Michael A. Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Jacob G. Malone
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
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17
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Nayar G, Terrizzano I, Seabolt E, Agarwal A, Boucher C, Ruiz J, Slizovskiy IB, Kaufman JH, Noyes NR. ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks. Front Genet 2022; 13:1024577. [PMID: 36568361 PMCID: PMC9779932 DOI: 10.3389/fgene.2022.1024577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.
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Affiliation(s)
- Gowri Nayar
- Department of Biomedical Informatics, Stanford University, Stanford, CA, United States
| | | | - Ed Seabolt
- IBM Research Almaden, San Jose, CA, United States
| | | | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States
| | - Jaime Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States
| | - Ilya B. Slizovskiy
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | | | - Noelle R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Noelle R. Noyes,
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18
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Ares-Arroyo M, Coluzzi C, P.C. Rocha E. Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation. Nucleic Acids Res 2022; 51:3001-3016. [PMID: 36442505 PMCID: PMC10123127 DOI: 10.1093/nar/gkac1079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Abstract
Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.
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Affiliation(s)
- Manuel Ares-Arroyo
- Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France
| | - Charles Coluzzi
- Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France
| | - Eduardo P.C. Rocha
- Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France
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19
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Chen H, Tao S, Li N, Wang F, Wang L, Tang Y, Liang W. Functional comparison of anti-restriction and anti-methylation activities of ArdA, KlcA, and KlcAHS from Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:916547. [PMID: 35967855 PMCID: PMC9366191 DOI: 10.3389/fcimb.2022.916547] [Citation(s) in RCA: 1] [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: 04/09/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Anti-restriction proteins are typically encoded by plasmids, conjugative transposons, or phages to improve their chances of entering a new bacterial host with a type I DNA restriction and modification (RM) system. The invading DNA is normally destroyed by the RM system. The anti-restriction proteins ArdA, KlcA, and their homologues are usually encoded on plasmid of carbapenemase-resistant Klebsiella pneumoniae. We found that the plasmid sequence and restriction proteins affected horizontal gene transfer, and confirmed the anti-restriction and anti-methylation activities of ArdA and KlcA during transformation and transduction. Among the three anti-restriction proteins, ArdA shows stronger anti-restriction and anti-methylation effects, and KlcAHS was weaker. KlcA shows anti-methylation only during transformation. Understanding the molecular mechanism underlying the clinical dissemination of K. pneumoniae and other clinically resistant strains from the perspective of restrictive and anti-restrictive systems will provide basic theoretical support for the prevention and control of multidrug-resistant bacteria, and new strategies for delaying or even controlling the clinical dissemination of resistant strains in the future.
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Affiliation(s)
- Huimin Chen
- Medical School of Jiangsu University, Zhenjiang, China
| | - Shuan Tao
- Medical School of Jiangsu University, Zhenjiang, China
| | - Na Li
- Department of Laboratory Medicine, Bengbu Medical College, Bengbu, China
| | - Fang Wang
- Department of Central Laboratory, Lianyungang Second People Hospital, Lianyungang, China
| | - Lei Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yu Tang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Wei Liang, ; Yu Tang,
| | - Wei Liang
- Lianyungang Clinical College of Jiangsu University, Lianyungang, China
- *Correspondence: Wei Liang, ; Yu Tang,
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20
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Darphorn TS, Koenders-van Sintanneland BB, Grootemaat AE, van der Wel NN, Brul S, ter Kuile BH. Transfer dynamics of multi-resistance plasmids in Escherichia coli isolated from meat. PLoS One 2022; 17:e0270205. [PMID: 35797379 PMCID: PMC9262221 DOI: 10.1371/journal.pone.0270205] [Citation(s) in RCA: 1] [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: 12/10/2021] [Accepted: 06/06/2022] [Indexed: 12/31/2022] Open
Abstract
Resistance plasmids are crucial for the transfer of antimicrobial resistance and thus form a matter of concern for veterinary and human healthcare. To study plasmid transfer, foodborne Escherichia coli isolates harboring one to five known plasmids were co-incubated with a general recipient strain. Plasmid transfer rates under standardized conditions varied by a factor of almost 106, depending on the recipient/donor strain combination. After 1 hour transconjugants never accounted for more than 3% of the total number of cells. Transconjugants were formed from 14 donors within 1 hour of co-incubation, but in the case of 3 donors 24 hours were needed. Transfer rates were also measured during longer co-incubation, between different species and during repeated back and forth transfer. Longer co-incubation resulted in the transfer of more types of resistance. Maximum growth rates of donor strains varied by a factor of 3. Donor strains often had higher growth rates than the corresponding transconjugants, which grew at the same rate as or slightly faster than the recipient. Hence, possessing one or more plasmids does not seem to burden the harboring strain metabolically. Transfer was species specific and repeated transfer of one plasmid did not result in different transfer rates over time. Transmission Electron microcopy was used to analyze the morphology of the connection between co-incubated strains. Connection by more pili between the cells resulted in better aggregate formation and corresponded with higher transfer rates.
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Affiliation(s)
- Tania S. Darphorn
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Belinda B. Koenders-van Sintanneland
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Anita E. Grootemaat
- Department of Cell Biology and Histology, Electron Microscopy Centre Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - Nicole N. van der Wel
- Department of Cell Biology and Histology, Electron Microscopy Centre Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H. ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands
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21
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Zhao C, Li J, Li C, Xue B, Wang S, Zhang X, Yang X, Shen Z, Bo L, Qiu Z, Wang J. Horizontal transfer of the multidrug resistance plasmid RP4 inhibits ammonia nitrogen removal dominated by ammonia-oxidizing bacteria. WATER RESEARCH 2022; 217:118434. [PMID: 35427829 DOI: 10.1016/j.watres.2022.118434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) have become an important public health concern. Particularly, although several ARGs have been identified in wastewater treatment plants (WWTPs), very few studies have characterized their impacts on reactor performance. Therefore, our study sought to investigate the effect of a representative conjugative transfer plasmid (RP4) encoding multidrug resistance genes on ammonia oxidation. To achieve this, we established sequencing batch reactors (SBRs) and a conjugation model with E. coli donor strains carrying the RP4 plasmid and a typical ammonia-oxidating (AOB) bacterial strain (Nitrosomonas europaea ATCC 25978) as a recipient to investigate the effect of conjugative transfer of plasmid RP4 on AOB. Our findings demonstrated that the RP4 plasmid carried by the donor strains could be transferred to AOB in the SBR and to Nitrosomonas europaea ATCC 25978. In SBR treated with donor strains carrying the RP4 plasmid, ammonia removal efficiency continuously decreased to 71%. Once the RP4 plasmid entered N. europaea ATCC 25978 in the conjugation model, ammonia removal was significantly inhibited and nitrite generation was decreased. Furthermore, the expression of several functional genes related to ammonia oxidation in AOB was suppressed following the transfer of the RP4 plasmid, including amoA, amoC, hao, nirK, and norB. In contrast, the cytL gene encoding cytochrome P460 was upregulated. These results demonstrated the ecological risk of ARGs in WWTPs, and therefore measures must be taken to avoid their transfer.
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Affiliation(s)
- Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Jia Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhiqiang Shen
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Lin Bo
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Tiangong University, Tianjin, China
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China.
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22
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Nohejl T, Valcek A, Papousek I, Palkovicova J, Wailan AM, Pratova H, Minoia M, Dolejska M. Genomic analysis of qnr-harbouring IncX plasmids and their transferability within different hosts under induced stress. BMC Microbiol 2022; 22:136. [PMID: 35590235 PMCID: PMC9118779 DOI: 10.1186/s12866-022-02546-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background Conjugative plasmids play a major role in the dissemination of antibiotic resistance genes. Knowledge of the plasmid characteristics and behaviour can allow development of control strategies. Here we focus on the IncX group of plasmids carrying genes conferring quinolone resistance (PMQR), reporting their transfer and persistence within host bacteria of various genotypes under distinct conditions and levels of induced stress in form of temperature change and various concentrations of ciprofloxacin supplementation. Methods Complete nucleotide sequences were determined for eight qnr-carrying IncX-type plasmids, of IncX1 (3), IncX2 (3) and a hybrid IncX1-2 (2) types, recovered from Escherichia coli of various origins. This data was compared with further complete sequences of IncX1 and IncX2 plasmids carrying qnr genes (n = 41) retrieved from GenBank and phylogenetic tree was constructed. Representatives of IncX1 (pHP2) and IncX2 (p194) and their qnrS knockout mutants, were studied for influence of induced stress and genetic background on conjugative transfer and maintenance. Results A high level of IncX core-genome similarity was found in plasmids of animal, environmental and clinical origin. Significant differences were found between the individual IncX plasmids, with IncX1 subgroup plasmids showing higher conjugative transfer rates than IncX2 plasmids. Knockout of qnr modified transfer frequency of both plasmids. Two stresses applied simultaneously were needed to affect transfer rate of wildtype plasmids, whereas a single stress was sufficient to affect the IncX ΔqnrS plasmids. The conjugative transfer was shown to be biased towards the host phylogenetic proximity. A long-term cultivation experiment pointed out the persistence of IncX plasmids in the antibiotic-free environment. Conclusions The study indicated the stimulating effect of ciprofloxacin supplementation on the plasmid transfer that can be nullified by the carriage of a single PMQR gene. The findings present the significant properties and behaviour of IncX plasmids carrying antibiotic resistance genes that are likely to play a role in their dissemination and stability in bacterial populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02546-6.
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Affiliation(s)
- Tomas Nohejl
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Adam Valcek
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic.,Faculty of Medicine, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Ivo Papousek
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jana Palkovicova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Alexander M Wailan
- Parasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Hana Pratova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Marco Minoia
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic. .,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic. .,Faculty of Medicine, Biomedical Center, Charles University, Pilsen, Czech Republic. .,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic.
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23
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Allard N, Neil K, Grenier F, Rodrigue S. The Type IV Pilus of Plasmid TP114 Displays Adhesins Conferring Conjugation Specificity and Is Important for DNA Transfer in the Mouse Gut Microbiota. Microbiol Spectr 2022; 10:e0230321. [PMID: 35293798 PMCID: PMC9045228 DOI: 10.1128/spectrum.02303-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Type IV pili (T4P) are common bacterial surface appendages involved in different biological processes such as adherence, motility, competence, pathogenesis, and conjugation. In this work, we describe the T4P of TP114, an IncI2 enterobacterial conjugative plasmid recently shown to disseminate at high rates in the mouse intestinal tract. This pilus is composed of the major PilS and minor PilV pilins that are both important for conjugation in broth and in the gut microbiota but not on a solid support. The PilV-coding sequence is part of a shufflon and can bear different C-terminal domains. The shufflon is a multiple DNA inversion system containing many DNA cassettes flanked by recombination sites that are recognized by a shufflon-specific tyrosine recombinase (shufflase) promoting the recombination between DNA segments. The different PilV variants act as adhesins that can modify the affinity for different recipient bacteria. Eight PilV variants were identified in TP114, including one that has not been described in other shufflons. All PilV variants allowed conjugative transfer with different recipient Escherichia coli strains. We conclude that the T4P carried by TP114 plays a major role in mating pair stabilization in broth as well as in the gut microbiota and that the shufflon acts as a biological switch modifying the conjugative host range specificity. IMPORTANCE Conjugative plasmids are involved in horizontal gene transfer in the gut microbiota, which constitutes an important antibiotic resistance gene reservoir. However, the molecular mechanisms used by conjugative plasmids to select recipient bacteria and transfer at high rates in the mouse gut microbiota remain poorly characterized. We studied the type IV pilus carried by TP114 and demonstrated that the minor pilin PilV acts as an adhesin that can efficiently select target cells for conjugative transfer. Moreover, the pilV gene can be rapidly modified by a shufflon, hence modulating the nature of the recipient bacteria during conjugation. Our study highlights the role of mating pair stabilization for conjugation in broth as well as in the gut microbiome and explains how the host spectrum of a plasmid can be expanded simply by remodeling the PilV adhesin.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Kevin Neil
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Frédéric Grenier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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24
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Wardell GE, Hynes MF, Young PJ, Harrison E. Why are rhizobial symbiosis genes mobile? Philos Trans R Soc Lond B Biol Sci 2022; 377:20200471. [PMID: 34839705 PMCID: PMC8628070 DOI: 10.1098/rstb.2020.0471] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022] Open
Abstract
Rhizobia are one of the most important and best studied groups of bacterial symbionts. They are defined by their ability to establish nitrogen-fixing intracellular infections within plant hosts. One surprising feature of this symbiosis is that the bacterial genes required for this complex trait are not fixed within the chromosome, but are encoded on mobile genetic elements (MGEs), namely plasmids or integrative and conjugative elements. Evidence suggests that many of these elements are actively mobilizing within rhizobial populations, suggesting that regular symbiosis gene transfer is part of the ecology of rhizobial symbionts. At first glance, this is counterintuitive. The symbiosis trait is highly complex, multipartite and tightly coevolved with the legume hosts, while transfer of genes can be costly and disrupt coadaptation between the chromosome and the symbiosis genes. However, horizontal gene transfer is a process driven not only by the interests of the host bacterium, but also, and perhaps predominantly, by the interests of the MGEs that facilitate it. Thus understanding the role of horizontal gene transfer in the rhizobium-legume symbiosis requires a 'mobile genetic element's-eye view' on the ecology and evolution of this important symbiosis. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Grace E. Wardell
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 1EA, UK
| | - Michael F. Hynes
- Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Peter J. Young
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Ellie Harrison
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 1EA, UK
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25
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Shen Z, Tang CM, Liu GY. Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids? Mil Med Res 2022; 9:3. [PMID: 35012680 PMCID: PMC8744291 DOI: 10.1186/s40779-021-00362-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/26/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.
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Affiliation(s)
- Zhen Shen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.,Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Guang-Yu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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26
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Liu G, Thomsen LE, Olsen JE. Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review. J Antimicrob Chemother 2021; 77:556-567. [PMID: 34894259 DOI: 10.1093/jac/dkab450] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.
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Affiliation(s)
- Gang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Line Elnif Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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27
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Brockhurst MA, Harrison E. Ecological and evolutionary solutions to the plasmid paradox. Trends Microbiol 2021; 30:534-543. [PMID: 34848115 DOI: 10.1016/j.tim.2021.11.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 12/22/2022]
Abstract
The 'plasmid paradox' arises because, although plasmids are common features of bacterial genomes, theoretically they should not exist: rates of conjugation were believed insufficient to allow plasmids to persist by infectious transmission, whereas the costs of plasmid maintenance meant that plasmids should be purged by negative selection regardless of whether they encoded beneficial accessory traits because these traits should eventually be captured by the chromosome, enabling the loss of the redundant plasmid. In the decade since the plasmid paradox was described, new data and theory show that a range of ecological and evolutionary mechanisms operate in bacterial populations and communities to explain the widespread distribution and stable maintenance of plasmids. We conclude, therefore, that multiple solutions to the plasmid paradox are now well understood. The current challenge for the field, however, is to better understand how these solutions operate in natural bacterial communities to explain and predict the distribution of plasmids and the dynamics of the horizontal gene transfer that they mediate in bacterial (pan)genomes.
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Affiliation(s)
- Michael A Brockhurst
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, M13 9PT, UK.
| | - Ellie Harrison
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, S10 2TN, UK
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28
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Sheppard RJ, Barraclough TG, Jansen VAA. The Evolution of Plasmid Transfer Rate in Bacteria and Its Effect on Plasmid Persistence. Am Nat 2021; 198:473-488. [PMID: 34559608 DOI: 10.1086/716063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractPlasmids are extrachromosomal segments of DNA that can transfer genes between bacterial cells. Many plasmid genes benefit bacteria but cause harm to human health by granting antibiotic resistance to pathogens. Transfer rate is a key parameter for predicting plasmid dynamics, but observed rates are highly variable, and the effects of selective forces on their evolution are unclear. We apply evolutionary analysis to plasmid conjugation models to investigate selective pressures affecting plasmid transfer rate, emphasizing host versus plasmid control, the costs of plasmid transfer, and the role of recipient cells. Our analyses show that plasmid-determined transfer rates can be predicted with three parameters (host growth rate, plasmid loss rate, and the cost of plasmid transfer on growth) under some conditions. We also show that low-frequency genetic variation in transfer rate can accumulate, facilitating rapid adaptation to changing conditions. Furthermore, reduced transfer rates due to host control have limited effects on plasmid prevalence until low enough to prevent plasmid persistence. These results provide a framework to predict plasmid transfer rate evolution in different environments and demonstrate the limited impact of host mechanisms to control the costs incurred when plasmids are present.
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29
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De R. Mobile Genetic Elements of Vibrio cholerae and the Evolution of Its Antimicrobial Resistance. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.691604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Vibrio cholerae (VC) is the causative agent of the severe dehydrating diarrheal disease cholera. The primary treatment for cholera is oral rehydration therapy (ORT). However, in case of moderate to severe dehydration, antibiotics are administered to reduce morbidity. Due to the emergence of multidrug resistant (MDR) strains of VC routinely used antibiotics fail to be effective in cholera patients. Antimicrobial resistance (AMR) is encoded in the genome of bacteria and is usually acquired from other organisms cohabiting in the environment or in the gut with which it interacts in the gut or environmental niche. The antimicrobial resistance genes (ARGs) are usually borne on mobile genetic elements (MGEs) like plasmids, transposons, integrons and SXT constin. Horizontal gene transfer (HGT) helps in the exchange of ARGs among bacteria leading to dissemination of AMR. In VC the acquisition and loss of AMR to many antibiotics have been found to be a dynamic process. This review describes the different AMR determinants and mechanisms of resistance that have been discovered in VC. These ARGs borne usually on MGEs have been recovered from isolates associated with past and present epidemics worldwide. These are responsible for resistance of VC to common antibiotics and are periodically lost and gained contributing to its genetic evolution. These resistance markers can be routinely used for AMR surveillance in VC. The review also presents a precise perspective on the importance of the gut microbiome in the emergence of MDR VC and concludes that the gut microbiome is a potential source of molecular markers and networks which can be manipulated for the interception of AMR in the future.
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30
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Detection of Quorum Sensing N-Acyl-Homoserine Lactone Molecules Produced by Different Resistant Klebsiella pneumoniae Isolates Recovered from Poultry and Different Environmental Niches. Appl Biochem Biotechnol 2021; 193:3351-3370. [PMID: 34196919 DOI: 10.1007/s12010-021-03605-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
This study aimed to detect and identify the N-acyl-homoserine lactones molecules (AHLs) produced by different resistant Klebsiella pneumoniae isolates recovered from poultry and environmental samples using a modified validated high-performance liquid chromatography method. A total of 56 K. pneumoniae isolates were recovered, investigated for their antibiotic susceptibility, and screened for AHLs production using the Agrobacterium tumefaciens NTL4 biosensor system and a validated high-performance liquid chromatography method. The results revealed the detection of different short- and long-chain AHLs molecules among 39 K. pneumoniae isolates recovered from poultry and environmental samples. All environmental isolates produced nine peaks with retention times for C4-HSL, C6-HSL, C12-HSL, C8-HSL, C14-HSL, C8-oxo-HSL, C10-HSL, C6-oxo-HSL, and C7-HSL. The most quantifiable AHL signal molecules in poultry isolates were C4-HSL, C6-HSL, and C12-HSL. No statistical correlation between the AHL-producing ability of K. pneumoniae isolates and antibiotic resistance was reported. To the best of our knowledge, this study provides the first detailed report on the detection and identification of AHLs in K. pneumoniae isolates recovered from poultry and environmental samples. Furthermore, it provides a new insight available tool other than LC-MS/MS for detection and identification of AHL molecules.
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31
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Ortiz Charneco G, Kelleher P, Buivydas A, Streekstra H, van Themaat EVL, de Waal PP, Mahony J, van Sinderen D. Genetic Dissection of a Prevalent Plasmid-Encoded Conjugation System in Lactococcus lactis. Front Microbiol 2021; 12:680920. [PMID: 34122391 PMCID: PMC8194271 DOI: 10.3389/fmicb.2021.680920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/20/2021] [Indexed: 01/02/2023] Open
Abstract
Plasmid pNP40, which was first identified nearly 40 years ago in Lactococcus lactis subsp. lactis biovar diacetylactis DRC3, encodes functions such as heavy metal-, bacteriophage-, and nisin-resistance, as well as plasmid transfer ability by conjugation. Here, we report an optimized conjugation protocol for this plasmid, yielding a transfer frequency that is approximately 4,000-fold higher than those previously reported in literature, while we also observed high-frequency plasmid co-mobilization. Individual mutations in 18 genes that encompass the presumed conjugation cluster of pNP40 were generated using ssDNA recombineering to evaluate the role of each gene in the conjugation process. A possible transcriptional repressor of this conjugation cluster, the product of the traR gene, was identified in this manner. This mutational analysis, paired with bioinformatic predictions as based on sequence and structural similarities, allowed us to generate a preliminary model of the pNP40 conjugation machinery.
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Affiliation(s)
| | - Philip Kelleher
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Andrius Buivydas
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | | | | | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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32
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pCTX-M3-Structure, Function, and Evolution of a Multi-Resistance Conjugative Plasmid of a Broad Recipient Range. Int J Mol Sci 2021; 22:ijms22094606. [PMID: 33925677 PMCID: PMC8125031 DOI: 10.3390/ijms22094606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022] Open
Abstract
pCTX-M3 is the archetypic member of the IncM incompatibility group of conjugative plasmids (recently referred to as IncM2). It is responsible for the worldwide dissemination of numerous antibiotic resistance genes, including those coding for extended-spectrum β-lactamases and conferring resistance to aminoglycosides. The IncM plasmids acquired during evolution diverse mobile genetic elements found in one or two multiple resistance regions, MRR(s), grouping antibiotic resistance genes as well as mobile genetic elements or their remnants. The IncM plasmids can be found in bacteria inhabiting various environments. The information on the structure and biology of pCTX-M3 is integrated in this review. It focuses on the functional modules of pCTX-M3 responsible for its replication, stable maintenance, and conjugative transfer, indicating that the host range of the pCTX-M3 replicon is limited to representatives of the family Enterobacteriaceae (Enterobacterales ord. nov.), while the range of recipients of its conjugation system is wide, comprising Alpha-, Beta-, and Gammaproteobacteria, and also Firmicutes.
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33
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Xiong R, Liu Y, Pu J, Liu J, Zheng D, Zeng J, Chen C, Lu Y, Huang B. Indole Inhibits IncP-1 Conjugation System Mainly Through Promoting korA and korB Expression. Front Microbiol 2021; 12:628133. [PMID: 33815310 PMCID: PMC8017341 DOI: 10.3389/fmicb.2021.628133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/12/2021] [Indexed: 11/26/2022] Open
Abstract
Indole works as an interspecies signal molecule to regulate multiple physiological activities, like antibiotic resistance, acid resistance, and virulence. However, the effect of indole on conjugation is unknown. Here, with Escherichia coli SM10λπ as a donor strain that carries a chromosomally integrated conjugative RP4 plasmid, we explored the effect of indole on conjugation of a mobilizable pUCP24T plasmid imparting gentamycin resistance. The results showed that exogenous indole treatment inhibited conjugative transfer of pUCP24T from SM10λπ to recipient strains, Pseudomonas aeruginosa PAO1 and E. coli EC600. Furthermore, raising endogenous indole production through overexpression of TnaA, a tryptophanase, in SM10λπ significantly inhibited both SM10λπ-PAO1 and SM10λπ-EC600 conjugation, whereas deficiency of tnaA reversed the phenotype. Subsequent mechanistic studies revealed that exogenous indole significantly inhibited the expression of mating pair formation gene (trbB) and the DNA transfer and replication gene (trfA), mainly due to the promotion of regulatory genes (korA and korB), and the result was confirmed in tnaA knockout and overexpression strains. Additionally, we found that both extracellular indole production and tnaA expression of SM10λπ were downregulated by ciprofloxacin (CIP). Intriguingly, one-eighth minimum inhibitory concentration of CIP treatment clearly facilitated both SM10λπ-PAO1 and SM10λπ-EC600 conjugation, and indole inhibited CIP-induced conjugation frequency. These data suggest that indole may play a negative role in the process of CIP-induced conjugation. This is the first study to reveal the biological function of indole-inhibiting conjugation and its role in CIP-induced conjugation, which may be developed into a new way of controlling the spread of antibiotic resistance.
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Affiliation(s)
- Rui Xiong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuyang Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jieying Pu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Jianping Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Dexiang Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Jianming Zeng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Yang Lu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Bin Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
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Meijer WJJ, Boer DR, Ares S, Alfonso C, Rojo F, Luque-Ortega JR, Wu LJ. Multiple Layered Control of the Conjugation Process of the Bacillus subtilis Plasmid pLS20. Front Mol Biosci 2021; 8:648468. [PMID: 33816561 PMCID: PMC8014075 DOI: 10.3389/fmolb.2021.648468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial conjugation is the main horizontal gene transfer route responsible for the spread of antibiotic resistance, virulence and toxin genes. During conjugation, DNA is transferred from a donor to a recipient cell via a sophisticated channel connecting the two cells. Conjugation not only affects many different aspects of the plasmid and the host, ranging from the properties of the membrane and the cell surface of the donor, to other developmental processes such as competence, it probably also poses a burden on the donor cell due to the expression of the large number of genes involved in the conjugation process. Therefore, expression of the conjugation genes must be strictly controlled. Over the past decade, the regulation of the conjugation genes present on the conjugative Bacillus subtilis plasmid pLS20 has been studied using a variety of methods including genetic, biochemical, biophysical and structural approaches. This review focuses on the interplay between RcopLS20, RappLS20 and Phr*pLS20, the proteins that control the activity of the main conjugation promoter Pc located upstream of the conjugation operon. Proper expression of the conjugation genes requires the following two fundamental elements. First, conjugation is repressed by default and an intercellular quorum-signaling system is used to sense conditions favorable for conjugation. Second, different layers of regulation act together to repress the Pc promoter in a strict manner but allowing rapid activation. During conjugation, ssDNA is exported from the cell by a membrane-embedded DNA translocation machine. Another membrane-embedded DNA translocation machine imports ssDNA in competent cells. Evidences are reviewed indicating that conjugation and competence are probably mutually exclusive processes. Some of the questions that remain unanswered are discussed.
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Affiliation(s)
- Wilfried J J Meijer
- Laboratory 402, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Saúl Ares
- Laboratory 35, C. Grupo Interdisciplinar de Sistemas Complejos and Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Carlos Alfonso
- Laboratory B08, Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Fernando Rojo
- Laboratory 216, Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Juan R Luque-Ortega
- Laboratory S07, Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
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Pessione E. The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions. Front Microbiol 2021; 11:571417. [PMID: 33584557 PMCID: PMC7873842 DOI: 10.3389/fmicb.2020.571417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria, the first organisms that appeared on Earth, continue to play a central role in ensuring life on the planet, both as biogeochemical agents and as higher organisms' symbionts. In the last decades, they have been employed both as bioremediation agents for cleaning polluted sites and as bioconversion effectors for obtaining a variety of products from wastes (including eco-friendly plastics and green energies). However, some recent reports suggest that bacterial biodiversity can be negatively affected by the present environmental crisis (global warming, soil desertification, and ocean acidification). This review analyzes the behaviors positively selected by evolution that render bacteria good models of sustainable practices (urgent in these times of climate change and scarcity of resources). Actually, bacteria display a tendency to optimize rather than maximize, to economize energy and building blocks (by using the same molecule for performing multiple functions), and to recycle and share metabolites, and these are winning strategies when dealing with sustainability. Furthermore, their ability to establish successful reciprocal relationships by means of anticipation, collective actions, and cooperation can also constitute an example highlighting how evolutionary selection favors behaviors that can be strategic to contain the present environmental crisis.
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Affiliation(s)
- Enrica Pessione
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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Zwanzig M. The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling. Comput Struct Biotechnol J 2020; 19:586-599. [PMID: 33510864 PMCID: PMC7807137 DOI: 10.1016/j.csbj.2020.12.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 12/27/2022] Open
Abstract
Many antibiotic resistance genes are associated with plasmids. The ecological success of these mobile genetic elements within microbial communities depends on varying mechanisms to secure their own propagation, not only on environmental selection. Among the most important are the cost of plasmids and their ability to be transferred to new hosts through mechanisms such as conjugation. These are regulated by dynamic control systems of the conjugation machinery and genetic adaptations that plasmid-host pairs can acquire in coevolution. However, in complex communities, these processes and mechanisms are subject to a variety of interactions with other bacterial species and other plasmid types. This article summarizes basic plasmid properties and ecological principles particularly important for understanding the persistence of plasmid-coded antibiotic resistance in aquatic environments. Through selected examples, it further introduces to the features of different types of simulation models such as systems of ordinary differential equations and individual-based models, which are considered to be important tools to understand these complex systems. This ecological perspective aims to improve the way we study and understand the dynamics, diversity and persistence of plasmids and associated antibiotic resistance genes.
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Affiliation(s)
- Martin Zwanzig
- Faculty of Environmental Sciences, Technische Universität Dresden, Pienner Str. 8, D-01737 Tharandt, Germany
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Hamed AA, Khedr M, Abdelraof M. Activation of LacZ gene in Escherichia coli DH5α via α-complementation mechanism for β-galactosidase production and its biochemical characterizations. J Genet Eng Biotechnol 2020; 18:80. [PMID: 33263861 PMCID: PMC7710787 DOI: 10.1186/s43141-020-00096-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/17/2020] [Indexed: 01/18/2023]
Abstract
Background Plasmid propagation in recombination strains such as Escherichia coli DH5α is regarded as a beneficial instrument for stable amplification of the DNA materials. Here, we show trans-conjugation of pGEM-T cloning vector (modified Promega PCR product cloning vector with tra genes, transposable element (Tn5)) and M13 sequence via α-complementation mechanism in order to activate β-d-galactosidase gene in DH5α strain (non-lactose-fermenting host). Results Trans-conjugation with pGEM-T allows correction of LacZ gene deletion through Tn5, and successful trans-conjugants in DH5α host cells can be able to produce active enzyme, thus described as lactose fermenting strain. The intracellular β-galactosidase was subjected to precipitation by ammonium sulfate and subsequently gel filtration, and the purified enzyme showed a molecular weight of approximately 72-kDa sodium dodecyl sulfate-polyacrylamid gel electrophoresis. The purified enzyme activity showed an optimal pH and temperature of 7.5 and 40 °C, respectively; it had a high stability within pH 6–8.5 and moderate thermal stability up to 50 °C. Conclusion Trans-conjugant of E. coli DH5α- lacZ∆M15 was successfully implemented. UV mutagenesis of the potent trans-conjugant isolate provides an improvement of the enzyme productivity. The enzymatic competitive inhibition by d-galactose and hydrolysis of lactose at ambient temperatures could make this enzyme a promising candidate for use in the dairy industry.
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Affiliation(s)
- Ahmed A Hamed
- Microbial Chemistry Department, Genetic engineering and Biotechnology research Division, National Research Centre, El-Buhouth St, Dokki, Cairo, 12622, Egypt
| | - Mohamed Khedr
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed Abdelraof
- Microbial Chemistry Department, Genetic engineering and Biotechnology research Division, National Research Centre, El-Buhouth St, Dokki, Cairo, 12622, Egypt.
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Virolle C, Goldlust K, Djermoun S, Bigot S, Lesterlin C. Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level. Genes (Basel) 2020; 11:genes11111239. [PMID: 33105635 PMCID: PMC7690428 DOI: 10.3390/genes11111239] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
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Protein Dynamics in F-like Bacterial Conjugation. Biomedicines 2020; 8:biomedicines8090362. [PMID: 32961700 PMCID: PMC7555446 DOI: 10.3390/biomedicines8090362] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/21/2023] Open
Abstract
Efficient in silico development of novel antibiotics requires high-resolution, dynamic models of drug targets. As conjugation is considered the prominent contributor to the spread of antibiotic resistance genes, targeted drug design to disrupt vital components of conjugative systems has been proposed to lessen the proliferation of bacterial antibiotic resistance. Advancements in structural imaging techniques of large macromolecular complexes has accelerated the discovery of novel protein-protein interactions in bacterial type IV secretion systems (T4SS). The known structural information regarding the F-like T4SS components and complexes has been summarized in the following review, revealing a complex network of protein-protein interactions involving domains with varying degrees of disorder. Structural predictions were performed to provide insight on the dynamicity of proteins within the F plasmid conjugative system that lack structural information.
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Gama JA, Zilhão R, Dionisio F. Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations. Front Microbiol 2020; 11:2033. [PMID: 32983032 PMCID: PMC7487452 DOI: 10.3389/fmicb.2020.02033] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/31/2020] [Indexed: 01/31/2023] Open
Abstract
It is difficult to understand plasmid maintenance in the absence of selection and theoretical models predict the conditions for plasmid persistence to be limited. Plasmid-associated fitness costs decrease bacterial competitivity, while imperfect partition allows the emergence of plasmid-free cells during cell division. Although plasmid conjugative transfer allows mobility into plasmid-free cells, the rate of such events is generally not high enough to ensure plasmid persistence. Experimental data suggest several factors that may expand the conditions favorable for plasmid maintenance, such as compensatory mutations and accessory genes that allow positive selection. Most of the previous studies focus on bacteria that carry a single plasmid. However, there is increasing evidence that multiple plasmids inhabit the same bacterial population and that interactions between them affect their transmission and persistence. Here, we adapt previous mathematical models to include multiple plasmids and perform computer simulations to study how interactions among them affect plasmid maintenance. We tested the contribution of different plasmid interaction parameters that impact three biological features: host fitness, conjugative transfer and plasmid loss – which affect plasmid persistence. The interaction affecting conjugation was studied in the contexts of intracellular and intercellular interactions, i.e., the plasmids interact when present in the same cell or when in different cells, respectively. First, we tested the effect of each type of interaction alone and concluded that only interactions affecting fitness (epistasis) prevented plasmid extinction. Although not allowing plasmid maintenance, intracellular interactions increasing conjugative efficiencies had a more determinant impact in delaying extinction than the remaining parameters. Then, we allowed multiple interactions between plasmids and concluded that, in a few cases, a combined effect of (intracellular) interactions increasing conjugation and fitness lead to plasmid maintenance. Our results show a hierarchy among these interaction parameters. Those affecting fitness favor plasmid persistence more than those affecting conjugative transfer and lastly plasmid loss. These results suggest that interactions between different plasmids can favor their persistence in bacterial communities.
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Affiliation(s)
- João Alves Gama
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Rita Zilhão
- Department of Plant Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Francisco Dionisio
- Department of Plant Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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The Conjugation Window in an Escherichia coli K-12 Strain with an IncFII Plasmid. Appl Environ Microbiol 2020; 86:AEM.00948-20. [PMID: 32591383 DOI: 10.1128/aem.00948-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/18/2020] [Indexed: 12/26/2022] Open
Abstract
Many studies have examined the role that conjugation plays in disseminating antibiotic resistance genes in bacteria. However, relatively little research has quantitively examined and modeled the dynamics of conjugation under growing and nongrowing conditions beyond a couple of hours. We therefore examined growing and nongrowing cultures of Escherichia coli over a 24-h period to understand the dynamics of bacterial conjugation in the presence and absence of antibiotics with pUUH239.2, an IncFII plasmid containing multiantibiotic- and metal-resistant genes. Our data indicate that conjugation occurs after E. coli cells divide and before they have transitioned to a nongrowing phase. The result is that there is only a small window of opportunity for E. coli to conjugate with pUUH239.2 under both growing and nongrowing conditions. Only a very small percentage of the donor cells likely are capable of even undergoing conjugation, and not all transconjugants can become donor cells due to molecular regulatory controls and not being in the correct growth phase. Once a growing culture enters stationary phase, the number of capable donor cells decreases rapidly and conjugation slows to produce a plateau. Published models did not provide accurate descriptions of conjugation under nongrowing conditions. We present here a modified modeling approach that accurately describes observed conjugation behavior under growing and nongrowing conditions.IMPORTANCE There has been growing interest in horizontal gene transfer of antibiotic resistance plasmids as the antibiotic resistance crisis has worsened over the years. Most studies examining conjugation of bacterial plasmids focus on growing cultures of bacteria for short periods, but in the environment, most bacteria grow episodically and at much lower rates than in the laboratory. We examined conjugation of an IncFII antibiotic resistance plasmid in E. coli under growing and nongrowing conditions to understand the dynamics of conjugation under which the plasmid is transferred. We found that conjugation occurs in a narrow time frame when E. coli is transitioning from a growing to nongrowing phase and that the conjugation plateau develops because of a lack of capable donor cells in growing cultures. From an environmental aspect, our results suggest that episodic growth in nutrient-depleted environments could result in more conjugation than sustained growth in a nutrient rich environment.
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Banderas A, Carcano A, Sia E, Li S, Lindner AB. Ratiometric quorum sensing governs the trade-off between bacterial vertical and horizontal antibiotic resistance propagation. PLoS Biol 2020; 18:e3000814. [PMID: 32797039 PMCID: PMC7449403 DOI: 10.1371/journal.pbio.3000814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/26/2020] [Accepted: 07/20/2020] [Indexed: 11/19/2022] Open
Abstract
Plasmid-mediated horizontal gene transfer of antibiotic resistance and virulence in pathogenic bacteria underlies a major public health issue. Understanding how, in the absence of antibiotic-mediated selection, plasmid-bearing cells avoid being outnumbered by plasmid-free cells is key to developing counterstrategies. Here, we quantified the induction of the plasmidial sex pheromone pathway of Enterococcus faecalis to show that the integration of the stimulatory (mate-sensing) and inhibitory (self-sensing) signaling modules from the pCF10 conjugative plasmid provides a precise measure of the recipient-to-donor ratio, agnostic to variations in population size. Such ratiometric control of conjugation favors vertical plasmid transfer under low mating likelihood and allows activation of conjugation functions only under high mating likelihood. We further show that this strategy constitutes a cost-effective investment into mating effort because overstimulation produces unproductive self-aggregation and growth rate reduction. A mathematical model suggests that ratiometric control of conjugation increases plasmid fitness and predicts a robust long-term, stable coexistence of donors and recipients. Our results demonstrate how population-level parameters can control transfer of antibiotic resistance in bacteria, opening the door for biotic control strategies. The pathogenic bacterium Enterococcus faecalis controls the horizontal gene transfer of antibiotic resistance according to the ratio of non-resistant to resistant bacteria, while remaining agnostic to variation in the total culture density. This ratiometric twist on the well-known phenomenon of quorum-sensing allows investment in expensive conjugative transfer of plasmids only when chances are high, akin to sexual systems in more complex organisms.
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Affiliation(s)
- Alvaro Banderas
- INSERM U1284, Systems engineering and evolution dynamics, Paris, France
- Center for Research and Interdisciplinarity, Université de Paris, Paris, France
- * E-mail: (AB); (ABL)
| | - Arthur Carcano
- INRIA Saclay–Ile-de-France, Palaiseau, France
- USR 3756 IP CNRS, Institut Pasteur, Paris, France
| | - Elisa Sia
- INSERM U1284, Systems engineering and evolution dynamics, Paris, France
- Center for Research and Interdisciplinarity, Université de Paris, Paris, France
| | - Shuang Li
- INSERM U1284, Systems engineering and evolution dynamics, Paris, France
- Center for Research and Interdisciplinarity, Université de Paris, Paris, France
| | - Ariel B. Lindner
- INSERM U1284, Systems engineering and evolution dynamics, Paris, France
- Center for Research and Interdisciplinarity, Université de Paris, Paris, France
- * E-mail: (AB); (ABL)
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Schwaiger KN, Voit A, Dobiašová H, Luley C, Wiltschi B, Nidetzky B. Plasmid Design for Tunable Two-Enzyme Co-Expression Promotes Whole-Cell Production of Cellobiose. Biotechnol J 2020; 15:e2000063. [PMID: 32668097 DOI: 10.1002/biot.202000063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/16/2020] [Indexed: 12/30/2022]
Abstract
Catalyst development for biochemical cascade reactions often follows a "whole-cell-approach" in which a single microbial cell is made to express all required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux necessitates precise balancing between activities. This study shows an effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors, enabling tunable two-enzyme co-expression in E. coli, for whole-cell-production of cellobiose. An efficient transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co-expression to cope with large differences in specific activity of cellobiose phosphorylase (14 U mg-1 ) and sucrose phosphorylase (122 U mg-1 ). Mono- and bicistronic co-expression strategies controlling transcription, transcription-translation coupling or plasmid replication are analyzed for effect on activity and stable producibility of the whole-cell-catalyst. A key role of bom (basis of mobility) for plasmid stability dependent on the ori is reported and the importance of RBS (ribosome binding site) strength is demonstrated. Whole cell catalysts show high specific rates (460 µmol cellobiose min-1 g-1 dry cells) and performance metrics (30 g L-1 ; ∼82% yield; 3.8 g L-1 h-1 overall productivity) promising for cellobiose production.
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Affiliation(s)
- Katharina N Schwaiger
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Alena Voit
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Hana Dobiašová
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Christiane Luley
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Birgit Wiltschi
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Bernd Nidetzky
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria.,Institute of Biotechnology and Biochemical Engineering, TU Graz, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
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Laskey A, Ottenbrite M, Devenish J, Kang M, Savic M, Nadin-Davis S, Chmara J, Lin M, Robertson J, Bessonov K, Gurnik S, Liu K, Nash JHE, Scott A, Topp E, Guan J. Mobility of β-Lactam Resistance Under Bacterial Co-infection and Ampicillin Treatment in a Mouse Model. Front Microbiol 2020; 11:1591. [PMID: 32733428 PMCID: PMC7358583 DOI: 10.3389/fmicb.2020.01591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/17/2020] [Indexed: 01/21/2023] Open
Abstract
Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to the dissemination of antibiotic-resistance genes in the gut microbiota and the development of antibiotic-resistant bacterial infection, a significant threat to animal and public health. Food or water may be contaminated with multiple resistant bacteria, but animal models on gene transfer were mainly based on single-strain infections. In this study, we investigated the mobility of β-lactam resistance following infection with single- versus multi-strain of resistant bacteria under ampicillin treatment. We characterized three bacterial strains isolated from food-animal production systems, Escherichia coli O80:H26 and Salmonella enterica serovars Bredeney and Heidelberg. Each strain carries at least one conjugative plasmid that encodes a β-lactamase. We orally infected mice with each or all three bacterial strain(s) in the presence or absence of ampicillin treatment. We assessed plasmid transfer from the three donor bacteria to an introduced E. coli CV601gfp recipient in the mouse gut, and evaluated the impacts of the bacterial infection on gut microbiota and gut health. In the absence of ampicillin treatment, none of the donor or recipient bacteria established in the normal gut microbiota and plasmid transfer was not detected. In contrast, the ampicillin treatment disrupted the gut microbiota and enabled S. Bredeney and Heidelberg to colonize and transfer their plasmids to the E. coli CV601gfp recipient. E. coli O80:H26 on its own failed to colonize the mouse gut. However, during co-infection with the two Salmonella strains, E. coli O80:H26 colonized and transferred its plasmid to the E. coli CV601gfp recipient and a residential E. coli O2:H6 strain. The co-infection significantly increased plasmid transfer frequency, enhanced Proteobacteria expansion and resulted in inflammation in the mouse gut. Our findings suggest that single-strain infection models for evaluating in vivo gene transfer may underrepresent the consequences of multi-strain infections following the consumption of heavily contaminated food or water.
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Affiliation(s)
- Alexander Laskey
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marie Ottenbrite
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Devenish
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mingsong Kang
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mirjana Savic
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Susan Nadin-Davis
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Chmara
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Min Lin
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Simone Gurnik
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kira Liu
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - John H. E. Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Andrew Scott
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Jiewen Guan
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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Bischof K, Schiffer D, Trunk S, Höfler T, Hopfer A, Rechberger G, Koraimann G. Regulation of R1 Plasmid Transfer by H-NS, ArcA, TraJ, and DNA Sequence Elements. Front Microbiol 2020; 11:1254. [PMID: 32595626 PMCID: PMC7303359 DOI: 10.3389/fmicb.2020.01254] [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: 03/07/2020] [Accepted: 05/18/2020] [Indexed: 11/17/2022] Open
Abstract
In conjugative elements such as integrating conjugative elements (ICEs) or conjugative plasmids (CPs) transcription of DNA transfer genes is a prerequisite for cells to become transfer competent, i.e., capable of delivering plasmid DNA via bacterial conjugation into new host bacteria. In the large family of F-like plasmids belonging to the MobF12A group, transcription of DNA transfer genes is tightly controlled and dependent on the activation of a single promoter, designated PY. Plasmid encoded TraJ and chromosomally encoded ArcA proteins are known activators, whereas the nucleoid associated protein heat-stable nucleoid structuring (H-NS) silences the PY promoter. To better understand the role of these proteins in PY promoter activation, we performed in vitro DNA binding studies using purified H-NS, ArcA, and TraJR1 (TraJ encoded by the conjugative resistance plasmid R1). All proteins could bind to R1PY DNA with high affinities; however, only ArcA was found to be highly sequence specific. DNase I footprinting studies revealed three H-NS binding sites, confirmed the binding site for ArcA, and suggested that TraJ contacts a dyad symmetry DNA sequence located between −51 and −38 in the R1PY promoter region. Moreover, TraJR1 and ArcA supplied together changed the H-NS specific protection pattern suggesting that these proteins are able to replace H-NS from R1PY regions proximal to the transcription start site. Our findings were corroborated by PY-lacZ reporter fusions with a series of site specific R1PY promoter mutations. Sequential changes of some critical DNA bases in the TraJ binding site (jbs) from plasmid R1 to plasmid F led to a remarkable specificity switch: The PY promoter became activatable by F encoded TraJ whereas TraJR1 lost its activation function. The R1PY mutagenesis approach also confirmed the requirement for the host-encoded response-regulator ArcA and indicated that the sequence context, especially in the −35 region is critical for PY regulation and function.
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Affiliation(s)
- Karin Bischof
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Doris Schiffer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Sarah Trunk
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Thomas Höfler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Anja Hopfer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Gerald Rechberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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Cenens W, Andrade MO, Llontop E, Alvarez-Martinez CE, Sgro GG, Farah CS. Bactericidal type IV secretion system homeostasis in Xanthomonas citri. PLoS Pathog 2020; 16:e1008561. [PMID: 32453788 PMCID: PMC7286519 DOI: 10.1371/journal.ppat.1008561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/10/2020] [Accepted: 04/18/2020] [Indexed: 11/19/2022] Open
Abstract
Several Xanthomonas species have a type IV secretion system (T4SS) that injects a cocktail of antibacterial proteins into neighbouring Gram-negative bacteria, often leading to rapid lysis upon cell contact. This capability represents an obvious fitness benefit since it can eliminate competition while the liberated contents of the lysed bacteria could provide an increase in the local availability of nutrients. However, the production of this Mega Dalton-sized molecular machine, with over a hundred subunits, also imposes a significant metabolic cost. Here we show that the chromosomal virB operon, which encodes the structural genes of this T4SS in X. citri, is regulated by the conserved global regulator CsrA. Relieving CsrA repression from the virB operon produced a greater number of T4SSs in the cell envelope and an increased efficiency in contact-dependent lysis of target cells. However, this was also accompanied by a physiological cost leading to reduced fitness when in co-culture with wild-type X. citri. We show that T4SS production is constitutive despite being downregulated by CsrA. Cells subjected to a wide range of rich and poor growth conditions maintain a constant density of T4SSs in the cell envelope and concomitant interbacterial competitiveness. These results show that CsrA provides a constant though partial repression on the virB operon, independent of the tested growth conditions, in this way controlling T4SS-related costs while at the same time maintaining X. citri's aggressive posture when confronted by competitors.
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Affiliation(s)
- William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
| | - Maxuel O. Andrade
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, R. Giuseppe Máximo Scolfaro, Campinas, SP, Brazil
| | - Edgar Llontop
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
| | - Cristina E. Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato, Campinas, SP, Brazil
| | - Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
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Chen L, Wilksch JJ, Liu H, Zhang X, Torres VVL, Bi W, Mandela E, Cao J, Li J, Lithgow T, Zhou T. Investigation of LuxS-mediated quorum sensing in Klebsiella pneumoniae. J Med Microbiol 2020; 69:402-413. [PMID: 32223838 PMCID: PMC7377169 DOI: 10.1099/jmm.0.001148] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction Autoinducer-2 (AI-2) quorum sensing is a bacterial communication system that responds to cell density. The system requires luxS activity to produce AI-2, which can regulate gene expression and processes such as biofilm formation. Aim To investigate the role of luxS in biofilm formation and gene expression in the nosocomial pathogen Klebsiella pneumoniae. Methodology A ΔluxS gene deletion was made in K. pneumoniae KP563, an extensively drug-resistant isolate. AI-2 production was assessed in wild-type and ΔluxS strains grown in media supplemented with different carbohydrates. Potential roles of luxS in biofilm formation were investigated using a microtiter plate biofilm assay and scanning electron microscopy. Quantitative RT-PCR evaluated the expression of lipopolysaccharide (wzm and wbbM), polysaccharide (pgaA), and type 3 fimbriae (mrkA) synthesis genes in wild-type and ΔluxS mutant biofilm extracts. Results AI-2 production was dependent on the presence of luxS. AI-2 accumulation was highest during early stationary phase in media supplemented with glucose, sucrose or glycerol. Changes in biofilm architecture were observed in the ΔluxS mutant, with less surface coverage and reduced macrocolony formation; however, no differences in biofilm formation between the wild-type and ΔluxS mutant using a microtiter plate assay were observed. In ΔluxS mutant biofilm extracts, the expression of wzm was down-regulated, and the expression of pgaA, which encodes a porin for poly-β−1,6-N-acetyl-d-glucosamine (PNAG) polysaccharide secretion, was upregulated. Conclusion Relationships among AI-2-mediated quorum sensing, biofilm formation and gene expression of outer-membrane components were identified in K. pneumoniae. These inter-connected processes could be important for bacterial group behaviour and persistence.
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Affiliation(s)
- Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, PR China
| | - Jonathan J Wilksch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Haiyang Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, PR China
| | - Xiaoxiao Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, PR China
| | - Von V L Torres
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Wenzi Bi
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, PR China
| | - Eric Mandela
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Jianming Cao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, PR China
| | - Jiahui Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, PR China
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, PR China
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Sheppard RJ, Beddis AE, Barraclough TG. The role of hosts, plasmids and environment in determining plasmid transfer rates: A meta-analysis. Plasmid 2020; 108:102489. [DOI: 10.1016/j.plasmid.2020.102489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/18/2019] [Accepted: 12/08/2019] [Indexed: 12/19/2022]
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Wang H, Qi H, Gong S, Huang Z, Meng C, Zhang Y, Chen X, Jiao X. Fe 3O 4 composited with MoS 2 blocks horizontal gene transfer. Colloids Surf B Biointerfaces 2020; 185:110569. [PMID: 31629970 DOI: 10.1016/j.colsurfb.2019.110569] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/13/2019] [Accepted: 10/06/2019] [Indexed: 11/25/2022]
Abstract
In this study, we found that Fe3O4 promoted horizontal gene transfer (HGT), but when Fe3O4 was composited with MoS2, the Fe3O4@MoS2 nanocomposite interacting with bacteria significantly blocked the HGT in the conjugation system. qPCR was used to analyze the expression of genes belonging to the chromosome and plasmid in the conjugation system. Results demonstrated that Fe3O4@MoS2 inhibited conjugation by promoting the expression of the global regulatory gene (trbA) and inhibiting the expression of conjugative transfer genes involved in mating pair formation (traF, trbB), DNA replication (trfA), and porins (outer membrane protein (omp) A and ompC). All of these genes are related to the permeability of the cell membrane, except for trfA. The results showed that Fe3O4@MoS2 interacted with bacteria to decrease their permeability against exogenous DNA. MoS2 may play an essential role in the HGT-inhibiting activity of Fe3O4@MoS2. This study highlights the diverse biological properties of nano-materials and provides clues for nano-scientists to develop environmentally friendly materials.
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Affiliation(s)
- Honggui Wang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University (26116120), Yangzhou, Jiangsu, 225009, PR China; School of Environmental Science and Engineering, Yangzhou University, 225127, Yangzhou, Jiangsu, PR China
| | - Huachen Qi
- School of Environmental Science and Engineering, Yangzhou University, 225127, Yangzhou, Jiangsu, PR China
| | - Shujun Gong
- School of Environmental Science and Engineering, Yangzhou University, 225127, Yangzhou, Jiangsu, PR China
| | - Zhihai Huang
- School of Environmental Science and Engineering, Yangzhou University, 225127, Yangzhou, Jiangsu, PR China
| | - Chuang Meng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University (26116120), Yangzhou, Jiangsu, 225009, PR China
| | - Ya Zhang
- School of Environmental Science and Engineering, Yangzhou University, 225127, Yangzhou, Jiangsu, PR China.
| | - Xiang Chen
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University (26116120), Yangzhou, Jiangsu, 225009, PR China
| | - Xin'an Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University (26116120), Yangzhou, Jiangsu, 225009, PR China.
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Conjugative Transfer of IncP-9 Catabolic Plasmids Requires a Previously Uncharacterized Gene, mpfK, Whose Homologs Are Conserved in Various MPF T-Type Plasmids. Appl Environ Microbiol 2019; 85:AEM.01850-19. [PMID: 31604768 DOI: 10.1128/aem.01850-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/02/2019] [Indexed: 11/20/2022] Open
Abstract
Conjugative transfer of bacterial plasmids to recipient cells is often mediated by type IV secretion machinery. Experimental investigations into the minimal gene sets required for efficient conjugative transfer suggest that such gene sets are variable, depending on plasmids. We have been analyzing the conjugative transfer of Pseudomonas-derived and IncP-9 plasmids, NAH7 and pWW0, whose conjugation systems belong to the MPFT type. Our deletion analysis and synthetic biology analysis in this study showed that these plasmids require previously uncharacterized genes, mpfK (formerly orf34) and its functional homolog, kikA, respectively, for their efficient conjugative transfer. MpfK was localized in periplasm and had four cysteine residues whose intramolecular or intermolecular disulfide bond formation was suggested to be important for efficient conjugative transfer. The mpfK homologs were specifically carried by many MPFT-type plasmids, including non-IncP-9 plasmids, such as R388 and R751. Intriguingly, the mpfK homologs from the two non-IncP-9 plasmids were not required for conjugation of their plasmids, but were able to complement efficiently the transfer defect of the NAH7 mpfK mutant. Our results suggested the importance of the mpfK homologs for conjugative transfer of MPFT-type plasmids.IMPORTANCE IncP-9 plasmids are important mobile genetic elements for the degradation of various aromatic hydrocarbons. Elucidation of conjugative transfer of such plasmids is expected to greatly contribute to our understanding of its role in the bioremediation of polluted environments. The present study mainly focused on the conjugation system of NAH7, a well-studied and naphthalene-catabolic IncP-9 plasmid. Our analysis showed that the NAH7 conjugation system uniquely requires, in addition to the conserved components of the type IV secretion system (T4SS), a previously uncharacterized periplasmic protein, MpfK, for successful conjugation. Our findings collectively revealed a unique type of T4SS-associated conjugation system in the IncP-9 plasmids.
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