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Liu Z, Gao Y, Wang M, Liu Y, Wang F, Shi J, Wang Z, Li R. Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli. THE ISME JOURNAL 2024; 18:wrae037. [PMID: 38438143 PMCID: PMC10976473 DOI: 10.1093/ismejo/wrae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Large cointegrate plasmids recruit genetic features of their parental plasmids and serve as important vectors in the spread of antibiotic resistance. They are now frequently found in clinical settings, raising the issue of how to limit their further transmission. Here, we conducted evolutionary research of a large blaNDM-positive cointegrate within Escherichia coli C600, and discovered that adaptive evolution of chromosome and plasmid jointly improved bacterial fitness, which was manifested as enhanced survival ability for in vivo and in vitro pairwise competition, biofilm formation, and gut colonization ability. From the plasmid aspect, large-scale DNA fragment loss is observed in an evolved clone. Although the evolved plasmid imposes a negligible fitness cost on host bacteria, its conjugation frequency is greatly reduced, and the deficiency of anti-SOS gene psiB is found responsible for the impaired horizontal transferability rather than the reduced fitness cost. These findings unveil an evolutionary strategy in which the plasmid horizontal transferability and fitness cost are balanced. From the chromosome perspective, all evolved clones exhibit parallel mutations in the transcriptional regulatory stringent starvation Protein A gene sspA. Through a sspA knockout mutant, transcriptome analysis, in vitro transcriptional activity assay, RT-qPCR, motility test, and scanning electron microscopy techniques, we demonstrated that the mutation in sspA reduces its transcriptional inhibitory capacity, thereby improving bacterial fitness, biofilm formation ability, and gut colonization ability by promoting bacterial flagella synthesis. These findings expand our knowledge of how cointegrate plasmids adapt to new bacterial hosts.
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Affiliation(s)
- Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- College of Animal Science and Technology & College of Veterinary medicine, Zhejiang Agriculture and Forestry University, Hangzhou, 311300 Zhejiang Province, People's Republic of China
| | - Yanyun Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 Jiangsu Province, People's Republic of China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 Jiangsu Province, People's Republic of China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Agricultural Science and Technology Development, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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Igler C, Huisman JS, Siedentop B, Bonhoeffer S, Lehtinen S. Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200478. [PMID: 34839701 PMCID: PMC8628072 DOI: 10.1098/rstb.2020.0478] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/09/2021] [Indexed: 12/27/2022] Open
Abstract
As infectious agents of bacteria and vehicles of horizontal gene transfer, plasmids play a key role in bacterial ecology and evolution. Plasmid dynamics are shaped not only by plasmid-host interactions but also by ecological interactions between plasmid variants. These interactions are complex: plasmids can co-infect the same cell and the consequences for the co-resident plasmid can be either beneficial or detrimental. Many of the biological processes that govern plasmid co-infection-from systems that exclude infection by other plasmids to interactions in the regulation of plasmid copy number-are well characterized at a mechanistic level. Modelling plays a central role in translating such mechanistic insights into predictions about plasmid dynamics and the impact of these dynamics on bacterial evolution. Theoretical work in evolutionary epidemiology has shown that formulating models of co-infection is not trivial, as some modelling choices can introduce unintended ecological assumptions. Here, we review how the biological processes that govern co-infection can be represented in a mathematical model, discuss potential modelling pitfalls, and analyse this model to provide general insights into how co-infection impacts ecological and evolutionary outcomes. In particular, we demonstrate how beneficial and detrimental effects of co-infection give rise to frequency-dependent selection on plasmid variants. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Claudia Igler
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Jana S. Huisman
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Berit Siedentop
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sonja Lehtinen
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
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Frequency and diversity of small plasmids in mesophilic Aeromonas isolates from fish, water and sediment. Plasmid 2021; 118:102607. [PMID: 34800545 DOI: 10.1016/j.plasmid.2021.102607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022]
Abstract
Plasmids are autonomous genetic elements ubiquitously present in bacteria. In addition to containing genetic determinants responsible for their replication and stability, some plasmids may carry genes that help bacteria adapt to different environments, while others without a known function are classified as cryptic. In this work we identified and characterized plasmids from a collection of mesophilic Aeromonas spp. (N = 90) isolated from water, sediments and fish. A total of 15 small plasmids ranging from 2287 to 10,558 bp, with an incidence of 16.7% (15/90) was found. Plasmids were detected in A. hydrophila (6), A. veronii (4), A. taiwanensis (2), A. jandaei (1), A. media (1) and Aeromonas sp. (1). There were no large or megaplasmids in the strains studied in this work. Analysis of coding sequences identified proteins associated to replication, mobilization, antibiotic resistance, virulence and stability. A considerable number of hypothetical proteins with unknown functions were also found. Some strains shared identical plasmid profiles, however, only two of them were clones. Small plasmids could be acting as a gene repositories as suggested by the presence of a gene encoding for a putative zonula occludens toxin (Zot) that causes diarrhea and the qnrB gene involved in quinolone resistance harbored in plasmids pAerXII and pAerXIII respectively.
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Pan Y, Zhang T, Yu L, Zong Z, Zhao S, Li R, Wang Q, Yuan L, Hu G, He D. IS 1294 Reorganizes Plasmids in a Multidrug-Resistant Escherichia coli Strain. Microbiol Spectr 2021; 9:e0050321. [PMID: 34612694 PMCID: PMC8510248 DOI: 10.1128/spectrum.00503-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/03/2021] [Indexed: 02/05/2023] Open
Abstract
The aims of this study were to elucidate the role of IS1294 in plasmid reorganization and to analyze biological characteristics of cointegrates derived from different daughter plasmids. The genetic profiles of plasmids in Escherichia coli strain C21 and its transconjugants were characterized by conjugation, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern hybridization, whole-genome sequencing (WGS) analysis, and PCR. The traits of cointegrates were characterized by conjugation and stability assays. blaCTX-M-55-bearing IncI2 pC21-1 and nonresistant IncI1 pC21-3, as conjugative helper plasmids, were fused with nonconjugative rmtB-bearing IncN-X1 pC21-2, generating cointegrates pC21-F1 and pC21-F2. Similarly, pC21-1 and pC21-3 were fused with nonconjugative IncF33:A-:B- pHB37-2 from another E. coli strain to generate cointegrates pC21-F3 and pC21-F4 under experimental conditions. Four cointegrates were further conjugated into the E. coli strain J53 recipient at high conjugation frequencies, ranging from 2.8 × 10-3 to 3.2 × 10-2. The formation of pC21-F1 and pC21-F4 was the result of host- and IS1294-mediated reactions and occurred at high fusion frequencies of 9.9 × 10-4 and 2.1 × 10-4, respectively. Knockout of RecA resulted in a 100-fold decrease in the frequency of plasmid reorganization. The phenomenon of cointegrate pC21-F2 and its daughter plasmids coexisting in transconjugants was detected for the first time in plasmid stability experiments. IS26-orf-oqxAB was excised from cointegrate pC21-F2 through a circular intermediate at a very low frequency, which was experimentally observed. To the best of our knowledge, this is the first report of IS1294-mediated fusion between plasmids with different replicons. This study provides insight into the formation and evolution of cointegrate plasmids under different drug selection pressures, which can promote the dissemination of MDR plasmids. IMPORTANCE The increasing resistance to β-lactams and aminoglycoside antibiotics, mainly due to extended-spectrum β-lactamases (ESBLs) and 16S rRNA methylase genes, is becoming a serious problem in Gram-negative bacteria. Plasmids, as the vehicles for resistance gene capture and horizontal gene transfer, serve a key role in terms of antibiotic resistance emergence and transmission. IS26, present in many antibiotic-resistant plasmids from Gram-negative bacteria, plays a critical role in the spread, clustering, and reorganization of resistance determinant-encoding plasmids and in plasmid reorganization through replicative transposition mechanisms and homologous recombination. However, the role of IS1294, present in many MDR plasmids, in the formation of cointegrates remains unclear. Here, we investigated experimentally the intermolecular recombination of IS1294, which occurred with high frequencies and led to the formation of conjugative MDR cointegrates and facilitated the cotransfer of blaCTX-M-55 and rmtB, and we further uncovered the significance of IS1294 in the formation of cointegrates and the common features of IS1294-driven cointegration of plasmids.
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Affiliation(s)
- Yushan Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tengli Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Lijie Yu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Zhiyong Zong
- West China Hospital, Sichuan University, Chengdu, China
| | - Shiyu Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, China
| | - Qianqian Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Li Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Gongzheng Hu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dandan He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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Shikov AE, Malovichko YV, Lobov AA, Belousova ME, Nizhnikov AA, Antonets KS. The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis. Int J Mol Sci 2021; 22:2244. [PMID: 33668147 PMCID: PMC7956386 DOI: 10.3390/ijms22052244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Bacillus thuringiensis, commonly referred to as Bt, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make Bt a prominent source of biologicals. To categorize the exuberance of Bt strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of Bt strains' phenotypes, neither it reflects actual phylogenetic relationships within the species. In this respect, comparative genomic and proteomic techniques appear more informative, but their use in Bt strain classification remains limited. In the present work, we used a bottom-up proteomic approach based on fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) coupled with liquid chromatography/tandem mass spectrometry(LC-MS/MS) protein identification to assess which stage of Bt culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the israelensis-attributed strains were assessed to compare sporulating cultures of the virulent derivative to the avirulent one as well as to the vegetative stage virulent bacteria. Using the same approach, virulent spores of the israelensis strain were also compared to the spores of strains belonging to two other major Bt serovars, namely darmstadiensis and thuringiensis. The identified proteins were analyzed regarding the presence of the respective genes in the 104 Bt genome assemblies available at open access with serovar attributions specified. Of 21 proteins identified, 15 were found to be encoded in all the present assemblies at 67% identity threshold, including several virulence factors. Notable, individual phylogenies of these core genes conferred neither the serotyping nor the flagellin-based phylogeny but corroborated the reconstruction based on phylogenomics approaches in terms of tree topology similarity. In its turn, the distribution of accessory protein genes was not confined to the existing serovars. The obtained results indicate that neither gene presence nor the core gene sequence may serve as distinctive bases for the serovar attribution, undermining the notion that the serotyping system reflects strains' phenotypic or genetic similarity. We also provide a set of loci, which fit in with the phylogenomics data plausibly and thus may serve for draft phylogeny estimation of the novel strains.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Arseniy A. Lobov
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
- Laboratory of Regenerative Biomedicine, Institute of Cytology of the Russian Academy of Science, 194064 St. Petersburg, Russia
| | - Maria E. Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
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7
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Gong L, Tang N, Chen D, Sun K, Lan R, Zhang W, Zhou H, Yuan M, Chen X, Zhao X, Che J, Bai X, Zhang Y, Xu H, Walsh TR, Lu J, Xu J, Li J, Feng J. A Nosocomial Respiratory Infection Outbreak of Carbapenem-Resistant Escherichia coli ST131 With Multiple Transmissible bla KPC-2 Carrying Plasmids. Front Microbiol 2020; 11:2068. [PMID: 33042037 PMCID: PMC7516988 DOI: 10.3389/fmicb.2020.02068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/06/2020] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) is well known for its multidrug resistance profile. Carbapenems have been considered the treatment of choice for E. coli ST131 infections, and resistance to carbapenems is emerging due to the acquisition of carbapenemase-encoding genes. In this study, 45 carbapenem-resistant E. coli strains were collected in a hospital. The resistance mechanisms, plasmid profiles, and genetic relatedness of these strains were determined. Phylogenetic relationships between these strains were assessed by molecular profiling and aligned with patient clinical details. The genetic context of bla KPC-2 was analyzed to trace the potential dissemination of bla KPC-2. The 45 carbapenem-resistant E. coli ST131 strains were closely related. Initially prevalent only in a single ward, ST131 subsequently spread to other ward, resulting in a respiratory infection outbreak of carbapenem-resistant E. coli ST131. Eight of the 30 patients died within 28 days of the first isolation of E. coli ST131. The bla KPC-2-positive plasmid profiles suggest that the carbapenem resistance was due to the acquisition by E. coli ST131 of transmissible plasmids pE0272_KPC and pE0171_KPC carrying bla KPC-2. Additionally, diverse multidrug resistance elements were transferred and rearranged between these plasmids mediated by IS26. Our research indicates that clinical attention should be paid to the importance of E. coli ST131 in respiratory infections and the spread of bla KPC -carrying E. coli ST131.
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Affiliation(s)
- Lin Gong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
- Wuhan Centers for Disease Prevention and Control, Wuhan, China
| | - Na Tang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Dongke Chen
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Kaiwen Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Min Yuan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Xia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Xiaofei Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Jie Che
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Xuemei Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Yunfei Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Hongtao Xu
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Timothy R. Walsh
- Department of Medical, Microbiology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jinxing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Juan Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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8
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Guzmán-Herrador DL, Llosa M. The secret life of conjugative relaxases. Plasmid 2019; 104:102415. [PMID: 31103521 DOI: 10.1016/j.plasmid.2019.102415] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/17/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
Conjugative relaxases are well-characterized proteins responsible for the site- and strand-specific endonucleolytic cleavage and strand transfer reactions taking place at the start and end of the conjugative DNA transfer process. Most of the relaxases characterized biochemically and structurally belong to the HUH family of endonucleases. However, an increasing number of new families of relaxases are revealing a variety of protein folds and catalytic alternatives to accomplish conjugative DNA processing. Relaxases show high specificity for their cognate target DNA sequences, but several recent reports underscore the importance of their activity on secondary targets, leading to widespread mobilization of plasmids containing an oriT-like sequence. Some relaxases perform other functions associated with their nicking and strand transfer ability, such as catalyzing site-specific recombination or initiation of plasmid replication. They perform these roles in the absence of conjugation, and the validation of these functions in several systems strongly suggest that they are not mere artifactual laboratory observations. Other unexpected roles recently assigned to relaxases include controlling plasmid copy number and promoting retrotransposition. Their capacity to mediate promiscuous mobilization and genetic reorganizations can be exploited for a number of imaginative biotechnological applications. Overall, there is increasing evidence that conjugative relaxases are not only key enzymes for horizontal gene transfer, but may have been adapted to perform other roles which contribute to prokaryotic genetic plasticity. Relaxed target specificity may be key to this versatility.
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Affiliation(s)
- Dolores Lucía Guzmán-Herrador
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain.
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Dionisio F, Zilhão R, Gama JA. Interactions between plasmids and other mobile genetic elements affect their transmission and persistence. Plasmid 2019; 102:29-36. [DOI: 10.1016/j.plasmid.2019.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 10/27/2022]
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10
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Zheng D, Zeng Z, Xue B, Deng Y, Sun M, Tang YJ, Ruan L. Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes. Microbiol Res 2018; 215:22-28. [DOI: 10.1016/j.micres.2018.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/23/2018] [Accepted: 06/02/2018] [Indexed: 11/28/2022]
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Wang P, Zhu Y, Shang H, Deng Y, Sun M. A minireplicon of plasmid pBMB26 represents a new typical replicon in the megaplasmids of Bacillus cereus group. J Basic Microbiol 2017; 58:263-272. [PMID: 29243837 DOI: 10.1002/jobm.201700525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/02/2017] [Accepted: 11/19/2017] [Indexed: 11/11/2022]
Abstract
A new minireplicon (rep26 minireplicon) from pBMB26, the 188 kb indigenous plasmid related to spore-crystal association (SCA) phenotype in Bacillus thuringiensis strain YBT-020, was characterized. A 12 kb EcoRI fragment, which encoded 10 putative open reading frames (ORFs), was capable of supporting replication when cloned in a replication probe vector. Deletion and frame shift mutation analysis showed that a 4.1 kb region encompassing two putative ORFs (orf21 and orf22) was essential for the plasmid replication in B. thuringiensis. Gene orf21 encoding a 49.8 kDa protein (named Rep26) with a helix-turn-helix motif showed no homology with known replication proteins and gene orf22 encoding a protein of 82.6 kDa showed homology to bacterial PcrA helicase. The replication origin of rep26 minireplicon was proved to be located in the coding region of orf21. Plasmid stability experiments indicated that the recombinant plasmid containing rep26 minireplicon has excellent segregational stability. BLASTP analysis revealed that amino acid sequences of ORF21 and ORF22 were well conserved among Bacillus cereus group strains. The rep26 minireplicon was widely distributed and could be defined as a new typical replicon in the megaplasmids of B. cereus group.
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Affiliation(s)
- Pengxia Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Yiguang Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Hui Shang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
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Wawrzyniak P, Płucienniczak G, Bartosik D. The Different Faces of Rolling-Circle Replication and Its Multifunctional Initiator Proteins. Front Microbiol 2017; 8:2353. [PMID: 29250047 PMCID: PMC5714925 DOI: 10.3389/fmicb.2017.02353] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR). RCR is one of the most well characterized models of DNA replication. Although many studies have focused on describing its mechanism, the role of replication initiator proteins has only recently been subject to in-depth analysis, which indicates their involvement in multiple biological process associated with RCR. In this review, we present a general overview of RCR and its impact in HGT. We focus on the molecular characteristics of RCR initiator proteins belonging to the HUH and Rep_trans protein families. Despite analogous mechanisms of action these are distinct groups of proteins with different catalytic domain structures. This is the first review describing the multifunctional character of various types of RCR initiator proteins, including the latest discoveries in the field. Recent reports provide evidence that (i) proteins initiating vegetative replication (Rep) or mobilization for conjugal transfer (Mob) may also have integrase (Int) activity, (ii) some Mob proteins are capable of initiating vegetative replication (Rep activity), and (iii) some Rep proteins can act like Mob proteins to mobilize plasmid DNA for conjugal transfer. These findings have significant consequences for our understanding of the role of RCR, not only in DNA metabolism but also in the biology of many MGEs.
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Affiliation(s)
- Paweł Wawrzyniak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland.,Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Grażyna Płucienniczak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Wang P, Zeng Z, Wang W, Wen Z, Li J, Wang X. Dissemination and loss of a biofilm-related genomic island in marine Pseudoalteromonas mediated by integrative and conjugative elements. Environ Microbiol 2017; 19:4620-4637. [PMID: 28892292 DOI: 10.1111/1462-2920.13925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 01/24/2023]
Abstract
Acquisition of genomic islands (GIs) plays a central role in the diversification and adaptation of bacteria. Some GIs can be mobilized in trans by integrative and conjugative elements (ICEs) or conjugative plasmids if the GIs carry specific transfer-related sequences. However, the transfer mechanism of GIs lacking such elements remains largely unexplored. Here, we investigated the transmissibility of a GI found in a coral-associated marine bacterium. This GI does not carry genes with transfer functions, but it carries four genes required for robust biofilm formation. Notably, this GI is inserted in the integration site for SXT/R391 ICEs. We demonstrated that acquisition of an SXT/R391 ICE results in either a tandem GI/ICE arrangement or the complete displacement of the GI. The GI displacement by the ICE greatly reduces biofilm formation. In contrast, the tandem integration of the ICE with the GI in cis allows the GI to hijack the transfer machinery of the ICE to excise, transfer and re-integrate into a new host. Collectively, our findings reveal that the integration of an ICE into a GI integration site enables rapid genome dynamics and a new mechanism by which SXT/R391 ICEs can augment genome plasticity.
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Affiliation(s)
- Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhenshun Zeng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongling Wen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer. Appl Environ Microbiol 2017; 83:AEM.00337-17. [PMID: 28432093 DOI: 10.1128/aem.00337-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 01/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.
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Wang P, Zhu Y, Zhang Y, Zhang C, Xu J, Deng Y, Peng D, Ruan L, Sun M. Mob/oriT, a mobilizable site-specific recombination system for unmarked genetic manipulation in Bacillus thuringiensis and Bacillus cereus. Microb Cell Fact 2016; 15:108. [PMID: 27286821 PMCID: PMC4902927 DOI: 10.1186/s12934-016-0492-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/23/2016] [Indexed: 11/29/2022] Open
Abstract
Background Bacillus thuringiensis and Bacillus cereus are two important species in B. cereus group. The intensive study of these strains at the molecular level and construction of genetically modified bacteria requires the development of efficient genetic tools. To insert genes into or delete genes from bacterial chromosomes, marker-less manipulation methods were employed. Results We present a novel genetic manipulation method for B. thuringiensis and B. cereus strains that does not leave selection markers. Our approach takes advantage of the relaxase Mob02281 encoded by plasmid pBMB0228 from Bacillus thuringiensis. In addition to its mobilization function, this Mob protein can mediate recombination between oriT sites. The Mob02281 mobilization module was associated with a spectinomycin-resistance gene to form a Mob-Spc cassette, which was flanked by the core 24-bp oriT sequences from pBMB0228. A strain in which the wild-type chromosome was replaced with the modified copy containing the Mob-Spc cassette at the target locus was obtained via homologous recombination. Thus, the spectinomycin-resistance gene can be used to screen for Mob-Spc cassette integration mutants. Recombination between the two oriT sequences mediated by Mob02281, encoded by the Mob-Spc cassette, resulted in the excision of the Mob-Spc cassette, producing the desired chromosomal alteration without introducing unwanted selection markers. We used this system to generate an in-frame deletion of a target gene in B. thuringiensis as well as a gene located in an operon of B. cereus. Moreover, we demonstrated that this system can be used to introduce a single gene or an expression cassette of interest in B. thuringiensis. Conclusion The Mob/oriT recombination system provides an efficient method for unmarked genetic manipulation and for constructing genetically modified bacteria of B. thuringiensis and B. cereus. Our method extends the available genetic tools for B. thuringiensis and B. cereus strains. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0492-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengxia Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yiguang Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuyang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chunyi Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianyi Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
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Peng D, Lin J, Huang Q, Zheng W, Liu G, Zheng J, Zhu L, Sun M. A novel metalloproteinase virulence factor is involved in Bacillus thuringiensis pathogenesis in nematodes and insects. Environ Microbiol 2015; 18:846-62. [PMID: 26995589 DOI: 10.1111/1462-2920.13069] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/25/2015] [Indexed: 11/29/2022]
Abstract
The Gram-positive soil bacterium Bacillus thuringiensis has been developed as the leading microbial insecticide for years. The pathogenesis of B. thuringiensis requires common extracellular factors that depend on the PlcR regulon, which regulates a large number of virulence factors; however, the precise role of many of these proteins is not known. In this study, we describe the complete lifecycle of a nematicidal B. thuringiensis strain in the free living nematode Caenorhabditis elegans using in vitro and in vivo molecular techniques to follow host and bacterial effectors during the infection process. We then focus on the metalloproteinase ColB, a collagenase, which was found highly important for destruction of the intestine thereby facilitates the adaptation and colonization of B. thuringiensis in C. elegans. In vivo green fluorescent protein (GFP) reporter-gene studies showed that ColB expression is highly induced and regulated by the global activator PlcR. Finally, we demonstrated that ColB also takes part in B. thuringiensis virulence in an insect model following injection and oral infection. Indeed, addition of purified ColB accelerates the action of Cry toxin proteins in insects, too. These results give novel insights into host adaptation for B. thuringiensis and other B. cereus group bacteria and highlight the role of collagenase metalloproteases to synergize infection process.
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Affiliation(s)
- Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jian Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiong Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Wen Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Guoqiang Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lei Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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17
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O'Brien FG, Yui Eto K, Murphy RJT, Fairhurst HM, Coombs GW, Grubb WB, Ramsay JP. Origin-of-transfer sequences facilitate mobilisation of non-conjugative antimicrobial-resistance plasmids in Staphylococcus aureus. Nucleic Acids Res 2015; 43:7971-83. [PMID: 26243776 PMCID: PMC4652767 DOI: 10.1093/nar/gkv755] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/14/2015] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is a common cause of hospital, community and livestock-associated infections and is increasingly resistant to multiple antimicrobials. A significant proportion of antimicrobial-resistance genes are plasmid-borne, but only a minority of S. aureus plasmids encode proteins required for conjugative transfer or Mob relaxase proteins required for mobilisation. The pWBG749 family of S. aureus conjugative plasmids can facilitate the horizontal transfer of diverse antimicrobial-resistance plasmids that lack Mob genes. Here we reveal that these mobilisable plasmids carry copies of the pWBG749 origin-of-transfer (oriT) sequence and that these oriT sequences facilitate mobilisation by pWBG749. Sequences resembling the pWBG749 oriT were identified on half of all sequenced S. aureus plasmids, including the most prevalent large antimicrobial-resistance/virulence-gene plasmids, pIB485, pMW2 and pUSA300HOUMR. oriT sequences formed five subfamilies with distinct inverted-repeat-2 (IR2) sequences. pWBG749-family plasmids encoding each IR2 were identified and pWBG749 mobilisation was found to be specific for plasmids carrying matching IR2 sequences. Specificity of mobilisation was conferred by a putative ribbon-helix-helix-protein gene smpO. Several plasmids carried 2–3 oriT variants and pWBG749-mediated recombination occurred between distinct oriT sites during mobilisation. These observations suggest this relaxase-in trans mechanism of mobilisation by pWBG749-family plasmids is a common mechanism of plasmid dissemination in S. aureus.
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Affiliation(s)
- Frances G O'Brien
- CHIRI Biosciences Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia Australian Collaborating Centre for Enterococcus and Staphylococcus Species (ACCESS) Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
| | - Karina Yui Eto
- CHIRI Biosciences Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia
| | - Riley J T Murphy
- CHIRI Biosciences Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia
| | - Heather M Fairhurst
- CHIRI Biosciences Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia
| | - Geoffrey W Coombs
- CHIRI Biosciences Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia Australian Collaborating Centre for Enterococcus and Staphylococcus Species (ACCESS) Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, Western Australia, Australia PathWest Laboratory Medicine, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Warren B Grubb
- CHIRI Biosciences Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia Australian Collaborating Centre for Enterococcus and Staphylococcus Species (ACCESS) Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
| | - Joshua P Ramsay
- CHIRI Biosciences Precinct, School of Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley WA 6102, Australia Australian Collaborating Centre for Enterococcus and Staphylococcus Species (ACCESS) Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
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Three Novel Lantibiotics, Ticins A1, A3, and A4, Have Extremely Stable Properties and Are Promising Food Biopreservatives. Appl Environ Microbiol 2015; 81:6964-72. [PMID: 26231642 DOI: 10.1128/aem.01851-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/16/2015] [Indexed: 02/06/2023] Open
Abstract
Lantibiotics are antimicrobial peptides with potential applications as the next generation of antimicrobials in the food industry and/or the pharmaceutical industry. Nisin has successfully been used as a food preservative for over 40 years, but its major drawback is its limited stability under neutral and alkaline pH conditions. To identify alternatives with better biochemical properties, we screened more than 100 strains of the Bacillus cereus group. Three novel lantibiotics, ticins A1 (4,062.98 Da), A3 (4,048.96 Da), and A4 (4,063.02 Da), which were highly thermostable (121°C for 30 min) and extremely pH tolerant (pH 2.0 to 9.0), were identified in Bacillus thuringiensis BMB3201. They all showed potent antimicrobial activities against all tested Gram-positive bacteria and greater activities than those of nisin A against Bacillus cereus and Listeria monocytogenes, two important foodborne pathogens. These three novel lantibiotics, with their extremely stable properties and potent antimicrobial activities, have the potential for use as biopreservatives.
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The Bacillus cereus group is an excellent reservoir of novel lanthipeptides. Appl Environ Microbiol 2014; 81:1765-74. [PMID: 25548056 DOI: 10.1128/aem.03758-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Lantibiotics are ribosomally synthesized peptides that contain multiple posttranslational modifications. Research on lantibiotics has increased recently, mainly due to their broad-spectrum antimicrobial activity, especially against some clinical Gram-positive pathogens. Many reports about various bacteriocins in the Bacillus cereus group have been published, but few were about lantibiotics. In this study, we identified 101 putative lanthipeptide gene clusters from 77 out of 223 strains of this group, and these gene clusters were further classified into 20 types according to their gene organization and the homologies of their functional genes. Among them, 18 types were novel and have not yet been experimentally verified. Two novel lantibiotics (thuricin 4A-4 and its derivative, thuricin 4A-4D) were identified in the type I-1 lanthipeptide gene cluster and showed activity against all tested Gram-positive bacteria. The mode of action of thuricin 4A-4 was studied, and we found that it acted as a bactericidal compound. The transcriptional analysis of four structural genes (thiA1, thiA2, thiA3, and thiA4) in the thuricin 4A gene cluster showed that only one structural gene, thiA4, showed efficient transcription in the exponential growth phase; the other three structural genes did not. In addition, the putative transmembrane protein ThiI was responsible for thuricin 4A-4 immunity. Genome analysis and functional verification illustrated that B. cereus group strains were a prolific source of novel lantibiotics.
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Abstract
Plasmid-encoded virulence factors are important in the pathogenesis of diseases caused by spore-forming bacteria. Unlike many other bacteria, the most common virulence factors encoded by plasmids in Clostridium and Bacillus species are protein toxins. Clostridium perfringens causes several histotoxic and enterotoxin diseases in both humans and animals and produces a broad range of toxins, including many pore-forming toxins such as C. perfringens enterotoxin, epsilon-toxin, beta-toxin, and NetB. Genetic studies have led to the determination of the role of these toxins in disease pathogenesis. The genes for these toxins are generally carried on large conjugative plasmids that have common core replication, maintenance, and conjugation regions. There is considerable functional information available about the unique tcp conjugation locus carried by these plasmids, but less is known about plasmid maintenance. The latter is intriguing because many C. perfringens isolates stably maintain up to four different, but closely related, toxin plasmids. Toxin genes may also be plasmid-encoded in the neurotoxic clostridia. The tetanus toxin gene is located on a plasmid in Clostridium tetani, but the botulinum toxin genes may be chromosomal, plasmid-determined, or located on bacteriophages in Clostridium botulinum. In Bacillus anthracis it is well established that virulence is plasmid determined, with anthrax toxin genes located on pXO1 and capsule genes on a separate plasmid, pXO2. Orthologs of these plasmids are also found in other members of the Bacillus cereus group such as B. cereus and Bacillus thuringiensis. In B. thuringiensis these plasmids may carry genes encoding one or more insecticidal toxins.
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Complete genome sequence of Bacillus thuringiensis YBT-1518, a typical strain with high toxicity to nematodes. J Biotechnol 2014; 171:1-2. [DOI: 10.1016/j.jbiotec.2013.11.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 11/29/2013] [Indexed: 11/19/2022]
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