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Elg CA, Mack E, Rolfsmeier M, McLean TC, Kosterlitz O, Soderling E, Narum S, Rowley PA, Thomas CM, Top EM. Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579024. [PMID: 38370613 PMCID: PMC10871194 DOI: 10.1101/2024.02.05.579024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Plasmids play a major role in rapid adaptation of bacteria by facilitating horizontal transfer of diverse genes, most notably those conferring antibiotic resistance. While most plasmids that replicate in a broad range of bacteria also persist well in diverse hosts, there are exceptions that are poorly understood. We investigated why a broad-host range plasmid, pBP136, originally found in clinical Bordetella pertussis isolates, quickly became extinct in laboratory Escherichia coli populations. Through experimental evolution we found that inactivation of a previously uncharacterized plasmid gene, upf31, drastically improved plasmid maintenance in E. coli. This gene inactivation resulted in decreased transcription of the global plasmid regulators (korA, korB, and korC) and numerous genes in their regulons. It also caused transcriptional changes in many chromosomal genes primarily related to metabolism. In silico analyses suggested that the change in plasmid transcriptome may be initiated by Upf31 interacting with the plasmid regulator KorB. Expression of upf31 in trans negatively affected persistence of pBP136Δupf31 as well as the closely related archetypal IncP-1β plasmid R751, which is stable in E. coli and natively encodes a truncated upf31 allele. Our results demonstrate that while the upf31 allele in pBP136 might advantageously modulate gene expression in its original host, B. pertussis, it has harmful effects in E. coli. Thus, evolution of a single plasmid gene can change the range of hosts in which that plasmid persists, due to effects on the regulation of plasmid gene transcription.
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Affiliation(s)
- Clinton A. Elg
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Erin Mack
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Michael Rolfsmeier
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Thomas C. McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Olivia Kosterlitz
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
- Biology Department, University of Washington, Seattle, Washington, USA
| | | | - Solana Narum
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | | | - Eva M. Top
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
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2
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Ma K, Feng Y, McNally A, Zong Z. Hijacking a small plasmid to confer high-level resistance to aztreonam-avibactam and ceftazidime-avibactam. Int J Antimicrob Agents 2023; 62:106985. [PMID: 37769749 DOI: 10.1016/j.ijantimicag.2023.106985] [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: 06/05/2023] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
Acquired β-lactamase-encoding genes are typically carried by large plasmids in Gram-negative bacteria, which also commonly carry multi-copy small plasmids. This study found that mobile genetic elements carrying antimicrobial resistance genes are capable of hijacking small plasmids. This study focused on aztreonam-avibactam (ATM-AVI) as this combination can be used to effectively counter almost all β-lactamases produced by bacteria, and has been recommended against carbapenem-resistant Enterobacterales. A clinical strain (085003) of carbapenem-resistant Escherichia coli was investigated, and mutants (085003R32 and 085003R512) able to grow under 32/4 and 512/4 mg/L of ATM-AVI were obtained as representatives of low- and high-level resistance, respectively, by induction. Comparative genomics showed that 085003R32 and 085003R512 had a single nucleotide mutation of β-lactamase gene blaCMY-2, encoding a novel CMY with a Thr319Ile substitution, assigned 'CMY-2R'. Cloning and enzyme kinetics were used to verify that CMY-2R conferred ATM-AVI resistance by compromising binding of AVI and subsequent protection of ATM. Mechanisms for the discrepant resistance between 085003R32 and 085003R512 were investigated. Three tandem copies of blaCMY-2R were identified on a self-transmissible IncP1 plasmid of 085003R32 due to IS1294 misrecognizing its end terIS and rolling-circle replication. 085003R512 had only a single copy of blaCMY-2R on the IncP1 plasmid, but possessed anther blaCMY-2R on an already present 4-kb small plasmid. IS1294-mediated mobilization on to this multi-copy small plasmid increased the copy number of blaCMY-2R significantly, rendering higher resistance. This study shows that bacteria can employ multiple approaches to accommodate selection pressures imposed by exposure to varied concentrations of antimicrobial agents.
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Affiliation(s)
- Ke Ma
- Centre of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China; Department of Infectious Diseases, The Affiliated Hospital, Guizhou Medical University, Guiyang, China
| | - Yu Feng
- Centre for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Zhiyong Zong
- Centre of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Centre for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
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Lazdins A, Maurya AP, Miller CE, Kamruzzaman M, Liu S, Stephens ER, Lloyd GS, Haratianfar M, Chamberlain M, Haines AS, Kreft JU, Webber MA, Iredell J, Thomas CM. Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR. PLoS One 2020; 15:e0225202. [PMID: 31940351 PMCID: PMC6961859 DOI: 10.1371/journal.pone.0225202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022] Open
Abstract
Plasmids are potent vehicles for spread of antibiotic resistance genes in bacterial populations and often persist in the absence of selection due to efficient maintenance mechanisms. We previously constructed non-conjugative high copy number plasmid vectors that efficiently displace stable plasmids from enteric bacteria in a laboratory context by blocking their replication and neutralising their addiction systems. Here we assess a low copy number broad-host-range self-transmissible IncP-1 plasmid as a vector for such curing cassettes to displace IncF and IncK plasmids. The wild type plasmid carrying the curing cassette displaces target plasmids poorly but derivatives with deletions near the IncP-1 replication origin that elevate copy number about two-fold are efficient. Verification of this in mini IncP-1 plasmids showed that elevated copy number was not sufficient and that the parB gene, korB, that is central to its partitioning and gene control system, also needs to be included. The resulting vector can displace target plasmids from a laboratory population without selection and demonstrated activity in a mouse model although spread is less efficient and requires additional selection pressure.
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Affiliation(s)
- Alessandro Lazdins
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Anand Prakash Maurya
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Claire E. Miller
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Muhammad Kamruzzaman
- University of Sydney, Centre for Infectious Disease & Microbiology, Westmead Institute of Medical Research, Westmead, New South Wales, Australia
| | - Shuting Liu
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Elton R. Stephens
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Georgina S. Lloyd
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Mona Haratianfar
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Melissa Chamberlain
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Anthony S. Haines
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Jan-Ulrich Kreft
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Mark. A. Webber
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Jonathan Iredell
- University of Sydney, Centre for Infectious Disease & Microbiology, Westmead Institute of Medical Research, Westmead, New South Wales, Australia
| | - Christopher M. Thomas
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
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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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5
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Wang H, Qi H, Zhu M, Gong S, Huang Z, Zhang Y, Chen X, Jiao X. MoS 2 decorated nanocomposite: Fe 2O 3@MoS 2 inhibits the conjugative transfer of antibiotic resistance genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 186:109781. [PMID: 31622879 DOI: 10.1016/j.ecoenv.2019.109781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 09/09/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Nanomaterials of Al2O3 and TiO2 have been proved to promote the spread of antibiotic resistance genes (ARGs) by horizontal gene transfer. In this work, we found that Fe2O3@MoS2 nanocomposite inhibited the horizontal gene transfer (HGT) by inhibiting the conjugative transfer mediated by RP4-7 plasmid. To discover the mechanism of Fe2O3@MoS2 inhibiting HGT, the bacterial cells were collected under the optimal mating conditions. The collected bacterial cells were used for analyzing the expression levels of genes unique to the plasmid and the bacterial chromosome in the conjugation system by qPCR. The results of genes expression demonstrated that the mechanism of Fe2O3@MoS2 inhibited conjugation by promoting the expression of global regulatory gene (trbA) and inhibiting the expression of conjugative transfer genes involved in mating pair formation (traF, trbB) and DNA replication (trfA). The risk assessment of Fe2O3@MoS2 showed that it had very low toxicity to organisms. The findings of this paper showed that Fe2O3@MoS2, as an inhibitor of horizontal gene transfer, is an environment-friendly material.
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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
| | - Ming Zhu
- 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
| | - 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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6
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Hyde EI, Callow P, Rajasekar KV, Timmins P, Patel TR, Siligardi G, Hussain R, White SA, Thomas CM, Scott DJ. Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA. Biochem J 2017; 474:3121-3135. [PMID: 28760886 PMCID: PMC5577506 DOI: 10.1042/bcj20170281] [Citation(s) in RCA: 5] [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: 04/14/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022]
Abstract
The ParB protein, KorB, from the RK2 plasmid is required for DNA partitioning and transcriptional repression. It acts co-operatively with other proteins, including the repressor KorA. Like many multifunctional proteins, KorB contains regions of intrinsically disordered structure, existing in a large ensemble of interconverting conformations. Using NMR spectroscopy, circular dichroism and small-angle neutron scattering, we studied KorB selectively within its binary complexes with KorA and DNA, and within the ternary KorA/KorB/DNA complex. The bound KorB protein remains disordered with a mobile C-terminal domain and no changes in the secondary structure, but increases in the radius of gyration on complex formation. Comparison of wild-type KorB with an N-terminal deletion mutant allows a model of the ensemble average distances between the domains when bound to DNA. We propose that the positive co-operativity between KorB, KorA and DNA results from conformational restriction of KorB on binding each partner, while maintaining disorder.
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Affiliation(s)
- Eva I Hyde
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Philip Callow
- Institut Laue Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | | | - Peter Timmins
- Institut Laue Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Trushar R Patel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Scott A White
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | | | - David J Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, U.K.
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, U.K
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7
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Perez-Cheeks BA, Planet PJ, Sarkar IN, Clock SA, Xu Q, Figurski DH. The product of tadZ, a new member of the parA/minD superfamily, localizes to a pole in Aggregatibacter actinomycetemcomitans. Mol Microbiol 2012; 83:694-711. [PMID: 22239271 DOI: 10.1111/j.1365-2958.2011.07955.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aggregatibacter actinomycetemcomitans establishes a tenacious biofilm that is important for periodontal disease. The tad locus encodes the components for the secretion and biogenesis of Flp pili, which are necessary for the biofilm to form. TadZ is required, but its function has been elusive. We show that tadZ genes belong to the parA/minD superfamily of genes and that TadZ from A. actinomycetemcomitans (AaTadZ) forms a polar focus in the cell independent of any other tad locus protein. Mutations indicate that regions in AaTadZ are required for polar localization and biofilm formation. We show that AaTadZ dimerizes and that all TadZ proteins are predicted to have a Walker-like A box. However, they all lack the conserved lysine at position 6 (K6) present in the canonical Walker-like A box. When the alanine residue (A6) in the atypical Walker-like A box of AaTadZ was converted to lysine, the mutant protein remained able to dimerize and localize, but it was unable to allow the formation of a biofilm. Another essential biofilm protein, the ATPase (AaTadA), also localizes to a pole. However, its correct localization depends on the presence of AaTadZ. We suggest that the TadZ proteins mediate polar localization of the Tad secretion apparatus.
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Affiliation(s)
- Brenda A Perez-Cheeks
- Department of Microbiology & Immunology, College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
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8
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Rajasekar K, Muntaha ST, Tame JRH, Kommareddy S, Morris G, Wharton CW, Thomas CM, White SA, Hyde EI, Scott DJ. Order and disorder in the domain organization of the plasmid partition protein KorB. J Biol Chem 2010; 285:15440-15449. [PMID: 20200158 PMCID: PMC2865260 DOI: 10.1074/jbc.m109.096099] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 02/23/2010] [Indexed: 01/16/2023] Open
Abstract
The plasmid partition protein KorB has a dual role: it is essential for the correct segregation of the low copy number broad host range RK2 plasmid while also being an important regulator of transcription. KorB belongs to the ParB family of proteins, and partitioning in RK2 has been studied as a simplified model of bacterial chromosome segregation. Structural information on full-length ParB proteins is limited, mainly due to the inability to grow crystals suitable for diffraction studies. We show, using CD and NMR, that KorB has regions of significant intrinsic disorder and hence it adopts a multiplicity of conformations in solution. The biophysical data are consistent with bioinformatic predictions based on the amino acid sequence that the N-terminal region and also the region between the central DNA-binding domain and the C-terminal dimerization domain are intrinsically disordered. We have used small angle x-ray scattering data to determine the ensemble of solution conformations for KorB and selected deletion mutants, based on models of the known domain structures. This conformational range of KorB is likely to be biologically required for DNA partitioning and for binding to a diverse set of partner proteins.
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Affiliation(s)
- Karthik Rajasekar
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Sidra Tul Muntaha
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jeremy R H Tame
- Protein Design Laboratory, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Sireesha Kommareddy
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Gordon Morris
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Leicestershire LE12 5RD, United Kingdom
| | - Christopher W Wharton
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Scott A White
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Eva I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.
| | - David J Scott
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Leicestershire LE12 5RD, United Kingdom.
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9
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König B, Müller JJ, Lanka E, Heinemann U. Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation. Nucleic Acids Res 2009; 37:1915-24. [PMID: 19190096 PMCID: PMC2665229 DOI: 10.1093/nar/gkp044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjugative transfer and stable inheritance. The structure of KorA bound to an 18-bp DNA duplex that contains the symmetric operator sequence and incorporates 5-bromo-deoxyuridine nucleosides has been determined by multiple-wavelength anomalous diffraction phasing at 1.96-Å resolution. KorA is present as a symmetric dimer and contacts DNA via a helix–turn–helix motif. Each half-site of the symmetric operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based on two KorA side chains forming hydrogen bonds to four bases within each operator half-site. KorA has a unique dimerization module shared by the RP4 proteins TrbA and KlcB. We propose that these proteins cooperate with the global RP4 repressor KorB in a similar manner via this dimerization module and thus regulate RP4 inheritance.
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Affiliation(s)
- Bettina König
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
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10
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Bingle LEH, Rajasekar KV, Muntaha ST, Nadella V, Hyde EI, Thomas CM. A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB. Mol Microbiol 2008; 70:1502-14. [PMID: 19019158 PMCID: PMC2680271 DOI: 10.1111/j.1365-2958.2008.06498.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2008] [Indexed: 01/08/2023]
Abstract
A central feature of broad host range IncP-1 plasmids is the set of regulatory circuits that tightly control plasmid core functions under steady-state conditions. Cooperativity between KorB and either KorA or TrbA repressor proteins is a key element of these circuits and deletion analysis has implicated the conserved C-terminal domain of KorA and TrbA in this interaction. By NMR we show that KorA and KorB interact directly and identify KorA amino acids that are affected on KorB binding. Studies on mutants showed that tyrosine 84 (or phenylalanine, in some alleles) is dispensable for repressor activity but critical for the specific interaction with KorB in both in vivo reporter gene assays and in vitro electrophoretic mobility shift and co-purification assays. This confirms that direct and specific protein-protein interactions are responsible for the cooperativity observed between KorB and its corepressors and lays the basis for determining the biological importance of this cooperativity.
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Affiliation(s)
| | | | - Sidra tul Muntaha
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Vinod Nadella
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, EdgbastonBirmingham B15 2TT, UK
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Abstract
Gene regulation circuits control all aspects of the life of plasmids. This review gives an overview of the current orchestration of the circuits that control plasmid replication, plasmid transfer, plasmid segregation and plasmid maintenance.
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Affiliation(s)
- C M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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12
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Rajasekar KV, Bingle LEH, Thomas CM, Hyde EI. 1H, 13C and 15N assignments of the KorA global transcriptional repressor protein from the low copy number IncP-1 plasmid, RK2. JOURNAL OF BIOMOLECULAR NMR 2006; 36 Suppl 1:71. [PMID: 16944275 DOI: 10.1007/s10858-006-9060-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 07/03/2006] [Indexed: 05/11/2023]
Affiliation(s)
- K V Rajasekar
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK,
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Rhodes G, Parkhill J, Bird C, Ambrose K, Jones MC, Huys G, Swings J, Pickup RW. Complete nucleotide sequence of the conjugative tetracycline resistance plasmid pFBAOT6, a member of a group of IncU plasmids with global ubiquity. Appl Environ Microbiol 2005; 70:7497-510. [PMID: 15574953 PMCID: PMC535204 DOI: 10.1128/aem.70.12.7497-7510.2004] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study presents the first complete sequence of an IncU plasmid, pFBAOT6. This plasmid was originally isolated from a strain of Aeromonas caviae from hospital effluent (Westmorland General Hospital, Kendal, United Kingdom) in September 1997 (G. Rhodes, G. Huys, J. Swings, P. McGann, M. Hiney, P. Smith, and R. W. Pickup, Appl. Environ. Microbiol. 66:3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pFBAOT6 is 84,748 bp long and has 94 predicted coding sequences, only 12 of which do not have a possible function that has been attributed. Putative replication, maintenance, and transfer functions have been identified and are located in a region in the first 31 kb of the plasmid. The replication region is poorly understood but exhibits some identity at the protein level with replication proteins from the gram-positive bacteria Bacillus and Clostridium. The mating pair formation system is a virB homologue, type IV secretory pathway that is similar in its structural organization to the mating pair formation systems of the related broad-host-range (BHR) environmental plasmids pIPO2, pXF51, and pSB102 from plant-associated bacteria. Partitioning and maintenance genes are homologues of genes in IncP plasmids. The DNA transfer genes and the putative oriT site also exhibit high levels of similarity with those of plasmids pIPO2, pXF51, and pSB102. The genetic load region encompasses 54 kb, comprises the resistance genes, and includes a class I integron, an IS630 relative, and other transposable elements in a 43-kb region that may be a novel Tn1721-flanked composite transposon. This region also contains 24 genes that exhibit the highest levels of identity to chromosomal genes of several plant-associated bacteria. The features of the backbone of pFBAOT6 that are shared with this newly defined group of environmental BHR plasmids suggest that pFBAOT6 may be a relative of this group, but a relative that was isolated from a clinical bacterial environment rather than a plant-associated bacterial environment.
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Affiliation(s)
- Glenn Rhodes
- Centre for Ecology and Hydrology, Lancaster, United Kingdom.
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Bingle LEH, Zatyka M, Manzoor SE, Thomas CM. Co-operative interactions control conjugative transfer of broad host-range plasmid RK2: full effect of minor changes in TrbA operator depends on KorB. Mol Microbiol 2003; 49:1095-108. [PMID: 12890031 DOI: 10.1046/j.1365-2958.2003.03620.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A network of circuits, with KorB and TrbA as key regulators, controls genes for conjugative transfer of broad host range plasmid RK2. To assess the importance of the TrbA regulon, mutational analysis was applied to the TrbA operator at the trbB promoter and then to other TrbA-regulated promoters in the tra region. All identified TrbA operators are submaximal; in the case of trbBp, a G to A transition that made the operator core a perfect palindrome increased repression by about 50% compared to the wild type. When this change was introduced into the RK2 genome, decreases in transfer frequency of up to three orders of magnitude were observed, with bigger effects when Escherichia coli was the donor compared to Pseudomonas putida. Western blotting showed a significant decrease in Trb protein levels. These effects were much greater than the effect of the mutation on repression by TrbA alone. When KorB was introduced into the reporter system, the effects were closer to those observed in the whole RK2 context. These results indicate that co-operativity, previously observed between TrbA and KorB, allows big changes in transfer gene expression to result from small changes in individual regulator activities.
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Affiliation(s)
- Lewis E H Bingle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Kostelidou K, Thomas CM. DNA recognition by the KorA proteins of IncP-1 plasmids RK2 and R751. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1576:110-8. [PMID: 12031490 DOI: 10.1016/s0167-4781(02)00306-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The KorA repressor proteins of IncP-1 plasmids belong to a growing family of plasmid-encoded repressors that regulate partitioning genes, and in the IncP-1 plasmids coordinate these with expression of replication and transfer genes as well. Both KorA(RK2) (IncP-1 alpha) and KorA(R751) (IncP-1 beta) recognise the 5'-GTTTAGCTAAAC-3' palindrome. Reporter gene assays showed that KorA proteins from these two main subgroups of IncP-1 plasmids show specificity for their own promoter/operators and this preference was confirmed with in vitro binding studies using gel mobility shift assays on one representative promoter. Class I (high affinity) operators for KorA(RK2) are flanked by an A-A-A/T sequence in the upstream half; the T base was shown to greatly influence strong repression. A C-A-G triplet was present in the same region in the R751 O(A) sequences and the G base was accordingly found to be important for strong KorA(R751) repression. An obvious difference between the two KorA proteins is a histidine to serine change at the C-proximal end of the putative recognition helix of the HTH motif (aa 56). An IncP-1 alpha KorAH56S mutant protein had higher affinity for all operators but had improved more on R751 operators than on RK2 operators. This indicates that KorA of RK2 is not maximised for DNA binding activity and that the aa difference at position 56 may play a role in differentiation between alpha and beta KorA operators.
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Affiliation(s)
- Kalliopi Kostelidou
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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