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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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Maurya AP, Lazdins A, Wilson H, Lloyd GS, Stephens ER, Haines AS, Thomas CM. Iteron control of oriV function in IncP-1 plasmid RK2. Plasmid 2023; 126:102681. [PMID: 36990191 DOI: 10.1016/j.plasmid.2023.102681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Replication control of many plasmids is mediated by the balance between the positive and negative effects of Rep protein binding repeated sequences (iterons) associated with the replication origin, oriV. Negative control is thought to be mediated by dimeric Rep protein linking iterons in a process termed "handcuffing". The well-studied oriV region of RK2 contains 9 iterons arranged as a singleton (iteron 1), a group of 3 (iterons 2-4) and a group of 5 (iterons 5-9), but only iterons 5 to 9 are essential for replication. An additional iteron (iteron 10), oriented in the opposite direction, is also involved and reduces copy-number nearly two-fold. Since iterons 1 and 10 share an identical upstream hexamer (5' TTTCAT 3') it has been hypothesised that they form a TrfA-mediated loop facilitated by their inverted orientation. Here we report that contrary to the hypothesis, flipping one or other so they are in direct orientation results in marginally lower rather than higher copy-number. In addition, following mutagenesis of the hexamer upstream of iteron 10, we report that the Logo for the hexamer "upstream" of the regulatory iterons (1 to 4 and 10) differs from that of the essential iterons, suggesting functional differences in their interaction with TrfA.
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Affiliation(s)
- Anand P Maurya
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alessandro Lazdins
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Helen Wilson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Georgina S Lloyd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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3
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New temperature-switchable acyl homoserine lactone-regulated expression vector. Appl Microbiol Biotechnol 2023; 107:807-818. [PMID: 36580089 DOI: 10.1007/s00253-022-12341-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/30/2022]
Abstract
Bacterial expression systems play an indispensable role in the biosynthesis of recombinant proteins. Different proteins and the tasks associated with them may require different systems. The purpose of this work is to make an expression vector that allows switching on and off the expression of the target gene during cell incubation. Several expression vectors for use in Escherichia coli cells were developed using elements of the luxR/luxI type quorum sensing system of psychrophilic bacterium Aliivibrio logei. These vectors contain A. logei luxR2 and (optionally) luxI genes and LuxR2-regulated promoter, under the control of which a target gene is intended to be inserted. The synthesis of the target protein depends directly on the temperature: gene expression starts when the temperature drops to 22 °C and stops when it rises to 37 °C, which makes it possible to fix the desired amount of the target protein in the cell. At the same time, the expression of the target gene at a low temperature depends on the concentration of the autoinducer (L-homoserine N-(3-oxohexanoyl)-lactone, AI) in the culture medium in a wide range from 1 nM to 10 μM, which makes it possible to smoothly regulate the rate of target protein synthesis. Presence of luxI in the vector provides the possibility of autoinduction. Constructed expression vectors were tested with gfp, ardA, and ardB genes. At maximum, we obtained the target protein in an amount of up to 33% of the total cellular protein. KEY POINTS: • A. logei quorum sensing system elements were applied in new expression vectors • Expression of target gene is inducible at 22 °C and it is switched off at 37 °C • Target gene expression at 22 °C is tunable by use different AI concentrations.
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4
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Chen H, Tao S, Li N, Wang F, Wang L, Tang Y, Liang W. Functional comparison of anti-restriction and anti-methylation activities of ArdA, KlcA, and KlcAHS from Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:916547. [PMID: 35967855 PMCID: PMC9366191 DOI: 10.3389/fcimb.2022.916547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Anti-restriction proteins are typically encoded by plasmids, conjugative transposons, or phages to improve their chances of entering a new bacterial host with a type I DNA restriction and modification (RM) system. The invading DNA is normally destroyed by the RM system. The anti-restriction proteins ArdA, KlcA, and their homologues are usually encoded on plasmid of carbapenemase-resistant Klebsiella pneumoniae. We found that the plasmid sequence and restriction proteins affected horizontal gene transfer, and confirmed the anti-restriction and anti-methylation activities of ArdA and KlcA during transformation and transduction. Among the three anti-restriction proteins, ArdA shows stronger anti-restriction and anti-methylation effects, and KlcAHS was weaker. KlcA shows anti-methylation only during transformation. Understanding the molecular mechanism underlying the clinical dissemination of K. pneumoniae and other clinically resistant strains from the perspective of restrictive and anti-restrictive systems will provide basic theoretical support for the prevention and control of multidrug-resistant bacteria, and new strategies for delaying or even controlling the clinical dissemination of resistant strains in the future.
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Affiliation(s)
- Huimin Chen
- Medical School of Jiangsu University, Zhenjiang, China
| | - Shuan Tao
- Medical School of Jiangsu University, Zhenjiang, China
| | - Na Li
- Department of Laboratory Medicine, Bengbu Medical College, Bengbu, China
| | - Fang Wang
- Department of Central Laboratory, Lianyungang Second People Hospital, Lianyungang, China
| | - Lei Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yu Tang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Wei Liang, ; Yu Tang,
| | - Wei Liang
- Lianyungang Clinical College of Jiangsu University, Lianyungang, China
- *Correspondence: Wei Liang, ; Yu Tang,
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5
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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] [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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Liang W, Tang Y, Li G, Shen P, Tian Y, Jiang H, Jiang X, Lu Y. KlcA HS genes are ubiquitous in clinical, bla KPC-2-positive, Klebsiella pneumoniae isolates. INFECTION GENETICS AND EVOLUTION 2019; 70:84-89. [PMID: 30807842 DOI: 10.1016/j.meegid.2019.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 01/28/2023]
Abstract
Carbapenemase-producing Klebsiella pneumoniae has emerged and spread widely throughout the world. The mechanisms involved remain unclear. To provide insight, five plasmids were obtained from carbapenemase-producing K. pneumoniae clinical isolates. The five sequences were acquired, aligned and analyzed. In addition to the blaKPC-2 gene, which encodes beta lactamase, essentially all the plasmids contained a putative anti-restriction protein-encoding gene, KlcAHS. The KlcAHS gene was found in 98.2% of the blaKPC-2-positive, imipenem-resistant K. pneumoniae clinical isolates and in <1% of the blaKPC-2-negative control group. A searched of the GenBank database indicated that KlcAHS was mainly submitted by Chinese investigators beginning in 2010. Seventeen different KlcA amino acid sequences were found in the database using the restricting words: KlcA and Klebsiella pneumoniae. These sequences were used to generate a phylogenetic tree via MEGA6 software, revealing a distant evolutionary relationship between KlcAHS and other KlcAs. The secondary structure of KlcAHS, predicted with PROMALS3D software, exhibited highly conserved α-helices and β-strands. KlcAHS expressed anti-restriction activity in vivo. In summary, KlcAHS genes are ubiquitous in blaKPC-2-positive Klebsiella pneumoniae clinical isolates collected at Huashan Hospital, China. The KlcAHS protein possesses a secondary structure similar to that exhibited by anti-restriction proteins and displays anti-restriction activity. As such, KlcAHS is a probable factor in the accelerated spread of blaKPC-2 and carbapenem-resistance among clinical, K. pneumoniae isolates.
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Affiliation(s)
- Wei Liang
- Department of Laboratory Medicine, the Second People's Hospital of Lianyungang City, Jiangsu Province, China
| | - Yu Tang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gang Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pinghua Shen
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yueru Tian
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haoqin Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yuan Lu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
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Kudryavtseva AA, Osetrova MS, Livinyuk VY, Manukhov IV, Zavilgelsky GB. The importance of C-terminal aspartic acid residue (D141) to the antirestriction activity of the ArdB (R64) protein. Mol Biol 2017. [DOI: 10.1134/s0026893317050119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG. Type I restriction enzymes and their relatives. Nucleic Acids Res 2014; 42:20-44. [PMID: 24068554 PMCID: PMC3874165 DOI: 10.1093/nar/gkt847] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/24/2022] Open
Abstract
Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction-modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - David T. F. Dryden
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
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9
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Ludwiczak M, Dolowy P, Markowska A, Szarlak J, Kulinska A, Jagura-Burdzy G. Global transcriptional regulator KorC coordinates expression of three backbone modules of the broad-host-range RA3 plasmid from IncU incompatibility group. Plasmid 2013; 70:131-45. [PMID: 23583562 DOI: 10.1016/j.plasmid.2013.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/28/2013] [Accepted: 03/29/2013] [Indexed: 11/17/2022]
Abstract
The broad-host-range conjugative RA3 plasmid from IncU incompatibility group has been isolated from the fish pathogen Aeromonas hydrophila. DNA sequencing has revealed a mosaic modular structure of RA3 with the stabilization module showing some similarity to IncP-1 genes and the conjugative transfer module highly similar to that from PromA plasmids. The integrity of the mosaic plasmid genome seems to be specified by its regulatory network. In this paper the transcriptional regulator KorC was analyzed. KorCRA3 (98 amino acids) is encoded in the stabilization region and represses four strong promoters by binding to a conserved palindrome sequence, designated OC on the basis of homology to the KorC operator sequences in IncP-1 plasmids. Two of the KorCRA3-regulated promoters precede the first two cistrons in the stabilization module, one fires towards replication module, remaining one controls a tricistronic operon, whose products are involved in the conjugative transfer process. Despite the similarity between the binding sites in IncU and IncP-1 plasmids, no cross-reactivity between their KorC proteins has been detected. KorC emerges as a global regulator of RA3, coordinating all its backbone functions: replication, stable maintenance and conjugative transfer.
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Affiliation(s)
- M Ludwiczak
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
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10
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Balabanov VP, Pustovoit KS, Zavilgelsky GB. Comparative analysis of antirestriction activity of the ArdA and ArdB proteins encoded by genes of the R64 transmissible plasmid (IncI1). Mol Biol 2012. [DOI: 10.1134/s0026893312010025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Kolatka K, Kubik S, Rajewska M, Konieczny I. Replication and partitioning of the broad-host-range plasmid RK2. Plasmid 2010; 64:119-34. [DOI: 10.1016/j.plasmid.2010.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/08/2010] [Accepted: 06/21/2010] [Indexed: 11/27/2022]
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12
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Serfiotis-Mitsa D, Herbert AP, Roberts GA, Soares DC, White JH, Blakely GW, Uhrín D, Dryden DTF. The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro. Nucleic Acids Res 2009; 38:1723-37. [PMID: 20007596 PMCID: PMC2836571 DOI: 10.1093/nar/gkp1144] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Plasmids, conjugative transposons and phage frequently encode anti-restriction proteins to enhance their chances of entering a new bacterial host that is highly likely to contain a Type I DNA restriction and modification (RM) system. The RM system usually destroys the invading DNA. Some of the anti-restriction proteins are DNA mimics and bind to the RM enzyme to prevent it binding to DNA. In this article, we characterize ArdB anti-restriction proteins and their close homologues, the KlcA proteins from a range of mobile genetic elements; including an ArdB encoded on a pathogenicity island from uropathogenic Escherichia coli and a KlcA from an IncP-1b plasmid, pBP136 isolated from Bordetella pertussis. We show that all the ArdB and KlcA act as anti-restriction proteins and inhibit the four main families of Type I RM systems in vivo, but fail to block the restriction endonuclease activity of the archetypal Type I RM enzyme, EcoKI, in vitro indicating that the action of ArdB is indirect and very different from that of the DNA mimics. We also present the structure determined by NMR spectroscopy of the pBP136 KlcA protein. The structure shows a novel protein fold and it is clearly not a DNA structural mimic.
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Affiliation(s)
- Dimitra Serfiotis-Mitsa
- EaStChem School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JJ, UK
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Brilli M, Mengoni A, Fondi M, Bazzicalupo M, Liò P, Fani R. Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network. BMC Bioinformatics 2008; 9:551. [PMID: 19099604 PMCID: PMC2640388 DOI: 10.1186/1471-2105-9-551] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 12/21/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple) horizontal gene transfer (HGT) events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of network-like relationships characterizing the evolution of prokaryotes. Actually, they can be transferred among different organisms allowing the dissemination of novel functions, thus playing a pivotal role in prokaryotic evolution. However, the study of their evolutionary dynamics is complicated by the absence of universally shared genes, a prerequisite for phylogenetic analyses. RESULTS To overcome such limitations we developed a bioinformatic package, named Blast2Network (B2N), allowing the automatic phylogenetic profiling and the visualization of homology relationships in a large number of plasmid sequences. The software was applied to the study of 47 completely sequenced plasmids coming from Escherichia, Salmonella and Shigella spps. CONCLUSION The tools implemented by B2N allow to describe and visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; in particular it helped to shed some light on the complex history of Escherichia, Salmonella and Shigella plasmids and to focus on possible roles of unannotated proteins.The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.
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Affiliation(s)
- Matteo Brilli
- Department of Evolutionary Biology, University of Florence, via Romana 17, I-50125 Florence, Italy.
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14
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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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15
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Genomic and functional characterization of the modular broad-host-range RA3 plasmid, the archetype of the IncU group. Appl Environ Microbiol 2008; 74:4119-32. [PMID: 18502921 PMCID: PMC2446526 DOI: 10.1128/aem.00229-08] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
IncU plasmids are a distinctive group of mobile elements with highly conserved backbone functions and variable antibiotic resistance gene cassettes. The IncU archetype is conjugative plasmid RA3, whose sequence (45,909 bp) shows it to be a mosaic, modular replicon with a class I integron different from that of other IncU replicons. Functional analysis demonstrated that RA3 possesses a broad host range and can efficiently self-transfer, replicate, and be maintained stably in alpha-, beta-, and gammaproteobacteria. RA3 contains 50 open reading frames clustered in distinct functional modules. The replication module encompasses the repA and repB genes embedded in long repetitive sequences. RepA, which is homologous to antitoxin proteins from alpha- and gammaproteobacteria, contains a Cro/cI-type DNA-binding domain present in the XRE family of transcriptional regulators. The repA promoter is repressed by RepA and RepB. The minireplicon encompasses repB and the downstream repetitive sequence r1/r2. RepB shows up to 80% similarity to putative replication initiation proteins from environmental plasmids of beta- and gammaproteobacteria, as well as similarity to replication proteins from alphaproteobacteria and Firmicutes. Stable maintenance functions of RA3 are most like those of IncP-1 broad-host-range plasmids and comprise the active partitioning apparatus formed by IncC (ParA) and KorB (ParB), the antirestriction protein KlcA, and accessory stability components KfrA and KfrC. The RA3 origin of transfer was localized experimentally between the maintenance and conjugative-transfer operons. The putative conjugative-transfer module is highly similar in organization and in its products to transfer regions of certain broad-host-range environmental plasmids.
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16
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Distribution of the partitioning protein KorB on the genome of IncP-1 plasmid RK2. Plasmid 2008; 59:163-75. [DOI: 10.1016/j.plasmid.2008.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 02/15/2008] [Accepted: 02/15/2008] [Indexed: 11/24/2022]
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Tock MR, Dryden DTF. The biology of restriction and anti-restriction. Curr Opin Microbiol 2005; 8:466-72. [PMID: 15979932 DOI: 10.1016/j.mib.2005.06.003] [Citation(s) in RCA: 351] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Accepted: 06/09/2005] [Indexed: 11/29/2022]
Abstract
The phenomena of prokaryotic restriction and modification, as well as anti-restriction, were first discovered five decades ago but have yielded only gradually to rigorous analysis. Work presented at the 5th New England Biolabs Meeting on Restriction-Modification (available on REBASE, http://www.rebase.com) and several recently published genetic, biochemical and biophysical analyses indicate that these fields continue to contribute significantly to basic science. Recently, there have been several studies that have shed light on the still developing field of restriction-modification and on the newly re-emerging field of anti-restriction.
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Affiliation(s)
- Mark R Tock
- School of Chemistry, The King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
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Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 2005; 3:711-21. [PMID: 16138099 DOI: 10.1038/nrmicro1234] [Citation(s) in RCA: 1214] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition.
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Affiliation(s)
- Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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19
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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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20
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Vedler E, Vahter M, Heinaru A. The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol 2004; 186:7161-74. [PMID: 15489427 PMCID: PMC523222 DOI: 10.1128/jb.186.21.7161-7174.2004] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D(+) phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D(+) phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 beta subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the alpha, beta, and gamma subgroups) that it belongs to a new IncP1subgroup, the delta subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids.
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Affiliation(s)
- Eve Vedler
- Department of Genetics, Institute of Molecular and Cell Biology, 23 Riia Street, Tartu 51010, Estonia.
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21
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Affiliation(s)
- Brian M Wilkins
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.
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22
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Wilson JW, Figurski DH. Host-specific incompatibility by 9-bp direct repeats indicates a role in the maintenance of broad-host-range plasmid RK2. Plasmid 2002; 47:216-23. [PMID: 12151237 DOI: 10.1016/s0147-619x(02)00015-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Broad-host-range incompatibility group P (IncP) plasmids RK2 and R751 have 9-bp direct repeats (DR) of unknown function located between their kilC and kilE loci. The nucleotide sequences of the 9-bp repeats are different for RK2 (an IncPalpha group plasmid) and R751 (IncPbeta group), but both DR regions are organized similarly, including an 11-bp spacer with identical 5'-CGCCA-3' cores and an adjacent binding site for KorB, a known partition protein and transcriptional repressor. The occurrence of similarly arranged DR elements with different repeat sequences is suggestive of an important plasmid-specific function for the DR regions. Here we show that the cloned RK2 DR region in trans to RK2 exhibits a host-specific incompatibility phenotype, in which RK2 is destabilized in Pseudomonas aeruginosa but not in Escherichia coli. Incompatibility was not dependent on the adjacent KorB-binding site. Deletion of the kilE locus, which is required for stable maintenance in P. aeruginosa, did not abolish DR-mediated incompatibility. Precise deletion of DR from RK2 had no effect on maintenance but eliminated sensitivity to DR in trans, showing that incompatibility requires DR to be present on both plasmids. These results raise the possibility that the DR region may be involved in a plasmid maintenance system for P. aeruginosa that is independent of the known stability functions on RK2.
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Affiliation(s)
- James W Wilson
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, 701 West 168th St., New York, NY 10032, USA
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23
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Bhattacharyya A, Figurski DH. A small protein-protein interaction domain common to KlcB and global regulators KorA and TrbA of promiscuous IncP plasmids. J Mol Biol 2001; 310:51-67. [PMID: 11419936 DOI: 10.1006/jmbi.2001.4729] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The kor regulon of broad host-range, incompatibility group P (IncP) plasmids uses the KorA, KorB, and KorC repressors to regulate expression of genes for replication, conjugation, segregation, and host range. One operon, kilC, encodes the KorC repressor and two genes of unknown function (klcA and klcB). The predicted sequences of the 51.1 kDa KlcB protein, the 11.3 kDa KorA repressor, and another small (13.5 kDa) regulatory protein, TrbA, show a highly related 35 amino acid residue segment (V-L-P domain). We found that induction of the klcB gene is toxic to Escherichia coli host cells harboring an IncP plasmid. We confirmed a model in which the V-L-P domain of KlcB interacts directly with the V-L-P domain of KorA to derepress KorA-regulated operons, thereby allowing expression of toxic genes. First, a lacZ reporter fused to the kleA promoter, which is regulated by KorA and KorC, revealed that klcB induction specifically releases KorA-repression but has no effect on KorC repression. Second, induced expression of the V-L-P domains from KorA or KlcB is sufficient to release KorA-repression at the kleA promoter. Third, purified GST-KlcB fusion protein interacts specifically with His-tagged KorA. Fourth, fusion of the V-L-P domains of KorA and TrbA and full-length KlcB polypeptide to the DNA-binding domain of bacteriophage lambda repressor leads to the formation of functional, dimeric repressors, and mutations that alter conserved residues of the V-L-P domain adversely affect dimerization. Fifth, crosslinking experiments demonstrated that the V-L-P domain of KorA is able to dimerize in solution and form heterodimers in mixtures with full-length KorA polypeptide. These findings show that the V-L-P domain is a protein-protein interaction module that is likely to be responsible for dimerization of KorA and TrbA, and important for KlcB dimerization. We speculate on the possible significance of KlcB-KorA heterodimers in IncP plasmid maintenance.
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Affiliation(s)
- A Bhattacharyya
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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24
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25
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Kostelidou K, Jones AC, Thomas CM. Conserved C-terminal region of global repressor KorA of broad-host-range plasmid RK2 is required for co-operativity between KorA and a second RK2 global regulator, KorB. J Mol Biol 1999; 289:211-21. [PMID: 10366500 DOI: 10.1006/jmbi.1999.2761] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
KorA and KorB proteins of IncP1 plasmid RK2 are encoded in the central control region (ccr) of the plasmid and act as global regulators of plasmid genes for replication, transfer and stable inheritance. KorA represses seven promoters on RK2, by binding to a defined operator site, OA, which always occurs in promoter regions. KorB recognises another operator, OB, which is found 12 times on the RK2 genome, but not always in promoter regions. At five of the KorA-regulated promoters, an OBsequence is also present. The presence of both KorA and KorB leads to severely decreased promoter activity. By measuring repression at different levels of KorA and KorB alone and in combination, we showed that there is at least 3. 4-fold co-operativity between them at korApin vivo. Testing the ability of previously isolated KorA mutants to act in a co-operative way in the presence of KorB in vivo or in vitro showed that the C-terminal part of KorA between amino acid positions 68 and 83 is required for this co-operativity. This region is part of a segment that is highly conserved between KorA and two other RK2 proteins, TrbA and KlcB. We propose that this conserved region may provide the basis for co-operativity with KorB either indirectly, by modulating DNA structure near the KorB binding site, or directly by serving as the "recognition" patch of each protein by KorB. It may thus serve as a key domain in allowing a sensitive response of the global circuits to changes in repressor concentration and thus modulation of replication, transfer and maintenance.
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Affiliation(s)
- K Kostelidou
- School of Biological Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
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26
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Abstract
The entire nucleotide sequence of the first DNA segment of the conjugative F plasmid to enter the recipient cell, the leading region, is described. Analysis of the sequence provides further evidence that products encoded within the 13.2-kb leading region are likely to be expressed and perform functions associated with the transferred strand in the recipient cell.
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Affiliation(s)
- N P Manwaring
- School of Biological Sciences, University of Sydney, New South Wales, 2006, Australia
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27
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Thorsted PB, Macartney DP, Akhtar P, Haines AS, Ali N, Davidson P, Stafford T, Pocklington MJ, Pansegrau W, Wilkins BM, Lanka E, Thomas CM. Complete sequence of the IncPbeta plasmid R751: implications for evolution and organisation of the IncP backbone. J Mol Biol 1998; 282:969-90. [PMID: 9753548 DOI: 10.1006/jmbi.1998.2060] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The broad host range IncP plasmids are of particular interest because of their ability to promote gene spread between diverse bacterial species. To facilitate study of these plasmids we have compiled the complete sequence of the IncPbeta plasmid R751. Comparison with the sequence of the IncPalpha plasmids confirms the conservation of the IncP backbone of replication, conjugative transfer and stable inheritance functions between the two branches of this family. As in the IncPalpha genome the DNA of this backbone appears to have been enriched for the GCCG/CGGC motifs characteristic of the genome of organisms with a high G+C content, such as P. aeruginosa, suggesting that IncPbeta plasmids have been subjected during their evolution to similar mutational and selective forces as IncPalpha plasmids and may have evolved in pseudomonad hosts. The IncP genome is consistently interrupted by insertion of phenotypic markers and/or transposable elements between oriV and trfA and between the tra and trb operons. The R751 genome reveals a family of repeated sequences in these regions which may form the basis of a hot spot for insertion of foreign DNA. Sequence analysis of the cryptic transposon Tn4321 revealed that it is not a member of the Tn21 family as we had proposed previously from an inspection of its ends. Rather it is a composite transposon defined by inverted repeats of a 1347 bp IS element belonging to a recently discovered family which is distributed throughout the prokaryotes. The central unique region of Tn4321 encodes two predicted proteins, one of which is a regulatory protein while the other is presumably responsible for an as yet unidentified phenotype. The most striking feature of the IncPalpha plasmids, the global regulation of replication and transfer by the KorA and KorB proteins encoded in the central control operon, is conserved between the two plasmids although there appear to be significant differences in the specificity of repressor-operator interactions. The importance of these global regulatory circuits is emphasised by the observation that the operator sequences for KorB are highly conserved even in contexts where the surrounding region, either a protein coding or intergenic sequence, has diverged considerably. There appears to be no equivalent of the parABCDE region which in the IncPalpha plasmids provides multimer resolution, lethality to plasmid-free segregants and active partitioning functions. However, we found that the continuous sector from co-ordinate 0 to 9100 bp, encoding the co-regulated klc and kle operons as well as the central control region, could confer a high degree of segregational stability on a low copy number test vector. Thus R751 appears to exhibit very clearly what was first revealed by study of the IncPalpha plasmids, namely a fully functional co-ordinately regulated set of replication, transfer and stable inheritance functions.
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Affiliation(s)
- P B Thorsted
- School of Biological Sciences, University of Birmingham, Birmingham, Edgbaston, B15 2TT, UK
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28
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Kostelidou K, Jagura-Burdzy G, Thomas CM. Mutational analysis of the global regulator KorA of broad-host-range plasmid RK2. J Mol Biol 1998; 281:453-63. [PMID: 9698561 DOI: 10.1006/jmbi.1998.1956] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
KorA protein encoded in the central control region of IncP plasmid RK2 binds to seven operators on the plasmid genome and acts as a global repressor of genes for replication and stable inheritance functions. At trfAp, the promoter for plasmid replication genes, KorA also causes derepression of trbAp, the promoter for trbA, encoding another global regulator (TrbA), which controls genes required for conjugative transfer. Both KorB, a second global repressor encoded in the central control region, and TrbA also act in the trfAp-trbAp region to down-regulate trfAp, but neither of these extra repressors allows derepression of trbAp. To initiate a functional dissection of KorA, we used random mutagenesis and a positive selection system to identify korA mutants which no longer repressed trfAp. Nine single amino acid changes were obtained, which did not affect polypeptide length or apparent stability. These clustered either in the N-terminal region of the protein (region I) or in the putative HTH motif (region II). No changes were obtained in the C-terminal region (region III). Four truncated KorA proteins, with deletions either from the N-terminal or the C-terminal end, were also screened together with the single mutants. Both the band-shift assay with trfAp DNA and the in vivo promoter-probe assays with either trfAp or trbAp showed that none of the region II mutants could bind to DNA and repress the promoter. The region I mutants with a conservative amino acid substitution retained some DNA binding and repressor activity, as well as the ability to dimerise. However, an in vivo system to detect trans-dominance of the mutants indicated that one region I point mutant together with the two N-terminally truncated mutants had lost their dimerisation ability. Deletions into the basic C terminus of KorA did not abolish dimerisation. The results implicate region I in dimerisation, region II in DNA binding and region III in a yet unspecified role, possibly interaction with other proteins such as KorB.
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Affiliation(s)
- K Kostelidou
- School of Biological Sciences, University of Birmingham, Birmingham, Edgbaston, B15 2TT, UK
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29
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Jovanovic OS, Figurski DH. A potential new gene (tccA) on IncP plasmid RK2 and transposon Tn1721: relationship of its product to the TrwC relaxase/helicase of IncW plasmid R388. Plasmid 1998; 38:220-3. [PMID: 9435024 DOI: 10.1006/plas.1997.1314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Computational analysis of the fully sequenced 60-kb genome of broad-host-range IncP alpha plasmid RK2 revealed a previously unreported potential protein-coding sequence, an 80-codon open reading frame (tccA), located in the region between the vegetative origin of replication (oriV) and the tetR gene of the tetracycline resistance determinant. The coding region is also present in the transposon Tn1721 tet region, which is nearly identical to the tet region of RK2. Remarkably, the predicted polypeptide product of the coding region displays 56% identity and 72% similarity with the C-terminal domain of the TrwC relaxase/helicase protein of IncW plasmid R388.
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Affiliation(s)
- O S Jovanovic
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York 10032. USA
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30
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Holčík M, Iyer VM. Conditionally lethal genes associated with bacterial plasmids. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 11):3403-3416. [PMID: 9387219 DOI: 10.1099/00221287-143-11-3403] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Martin Holčík
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa Ontario Canada K1S5B6
| | - V M Iyer
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa Ontario Canada K1S5B6
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31
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Wilson JW, Sia EA, Figurski DH. The kilE locus of promiscuous IncP alpha plasmid RK2 is required for stable maintenance in Pseudomonas aeruginosa. J Bacteriol 1997; 179:2339-47. [PMID: 9079921 PMCID: PMC178972 DOI: 10.1128/jb.179.7.2339-2347.1997] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Eight coordinately regulated operons constitute the kor regulon of the IncP alpha plasmid RK2. Three operons specify functions required for replication initiation, conjugative transfer, and control of gene expression. The functions of the other operons, including those of the four coregulated operons that compose the kilA, kilC, and kilE loci, have not been determined. Here, we present the first evidence that a kil determinant is involved in IncP plasmid maintenance. Elevation of KorC levels specifically to reduce the expression of the KorC-regulated kilC and kilE operons severely affected the maintenance of both the IncP alpha plasmid RK2lac and the IncP beta plasmid R751 in Pseudomonas aeruginosa but had little effect on plasmid maintenance in Escherichia coli. Precise deletion of the two kilE operons from RK2lac was achieved with the VEX mutagenesis system for large genomes. The resulting plasmid showed significant loss of stability in P. aeruginosa only. The defect could be complemented by reintroduction of kilE at a different position on the plasmid. The instability of the RK2lac delta kilE mutant did not result from a reduction in average plasmid copy number, reduced expression of kilC, decreased conjugative transfer, or loss of the korE regulator. We found that both the par and kilE loci are required for full stability of RK2lac in P. aeruginosa and that the par and kilE functions act independently. These results demonstrate a critical role for the kilE locus in the stable inheritance of RK2 in P. aeruginosa.
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Affiliation(s)
- J W Wilson
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
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32
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Chattoraj DK, Schneider TD. Replication control of plasmid P1 and its host chromosome: the common ground. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 57:145-86. [PMID: 9175433 DOI: 10.1016/s0079-6603(08)60280-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- D K Chattoraj
- Laboratory of Biochemistry NCI, NIH Bethesda, Maryland 20892, USA
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33
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Whelan KF, Sherburne RK, Taylor DE. Characterization of a region of the IncHI2 plasmid R478 which protects Escherichia coli from toxic effects specified by components of the tellurite, phage, and colicin resistance cluster. J Bacteriol 1997; 179:63-71. [PMID: 8981981 PMCID: PMC178662 DOI: 10.1128/jb.179.1.63-71.1997] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The IncHI2 plasmid R478 specifies resistance to potassium tellurite (Te(r)), to some bacteriophages (Phi), and to pore-forming colicins (PacB). The genes encoding the three phenotypes are linked, and an 8.4-kb fragment of R478 DNA encoding them cannot be subcloned unless cocloned with a second section of the plasmid. Subclone pKFW4A contains a 5.9-kb BamHI-EcoRI fragment which caused some toxicity when present in Escherichia coli cells. Bacterial cells containing freshly transformed pKFW4A, examined by light microscopy and electron microscopy, had a filamentous morphology consistent with a block in septation. Insertion of transposon Tn1000 into terZ, -A, -B, and -C genes of pKFW4A resulted in the loss of the filamentation phenotype. Deletion of several regions of the clone confirmed that these latter components are involved in the filamentation phenotype. The region specifying protection from toxicity caused by the larger 8.4-kb fragment (encompassing this cluster and the entire 5.9-kb section of pKFW4A) was sequenced and analyzed by T7 polymerase expression and Tn1000 mutagenesis. Three open reading frames, terW, terY, and terX, were identified in a 2.6-kb region. Two polypeptides with approximate molecular masses of 18 and 28 kDa were expressed in CSRDE3 cells and were consistent with TerW (17.1 kDa; 155 amino acids [aa]) and TerY (26.9 kDa; 248 aa), whereas a protein of 213 aa deduced from terX was not observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The terX gene product shows strong identity with the previously identified TerE, TerD, and TerZ polypeptides, and there is a conserved motif of 13 residues, GDN(R/L)TG(E/A)GDGDDE, within this group of polypeptides. Complementation analysis indicated that terW, located approximately 6.0 kb upstream of terZ, brings about protection of cells from toxic effects of components of the Te(r), Phi, and PacB cluster.
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Affiliation(s)
- K F Whelan
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Canada
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34
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Toukdarian AE, Helinski DR, Perri S. The plasmid RK2 initiation protein binds to the origin of replication as a monomer. J Biol Chem 1996; 271:7072-8. [PMID: 8636140 DOI: 10.1074/jbc.271.12.7072] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The TrfA protein encoded by the broad host range bacterial plasmid RK2 specifically binds to eight direct repeats (iterons) present at the plasmid replication origin to initiate DNA replication. Purified TrfA protein is largely in the form of a dimer, and using a dimerization test system that involves the fusion of the amino-terminal domain of the lambda cI repressor protein to TrfA, we show that the TrfA protein forms dimers in vivo. Because of the high stability of the dimer form of TrfA, the formation of heterodimers between the wild-type and different sized TrfA proteins requires in vivo de novo folding of the primary protein sequence or in vitro denaturation and renaturation. The results of gel mobility shift assays using in vitro or in vivo formed heterodimers indicated that the TrfA protein binds to the iteron DNA as a monomer. Furthermore, when the monomeric and dimeric forms of TrfA are separated by gel filtration chromatography, only the protein in the chromatographic position of the monomeric form demonstrated significant DNA binding activity. These results indicate that only the monomer form of the TrfA protein is active for binding to the iterons at the RK2 replication origin.
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Affiliation(s)
- A E Toukdarian
- Center for Molecular Genetics and Department of Biology, University of California, San Diego, La Jolla, California 92093-0634, USA
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Thomas CM, Smith CA, Ibbotson JP, Johnston L, Wang N. Evolution of the korA-oriV segment of promiscuous IncP plasmids. MICROBIOLOGY (READING, ENGLAND) 1995; 141 ( Pt 5):1201-1210. [PMID: 7773415 DOI: 10.1099/13500872-141-5-1201] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Plasmids belonging to Escherichia coli incompatibility group P are of particular interest because they can transfer between, and be stably maintained in, almost all Gram-negative bacterial species. The segment of the IncP alpha plasmid genome between the key regulatory gene korA and the vegetative replication origin, oriV, encodes a series of operons co-regulated with replication and transfer functions by the KorA protein. To determine which of these genes are likely to have an important role in IncP plasmid survival the equivalent region of the distantly related IncP beta plasmid R751 was sequenced. Sequence comparisons show that the kla operon (formerly the kilA locus, which is also responsible for a cryptic tellurite-resistance determinant) is completely absent from R751. Similarly in the kle region, which encodes genes associated with the KilE+ phenotype of unknown function, kleC and kleD, which we proposed arose by a duplication of kleA and kleB, are also completely absent. The genes that are conserved are klcA (formerly kilC, responsible for the KilC+, and recently proposed to be involved in overcoming restriction barriers during transfer), klcB (an ORF interrupted by Tn1 insertion in RK2), korC (a transcriptional repressor which controls the klcK and kle operons), and kleA, kleB, kleE and kleF. A striking feature of the organization in R751 is the lack of the strong transcriptional termination signals which are present in IncP alpha plasmids. The degree of divergence between the plasmids facilitates the identification of motifs of probable functional importance in the primary protein sequences.
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Affiliation(s)
- Christopher M Thomas
- School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher A Smith
- School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - John P Ibbotson
- School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Lynda Johnston
- School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Naijin Wang
- School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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