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Couturier A, Virolle C, Goldlust K, Berne-Dedieu A, Reuter A, Nolivos S, Yamaichi Y, Bigot S, Lesterlin C. Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer. Nat Commun 2023; 14:294. [PMID: 36653393 PMCID: PMC9849209 DOI: 10.1038/s41467-023-35978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.
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Affiliation(s)
- Agathe Couturier
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Chloé Virolle
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Kelly Goldlust
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Annick Berne-Dedieu
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Audrey Reuter
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Sophie Nolivos
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Yoshiharu Yamaichi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
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2
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Virolle C, Goldlust K, Djermoun S, Bigot S, Lesterlin C. Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level. Genes (Basel) 2020; 11:genes11111239. [PMID: 33105635 PMCID: PMC7690428 DOI: 10.3390/genes11111239] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
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3
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Wagner MA, Bischof K, Kati D, Koraimann G. Silencing and activating type IV secretion genes of the F-like conjugative resistance plasmid R1. Microbiology (Reading) 2013; 159:2481-2491. [DOI: 10.1099/mic.0.071738-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Maria Anna Wagner
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Karin Bischof
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Dominiki Kati
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - Günther Koraimann
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Humboldtstrasse 50, A-8010 Graz, Austria
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4
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Wong JJW, Lu J, Glover JNM. Relaxosome function and conjugation regulation in F-like plasmids - a structural biology perspective. Mol Microbiol 2012; 85:602-17. [PMID: 22788760 DOI: 10.1111/j.1365-2958.2012.08131.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The tra operon of the prototypical F plasmid and its relatives enables transfer of a copy of the plasmid to other bacterial cells via the process of conjugation. Tra proteins assemble to form the transferosome, the transmembrane pore through which the DNA is transferred, and the relaxosome, a complex of DNA-binding proteins at the origin of DNA transfer. F-like plasmid conjugation is characterized by a high degree of plasmid specificity in the interactions of tra components, and is tightly regulated at the transcriptional, translational and post-translational levels. Over the past decade, X-ray crystallography of conjugative components has yielded insights into both specificity and regulatory mechanisms. Conjugation is repressed by FinO, an RNA chaperone which increases the lifetime of the small RNA, FinP. Recent work has resulted in a detailed model of FinO/FinP interactions and the discovery of a family of FinO-like RNA chaperones. Relaxosome components include TraI, a relaxase/helicase, and TraM, which mediates signalling between the transferosome and relaxosome for transfer initiation. The structures of TraI and TraM bound to oriT DNA reveal the basis of specific recognition of DNA for their cognate plasmid. Specificity also exists in TraI and TraM interactions with the transferosome protein TraD.
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Affiliation(s)
- Joyce J W Wong
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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5
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de la Cruz F, Frost LS, Meyer RJ, Zechner EL. Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 2010; 34:18-40. [PMID: 19919603 DOI: 10.1111/j.1574-6976.2009.00195.x] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial conjugation in Gram-negative bacteria is triggered by a signal that connects the relaxosome to the coupling protein (T4CP) and transferosome, a type IV secretion system. The relaxosome, a nucleoprotein complex formed at the origin of transfer (oriT), consists of a relaxase, directed to the nic site by auxiliary DNA-binding proteins. The nic site undergoes cleavage and religation during vegetative growth, but this is converted to a cleavage and unwinding reaction when a competent mating pair has formed. Here, we review the biochemistry of relaxosomes and ponder some of the remaining questions about the nature of the signal that begins the process.
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6
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Analysis of ColE1 MbeC unveils an extended ribbon-helix-helix family of nicking accessory proteins. J Bacteriol 2008; 191:1446-55. [PMID: 19114496 DOI: 10.1128/jb.01342-08] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MbeC is a 13-kDa ColE1-encoded protein required for efficient mobilization of ColE1, a plasmid widely used in cloning vector technology. MbeC protein was purified and used for in vitro DNA binding, which showed that it binds specifically double-stranded DNA (dsDNA) containing the ColE1 oriT. Amino acid sequence comparison and secondary structure prediction imply that MbeC is related to the ribbon-helix-helix (RHH) protein family. Alignment with RHH members pointed to a conserved arginine (R13 in MbeC) that was mutated to alanine. The mutant MbeC(R13A) was unable to bind either single-stranded DNA or dsDNA. Limited proteolysis fragmented MbeC in two stable folding domains: the N-terminal domain, which contains the RHH motif, and the C-terminal domain, which comprises a signature shared by nicking accessory proteins. The results indicate that MbeC plays a similar role in conjugation as TraY and TrwA of plasmids F and R388, respectively. Thus, it appears that an extended, possibly universal mechanism of DNA conjugative processing exists, in which oriT-processing is carried out by relaxases assisted by homologous nicking accessory proteins. This mechanism seems to be shared by all major conjugative systems analyzed thus far.
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7
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Using fluorophore-labeled oligonucleotides to measure affinities of protein-DNA interactions. Methods Enzymol 2008; 450:253-72. [PMID: 19152864 DOI: 10.1016/s0076-6879(08)03412-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Changes in fluorescence emission intensity and anisotropy can reflect changes in the environment and molecular motion of a fluorophore. Researchers can capitalize on these characteristics to assess the affinity and specificity of DNA-binding proteins using fluorophore-labeled oligonucleotides. While there are many advantages to measuring binding using fluorescent oligonucleotides, there are also some distinct disadvantages. Here we describe some of the relevant issues for the novice, illustrating key points using data collected with a variety of labeled oligonucleotides and the relaxase domain of F plasmid TraI. Topics include selection of a fluorophore, experimental design using a fluorometer equipped with an automatic titrating unit, and analysis of direct binding and competition assays.
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8
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Zahrl D, Wagner A, Tscherner M, Koraimann G. GroEL plays a central role in stress-induced negative regulation of bacterial conjugation by promoting proteolytic degradation of the activator protein TraJ. J Bacteriol 2007; 189:5885-94. [PMID: 17586648 PMCID: PMC1952051 DOI: 10.1128/jb.00005-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of DNA transfer genes is a prerequisite for conjugative DNA transfer of F-like plasmids. Transfer gene expression is sensed by the donor cell and is regulated by a complex network of plasmid- and host-encoded factors. In this study we analyzed the effect of induction of the heat shock regulon on transfer gene expression and DNA transfer in Escherichia coli. Raising the growth temperature from 22 degrees C to 43 degrees C transiently reduced transfer gene expression to undetectable levels and reduced conjugative transfer by 2 to 3 orders of magnitude. In contrast, when host cells carried the temperature-sensitive groEL44 allele, heat shock-mediated repression was alleviated. These data implied that the chaperonin GroEL was involved in negative regulation after heat shock. Investigation of the role of GroEL in this regulatory process revealed that, in groEL(Ts) cells, TraJ, the plasmid-encoded master activator of type IV secretion (T4S) system genes, was less susceptible to proteolysis and had a prolonged half-life compared to isogenic wild-type E. coli cells. This result suggested a direct role for GroEL in proteolysis of TraJ, down-regulation of T4S system gene expression, and conjugation after heat shock. Strong support for this novel role for GroEL in regulation of bacterial conjugation was the finding that GroEL specifically interacted with TraJ in vivo. Our results further suggested that in wild-type cells this interaction was followed by rapid degradation of TraJ whereas in groEL(Ts) cells TraJ remained trapped in the temperature-sensitive GroEL protein and thus was not amenable to proteolysis.
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Affiliation(s)
- Doris Zahrl
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
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9
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Williams SL, Schildbach JF. TraY and integration host factor oriT binding sites and F conjugal transfer: sequence variations, but not altered spacing, are tolerated. J Bacteriol 2007; 189:3813-23. [PMID: 17351033 PMCID: PMC1913323 DOI: 10.1128/jb.01783-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial conjugation is the process by which a single strand of a conjugative plasmid is transferred from donor to recipient. For F plasmid, TraI, a relaxase or nickase, binds a single plasmid DNA strand at its specific origin of transfer (oriT) binding site, sbi, and cleaves at a site called nic. In vitro studies suggest TraI is recruited to sbi by its accessory proteins, TraY and integration host factor (IHF). TraY and IHF bind conserved oriT sites sbyA and ihfA, respectively, and bend DNA. The resulting conformational changes may propagate to nic, generating the single-stranded region that TraI can bind. Previous deletion studies performed by others showed transfer efficiency of a plasmid containing F oriT decreased progressively as increasingly longer segments, ultimately containing both sbyA and ihfA, were deleted. Here we describe our efforts to more precisely define the role of sbyA and ihfA by examining the effects of multiple base substitutions at sbyA and ihfA on binding and plasmid mobilization. While we observed significant decreases in in vitro DNA-binding affinities, we saw little effect on plasmid mobilization even when sbyA and ihfA variants were combined. In contrast, when half or full helical turns were inserted between the relaxosome protein-binding sites, mobilization was dramatically reduced, in some cases below the detectable limit of the assay. These results are consistent with TraY and IHF recognizing sbyA and ihfA with limited sequence specificity and with relaxosome proteins requiring proper spacing and orientation with respect to each other.
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Affiliation(s)
- Sarah L Williams
- Department of Biology, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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10
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Abraham LO, Li Y, Zamble DB. The metal- and DNA-binding activities of Helicobacter pylori NikR. J Inorg Biochem 2005; 100:1005-14. [PMID: 16343630 DOI: 10.1016/j.jinorgbio.2005.10.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 10/19/2005] [Accepted: 10/27/2005] [Indexed: 11/17/2022]
Abstract
The pathogenic bacteria Helicobacter pylori require nickel as a cofactor of the enzymes urease and hydrogenase. One of the proteins that controls nickel homeostasis in this organism is Helicobacter pylori NikR (HpNikR), a homologue of nickel-dependent transcription factors from other organisms, which regulates the expression of multiple proteins such as the urease structural subunits and itself. To examine the properties of this protein, metal analysis was used to demonstrate that HpNikR can bind stoichiometric nickel or copper, and electronic absorption spectroscopy revealed that HpNikR binds nickel with picomolar affinity in what is likely a conserved square-planar site. In vitro DNA-binding assays revealed that HpNikR can bind directly to the promoter region of the ureA operon in response to nickel, and the location of the binding site was defined. Nickel also induces DNA binding to the nikR promoter sequence but the complex is much weaker. These experiments suggest that HpNikR directly controls the expression of multiple genes by binding to separate DNA sequences, and the possible mechanisms for differential regulation are discussed.
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Affiliation(s)
- Lihor O Abraham
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, Ont., Canada M5S 3H6
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11
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Csitkovits VC, Dermić D, Zechner EL. Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem 2004; 279:45477-84. [PMID: 15322083 DOI: 10.1074/jbc.m407970200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TraI protein of plasmid R1 possesses two activities, a DNA transesterase and a highly processive 5'-3' DNA helicase, which are essential for bacterial conjugation. Regulation of the functional domains of the enzyme is poorly understood. TraI cleaves supercoiled oriT DNA with site and strand specificity in vitro but fails to initiate unwinding from this site (nic). The helicase requires an extended region of adjacent single-stranded DNA to enter the duplex, yet interaction of purified TraI with oriT DNA alone or as an integral part of the IncF relaxosome does not melt sufficient duplex to load the helicase. This study aims to gain insights into the controlled initiation of both TraI-catalyzed activities. Linear double-stranded DNA substrates with a central region of sequence heterogeneity were used to trap defined lengths of R1 oriT sequence in unwound conformation. Concomitant reconstitution of TraI DNA transesterase and helicase activities was observed. Efficient helicase activity was measured on substrates containing 60 bases of open duplex but not on substrates containing < or =30 bases in open conformation. The additional presence of auxiliary DNA-binding proteins TraY and Escherichia coli integration host factor did not stimulate TraI activities on these substrates. This model system offers a novel approach to investigate factors controlling helicase loading and the directionality of DNA unwinding from nic.
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Affiliation(s)
- Vanessa C Csitkovits
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, Universitätsplatz 2, A-8010 Graz, Austria
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12
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Abstract
F factor TraY, a ribbon-helix-helix DNA-binding protein, performs two roles in bacterial conjugation. TraY binds the F origin of transfer (oriT) to promote nicking of plasmid DNA prior to conjugative transfer. TraY also binds the P(Y) promoter to up-regulate tra gene expression. The two plasmid regions bound by TraY share limited sequence identity, yet TraY binds them with similar affinities. TraY recognition of the two sites was first probed using in vitro footprinting methods. Hydroxyl radical footprinting at both oriT and P(Y) sites indicated that bound TraY protected the DNA backbone bordering three adjacent DNA subsites. Analytical ultracentrifugation results for TraY:oligonucleotide complexes were consistent with two of these subsites being bound cooperatively, and the third being occupied at higher TraY concentrations. Methylation protection and interference footprinting identified several guanine bases contacted by or proximal to bound TraY, most located within these subsites. TraY affinity for variant oriT sequences with base substitutions at or near these guanine bases suggested that two of the three subsites correspond to high-affinity, cooperatively bound imperfect inverted GA(G/T)A repeats. Altering the spacing or orientation of these sites reduced binding. TraY mutant R73A failed to protect two symmetry-related oriT guanine bases in these repeats from methylation, identifying possible direct TraY-DNA contacts. The third subsite appears to be oriented as an imperfect direct repeat with its adjacent subsite, although base substitutions at this subsite did not reduce binding. Although unusual for ribbon-helix-helix proteins, this binding site arrangement occurs at both F TraY sites, consistent with it being functionally relevant.
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Affiliation(s)
- Pamela L Lum
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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13
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Krasilnikova MM, Smirnova EV, Krasilnikov AS, Mirkin SM. A new trick for an old dog: TraY binding to a homopurine-homopyrimidine run attenuates DNA replication. J Mol Biol 2001; 313:271-82. [PMID: 11800556 DOI: 10.1006/jmbi.2001.5059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effects of the d(GA)(n).d(TC)(n) repeat on plasmid replication in Escherichia coli cells were analyzed using electrophoretic analysis of replication intermediates. This repeat appeared to stall the replication fork progression in E. coli strains carrying F' episomes. The potency of replication stalling increased with the repeat's length but did not depend on its orientation relative to the replication origin, or transcription through the repeat. Treatment of E. coli cells with the protein synthesis inhibitor chloramphenicol abolished replication blockage, indicating that protein binding might be responsible for the repeat-caused replication blockage. Concordantly, dimethylsulfate footprinting in vivo revealed methylation protection of all guanine residues within the d(GA)(n).d(TC)(n). Gel retardation assays with crude cell extracts confirmed the presence of a d(GA)(n).d(TC)(n) -binding activity in F', but not F(-), strains. Further, strains cured from the F' episome lost this activity, while F(-) strains that acquired the F' factor via conjugation, acquired d(GA)(n).d(TC)(n)-binding activity as well. Thus, this d(GA)(n).d(TC)(n)-binding protein is encoded by the F' factor. Purification of this protein by affinity chromatography revealed a single polypeptide with an apparent molecular mass of 15.2 kDa. Microsequencing of its two tryptic peptides revealed two perfect matches with the TraY protein, which is encoded by the F factor. Overexpression of an individual TraY protein in the F(-) E. coli strain conveyed d(GA)(n).d(TC)(n)-binding activity in vitro and replication stalling at d(GA)(n).d(TC)(n) repeats in vivo. We conclude that TraY binding to a homopurine-homopyrimidine repeat is responsible for stalling DNA replication. Biological applications of this phenomenon are discussed.
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Affiliation(s)
- M M Krasilnikova
- Department of Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
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14
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Stern JC, Schildbach JF. DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA. Biochemistry 2001; 40:11586-95. [PMID: 11560509 DOI: 10.1021/bi010877q] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The TraI protein has two essential roles in transfer of conjugative plasmid F Factor. As part of a complex of DNA-binding proteins, TraI introduces a site- and strand-specific nick at the plasmid origin of transfer (oriT), cutting the DNA strand that is transferred to the recipient cell. TraI also acts as a helicase, presumably unwinding the plasmid strands prior to transfer. As an essential feature of its nicking activity, TraI is capable of binding and cleaving single-stranded DNA oligonucleotides containing an oriT sequence. The specificity of TraI DNA recognition was examined by measuring the binding of oriT oligonucleotide variants to TraI36, a 36-kD amino-terminal domain of TraI that retains the sequence-specific nucleolytic activity. TraI36 recognition is highly sequence-specific for an 11-base region of oriT, with single base changes reducing affinity by as much as 8000-fold. The binding data correlate with plasmid mobilization efficiencies: plasmids containing sequences bound with lower affinities by TraI36 are transferred between cells at reduced frequencies. In addition to the requirement for high affinity binding to oriT, efficient in vitro nicking and in vivo plasmid mobilization requires a pyrimidine immediately 5' of the nick site. The high sequence specificity of TraI single-stranded DNA recognition suggests that despite its recognition of single-stranded DNA, TraI is capable of playing a major regulatory role in initiation and/or termination of plasmid transfer.
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Affiliation(s)
- J C Stern
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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15
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Karl W, Bamberger M, Zechner EL. Transfer protein TraY of plasmid R1 stimulates TraI-catalyzed oriT cleavage in vivo. J Bacteriol 2001; 183:909-14. [PMID: 11208788 PMCID: PMC94957 DOI: 10.1128/jb.183.3.909-914.2001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of TraY protein on TraI-catalyzed strand scission at the R1 transfer origin (oriT) in vivo was investigated. As expected, the cleavage reaction was not detected in Escherichia coli cells expressing tral and the integration host factor (IHF) in the absence of other transfer proteins. The TraM dependence of strand scission was found to be inversely correlated with the presence of TraY. Thus, the TraY and TraM proteins could each enhance cleaving activity at oriT in the absence of the other. In contrast, no detectable intracellular cleaving activity was exhibited by TraI in an IHF mutant strain despite the additional presence of both TraM and TraY. An essential role for IHF in this reaction in vivo is, therefore, implied. Mobilization experiments employing recombinant R1 oriT constructions and a heterologous conjugative helper plasmid were used to investigate the independent contributions of TraY and TraM to the R1 relaxosome during bacterial conjugation. In accordance with earlier observations, traY was dispensable for mobilization in the presence of traM, but mobilization did not occur in the absence of both traM and traY. Interestingly, although the cleavage assays demonstrate that TraM and TraY independently promote strand scission in vivo, TraM remained essential for mobilization of the R1 origin even in the presence of TraY. These findings suggest that, whereas TraY and TraM function may overlap to a certain extent in the R1 relaxosome, TraM additionally performs a second function that is essential for successful conjugative transmission of plasmid DNA.
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Affiliation(s)
- W Karl
- Institut für Molekularbiologie, Biochemie und Mikrobiologie, Karl-Franzens-Universität Graz, A-8010 Graz, Austria
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16
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Stockwell D, Lelianova V, Thompson T, Dempsey WB. Transcription of the transfer genes traY and traM of the antibiotic resistance plasmid R100-1 is linked. Plasmid 2000; 43:35-48. [PMID: 10610818 DOI: 10.1006/plas.1999.1435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three separate traY deletion mutants of R100-1 were prepared by allele replacement. These mutants retained the ability to transfer at a level 100 times greater than R100 and 1/50 that of the parental R100-1. The mutants were complemented to normal R100-1 transfer levels by pDSP06, a multicopy traY clone. Comparison of transcripts initiated at the traY promoter, P(Y), by primer extension experiments showed that there was no detectable P(Y) activity in R100 and that the level of P(Y) activity in the traY deletion mutants was lower than that in R100-1. Similar measurements performed on RNA from a set of previously described traM deletion mutants showed that those traM deletion mutants that produced more traM and finM (M) transcripts than the parental R100-1 also produced more traY transcripts than R100-1 and that those traM mutants that produced fewer M transcripts than R100-1 also produced fewer traY transcripts than R100-1. We conclude that in R100, TraY regulates P(Y) activity and that transcripts originating in traM affect P(Y) activity.
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Affiliation(s)
- D Stockwell
- Veterans Affairs Medical Center and University of Texas Southwestern Medical Center, Dallas, Texas, 75216, USA
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17
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Lum PL, Schildbach JF. Specific DNA recognition by F Factor TraY involves beta-sheet residues. J Biol Chem 1999; 274:19644-8. [PMID: 10391902 DOI: 10.1074/jbc.274.28.19644] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The F Factor TraY protein is a sequence-specific DNA-binding protein required for efficient conjugal transfer. Genetic and biochemical studies indicate that TraY has two functional roles in conjugation. TraY binds to the PY promoter to up-regulate transcription of tra genes. TraY also binds to the plasmid origin of transfer (oriT), serving as an accessory protein in the nicking of F Factor in preparation for transfer. TraY is thought to belong to the ribbon-helix-helix family of transcription factors. These proteins contact DNA using residues of an antiparallel beta-sheet. We engineered and characterized six TraY mutants each having a single potential beta-sheet DNA contact residue replaced with Ala. Most TraY mutants had significantly reduced affinity for the TraY oriT binding site while possessing near wild-type stability and nonspecific DNA recognition. These results indicate that TraY beta-sheet residues participate in DNA recognition, and support inclusion of TraY in the ribbon-helix-helix family.
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Affiliation(s)
- P L Lum
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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Moncalián G, Valle M, Valpuesta JM, de la Cruz F. IHF protein inhibits cleavage but not assembly of plasmid R388 relaxosomes. Mol Microbiol 1999; 31:1643-52. [PMID: 10209739 DOI: 10.1046/j.1365-2958.1999.01288.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Relaxosomes are specific nucleoprotein structures involved in DNA-processing reactions during bacterial conjugation. In this work, we present evidence indicating that plasmid R388 relaxosomes are composed of origin of transfer (oriT) DNA plus three proteins TrwC relaxase, TrwA nic-cleavage accessory protein and integration host factor (IHF), which acts as a regulatory protein. Protein IHF bound to two sites (ihfA and ihfB) in R388 oriT, as shown by gel retardation and DNase I footprinting analysis. IHF binding in vitro was found to inhibit nic-cleavage, but not TrwC binding to supercoiled DNA. However, no differences in the frequency of R388 conjugation were found between IHF- and IHF+ donor strains. In contrast, examination of plasmid DNA obtained from IHF- strains revealed that R388 was obtained mostly in relaxed form from these strains, whereas it was mostly supercoiled in IHF+ strains. Thus, IHF could have an inhibitory role in the nic-cleavage reaction in vivo. It can be speculated that triggering of conjugative DNA processing during R388 conjugation can be mediated by IHF release from oriT.
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Affiliation(s)
- G Moncalián
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
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19
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Taki K, Abo T, Ohtsubo E. Regulatory mechanisms in expression of the traY-I operon of sex factor plasmid R100: involvement of traJ and traY gene products. Genes Cells 1998; 3:331-45. [PMID: 9734780 DOI: 10.1046/j.1365-2443.1998.00194.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The plasmid R100 encodes tra genes essential for conjugal DNA transfer in Escherichia coli. Genetic evidence suggests that the traJ gene encodes a positive regulator for the traY-I operon, which includes almost all the tra genes located downstream of traJ. The molecular mechanism of regulation by TraJ, however, is not yet understood. traY is the most proximal gene in the traY-I operon. TraY promotes DNA transfer by binding to a site, sbyA, near the origin of transfer. TraY is suggested to have another role in regulation of the traY-I operon, since it binds to two other sites, named sbyB and sbyC, located in the region preceding traY-I. RESULTS Using a traY-lacZ fusion gene, we showed that the traY-I operon was expressed only in the presence of traJ. The TraJ-dependent expression of traY-I required the E. coli arcA gene, which encodes a host factor required for conjugation. TraJ-dependent transcription occurred from a promoter (named pY) located upstream of traY-I. The isolated TraJ protein was found to bind to a dyad symmetry sequence, named sbj (specific binding site of TraJ), which existed in the intergenic region between traJ and traY-I. We also demonstrated that TraY repressed the TraJ-dependent expression of traY-I at the TraY binding sites, sbyB and sbyC, which overlapped with pY. CONCLUSIONS TraJ is a protein which binds to the sbj site in the region upstream of the promoter pY and positively regulates expression of the traY-I operon in the presence of the E. coli arcA gene. Since sbj is located 93bp upstream of pY in the intergenic region between traJ and traY-I, TraJ presumably contacts with a transcription apparatus to promote transcription from pY. TraY, which is known to activate the initiation of conjugal DNA transfer, has a new role in the transcriptional autoregulation of traY-I expression. At levels which are sufficient to initiate conjugal DNA transfer, TraY represses traY-I transcription in the presence of TraJ.
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Affiliation(s)
- K Taki
- Institute of Molecular and Cellular Biosciences, the University of Tokyo, Japan
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20
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Strohmaier H, Noiges R, Kotschan S, Sawers G, Högenauer G, Zechner EL, Koraimann G. Signal transduction and bacterial conjugation: characterization of the role of ArcA in regulating conjugative transfer of the resistance plasmid R1. J Mol Biol 1998; 277:309-16. [PMID: 9514749 DOI: 10.1006/jmbi.1997.1598] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of the two-component response regulator ArcA protein in the transfer of the conjugative resistance plasmid R1 was investigated using a variety of in vivo and in vitro assays. The frequency of conjugal DNA transfer of plasmid R1-16, a derepressed variant of R1, was reduced by four orders of magnitude in an Escherichia coli host with a mutation in the arcA gene. Measurements of mRNAs transcribed from key plasmid transfer genes revealed that the abundance of each of the mRNA species investigated was reduced significantly in an arcA background. Gene fusion studies with the R1 PY promoter, the major promoter of the transfer operon, and a lacZ reporter gene, indicated that arcA is required for maximal expression from this promoter. However, a stimulating effect of arcA could only be detected when the plasmid-specified positive regulator of the transfer genes, traJ, was present. Electrophoretic mobility shift assays were used to demonstrate specific binding of purified ArcA protein and a purified and phosphorylated oligohistidine-tagged ArcA (His6-ArcA) to a DNA fragment containing the PY promoter region. The binding of phosphorylated His6-ArcA to the PY promoter was further characterized by DNase I footprinting. The observed protection pattern was characteristic for ArcA acting as a transcriptional activator.
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Affiliation(s)
- H Strohmaier
- Institut für Mikrobiologie, Universität Graz, Universitätsplatz 2, Graz, A-8010, Austria
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21
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Schildbach JF, Robinson CR, Sauer RT. Biophysical characterization of the TraY protein of Escherichia coli F factor. J Biol Chem 1998; 273:1329-33. [PMID: 9430665 DOI: 10.1074/jbc.273.3.1329] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The TraY protein is required for efficient bacterial conjugation by Escherichia coli F factor. TraY has two functional roles: participating in the "relaxosome," a protein-DNA complex that nicks one strand of the F factor plasmid, and up-regulating transcription from the traYI promoter. The traY gene was cloned, and the TraY protein was expressed, purified, and characterized. TraY has a mixed alpha-helix and beta-sheet secondary structure as judged by its circular dichroism spectrum, is monomeric, and undergoes reversible urea denaturation with delta Gu = 6 kcal/mol at 25 degrees C. The kinetics of protein unfolding and refolding, as measured by changes in fluorescence, are complex, suggesting the presence of intermediates or of heterogeneity in the folding reaction. TraY has been classified as a member of the ribbon-helix-helix family of transcription factors but is unusual in appearing to have tandem repeats of the beta alpha alpha motif in the same polypeptide chain. The data presented here show that folding and assembly of the functional (beta alpha alpha)2 unit occurs as an intramolecular reaction and not by cross-folding between different polypeptide chains.
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Affiliation(s)
- J F Schildbach
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.
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22
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Furuya N, Komano T. Mutational analysis of the R64 oriT region: requirement for precise location of the NikA-binding sequence. J Bacteriol 1997; 179:7291-7. [PMID: 9393692 PMCID: PMC179678 DOI: 10.1128/jb.179.23.7291-7297.1997] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Conjugative DNA transfer of IncI1 plasmid R64 is initiated by the introduction of a site- and strand-specific nick into the origin of transfer (oriT). In R64 oriT, 17-bp (repeat A and B) and 8-bp inverted-repeat sequences with mismatches are located 8 bp away from the nick site. The nicking is mediated by R64 NikA and NikB proteins. To analyze the functional organization of the R64 oriT region, various deletion, insertion, and substitution mutations were introduced into a 92-bp minimal R64 oriT sequence and their effects on oriT function were investigated. This detailed analysis confirms our previous prediction that the R64 oriT region consists of an oriT core sequence and additional sequences necessary for full oriT activity. The oriT core sequence consists of the repeat A sequence, which is recognized by R64 NikA protein, and the nick region sequence, which is conserved among various origins of transfer and is most probably recognized by NikB protein. The oriT core sequence is sufficient for NikAB-mediated oriT-specific nicking. Furthermore, it was shown that the repeat A sequence is essential for localization to a precise position relative to the nick site for oriT function. This seems to be required for the formation of a functional ternary complex consisting of NikA and NikB proteins and oriT DNA. The repeat B sequence and 8-bp inverted repeat sequences are suggested to be required for the termination of DNA transfer.
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Affiliation(s)
- N Furuya
- Department of Biology, Tokyo Metropolitan University, Hachioji, Japan
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23
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Disqué-Kochem C, Dreiseikelmann B. The cytoplasmic DNA-binding protein TraM binds to the inner membrane protein TraD in vitro. J Bacteriol 1997; 179:6133-7. [PMID: 9324263 PMCID: PMC179519 DOI: 10.1128/jb.179.19.6133-6137.1997] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The cytoplasmic protein TraM is one of four essential gene products of the F factor which are involved in DNA transfer after mating pair formation. TraM binds to three specific sites within the oriT region. Besides regulation of its own synthesis, the precise function of TraM during conjugation is not yet known. In the present work, the affinity of TraM to TraD was studied in vitro by an overlay assay and by affinity chromatography. Whether the interaction between TraM and TraD causes a transient or permanent anchoring of the F factor to the site of transfer is discussed. A 35-kDa host membrane protein of yet unknown function also shows affinity to TraM and may be involved in this anchoring process as well.
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Affiliation(s)
- C Disqué-Kochem
- Mikrobiologie/Gentechnologie, Universität Bielefeld, Germany
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24
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Paterson ES, Iyer VN. Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. J Bacteriol 1997; 179:5768-76. [PMID: 9294433 PMCID: PMC179465 DOI: 10.1128/jb.179.18.5768-5776.1997] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The N-type oriT of plasmid pMUR274 was cloned on a 474-bp RsaI-SspI fragment, and the nucleotide sequence was determined. A comparison of the pMUR274 oriT sequence and the sequence of the oriTs of IncN plasmid pCU1 and IncW plasmid R388 demonstrated 57 and 28% identity, respectively. Intramolecular, site-specific recombination between the pCU1 oriT and the oriT of pMUR274 resulted in the formation of a hybrid oriT containing one half of each parental sequence. The junction point of the hybrid occurred within a 10-bp sequence, GCTATACACC, present in both parental sequences and represents the nic site of each oriT. Mutation of the first A or second T residue within the 10-bp junction sequence reduced transfer less than 20-fold, while mutation of either the second or third A residue reduced transfer over 1,000-fold. Site-specific recombination between a wild-type pCU1 oriT and these four mutant pCU1 oriTs demonstrated that nic lies between the second T and second A residues of the 10-bp junction sequence. Site-specific recombination between wild-type and mutant pCU1 oriTs also demonstrated that point mutations to the right of nic reduced both initiation and termination of transfer while point mutations to the left of nic reduced termination but had little or no effect on initiation. A 28-bp deletion within the AT-rich region 39 bases to the right of nic reduced both initiation and termination, while deletion of a 6-bp inverted repeat sequence at the right-most boundary of the minimal oriT region reduced initiation but not termination.
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Affiliation(s)
- E S Paterson
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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25
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Moncalián G, Grandoso G, Llosa M, de la Cruz F. oriT-processing and regulatory roles of TrwA protein in plasmid R388 conjugation. J Mol Biol 1997; 270:188-200. [PMID: 9236121 DOI: 10.1006/jmbi.1997.1082] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
TrwA protein was purified from an overproducing Escherichia coli strain and characterized as a 53 kDa tetrameric DNA-binding protein. Gel shift assays showed that TrwA bound specifically to the oriT sequence of plasmid R388. DNAse I footprinting analysis defined two DNA regions within oriT (sites A and B) that were protected by TrwA. At low TrwA concentrations only region A was protected (K(D) = 4 x 10(-8) M) while region B required higher TrwA concentrations (K(D) = 4 x 10(-7) M). As a result of its binding to oriT, TrwA was found to perform two biochemical activities related to its role in R388 conjugation. First, TrwA binding to oriT resulted in transcriptional repression of the trwABC operon as indicated by its effect on the beta-galactosidase activity of transcriptional fusions in trwB and trwC, and by direct measurement of the trwA mRNA levels by hybridization. This result was further confirmed by the fact that TrwA overexpression resulted in lowered conjugation frequencies. Second, TrwA enhanced the relaxation activity of TrwC in vitro. This effect was correlated to a 10(5)-fold increase in the frequency of conjugation in vivo and was shown to be independent of the regulation of transcription. Thus, TrwA shows functional similarities to protein TraY of F-like plasmids, that could be correlated to a structural similarity in their DNA-binding motifs.
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Affiliation(s)
- G Moncalián
- Departamento de Biologia Molecular, Universidad de Cantabria, Santander, Spain
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26
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Abstract
We have examined the effect of the F plasmid TraY protein on tra gene expression in vivo. Expression was assayed as alkaline phosphatase activity in cells containing a traY phi(traA'-'phoA)hyb operon under traY promoter control. Amber mutations in traY significantly reduced alkaline phosphatase activity. Since nonsense polarity effects were minimal, if they occurred at all, these data provide the first direct evidence that TraY regulates tra gene expression.
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Affiliation(s)
- P M Silverman
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City 73104, USA.
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27
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Nelson WC, Matson SW. The F plasmid traY gene product binds DNA as a monomer or a dimer: structural and functional implications. Mol Microbiol 1996; 20:1179-87. [PMID: 8809770 DOI: 10.1111/j.1365-2958.1996.tb02638.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The F factor traY gene product (TraYp) is a site-specific DNA-binding protein involved in initiation of DNA transfer during bacterial conjugation. The sequence of TraYp exhibits a unique direct-repeat structure predicted to have a ribbon-helix-helix DNA-binding motif in each repeat unit. The stoichiometry of TraYp binding to DNA was determined to further support the hypothesis that TraYp is a member of the ribbon-helix-helix family of DNA-binding proteins. A glutathione-S-transferase-traY fusion protein was purified and shown to possess almost wild-type DNA-binding activity. DNA-binding experiments were performed in which the DNA ligand was incubated with either the fusion protein, the wild-type protein, or both. The results indicate that TraYp can bind DNA as a monomer or a dimer. Thus a TraYp monomer folds into a stable three-dimensional structure similar to that of a dimer of the ribbon-helix-helix proteins Arc or Mnt. A homology model of a TraYp monomer has been constructed using the co-crystal structure of Arc bound to DNA as a template to provide additional support for this conclusion. In addition, we have shown that an origin of the transfer-deletion mutant lacking approximately half of the TraYp-binding site can only be bound by a monomer of TraYp. The functional implications of this result are discussed.
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Affiliation(s)
- W C Nelson
- Department of Biology CB#3280, University of North Carolina at Chapel Hill 27599-3280, USA
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28
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Howard MT, Nelson WC, Matson SW. Stepwise Assembly of a Relaxosome at the F Plasmid Origin of Transfer. J Biol Chem 1995. [DOI: 10.1074/jbc.270.47.28381] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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29
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Nelson WC, Howard MT, Sherman JA, Matson SW. The traY Gene Product and Integration Host Factor Stimulate Escherichia coli DNA Helicase I-catalyzed Nicking at the F Plasmid oriT. J Biol Chem 1995. [DOI: 10.1074/jbc.270.47.28374] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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30
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Di Laurenzio L, Scraba DG, Paranchych W, Frost LS. Studies on the binding of integration host factor (IHF) and TraM to the origin of transfer of the IncFV plasmid pED208. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:726-34. [PMID: 7616964 DOI: 10.1007/bf00290404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The origin of transfer (oriT) of the IncFV plasmid pED208 contains a region with three binding sites for both the plasmid-encoded TraM protein and the integration host factor (IHF) of Escherichia coli, a sequence-specific DNA-binding protein. One region, containing overlapping TraM and IHF binding sites, could be interpreted as containing two binding sites for each protein. Using gel retardation assays, an affinity constant for IHF binding to the three main sites was estimated in the presence and absence of 0.1 M potassium glutamate, which increased the avidity of IHF binding to the weaker sites by two orders of magnitude. DNase I protection analyses and electron microscopy were used to determine the affinity of IHF for oriT-containing DNA in the presence and absence of TraM. The binding of IHF and TraM was found to be non-cooperative by the two techniques employed. Electron microscopy also demonstrated that IHF bent the oriT region in a manner consistent with its previously determined mode of action, while TraM had no discernible effect on the appearance of the DNA. This suggested that IHF and TraM interact with a 295 bp sequence in the oriT region and organize it into a higher order structure that may have a role in the initiation of DNA transfer and control of traM expression.
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Affiliation(s)
- L Di Laurenzio
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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31
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Abstract
The extent of the F plasmid oriT nicking region was determined from the properties of successive substitution mutations in the region from base pair 121 to base pair 174 and from KMnO4 probing of DNA structural distortions induced in vivo by tra gene products. Nicking and transfer assays indicated that the left margin of oriT lies predominantly at the nick site, and that the nicking domain primarily lies within 17 bp to the right of the nick. Some mutants that were proficient for nicking showed reduced frequencies of termination, indicating that oriT nicking does not guarantee efficient termination. DNA in the vicinity of the nick (G137, T138, G140, and T141 on the nicked strand) showed elevated sensitivity to KMnO4 when tra gene products were present in the donor. Bases C145, C146, C147, C149, and G150 on the unnicked strand also became more sensitive to oxidation under tra+ conditions. The bases preferentially oxidized by KMnO4 lie within the nicking domain, as defined by the substitution mutants, and they include dinucleotides that can produce kinks in the DNA. Base pairs in the nicking region are calculated to be more thermodynamically stable than base pairs in the flanking regions.
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Affiliation(s)
- Y Luo
- Department of Biological Sciences, University of Southern California, Los Angeles 90089-1340, USA
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32
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Sherman JA, Matson SW. Escherichia coli DNA helicase I catalyzes a sequence-specific cleavage/ligation reaction at the F plasmid origin of transfer. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)47182-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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33
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Frost LS, Ippen-Ihler K, Skurray RA. Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol Rev 1994; 58:162-210. [PMID: 7915817 PMCID: PMC372961 DOI: 10.1128/mr.58.2.162-210.1994] [Citation(s) in RCA: 274] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacterial conjugation results in the transfer of DNA of either plasmid or chromosomal origin between microorganisms. Transfer begins at a defined point in the DNA sequence, usually called the origin of transfer (oriT). The capacity of conjugative DNA transfer is a property of self-transmissible plasmids and conjugative transposons, which will mobilize other plasmids and DNA sequences that include a compatible oriT locus. This review will concentrate on the genes required for bacterial conjugation that are encoded within the transfer region (or regions) of conjugative plasmids. One of the best-defined conjugation systems is that of the F plasmid, which has been the paradigm for conjugation systems since it was discovered nearly 50 years ago. The F transfer region (over 33 kb) contains about 40 genes, arranged contiguously. These are involved in the synthesis of pili, extracellular filaments which establish contact between donor and recipient cells; mating-pair stabilization; prevention of mating between similar donor cells in a process termed surface exclusions; DNA nicking and transfer during conjugation; and the regulation of expression of these functions. This review is a compendium of the products and other features found in the F transfer region as well as a discussion of their role in conjugation. While the genetics of F transfer have been described extensively, the mechanism of conjugation has proved elusive, in large part because of the low levels of expression of the pilus and the numerous envelope components essential for F plasmid transfer. The advent of molecular genetic techniques has, however, resulted in considerable recent progress. This summary of the known properties of the F transfer region is provided in the hope that it will form a useful basis for future comparison with other conjugation systems.
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Affiliation(s)
- L S Frost
- Department of Microbiology, University of Alberta, Edmonton, Canada
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34
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Abstract
F plasmid traY protein binding to wild-type or deleted regions containing the TraY-binding site, sbyA, was studied in vitro. The principal DNA-protein complex was formed with DNA segments including the sbyA site defined by footprinting and (with lesser affinity) with truncated segments that retained the leftward two-thirds of sbyA. This located the major sequence determinants for TraY binding between bp 204 and 227 on the oriT map. For all sequences tested, bound TraY induced bending of approximately 50 to 55 degrees, and centred between bp 214 and 221. Thermodynamic and mobility analyses indicated that two TraY protomers bind to sbyA. At higher TraY concentrations, additional TraY bound to the left of the sbyA in a region previously shown to bind IHF (site IHF A). TraY binding to this additional site (sbyC) was inhibited by IHF. Sequence similarities shared by sbyA, sbyB, and sbyC may include the critical base pairs for TraY binding.
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Affiliation(s)
- Y Luo
- Department of Biological Sciences, University of Southern California, Los Angeles 90089-1340
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35
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Abstract
DNA sequences within the F plasmid transfer origin (oriT) were tested for their ability to initiate or terminate conjugal transfer. Mutant and wild-type oriT elements were cloned as direct repetitions flanking the rpsL gene on a pBR322-based plasmid, and the frequency of deletion of this segment during matings sponsored by F'lac (F42) with streptomycin-resistant recipients was measured. Shortened oriT elements that lacked adjacent TraM-binding sites allowed efficient initiation and termination. Some truncated oriT segments lacking the TraM-binding sites and the TraY-binding site, sbyA, initiated transfer inefficiently, but nevertheless promoted efficient termination. Removal of TraM-, TraY-, and IHF-binding sites severely reduced both nicking and termination. Point mutations that previously had been reported to prevent nicking caused reduced levels of both initiation and termination. These results indicate that regions of oriT supporting initiation are more extensive than those needed for termination, although some regions are required for both. Moreover, termination can be effective for some mutant loci that do not support efficient nicking.
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Affiliation(s)
- Q Gao
- Department of Biological Sciences, University of Southern California, Los Angeles 90089-1340
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36
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Raumann BE, Brown BM, Sauer RT. Major groove DNA recognition by β-sheets: the ribbon-helix-helix family of gene regulatory proteins. Curr Opin Struct Biol 1994. [DOI: 10.1016/s0959-440x(94)90057-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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