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Peng Y, Lu J, Wong JJW, Edwards RA, Frost LS, Mark Glover JN. Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM. J Mol Biol 2014; 426:3783-3795. [PMID: 25284757 DOI: 10.1016/j.jmb.2014.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/04/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022]
Abstract
The conjugative transfer of bacterial F plasmids relies on TraM, a plasmid-encoded protein that recognizes multiple DNA sites to recruit the plasmid to the conjugative pore. In spite of the high degree of amino acid sequence conservation between TraM proteins, many of these proteins have markedly different DNA binding specificities that ensure the selective recruitment of a plasmid to its cognate pore. Here we present the structure of F TraM RHH (ribbon-helix-helix) domain bound to its sbmA site. The structure indicates that a pair of TraM tetramers cooperatively binds an underwound sbmA site containing 12 base pairs per turn. The sbmA is composed of 4 copies of a 5-base-pair motif, each of which is recognized by an RHH domain. The structure reveals that a single conservative amino acid difference in the RHH β-ribbon between F and pED208 TraM changes its specificity for its cognate 5-base-pair sequence motif. Specificity is also dictated by the positioning of 2-base-pair spacer elements within sbmA; in F sbmA, the spacers are positioned between motifs 1 and 2 and between motifs 3 and 4, whereas in pED208 sbmA, there is a single spacer between motifs 2 and 3. We also demonstrate that a pair of F TraM tetramers can cooperatively bind its sbmC site with an affinity similar to that of sbmA in spite of a lack of sequence similarity between these DNA elements. These results provide a basis for the prediction of the DNA binding properties of the family of TraM proteins.
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Affiliation(s)
- Yun Peng
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Jun Lu
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Joyce J W Wong
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ross A Edwards
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Laura S Frost
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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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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Wang S, Leng XY, Yan YB. The Benefits of Being β-Crystallin Heteromers: βB1-Crystallin Protects βA3-Crystallin against Aggregation during Co-refolding. Biochemistry 2011; 50:10451-61. [DOI: 10.1021/bi201375p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Sha Wang
- State Key
Laboratory of Biomembrane and Membrane Biotechnology, School of Life
Sciences, Tsinghua University, Beijing
100084, China
| | - Xiao-Yao Leng
- State Key
Laboratory of Biomembrane and Membrane Biotechnology, School of Life
Sciences, Tsinghua University, Beijing
100084, China
| | - Yong-Bin Yan
- State Key
Laboratory of Biomembrane and Membrane Biotechnology, School of Life
Sciences, Tsinghua University, Beijing
100084, China
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Wong JJW, Lu J, Edwards RA, Frost LS, Glover JNM. Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM. Nucleic Acids Res 2011; 39:6775-88. [PMID: 21565799 PMCID: PMC3159463 DOI: 10.1093/nar/gkr296] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The conjugative transfer of F-like plasmids such as F, R1, R100 and pED208, between bacterial cells requires TraM, a plasmid-encoded DNA-binding protein. TraM tetramers bridge the origin of transfer (oriT) to a key component of the conjugative pore, the coupling protein TraD. Here we show that TraM recognizes a high-affinity DNA-binding site, sbmA, as a cooperative dimer of tetramers. The crystal structure of the TraM-sbmA complex from the plasmid pED208 shows that binding cooperativity is mediated by DNA kinking and unwinding, without any direct contact between tetramers. Sequence-specific DNA recognition is carried out by TraM's N-terminal ribbon-helix-helix (RHH) domains, which bind DNA in a staggered arrangement. We demonstrate that both DNA-binding specificity, as well as selective interactions between TraM and the C-terminal tail of its cognate TraD mediate conjugation specificity within the F-like family of plasmids. The ability of TraM to cooperatively bind DNA without interaction between tetramers leaves the C-terminal TraM tetramerization domains free to make multiple interactions with TraD, driving recruitment of the plasmid to the conjugative pore.
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Affiliation(s)
- Joyce J W Wong
- Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Silanskas A, Foss M, Wende W, Urbanke C, Lagunavicius A, Pingoud A, Siksnys V. Photocaged variants of the MunI and PvuII restriction enzymes. Biochemistry 2011; 50:2800-7. [PMID: 21410225 DOI: 10.1021/bi2000609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Regulation of proteins by light is a new and promising strategy for the external control of biological processes. In this study, we demonstrate the ability to regulate the catalytic activity of the MunI and PvuII restriction endonucleases with light. We used two different approaches to attach a photoremovable caging compound, 2-nitrobenzyl bromide (NBB), to functionally important regions of the two enzymes. First, we covalently attached a caging molecule at the dimer interface of MunI to generate an inactive monomer. Second, we attached NBB at the DNA binding site of the single-chain variant of PvuII (scPvuII) to prevent binding and cleavage of the DNA substrate. Upon removal of the caging group by UV irradiation, nearly 50% of the catalytic activity of MunI and 80% of the catalytic activity of PvuII could be restored.
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Affiliation(s)
- Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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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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Lu J, Wong JJW, Edwards RA, Manchak J, Frost LS, Glover JNM. Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation. Mol Microbiol 2008; 70:89-99. [PMID: 18717787 DOI: 10.1111/j.1365-2958.2008.06391.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
F plasmid-mediated bacterial conjugation requires interactions between a relaxosome component, TraM, and the coupling protein TraD, a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. Here we present the crystal structure of the C-terminal tail of TraD bound to the TraM tetramerization domain, the first structural evidence of relaxosome-coupling protein interactions. The structure reveals the TraD C-terminal peptide bound to each of four symmetry-related grooves on the surface of the TraM tetramer. Extensive protein-protein interactions were observed between the two proteins. Mutational analysis indicates that these interactions are specific and required for efficient F conjugation in vivo. Our results suggest that specific interactions between the C-terminal tail of TraD and the TraM tetramerization domain might lead to more generalized interactions that stabilize the relaxosome-coupling protein complex in preparation for conjugative DNA transfer.
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Affiliation(s)
- Jun Lu
- Departments of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Lu J, Edwards RA, Wong JJW, Manchak J, Scott PG, Frost LS, Glover JNM. Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM. EMBO J 2006; 25:2930-9. [PMID: 16710295 PMCID: PMC1500842 DOI: 10.1038/sj.emboj.7601151] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2005] [Accepted: 04/27/2006] [Indexed: 11/09/2022] Open
Abstract
TraM is essential for F plasmid-mediated bacterial conjugation, where it binds to the plasmid DNA near the origin of transfer, and recognizes a component of the transmembrane DNA transfer complex, TraD. Here we report the 1.40 A crystal structure of the TraM core tetramer (TraM58-127). TraM58-127 is a compact eight-helical bundle, in which the N-terminal helices from each protomer interact to form a central, parallel four-stranded coiled-coil, whereas each C-terminal helix packs in an antiparallel arrangement around the outside of the structure. Four protonated glutamic acid residues (Glu88) are packed in a hydrogen-bonded arrangement within the central four-helix bundle. Mutational and biophysical analyses indicate that this protonated state is in equilibrium with a deprotonated tetrameric form characterized by a lower helical content at physiological pH and temperature. Comparison of TraM to its Glu88 mutants predicted to stabilize the helical structure suggests that the protonated state is the active form for binding TraD in conjugation.
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Affiliation(s)
- Jun Lu
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ross A Edwards
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joyce J W Wong
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jan Manchak
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Paul G Scott
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Laura S Frost
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7. Tel.: +1 780 492 2136; Fax: +1 780 492 0886; E-mail:
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Zaremba M, Sasnauskas G, Urbanke C, Siksnys V. Conversion of the Tetrameric Restriction Endonuclease Bse634I into a Dimer: Oligomeric Structure–Stability–Function Correlations. J Mol Biol 2005; 348:459-78. [PMID: 15811381 DOI: 10.1016/j.jmb.2005.02.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Revised: 02/02/2005] [Accepted: 02/20/2005] [Indexed: 11/30/2022]
Abstract
The Bse634I restriction endonuclease is a tetramer and belongs to the type IIF subtype of restriction enzymes. It requires two recognition sites for its optimal activity and cleaves plasmid DNA with two sites much faster than a single-site DNA. We show that disruption of the tetramerisation interface of Bse634I by site-directed mutagenesis converts the tetrameric enzyme into a dimer. Dimeric W228A mutant cleaves plasmid DNA containing one or two sites with the same efficiency as the tetramer cleaves the two-site plasmid. Hence, the catalytic activity of the Bse634I tetramer on a single-site DNA is down-regulated due to the cross-talking interactions between the individual dimers. The autoinhibition within the Bse634I tetramer is relieved by bridging two DNA copies into the synaptic complex that promotes fast and concerted cleavage at both sites. Cleavage analysis of the oligonucleotide attached to the solid support revealed that Bse634I is able to form catalytically competent synaptic complexes by bridging two molecules of the cognate DNA, cognate DNA-miscognate DNA and cognate DNA-product DNA. Taken together, our data demonstrate that a single W228A mutation converts a tetrameric type IIF restriction enzyme Bse634I into the orthodox dimeric type IIP restriction endonuclease. However, the stability of the dimer towards chemical denaturants, thermal inactivation and proteolytic degradation are compromised.
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Affiliation(s)
- M Zaremba
- Institute of Biotechnology, Graiciuno 8, Vilnius LT-02241, Lithuania
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Lu J, Zhao W, Frost LS. Mutational analysis of TraM correlates oligomerization and DNA binding with autoregulation and conjugative DNA transfer. J Biol Chem 2004; 279:55324-33. [PMID: 15509578 DOI: 10.1074/jbc.m409352200] [Citation(s) in RCA: 14] [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
F plasmid TraM, an autoregulatory homotetramer, is essential for F plasmid bacterial conjugative transfer, one of the major mechanisms for horizontal gene dissemination. TraM cooperatively binds to three sites (sbmA, -B, and -C) near the origin of transfer in the F plasmid. To examine whether or not tetramerization of TraM is required for autoregulation and F conjugation, we used a two-plasmid system to screen for autoregulation-defective traM mutants generated by random PCR mutagenesis. A total of 72 missense mutations in TraM affecting autoregulation were selected, all of which also resulted in a loss of TraM function during F conjugation. Mutational analysis of TraM defined three regions important for F conjugation, including residues 3-10 (region I), 31-53 (region II), and 80-121 (region III); in addition, residues 3-47 were also important for the immunoreactivity of TraM. Biochemical analysis of mutant proteins indicated that region I defined a DNA binding domain that was not involved in tetramerization, whereas regions II and III were important for both tetramerization and efficient DNA binding. Mutations in region III affected the cooperativity of binding of TraM to sbmA, -B, and -C. Our results suggest that tetramerization is important for specific DNA binding, which, in turn, is essential for traM autoregulation and F conjugation. These findings support the hypothesis that TraM functions as a "signaling" factor that triggers DNA transport during F conjugation.
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Affiliation(s)
- Jun Lu
- Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Zaremba M, Urbanke C, Halford SE, Siksnys V. Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the phospholipase D superfamily. J Mol Biol 2004; 336:81-92. [PMID: 14741205 DOI: 10.1016/j.jmb.2003.12.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The BfiI endonuclease cleaves DNA at fixed positions downstream of an asymmetric sequence. Unlike other restriction enzymes, it functions without metal ions. The N-terminal half of BfiI is similar to Nuc, an EDTA-resistant nuclease from Salmonella typhimurium that belongs to the phosphoplipase D superfamily. Nuc is a dimer with one active site at its subunit interface, as is BfiI, but it cuts DNA non-specifically. BfiI was cleaved by thermolysin into an N-terminal domain, which forms a dimer with non-specific nuclease activity, and a C-terminal domain, which lacks catalytic activity but binds specifically to the recognition sequence as a monomer. On denaturation with guanidinium, BfiI underwent two unfolding transitions: one at a relatively low concentration of guanidinium, to a dimeric non-specific nuclease; a second at a higher concentration, to an inactive monomer. The isolated C-terminal domain unfolded at the first (relatively low) concentration, the isolated N-terminal at the second. Hence, BfiI consists of two physically separate domains, with catalytic and dimerisation functions in the N terminus and DNA recognition functions in the C terminus. It is the first example of a restriction enzyme generated by the evolutionary fusion of a DNA recognition domain to a phosphodiesterase from the phospholipase D superfamily. BfiI may consist of three structural units: a stable central core with the active site, made from two copies of the N-terminal domain, flanked by relatively unstable C-terminal domains, that each bind a copy of the recognition sequence.
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