1
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Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped, cold-tolerant bacterium, designated F01003T, was isolated from soil sampled near Happiness Bay on the west coast of Antarctica. Strain F01003T was found to grow at 4-30 °C (optimum, 25 °C), pH 5.5-8.0 (pH 6.5-7.0) and in the presence of 0-1 % NaCl (0 %, w/v). Cells were oxidase-positive and catalase-positive. Strain F01003T contained menaquinone 7 (MK-7) as the predominant respiratory quinone. The main cellular fatty acids included summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0. Phosphatidylethanolamine and an unidentified aminolipid were identified as the major polar lipids. The DNA G+C content of strain F01003T was 44.8 mol%. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence revealed that strain F01003T was most closely related to the genus Mucilaginibacter and exhibited the highest sequence similarity to Mucilaginibacter phyllosphaerae LMG 29118T (97.3 %). On the basis of the evidence presented in this polyphasic taxonomic study, strain F01003T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibactergilvus sp. nov. is proposed. The type strain is F01003T (=KCTC 62991T=CCTCC AB 2019023T).
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Affiliation(s)
- Yu-Qi Yan
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Yong-Xin Hao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Rui-Han He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University, Weihai 264209, PR China.,SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
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2
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Heilers JH, Reiners J, Heller EM, Golzer A, Smits SHJ, van der Does C. DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island. Nucleic Acids Res 2019; 47:8136-8153. [PMID: 31276596 PMCID: PMC6736028 DOI: 10.1093/nar/gkz577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022] Open
Abstract
Relaxases of the MOBH family are often found on large plasmids, genetic islands and integrative conjugative elements. Many members of this family contain an N-terminal relaxase domain (TraI_2) followed by a disordered middle part and a C-terminal domain of unknown function (TraI_2_C). The TraI_2 domain contains two putative metal-binding motifs, an HD domain motif and an alternative 3H motif. TraI, encoded within the gonococcal genetic island of Neisseria gonorrhoeae, is the prototype of the MOBH family. SAXS experiments showed that TraI_2 and TraI_2_C form globular structures separated by an extended middle domain. The TraI_2 domain cleaves oriT-ssDNA in a site-specific Mn2+ or Co2+ dependent manner. The minimal oriT encompasses 50 nucleotides, requires an inverted repeat 3′ of the nic-site and several nucleotides around nic for efficient cleavage. Surprisingly, no stable covalent relaxase-DNA intermediate was observed. Mutagenesis of conserved tyrosines showed that cleavage was abolished in the Y212A mutant, whereas the Y212F and Y212H mutants retained residual activity. The HD and the alternative 3H motifs were essential for cleavage and the HD domain residues D162 and D267 for metal ion binding. We propose that the active site binds two metal ions, one in a high-affinity and one in a low-affinity site.
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Affiliation(s)
- Jan-Hendrik Heilers
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
| | - Jens Reiners
- Biochemie I, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University, 40225 Düsseldorf, Germany
| | | | - Annika Golzer
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
| | - Sander H J Smits
- Biochemie I, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Chris van der Does
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
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3
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Krishna B, Gubensäk N, Wagner GE, Zechner E, Raffl S, Becker W, Schrank E, Zangger K. 1H, 13C, 15N resonance assignment of the C-terminal domain of the bifunctional enzyme TraI of plasmid R1. Biomol NMR Assign 2019; 13:121-125. [PMID: 30617945 PMCID: PMC6439144 DOI: 10.1007/s12104-018-9863-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Transfer of genetic material is the main mechanism underlying the spread of antibiotic resistance and virulence factors within the bacterial community. Conjugation is one such process by which the genetic material is shared from one bacterium to another. The DNA substrate is processed and prepared for transfer by a multi-protein complex called the relaxosome .The relaxosome of plasmid R1 possesses the most crucial enzyme TraI which, both nicks and unwinds the dsDNA substrate. TraI comprises 1765 residues and multiple functional domains, including those catalyzing the DNA trans-esterase (relaxase) on the dsDNA designated for a conjugative transfer and DNA helicase activities. Structural and functional studies have been reported for most of the TraI except the C-terminal domain spanning from residue 1630 to 1765. This region is the least understood part of TraI and is thought to be highly disordered and flexible. This region, being intrinsically disordered, is hypothesized to be serving as an interacting platform for other proteins involved in this DNA transfer initiation mechanism. In this work, we report the 1H, 13C, 15N resonance assignment of this region as well as the secondary structure information based on the backbone chemical shifts.
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Affiliation(s)
| | - Nina Gubensäk
- Institute of Chemistry, University of Graz, 8010, Graz, Austria
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010, Graz, Austria
| | - Ellen Zechner
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, 8010, Graz, Austria
| | - Sandra Raffl
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, 8010, Graz, Austria
| | - Walter Becker
- Institute of Chemistry, University of Graz, 8010, Graz, Austria
| | - Evelyne Schrank
- Institute of Chemistry, University of Graz, 8010, Graz, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, 8010, Graz, Austria.
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4
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Kiss J, Szabó M, Hegyi A, Douard G, Praud K, Nagy I, Olasz F, Cloeckaert A, Doublet B. Identification and Characterization of oriT and Two Mobilization Genes Required for Conjugative Transfer of Salmonella Genomic Island 1. Front Microbiol 2019; 10:457. [PMID: 30894848 PMCID: PMC6414798 DOI: 10.3389/fmicb.2019.00457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/20/2019] [Indexed: 11/13/2022] Open
Abstract
The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resistance to critically important antibiotics among enteric bacteria. Even though many aspects of SGI1 mobilization by IncA and IncC plasmids have been explored, the basic transfer elements such as oriT and self-encoded mobilization proteins remain undiscovered. Here we describe the mobilization region of SGI1 that is well conserved throughout the family and carries the oriT SGI1 and two genes, mpsA and mpsB (originally annotated as S020 and S019, respectively) that are essential for the conjugative transfer of SGI1. OriT SGI1, which is located in the vicinity of the two mobilization genes proved to be a 125-bp GC-rich sequence with several important inverted repeat motifs. The mobilization proteins MpsA and MpsB are expressed from a bicistronic mRNA, although MpsB can be produced from its own mRNA as well. The protein structure predictions imply that MpsA belongs to the lambda tyrosine recombinase family, while MpsB resembles the N-terminal core DNA binding domains of these enzymes. The results suggest that MpsA may act as an atypical relaxase, which needs MpsB for SGI1 transfer. Although the helper plasmid-encoded relaxase proved not to be essential for SGI1 transfer, it appeared to be important to achieve the high transfer rate of the island observed with the IncA/IncC-SGI1 system.
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Affiliation(s)
- János Kiss
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Mónika Szabó
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Anna Hegyi
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary.,ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - Gregory Douard
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - Karine Praud
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - István Nagy
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Ferenc Olasz
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Axel Cloeckaert
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - Benoît Doublet
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
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5
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Shala-Lawrence A, Bragagnolo N, Nowroozi-Dayeni R, Kheyson S, Audette GF. The interaction of TraW and TrbC is required to facilitate conjugation in F-like plasmids. Biochem Biophys Res Commun 2018; 503:2386-2392. [PMID: 29966652 DOI: 10.1016/j.bbrc.2018.06.166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 12/20/2022]
Abstract
Bacterial conjugation, such as that mediated by the E. coli F plasmid, is a main mechanism driving bacterial evolution. Two important proteins required for F-pilus assembly and DNA transfer proficiency are TraW and TrbC. As members of a larger complex, these proteins assemble into a type IV secretion system and are essential components of pore formation and mating pair stabilization between the donor and the recipient cells. In the current report, we demonstrate the physical interaction of TraW and TrbC, show that TraW preferentially interacts with the N-terminal domain of TrbC, and that this interaction is important in restoring conjugation in traW/trbC knockouts.
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Affiliation(s)
- Agnesa Shala-Lawrence
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Nicholas Bragagnolo
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Roksana Nowroozi-Dayeni
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Sasha Kheyson
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Gerald F Audette
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada.
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6
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Abstract
All plasmids that spread by conjugative transfer encode a relaxase. That includes plasmids that encode the type IV secretion machinery necessary to mediate cell to cell transfer, as well as mobilizable plasmids that exploit the existence of other plasmids' type IV secretion machinery to enable their own lateral spread. Relaxases perform key functions in plasmid transfer by first binding to their cognate plasmid as part of a multiprotein complex called the relaxosome, which is then specifically recognized by a receptor protein at the opening of the secretion channel. Relaxases catalyze a site- and DNA-strand-specific cleavage reaction on the plasmid then pilot the single strand of plasmid DNA through the membrane-spanning type IV secretion channel as a nucleoprotein complex. In the recipient cell, relaxases help terminate the transfer process efficiently and stabilize the incoming plasmid DNA. Here, we review the well-studied MOBF family of relaxases to describe the biochemistry of these versatile enzymes and integrate current knowledge into a mechanistic model of plasmid transfer in Gram-negative bacteria.
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7
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Abstract
Bacterial conjugation is one of the main mechanisms for horizontal gene transfer. It constitutes a key element in the dissemination of antibiotic resistance and virulence genes to human pathogenic bacteria. DNA transfer is mediated by a membrane-associated macromolecular machinery called Type IV secretion system (T4SS). T4SSs are involved not only in bacterial conjugation but also in the transport of virulence factors by pathogenic bacteria. Thus, the search for specific inhibitors of different T4SS components opens a novel approach to restrict plasmid dissemination. This review highlights recent biochemical and structural findings that shed new light on the molecular mechanisms of DNA and protein transport by T4SS. Based on these data, a model for pilus biogenesis and substrate transfer in conjugative systems is proposed. This model provides a renewed view of the mechanism that might help to envisage new strategies to curb the threating expansion of antibiotic resistance.
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Affiliation(s)
- Elena Cabezón
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Jorge Ripoll-Rozada
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Alejandro Peña
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
| | - Ignacio Arechaga
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, (Universidad de Cantabria, CSIC) Santander, Spain
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8
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McLaughlin KJ, Nash RP, Redinbo MR. Unique helicase determinants in the essential conjugative TraI factor from Salmonella enterica serovar Typhimurium plasmid pCU1. J Bacteriol 2014; 196:3082-90. [PMID: 24936053 DOI: 10.1128/JB.01496-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread development of multidrug-resistant bacteria is a major health emergency. Conjugative DNA plasmids, which harbor a wide range of antibiotic resistance genes, also encode the protein factors necessary to orchestrate the propagation of plasmid DNA between bacterial cells through conjugative transfer. Successful conjugative DNA transfer depends on key catalytic components to nick one strand of the duplex DNA plasmid and separate the DNA strands while cell-to-cell transfer occurs. The TraI protein from the conjugative Salmonella plasmid pCU1 fulfills these key catalytic roles, as it contains both single-stranded DNA-nicking relaxase and ATP-dependent helicase domains within a single, 1,078-residue polypeptide. In this work, we unraveled the helicase determinants of Salmonella pCU1 TraI through DNA binding, ATPase, and DNA strand separation assays. TraI binds DNA substrates with high affinity in a manner influenced by nucleic acid length and the presence of a DNA hairpin structure adjacent to the nick site. TraI selectively hydrolyzes ATP, and mutations in conserved helicase motifs eliminate ATPase activity. Surprisingly, the absence of a relatively short (144-residue) domain at the extreme C terminus of the protein severely diminishes ATP-dependent strand separation. Collectively, these data define the helicase motifs of the conjugative factor TraI from Salmonella pCU1 and reveal a previously uncharacterized C-terminal functional domain that uncouples ATP hydrolysis from strand separation activity.
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9
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Clark NJ, Raththagala M, Wright NT, Buenger EA, Schildbach JF, Krueger S, Curtis JE. Structures of TraI in solution. J Mol Model 2014; 20:2308. [PMID: 24898939 DOI: 10.1007/s00894-014-2308-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Bacterial conjugation, a DNA transfer mechanism involving transport of one plasmid strand from donor to recipient, is driven by plasmid-encoded proteins. The F TraI protein nicks one F plasmid strand, separates cut and uncut strands, and pilots the cut strand through a secretion pore into the recipient. TraI is a modular protein with identifiable nickase, ssDNA-binding, helicase and protein-protein interaction domains. While domain structures corresponding to roughly 1/3 of TraI have been determined, there has been no comprehensive structural study of the entire TraI molecule, nor an examination of structural changes to TraI upon binding DNA. Here, we combine solution studies using small-angle scattering and circular dichroism spectroscopy with molecular Monte Carlo and molecular dynamics simulations to assess solution behavior of individual and groups of domains. Despite having several long (>100 residues) apparently disordered or highly dynamic regions, TraI folds into a compact molecule. Based on the biophysical characterization, we have generated models of intact TraI. These data and the resulting models have provided clues to the regulation of TraI function.
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Affiliation(s)
- Nicholas J Clark
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD, 20899, USA
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10
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Redzej A, Ilangovan A, Lang S, Gruber CJ, Topf M, Zangger K, Zechner EL, Waksman G. Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems. Mol Microbiol 2013; 89:324-33. [PMID: 23710762 PMCID: PMC3912908 DOI: 10.1111/mmi.12275] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2013] [Indexed: 01/26/2023]
Abstract
Relaxases are proteins responsible for the transfer of plasmid and chromosomal DNA from one bacterium to another during conjugation. They covalently react with a specific phosphodiester bond within DNA origin of transfer sequences, forming a nucleo-protein complex which is subsequently recruited for transport by a plasmid-encoded type IV secretion system. In previous work we identified the targeting translocation signals presented by the conjugative relaxase TraI of plasmid R1. Here we report the structure of TraI translocation signal TSA. In contrast to known translocation signals we show that TSA is an independent folding unit and thus forms a bona fide structural domain. This domain can be further divided into three subdomains with striking structural homology with helicase subdomains of the SF1B family. We also show that TSA is part of a larger vestigial helicase domain which has lost its helicase activity but not its single-stranded DNA binding capability. Finally, we further delineate the binding site responsible for translocation activity of TSA by targeting single residues for mutations. Overall, this study provides the first evidence that translocation signals can be part of larger structural scaffolds, overlapping with translocation-independent activities.
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Affiliation(s)
- Adam Redzej
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
| | - Aravindan Ilangovan
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
| | - Silvia Lang
- University of Graz, Institute of Molecular BiosciencesHumboldtstrasse 50, 8010, Graz, Austria
| | - Christian J Gruber
- University of Graz, Institute of Molecular BiosciencesHumboldtstrasse 50, 8010, Graz, Austria
| | - Maya Topf
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
| | - Klaus Zangger
- University of Graz, Institute of ChemistryHeinrichstrasse 28, 8010, Graz, Austria
| | - Ellen L Zechner
- University of Graz, Institute of Molecular BiosciencesHumboldtstrasse 50, 8010, Graz, Austria
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, UCL and BirkbeckMalet Street, London, WC1E 7HX, UK
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11
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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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12
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Wright NT, Raththagala M, Hemmis CW, Edwards S, Curtis JE, Krueger S, Schildbach JF. Solution structure and small angle scattering analysis of TraI (381-569). Proteins 2012; 80:2250-61. [PMID: 22611034 DOI: 10.1002/prot.24114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 04/15/2012] [Accepted: 05/02/2012] [Indexed: 12/12/2022]
Abstract
TraI, the F plasmid-encoded nickase, is a 1756 amino acid protein essential for conjugative transfer of plasmid DNA from one bacterium to another. Although crystal structures of N- and C-terminal domains of F TraI have been determined, central domains of the protein are structurally unexplored. The central region (between residues 306 and 1520) is known to both bind single-stranded DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Here, we show that the ssDNA binding site is located between residues 381 and 858, and we also present the high-resolution solution structure of the N-terminus of this region (residues 381-569). This fragment folds into a four-strand parallel β sheet surrounded by α helices, and it resembles the structure of the N-terminus of helicases such as RecD and RecQ despite little sequence similarity. The structure supports the model that F TraI resulted from duplication of a RecD-like domain and subsequent specialization of domains into the more N-terminal ssDNA binding domain and the more C-terminal domain containing helicase motifs. In addition, we provide evidence that the nickase and ssDNA binding domains of TraI are held close together by an 80-residue linker sequence that connects the two domains. These results suggest a possible physical explanation for the apparent negative cooperativity between the nickase and ssDNA binding domain.
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Affiliation(s)
- Nathan T Wright
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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13
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Cheng Y, Frazier M, Lu F, Cao X, Redinbo MR. Crystal structure of the plant epigenetic protein arginine methyltransferase 10. J Mol Biol 2011; 414:106-22. [PMID: 21986201 PMCID: PMC3217299 DOI: 10.1016/j.jmb.2011.09.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/20/2011] [Accepted: 09/24/2011] [Indexed: 01/07/2023]
Abstract
Protein arginine methyltransferase 10 (PRMT10) is a type I arginine methyltransferase that is essential for regulating flowering time in Arabidopsis thaliana. We present a 2.6 Å resolution crystal structure of A. thaliana PRMT 10 (AtPRMT10) in complex with a reaction product, S-adenosylhomocysteine. The structure reveals a dimerization arm that is 12-20 residues longer than PRMT structures elucidated previously; as a result, the essential AtPRMT10 dimer exhibits a large central cavity and a distinctly accessible active site. We employ molecular dynamics to examine how dimerization facilitates AtPRMT10 motions necessary for activity, and we show that these motions are conserved in other PRMT enzymes. Finally, functional data reveal that the 10 N-terminal residues of AtPRMT10 influence substrate specificity, and that enzyme activity is dependent on substrate protein sequences distal from the methylation site. Taken together, these data provide insights into the molecular mechanism of AtPRMT10, as well as other members of the PRMT family of enzymes. They highlight differences between AtPRMT10 and other PRMTs but also indicate that motions are a conserved element of PRMT function.
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Affiliation(s)
- Yuan Cheng
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Monica Frazier
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Falong Lu
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China,Graduate School, Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Matthew R. Redinbo
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Correspondence: Matthew R. Redinbo, Ph.D., Department of Chemistry, Campus Box 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. Tel.:919-843-8910, Fax: 919-962-2388,
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