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Cabezón E, Ripoll-Rozada J, Peña A, de la Cruz F, Arechaga I. Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev 2014; 39:81-95. [PMID: 25154632 DOI: 10.1111/1574-6976.12085] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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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52
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Rzechorzek NJ, Blackwood JK, Bray SM, Maman JD, Pellegrini L, Robinson NP. Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea. Nat Commun 2014; 5:5506. [PMID: 25420454 PMCID: PMC4376295 DOI: 10.1038/ncomms6506] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/07/2014] [Indexed: 11/25/2022] Open
Abstract
The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualises at atomic resolution the N-terminal HerA-ATP Synthase (HAS) domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.
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Affiliation(s)
- Neil J Rzechorzek
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - John K Blackwood
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sian M Bray
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Joseph D Maman
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Nicholas P Robinson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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53
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Byrne RT, Schuller JM, Unverdorben P, Förster F, Hopfner KP. Molecular architecture of the HerA-NurA DNA double-strand break resection complex. FEBS Lett 2014; 588:4637-44. [PMID: 25447518 DOI: 10.1016/j.febslet.2014.10.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 11/27/2022]
Abstract
DNA double-strand breaks can be repaired by homologous recombination, during which the DNA ends are long-range resected by helicase-nuclease systems to generate 3' single strand tails. In archaea, this requires the Mre11-Rad50 complex and the ATP-dependent helicase-nuclease complex HerA-NurA. We report the cryo-EM structure of Sulfolobus solfataricus HerA-NurA at 7.4Å resolution and present the pseudo-atomic model of the complex. HerA forms an ASCE hexamer that tightly interacts with a NurA dimer, with each NurA protomer binding three adjacent HerA HAS domains. Entry to NurA's nuclease active sites requires dsDNA to pass through a 23Å wide channel in the HerA hexamer. The structure suggests that HerA is a dsDNA translocase that feeds DNA into the NurA nuclease sites.
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Affiliation(s)
- Robert Thomas Byrne
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Jan Michael Schuller
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Pia Unverdorben
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Straße 25, D-81377 Munich, Germany; Center for Integrated Protein Sciences, Munich, Germany.
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54
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Goessweiner-Mohr N, Eder M, Hofer G, Fercher C, Arends K, Birner-Gruenberger R, Grohmann E, Keller W. Structure of the double-stranded DNA-binding type IV secretion protein TraN from Enterococcus. ACTA ACUST UNITED AC 2014; 70:2376-89. [PMID: 25195751 DOI: 10.1107/s1399004714014187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/17/2014] [Indexed: 11/10/2022]
Abstract
Conjugative transfer through type IV secretion multiprotein complexes is the most important means of spreading antimicrobial resistance. Plasmid pIP501, frequently found in clinical Enterococcus faecalis and Enterococcus faecium isolates, is the first Gram-positive (G+) conjugative plasmid for which self-transfer to Gram-negative (G-) bacteria has been demonstrated. The pIP501-encoded type IV secretion system (T4SS) protein TraN localizes to the cytoplasm and shows specific DNA binding. The specific DNA-binding site upstream of the pIP501 origin of transfer (oriT) was identified by a novel footprinting technique based on exonuclease digestion and sequencing, suggesting TraN to be an accessory protein of the pIP501 relaxase TraA. The structure of TraN was determined to 1.35 Å resolution. It revealed an internal dimer fold with antiparallel β-sheets in the centre and a helix-turn-helix (HTH) motif at both ends. Surprisingly, structurally related proteins (excisionases from T4SSs of G+ conjugative transposons and transcriptional regulators of the MerR family) resembling only one half of TraN were found. Thus, TraN may be involved in the early steps of pIP501 transfer, possibly triggering pIP501 TraA relaxase activity by recruiting the relaxosome to the assembled mating pore.
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Affiliation(s)
| | - Markus Eder
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Gerhard Hofer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Christian Fercher
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Karsten Arends
- Robert Koch Institute Berlin, Nordufer 20, 13353 Berlin, Germany
| | - Ruth Birner-Gruenberger
- Institute for Pathology and Omics Center Graz, Medical University Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
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55
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Low HH, Gubellini F, Rivera-Calzada A, Braun N, Connery S, Dujeancourt A, Lu F, Redzej A, Fronzes R, Orlova EV, Waksman G. Structure of a type IV secretion system. Nature 2014; 508:550-553. [PMID: 24670658 PMCID: PMC3998870 DOI: 10.1038/nature13081] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/27/2014] [Indexed: 02/08/2023]
Abstract
Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification of human cells. Given the complex choreography of the substrate through the secretion apparatus, the molecular mechanism of the type IV secretion system has proved difficult to dissect in the absence of structural data for the entire machinery. Here we use electron microscopy to reconstruct the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid. We show that eight proteins assemble in an intricate stoichiometric relationship to form an approximately 3 megadalton nanomachine that spans the entire cell envelope. The structure comprises an outer membrane-associated core complex connected by a central stalk to a substantial inner membrane complex that is dominated by a battery of 12 VirB4 ATPase subunits organized as side-by-side hexameric barrels. Our results show a secretion system with markedly different architecture, and consequently mechanism, to other known bacterial secretion systems.
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Affiliation(s)
- Harry H. Low
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
| | - Francesca Gubellini
- Institut Pasteur, G5 Biologie structurale de la sécrétion bactérienne and UMR 3528-CNRS, 25 rue du Docteur Roux, 75015 Paris, France
| | - Angel Rivera-Calzada
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
| | - Nathalie Braun
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
| | - Sarah Connery
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
| | - Annick Dujeancourt
- Institut Pasteur, G5 Biologie structurale de la sécrétion bactérienne and UMR 3528-CNRS, 25 rue du Docteur Roux, 75015 Paris, France
| | - Fang Lu
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
| | - Adam Redzej
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
| | - Rémi Fronzes
- Institut Pasteur, G5 Biologie structurale de la sécrétion bactérienne and UMR 3528-CNRS, 25 rue du Docteur Roux, 75015 Paris, France
| | - Elena V. Orlova
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
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56
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Trokter M, Felisberto-Rodrigues C, Christie PJ, Waksman G. Recent advances in the structural and molecular biology of type IV secretion systems. Curr Opin Struct Biol 2014; 27:16-23. [PMID: 24709394 PMCID: PMC4182333 DOI: 10.1016/j.sbi.2014.02.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/28/2014] [Indexed: 11/28/2022]
Abstract
We describe the first structure of a type IV secretion (T4S) system. The previously reported core complex is mostly an outer membrane complex. We describe the newly discovered inner membrane complex and the stalk. We discuss proposed translocation mechanisms of T4S systems. We discuss the regulation of pilus biogenesis and substrate transfer by T4S systems.
Bacteria use type IV secretion (T4S) systems to deliver DNA and protein substrates to a diverse range of prokaryotic and eukaryotic target cells. T4S systems have great impact on human health, as they are a major source of antibiotic resistance spread among bacteria and are central to infection processes of many pathogens. Therefore, deciphering the structure and underlying translocation mechanism of T4S systems is crucial to facilitate development of new drugs. The last five years have witnessed considerable progress in unraveling the structure of T4S system subassemblies, notably that of the T4S system core complex, a large 1 MegaDalton (MDa) structure embedded in the double membrane of Gram-negative bacteria and made of 3 of the 12 T4S system components. However, the recent determination of the structure of ∼3 MDa assembly of 8 of these components has revolutionized our views of T4S system architecture and opened up new avenues of research, which are discussed in this review.
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Affiliation(s)
- Martina Trokter
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Catarina Felisberto-Rodrigues
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, 6431 Fannin Street, Houston, TX 77030, USA
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK.
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57
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Goessweiner-Mohr N, Fercher C, Arends K, Birner-Gruenberger R, Laverde-Gomez D, Huebner J, Grohmann E, Keller W. The type IV secretion protein TraK from the Enterococcus conjugative plasmid pIP501 exhibits a novel fold. ACTA ACUST UNITED AC 2014; 70:1124-35. [PMID: 24699656 DOI: 10.1107/s1399004714001606] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 01/22/2014] [Indexed: 11/11/2022]
Abstract
Conjugative plasmid transfer presents a serious threat to human health as the most important means of spreading antibiotic resistance and virulence genes among bacteria. The required direct cell-cell contact is established by a multi-protein complex, the conjugative type IV secretion system (T4SS). The conjugative core complex spans the cellular envelope and serves as a channel for macromolecular secretion. T4SSs of Gram-negative (G-) origin have been studied in great detail. In contrast, T4SSs of Gram-positive (G+) bacteria have only received little attention thus far, despite the medical relevance of numerous G+ pathogens (e.g. enterococci, staphylococci and streptococci). This study provides structural information on the type IV secretion (T4S) protein TraK of the G+ broad host range Enterococcus conjugative plasmid pIP501. The crystal structure of the N-terminally truncated construct TraKΔ was determined to 3.0 Å resolution and exhibits a novel fold. Immunolocalization demonstrated that the protein localizes to the cell wall facing towards the cell exterior, but does not exhibit surface accessibility. Circular dichroism, dynamic light scattering and size-exclusion chromatography confirmed the protein to be a monomer. With the exception of proteins from closely related T4SSs, no significant sequence or structural relatives were found. This observation marks the protein as a very exclusive, specialized member of the pIP501 T4SS.
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Affiliation(s)
- Nikolaus Goessweiner-Mohr
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Christian Fercher
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | | | - Ruth Birner-Gruenberger
- Institute for Pathology and Center of Medical Research, Medical University Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Diana Laverde-Gomez
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Johannes Huebner
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Walter Keller
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
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58
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Christie PJ, Whitaker N, González-Rivera C. Mechanism and structure of the bacterial type IV secretion systems. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1578-91. [PMID: 24389247 DOI: 10.1016/j.bbamcr.2013.12.019] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 01/25/2023]
Abstract
The bacterial type IV secretion systems (T4SSs) translocate DNA and protein substrates to bacterial or eukaryotic target cells generally by a mechanism dependent on direct cell-to-cell contact. The T4SSs encompass two large subfamilies, the conjugation systems and the effector translocators. The conjugation systems mediate interbacterial DNA transfer and are responsible for the rapid dissemination of antibiotic resistance genes and virulence determinants in clinical settings. The effector translocators are used by many Gram-negative bacterial pathogens for delivery of potentially hundreds of virulence proteins to eukaryotic cells for modulation of different physiological processes during infection. Recently, there has been considerable progress in defining the structures of T4SS machine subunits and large machine subassemblies. Additionally, the nature of substrate translocation sequences and the contributions of accessory proteins to substrate docking with the translocation channel have been elucidated. A DNA translocation route through the Agrobacterium tumefaciens VirB/VirD4 system was defined, and both intracellular (DNA ligand, ATP energy) and extracellular (phage binding) signals were shown to activate type IV-dependent translocation. Finally, phylogenetic studies have shed light on the evolution and distribution of T4SSs, and complementary structure-function studies of diverse systems have identified adaptations tailored for novel functions in pathogenic settings. This review summarizes the recent progress in our understanding of the architecture and mechanism of action of these fascinating machines, with emphasis on the 'archetypal' A. tumefaciens VirB/VirD4 T4SS and related conjugation systems. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Peter J Christie
- Department of Microbiology and Molecular Genetics, UT-Houston Medical School, 6431 Fannin, JFB1.765, Houston, TX 77030, USA.
| | - Neal Whitaker
- Department of Microbiology and Molecular Genetics, UT-Houston Medical School, 6431 Fannin, JFB1.765, Houston, TX 77030, USA
| | - Christian González-Rivera
- Department of Microbiology and Molecular Genetics, UT-Houston Medical School, 6431 Fannin, JFB1.765, Houston, TX 77030, USA
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59
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Chang JH, Desveaux D, Creason AL. The ABCs and 123s of bacterial secretion systems in plant pathogenesis. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:317-45. [PMID: 24906130 DOI: 10.1146/annurev-phyto-011014-015624] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Bacteria have many export and secretion systems that translocate cargo into and across biological membranes. Seven secretion systems contribute to pathogenicity by translocating proteinaceous cargos that can be released into the extracellular milieu or directly into recipient cells. In this review, we describe these secretion systems and how their complexities and functions reflect differences in the destinations, states, functions, and sizes of the translocated cargos as well as the architecture of the bacterial cell envelope. We examine the secretion systems from the perspective of pathogenic bacteria that proliferate within plant tissues and highlight examples of translocated proteins that contribute to the infection and disease of plant hosts.
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Affiliation(s)
- Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331; ,
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60
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Structural organisation of the type IV secretion systems. Curr Opin Microbiol 2013; 17:24-31. [PMID: 24581689 PMCID: PMC3969286 DOI: 10.1016/j.mib.2013.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/06/2013] [Accepted: 11/07/2013] [Indexed: 02/04/2023]
Abstract
Type IV secretion systems are nanomachines that transport substrates through bacterial membranes. Structures of components obtained by crystallography are presented. Higher resolution core complex structures revealed localisations of protein components. Docking of known and modelled atomic structures uncovers interactions between components.
Type IV secretion (T4S) systems are large dynamic nanomachines that transport DNAs and/or proteins through the membranes of bacteria. Because of their complexity and multi-protein organisation, T4S systems have been extremely challenging to study structurally. However in the past five years significant milestones have been achieved by X-ray crystallography and cryo-electron microscopy. This review describes some of the more recent advances: the structures of some of the protein components of the T4S systems and the complete core complex structure that was determined using electron microscopy.
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61
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Allen SJ, Schwartz AM, Bush MF. Effects of Polarity on the Structures and Charge States of Native-Like Proteins and Protein Complexes in the Gas Phase. Anal Chem 2013; 85:12055-61. [DOI: 10.1021/ac403139d] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samuel J. Allen
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Alicia M. Schwartz
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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62
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Goessweiner-Mohr N, Arends K, Keller W, Grohmann E. Conjugative type IV secretion systems in Gram-positive bacteria. Plasmid 2013; 70:289-302. [PMID: 24129002 PMCID: PMC3913187 DOI: 10.1016/j.plasmid.2013.09.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 09/21/2013] [Accepted: 09/30/2013] [Indexed: 01/17/2023]
Abstract
The conjugative transfer mechanism of broad-host-range, Enterococcus sex pheromone and Clostridium plasmids is reviewed. Comparisons with Gram-negative type IV secretion systems are presented. The current understanding of the unique Streptomyces double stranded DNA transfer mechanism is reviewed.
Bacterial conjugation presents the most important means to spread antibiotic resistance and virulence factors among closely and distantly related bacteria. Conjugative plasmids are the mobile genetic elements mainly responsible for this task. All the genetic information required for the horizontal transmission is encoded on the conjugative plasmids themselves. Two distinct concepts for horizontal plasmid transfer in Gram-positive bacteria exist, the most prominent one transports single stranded plasmid DNA via a multi-protein complex, termed type IV secretion system, across the Gram-positive cell envelope. Type IV secretion systems have been found in virtually all unicellular Gram-positive bacteria, whereas multicellular Streptomycetes seem to have developed a specialized system more closely related to the machinery involved in bacterial cell division and sporulation, which transports double stranded DNA from donor to recipient cells. This review intends to summarize the state of the art of prototype systems belonging to the two distinct concepts; it focuses on protein key players identified so far and gives future directions for research in this emerging field of promiscuous interbacterial transport.
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63
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Abstract
Secretion of effectors across bacterial membranes is usually mediated by large multisubunit complexes. In most cases, the secreted effectors are virulent factors normally associated to pathogenic diseases. The biogenesis of these secretion systems and the transport of the effectors are processes that require energy. This energy could be directly obtained by using the proton motive force, but in most cases the energy associated to these processes is derived from ATP hydrolysis. Here, a description of the machineries involved in generating the energy required for system biogenesis and substrate transport by type II, III and IV secretion systems is provided, with special emphasis on highlighting the structural similarities and evolutionary relationships among the secretion ATPases.
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Affiliation(s)
- Alejandro Peña
- Departamento de Biología Molecular, Universidad de Cantabria, UC-CSIC-SODERCAN, Santander, Spain
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64
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Functional interactions of VirB11 traffic ATPases with VirB4 and VirD4 molecular motors in type IV secretion systems. J Bacteriol 2013; 195:4195-201. [PMID: 23852869 DOI: 10.1128/jb.00437-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pilus biogenesis and substrate transport by type IV secretion systems require energy, which is provided by three molecular motors localized at the base of the secretion channel. One of these motors, VirB11, belongs to the superfamily of traffic ATPases, which includes members of the type II secretion system and the type IV pilus and archaeal flagellar assembly apparatus. Here, we report the functional interactions between TrwD, the VirB11 homolog of the conjugative plasmid R388, and TrwK and TrwB, the motors involved in pilus biogenesis and DNA transport, respectively. Although these interactions remained standing upon replacement of the traffic ATPase by a homolog from a phylogenetically related conjugative system, namely, TraG of plasmid pKM101, this homolog could not replace the TrwD function for DNA transfer. This result suggests that VirB11 works as a switch between pilus biogenesis and DNA transport and reinforces a mechanistic model in which VirB11 proteins act as traffic ATPases by regulating both events in type IV secretion systems.
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65
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A putative transmembrane leucine zipper of agrobacterium VirB10 is essential for t-pilus biogenesis but not type IV secretion. J Bacteriol 2013; 195:3022-34. [PMID: 23625845 DOI: 10.1128/jb.00287-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Agrobacterium tumefaciens VirB/VirD4 type IV secretion system is composed of a translocation channel and an extracellular T pilus. Bitopic VirB10, the VirB7 lipoprotein, and VirB9 interact to form a cell envelope-spanning structural scaffold termed the "core complex" that is required for the assembly of both structures. The related pKM101-encoded core complex is composed of 14 copies each of these VirB homologs, and the transmembrane (TM) α helices of VirB10-like TraF form a 55-Å-diameter ring at the inner membrane. Here, we report that the VirB10 TM helix possesses two types of putative dimerization motifs, a GxxxA (GA4) motif and two leucine (Leu1, Leu2) zippers. Mutations in the Leu1 motif disrupted T-pilus biogenesis, but these or other mutations in the GA4 or Leu2 motif did not abolish substrate transfer. Replacement of the VirB10 TM domain with a nondimerizing poly-Leu/Ala TM domain sequence also blocked pilus production but not substrate transfer or formation of immunoprecipitable complexes with the core subunits VirB7 and VirB9 and the substrate receptor VirD4. The VirB10 TM helix formed weak homodimers in Escherichia coli, as determined with the TOXCAT assay, whereas replacement of the VirB10 TM helix with the strongly dimerizing TM helix from glycophorin A blocked T-pilus biogenesis in A. tumefaciens. Our findings support a model in which VirB10's TM helix contributes to the assembly or activity of the translocation channel as a weakly self-interacting membrane anchor but establishes a heteromeric TM-TM helix interaction via its Leu1 motif that is critical for T-pilus biogenesis.
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66
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Structural independence of conjugative coupling protein TrwB from its Type IV secretion machinery. Plasmid 2013; 70:146-53. [PMID: 23583564 DOI: 10.1016/j.plasmid.2013.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/27/2013] [Accepted: 03/30/2013] [Indexed: 11/21/2022]
Abstract
The stability of components of multiprotein complexes often relies on the presence of the functional complex. To assess structural dependence among the components of the R388 Type IV secretion system (T4SS), the steady-state level of several Trw proteins was determined in the absence of other Trw components. While several Trw proteins were affected by the lack of others, we found that the coupling protein TrwB is not affected by the absence of other T4SS components, nor did its absence alter significantly the levels of integral components of the complex, underscoring the independent role of the coupling protein on the T4SS architecture. The cytoplasmic ATPases TrwK (VirB4) and TrwD (VirB11) were affected by the absence of several core complex components, while the pilus component TrwJ (VirB5) required the presence of all other Trw proteins (except for TrwB) to be detectable. Overall, the results delineate a possible assembly pathway for the T4SS of R388. We have also tested structural complementation of TrwD (VirB11) and TrwJ (VirB5) by their homologues in the highly related Trw system of Bartonella tribocorum (Bt). The results reveal a correlation with the functional complementation data previously reported.
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Bhatty M, Laverde Gomez JA, Christie PJ. The expanding bacterial type IV secretion lexicon. Res Microbiol 2013; 164:620-39. [PMID: 23542405 DOI: 10.1016/j.resmic.2013.03.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/01/2012] [Accepted: 02/05/2013] [Indexed: 02/06/2023]
Abstract
The bacterial type IV secretion systems (T4SSs) comprise a biologically diverse group of translocation systems functioning to deliver DNA or protein substrates from donor to target cells generally by a mechanism dependent on establishment of direct cell-to-cell contact. Members of one T4SS subfamily, the conjugation systems, mediate the widespread and rapid dissemination of antibiotic resistance and virulence traits among bacterial pathogens. Members of a second subfamily, the effector translocators, are used by often medically-important pathogens to deliver effector proteins to eukaryotic target cells during the course of infection. Here we summarize our current understanding of the structural and functional diversity of T4SSs and of the evolutionary processes shaping this diversity. We compare mechanistic and architectural features of T4SSs from Gram-negative and -positive species. Finally, we introduce the concept of the 'minimized' T4SSs; these are systems composed of a conserved set of 5-6 subunits that are distributed among many Gram-positive and some Gram-negative species.
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Affiliation(s)
- Minny Bhatty
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin, Houston, TX 77030, USA
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68
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Structure of a bacterial type IV secretion core complex at subnanometre resolution. EMBO J 2013; 32:1195-204. [PMID: 23511972 PMCID: PMC3630358 DOI: 10.1038/emboj.2013.58] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/19/2013] [Indexed: 01/28/2023] Open
Abstract
Type IV secretion (T4S) systems are able to transport DNAs and/or proteins through the membranes of bacteria. They form large multiprotein complexes consisting of 12 proteins termed VirB1-11 and VirD4. VirB7, 9 and 10 assemble into a 1.07 MegaDalton membrane-spanning core complex (CC), around which all other components assemble. This complex is made of two parts, the O-layer inserted in the outer membrane and the I-layer inserted in the inner membrane. While the structure of the O-layer has been solved by X-ray crystallography, there is no detailed structural information on the I-layer. Using high-resolution cryo-electron microscopy and molecular modelling combined with biochemical approaches, we determined the I-layer structure and located its various components in the electron density. Our results provide new structural insights on the CC, from which the essential features of T4S system mechanisms can be derived. The core of the bacterial type IV secretion system consists of the O-layer in the outer membrane and the inner-membrane I-layer. The first high-resolution cryo-electron microscopy structure of the I-layer provides insights into T4SS secretion mechanism.
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69
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Goessweiner-Mohr N, Grumet L, Pavkov-Keller T, Birner-Gruenberger R, Grohmann E, Keller W. Crystallization and preliminary structure determination of the transfer protein TraM from the Gram-positive conjugative plasmid pIP501. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:178-83. [PMID: 23385763 PMCID: PMC3564624 DOI: 10.1107/s1744309113000134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/02/2013] [Indexed: 11/07/2023]
Abstract
The major means of horizontal gene spread (e.g. of antibiotic resistance) is conjugative plasmid transfer. It presents a serious threat especially for hospitalized and immuno-suppressed patients, as it can lead to the accelerated spread of bacteria with multiple antibiotic resistances. Detailed information about the process is available only for bacteria of Gram-negative (G-) origin and little is known about the corresponding mechanisms in Gram-positive (G+) bacteria. Here we present the purification, biophysical characterization, crystallization and preliminary structure determination of the TraM C-terminal domain (TraMΔ, comprising residues 190-322 of the full-length protein), a putative transfer protein from the G+ conjugative model plasmid pIP501. The crystals diffracted to 2.5 Å resolution and belonged to space group P1, with unit-cell parameters a = 39.21, b = 54.98, c = 93.47 Å, α = 89.91, β = 86.44, γ = 78.63° and six molecules per asymmetric unit. The preliminary structure was solved by selenomethionine single-wavelength anomalous diffraction.
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Affiliation(s)
- Nikolaus Goessweiner-Mohr
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Styria, Austria
| | - Lukas Grumet
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Styria, Austria
| | - Tea Pavkov-Keller
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Styria, Austria
| | - Ruth Birner-Gruenberger
- Institute of Pathology and Center of Medical Research – Core Facility Mass Spectrometry, Medical University Graz, Stiftingtalstrasse 24, 8010 Graz, Styria, Austria
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Str. 55, Freiburg, 79106, Germany
| | - Walter Keller
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Styria, Austria
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70
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Abstract
Bacteria have evolved several secretion machineries to bring about transport of various virulence factors, nutrients, nucleic acids and cell-surface appendages that are essential for their pathogenesis. T4S (Type IV secretion) systems are versatile secretion systems found in various Gram-negative and Gram-positive bacteria and in few archaea. They are large multisubunit translocons secreting a diverse array of substrates varying in size and nature from monomeric proteins to nucleoprotein complexes. T4S systems have evolved from conjugation machineries and are implicated in antibiotic resistance gene transfer and transport of virulence factors in Legionella pneumophila causing Legionnaires’ disease, Brucella suis causing brucellosis and Helicobacter pylori causing gastroduodenal diseases. The best-studied are the Agrobacterium tumefaciens VirB/D4 and the Escherichia coli plasmid pKM101 T4S systems. Recent structural advances revealing the cryo-EM (electron microscopy) structure of the core translocation assembly and high-resolution structure of the outer-membrane pore of T4S systems have made paradigm shifts in the understanding of T4S systems. The present paper reviews the advances made in biochemical and structural studies and summarizes our current understanding of the molecular architecture of this mega-assembly.
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71
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Goessweiner-Mohr N, Grumet L, Arends K, Pavkov-Keller T, Gruber CC, Gruber K, Birner-Gruenberger R, Kropec-Huebner A, Huebner J, Grohmann E, Keller W. The 2.5 Å structure of the enterococcus conjugation protein TraM resembles VirB8 type IV secretion proteins. J Biol Chem 2013; 288:2018-28. [PMID: 23188825 PMCID: PMC3548508 DOI: 10.1074/jbc.m112.428847] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/20/2012] [Indexed: 11/24/2022] Open
Abstract
Conjugative plasmid transfer is the most important means of spreading antibiotic resistance and virulence genes among bacteria and therefore presents a serious threat to human health. The process requires direct cell-cell contact made possible by a multiprotein complex that spans cellular membranes and serves as a channel for macromolecular secretion. Thus far, well studied conjugative type IV secretion systems (T4SS) are of Gram-negative (G-) origin. Although many medically relevant pathogens (e.g., enterococci, staphylococci, and streptococci) are Gram-positive (G+), their conjugation systems have received little attention. This study provides structural information for the transfer protein TraM of the G+ broad host range Enterococcus conjugative plasmid pIP501. Immunolocalization demonstrated that the protein localizes to the cell wall. We then used opsonophagocytosis as a novel tool to verify that TraM was exposed on the cell surface. In these assays, antibodies generated to TraM recruited macrophages and enabled killing of pIP501 harboring Enteroccocus faecalis cells. The crystal structure of the C-terminal, surface-exposed domain of TraM was determined to 2.5 Å resolution. The structure, molecular dynamics, and cross-linking studies indicated that a TraM trimer acts as the biological unit. Despite the absence of sequence-based similarity, TraM unexpectedly displayed a fold similar to the T4SS VirB8 proteins from Agrobacterium tumefaciens and Brucella suis (G-) and to the transfer protein TcpC from Clostridium perfringens plasmid pCW3 (G+). Based on the alignments of secondary structure elements of VirB8-like proteins from mobile genetic elements and chromosomally encoded T4SS from G+ and G- bacteria, we propose a new classification scheme of VirB8-like proteins.
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Affiliation(s)
- Nikolaus Goessweiner-Mohr
- From the Karl-Franzens-University Graz, Institute of Molecular Biosciences, Structural Biology, 8010 Graz, Austria
| | - Lukas Grumet
- From the Karl-Franzens-University Graz, Institute of Molecular Biosciences, Structural Biology, 8010 Graz, Austria
| | - Karsten Arends
- the Technical University Berlin, Environmental Microbiology/Genetics, 10587 Berlin, Germany
- the Robert Koch Institute, 13086 Berlin, Germany
| | - Tea Pavkov-Keller
- the Austrian Centre of Industrial Biotechnology GmbH, 8010 Graz, Austria
| | | | - Karl Gruber
- From the Karl-Franzens-University Graz, Institute of Molecular Biosciences, Structural Biology, 8010 Graz, Austria
| | - Ruth Birner-Gruenberger
- the Medical University Graz, Institute for Pathology and Center of Medical Research, Core Facility Mass Spectrometry, 8010 Graz, Austria, and
| | - Andrea Kropec-Huebner
- the Division of Infectious Diseases, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Johannes Huebner
- the Division of Infectious Diseases, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Elisabeth Grohmann
- the Technical University Berlin, Environmental Microbiology/Genetics, 10587 Berlin, Germany
- the Division of Infectious Diseases, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Walter Keller
- From the Karl-Franzens-University Graz, Institute of Molecular Biosciences, Structural Biology, 8010 Graz, Austria
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Goessweiner-Mohr N, Fercher C, Abajy MY, Grohmann E, Keller W. Crystallization and first data collection of the putative transfer protein TraN from the Gram-positive conjugative plasmid pIP501. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1402-5. [PMID: 23143259 PMCID: PMC3515391 DOI: 10.1107/s174430911204184x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/05/2012] [Indexed: 11/13/2022]
Abstract
Conjugative plasmid transfer is the most important route for the spread of resistance and virulence genes among bacteria. Consequently, bacteria carrying conjugative plasmids are a substantial threat to human health, especially hospitalized patients. Whilst detailed information about the process has been obtained for Gram-negative type-4 secretion systems, little is known about the corresponding mechanisms in Gram-positive (G+) bacteria. The successful purification and crystallization of the putative transfer protein TraN from the G+ conjugative model plasmid pIP501 of Enterococcus faecalis are presented. Native crystals diffracted to 1.8 Å resolution on a synchrotron beamline. The crystals belonged to space group P2(1), with unit-cell parameters a=32.88, b=54.94, c=57.71 Å, β=91.89° and two molecules per asymmetric unit.
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Affiliation(s)
- Nikolaus Goessweiner-Mohr
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Christian Fercher
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Mohammad Yaser Abajy
- Environmental Microbiology/Genetics, Technical University Berlin, Franklinstrasse 28/29, 10587 Berlin, Germany
| | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Walter Keller
- Institute for Molecular Biosciences, Karl-Franzens-University Graz, Humboldtstrasse 50/III, 8010 Graz, Austria
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Peña A, Matilla I, Martín-Benito J, Valpuesta JM, Carrascosa JL, de la Cruz F, Cabezón E, Arechaga I. The hexameric structure of a conjugative VirB4 protein ATPase provides new insights for a functional and phylogenetic relationship with DNA translocases. J Biol Chem 2012; 287:39925-32. [PMID: 23035111 DOI: 10.1074/jbc.m112.413849] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
VirB4 proteins are ATPases essential for pilus biogenesis and protein transport in type IV secretion systems. These proteins contain a motor domain that shares structural similarities with the motor domains of DNA translocases, such as the VirD4/TrwB conjugative coupling proteins and the chromosome segregation pump FtsK. Here, we report the three-dimensional structure of full-length TrwK, the VirB4 homologue in the conjugative plasmid R388, determined by single-particle electron microscopy. The structure consists of a hexameric double ring with a barrel-shaped structure. The C-terminal half of VirB4 proteins shares a striking structural similarity with the DNA translocase TrwB. Docking the atomic coordinates of the crystal structures of TrwB and FtsK into the EM map revealed a better fit for FtsK. Interestingly, we have found that like TrwB, TrwK is able to bind DNA with a higher affinity for G4 quadruplex structures than for single-stranded DNA. Furthermore, TrwK exerts a dominant negative effect on the ATPase activity of TrwB, which reflects an interaction between the two proteins. Our studies provide new insights into the structure-function relationship and the evolution of these DNA and protein translocases.
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Affiliation(s)
- Alejandro Peña
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-SODERCAN, Santander, Spain
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Guglielmini J, de la Cruz F, Rocha EPC. Evolution of conjugation and type IV secretion systems. Mol Biol Evol 2012; 30:315-31. [PMID: 22977114 PMCID: PMC3548315 DOI: 10.1093/molbev/mss221] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic exchange by conjugation is responsible for the spread of resistance, virulence,
and social traits among prokaryotes. Recent works unraveled the functioning of the
underlying type IV secretion systems (T4SS) and its distribution and recruitment for other
biological processes (exaptation), notably pathogenesis. We analyzed the phylogeny of key
conjugation proteins to infer the evolutionary history of conjugation and T4SS. We show
that single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) conjugation, while both
based on a key AAA+ ATPase, diverged before the last common ancestor of
bacteria. The two key ATPases of ssDNA conjugation are monophyletic, having diverged at an
early stage from dsDNA translocases. Our data suggest that ssDNA conjugation arose first
in diderm bacteria, possibly Proteobacteria, and then spread to other bacterial phyla,
including bacterial monoderms and Archaea. Identifiable T4SS fall within the eight
monophyletic groups, determined by both taxonomy and structure of the cell envelope.
Transfer to monoderms might have occurred only once, but followed diverse adaptive paths.
Remarkably, some Firmicutes developed a new conjugation system based on an atypical
relaxase and an ATPase derived from a dsDNA translocase. The observed evolutionary rates
and patterns of presence/absence of specific T4SS proteins show that conjugation systems
are often and independently exapted for other functions. This work brings a natural basis
for the classification of all kinds of conjugative systems, thus tackling a problem that
is growing as fast as genomic databases. Our analysis provides the first global picture of
the evolution of conjugation and shows how a self-transferrable complex multiprotein
system has adapted to different taxa and often been recruited by the host. As conjugation
systems became specific to certain clades and cell envelopes, they may have biased the
rate and direction of gene transfer by conjugation within prokaryotes.
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Affiliation(s)
- Julien Guglielmini
- Département Génomes et Génétique, Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.
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