1
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Dugelay C, Gueguen-Chaignon V, Terradot L. Structural Analyses of Bacterial Effectors by X-Ray Crystallography. Methods Mol Biol 2024; 2715:485-502. [PMID: 37930546 DOI: 10.1007/978-1-0716-3445-5_29] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
X-ray crystallography is a method of choice to determine and analyze protein structures. Although large complexes are challenging to crystallize and cryo-electron microscopy is thus better suited for these, crystallography can still be efficient in solving structures of single components of secretion systems or effectors. Many of the different steps leading to structure determination by X-ray crystallography have been automatized. Here, we describe a generic approach to obtain crystals, solve the structure of a given protein, and perform a preliminary analysis, highlighting novel and efficient possibilities offered by automatization and contribution of Alpha Fold 2 structure prediction.
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Affiliation(s)
- Chloé Dugelay
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, UMR5086, Lyon, France
| | - Virginie Gueguen-Chaignon
- Protein Science Facility, SFR Biosciences, Centre National de la Recherche Scientifique UAR3444, Université de Lyon, Lyon, France
| | - Laurent Terradot
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, UMR5086, Lyon, France.
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2
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Blanc M, Lettl C, Guérin J, Vieille A, Furler S, Briand-Schumacher S, Dreier B, Bergé C, Plückthun A, Vadon-Le Goff S, Fronzes R, Rousselle P, Fischer W, Terradot L. Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system. PLoS Pathog 2023; 19:e1011368. [PMID: 37155700 DOI: 10.1371/journal.ppat.1011368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/18/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The bacterial human pathogen Helicobacter pylori produces a type IV secretion system (cagT4SS) to inject the oncoprotein CagA into gastric cells. The cagT4SS external pilus mediates attachment of the apparatus to the target cell and the delivery of CagA. While the composition of the pilus is unclear, CagI is present at the surface of the bacterium and required for pilus formation. Here, we have investigated the properties of CagI by an integrative structural biology approach. Using Alpha Fold 2 and Small Angle X-ray scattering, it was found that CagI forms elongated dimers mediated by rod-shape N-terminal domains (CagIN) prolonged by globular C-terminal domains (CagIC). Three Designed Ankyrin Repeat Proteins (DARPins) K2, K5 and K8 selected against CagI interacted with CagIC with subnanomolar affinities. The crystal structures of the CagI:K2 and CagI:K5 complexes were solved and identified the interfaces between the molecules, thereby providing a structural explanation for the difference in affinity between the two binders. Purified CagI and CagIC were found to interact with adenocarcinoma gastric (AGS) cells, induced cell spreading and the interaction was inhibited by K2. The same DARPin inhibited CagA translocation by up to 65% in AGS cells while inhibition levels were 40% and 30% with K8 and K5, respectively. Our study suggests that CagIC plays a key role in cagT4SS-mediated CagA translocation and that DARPins targeting CagI represent potent inhibitors of the cagT4SS, a crucial risk factor for gastric cancer development.
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Affiliation(s)
- Marine Blanc
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jérémy Guérin
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Anaïs Vieille
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Sven Furler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Célia Bergé
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sandrine Vadon-Le Goff
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Rémi Fronzes
- European Institute of Chemistry and Biology, CNRS UMR 5234 Microbiologie Fondamentale et Pathogénicité, Univ. Bordeaux, Pessac, France
| | - Patricia Rousselle
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
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3
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Jurėnas D, Rey M, Byrne D, Chamot-Rooke J, Terradot L, Cascales E. Salmonella antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of EF-Tu P-loop. Nucleic Acids Res 2022; 50:13114-13127. [PMID: 36484105 PMCID: PMC9825190 DOI: 10.1093/nar/gkac1162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 11/11/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Rearrangement hot spot (Rhs) proteins are members of the broad family of polymorphic toxins. Polymorphic toxins are modular proteins composed of an N-terminal region that specifies their mode of secretion into the medium or into the target cell, a central delivery module, and a C-terminal domain that has toxic activity. Here, we structurally and functionally characterize the C-terminal toxic domain of the antibacterial Rhsmain protein, TreTu, which is delivered by the type VI secretion system of Salmonella enterica Typhimurium. We show that this domain adopts an ADP-ribosyltransferase fold and inhibits protein synthesis by transferring an ADP-ribose group from NAD+ to the elongation factor Tu (EF-Tu). This modification is specifically placed on the side chain of the conserved D21 residue located on the P-loop of the EF-Tu G-domain. Finally, we demonstrate that the TriTu immunity protein neutralizes TreTu activity by acting like a lid that closes the catalytic site and traps the NAD+.
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Affiliation(s)
- Dukas Jurėnas
- Correspondence may also be addressed to Dukas Jurėnas.
| | - Martial Rey
- Mass Spectrometry for Biology Unit, Université Paris Cité, Institut Pasteur, CNRS, UAR 2024, 75015 Paris, France
| | - Deborah Byrne
- Protein Expression Facility, Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, 13009 Marseille, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Université Paris Cité, Institut Pasteur, CNRS, UAR 2024, 75015 Paris, France
| | - Laurent Terradot
- Laboratory of Molecular Microbiology and Structural Biochemistry, Institut de Biologie et Chimie des Protéines, Centre National de la Recherche Scientifique, Université de Lyon, UMR 5086, 69367 Lyon, France
| | - Eric Cascales
- To whom correspondence should be addressed. Tel: +33 491164462; Fax: +33 491712124;
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4
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Abstract
Bacterial genomes are highly plastic and evolve rapidly by acquiring new genetic information through horizontal gene transfer mechanisms. Capturing DNA transfer by conjugation between bacterial cells in real time is relevant to address bacterial genomes' dynamic architecture comprehensively. Here, we describe a method allowing the direct visualization of bacterial conjugation in live cells, including the fluorescent labeling of the conjugative pilus and the monitoring of plasmid DNA transfer from donor to recipient cells.
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Affiliation(s)
- Kelly Goldlust
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon Cedex 07, France
| | - Agathe Couturier
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon Cedex 07, France
| | - Laurent Terradot
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon Cedex 07, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon Cedex 07, France.
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5
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Zehnder J, Cadalbert R, Terradot L, Ernst M, Böckmann A, Güntert P, Meier BH, Wiegand T. Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase. Chemistry 2021; 27:7745-7755. [PMID: 33822417 PMCID: PMC8252064 DOI: 10.1002/chem.202100462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.
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Affiliation(s)
- Johannes Zehnder
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Riccardo Cadalbert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Matthias Ernst
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Peter Güntert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
- Institute of Biophysical ChemistryCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt am Main60438Frankfurt am MainGermany
- Department of ChemistryTokyo Metropolitan UniversityHachiojiTokyo1920397Japan
| | - Beat H. Meier
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas Wiegand
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
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6
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Wiegand T, Schledorn M, Malär AA, Cadalbert R, Däpp A, Terradot L, Meier BH, Böckmann A. Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy. Chembiochem 2020; 21:324-330. [PMID: 31310428 PMCID: PMC7318265 DOI: 10.1002/cbic.201900439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 12/16/2022]
Abstract
Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.
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Affiliation(s)
- Thomas Wiegand
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Maarten Schledorn
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander A. Malär
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Riccardo Cadalbert
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander Däpp
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Laurent Terradot
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRS/Université de Lyon7 Passage du vercors69367LyonFrance
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7
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Liu L, Gueguen-Chaignon V, Gonçalves IR, Rascle C, Rigault M, Dellagi A, Loisel E, Poussereau N, Rodrigue A, Terradot L, Condemine G. A secreted metal-binding protein protects necrotrophic phytopathogens from reactive oxygen species. Nat Commun 2019; 10:4853. [PMID: 31649262 PMCID: PMC6813330 DOI: 10.1038/s41467-019-12826-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/27/2019] [Indexed: 11/13/2022] Open
Abstract
Few secreted proteins involved in plant infection common to necrotrophic bacteria, fungi and oomycetes have been identified except for plant cell wall-degrading enzymes. Here we study a family of iron-binding proteins that is present in Gram-negative and Gram-positive bacteria, fungi, oomycetes and some animals. Homolog proteins in the phytopathogenic bacterium Dickeya dadantii (IbpS) and the fungal necrotroph Botrytis cinerea (BcIbp) are involved in plant infection. IbpS is secreted, can bind iron and copper, and protects the bacteria against H2O2-induced death. Its 1.7 Å crystal structure reveals a classical Venus Fly trap fold that forms dimers in solution and in the crystal. We propose that secreted Ibp proteins binds exogenous metals and thus limit intracellular metal accumulation and ROS formation in the microorganisms. The authors identify a family of iron-binding proteins that is present in phytopathogenic bacteria, fungi and oomycetes. Some of these proteins are secreted, bind metals, protect the pathogen from H2O2-induced death, and are involved in plant infection.
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Affiliation(s)
- Lulu Liu
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France
| | | | - Isabelle R Gonçalves
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France
| | - Christine Rascle
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France
| | - Martine Rigault
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, 78026, Versailles, France
| | - Alia Dellagi
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, 78026, Versailles, France
| | - Elise Loisel
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France
| | - Nathalie Poussereau
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France
| | - Agnès Rodrigue
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Institut de Biologie et Chimie des Protéines, Université de Lyon, 69367, Lyon, France.
| | - Guy Condemine
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France.
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8
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Wiegand T, Cadalbert R, Lacabanne D, Timmins J, Terradot L, Böckmann A, Meier BH. The conformational changes coupling ATP hydrolysis and translocation in a bacterial DnaB helicase. Nat Commun 2019; 10:31. [PMID: 30604765 PMCID: PMC6318325 DOI: 10.1038/s41467-018-07968-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/10/2018] [Indexed: 11/08/2022] Open
Abstract
DnaB helicases are motor proteins that couple ATP-hydrolysis to the loading of the protein onto DNA at the replication fork and to translocation along DNA to separate double-stranded DNA into single strands during replication. Using a network of conformational states, arrested by nucleotide mimics, we herein characterize the reaction coordinates for ATP hydrolysis, DNA loading and DNA translocation using solid-state NMR spectroscopy. AMP-PCP is used as pre-hydrolytic, ADP:AlF4- as transition state, and ADP as post-hydrolytic ATP mimic. 31P and 13C NMR spectra reveal conformational and dynamic responses to ATP hydrolysis and the resulting DNA loading and translocation with single amino-acid resolution. This allows us to identify residues guiding the DNA translocation process and to explain the high binding affinities for DNA observed for ADP:AlF4-, which turns out to be optimally preconfigured to bind DNA.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Denis Lacabanne
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Joanna Timmins
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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9
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Sodolescu A, Dian C, Terradot L, Bouzhir-Sima L, Lestini R, Myllykallio H, Skouloubris S, Liebl U. Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori. PLoS One 2018; 13:e0208850. [PMID: 30550583 PMCID: PMC6294363 DOI: 10.1371/journal.pone.0208850] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Received: 08/23/2018] [Accepted: 11/23/2018] [Indexed: 11/19/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX. Here the distinct catalytic reaction directly produces tetrahydrofolate (THF) and consequently in most ThyX-containing organisms, DHFR is absent. While the resulting influence on the folate metabolism of ThyX-containing bacteria is not fully understood, the presence of ThyX may provide growth benefits under conditions where the level of reduced folate derivatives is compromised. Interestingly, the third key enzyme implicated in generation of MTHF, serine hydroxymethyltransferase (SHMT), has a universal phylogenetic distribution, but remains understudied in ThyX-containg bacteria. To obtain functional insight into these ThyX-dependent thymidylate/folate cycles, we characterized the predicted SHMT from the ThyX-containing bacterium Helicobacter pylori. Serine hydroxymethyltransferase activity was confirmed by functional genetic complementation of a glyA-inactivated E. coli strain. A H. pylori ΔglyA strain was obtained, but exhibited markedly slowed growth and had lost the virulence factor CagA. Biochemical and spectroscopic evidence indicated formation of a characteristic enzyme-PLP-glycine-folate complex and revealed unexpectedly weak binding affinity of PLP. The three-dimensional structure of the H. pylori SHMT apoprotein was determined at 2.8Ǻ resolution, suggesting a structural basis for the low affinity of the enzyme for its cofactor. Stabilization of the proposed inactive configuration using small molecules has potential to provide a specific way for inhibiting HpSHMT.
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Affiliation(s)
- Andreea Sodolescu
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Cyril Dian
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette, France
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry, Institut de Biologie et Chimie des Protéines, CNRS, Université de Lyon, Lyon, France
| | - Latifa Bouzhir-Sima
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Roxane Lestini
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Hannu Myllykallio
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Stéphane Skouloubris
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
- Department of Biology, Université Paris-Sud, Université Paris Saclay, Orsay, France
| | - Ursula Liebl
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
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10
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Bats SH, Bergé C, Coombs N, Terradot L, Josenhans C. Biochemical characterization of the Helicobacter pylori Cag Type 4 Secretion System protein CagN and its interaction partner CagM. Int J Med Microbiol 2018; 308:425-437. [PMID: 29572102 DOI: 10.1016/j.ijmm.2018.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 02/12/2018] [Revised: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 12/26/2022] Open
Abstract
Highly virulent Helicobacter pylori strains contain the cag pathogenicity island (cagPAI). It codes for about 30 proteins forming a type IV secretion system (T4SS) which translocates the pro-inflammatory protein CagA into epithelial host cells. While CagA and various other Cag proteins have been extensively studied, several cagPAI proteins are poorly characterized or of unknown function. CagN (HP0538) is of unknown function but highly conserved in the cagPAI suggesting an important role. cagM (HP0537) is the first gene of the cagMN operon and its product is part of the CagT4SS core complex. Both proteins do not have detectable homologs in other type IV secretion systems. We have characterized the biochemical and structural properties of CagN and CagM and their interaction. We demonstrate by circular dichroism, Multi-Angle Light Scattering (MALS) and small angle X-ray scattering (SAXS) that CagN is a folded, predominantly monomeric protein with an elongated shape in solution. CagM is folded and forms predominantly dimers that are also elongated in solution. We found by various in vivo and in vitro methods that CagN and CagM directly interact with each other. CagM self-interacts stably with a low nanomolar KD and can form stable multimers. Finally, in vivo experiments show that deletion of CagM reduces the amounts of CagN and other outer CagPAI proteins in H. pylori cells.
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Affiliation(s)
- Simon H Bats
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; Max von Pettenkofer Institute, Ludwig Maximilians Universität LMU München, Pettenkoferstraße 9a, 80336 München, Germany
| | - Célia Bergé
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon 1, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69367 Lyon, Cedex 07, France
| | - Nina Coombs
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon 1, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69367 Lyon, Cedex 07, France
| | - Christine Josenhans
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; Max von Pettenkofer Institute, Ludwig Maximilians Universität LMU München, Pettenkoferstraße 9a, 80336 München, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany.
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11
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Koelblen T, Bergé C, Cherrier MV, Brillet K, Jimenez-Soto L, Ballut L, Takagi J, Montserret R, Rousselle P, Fischer W, Haas R, Fronzes R, Terradot L. Molecular dissection of protein-protein interactions between integrin α5β1 and the Helicobacter pylori
Cag type IV secretion system. FEBS J 2017; 284:4143-4157. [DOI: 10.1111/febs.14299] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/04/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Thomas Koelblen
- UMR 5086 Molecular Microbiology and Structural Biochemistry; Institut de Biologie et Chimie des Protéines; CNRS-Université de Lyon; France
| | - Célia Bergé
- UMR 5086 Molecular Microbiology and Structural Biochemistry; Institut de Biologie et Chimie des Protéines; CNRS-Université de Lyon; France
| | - Mickaël V. Cherrier
- UMR 5086 Molecular Microbiology and Structural Biochemistry; Institut de Biologie et Chimie des Protéines; CNRS-Université de Lyon; France
| | - Karl Brillet
- UMR 5086 Molecular Microbiology and Structural Biochemistry; Institut de Biologie et Chimie des Protéines; CNRS-Université de Lyon; France
| | - Luisa Jimenez-Soto
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie; Ludwig-Maximilians-Universität; München Germany
| | - Lionel Ballut
- UMR 5086 Molecular Microbiology and Structural Biochemistry; Institut de Biologie et Chimie des Protéines; CNRS-Université de Lyon; France
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression; Institute for Protein Research; Osaka University; Japan
| | - Roland Montserret
- UMR 5086 Molecular Microbiology and Structural Biochemistry; Institut de Biologie et Chimie des Protéines; CNRS-Université de Lyon; France
| | - Patricia Rousselle
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique; UMR 5305; CNRS; University Lyon 1; France
| | - Wolfgang Fischer
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie; Ludwig-Maximilians-Universität; München Germany
| | - Rainer Haas
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie; Ludwig-Maximilians-Universität; München Germany
- German Center for Infection Research (DZIF); Partner Site LMU; München Germany
| | - Rémi Fronzes
- European Institute of Chemistry and Biology; CNRS; UMR 5234; Microbiologie Fondamentale et Pathogénicité; University of Bordeaux; Pessac France
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry; Institut de Biologie et Chimie des Protéines; CNRS-Université de Lyon; France
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12
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Imbert PR, Louche A, Luizet JB, Grandjean T, Bigot S, Wood TE, Gagné S, Blanco A, Wunderley L, Terradot L, Woodman P, Garvis S, Filloux A, Guery B, Salcedo SP. A Pseudomonas aeruginosa TIR effector mediates immune evasion by targeting UBAP1 and TLR adaptors. EMBO J 2017; 36:1869-1887. [PMID: 28483816 PMCID: PMC5494471 DOI: 10.15252/embj.201695343] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 07/27/2016] [Revised: 03/29/2017] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Bacterial pathogens often subvert the innate immune system to establish a successful infection. The direct inhibition of downstream components of innate immune pathways is particularly well documented but how bacteria interfere with receptor proximal events is far less well understood. Here, we describe a Toll/interleukin 1 receptor (TIR) domain‐containing protein (PumA) of the multi‐drug resistant Pseudomonas aeruginosa PA7 strain. We found that PumA is essential for virulence and inhibits NF‐κB, a property transferable to non‐PumA strain PA14, suggesting no additional factors are needed for PumA function. The TIR domain is able to interact with the Toll‐like receptor (TLR) adaptors TIRAP and MyD88, as well as the ubiquitin‐associated protein 1 (UBAP1), a component of the endosomal‐sorting complex required for transport I (ESCRT‐I). These interactions are not spatially exclusive as we show UBAP1 can associate with MyD88, enhancing its plasma membrane localization. Combined targeting of UBAP1 and TLR adaptors by PumA impedes both cytokine and TLR receptor signalling, highlighting a novel strategy for innate immune evasion.
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Affiliation(s)
- Paul Rc Imbert
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
| | - Arthur Louche
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
| | - Jean-Baptiste Luizet
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
| | - Teddy Grandjean
- EA 7366 Recherche Translationelle Relations Hôte-Pathogènes, Faculté de Médecine Pôle Recherche, Université Lille 2, Lille, France
| | - Sarah Bigot
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
| | - Thomas E Wood
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Stéphanie Gagné
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
| | - Amandine Blanco
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
| | - Lydia Wunderley
- School of Biological Sciences, Faculty of Biology Medicine and Health University of Manchester Manchester Academic Health Science Centre, Manchester, UK†
| | - Laurent Terradot
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
| | - Philip Woodman
- School of Biological Sciences, Faculty of Biology Medicine and Health University of Manchester Manchester Academic Health Science Centre, Manchester, UK†
| | - Steve Garvis
- Laboratoire de Biologie et Modelisation, Ecole Normal Supérieur, UMR5239, Lyon, France
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Benoit Guery
- EA 7366 Recherche Translationelle Relations Hôte-Pathogènes, Faculté de Médecine Pôle Recherche, Université Lille 2, Lille, France
| | - Suzana P Salcedo
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique, University of Lyon, Lyon, France
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13
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Wiegand T, Lacabanne D, Keller K, Cadalbert R, Lecoq L, Yulikov M, Terradot L, Jeschke G, Meier BH, Böckmann A. Solid-state NMR and EPR Spectroscopy of Mn 2+ -Substituted ATP-Fueled Protein Engines. Angew Chem Int Ed Engl 2017; 56:3369-3373. [PMID: 28191714 DOI: 10.1002/anie.201610551] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Indexed: 12/16/2022]
Abstract
Paramagnetic metal ions deliver structural information both in EPR and solid-state NMR experiments, offering a profitable synergetic approach to study bio-macromolecules. We demonstrate the spectral consequences of Mg2+ / Mn2+ substitution and the resulting information contents for two different ATP:Mg2+ -fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | | | | | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Maxim Yulikov
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Gunnar Jeschke
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
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14
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Wiegand T, Lacabanne D, Keller K, Cadalbert R, Lecoq L, Yulikov M, Terradot L, Jeschke G, Meier BH, Böckmann A. Festkörper-NMR- und EPR-Spektroskopie an Mn2+-substituierten ATP-angetriebenen Proteinmaschinen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
| | | | | | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
| | - Maxim Yulikov
- Physikalische Chemie; ETH Zürich; 8093 Zürich Schweiz
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
| | | | - Beat H. Meier
- Physikalische Chemie; ETH Zürich; 8093 Zürich Schweiz
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
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15
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Wiegand T, Cadalbert R, Gardiennet C, Timmins J, Terradot L, Böckmann A, Meier BH. Beobachtung von ssDNA-Bindung an die DnaB-Helikase von Helicobacter pylori
mittels Festkörper-NMR-Spektroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry; UMR 5086 CNRS; Université de Lyon; 7 passage du Vercors 69367 Lyon Frankreich
- CRM2, UMR 7036 CNRS/; Université de Lorraine; Faculté des Sciences et Technologies, BP 70239; Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy Frankreich
| | - Joanna Timmins
- Univ. Grenoble Alpes; CEA, CNRS; 38044 Grenoble Frankreich
| | - Laurent Terradot
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry; UMR 5086 CNRS; Université de Lyon; 7 passage du Vercors 69367 Lyon Frankreich
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry; UMR 5086 CNRS; Université de Lyon; 7 passage du Vercors 69367 Lyon Frankreich
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16
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Wiegand T, Cadalbert R, Gardiennet C, Timmins J, Terradot L, Böckmann A, Meier BH. Monitoring ssDNA Binding to the DnaB Helicase from Helicobacter pylori by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:14164-14168. [PMID: 27709753 DOI: 10.1002/anie.201607295] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 07/28/2016] [Revised: 08/23/2016] [Indexed: 11/11/2022]
Abstract
DnaB helicases are bacterial, ATP-driven enzymes that unwind double-stranded DNA during DNA replication. Herein, we study the sequential binding of the "non-hydrolysable" ATP analogue AMP-PNP and of single-stranded (ss) DNA to the dodecameric DnaB helicase from Helicobacter pylori using solid-state NMR. Phosphorus cross-polarization experiments monitor the binding of AMP-PNP and DNA to the helicase. 13 C chemical-shift perturbations (CSPs) are used to detect conformational changes in the protein upon binding. The helicase switches upon AMP-PNP addition into a conformation apt for ssDNA binding, and AMP-PNP is hydrolyzed and released upon binding of ssDNA. Our study sheds light on the conformational changes which are triggered by the interaction with AMP-PNP and are needed for ssDNA binding of H. pylori DnaB in vitro. They also demonstrate the level of detail solid-state NMR can provide for the characterization of protein-DNA interactions and the interplay with ATP or its analogues.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.,CRM2, UMR 7036 CNRS/, Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, Boulevard des Aiguillettes, 54506, Vandoeuvre-lès-Nancy, France
| | - Joanna Timmins
- Univ. Grenoble Alpes, CEA,CNRS, F-, 38044, Grenoble, France
| | - Laurent Terradot
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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17
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Rigard M, Bröms JE, Mosnier A, Hologne M, Martin A, Lindgren L, Punginelli C, Lays C, Walker O, Charbit A, Telouk P, Conlan W, Terradot L, Sjöstedt A, Henry T. Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence. PLoS Pathog 2016; 12:e1005821. [PMID: 27602570 PMCID: PMC5014421 DOI: 10.1371/journal.ppat.1005821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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] [Received: 01/14/2016] [Accepted: 07/20/2016] [Indexed: 12/12/2022] Open
Abstract
The virulence of Francisella tularensis, the etiological agent of tularemia, relies on an atypical type VI secretion system (T6SS) encoded by a genomic island termed the Francisella Pathogenicity Island (FPI). While the importance of the FPI in F. tularensis virulence is clearly established, the precise role of most of the FPI-encoded proteins remains to be deciphered. In this study, using highly virulent F. tularensis strains and the closely related species F. novicida, IglG was characterized as a protein featuring a unique α-helical N-terminal extension and a domain of unknown function (DUF4280), present in more than 250 bacterial species. Three dimensional modeling of IglG and of the DUF4280 consensus protein sequence indicates that these proteins adopt a PAAR-like fold, suggesting they could cap the T6SS in a similar way as the recently described PAAR proteins. The newly identified PAAR-like motif is characterized by four conserved cysteine residues, also present in IglG, which may bind a metal atom. We demonstrate that IglG binds metal ions and that each individual cysteine is required for T6SS-dependent secretion of IglG and of the Hcp homologue, IglC and for the F. novicida intracellular life cycle. In contrast, the Francisella-specific N-terminal α-helical extension is not required for IglG secretion, but is critical for F. novicida virulence and for the interaction of IglG with another FPI-encoded protein, IglF. Altogether, our data suggest that IglG is a PAAR-like protein acting as a bi-modal protein that may connect the tip of the Francisella T6SS with a putative T6SS effector, IglF. Francisella tularensis is a highly pathogenic bacterium causing tularemia. Its ability to cause disease is linked to its ability to replicate in the macrophage cytosol. The intracellular life cycle of Francisella is controlled by a type VI secretion system (T6SS), which is thought to inject effectors into the host cell to allow bacterial escape into the host cytosol. The molecular mechanisms behind this process are still largely unclear. In this work, we identify IglG as a protein with two important domains, one conserved in proteins from more than 250 bacterial species (DUF4280, renamed here as PAAR-like domain) and one specific for the Francisella genus. Using protein sequence analysis and three-dimensional structure predictions, comparative modeling and biochemistry approaches, our data demonstrate that IglG is a metal-binding protein that based on its PAAR-like domain might cap the VgrG spike of the T6SS and act as a membrane-puncturing protein. Furthermore, we identified that the Francisella-specific domain is directly involved in forming a protein complex with another virulence protein, IglF. This work, in addition to enhancing the molecular understanding of the Francisella T6SS, defines the features of the conserved DUF4280, a novel PAAR-like domain involved in type VI secretion (T6S) of many bacterial species.
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Affiliation(s)
- Mélanie Rigard
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jeanette E. Bröms
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Amandine Mosnier
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Amandine Martin
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Lena Lindgren
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Claire Punginelli
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Claire Lays
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Olivier Walker
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Alain Charbit
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France
- Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Philippe Telouk
- University of Lyon, Lyon, France
- Laboratoire de Geologie de Lyon; Ecole Normale Supérieure de Lyon, Lyon, France
| | - Wayne Conlan
- National Research Council Canada, Human Health Therapeutics Portfolio, Ottawa, Ontario, Canada
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
- * E-mail: (LT); (AS); (TH)
| | - Anders Sjöstedt
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- * E-mail: (LT); (AS); (TH)
| | - Thomas Henry
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail: (LT); (AS); (TH)
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18
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Wiegand T, Gardiennet C, Cadalbert R, Lacabanne D, Kunert B, Terradot L, Böckmann A, Meier BH. Variability and conservation of structural domains in divide-and-conquer approaches. J Biomol NMR 2016; 65:79-86. [PMID: 27240588 DOI: 10.1007/s10858-016-0039-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/19/2016] [Indexed: 05/26/2023]
Abstract
The use of protein building blocks for the structure determination of multidomain proteins and protein-protein complexes, also known as the "divide and conquer" approach, is an important strategy for obtaining protein structures. Atomic-resolution X-ray or NMR data of the individual domains are combined with lower-resolution electron microscopy maps or X-ray data of the full-length protein or the protein complex. Doing so, it is often assumed that the individual domain structures remain invariant in the context of the superstructure. In this work, we show the potentials and limitations of NMR to validate this approach at the example of the dodecameric DnaB helicase from Helicobacter pylori. We investigate how sequentially assigned spectra, as well as unassigned spectral fingerprints can be used to indicate the conservation of individual domains, and also to highlight conformational differences.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
- CRM2, UMR 7036, CNRS, Université de Lorraine, 54506, Vandoeuvre-lès-Nancy, France
| | | | - Denis Lacabanne
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Britta Kunert
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Laurent Terradot
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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19
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Wiegand T, Gardiennet C, Ravotti F, Bazin A, Kunert B, Lacabanne D, Cadalbert R, Güntert P, Terradot L, Böckmann A, Meier BH. Solid-state NMR sequential assignments of the N-terminal domain of HpDnaB helicase. Biomol NMR Assign 2016; 10:13-23. [PMID: 26280528 DOI: 10.1007/s12104-015-9629-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 08/11/2015] [Indexed: 05/21/2023]
Abstract
We present solid-state NMR assignments of the N-terminal domain of the DnaB helicase from Helicobacter pylori (153 residues) in its microcrystalline form. We use a sequential resonance assignment strategy based on three-dimensional NMR experiments. The resonance assignments obtained are compared with automated resonance assignments computed with the ssFLYA algorithm. An analysis of the (13)C secondary chemical shifts determines the position of the secondary structure elements in this α-helical protein.
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Affiliation(s)
- Thomas Wiegand
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Carole Gardiennet
- Institut de Biologie et Chemie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercor, 69007, Lyon, France
| | - Francesco Ravotti
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Alexandre Bazin
- Institut de Biologie et Chemie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercor, 69007, Lyon, France
| | - Britta Kunert
- Institut de Biologie et Chemie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercor, 69007, Lyon, France
| | - Denis Lacabanne
- Institut de Biologie et Chemie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercor, 69007, Lyon, France
| | - Riccardo Cadalbert
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Peter Güntert
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Laurent Terradot
- Institut de Biologie et Chemie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercor, 69007, Lyon, France.
| | - Anja Böckmann
- Institut de Biologie et Chemie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercor, 69007, Lyon, France.
| | - Beat H Meier
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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Gardiennet C, Wiegand T, Bazin A, Cadalbert R, Kunert B, Lacabanne D, Gutsche I, Terradot L, Meier BH, Böckmann A. Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori. J Biomol NMR 2016; 64:189-95. [PMID: 26961129 DOI: 10.1007/s10858-016-0018-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/24/2016] [Indexed: 05/09/2023]
Abstract
We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387 kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information that can be extracted from such a large protein is still limited, we can assign a number of amino-acid residues experiencing significant chemical-shift perturbations upon helicase-primase complex formation. The location of these residues is used as a guide to model the interaction interface between the two proteins in the complex. Chemical-shift perturbations also reveal changes at the interaction interfaces of the hexameric HpDnaB assembly on HpDnaG binding. A structural model of the complex that explains the experimental findings is obtained.
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Affiliation(s)
- Carole Gardiennet
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69007, Lyon, France
- CNRS, CRM2, UMR 7036, Université de Lorraine, 54506, Vandoeuvre-lès-Nancy, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Alexandre Bazin
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69007, Lyon, France
| | - Riccardo Cadalbert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69007, Lyon, France
| | - Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69007, Lyon, France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS), CNRS, IBS; CEA, IBS, Université Grenoble Alpes, 38044, Grenoble, France
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69007, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69007, Lyon, France.
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Flayhan A, Bergé C, Baïlo N, Doublet P, Bayliss R, Terradot L. Erratum: The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase. Sci Rep 2016; 6:20746. [PMID: 26839176 PMCID: PMC4738274 DOI: 10.1038/srep20746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Cheng B, Montmasson M, Terradot L, Rousselle P. Syndecans as Cell Surface Receptors in Cancer Biology. A Focus on their Interaction with PDZ Domain Proteins. Front Pharmacol 2016; 7:10. [PMID: 26869927 PMCID: PMC4735372 DOI: 10.3389/fphar.2016.00010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 11/26/2015] [Accepted: 01/12/2016] [Indexed: 01/23/2023] Open
Abstract
Syndecans are transmembrane receptors with ectodomains that are modified by glycosaminoglycan chains. The ectodomains can interact with a wide variety of molecules, including growth factors, cytokines, proteinases, adhesion receptors, and extracellular matrix (ECM) components. The four syndecans in mammals are expressed in a development-, cell-type-, and tissue-specific manner and can function either as co-receptors with other cell surface receptors or as independent adhesion receptors that mediate cell signaling. They help regulate cell proliferation and migration, angiogenesis, cell/cell and cell/ECM adhesion, and they may participate in several key tumorigenesis processes. In some cancers, syndecan expression regulates tumor cell proliferation, adhesion, motility, and other functions, and may be a prognostic marker for tumor progression and patient survival. The short cytoplasmic tail is likely to be involved in these events through recruitment of signaling partners. In particular, the conserved carboxyl-terminal EFYA tetrapeptide sequence that is present in all syndecans binds to some PDZ domain-containing proteins that may function as scaffold proteins that recruit signaling and cytoskeletal proteins to the plasma membrane. There is growing interest in understanding these interactions at both the structural and biological levels, and recent findings show their high degree of complexity. Parameters that influence the recruitment of PDZ domain proteins by syndecans, such as binding specificity and affinity, are the focus of active investigations and are important for understanding regulatory mechanisms. Recent studies show that binding may be affected by post-translational events that influence regulatory mechanisms, such as phosphorylation within the syndecan cytoplasmic tail.
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Affiliation(s)
- Bill Cheng
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS, Institut de Biologie et Chimie des Protéines, SFR BioSciences Gerland-Lyon Sud, Université Lyon 1 Lyon, France
| | - Marine Montmasson
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS, Institut de Biologie et Chimie des Protéines, SFR BioSciences Gerland-Lyon Sud, Université Lyon 1 Lyon, France
| | - Laurent Terradot
- Bases Moléculaires et Structurales des Systèmes Infectieux UMR 5086, CNRS, Institut de Biologie et Chimie des Protéines, SFR BioSciences Gerland-Lyon Sud, Université Lyon 1 Lyon, France
| | - Patricia Rousselle
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS, Institut de Biologie et Chimie des Protéines, SFR BioSciences Gerland-Lyon Sud, Université Lyon 1 Lyon, France
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Felicori L, Jameson KH, Roblin P, Fogg MJ, Garcia-Garcia T, Ventroux M, Cherrier MV, Bazin A, Noirot P, Wilkinson AJ, Molina F, Terradot L, Noirot-Gros MF. Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners. Nucleic Acids Res 2016; 44:449-63. [PMID: 26615189 PMCID: PMC4705661 DOI: 10.1093/nar/gkv1318] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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] [Received: 08/24/2015] [Revised: 11/06/2015] [Accepted: 11/10/2015] [Indexed: 11/12/2022] Open
Abstract
YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell.
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Affiliation(s)
- Liza Felicori
- Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, UFMG, 31270-901, Belo Horizonte, MG, Brazil Sys2Diag FRE3690-CNRS/ALCEDIAG, Montpellier, France
| | - Katie H Jameson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Pierre Roblin
- Synchrotron SOLEIL-L'Orme des Merisiers Saint-Aubin- BP 48 91192 GIF-sur-YVETTE CEDEX, France
| | - Mark J Fogg
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Transito Garcia-Garcia
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
| | - Magali Ventroux
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
| | - Mickaël V Cherrier
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon, France Université de Lyon, F-69622 Lyon, France Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Alexandre Bazin
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon, France Université de Lyon, F-69622 Lyon, France Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Philippe Noirot
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Laurent Terradot
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon, France Université de Lyon, F-69622 Lyon, France Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Marie-Françoise Noirot-Gros
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
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Flayhan A, Bergé C, Baïlo N, Doublet P, Bayliss R, Terradot L. The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase. Sci Rep 2015; 5:14602. [PMID: 26419332 PMCID: PMC4588518 DOI: 10.1038/srep14602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/28/2015] [Indexed: 01/24/2023] Open
Abstract
Bacterial pathogens subvert signalling pathways to promote invasion and/or replication into the host. LegK1-4 proteins are eukaryotic-like serine/threonine kinases that are translocated by the Dot/Icm type IV secretion system (T4SS) of several Legionella pneumophila strains. We present the crystal structures of an active fragment of the LegK4 protein in apo and substrate-bound states. The structure of LegK41–445 reveals a eukaryotic-like kinase domain flanked by a novel cap domain and a four-helix bundle. The protein self-assembles through interactions mediated by helices αF and αG that generate a dimeric interface not previously observed in a protein kinase. The helix αG is displaced compared to previous kinase structures, and its role in stabilization of the activation loop is taken on by the dimerisation interface. The apo-form of the protein has an open conformation with a disordered P-loop but a structured activation segment in absence of targeted phosphorylation. The nucleotide-binding site of LegK4 contains an unusual set of residues that mediate non-canonical interactions with AMP-PNP. Nucleotide binding results in limited changes in the active site, suggesting that LegK4 constitutive kinase activity does not depend on phosphorylation of the activation loop but on the stabilizing effects of the dimer.
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Affiliation(s)
- Ali Flayhan
- UMR 5086 BMSSI CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Célia Bergé
- UMR 5086 BMSSI CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Nathalie Baïlo
- Legionella Pathogenesis Group, International Center for Infectiology Research, Université de Lyon Lyon, France.,INSERM U1111 Lyon, France.,Ecole Normale Suptérieure de Lyon Lyon, France.,Centre International de Recherche en Infectiologie, Université Lyon 1 Lyon, France.,CNRS, UMR5308 Lyon, France
| | - Patricia Doublet
- Legionella Pathogenesis Group, International Center for Infectiology Research, Université de Lyon Lyon, France.,INSERM U1111 Lyon, France.,Ecole Normale Suptérieure de Lyon Lyon, France.,Centre International de Recherche en Infectiologie, Université Lyon 1 Lyon, France.,CNRS, UMR5308 Lyon, France
| | - Richard Bayliss
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Laurent Terradot
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
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Bazin A, Cherrier MV, Gutsche I, Timmins J, Terradot L. Structure and primase-mediated activation of a bacterial dodecameric replicative helicase. Nucleic Acids Res 2015; 43:8564-76. [PMID: 26264665 PMCID: PMC4787810 DOI: 10.1093/nar/gkv792] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/22/2015] [Indexed: 01/29/2023] Open
Abstract
Replicative helicases are essential ATPases that unwind DNA to initiate chromosomal replication. While bacterial replicative DnaB helicases are hexameric, Helicobacter pylori DnaB (HpDnaB) was found to form double hexamers, similar to some archaeal and eukaryotic replicative helicases. Here we present a structural and functional analysis of HpDnaB protein during primosome formation. The crystal structure of the HpDnaB at 6.7 Å resolution reveals a dodecameric organization consisting of two hexamers assembled via their N-terminal rings in a stack-twisted mode. Using fluorescence anisotropy we show that HpDnaB dodecamer interacts with single-stranded DNA in the presence of ATP but has a low DNA unwinding activity. Multi-angle light scattering and small angle X-ray scattering demonstrate that interaction with the DnaG primase helicase-binding domain dissociates the helicase dodecamer into single ringed primosomes. Functional assays on the proteins and associated complexes indicate that these single ringed primosomes are the most active form of the helicase for ATP hydrolysis, DNA binding and unwinding. These findings shed light onto an activation mechanism of HpDnaB by the primase that might be relevant in other bacteria and possibly other organisms exploiting dodecameric helicases for DNA replication.
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Affiliation(s)
- Alexandre Bazin
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367, Lyon, France. Université de Lyon, F-69622, Lyon, France; Université Claude Bernard Lyon 1, F-69622, Villeurbanne, France
| | - Mickaël V Cherrier
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367, Lyon, France. Université de Lyon, F-69622, Lyon, France; Université Claude Bernard Lyon 1, F-69622, Villeurbanne, France
| | - Irina Gutsche
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, F-38044 Grenoble Cedex 9, France
| | - Joanna Timmins
- Univ. Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France CEA, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Laurent Terradot
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367, Lyon, France. Université de Lyon, F-69622, Lyon, France; Université Claude Bernard Lyon 1, F-69622, Villeurbanne, France
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Felix C, Kaplan Türköz B, Ranaldi S, Koelblen T, Terradot L, O'Callaghan D, Vergunst AC. The Brucella TIR domain containing proteins BtpA and BtpB have a structural WxxxE motif important for protection against microtubule depolymerisation. Cell Commun Signal 2014; 12:53. [PMID: 25304327 PMCID: PMC4203976 DOI: 10.1186/s12964-014-0053-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/27/2014] [Indexed: 01/12/2023] Open
Abstract
Background The TIR domain-containing proteins BtpA/Btp1/TcpB and BtpB are translocated into host cells by the facultative intracellular bacterial pathogen Brucella. Here, they interfere with Toll like receptor signalling to temper the host inflammatory response. BtpA has also been found to modulate microtubule dynamics. In both proteins we identified a WxxxE motif, previously shown to be an essential structural component in a family of bacterial type III secretion system effectors that modulate host actin dynamics by functioning as guanine nucleotide exchange factors of host GTPases. We analysed a role for the WxxxE motif in association of BtpA and BtpB with the cytoskeleton. Results Unlike BtpA, ectopically expressed BtpB did not show a tubular localisation, but was found ubiquitously in the cytoplasm and the nucleus, and often appeared in discrete punctae in HeLa cells. BtpB was able to protect microtubules from drug-induced destabilisation similar to BtpA. The WxxxE motif was important for the ability of BtpA and BtpB to protect microtubules against destabilising drugs. Surprisingly, ectopic expression of BtpA, although not BtpB, in HeLa cells induced the formation of filopodia. This process was invariably dependent of the WxxxE motif. Our recent resolution of the crystal structure of the BtpA TIR domain reveals that the motif positions a glycine residue that has previously been shown to be essential for interaction of BtpA with microtubules. Conclusions Our results suggest a structural role for the WxxxE motif in the association of BtpA and BtpB with microtubules, as with the WxxxE GEF family proteins where the motif positions an adjacent catalytic loop important for interaction with specific Rho GTPases. In addition, the ability of ectopically expressed BtpA to induce filopodia in a WxxxE-dependent manner suggests a novel property for BtpA. A conserved WxxxE motif is found in most bacterial and several eukaryotic TIR domain proteins. Despite the similarity between ectopically expressed BtpA and WxxxE GEFs to modulate host actin dynamics, our results suggest that BtpA is not part of this WxxxE GEF family. The WxxxE motif may therefore be a more common structural motif than thus far described. BtpA may provide clues to cross-talk between the TLR and GTPase signalling pathways. Electronic supplementary material The online version of this article (doi:10.1186/s12964-014-0053-y) contains supplementary material, which is available to authorized users.
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Bazin A, Cherrier M, Terradot L. Structural insights into DNA replication initiation in Helicobacter pylori. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314083673] [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: 11/10/2022] Open
Abstract
In Gram-negative bacteria, opening of DNA double strand during replication is performed by the replicative helicase DnaB. This protein allows for replication fork elongation by unwinding DNA and interacting with DnaG primase. DnaB is composed of two domains: an N-terminal domain (NTD) and a C-terminal domain (CTD) connected by a flexible linker. The protein forms two-tiered hexamers composed of a NTD-ring and a CTD-ring. In Escherichia coli, the initiator protein DnaA binds to the origin of replication oriC and induces the opening of a AT-rich region. The replicative helicase DnaB is then loaded onto single stranded DNA by interacting with DnaA and with the AAA+ helicase loader DnaC. However, AAA+ loaders are absent in 80% of the bacterial genome, raising the question of how helicases are loaded in these bacteria [1]. In the genome of human pathogen Helicobacter pylori, no AAA+ loader has been identified. Moreover H. pylori DnaB (HpDnaB) has the ability to support replication of an otherwise unviable E. coli strain that bears a defective copy of DnaC by complementation [2]. In order to better understand the properties of HpDnaB we have first shown that HpDnaB forms double hexamers by negative stain electron microscopy [3]. Then, we have then solved the crystal structure of HpDnaB at a resolution of 6.7Å by X-ray crystallography with Rfree/Rfactor of 0.29/0.25. The structure reveals that the protein adopts a new dodecameric arrangement generated by crystallographic three fold symmetry. When compared to hexameric DnaBs, the hexamer of HpDnaB displays an original combination of NTD-ring and CTD-ring symmetries, intermediate between apo and ADP-bound structure. Biochemistry studies of HpDnaB interaction with HpDnaG-CTD and ssDNA provides mechanistic insights into the initial steps of DNA replication in H. pylori. Our results offer an alternative solution of helicase loading and DNA replication initiation in H. pylori and possibly other bacteria that do not employ helicase loaders.
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Kaplan-Türköz B, Koelblen T, Felix C, Candusso MP, O'Callaghan D, Vergunst AC, Terradot L. Structure of the Toll/interleukin 1 receptor (TIR) domain of the immunosuppressive Brucella effector BtpA/Btp1/TcpB. FEBS Lett 2013; 587:3412-6. [PMID: 24076024 DOI: 10.1016/j.febslet.2013.09.007] [Citation(s) in RCA: 31] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 11/15/2022]
Abstract
BtpA/Btp1/TcpB is a virulence factor produced by Brucella species that possesses a Toll interleukin-1 receptor (TIR) domain. Once delivered into the host cell, BtpA interacts with MyD88 to interfere with TLR signalling and modulates microtubule dynamics. Here the crystal structure of the BtpA TIR domain at 3.15 Å is presented. The structure shows a dimeric arrangement of a canonical TIR domain, similar to the Paracoccus denitrificans Tir protein but secured by a unique long N-terminal α-tail that packs against the TIR:TIR dimer. Structure-based mutations and multi-angle light scattering experiments characterized the BtpA dimer conformation in solution. The structure of BtpA will help with studies to understand the mechanisms involved in its interactions with MyD88 and with microtubules.
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Affiliation(s)
- Burcu Kaplan-Türköz
- UMR 5086, BMSSI, CNRS - Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, F-69367, France
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Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. Hochaufgelöste Festkörper-NMR-Spektren einer sedimentierten, nichtkristallinen dodekameren Helicase (59 kDa). Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200779] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Gardiennet C, Schütz AK, Hunkeler A, Kunert B, Terradot L, Böckmann A, Meier BH. A Sedimented Sample of a 59 kDa Dodecameric Helicase Yields High-Resolution Solid-State NMR Spectra. Angew Chem Int Ed Engl 2012; 51:7855-8. [DOI: 10.1002/anie.201200779] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 04/10/2012] [Indexed: 11/10/2022]
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Stelter M, Gutsche I, Kapp U, Bazin A, Bajic G, Goret G, Jamin M, Timmins J, Terradot L. Architecture of a Dodecameric Bacterial Replicative Helicase. Structure 2012; 20:554-64. [DOI: 10.1016/j.str.2012.01.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 01/17/2012] [Accepted: 01/22/2012] [Indexed: 10/28/2022]
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Terradot L, Noirot-Gros MF. Bacterial protein interaction networks: puzzle stones from solved complex structures add to a clearer picture. Integr Biol (Camb) 2011; 3:645-52. [PMID: 21584322 DOI: 10.1039/c0ib00023j] [Citation(s) in RCA: 5] [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] [Indexed: 12/18/2022]
Abstract
Global scale studies of protein-protein interaction (PPI) networks have considerably expanded our view of how proteins act in the cell. In particular, bacterial "interactome" surveys have revealed that proteins can sometimes interact with a large number of protein partners and connect different cellular processes. More targeted, pathway-orientated PPI studies have also helped to propose functions for unknown proteins based on the "guilty by association" principle. However, given the immense repertoire of PPIs generated and the variability of PPI networks, more studies are required to understand the role(s) of these interactions in the cell. With the availability of bioinformatic analysis tools, transcriptomics and co-expression experiments for a given interaction, interactomes are being deciphered. More recently, functional and structural studies have been derived from these PPI networks. In this review, we will give a number of examples of how combining functional and structural studies into PPI networks has contributed to understanding the functions of some of these interactions. We discuss how interactomes now represent a unique opportunity to determine the structures of bacterial protein complexes on a large scale by the integration of multiple technologies.
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Affiliation(s)
- Laurent Terradot
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université de Lyon, IFR128, Biologie Structurale des Complexes Macromoléculaires Bactériens, 7 Passage du Vercors, F-69367, Lyon Cedex 07, France.
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Cioci G, Terradot L, Dian C, Mueller-Dieckmann C, Leonard G. Crystal structure of HP0721, a novel secreted protein from Helicobacter pylori. Proteins 2011; 79:1678-81. [PMID: 21365686 DOI: 10.1002/prot.22988] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/08/2010] [Accepted: 12/14/2010] [Indexed: 12/16/2022]
Affiliation(s)
- Gianluca Cioci
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France.
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Zawilak-Pawlik A, Donczew R, Szafrański S, Mackiewicz P, Terradot L, Zakrzewska-Czerwińska J. DiaA/HobA and DnaA: a pair of proteins co-evolved to cooperate during bacterial orisome assembly. J Mol Biol 2011; 408:238-51. [PMID: 21354425 DOI: 10.1016/j.jmb.2011.02.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 02/08/2011] [Accepted: 02/17/2011] [Indexed: 11/26/2022]
Abstract
Replication of the bacterial chromosome is initiated by binding the DnaA protein to oriC. Various factors control the ability of DnaA to bind and unwind DNA. Among them, Escherichia coli DiaA and Helicobacter pylori HobA have been characterized recently. They were found to interact with domain I of DnaA and stimulate DnaA binding to oriC. We examined HobA and DiaA functional homology and showed that, despite a high degree of structural similarity, they are not interchangeable because they are unable to interact with heterologous DnaA proteins. We revealed particular structural differences impeding formation of heterologous complexes and, consistently, we restored DiaA-enhanced oriC binding by the hybrid Ec(I)-Hp(II-IV)DnaA protein; i.e. H. pylori DnaA in which domain I was exchanged with that of E. coli. This proved that DiaA and HobA are functional homologs and upon binding to DnaA they exert a similar effect on orisome formation. Interestingly, we showed for the first time that the dynamics of DiaA- and HobA-stimulated orisome assembly are different. HobA enhances and accelerates HpDnaA binding to oriC, whereas DiaA increases but decelerates EcDnaA binding with oriC. We postulate that the different dynamics of orisome formation reflect the distinct strategies adopted by E. coli and H. pylori to regulate the frequency of the replication of their chromosomes. DiaA/HobA homolog have been identified in many proteobacteria and therefore might constitute a common, though species-specific, factor modulating bacterial orisome assembly.
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Affiliation(s)
- Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Department of Microbiology, Weigla 12, 53-114 Wrocław, Poland.
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Abstract
Type IV secretion systems (T4SS) are macromolecular assemblies used by bacteria to transport material across their membranes. T4SS are generally composed of a set of twelve proteins (VirB1-11 and VirD4). This represents a dynamic machine powered by three ATPases. T4SS are widespread in pathogenic bacteria where they are often used to deliver effectors into host cells. For example, the human pathogen Helicobacter pylori encodes a T4SS, the Cag-T4SS, which mediates the injection of the toxin CagA. We review the progress made in the past decade in our understanding of T4SS architecture. We translate this new knowledge to derive an understanding of the structure of the H. pylori Cag system, and use recent protein-protein interaction data to refine this model.
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Affiliation(s)
- Laurent Terradot
- Institut de Biologie et Chimie des Protéines, Biologie Structurale des Complexes Macromoléculaires Bactériens, UMR 5086 CNRS Université de Lyon, Lyon, France.
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Dian C, Vitale S, Leonard GA, Bahlawane C, Fauquant C, Leduc D, Muller C, de Reuse H, Michaud-Soret I, Terradot L. The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites. Mol Microbiol 2011; 79:1260-75. [PMID: 21208302 DOI: 10.1111/j.1365-2958.2010.07517.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fur, the ferric uptake regulator, is a transcription factor that controls iron metabolism in bacteria. Binding of ferrous iron to Fur triggers a conformational change that activates the protein for binding to specific DNA sequences named Fur boxes. In Helicobacter pylori, HpFur is involved in acid response and is important for gastric colonization in model animals. Here we present the crystal structure of a functionally active HpFur mutant (HpFur2M; C78S-C150S) bound to zinc. Although its fold is similar to that of other Fur and Fur-like proteins, the crystal structure of HpFur reveals a unique structured N-terminal extension and an unusual C-terminal helix. The structure also shows three metal binding sites: S1 the structural ZnS₄ site previously characterized biochemically in HpFur and the two zinc sites identified in other Fur proteins. Site-directed mutagenesis and spectroscopy analyses of purified wild-type HpFur and various mutants show that the two metal binding sites common to other Fur proteins can be also metallated by cobalt. DNA protection and circular dichroism experiments demonstrate that, while these two sites influence the affinity of HpFur for DNA, only one is absolutely required for DNA binding and could be responsible for the conformational changes of Fur upon metal binding while the other is a secondary site.
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Affiliation(s)
- Cyril Dian
- Structural Biology Group, European Synchrotron Radiation Facility, BP 220 F-38043 Grenoble cedex 9, France
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Bahlawane C, Dian C, Muller C, Round A, Fauquant C, Schauer K, de Reuse H, Terradot L, Michaud-Soret I. Structural and mechanistic insights into Helicobacter pylori NikR activation. Nucleic Acids Res 2010; 38:3106-18. [PMID: 20089510 PMCID: PMC2875016 DOI: 10.1093/nar/gkp1216] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly secondary external (X) sites. We describe a biochemical characterization of HpNikR mutants that shows that the HA sites are essential but not sufficient for DNA binding, while the secondary external (X) sites and residues from the HpNikR dimer–dimer interface are important for DNA binding. We show that a second metal is necessary for HpNikR/DNA binding, but only to some promoters. Small-angle X-ray scattering shows that HpNikR adopts a defined conformation in solution, resembling the cis-conformation and suggests that nickel does not trigger large conformational changes in HpNikR. The crystal structures of selected mutants identify the effects of each mutation on HpNikR structure. This study unravels key structural features from which we derive a model for HpNikR activation where: (i) HA sites and an hydrogen bond network are required for DNA binding and (ii) metallation of a unique secondary external site (X) modulates HpNikR DNA binding to low-affinity promoters by disruption of a salt bridge.
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Affiliation(s)
- C Bahlawane
- CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, France
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39
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Terradot L, Zawilak-Pawlik A. Structural insight into Helicobacter pylori DNA replication initiation. Gut Microbes 2010; 1:330-334. [PMID: 21327042 PMCID: PMC3023618 DOI: 10.4161/gmic.1.5.13115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/21/2010] [Accepted: 07/21/2010] [Indexed: 02/03/2023] Open
Abstract
While increasing knowledge is accumulating about the molecular mechanisms allowing the human pathogen Helicobacter pylori to survive and to subvert host defenses, much less is known about fundamental aspects of its biology, including DNA replication. We have studied the initiation step of chromosome replication of H. pylori and particularly the interaction between the initiator protein DnaA and its recently identified regulator HobA. This work has recently culminated in the determination of the crystal structure of the domains I and II of DnaA (DnaA(I-II)) in complex with HobA. By combining the structure with a variety of biochemical experiments we show that a tetramer of HobA can accommodate up to four DnaA molecules organized in a particular conformation within the complex. Mutations of the HobA interface that impaired the binding with DnaA were designed and proved to be lethal once introduced into H. pylori. These features suggest that HobA provides a molecular scaffold onto which regular oligomers of DnaA can assemble. The HobA-promoted oligomerization of DnaA could have a determinant role in the formation of the open complex. We propose a speculative model of HobA-dependent DnaA oligomerization leading to DNA unwinding. More generally, the parallel we draw with Escherichia coli DnaA and DiaA (HobA-like E. coli protein) will direct new studies that will contribute to the understanding of bacterial DNA replication.
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Affiliation(s)
- Laurent Terradot
- Macromolecular Crystallography Group ESRF; Grenoble Cedex, France,Institut de Biologie et Chimie des Protéines; UMR 5086 CNRS Université de Lyon; IFR128; Biologie Structurale des Complexes Macromoléculaires Bactériens; Lyon, France
| | - Anna Zawilak-Pawlik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy; Polish Academy of Sciences; Microbiology Department; Wroclaw, Poland
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Jiménez-Soto LF, Kutter S, Sewald X, Ertl C, Weiss E, Kapp U, Rohde M, Pirch T, Jung K, Retta SF, Terradot L, Fischer W, Haas R. Helicobacter pylori type IV secretion apparatus exploits beta1 integrin in a novel RGD-independent manner. PLoS Pathog 2009. [PMID: 19997503 DOI: 10.1371/journal.ppat.1000684.t001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Translocation of the Helicobacter pylori (Hp) cytotoxin-associated gene A (CagA) effector protein via the cag-Type IV Secretion System (T4SS) into host cells is a major risk factor for severe gastric diseases, including gastric cancer. However, the mechanism of translocation and the requirements from the host cell for that event are not well understood. The T4SS consists of inner- and outer membrane-spanning Cag protein complexes and a surface-located pilus. Previously an arginine-glycine-aspartate (RGD)-dependent typical integrin/ligand type interaction of CagL with alpha5beta1 integrin was reported to be essential for CagA translocation. Here we report a specific binding of the T4SS-pilus-associated components CagY and the effector protein CagA to the host cell beta1 Integrin receptor. Surface plasmon resonance measurements revealed that CagA binding to alpha5beta1 integrin is rather strong (dissociation constant, K(D) of 0.15 nM), in comparison to the reported RGD-dependent integrin/fibronectin interaction (K(D) of 15 nM). For CagA translocation the extracellular part of the beta1 integrin subunit is necessary, but not its cytoplasmic domain, nor downstream signalling via integrin-linked kinase. A set of beta1 integrin-specific monoclonal antibodies directed against various defined beta1 integrin epitopes, such as the PSI, the I-like, the EGF or the beta-tail domain, were unable to interfere with CagA translocation. However, a specific antibody (9EG7), which stabilises the open active conformation of beta1 integrin heterodimers, efficiently blocked CagA translocation. Our data support a novel model in which the cag-T4SS exploits the beta1 integrin receptor by an RGD-independent interaction that involves a conformational switch from the open (extended) to the closed (bent) conformation, to initiate effector protein translocation.
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Affiliation(s)
- Luisa F Jiménez-Soto
- Max von Pettenkofer-Institute for Hygiene and Medical Microbiology, Ludwig-Maximilians-Universität, München, Germany
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41
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Tosi T, Cioci G, Jouravleva K, Dian C, Terradot L. Structures of the tumor necrosis factor alpha inducing protein Tipalpha: a novel virulence factor from Helicobacter pylori. FEBS Lett 2009; 583:1581-5. [PMID: 19401200 DOI: 10.1016/j.febslet.2009.04.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 04/08/2009] [Accepted: 04/20/2009] [Indexed: 12/15/2022]
Abstract
Helicobacter pylori secretes a unique virulence factor, Tipalpha, that enters gastric cells and both stimulates the production of the TNF-alpha and activates the NF-kappaB pathway. The structures of a truncated version of Tipalpha (TipalphaN34) in two crystal forms are presented here. Tipalpha adopts a novel beta(1)alpha(1)alpha(2)beta(2)beta(3)alpha(3)alpha(4) topology that can be described as a combination of three domains. A first region consists in a short flexible extension, a second displays a dodecin-like fold and a third is a helical bundle domain similar to the sterile alpha motif (SAM). Analysis of the oligomerisation states of TipalphaN34 in the crystals and in solution suggests that the disulfide bridges could hold together Tipalpha monomers during their secretion in the gastric environment.
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Affiliation(s)
- Tommaso Tosi
- European Synchrotron Radiation Facility, MX Group, Grenoble Cedex 9, France
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42
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Angelini A, Cendron L, Goncalves S, Zanotti G, Terradot L. Structural and enzymatic characterization of HP0496, a YbgC thioesterase from Helicobacter pylori. Proteins 2009; 72:1212-21. [PMID: 18338382 DOI: 10.1002/prot.22014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
YbgC proteins are bacterial acyl-CoA thioesterases associated with the Tol-Pal system. This system is important for cell envelope integrity and is part of the cell division machinery. In E. coli, YbgC associates with the cell membrane and is part of a protein network involved in lipid biogenesis. In the human pathogen Helicobacter pylori, a putative homologue of YbgC, named HP0496, was found to interact with the cytotoxin CagA by two different studies. We have determined its crystal structure and characterized its enzymatic activity. The structure of HP0496 shows that it is a member of the hot-dog family of proteins, with a epsilongamma tetrameric arrangement. Finally, enzymatic assays performed with the purified protein showed that HP0496 is an acyl-CoA thioesterase that favors long-chain substrates.
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Affiliation(s)
- Alessandro Angelini
- Macromolecular Crystallography Group, European Synchrotron Radiation Facility, B.P. 220, 6 rue Jules Horowitz, F-38043 Grenoble Cedex, France
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Angelini A, Tosi T, Mas P, Acajjaoui S, Zanotti G, Terradot L, Hart DJ. Expression of Helicobacter pylori CagA domains by library-based construct screening. FEBS J 2009; 276:816-24. [DOI: 10.1111/j.1742-4658.2008.06826.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Loguercio S, Dian C, Flagiello A, Scannella A, Pucci P, Terradot L, Zagari A. In HspA from Helicobacter pylori vicinal disulfide bridges are a key determinant of domain B structure. FEBS Lett 2008; 582:3537-41. [PMID: 18805417 DOI: 10.1016/j.febslet.2008.09.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 09/10/2008] [Indexed: 01/22/2023]
Abstract
Helicobacter pylori produces a heat shock protein A (HspA) that is unique to this bacteria. While the first 91 residues (domain A) of the protein are similar to GroES, the last 26 (domain B) are unique to HspA. Domain B contains eight histidines and four cysteines and was suggested to bind nickel. We have produced HspA and two mutants: Cys94Ala and Cys94Ala/Cys111Ala and identified the disulfide bridge pattern of the protein. We found that the cysteines are engaged in three disulfide bonds: Cys51/Cys53, Cys94/Cys111 and Cys95/Cys112 that result in a unique closed loop structure for the domain B.
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Affiliation(s)
- Salvatore Loguercio
- Department of Biological Sciences and CNISM, University of Naples "Federico II", Via Mezzocannone 16, I-80134 Naples, Italy
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Natrajan G, Hall DR, Thompson AC, Gutsche I, Terradot L. Structural similarity between the DnaA-binding proteins HobA (HP1230) from Helicobacter pylori and DiaA from Escherichia coli. Mol Microbiol 2007; 65:995-1005. [PMID: 17683397 DOI: 10.1111/j.1365-2958.2007.05843.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In prokaryotes, DNA replication is initiated by the binding of DnaA to the oriC region of the chromosome to load the primosome machinery and start a new replication round. Several proteins control these events in Escherichia coli to ensure that replication is precisely timed during the cell cycle. Here, we report the crystal structure of HobA (HP1230) at 1.7 A, a recently discovered protein that specifically interacts with DnaA protein from Helicobacter pylori (HpDnaA). We found that the closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. Remarkably, SIS proteins share strong sequence homology with DiaA from E. coli; yet, HobA and DiaA share no sequence homology. Thus, by solving the structure of HobA, we unexpectedly discovered that HobA is a H. pylori structural homologue of DiaA. By comparing the structure of HobA to a homology model of DiaA, we identified conserved, surface-accessible residues that could be involved in protein-protein interaction. Finally, we show that HobA specifically interacts with the N-terminal part of HpDnaA. The structural homology between DiaA and HobA strongly supports their involvement in the replication process and these proteins could define a new structural family of replication regulators in bacteria.
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Affiliation(s)
- Ganesh Natrajan
- Macromolecular Crystallography Group, European Synchrotron Radiation Facility, B.P. 220, 6 rue Jules Horowitz, F-38043 Grenoble Cedex, France
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Fauquant C, Diederix REM, Rodrigue A, Dian C, Kapp U, Terradot L, Mandrand-Berthelot MA, Michaud-Soret I. pH dependent Ni(II) binding and aggregation of Escherichia coli and Helicobacter pylori NikR. Biochimie 2006; 88:1693-705. [PMID: 16930800 DOI: 10.1016/j.biochi.2006.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Accepted: 07/19/2006] [Indexed: 11/30/2022]
Abstract
NikR proteins are bacterial metallo-regulatory transcription factors that control the expression of the nickel uptake system and/or nickel containing enzymes such as urease, and are involved in the acid stress response. Here, a comparative study is reported on NikR from Helicobacter pylori (HpNikR) and Escherichia coli (EcNikR), as well as the Q2E mutant of EcNikR. Most attention was focused on the Ni(II) binding properties of these proteins, as a function of pH. The influence of the pH on the Ni(II) binding and aggregation properties was studied using gel filtration analysis and UV-visible absorption spectroscopy in the presence of an increasing concentration of nickel. Q2E and wt EcNikR are identical in Ni(II) binding but the Q2E mutant is impaired to some extent in DNA-binding. For EcNikR it is shown that between pH 6 and 8, addition of Ni(II) above 1 equiv. induces mass aggregation and precipitation, concomitant with binding of Ni(II) up to a maximum of 5-8 Ni(II) ions per monomer. The Ni(II) site with highest affinity is the well-described square planar site with three histidines and one cysteine ligands. Aggregation is complete in the presence of less than 1 extra equiv. of Ni(II) and aggregation is fully reversible and precipitates are rapidly solubilized by addition of EDTA. The sensitivity of EcNikR to aggregation decreases with decreasing pH, concurrent with histidines being the main ligands of the site responsible for aggregation. HpNikR does not display aggregation except at alkaline pH, where 3 Ni(II) equiv. are needed. The participation of a cluster consisting of surface-exposed histidines present in EcNikR but not in HpNikR, is proposed to be involved in aggregation. Our results on HpNikR are compatible with the crystallographic data and with the ability of this protein to bind more than one nickel.
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Affiliation(s)
- C Fauquant
- Laboratoire de Physicochimie Des Métaux en Biologie, Département Réponse et Dynamique et Cellulaires, CEA-Grenoble, 17, avenue des Martyrs, 38054 Grenoble cedex 9, France
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47
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Dian C, Schauer K, Kapp U, McSweeney SM, Labigne A, Terradot L. Structural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel-bound states. J Mol Biol 2006; 361:715-30. [PMID: 16872629 DOI: 10.1016/j.jmb.2006.06.058] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 06/13/2006] [Accepted: 06/22/2006] [Indexed: 12/28/2022]
Abstract
The survival of Helicobacter pylori in the human stomach critically relies on the availability and use of nickel, an absolute cofactor of the important virulence determinant urease. Nickel-responsive gene regulation is mediated by HpNikR, a protein belonging to the ribbon-helix-helix family of transcriptional regulators. Unlike its homologues, HpNikR acts as both a repressor and an activator within an acid adaptation cascade. We report the crystal structure of the full-length HpNikR in a nickel-free conformation and two nickel-bound structures obtained in different conditions: Ni1-HpNikR and Ni2-HpNikR. Apo-HpNikR shows the same global fold as its bacterial homologues although with an unusual closed trans-conformation and asymmetrical quaternary arrangement. The structure of Ni1-HpNikR in the presence of nickel has two different sides, one showing nickel binding similar to that of known NikRs and the other reflecting an intermediate state. The structure of Ni2-HpNikR obtained using a shorter exposure to nickel provides another snapshot of the nickel incorporation. Altogether, the three structures have allowed us to determine the route for nickel within HpNikR and reveal the cooperativity between the tetramerization domain and the DNA-binding domain. Experiments using point mutations of HpnikR residues involved in nickel internalisation confirm that these residues are critical for HpNikR functions in vivo.
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Affiliation(s)
- Cyril Dian
- The European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble Cedex 9, France
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48
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Terradot L, Bayliss R, Oomen C, Leonard G, Waksman G. Structural biology of Type IV secretion system. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305089798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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49
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Terradot L, Bayliss R, Oomen C, Leonard GA, Baron C, Waksman G. Structures of two core subunits of the bacterial type IV secretion system, VirB8 from Brucella suis and ComB10 from Helicobacter pylori. Proc Natl Acad Sci U S A 2005; 102:4596-601. [PMID: 15764702 PMCID: PMC555499 DOI: 10.1073/pnas.0408927102] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Type IV secretion systems (T4SSs) are commonly used secretion machineries in Gram-negative bacteria. They are used in the infection of human, animal, or plant cells and the propagation of antibiotic resistance. The T4SS apparatus spans both membranes of the bacterium and generally is composed of 12 proteins, named VirB1-11 and VirD4 after proteins of the canonical Agrobacterium tumefaciens T4SS. The periplasmic core complex of VirB8/VirB10 structurally and functionally links the cytoplasmic NTPases of the system with its outer membrane and pilus components. Here we present crystal structures of VirB8 of Brucella suis, the causative agent of brucellosis, and ComB10, a VirB10 homolog of Helicobacter pylori, the causative agent of gastric ulcers. The structures of VirB8 and ComB10 resemble known folds, albeit with novel secondary-structure modifications unique to and conserved within their respective families. Both proteins crystallized as dimers, providing detailed predictions about their self associations. These structures make a substantial contribution to the repertoire of T4SS component structures and will serve as springboards for future functional and protein-protein interaction studies by using knowledge-based site-directed and deletion mutagenesis.
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Affiliation(s)
- Laurent Terradot
- Institute of Structural Molecular Biology, Malet Street, London WC1E 7HX, UK
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50
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Leiros HKS, Kozielski-Stuhrmann S, Kapp U, Terradot L, Leonard GA, McSweeney SM. Structural basis of 5-nitroimidazole antibiotic resistance: the crystal structure of NimA from Deinococcus radiodurans. J Biol Chem 2004; 279:55840-9. [PMID: 15492014 DOI: 10.1074/jbc.m408044200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
5-Nitroimidazole-based antibiotics are compounds extensively used for treating infections in humans and animals caused by several important pathogens. They are administered as prodrugs, and their activation depends upon an anaerobic 1-electron reduction of the nitro group by a reduction pathway in the cells. Bacterial resistance toward these drugs is thought to be caused by decreased drug uptake and/or an altered reduction efficiency. One class of resistant strains, identified in Bacteroides, has been shown to carry Nim genes (NimA, -B, -C, -D, and -E), which encode for reductases that convert the nitro group on the antibiotic into a non-bactericidal amine. In this paper, we have described the crystal structure of NimA from Deinococcus radiodurans (drNimA) at 1.6 A resolution. We have shown that drNimA is a homodimer in which each monomer adopts a beta-barrel fold. We have identified the catalytically important His-71 along with the cofactor pyruvate and antibiotic binding sites, all of which are found at the monomer-monomer interface. We have reported three additional crystal structures of drNimA, one in which the antibiotic metronidazole is bound to the protein, one with pyruvate covalently bound to His-71, and one with lactate covalently bound to His-71. Based on these structures, a reaction mechanism has been proposed in which the 2-electron reduction of the antibiotic prevents accumulation of the toxic nitro radical. This mechanism suggests that Nim proteins form a new class of reductases, conferring resistance against 5-nitroimidazole-based antibiotics.
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Affiliation(s)
- Hanna-Kirsti S Leiros
- Macromolecular Crystallography Group, European Synchrotron Radiation Facility, BP 220, 6 Rue Jules Horowitz, F-38043 Grenoble Cedex 09, France
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