1
|
Petit-Hartlein I, Vermot A, Thepaut M, Humm AS, Dupeux F, Dupuy J, Chaptal V, Marquez JA, Smith SME, Fieschi F. X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX. eLife 2024; 13:RP93759. [PMID: 38640072 PMCID: PMC11031084 DOI: 10.7554/elife.93759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024] Open
Abstract
NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2's requirement for activation.
Collapse
Affiliation(s)
| | - Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | - Michel Thepaut
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | | | - Florine Dupeux
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
- European Molecular Biology LaboratoryGrenobleFrance
| | - Jerome Dupuy
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | | | | | - Susan ME Smith
- Department of Molecular and Cellular Biology, Kennesaw State UniversityKennesawUnited States
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
- Institut Universitaire de FranceParisFrance
| |
Collapse
|
2
|
Caux C, Guigliarelli B, Vivès C, Biaso F, Horeau M, Hassoune H, Petit-Hartlein I, Juillan-Binard C, Torelli S, Fieschi F, Nivière V. Membrane-Bound Flavocytochrome MsrQ Is a Substrate of the Flavin Reductase Fre in Escherichia coli. ACS Chem Biol 2021; 16:2547-2559. [PMID: 34550690 DOI: 10.1021/acschembio.1c00613] [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] [Indexed: 11/30/2022]
Abstract
MsrPQ is a new type of methionine sulfoxide reductase (Msr) system found in bacteria. It is specifically involved in the repair of periplasmic methionine residues that are oxidized by hypochlorous acid. MsrP is a periplasmic molybdoenzyme that carries out the Msr activity, whereas MsrQ, an integral membrane-bound hemoprotein, acts as the physiological partner of MsrP to provide electrons for catalysis. Although MsrQ (YedZ) was associated since long with a protein superfamily named FRD (ferric reductase domain), including the eukaryotic NADPH oxidases and STEAP proteins, its biochemical properties are still sparsely documented. Here, we have investigated the cofactor content of the E. coli MsrQ and its mechanism of reduction by the flavin reductase Fre. We showed by electron paramagnetic resonance (EPR) spectroscopy that MsrQ contains a single highly anisotropic low-spin (HALS) b-type heme located on the periplasmic side of the membrane. We further demonstrated that MsrQ holds a flavin mononucleotide (FMN) cofactor that occupies the site where a second heme binds in other members of the FDR superfamily on the cytosolic side of the membrane. EPR spectroscopy indicates that the FMN cofactor can accommodate a radical semiquinone species. The cytosolic flavin reductase Fre was previously shown to reduce the MsrQ heme. Here, we demonstrated that Fre uses the FMN MsrQ cofactor as a substrate to catalyze the electron transfer from cytosolic NADH to the heme. Formation of a specific complex between MsrQ and Fre could favor this unprecedented mechanism, which most likely involves transfer of the reduced FMN cofactor from the Fre active site to MsrQ.
Collapse
Affiliation(s)
- Christelle Caux
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Bruno Guigliarelli
- CNRS, BIP-UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Univ., Marseille 13402, France
| | - Corinne Vivès
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Frédéric Biaso
- CNRS, BIP-UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Univ., Marseille 13402, France
| | - Marius Horeau
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Hawra Hassoune
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | | | - Céline Juillan-Binard
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Stephane Torelli
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| | - Franck Fieschi
- CNRS, CEA, Institut de Biologie Structurale, Univ. Grenoble Alpes, Grenoble 38044, France
| | - Vincent Nivière
- CNRS, CEA, IRIG-LCBM, Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, Grenoble 38054, France
| |
Collapse
|
3
|
Breyton C, Javed W, Vermot A, Arnaud CA, Hajjar C, Dupuy J, Petit-Hartlein I, Le Roy A, Martel A, Thépaut M, Orelle C, Jault JM, Fieschi F, Porcar L, Ebel C. Assemblies of lauryl maltose neopentyl glycol (LMNG) and LMNG-solubilized membrane proteins. Biochim Biophys Acta Biomembr 2019; 1861:939-957. [PMID: 30776334 DOI: 10.1016/j.bbamem.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
Laurylmaltose neopentylglycol (LMNG) bears two linked hydrophobic chains of equal length and two hydrophilic maltoside groups. It arouses a strong interest in the field of membrane protein biochemistry, since it was shown to efficiently solubilize and stabilize membrane proteins often better than the commonly used dodecylmaltopyranoside (DDM), and to allow structure determination of some challenging membrane proteins. However, LMNG was described to form large micelles, which could be unfavorable for structural purposes. We thus investigated its auto-assemblies and the association state of different membrane proteins solubilized in LMNG by analytical ultracentrifugation, size exclusion chromatography coupled to light scattering, centrifugation on sucrose gradient and/or small angle scattering. At high concentrations (in the mM range), LMNG forms long rods, and it stabilized the membrane proteins investigated herein, i.e. a bacterial multidrug transporter, BmrA; a prokaryotic analogous of the eukaryotic NADPH oxidases, SpNOX; an E. coli outer membrane transporter, FhuA; and the halobacterial bacteriorhodopsin, bR. BmrA, in the Apo and the vanadate-inhibited forms showed reduced kinetics of limited proteolysis in LMNG compared to DDM. Both SpNOX and BmrA display an increased specific activity in LMNG compared to DDM. The four proteins form LMNG complexes with their usual quaternary structure and with usual amount of bound detergent. No heterogeneous complexes related to the large micelle size of LMNG alone were observed. In conditions where LMNG forms assemblies of large size, FhuA crystals diffracting to 4.0 Å were obtained by vapor diffusion. LMNG large micelle size thus does not preclude membrane protein homogeneity and crystallization.
Collapse
Affiliation(s)
- Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Waqas Javed
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France; University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Charles-Adrien Arnaud
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Christine Hajjar
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Jérôme Dupuy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Isabelle Petit-Hartlein
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Anne Martel
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Lionel Porcar
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France.
| |
Collapse
|
4
|
Juillan-Binard C, Picciocchi A, Andrieu JP, Dupuy J, Petit-Hartlein I, Caux-Thang C, Vivès C, Nivière V, Fieschi F. A Two-component NADPH Oxidase (NOX)-like System in Bacteria Is Involved in the Electron Transfer Chain to the Methionine Sulfoxide Reductase MsrP. J Biol Chem 2016; 292:2485-2494. [PMID: 28028176 DOI: 10.1074/jbc.m116.752014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 08/04/2016] [Revised: 12/21/2016] [Indexed: 01/22/2023] Open
Abstract
MsrPQ is a newly identified methionine sulfoxide reductase system found in bacteria, which appears to be specifically involved in the repair of periplasmic proteins oxidized by hypochlorous acid. It involves two proteins: a periplasmic one, MsrP, previously named YedY, carrying out the Msr activity, and MsrQ, an integral b-type heme membrane-spanning protein, which acts as the specific electron donor to MsrP. MsrQ, previously named YedZ, was mainly characterized by bioinformatics as a member of the FRD superfamily of heme-containing membrane proteins, which include the NADPH oxidase proteins (NOX/DUOX). Here we report a detailed biochemical characterization of the MsrQ protein from Escherichia coli We optimized conditions for the overexpression and membrane solubilization of an MsrQ-GFP fusion and set up a purification scheme allowing the production of pure MsrQ. Combining UV-visible spectroscopy, heme quantification, and site-directed mutagenesis of histidine residues, we demonstrated that MsrQ is able to bind two b-type hemes through the histidine residues conserved between the MsrQ and NOX protein families. In addition, we identify the E. coli flavin reductase Fre, which is related to the dehydrogenase domain of eukaryotic NOX enzymes, as an efficient cytosolic electron donor to the MsrQ heme moieties. Cross-linking experiments as well as surface Plasmon resonance showed that Fre interacts with MsrQ to form a specific complex. Taken together, these data support the identification of the first prokaryotic two-component protein system related to the eukaryotic NOX family and involved in the reduction of periplasmic oxidized proteins.
Collapse
Affiliation(s)
- Céline Juillan-Binard
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Antoine Picciocchi
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Jean-Pierre Andrieu
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Jerome Dupuy
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Isabelle Petit-Hartlein
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Christelle Caux-Thang
- the Université Grenoble Alpes, Grenoble.,CNRS LCBM UMR 5249, Grenoble, and.,CEA-DRF-BIG-Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, 38054 Grenoble, France
| | - Corinne Vivès
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble.,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| | - Vincent Nivière
- the Université Grenoble Alpes, Grenoble.,CNRS LCBM UMR 5249, Grenoble, and.,CEA-DRF-BIG-Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, 38054 Grenoble, France
| | - Franck Fieschi
- From the Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 38044 Grenoble, .,the IBS, Commissariat à l'Energie Atomique (CEA), 38027 Grenoble.,the IBS, CNRS, 38027 Grenoble
| |
Collapse
|
5
|
Picciocchi A, Šiaučiūnaiteė-Gaubard L, Petit-Hartlein I, Sadir R, Revilloud J, Caro L, Vivaudou M, Fieschi F, Moreau C, Vivès C. C-terminal engineering of CXCL12 and CCL5 chemokines: functional characterization by electrophysiological recordings. PLoS One 2014; 9:e87394. [PMID: 24498095 PMCID: PMC3909184 DOI: 10.1371/journal.pone.0087394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 07/26/2013] [Accepted: 12/21/2013] [Indexed: 11/18/2022] Open
Abstract
Chemokines are chemotactic cytokines comprised of 70–100 amino acids. The chemokines CXCL12 and CCL5 are the endogenous ligands of the CXCR4 and CCR5 G protein-coupled receptors that are also HIV co-receptors. Biochemical, structural and functional studies of receptors are ligand-consuming and the cost of commercial chemokines hinders their use in such studies. Here, we describe methods for the expression, refolding, purification, and functional characterization of CXCL12 and CCL5 constructs incorporating C-terminal epitope tags. The model tags used were hexahistidines and Strep-Tag for affinity purification, and the double lanthanoid binding tag for fluorescence imaging and crystal structure resolution. The ability of modified and purified chemokines to bind and activate CXCR4 and CCR5 receptors was tested in Xenopus oocytes expressing the receptors, together with a Kir3 G-protein activated K+ channel that served as a reporter of receptor activation. Results demonstrate that tags greatly influence the biochemical properties of the recombinant chemokines. Besides, despite the absence of any evidence for CXCL12 or CCL5 C-terminus involvement in receptor binding and activation, we demonstrated unpredictable effects of tag insertion on the ligand apparent affinity and efficacy or on the ligand dissociation. These tagged chemokines should constitute useful tools for the selective purification of properly-folded chemokines receptors and the study of their native quaternary structures.
Collapse
Affiliation(s)
- Antoine Picciocchi
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Lina Šiaučiūnaiteė-Gaubard
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Isabelle Petit-Hartlein
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Rabia Sadir
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Jean Revilloud
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Lydia Caro
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Michel Vivaudou
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Franck Fieschi
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- Institut Universitaire de France, Paris, France
| | - Christophe Moreau
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- * E-mail: (CM); (CV)
| | - Corinne Vivès
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CEA, DSV/IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- * E-mail: (CM); (CV)
| |
Collapse
|
6
|
Trepreau J, de Rosny E, Duboc C, Sarret G, Petit-Hartlein I, Maillard AP, Imberty A, Proux O, Covès J. Spectroscopic characterization of the metal-binding sites in the periplasmic metal-sensor domain of CnrX from Cupriavidus metallidurans CH34. Biochemistry 2011; 50:9036-45. [PMID: 21942751 DOI: 10.1021/bi201031q] [Citation(s) in RCA: 10] [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] [Indexed: 11/30/2022]
Abstract
CnrX, the dimeric metal sensor of the three-protein transmembrane signal transduction complex CnrYXH of Cupriavidus metallidurans CH34, contains one metal-binding site per monomer. Both Ni and Co elicit a biological response and bind the protein in a 3N2O1S coordination sphere with a nearly identical octahedral geometry as shown by the X-ray structure of CnrXs, the soluble domain of CnrX. However, in solution CnrXs is titrated by 4 Co-equiv and exhibits an unexpected intense band at 384 nm that was detected neither by single-crystal spectroscopy nor under anaerobiosis. The data from a combination of spectroscopic techniques (spectrophotometry, electron paramagnetic resonance, X-ray absorption spectroscopy) showed that two sites correspond to those identified by crystallography. The two extra binding sites accommodate Co(II) in an octahedral geometry in the absence of oxygen and are occupied in air by a mixture of low-spin Co(II) as well as EPR-silent Co(III). These extra sites, located at the N-terminus of the protein, are believed to participate to the formation of peroxo-bridged dimers. Accordingly, we hypothesize that the intense band at 384 nm relies on the formation of a binuclear μ-peroxo Co(III) complex. These metal binding sites are not physiologically relevant since they are not detected in full-length NccX, the closest homologue of CnrX. X-ray absorption spectroscopy demonstrates that NccX stabilizes Co(II) in two-binding sites similar to those characterized by crystallography in its soluble counterpart. Nevertheless, the original spectroscopic properties of the extra Co-binding sites are of interest because they are susceptible to be detected in other Co-bound proteins.
Collapse
Affiliation(s)
- Juliette Trepreau
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR 5075, CNRS-CEA-UJF-Grenoble-1, 41, rue Jules Horowitz, 38027 Grenoble Cedex, France
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Mitschler A, Blakeley M, Petit-Hartlein I, Mueller-Dieckmann C, Popov A, Howard E, Haertlein M, Podjarny A. High-resolution X-ray and neutron data collection on antifreeze protein. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309096445] [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: 11/10/2022] Open
|