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Denic M, Turlin E, Michel V, Fischer F, Khorasani-Motlagh M, Zamble D, Vinella D, de Reuse H. A novel mode of control of nickel uptake by a multifunctional metallochaperone. PLoS Pathog 2021; 17:e1009193. [PMID: 33444370 PMCID: PMC7840056 DOI: 10.1371/journal.ppat.1009193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/27/2021] [Accepted: 11/26/2020] [Indexed: 01/08/2023] Open
Abstract
Cellular metal homeostasis is a critical process for all organisms, requiring tight regulation. In the major pathogen Helicobacter pylori, the acquisition of nickel is an essential virulence determinant as this metal is a cofactor for the acid-resistance enzyme, urease. Nickel uptake relies on the NixA permease and the NiuBDE ABC transporter. Till now, bacterial metal transporters were reported to be controlled at their transcriptional level. Here we uncovered post-translational regulation of the essential Niu transporter in H. pylori. Indeed, we demonstrate that SlyD, a protein combining peptidyl-prolyl isomerase (PPIase), chaperone, and metal-binding properties, is required for the activity of the Niu transporter. Using two-hybrid assays, we found that SlyD directly interacts with the NiuD permease subunit and identified a motif critical for this contact. Mutants of the different SlyD functional domains were constructed and used to perform in vitro PPIase activity assays and four different in vivo tests measuring nickel intracellular accumulation or transport in H. pylori. In vitro, SlyD PPIase activity is down-regulated by nickel, independently of its C-terminal region reported to bind metals. In vivo, a role of SlyD PPIase function was only revealed upon exposure to high nickel concentrations. Most importantly, the IF chaperone domain of SlyD was shown to be mandatory for Niu activation under all in vivo conditions. These data suggest that SlyD is required for the active functional conformation of the Niu permease and regulates its activity through a novel mechanism implying direct protein interaction, thereby acting as a gatekeeper of nickel uptake. Finally, in agreement with a central role of SlyD, this protein is essential for the colonization of the mouse model by H. pylori. Metal ions are essential for the viability of all living organisms. Indeed, more than one-third of all proteins need metal cofactors for their function. Intracellular metal concentrations require tight control as non-physiological amounts are very toxic. In particular, nickel plays a unique role in Helicobacter pylori, a bacterial pathogen that colonizes the stomach of about half of the human population worldwide and is associated with the development of gastric cancer. Nickel is essential for H. pylori as it is the cofactor of urease, an enzyme indispensable for resistance to the gastric acidity of the stomach and thus for in vivo colonization. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms. Till now, control of nickel uptake was only reported to rely on transcriptional regulators. In the present study, we uncovered a novel mechanism of regulation of nickel acquisition. SlyD, a multifunctional enzyme was found to control, by direct protein interaction, the activity of an essential nickel uptake system in H. pylori. We revealed that the SlyD chaperone activity is mandatory for the active conformation and thus functionality of the nickel permease.
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Affiliation(s)
- Milica Denic
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
- Université de Paris, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Evelyne Turlin
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
| | - Valérie Michel
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
| | - Frédéric Fischer
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, Strasbourg, France
| | | | - Deborah Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Vinella
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
- * E-mail: (DV); (HDR)
| | - Hilde de Reuse
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
- * E-mail: (DV); (HDR)
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Yaseen A, Audette GF. Structural flexibility in the Helicobacter pylori peptidyl-prolyl cis,trans-isomerase HP0175 is achieved through an extension of the chaperone helices. J Struct Biol 2018; 204:261-269. [PMID: 30179659 DOI: 10.1016/j.jsb.2018.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 01/19/2023]
Abstract
Helicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like receptor 4 (TLR4). Here, we report the structure of apo-HP0175 at 2.09 Å with a single monomer in the asymmetric unit. Chromatographic, light scattering and mass spectrometric analysis of HP0175 in solution indicate that the protein is mainly monomeric under low salt conditions, while increasing ionic interactions facilitates protein dimerization. A comparison of the apo-HP0175 structure to that of the indole-2-carboxylic acid-bound form shows movement of the N- and C-terminal helices upon interaction of the catalytic residues in the binding pocket. Helix extension of the N/C chaperone domains between apo and I2CA-bound HP0175 supports previous findings in parvulin PPIases for their role in protein stabilization (and accommodation of variable protein lengths) of those undergoing catalysis.
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Affiliation(s)
- Ayat Yaseen
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Gerald F Audette
- Department of Chemistry, York University, Toronto M3J 1P3, Canada; Centre for Research of Biomolecular Interactions, York University, Toronto M3J 1P3, Canada.
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Dantu SC, Khavnekar S, Kale A. Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study. J Biomol Struct Dyn 2016; 35:2186-2196. [DOI: 10.1080/07391102.2016.1209131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sarath Chandra Dantu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sagar Khavnekar
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
| | - Avinash Kale
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
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