51
|
Caux-Thang C, Parent A, Sethu R, Maïga A, Blondin G, Latour JM, Duarte V. Single asparagine to arginine mutation allows PerR to switch from PerR box to fur box. ACS Chem Biol 2015; 10:682-6. [PMID: 25486128 DOI: 10.1021/cb500783g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fur family proteins, ubiquitous in prokaryotes, play a pivotal role in microbial survival and virulence in most pathogens. Metalloregulators, such as Fur and PerR, regulate the transcription of genes connected to iron homeostasis and response to oxidative stress, respectively. In Bacillus subtilis, Fur and PerR bind with high affinity to DNA sequences differing at only two nucleotides. In addition to these differences in the PerR and Fur boxes, we identify in this study a residue located on the DNA binding motif of the Fur protein that is critical to discrimination between the two close DNA sequences. Interestingly, when this residue is introduced into PerR, it lowers the affinity of PerR for its own DNA target but confers to the protein the ability to interact strongly with the Fur DNA binding sequence. The present data show how two closely related proteins have distinct biological properties just by changing a single residue.
Collapse
Affiliation(s)
| | - Aubérie Parent
- Université Grenoble Alpes, LCBM, F-38054 Grenoble, France
| | | | | | | | | | | |
Collapse
|
52
|
Molecular characterization of a homolog of the ferric-uptake regulator, Fur, from the marine bacterium Marinobacter algicola DG893. Biometals 2014; 28:197-206. [PMID: 25528647 DOI: 10.1007/s10534-014-9815-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
Abstract
Full length recombinant iron regulatory protein, Fur, has been isolated and characterized from the algal-associated marine bacterium Marinobacter algicola DG893. Under nondenaturing conditions the Fur protein behaves on size exclusion chromatography as a dimer while it is monomeric under SDS PAGE conditions. ICP-MS and fluorescence quenching experiments show that Mb-Fur binds a single metal ion (Zn, Mn, or Co) per monomer. Electrophoretic mobility shift assays were used to probe the interaction of Mb-Fur with the purported Fur box in the promoter region upstream of the vibrioferrin biosynthetic operon. Interaction of Mb-Fur with a 100 bp DNA fragment containing the Fur box in the presence of 10 µM Mn, Co or Zn(II) resulted in decreased migration of DNA on a 7.5% polyacrylamide gel. In the absence of the Fur protein or the metal, no interaction is seen. The presence of EDTA in the binding, loading or running buffers also abolished all activity demonstrating the importance of the metal in formation of the promoter-repressor complex. Based on a high degree of similarity between Mb-Fur and its homolog from Pseudomonas aeruginosa (PA) whose X-ray structure is known we developed a structural model for the former which suggested that only one of the several metal binding sites found in other Fur's would be functional. This is consistent with the single metal binding stoichiometry we observed. Since the purported metal binding site was one that has been described as "structural" rather than "functional" in PA and yet the monometallic Mb-Fur retains DNA Fur box binding ability it reopens the question of which site is which, or if different species have adapted the sites for different purposes.
Collapse
|
53
|
Schild F, Kieffer-Jaquinod S, Palencia A, Cobessi D, Sarret G, Zubieta C, Jourdain A, Dumas R, Forge V, Testemale D, Bourguignon J, Hugouvieux V. Biochemical and biophysical characterization of the selenium-binding and reducing site in Arabidopsis thaliana homologue to mammals selenium-binding protein 1. J Biol Chem 2014; 289:31765-31776. [PMID: 25274629 PMCID: PMC4231655 DOI: 10.1074/jbc.m114.571208] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 09/17/2014] [Indexed: 12/19/2022] Open
Abstract
The function of selenium-binding protein 1 (SBP1), present in almost all organisms, has not yet been established. In mammals, SBP1 is known to bind the essential element selenium but the binding site has not been identified. In addition, the SBP family has numerous potential metal-binding sites that may play a role in detoxification pathways in plants. In Arabidopsis thaliana, AtSBP1 over-expression increases tolerance to two toxic compounds for plants, selenium and cadmium, often found as soil pollutants. For a better understanding of AtSBP1 function in detoxification mechanisms, we investigated the chelating properties of the protein toward different ligands with a focus on selenium using biochemical and biophysical techniques. Thermal shift assays together with inductively coupled plasma mass spectrometry revealed that AtSBP1 binds selenium after incubation with selenite (SeO3(2-)) with a ligand to protein molar ratio of 1:1. Isothermal titration calorimetry confirmed the 1:1 stoichiometry and revealed an unexpectedly large value of binding enthalpy suggesting a covalent bond between selenium and AtSBP1. Titration of reduced Cys residues and comparative mass spectrometry on AtSBP1 and the purified selenium-AtSBP1 complex identified Cys(21) and Cys(22) as being responsible for the binding of one selenium. These results were validated by site-directed mutagenesis. Selenium K-edge x-ray absorption near edge spectroscopy performed on the selenium-AtSBP1 complex demonstrated that AtSBP1 reduced SeO3(2-) to form a R-S-Se(II)-S-R-type complex. The capacity of AtSBP1 to bind different metals and selenium is discussed with respect to the potential function of AtSBP1 in detoxification mechanisms and selenium metabolism.
Collapse
Affiliation(s)
- Florie Schild
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Sylvie Kieffer-Jaquinod
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Biologie à Grande Echelle, Université Grenoble Alpes, CEA, INSERM, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Andrés Palencia
- European Molecular Biology Laboratory Outstation, 71 avenue des Martyrs, F-38042 Grenoble, France and Unit for Virus Host-Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, Direction des Sciences du Vivant, Institut de Biologie Structurale, 6 rue Jules Horowitz, F-38044 Grenoble, France
| | - Géraldine Sarret
- Université Grenoble Alpes, CNRS & IRD, ISTerre, BP 53, F-38041 Grenoble, France
| | - Chloé Zubieta
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Agnès Jourdain
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Renaud Dumas
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Vincent Forge
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CEA, CNRS, Institut de Recherches en Technologies et Sciences pour le Vivant, 17 rue des Martyrs, F-38000 Grenoble, France, and
| | - Denis Testemale
- Université Grenoble Alpes, CNRS, Institut NEEL, 25 rue des Martyrs, F-38042 Grenoble, France
| | - Jacques Bourguignon
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359
| | - Véronique Hugouvieux
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CEA, Université Grenoble Alpes, CNRS UMR5168, INRA USC1359,.
| |
Collapse
|
54
|
Butler CA, Dashper SG, Zhang L, Seers CA, Mitchell HL, Catmull DV, Glew MD, Heath JE, Tan Y, Khan HSG, Reynolds EC. The Porphyromonas gingivalis ferric uptake regulator orthologue binds hemin and regulates hemin-responsive biofilm development. PLoS One 2014; 9:e111168. [PMID: 25375181 PMCID: PMC4222909 DOI: 10.1371/journal.pone.0111168] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/26/2014] [Indexed: 12/27/2022] Open
Abstract
Porphyromonas gingivalis is a Gram-negative pathogen associated with the biofilm-mediated disease chronic periodontitis. P. gingivalis biofilm formation is dependent on environmental heme for which P. gingivalis has an obligate requirement as it is unable to synthesize protoporphyrin IX de novo, hence P. gingivalis transports iron and heme liberated from the human host. Homeostasis of a variety of transition metal ions is often mediated in Gram-negative bacteria at the transcriptional level by members of the Ferric Uptake Regulator (Fur) superfamily. P. gingivalis has a single predicted Fur superfamily orthologue which we have designated Har (heme associated regulator). Recombinant Har formed dimers in the presence of Zn2+ and bound one hemin molecule per monomer with high affinity (Kd of 0.23 µM). The binding of hemin resulted in conformational changes of Zn(II)Har and residue 97Cys was involved in hemin binding as part of a predicted -97C-98P-99L- hemin binding motif. The expression of 35 genes was down-regulated and 9 up-regulated in a Har mutant (ECR455) relative to wild-type. Twenty six of the down-regulated genes were previously found to be up-regulated in P. gingivalis grown as a biofilm and 11 were up-regulated under hemin limitation. A truncated Zn(II)Har bound the promoter region of dnaA (PGN_0001), one of the up-regulated genes in the ECR455 mutant. This binding decreased as hemin concentration increased which was consistent with gene expression being regulated by hemin availability. ECR455 formed significantly less biofilm than the wild-type and unlike wild-type biofilm formation was independent of hemin availability. P. gingivalis possesses a hemin-binding Fur orthologue that regulates hemin-dependent biofilm formation.
Collapse
Affiliation(s)
- Catherine A. Butler
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Stuart G. Dashper
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Lianyi Zhang
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Christine A. Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Helen L. Mitchell
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Deanne V. Catmull
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Michelle D. Glew
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Jacqueline E. Heath
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Yan Tan
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Hasnah S. G. Khan
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Eric C. Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
- * E-mail:
| |
Collapse
|
55
|
Gilston BA, Wang S, Marcus MD, Canalizo-Hernández MA, Swindell EP, Xue Y, Mondragón A, O'Halloran TV. Structural and mechanistic basis of zinc regulation across the E. coli Zur regulon. PLoS Biol 2014; 12:e1001987. [PMID: 25369000 PMCID: PMC4219657 DOI: 10.1371/journal.pbio.1001987] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/22/2014] [Indexed: 11/18/2022] Open
Abstract
Structural, thermodynamic, and gene expression studies provide a comprehensive picture of how the bacterial metalloregulatory transcriptional repressor Zur achieves its exquisite sensitivity to zinc concentrations. Commensal microbes, whether they are beneficial or pathogenic, are sensitive to host processes that starve or swamp the prokaryote with large fluctuations in local zinc concentration. To understand how microorganisms coordinate a dynamic response to changes in zinc availability at the molecular level, we evaluated the molecular mechanism of the zinc-sensing zinc uptake regulator (Zur) protein at each of the known Zur-regulated genes in Escherichia coli. We solved the structure of zinc-loaded Zur bound to the PznuABC promoter and show that this metalloregulatory protein represses gene expression by a highly cooperative binding of two adjacent dimers to essentially encircle the core element of each of the Zur-regulated promoters. Cooperativity in these protein-DNA interactions requires a pair of asymmetric salt bridges between Arg52 and Asp49′ that connect otherwise independent dimers. Analysis of the protein-DNA interface led to the discovery of a new member of the Zur-regulon: pliG. We demonstrate this gene is directly regulated by Zur in a zinc responsive manner. The pliG promoter forms stable complexes with either one or two Zur dimers with significantly less protein-DNA cooperativity than observed at other Zur regulon promoters. Comparison of the in vitro Zur-DNA binding affinity at each of four Zur-regulon promoters reveals ca. 10,000-fold variation Zur-DNA binding constants. The degree of Zur repression observed in vivo by comparison of transcript copy number in wild-type and Δzur strains parallels this trend spanning a 100-fold difference. We conclude that the number of ferric uptake regulator (Fur)-family dimers that bind within any given promoter varies significantly and that the thermodynamic profile of the Zur-DNA interactions directly correlates with the physiological response at different promoters. Zinc is an essential nutrient for most organisms, with the Zn2+ ion performing numerous structural, regulatory, and catalytic roles in a range of proteins. However, this nutrient can neither be synthesized nor degraded and individual cells need to be able to maintain steady levels of zinc in the face of near-zero or excessively high environmental concentrations. Here we look at how the bacterium E. coli does this, by examining the structure and function of Zur, a transcriptional repressor that is exquisitely sensitive to Zn2+ concentration. Although the structures of related Zur proteins on their own are known, here we show how E. coli protein binds to DNA and explain its extreme sensitivity and specificity (it responds to Zn2+ concentrations in the femtomolar range). Our results reveal how the Zur protein switches on and off a bank of bacterial genes that control zinc physiology. Extensive analysis of protein-DNA interactions revealed both a surprising degree of cooperativity and an extremely large range of Zur-DNA binding affinities across the set of genes known as the Zur regulon. The results provide strong support for a controversial idea that the thermodynamics of an ensemble of protein-DNA interactions play a dominant role in the physiological control of gene regulation networks. In addition, we have used our structural and thermodynamic analysis to identify a novel gene target of Zur regulation.
Collapse
Affiliation(s)
- Benjamin A. Gilston
- Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Suning Wang
- Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Mason D. Marcus
- Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Mónica A. Canalizo-Hernández
- Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Elden P. Swindell
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Yi Xue
- Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail: (AM); (TVO)
| | - Thomas V. O'Halloran
- Department of Chemistry and The Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail: (AM); (TVO)
| |
Collapse
|
56
|
Mukherjee D, Datta AB, Chakrabarti P. Crystal structure of HlyU, the hemolysin gene transcription activator, from Vibrio cholerae N16961 and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2346-54. [PMID: 25450504 DOI: 10.1016/j.bbapap.2014.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/29/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022]
Abstract
HlyU in Vibrio cholerae is known to be the transcriptional activator of the hemolysin gene, HlyA and possibly a regulator of other virulence factors influencing growth, colonization and pathogenicity of this infective agent. Here we report the crystal structure of HlyU from V. cholerae N16961 (HlyU_Vc) at 1.8Å. The protein, with five α-helices and three β-strands in the topology of α1-α2-β1-α3-α4-β2-β3-α5, forms a homodimer. Helices α3-α4 and a β sheet form the winged helix-turn-helix (wHTH) DNA-binding motif common to the transcription regulators of the SmtB/ArsR family. In spite of an overall fold similar to SmtB/ArsR family, it lacks any metal binding site seen in SmtB. A comparison of the dimeric interfaces showed that the one in SmtB is much larger and have salt bridges that can be disrupted to accommodate metal ions. A model of HlyU-DNA complex suggests bending of the DNA. Cys38 in the structure was found to be modified as sulfenic acid; the oxidized form was not seen in another structure solved under reducing condition. Although devoid of any metal binding site, the presence of a Cys residue exhibiting oxidation-reduction suggests the possibility of the existence of a redox switch in transcription regulation. A structure-based phylogenetic analysis of wHTH proteins revealed the segregation of metal and non-metal binding proteins as well as those in the latter group that are under redox control.
Collapse
Affiliation(s)
- Debadrita Mukherjee
- Bioinformatics Centre, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Ajit Bikram Datta
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Bioinformatics Centre, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India; Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
| |
Collapse
|
57
|
Ciuraszkiewicz J, Śmiga M, Mackiewicz P, Gmiterek A, Bielecki M, Olczak M, Olczak T. Fur homolog regulatesPorphyromonas gingivalisvirulence under low-iron/heme conditions through a complex regulatory network. Mol Oral Microbiol 2014; 29:333-53. [DOI: 10.1111/omi.12077] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2014] [Indexed: 12/22/2022]
Affiliation(s)
- J. Ciuraszkiewicz
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - M. Śmiga
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - P. Mackiewicz
- Department of Genomics; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - A. Gmiterek
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - M. Bielecki
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - M. Olczak
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - T. Olczak
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| |
Collapse
|
58
|
A Mur regulator protein in the extremophilic bacterium Deinococcus radiodurans. PLoS One 2014; 9:e106341. [PMID: 25243898 PMCID: PMC4171365 DOI: 10.1371/journal.pone.0106341] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/29/2014] [Indexed: 12/11/2022] Open
Abstract
Ferric uptake regulator (Fur) is a transcriptional regulator that controls the expression of genes involved in the uptake of iron and manganese, as well as vital nutrients, and is essential for intracellular redox cycling. We identified a unique Fur homolog (DR0865) from Deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. A dr0865 mutant (Mt-0865) showed a higher sensitivity to manganese stress, hydrogen peroxide, gamma irradiation and ultraviolet (UV) irradiation than the wild-type R1 strain. Cellular manganese (Mn) ion (Mn2+) analysis showed that Mn2+, copper (Cu2+), and ferric (Fe3+) ions accumulated significantly in the mutant, which suggests that the dr0865 gene is not only involved in the regulation of Mn2+ homeostasis, but also affects the uptake of other ions. In addition, transcriptome profiles under MnCl2 stress showed that the expression of many genes involved in Mn metabolism was significantly different in the wild-type R1 and DR0865 mutant (Mt-0865). Furthermore, we found that the dr0865 gene serves as a positive regulator of the manganese efflux pump gene mntE (dr1236), and as a negative regulator of Mn ABC transporter genes, such as dr2283, dr2284 and dr2523. Therefore, it plays an important role in maintaining the homoeostasis of intracellular Mn (II), and also other Mn2+, zinc (Zn2+) and Cu2+ ions. Based on its role in manganese homeostasis, DR0865 likely belongs to the Mur sub-family of Fur homolog.
Collapse
|
59
|
Krynická V, Tichý M, Krafl J, Yu J, Kaňa R, Boehm M, Nixon PJ, Komenda J. Two essential FtsH proteases control the level of the Fur repressor during iron deficiency in the cyanobacterium Synechocystis sp. PCC 6803. Mol Microbiol 2014; 94:609-24. [PMID: 25238320 DOI: 10.1111/mmi.12782] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2014] [Indexed: 12/18/2022]
Abstract
The cyanobacterium Synechocystis sp. PCC 6803 expresses four different FtsH protease subunits (FtsH1-4) that assemble into specific homo- and heterocomplexes. The FtsH2/FtsH3 complex is involved in photoprotection but the physiological roles of the other complexes, notably the essential FtsH1/FtsH3 complex, remain unclear. Here we show that the FtsH1 and FtsH3 proteases are involved in the acclimation of cells to iron deficiency. A mutant conditionally depleted in FtsH3 was unable to induce normal expression of the IsiA chlorophyll-protein and FutA1 iron transporter upon iron deficiency due to a block in transcription, which is regulated by the Fur transcriptional repressor. Levels of Fur declined in the WT and the FtsH2 null mutant upon iron depletion but not in the FtsH3 downregulated strain. A similar stabilizing effect on Fur was also observed in a mutant conditionally depleted in the FtsH1 subunit. Moreover, a mutant overexpressing FtsH1 showed reduced levels of Fur and enhanced accumulation of both IsiA and FutA1 even under iron sufficiency. Analysis of GFP-tagged derivatives and biochemical fractionation supported a common location for FtsH1 and FtsH3 in the cytoplasmic membrane. Overall we propose that degradation of the Fur repressor mediated by the FtsH1/FtsH3 heterocomplex is critical for acclimation to iron depletion.
Collapse
Affiliation(s)
- Vendula Krynická
- Institute of Microbiology, Academy of Sciences, Opatovický mlýn, 37981, Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | | | | | | | | | | | | | | |
Collapse
|
60
|
Botello-Morte L, Bes MT, Heras B, Fernández-Otal Á, Peleato ML, Fillat MF. Unraveling the redox properties of the global regulator FurA from Anabaena sp. PCC 7120: disulfide reductase activity based on its CXXC motifs. Antioxid Redox Signal 2014; 20:1396-406. [PMID: 24093463 PMCID: PMC3936511 DOI: 10.1089/ars.2013.5376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED Cyanobacterial FurA works as a global regulator linking iron homeostasis to photosynthetic metabolism and the responses to different environmental stresses. Additionally, FurA modulates several genes involved in redox homeostasis and fulfills the characteristics of a heme-sensor protein whose interaction with this cofactor negatively affects its DNA binding ability. FurA from Anabaena PCC 7120 contains five cysteine residues, four of them arranged in two redox CXXC motifs. AIMS Our goals were to analyze in depth the putative contribution of these CXXC motifs in the redox properties of FurA and to identify potential interacting partners of this regulator. RESULTS Insulin reduction assays unravel that FurA exhibits disulfide reductase activity. Simultaneous presence of both CXXC signatures greatly enhances the reduction rate, although the redox motif containing Cys(101) and Cys(104) seems a major contributor to this activity. Disulfide reductase activity was not detected in other ferric uptake regulator (Fur) proteins isolated from heterotrophic bacteria. In vivo, FurA presents different redox states involving intramolecular disulfide bonds when is partially oxidized. Redox potential values for CXXC motifs, -235 and -238 mV, are consistent with those reported for other proteins displaying disulfide reductase activity. Pull-down and two-hybrid assays unveil potential FurA interacting partners, namely phosphoribulokinase Alr4123, the hypothetical amidase-containing domain All1140 and the DNA-binding protein HU. INNOVATION A novel biochemical activity of cyanobacterial FurA based on its cysteine arrangements and the identification of novel interacting partners are reported. CONCLUSION The present study discloses a putative connection of FurA with the cyanobacterial redox-signaling pathway.
Collapse
Affiliation(s)
- Laura Botello-Morte
- 1 Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza , Zaragoza, Spain
| | | | | | | | | | | |
Collapse
|
61
|
Fillat MF. The FUR (ferric uptake regulator) superfamily: diversity and versatility of key transcriptional regulators. Arch Biochem Biophys 2014; 546:41-52. [PMID: 24513162 DOI: 10.1016/j.abb.2014.01.029] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/27/2014] [Accepted: 01/31/2014] [Indexed: 11/17/2022]
Abstract
Control of metal homeostasis is essential for life in all kingdoms. In most prokaryotic organisms the FUR (ferric uptake regulator) family of transcriptional regulators is involved in the regulation of iron and zinc metabolism through control by Fur and Zur proteins. A third member of this family, the peroxide-stress response PerR, is present in most Gram-positives, establishing a tight functional interaction with the global regulator Fur. These proteins play a pivotal role for microbial survival under adverse conditions and in the expression of virulence in most pathogens. In this paper we present the current state of the art in the knowledge of the FUR family, including those members only present in more reduced numbers of bacteria, namely Mur, Nur and Irr. The huge amount of work done in the two last decades shows that FUR proteins present considerable diversity in their regulatory mechanisms and interesting structural differences. However, much work needs to be done to obtain a more complete picture of this family, especially in connection with the roles of some members as gas and redox sensors as well as to fully characterize their participation in bacterial adaptative responses.
Collapse
Affiliation(s)
- María F Fillat
- Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Pedro Cerbuna, 12, 50009 Zaragoza, Spain.
| |
Collapse
|
62
|
Agriesti F, Roncarati D, Musiani F, Del Campo C, Iurlaro M, Sparla F, Ciurli S, Danielli A, Scarlato V. FeON-FeOFF: the Helicobacter pylori Fur regulator commutates iron-responsive transcription by discriminative readout of opposed DNA grooves. Nucleic Acids Res 2013; 42:3138-51. [PMID: 24322295 PMCID: PMC3950669 DOI: 10.1093/nar/gkt1258] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Most transcriptional regulators bind nucleotide motifs in the major groove, although some are able to recognize molecular determinants conferred by the minor groove of DNA. Here we report a transcriptional commutator switch that exploits the alternative readout of grooves to mediate opposite output regulation for the same input signal. This mechanism accounts for the ability of the Helicobacter pylori Fur regulator to repress the expression of both iron-inducible and iron-repressible genes. When iron is scarce, Fur binds to DNA as a dimer, through the readout of thymine pairs in the major groove, repressing iron-inducible transcription (FeON). Conversely, on iron-repressible elements the metal ion acts as corepressor, inducing Fur multimerization with consequent minor groove readout of AT-rich inverted repeats (FeOFF). Our results provide first evidence for a novel regulatory paradigm, in which the discriminative readout of DNA grooves enables to toggle between the repression of genes in a mutually exclusive manner.
Collapse
Affiliation(s)
- Francesca Agriesti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
63
|
Experimental phasing using zinc and sulfur anomalous signals measured at the zinc absorption peak. J Microbiol 2013; 51:639-43. [PMID: 24173644 DOI: 10.1007/s12275-013-3412-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/27/2013] [Indexed: 10/26/2022]
Abstract
Iron is an essential transition metal required for bacterial growth and survival. Excess free iron can lead to the generation of reactive oxygen species that can cause severe damage to cellular functions. Cells have developed iron-sensing regulators to maintain iron homeostasis at the transcription level. The ferric uptake regulator (Fur) is an iron-responsive regulator that controls the expression of genes involved in iron homeostasis, bacterial virulence, stress resistance, and redox metabolism. Here, we report the expression, purification, crystallization, and phasing of the apo-form of Bacillus subtilis Fur (BsFur) in the absence of regulatory metal ions. Crystals were obtained by microbatch crystallization method at 295 K and diffraction data at a resolution of 2.6 Å was collected at the zinc peak wavelength (λ=1.2823 Å). Experimental phasing identified the positions of one zinc atom and four sulfur atoms of cysteine residues coordinating the zinc atom, indicating that the data contained a meaningful anomalous scattering originating from the ordered zinc-coordinating sulfur atoms, in spite of the small anomalous signals of sulfur atoms at the examined wavelength.
Collapse
|
64
|
Wang Q, Liu JX, Zhang WJ, Zhang TW, Yang J, Li Y. Expression patterns of key iron and oxygen metabolism genes during magnetosome formation in Magnetospirillum gryphiswaldense MSR-1. FEMS Microbiol Lett 2013; 347:163-72. [PMID: 23937222 DOI: 10.1111/1574-6968.12234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/06/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022] Open
Abstract
To evaluate the expression patterns of genes involved in iron and oxygen metabolism during magnetosome formation, the profiles of 13 key genes in Magnetospirillum gryphiswaldense MSR-1 cells cultured under high-iron vs. low-iron conditions were examined. Cell growth rates did not differ between the two conditions. Only the high-iron cells produced magnetosomes. Transmission electron microscopy observations revealed that magnetosome formation began at 6 h and crystal maturation occurred from 10 to 18 h. Real-time polymerase chain reaction analysis showed that expression of these genes increased during cell growth and magnetosome synthesis, particularly for ferric reductase gene (fer6) and ferrous transport system-related genes feoAB1, feoAB2, sodB, and katG. The low-iron cells showed increased expression of feoAB1 and feoB2 from 12 to 18 h but no clear expression changes for the other genes. Expression patterns of the genes were divided by hierarchical clustering into four clusters for the high-iron cells and three clusters for the low-iron cells. Each cluster included both iron and oxygen metabolism genes showing similar expression patterns. The findings indicate the coordination and co-dependence of iron and oxygen metabolism gene activity to achieve a balance during the biomineralization process. Future transcriptome analysis will help elucidate the mechanism of biomineralization in MSR-1 magnetosome formation.
Collapse
Affiliation(s)
- Qing Wang
- State Key Laboratories for Agro-biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China; France-China Bio-mineralization and Nano-structure Laboratory, Beijing, China
| | | | | | | | | | | |
Collapse
|
65
|
Gentry LE, Thacker MA, Doughty R, Timkovich R, Busenlehner LS. His86 from the N-terminus of frataxin coordinates iron and is required for Fe-S cluster synthesis. Biochemistry 2013; 52:6085-96. [PMID: 23909240 PMCID: PMC3871887 DOI: 10.1021/bi400443n] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human frataxin has a vital role in the biosynthesis of iron-sulfur (Fe-S) clusters in mitochondria, and its deficiency causes the neurodegenerative disease Friedreich's ataxia. Proposed functions for frataxin in the Fe-S pathway include iron donation to the Fe-S cluster machinery and regulation of cysteine desulfurase activity to control the rate of Fe-S production, although further molecular detail is required to distinguish these two possibilities. It is well established that frataxin can coordinate iron using glutamate and aspartate side chains on the protein surface; however, in this work we identify a new iron coordinating residue in the N-terminus of human frataxin using complementary spectroscopic and structural approaches. Further, we demonstrate that His86 in this N-terminal region is required for high affinity iron coordination and iron assembly of Fe-S clusters by ISCU as part of the Fe-S cluster biosynthetic complex. If a binding site that includes His86 is important for Fe-S cluster synthesis as part of its chaperone function, this raises the possibility that either iron binding at the acidic surface of frataxin may be spurious or that it is required for protein-protein interactions with the Fe-S biosynthetic quaternary complex. Our data suggest that iron coordination to frataxin may be significant to the Fe-S cluster biosynthesis pathway in mitochondria.
Collapse
Affiliation(s)
- Leslie E. Gentry
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | - Matthew A. Thacker
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | | | - Russell Timkovich
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | - Laura S. Busenlehner
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| |
Collapse
|
66
|
Wang P, Dadhwal P, Cheng Z, Zianni MR, Rikihisa Y, Liang FT, Li X. Borrelia burgdorferi oxidative stress regulator BosR directly represses lipoproteins primarily expressed in the tick during mammalian infection. Mol Microbiol 2013; 89:1140-53. [PMID: 23869590 DOI: 10.1111/mmi.12337] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2013] [Indexed: 12/16/2022]
Abstract
Differential gene expression is a key strategy adopted by the Lyme disease spirochaete, Borrelia burgdorferi, for adaptation and survival in the mammalian host and the tick vector. Many B. burgdorferi surface lipoproteins fall into two distinct groups according to their expression patterns: one group primarily expressed in the tick and the other group primarily expressed in the mammal. Here, we show that the Fur homologue in this bacterium, also known as Borrelia oxidative stress regulator (BosR), is required for repression of outer surface protein A (OspA) and OspD in the mammal. Furthermore, BosR binds directly to sequences upstream of the ospAB operon and the ospD gene through recognition of palindromic motifs similar to those recognized by other Fur homologues but with a 1 bp variation in the spacer length. Putative BosR binding sites have been identified upstream of 156 B. burgdorferi genes. Some of these genes share the same expression pattern as ospA and ospD. Most notably, 12 (67%) of the 18 genes previously identified in a genome-wide microarray study to be most significantly repressed in the mammal are among the putative BosR regulon. These data indicate that BosR may directly repress transcription of many genes that are downregulated in the mammal.
Collapse
Affiliation(s)
- Peng Wang
- Department of Veterinary Biosciences, The Ohio State University, 1900 Coffey Road, Columbus, OH, 43210, USA
| | | | | | | | | | | | | |
Collapse
|
67
|
Parent A, Caux-Thang C, Signor L, Clémancey M, Sethu R, Blondin G, Maldivi P, Duarte V, Latour JM. Single Glutamate to Aspartate Mutation Makes Ferric Uptake Regulator (Fur) as Sensitive to H2O2as Peroxide Resistance Regulator (PerR). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
68
|
Parent A, Caux-Thang C, Signor L, Clémancey M, Sethu R, Blondin G, Maldivi P, Duarte V, Latour JM. Single Glutamate to Aspartate Mutation Makes Ferric Uptake Regulator (Fur) as Sensitive to H2O2as Peroxide Resistance Regulator (PerR). Angew Chem Int Ed Engl 2013; 52:10339-43. [DOI: 10.1002/anie.201304021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/24/2013] [Indexed: 11/09/2022]
|
69
|
Barison N, Cendron L, Loconte V, Proctor EA, Dokholyan NV, Zanotti G. Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1387-94. [PMID: 23897462 DOI: 10.1107/s0907444913008160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/25/2013] [Indexed: 11/10/2022]
Abstract
Helicobacter pylori is a bacterial pathogen that causes severe diseases, including gastritis, ulcers and gastric cancer. Although this bacterium has been extensively studied, the physiological functions of a large number of the proteins encoded by its genome are unknown. HP1028 is a protein that is relevant to colonization and to the survival of the bacterium in the stomach, but its function is not clearly understood. Bioinformatics studies suggest that HP1028 is a monomeric protein that is secreted in the H. pylori periplasm. The crystal structure of HP1028 has been determined at 2.6 Å resolution using the SAD method. The three-dimensional structure of the protein reveals that it belongs to the lipocalin family, a group of proteins that bind and transport (often hydrophobic) small molecules. The structure of HP1028, together with the possible localization of the mature protein in the bacterial periplasm and the position of the hp1028 gene in the bacterial genome, point to a role in H. pylori chemotaxis.
Collapse
Affiliation(s)
- Nicola Barison
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | | | | | | | | | | |
Collapse
|
70
|
Kim MK, Lee S, An YJ, Jeong CS, Ji CJ, Lee JW, Cha SS. In-house zinc SAD phasing at Cu Kα edge. Mol Cells 2013; 36:74-81. [PMID: 23686432 PMCID: PMC3887929 DOI: 10.1007/s10059-013-0074-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022] Open
Abstract
De novo zinc single-wavelength anomalous dispersion (Zn-SAD) phasing has been demonstrated with the 1.9 Å resolution data of glucose isomerase and 2.6 Å resolution data of Staphylococcus aureus Fur (SaFur) collected using in-house Cu Kα X-ray source. The successful in-house Zn-SAD phasing of glucose isomerase, based on the anomalous signals of both zinc ions introduced to crystals by soaking and native sulfur atoms, drove us to determine the structure of SaFur, a zinc-containing transcription factor, by Zn-SAD phasing using in-house X-ray source. The abundance of zinc-containing proteins in nature, the easy zinc derivatization of the protein surface, no need of synchrotron access, and the successful experimental phasing with the modest 2.6 Å resolution SAD data indicate that inhouse Zn-SAD phasing can be widely applicable to structure determination.
Collapse
Affiliation(s)
- Min-Kyu Kim
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Sangmin Lee
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
- Ocean Science and Technology School, Pusan 606-791,
Korea
| | - Young Jun An
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Chang-Sook Jeong
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Chang-Jun Ji
- Department of Life Science and Institute for Natural Sciences, Hanyang University, Seoul 133-791,
Korea
| | - Jin-Won Lee
- Department of Life Science and Institute for Natural Sciences, Hanyang University, Seoul 133-791,
Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
- Ocean Science and Technology School, Pusan 606-791,
Korea
- Department of Marine Biotechnology, University of Science and Technology, Daejeon 305-333
Korea
| |
Collapse
|
71
|
Gilbreath JJ, Pich OQ, Benoit SL, Besold AN, Cha JH, Maier RJ, Michel SLJ, Maynard EL, Merrell DS. Random and site-specific mutagenesis of the Helicobacter pylori ferric uptake regulator provides insight into Fur structure-function relationships. Mol Microbiol 2013; 89:304-23. [PMID: 23710935 DOI: 10.1111/mmi.12278] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2013] [Indexed: 12/29/2022]
Abstract
The ferric uptake regulator (Fur) of Helicobacter pylori is a global regulator that is important for colonization and survival within the gastric mucosa. H. pylori Fur is unique in its ability to activate and repress gene expression in both the iron-bound (Fe-Fur) and apo forms (apo-Fur). In the current study we combined random and site-specific mutagenesis to identify amino acid residues important for both Fe-Fur and apo-Fur function. We identified 25 mutations that affected Fe-Fur repression and 23 mutations that affected apo-Fur repression, as determined by transcriptional analyses of the Fe-Fur target gene amiE, and the apo-Fur target gene, pfr. In addition, eight of these mutations also significantly affected levels of Fur in the cell. Based on regulatory phenotypes, we selected several representative mutations to characterize further. Of those selected, we purified the wild-type (HpFurWT) and three mutant Fur proteins (HpFurE5A, HpFurA92T and HpFurH134Y), which represent mutations in the N-terminal extension, the regulatory metal binding site (S2) and the structural metal binding site (S3) respectively. Purified proteins were evaluated for secondary structure by circular dichroism spectroscopy, iron-binding by atomic absorption spectrophotometry, oligomerization in manganese-substituted and apo conditions by in vitro cross-linking assays, and DNA binding to Fe-Fur and apo-Fur target sequences by fluorescence anisotropy. The results showed that the N-terminal, S2 and S3 regions play distinct roles in terms of Fur structure-function relationships. Overall, these studies provide novel information regarding the role of these residues in Fur function, and provide mechanistic insight into how H. pylori Fur regulates gene expression in both the iron-bound and apo forms of the protein.
Collapse
Affiliation(s)
- Jeremy J Gilbreath
- Department of Microbiology and Immunology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
72
|
Makthal N, Rastegari S, Sanson M, Ma Z, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Crystal structure of peroxide stress regulator from Streptococcus pyogenes provides functional insights into the mechanism of oxidative stress sensing. J Biol Chem 2013; 288:18311-24. [PMID: 23645680 DOI: 10.1074/jbc.m113.456590] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Regulation of oxidative stress responses by the peroxide stress regulator (PerR) is critical for the in vivo fitness and virulence of group A Streptococcus. To elucidate the molecular mechanism of DNA binding, peroxide sensing, and gene regulation by PerR, we performed biochemical and structural characterization of PerR. Sequence-specific DNA binding by PerR does not require regulatory metal occupancy. However, metal binding promotes higher affinity PerR-DNA interactions. PerR metallated with iron directly senses peroxide stress and dissociates from operator sequences. The crystal structure revealed that PerR exists as a homodimer with two metal-binding sites per subunit as follows: a structural zinc site and a regulatory metal site that is occupied in the crystals by nickel. The regulatory metal-binding site in PerR involves a previously unobserved HXH motif located in its unique N-terminal extension. Mutational analysis of the regulatory site showed that the PerR metal ligands are involved in regulatory metal binding, and integrity of this site is critical for group A Streptococcus virulence. Interestingly, the metal-binding HXH motif is not present in the structurally characterized members of ferric uptake regulator (Fur) family but is fully conserved among PerR from the genus Streptococcus. Thus, it is likely that the PerR orthologs from streptococci share a common mechanism of metal binding, peroxide sensing, and gene regulation that is different from that of well characterized PerR from Bacillus subtilis. Together, our findings provide key insights into the peroxide sensing and regulation of the oxidative stress-adaptive responses by the streptococcal subfamily of PerR.
Collapse
Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | |
Collapse
|
73
|
Harrison A, Santana EA, Szelestey BR, Newsom DE, White P, Mason KM. Ferric uptake regulator and its role in the pathogenesis of nontypeable Haemophilus influenzae. Infect Immun 2013; 81:1221-33. [PMID: 23381990 PMCID: PMC3639608 DOI: 10.1128/iai.01227-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/21/2013] [Indexed: 11/20/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the human nasopharynx, and yet is also an opportunistic pathogen of the upper and lower respiratory tracts. Host microenvironments influence gene expression patterns, likely critical for NTHi persistence. The host sequesters iron as a mechanism to control microbial growth, and yet iron limitation influences gene expression and subsequent production of proteins involved in iron homeostasis. Careful regulation of iron uptake, via the ferric uptake regulator Fur, is essential in multiple bacteria, including NTHi. We hypothesized therefore that Fur contributes to iron homeostasis in NTHi, is critical for bacterial persistence, and likely regulates expression of virulence factors. Toward this end, fur was deleted in the prototypic NTHi clinical isolate, 86-028NP, and we assessed gene expression regulated by Fur. As expected, expression of the majority of genes that encode proteins with predicted roles in iron utilization was repressed by Fur. However, 14 Fur-regulated genes encode proteins with no known function, and yet may contribute to iron utilization or other biological functions. In a mammalian model of human otitis media, we determined that Fur was critical for bacterial persistence, indicating an important role for Fur-mediated iron homeostasis in disease progression. These data provide a profile of genes regulated by Fur in NTHi and likely identify additional regulatory pathways involved in iron utilization. Identification of such pathways will increase our understanding of how this pathogen can persist within host microenvironments, as a common commensal and, importantly, as a pathogen with significant clinical impact.
Collapse
Affiliation(s)
- Alistair Harrison
- The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, The Center for Microbial Interface Biology, and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.
| | | | | | | | | | | |
Collapse
|
74
|
Braun V, Hantke K. The Tricky Ways Bacteria Cope with Iron Limitation. IRON UPTAKE IN BACTERIA WITH EMPHASIS ON E. COLI AND PSEUDOMONAS 2013. [DOI: 10.1007/978-94-007-6088-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
75
|
Katigbak J, Zhang Y. Iron Binding Site in a Global Regulator in Bacteria - Ferric Uptake Regulator (Fur) Protein: Structure, Mössbauer Properties, and Functional Implication. J Phys Chem Lett 2012; 2012:3503-3508. [PMID: 23205186 PMCID: PMC3507992 DOI: 10.1021/jz301689b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fur protein plays key roles in regulating numerous genes in bacteria and is essential for intracellular iron concentration regulation. However, atomic level pictures of the iron binding site and its functional mechanism remain to be established. Here we present results of the first quantum chemical investigation of various first- and second-shell models and experimental Mössbauer data of E. Coli Fur, including 1) the first robust evidence that site 2 is the Fe binding site with a 3His/2Glu ligand set, being the first case in non-heme proteins, with computed Mössbauer data in excellent accord with experiment; 2) the first discovery of a conservative hydrogen bonding interaction in the iron binding site based on X-ray and homology structures; 3) the first atomic level hypothesis of active site reorganization upon iron concentration increase, triggering the conformational change needed for its function. These results shall facilitate structural and functional studies of Fur family proteins.
Collapse
|
76
|
Abstract
SIGNIFICANCE In bacteria, transcriptional responses to reactive oxygen and nitrogen species (ROS and RNS, respectively) are typically coordinated by regulatory proteins that employ metal centers or reactive thiols to detect the presence of those species. This review is focused on the structure, function and mechanism of three regulatory proteins (Fur, PerR, and NorR) that contain non-heme iron and regulate the transcription of target genes in response to ROS and/or RNS. The targets for regulation include genes encoding detoxification activities, and genes encoding proteins involved in the repair of the damage caused by ROS and RNS. RECENT ADVANCES Three-dimensional structures of several Fur proteins and of PerR are revealing important details of the metal binding sites of these proteins, showing a surprising degree of structural diversity in the Fur family. CRITICAL ISSUES Discussion of the interaction of Fur with ROS and RNS will illustrate the difficulty that sometimes exists in distinguishing between true physiological responses and adventitious reactions of a regulatory protein with a reactive ligand. FUTURE DIRECTIONS Consideration of these three sensor proteins illuminates some of the key questions that remain unanswered, for example, the nature of the biochemical determinants that dictate the sensitivity and specificity of the interaction of the sensor proteins with their cognate signals.
Collapse
Affiliation(s)
- Stephen Spiro
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75080, USA.
| | | |
Collapse
|
77
|
Ma Z, Faulkner MJ, Helmann JD. Origins of specificity and cross-talk in metal ion sensing by Bacillus subtilis Fur. Mol Microbiol 2012; 86:1144-55. [PMID: 23057863 DOI: 10.1111/mmi.12049] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2012] [Indexed: 11/28/2022]
Abstract
Fur (ferric uptake regulator) is the master regulator of iron homeostasis in many bacteria, but how it responds specifically to Fe(II) in vivo is not clear. Biochemical analyses of Bacillus subtilis Fur (BsFur) reveal that in addition to Fe(II), both Zn(II) and Mn(II) allosterically activate BsFur-DNA binding. Dimeric BsFur co-purifies with site 1 structural Zn(II) (Fur(2) Zn(2) ) and can bind four additional Zn(II) or Mn(II) ions per dimer. Metal ion binding at previously described site 3 occurs with highest affinity, but the Fur(2) Zn(2) :Me(2) form has only a modest increase in DNA binding affinity (approximately sevenfold). Metallation of site 2 (Fur(2) Zn(2) :Me(4) ) leads to a ~ 150-fold further enhancement in DNA binding affinity. Fe(II) binding studies indicate that BsFur buffers the intracellular Fe(II) concentration at ~ 1 μM. Both Mn(II) and Zn(II) are normally buffered at levels insufficient for metallation of BsFur site 2, thereby accounting for the lack of cross-talk observed in vivo. However, in a perR mutant, where the BsFur concentration is elevated, BsFur may now use Mn(II) as a co-repressor and inappropriately repress iron uptake. Since PerR repression of fur is enhanced by Mn(II), and antagonized by Fe(II), PerR may co-regulate Fe(II) homeostasis by modulating BsFur levels in response to the Mn(II)/Fe(II) ratio.
Collapse
Affiliation(s)
- Zhen Ma
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | | | | |
Collapse
|
78
|
Abstract
The ferric uptake regulator (Fur) protein has been shown to function as a repressor of transcription in a number of diverse microorganisms. However, recent studies have established that Fur can function at a global level as both an activator and a repressor of transcription through both direct and indirect mechanisms. Fur-mediated indirect activation occurs via the repression of additional repressor proteins, or small regulatory RNAs, thereby activating transcription of a previously silent gene. Fur mediates direct activation through binding of Fur to the promoter regions of genes. Whereas the repressive mechanism of Fur has been thoroughly investigated, emerging studies on direct and indirect Fur-mediated activation mechanisms have revealed novel global regulatory circuits.
Collapse
|
79
|
Bhubhanil S, Ruangkiattikul N, Niamyim P, Chamsing J, Ngok-Ngam P, Sukchawalit R, Mongkolsuk S. Identification of amino acid residues important for the function of Agrobacterium tumefaciens Irr protein. FEMS Microbiol Lett 2012; 335:68-77. [PMID: 22817265 DOI: 10.1111/j.1574-6968.2012.02638.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 07/14/2012] [Accepted: 07/16/2012] [Indexed: 11/29/2022] Open
Abstract
The key amino acid residues that influence the function of the Agrobacterium tumefaciens iron response regulator protein (Irr(At) ) were investigated. Several Irr(At) mutant proteins containing substitutions in amino acids corresponding to candidate metal- and haem-binding sites were constructed. The ability of the mutant proteins to repress the promoter of the membrane bound ferritin (mbfA) gene was investigated using a promoter-lacZ fusion assay. A single mutation at residue H94 significantly decreased the repressive activity of Irr(At) . Multiple mutation analysis revealed the importance of H45, H65, the HHH motif (H92, H93 and H94) and H127 for the repressor function of Irr(At) . H94 is essential for the iron responsiveness of Irr(At) . Furthermore, the Irr(At) mutant proteins showed differential abilities to complement the H(2) O(2) -hyper-resistant phenotype of an irr mutant.
Collapse
Affiliation(s)
- Sakkarin Bhubhanil
- Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | | | | | | | | | | |
Collapse
|
80
|
Structure and regulon of Campylobacter jejuni ferric uptake regulator Fur define apo-Fur regulation. Proc Natl Acad Sci U S A 2012; 109:10047-52. [PMID: 22665794 DOI: 10.1073/pnas.1118321109] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The full regulatory potential of the ferric uptake regulator (Fur) family of proteins remains undefined despite over 20 years of study. We report herein an integrated approach that combines both genome-wide technologies and structural studies to define the role of Fur in Campylobacter jejuni (Cj). CjFur ChIP-chip assays identified 95 genomic loci bound by CjFur associated with functions as diverse as iron acquisition, flagellar biogenesis, and non-iron ion transport. Comparative analysis with transcriptomic data revealed that CjFur regulation extends beyond solely repression and also includes both gene activation and iron-independent regulation. Computational analysis revealed the presence of an elongated holo-Fur repression motif along with a divergent holo-Fur activation motif. This diversity of CjFur DNA-binding elements is supported by the crystal structure of CjFur, which revealed a unique conformation of its DNA-binding domain and the absence of metal in the regulatory site. Strikingly, our results indicate that the apo-CjFur structure retains the canonical V-shaped dimer reminiscent of previously characterized holo-Fur proteins enabling DNA interaction. This conformation stems from a structurally unique hinge domain that is poised to further contribute to CjFur's regulatory functions by modulating the orientation of the DNA-binding domain upon binding of iron. The unique features of the CjFur crystal structure rationalize the binding sequence diversity that was uncovered during ChIP-chip analysis and defines apo-Fur regulation.
Collapse
|
81
|
Pellicer S, González A, Peleato ML, Martinez JI, Fillat MF, Bes MT. Site-directed mutagenesis and spectral studies suggest a putative role of FurA from Anabaena sp. PCC 7120 as a heme sensor protein. FEBS J 2012; 279:2231-46. [DOI: 10.1111/j.1742-4658.2012.08606.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
82
|
Pich OQ, Carpenter BM, Gilbreath JJ, Merrell DS. Detailed analysis of Helicobacter pylori Fur-regulated promoters reveals a Fur box core sequence and novel Fur-regulated genes. Mol Microbiol 2012; 84:921-41. [PMID: 22507395 DOI: 10.1111/j.1365-2958.2012.08066.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In Helicobacter pylori, iron balance is controlled by the Ferric uptake regulator (Fur), an iron-sensing repressor protein that typically regulates expression of genes implicated in iron transport and storage. Herein, we carried out extensive analysis of Fur-regulated promoters and identified a 7-1-7 motif with dyad symmetry (5'-TAATAATnATTATTA-3'), which functions as the Fur box core sequence of H. pylori. Addition of this sequence to the promoter region of a typically non-Fur regulated gene was sufficient to impose Fur-dependent regulation in vivo. Moreover, mutation of this sequence within Fur-controlled promoters negated regulation. Analysis of the H. pylori chromosome for the occurrence of the Fur box established the existence of well-conserved Fur boxes in the promoters of numerous known Fur-regulated genes, and revealed novel putative Fur targets. Transcriptional analysis of the new candidate genes demonstrated Fur-dependent repression of HPG27_51, HPG27_52, HPG27_199, HPG27_445, HPG27_825 and HPG27_1063, as well as Fur-mediated activation of the cytotoxin associated gene A, cagA (HPG27_507). Furthermore, electrophoretic mobility shift assays confirmed specific binding of Fur to the promoters of each of these genes. Future experiments will determine whether loss of Fur regulation of any of these particular genes contributes to the defects in colonization exhibited by the H. pylori fur mutant.
Collapse
Affiliation(s)
- Oscar Q Pich
- Department of Microbiology and Immunology, Uniformed Services University of the Heath Sciences, Bethesda, MD 20814, USA
| | | | | | | |
Collapse
|
83
|
Abstract
In this paper, we report a novel normal-mode analysis for supramolecular complexes, named fSUB. The method models a complex as a group of flexible substructures. The low-frequency substructure modes are first determined with substructures in isolation, and the motions of the whole complex are then calculated on the basis of substructure modes and substructure-substructure interactions. The calculation of modes in fSUB requires modal analysis without initial energy minimization, which is essential for maintaining energetic and structural consistency between substructures and whole complex. Compared with other coarse-grained methods, such as the RTB method, fSUB delivers much more accurate modes for the complex and allows for the choice of much larger substructures. The method can also accommodate any type of substructure arrangement including covalent bonds across the interface. In tests on molecular chaperonin GroEL (7350 residues) and HK97 capsid complex (118,092 residues), fSUB was shown to be much more efficient in terms of combined accuracy and demand of computing resources. Our results clearly demonstrated the vital importance of including substructure flexibility in complex modal analysis, as the deformational patterns of substructures were found to play an important role even in the lowest frequency modes of the whole complex.
Collapse
Affiliation(s)
- Mingyang Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza Houston, Texas 77030, United States
| | | | | |
Collapse
|
84
|
Tsugawa H, Suzuki H, Matsuzaki J, Hirata K, Hibi T. FecA1, a bacterial iron transporter, determines the survival of Helicobacter pylori in the stomach. Free Radic Biol Med 2012; 52:1003-10. [PMID: 22245091 DOI: 10.1016/j.freeradbiomed.2011.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 11/16/2011] [Accepted: 12/14/2011] [Indexed: 01/14/2023]
Abstract
Helicobacter pylori encodes a single iron-cofactored superoxide dismutase (SodB), which is regulated by the ferric uptake regulator (Fur). Ferrous ion (Fe(2+)) is necessary for the activation of SodB. The activity of SodB is an important determinant of the capability of H. pylori for long-term colonization of the stomach and of the development of metronidazole (Mtz) resistance of the bacterium. This study is conducted to characterize the Fe(2+)-supply mechanisms for the activation of SodB in H. pylori, which, as mentioned above, is associated with the host-colonization ability and Mtz resistance of H. pylori. In this study, we demonstrate that fecA1, a Fe(3+)-dicitrate transporter homolog, is an essential gene for SodB activation, but not for the biogenic activity of H. pylori. H. pylori with SodB inactivation by fecA1 deletion showed reduced resistance to H(2)O(2), reduced gastric mucosal-colonization ability in Mongolian gerbils, and also reduced resistance to Mtz. Our experiment demonstrated that FecA1 is an important determinant of the host-colonization ability and Mtz resistance of H. pylori through Fe(2+) supply to SodB, suggesting that FecA1 may be a possible target for the development of a novel bactericidal drug.
Collapse
Affiliation(s)
- Hitoshi Tsugawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | | | | | | | | |
Collapse
|
85
|
Guerra AJ, Giedroc DP. Metal site occupancy and allosteric switching in bacterial metal sensor proteins. Arch Biochem Biophys 2012; 519:210-22. [PMID: 22178748 PMCID: PMC3312040 DOI: 10.1016/j.abb.2011.11.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/23/2011] [Accepted: 11/29/2011] [Indexed: 12/22/2022]
Abstract
All prokaryotes encode a panel of metal sensor or metalloregulatory proteins that govern the expression of genes that allows an organism to quickly adapt to toxicity or deprivation of both biologically essential transition metal ions, e.g., Zn, Cu, Fe, and heavy metal pollutants. As such, metal sensor proteins can be considered arbiters of intracellular transition metal bioavailability and thus potentially control the metallation state of the metalloproteins in the cell. Metal sensor proteins are specialized allosteric proteins that regulate transcription as a result direct binding of one or two cognate metal ions, to the exclusion of all others. In most cases, the binding of the cognate metal ion induces a structural change in a protein oligomer that either activates or inhibits operator DNA binding. A quantitative measure of the degree to which a particular metal drives metalloregulation of operator DNA-binding is the allosteric coupling free energy, ΔGc. In this review, we summarize recent work directed toward understanding metal occupancy and metal selectivity of these allosteric switches in selected families of metal sensor proteins and examine the structural origins of ΔGc in the functional context a thermodynamic "set-point" model of intracellular metal homeostasis.
Collapse
Affiliation(s)
- Alfredo J. Guerra
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN USA 47405-7102
| | - David P. Giedroc
- Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN USA 47405-7102
| |
Collapse
|
86
|
Abstract
The dramatic changes in the environmental conditions that organisms encountered during evolution and adaptation to life in specific niches, have influenced intracellular and extracellular metal ion contents and, as a consequence, the cellular ability to sense and utilize different metal ions. This metal-driven differentiation is reflected in the specific panels of metal-responsive transcriptional regulators found in different organisms, which finely tune the intracellular metal ion content and all metal-dependent processes. In order to understand the processes underlying this complex metal homeostasis network, the study of the molecular processes that determine the protein-metal ion recognition, as well as how this event is transduced into a transcriptional output, is necessary. This chapter describes how metal ion binding to specific proteins influences protein interaction with DNA and how this event can influence the fate of genetic expression, leading to specific transcriptional outputs. The features of representative metal-responsive transcriptional regulators, as well as the molecular basis of metal-protein and protein-DNA interactions, are discussed on the basis of the structural information available. An overview of the recent advances in the understanding of how these proteins choose specific metal ions among the intracellular metal ion pool, as well as how they allosterically respond to their effector binding, is given.
Collapse
|
87
|
Iron trafficking system in Helicobacter pylori. Biometals 2011; 25:247-58. [PMID: 22127376 DOI: 10.1007/s10534-011-9512-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 11/16/2011] [Indexed: 12/14/2022]
Abstract
Helicobacter pylori infections are closely associated with peptic ulcers, gastric malignancy and iron deficiency anemia. Iron is essential for almost all living organisms and the investigation of iron uptake and trafficking system is thus important to understand the pathological roles of H. pylori. Up to now, the iron trafficking system of H. pylori is not yet fully clear and merits further efforts in this regards. The available information about iron uptake and regulation has been discussed in this concise review, such as FeoB in ferrous transportation, FrpB2 in hemoglobin uptake, HugZ in heme processing, virulence factors (VacA and CagA) in transferrin utilization, Pfr and NapA in iron storage and Fur in iron regulation. The identified iron trafficking system will help us to understand the pathological roles of H. pylori in the various gastric diseases and iron deficiency anemia and stimulates further development of effective anti-bacterial drugs.
Collapse
|
88
|
Guerra AJ, Dann CE, Giedroc DP. Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state. J Am Chem Soc 2011; 133:19614-7. [PMID: 22085181 DOI: 10.1021/ja2080532] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Streptococcus pneumoniae adhesin competence regulator (AdcR), the first metal-dependent member of the multiple antibiotic resistance regulator (MarR) family of proteins, represses the transcription of a high-affinity zinc-specific uptake transporter, a group of surface antigen zinc-binding pneumococcal histidine triad proteins (PhtA, PhtB, PhtD, and PhtE), and an AdcA homologue (AdcAII). The 2.0 Å resolution structure of Zn(II)-bound AdcR reveals a highly helical two-fold-symmetric dimer with two distinct metal-binding sites per protomer. Zn(II) is tetrahedrally coordinated by E24, H42, H108, and H112 in what defines the primary sensing site in AdcR. Site 2 is a tetracoordinate site whose function is currently unknown. NMR methyl group perturbation experiments reveal that Zn(II) drives a global change in the structure of apo-AdcR that stabilizes a conformation that is compatible with DNA binding. This co-repression mechanism is unprecedented in MarR transcriptional regulators.
Collapse
Affiliation(s)
- Alfredo J Guerra
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | | | | |
Collapse
|
89
|
Graham AI, Sanguinetti G, Bramall N, McLeod CW, Poole RK. Dynamics of a starvation-to-surfeit shift: a transcriptomic and modelling analysis of the bacterial response to zinc reveals transient behaviour of the Fur and SoxS regulators. MICROBIOLOGY-SGM 2011; 158:284-292. [PMID: 22016571 DOI: 10.1099/mic.0.053843-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We describe a hybrid transcriptomic and modelling analysis of the dynamics of a bacterial response to stress, namely the addition of 200 µM Zn to Escherichia coli growing in severely Zn-depleted medium and of cells growing at different Zn concentrations at steady state. Genes that changed significantly in response to the transition were those reported previously to be associated with zinc deficiency (zinT, znuA, ykgM) or excess (basR, cpxP, cusF). Cellular Zn levels were confirmed by ICP-AES to be 14- to 28-fold greater after Zn addition but there was also 6- to 8-fold more cellular Fe 30 min after Zn addition. Statistical modelling of the transcriptomic data generated from the Zn shift focused on the role of ten key regulators; ArsR, BaeR, CpxR, CusR, Fur, OxyR, SoxS, ZntR, ZraR and Zur. The data and modelling reveal a transient change in the activity of the iron regulator Fur and of the oxidative stress regulator SoxS, neither of which is evident from the steady-state transcriptomic analyses. We hypothesize a competitive binding mechanism that combines these observations and existing data on the physiology of Zn and Fe uptake. Formalizing the mechanism in a differential equation model shows that it can reproduce qualitatively the behaviour seen in the data. This gives new insights into the interplay of these two fundamental metal ions in gene regulation and bacterial physiology, as well as highlighting the importance of dynamic studies to reverse-engineer systems behaviour.
Collapse
Affiliation(s)
- Alison I Graham
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Informatics Forum, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - Neil Bramall
- Centre for Analytical Sciences, The University of Sheffield, Western Bank, Sheffield S3 7HF, UK
| | - Cameron W McLeod
- Centre for Analytical Sciences, The University of Sheffield, Western Bank, Sheffield S3 7HF, UK
| | - Robert K Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| |
Collapse
|
90
|
Schalk IJ, Hannauer M, Braud A. New roles for bacterial siderophores in metal transport and tolerance. Environ Microbiol 2011; 13:2844-54. [PMID: 21883800 DOI: 10.1111/j.1462-2920.2011.02556.x] [Citation(s) in RCA: 286] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Siderophores are chelators with extremely strong affinity for ferric iron and are best known for their capacity to feed microorganisms with this metal. Despite their preference for iron, they can also chelate numerous other metals with variable affinities. There is also increasing evidence that metals other than iron can activate the production of siderophores by bacteria, thereby implicating siderophores in the homeostasis of metals other than iron and especially heavy metal tolerance. This article considers this new concept that siderophores play a role in protecting bacteria against metal toxicity and discusses the possible contribution of these chelators to the transport of biological relevant metals in addition to iron.
Collapse
Affiliation(s)
- Isabelle J Schalk
- UMR7242, University of Strasbourg-CNRS, ESBS, Blvd Sébastien Brant, F-67413 Illkirch, Strasbourg, France.
| | | | | |
Collapse
|
91
|
Reyes-Caballero H, Lee CW, Giedroc DP. Mycobacterium tuberculosis NmtR harbors a nickel sensing site with parallels to Escherichia coli RcnR. Biochemistry 2011; 50:7941-52. [PMID: 21819125 DOI: 10.1021/bi200737a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis NmtR is a Ni(II)/Co(II)-sensing metalloregulatory protein from the extensively studied ArsR/SmtB family. Two Ni(II) ions bind to the NmtR dimer to form octahedral coordination complexes with the following stepwise binding affinities: K(Ni1) = (1.2 ± 0.1) × 10(10) M(-1), and K(Ni2) = (0.7 ± 0.4) × 10(10) M(-1) (pH 7.0). A glutamine scanning mutagenesis approach reveals that Asp91, His93, His104, and His107, all contained within the C-terminal α5 helix, and His3 as part of the conserved α-NH(2)-Gly2-His3-Gly4 motif at the N-terminus make significant contributions to the magnitude of K(Ni). In contrast, substitution of residues from the C-terminal region, His109, Asp114, and His116, previously implicated in Ni(II) binding and metalloregulation in cells, gives rise to wild-type K(Ni) and Ni(II)-dependent allosteric coupling free energies. Interestingly, deletion of residues 112-120 from the C-terminal region (Δ111 NmtR) reduces the Ni(II) binding stoichiometry to one per dimer and greatly reduces Ni(II) responsiveness. H3Q and Δ111 NmtRs also show clear perturbations in the rank order of metal responsiveness to Ni(II), Co(II), and Zn(II) that is distinct from that of wild-type NmtR. (15)N relaxation experiments with apo-NmtR reveal that both N-terminal (residues 2-14) and C- terminal (residues 110-120) regions are unstructured in solution, and this property likely dictates the metal specificity profile characteristic of the Ni(II) sensor NmtR relative to other ArsR family regulators.
Collapse
|
92
|
Ma Z, Gabriel SE, Helmann JD. Sequential binding and sensing of Zn(II) by Bacillus subtilis Zur. Nucleic Acids Res 2011; 39:9130-8. [PMID: 21821657 PMCID: PMC3241647 DOI: 10.1093/nar/gkr625] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacillus subtilis Zur (BsZur) represses high-affinity zinc-uptake systems and alternative ribosomal proteins in response to zinc replete conditions. Sequence alignments and structural studies of related Fur family proteins suggest that BsZur may contain three zinc-binding sites (sites 1–3). Mutational analyses confirm the essential structural role of site 1, while mutants affected in sites 2 and 3 retain partial repressor function. Purified BsZur binds a maximum of two Zn(II) per monomer at site 1 and site 2. Site 3 residues are important for dimerization, but do not directly bind Zn(II). Analyses of metal-binding affinities reveals negative cooperativity between the two site 2 binding events in each dimer. DNA-binding studies indicate that BsZur is sequentially activated from an inactive dimer (Zur2:Zn2) to a partially active asymmetric dimer (Zur2:Zn3), and finally to the fully zinc-loaded active form (Zur2:Zn4). BsZur with a C84S mutation in site 2 forms a Zur2:Zn3 form with normal metal- and DNA-binding affinities but is impaired in formation of the Zur2:Zn4 high affinity DNA-binding state. This mutant retains partial repressor activity in vivo, thereby supporting a model in which stepwise activation by zinc serves to broaden the physiological response to a wider range of metal concentrations.
Collapse
Affiliation(s)
- Zhen Ma
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | | | | |
Collapse
|
93
|
Helicobacter pylori and effects on iron status in children: delineating causality. J Pediatr Gastroenterol Nutr 2011; 52:646-7. [PMID: 21593639 DOI: 10.1097/mpg.0b013e318219cbc4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
|
94
|
Reyes-Caballero H, Campanello GC, Giedroc DP. Metalloregulatory proteins: metal selectivity and allosteric switching. Biophys Chem 2011; 156:103-14. [PMID: 21511390 DOI: 10.1016/j.bpc.2011.03.010] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 01/13/2023]
Abstract
Prokaryotic organisms have evolved the capacity to quickly adapt to a changing and challenging microenvironment in which the availability of both biologically required and non-essential transition metal ions can vary dramatically. In all bacteria, a panel of metalloregulatory proteins controls the expression of genes encoding membrane transporters and metal trafficking proteins that collectively manage metal homeostasis and resistance. These "metal sensors" are specialized allosteric proteins, in which the direct binding of a specific or small number of "cognate" metal ion(s) drives a conformational change in the regulator that allosterically activates or inhibits operator DNA binding, or alternatively, distorts the promoter structure thereby converting a poor promoter to a strong one. In this review, we discuss our current understanding of the features that control metal specificity of the allosteric response in these systems, and the role that structure, thermodynamics and conformational dynamics play in mediating allosteric activation or inhibition of DNA binding.
Collapse
|
95
|
Choi SS, Chivers PT, Berg DE. Point mutations in Helicobacter pylori's fur regulatory gene that alter resistance to metronidazole, a prodrug activated by chemical reduction. PLoS One 2011; 6:e18236. [PMID: 21464913 PMCID: PMC3064673 DOI: 10.1371/journal.pone.0018236] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 02/23/2011] [Indexed: 02/08/2023] Open
Abstract
Background Helicobacter pylori's Fur regulatory protein controls transcription of dozens of genes in response to iron availability, acidity and oxidative stress, and affects the vigor of infection and severity of disease. It is unusual among Fur family proteins in being active both when iron-loaded and iron-free. Metholodolgy/Principal Findings We tested if H. pylori fur mutations could affect resistance to metronidazole (Mtz), an anti-H. pylori prodrug rendered bactericidal by chemical reduction. Point mutations were made by PCR in DNA containing fur and a downstream chloramphenicol resistance gene, and were placed in the H. pylori chromosome by transformation of a fur-deletion (Δfur) strain. Several substitutions affecting H. pylori Fur's ∼10 residue N terminal arm, which has no counterpart in prototype (E. coli-type) Fur proteins, increased Mtz resistance, as did mutations affecting the region between DNA binding and dimerization domains. Three types of mutations decreased resistance more than did Δfur: substitutions affecting the N-terminal arm; substitutions affecting the metal binding pocket; and nonsense mutations that resulted in a truncated Fur protein with no C-terminal dimerization domain. Most metal binding pocket mutations were obtained only in fur genes with additional inactivating mutations, and thus seemed deleterious or lethal because they. Conclusions/Significance These results establish that H. pylori Fur's distinctive N terminal arm is functional, and more generally illustrate that point mutations can confer informative phenotypes, distinct from those conferred by null mutations. We propose that fur mutations can affect Mtz susceptibility by altering the balance among Fur's several competing activities, and thereby the expression of genes that control cellular redox potential or elimination of bactericidal Mtz activation products. Further analyses of selected mutants should provide insights into Fur interactions with other cellular components, metabolic circuitry, and how H. pylori thrives in its special gastric niche.
Collapse
Affiliation(s)
- Sung Sook Choi
- Department of Molecular Microbiology, Washington University Medical School, St Louis, Missouri, United States of America
| | - Peter T. Chivers
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St Louis, Missouri, United States of America
| | - Douglas E. Berg
- Department of Molecular Microbiology, Washington University Medical School, St Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
96
|
Ma Z, Lee JW, Helmann JD. Identification of altered function alleles that affect Bacillus subtilis PerR metal ion selectivity. Nucleic Acids Res 2011; 39:5036-44. [PMID: 21398634 PMCID: PMC3130269 DOI: 10.1093/nar/gkr095] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis PerR is a Fur family repressor that senses hydrogen peroxide by metal-catalyzed oxidation. PerR contains a structural Zn(II) ion (Site 1) and a regulatory metal binding site (Site 2) that, upon association with either Mn(II) or Fe(II), allosterically activates DNA binding. In addition, a third less conserved metal binding site (Site 3) is present near the dimer interface in several crystal structures of homologous Fur family proteins. Here, we show that PerR proteins with substitutions of putative Site 3 residues (Y92A, E114A and H128A) are functional as repressors, but are unexpectedly compromised in their ability to sense H(2)O(2). Consistently, these mutants utilize Mn(II) but not Fe(II) as a co-repressor in vivo. Metal titrations failed to identify a third binding site in PerR, and inspection of the PerR structure suggests that these residues instead constitute a hydrogen binding network that modulates the architecture, and consequently the metal selectivity, of Site 2. PerR H128A binds DNA with high affinity, but has a significantly reduced affinity for Fe(II), and to a lesser extent for Mn(II). The ability of PerR H128A to bind Fe(II) in vivo and to thereby respond efficiently to H(2)O(2) was restored in a fur mutant strain with elevated cytosolic iron concentration.
Collapse
Affiliation(s)
- Zhen Ma
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | | | | |
Collapse
|
97
|
Graded expression of zinc-responsive genes through two regulatory zinc-binding sites in Zur. Proc Natl Acad Sci U S A 2011; 108:5045-50. [PMID: 21383173 DOI: 10.1073/pnas.1017744108] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Zinc is one of the essential transition metals in cells. Excess or lack of zinc is detrimental, and cells exploit highly sensitive zinc-binding regulators to achieve homeostasis. In this article, we present a crystal structure of active Zur from Streptomyces coelicolor with three zinc-binding sites (C-, M-, and D-sites). Mutations of the three sites differentially affected sporulation and transcription of target genes, such that C- and M-site mutations inhibited sporulation and derepressed all target genes examined, whereas D-site mutations did not affect sporulation and derepressed only a sensitive gene. Biochemical and spectroscopic analyses of representative metal site mutants revealed that the C-site serves a structural role, whereas the M- and D-sites regulate DNA-binding activity as an on-off switch and a fine-tuner, respectively. Consistent with differential effect of mutations on target genes, zinc chelation by TPEN derepressed some genes (znuA, rpmF2) more sensitively than others (rpmG2, SCO7682) in vivo. Similar pattern of TPEN-sensitivity was observed for Zur-DNA complexes formed on different promoters in vitro. The sensitive promoters bound Zur with lower affinity than the less sensitive ones. EDTA-treated apo-Zur gained its DNA binding activity at different concentrations of added zinc for the two promoter groups, corresponding to free zinc concentrations of 4.5×10(-16) M and 7.9×10(-16) M for the less sensitive and sensitive promoters, respectively. The graded expression of target genes is a clever outcome of subtly modulating Zur-DNA binding affinities in response to zinc availability. It enables bacteria to detect metal depletion with improved sensitivity and optimize gene-expression pattern.
Collapse
|