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Gu Y, Liu Y, Mao W, Peng Y, Han X, Jin H, Xu J, Chang L, Hou Y, Shen X, Liu X, Yang Y. Functional versatility of Zur in metal homeostasis, motility, biofilm formation, and stress resistance in Yersinia pseudotuberculosis. Microbiol Spectr 2024; 12:e0375623. [PMID: 38534119 PMCID: PMC11064496 DOI: 10.1128/spectrum.03756-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Zur (zinc uptake regulator) is a significant member of the Fur (ferric uptake regulator) superfamily, which is widely distributed in bacteria. Zur plays crucial roles in zinc homeostasis and influences cell development and environmental adaptation in various species. Yersinia pseudotuberculosis is a Gram-negative enteric that pathogen usually serves as a model organism in pathogenicity studies. The regulatory effects of Zur on the zinc transporter ZnuABC and the protein secretion system T6SS have been documented in Y. pseudotuberculosis. In this study, a comparative transcriptomics analysis between a ∆zur mutant and the wild-type (WT) strain of Y. pseudotuberculosis was conducted using RNA-seq. This analysis revealed global regulation by Zur across multiple functional categories, including membrane transport, cell motility, and molecular and energy metabolism. Additionally, Zur mediates the homeostasis not only of zinc but also ferric and magnesium in vivo. There was a notable decrease in 35 flagellar biosynthesis and assembly-related genes, leading to reduced swimming motility in the ∆zur mutant strain. Furthermore, Zur upregulated multiple simple sugar and oligopeptide transport system genes by directly binding to their promoters. The absence of Zur inhibited biofilm formation as well as reduced resistance to chloramphenicol and acidic stress. This study illustrates the comprehensive regulatory functions of Zur, emphasizing its importance in stress resistance and pathogenicity in Y. pseudotuberculosis. IMPORTANCE Bacteria encounter diverse stresses in the environment and possess essential regulators to modulate the expression of genes in responding to the stresses for better fitness and survival. Zur (zinc uptake regulator) plays a vital role in zinc homeostasis. Studies of Zur from multiple species reviewed that it influences cell development, stress resistance, and virulence of bacteria. Y. pseudotuberculosis is an enteric pathogen that serves a model organism in the study of pathogenicity, virulence factors, and mechanism of environmental adaptation. In this study, transcriptomics analysis of Zur's regulons was conducted in Y. pseudotuberculosis. The functions of Zur as a global regulator in metal homeostasis, motility, nutrient acquisition, glycan metabolism, and nucleotide metabolism, in turn, increasing the biofilm formation, stress resistance, and virulence were reviewed. The importance of Zur in environmental adaptation and pathogenicity of Y. pseudotuberculosis was emphasized.
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Affiliation(s)
- Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yongde Liu
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd, Qingyang, China
| | - Wei Mao
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd, Qingyang, China
| | - Ying Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiaoru Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Han Jin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jingling Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Liyang Chang
- College of Enology, Northwest A&F University, Yangling, China
| | - Yixin Hou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xingyu Liu
- General Research Institute for Nonferrous Metals, Beijing, China
| | - Yantao Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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2
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Berg K, Pedersen HL, Leiros I. Biochemical characterization of ferric uptake regulator (Fur) from Aliivibrio salmonicida. Mapping the DNA sequence specificity through binding studies and structural modelling. Biometals 2020; 33:169-185. [PMID: 32648080 PMCID: PMC7536154 DOI: 10.1007/s10534-020-00240-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 06/28/2020] [Indexed: 11/25/2022]
Abstract
Iron is an essential nutrient for bacteria, however its propensity to form toxic hydroxyl radicals at high intracellular concentrations, requires its acquisition to be tightly regulated. Ferric uptake regulator (Fur) is a metal-dependent DNA-binding protein that acts as a transcriptional regulator in maintaining iron metabolism in bacteria and is a highly interesting target in the design of new antibacterial drugs. Fur mutants have been shown to exhibit decreased virulence in infection models. The protein interacts specifically with DNA at binding sites designated as 'Fur boxes'. In the present study, we have investigated the interaction between Fur from the fish pathogen Aliivibrio salmonicida (AsFur) and its target DNA using a combination of biochemical and in silico methods. A series of target DNA oligomers were designed based on analyses of Fur boxes from other species, and affinities assessed using electrophoretic mobility shift assay. Binding strengths were interpreted in the context of homology models of AsFur to gain molecular-level insight into binding specificity.
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Affiliation(s)
- Kristel Berg
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Hege Lynum Pedersen
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Ingar Leiros
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT the Arctic University of Norway, 9037, Tromsø, Norway.
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3
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Nam D, Matsumoto Y, Uchida T, O'Brian MR, Ishimori K. Mechanistic insights into heme-mediated transcriptional regulation via a bacterial manganese-binding iron regulator, iron response regulator (Irr). J Biol Chem 2020; 295:11316-11325. [PMID: 32554810 DOI: 10.1074/jbc.ra119.011855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/15/2020] [Indexed: 11/06/2022] Open
Abstract
The transcription factor iron response regulator (Irr) is a key regulator of iron homeostasis in the nitrogen-fixating bacterium Bradyrhizobium japonicum Irr acts by binding to target genes, including the iron control element (ICE), and is degraded in response to heme binding. Here, we examined this binding activity using fluorescence anisotropy with a 6-carboxyfluorescein-labeled ICE-like oligomer (FAM-ICE). In the presence of Mn2+, Irr addition increased the fluorescence anisotropy, corresponding to formation of the Irr-ICE complex. The addition of EDTA to the Irr-ICE complex reduced fluorescence anisotropy, but fluorescence was recovered after Mn2+ addition, indicating that Mn2+ binding is a prerequisite for complex formation. Binding activity toward ICE was lost upon introduction of substitutions in a His-cluster region of Irr, revealing that Mn2+ binds to this region. We observed that the His-cluster region is also the heme binding site; results from fluorescence anisotropy and electrophoretic mobility shift analyses disclosed that the addition of a half-equivalent of heme dissociates Irr from ICE, likely because of Mn2+ release due to heme binding. We hypothesized that heme binding to another heme binding site, Cys-29, would also inhibit the formation of the Irr-ICE complex because it is proximal to the ICE binding site, which was supported by the loss of ICE binding activity in a Cys-29-mutated Irr. These results indicate that Irr requires Mn2+ binding to form the Irr-ICE complex and that the addition of heme dissociates Irr from ICE by replacing Mn2+ with heme or by heme binding to Cys-29.
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Affiliation(s)
- Dayeon Nam
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Yuki Matsumoto
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Mark R O'Brian
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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Mason C, Liu X, Prabhudeva S, Ouyang Z. The CXXC Motifs Are Essential for the Function of BosR in Borrelia burgdorferi. Front Cell Infect Microbiol 2019; 9:109. [PMID: 31041197 PMCID: PMC6476982 DOI: 10.3389/fcimb.2019.00109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/28/2019] [Indexed: 01/07/2023] Open
Abstract
BosR, a Fur family member, is essential for the pathogenesis of the Lyme disease pathogen, Borrelia burgdorferi. Unlike typical Fur proteins in which DNA binding represses gene expression, binding of BosR to the rpoS promoter directly activates rpoS transcription in B. burgdorferi. However, virtually nothing is known concerning potential structural features and amino acid residues of BosR that are important for protein function and virulence regulation in B. burgdorferi. Particularly, it remains unknown what structural motifs or residues of BosR coordinate Zn, although previous analyses have indicated that the function of BosR may depend on Zn. To address these information gaps, we herein introduced mutations into four conserved cysteine residues in two putative CXXC motifs of BosR. Our data showed that the ability of BosR to bind Zn was dramatically reduced when the CXXC motifs were mutated. Moreover, we found that the two CXXC motifs contributed to the ability of BosR to form dimers. By using a trans-complementation genetic approach, we additionally demonstrated that both CXXC motifs of BosR were essential for in vivo gene expression regulation. Mutation of any of the four cysteines abolished the transcriptional activation of rpoS. In contrast to wild type BosR, each mutant protein was incapable of binding the rpoS promoter in electrophoretic mobility shift assays. The combined data strongly support that the two CXXC motifs and four cysteines constitute the structural site essential for Zn-coordination, protein dimerization, and the unique regulatory activity of BosR.
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Affiliation(s)
- Charlotte Mason
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
| | - Xiaoyan Liu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Spoorthy Prabhudeva
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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5
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Sato R, Harada R, Shigeta Y. The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study. Biophys Physicobiol 2018; 15:18-27. [PMID: 29450111 PMCID: PMC5812317 DOI: 10.2142/biophysico.15.0_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/30/2017] [Indexed: 12/01/2022] Open
Abstract
Photolyases (PHRs) and cryptochromes (CRYs) belong to the same family known as blue-light photoreceptors. Although their amino acid sequences and corresponding structures are similar to each other, they exert different functions. PHRs function as an enzyme to repair UV-induced deoxyribonucleic acid (DNA) lesions such as a cyclobutane pyrimidine dimer (CPD) and a (6-4) photoproduct ((6-4)pp), whereas CRYs are a circadian photoreceptor in plants and animals and at the same time they control the photoperiodic induction of flowering in plants. When a new type cryptochrome was identified, it was assumed that another type of CRYs, cryptochrome-DASH (CRY-DASH), which is categorized as a subfamily of photolyase/cryptochrome family, would possess the DNA photolyase activity. However, CRY-DASH had a weak DNA photolyase activity, but the reason for this is still unclear. To clarify the reason, we performed molecular dynamics (MD) simulations for a complex of CPD-PHR or CRY-DASH with damaged double-stranded DNA (dsDNA) and estimated the binding free energy, ΔGbind, between the protein and the damaged dsDNA by using a molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) method. ΔGbind for both proteins were −35 and 57 kcal mol−1, respectively, indicating that the structural stability of CRY-DASH was lower than that of CPD-PHR upon the damaged dsDNA binding. In particular, the number of amino acid residues relevant to the damaged dsDNA binding on the CRY-DASH surface was smaller than that on CPD-PHR. Therefore, the present result suggests that CRY-DASH has a weak DNA photolyase activity because it has a lower binding affinity than CPD-PHR.
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Affiliation(s)
- Ryuma Sato
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577 Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577 Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577 Japan
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6
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Osajima T, Hoshino T. Roles of the respective loops at complementarity determining region on the antigen-antibody recognition. Comput Biol Chem 2016; 64:368-383. [DOI: 10.1016/j.compbiolchem.2016.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 01/25/2023]
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7
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Mathieu S, Cissé C, Vitale S, Ahmadova A, Degardin M, Pérard J, Colas P, Miras R, Boturyn D, Covès J, Crouzy S, Michaud-Soret I. From Peptide Aptamers to Inhibitors of FUR, Bacterial Transcriptional Regulator of Iron Homeostasis and Virulence. ACS Chem Biol 2016; 11:2519-28. [PMID: 27409249 DOI: 10.1021/acschembio.6b00360] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
FUR (Ferric Uptake Regulator) protein is a global transcriptional regulator that senses iron status and controls the expression of genes involved in iron homeostasis, virulence, and oxidative stress. Ubiquitous in Gram-negative bacteria and absent in eukaryotes, FUR is an attractive antivirulence target since the inactivation of the fur gene in various pathogens attenuates their virulence. The characterization of 13-aa-long anti-FUR linear peptides derived from the variable part of the anti-FUR peptide aptamers, that were previously shown to decrease pathogenic E. coli strain virulence in a fly infection model, is described herein. Modeling, docking, and experimental approaches in vitro (activity and interaction assays, mutations) and in cells (yeast two-hybrid assays) were combined to characterize the interactions of the peptides with FUR, and to understand their mechanism of inhibition. As a result, reliable structure models of two peptide-FUR complexes are given. Inhibition sites are mapped in the groove between the two FUR subunits where DNA should also bind. Another peptide behaves differently and interferes with the dimerization itself. These results define these novel small peptide inhibitors as lead compounds for inhibition of the FUR transcription factor.
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Affiliation(s)
- Sophie Mathieu
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
| | - Cheickna Cissé
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
| | - Sylvia Vitale
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
| | - Aynur Ahmadova
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
| | - Mélissa Degardin
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
- Univ. Grenoble
Alpes, DCM UMR 5250, F-38000 Grenoble, France
- CNRS, DCM UMR
5250, F-38000 Grenoble, France
| | - Julien Pérard
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
| | - Pierre Colas
- P2I2 Group, Protein Phosphorylation
and Human Disease Unit, CNRS Unité de Service et de Recherche
USR3151, Station Biologique de Roscoff, F-29680 Roscoff, France
| | - Roger Miras
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
| | - Didier Boturyn
- Univ. Grenoble
Alpes, DCM UMR 5250, F-38000 Grenoble, France
- CNRS, DCM UMR
5250, F-38000 Grenoble, France
| | - Jacques Covès
- Univ. Grenoble
Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Serge Crouzy
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
| | - Isabelle Michaud-Soret
- CNRS,
Laboratoire
de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France
- CEA, LCBM, F-38054 Grenoble, France
- Univ. Grenoble Alpes,
LCBM, F-38054 Grenoble, France
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8
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Ding F, Peng W. Biophysical evaluation of protein structural flexibility for ligand biorecognition in solid solution. Phys Chem Chem Phys 2016; 18:6595-606. [DOI: 10.1039/c5cp07385e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural flexibility of biomolecules may have a large influence on ligand–receptor recognition.
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Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection
- Qingdao Agricultural University
- Qingdao 266109
- China
- Department of Chemistry
| | - Wei Peng
- College of Agriculture and Plant Protection
- Qingdao Agricultural University
- Qingdao 266109
- China
- College of Food Science and Engineering
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9
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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.
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Affiliation(s)
| | - Aubérie Parent
- Université Grenoble Alpes, LCBM, F-38054 Grenoble, France
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10
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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.
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11
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Cissé C, Mathieu SV, Abeih MBO, Flanagan L, Vitale S, Catty P, Boturyn D, Michaud-Soret I, Crouzy S. Inhibition of the ferric uptake regulator by peptides derived from anti-FUR peptide aptamers: coupled theoretical and experimental approaches. ACS Chem Biol 2014; 9:2779-86. [PMID: 25238402 DOI: 10.1021/cb5005977] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The FUR protein (ferric uptake regulator) is an iron-dependent global transcriptional regulator. Specific to bacteria, FUR is an attractive antibacterial target since virulence is correlated to iron bioavailability. Recently, four anti-FUR peptide aptamers, composed of 13 amino acid variable loops inserted into a thioredoxinA scaffold, were identified, which were able to interact with Escherichia coli FUR (EcFUR), inhibit its binding to DNA and to decrease the virulence of pathogenic E. coli in a fly infection model. The first characterization of anti-FUR linear peptides (pF1 6 to 13 amino acids) derived from the variable part of the F1 anti-FUR peptide aptamer is described herein. Theoretical and experimental approaches, in original combination, were used to study interactions of these peptides with FUR in order to understand their mechanism of inhibition. After modeling EcFUR by homology, docking with Autodock was combined with molecular dynamics simulations in implicit solvent to take into account the flexibility of the partners. All calculations were cross-checked either with other programs or with experimental data. As a result, reliable structures of EcFUR and its complex with pF1 are given and an inhibition pocket formed by the groove between the two FUR subunits is proposed. The location of the pocket was validated through experimental mutation of key EcFUR residues at the site of proposed peptide interaction. Cyclisation of pF1, mimicking the peptide constraint in F1, improved inhibition. The details of the interactions between peptide and protein were analyzed and a mechanism of inhibition of these anti-FUR molecules is proposed.
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Affiliation(s)
- Cheickna Cissé
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
| | - Sophie V. Mathieu
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
| | - Mohamed B. Ould Abeih
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
| | - Lindsey Flanagan
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
| | - Sylvia Vitale
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
| | - Patrice Catty
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
| | - Didier Boturyn
- Univ. Grenoble Alpes, DCM, CRNS, UMR 5250, F-38000 Grenoble, France
| | - Isabelle Michaud-Soret
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
| | - Serge Crouzy
- CEA, Laboratoire
de Chimie et Biologie des Métaux
(LCBM), F-38000 Grenoble, France
- CNRS, LCBM, F-38000 Grenoble, France
- Univ. Grenoble Alpes, LCBM, F-38000 Grenoble, France
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12
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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.
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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:
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13
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Bagul P, Khomane KS, Kesharwani SS, Pragyan P, Nandekar PP, Meena CL, Bansal AK, Jain R, Tikoo K, Sangamwar AT. Intestinal transport of TRH analogs through PepT1: the role ofin silicoandin vitromodeling. J Mol Recognit 2014; 27:609-17. [DOI: 10.1002/jmr.2385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/22/2014] [Accepted: 04/22/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Pravin Bagul
- Department of Pharmaceutics; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Kailas S. Khomane
- Department of Pharmaceutics; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Siddharth S. Kesharwani
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Preeti Pragyan
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Prajwal P. Nandekar
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Chhuttan Lal Meena
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Arvind K. Bansal
- Department of Pharmaceutics; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Rahul Jain
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Kulbhushan Tikoo
- Department of Pharmacology and Toxicology; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
| | - Abhay T. Sangamwar
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); Sector-67, S.A.S. Nagar Mohali Punjab 160062 India
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14
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Tobe T, Yen H, Takahashi H, Kagayama Y, Ogasawara N, Oshima T. Antisense transcription regulates the expression of the enterohemorrhagic Escherichia coli virulence regulatory gene ler in response to the intracellular iron concentration. PLoS One 2014; 9:e101582. [PMID: 25006810 PMCID: PMC4090186 DOI: 10.1371/journal.pone.0101582] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/08/2014] [Indexed: 12/12/2022] Open
Abstract
Enteric pathogens, such as enterohemorrhagic E. coli (EHEC) O157:H7, encounter varying concentrations of iron during their life cycle. In the gastrointestinal tract, the amount of available free iron is limited because of absorption by host factors. EHEC and other enteric pathogens have developed sophisticated iron-responsive systems to utilize limited iron resources, and these systems are primarily regulated by the Fur repressor protein. The iron concentration could be a signal that controls gene expression in the intestines. In this study, we explored the role of iron in LEE (locus for enterocyte effacement) virulence gene expression in EHEC. In contrast to the expression of Fur-regulated genes, the expression of LEE genes was greatly reduced in fur mutants irrespective of the iron concentration. The expression of the ler gene, the LEE-encoded master regulator, was affected at a post-transcription step by fur mutation. Further analysis showed that the loss of Fur affected the translation of the ler gene by increasing the intracellular concentration of free iron, and the transcription of the antisense strand was necessary for regulation. The results indicate that LEE gene expression is closely linked to the control of intracellular free iron homeostasis.
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Affiliation(s)
- Toru Tobe
- Department of Biomedical Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- * E-mail:
| | - Hilo Yen
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Chiba, Japan
| | - Yoko Kagayama
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Naotake Ogasawara
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Taku Oshima
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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15
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Zhao WW, Liu FF, Shi QH, Dong XY, Sun Y. Biomimetic design of affinity peptide ligands for human IgG based on protein A-IgG complex. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.03.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Ikeda Y, Minoshima H, Satoh M, Ishikawa T, Kawashima-Ohya Y, Tomobe K, Omata Y, Kawashima T. Transcriptional factor fur from Thermoplasma volcanium binds its own promoter DNA in a divalent cation-dependent manner. J GEN APPL MICROBIOL 2013; 58:465-73. [PMID: 23337582 DOI: 10.2323/jgam.58.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Because archaea possess many respiratory enzymes or radical scavengers with catalytic domains that contain iron, the expression of the genes encoding these enzymes might be regulated by iron acquisition. The genome of an archaeon, Thermoplasma volcanium contains a gene that encodes Fur (TVN0292). The fur gene of T. volcanium was amplified by PCR, and cloned into plasmid pET28a. TvFur (T. volcanium Fur protein) was expressed in E. coli cells and then purified. EMSA revealed that TvFur binds to its own promoter DNA. The binding to its own promoter was in an Mn(2+)-, Zn(2+)-, and Ni(2+)-dependent manner. DNase I footprinting analysis revealed that the binding sequence of tvfur promoter was 5'-G TTATTAT G TTTATAT A TTAATTA G-3'. An analysis utilizing oligonucleotides in TvFur-binding sequences revealed that TvFur binds to the TATA-box or regions in the vicinity of the TATA-box in the promoter. These results indicated that TvFur regulates transcription depending on the availability of environmental divalent cations.
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Affiliation(s)
- Yu Ikeda
- Department of Molecular Biology, Faculty of Pharmaceutical Science, Yokohama College of Pharmacy, Yokohama 245-0066, Japan
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17
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Effect of the amino acid substitution in the DNA-binding domain of the Fur regulator on production of pyoverdine. Folia Microbiol (Praha) 2012. [PMID: 23180123 DOI: 10.1007/s12223-012-0210-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The ferric uptake regulator gene (fur), its promoter region and Fur box of pvdS gene involved in siderophore-mediated iron uptake system were sequenced in the parent strain Pseudomonas aeruginosa PAO1 and in the fur mutant FPA121 derived from the strain PAO1. We identified the gene fur 179 bearing a novel, single-point mutation that changed the amino acid residue Gln60Pro in the DNA-binding domain of the Fur protein. The synthesis of pyoverdine was studied in cultures of the strains PAO1 and FPA121 grown in iron-deplete and iron-replete (60 μmol/L FeIII) medium. The amino acid replacement in the regulatory Fur protein is responsible for the overproduction of pyoverdine in iron-deplete and iron-replete medium. No mutation was identified in the Fur box of the gene pvdS.
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18
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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.
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19
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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.
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Affiliation(s)
- Stephen Spiro
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75080, USA.
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20
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Gu J, Yu H. The role of residue S139 of mandelate racemase: synergistic effect of S139 and E317 on transition state stabilization. J Biomol Struct Dyn 2012; 30:585-93. [DOI: 10.1080/07391102.2012.687524] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Khomane KS, Nandekar PP, Wahlang B, Bagul P, Shaikh N, Pawar YB, Meena CL, Sangamwar AT, Jain R, Tikoo K, Bansal AK. Mechanistic Insights into PEPT1-Mediated Transport of a Novel Antiepileptic, NP-647. Mol Pharm 2012; 9:2458-68. [DOI: 10.1021/mp200672d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kailas S. Khomane
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Prajwal P. Nandekar
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Banrida Wahlang
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Pravin Bagul
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Naeem Shaikh
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Yogesh B. Pawar
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Chhuttan Lal Meena
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Abhay T. Sangamwar
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Rahul Jain
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - K. Tikoo
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
| | - Arvind K. Bansal
- Department
of Pharmaceutics, ‡Department of Pharmacoinformatics, §Department of Medicinal Chemistry, and ∥Department of
Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67,
SAS Nagar, Mohali, Punjab, India
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22
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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.
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23
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Huang B, Liu FF, Dong XY, Sun Y. Molecular Mechanism of the Affinity Interactions between Protein A and Human Immunoglobulin G1 Revealed by Molecular Simulations. J Phys Chem B 2011; 115:4168-76. [DOI: 10.1021/jp111216g] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bo Huang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fu-Feng Liu
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiao-Yan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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24
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Fleischhacker AS, Kiley PJ. Iron-containing transcription factors and their roles as sensors. Curr Opin Chem Biol 2011; 15:335-41. [PMID: 21292540 DOI: 10.1016/j.cbpa.2011.01.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 12/23/2022]
Abstract
Iron-binding transcription factors are widespread throughout the bacterial world and to date are known to bind several types of cofactors, such as Fe2+, heme, or iron-sulfur clusters. The known chemistry of these cofactors is exploited by transcription factors, including Fur, FNR, and NsrR, to sense molecules such as Fe2+, gases (e.g. oxygen and nitric oxide), or reactive oxygen species. New structural data and information generated by genome-wide analysis studies have provided additional details about the mechanism and function of iron-binding transcription factors that act as sensors.
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Affiliation(s)
- Angela S Fleischhacker
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
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25
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Dian C, Vitale S, Leonard GA, Bahlawane C, Fauquant C, Leduc D, Muller C, de Reuse H, Michaud-Soret I, Terradot L. The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites. Mol Microbiol 2011; 79:1260-75. [PMID: 21208302 DOI: 10.1111/j.1365-2958.2010.07517.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fur, the ferric uptake regulator, is a transcription factor that controls iron metabolism in bacteria. Binding of ferrous iron to Fur triggers a conformational change that activates the protein for binding to specific DNA sequences named Fur boxes. In Helicobacter pylori, HpFur is involved in acid response and is important for gastric colonization in model animals. Here we present the crystal structure of a functionally active HpFur mutant (HpFur2M; C78S-C150S) bound to zinc. Although its fold is similar to that of other Fur and Fur-like proteins, the crystal structure of HpFur reveals a unique structured N-terminal extension and an unusual C-terminal helix. The structure also shows three metal binding sites: S1 the structural ZnS₄ site previously characterized biochemically in HpFur and the two zinc sites identified in other Fur proteins. Site-directed mutagenesis and spectroscopy analyses of purified wild-type HpFur and various mutants show that the two metal binding sites common to other Fur proteins can be also metallated by cobalt. DNA protection and circular dichroism experiments demonstrate that, while these two sites influence the affinity of HpFur for DNA, only one is absolutely required for DNA binding and could be responsible for the conformational changes of Fur upon metal binding while the other is a secondary site.
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Affiliation(s)
- Cyril Dian
- Structural Biology Group, European Synchrotron Radiation Facility, BP 220 F-38043 Grenoble cedex 9, France
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26
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Abstract
Both the essentiality and toxicity of transition metals are exploited as part of mammalian immune defenses against bacterial infection. Salmonella serovars continue to cause serious medical and veterinary problems worldwide and detecting deficiency and excess of different metal ions (such as copper, iron, zinc, manganese, nickel, and cobalt) is fundamental to their virulence. This involves multiple DNA-binding metal-responsive transcription factors that discriminate between elements and trigger expression of genes that mediate appropriate responses to metal fluxes. This review focuses on the metal stresses encountered by Salmonella during infection and the roles of the different metal-sensing regulatory proteins and their target genes in adapting to these changing metal levels. Current knowledge regarding the mechanisms of metal-regulated gene expression and the structural features of sensory metal binding sites are described. In addition, the principles governing the ability of the different sensors to detect specific metals within a cell to control cytosolic metal levels are also discussed. These proteins represent potential targets for the development of new therapeutic approaches.
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27
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Mutagenesis of conserved amino acids of Helicobacter pylori fur reveals residues important for function. J Bacteriol 2010; 192:5037-52. [PMID: 20644138 DOI: 10.1128/jb.00198-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The ferric uptake regulator (Fur) of the medically important pathogen Helicobacter pylori is unique in that it has been shown to function as a repressor both in the presence of an Fe2+ cofactor and in its apo (non-Fe2+-bound) form. However, virtually nothing is known concerning the amino acid residues that are important for Fur functioning. Therefore, mutations in six conserved amino acid residues of H. pylori Fur were constructed and analyzed for their impact on both iron-bound and apo repression. In addition, accumulation of the mutant proteins, protein secondary structure, DNA binding ability, iron binding capacity, and the ability to form higher-order structures were also examined for each mutant protein. While none of the mutated residues completely abrogated the function of Fur, we were able to identify residues that were critical for both iron-bound and apo-Fur repression. One mutation, V64A, did not alter regulation of any target genes. However, each of the five remaining mutations showed an effect on either iron-bound or apo regulation. Of these, H96A, E110A, and E117A mutations altered iron-bound Fur regulation and were all shown to influence iron binding to different extents. Additionally, the H96A mutation was shown to alter Fur oligomerization, and the E110A mutation was shown to impact oligomerization and DNA binding. Conversely, the H134A mutant exhibited changes in apo-Fur regulation that were the result of alterations in DNA binding. Although the E90A mutant exhibited alterations in apo-Fur regulation, this mutation did not affect any of the assessed protein functions. This study is the first for H. pylori to analyze the roles of specific amino acid residues of Fur in function and continues to highlight the complexity of Fur regulation in this organism.
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28
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Furini S, Domene C, Cavalcanti S. Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. J Phys Chem B 2010; 114:2238-45. [PMID: 20095570 DOI: 10.1021/jp906504m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The Lac repressor finds its DNA binding sequences with an association rate 2 orders of magnitude higher than what is expected for a random diffusive process. This experimental data stimulated numerous theoretical and experimental studies, which led to the facilitated diffusion model. In facilitated diffusion, the Lac repressor binds nonspecifically to DNA. This nonspecific binding is followed by an exploration of the DNA molecule in a reduced space. Single-molecule imaging confirmed that the Lac repressor may move along the DNA molecule; however, it is still under debate whether the LacI movement proceeds through sliding, with a continuous close contact between the protein and DNA, or through hopping between adjacent binding sites. We have investigated the one-dimensional sliding movement of the Lac repressor along nonspecific DNA by full-atomistic molecular dynamics simulations and free-energy calculations based on the umbrella sampling technique. The computed free-energy profile along a helical trajectory was periodic, with periodicity equal to the distance between successive nucleotides and an energy barrier between successive minima of 8.7 +/- 0.7 kcal/mol. The results from the molecular simulations were subsequently used in a Langevin dynamics framework to estimate the diffusion coefficient of the Lac repressor sliding along nonspecific DNA. The computed diffusion coefficient is close to the lower limit of the experimental range.
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Affiliation(s)
- Simone Furini
- Department of Electronics, Computer Science and Systems, University of Bologna, Bologna, Italy.
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Pedersen HL, Ahmad R, Riise EK, Leiros HKS, Hauglid S, Espelid S, Brandsdal BO, Leiros I, Willassen NP, Haugen P. Experimental and computational characterization of the ferric uptake regulator from Aliivibrio salmonicida (Vibrio salmonicida). J Microbiol 2010; 48:174-83. [DOI: 10.1007/s12275-010-9199-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 09/17/2009] [Indexed: 11/29/2022]
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Vitale S, Fauquant C, Lascoux D, Schauer K, Saint-Pierre C, Michaud-Soret I. A ZnS4 Structural Zinc Site in the Helicobacter pylori Ferric Uptake Regulator. Biochemistry 2009; 48:5582-91. [DOI: 10.1021/bi9004396] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sylvia Vitale
- CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), l’Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), and Université Joseph Fourier, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Caroline Fauquant
- CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), l’Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), and Université Joseph Fourier, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - David Lascoux
- Laboratoire de Spectrométrie de Masse des Protéines, Institut de Biologie Structurale, Jean-Pierre Ebel (UMR 5075 CNRS/CEA/UJF), F-38027 Grenoble Cedex 1, France
| | - Kristine Schauer
- Unité Pathogenèse de Helicobacter, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Christine Saint-Pierre
- Laboratoire des Lésions des Acides Nucléiques, DSM/INAC/Service de Chimie Inorganique et Biologique, UMR E-3 CEA/UJF CNRS FRE 3200, 17 rue des Martyrs, Grenoble F-38054 Cedex 9, France
| | - Isabelle Michaud-Soret
- CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), l’Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), and Université Joseph Fourier, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
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31
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Sheikh MA, Taylor GL. Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals insights into metal co-ordination. Mol Microbiol 2009; 72:1208-20. [PMID: 19400801 DOI: 10.1111/j.1365-2958.2009.06718.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ferric uptake regulator (Fur) is a metal-dependent DNA-binding protein that acts as both a repressor and an activator of numerous genes involved in maintaining iron homeostasis in bacteria. It has also been demonstrated in Vibrio cholerae that Fur plays an additional role in pathogenesis, opening up the potential of Fur as a drug target for cholera. Here we present the crystal structure of V. cholerae Fur that reveals a very different orientation of the DNA-binding domains compared with that observed in Pseudomonas aeruginosa Fur. Each monomer of the dimeric Fur protein contains two metal binding sites occupied by zinc in the crystal structure. In the P. aeruginosa study these were designated as the regulatory site (Zn1) and structural site (Zn2). This V. cholerae Fur study, together with studies on Fur homologues and paralogues, suggests that in fact the Zn2 site is the regulatory iron binding site and the Zn1 site plays an auxiliary role. There is no evidence of metal binding to the cysteines that are conserved in many Fur homologues, including Escherichia coli Fur. An analysis of the metal binding properties shows that V. cholerae Fur can be activated by a range of divalent metals.
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Affiliation(s)
- Md Arif Sheikh
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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