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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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Molecular basis for the integration of environmental signals by FurB from Anabaena sp. PCC 7120. Biochem J 2018; 475:151-168. [DOI: 10.1042/bcj20170692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/22/2017] [Accepted: 12/04/2017] [Indexed: 12/29/2022]
Abstract
FUR (Ferric uptake regulator) proteins are among the most important families of transcriptional regulators in prokaryotes, often behaving as global regulators. In the cyanobacterium Anabaena PCC 7120, FurB (Zur, Zinc uptake regulator) controls zinc and redox homeostasis through the repression of target genes in a zinc-dependent manner. In vitro, non-specific binding of FurB to DNA elicits protection against oxidative damage and avoids cleavage by deoxyribonuclease I. The present study provides, for the first time, evidence of the influence of redox environment in the interaction of FurB with regulatory zinc and its consequences in FurB–DNA-binding affinity. Calorimetry studies showed that, in addition to one structural Zn(II), FurB is able to bind two additional Zn(II) per monomer and demonstrated the implication of cysteine C93 in regulatory Zn(II) coordination. The interaction of FurB with the second regulatory zinc occurred only under reducing conditions. While non-specific FurB–DNA interaction is Zn(II)-independent, the optimal binding of FurB to target promoters required loading of two regulatory zinc ions. Those results combined with site-directed mutagenesis and gel-shift assays evidenced that the redox state of cysteine C93 conditions the binding of the second regulatory Zn(II) and, in turn, modulates the affinity for a specific DNA target. Furthermore, differential spectroscopy studies showed that cysteine C93 could also be involved in heme coordination by FurB, either as a direct ligand or being located near the binding site. The results indicate that besides controlling zinc homeostasis, FurB could work as a redox-sensing protein probably modifying its zinc and DNA-binding abilities depending upon environmental conditions.
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Kaushik MS, Singh P, Tiwari B, Mishra AK. Ferric Uptake Regulator (FUR) protein: properties and implications in cyanobacteria. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1134-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Doménech R, Hernández-Cifre JG, Bacarizo J, Díez-Peña AI, Martínez-Rodríguez S, Cavasotto CN, de la Torre JG, Cámara-Artigás A, Velázquez-Campoy A, Neira JL. The histidine-phosphocarrier protein of the phosphoenolpyruvate: sugar phosphotransferase system of Bacillus sphaericus self-associates. PLoS One 2013; 8:e69307. [PMID: 23922699 PMCID: PMC3724859 DOI: 10.1371/journal.pone.0069307] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/12/2013] [Indexed: 12/12/2022] Open
Abstract
The phosphotransferase system (PTS) is involved in the use of carbon sources in bacteria. Bacillus sphaericus, a bacterium with the ability to produce insecticidal proteins, is unable to use hexoses and pentoses as the sole carbon source, but it has ptsHI genes encoding the two general proteins of the PTS: enzyme I (EI) and the histidine phosphocarrier (HPr). In this work, we describe the biophysical and structural properties of HPr from B. sphaericus, HPrbs, and its affinity towards EI of other species to find out whether there is inter-species binding. Conversely to what happens to other members of the HPr family, HPrbs forms several self-associated species. The conformational stability of the protein is low, and it unfolds irreversibly during heating. The protein binds to the N-terminal domain of EI from Streptomyces coelicolor, EINsc, with a higher affinity than that of the natural partner of EINsc, HPrsc. Modelling of the complex between EINsc and HPrbs suggests that binding occurs similarly to that observed in other HPr species. We discuss the functional implications of the oligomeric states of HPrbs for the glycolytic activity of B. sphaericus, as well as a strategy to inhibit binding between HPrsc and EINsc.
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Affiliation(s)
- Rosa Doménech
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
| | | | - Julio Bacarizo
- Departamento de Química y Física, Campus de Excelencia Internacional Agroalimentario, Universidad de Almería, Almería, Spain
| | - Ana I. Díez-Peña
- Departamento de Química Física, Universidad de Murcia, Murcia, Spain
| | - Sergio Martínez-Rodríguez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
- Departamento de Química y Física, Campus de Excelencia Internacional Agroalimentario, Universidad de Almería, Almería, Spain
| | - Claudio N. Cavasotto
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET- Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | | | - Ana Cámara-Artigás
- Departamento de Química y Física, Campus de Excelencia Internacional Agroalimentario, Universidad de Almería, Almería, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - José L. Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- * E-mail:
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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]
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Pellicer S, Bes MT, González A, Neira JL, Peleato ML, Fillat MF. High-recovery one-step purification of the DNA-binding protein Fur by mild guanidinium chloride treatment. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hernández JA, Pellicer S, Huang L, Peleato ML, Fillat MF. FurA modulates gene expression of alr3808, a DpsA homologue in Nostoc (Anabaena) sp. PCC7120. FEBS Lett 2007; 581:1351-6. [PMID: 17350003 DOI: 10.1016/j.febslet.2007.02.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 02/15/2007] [Accepted: 02/18/2007] [Indexed: 10/23/2022]
Abstract
The DNA-binding protein from stationary phase (Dps) protein family plays an important role in protecting microorganisms from oxidative and nutritional stresses. In silico analysis of the promoter region of alr3808, a dpsA homologue from the cyanobacterium Nostoc sp. PCC7120 shows putative iron-boxes with high homology with those recognized by FurA (ferric uptake regulator). Evidence for the modulation of dpsA by FurA was obtained using in vitro and in vivo approaches. SELEX linked to PCR was used to identify P(dpsA) as a FurA target. Concurrently, EMSA assays showed high affinity of FurA for the dpsA promoter region. DpsA expression analysis in an insertional mutant of the alr1690-alphafurA message (that exhibited an increased expression of FurA) showed a reduced synthesis of DpsA. These studies suggest that FurA plays a significant role in the regulation of the DpsA.
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Affiliation(s)
- José A Hernández
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Pedro Cerbuna 12, 50009-Zaragoza, Spain
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