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Oney-Hawthorne SD, Barondeau DP. Fe-S cluster biosynthesis and maturation: Mass spectrometry-based methods advancing the field. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119784. [PMID: 38908802 DOI: 10.1016/j.bbamcr.2024.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
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Affiliation(s)
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA.
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2
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Vallières C, Benoit O, Guittet O, Huang ME, Lepoivre M, Golinelli-Cohen MP, Vernis L. Iron-sulfur protein odyssey: exploring their cluster functional versatility and challenging identification. Metallomics 2024; 16:mfae025. [PMID: 38744662 PMCID: PMC11138216 DOI: 10.1093/mtomcs/mfae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Iron-sulfur (Fe-S) clusters are an essential and ubiquitous class of protein-bound prosthetic centers that are involved in a broad range of biological processes (e.g. respiration, photosynthesis, DNA replication and repair and gene regulation) performing a wide range of functions including electron transfer, enzyme catalysis, and sensing. In a general manner, Fe-S clusters can gain or lose electrons through redox reactions, and are highly sensitive to oxidation, notably by small molecules such as oxygen and nitric oxide. The [2Fe-2S] and [4Fe-4S] clusters, the most common Fe-S cofactors, are typically coordinated by four amino acid side chains from the protein, usually cysteine thiolates, but other residues (e.g. histidine, aspartic acid) can also be found. While diversity in cluster coordination ensures the functional variety of the Fe-S clusters, the lack of conserved motifs makes new Fe-S protein identification challenging especially when the Fe-S cluster is also shared between two proteins as observed in several dimeric transcriptional regulators and in the mitoribosome. Thanks to the recent development of in cellulo, in vitro, and in silico approaches, new Fe-S proteins are still regularly identified, highlighting the functional diversity of this class of proteins. In this review, we will present three main functions of the Fe-S clusters and explain the difficulties encountered to identify Fe-S proteins and methods that have been employed to overcome these issues.
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Affiliation(s)
- Cindy Vallières
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Orane Benoit
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Olivier Guittet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Meng-Er Huang
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Michel Lepoivre
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Laurence Vernis
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
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Dodd EL, Le Brun NE. Probing the mechanism of the dedicated NO sensor [4Fe-4S] NsrR: the effect of cluster ligand environment. J Inorg Biochem 2024; 252:112457. [PMID: 38176366 DOI: 10.1016/j.jinorgbio.2023.112457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 01/06/2024]
Abstract
NsrR from Streptomyces coelicolor is a bacterial nitric oxide (NO) sensor/nitrosative stress regulator as its primary function, and has been shown to have differential response at low, mid, and high levels of NO. These must correspond to discrete structural changes at the protein-bound [4Fe-4S] cluster in response to stepwise nitrosylation of the cluster. We have investigated the effect of the monohapto carboxylate ligand in the site differentiated [4Fe-4S] cluster cofactor of the protein NsrR on modulating its reactivity to NO with a focus on indentifying mechanistic intermediates. We have prepared a synthetic model [4Fe-4S] cluster complex with tripodal ligand and one single site differentiated site occupied by either thiolate or carboxylate ligand. We report here the mechanistic details of sequential steps of nitrosylation as observed by ESI MS and IR spectroscopy. Parallel non-denaturing mass spectrometry analyses were performed using site-differentiated variants of NsrR with the native aspartic acid, cysteine, or alanine in the position of the forth ligand to the cluster. A mono-nitrosylated synthetic [4Fe-4S] cluster was observed for the first time in a biologically-relevant thiolate-based coordination environment. Combined synthetic and protein data give unprecedented clarity in the modulation of nitrosylation of a [4Fe-4S] cluster.
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Affiliation(s)
- Erin L Dodd
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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4
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Rohac R, Crack JC, de Rosny E, Gigarel O, Le Brun NE, Fontecilla-Camps JC, Volbeda A. Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors. Commun Biol 2022; 5:769. [PMID: 35908109 PMCID: PMC9338935 DOI: 10.1038/s42003-022-03745-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/21/2022] [Indexed: 11/20/2022] Open
Abstract
Several transcription factors of the Rrf2 family use an iron-sulfur cluster to regulate DNA binding through effectors such as nitric oxide (NO), cellular redox status and iron levels. [4Fe-4S]-NsrR from Streptomyces coelicolor (ScNsrR) modulates expression of three different genes via reaction and complex formation with variable amounts of NO, which results in detoxification of this gas. Here, we report the crystal structure of ScNsrR complexed with an hmpA1 gene operator fragment and compare it with those previously reported for [2Fe-2S]-RsrR/rsrR and apo-IscR/hyA complexes. Important structural differences reside in the variation of the DNA minor and major groove widths. In addition, different DNA curvatures and different interactions with the protein sensors are observed. We also report studies of NsrR binding to four hmpA1 variants, which indicate that flexibility in the central region is not a key binding determinant. Our study explores the promotor binding specificities of three closely related transcriptional regulators. The crystal structure of the iron-sulfur protein NsrR from Streptomyces coelicolor bound to a gene operator fragment is reported and compared with other structures, giving insight into the structural determinants of DNA recognition by the NO sensor.
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Affiliation(s)
- Roman Rohac
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Eve de Rosny
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Océane Gigarel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Juan C Fontecilla-Camps
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Anne Volbeda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France.
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5
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Sawa T, Takata T, Matsunaga T, Ihara H, Motohashi H, Akaike T. Chemical Biology of Reactive Sulfur Species: Hydrolysis-Driven Equilibrium of Polysulfides as a Determinant of Physiological Functions. Antioxid Redox Signal 2022; 36:327-336. [PMID: 34409860 PMCID: PMC8865625 DOI: 10.1089/ars.2021.0170] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Significance: Polysulfide species (i.e., R-Sn-R', n > 2; and R-Sn-H, n > 1) exist in many organisms. The highly nucleophilic nature of hydropersulfides and hydropolysulfides contributes to the potent antioxidant activities of polysulfide species that protect organisms against oxidative and electrophilic stresses. Recent Advances: Accumulating evidence suggests that organic polysulfides (R-Sn-R') readily undergo alkaline hydrolysis, which results in formation of both nucleophilic hydrosulfide/polysulfide (R-Sn-1H) and electrophilic sulfenic acid (R'SOH) species. Polysulfides maintain a steady-state equilibrium that is driven by hydrolysis even in aqueous physiological milieus. This unique property makes polysulfide chemistry and biology more complex than previously believed. Critical Issues: The hydrolysis equilibrium of polysulfides shifts to the right when electrophiles are present. Strong electrophilic alkylating agents (e.g., monobromobimane) greatly enhance polysulfide hydrolysis, which leads to increased polysulfide degradation and artifactual formation of bis-S-bimane adducts in the absence of free hydrogen sulfide. The finding that hydroxyl group-containing substances such as tyrosine efficiently protected polysulfides from hydrolysis led to development of the new alkylating agent, N-iodoacetyl l-tyrosine methyl ester (TME-IAM). TME-IAM efficiently and specifically traps and stabilizes hydropolysulfides and protects polysulfide chains from hydrolysis, and, when used with mass spectrometry, TME-IAM allows speciation of the reactive sulfur metabolome. In addition, the polyethylene glycol-conjugated maleimide-labeling gel shift assay, which relies on unique hydrolysis equilibrium of polysulfides, will be a reliable technique for proteomics of polysulfide-containing proteins. Future Directions: Using precise methodologies to achieve a better understanding of the occurrence and metabolism of polysulfide species is necessary to gain insights into the undefined biology of polysulfide species. Antioxid. Redox Signal. 36, 327-336.
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Affiliation(s)
- Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tsuyoshi Takata
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuro Matsunaga
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hideshi Ihara
- Department of Biological Sciences, Graduate School of Science, Osaka Prefecture University, Osaka, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
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6
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Oakley KM, Lehane RL, Zhao Z, Kim E. Dioxygen reactivity of a biomimetic [4Fe-4S] compound exhibits [4Fe-4S] to [2Fe-2S] cluster conversion. J Inorg Biochem 2022; 228:111714. [PMID: 35032923 DOI: 10.1016/j.jinorgbio.2022.111714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/16/2021] [Accepted: 01/01/2022] [Indexed: 10/19/2022]
Abstract
Fumarate and nitrate reductase (FNR) is a gene regulatory protein that controls anaerobic to aerobic respiration in Escherichia coli, for which O2 serves as a control switch to induce a protein structural change by converting [4Fe-4S] cofactors to [2Fe-2S] clusters. Although biomimetic models can aid in understanding the complex functions of their protein counterparts, the inherent sensitivity of discrete [Fe-S] molecules to aerobic conditions poses a unique challenge to mimic the O2-sensing capability of FNR. Herein, we report unprecedented biomimetic O2 reactivity of a discrete [4Fe-4S] complex, [Fe4S4(SPhF)4]2- (1) where SPhF is 4-fluorothiophenolate, in which the reaction of 1 with O2(g) in the presence of thiolate produces its [2Fe-2S] analogue, [Fe2S2(SPhF)4]2- (2), at room temperature. The cluster conversion of 1 to 2 can also be achieved by employing disulfide as an oxidant under the same reaction conditions. The [4Fe-4S] to [2Fe-2S] cluster conversion by O2 was found to be significantly faster than that by disulfide, while the reaction with disulfide produced higher yields of 2.
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Affiliation(s)
- Kady M Oakley
- Brown University, Providence, RI, United States of America
| | - Ryan L Lehane
- Brown University, Providence, RI, United States of America
| | - Ziyi Zhao
- Brown University, Providence, RI, United States of America
| | - Eunsuk Kim
- Brown University, Providence, RI, United States of America.
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7
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Butt AT, Banyard CD, Haldipurkar SS, Agnoli K, Mohsin M, Vitovski S, Paleja A, Tang Y, Lomax R, Ye F, Green J, Thomas M. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3709-3726. [PMID: 35234897 PMCID: PMC9023288 DOI: 10.1093/nar/gkac137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/14/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen that causes severe infections of the cystic fibrosis (CF) lung. To acquire iron, B. cenocepacia secretes the Fe(III)-binding compound, ornibactin. Genes for synthesis and utilisation of ornibactin are served by the iron starvation (IS) extracytoplasmic function (ECF) σ factor, OrbS. Transcription of orbS is regulated in response to the prevailing iron concentration by the ferric uptake regulator (Fur), such that orbS expression is repressed under iron-sufficient conditions. Here we show that, in addition to Fur-mediated regulation of orbS, the OrbS protein itself responds to intracellular iron availability. Substitution of cysteine residues in the C-terminal region of OrbS diminished the ability to respond to Fe(II) in vivo. Accordingly, whilst Fe(II) impaired transcription from and recognition of OrbS-dependent promoters in vitro by inhibiting the binding of OrbS to core RNA polymerase (RNAP), the cysteine-substituted OrbS variant was less responsive to Fe(II). Thus, the cysteine residues within the C-terminal region of OrbS contribute to an iron-sensing motif that serves as an on-board ‘anti-σ factor’ in the presence of Fe(II). A model to account for the presence two regulators (Fur and OrbS) that respond to the same intracellular Fe(II) signal to control ornibactin synthesis and utilisation is discussed.
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Affiliation(s)
- Aaron T Butt
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Christopher D Banyard
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Sayali S Haldipurkar
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Kirsty Agnoli
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Muslim I Mohsin
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Srdjan Vitovski
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Ameya Paleja
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Yingzhi Tang
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Rebecca Lomax
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Fuzhou Ye
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
| | - Jeffrey Green
- Correspondence may also be addressed to Jeffrey Green. Tel: +44 114 222 4403; Fax: +44 114 222 2800;
| | - Mark S Thomas
- To whom correspondence should be addressed. Tel: +44 114 215 9557; Fax: +44 114 271 1863;
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8
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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10
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Rydz L, Wróbel M, Jurkowska H. Sulfur Administration in Fe-S Cluster Homeostasis. Antioxidants (Basel) 2021; 10:antiox10111738. [PMID: 34829609 PMCID: PMC8614886 DOI: 10.3390/antiox10111738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022] Open
Abstract
Mitochondria are the key organelles of Fe–S cluster synthesis. They contain the enzyme cysteine desulfurase, a scaffold protein, iron and electron donors, and specific chaperons all required for the formation of Fe–S clusters. The newly formed cluster can be utilized by mitochondrial Fe–S protein synthesis or undergo further transformation. Mitochondrial Fe–S cluster biogenesis components are required in the cytosolic iron–sulfur cluster assembly machinery for cytosolic and nuclear cluster supplies. Clusters that are the key components of Fe–S proteins are vulnerable and prone to degradation whenever exposed to oxidative stress. However, once degraded, the Fe–S cluster can be resynthesized or repaired. It has been proposed that sulfurtransferases, rhodanese, and 3-mercaptopyruvate sulfurtransferase, responsible for sulfur transfer from donor to nucleophilic acceptor, are involved in the Fe–S cluster formation, maturation, or reconstitution. In the present paper, we attempt to sum up our knowledge on the involvement of sulfurtransferases not only in sulfur administration but also in the Fe–S cluster formation in mammals and yeasts, and on reconstitution-damaged cluster or restoration of enzyme’s attenuated activity.
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11
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Pardoux R, Dolla A, Aubert C. Metal-containing PAS/GAF domains in bacterial sensors. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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12
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Dillon KM, Matson JB. A Review of Chemical Tools for Studying Small Molecule Persulfides: Detection and Delivery. ACS Chem Biol 2021; 16:1128-1141. [PMID: 34114796 DOI: 10.1021/acschembio.1c00255] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hydrogen sulfide (H2S) has gained significant attention as a potent bioregulator in the redox metabolome, but it is just one of many reactive sulfur species (RSS). Recently, small molecule persulfides (structure RSSH) have emerged as RSS of particular interest due to their enhanced antioxidant abilities compared to H2S and their ability to directly convert protein thiols into protein persulfides, suggesting that persulfides may have distinct physiological functions from H2S. However, persulfides exhibit instability and cross-reactivity that hampers the elucidation of their precise biological roles. As such, chemists have designed chemical tools and techniques to facilitate the study of persulfides under various conditions. These molecules and methods include persulfide trapping reagents and sensors, as well as compounds that degrade in response to various triggers to release persulfides, termed persulfide donors. There now exist a variety of persulfide donor classes, some of which possess tissue-targeting capabilities designed to mimic localized endogenous production of RSS. This Review briefly covers the physicochemical properties of persulfides, the endogenous production of small molecule persulfides, and their reactions with protein thiols and other reactive species. These introductory sections are followed by a discussion of chemical tools used in persulfide chemical biology, with critical analysis of recent advancements in the field and commentary on potential directions for future research.
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Affiliation(s)
- Kearsley M. Dillon
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - John B. Matson
- Department of Chemistry, Virginia Tech Center for Drug Discovery, and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
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13
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Crack JC, Gray E, Le Brun NE. Sensing mechanisms of iron-sulfur cluster regulatory proteins elucidated using native mass spectrometry. Dalton Trans 2021; 50:7887-7897. [PMID: 34037038 PMCID: PMC8204329 DOI: 10.1039/d1dt00993a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/17/2021] [Indexed: 12/02/2022]
Abstract
The ability to sense and respond to various key environmental cues is important for the survival and adaptability of many bacteria, including pathogens. The particular sensitivity of iron-sulfur (Fe-S) clusters is exploited in nature, such that multiple sensor-regulator proteins, which coordinate the detection of analytes with a (in many cases) global transcriptional response, are Fe-S cluster proteins. The fragility and sensitivity of these Fe-S clusters make studying such proteins difficult, and gaining insight of what they sense, and how they sense it and transduce the signal to affect transcription, is a major challenge. While mass spectrometry is very widely used in biological research, it is normally employed under denaturing conditions where non-covalently attached cofactors are lost. However, mass spectrometry under conditions where the protein retains its native structure and, thus, cofactors, is now itself a flourishing field, and the application of such 'native' mass spectrometry to study metalloproteins is now relatively widespread. Here we describe recent advances in using native MS to study Fe-S cluster proteins. Through its ability to accurately measure mass changes that reflect chemistry occurring at the cluster, this approach has yielded a remarkable richness of information that is not accessible by other, more traditional techniques.
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Affiliation(s)
- Jason C. Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research ParkNorwichNR4 7TJUK
| | - Elizabeth Gray
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research ParkNorwichNR4 7TJUK
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research ParkNorwichNR4 7TJUK
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14
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Abstract
Iron-sulfur clusters constitute a large and widely distributed group of protein cofactors that play key roles in a wide range of metabolic processes. The inherent reactivity of iron-sulfur clusters toward small molecules, for example, O2, NO, or free Fe, makes them ideal for sensing changes in the cellular environment. Nondenaturing, or native, MS is unique in its ability to preserve the noncovalent interactions of many (if not all) species, including stable intermediates, while providing accurate mass measurements in both thermodynamic and kinetic experimental regimes. Here, we provide practical guidance for the study of iron-sulfur proteins by native MS, illustrated by examples where it has been used to unambiguously determine the type of cluster coordinated to the protein framework. We also describe the use of time-resolved native MS to follow the kinetics of cluster conversion, allowing the elucidation of the precise series of molecular events for all species involved. Finally, we provide advice on a unique approach to a typical thermodynamic titration, uncovering early, quasi-stable, intermediates in the reaction of a cluster with nitric oxide, resulting in cluster nitrosylation.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, UK.
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15
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Azam T, Przybyla-Toscano J, Vignols F, Couturier J, Rouhier N, Johnson MK. [4Fe-4S] cluster trafficking mediated by Arabidopsis mitochondrial ISCA and NFU proteins. J Biol Chem 2020; 295:18367-18378. [PMID: 33122194 PMCID: PMC7939391 DOI: 10.1074/jbc.ra120.015726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/12/2020] [Indexed: 12/17/2022] Open
Abstract
Numerous iron-sulfur (Fe-S) proteins with diverse functions are present in the matrix and respiratory chain complexes of mitochondria. Although [4Fe-4S] clusters are the most common type of Fe-S cluster in mitochondria, the molecular mechanism of [4Fe-4S] cluster assembly and insertion into target proteins by the mitochondrial iron-sulfur cluster (ISC) maturation system is not well-understood. Here we report a detailed characterization of two late-acting Fe-S cluster-carrier proteins from Arabidopsis thaliana, NFU4 and NFU5. Yeast two-hybrid and bimolecular fluorescence complementation studies demonstrated interaction of both the NFU4 and NFU5 proteins with the ISCA class of Fe-S carrier proteins. Recombinant NFU4 and NFU5 were purified as apo-proteins after expression in Escherichia coliIn vitro Fe-S cluster reconstitution led to the insertion of one [4Fe-4S]2+ cluster per homodimer as determined by UV-visible absorption/CD, resonance Raman and EPR spectroscopy, and analytical studies. Cluster transfer reactions, monitored by UV-visible absorption and CD spectroscopy, showed that a [4Fe-4S]2+ cluster-bound ISCA1a/2 heterodimer is effective in transferring [4Fe-4S]2+ clusters to both NFU4 and NFU5 with negligible back reaction. In addition, [4Fe-4S]2+ cluster-bound ISCA1a/2, NFU4, and NFU5 were all found to be effective [4Fe-4S]2+ cluster donors for maturation of the mitochondrial apo-aconitase 2 as assessed by enzyme activity measurements. The results demonstrate rapid, unidirectional, and quantitative [4Fe-4S]2+ cluster transfer from ISCA1a/2 to NFU4 or NFU5 that further delineates their respective positions in the plant ISC machinery and their contributions to the maturation of client [4Fe-4S] cluster-containing proteins.
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Affiliation(s)
- Tamanna Azam
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA
| | | | - Florence Vignols
- BPMP, Université de Montpellier, INRAE, CNRS, SupAgro, Montpellier, France
| | | | | | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA.
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Enzymatic Regulation and Biological Functions of Reactive Cysteine Persulfides and Polysulfides. Biomolecules 2020; 10:biom10091245. [PMID: 32867265 PMCID: PMC7563103 DOI: 10.3390/biom10091245] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/15/2020] [Accepted: 08/25/2020] [Indexed: 01/15/2023] Open
Abstract
Cysteine persulfide (CysSSH) and cysteine polysulfides (CysSSnH, n > 1) are cysteine derivatives that have sulfane sulfur atoms bound to cysteine thiol. Advances in analytical methods that detect and quantify persulfides and polysulfides have shown that CysSSH and related species such as glutathione persulfide occur physiologically and are prevalent in prokaryotes, eukaryotes, and mammals in vivo. The chemical properties and abundance of these compounds suggest a central role for reactive persulfides in cell-regulatory processes. CysSSH and related species have been suggested to act as powerful antioxidants and cellular protectants and may serve as redox signaling intermediates. It was recently shown that cysteinyl-tRNA synthetase (CARS) is a new cysteine persulfide synthase. In addition, we discovered that CARS is involved in protein polysulfidation that is coupled with translation. Mitochondrial activity in biogenesis and bioenergetics is supported and upregulated by CysSSH derived from mitochondrial CARS. In this review article, we discuss the mechanisms of the biosynthesis of CysSSH and related persulfide species, with a particular focus on the roles of CARS. We also review the antioxidative and anti-inflammatory actions of persulfides.
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17
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Zhang T, Tsutsuki H, Ono K, Akaike T, Sawa T. Antioxidative and anti-inflammatory actions of reactive cysteine persulfides. J Clin Biochem Nutr 2020; 68:5-8. [PMID: 33536706 PMCID: PMC7844669 DOI: 10.3164/jcbn.20-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/07/2020] [Indexed: 12/19/2022] Open
Abstract
Cysteine persulfide (CysSSH) and polysulfides (CysS[S]nH, n>1) are cysteine derivatives having sulfane sulfur atoms bound to cysteine thiol. Recent advances in the development of analytical methods for detection and quantification of persulfides and polysulfides have revealed the biological presence, in both prokaryotes and eukaryotes, of persulfide/polysulfide in diverse forms such as CysSSH, glutathione persulfide and protein persulfides. Accumulating evidence has suggested that persulfide/polysulfide species may involve in a variety of biological events such as biosyntheses of sulfur-containing molecules, tRNA modification, regulation of redox-dependent signal transduction, mitochondrial energy metabolism via sulfur respiration, cytoprotection from oxidative stress via their antioxidant activities, and anti-inflammation against Toll-like receptor-mediated inflammatory responses. Development of chemical sulfur donors may facilitate further understanding of physiological and pathophysiological roles of persulfide/polysulfide species, including regulatory roles of these species in immune responses.
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Affiliation(s)
- Tianli Zhang
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Hiroyasu Tsutsuki
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Katushiko Ono
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
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18
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Crack JC, Stewart MYY, Le Brun NE. Generation of 34S-substituted protein-bound [4Fe-4S] clusters using 34S-L-cysteine. Biol Methods Protoc 2019; 4:bpy015. [PMID: 32395620 PMCID: PMC7200944 DOI: 10.1093/biomethods/bpy015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 01/30/2023] Open
Abstract
The ability to specifically label the sulphide ions of protein-bound iron-sulphur (FeS) clusters with 34S isotope greatly facilitates structure-function studies. In particular, it provides insight when using either spectroscopic techniques that probe cluster-associated vibrations, or non-denaturing mass spectrometry, where the ∼+2 Da average increase per sulphide enables unambiguous assignment of the FeS cluster and, where relevant, its conversion/degradation products. Here, we employ a thermostable homologue of the O-acetyl-l-serine sulfhydrylase CysK to generate 34S-substituted l-cysteine and subsequently use it as a substrate for the l-cysteine desulfurase NifS to gradually supply 34S2- for in vitro FeS cluster assembly in an otherwise standard cluster reconstitution protocol.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR47 TJ, UK
| | - Melissa Y Y Stewart
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR47 TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR47 TJ, UK
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19
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out multiple functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters with small/redox-active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial reprogramming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances: Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high-resolution structural data. Although this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
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20
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Mettert EL, Kiley PJ. Reassessing the Structure and Function Relationship of the O 2 Sensing Transcription Factor FNR. Antioxid Redox Signal 2018; 29:1830-1840. [PMID: 28990402 PMCID: PMC6217745 DOI: 10.1089/ars.2017.7365] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE The Escherichia coli regulatory protein fumarate nitrate reduction (FNR) mediates a global transcriptional response upon O2 deprivation. Spanning nearly 40 years of research investigations, our understanding of how FNR senses and responds to O2 has considerably progressed despite a lack of structural information for most of that period. This knowledge has established the paradigm for how facultative anaerobic bacteria sense changes in O2 tension. Recent Advances: Recently, the X-ray crystal structure of Aliivibrio fischeri FNR with its [4Fe-4S] cluster cofactor was solved and has provided valuable new insight into FNR structure and function. These findings have alluded to the conformational changes that may occur to alter FNR activity in response to O2. CRITICAL ISSUES Here, we review the major features of this structure in context of previously acquired data. In doing so, we discuss additional mechanistic aspects of FNR function that warrant further investigation. FUTURE DIRECTIONS To complement the [4Fe-4S]-FNR structure, the structures of apo-FNR and FNR bound to DNA or RNA polymerase are needed. Together, these structures would elevate our understanding of how ligation of its [4Fe-4S] cluster allows FNR to regulate transcription according to the level of environmental O2.
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Affiliation(s)
- Erin L Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison , Madison, Wisconsin
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison , Madison, Wisconsin
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21
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Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
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Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
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22
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Romsang A, Duang-Nkern J, Khemsom K, Wongsaroj L, Saninjuk K, Fuangthong M, Vattanaviboon P, Mongkolsuk S. Pseudomonas aeruginosa ttcA encoding tRNA-thiolating protein requires an iron-sulfur cluster to participate in hydrogen peroxide-mediated stress protection and pathogenicity. Sci Rep 2018; 8:11882. [PMID: 30089777 PMCID: PMC6082896 DOI: 10.1038/s41598-018-30368-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/27/2018] [Indexed: 01/21/2023] Open
Abstract
During the translation process, transfer RNA (tRNA) carries amino acids to ribosomes for protein synthesis. Each codon of mRNA is recognized by a specific tRNA, and enzyme-catalysed modifications to tRNA regulate translation. TtcA is a unique tRNA-thiolating enzyme that requires an iron-sulfur ([Fe-S]) cluster to catalyse thiolation of tRNA. In this study, the physiological functions of a putative ttcA in Pseudomonas aeruginosa, an opportunistic human pathogen that causes serious problems in hospitals, were characterized. A P. aeruginosa ttcA-deleted mutant was constructed, and mutant cells were rendered hypersensitive to oxidative stress, such as hydrogen peroxide (H2O2) treatment. Catalase activity was lower in the ttcA mutant, suggesting that this gene plays a role in protecting against oxidative stress. Moreover, the ttcA mutant demonstrated attenuated virulence in a Drosophila melanogaster host model. Site-directed mutagenesis analysis revealed that the conserved cysteine motifs involved in [Fe-S] cluster ligation were required for TtcA function. Furthermore, ttcA expression increased upon H2O2 exposure, implying that enzyme levels are induced under stress conditions. Overall, the data suggest that P. aeruginosa ttcA plays a critical role in protecting against oxidative stress via catalase activity and is required for successful bacterial infection of the host.
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Affiliation(s)
- Adisak Romsang
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand. .,Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Jintana Duang-Nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Khwannarin Khemsom
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Lampet Wongsaroj
- Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kritsakorn Saninjuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Mayuree Fuangthong
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Paiboon Vattanaviboon
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Skorn Mongkolsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand.,Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
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23
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Crack JC, Hamilton CJ, Le Brun NE. Mass spectrometric detection of iron nitrosyls, sulfide oxidation and mycothiolation during nitrosylation of the NO sensor [4Fe-4S] NsrR. Chem Commun (Camb) 2018; 54:5992-5995. [PMID: 29790499 PMCID: PMC5994877 DOI: 10.1039/c8cc01339j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Identification of RRE-type iron-nitrosyl species formed upon nitrosylation of [4Fe–4S] NsrR.
The bacterial nitric oxide (NO)-sensing transcriptional regulator NsrR binds a [4Fe–4S] cluster that enables DNA-binding and thus repression of the cell's NO stress response. Upon exposure to NO, the cluster undergoes a complex nitrosylation reaction resulting in a mixture of iron-nitrosyl species, which spectroscopic studies have indicated are similar to well characterized low molecular weight dinitrosyl iron complex (DNIC), Roussin's Red Ester (RRE) and Roussin's Black Salt (RBS). Here we report mass spectrometric studies that enable the unambiguous identification of NsrR-bound RRE-type species, including a persulfide bound form that results from the oxidation of cluster sulfide. In the presence of the low molecular weight thiols glutathione and mycothiol, glutathionylated and mycothiolated forms of NsrR were readily formed.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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24
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Todorovic S, Teixeira M. Resonance Raman spectroscopy of Fe-S proteins and their redox properties. J Biol Inorg Chem 2018; 23:647-661. [PMID: 29368020 PMCID: PMC6006211 DOI: 10.1007/s00775-018-1533-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/14/2017] [Indexed: 12/02/2022]
Abstract
Resonance Raman spectra of Fe-S proteins are sensitive to the cluster type, structure and symmetry. Furthermore, bands that originate from bridging and terminal Fe-S vibrations in the 2Fe-2S, 3Fe-4S and 4Fe-4S clusters can be sensitively distinguished in the spectra, as well as the type of non-cysteinyl coordinating ligands, if present. For these reasons, resonance Raman spectroscopy has been playing an exceptionally active role in the studies of Fe-S proteins of diverse structures and functions. We provide here a concise overview of the structural information that can be obtained from resonance Raman spectroscopy on Fe-S clusters, and in parallel, refer to their thermodynamic properties (e.g., reduction potential), which together define the physiological roles of Fe-S proteins. We demonstrate how the knowledge gained over the past several decades on simple clusters nowadays enables studies of complex structures that include Fe-S clusters coupled to other centers and transient processes that involve cluster inter-conversion, biogenesis, disassembly and catalysis.
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Affiliation(s)
- Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
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25
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Hall AR, Geoghegan M. Polymers and biopolymers at interfaces. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:036601. [PMID: 29368695 DOI: 10.1088/1361-6633/aa9e9c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This review updates recent progress in the understanding of the behaviour of polymers at surfaces and interfaces, highlighting examples in the areas of wetting, dewetting, crystallization, and 'smart' materials. Recent developments in analysis tools have yielded a large increase in the study of biological systems, and some of these will also be discussed, focussing on areas where surfaces are important. These areas include molecular binding events and protein adsorption as well as the mapping of the surfaces of cells. Important techniques commonly used for the analysis of surfaces and interfaces are discussed separately to aid the understanding of their application.
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Affiliation(s)
- A R Hall
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield S3 7RH, United Kingdom. Fraunhofer Project Centre for Embedded Bioanalytical Systems, Dublin City University, Glasnevin, Dublin 9, Ireland
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26
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Sánchez LA, Gómez-Gallardo M, Díaz-Pérez AL, Cortés-Rojo C, Campos-García J. Iba57p participates in maturation of a [2Fe-2S]-cluster Rieske protein and in formation of supercomplexes III/IV of Saccharomyces cerevisiae electron transport chain. Mitochondrion 2018; 44:75-84. [PMID: 29343425 DOI: 10.1016/j.mito.2018.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/20/2017] [Accepted: 01/10/2018] [Indexed: 11/15/2022]
Abstract
The [Fe-S] late-acting subsystem comprised of Isa1p/Isa2p, Grx5p, and Iba57p proteins (Fe-S-IBG subsystem) is involved in [4Fe-4S]-cluster protein assembly. The effect of deleting IBA57 in Saccharomyces cerevisiae on mitochondrial respiratory complex integration and functionality associated with Rieske protein maturation was evaluated. The iba57Δ mutant showed decreased expression and maturation of the Rieske protein. The loss of Rieske protein caused by IBA57 deletion affected the structure of supercomplexes III2IV2 and III2IV1 and their integration into the mitochondria, causing dysfunction in the electron transport chain. These effects were correlated with decreased cytochrome functionality and content in the iba57Δ mutant. These findings suggest that Iba57p participates in maturation of the [2Fe-2S]-cluster into the Rieske protein and that Rieske protein plays important roles in the conformation and functionality of mitochondrial supercomplex III/IV in the electron transport chain.
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Affiliation(s)
- Luis A Sánchez
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Mauricio Gómez-Gallardo
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Alma L Díaz-Pérez
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Christian Cortés-Rojo
- Lab. de Bioquímica, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Jesús Campos-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico.
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27
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Zhang H, Krämer U. Differential Diel Translation of Transcripts With Roles in the Transfer and Utilization of Iron-Sulfur Clusters in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1641. [PMID: 30483293 PMCID: PMC6243122 DOI: 10.3389/fpls.2018.01641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/22/2018] [Indexed: 05/07/2023]
Abstract
Iron-sulfur (Fe-S) clusters are evolutionarily ancient ubiquitous protein cofactors which have mostly catalytic functions but can also have structural roles. In Arabidopsis thaliana, we presently know a total of 124 Fe-S metalloproteins that are encoded in the genome. Fe-S clusters are highly sensitive to oxidation. Therefore, we hypothesized that Fe-S cluster protein biogenesis is adjusted following the daily rhythms in metabolism driven by photosynthesis at the whole-plant, organ, cellular and sub-cellular levels. It had been concluded previously that little such regulation occurs at the transcript level among the genes functioning in Fe-S cluster assembly. As an initial step toward testing our hypothesis, we thus addressed the diel time course of the translation state of relevant transcripts based on publicly available genome-wide microarray data. This analysis can answer whether the translation of the pool of transcripts of a given gene is temporarily either enhanced or suppressed, and when during the day. Thirty-three percent of the transcripts with functions in Fe-S cluster assembly exhibited significant changes in translation state over a diurnal time course, compared to 26% of all detected transcripts. These transcripts comprised functions in all three steps of cluster assembly including persulfide formation, Fe-S cluster formation and Fe-S cluster transfer to target apoproteins. The number of Fe-S cluster carrier/transfer functions contributed more than half of these transcripts, which reached maxima in translation state either during the night or the end of the night. Similarly, translation state of mitochondrial frataxin and ferredoxin, which are thought to contribute Fe and electrons during cluster formation, peaked during the night. By contrast, translation state of chloroplast SUFE2 in persulfide formation and cytosolic Fe-S cluster formation scaffold protein NBP35 reached maxima in translation state during the day. Among the transcripts encoding target Fe-S cluster-utilizing proteins, 19% exhibited diurnal variation in translation state. Day-time maxima of translation state were most common among these transcripts, with none of the maxima during the night (ZT18). We conclude that diurnal regulation of translation state is important in metalloprotein biogenesis. Future models of Fe-S protein biogenesis require more comprehensive data and will have to accommodate diurnal dynamics.
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28
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Lu Y. Assembly and Transfer of Iron-Sulfur Clusters in the Plastid. FRONTIERS IN PLANT SCIENCE 2018; 9:336. [PMID: 29662496 PMCID: PMC5890173 DOI: 10.3389/fpls.2018.00336] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/28/2018] [Indexed: 05/09/2023]
Abstract
Iron-Sulfur (Fe-S) clusters and proteins are essential to many growth and developmental processes. In plants, they exist in the plastids, mitochondria, cytosol, and nucleus. Six types of Fe-S clusters are found in the plastid: classic 2Fe-2S, NEET-type 2Fe-2S, Rieske-type 2Fe-2S, 3Fe-4S, 4Fe-4S, and siroheme 4Fe-4S. Classic, NEET-type, and Rieske-type 2Fe-2S clusters have the same 2Fe-2S core; similarly, common and siroheme 4Fe-4S clusters have the same 4Fe-4S core. Plastidial Fe-S clusters are assembled by the sulfur mobilization (SUF) pathway, which contains cysteine desulfurase (EC 2.8.1.7), sulfur transferase (EC 2.8.1.3), Fe-S scaffold complex, and Fe-S carrier proteins. The plastidial cysteine desulfurase-sulfur transferase-Fe-S-scaffold complex system is responsible for de novo assembly of all plastidial Fe-S clusters. However, different types of Fe-S clusters are transferred to recipient proteins via respective Fe-S carrier proteins. This review focuses on recent discoveries on the molecular functions of different assembly and transfer factors involved in the plastidial SUF pathway. It also discusses potential points for regulation of the SUF pathway, relationships among the plastidial, mitochondrial, and cytosolic Fe-S assembly and transfer pathways, as well as several open questions about the carrier proteins for Rieske-type 2Fe-2S, NEET-type 2Fe-2S, and 3F-4S clusters.
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29
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Reactive Cysteine Persulphides: Occurrence, Biosynthesis, Antioxidant Activity, Methodologies, and Bacterial Persulphide Signalling. Adv Microb Physiol 2018; 72:1-28. [PMID: 29778212 DOI: 10.1016/bs.ampbs.2018.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cysteine hydropersulphide (CysSSH) is a cysteine derivative having one additional sulphur atom bound to a cysteinyl thiol group. Recent advances in the development of analytical methods for detection and quantification of persulphides and polysulphides have revealed the biological presence, in both prokaryotes and eukaryotes, of hydropersulphides in diverse forms such as CysSSH, homocysteine hydropersulphide, glutathione hydropersulphide, bacillithiol hydropersulphide, coenzyme A hydropersulphide, and protein hydropersulphides. Owing to the chemical reactivity of the persulphide moiety, biological systems utilize persulphides as important intermediates in the synthesis of various sulphur-containing biomolecules. Accumulating evidence has revealed another important feature of persulphides: their potent reducing activity, which implies that they are implicated in the regulation of redox signalling and antioxidant functions. In this chapter, we discuss the biological occurrence and possible biosynthetic mechanisms of CysSSH and related persulphides, and we include descriptions of recent advances in the analytical methods that have been used to detect and quantitate persulphide species. We also discuss the antioxidant activity of persulphide species that contributes to protecting cells from reactive oxygen species-associated damage, and we examine the signalling roles of CysSSH in bacteria.
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30
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Structure of a Wbl protein and implications for NO sensing by M. tuberculosis. Nat Commun 2017; 8:2280. [PMID: 29273788 PMCID: PMC5741622 DOI: 10.1038/s41467-017-02418-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/29/2017] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis causes pulmonary tuberculosis (TB) and claims ~1.8 million human lives per annum. Host nitric oxide (NO) is important in controlling TB infection. M. tuberculosis WhiB1 is a NO-responsive Wbl protein (actinobacterial iron–sulfur proteins first identified in the 1970s). Until now, the structure of a Wbl protein has not been available. Here a NMR structural model of WhiB1 reveals that Wbl proteins are four-helix bundles with a core of three α-helices held together by a [4Fe-4S] cluster. The iron–sulfur cluster is required for formation of a complex with the major sigma factor (σA) and reaction with NO disassembles this complex. The WhiB1 structure suggests that loss of the iron–sulfur cluster (by nitrosylation) permits positively charged residues in the C-terminal helix to engage in DNA binding, triggering a major reprogramming of gene expression that includes components of the virulence-critical ESX-1 secretion system. Mycobacterium tuberculosis WhiB1 is a DNA-binding protein with a NO sensitive [4Fe-4S] cluster. Here the authors present the NMR structure of WhiB1 and suggest how loss of the iron-sulfur cluster through nitrosylation affects WhiB1 DNA binding and leads to transcriptional reprogramming.
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31
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out a wide range of functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters towards small/redox active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial re-programming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances. Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high resolution structural data. Though this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- School of Chemistry , University of East Anglia , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry , University plain , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
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32
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Pellicer Martinez MT, Martinez AB, Crack JC, Holmes JD, Svistunenko DA, Johnston AWB, Cheesman MR, Todd JD, Le Brun NE. Sensing iron availability via the fragile [4Fe-4S] cluster of the bacterial transcriptional repressor RirA. Chem Sci 2017; 8:8451-8463. [PMID: 29619193 PMCID: PMC5863699 DOI: 10.1039/c7sc02801f] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/20/2017] [Indexed: 01/02/2023] Open
Abstract
The global iron regulator RirA controls transcription of iron metabolism genes via the binding of a fragile [4Fe–4S] cluster.
Rhizobial iron regulator A (RirA) is a global regulator of iron homeostasis in many nitrogen-fixing Rhizobia and related species of α-proteobacteria. It belongs to the widespread Rrf2 super-family of transcriptional regulators and features three conserved Cys residues that characterise the binding of an iron–sulfur cluster in other Rrf2 family regulators. Here we report biophysical studies demonstrating that RirA contains a [4Fe–4S] cluster, and that this form of the protein binds RirA-regulated DNA, consistent with its function as a repressor of expression of many genes involved in iron uptake. Under low iron conditions, [4Fe–4S] RirA undergoes a cluster conversion reaction resulting in a [2Fe–2S] form, which exhibits much lower affinity for DNA. Under prolonged low iron conditions, the [2Fe–2S] cluster degrades to apo-RirA, which does not bind DNA and can no longer function as a repressor of the cell's iron-uptake machinery. [4Fe–4S] RirA was also found to be sensitive to O2, suggesting that both iron and O2 are important signals for iron metabolism. Consistent with this, in vivo data showed that expression of RirA-regulated genes is also affected by O2. These data lead us to propose a novel regulatory model for iron homeostasis, in which RirA senses iron via the incorporation of a fragile iron–sulfur cluster that is sensitive to iron and O2 concentrations.
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Affiliation(s)
- Ma Teresa Pellicer Martinez
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK . ; ; Tel: +44 1603 592699
| | - Ana Bermejo Martinez
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK . ; ; Tel: +44 1603 592699
| | - John D Holmes
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK . ; ; Tel: +44 1603 592699
| | - Dimitri A Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester CO4 3SQ , UK
| | - Andrew W B Johnston
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK
| | - Myles R Cheesman
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK . ; ; Tel: +44 1603 592699
| | - Jonathan D Todd
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK . ; ; Tel: +44 1603 592699
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33
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Vaccaro BJ, Clarkson SM, Holden JF, Lee DW, Wu CH, Poole Ii FL, Cotelesage JJH, Hackett MJ, Mohebbi S, Sun J, Li H, Johnson MK, George GN, Adams MWW. Biological iron-sulfur storage in a thioferrate-protein nanoparticle. Nat Commun 2017; 8:16110. [PMID: 28726794 PMCID: PMC5524996 DOI: 10.1038/ncomms16110] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/30/2017] [Indexed: 11/09/2022] Open
Abstract
Iron–sulfur clusters are ubiquitous in biology and function in electron transfer and catalysis. They are assembled from iron and cysteine sulfur on protein scaffolds. Iron is typically stored as iron oxyhydroxide, ferrihydrite, encapsulated in 12 nm shells of ferritin, which buffers cellular iron availability. Here we have characterized IssA, a protein that stores iron and sulfur as thioferrate, an inorganic anionic polymer previously unknown in biology. IssA forms nanoparticles reaching 300 nm in diameter and is the largest natural metalloprotein complex known. It is a member of a widely distributed protein family that includes nitrogenase maturation factors, NifB and NifX. IssA nanoparticles are visible by electron microscopy as electron-dense bodies in the cytoplasm. Purified nanoparticles appear to be generated from 20 nm units containing ∼6,400 Fe atoms and ∼170 IssA monomers. In support of roles in both iron–sulfur storage and cluster biosynthesis, IssA reconstitutes the [4Fe-4S] cluster in ferredoxin in vitro. The biosynthesis of iron-sulfur clusters in anaerobic organisms has not been extensively investigated. Here, the authors identify and characterize a multi-subunit protein that stores iron and sulfur in thioferrate for the assembly of the clusters in Pyrococcus furiosus.
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Affiliation(s)
- Brian J Vaccaro
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Sonya M Clarkson
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - James F Holden
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Dong-Woo Lee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Farris L Poole Ii
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Julien J H Cotelesage
- Department of Geological Sciences and Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C5, Canada
| | - Mark J Hackett
- Department of Geological Sciences and Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C5, Canada
| | - Sahel Mohebbi
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Jingchuan Sun
- Cryo-EM Structural Biology Laboratory, Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Michael K Johnson
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Graham N George
- Department of Geological Sciences and Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C5, Canada
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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34
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Ono K, Jung M, Zhang T, Tsutsuki H, Sezaki H, Ihara H, Wei FY, Tomizawa K, Akaike T, Sawa T. Synthesis of l-cysteine derivatives containing stable sulfur isotopes and application of this synthesis to reactive sulfur metabolome. Free Radic Biol Med 2017; 106:69-79. [PMID: 28189853 DOI: 10.1016/j.freeradbiomed.2017.02.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 01/11/2023]
Abstract
Cysteine persulfide is an L-cysteine derivative having one additional sulfur atom bound to a cysteinyl thiol group, and it serves as a reactive sulfur species that regulates redox homeostasis in cells. Here, we describe a rapid and efficient method of synthesis of L-cysteine derivatives containing isotopic sulfur atoms and application of this method to a reactive sulfur metabolome. We used bacterial cysteine syntheses to incorporate isotopic sulfur atoms into the sulfhydryl moiety of L-cysteine. We cloned three cysteine synthases-CysE, CysK, and CysM-from the Gram-negative bacterium Salmonella enterica serovar Typhimurium LT2, and we generated their recombinant enzymes. We synthesized 34S-labeled L-cysteine from O-acetyl-L-serine and 34S-labeled sodium sulfide as substrates for the CysK or CysM reactions. Isotopic labeling of L-cysteine at both sulfur (34S) and nitrogen (15N) atoms was also achieved by performing enzyme reactions with 15N-labeled L-serine, acetyl-CoA, and 34S-labeled sodium sulfide in the presence of CysE and CysK. The present enzyme systems can be applied to syntheses of a series of L-cysteine derivatives including L-cystine, L-cystine persulfide, S-sulfo-L-cysteine, L-cysteine sulfonate, and L-selenocystine. We also prepared 34S-labeled N-acetyl-L-cysteine (NAC) by incubating 34S-labeled L-cysteine with acetyl coenzyme A in test tubes. Tandem mass spectrometric identification of low-molecular-weight thiols after monobromobimane derivatization revealed the endogenous occurrence of NAC in the cultured mammalian cells such as HeLa cells and J774.1 cells. Furthermore, we successfully demonstrated, by using 34S-labeled NAC, metabolic conversion of NAC to glutathione and its persulfide, via intermediate formation of L-cysteine, in the cells. The approach using isotopic sulfur labeling combined with mass spectrometry may thus contribute to greater understanding of reactive sulfur metabolome and redox biology.
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Affiliation(s)
- Katsuhiko Ono
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Minkyung Jung
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8577, Japan
| | - Tianli Zhang
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroyasu Tsutsuki
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroshi Sezaki
- Life Sciences and Applied Markets Group, Agilent Technologies, Tokyo 192-8510, Japan
| | - Hideshi Ihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8577, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
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35
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Tanner AW, Carabetta VJ, Martinie RJ, Mashruwala AA, Boyd JM, Krebs C, Dubnau D. The RicAFT (YmcA-YlbF-YaaT) complex carries two [4Fe-4S] 2+ clusters and may respond to redox changes. Mol Microbiol 2017; 104:837-850. [PMID: 28295778 DOI: 10.1111/mmi.13667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2017] [Indexed: 01/10/2023]
Abstract
During times of environmental insult, Bacillus subtilis undergoes developmental changes leading to biofilm formation, sporulation and competence. Each of these states is regulated in part by the phosphorylated form of the master response regulator Spo0A (Spo0A∼P). The phosphorylation state of Spo0A is controlled by a multi-component phosphorelay. RicA, RicF and RicT (previously YmcA, YlbF and YaaT) have been shown to be important regulatory proteins for multiple developmental fates. These proteins directly interact and form a stable complex, which has been proposed to accelerate the phosphorelay. Indeed, this complex is sufficient to stimulate the rate of phosphotransfer amongst the phosphorelay proteins in vitro. In this study, we demonstrate that two [4Fe-4S]2+ clusters can be assembled on the complex. As with other iron-sulfur cluster-binding proteins, the complex was also found to bind FAD, hinting that these cofactors may be involved in sensing the cellular redox state. This work provides the first comprehensive characterization of an iron-sulfur protein complex that regulates Spo0A∼P levels. Phylogenetic and genetic evidence suggests that the complex plays a broader role beyond stimulation of the phosphorelay.
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Affiliation(s)
- Andrew W Tanner
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Valerie J Carabetta
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.,Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Ryan J Martinie
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ameya A Mashruwala
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - David Dubnau
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.,Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
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36
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Mass spectrometric identification of intermediates in the O 2-driven [4Fe-4S] to [2Fe-2S] cluster conversion in FNR. Proc Natl Acad Sci U S A 2017; 114:E3215-E3223. [PMID: 28373574 DOI: 10.1073/pnas.1620987114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The iron-sulfur cluster containing protein Fumarate and Nitrate Reduction (FNR) is the master regulator for the switch between anaerobic and aerobic respiration in Escherichia coli and many other bacteria. The [4Fe-4S] cluster functions as the sensory module, undergoing reaction with O2 that leads to conversion to a [2Fe-2S] form with loss of high-affinity DNA binding. Here, we report studies of the FNR cluster conversion reaction using time-resolved electrospray ionization mass spectrometry. The data provide insight into the reaction, permitting the detection of cluster conversion intermediates and products, including a [3Fe-3S] cluster and persulfide-coordinated [2Fe-2S] clusters [[2Fe-2S](S) n , where n = 1 or 2]. Analysis of kinetic data revealed a branched mechanism in which cluster sulfide oxidation occurs in parallel with cluster conversion and not as a subsequent, secondary reaction to generate [2Fe-2S](S) n species. This methodology shows great potential for broad application to studies of protein cofactor-small molecule interactions.
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37
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Biological chemistry of hydrogen sulfide and persulfides. Arch Biochem Biophys 2017; 617:9-25. [DOI: 10.1016/j.abb.2016.09.018] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 02/08/2023]
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38
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Ruetz M, Kumutima J, Lewis BE, Filipovic MR, Lehnert N, Stemmler TL, Banerjee R. A distal ligand mutes the interaction of hydrogen sulfide with human neuroglobin. J Biol Chem 2017; 292:6512-6528. [PMID: 28246171 DOI: 10.1074/jbc.m116.770370] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/16/2017] [Indexed: 11/06/2022] Open
Abstract
Hydrogen sulfide is a critical signaling molecule, but high concentrations cause cellular toxicity. A four-enzyme pathway in the mitochondrion detoxifies H2S by converting it to thiosulfate and sulfate. Recent studies have shown that globins like hemoglobin and myoglobin can also oxidize H2S to thiosulfate and hydropolysulfides. Neuroglobin, a globin enriched in the brain, was reported to bind H2S tightly and was postulated to play a role in modulating neuronal sensitivity to H2S in conditions such as stroke. However, the H2S reactivity of the coordinately saturated heme in neuroglobin is expected a priori to be substantially lower than that of the 5-coordinate hemes present in myoglobin and hemoglobin. To resolve this discrepancy, we explored the role of the distal histidine residue in muting the reactivity of human neuroglobin toward H2S. Ferric neuroglobin is slowly reduced by H2S and catalyzes its inefficient oxidative conversion to thiosulfate. Mutation of the distal His64 residue to alanine promotes rapid binding of H2S and its efficient conversion to oxidized products. X-ray absorption, EPR, and resonance Raman spectroscopy highlight the chemically different reaction options influenced by the distal histidine ligand. This study provides mechanistic insights into how the distal heme ligand in neuroglobin caps its reactivity toward H2S and identifies by cryo-mass spectrometry a range of sulfide oxidation products with 2-6 catenated sulfur atoms with or without oxygen insertion, which accumulate in the absence of the His64 ligand.
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Affiliation(s)
| | - Jacques Kumutima
- the Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
| | - Brianne E Lewis
- the Department of Pharmaceutical Science, Wayne State University, Detroit, Michigan 48201-2417
| | - Milos R Filipovic
- the University of Bordeaux, IBGC, UMR 5090, F33077 Bordeaux, France, and.,CNRS, Institute of Biochemistry and Cellular Genetics, UMR 5095, F33077 Bordeaux, France
| | - Nicolai Lehnert
- the Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
| | - Timothy L Stemmler
- the Department of Pharmaceutical Science, Wayne State University, Detroit, Michigan 48201-2417
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39
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Serrano PN, Wang H, Crack JC, Prior C, Hutchings MI, Thomson AJ, Kamali S, Yoda Y, Zhao J, Hu MY, Alp EE, Oganesyan VS, Le Brun NE, Cramer SP. Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes. Angew Chem Int Ed Engl 2016; 55:14575-14579. [PMID: 27778474 PMCID: PMC5204455 DOI: 10.1002/anie.201607033] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/05/2016] [Indexed: 12/13/2022]
Abstract
The reaction of protein-bound iron-sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2 (NO)4 (Cys)2 ]) and Roussin's Black Salt (RBS, [Fe4 (NO)7 S3 ]. In the latter case, the absence of 32 S/34 S shifts in the Fe-S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates.
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Affiliation(s)
| | - Hongxin Wang
- Department of ChemistryUniversity of CaliforniaDavisCA95616USA
- Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Jason C. Crack
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Christopher Prior
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | | | - Andrew J. Thomson
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Saeed Kamali
- University of Tennessee Space InstituteTullahomeTN37388-9700USA
| | - Yoshitaka Yoda
- Research and Utilization DivisionSPring-8/JASRI1-1-1 Kouto, SayoHyogo679-5198Japan
| | - Jiyong Zhao
- Advanced Photon SourceArgonne National LaboratoryArgonneIL60439USA
| | - Michael Y. Hu
- Advanced Photon SourceArgonne National LaboratoryArgonneIL60439USA
| | - Ercan E. Alp
- Advanced Photon SourceArgonne National LaboratoryArgonneIL60439USA
| | - Vasily S. Oganesyan
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Nick E. Le Brun
- Centre for Molecular and Structural BiochemistrySchool of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Stephen P. Cramer
- Department of ChemistryUniversity of CaliforniaDavisCA95616USA
- Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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40
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Holm RH, Lo W. Structural Conversions of Synthetic and Protein-Bound Iron–Sulfur Clusters. Chem Rev 2016; 116:13685-13713. [DOI: 10.1021/acs.chemrev.6b00276] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. H. Holm
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Wayne Lo
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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41
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Serrano PN, Wang H, Crack JC, Prior C, Hutchings MI, Thomson AJ, Kamali S, Yoda Y, Zhao J, Hu MY, Alp EE, Oganesyan VS, Le Brun NE, Cramer SP. Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Hongxin Wang
- Department of Chemistry; University of California; Davis CA 95616 USA
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
| | - Jason C. Crack
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Christopher Prior
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | | | - Andrew J. Thomson
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Saeed Kamali
- University of Tennessee Space Institute; Tullahome TN 37388-9700 USA
| | - Yoshitaka Yoda
- Research and Utilization Division; SPring-8/JASRI; 1-1-1 Kouto, Sayo Hyogo 679-5198 Japan
| | - Jiyong Zhao
- Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Michael Y. Hu
- Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Ercan E. Alp
- Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Vasily S. Oganesyan
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry; School of Chemistry; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - Stephen P. Cramer
- Department of Chemistry; University of California; Davis CA 95616 USA
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
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42
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A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc Natl Acad Sci U S A 2016; 113:12703-12708. [PMID: 27791189 DOI: 10.1073/pnas.1615732113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sulfur-containing nucleosides in transfer RNA (tRNAs) are present in all three domains of life; they have critical functions for accurate and efficient translation, such as tRNA structure stabilization and proper codon recognition. The tRNA modification enzymes ThiI (in bacteria and archaea) and Ncs6 (in archaea and eukaryotic cytosols) catalyze the formation of 4-thiouridine (s4U) and 2-thiouridine (s2U), respectively. The ThiI homologs were proposed to transfer sulfur via cysteine persulfide enzyme adducts, whereas the reaction mechanism of Ncs6 remains unknown. Here we show that ThiI from the archaeon Methanococcus maripaludis contains a [3Fe-4S] cluster that is essential for its tRNA thiolation activity. Furthermore, the archaeal and eukaryotic Ncs6 homologs as well as phosphoseryl-tRNA (Sep-tRNA):Cys-tRNA synthase (SepCysS), which catalyzes the Sep-tRNA to Cys-tRNA conversion in methanogens, also possess a [3Fe-4S] cluster similar to the methanogenic archaeal ThiI. These results suggest that the diverse tRNA thiolation processes in archaea and eukaryotic cytosols share a common mechanism dependent on a [3Fe-4S] cluster for sulfur transfer.
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43
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Cadby IT, Ibrahim SA, Faulkner M, Lee DJ, Browning D, Busby SJ, Lovering AL, Stapleton MR, Green J, Cole JA. Regulation, sensory domains and roles of twoDesulfovibrio desulfuricansATCC27774 Crp family transcription factors, HcpR1 and HcpR2, in response to nitrosative stress. Mol Microbiol 2016; 102:1120-1137. [DOI: 10.1111/mmi.13540] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Ian T. Cadby
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Susan A. Ibrahim
- Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Matthew Faulkner
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - David J. Lee
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Douglas Browning
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Stephen J. Busby
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Andrew L. Lovering
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Melanie R. Stapleton
- Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Jeffrey Green
- Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Jeffrey A. Cole
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
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44
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Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily. Sci Rep 2016; 6:31597. [PMID: 27605472 PMCID: PMC5015018 DOI: 10.1038/srep31597] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/25/2016] [Indexed: 01/06/2023] Open
Abstract
Members of the Rrf2 superfamily of transcription factors are widespread in bacteria but their functions are largely unexplored. The few that have been characterized in detail sense nitric oxide (NsrR), iron limitation (RirA), cysteine availability (CymR) and the iron sulfur (Fe-S) cluster status of the cell (IscR). In this study we combined ChIP- and dRNA-seq with in vitro biochemistry to characterize a putative NsrR homologue in Streptomyces venezuelae. ChIP-seq analysis revealed that rather than regulating the nitrosative stress response like Streptomyces coelicolor NsrR, Sven6563 binds to a conserved motif at a different, much larger set of genes with a diverse range of functions, including a number of regulators, genes required for glutamine synthesis, NADH/NAD(P)H metabolism, as well as general DNA/RNA and amino acid/protein turn over. Our biochemical experiments further show that Sven6563 has a [2Fe-2S] cluster and that the switch between oxidized and reduced cluster controls its DNA binding activity in vitro. To our knowledge, both the sensing domain and the putative target genes are novel for an Rrf2 protein, suggesting Sven6563 represents a new member of the Rrf2 superfamily. Given the redox sensitivity of its Fe-S cluster we have tentatively named the protein RsrR for Redox sensitive response Regulator.
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45
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The conserved protein Dre2 uses essential [2Fe–2S] and [4Fe–4S] clusters for its function in cytosolic iron–sulfur protein assembly. Biochem J 2016; 473:2073-85. [DOI: 10.1042/bcj20160416] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/10/2016] [Indexed: 11/17/2022]
Abstract
The essential protein Dre2 uses iron–sulfur (Fe–S) clusters to transfer electrons for cytosolic Fe–S protein biogenesis. Biochemical, cell biological and spectroscopic approaches demonstrate that recombinant Dre2 binds oxygen-labile [2Fe–2S] and [4Fe–4S] clusters at two conserved C-terminal motifs with four cysteine residues each.
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46
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Christ S, Leichert LI, Willms A, Lill R, Mühlenhoff U. Defects in Mitochondrial Iron–Sulfur Cluster Assembly Induce Cysteine S-Polythiolation on Iron–Sulfur Apoproteins. Antioxid Redox Signal 2016; 25:28-40. [DOI: 10.1089/ars.2015.6599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Stefan Christ
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
| | - Lars I. Leichert
- Institute for Biochemistry and Pathobiochemistry—Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Anna Willms
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Zentrum für Synthetische Mikrobiologie SYNMIKRO, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
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47
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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48
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Tanifuji K, Tajima S, Ohki Y, Tatsumi K. Interconversion between [Fe4S4] and [Fe2S2] Clusters Bearing Amide Ligands. Inorg Chem 2016; 55:4512-8. [DOI: 10.1021/acs.inorgchem.6b00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kazuki Tanifuji
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shunichi Tajima
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yasuhiro Ohki
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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49
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Golinelli-Cohen MP, Lescop E, Mons C, Gonçalves S, Clémancey M, Santolini J, Guittet E, Blondin G, Latour JM, Bouton C. Redox Control of the Human Iron-Sulfur Repair Protein MitoNEET Activity via Its Iron-Sulfur Cluster. J Biol Chem 2016; 291:7583-93. [PMID: 26887944 DOI: 10.1074/jbc.m115.711218] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/06/2022] Open
Abstract
Human mitoNEET (mNT) is the first identified Fe-S protein of the mammalian outer mitochondrial membrane. Recently, mNT has been implicated in cytosolic Fe-S repair of a key regulator of cellular iron homeostasis. Here, we aimed to decipher the mechanism by which mNT triggers its Fe-S repair capacity. By using tightly controlled reactions combined with complementary spectroscopic approaches, we have determined the differential roles played by both the redox state of the mNT cluster and dioxygen in cluster transfer and protein stability. We unambiguously demonstrated that only the oxidized state of the mNT cluster triggers cluster transfer to a generic acceptor protein and that dioxygen is neither required for the cluster transfer reaction nor does it affect the transfer rate. In the absence of apo-acceptors, a large fraction of the oxidized holo-mNT form is converted back to reduced holo-mNT under low oxygen tension. Reduced holo-mNT, which holds a [2Fe-2S](+)with a global protein fold similar to that of the oxidized form is, by contrast, resistant in losing its cluster or in transferring it. Our findings thus demonstrate that mNT uses an iron-based redox switch mechanism to regulate the transfer of its cluster. The oxidized state is the "active state," which reacts promptly to initiate Fe-S transfer independently of dioxygen, whereas the reduced state is a "dormant form." Finally, we propose that the redox-sensing function of mNT is a key component of the cellular adaptive response to help stress-sensitive Fe-S proteins recover from oxidative injury.
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Affiliation(s)
- Marie-Pierre Golinelli-Cohen
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France,
| | - Ewen Lescop
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Cécile Mons
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sergio Gonçalves
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Martin Clémancey
- Université Grenoble Alpes, Laboratoire Chimie et Biologie des Métaux (LCBM), and Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherche en Technologies et Sciences pour le Vivant (iRTSV), LCBM, Equipe Physicochimie des Métaux en Biologie (PMB), and CNRS UMR 5249, LCBM, 38054 Grenoble, France, and
| | - Jérôme Santolini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Eric Guittet
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Geneviève Blondin
- Université Grenoble Alpes, Laboratoire Chimie et Biologie des Métaux (LCBM), and Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherche en Technologies et Sciences pour le Vivant (iRTSV), LCBM, Equipe Physicochimie des Métaux en Biologie (PMB), and CNRS UMR 5249, LCBM, 38054 Grenoble, France, and
| | - Jean-Marc Latour
- Université Grenoble Alpes, Laboratoire Chimie et Biologie des Métaux (LCBM), and Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherche en Technologies et Sciences pour le Vivant (iRTSV), LCBM, Equipe Physicochimie des Métaux en Biologie (PMB), and CNRS UMR 5249, LCBM, 38054 Grenoble, France, and
| | - Cécile Bouton
- From the Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France,
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50
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Crack JC, Hutchings MI, Thomson AJ, Le Brun NE. Biochemical properties of Paracoccus denitrificans FnrP: reactions with molecular oxygen and nitric oxide. J Biol Inorg Chem 2016; 21:71-82. [PMID: 26790880 PMCID: PMC4771820 DOI: 10.1007/s00775-015-1326-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
In Paracoccus denitrificans, three CRP/FNR family regulatory proteins, NarR, NnrR and FnrP, control the switch between aerobic and anaerobic (denitrification) respiration. FnrP is a [4Fe–4S] cluster-containing homologue of the archetypal O2 sensor FNR from E. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to O2, and also NO, availability. Here we show that FnrP undergoes O2-driven [4Fe–4S] to [2Fe–2S] cluster conversion that involves up to 2 O2 per cluster, with significant oxidation of released cluster sulfide to sulfane observed at higher O2 concentrations. The rate of the cluster reaction was found to be ~sixfold lower than that of E. coli FNR, suggesting that FnrP can remain transcriptionally active under microaerobic conditions. This is consistent with a role for FnrP in activating expression of the high O2 affinity cytochrome c oxidase under microaerobic conditions. Cluster conversion resulted in dissociation of the transcriptionally active FnrP dimer into monomers. Therefore, along with E. coli FNR, FnrP belongs to the subset of FNR proteins in which cluster type is correlated with association state. Interestingly, two key charged residues, Arg140 and Asp154, that have been shown to play key roles in the monomer–dimer equilibrium in E. coli FNR are not conserved in FnrP, indicating that different protomer interactions are important for this equilibrium. Finally, the FnrP [4Fe–4S] cluster is shown to undergo reaction with multiple NO molecules, resulting in iron nitrosyl species and dissociation into monomers.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew J Thomson
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK.
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