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Muras V, Toulouse C, Fritz G, Steuber J. Respiratory Membrane Protein Complexes Convert Chemical Energy. Subcell Biochem 2019; 92:301-335. [PMID: 31214991 DOI: 10.1007/978-3-030-18768-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The invention of a biological membrane which is used as energy storage system to drive the metabolism of a primordial, unicellular organism represents a key event in the evolution of life. The innovative, underlying principle of this key event is respiration. In respiration, a lipid bilayer with insulating properties is chosen as the site for catalysis of an exergonic redox reaction converting substrates offered from the environment, using the liberated Gibbs free energy (ΔG) for the build-up of an electrochemical H+ (proton motive force, PMF) or Na+ gradient (sodium motive force, SMF) across the lipid bilayer. Very frequently , several redox reactions are performed in a consecutive manner, with the first reaction delivering a product which is used as substrate for the second redox reaction, resulting in a respiratory chain. From today's perspective, the (mostly) unicellular bacteria and archaea seem to be much simpler and less evolved when compared to multicellular eukaryotes. However, they are overwhelmingly complex with regard to the various respiratory chains which permit survival in very different habitats of our planet, utilizing a plethora of substances to drive metabolism. This includes nitrogen, sulfur and carbon compounds which are oxidized or reduced by specialized, respiratory enzymes of bacteria and archaea which lie at the heart of the geochemical N, S and C-cycles. This chapter gives an overview of general principles of microbial respiration considering thermodynamic aspects, chemical reactions and kinetic restraints. The respiratory chains of Escherichia coli and Vibrio cholerae are discussed as models for PMF- versus SMF-generating processes, respectively. We introduce main redox cofactors of microbial respiratory enzymes, and the concept of intra-and interelectron transfer. Since oxygen is an electron acceptor used by many respiratory chains, the formation and removal of toxic oxygen radicals is described. Promising directions of future research are respiratory enzymes as novel bacterial targets, and biotechnological applications relying on respiratory complexes.
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Affiliation(s)
- Valentin Muras
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Charlotte Toulouse
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Günter Fritz
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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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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Child SA, Bradley JM, Pukala TL, Svistunenko DA, Le Brun NE, Bell SG. Electron transfer ferredoxins with unusual cluster binding motifs support secondary metabolism in many bacteria. Chem Sci 2018; 9:7948-7957. [PMID: 30542550 PMCID: PMC6237146 DOI: 10.1039/c8sc01286e] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/21/2018] [Indexed: 01/06/2023] Open
Abstract
The proteins responsible for controlling electron transfer in bacterial secondary metabolism are not always known or characterised. Here we demonstrate that many bacteria contain a set of unfamiliar ferredoxin encoding genes which are associated with those of cytochrome P450 (CYP) monooxygenases and as such are involved in anabolic and catabolic metabolism. The model organism Mycobacterium marinum M contains eleven of these genes which encode [3Fe-4S] or [4Fe-4S] single cluster containing ferredoxins but which have unusual iron-sulfur cluster binding motif sequences, CXX?XXC(X) n CP, where '?' indicates a variable amino acid residue. Rather than a cysteine residue, which is highly conserved in [4Fe-4S] clusters, or alanine or glycine residues, which are common in [3Fe-4S] ferredoxins, these genes encode at this position histidine, asparagine, tyrosine, serine, threonine or phenylalanine. We have purified, characterised and reconstituted the activity of several of these CYP/electron transfer partner systems and show that all those examined contain a [3Fe-4S] cluster. Furthermore, the ferredoxin used and the identity of the variable motif residue in these proteins affects the functionality of the monooxygenase system and has a significant influence on the redox properties of the ferredoxins. Similar ferredoxin encoding genes were identified across Mycobacterium species, including in the pathogenic M. tuberculosis and M. ulcerans, as well as in a wide range of other bacteria such as Rhodococcus and Streptomyces. In the majority of instances these are associated with CYP genes. These ferredoxin systems are important in controlling electron transfer across bacterial secondary metabolite production processes which include antibiotic and pigment formation among others.
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Affiliation(s)
- Stella A Child
- Department of Chemistry , University of Adelaide , SA 5005 , Australia .
| | - Justin M Bradley
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK
| | - Tara L Pukala
- Department of Chemistry , University of Adelaide , SA 5005 , Australia .
| | - Dimitri A Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester CO4 3SQ , 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 G Bell
- Department of Chemistry , University of Adelaide , SA 5005 , Australia .
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Abstract
Abstract
Metal ions are essential cofactors required by the proteome of organisms from any kingdom of life to correctly exert their functions. Dedicated cellular import, transport and homeostasis systems assure that the needed metal ion is correctly delivered and inserted into the target proteins and avoid the presence of free metal ions in the cell, preventing oxidative damaging. Among metal ions, in eukaryotic organisms copper and iron are required by proteins involved in absolutely essential functions, such as respiration, oxidative stress protection, catalysis, gene expression regulation. Copper and iron binding proteins are localized in essentially all cellular compartments. Copper is physiologically present mainly as individual metal ion. Iron can be present both as individual metal ion or as part of cofactors, such as hemes and iron-sulfur (Fe-S) clusters. Both metal ions are characterized by the ability to cycle between different oxidation states, which enable them to catalyze redox reactions and to participate in electron transfer processes. Here we describe in detail the main processes responsible for the trafficking of copper and iron sulfur clusters, with particular interest for the structural aspects of the maturation of copper and iron-sulfur-binding proteins.
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56
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Zhang W, Du L, Li F, Zhang X, Qu Z, Han L, Li Z, Sun J, Qi F, Yao Q, Sun Y, Geng C, Li S. Mechanistic Insights into Interactions between Bacterial Class I P450 Enzymes and Redox Partners. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02913] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Lei Du
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Fengwei Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Zepeng Qu
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Lei Han
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Jingran Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Fengxia Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Qiuping Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Yue Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
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57
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Kurniawan I, Kawaguchi K, Shoji M, Matsui T, Shigeta Y, Nagao H. A Theoretical Study on Redox Potential and p Kaof [2Fe-2S] Cluster Model from Iron-Sulfur Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Isman Kurniawan
- Division of Mathematical and Physical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- School of Computing, Telkom University, Terusan Buah Batu, Bandung, 40257 Indonesia
| | - Kazutomo Kawaguchi
- Division of Mathematical and Physical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Toru Matsui
- College of Chemistry, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hidemi Nagao
- Division of Mathematical and Physical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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58
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Wijerathne H, Yao H, Wang Y, Lovell S, Battaile KP, Rivera M. Bfd, a New Class of [2Fe-2S] Protein That Functions in Bacterial Iron Homeostasis, Requires a Structural Anion Binding Site. Biochemistry 2018; 57:5533-5543. [PMID: 30183257 DOI: 10.1021/acs.biochem.8b00823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mobilization of iron from bacterioferritin (BfrB) requires specific interactions with a [2Fe-2S] ferredoxin (Bfd). Blocking the BfrB:Bfd interaction results in irreversible iron accumulation in BfrB and iron deficiency in the cytosol [Eshelman, K., et al. (2017) Metallomics 9, 646-659]. The only known Bfd structure, which was obtained in complex with BfrB (Protein Data Bank entry 4E6K ), indicated a new fold and suggested that the stability of Bfd is aided by an anion binding site consisting of R26, R29, and K46. We investigated the Bfd fold using site-directed mutagenesis, X-ray crystallography, and biochemistry in solution. The X-ray structure, which is nearly identical to that of Bfd in the BfrB:Bfd complex, shows that the [2Fe-2S] cluster preorganizes residues at the BfrB:Bfd interface into a structure complementary to the Bfd binding site on BfrB. Studies in solution showed rapid loss of the [2Fe-2S] cluster at a low ionic strength but higher stability with an increasing ionic strength, thus supporting a structural anion binding site. Structures of the R26E and R26E/K46Y mutants are nearly identical to that of Bfd, except for a new network of hydrogen bonds stabilizing the region encompassing the former anion binding site. The stability of the R26E and R26E/K46Y mutants, which is weakly and completely independent of solution ionic strength, respectively, corroborates that Bfd requires an anion binding site. The mutations, which caused only small changes to the strength of the BfrB:Bfd interaction and mobilization of iron from BfrB, indicate that the anion binding site in Bfd serves primarily a structural role.
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Affiliation(s)
- Harshani Wijerathne
- Department of Chemistry , University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Huili Yao
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
| | - Yan Wang
- Department of Chemistry , University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Kevin P Battaile
- IMCA-CAT , Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A , Argonne , Illinois 60439 , United States
| | - Mario Rivera
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
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59
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Linking cytochrome P450 enzymes from Mycobacterium tuberculosis to their cognate ferredoxin partners. Appl Microbiol Biotechnol 2018; 102:9231-9242. [PMID: 30136203 PMCID: PMC6208970 DOI: 10.1007/s00253-018-9299-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/27/2018] [Accepted: 08/02/2018] [Indexed: 01/13/2023]
Abstract
Mycobacterium tuberculosis (Mtb) codes for 20 cytochrome P450 enzymes (CYPs), considered potential drug-targets due to their essential roles in bacterial viability and host infection. Catalytic activity of mycobacterial CYPs is dependent on electron transfer from a NAD (P)H-ferredoxin-reductase (FNR) and a ferredoxin (Fd). Two FNRs (FdrA and FprA) and five ferredoxins (Fdx, FdxA, FdxC, FdxD, and Rv1786) have been found in the Mtb genome. However, as of yet, the cognate redox partnerships have not been fully established. This is confounded by the fact that heterologous redox partners are routinely used to reconstitute Mtb CYP metabolism. To this end, this study aimed to biochemically characterize and identify cognate redox partnerships for Mtb CYPs. Interestingly, all combinations of FNRs and ferredoxins were active in the reduction of oxidized cytochrome c, but steady-state kinetic assays revealed FdxD as the most efficient redox partner for FdrA, whereas Fdx coupled preferably with FprA. CYP121A1, CYP124A1, CYP125A1, and CYP142A1 metabolism with the cognate redox partners was reconstituted in vitro showing an unanticipated selectivity in the requirement for electron transfer partnership, which did not necessarily correlate with proximity in the genome. This is the first description of microbial P450 metabolism in which multiple ferredoxins are functionally linked to multiple CYPs.
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60
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Hemschemeier A, Happe T. The plasticity of redox cofactors: from metalloenzymes to redox-active DNA. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0029-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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61
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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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62
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Ferecatu I, Canal F, Fabbri L, Mazure NM, Bouton C, Golinelli-Cohen MP. Dysfunction in the mitochondrial Fe-S assembly machinery leads to formation of the chemoresistant truncated VDAC1 isoform without HIF-1α activation. PLoS One 2018; 13:e0194782. [PMID: 29596470 PMCID: PMC5875801 DOI: 10.1371/journal.pone.0194782] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/11/2018] [Indexed: 01/09/2023] Open
Abstract
Biogenesis of iron-sulfur clusters (ISC) is essential to almost all forms of life and involves complex protein machineries. This process is initiated within the mitochondrial matrix by the ISC assembly machinery. Cohort and case report studies have linked mutations in ISC assembly machinery to severe mitochondrial diseases. The voltage-dependent anion channel (VDAC) located within the mitochondrial outer membrane regulates both cell metabolism and apoptosis. Recently, the C-terminal truncation of the VDAC1 isoform, termed VDAC1-ΔC, has been observed in chemoresistant late-stage tumor cells grown under hypoxic conditions with activation of the hypoxia-response nuclear factor HIF-1α. These cells harbored atypical enlarged mitochondria. Here, we show for the first time that depletion of several proteins of the mitochondrial ISC machinery in normoxia leads to a similar enlarged mitochondria phenotype associated with accumulation of VDAC1-ΔC. This truncated form of VDAC1 accumulates in the absence of HIF-1α and HIF-2α activations and confers cell resistance to drug-induced apoptosis. Furthermore, we show that when hypoxia and siRNA knock-down of the ISC machinery core components are coupled, the cell phenotype is further accentuated, with greater accumulation of VDAC1-ΔC. Interestingly, we show that hypoxia promotes the downregulation of several proteins (ISCU, NFS1, FXN) involved in the early steps of mitochondrial Fe-S cluster biogenesis. Finally, we have identified the mitochondria-associated membrane (MAM) localized Fe-S protein CISD2 as a link between ISC machinery downregulation and accumulation of anti-apoptotic VDAC1-ΔC. Our results are the first to associate dysfunction in Fe-S cluster biogenesis with cleavage of VDAC1, a form which has previously been shown to promote tumor resistance to chemotherapy, and raise new perspectives for targets in cancer therapy.
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Affiliation(s)
- Ioana Ferecatu
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Frédéric Canal
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Lucilla Fabbri
- Institute for Research on Cancer and Aging of Nice, CNRS-UMR 7284-Inserm U1081, University of Nice Sophia-Antipolis, Centre Antoine Lacassagne, Nice, France
| | - Nathalie M. Mazure
- Institute for Research on Cancer and Aging of Nice, CNRS-UMR 7284-Inserm U1081, University of Nice Sophia-Antipolis, Centre Antoine Lacassagne, Nice, France
| | - Cécile Bouton
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail: (CB); (MPG)
| | - Marie-Pierre Golinelli-Cohen
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail: (CB); (MPG)
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63
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Mao Z, Liou SH, Khadka N, Jenney FE, Goodin DB, Seefeldt LC, Adams MWW, Cramer SP, Larsen DS. Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins. Biochemistry 2018; 57:978-990. [PMID: 29303562 DOI: 10.1021/acs.biochem.7b01159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin, the 2Fe-2S cluster in Pseudomonas putida putidaredoxin, the 4Fe-4S cluster in nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein. Laser excitation promotes the iron-sulfur clusters to excited electronic states that relax to lower states. The electronic relaxation lifetimes of the 1Fe-4S, 8Fe-7S, and 7Fe-9S-1Mo clusters are on the picosecond time scale, although the dynamics of the MoFe protein is a mixture of the dynamics of the latter two clusters. The lifetimes of the 2Fe-2S and 4Fe-4S clusters, however, extend to several nanoseconds. A competition between reorganization energies and the density of electronic states (thus electronic coupling between states) mediates the charge-transfer lifetimes, with the 2Fe-2S cluster of Pdx and the 4Fe-4S cluster of Fe protein lying at the optimum leading to them having significantly longer lifetimes. Their long lifetimes make them the optimal candidates for long-range electron transfer and as external photosensitizers for other photoactivated chemical reactions like solar hydrogen production. Potential electron-transfer and hole-transfer pathways that possibly facilitate these charge transfers are proposed.
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Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Shu-Hao Liou
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine , Suwanee, Georgia 30024, United States
| | - David B Goodin
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Michael W W Adams
- Department of Biochemistry, The University of Georgia , Athens, Georgia 30602, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
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64
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Pierella Karlusich JJ, Carrillo N. Evolution of the acceptor side of photosystem I: ferredoxin, flavodoxin, and ferredoxin-NADP + oxidoreductase. PHOTOSYNTHESIS RESEARCH 2017; 134:235-250. [PMID: 28150152 DOI: 10.1007/s11120-017-0338-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/12/2017] [Indexed: 05/21/2023]
Abstract
The development of oxygenic photosynthesis by primordial cyanobacteria ~2.7 billion years ago led to major changes in the components and organization of photosynthetic electron transport to cope with the challenges of an oxygen-enriched atmosphere. We review herein, following the seminal contributions as reported by Jaganathan et al. (Functional genomics and evolution of photosynthetic systems, vol 33, advances in photosynthesis and respiration, Springer, Dordrecht, 2012), how these changes affected carriers and enzymes at the acceptor side of photosystem I (PSI): the electron shuttle ferredoxin (Fd), its isofunctional counterpart flavodoxin (Fld), their redox partner ferredoxin-NADP+ reductase (FNR), and the primary PSI acceptors F x and F A/F B. Protection of the [4Fe-4S] centers of these proteins from oxidative damage was achieved by strengthening binding between the F A/F B polypeptide and the reaction center core containing F x, therefore impairing O2 access to the clusters. Immobilization of F A/F B in the PSI complex led in turn to the recruitment of new soluble electron shuttles. This function was fulfilled by oxygen-insensitive [2Fe-2S] Fd, in which the reactive sulfide atoms of the cluster are shielded from solvent by the polypeptide backbone, and in some algae and cyanobacteria by Fld, which employs a flavin as prosthetic group and is tolerant to oxidants and iron limitation. Tight membrane binding of FNR allowed solid-state electron transfer from PSI bridged by Fd/Fld. Fine tuning of FNR catalytic mechanism led to formidable increases in turnover rates compared with FNRs acting in heterotrophic pathways, favoring Fd/Fld reduction instead of oxygen reduction.
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Affiliation(s)
- Juan José Pierella Karlusich
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, 2000, Rosario, Argentina
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, 2000, Rosario, Argentina.
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Lakhal-Littleton S, Robbins PA. The interplay between iron and oxygen homeostasis with a particular focus on the heart. J Appl Physiol (1985) 2017; 123:967-973. [PMID: 28775066 DOI: 10.1152/japplphysiol.00237.2017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/10/2017] [Accepted: 07/29/2017] [Indexed: 12/11/2022] Open
Abstract
Iron is subject to tight homeostatic control in mammals. At the systemic level, iron homeostasis is controlled by the liver-derived hormone hepcidin acting on its target ferroportin in the gut, spleen, and liver, which form the sites of iron uptake, recycling, and storage, respectively. At the cellular level, iron homeostasis is dependent on the iron regulatory proteins IRP1/IRP2. Unique chemical properties of iron underpin its importance in biochemical reactions involving oxygen. As such, it is not surprising that there are reciprocal regulatory links between iron and oxygen homeostasis, operating both at the systemic and cellular levels. Hypoxia activates the IRP pathway, and in addition suppresses liver hepcidin through endocrine factors that have yet to be fully elucidated. This review summarizes current knowledge on the interplay between oxygen and iron homeostasis and describes recent insights gained into this interaction in the context of the heart. These include the recognition that the hepcidin/ferroportin axis plays a vital role in the regulation of intracellular iron homeostasis as well as regulating systemic iron availability. As is the case for other aspects of iron homeostasis, hypoxia significantly modulates the function of the hepcidin/ferroportin pathway in the heart. Key areas still to understand are the interactions between cardiac iron and diseases of the heart where hypoxia is a recognized component.
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Affiliation(s)
- Samira Lakhal-Littleton
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter Alistair Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Kobayashi K. Sensing Mechanisms in the Redox-Regulated, [2Fe-2S] Cluster-Containing, Bacterial Transcriptional Factor SoxR. Acc Chem Res 2017. [PMID: 28636310 DOI: 10.1021/acs.accounts.7b00137] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess molecular biosensors that enable responses to a variety of stressful conditions, including oxidative stress, toxic compounds, and interactions with other organisms, through elaborately coordinated regulation of gene expression. In Escherichia coli and related bacteria, the transcription factor SoxR functions as a sensor of oxidative stress and nitric oxide (NO). SoxR protein contains a [2Fe-2S] cluster essential for its transcription-enhancing activity, which is regulated by redox changes in the [2Fe-2S] cluster. We have explored the mechanistic and structural basis of SoxR proteins function and determined how the chemistry at the [2Fe-2S] cluster causes the subsequent regulatory response. In this Account, I describe our recent achievements in three different areas using physicochemical techniques, primarily pulse radiolysis. First, redox-dependent conformational changes in SoxR-bound DNA were studied by site-specifically replacing selected bases with the fluorescent probes 2-aminopurine and pyrrolocytosine. X-ray analyses of the DNA-SoxR complex in the oxidized state revealed that the DNA structure is distorted in the center regions, resulting in local untwisting of base pairs. However, the inactive, reduced state had remained uncharacterized. We found that reduction of the [2Fe-2S] cluster in the SoxR-DNA complex weakens the fluorescence intensity within a region confined to the central base pairs in the promoter region. Second, the reactions of NO with [2Fe-2S] clusters of E. coli SoxR were analyzed using pulse radiolysis. The transcriptional activation of SoxR in E. coli occurs through direct modification of [2Fe-2S] by NO to form a dinitrosyl iron complex (DNIC). The reaction of NO with [2Fe-2S] cluster of SoxR proceeded nearly quantitatively with concomitant reductive elimination of two equivalents S0 atoms. Intermediate nitrosylation products, however, were too unstable to observe. We found that the conversion proceeds through at least two steps, with the faster phase being the first reaction of the NO molecule with the [2Fe-2S] cluster. The slower reaction with the second equivalent NO molecule, however, was important for the formation of DNIC. Third, to elucidate the differences between the distinct responses of SoxR proteins from two different species, we studied the interaction of E. coli and Pseudomonas aeruginosa SoxR with superoxide anion using a mutagenic approach. Despite the homology between E. coli SoxR and P. aeruginosa SoxR, the function of P. aeruginosa SoxR differs from that of E. coli. The substitution of E. coli SoxR lysine residues, located close to [2Fe-2S] clusters, into P. aeruginosa SoxR dramatically affected the reaction with superoxide anion.
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific
and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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69
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Natarajan M, Pandey IK, Kaur-Ghumaan S. Synthesis and Electrocatalysis of Diiron Monothiolate Complexes: Small Molecule Mimics of the [FeFe] Hydrogenase Enzyme. ChemistrySelect 2017. [DOI: 10.1002/slct.201700084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mookan Natarajan
- Department of Chemistry; University of Delhi; Delhi- 110007 India
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Andreini C, Rosato A, Banci L. The Relationship between Environmental Dioxygen and Iron-Sulfur Proteins Explored at the Genome Level. PLoS One 2017; 12:e0171279. [PMID: 28135316 PMCID: PMC5279795 DOI: 10.1371/journal.pone.0171279] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/18/2017] [Indexed: 12/31/2022] Open
Abstract
About 2 billion years ago, the atmosphere of the Earth experienced a great change due to the buildup of dioxygen produced by photosynthetic organisms. This transition caused a reduction of iron bioavailability and at the same time exposed living organisms to the threat of oxidative stress. Iron-sulfur (Fe-S) clusters require iron ions for their biosynthesis and are labile if exposed to reactive oxygen species. To assess how the above transition influenced the usage of Fe-S clusters by organisms, we compared the distribution of the Fe-S proteins encoded by the genomes of more than 400 prokaryotic organisms as a function of their dioxygen requirements. Aerobic organisms use less Fe-S proteins than the majority of anaerobic organisms with a similar genome size. Furthermore, aerobes have evolved specific Fe-S proteins that bind the less iron-demanding and more chemically stable Fe2S2 clusters while reducing the number of Fe4S4-binding proteins in their genomes. However, there is a shared core of Fe-S protein families composed mainly by Fe4S4-binding proteins. Members of these families are present also in humans. The distribution of human Fe-S proteins within cell compartments shows that mitochondrial proteins are inherited from prokaryotic proteins of aerobes, whereas nuclear and cytoplasmic Fe-S proteins are inherited from anaerobic organisms.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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71
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Stiban J, So M, Kaguni LS. Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor. BIOCHEMISTRY (MOSCOW) 2017; 81:1066-1080. [PMID: 27908232 DOI: 10.1134/s0006297916100059] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis. Whereas the identification of iron-sulfur containing proteins and their roles in numerous aspects of cellular function has been a long-standing research area, that in mitochondria is comparatively recent, and it is likely that their roles within mitochondria have been only partially revealed. We review the status of the field and provide examples of other cellular iron-sulfur proteins to highlight their multifarious roles.
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Affiliation(s)
- Johnny Stiban
- Birzeit University, Department of Biology and Biochemistry, West Bank Birzeit, 627, Palestine.
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72
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Cheng Z, Landry AP, Wang Y, Ding H. Binding of Nitric Oxide in CDGSH-type [2Fe-2S] Clusters of the Human Mitochondrial Protein Miner2. J Biol Chem 2017; 292:3146-3153. [PMID: 28082676 DOI: 10.1074/jbc.m116.766774] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/10/2017] [Indexed: 12/31/2022] Open
Abstract
Iron-sulfur proteins are among the primary targets of nitric oxide in cells. Previous studies have shown that iron-sulfur clusters hosted by cysteine residues in proteins are readily disrupted by nitric oxide forming a protein-bound dinitrosyl iron complex, thiolate-bridged di-iron tetranitrosyl complex, or octanitrosyl cluster. Here we report that human mitochondrial protein Miner2 [2Fe-2S] clusters can bind nitric oxide without disruption of the clusters. Miner2 is a member of a new CDGSH iron-sulfur protein family that also includes two mitochondrial proteins: the type II diabetes-related mitoNEET and the Wolfram syndrome 2-linked Miner1. Miner2 contains two CDGSH motifs, and each CDGSH motif hosts a [2Fe-2S] cluster via three cysteine and one histidine residues. Binding of nitric oxide in the reduced Miner2 [2Fe-2S] clusters produces a major absorption peak at 422 nm without releasing iron or sulfide from the clusters. The EPR measurements and mass spectrometry analyses further reveal that nitric oxide binds to the reduced [2Fe-2S] clusters in Miner2, with each cluster binding one nitric oxide. Although the [2Fe-2S] cluster in purified human mitoNEET and Miner1 fails to bind nitric oxide, a single mutation of Asp-96 to Val in mitoNEET or Asp-123 to Val in Miner1 facilitates nitric oxide binding in the [2Fe-2S] cluster, indicating that a subtle change of protein structure may switch mitoNEET and Miner1 to bind nitric oxide. The results suggest that binding of nitric oxide in the CDGSH-type [2Fe-2S] clusters in mitochondrial protein Miner2 may represent a new nitric oxide signaling mode in cells.
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Affiliation(s)
- Zishuo Cheng
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Aaron P Landry
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Yiming Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Huangen Ding
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803.
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73
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Pallares IG, Moore TC, Escalante-Semerena JC, Brunold TC. Spectroscopic Studies of the EutT Adenosyltransferase from Salmonella enterica: Evidence of a Tetrahedrally Coordinated Divalent Transition Metal Cofactor with Cysteine Ligation. Biochemistry 2017; 56:364-375. [PMID: 28045498 DOI: 10.1021/acs.biochem.6b00750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The EutT enzyme from Salmonella enterica, a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes, requires a divalent transition metal ion for catalysis, with Fe(II) yielding the highest activity. EutT contains a unique cysteine-rich HX11CCX2C(83) motif (where H and the last C occupy the 67th and 83rd positions, respectively, in the amino acid sequence) not found in other ACATs and employs an unprecedented mechanism for the formation of adenosylcobalamin. Recent kinetic and spectroscopic studies of this enzyme revealed that residues in the HX11CCX2C(83) motif are required for the tight binding of the divalent metal ion and are critical for the formation of a four-coordinate (4c) cob(II)alamin [Co(II)Cbl] intermediate in the catalytic cycle. However, it remained unknown which, if any, of the residues in the HX11CCX2C(83) motif bind the divalent metal ion. To address this issue, we have characterized Co(II)-substituted wild-type EutT (EutTWT/Co) by using electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism (MCD) spectroscopies. Our results indicate that the reduced catalytic activity of EutTWT/Co relative to that of the Fe(II)-containing enzyme arises from the incomplete incorporation of Co(II) ions and, thus, a decrease in the relative population of 4c Co(II)Cbl. Our MCD data for EutTWT/Co also reveal that the Co(II) ions reside in a distorted tetrahedral coordination environment with direct cysteine sulfur ligation. Additional spectroscopic studies of EutT/Co variants possessing a single alanine substitution of either His67, His75, Cys79, Cys80, or Cys83 indicate that Cys80 coordinates to the Co(II) ion, while the additional residues are important for maintaining the structural integrity and/or high affinity of the metal binding site.
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Affiliation(s)
- Ivan G Pallares
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Theodore C Moore
- Department of Microbiology, University of Georgia , Athens, Georgia 30602, United States
| | | | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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Dizicheh ZB, Halloran N, Asma W, Ghirlanda G. De Novo Design of Iron–Sulfur Proteins. Methods Enzymol 2017; 595:33-53. [DOI: 10.1016/bs.mie.2017.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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75
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Atkinson JT, Campbell I, Bennett GN, Silberg JJ. Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways. Biochemistry 2016; 55:7047-7064. [DOI: 10.1021/acs.biochem.6b00831] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joshua T. Atkinson
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, MS-180, 6100 Main Street, Houston, Texas 77005, United States
| | - Ian Campbell
- Biochemistry
and Cell Biology Graduate Program, Rice University, MS-140, 6100
Main Street, Houston, Texas 77005, United States
| | - George N. Bennett
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemical and Biomolecular Engineering, Rice University, MS-362,
6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
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76
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Functional characterization of aconitase X as a cis-3-hydroxy-L-proline dehydratase. Sci Rep 2016; 6:38720. [PMID: 27929065 PMCID: PMC5144071 DOI: 10.1038/srep38720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/11/2016] [Indexed: 01/30/2023] Open
Abstract
In the aconitase superfamily, which includes the archetypical aconitase, homoaconitase, and isopropylmalate isomerase, only aconitase X is not functionally annotated. The corresponding gene (LhpI) was often located within the bacterial gene cluster involved in L-hydroxyproline metabolism. Screening of a library of (hydroxy)proline analogues revealed that this protein catalyzes the dehydration of cis-3-hydroxy-L-proline to Δ1-pyrroline-2-carboxylate. Furthermore, electron paramagnetic resonance and site-directed mutagenic analyses suggests the presence of a mononuclear Fe(III) center, which may be coordinated with one glutamate and two cysteine residues. These properties were significantly different from those of other aconitase members, which catalyze the isomerization of α- to β-hydroxy acids, and have a [4Fe-4S] cluster-binding site composed of three cysteine residues. Bacteria with the LhpI gene could degrade cis-3-hydroxy-L-proline as the sole carbon source, and LhpI transcription was up-regulated not only by cis-3-hydroxy-L-proline, but also by several isomeric 3- and 4-hydroxyprolines.
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Lakhal-Littleton S, Wolna M, Chung YJ, Christian HC, Heather LC, Brescia M, Ball V, Diaz R, Santos A, Biggs D, Clarke K, Davies B, Robbins PA. An essential cell-autonomous role for hepcidin in cardiac iron homeostasis. eLife 2016; 5. [PMID: 27897970 PMCID: PMC5176354 DOI: 10.7554/elife.19804] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/24/2016] [Indexed: 12/16/2022] Open
Abstract
Hepcidin is the master regulator of systemic iron homeostasis. Derived primarily from the liver, it inhibits the iron exporter ferroportin in the gut and spleen, the sites of iron absorption and recycling respectively. Recently, we demonstrated that ferroportin is also found in cardiomyocytes, and that its cardiac-specific deletion leads to fatal cardiac iron overload. Hepcidin is also expressed in cardiomyocytes, where its function remains unknown. To define the function of cardiomyocyte hepcidin, we generated mice with cardiomyocyte-specific deletion of hepcidin, or knock-in of hepcidin-resistant ferroportin. We find that while both models maintain normal systemic iron homeostasis, they nonetheless develop fatal contractile and metabolic dysfunction as a consequence of cardiomyocyte iron deficiency. These findings are the first demonstration of a cell-autonomous role for hepcidin in iron homeostasis. They raise the possibility that such function may also be important in other tissues that express both hepcidin and ferroportin, such as the kidney and the brain. DOI:http://dx.doi.org/10.7554/eLife.19804.001 Many proteins inside cells require iron to work properly, and so this mineral is an essential part of the diets of most mammals. However, because too much iron in the body is also bad for health, mammals possess several proteins whose role is to maintain the balance of iron. Two proteins in particular, called hepcidin and ferroportin, are thought to be important in this process. Some ferroportin is found in the cells that line the gut (where iron is absorbed into the body) and is required to release this iron into the bloodstream. It is also found in the spleen, which is where iron is removed from old red blood cells so that it can be recycled. The liver produces hepcidin to control when ferroportin is active in the gut and spleen. Both hepcidin and ferroportin are also found in heart cells. In 2015, a study reported that that heart ferroportin plays an important role in heart activity. However, it was not clear what role hepcidin plays in this organ. Now, Lakhal-Littleton et al. – including many of the researchers from the previous work – have genetically engineered mice such that they specifically lacked heart hepcidin, or had a version of ferroportin in their heart that does not respond to hepcidin. The experiments show that these changes caused fatal heart failure in the mice because ferroportin releases iron from heart cells in an uncontrolled manner. Lakhal-Littleton et al. were able to prevent heart failure by injecting the animals with iron directly into the bloodstream. These findings show that hepcidin produced outside the liver has a role in controlling the levels of iron in the body’s organs. Other organs such as the brain, kidney and placenta all have their own forms of hepcidin and ferroportin; further work could investigate the roles of these proteins. Finally, another challenge for the future will be to test whether new drugs that are being developed to block or mimic hepcidin from the liver have the potential to treat heart conditions in humans. DOI:http://dx.doi.org/10.7554/eLife.19804.002
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Affiliation(s)
- Samira Lakhal-Littleton
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Magda Wolna
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Yu Jin Chung
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Helen C Christian
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Lisa C Heather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Marcella Brescia
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Vicky Ball
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Rebeca Diaz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ana Santos
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Daniel Biggs
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kieran Clarke
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Benjamin Davies
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter A Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Koval AM, Jagger BR, Wheeler RA. Distinguishing the Protonation State of the Histidine Ligand to the Oxidized Iron-Sulfur Cluster from the MitoNEET Family of Proteins. Chemphyschem 2016; 18:39-41. [PMID: 27870532 DOI: 10.1002/cphc.201600957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Indexed: 11/10/2022]
Abstract
The iron-sulfur cluster located in the recently discovered human mitoNEET protein (and related proteins) is structurally similar to the more well-known ferredoxin and Rieske clusters. Although its biological function is uncertain, the iron-sulfur cluster in mitoNEET has been proposed to undergo proton-coupled electron transfer involving the histidine ligand to the cluster. The cluster is also released from the protein at low pH. This contribution reports density functional calculations to model the structures, vibrations, and Heisenberg coupling constants (J) for high-spin (HS), broken symmetry (BS) singlet, and extended broken symmetry (EBS) singlet states of the oxidized iron-sulfur cluster from mitoNEET. This work suggests that J values or 15 N isotopic frequency shifts may provide methods for determining experimentally whether the histidine ligand to the oxidized iron-sulfur cluster in human mitoNEET and mitoNEET-related proteins is protonated or deprotonated.
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Affiliation(s)
- Ashlyn M Koval
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA
| | - Benjamin R Jagger
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA
| | - Ralph A Wheeler
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy., DeKalb, IL, 60115, USA
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Romero Romero ML, Rabin A, Tawfik DS. Funktionelle Proteine aus kurzen Peptiden: 50 Jahre nach Margaret Dayhoffs Hypothese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609977] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- M. Luisa Romero Romero
- Department of Biomolecular Sciences; The Weizmann Institute of Science; Rehovot 76100 Israel
| | - Avigayel Rabin
- Derzeitige Adresse: Department of Biological Chemistry, Alexander Silberman Inst. of Life Sciences; The Hebrew University of Jerusalem; Edmond J. Safra Campus Jerusalem 91904 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences; The Weizmann Institute of Science; Rehovot 76100 Israel
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80
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Romero Romero ML, Rabin A, Tawfik DS. Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50. Angew Chem Int Ed Engl 2016; 55:15966-15971. [PMID: 27865046 DOI: 10.1002/anie.201609977] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 01/08/2023]
Abstract
First and foremost: Margaret Dayhoff's 1966 hypothesis on the origin of proteins is now an accepted model for the emergence of large, globular, functional proteins from short, simple peptides. However, the fundamental question of how the first protein(s) emerged still stands. The tools and hypotheses pioneered by Dayhoff, and the over 65 million protein sequences and 12 000 structures known today, enable those who follow in her footsteps to address this question.
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Affiliation(s)
- M Luisa Romero Romero
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Avigayel Rabin
- Current address: Department of Biological Chemistry the Alexander Silberman Inst. of Life Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 91904, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
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81
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Mahadevan A, Fernando S. An improved glycerol biosensor with an Au-FeS-NAD-glycerol-dehydrogenase anode. Biosens Bioelectron 2016; 92:417-424. [PMID: 27836608 DOI: 10.1016/j.bios.2016.10.085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 11/26/2022]
Abstract
An improved glycerol biosensor was developed via direct attachment of NAD+-glycerol dehydrogenase coenzyme-apoenzyme complex onto supporting gold electrodes, using novel inorganic iron (II) sulfide (FeS)-based single molecular wires. Sensing performance factors, i.e., sensitivity, a detection limit and response time of the FeS and conventional pyrroloquinoline quinone (PQQ)-based biosensor were evaluated by dynamic constant potential amperometry at 1.3V under non-buffered conditions. For glycerol concentrations ranging from 1 to 25mM, a 77% increase in sensitivity and a 53% decrease in detection limit were observed for the FeS-based biosensor when compared to the conventional PQQ-based counterpart. The electrochemical behavior of the FeS-based glycerol biosensor was analyzed at different concentrations of glycerol, accompanied by an investigation into the effects of applied potential and scan rate on the current response. Effects of enzyme stimulants ((NH4)2SO4 and MnCl2·4H2O) concentrations and buffers/pH (potassium phosphate buffer pH 6-8, Tris buffer pH 8-10) on the current responses generated by the FeS-based glycerol biosensor were also studied. The optimal detection conditions were 0.03M (NH4)2SO4 and 0.3µm MnCl2·4H2O in non-buffered aqueous electrolyte under stirring whereas under non-stirring, Tris buffer at pH 10 with 0.03M (NH4)2SO4 and 30µm MnCl2·4H2O were found to be optimal detection conditions. Interference by glucose, fructose, ethanol, and acetic acid in glycerol detection was studied. The observations indicated a promising enhancement in glycerol detection using the novel FeS-based glycerol sensing electrode compared to the conventional PQQ-based one. These findings support the premise that FeS-based bioanodes are capable of biosensing glycerol successfully and may be applicable for other enzymatic biosensors.
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Affiliation(s)
- Aishwarya Mahadevan
- Department of Biological and Agricultural Engineering, Texas A&M University, 303C Scoates Hall, College Station TX 77843, USA
| | - Sandun Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, 303C Scoates Hall, College Station TX 77843, USA.
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82
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A synthetic redox biofilm made from metalloprotein–prion domain chimera nanowires. Nat Chem 2016; 9:157-163. [DOI: 10.1038/nchem.2616] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/16/2016] [Indexed: 11/08/2022]
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83
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Abstract
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.
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Affiliation(s)
- Elizabeth O’Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Rebekah M.B. Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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84
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Design of Redox-Active Peptides: Towards Functional Materials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27677515 DOI: 10.1007/978-3-319-39196-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In nature, the majority of processes that occur in the cell involve the cycling of electrons and protons, changing the reduction and oxidation state of substrates to alter their chemical reactivity and usefulness in vivo. One of the most relevant examples of these processes is the electron transport chain, a series of oxidoreductase proteins that shuttle electrons through well-defined pathways, concurrently moving protons across the cell membrane. Inspired by these processes, researchers have sought to develop materials to mimic natural systems for a number of applications, including fuel production. The most common cofactors found in proteins to carry out electron transfer are iron sulfur clusters and porphyrin-like molecules. Both types have been studied within natural proteins, such as in photosynthetic machinery or soluble electron carriers; in parallel, an extensive literature has developed over recent years attempting to model and study these cofactors within peptide-based materials. This chapter will focus on major designs that have significantly advanced the field.
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85
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Sommer DJ, Roy A, Astashkin A, Ghirlanda G. Modulation of cluster incorporation specificity in a de novo iron-sulfur cluster binding peptide. Biopolymers 2016; 104:412-8. [PMID: 25808361 DOI: 10.1002/bip.22635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/20/2022]
Abstract
iron-sulfur cluster binding proteins perform an astounding variety of functions, and represent one of the most abundant classes of metalloproteins. Most often, they constitute pairs or chains and act as electron transfer modules either within complex redox enzymes or within small diffusible proteins. We have previously described the design of a three-helix bundle that can bind two clusters within its hydrophobic core. Here, we use single-point mutations to exchange one of the Cys ligands coordinating the cluster to either Leu or Ser. We show that the mutants modulate the redox potential of the clusters and stabilize the [3Fe-4S] form over the [4Fe-4S] form, supporting the use of model iron-sulfur cluster proteins as modules in the design of complex redox enzymes.
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Affiliation(s)
| | - Anindya Roy
- Chemistry and Biochemistry, Arizona State University, Tempe, AZ
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86
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Shepard EM, Byer AS, Betz JN, Peters JW, Broderick JB. A Redox Active [2Fe-2S] Cluster on the Hydrogenase Maturase HydF. Biochemistry 2016; 55:3514-27. [PMID: 27232385 DOI: 10.1021/acs.biochem.6b00528] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
[FeFe]-hydrogenases are nature's most prolific hydrogen catalysts, excelling at facilely interconverting H2 and protons. The catalytic core common to all [FeFe]-hydrogenases is a complex metallocofactor, referred to as the H-cluster, which is composed of a standard [4Fe-4S] cluster linked through a bridging thiolate to a 2Fe subcluster harboring dithiomethylamine, carbon monoxide, and cyanide ligands. This 2Fe subcluster is synthesized and inserted into [FeFe]-hydrogenase by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG are radical S-adenosylmethionine enzymes and synthesize the nonprotein ligands of the H-cluster. HydF is a GTPase that functions as a scaffold or carrier for 2Fe subcluster production. Herein, we utilize UV-visible, circular dichroism, and electron paramagnetic resonance spectroscopic studies to establish the existence of redox active [4Fe-4S] and [2Fe-2S] clusters bound to HydF. We have used spectroelectrochemical titrations to assign iron-sulfur cluster midpoint potentials, have shown that HydF purifies with a reduced [2Fe-2S] cluster in the absence of exogenous reducing agents, and have tracked iron-sulfur cluster spectroscopic changes with quaternary structural perturbations. Our results provide an important foundation for understanding the maturation process by defining the iron-sulfur cluster content of HydF prior to its interaction with HydE and HydG. We speculate that the [2Fe-2S] cluster of HydF either acts as a placeholder for HydG-derived Fe(CO)2CN species or serves as a scaffold for 2Fe subcluster assembly.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Jeremiah N Betz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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87
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Li Y, Liu P, Takano T, Liu S. A Chloroplast-Localized Rubredoxin Family Protein Gene from Puccinellia tenuiflora (PutRUB) Increases NaCl and NaHCO₃ Tolerance by Decreasing H₂O₂ Accumulation. Int J Mol Sci 2016; 17:ijms17060804. [PMID: 27248998 PMCID: PMC4926338 DOI: 10.3390/ijms17060804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 11/24/2022] Open
Abstract
Rubredoxin is one of the simplest iron–sulfur (Fe–S) proteins. It is found primarily in strict anaerobic bacteria and acts as a mediator of electron transfer participation in different biochemical reactions. The PutRUB gene encoding a chloroplast-localized rubredoxin family protein was screened from a yeast full-length cDNA library of Puccinellia tenuiflora under NaCl and NaHCO3 stress. We found that PutRUB expression was induced by abiotic stresses such as NaCl, NaHCO3, CuCl2 and H2O2. These findings suggested that PutRUB might be involved in plant responses to adversity. In order to study the function of this gene, we analyzed the phenotypic and physiological characteristics of PutRUB transgenic plants treated with NaCl and NaHCO3. The results showed that PutRUB overexpression inhibited H2O2 accumulation, and enhanced transgenic plant adaptability to NaCl and NaHCO3 stresses. This indicated PutRUB might be involved in maintaining normal electron transfer to reduce reactive oxygen species (ROS) accumulation.
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Affiliation(s)
- Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin Hexing Road, Harbin 150040, China.
| | - Panpan Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin Hexing Road, Harbin 150040, China.
| | - Tetsuo Takano
- Asian Natural Environmental Science Center, University of Tokyo, Nishitokyo-shi, Tokyo 188-0002, Japan.
| | - Shenkui Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin Hexing Road, Harbin 150040, China.
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88
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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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89
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Andberg M, Aro-Kärkkäinen N, Carlson P, Oja M, Bozonnet S, Toivari M, Hakulinen N, O'Donohue M, Penttilä M, Koivula A. Characterization and mutagenesis of two novel iron-sulphur cluster pentonate dehydratases. Appl Microbiol Biotechnol 2016; 100:7549-63. [PMID: 27102126 DOI: 10.1007/s00253-016-7530-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 10/21/2022]
Abstract
We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-arabonate dehydratase from Rhizobium leguminosarum bv. trifolii, Rl ArDHT (EC 4.2.1.25), that produce the corresponding 2-keto-3-deoxy-sugar acids. There is only a very limited amount of characterization data available on pentonate dehydratases, even though the enzymes from these oxidative pathways have potential applications with plant biomass pentose sugars. The two bacterial enzymes share 41 % amino acid sequence identity and were expressed and purified from Escherichia coli as homotetrameric proteins. Both dehydratases were shown to accept pentonate and hexonate sugar acids as their substrates and require Mg(2+) for their activity. Cc XyDHT displayed the highest activity on D-xylonate and D-gluconate, while Rl ArDHT functioned best on D-fuconate, L-arabonate and D-galactonate. The configuration of the OH groups at C2 and C3 position of the sugar acid were shown to be critical, and the C4 configuration also contributed substantially to the substrate recognition. The two enzymes were also shown to contain an iron-sulphur [Fe-S] cluster. Our phylogenetic analysis and mutagenesis studies demonstrated that the three conserved cysteine residues in the aldonic acid dehydratase group of IlvD/EDD family members, those of C60, C128 and C201 in Cc XyDHT, and of C59, C127 and C200 in Rl ArDHT, are needed for coordination of the [Fe-S] cluster. The iron-sulphur cluster was shown to be crucial for the catalytic activity (kcat) but not for the substrate binding (Km) of the two pentonate dehydratases.
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Affiliation(s)
- Martina Andberg
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland.
| | - Niina Aro-Kärkkäinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Paul Carlson
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Sophie Bozonnet
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.,CNRS, UMR5504, F-31400, Toulouse, France
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Michael O'Donohue
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.,CNRS, UMR5504, F-31400, Toulouse, France
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
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90
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Andreini C, Banci L, Rosato A. Exploiting Bacterial Operons To Illuminate Human Iron–Sulfur Proteins. J Proteome Res 2016; 15:1308-22. [DOI: 10.1021/acs.jproteome.6b00045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center and ‡Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center and ‡Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center and ‡Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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91
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Griffin A, Parajes S, Weger M, Zaucker A, Taylor AE, O'Neil DM, Müller F, Krone N. Ferredoxin 1b (Fdx1b) Is the Essential Mitochondrial Redox Partner for Cortisol Biosynthesis in Zebrafish. Endocrinology 2016; 157:1122-34. [PMID: 26650568 PMCID: PMC4769370 DOI: 10.1210/en.2015-1480] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mitochondrial cytochrome P450 (CYP) enzymes rely on electron transfer from the redox partner ferredoxin 1 (FDX1) for catalytic activity. Key steps in steroidogenesis require mitochondrial CYP enzymes and FDX1. Over 30 ferredoxin mutations have been explored in vitro; however, no spontaneously occurring mutations have been identified in humans leaving the impact of FDX1 on steroidogenesis in the whole organism largely unknown. Zebrafish are an important model to study human steroidogenesis, because they have similar steroid products and endocrine tissues. This study aimed to characterize the influence of ferredoxin on steroidogenic capacity in vivo by using zebrafish. Zebrafish have duplicate ferredoxin paralogs: fdx1 and fdx1b. Although fdx1 was observed throughout development and in most tissues, fdx1b was expressed after development of the zebrafish interrenal gland (counterpart to the mammalian adrenal gland). Additionally, fdx1b was restricted to adult steroidogenic tissues, such as the interrenal, gonads, and brain, suggesting that fdx1b was interacting with steroidogenic CYP enzymes. By using transcription activator-like effector nucleases, we generated fdx1b mutant zebrafish lines. Larvae with genetic disruption of fdx1b were morphologically inconspicuous. However, steroid hormone analysis by liquid chromatography tandem mass spectrometry revealed fdx1b mutants failed to synthesize glucocorticoids. Additionally, these mutants had an up-regulation of the hypothalamus-pituitary-interrenal axis and showed altered dark-light adaptation, suggesting impaired cortisol signaling. Antisense morpholino knockdown confirmed Fdx1b is required for de novo cortisol biosynthesis. In summary, by using zebrafish, we generated a ferredoxin knockout model system, which demonstrates for the first time the impact of mitochondrial redox regulation on glucocorticoid biosynthesis in vivo.
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Affiliation(s)
- Aliesha Griffin
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
| | - Silvia Parajes
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
| | - Meltem Weger
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
| | - Andreas Zaucker
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
| | - Angela E Taylor
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
| | - Donna M O'Neil
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
| | - Ferenc Müller
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
| | - Nils Krone
- Centre for Endocrinology, Diabetes, and Metabolism (A.G., S.P., M.W., A.Z., A.E.T., D.M.O., N.K.), School of Clinical and Experimental Medicine (F.M.), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and Department of Oncology and Metabolism (N.K.), University of Sheffield, Sheffield S10 2TG, United Kingdom
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92
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Wisener JC, Patton KT, Agbo JK, Mebi CA. Phenylthiolate-diironhexacarbonyl complexes: a comparative conceptual DFT and electrochemical study. TRANSIT METAL CHEM 2016. [DOI: 10.1007/s11243-016-0028-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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93
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Trasviña-Arenas CH, Lopez-Castillo LM, Sanchez-Sandoval E, Brieba LG. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY. FEBS J 2016; 283:521-40. [PMID: 26613369 DOI: 10.1111/febs.13608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 11/15/2015] [Accepted: 11/24/2015] [Indexed: 01/31/2023]
Abstract
7,8-Dihydro-8-deoxyguanine (8oG) is one of the most common oxidative lesions in DNA. DNA polymerases misincorporate an adenine across from this lesion. Thus, 8oG is a highly mutagenic lesion responsible for G:C→T:A transversions. MutY is an adenine glycosylase, part of the base excision repair pathway that removes adenines, when mispaired with 8oG or guanine. Its catalytic domain includes a [4Fe-4S] cluster motif coordinated by cysteinyl ligands. When this cluster is absent, MutY activity is depleted and several studies concluded that the [4Fe-4S] cluster motif is an indispensable component for DNA binding, substrate recognition and enzymatic activity. In the present study, we identified 46 MutY homologues that lack the canonical cysteinyl ligands, suggesting an absence of the [4Fe-4S] cluster. A phylogenetic analysis groups these novel MutYs into two different clades. One clade is exclusive of the order Lactobacillales and another clade has a mixed composition of anaerobic and microaerophilic bacteria and species from the protozoan genus Entamoeba. Structural modeling and sequence analysis suggests that the loss of the [4Fe-4S] cluster is compensated by a convergent solution in which bulky amino acids substitute the [4Fe-4S] cluster. We functionally characterized MutYs from Lactobacillus brevis and Entamoeba histolytica as representative members from each clade and found that both enzymes are active adenine glycosylases. Furthermore, chimeric glycosylases, in which the [4Fe-4S] cluster of Escherichia coli MutY is replaced by the corresponding amino acids of LbY and EhY, are also active. Our data indicates that the [4Fe-4S] cluster plays a structural role in MutYs and evidences the existence of alternative functional solutions in nature.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Laura M Lopez-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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94
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Mahadevan A, Fernando T, Fernando S. Iron-sulfur-based single molecular wires for enhancing charge transport in enzyme-based bioelectronic systems. Biosens Bioelectron 2015; 78:477-482. [PMID: 26657591 DOI: 10.1016/j.bios.2015.11.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/22/2015] [Accepted: 11/27/2015] [Indexed: 10/22/2022]
Abstract
When redox enzymes are wired to electrodes outside a living cell (ex vivo), their ability to produce a sufficiently powerful electrical current diminishes significantly due to the thermodynamic and kinetic limitations associated with the wiring systems. Therefore, we are yet to harness the full potential of redox enzymes for the development of self-powering bioelectronics devices (such as sensors and fuel cells). Interestingly, nature uses iron-sulfur complexes ([Fe-S]), to circumvent these issues in vivo. Yet, we have not been able to utilize [Fe-S]-based chains ex vivo, primarily due to their instability in aqueous media. Here, a simple technique to attach iron (II) sulfide (FeS) to a gold surface in ethanol media and then complete the attachment of the enzyme in aqueous media is reported. Cyclic voltammetry and spectroscopy techniques confirmed the concatenation of FeS and glycerol-dehydrogenase/nicotinamide-adenine-dinucleotide (GlDH-NAD(+)) apoenzyme-coenzyme molecular wiring system on the base gold electrode. The resultant FeS-based enzyme electrode reached an open circuit voltage closer to its standard potential under a wide range of glycerol concentrations (0.001-1M). When probed under constant potential conditions, the FeS-based electrode was able to amplify current by over 10 fold as compared to electrodes fabricated with the conventional pyrroloquinoline quinone-based composite molecular wiring system. These improvements in current/voltage responses open up a wide range of possibilities for fabricating self-powering, bio-electronic devices.
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Affiliation(s)
- Aishwarya Mahadevan
- Department of Biological and Agricultural Engineering, Texas A&M University, 303C Scoates Hall, College Station, TX 77843, USA
| | - Teshan Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, 303C Scoates Hall, College Station, TX 77843, USA
| | - Sandun Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, 303C Scoates Hall, College Station, TX 77843, USA.
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95
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The Oncogenic Small Tumor Antigen of Merkel Cell Polyomavirus Is an Iron-Sulfur Cluster Protein That Enhances Viral DNA Replication. J Virol 2015; 90:1544-56. [PMID: 26608318 DOI: 10.1128/jvi.02121-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/17/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Merkel cell polyomavirus (MCPyV) plays an important role in Merkel cell carcinoma (MCC). MCPyV small T (sT) antigen has emerged as the key oncogenic driver in MCC carcinogenesis. It has also been shown to promote MCPyV LT-mediated replication by stabilizing LT. The importance of MCPyV sT led us to investigate sT functions and to identify potential ways to target this protein. We discovered that MCPyV sT purified from bacteria contains iron-sulfur (Fe/S) clusters. Electron paramagnetic resonance analysis showed that MCPyV sT coordinates a [2Fe-2S] and a [4Fe-4S] cluster. We also observed phenotypic conservation of Fe/S coordination in the sTs of other polyomaviruses. Since Fe/S clusters are critical cofactors in many nucleic acid processing enzymes involved in DNA unwinding and polymerization, our results suggested the hypothesis that MCPyV sT might be directly involved in viral replication. Indeed, we demonstrated that MCPyV sT enhances LT-mediated replication in a manner that is independent of its previously reported ability to stabilize LT. MCPyV sT translocates to nuclear foci containing actively replicating viral DNA, supporting a direct role for sT in promoting viral replication. Mutations of Fe/S cluster-coordinating cysteines in MCPyV sT abolish its ability to stimulate viral replication. Moreover, treatment with cidofovir, a potent antiviral agent, robustly inhibits the sT-mediated enhancement of MCPyV replication but has little effect on the basal viral replication driven by LT alone. This finding further indicates that MCPyV sT plays a direct role in stimulating viral DNA replication and introduces cidofovir as a possible drug for controlling MCPyV infection. IMPORTANCE MCPyV is associated with a highly aggressive form of skin cancer in humans. Epidemiological surveys for MCPyV seropositivity and sequencing analyses of healthy human skin suggest that MCPyV may represent a common component of the human skin microbial flora. However, much of the biology of the virus and its oncogenic ability remain to be investigated. In this report, we identify MCPyV sT as a novel Fe/S cluster protein and show that conserved cysteine clusters are important for sT's ability to enhance viral replication. Moreover, we show that sT sensitizes MCPyV replication to cidofovir inhibition. The discovery of Fe/S clusters in MCPyV sT opens new avenues to the study of the structure and functionality of this protein. Moreover, this study supports the notion that sT is a potential drug target for dampening MCPyV infection.
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96
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Saha PP, Srivastava S, Kumar S K P, Sinha D, D'Silva P. Mapping Key Residues of ISD11 Critical for NFS1-ISD11 Subcomplex Stability: IMPLICATIONS IN THE DEVELOPMENT OF MITOCHONDRIAL DISORDER, COXPD19. J Biol Chem 2015; 290:25876-90. [PMID: 26342079 DOI: 10.1074/jbc.m115.678508] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 11/06/2022] Open
Abstract
Biogenesis of the iron-sulfur (Fe-S) cluster is an indispensable process in living cells. In mammalian mitochondria, the initial step of the Fe-S cluster assembly process is assisted by the NFS1-ISD11 complex, which delivers sulfur to scaffold protein ISCU during Fe-S cluster synthesis. Although ISD11 is an essential protein, its cellular role in Fe-S cluster biogenesis is still not defined. Our study maps the important ISD11 amino acid residues belonging to putative helix 1 (Phe-40), helix 3 (Leu-63, Arg-68, Gln-69, Ile-72, Tyr-76), and C-terminal segment (Leu-81, Glu-84) are critical for in vivo Fe-S cluster biogenesis. Importantly, mutation of these conserved ISD11 residues into alanine leads to its compromised interaction with NFS1, resulting in reduced stability and enhanced aggregation of NFS1 in the mitochondria. Due to altered interaction with ISD11 mutants, the levels of NFS1 and Isu1 were significantly depleted, which affects Fe-S cluster biosynthesis, leading to reduced electron transport chain complex (ETC) activity and mitochondrial respiration. In humans, a clinically relevant ISD11 mutation (R68L) has been associated in the development of a mitochondrial genetic disorder, COXPD19. Our findings highlight that the ISD11 R68A/R68L mutation display reduced affinity to form a stable subcomplex with NFS1, and thereby fails to prevent NFS1 aggregation resulting in impairment of the Fe-S cluster biogenesis. The prime affected machinery is the ETC complex, which showed compromised redox properties, causing diminished mitochondrial respiration. Furthermore, the R68L ISD11 mutant displayed accumulation of mitochondrial iron and reactive oxygen species, leading to mitochondrial dysfunction, which correlates with the phenotype observed in COXPD19 patients.
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Affiliation(s)
- Prasenjit Prasad Saha
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
| | - Shubhi Srivastava
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
| | - Praveen Kumar S K
- the Department of Biochemistry, Karnatak University, Dharwad 580003, Karnataka, India
| | - Devanjan Sinha
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
| | - Patrick D'Silva
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
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97
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Albertini M, Berto P, Vallese F, Di Valentin M, Costantini P, Carbonera D. Probing the Solvent Accessibility of the [4Fe-4S] Cluster of the Hydrogenase Maturation Protein HydF from Thermotoga neapolitana by HYSCORE and 3p-ESEEM. J Phys Chem B 2015; 119:13680-9. [PMID: 25978307 DOI: 10.1021/acs.jpcb.5b03110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The catalytic site of [FeFe]-hydrogenase, the "H-cluster", composed of a [4Fe-4S] unit connected by a cysteinyl residue to a [2Fe] center coordinated by three CO, two CN(-), and a bridging dithiolate, is assembled in a complex maturation pathway, at present not fully characterized, involving three conserved proteins, HydG, HydE, and HydF. HydF is a complex enzyme, which is thought to act as a scaffold and carrier for the [2Fe] subunit of the H-cluster. This maturase protein contains itself a [4Fe-4S] cluster binding site, with three conserved cysteine residues and a noncysteinyl fourth ligand. In this work, we have exploited 3p-ESEEM and HYSCORE spectroscopies to get insight into the structure and the chemical environment of the [4Fe-4S] cluster of HydF from the hyperthermophilic organism Thermotoga neapolitana. The nature of the fourth ligand and the solvent accessibility of the active site comprising the [4Fe-4S] cluster are discussed on the basis of the spectroscopic results obtained upon H/D exchange. We propose that the noncysteinyl ligated Fe atom of the [4Fe-4S] cluster is the site where the [2Fe] subcluster precursor is anchored and finally processed to be delivered to the hydrogenase (HydA).
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Affiliation(s)
- Marco Albertini
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
| | - Paola Berto
- Department of Biomedical Sciences, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Francesca Vallese
- Department of Biomedical Sciences, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
| | - Paola Costantini
- Department of Biology, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
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98
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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99
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Piccioli M, Turano P. Transient iron coordination sites in proteins: Exploiting the dual nature of paramagnetic NMR. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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100
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Kobayashi K, Fujikawa M, Kozawa T. Binding of promoter DNA to SoxR protein decreases the reduction potential of the [2Fe-2S] cluster. Biochemistry 2014; 54:334-9. [PMID: 25490746 DOI: 10.1021/bi500931w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The [2Fe-2S] transcriptional factor SoxR, a member of the MerR family, functions as a sensor of oxidative stress in Escherichia coli. The transcriptional activity of SoxR is regulated by the reversible oxidation and reduction of [2Fe-2S] clusters. Electrochemistry measurements on DNA-modified electrodes have shown a dramatic shift in the reduction potential of SoxR from -290 to +200 mV with the promoter DNA-bound [ Gorodetsky , A. A. , Dietrich , L. E. P. , Lee , P. E. , Demple , B. , , Newman , D. K. , and Barton , J. K. ( 2008 ) DNA binding shifts the reduction potential of the transcription factor SoxR , Proc. Natl. Acad. Sci. U.S.A. 105 , 3684 - 3689 ]. To determine the change of the SoxR reduction potential using the new condition, the one-electron oxidation-reduction properties of [2Fe-2S] cluster in SoxR were investigated in the absence and presence of the DNA. The [2Fe-2S] cluster of SoxR was completely reduced by nicotinamide adenine dinucleotide phosphate (NADPH)-cytochrome P450 reductase (CRP) in the presence of a NADPH generating system (glucose 6-dehydrogenase and glucose-6 phosphate), indicating that CRP can serve as an NADPH-dependent electron carrier for SoxR. The reduction potential of SoxR was measured from equilibrium data coupled with NADPH and CRP in the presence of electron mediators. The reduction potentials of DNA-bound and DNA-free states of SoxR were -320 and -293 mV versus NHE (normal hydrogen electrode), respectively. These results indicate that DNA binding causes a moderate shift in the reduction potential of SoxR.
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University , Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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