1
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Want K, D'Autréaux B. Mechanism of mitochondrial [2Fe-2S] cluster biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119811. [PMID: 39128597 DOI: 10.1016/j.bbamcr.2024.119811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/13/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024]
Abstract
Iron‑sulfur (Fe-S) clusters constitute ancient cofactors that accompany a versatile range of fundamental biological reactions across eukaryotes and prokaryotes. Several cellular pathways exist to coordinate iron acquisition and sulfur mobilization towards a scaffold protein during the tightly regulated synthesis of Fe-S clusters. The mechanism of mitochondrial eukaryotic [2Fe-2S] cluster synthesis is coordinated by the Iron-Sulfur Cluster (ISC) machinery and its aberrations herein have strong implications to the field of disease and medicine which is therefore of particular interest. Here, we describe our current knowledge on the step-by-step mechanism leading to the production of mitochondrial [2Fe-2S] clusters while highlighting the recent developments in the field alongside the challenges that are yet to be overcome.
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Affiliation(s)
- Kristian Want
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Benoit D'Autréaux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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2
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Olivieri P, Zupok A, Yildiz T, Oltmanns J, Lehmann A, Sokolowska E, Skirycz A, Schünemann V, Leimkühler S. TusA influences Fe-S cluster assembly and iron homeostasis in E. coli by reducing the translation efficiency of Fur. Microbiol Spectr 2024; 12:e0055624. [PMID: 38916309 PMCID: PMC11302051 DOI: 10.1128/spectrum.00556-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 06/26/2024] Open
Abstract
All sulfur transfer pathways have generally a l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of numerous sulfur-containing biomolecules in the cell. In Escherichia coli, the housekeeping l-cysteine desulfurase IscS has several interaction partners, which bind at different sites of the protein. So far, the interaction sites of IscU, Fdx, CyaY, and IscX involved in iron-sulfur (Fe-S) cluster assembly have been mapped, in addition to TusA, which is required for molybdenum cofactor biosynthesis and mnm5s2U34 tRNA modifications, and ThiI, which is involved in thiamine biosynthesis and s4U8 tRNA modifications. Previous studies predicted that the sulfur acceptor proteins bind to IscS one at a time. E. coli TusA has, however, been suggested to be involved in Fe-S cluster assembly, as fewer Fe-S clusters were detected in a ∆tusA mutant. The basis for this reduction in Fe-S cluster content is unknown. In this work, we investigated the role of TusA in iron-sulfur cluster assembly and iron homeostasis. We show that the absence of TusA reduces the translation of fur, thereby leading to pleiotropic cellular effects, which we dissect in detail in this study.IMPORTANCEIron-sulfur clusters are evolutionarily ancient prosthetic groups. The ferric uptake regulator plays a major role in controlling the expression of iron homeostasis genes in bacteria. We show that a ∆tusA mutant is impaired in the assembly of Fe-S clusters and accumulates iron. TusA, therefore, reduces fur mRNA translation leading to pleiotropic cellular effects.
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Affiliation(s)
- Paolo Olivieri
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Arkadiuz Zupok
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Tugba Yildiz
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Jonathan Oltmanns
- Department of Physics, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Angelika Lehmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Ewelina Sokolowska
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Volker Schünemann
- Department of Physics, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
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3
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Benisch R, Giessen TW. Structural and biochemical characterization of an encapsulin-associated rhodanese from Acinetobacter baumannii. Protein Sci 2024; 33:e5129. [PMID: 39073218 PMCID: PMC11284452 DOI: 10.1002/pro.5129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/07/2024] [Accepted: 07/14/2024] [Indexed: 07/30/2024]
Abstract
Rhodanese-like domains (RLDs) represent a widespread protein family canonically involved in sulfur transfer reactions between diverse donor and acceptor molecules. RLDs mediate these transsulfuration reactions via a transient persulfide intermediate, created by modifying a conserved cysteine residue in their active sites. RLDs are involved in various aspects of sulfur metabolism, including sulfide oxidation in mitochondria, iron-sulfur cluster biogenesis, and thio-cofactor biosynthesis. However, due to the inherent complexity of sulfur metabolism caused by the intrinsically high nucleophilicity and redox sensitivity of thiol-containing compounds, the physiological functions of many RLDs remain to be explored. Here, we focus on a single domain Acinetobacter baumannii RLD (Ab-RLD) associated with a desulfurase encapsulin which is able to store substantial amounts of sulfur inside its protein shell. We determine the 1.6 Å x-ray crystal structure of Ab-RLD, highlighting a homodimeric structure with a number of unusual features. We show through kinetic analysis that Ab-RLD exhibits thiosulfate sulfurtransferase activity with both cyanide and glutathione acceptors. Using native mass spectrometry and in vitro assays, we provide evidence that Ab-RLD can stably carry a persulfide and thiosulfate modification and may employ a ternary catalytic mechanism. Our results will inform future studies aimed at investigating the functional link between Ab-RLD and the desulfurase encapsulin.
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Affiliation(s)
- Robert Benisch
- Program in Chemical BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Tobias W. Giessen
- Program in Chemical BiologyUniversity of MichiganAnn ArborMichiganUSA
- Department of Biological ChemistryUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
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4
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Olivieri P, Klabes M, Crack JC, Lehmann A, Bennett SP, Le Brun NE, Leimkühler S. Binding of IscU and TusA to different but competing sites of IscS influences the activity of IscS and directs sulfur to the respective biomolecular synthesis pathway. Microbiol Spectr 2024; 12:e0094924. [PMID: 38980029 PMCID: PMC11302665 DOI: 10.1128/spectrum.00949-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/05/2024] [Indexed: 07/10/2024] Open
Abstract
All sulfur transfer pathways generally have in common an l-cysteine desulfurase as the initial sulfur-mobilizing enzyme, which serves as a sulfur donor for the biosynthesis of numerous sulfur-containing biomolecules in the cell. In Escherichia coli, the housekeeping l-cysteine desulfurase IscS functions as a hub for sulfur transfer through interactions with several partner proteins, which bind at different sites on IscS. So far, the interaction sites of IscU, Fdx, CyaY, and IscX involved in iron sulfur (Fe-S) cluster assembly, TusA, required for molybdenum cofactor biosynthesis and mnm5s2U34 transfer RNA (tRNA) modifications, and ThiI, involved in both the biosynthesis of thiamine and s4U8 tRNA modifications, have been mapped. Previous studies have suggested that IscS partner proteins bind only one at a time, with the exception of Fe-S cluster assembly, which involves the formation of a ternary complex involving IscS, IscU, and one of CyaY, Fdx, or IscX. Here, we show that the affinity of TusA for IscS is similar to but lower than that of IscU and that these proteins compete for binding to IscS. We show that heterocomplexes involving the IscS dimer and single IscU and TusA molecules are readily formed and that binding of both TusA and IscU to IscS affects its l-cysteine desulfurase activity. A model is proposed in which the delivery of sulfur to different sulfur-requiring pathways is controlled by sulfur acceptor protein levels, IscS-binding affinities, and acceptor protein-modulated IscS desulfurase activity.IMPORTANCEIron-sulfur clusters are evolutionarily ancient prosthetic groups. The housekeeping l-cysteine desulfurase IscS functions as a central core for sulfur transfer through interactions with several partner proteins, which bind at different sites on each IscS monomer with different affinities and partially overlapping binding sites. We show that heterocomplexes involving the IscS dimer and single IscU and TusA molecules at each site of the dimer are formed, thereby influencing the activity of IscS.
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Affiliation(s)
- Paolo Olivieri
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Moritz Klabes
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jason C. Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Angelika Lehmann
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Sophie P. Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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5
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Hasnat MA, Leimkühler S. Shared functions of Fe-S cluster assembly and Moco biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119731. [PMID: 38631442 DOI: 10.1016/j.bbamcr.2024.119731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In the recent years it has become evident that the availability of Fe-S clusters play an important role for the biosynthesis of Moco. First, the MoaA protein binds two [4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional [4Fe-4S] cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is an enzyme involved in the transfer of sulfur to various acceptor proteins with a main role in the assembly of Fe-S clusters. In this review, we dissect the dependence of the production of active molybdoenzymes in detail, starting from the regulation of gene expression and further explaining sulfur delivery and Fe-S cluster insertion into target enzymes. Further, Fe-S cluster assembly is also linked to iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, we explain that the expression of the genes is dependent on an active FNR protein. FNR is a very important transcription factor that represents the master-switch for the expression of target genes in response to anaerobiosis. Moco biosynthesis is further directly dependent on the presence of ArcA and also on an active Fur protein.
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Affiliation(s)
- Muhammad Abrar Hasnat
- University of Potsdam, Institute of Biochemistry and Biology, Department of Molecular Enzymology, Karl-Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Silke Leimkühler
- University of Potsdam, Institute of Biochemistry and Biology, Department of Molecular Enzymology, Karl-Liebknecht Str. 24-25, 14476 Potsdam-Golm, Germany.
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6
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Benisch R, Giessen TW. Structural and biochemical characterization of an encapsulin-associated rhodanese from Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.581022. [PMID: 38464153 PMCID: PMC10925157 DOI: 10.1101/2024.02.19.581022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Rhodanese-like domains (RLDs) represent a widespread protein family canonically involved in sulfur transfer reactions between diverse donor and acceptor molecules. RLDs mediate these transsulfuration reactions via a transient persulfide intermediate, created by modifying a conserved cysteine residue in their active sites. RLDs are involved in various aspects of sulfur metabolism, including sulfide oxidation in mitochondria, iron-sulfur cluster biogenesis, and thio-cofactor biosynthesis. However, due to the inherent complexity of sulfur metabolism caused by the intrinsically high nucleophilicity and redox sensitivity of thiol-containing compounds, the physiological functions of many RLDs remain to be explored. Here, we focus on a single domain Acinetobacter baumannii RLD (Ab-RLD) associated with a desulfurase encapsulin which is able to store substantial amounts of sulfur inside its protein shell. We determine the 1.6 Å x-ray crystal structure of Ab-RLD, highlighting a homodimeric structure with a number of unusual features. We show through kinetic analysis that Ab-RLD exhibits thiosulfate sulfurtransferase activity with both cyanide and glutathione acceptors. Using native mass spectrometry and in vitro assays, we provide evidence that Ab-RLD can stably carry a persulfide and thiosulfate modification and may employ a ternary catalytic mechanism. Our results will inform future studies aimed at investigating the functional link between Ab-RLD and the desulfurase encapsulin.
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Affiliation(s)
- Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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7
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Bennett SP, Crack JC, Puglisi R, Pastore A, Le Brun NE. Native mass spectrometric studies of IscSU reveal a concerted, sulfur-initiated mechanism of iron-sulfur cluster assembly. Chem Sci 2022; 14:78-95. [PMID: 36605734 PMCID: PMC9769115 DOI: 10.1039/d2sc04169c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are cofactors essential for life. Though the proteins that function in the assembly of Fe-S clusters are well known, details of the molecular mechanism are less well established. The Isc (iron-sulfur cluster) biogenesis apparatus is widespread in bacteria and is the closest homologue to the human system. Mutations in certain components of the human system lead to disease, and so further studies of this system could be important for developing strategies for medical treatments. We have studied two core components of the Isc biogenesis system: IscS, a cysteine desulfurase; and IscU, a scaffold protein on which clusters are built before subsequent transfer onto recipient apo-proteins. Fe2+-binding, sulfur transfer, and formation of a [2Fe-2S] was followed by a range of techniques, including time-resolved mass spectrometry, and intermediate and product species were unambiguously identified through isotopic substitution experiments using 57Fe and 34S. Under cluster synthesis conditions, sulfur adducts and the [2Fe-2S] cluster product readily accumulated on IscU, but iron adducts (other than the cluster itself) were not observed at physiologically relevant Fe2+ concentrations. Our data indicate that either Fe2+ or sulfur transfer can occur first, but that the transfer of sulfane sulfur (S0) to IscU must occur first if Zn2+ is bound to IscU, suggesting that it is the key step that initiates cluster assembly. Following this, [2Fe-2S] cluster formation is a largely concerted reaction once Fe2+ is introduced.
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Affiliation(s)
- Sophie P Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Rita Puglisi
- The Wohl Institute, King's College London, Denmark Hill Campus London SE5 8AF UK
| | - Annalisa Pastore
- The Wohl Institute, King's College London, Denmark Hill Campus London SE5 8AF UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
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8
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Li M, Wu B, Zhang P, Li Y, Xu W, Wang K, Qiu Q, Zhang J, Li J, Zhang C, Fan J, Feng C, Chen Z. Genomes of Two Flying Squid Species Provide Novel Sights into Adaptations of Cephalopods to Pelagic Life. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1053-1065. [PMID: 36216027 DOI: 10.1016/j.gpb.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/25/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
Abstract
Pelagic cephalopods have evolved a series of fascinating traits, such as excellent visual acuity, high-speed agility, and photophores for adaptation to open pelagic oceans. However, the genetic mechanisms underpinning these traits are not well understood. Thus, in this study, we obtained high-quality genomes of two purpleback flying squid species (Sthenoteuthis oualaniensis and Sthenoteuthis sp.), with sizes of 5450 Mb and 5651 Mb, respectively. Comparative genomic analyses revealed that the S-crystallin subfamily SL20-1 associated with visual acuity in the purpleback flying squid lineage was significantly expanded, and the evolution of high-speed agility for the species was accompanied by significant positive selection pressure on genes related to energy metabolism. These molecular signals might have contributed to the evolution of their adaptative predatory and anti-predatory traits. In addition, the transcriptomic analysis provided clear indications of the evolution of the photophores of purpleback flying squids, especially the recruitment of new genes and energy metabolism-related genes which may have played key functional roles in the process.
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Affiliation(s)
- Min Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Key Laboratory for Sustainable Utilization of Open-Sea Fishery, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Peng Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Ye Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jun Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Jie Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Chi Zhang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Jiangtao Fan
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Zuozhi Chen
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Key Laboratory for Sustainable Utilization of Open-Sea Fishery, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China.
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9
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Schachterle JK, Gdanetz K, Pandya I, Sundin GW. Identification of novel virulence factors in Erwinia amylovora through temporal transcriptomic analysis of infected apple flowers under field conditions. MOLECULAR PLANT PATHOLOGY 2022; 23:855-869. [PMID: 35246928 PMCID: PMC9104256 DOI: 10.1111/mpp.13199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
The enterobacterial pathogen Erwinia amylovora uses multiple virulence-associated traits to cause fire blight, a devastating disease of apple and pear trees. Many virulence-associated phenotypes have been studied that are critical for virulence and pathogenicity. Despite the in vitro testing that has revealed how these systems are transcriptionally regulated, information on when and where in infected tissues these genes are being expressed is lacking. Here, we used a high-throughput sequencing approach to characterize the transcriptome of E. amylovora during disease progression on apple flowers under field infection conditions. We report that type III secretion system genes and flagellar genes are strongly co-expressed. Likewise, genes involved in biosynthesis of the exopolysaccharide amylovoran and sorbitol utilization had similar expression patterns. We further identified a group of 16 genes whose expression is increased and maintained at high levels throughout disease progression across time and tissues. We chose five of these genes for mutational analysis and observed that deletion mutants lacking these genes all display reduced symptom development on apple shoots. Furthermore, these induced genes were over-represented for genes involved in sulphur metabolism and cycling, suggesting the possibility of an important role for maintenance of oxidative homeostasis during apple flower infection.
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Affiliation(s)
- Jeffrey K. Schachterle
- Genetics and Genome Sciences ProgramMichigan State UniversityEast LansingMIUSA
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMIUSA
- Present address:
USDAARS, Cereal Crops Research UnitFargoNDUSA
| | - Kristi Gdanetz
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Ishani Pandya
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - George W. Sundin
- Genetics and Genome Sciences ProgramMichigan State UniversityEast LansingMIUSA
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMIUSA
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10
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Puglisi R. Protein Mutations and Stability, a Link with Disease: The Case Study of Frataxin. Biomedicines 2022; 10:biomedicines10020425. [PMID: 35203634 PMCID: PMC8962269 DOI: 10.3390/biomedicines10020425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Protein mutations may lead to pathologies by causing protein misfunction or propensity to degradation. For this reason, several studies have been performed over the years to determine the capability of proteins to retain their native conformation under stress condition as well as factors to explain protein stabilization and the mechanisms behind unfolding. In this review, we explore the paradigmatic example of frataxin, an iron binding protein involved in Fe–S cluster biogenesis, and whose impairment causes a neurodegenerative disease called Friedreich’s Ataxia (FRDA). We summarize what is known about most common point mutations identified so far in heterozygous FRDA patients, their effects on frataxin structure and function and the consequences of its binding with partners.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, London SE59RT, UK
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11
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Fujishiro T, Nakamura R, Kunichika K, Takahashi Y. Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis. Biophys Physicobiol 2022; 19:1-18. [PMID: 35377584 PMCID: PMC8918507 DOI: 10.2142/biophysico.bppb-v19.0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ryosuke Nakamura
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Kouhei Kunichika
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Yasuhiro Takahashi
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
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12
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Petronek MS, Spitz DR, Allen BG. Iron-Sulfur Cluster Biogenesis as a Critical Target in Cancer. Antioxidants (Basel) 2021; 10:1458. [PMID: 34573089 PMCID: PMC8465902 DOI: 10.3390/antiox10091458] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Cancer cells preferentially accumulate iron (Fe) relative to non-malignant cells; however, the underlying rationale remains elusive. Iron-sulfur (Fe-S) clusters are critical cofactors that aid in a wide variety of cellular functions (e.g., DNA metabolism and electron transport). In this article, we theorize that a differential need for Fe-S biogenesis in tumor versus non-malignant cells underlies the Fe-dependent cell growth demand of cancer cells to promote cell division and survival by promoting genomic stability via Fe-S containing DNA metabolic enzymes. In this review, we outline the complex Fe-S biogenesis process and its potential upregulation in cancer. We also discuss three therapeutic strategies to target Fe-S biogenesis: (i) redox manipulation, (ii) Fe chelation, and (iii) Fe mimicry.
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Affiliation(s)
- Michael S. Petronek
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Douglas R. Spitz
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Bryan G. Allen
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
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13
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Mohammad Sadik, Mohammad Afsar, Ramachandran R, Habib S. [Fe-S] biogenesis and unusual assembly of the ISC scaffold complex in the Plasmodium falciparum mitochondrion. Mol Microbiol 2021; 116:606-623. [PMID: 34032321 DOI: 10.1111/mmi.14735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022]
Abstract
The malaria parasite harbors two [Fe-S] biogenesis pathways of prokaryotic origin-the SUF and ISC systems in the apicoplast and mitochondrion, respectively. While the SUF machinery has been delineated, there is little experimental evidence on the ISC pathway. We confirmed mitochondrial targeting of Plasmodium falciparum ISC proteins followed by analyses of cysteine desulfurase, scaffold, and [Fe-S]-carrier components. PfIscU functioned as the scaffold in complex with the PfIscS-PfIsd11 cysteine desulfurase and could directly assemble [4Fe-4S] without prior [2Fe-2S] formation seen in other homologs. Small angle X-ray scattering and spectral studies showed that PfIscU, a trimer, bound one [4Fe-4S]. In a deviation from reported complexes from other organisms, the P. falciparum desulfurase-scaffold complex assembled around a PfIscS tetramer instead of a dimer, resulting in a symmetric hetero-hexamer [2× (2PfIscS-2PfIsd11-2PfIscU)]. PfIscU directly transferred [4Fe-4S] to the apo-protein aconitase B thus abrogating the requirement of intermediary proteins for conversion of [2Fe-2S] to [4Fe-4S] before transfer to [4Fe-4S]-recipients. Among the putative cluster-carriers, PfIscA2 was more efficient than PfNifU-like protein; PfIscA1 primarily bound iron, suggesting its potential role as a Fe2+ carrier/donor. Our results identify the core P. falciparum ISC machinery and reveal unique features compared with those in bacteria or yeast and human mitochondria.
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Affiliation(s)
- Mohammad Sadik
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Afsar
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ravishankar Ramachandran
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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14
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Liu A, Krushnamurthy PH, Subramanya KS, Mitchell DA, Mahanta N. Enzymatic thioamidation of peptide backbones. Methods Enzymol 2021; 656:459-494. [PMID: 34325795 DOI: 10.1016/bs.mie.2021.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Thioamides are found in a few natural products and two known protein assemblies: the Escherichia coli ribosome and methyl-coenzyme M reductase (MCR) from methane-metabolizing archaea. Compared to an amide, thioamides alter the physical and chemical properties of peptide backbones, including the conformation dynamics, proteolytic stability, hydrogen-bonding capabilities, and possibly reactivity of a protein when installed. Recently, there has been significant progress in elucidating enzymatic post-translational thioamide installation, with most work leveraging the archaeal MCR-modifying enzymes. This chapter describes the protocols used for the in vitro enzymatic thioamidation of MCR-derived peptides, including polypeptide overexpression, purification, reaction reconstitution, and mass spectrometry-based product analysis. In addition, we highlight the protocols used for the biochemical, kinetics, and binding studies using recombinant enzymes obtained heterologously from E. coli. We anticipate that these methods will serve to guide future studies on peptide post-translational thioamidation, as well as other peptide backbone modifications using a parallel workflow.
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Affiliation(s)
- Andi Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States; Department of Microbiology, University of Illinois, Urbana, IL, United States
| | - P H Krushnamurthy
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - K S Subramanya
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States; Department of Microbiology, University of Illinois, Urbana, IL, United States; Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Nilkamal Mahanta
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India.
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15
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Kunichika K, Nakamura R, Fujishiro T, Takahashi Y. The Structure of the Dimeric State of IscU Harboring Two Adjacent [2Fe-2S] Clusters Provides Mechanistic Insights into Cluster Conversion to [4Fe-4S]. Biochemistry 2021; 60:1569-1572. [PMID: 33938220 DOI: 10.1021/acs.biochem.1c00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IscU serves as a scaffold for the de novo assembly of a [2Fe-2S] cluster prior to its delivery to recipient protein. It has also been proposed that on one dimer of bacterial IscU, two [2Fe-2S] clusters can be converted into a single [4Fe-4S] cluster. However, lack of structural information about the dimeric state of IscU has hindered our understanding of the underlying mechanisms. In this study, we determine the X-ray crystal structure of IscU from the thermophilic archaeon Methanothrix thermoacetophila and demonstrate a dimer structure of IscU in which two [2Fe-2S] clusters are facing each other in close proximity at the dimer interface. Our structure also reveals for the first time that Asp40 serves as a fourth ligand to the [2Fe-2S] cluster with three Cys ligands in each monomer, consistent with previous spectroscopic data. We confirm by EPR spectroscopic analysis that in solution two adjacent [2Fe-2S] clusters in the wild-type dimer are converted to a [4Fe-4S] cluster via reductive coupling. Furthermore, we find that the H106A substitution abolishes the reductive conversion to the [4Fe-4S] cluster without structural alteration, suggesting that His106 is functionally involved in this process. Overall, these findings provide a structural explanation for the assembly and conversion of Fe-S clusters on IscU and highlight a dynamic process that advances via association and dissociation of the IscU dimer.
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Affiliation(s)
- Kouhei Kunichika
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
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16
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Sato S, Matsushima Y, Kanazawa M, Tanaka N, Fujishiro T, Kunichika K, Nakamura R, Tomioka H, Wada K, Takahashi Y. Evidence for dynamic in vivo interconversion of the conformational states of IscU during iron-sulfur cluster biosynthesis. Mol Microbiol 2020; 115:807-818. [PMID: 33202070 DOI: 10.1111/mmi.14646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/02/2020] [Accepted: 11/12/2020] [Indexed: 11/28/2022]
Abstract
IscU is a central component of the ISC machinery and serves as a scaffold for de novo assembly of Fe-S clusters. The dedicated chaperone system composed of the Hsp70-chaperone HscA and the J-protein cochaperone HscB synergistically interacts with IscU and facilitates cluster transfer from IscU to recipient apo-proteins. Here, we report that the otherwise essential roles of HscA and HscB can be bypassed in vivo by a number of single amino acid substitutions in IscU. CD spectroscopic studies of the variant IscU proteins capable of this bypass activity revealed dynamic interconversion between two conformations: the denatured (D) and the structured (S) state in the absence and presence of Zn2+ , respectively, which was far more prominent than interconversion observed in wild-type IscU. Furthermore, we found that neither the S-shifted (more structured) variants of IscU nor the perpetually denatured variants could perform their in vivo role regardless of whether the chaperone system was present or not. The present study thus provides for the first time evidence that an in vivo D-state of IscU exists and implies that conformational interconversion between the S- and D-states of the scaffolding protein is a fundamental requirement for the assembly and transfer of the Fe-S cluster.
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Affiliation(s)
- Sakiko Sato
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yumeka Matsushima
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miaki Kanazawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kouhei Kunichika
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Hiroaki Tomioka
- Department of Science Education, Graduate School of Education, Saitama University, Saitama, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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17
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Abstract
Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.
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18
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The Requirement of Inorganic Fe-S Clusters for the Biosynthesis of the Organometallic Molybdenum Cofactor. INORGANICS 2020. [DOI: 10.3390/inorganics8070043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are essential protein cofactors. In enzymes, they are present either in the rhombic [2Fe-2S] or the cubic [4Fe-4S] form, where they are involved in catalysis and electron transfer and in the biosynthesis of metal-containing prosthetic groups like the molybdenum cofactor (Moco). Here, we give an overview of the assembly of Fe-S clusters in bacteria and humans and present their connection to the Moco biosynthesis pathway. In all organisms, Fe-S cluster assembly starts with the abstraction of sulfur from l-cysteine and its transfer to a scaffold protein. After formation, Fe-S clusters are transferred to carrier proteins that insert them into recipient apo-proteins. In eukaryotes like humans and plants, Fe-S cluster assembly takes place both in mitochondria and in the cytosol. Both Moco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. Moco is a tricyclic pterin compound with molybdenum coordinated through its unique dithiolene group. Moco biosynthesis begins in the mitochondria in a Fe-S cluster dependent step involving radical/S-adenosylmethionine (SAM) chemistry. An intermediate is transferred to the cytosol where the dithiolene group is formed, to which molybdenum is finally added. Further connections between Fe-S cluster assembly and Moco biosynthesis are discussed in detail.
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19
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Puglisi R, Boeri Erba E, Pastore A. A Guide to Native Mass Spectrometry to determine complex interactomes of molecular machines. FEBS J 2020; 287:2428-2439. [PMID: 32142206 PMCID: PMC8647915 DOI: 10.1111/febs.15281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/01/2020] [Accepted: 03/04/2020] [Indexed: 01/17/2023]
Abstract
Native mass spectrometry is an emerging technique in biology that gives the possibility to study noncovalently bound complexes with high sensitivity and accuracy. It thus allows the characterization of macromolecular assemblies, assessing their mass and stoichiometries and mapping the interacting surfaces. In this review, we discuss the application of native mass spectrometry to dynamic molecular machines based on multiple weak interactions. In the study of these machines, it is crucial to understand which and under which conditions various complexes form at any time point. We focus on the specific example of the iron-sulfur cluster biogenesis machine because this is an archetype of a dynamic machine that requires very specific and demanding experimental conditions, such as anaerobicity and the need of retaining the fold of marginally folded proteins. We describe the advantages, challenges and current limitations of the technique by providing examples from our own experience and suggesting possible future solutions.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King’s College LondonUK
| | | | - Annalisa Pastore
- UK Dementia Research Institute at the Wohl Institute of King’s College LondonUK
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20
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Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System. mBio 2020; 11:mBio.00488-20. [PMID: 32345643 PMCID: PMC7188994 DOI: 10.1128/mbio.00488-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Apart from its roles in Fe-S cluster assembly, tRNA thiolation, and sulfur-containing cofactor biosynthesis, cysteine desulfurase serves as a sulfur donor in the DNA PT modification, in which a sulfur atom substitutes a nonbridging oxygen in the DNA phosphodiester backbone. The initial sulfur mobilization from l-cysteine is catalyzed by the SspA cysteine desulfurase in the SspABCD-mediated DNA PT modification system. By determining the crystal structure of SspA, the study presents the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor. To overcome the long distance (8.9 Å) between the catalytic Cys314 and the cysteine substrate, a conformational change occurs to bring Cys314 to the vicinity of the substrate, allowing for nucleophilic attack. DNA phosphorothioate (PT) modification, in which the nonbridging oxygen in the sugar-phosphate backbone is substituted by sulfur, is catalyzed by DndABCDE or SspABCD in a double-stranded or single-stranded manner, respectively. In Dnd and Ssp systems, mobilization of sulfur in PT formation starts with the activation of the sulfur atom of cysteine catalyzed by the DndA and SspA cysteine desulfurases, respectively. Despite playing the same biochemical role, SspA cannot be functionally replaced by DndA, indicating its unique physiological properties. In this study, we solved the crystal structure of Vibrio cyclitrophicus SspA in complex with its natural substrate, cysteine, and cofactor, pyridoxal phosphate (PLP), at a resolution of 1.80 Å. Our solved structure revealed the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor, suggesting a common binding mode shared by cysteine desulfurases. In addition, although the distance between the catalytic Cys314 and the substrate cysteine is 8.9 Å, which is too far for direct interaction, our structural modeling and biochemical analysis revealed a conformational change in the active site region toward the cysteine substrate to move them close to each other to facilitate the nucleophilic attack. Finally, the pulldown analysis showed that SspA could form a complex with SspD, an ATP pyrophosphatase, suggesting that SspD might potentially accept the activated sulfur atom directly from SspA, providing further insights into the biochemical pathway of Ssp-mediated PT modification.
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21
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Baussier C, Fakroun S, Aubert C, Dubrac S, Mandin P, Py B, Barras F. Making iron-sulfur cluster: structure, regulation and evolution of the bacterial ISC system. Adv Microb Physiol 2020; 76:1-39. [PMID: 32408945 DOI: 10.1016/bs.ampbs.2020.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron sulfur (Fe-S) clusters rank among the most ancient and conserved prosthetic groups. Fe-S clusters containing proteins are present in most, if not all, organisms. Fe-S clusters containing proteins are involved in a wide range of cellular processes, from gene regulation to central metabolism, via gene expression, RNA modification or bioenergetics. Fe-S clusters are built by biogenesis machineries conserved throughout both prokaryotes and eukaryotes. We focus mostly on bacterial ISC machinery, but not exclusively, as we refer to eukaryotic ISC system when it brings significant complementary information. Besides covering the structural and regulatory aspects of Fe-S biogenesis, this review aims to highlight Fe-S biogenesis facets remaining matters of discussion, such as the role of frataxin, or the link between fatty acid metabolism and Fe-S homeostasis. Last, we discuss recent advances on strategies used by different species to make and use Fe-S clusters in changing redox environmental conditions.
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Affiliation(s)
- Corentin Baussier
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Soufyan Fakroun
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Sarah Dubrac
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
| | - Pierre Mandin
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Frédéric Barras
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
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22
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Lin CW, McCabe JW, Russell DH, Barondeau DP. Molecular Mechanism of ISC Iron-Sulfur Cluster Biogenesis Revealed by High-Resolution Native Mass Spectrometry. J Am Chem Soc 2020; 142:6018-6029. [PMID: 32131593 DOI: 10.1021/jacs.9b11454] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous protein cofactors that are required for many important biological processes including oxidative respiration, nitrogen fixation, and photosynthesis. Biosynthetic pathways assemble Fe-S clusters with different iron-to-sulfur stoichiometries and distribute these clusters to appropriate apoproteins. In the ISC pathway, the pyridoxal 5'-phosphate-dependent cysteine desulfurase enzyme IscS provides sulfur to the scaffold protein IscU, which templates the Fe-S cluster assembly. Despite their functional importance, mechanistic details for cluster synthesis have remained elusive. Recent advances in native mass spectrometry (MS) have allowed proteins to be preserved in native-like structures and support applications in the investigation of protein structure, dynamics, ligand interactions, and the identification of protein-associated intermediates. Here, we prepared samples under anaerobic conditions and then applied native MS to investigate the molecular mechanism for Fe-S cluster synthesis. This approach was validated by the high agreement between native MS and traditional visible circular dichroism spectroscopic assays. Time-dependent native MS experiments revealed potential iron- and sulfur-based intermediates that decay as the [2Fe-2S] cluster signal developed. Additional experiments establish that (i) Zn(II) binding stabilizes IscU and protects the cysteine residues from oxidation, weakens the interactions between IscU and IscS, and inhibits Fe-S cluster biosynthesis; and (ii) Fe(II) ions bind to the IscU active site cysteine residues and another lower affinity binding site and promote the intermolecular sulfur transfer reaction from IscS to IscU. Overall, these results support an iron-first model for Fe-S cluster synthesis and highlight the power of native MS in defining protein-associated intermediates and elucidating mechanistic details of enzymatic processes.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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23
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Lu HM, Li JD, Zhang YD, Lu XL, Xu C, Huang Y, Gribskov M. The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs. Genome Biol Evol 2020; 12:160-173. [PMID: 32108236 PMCID: PMC7144353 DOI: 10.1093/gbe/evaa038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 01/15/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe-S clusters is therefore relevant to many fields. In the complex process of Fe-S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe-S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.
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Affiliation(s)
- Hui-Meng Lu
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Jing-Di Li
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Yu-Dan Zhang
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Xiao-Li Lu
- School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, Shaanxi, PR China
| | - Chang Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, PR China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, PR China
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University
- Department of Computer Science, Purdue University
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24
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Wang J, Guo X, Li H, Qi H, Qian J, Yan S, Shi J, Niu W. Hydrogen Sulfide From Cysteine Desulfurase, Not 3-Mercaptopyruvate Sulfurtransferase, Contributes to Sustaining Cell Growth and Bioenergetics in E. coli Under Anaerobic Conditions. Front Microbiol 2019; 10:2357. [PMID: 31681220 PMCID: PMC6797615 DOI: 10.3389/fmicb.2019.02357] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 09/27/2019] [Indexed: 01/09/2023] Open
Abstract
Endogenous hydrogen sulfide (H2S), which is primarily generated by 3-mercaptopyruvate sulfurtransferase (3-MST) in Escherichia coli (E. coli) under aerobic conditions, renders bacteria highly resistant to oxidative stress. However, the biosynthetic pathway and physiological role of this gas under anaerobic conditions remains largely unknown. In the present study, we demonstrate that cysteine desulfurase (IscS), not 3-MST, is the primary source of endogenous H2S in E. coli under anaerobic conditions. A significant decrease in H2S production under anaerobic conditions was observed in E. coli upon deletion of IscS, but not in 3-MST-deficient bacteria (ΔmstA). Furthermore, the H2S-producing activity of recombinant IscS using L-cysteine as a substrate exhibited an approximately 2.6-fold increase in the presence of dithiothreitol (DTT), indicating that H2S production catalyzed by IscS was greatly increased under reducing conditions. The activity of IscS was regulated under the different redox conditions and the midpoint redox potential was determined to be −329 ± 1.6 mV. Moreover, in E. coli cells H2S production from IscS is regulated under oxidative and reductive stress. A mutant E. coli (ΔiscS) strain lacking a chromosomal copy of the IscS-encoding gene iscS showed significant growth defects and low levels of ATP under both aerobic and anaerobic conditions. The growth defects could be fully restored after addition of 500 μM Na2S (an H2S donor) under anaerobic conditions, but not by the addition of cysteine, sodium sulfite or sodium sulfate. We also showed that the addition of 500 μM Na2S to culture medium stimulates ATP synthesis in the mutant E. coli (ΔiscS) strain in the logarithmic growth phase but suppresses ATP synthesis in wild-type E. coli. Our results reveal a new H2S-producing pathway in E. coli under anaerobic conditions and show that hydrogen sulfide from IscS contributes to sustaining cell growth and bioenergetics under oxygen-deficient conditions.
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Affiliation(s)
- Jun Wang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xin Guo
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Heng Li
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Haizhen Qi
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Jing Qian
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Shasha Yan
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Junling Shi
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Weining Niu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
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25
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Tanaka N, Yuda E, Fujishiro T, Hirabayashi K, Wada K, Takahashi Y. Identification of IscU residues critical for de novo iron-sulfur cluster assembly. Mol Microbiol 2019; 112:1769-1783. [PMID: 31532036 DOI: 10.1111/mmi.14392] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 01/16/2023]
Abstract
IscU is a central component of the ISC machinery and serves as a scaffold for the de novo assembly of iron-sulfur (Fe-S) clusters prior to their delivery to target apo-Fe-S proteins. However, the molecular mechanism is not yet fully understood. In this study, we have conducted mutational analysis of E. coli IscU using the recently developed genetic complementation system of a mutant that can survive without Fe-S clusters. The Fe-S cluster ligands (C37, C63, H105, C106) and the proximal D39 and K103 residues are essential for in vivo function of IscU and could not be substituted with any other amino acids. Furthermore, we found that substitution of Y3, a strictly conserved residue among IscU homologs, abolished in vivo functions. Surprisingly, a second-site suppressor mutation in IscS (A349V) reverted the defect caused by IscU Y3 substitutions. Biochemical analysis revealed that IscU Y3 was crucial for functional interaction with IscS and sulfur transfer between the two proteins. Our findings suggest that the critical role of IscU Y3 is linked to the conformational dynamics of the flexible loop of IscS, which is required for the ingenious sulfur transfer to IscU.
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Affiliation(s)
- Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Eiki Yuda
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kei Hirabayashi
- Department of Medical Sciences, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
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26
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Gervason S, Larkem D, Mansour AB, Botzanowski T, Müller CS, Pecqueur L, Le Pavec G, Delaunay-Moisan A, Brun O, Agramunt J, Grandas A, Fontecave M, Schünemann V, Cianférani S, Sizun C, Tolédano MB, D'Autréaux B. Physiologically relevant reconstitution of iron-sulfur cluster biosynthesis uncovers persulfide-processing functions of ferredoxin-2 and frataxin. Nat Commun 2019; 10:3566. [PMID: 31395877 PMCID: PMC6687725 DOI: 10.1038/s41467-019-11470-9] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/04/2019] [Indexed: 12/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are essential protein cofactors whose biosynthetic defects lead to severe diseases among which is Friedreich's ataxia caused by impaired expression of frataxin (FXN). Fe-S clusters are biosynthesized on the scaffold protein ISCU, with cysteine desulfurase NFS1 providing sulfur as persulfide and ferredoxin FDX2 supplying electrons, in a process stimulated by FXN but not clearly understood. Here, we report the breakdown of this process, made possible by removing a zinc ion in ISCU that hinders iron insertion and promotes non-physiological Fe-S cluster synthesis from free sulfide in vitro. By binding zinc-free ISCU, iron drives persulfide uptake from NFS1 and allows persulfide reduction into sulfide by FDX2, thereby coordinating sulfide production with its availability to generate Fe-S clusters. FXN stimulates the whole process by accelerating persulfide transfer. We propose that this reconstitution recapitulates physiological conditions which provides a model for Fe-S cluster biosynthesis, clarifies the roles of FDX2 and FXN and may help develop Friedreich's ataxia therapies.
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Affiliation(s)
- Sylvain Gervason
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Djabir Larkem
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Amir Ben Mansour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Christina S Müller
- Fachbreich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663, Kaiserslautern, Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR 8229, PSL Research University, 11 place Marcelin Berthelot, 75005, Paris, France
| | - Gwenaelle Le Pavec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Agnès Delaunay-Moisan
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Omar Brun
- Departament de Química Orgànica i IBUB, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1-11, E-08028, Barcelona, Spain
| | - Jordi Agramunt
- Departament de Química Orgànica i IBUB, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1-11, E-08028, Barcelona, Spain
| | - Anna Grandas
- Departament de Química Orgànica i IBUB, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1-11, E-08028, Barcelona, Spain
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR 8229, PSL Research University, 11 place Marcelin Berthelot, 75005, Paris, France
| | - Volker Schünemann
- Fachbreich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663, Kaiserslautern, Germany
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190, Gif-sur-Yvette, France
| | - Michel B Tolédano
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Benoit D'Autréaux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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27
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Zheng C, Guo S, Tennant WG, Pradhan PK, Black KA, Dos Santos PC. The Thioredoxin System Reduces Protein Persulfide Intermediates Formed during the Synthesis of Thio-Cofactors in Bacillus subtilis. Biochemistry 2019; 58:1892-1904. [PMID: 30855939 DOI: 10.1021/acs.biochem.9b00045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biosynthesis of Fe-S clusters and other thio-cofactors requires the participation of redox agents. A shared feature in these pathways is the formation of transient protein persulfides, which are susceptible to reduction by artificial reducing agents commonly used in reactions in vitro. These agents modulate the reactivity and catalytic efficiency of biosynthetic reactions and, in some cases, skew the enzymes' kinetic behavior, bypassing sulfur acceptors known to be critical for the functionality of these pathways in vivo. Here, we provide kinetic evidence for the selective reactivity of the Bacillus subtilis Trx (thioredoxin) system toward protein-bound persulfide intermediates. Our results demonstrate that the redox flux of the Trx system modulates the rate of sulfide production in cysteine desulfurase assays. Likewise, the activity of the Trx system is dependent on the rate of persulfide formation, suggesting the occurrence of coupled reaction schemes between both enzymatic systems in vitro. Inactivation of TrxA (thioredoxin) or TrxR (thioredoxin reductase) impairs the activity of Fe-S enzymes in B. subtilis, indicating the involvement of the Trx system in Fe-S cluster metabolism. Surprisingly, biochemical characterization of TrxA reveals that this enzyme is able to coordinate Fe-S species, resulting in the loss of its reductase activity. The inactivation of TrxA through the coordination of a labile cluster, combined with its proposed role as a physiological reducing agent in sulfur transfer pathways, suggests a model for redox regulation. These findings provide a potential link between redox regulation and Fe-S metabolism.
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Affiliation(s)
- Chenkang Zheng
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Selina Guo
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - William G Tennant
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Pradyumna K Pradhan
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States.,Department of Chemistry and Biochemistry , The University of North Carolina at Greensboro , Greensboro , North Carolina 27412 , United States
| | - Katherine A Black
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States.,Department of Medicine , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Patricia C Dos Santos
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
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28
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Zupok A, Iobbi-Nivol C, Méjean V, Leimkühler S. The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria. Metallomics 2019; 11:1602-1624. [DOI: 10.1039/c9mt00186g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.
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Affiliation(s)
- Arkadiusz Zupok
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Vincent Méjean
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Silke Leimkühler
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
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29
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Castro IH, Pignataro MF, Sewell KE, Espeche LD, Herrera MG, Noguera ME, Dain L, Nadra AD, Aran M, Smal C, Gallo M, Santos J. Frataxin Structure and Function. Subcell Biochem 2019; 93:393-438. [PMID: 31939159 DOI: 10.1007/978-3-030-28151-9_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian frataxin is a small mitochondrial protein involved in iron sulfur cluster assembly. Frataxin deficiency causes the neurodegenerative disease Friedreich's Ataxia. Valuable knowledge has been gained on the structural dynamics of frataxin, metal-ion-protein interactions, as well as on the effect of mutations on protein conformation, stability and internal motions. Additionally, laborious studies concerning the enzymatic reactions involved have allowed for understanding the capability of frataxin to modulate Fe-S cluster assembly function. Remarkably, frataxin biological function depends on its interaction with some proteins to form a supercomplex, among them NFS1 desulfurase and ISCU, the scaffolding protein. By combining multiple experimental tools including high resolution techniques like NMR and X-ray, but also SAXS, crosslinking and mass-spectrometry, it was possible to build a reliable model of the structure of the desulfurase supercomplex NFS1/ACP-ISD11/ISCU/frataxin. In this chapter, we explore these issues showing how the scientific view concerning frataxin structure-function relationships has evolved over the last years.
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Affiliation(s)
- Ignacio Hugo Castro
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - María Florencia Pignataro
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - Karl Ellioth Sewell
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - Lucía Daniela Espeche
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla"-A.N.L.I.S, Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina
| | - María Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Liliana Dain
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla"-A.N.L.I.S, Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina
| | - Alejandro Daniel Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Martín Aran
- Fundación Instituto Leloir E IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Clara Smal
- Fundación Instituto Leloir E IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Mariana Gallo
- IRBM Science Park S.p.A, Via Pontina km 30,600, 00071, Pomezia, RM, Italy
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina.
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina.
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30
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Schwanhold N, Iobbi-Nivol C, Lehmann A, Leimkühler S. Same but different: Comparison of two system-specific molecular chaperones for the maturation of formate dehydrogenases. PLoS One 2018; 13:e0201935. [PMID: 30444874 PMCID: PMC6239281 DOI: 10.1371/journal.pone.0201935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022] Open
Abstract
The maturation of bacterial molybdoenzymes is a complex process leading to the insertion of the bulky bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor into the apo-enzyme. Most molybdoenzymes were shown to contain a specific chaperone for the insertion of the bis-MGD cofactor. Formate dehydrogenases (FDH) together with their molecular chaperone partner seem to display an exception to this specificity rule, since the chaperone FdhD has been proven to be involved in the maturation of all three FDH enzymes present in Escherichia coli. Multiple roles have been suggested for FdhD-like chaperones in the past, including the involvement in a sulfur transfer reaction from the l-cysteine desulfurase IscS to bis-MGD by the action of two cysteine residues present in a conserved CXXC motif of the chaperones. However, in this study we show by phylogenetic analyses that the CXXC motif is not conserved among FdhD-like chaperones. We compared in detail the FdhD-like homologues from Rhodobacter capsulatus and E. coli and show that their roles in the maturation of FDH enzymes from different subgroups can be exchanged. We reveal that bis-MGD-binding is a common characteristic of FdhD-like proteins and that the cofactor is bound with a sulfido-ligand at the molybdenum atom to the chaperone. Generally, we reveal that the cysteine residues in the motif CXXC of the chaperone are not essential for the production of active FDH enzymes.
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Affiliation(s)
- Nadine Schwanhold
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | | | - Angelika Lehmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Potsdam, Germany
- * E-mail:
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31
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LdIscU is a [2Fe-2S] scaffold protein which interacts with LdIscS and its expression is modulated by Fe-S proteins in Leishmania donovani. Int J Biol Macromol 2018; 116:1128-1145. [PMID: 29782976 DOI: 10.1016/j.ijbiomac.2018.05.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 11/20/2022]
Abstract
The pathogenicity of protozoan parasites is frequently attributed to their ability to circumvent the deleterious effects of ROS and Fe-S clusters are among their susceptible targets with paramount importance for parasite survival. The biogenesis of Fe-S clusters is orchestrated by ISC system; the sulfur donor IscS and scaffold protein IscU being its core components. However, among protozoan parasites including Leishmania, no information is available regarding biochemical aspect of IscU, its interaction partners and regulation. Here, we show that Leishmania donovani IscU homolog, LdIscU, readily assembles [2Fe-2S] clusters and, interestingly, follows Michaelis-Menten enzyme kinetics. It is localized in the mitochondria of the parasite and interacts with LdIscS to form a stable complex. Additionally, LdIscU and Fe-S proteins activity is significantly upregulated in resistant isolates and during stationary growth stage indicating an association between them. The differential expression of LdIscU modulated by Fe-S proteins demand suggests its potential role in parasite survival and drug resistance. Thus, our study provides novel insight into the Fe-S scaffold protein of a protozoan parasite.
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32
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Dos Santos PC. B. subtilis as a Model for Studying the Assembly of Fe-S Clusters in Gram-Positive Bacteria. Methods Enzymol 2018; 595:185-212. [PMID: 28882201 DOI: 10.1016/bs.mie.2017.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complexes of iron and sulfur (Fe-S clusters) are widely distributed in nature and participate in essential biochemical reactions. The biological formation of Fe-S clusters involves dedicated pathways responsible for the mobilization of sulfur, the assembly of Fe-S clusters, and the transfer of these clusters to target proteins. Genomic analysis of Bacillus subtilis and other Gram-positive bacteria indicated the presence of only one Fe-S cluster biosynthesis pathway, which is distinct in number of components and organization from previously studied systems. B. subtilis has been used as a model system for the characterization of cysteine desulfurases responsible for sulfur mobilization reactions in the biogenesis of Fe-S clusters and other sulfur-containing cofactors. Cysteine desulfurases catalyze the cleavage of the C-S bond from the amino acid cysteine and subsequent transfer of sulfur to acceptor molecules. These reactions can be monitored by the rate of alanine formation, the first product in the reaction, and sulfide formation, a byproduct of reactions performed under reducing conditions. The assembly of Fe-S clusters on protein scaffolds and the transfer of these clusters to target acceptors are determined through a combination of spectroscopic methods probing the rate of cluster assembly and transfer. This chapter provides a description of reactions promoting the assembly of Fe-S clusters in bacteria as well as methods used to study functions of each biosynthetic component and identify mechanistic differences employed by these enzymes across different pathways.
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33
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Marelja Z, Leimkühler S, Missirlis F. Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism. Front Physiol 2018; 9:50. [PMID: 29491838 PMCID: PMC5817353 DOI: 10.3389/fphys.2018.00050] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which may function as a mitochondrial iron sensor since it is inactivated by iron; (iii) with the Krebs cycle thus disrupted, citrate is exported to the cytosol for fatty acid synthesis, while succinyl-CoA and the iron are used for heme biosynthesis; (iv) as iron is used for heme biosynthesis its concentration in the matrix drops allowing for manganese to reactivate superoxide dismutase and Fe-S cluster biosynthesis to reestablish the Krebs cycle.
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Affiliation(s)
- Zvonimir Marelja
- Imagine Institute, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Fanis Missirlis
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
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Adinolfi S, Puglisi R, Crack JC, Iannuzzi C, Dal Piaz F, Konarev PV, Svergun DI, Martin S, Le Brun NE, Pastore A. The Molecular Bases of the Dual Regulation of Bacterial Iron Sulfur Cluster Biogenesis by CyaY and IscX. Front Mol Biosci 2018; 4:97. [PMID: 29457004 PMCID: PMC5801593 DOI: 10.3389/fmolb.2017.00097] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/22/2017] [Indexed: 12/11/2022] Open
Abstract
IscX (or YfhJ) is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialized and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach based on nuclear magnetic resonance, small angle scattering and biochemical methods, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest the mechanism of the dual regulation of iron sulfur cluster assembly under the control of iron as the effector.
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Affiliation(s)
| | - Rita Puglisi
- The Wohl Institute, King's College London, London, United Kingdom
| | - Jason C Crack
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Clara Iannuzzi
- The Wohl Institute, King's College London, London, United Kingdom.,DBBGP, Università degli Studi della Campania "L. Vanvitelli,", Naples, Italy
| | - Fabrizio Dal Piaz
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana"/DIPMED, Universita' di Salerno, Fisciano, Italy
| | - Petr V Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia.,National Research Centre "Kurchatov Institute, ", Moscow, Russia
| | | | | | - Nick E Le Brun
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Annalisa Pastore
- The Wohl Institute, King's College London, London, United Kingdom.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
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35
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Yokoyama N, Nonaka C, Ohashi Y, Shioda M, Terahata T, Chen W, Sakamoto K, Maruyama C, Saito T, Yuda E, Tanaka N, Fujishiro T, Kuzuyama T, Asai K, Takahashi Y. Distinct roles for U-type proteins in iron-sulfur cluster biosynthesis revealed by genetic analysis of the Bacillus subtilis sufCDSUB operon. Mol Microbiol 2018; 107:688-703. [PMID: 29292548 DOI: 10.1111/mmi.13907] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/24/2017] [Accepted: 12/29/2017] [Indexed: 01/09/2023]
Abstract
The biosynthesis of iron-sulfur (Fe-S) clusters in Bacillus subtilis is mediated by the SUF-like system composed of the sufCDSUB gene products. This system is unique in that it is a chimeric machinery comprising homologues of E. coli SUF components (SufS, SufB, SufC and SufD) and an ISC component (IscU). B. subtilis SufS cysteine desulfurase transfers persulfide sulfur to SufU (the IscU homologue); however, it has remained controversial whether SufU serves as a scaffold for Fe-S cluster assembly, like IscU, or acts as a sulfur shuttle protein, like E. coli SufE. Here we report that reengineering of the isoprenoid biosynthetic pathway in B. subtilis can offset the indispensability of the sufCDSUB operon, allowing the resultant Δsuf mutants to grow without detectable Fe-S proteins. Heterologous bidirectional complementation studies using B. subtilis and E. coli mutants showed that B. subtilis SufSU is interchangeable with E. coli SufSE but not with IscSU. In addition, functional similarity in SufB, SufC and SufD was observed between B. subtilis and E. coli. Our findings thus indicate that B. subtilis SufU is the protein that transfers sulfur from SufS to SufB, and that the SufBCD complex is the site of Fe-S cluster assembly.
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Affiliation(s)
- Nao Yokoyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Chihiro Nonaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yukari Ohashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masaharu Shioda
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takuya Terahata
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Wen Chen
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kotomi Sakamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Chihiro Maruyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takuya Saito
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Eiki Yuda
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kei Asai
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
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Fujishiro T, Terahata T, Kunichika K, Yokoyama N, Maruyama C, Asai K, Takahashi Y. Zinc-Ligand Swapping Mediated Complex Formation and Sulfur Transfer between SufS and SufU for Iron–Sulfur Cluster Biogenesis in Bacillus subtilis. J Am Chem Soc 2017; 139:18464-18467. [DOI: 10.1021/jacs.7b11307] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Takashi Fujishiro
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Takuya Terahata
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kouhei Kunichika
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nao Yokoyama
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Chihiro Maruyama
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kei Asai
- Department
of Bioscience, Graduate School of Agriculture, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuhiro Takahashi
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
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Abstract
Iron-sulfur clusters (Fe/S clusters) are essential cofactors required throughout the clades of biology for performing a myriad of unique functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. Although Fe/S clusters can be synthesized in vitro and transferred to a client protein without enzymatic assistance, biology has evolved intricate mechanisms to assemble and transfer Fe/S clusters within the cellular environment. In eukaryotes, the foundation of all cellular clusters starts within the mitochondria. The focus of this review is to detail the mitochondrial Fe/S biogenesis (ISC) pathway along with the Fe/S cluster transfer steps necessary to mature Fe/S proteins. New advances in our understanding of the mitochondrial Fe/S biogenesis machinery will be highlighted. Additionally, we will address various experimental approaches that have been successful in the identification and characterization of components of the ISC pathway.
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Affiliation(s)
- Andrew Melber
- University of Utah Health Sciences Center, Salt Lake City, Utah, United States
| | - Dennis R Winge
- University of Utah Health Sciences Center, Salt Lake City, Utah, United States.
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38
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Dzul SP, Rocha AG, Rawat S, Kandegedara A, Kusowski A, Pain J, Murari A, Pain D, Dancis A, Stemmler TL. In vitro characterization of a novel Isu homologue from Drosophila melanogaster for de novo FeS-cluster formation. Metallomics 2017; 9:48-60. [PMID: 27738674 DOI: 10.1039/c6mt00163g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
FeS-clusters are utilized by numerous proteins within several biological pathways that are essential for life. In eukaryotes, the primary FeS-cluster production pathway is the mitochondrial iron-sulfur cluster (ISC) pathway. In Saccharomyces cerevisiae, de novo FeS-cluster formation is accomplished through coordinated assembly with the substrates iron and sulfur by the scaffold assembly protein "Isu1". Sulfur for cluster assembly is provided by cysteine desulfurase "Nfs1", a protein that works in union with its accessory protein "Isd11". Frataxin "Yfh1" helps direct cluster assembly by serving as a modulator of Nfs1 activity, by assisting in the delivery of sulfur and Fe(ii) to Isu1, or more likely through a combination of these and other possible roles. In vitro studies on the yeast ISC machinery have been limited, however, due to the inherent instability of recombinant Isu1. Isu1 is a molecule prone to degradation and aggregation. To circumvent Isu1 instability, we have replaced yeast Isu1 with the fly ortholog to stabilize our in vitro ISC assembly system and assist us in elucidating molecular details of the yeast ISC pathway. Our laboratory previously observed that recombinant frataxin from Drosophila melanogaster has remarkable stability compared to the yeast ortholog. Here we provide the first characterization of D. melanogaster Isu1 (fIscU) and demonstrate its ability to function within the yeast ISC machinery both in vivo and in vitro. Recombinant fIscU has physical properties similar to that of yeast Isu1. It functions as a stable dimer with similar Fe(ii) affinity and ability to form two 2Fe-2S clusters as the yeast dimer. The fIscU and yeast ISC proteins are compatible in vitro; addition of Yfh1 to Nfs1-Isd11 increases the rate of FeS-cluster formation on fIscU to a similar extent observed with Isu1. Finally, fIscU expressed in mitochondria of a yeast strain lacking Isu1 (and its paralog Isu2) is able to completely reverse the deletion phenotypes. These results demonstrate fIscU can functionally replace yeast Isu1 and it can serve as a powerful tool for exploring molecular details within the yeast ISC pathway.
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Affiliation(s)
- Stephen P Dzul
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - Agostinho G Rocha
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Swati Rawat
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - Ashoka Kandegedara
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - April Kusowski
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - Jayashree Pain
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Anjaneyulu Murari
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Debkumar Pain
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Timothy L Stemmler
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
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40
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Bühning M, Friemel M, Leimkühler S. Functional Complementation Studies Reveal Different Interaction Partners of Escherichia coli IscS and Human NFS1. Biochemistry 2017; 56:4592-4605. [PMID: 28766335 DOI: 10.1021/acs.biochem.7b00627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The trafficking and delivery of sulfur to cofactors and nucleosides is a highly regulated and conserved process among all organisms. All sulfur transfer pathways generally have an l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of sulfur-containing biomolecules like iron-sulfur (Fe-S) clusters, thiamine, biotin, lipoic acid, the molybdenum cofactor (Moco), and thiolated nucleosides in tRNA. The human l-cysteine desulfurase NFS1 and the Escherichia coli homologue IscS share a level of amino acid sequence identity of ∼60%. While E. coli IscS has a versatile role in the cell and was shown to have numerous interaction partners, NFS1 is mainly localized in mitochondria with a crucial role in the biosynthesis of Fe-S clusters. Additionally, NFS1 is also located in smaller amounts in the cytosol with a role in Moco biosynthesis and mcm5s2U34 thio modifications of nucleosides in tRNA. NFS1 and IscS were conclusively shown to have different interaction partners in their respective organisms. Here, we used functional complementation studies of an E. coli iscS deletion strain with human NFS1 to dissect their conserved roles in the transfer of sulfur to a specific target protein. Our results show that human NFS1 and E. coli IscS share conserved binding sites for proteins involved in Fe-S cluster assembly like IscU, but not with proteins for tRNA thio modifications or Moco biosynthesis. In addition, we show that human NFS1 was almost fully able to complement the role of IscS in Moco biosynthesis when its specific interaction partner protein MOCS3 from humans was also present.
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Affiliation(s)
- Martin Bühning
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
| | - Martin Friemel
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
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41
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Abstract
The biogenesis of iron-sulfur (Fe/S) proteins in eukaryotes is a multistage, multicompartment process that is essential for a broad range of cellular functions, including genome maintenance, protein translation, energy conversion, and the antiviral response. Genetic and cell biological studies over almost 2 decades have revealed some 30 proteins involved in the synthesis of cellular [2Fe-2S] and [4Fe-4S] clusters and their incorporation into numerous apoproteins. Mechanistic aspects of Fe/S protein biogenesis continue to be elucidated by biochemical and ultrastructural investigations. Here, we review recent developments in the pursuit of constructing a comprehensive model of Fe/S protein assembly in the mitochondrion.
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Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
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42
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Kumaresan V, Nizam F, Ravichandran G, Viswanathan K, Palanisamy R, Bhatt P, Arasu MV, Al-Dhabi NA, Mala K, Arockiaraj J. Transcriptome changes of blue-green algae, Arthrospira sp. in response to sulfate stress. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.01.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Friemel M, Marelja Z, Li K, Leimkühler S. The N-Terminus of Iron-Sulfur Cluster Assembly Factor ISD11 Is Crucial for Subcellular Targeting and Interaction with l-Cysteine Desulfurase NFS1. Biochemistry 2017; 56:1797-1808. [PMID: 28271877 DOI: 10.1021/acs.biochem.6b01239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Assembly of iron-sulfur (FeS) clusters is an important process in living cells. The initial sulfur mobilization step for FeS cluster biosynthesis is catalyzed by l-cysteine desulfurase NFS1, a reaction that is localized in mitochondria in humans. In humans, the function of NFS1 depends on the ISD11 protein, which is required to stabilize its structure. The NFS1/ISD11 complex further interacts with scaffold protein ISCU and regulator protein frataxin, thereby forming a quaternary complex for FeS cluster formation. It has been suggested that the role of ISD11 is not restricted to its role in stabilizing the structure of NFS1, because studies of single-amino acid variants of ISD11 additionally demonstrated its importance for the correct assembly of the quaternary complex. In this study, we are focusing on the N-terminal region of ISD11 to determine the role of N-terminal amino acids in the formation of the complex with NFS1 and to reveal the mitochondrial targeting sequence for subcellular localization. Our in vitro studies with the purified proteins and in vivo studies in a cellular system show that the first 10 N-terminal amino acids of ISD11 are indispensable for the activity of NFS1 and especially the conserved "LYR" motif is essential for the role of ISD11 in forming a stable and active complex with NFS1.
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Affiliation(s)
- Martin Friemel
- Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam , Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Zvonimir Marelja
- Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité , 75015 Paris, France
| | - Kuanyu Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University , Nanjing, China
| | - Silke Leimkühler
- Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam , Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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44
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Leimkühler S, Bühning M, Beilschmidt L. Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes. Biomolecules 2017; 7:biom7010005. [PMID: 28098827 PMCID: PMC5372717 DOI: 10.3390/biom7010005] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 11/18/2022] Open
Abstract
Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm5s2U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT). Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco) and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes.
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Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| | - Martin Bühning
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| | - Lena Beilschmidt
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
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45
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Vranish JN, Das D, Barondeau DP. Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe-S Cluster Biosynthetic Pathways. ACS Chem Biol 2016; 11:3114-3121. [PMID: 27653419 DOI: 10.1021/acschembio.6b00632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Iron-sulfur (Fe-S) clusters are protein cofactors that are required for many essential cellular functions. Fe-S clusters are synthesized and inserted into target proteins by an elaborate biosynthetic process. The insensitivity of most Fe-S assembly and transfer assays requires high concentrations for components and places major limits on reaction complexity. Recently, fluorophore labels were shown to be effective at reporting cluster content for Fe-S proteins. Here, the incorporation of this labeling approach allowed the design and interrogation of complex Fe-S cluster biosynthetic reactions that mimic in vivo conditions. A bacterial Fe-S assembly complex, composed of the cysteine desulfurase IscS and scaffold protein IscU, was used to generate [2Fe-2S] clusters for transfer to mixtures of putative intermediate carrier and acceptor proteins. The focus of this study was to test whether the monothiol glutaredoxin, Grx4, functions as an obligate [2Fe-2S] carrier protein in the Fe-S cluster distribution network. Interestingly, [2Fe-2S] clusters generated by the IscS-IscU complex transferred to Grx4 at rates comparable to previous assays using uncomplexed IscU as a cluster source in chaperone-assisted transfer reactions. Further, we provide evidence that [2Fe-2S]-Grx4 delivers clusters to multiple classes of Fe-S targets via direct ligand exchange in a process that is both dynamic and reversible. Global fits of cluster transfer kinetics support a model in which Grx4 outcompetes terminal target proteins for IscU-bound [2Fe-2S] clusters and functions as an intermediate cluster carrier. Overall, these studies demonstrate the power of chemically conjugated fluorophore reporters for unraveling mechanistic details of biological metal cofactor assembly and distribution networks.
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Affiliation(s)
- James N. Vranish
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States
| | - Deepika Das
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - David P. Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
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46
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Puglisi R, Yan R, Adinolfi S, Pastore A. A New Tessera into the Interactome of the isc Operon: A Novel Interaction between HscB and IscS. Front Mol Biosci 2016; 3:48. [PMID: 27730125 PMCID: PMC5037179 DOI: 10.3389/fmolb.2016.00048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 08/22/2016] [Indexed: 12/05/2022] Open
Abstract
Iron sulfur clusters are essential universal prosthetic groups which can be formed inorganically but, in biology, are bound to proteins and produced enzymatically. Most of the components of the machine that produces the clusters are conserved throughout evolution. In bacteria, they are encoded in the isc operon. Previous reports provide information on the role of specific components but a clear picture of how the whole machine works is still missing. We have carried out a study of the effects of the co-chaperone HscB from the model system E. coli. We document a previously undetected weak interaction between the chaperone HscB and the desulfurase IscS, one of the two main players of the machine. The binding site involves a region of HscB in the longer stem of the approximately L-shaped molecule, whereas the interacting surface of IscS overlaps with the surface previously involved in binding other proteins, such as ferredoxin and frataxin. Our findings provide an entirely new perspective to our comprehension of the role of HscB and propose this protein as a component of the IscS complex.
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Affiliation(s)
- Rita Puglisi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Robert Yan
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Salvatore Adinolfi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College LondonLondon, UK; Molecular Medicine Department, University of PaviaPavia, Italy
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47
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Yan R, Friemel M, Aloisi C, Huynen M, Taylor IA, Leimkühler S, Pastore A. The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS. PLoS One 2016; 11:e0157895. [PMID: 27427956 PMCID: PMC4948766 DOI: 10.1371/journal.pone.0157895] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022] Open
Abstract
The eukaryotic protein Isd11 is a chaperone that binds and stabilizes the central component of the essential metabolic pathway responsible for formation of iron-sulfur clusters in mitochondria, the desulfurase Nfs1. Little is known about the exact role of Isd11. Here, we show that human Isd11 (ISD11) is a helical protein which exists in solution as an equilibrium between monomer, dimeric and tetrameric species when in the absence of human Nfs1 (NFS1). We also show that, surprisingly, recombinant ISD11 expressed in E. coli co-purifies with the bacterial orthologue of NFS1, IscS. Binding is weak but specific suggesting that, despite the absence of Isd11 sequences in bacteria, there is enough conservation between the two desulfurases to retain a similar mode of interaction. This knowledge may inform us on the conservation of the mode of binding of Isd11 to the desulfurase. We used evolutionary evidence to suggest Isd11 residues involved in the interaction.
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Affiliation(s)
- Robert Yan
- Maurice Wohl Institute, King’s College London, 5 Cutcombe Rd, SE5, London, United Kingdom
| | - Martin Friemel
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Claudia Aloisi
- Maurice Wohl Institute, King’s College London, 5 Cutcombe Rd, SE5, London, United Kingdom
| | - Martijn Huynen
- CMBI 260, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ian A. Taylor
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, NW7 1AA, United Kingdom
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Annalisa Pastore
- Maurice Wohl Institute, King’s College London, 5 Cutcombe Rd, SE5, London, United Kingdom
- * E-mail:
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48
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Fernández FJ, Ardá A, López-Estepa M, Aranda J, Peña-Soler E, Garces F, Round A, Campos-Olivas R, Bruix M, Coll M, Tuñón I, Jiménez-Barbero J, Vega MC. Mechanism of Sulfur Transfer Across Protein–Protein Interfaces: The Cysteine Desulfurase Model System. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Francisco J. Fernández
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Ana Ardá
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
| | - Miguel López-Estepa
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Juan Aranda
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esther Peña-Soler
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La
Jolla, 92037 California, United States
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for
Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | | | - Marta Bruix
- Instituto de Química Física Rocasolano (IQFR-CSIC), 28006 Madrid, Spain
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), 08028 Barcelona, Spain
| | - Iñaki Tuñón
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Jesús Jiménez-Barbero
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - M. Cristina Vega
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
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49
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Barupala DP, Dzul SP, Riggs-Gelasco PJ, Stemmler TL. Synthesis, delivery and regulation of eukaryotic heme and Fe-S cluster cofactors. Arch Biochem Biophys 2016; 592:60-75. [PMID: 26785297 PMCID: PMC4784227 DOI: 10.1016/j.abb.2016.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 11/25/2022]
Abstract
In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways.
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Affiliation(s)
- Dulmini P Barupala
- Departments of Biochemistry and Molecular Biology, and Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Stephen P Dzul
- Departments of Biochemistry and Molecular Biology, and Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA
| | | | - Timothy L Stemmler
- Departments of Biochemistry and Molecular Biology, and Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA.
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50
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Prischi F, Pastore A. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:351-68. [PMID: 27165336 DOI: 10.1007/978-3-319-27216-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.
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Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King's College London, Denmark Hill Campus, London, UK.
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