1
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Dussouchaud M, Barras F, de Choudens SO. Fe-S biogenesis by SMS and SUF pathways: A focus on the assembly step. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119772. [PMID: 38838856 DOI: 10.1016/j.bbamcr.2024.119772] [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: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
FeS clusters are prosthetic groups present in all organisms. Proteins with FeS centers are involved in most cellular processes. ISC and SUF are machineries necessary for the formation and insertion of FeS in proteins. Recently, a phylogenetic analysis on more than 10,000 genomes of prokaryotes have uncovered two new systems, MIS and SMS, which were proposed to be ancestral to ISC and SUF. SMS is composed of SmsBC, two homologs of SufBC(D), the scaffolding complex of SUF. In this review, we will specifically focus on the current knowledge of the SUF system and on the new perspectives given by the recent discovery of its ancestor, the SMS system.
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Affiliation(s)
- Macha Dussouchaud
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Department of Microbiology, Unit Stress Adaptation and Metabolism in enterobacteria, Paris, France
| | - Frédéric Barras
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Department of Microbiology, Unit Stress Adaptation and Metabolism in enterobacteria, Paris, France
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2
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Pavlova ON, Tupikin AE, Chernitsyna SM, Bukin YS, Lomakina AV, Pogodaeva TV, Nikonova AA, Bukin SV, Zemskaya TI, Kabilov MR. Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal. MICROBIAL ECOLOGY 2023; 86:1604-1619. [PMID: 36717392 DOI: 10.1007/s00248-023-02182-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151T), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.
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Affiliation(s)
- O N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
| | - A E Tupikin
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - S M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Y S Bukin
- Laboratory of Genosystematics, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A V Lomakina
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A A Nikonova
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - S V Bukin
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - M R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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3
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Selles B, Moseler A, Caubrière D, Sun SK, Ziesel M, Dhalleine T, Hériché M, Wirtz M, Rouhier N, Couturier J. The cytosolic Arabidopsis thaliana cysteine desulfurase ABA3 delivers sulfur to the sulfurtransferase STR18. J Biol Chem 2022; 298:101749. [PMID: 35189141 PMCID: PMC8931425 DOI: 10.1016/j.jbc.2022.101749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of many sulfur-containing molecules depends on cysteine as a sulfur source. Both the cysteine desulfurase (CD) and rhodanese (Rhd) domain–containing protein families participate in the trafficking of sulfur for various metabolic pathways in bacteria and human, but their connection is not yet described in plants. The existence of natural chimeric proteins containing both CD and Rhd domains in specific bacterial genera, however, suggests a general interaction between these proteins. We report here the biochemical relationships between two cytosolic proteins from Arabidopsis thaliana, a Rhd domain–containing protein, the sulfurtransferase 18 (STR18), and a CD isoform referred to as ABA3, and compare these biochemical features to those of a natural CD–Rhd fusion protein from the bacterium Pseudorhodoferax sp. We observed that the bacterial enzyme is bifunctional exhibiting both CD and STR activities using l-cysteine and thiosulfate as sulfur donors but preferentially using l-cysteine to catalyze transpersulfidation reactions. In vitro activity assays and mass spectrometry analyses revealed that STR18 stimulates the CD activity of ABA3 by reducing the intermediate persulfide on its catalytic cysteine, thereby accelerating the overall transfer reaction. We also show that both proteins interact in planta and form an efficient sulfur relay system, whereby STR18 catalyzes transpersulfidation reactions from ABA3 to the model acceptor protein roGFP2. In conclusion, the ABA3–STR18 couple likely represents an uncharacterized pathway of sulfur trafficking in the cytosol of plant cells, independent of ABA3 function in molybdenum cofactor maturation.
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Affiliation(s)
| | - Anna Moseler
- Université de Lorraine, INRAE, IAM, Nancy, France
| | | | - Sheng-Kai Sun
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | | | | | | | - Markus Wirtz
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | | | - Jérémy Couturier
- Université de Lorraine, INRAE, IAM, Nancy, France; Institut Universitaire de France, France.
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4
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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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5
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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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6
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Blahut M, Sanchez E, Fisher CE, Outten FW. Fe-S cluster biogenesis by the bacterial Suf pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118829. [PMID: 32822728 DOI: 10.1016/j.bbamcr.2020.118829] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023]
Abstract
Biogenesis of iron-sulfur (FeS) clusters in an essential process in living organisms due to the critical role of FeS cluster proteins in myriad cell functions. During biogenesis of FeS clusters, multi-protein complexes are used to drive the mobilization and protection of reactive sulfur and iron intermediates, regulate assembly of various FeS clusters on an ATPase-dependent, multi-protein scaffold, and target nascent clusters to their downstream protein targets. The evolutionarily ancient sulfur formation (Suf) pathway for FeS cluster assembly is found in bacteria and archaea. In Escherichia coli, the Suf pathway functions as an emergency pathway under conditions of iron limitation or oxidative stress. In other pathogenic bacteria, such as Mycobacterium tuberculosis and Enterococcus faecalis, the Suf pathway is the sole source for FeS clusters and therefore is a potential target for the development of novel antibacterial compounds. Here we summarize the considerable progress that has been made in characterizing the first step of mobilization and protection of reactive sulfur carried out by the SufS-SufE or SufS-SufU complex, FeS cluster assembly on SufBC2D scaffold complexes, and the downstream trafficking of nascent FeS clusters to A-type carrier (ATC) proteins. Cell Biology of Metals III edited by Roland Lill and Mick Petris.
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Affiliation(s)
- Matthew Blahut
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Enis Sanchez
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Claire E Fisher
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - F Wayne Outten
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.
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7
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Blahut M, Wise CE, Bruno MR, Dong G, Makris TM, Frantom PA, Dunkle JA, Outten FW. Direct observation of intermediates in the SufS cysteine desulfurase reaction reveals functional roles of conserved active-site residues. J Biol Chem 2019; 294:12444-12458. [PMID: 31248989 DOI: 10.1074/jbc.ra119.009471] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/16/2019] [Indexed: 12/25/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are necessary for the proper functioning of numerous metalloproteins. Fe-S cluster (Isc) and sulfur utilization factor (Suf) pathways are the key biosynthetic routes responsible for generating these Fe-S cluster prosthetic groups in Escherichia coli Although Isc dominates under normal conditions, Suf takes over during periods of iron depletion and oxidative stress. Sulfur acquisition via these systems relies on the ability to remove sulfur from free cysteine using a cysteine desulfurase mechanism. In the Suf pathway, the dimeric SufS protein uses the cofactor pyridoxal 5'-phosphate (PLP) to abstract sulfur from free cysteine, resulting in the production of alanine and persulfide. Despite much progress, the stepwise mechanism by which this PLP-dependent enzyme operates remains unclear. Here, using rapid-mixing kinetics in conjunction with X-ray crystallography, we analyzed the pre-steady-state kinetics of this process while assigning early intermediates of the mechanism. We employed H123A and C364A SufS variants to trap Cys-aldimine and Cys-ketimine intermediates of the cysteine desulfurase reaction, enabling direct observations of these intermediates and associated conformational changes of the SufS active site. Of note, we propose that Cys-364 is essential for positioning the Cys-aldimine for Cα deprotonation, His-123 acts to protonate the Ala-enamine intermediate, and Arg-56 facilitates catalysis by hydrogen bonding with the sulfhydryl of Cys-aldimine. Our results, along with previous SufS structural findings, suggest a detailed model of the SufS-catalyzed reaction from Cys binding to C-S bond cleavage and indicate that Arg-56, His-123, and Cys-364 are critical SufS residues in this C-S bond cleavage pathway.
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Affiliation(s)
- Matthew Blahut
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Courtney E Wise
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Michael R Bruno
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487
| | - Guangchao Dong
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Patrick A Frantom
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487
| | - Jack A Dunkle
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487.
| | - F Wayne Outten
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208.
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8
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Vacek V, Novák LVF, Treitli SC, Táborský P, Cepicka I, Kolísko M, Keeling PJ, Hampl V. Fe-S Cluster Assembly in Oxymonads and Related Protists. Mol Biol Evol 2019; 35:2712-2718. [PMID: 30184127 PMCID: PMC6231488 DOI: 10.1093/molbev/msy168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The oxymonad Monocercomonoides exilis was recently reported to be the first eukaryote that has completely lost the mitochondrial compartment. It was proposed that an important prerequisite for such a radical evolutionary step was the acquisition of the SUF Fe–S cluster assembly pathway from prokaryotes, making the mitochondrial ISC pathway dispensable. We have investigated genomic and transcriptomic data from six oxymonad species and their relatives, composing the group Preaxostyla (Metamonada, Excavata), for the presence and absence of enzymes involved in Fe–S cluster biosynthesis. None possesses enzymes of mitochondrial ISC pathway and all apparently possess the SUF pathway, composed of SufB, C, D, S, and U proteins, altogether suggesting that the transition from ISC to SUF preceded their last common ancestor. Interestingly, we observed that SufDSU were fused in all three oxymonad genomes, and in the genome of Paratrimastix pyriformis. The donor of the SUF genes is not clear from phylogenetic analyses, but the enzyme composition of the pathway and the presence of SufDSU fusion suggests Firmicutes, Thermotogae, Spirochaetes, Proteobacteria, or Chloroflexi as donors. The inventory of the downstream CIA pathway enzymes is consistent with that of closely related species that retain ISC, indicating that the switch from ISC to SUF did not markedly affect the downstream process of maturation of cytosolic and nuclear Fe–S proteins.
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Affiliation(s)
- Vojtech Vacek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lukáš V F Novák
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Cepicka
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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9
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Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nat Commun 2019; 10:10. [PMID: 30602777 PMCID: PMC6315030 DOI: 10.1038/s41467-018-07709-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/15/2018] [Indexed: 01/26/2023] Open
Abstract
The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release. Genetic variants might exert their functional effects via influencing molecular interaction. Here, the authors present a resource featuring almost 28,000 annotations describing the effect of small sequence changes on physical protein interactions, curated by IMEx Consortium curators.
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10
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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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11
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Pérard J, Ollagnier de Choudens S. Iron-sulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding. J Biol Inorg Chem 2017; 23:581-596. [PMID: 29280002 PMCID: PMC6006206 DOI: 10.1007/s00775-017-1527-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/11/2017] [Indexed: 11/30/2022]
Abstract
Iron–sulfur clusters (Fe–S) are amongst the most ancient and versatile inorganic cofactors in nature which are used by proteins for fundamental biological processes. Multiprotein machineries (NIF, ISC, SUF) exist for Fe–S cluster biogenesis which are mainly conserved from bacteria to human. SUF system (sufABCDSE operon) plays a general role in many bacteria under conditions of iron limitation or oxidative stress. In this mini-review, we will summarize the current understanding of the molecular mechanism of Fe–S biogenesis by SUF. The advances in our understanding of the molecular aspects of SUF originate from biochemical, biophysical and recent structural studies. Combined with recent in vivo experiments, the understanding of the Fe–S biogenesis mechanism considerably moved forward.
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Affiliation(s)
- J Pérard
- Laboratoire de Chimie et Biologie des Métaux, Biocat, Université Grenoble Alpes, Grenoble, France.,Laboratoire de Chimie et Biologie des Métaux, CNRS, BioCat, UMR 5249, Grenoble, France.,CEA-Grenoble, DRF/BIG/CBM, Grenoble, France
| | - Sandrine Ollagnier de Choudens
- Laboratoire de Chimie et Biologie des Métaux, Biocat, Université Grenoble Alpes, Grenoble, France. .,Laboratoire de Chimie et Biologie des Métaux, CNRS, BioCat, UMR 5249, Grenoble, France. .,CEA-Grenoble, DRF/BIG/CBM, Grenoble, France.
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12
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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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13
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Blauenburg B, Mielcarek A, Altegoer F, Fage CD, Linne U, Bange G, Marahiel MA. Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU. PLoS One 2016; 11:e0158749. [PMID: 27382962 PMCID: PMC4934914 DOI: 10.1371/journal.pone.0158749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/21/2016] [Indexed: 12/31/2022] Open
Abstract
The biosynthesis of iron sulfur (Fe-S) clusters in Bacillus subtilis is mediated by a SUF-type gene cluster, consisting of the cysteine desulfurase SufS, the scaffold protein SufU, and the putative chaperone complex SufB/SufC/SufD. Here, we present the high-resolution crystal structure of the SufS homodimer in its product-bound state (i.e., in complex with pyrodoxal-5'-phosphate, alanine, Cys361-persulfide). By performing hydrogen/deuterium exchange (H/DX) experiments, we characterized the interaction of SufS with SufU and demonstrate that SufU induces an opening of the active site pocket of SufS. Recent data indicate that frataxin could be involved in Fe-S cluster biosynthesis by facilitating iron incorporation. H/DX experiments show that frataxin indeed interacts with the SufS/SufU complex at the active site. Our findings deepen the current understanding of Fe-S cluster biosynthesis, a complex yet essential process, in the model organism B. subtilis.
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Affiliation(s)
- Bastian Blauenburg
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Andreas Mielcarek
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Florian Altegoer
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Christopher D. Fage
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
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14
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Abstract
Twin-arginine protein translocation systems (Tat) translocate fully folded and co-factor-containing proteins across biological membranes. In this review, we focus on the Tat pathway of Gram-positive bacteria. The minimal Tat pathway is composed of two components, namely a TatA and TatC pair, which are often complemented with additional TatA-like proteins. We provide overviews of our current understanding of Tat pathway composition and mechanistic aspects related to Tat-dependent cargo protein translocation. This includes Tat pathway flexibility, requirements for the correct folding and incorporation of co-factors in cargo proteins and the functions of known cargo proteins. Tat pathways of several Gram-positive bacteria are discussed in detail, with emphasis on the Tat pathway of Bacillus subtilis. We discuss both shared and unique features of the different Gram-positive bacterial Tat pathways. Lastly, we highlight topics for future research on Tat, including the development of this protein transport pathway for the biotechnological secretion of high-value proteins and its potential applicability as an antimicrobial drug target in pathogens.
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Affiliation(s)
- Vivianne J Goosens
- MRC Centre for Molecular Bacteriology and Infection, Section of Microbiology, Imperial College London, London, SW7 2AZ, UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700, RB, Groningen, The Netherlands.
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15
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Outten FW. Recent advances in the Suf Fe-S cluster biogenesis pathway: Beyond the Proteobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1464-9. [PMID: 25447545 DOI: 10.1016/j.bbamcr.2014.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/21/2023]
Abstract
Fe-S clusters play critical roles in cellular function throughout all three kingdoms of life. Consequently, Fe-S cluster biogenesis systems are present in most organisms. The Suf (sulfur formation) system is the most ancient of the three characterized Fe-S cluster biogenesis pathways, which also include the Isc and Nif systems. Much of the first work on the Suf system took place in Gram-negative Proteobacteria used as model organisms. These early studies led to a wealth of biochemical, genetic, and physiological information on Suf function. From those studies we have learned that SufB functions as an Fe-S scaffold in conjunction with SufC (and in some cases SufD). SufS and SufE together mobilize sulfur for cluster assembly and SufA traffics the complete Fe-S cluster from SufB to target apo-proteins. However, recent progress on the Suf system in other organisms has opened up new avenues of research and new hypotheses about Suf function. This review focuses primarily on the most recent discoveries about the Suf pathway and where those new models may lead the field. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- F Wayne Outten
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC 29208, USA.
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16
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Boyd ES, Thomas KM, Dai Y, Boyd JM, Outten FW. Interplay between oxygen and Fe-S cluster biogenesis: insights from the Suf pathway. Biochemistry 2014; 53:5834-47. [PMID: 25153801 PMCID: PMC4172210 DOI: 10.1021/bi500488r] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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Iron–sulfur (Fe–S)
cluster metalloproteins conduct
essential functions in nearly all contemporary forms of life. The
nearly ubiquitous presence of Fe–S clusters and the fundamental
requirement for Fe–S clusters in both aerobic and anaerobic
Archaea, Bacteria, and Eukarya suggest that these clusters were likely
integrated into central metabolic pathways early in the evolution
of life prior to the widespread oxidation of Earth’s atmosphere.
Intriguingly, Fe–S cluster-dependent metabolism is sensitive
to disruption by oxygen because of the decreased bioavailability of
ferric iron as well as direct oxidation of sulfur trafficking intermediates
and Fe–S clusters by reactive oxygen species. This fact, coupled
with the ubiquity of Fe–S clusters in aerobic organisms, suggests
that organisms evolved with mechanisms that facilitate the biogenesis
and use of these essential cofactors in the presence of oxygen, which
gradually began to accumulate around 2.5 billion years ago as oxygenic
photosynthesis proliferated and reduced minerals that buffered against
oxidation were depleted. This review highlights the most ancient of
the Fe–S cluster biogenesis pathways, the Suf system, which
likely was present in early anaerobic forms of life. Herein, we use
the evolution of the Suf pathway to assess the relationships between
the biochemical functions and physiological roles of Suf proteins,
with an emphasis on the selective pressure of oxygen toxicity. Our
analysis suggests that diversification into oxygen-containing environments
disrupted iron and sulfur metabolism and was a main driving force
in the acquisition of accessory Suf proteins (such as SufD, SufE,
and SufS) by the core SufB–SufC scaffold complex. This analysis
provides a new framework for the study of Fe–S cluster biogenesis
pathways and Fe–S cluster-containing metalloenzymes and their
complicated patterns of divergence in response to oxygen.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Immunology, Montana State University , 109 Lewis Hall, Bozeman, Montana 59717, United States
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17
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The cysteine desulfurase IscS of Mycobacterium tuberculosis is involved in iron-sulfur cluster biogenesis and oxidative stress defence. Biochem J 2014; 459:467-78. [PMID: 24548275 DOI: 10.1042/bj20130732] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The complex multiprotein systems for the assembly of protein-bound iron-sulfur (Fe-S) clusters are well defined in Gram-negative model organisms. However, little is known about Fe-S cluster biogenesis in other bacterial species. The ISC (iron-sulfur cluster) operon of Mycobacterium tuberculosis lacks several genes known to be essential for the function of this system in other organisms. However, the cysteine desulfurase IscSMtb (Rv number Rv3025c; Mtb denotes M. tuberculosis) is conserved in this important pathogen. The present study demonstrates that deleting iscSMtb renders the cells microaerophilic and hypersensitive to oxidative stress. Moreover, the ∆iscSMtb mutant shows impaired Fe-S cluster-dependent enzyme activity, clearly indicating that IscSMtb is associated with Fe-S cluster assembly. An extensive interaction network of IscSMtb with Fe-S proteins was identified, suggesting a novel mechanism of sulfur transfer by direct interaction with apoproteins. Interestingly, the highly homologous IscS of Escherichia coli failed to complement the ∆iscSMtb mutant and showed a less diverse protein-interaction profile. To identify a structural basis for these observations we determined the crystal structure of IscSMtb, which mirrors adaptations made in response to an ISC operon devoid of IscU-like Fe-S cluster scaffold proteins. We conclude that in M. tuberculosis IscS has been redesigned during evolution to compensate for the deletion of large parts of the ISC operon.
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18
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Grosjean H, Breton M, Sirand-Pugnet P, Tardy F, Thiaucourt F, Citti C, Barré A, Yoshizawa S, Fourmy D, de Crécy-Lagard V, Blanchard A. Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PLoS Genet 2014; 10:e1004363. [PMID: 24809820 PMCID: PMC4014445 DOI: 10.1371/journal.pgen.1004363] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 03/24/2014] [Indexed: 11/18/2022] Open
Abstract
Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction. With genomes under 1 Mbp in size, most Mollicutes species retain the capacity to replicate and grow autonomously. The major goal of this work was to identify the minimal set of proteins that can sustain ribosome biogenesis and translation of the genetic code in these bacteria. Using the experimentally validated genes from the model bacteria Escherichia coli and Bacillus subtilis as input, genes encoding proteins of the core translation machinery were predicted in 39 distinct Mollicutes species, 33 of which are culturable. The set of 260 input genes encodes proteins involved in ribosome biogenesis, tRNA maturation and aminoacylation, as well as proteins cofactors required for mRNA translation and RNA decay. A core set of 104 of these proteins is found in all species analyzed. Genes encoding proteins involved in post-translational modifications of ribosomal proteins and translation cofactors, post-transcriptional modifications of t+rRNA, in ribosome assembly and RNA degradation are the most frequently lost. As expected, genes coding for aminoacyl-tRNA synthetases, ribosomal proteins and initiation, elongation and termination factors are the most persistent (i.e. conserved in a majority of genomes). Enzymes introducing nucleotides modifications in the anticodon loop of tRNA, in helix 44 of 16S rRNA and in helices 69 and 80 of 23S rRNA, all essential for decoding and facilitating peptidyl transfer, are maintained in all species. Reconstruction of genome evolution in Mollicutes revealed that, beside many gene losses, occasional gains by horizontal gene transfer also occurred. This analysis not only showed that slightly different solutions for preserving a functional, albeit minimal, protein synthetizing machinery have emerged in these successive rounds of reductive evolution but also has broad implications in guiding the reconstruction of a minimal cell by synthetic biology approaches.
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Affiliation(s)
- Henri Grosjean
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Marc Breton
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Pascal Sirand-Pugnet
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Florence Tardy
- Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, Lyon, France
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, Marcy L'Etoile, France
| | - François Thiaucourt
- Centre International de Recherche en Agronomie pour le Développement, UMR CMAEE, Montpellier, France
| | - Christine Citti
- INRA, UMR1225, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
- Université de Toulouse, INP-ENVT, UMR1225, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Aurélien Barré
- Univ. Bordeaux, Centre de bioinformatique et de génomique fonctionnelle, CBiB, Bordeaux, France
| | - Satoko Yoshizawa
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Dominique Fourmy
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University Florida, Gainesville, Florida, United States of America
| | - Alain Blanchard
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- * E-mail:
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19
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Selbach BP, Chung AH, Scott AD, George SJ, Cramer SP, Dos Santos PC. Fe-S cluster biogenesis in Gram-positive bacteria: SufU is a zinc-dependent sulfur transfer protein. Biochemistry 2013; 53:152-60. [PMID: 24321018 DOI: 10.1021/bi4011978] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The biosynthesis of Fe-S clusters in Bacillus subtilis and other Gram-positive bacteria is catalyzed by the SufCDSUB system. The first step in this pathway involves the sulfur mobilization from the free amino acid cysteine to a sulfur acceptor protein SufU via a PLP-dependent cysteine desulfurase SufS. In this reaction scheme, the formation of an enzyme S-covalent intermediate is followed by the binding of SufU. This event leads to the second half of the reaction where a deprotonated thiol of SufU promotes the nucleophilic attack onto the persulfide intermediate of SufS. Kinetic analysis combined with spectroscopic methods identified that the presence of a zinc atom tightly bound to SufU (Ka = 10(17) M(-1)) is crucial for its structural and catalytic competency. Fe-S cluster assembly experiments showed that despite the high degree of sequence and structural similarity to the ortholog enzyme IscU, the B. subtilis SufU does not act as a standard Fe-S cluster scaffold protein. The involvement of SufU as a dedicated agent of sulfur transfer, rather than as an assembly scaffold, in the biogenesis of Fe-S clusters in Gram-positive microbes indicates distinct strategies used by bacterial systems to assemble Fe-S clusters.
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Affiliation(s)
- Bruna P Selbach
- Department of Chemistry, Wake Forest University , Winston-Salem, North Carolina, United States
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20
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Biogenesis of [Fe–S] cluster in Firmicutes: an unexploited field of investigation. Antonie Van Leeuwenhoek 2013; 104:283-300. [DOI: 10.1007/s10482-013-9966-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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21
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Reprint of: Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:923-37. [PMID: 23660107 DOI: 10.1016/j.bbabio.2013.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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22
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Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F. Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:455-69. [PMID: 23298813 DOI: 10.1016/j.bbabio.2012.12.010] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/17/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Béatrice Roche
- Institut de Microbiologie de la Méditerranée, Marseille, France
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23
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Miethke M. Molecular strategies of microbial iron assimilation: from high-affinity complexes to cofactor assembly systems. Metallomics 2013. [DOI: 10.1039/c2mt20193c] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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24
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Enterococcus faecalis SufU scaffold protein enhances SufS desulfurase activity by acquiring sulfur from its cysteine-153. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1910-8. [DOI: 10.1016/j.bbapap.2011.06.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/07/2011] [Accepted: 06/29/2011] [Indexed: 11/20/2022]
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25
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Albrecht AG, Landmann H, Nette D, Burghaus O, Peuckert F, Seubert A, Miethke M, Marahiel MA. The frataxin homologue Fra plays a key role in intracellular iron channeling in Bacillus subtilis. Chembiochem 2011; 12:2052-61. [PMID: 21744456 DOI: 10.1002/cbic.201100190] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Indexed: 12/16/2023]
Abstract
Frataxin homologues are important iron chaperones in eukarya and prokarya. Using a native proteomics approach we were able to identify the structural frataxin homologue Fra (formerly YdhG) of Bacillus subtilis and to quantify its native iron-binding stoichiometry. Using recombinant proteins we could show in vitro that Fra is able to transfer iron onto the B. subtilis SUF system for iron-sulfur cluster biosynthesis. In a four-constituents reconstitution system (including SufU, SufS, Fra and CitB) we observed a Fra-dependent formation of a [4 Fe-4 S] cluster on SufU that could be efficiently transferred onto the target apo-aconitase (CitB). A Δfra deletion mutant showed a severe growth phenotype associated with a broadly disturbed iron homeostasis; this indicates that Fra is a central component of intracellular iron channeling in B. subtilis.
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Affiliation(s)
- Alexander G Albrecht
- Fachbereich Chemie/Biochemie der Philipps Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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26
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Riboldi GP, Larson TJ, Frazzon J. Enterococcus faecalis sufCDSUB complements Escherichia coli sufABCDSE. FEMS Microbiol Lett 2011; 320:15-24. [PMID: 21480963 DOI: 10.1111/j.1574-6968.2011.02284.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Iron-sulfur [Fe-S] clusters are inorganic prosthetic groups that play essential roles in all living organisms. Iron and sulfur mobilization, formation of [Fe-S] clusters, and delivery to its final protein targets involves a complex set of specific protein machinery. Proteobacteria has three systems of [Fe-S] biogenesis, designated NIF, ISC, and SUF. In contrast, the Firmicutes system is not well characterized and has only one system, formed mostly by SUF homologs. The Firmicutes phylum corresponds to a group of pathological bacteria, of which Enterococcus faecalis is a clinically relevant representative. Recently, the E. faecalis sufCDSUB [Fe-S] cluster biosynthetic machinery has been identified, although there is no further information available about the similarities and/or variations of Proteobacteria and Firmicutes systems. The aim of the present work was to compare the ability of the different Proteobacteria and Firmicutes systems to complement the Azotobacter vinelandii and Escherichia coli ISC and SUF systems. Indeed, E. faecalis sufCDSUB is able to complement the E. coli SUF system, allowing viable mutants of both sufABCDSE and iscRSU-hscBA-fdx systems. The presence of all E. faecalis SUF factors enables proper functional interactions, which would not otherwise occur in proteins from different systems.
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Affiliation(s)
- Gustavo P Riboldi
- Biotechnology Center (CBIOT), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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