1
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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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2
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Dean DR. On the path to [Fe-S] protein maturation: A personal perspective. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119750. [PMID: 38762171 DOI: 10.1016/j.bbamcr.2024.119750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
Azotobacter vinelandii is a genetically tractable Gram-negative proteobacterium able to fix nitrogen (N2) under aerobic growth conditions. This narrative describes how biochemical-genetic approaches using A. vinelandii to study nitrogen fixation led to the formulation of the "scaffold hypothesis" for the assembly of both simple and complex [Fe-S] clusters associated with biological nitrogen fixation. These studies also led to the discovery of a parallel, but genetically distinct, pathway for maturation of [Fe-S] proteins that support central metabolic processes.
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Affiliation(s)
- Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061-0346, United States of America.
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3
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Xi J, Chen X, Du J, Zhong L, Hu Q, Zhao L. Biosynthesis, behavior and fate of volatile organic sulfide in Lentinus edodes (Berk.) upon hot-air drying treatment. Food Chem 2023; 412:135528. [PMID: 36716624 DOI: 10.1016/j.foodchem.2023.135528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/28/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
This study elucidated the biosynthesis and changing behaviors of organic sulfide in shiitake mushrooms upon hot-air drying treatment. The changes of aw, moisture migration, contours of taste and flavor, organic sulfide, and 4 key enzyme activities were monitored throughout three drying procedures (CT/ST1/ST2). Results showed that drying rate was related to the moisture migration. Key enzymes of γ-GTase, ASFase and CS lyase were heat-resistant proteases, while C-Dase exhibited low thermal stability with the activity decreased during treatment. A total of 17 organic sulfides were identified and PLS analyses suggested 6 cyclic polysulfides were formed by C-Dase desulfurization, while 5 thioethers generation were related to the thermal cleavage of direct precursors (straight-chain di/tris/tetrasulfonyl esters) and Maillard reaction. These results indicated that ST2 drying procedures had a positive effect on the formation of cyclic polysulfides at the end of drying pried and the achievement of premium flavor qualities.
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Affiliation(s)
- Jiapei Xi
- Nanjing Agricultural University, College of Food Science and Technology, Nanjing 210095, China
| | - Xiao Chen
- Nanjing Agricultural University, College of Food Science and Technology, Nanjing 210095, China
| | - Jiaxin Du
- Nanjing Agricultural University, College of Food Science and Technology, Nanjing 210095, China
| | - Lei Zhong
- Nanjing Agricultural University, College of Food Science and Technology, Nanjing 210095, China
| | - Qiuhui Hu
- Nanjing Agricultural University, College of Food Science and Technology, Nanjing 210095, China; Nanjing University of Finance and Economics, College of Food Science & Engineering, Nanjing 210023, China
| | - Liyan Zhao
- Nanjing Agricultural University, College of Food Science and Technology, Nanjing 210095, China.
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4
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Alsohaibani R, Claudel AL, Perchat-Varlet R, Boutserin S, Talfournier F, Boschi-Muller S, Selles B. Rhodanese-Fold Containing Proteins in Humans: Not Just Key Players in Sulfur Trafficking. Antioxidants (Basel) 2023; 12:antiox12040843. [PMID: 37107218 PMCID: PMC10135228 DOI: 10.3390/antiox12040843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The Rhodanese-fold is a ubiquitous structural domain present in various protein subfamilies associated with different physiological functions or pathophysiological conditions in humans. Proteins harboring a Rhodanese domain are diverse in terms of domain architecture, with some representatives exhibiting one or several Rhodanese domains, fused or not to other structural domains. The most famous Rhodanese domains are catalytically active, thanks to an active-site loop containing an essential cysteine residue which allows for catalyzing sulfur transfer reactions involved in sulfur trafficking, hydrogen sulfide metabolism, biosynthesis of molybdenum cofactor, thio-modification of tRNAs or protein urmylation. In addition, they also catalyse phosphatase reactions linked to cell cycle regulation, and recent advances proposed a new role into tRNA hydroxylation, illustrating the catalytic versatility of Rhodanese domain. To date, no exhaustive analysis of Rhodanese containing protein equipment from humans is available. In this review, we focus on structural and biochemical properties of human-active Rhodanese-containing proteins, in order to provide a picture of their established or putative key roles in many essential biological functions.
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5
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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6
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Lin CW, Oney-Hawthorne SD, Kuo ST, Barondeau DP, Russell DH. Mechanistic Insights into IscU Conformation Regulation for Fe-S Cluster Biogenesis Revealed by Variable Temperature Electrospray Ionization Native Ion Mobility Mass Spectrometry. Biochemistry 2022; 61:2733-2741. [PMID: 36351081 PMCID: PMC10009881 DOI: 10.1021/acs.biochem.2c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Iron-sulfur (Fe-S) cluster (ISC) cofactors are required for the function of many critical cellular processes. In the ISC Fe-S cluster biosynthetic pathway, IscU assembles Fe-S cluster intermediates from iron, electrons, and inorganic sulfur, which is provided by the cysteine desulfurase enzyme IscS. IscU also binds to Zn, which mimics and competes for binding with the Fe-S cluster. Crystallographic and nuclear magnetic resonance spectroscopic studies reveal that IscU is a metamorphic protein that exists in multiple conformational states, which include at least a structured form and a disordered form. The structured form of IscU is favored by metal binding and is stable in a narrow temperature range, undergoing both cold and hot denaturation. Interestingly, the form of IscU that binds IscS and functions in Fe-S cluster assembly remains controversial. Here, results from variable temperature electrospray ionization (vT-ESI) native ion mobility mass spectrometry (nIM-MS) establish that IscU exists in structured, intermediate, and disordered forms that rearrange to more extended conformations at higher temperatures. A comparison of Zn-IscU and apo-IscU reveals that Zn(II) binding attenuates the cold/heat denaturation of IscU, promotes refolding of IscU, favors the structured and intermediate conformations, and inhibits the disordered high charge states. Overall, these findings provide a structural rationalization for the role of Zn(II) in stabilizing IscU conformations and IscS in altering the IscU active site to prepare for Zn(II) release and cluster synthesis. This work highlights how vT-ESI-nIM-MS can be applied as a powerful tool in mechanistic enzymology by providing details of relationships among temperature, protein conformations, and ligand/protein binding.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Shelby D Oney-Hawthorne
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Syuan-Ting Kuo
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David P Barondeau
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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7
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Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes. Int J Mol Sci 2022; 23:ijms231810611. [PMID: 36142529 PMCID: PMC9502317 DOI: 10.3390/ijms231810611] [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: 07/28/2022] [Revised: 08/23/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.
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8
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Tachezy J, Makki A, Hrdý I. The hydrogenosomes of Trichomonas vaginalis. J Eukaryot Microbiol 2022; 69:e12922. [PMID: 35567536 DOI: 10.1111/jeu.12922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.
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Affiliation(s)
- Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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9
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Solomon JB, Tanifuji K, Lee CC, Jasniewski AJ, Hedman B, Hodgson KO, Hu Y, Ribbe MW. Characterization of a Nitrogenase Iron Protein Substituted with a Synthetic [Fe 4 Se 4 ] Cluster. Angew Chem Int Ed Engl 2022; 61:e202202271. [PMID: 35218104 PMCID: PMC9038695 DOI: 10.1002/anie.202202271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 11/08/2022]
Abstract
The Fe protein of nitrogenase plays multiple roles in substrate reduction and cluster maturation via its redox-active [Fe4 S4 ] cluster. Here we report the synthesis and characterization of a water-soluble [Fe4 Se4 ] cluster that is used to substitute the [Fe4 S4 ] cluster of the Azotobacter vinelandii Fe protein (AvNifH). Biochemical, EPR and XAS/EXAFS analyses demonstrate the ability of the [Fe4 Se4 ] cluster to adopt the super-reduced, all-ferrous state upon its incorporation into AvNifH. Moreover, these studies reveal that the [Fe4 Se4 ] cluster in AvNifH already assumes a partial all-ferrous state ([Fe4 Se4 ]0 ) in the presence of dithionite, where its [Fe4 S4 ] counterpart in AvNifH exists solely in the reduced state ([Fe4 S4 ]1+ ). Such a discrepancy in the redox properties of the AvNifH-associated [Fe4 Se4 ] and [Fe4 S4 ] clusters can be used to distinguish the differential redox requirements for the substrate reduction and cluster maturation of nitrogenase, pointing to the utility of chalcogen-substituted FeS clusters in future mechanistic studies of nitrogenase catalysis and assembly.
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Affiliation(s)
- Joseph B Solomon
- Department of Molecular Biology and Biochemistry, University of Califronia, Irvine, Irvine, CA 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of Califronia, Irvine, Irvine, CA 92697-3900, USA.,Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of Califronia, Irvine, Irvine, CA 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of Califronia, Irvine, Irvine, CA 92697-3900, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.,Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of Califronia, Irvine, Irvine, CA 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of Califronia, Irvine, Irvine, CA 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
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10
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Nakamura R, Ogawa S, Takahashi Y, Fujishiro T. Cycloserine enantiomers inhibit PLP‐dependent cysteine desulfurase SufS via distinct mechanisms. FEBS J 2022; 289:5947-5970. [DOI: 10.1111/febs.16455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/20/2022] [Accepted: 04/07/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
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11
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Das JK, Heryakusuma C, Susanti D, Choudhury PP, Mukhopadhyay B. Reduced Protein Sequence Patterns in Identifying Key Structural Elements of Dissimilatory Sulfite Reductase Homologs. Comput Biol Chem 2022; 98:107691. [DOI: 10.1016/j.compbiolchem.2022.107691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
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12
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Solomon J, Tanifuji K, Lee CC, Jasniewski A, Hedman B, Hodgson K, Hu Y, Ribbe M. Characterization of a Nitrogenase Iron Protein Substituted with a Synthetic [Fe4Se4] Cluster. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Kazuki Tanifuji
- Kyoto University Institute for Chemical Research UNITED STATES
| | - Chi Chung Lee
- University of California Irvine Molecular Biology and Biochemistry UNITED STATES
| | - Andrew Jasniewski
- University of California Irvine Molecular Biology and Biochemistry UNITED STATES
| | - Britt Hedman
- Stanford University Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory UNITED STATES
| | | | - Yilin Hu
- University of California Irvine Molecular Biology and Biochemistry UNITED STATES
| | - Markus Ribbe
- Irvine Molecular Biology & Biochemistry 2236 McGaugh Hall 92697 Irvine UNITED STATES
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13
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Oikawa T, Okajima K, Yamanaka K, Kato S. First enzymological characterization of selenocysteine β-lyase from a lactic acid bacterium, Leuconostoc mesenteroides. Amino Acids 2022; 54:787-798. [PMID: 35122135 DOI: 10.1007/s00726-022-03133-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022]
Abstract
We succeeded in expressing selenocysteine β-lyase (SCL) from a lactic acid bacterium, Leuconostoc mesenteroides LK-151 (Lm-SCL), in the soluble fractions of Escherichia coli Rosetta (DE3) using a novel expression vector of pET21malb constructed by ourselves that has both maltose binding protein (MBP)- and 6 × His-tag. Lm-SCL acted on L-selenocysteine, L-cysteine, and L-cysteine sulfinic acid but showed a high preference for L-selenocysteine. The kcat and kcat/Km values of Lm-SCL were determined to be 108 (min-1) and 42.0 (min-1・mM-1), respectively, and this was enough catalytic efficiency to suggest that Lm-SCL might also be involved in supplying elemental selenium from L-selenocysteine to selenoproteins like other SCLs. The optimum temperature and optimum pH of Lm-SCL were determined to be 37 °C and pH 6.5, respectively. Lm-SCL was stable at 37-45 °C and pH 6.5-7.5. Lm-SCL was completely inhibited by the addition of hydroxylamine, semicarbazide, and iodoacetic acid. The enzyme activity of Lm-SCL was decreased in the presence of various metal ions, especially Cu2+. The quaternary structure of Lm-SCL is a homodimer with a subunit molecular mass of 47.5 kDa. The similarity of the primary structure of Lm-SCL to other SCLs from Citrobacter freundii, Escherichia coli, humans, or mouse was calculated to be 47.0, 48.0, 12.5, or 24.0%, respectively. Unlike Ec-SCL, our mutational and molecular docking simulation studies revealed that C362 of Lm-SCL might also catalyze the deselenation of L-selenocysteine in addition to the desulfuration of L-cysteine.
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Affiliation(s)
- Tadao Oikawa
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka-Fu, 564-8680, Japan.
| | - Kouhei Okajima
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka-Fu, 564-8680, Japan
| | - Kazuya Yamanaka
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka-Fu, 564-8680, Japan
| | - Shiro Kato
- International Institute of Rare Sugar Research and Education, Kagawa University, 2393 Ikenobe, Miki, Kagawa, 761-0795, Japan
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14
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Karunakaran G, Yang Y, Tremblay V, Ning Z, Martin J, Belaouad A, Figeys D, Brunzelle J, Giguere PM, Stintzi A, Couture JF. Structural analysis of Atopobium parvulum SufS cysteine desulfurase linked to Crohn's disease. FEBS Lett 2022; 596:898-909. [PMID: 35122247 DOI: 10.1002/1873-3468.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/09/2022]
Abstract
Crohn's Disease (CD) is characterized by the chronic inflammation of the gastrointestinal tract. A dysbiotic microbiome and a defective immune system are linked to CD, where hydrogen sulfide (H2 S) microbial producers positively correlate with the severity of the disease. Atopobium parvulum is a key H2 S producer from the microbiome of CD patients. In this study, the biochemical characterization of two Atopobium parvulum cysteine desulfurases, ApSufS and ApCsdB, show that the enzymes are allosterically regulated. Structural analyses reveal that ApSufS forms a dimer with conserved characteristics observed in type II cysteine desulfurases. Four residues surrounding the active site are essential to catalyze cysteine desulfurylation, and a segment of short-chain residues grant access for substrate binding. A better understanding of ApSufS will help future avenues for CD treatment.
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Affiliation(s)
- Gapisha Karunakaran
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Yidai Yang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Véronique Tremblay
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Jade Martin
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Amine Belaouad
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Joseph Brunzelle
- Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, 60611, USA
| | - Patrick M Giguere
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
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15
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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: 2] [Impact Index Per Article: 1.0] [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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16
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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17
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Hinton TV, Batelu S, Gleason N, Stemmler TL. Molecular characteristics of proteins within the mitochondrial Fe-S cluster assembly complex. Micron 2021; 153:103181. [PMID: 34823116 DOI: 10.1016/j.micron.2021.103181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022]
Abstract
Iron-Sulfur (Fe-S) clusters are essential for life, as they are widely utilized in nearly every biochemical pathway. When bound to proteins, Fe-S clusters assist in catalysis, signal recognition, and energy transfer events, as well as additional cellular pathways including cellular respiration and DNA repair and replication. In Eukaryotes, Fe-S clusters are produced through coordinated activity by mitochondrial Iron-Sulfur Cluster (ISC) assembly pathway proteins through direct assembly, or through the production of the activated sulfur substrate used by the Cytosolic Iron-Sulfur Cluster Assembly (CIA) pathway. In the mitochondria, Fe-S cluster assembly is accomplished through the coordinated activity of the ISC pathway protein complex composed of a cysteine desulfurase, a scaffold protein, the accessory ISD11 protein, the acyl carrier protein, frataxin, and a ferredoxin; downstream events that accomplish Fe-S cluster transfer and delivery are driven by additional chaperone/delivery proteins that interact with the ISC assembly complex. Deficiency in human production or activity of Fe-S cluster containing proteins is often detrimental to cell and organism viability. Here we summarize what is known about the structure and functional activities of the proteins involved in the early steps of assembling [2Fe-2S] clusters before they are transferred to proteins devoted to their delivery. Our goal is to provide a comprehensive overview of how the ISC assembly apparatus proteins interact to make the Fe-S cluster which can be delivered to proteins downstream to the assembly event.
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Affiliation(s)
- Tiara V Hinton
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.
| | - Noah Gleason
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.
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18
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Methods to Investigate the Kinetic Profile of Cysteine Desulfurases. Methods Mol Biol 2021. [PMID: 34292550 DOI: 10.1007/978-1-0716-1605-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Biological iron-sulfur (Fe-S) clusters are essential protein prosthetic groups that promote a range of biochemical reactions. In vivo, these clusters are synthesized by specialized protein machineries involved in sulfur mobilization, cluster assembly, and cluster transfer to their target proteins. Cysteine desulfurases initiate the first step of sulfur activation and mobilization in cluster biosynthetic pathways. The reaction catalyzed by these enzymes involves the abstraction of sulfur from the amino acid L-cysteine, with concomitant formation of alanine. The presence and availability of a sulfur acceptor modulate the sulfurtransferase activity of this class of enzymes by altering their reaction profile and catalytic turnover rate. Herein, we describe two methods used to probe the reaction profile of cysteine desulfurases through quantification of alanine and sulfide production in these reactions.
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19
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Jiang C, Ge J, He B, Zeng B. Glycosphingolipids in Filamentous Fungi: Biological Roles and Potential Applications in Cosmetics and Health Foods. Front Microbiol 2021; 12:690211. [PMID: 34367090 PMCID: PMC8341767 DOI: 10.3389/fmicb.2021.690211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungi are a group of economically important fungi used in the production of fermented foods, industrial enzymes, and secondary metabolites. Glycosphingolipids (GSLs) as constituents of lipid rafts are involved in growth, differentiation, and response to environment stress in filamentous fungi. In addition to these key roles, GSLs are also important in the barrier function of skin to retain moisture as a moisturizing ingredient in cosmetics or health products for their strong biological activity as a functional component. GSLs found in filamentous fungi are divided in two major classes: neutral GSLs (glycosylceramides), glucosylceramides (GlcCers), and/or galactosylceramides (GalCers) and acidic GSLs, mannosylinositol phosphorylceramide (MIPC) and mannosyldiinositol phosphorylceramide [M(IP)2C]. Glycosylceramides are one of the abundant GSLs in Aspergillus and known to improve skin-barrier function and prevent intestinal impairment as a prebiotic. Some filamentous fungi of Aspergillus spp., synthesizing both GlcCer and GalCer, would be an amenable source to exploit glycosylceramides that wildly adding in cosmetics as moisturizing ingredients or health food as dietary supplements. In this minireview, the types, structures, and biosynthetic pathways of GSLs in filamentous fungi, and the relevance of GSLs in fungal growth, spore formation, and environmental stress response are explained. Furthermore, the advantage, potential development, and application of GlcCer and GalCer from filamentous fungi Aspergillus spp. are also investigate based on the use of plant GlcCer in health foods and cosmetics.
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Affiliation(s)
- Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Jinxin Ge
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
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20
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Schulte CCM, Borah K, Wheatley RM, Terpolilli JJ, Saalbach G, Crang N, de Groot DH, Ratcliffe RG, Kruger NJ, Papachristodoulou A, Poole PS. Metabolic control of nitrogen fixation in rhizobium-legume symbioses. SCIENCE ADVANCES 2021; 7:7/31/eabh2433. [PMID: 34330708 PMCID: PMC8324050 DOI: 10.1126/sciadv.abh2433] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/14/2021] [Indexed: 05/16/2023]
Abstract
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD+ ratio than sugars. Modeling and 13C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N2 fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.
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Affiliation(s)
- Carolin C M Schulte
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Khushboo Borah
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Nick Crang
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Daan H de Groot
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | | | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, UK.
- John Innes Centre, Norwich Research Park, Norwich, UK
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21
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Das M, Dewan A, Shee S, Singh A. The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis. Antioxidants (Basel) 2021; 10:antiox10070997. [PMID: 34201508 PMCID: PMC8300815 DOI: 10.3390/antiox10070997] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 12/02/2022] Open
Abstract
Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2−). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.
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22
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Chavan SP, Kawale SA, Patil NB, Kalbhor DB. Application of allylic amine formation from aziridine-2-ol under Appel reaction condition: Synthesis of N-(tert-butoxycarbonyl)-D-vinyl glycine methyl ester. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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23
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Jin H, Dhanasingh I, Sung J, La JW, Lee Y, Lee EM, Kang Y, Lee DY, Lee SH, Lee D. The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation. Microb Biotechnol 2021; 14:938-952. [PMID: 33320434 PMCID: PMC8085985 DOI: 10.1111/1751-7915.13717] [Citation(s) in RCA: 3] [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: 09/09/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 11/27/2022] Open
Abstract
Most extremophilic anaerobes possess a sulfur formation (Suf) system for Fe-S cluster biogenesis. In addition to its essential role in redox chemistry and stress responses of Fe-S cluster proteins, the Suf system may play an important role in keratin degradation by Fervidobacterium islandicum AW-1. Comparative genomics of the order Thermotogales revealed that the feather-degrading F. islandicum AW-1 has a complete Suf-like machinery (SufCBDSU) that is highly expressed in cells grown on native feathers in the absence of elemental sulfur (S0 ). On the other hand, F. islandicum AW-1 exhibited a significant retardation in the Suf system-mediated keratin degradation in the presence of S0 . Detailed differential expression analysis of sulfur assimilation machineries unveiled the mechanism by which an efficient sulfur delivery from persulfurated SufS to SufU is achieved during keratinolysis under sulfur starvation. Indeed, addition of SufS-SufU to cell extracts containing keratinolytic proteases accelerated keratin decomposition in vitro under reducing conditions. Remarkably, mass spectrometric analysis of extracellular and intracellular levels of amino acids suggested that redox homeostasis within cells coupled to extracellular cysteine and cystine recycling might be a prerequisite for keratinolysis. Taken together, these results suggest that the Suf-like machinery including the SufS-SufU complex may contribute to sulfur availability for an extracellular reducing environment as well as intracellular redox homeostasis through cysteine released from keratin hydrolysate under starvation conditions.
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Affiliation(s)
- Hyeon‐Su Jin
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Immanuel Dhanasingh
- Department of Cellular and Molecular MedicineChosun University School of MedicineGwangju61452South Korea
| | - Jae‐Yoon Sung
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Jae Won La
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Yena Lee
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
| | - Eun Mi Lee
- Department of Agricultural BiotechnologyCenter for Food and BioconvergenceResearch Institute for Agricultural and Life SciencesSeoul National UniversitySeoul08826South Korea
| | - Yujin Kang
- Department of Bio and Fermentation Convergence TechnologyBK21 PLUS ProgramKookmin UniversitySeoul02707Korea
| | - Do Yup Lee
- Department of Agricultural BiotechnologyCenter for Food and BioconvergenceResearch Institute for Agricultural and Life SciencesSeoul National UniversitySeoul08826South Korea
| | - Sung Haeng Lee
- Department of Cellular and Molecular MedicineChosun University School of MedicineGwangju61452South Korea
| | - Dong‐Woo Lee
- Department of BiotechnologyYonsei UniversitySeoul03722South Korea
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24
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A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical SAM protein MoaA for the synthesis of active molybdoenzymes. J Bacteriol 2021; 203:e0008621. [PMID: 33782054 DOI: 10.1128/jb.00086-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them were characterized in detail in Escherichia coli, namely IscA, SufA and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli Our studies include the identification of the A-type carrier proteins ErpA and IscA involved in [4Fe-4S] cluster insertion into the S-adenosyl-methionine dependent radical SAM protein MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth of nitrate respiration, based on low gene expression levels.IMPORTANCEUnderstanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics and gene regulation. Still remaining critical gaps in our knowledge are how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SusA and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.
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25
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TusA Is a Versatile Protein That Links Translation Efficiency to Cell Division in Escherichia coli. J Bacteriol 2021; 203:JB.00659-20. [PMID: 33526615 DOI: 10.1128/jb.00659-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/11/2021] [Indexed: 11/20/2022] Open
Abstract
To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm5s2U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation.IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm5s2U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm5s2U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis.
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26
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Abstract
Rhizobia are a phylogenetically diverse group of soil bacteria that engage in mutualistic interactions with legume plants. Although specifics of the symbioses differ between strains and plants, all symbioses ultimately result in the formation of specialized root nodule organs which host the nitrogen-fixing microsymbionts called bacteroids. Inside nodules, bacteroids encounter unique conditions that necessitate global reprogramming of physiological processes and rerouting of their metabolism. Decades of research have addressed these questions using genetics, omics approaches, and more recently computational modelling. Here we discuss the common adaptations of rhizobia to the nodule environment that define the core principles of bacteroid functioning. All bacteroids are growth-arrested and perform energy-intensive nitrogen fixation fueled by plant-provided C4-dicarboxylates at nanomolar oxygen levels. At the same time, bacteroids are subject to host control and sanctioning that ultimately determine their fitness and have fundamental importance for the evolution of a stable mutualistic relationship.
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27
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Gomez-Casati DF, Busi MV, Barchiesi J, Pagani MA, Marchetti-Acosta NS, Terenzi A. Fe-S Protein Synthesis in Green Algae Mitochondria. PLANTS 2021; 10:plants10020200. [PMID: 33494487 PMCID: PMC7911964 DOI: 10.3390/plants10020200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/28/2022]
Abstract
Iron and sulfur are two essential elements for all organisms. These elements form the Fe-S clusters that are present as cofactors in numerous proteins and protein complexes related to key processes in cells, such as respiration and photosynthesis, and participate in numerous enzymatic reactions. In photosynthetic organisms, the ISC and SUF Fe-S cluster synthesis pathways are located in organelles, mitochondria, and chloroplasts, respectively. There is also a third biosynthetic machinery in the cytosol (CIA) that is dependent on the mitochondria for its function. The genes and proteins that participate in these assembly pathways have been described mainly in bacteria, yeasts, humans, and recently in higher plants. However, little is known about the proteins that participate in these processes in algae. This review work is mainly focused on releasing the information on the existence of genes and proteins of green algae (chlorophytes) that could participate in the assembly process of Fe-S groups, especially in the mitochondrial ISC and CIA pathways.
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Affiliation(s)
- Diego F. Gomez-Casati
- Correspondence: (D.F.G.-C.); (M.V.B.); Tel.: +54-341-4391955 (ext. 113) (D.F.G.-C. & M.V.B.)
| | - Maria V. Busi
- Correspondence: (D.F.G.-C.); (M.V.B.); Tel.: +54-341-4391955 (ext. 113) (D.F.G.-C. & M.V.B.)
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28
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Johnstone MA, Nelson SJ, O'Leary C, Self WT. Exploring the selenium-over-sulfur substrate specificity and kinetics of a bacterial selenocysteine lyase. Biochimie 2021; 182:166-176. [PMID: 33444662 DOI: 10.1016/j.biochi.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/15/2022]
Abstract
Selenium is a vital micronutrient in many organisms. While traces are required for microbial utilization, excess amounts are toxic; thus, selenium can be regarded as a biological double-edged sword. Selenium is chemically similar to the essential element sulfur, but curiously, evolution has selected the former over the latter for a subset of oxidoreductases. Enzymes involved in sulfur metabolism are less discriminate in terms of preventing selenium incorporation; however, its specific incorporation into selenoproteins reveals a highly discriminate process that is not completely understood. We have identified SclA, a NifS-like protein in the nosocomial pathogen, Enterococcus faecalis, and characterized its enzymatic activity and specificity for l-selenocysteine over l-cysteine. It is known that Asp-146 is required for selenocysteine specificity in the human selenocysteine lyase. Thus, using computational biology, we compared the bacterial and mammalian enzymes and identified His-100, an Asp-146 ortholog in SclA, and generated site-directed mutants in order to study the residue's potential role in the l-selenocysteine discrimination mechanism. The proteins were overexpressed, purified, and characterized for their biochemical properties. All mutants exhibited varying Michaelis-Menten behavior towards l-selenocysteine, but His-100 was not found to be essential for this activity. Additionally, l-cysteine acted as a competitive inhibitor of all enzymes with higher affinity than l-selenocysteine. Finally, we discovered that SclA exhibited low activity with l-cysteine as a poor substrate regardless of mutations. We conclude that His-100 is not required for l-selenocysteine specificity, underscoring the inherent differences in discriminatory mechanisms between bacterial NifS-like proteins and mammalian selenocysteine lyases.
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Affiliation(s)
- Michael A Johnstone
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Samantha J Nelson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Christine O'Leary
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - William T Self
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA.
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29
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Yang CT, Devarie-Baez NO, Hamsath A, Fu XD, Xian M. S-Persulfidation: Chemistry, Chemical Biology, and Significance in Health and Disease. Antioxid Redox Signal 2020; 33:1092-1114. [PMID: 31547682 PMCID: PMC7583347 DOI: 10.1089/ars.2019.7889] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Significance: S-Persulfidation generates persulfide adducts (RSSH) on both small molecules and proteins. This process is believed to be critical in the regulation of biological functions of reactive sulfur species such as H2S, as well as in signal transduction. S-Persulfidation also plays regulatory roles in human health and diseases. Recent Advances: Some mechanisms underlying the generation of low-molecular-weight persulfides and protein S-persulfidation in living organisms have been uncovered. Some methods for the specific delivery of persulfides and the detection of persulfides in biological systems have been developed. These advances help to pave the road to better understand the functions of S-persulfidation. Critical Issues: Persulfides are highly reactive and unstable. Currently, their identification relies on trapping them by S-alkylation, but this is not always reliable due to rapid sulfur exchange reactions. Therefore, the presence, identity, and fates of persulfides in biological environments are sometimes difficult to track. Future Directions: Further understanding the fundamental chemistry/biochemistry of persulfides and development of more reliable detection methods are needed. S-Persulfidation in specific protein targets is essential in organismal physiological health and human disease states. Besides cardiovascular and neuronal systems, the roles of persulfidation in other systems need to be further explored. Contradictory results of persulfidation in biology, especially in cancer, need to be clarified.
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Affiliation(s)
- Chun-Tao Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Protein Modification and Degradation Key Lab of Guangzhou and Guangdong, Key Laboratory of Molecular Clinical Pharmacology in School of Pharmaceutics Science, Guangzhou Medical University, Guangzhou, China.,Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Nelmi O Devarie-Baez
- Department of Chemistry, Washington State University-Tri Cities, Richland, Washington, USA
| | - Akil Hamsath
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Xiao-Dong Fu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Protein Modification and Degradation Key Lab of Guangzhou and Guangdong, Key Laboratory of Molecular Clinical Pharmacology in School of Pharmaceutics Science, Guangzhou Medical University, Guangzhou, China
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, Washington, USA
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30
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Zhao L, Zhou Y, Li J, Xia Y, Wang W, Luo X, Yin J, Zhong J. Transcriptional response of Bacillus megaterium FDU301 to PEG200-mediated arid stress. BMC Microbiol 2020; 20:351. [PMID: 33198631 PMCID: PMC7670681 DOI: 10.1186/s12866-020-02039-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/08/2020] [Indexed: 11/12/2022] Open
Abstract
Background For microorganisms on a paper surface, the lack of water is one of the most important stress factors. A strain of Bacillus megaterium FDU301 was isolated from plaques on a paper surface using culture medium with polyethylene glycol 200 (PEG200) to simulate an arid condition. Global transcriptomic analysis of B. megaterium FDU301 grown under normal and simulated arid conditions was performed via RNA-seq technology to identify genes involved in arid stress adaptation. Results The transcriptome of B. megaterium FDU301 grown in LB medium under arid (15% PEG200 (w/w)) and normal conditions were compared. A total of 2941 genes were differentially expressed, including 1422 genes upregulated and 1519 genes downregulated under arid conditions. Oxidative stress-responsive regulatory genes perR, fur, and tipA were significantly upregulated, along with DNA protecting protein (dps), and catalase (katE). Genes related to Fe2+ uptake (feoB), sporulation stage II (spoIIB, spoIIE, spoIIGA), small acid-soluble spore protein (sspD), and biosynthesis of compatible solute ectoine (ectB, ectA) were also highly expressed to various degrees. Oxidative phosphorylation-related genes (atpB, atpE, atpF, atpH, atpA, atpG, atpD, atpC) and glycolysis-related genes (pgk, tpiA, frmA) were significantly downregulated. Conclusion This is the first report about transcriptomic analysis of a B. megaterium to explore the mechanism of arid resistance. Major changes in transcription were seen in the arid condition simulated by PEG200 (15%), with the most important one being genes related to oxidative stress. The results showed a complex mechanism for the bacteria to adapt to arid stress. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02039-4.
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Affiliation(s)
- Lei Zhao
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Institute for Preservation and Conservation of Chinese Ancient Books, Fudan University, Shanghai, 200433, China
| | - Yanjun Zhou
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jianbei Li
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yucheng Xia
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weiyun Wang
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiuqi Luo
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Juan Yin
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jiang Zhong
- Department of Microbiology and Microbial Engineering and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Institute for Preservation and Conservation of Chinese Ancient Books, Fudan University, Shanghai, 200433, China.
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31
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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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32
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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33
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Abstract
Mitochondria are essential in most eukaryotes and are involved in numerous biological functions including ATP production, cofactor biosyntheses, apoptosis, lipid synthesis, and steroid metabolism. Work over the past two decades has uncovered the biogenesis of cellular iron-sulfur (Fe/S) proteins as the essential and minimal function of mitochondria. This process is catalyzed by the bacteria-derived iron-sulfur cluster assembly (ISC) machinery and has been dissected into three major steps: de novo synthesis of a [2Fe-2S] cluster on a scaffold protein; Hsp70 chaperone-mediated trafficking of the cluster and insertion into [2Fe-2S] target apoproteins; and catalytic conversion of the [2Fe-2S] into a [4Fe-4S] cluster and subsequent insertion into recipient apoproteins. ISC components of the first two steps are also required for biogenesis of numerous essential cytosolic and nuclear Fe/S proteins, explaining the essentiality of mitochondria. This review summarizes the molecular mechanisms underlying the ISC protein-mediated maturation of mitochondrial Fe/S proteins and the importance for human disease.
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Affiliation(s)
- Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany;
- SYNMIKRO Zentrum für synthetische Mikrobiologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Sven-A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany;
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34
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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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35
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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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36
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Hoffarth ER, Rothchild KW, Ryan KS. Emergence of oxygen- and pyridoxal phosphate-dependent reactions. FEBS J 2020; 287:1403-1428. [PMID: 32142210 DOI: 10.1111/febs.15277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/29/2019] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) is an organic cofactor employed by ~ 4% of enzymes. The structure of the PLP cofactor allows for the stabilization of carbanions through resonance. A small number of PLP-dependent enzymes employ molecular oxygen as a cosubstrate. Here, we review the biological roles and possible mechanisms of these enzymes, and we observe that these enzymes are found in multiple protein families, suggesting that reaction with oxygen might have emerged de novo in several protein families and thus could be directed to emerge again through laboratory evolution experiments.
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Affiliation(s)
- Elesha R Hoffarth
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
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37
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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: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [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 London, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Annalisa Pastore
- UK Dementia Research Institute at the Wohl Institute of King's College London, UK
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38
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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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39
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Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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40
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Abstract
![]()
Nitrogenase harbors three distinct
metal prosthetic groups that
are required for its activity. The simplest one is a [4Fe-4S] cluster
located at the Fe protein nitrogenase component. The MoFe protein
component carries an [8Fe-7S] group called P-cluster and a [7Fe-9S-C-Mo-R-homocitrate] group called FeMo-co. Formation of nitrogenase
metalloclusters requires the participation of the structural nitrogenase
components and many accessory proteins, and occurs both in
situ, for the P-cluster, and in external assembly sites for
FeMo-co. The biosynthesis of FeMo-co is performed stepwise and involves
molecular scaffolds, metallochaperones, radical chemistry, and novel
and unique biosynthetic intermediates. This review provides a critical
overview of discoveries on nitrogenase cofactor structure, function,
and activity over the last four decades.
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Affiliation(s)
- Stefan Burén
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Emilio Jiménez-Vicente
- Department of Biochemistry, Virginia Polytechnic Institute, Blacksburg, Virginia 24061, United States
| | - Carlos Echavarri-Erasun
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnologı́a y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
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41
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Nakamura R, Hikita M, Ogawa S, Takahashi Y, Fujishiro T. Snapshots of PLP‐substrate and PLP‐product external aldimines as intermediates in two types of cysteine desulfurase enzymes. FEBS J 2019; 287:1138-1154. [DOI: 10.1111/febs.15081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/11/2019] [Accepted: 10/01/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Masahide Hikita
- Structural Biology Research Center, Photon Factory Institute of Materials Structure Science High Energy Accelerator Research Organization Tsukuba Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Yasuhiro Takahashi
- 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
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42
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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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Patra S, Barondeau DP. Mechanism of activation of the human cysteine desulfurase complex by frataxin. Proc Natl Acad Sci U S A 2019; 116:19421-19430. [PMID: 31511419 PMCID: PMC6765240 DOI: 10.1073/pnas.1909535116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The function of frataxin (FXN) has garnered great scientific interest since its depletion was linked to the incurable neurodegenerative disease Friedreich's ataxia (FRDA). FXN has been shown to be necessary for iron-sulfur (Fe-S) cluster biosynthesis and proper mitochondrial function. The structural and functional core of the Fe-S cluster assembly complex is a low-activity pyridoxal 5'-phosphate (PLP)-dependent cysteine desulfurase enzyme that consists of catalytic (NFS1), LYRM protein (ISD11), and acyl carrier protein (ACP) subunits. Although previous studies show that FXN stimulates the activity of this assembly complex, the mechanism of FXN activation is poorly understood. Here, we develop a radiolabeling assay and use stopped-flow kinetics to establish that FXN is functionally linked to the mobile S-transfer loop cysteine of NFS1. Our results support key roles for this essential cysteine residue in substrate binding, as a general acid to advance the Cys-quinonoid PLP intermediate, as a nucleophile to form an NFS1 persulfide, and as a sulfur delivery agent to generate a persulfide species on the Fe-S scaffold protein ISCU2. FXN specifically accelerates each of these individual steps in the mechanism. Our resulting architectural switch model explains why the human Fe-S assembly system has low inherent activity and requires activation, the connection between the functional mobile S-transfer loop cysteine and FXN binding, and why the prokaryotic system does not require a similar FXN-based activation. Together, these results provide mechanistic insights into the allosteric-activator role of FXN and suggest new strategies to replace FXN function in the treatment of FRDA.
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Affiliation(s)
- Shachin Patra
- Department of Chemistry, Texas A&M University, College Station, TX 77842
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842
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Alfadhel M, Nashabat M, Abu Ali Q, Hundallah K. Mitochondrial iron-sulfur cluster biogenesis from molecular understanding to clinical disease. ACTA ACUST UNITED AC 2019; 22:4-13. [PMID: 28064324 PMCID: PMC5726836 DOI: 10.17712/nsj.2017.1.20160542] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Iron–sulfur clusters (ISCs) are known to play a major role in various protein functions. Located in the mitochondria, cytosol, endoplasmic reticulum and nucleus, they contribute to various core cellular functions. Until recently, only a few human diseases related to mitochondrial ISC biogenesis defects have been described. Such diseases include Friedreich ataxia, combined oxidative phosphorylation deficiency 19, infantile complex II/III deficiency defect, hereditary myopathy with lactic acidosis and mitochondrial muscle myopathy, lipoic acid biosynthesis defects, multiple mitochondrial dysfunctions syndromes and non ketotic hyperglycinemia due to glutaredoxin 5 gene defect. Disorders of mitochondrial import, export and translation, including sideroblastic anemia with ataxia, EVEN-PLUS syndrome and mitochondrial complex I deficiency due to nucleotide-binding protein-like protein gene defect, have also been implicated in ISC biogenesis defects. With advances in next generation sequencing technologies, more disorders related to ISC biogenesis defects are expected to be elucidated. In this article, we aim to shed the light on mitochondrial ISC biogenesis, related proteins and their function, pathophysiology, clinical phenotypes of related disorders, diagnostic approach, and future implications.
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Affiliation(s)
- Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Kingdom of Saudi Arabia
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Igiehon NO, Babalola OO, Aremu BR. Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress. BMC Microbiol 2019; 19:159. [PMID: 31296165 PMCID: PMC6624879 DOI: 10.1186/s12866-019-1536-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The role of soil microorganisms in plant growth, nutrient utilization, drought tolerance as well as biocontrol activity cannot be over-emphasized, especially in this era when food crisis is a global challenge. This research was therefore designed to gain genomic insights into plant growth promoting (PGP) Rhizobium species capable of enhancing soybean (Glycine max L.) seeds germination under drought condition. RESULTS Rhizobium sp. strain R1, Rhizobium tropici strain R2, Rhizobium cellulosilyticum strain R3, Rhizobium taibaishanense strain R4 and Ensifer meliloti strain R5 were found to possess the entire PGP traits tested. Specifically, these rhizobial strains were able to solubilize phosphate, produce exopolysaccharide (EPS), 1-aminocyclopropane-1-carboxylate (ACC), siderophore and indole-acetic-acid (IAA). These strains also survived and grew at a temperature of 45 °C and in an acidic condition with a pH 4. Consequently, all the Rhizobium strains enhanced the germination of soybean seeds (PAN 1532 R) under drought condition imposed by 4% poly-ethylene glycol (PEG); nevertheless, Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 inoculations were able to improve seeds germination more than R2, R4 and R5 strains. Thus, genomic insights into Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 revealed the presence of some genes with their respective proteins involved in symbiotic establishment, nitrogen fixation, drought tolerance and plant growth promotion. In particular, exoX, htrA, Nif, nodA, eptA, IAA and siderophore-producing genes were found in the two rhizobial strains. CONCLUSIONS Therefore, the availability of the whole genome sequences of R1 and R3 strains may further be exploited to comprehend the interaction of drought tolerant rhizobia with soybean and other legumes and the PGP ability of these rhizobial strains can also be harnessed for biotechnological application in the field especially in semiarid and arid regions of the globe.
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Affiliation(s)
- Nicholas O Igiehon
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, Mmabatho, 2735, South Africa
| | - Olubukola O Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, Mmabatho, 2735, South Africa.
| | - Bukola R Aremu
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, Mmabatho, 2735, South Africa
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46
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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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47
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Abstract
Biological nitrogen fixation, the conversion of dinitrogen (N2) into ammonia (NH3), stands as a particularly challenging chemical process. As the entry point into a bioavailable form of nitrogen, biological nitrogen fixation is a critical step in the global nitrogen cycle. In Nature, only one enzyme, nitrogenase, is competent in performing this reaction. Study of this complex metalloenzyme has revealed a potent substrate reduction system that utilizes some of the most sophisticated metalloclusters known. This chapter discusses the structure and function of nitrogenase, covers methods that have proven useful in the elucidation of enzyme properties, and provides an overview of the three known nitrogenase variants.
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48
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Fox NG, Yu X, Feng X, Bailey HJ, Martelli A, Nabhan JF, Strain-Damerell C, Bulawa C, Yue WW, Han S. Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism. Nat Commun 2019; 10:2210. [PMID: 31101807 PMCID: PMC6525205 DOI: 10.1038/s41467-019-09989-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022] Open
Abstract
The core machinery for de novo biosynthesis of iron-sulfur clusters (ISC), located in the mitochondria matrix, is a five-protein complex containing the cysteine desulfurase NFS1 that is activated by frataxin (FXN), scaffold protein ISCU, accessory protein ISD11, and acyl-carrier protein ACP. Deficiency in FXN leads to the loss-of-function neurodegenerative disorder Friedreich's ataxia (FRDA). Here the 3.2 Å resolution cryo-electron microscopy structure of the FXN-bound active human complex, containing two copies of the NFS1-ISD11-ACP-ISCU-FXN hetero-pentamer, delineates the interactions of FXN with other component proteins of the complex. FXN binds at the interface of two NFS1 and one ISCU subunits, modifying the local environment of a bound zinc ion that would otherwise inhibit NFS1 activity in complexes without FXN. Our structure reveals how FXN facilitates ISC production through stabilizing key loop conformations of NFS1 and ISCU at the protein-protein interfaces, and suggests how FRDA clinical mutations affect complex formation and FXN activation.
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Affiliation(s)
- Nicholas G Fox
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Merck & Co, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Xiaodi Yu
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
- SMPS, Janssen Research and Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Xidong Feng
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
| | - Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alain Martelli
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Joseph F Nabhan
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Claire Strain-Damerell
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Christine Bulawa
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Seungil Han
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA.
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49
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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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50
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Ciofi-Baffoni S, Nasta V, Banci L. Protein networks in the maturation of human iron-sulfur proteins. Metallomics 2019; 10:49-72. [PMID: 29219157 DOI: 10.1039/c7mt00269f] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The biogenesis of iron-sulfur (Fe-S) proteins in humans is a multistage process occurring in different cellular compartments. The mitochondrial iron-sulfur cluster (ISC) assembly machinery composed of at least 17 proteins assembles mitochondrial Fe-S proteins. A cytosolic iron-sulfur assembly (CIA) machinery composed of at least 13 proteins has been more recently identified and shown to be responsible for the Fe-S cluster incorporation into cytosolic and nuclear Fe-S proteins. Cytosolic and nuclear Fe-S protein maturation requires not only the CIA machinery, but also the components of the mitochondrial ISC assembly machinery. An ISC export machinery, composed of a protein transporter located in the mitochondrial inner membrane, has been proposed to act in mediating the export process of a still unknown component that is required for the CIA machinery. Several functional and molecular aspects of the protein networks operative in the three machineries are still largely obscure. This Review focuses on the Fe-S protein maturation processes in humans with the specific aim of providing a molecular picture of the currently known protein-protein interaction networks. The human ISC and CIA machineries are presented, and the ISC export machinery is discussed with respect to possible molecules being the substrates of the mitochondrial protein transporter.
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Affiliation(s)
- Simone Ciofi-Baffoni
- Magnetic Resonance Center-CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.
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