1
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Bak DW, Weerapana E. Proteomic strategies to interrogate the Fe-S proteome. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119791. [PMID: 38925478 DOI: 10.1016/j.bbamcr.2024.119791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Iron‑sulfur (Fe-S) clusters, inorganic cofactors composed of iron and sulfide, participate in numerous essential redox, non-redox, structural, and regulatory biological processes within the cell. Though structurally and functionally diverse, the list of all proteins in an organism capable of binding one or more Fe-S clusters is referred to as its Fe-S proteome. Importantly, the Fe-S proteome is highly dynamic, with continuous cluster synthesis and delivery by complex Fe-S cluster biogenesis pathways. This cluster delivery is balanced out by processes that can result in loss of Fe-S cluster binding, such as redox state changes, iron availability, and oxygen sensitivity. Despite continued expansion of the Fe-S protein catalogue, it remains a challenge to reliably identify novel Fe-S proteins. As such, high-throughput techniques that can report on native Fe-S cluster binding are required to both identify new Fe-S proteins, as well as characterize the in vivo dynamics of Fe-S cluster binding. Due to the recent rapid growth in mass spectrometry, proteomics, and chemical biology, there has been a host of techniques developed that are applicable to the study of native Fe-S proteins. This review will detail both the current understanding of the Fe-S proteome and Fe-S cluster biology as well as describing state-of-the-art proteomic strategies for the study of Fe-S clusters within the context of a native proteome.
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Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
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2
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Braymer JJ, Stehling O, Stümpfig M, Rösser R, Spantgar F, Blinn CM, Mühlenhoff U, Pierik AJ, Lill R. Requirements for the biogenesis of [2Fe-2S] proteins in the human and yeast cytosol. Proc Natl Acad Sci U S A 2024; 121:e2400740121. [PMID: 38743629 PMCID: PMC11126956 DOI: 10.1073/pnas.2400740121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
The biogenesis of iron-sulfur (Fe/S) proteins entails the synthesis and trafficking of Fe/S clusters, followed by their insertion into target apoproteins. In eukaryotes, the multiple steps of biogenesis are accomplished by complex protein machineries in both mitochondria and cytosol. The underlying biochemical pathways have been elucidated over the past decades, yet the mechanisms of cytosolic [2Fe-2S] protein assembly have remained ill-defined. Similarly, the precise site of glutathione (GSH) requirement in cytosolic and nuclear Fe/S protein biogenesis is unclear, as is the molecular role of the GSH-dependent cytosolic monothiol glutaredoxins (cGrxs). Here, we investigated these questions in human and yeast cells by various in vivo approaches. [2Fe-2S] cluster assembly of cytosolic target apoproteins required the mitochondrial ISC machinery, the mitochondrial transporter Atm1/ABCB7 and GSH, yet occurred independently of both the CIA system and cGrxs. This mechanism was strikingly different from the ISC-, Atm1/ABCB7-, GSH-, and CIA-dependent assembly of cytosolic-nuclear [4Fe-4S] proteins. One notable exception to this cytosolic [2Fe-2S] protein maturation pathway defined here was yeast Apd1 which used the CIA system via binding to the CIA targeting complex through its C-terminal tryptophan. cGrxs, although attributed as [2Fe-2S] cluster chaperones or trafficking proteins, were not essential in vivo for delivering [2Fe-2S] clusters to either CIA components or target apoproteins. Finally, the most critical GSH requirement was assigned to Atm1-dependent export, i.e. a step before GSH-dependent cGrxs function. Our findings extend the general model of eukaryotic Fe/S protein biogenesis by adding the molecular requirements for cytosolic [2Fe-2S] protein maturation.
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Affiliation(s)
- Joseph J. Braymer
- Institut für Zytobiologie und Zytopathologie, Fachbereich Medizin, Philipps-Universität Marburg, Marburg35032, Germany
- Zentrum für Synthetische Mikrobiologie Synmikro, Philipps-Universität Marburg, Marburg35032, Germany
| | - Oliver Stehling
- Institut für Zytobiologie und Zytopathologie, Fachbereich Medizin, Philipps-Universität Marburg, Marburg35032, Germany
- Zentrum für Synthetische Mikrobiologie Synmikro, Philipps-Universität Marburg, Marburg35032, Germany
| | - Martin Stümpfig
- Institut für Zytobiologie und Zytopathologie, Fachbereich Medizin, Philipps-Universität Marburg, Marburg35032, Germany
- Zentrum für Synthetische Mikrobiologie Synmikro, Philipps-Universität Marburg, Marburg35032, Germany
| | - Ralf Rösser
- Institut für Zytobiologie und Zytopathologie, Fachbereich Medizin, Philipps-Universität Marburg, Marburg35032, Germany
- Zentrum für Synthetische Mikrobiologie Synmikro, Philipps-Universität Marburg, Marburg35032, Germany
| | - Farah Spantgar
- Institut für Zytobiologie und Zytopathologie, Fachbereich Medizin, Philipps-Universität Marburg, Marburg35032, Germany
- Zentrum für Synthetische Mikrobiologie Synmikro, Philipps-Universität Marburg, Marburg35032, Germany
| | - Catharina M. Blinn
- Department of Chemistry, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Fachbereich Medizin, Philipps-Universität Marburg, Marburg35032, Germany
- Zentrum für Synthetische Mikrobiologie Synmikro, Philipps-Universität Marburg, Marburg35032, Germany
| | - Antonio J. Pierik
- Department of Chemistry, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Fachbereich Medizin, Philipps-Universität Marburg, Marburg35032, Germany
- Zentrum für Synthetische Mikrobiologie Synmikro, Philipps-Universität Marburg, Marburg35032, Germany
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3
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Gupta P, Mansuri R, Priydarshni P, Behera S, Zaidi A, Nehar S, Sahoo GC, Pandey K, Ali V. Interaction between Cfd1 and Nbp35 proteins involved in cytosolic FeS cluster assembly machinery deciphers a stable complexation in Leishmania donovani. Int J Biol Macromol 2023; 253:127073. [PMID: 37774824 DOI: 10.1016/j.ijbiomac.2023.127073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
Leishmania donovani is the causative unicellular parasite for visceral leishmaniasis (VL); and FeS proteins are likely to be very essential for their survival and viability. Cytosolic FeS cluster assembly (CIA) machinery is one of the four systems for the biosynthesis and transfer of FeS clusters among eukaryotes; Cfd1 and Nbp35 are the scaffold components for cytosolic FeS cluster biogenesis. We investigated the role of CIA machinery components and purified Cfd1 and Nbp35 proteins of L. donovani. We also investigated the interactive nature between LdCfd1 and LdNbp35 proteins by in silico analysis, in vitro co-purification, pull down assays along with in vivo immuno-precipitation; which inferred that both LdCfd1 and LdNbp35 proteins are interacting with each other. Thus, our collective data revealed the interaction between these two proteins which forms a stable complex that can be attributed to the cellular process of FeS clusters biogenesis, and transfer to target apo-proteins of L. donovani. The expression of Cfd1 and Nbp35 proteins in Amp B resistant parasites is up-regulated leading to increased amount of FeS proteins. Hence, it favors increased tolerance towards ROS level, which helps parasites survival under drug pressure contributing in Amphotericin B resistance.
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Affiliation(s)
- Parool Gupta
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Rani Mansuri
- Department of Bio-informatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Priya Priydarshni
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Sachidananda Behera
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Amir Zaidi
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Shamshun Nehar
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Ganesh Chandra Sahoo
- Department of Bio-informatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India
| | - Vahab Ali
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam Kuan, Patna 800007, India.
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4
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Zulkifli M, Okonkwo AU, Gohil VM. FDX1 Is Required for the Biogenesis of Mitochondrial Cytochrome c Oxidase in Mammalian Cells. J Mol Biol 2023; 435:168317. [PMID: 37858707 DOI: 10.1016/j.jmb.2023.168317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
Ferredoxins (FDXs) are evolutionarily conserved iron-sulfur (Fe-S) proteins that function as electron transfer proteins in diverse metabolic pathways. Mammalian mitochondria contain two ferredoxins, FDX1 and FDX2, which share a high degree of structural similarity but exhibit different functionalities. Previous studies have established the unique role of FDX2 in the biogenesis of Fe-S clusters; however, FDX1 seems to have multiple targets in vivo, some of which are only recently emerging. Using CRISPR-Cas9-based loss-of-function studies in rat cardiomyocyte cell line, we demonstrate an essential requirement of FDX1 in mitochondrial respiration and energy production. We attribute reduced mitochondrial respiration to a specific decrease in the abundance and assembly of cytochrome c oxidase (CcO), a mitochondrial heme-copper oxidase and the terminal enzyme of the mitochondrial respiratory chain. FDX1 knockout cells have reduced levels of copper and heme a/a3, factors that are essential for the maturation of the CcO enzyme complex. Copper supplementation failed to rescue CcO biogenesis, but overexpression of heme a synthase, COX15, partially rescued COX1 abundance in FDX1 knockout cells. This finding links FDX1 function to heme a biosynthesis, and places it upstream of COX15 in CcO biogenesis like its ancestral yeast homolog. Taken together, our work has identified FDX1 as a critical CcO biogenesis factor in mammalian cells.
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Affiliation(s)
- Mohammad Zulkifli
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA.
| | - Adriana U Okonkwo
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA.
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5
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Marquez MD, Greth C, Buzuk A, Liu Y, Blinn CM, Beller S, Leiskau L, Hushka A, Wu K, Nur K, Netz DJA, Perlstein DL, Pierik AJ. Cytosolic iron-sulfur protein assembly system identifies clients by a C-terminal tripeptide. Proc Natl Acad Sci U S A 2023; 120:e2311057120. [PMID: 37883440 PMCID: PMC10623007 DOI: 10.1073/pnas.2311057120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
The eukaryotic cytosolic Fe-S protein assembly (CIA) machinery inserts iron-sulfur (Fe-S) clusters into cytosolic and nuclear proteins. In the final maturation step, the Fe-S cluster is transferred to the apo-proteins by the CIA-targeting complex (CTC). However, the molecular recognition determinants of client proteins are unknown. We show that a conserved [LIM]-[DES]-[WF]-COO- tripeptide is present at the C-terminus of more than a quarter of clients or their adaptors. When present, this targeting complex recognition (TCR) motif is necessary and sufficient for binding to the CTC in vitro and for directing Fe-S cluster delivery in vivo. Remarkably, fusion of this TCR signal enables engineering of cluster maturation on a nonnative protein via recruitment of the CIA machinery. Our study advances our understanding of Fe-S protein maturation and paves the way for bioengineering novel pathways containing Fe-S enzymes.
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Affiliation(s)
| | - Carina Greth
- Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | | | - Yaxi Liu
- Department of Chemistry, Boston University, Boston, MA02215
| | - Catharina M. Blinn
- Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | - Simone Beller
- Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | - Laura Leiskau
- Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | - Anthony Hushka
- Department of Chemistry, Boston University, Boston, MA02215
| | - Kassandra Wu
- Department of Chemistry, Boston University, Boston, MA02215
| | - Kübra Nur
- Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | - Daili J. A. Netz
- Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern67663, Germany
| | | | - Antonio J. Pierik
- Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern67663, Germany
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6
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Marquez MD, Greth C, Buzuk A, Liu Y, Blinn CM, Beller S, Leiskau L, Hushka A, Wu K, Nur K, Netz DJ, Perlstein DL, Pierik AJ. Cytosolic iron-sulfur protein assembly system identifies clients by a C-terminal tripeptide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541488. [PMID: 37292740 PMCID: PMC10245660 DOI: 10.1101/2023.05.19.541488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The eukaryotic cytosolic Fe-S protein assembly (CIA) machinery inserts iron-sulfur (Fe-S) clusters into cytosolic and nuclear proteins. In the final maturation step, the Fe-S cluster is transferred to the apo-proteins by the CIA-targeting complex (CTC). However, the molecular recognition determinants of client proteins are unknown. We show that a conserved [LIM]-[DES]-[WF]-COO- tripeptide present at the C-terminus of clients is necessary and sufficient for binding to the CTC in vitro and directing Fe-S cluster delivery in vivo. Remarkably, fusion of this TCR (target complex recognition) signal enables engineering of cluster maturation on a non-native protein via recruitment of the CIA machinery. Our study significantly advances our understanding of Fe-S protein maturation and paves the way for bioengineering applications.
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Affiliation(s)
| | - Carina Greth
- Department of Chemistry, RPTU Kaiserslautern-Landau; 67663 Kaiserslautern, Germany
| | | | - Yaxi Liu
- Department of Chemistry, Boston University; Boston, MA, USA
| | - Catharina M. Blinn
- Department of Chemistry, RPTU Kaiserslautern-Landau; 67663 Kaiserslautern, Germany
| | - Simone Beller
- Department of Chemistry, RPTU Kaiserslautern-Landau; 67663 Kaiserslautern, Germany
| | - Laura Leiskau
- Department of Chemistry, RPTU Kaiserslautern-Landau; 67663 Kaiserslautern, Germany
| | - Anthony Hushka
- Department of Chemistry, Boston University; Boston, MA, USA
| | - Kassandra Wu
- Department of Chemistry, Boston University; Boston, MA, USA
| | - Kübra Nur
- Department of Chemistry, RPTU Kaiserslautern-Landau; 67663 Kaiserslautern, Germany
| | - Daili J. Netz
- Department of Chemistry, RPTU Kaiserslautern-Landau; 67663 Kaiserslautern, Germany
| | | | - Antonio J. Pierik
- Department of Chemistry, RPTU Kaiserslautern-Landau; 67663 Kaiserslautern, Germany
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7
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Bak DW, Weerapana E. Monitoring Fe-S cluster occupancy across the E. coli proteome using chemoproteomics. Nat Chem Biol 2023; 19:356-366. [PMID: 36635565 PMCID: PMC9992348 DOI: 10.1038/s41589-022-01227-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous metallocofactors involved in redox chemistry, radical generation and gene regulation. Common methods to monitor Fe-S clusters include spectroscopic analysis of purified proteins and autoradiographic visualization of radiolabeled iron distribution in proteomes. Here, we report a chemoproteomic strategy that monitors changes in the reactivity of Fe-S cysteine ligands to inform on Fe-S cluster occupancy. We highlight the utility of this platform in Escherichia coli by (1) demonstrating global disruptions in Fe-S incorporation in cells cultured under iron-depleted conditions, (2) determining Fe-S client proteins reliant on five scaffold, carrier and chaperone proteins within the Isc Fe-S biogenesis pathway and (3) identifying two previously unannotated Fe-S proteins, TrhP and DppD. In summary, the chemoproteomic strategy described herein is a powerful tool that reports on Fe-S cluster incorporation directly within a native proteome, enabling the interrogation of Fe-S biogenesis pathways and the identification of previously uncharacterized Fe-S proteins.
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Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA.
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8
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Pandey AK, Pain J, J B, Dancis A, Pain D. Essential mitochondrial role in iron-sulfur cluster assembly of the cytoplasmic isopropylmalate isomerase Leu1 in Saccharomyces cerevisiae. Mitochondrion 2023; 69:104-115. [PMID: 36773733 DOI: 10.1016/j.mito.2023.02.006] [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: 11/11/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Iron-sulfur (Fe-S) cluster assembly in mitochondria and cytoplasm is essential for cell viability. In the yeast S. cerevisiae, Leu1 [4Fe-4S] is the cytoplasmic isopropylmalate isomerase involved in leucine biosynthesis. Using permeabilized Δleu1 cells and recombinant apo-Leu1R, here we show that the [4Fe-4S] cluster assembly on Leu1R can be reconstituted in a physiologic manner requiring both mitochondria and cytoplasm, as judged by conversion of the inactive enzyme to an active form. The mitochondrial contribution to this reconstitution assay is abrogated by inactivating mutations in the mitochondrial ISC (iron-sulfur cluster assembly) machinery components (such as Nfs1 cysteine desulfurase and Ssq1 chaperone) or the mitochondrial exporter Atm1. Likewise, depletion of a CIA (cytoplasmic iron-sulfur protein assembly) component Dre2 leads to impaired Leu1R reconstitution. Mitochondria likely make and export an intermediate, called X-S or (Fe-S)int, that is needed for cytoplasmic Fe-S cluster biosynthesis. Here we show that once exported, the same intermediate can be used for both [2Fe-2S] and [4Fe-4S] cluster biogenesis in the cytoplasm, with no further requirement of mitochondria. Our data also suggest that the exported intermediate can activate defective/latent CIA components in cytoplasm isolated from nfs1 or Δatm1 mutant cells. These findings may provide a way to isolate X-S or (Fe-S)int.
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Affiliation(s)
- Ashutosh K Pandey
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, United States
| | - Jayashree Pain
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, United States
| | - Brindha J
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, United States
| | - Andrew Dancis
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, United States
| | - Debkumar Pain
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, United States.
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9
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Yang Y, Wang L, Che Z, Wang R, Cui R, Xu H, Chu S, Jiao Y, Zhang H, Yu D, Zhang D. Novel target sites for soybean yield enhancement by photosynthesis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153580. [PMID: 34871989 DOI: 10.1016/j.jplph.2021.153580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Photosynthesis plays an important role in plant growth and development. Increasing photosynthetic rate is a main objective of improving crop productivity. Chlorophyll fluorescence is an effective method for quickly evaluating photosynthesis. In this study, four representative chlorophyll fluorescence parameters, that is, maximum quantum efficiency of photosystem II, quantum efficiency of PSII, photochemical quenching, and non-photochemical quenching, of 219 diverse soybean accessions were measured across three environments. The underlying genetic architecture was analyzed by genome-wide association study. Forty-eight SNPs were detected to associate with the four traits and explained 10.43-20.41% of the phenotypic variation. Nine candidate genes in the stable QTLs were predicted. Great differences in the expression levels of the candidate genes existed between the high photosynthetic efficiency accessions and low photosynthetic efficiency accessions. In all, we uncover 17 QTLs associated with photosynthesis-related traits and nine genes that may participate in the regulation of photosynthesis, which can provide references for revealing the genetic mechanism of photosynthesis. These QTLs and candidate genes will provide new targets for crop yield improvement through increasing photosynthesis.
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Affiliation(s)
- Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Li Wang
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210014, China
| | - Zhijun Che
- Ningxia University, Yinchuan, 750021, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Ruifang Cui
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Hengyou Zhang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, 150081, China
| | - Deyue Yu
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210014, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China.
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10
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Campos OA, Attar N, Cheng C, Vogelauer M, Mallipeddi NV, Schmollinger S, Matulionis N, Christofk HR, Merchant SS, Kurdistani SK. A pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich's ataxia. SCIENCE ADVANCES 2021; 7:eabj9889. [PMID: 34919435 PMCID: PMC8682991 DOI: 10.1126/sciadv.abj9889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Disruptions to iron-sulfur (Fe-S) clusters, essential cofactors for a broad range of proteins, cause widespread cellular defects resulting in human disease. A source of damage to Fe-S clusters is cuprous (Cu1+) ions. Since histone H3 enzymatically produces Cu1+ for copper-dependent functions, we asked whether this activity could become detrimental to Fe-S clusters. Here, we report that histone H3–mediated Cu1+ toxicity is a major determinant of cellular functional pool of Fe-S clusters. Inadequate Fe-S cluster supply, due to diminished assembly as occurs in Friedreich’s ataxia or defective distribution, causes severe metabolic and growth defects in Saccharomyces cerevisiae. Decreasing Cu1+ abundance, through attenuation of histone cupric reductase activity or depletion of total cellular copper, restored Fe-S cluster–dependent metabolism and growth. Our findings reveal an interplay between chromatin and mitochondria in Fe-S cluster homeostasis and a potential pathogenic role for histone enzyme activity and Cu1+ in diseases with Fe-S cluster dysfunction.
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Affiliation(s)
- Oscar A. Campos
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Narsis Attar
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan V. Mallipeddi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Nedas Matulionis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sabeeha S. Merchant
- QB3-Berkeley, University of California, Berkeley, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Siavash K. Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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11
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Kim JE, Vali SW, Nguyen TQ, Dancis A, Lindahl PA. Mössbauer and LC-ICP-MS investigation of iron trafficking between vacuoles and mitochondria in vma2ΔSaccharomyces cerevisiae. J Biol Chem 2020; 296:100141. [PMID: 33268384 PMCID: PMC7948489 DOI: 10.1074/jbc.ra120.015907] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/24/2020] [Accepted: 12/02/2020] [Indexed: 01/09/2023] Open
Abstract
Vacuoles are acidic organelles that store FeIII polyphosphate, participate in iron homeostasis, and have been proposed to deliver iron to mitochondria for iron–sulfur cluster (ISC) and heme biosynthesis. Vma2Δ cells have dysfunctional V-ATPases, rendering their vacuoles nonacidic. These cells have mitochondria that are iron-dysregulated, suggesting disruption of a putative vacuole-to-mitochondria iron trafficking pathway. To investigate this potential pathway, we examined the iron content of a vma2Δ mutant derived from W303 cells using Mössbauer and EPR spectroscopies and liquid chromatography interfaced with inductively-coupled-plasma mass spectrometry. Relative to WT cells, vma2Δ cells contained WT concentrations of iron but nonheme FeII dominated the iron content of fermenting and respiring vma2Δ cells, indicating that the vacuolar FeIII ions present in WT cells had been reduced. However, vma2Δ cells synthesized WT levels of ISCs/hemes and had normal aconitase activity. The iron content of vma2Δ mitochondria was similar to WT, all suggesting that iron delivery to mitochondria was not disrupted. Chromatograms of cytosolic flow–through solutions exhibited iron species with apparent masses of 600 and 800 Da for WT and vma2∆, respectively. Mutant cells contained high copper concentrations and high concentrations of a species assigned to metallothionein, indicating copper dysregulation. vma2Δ cells from previously studied strain BY4741 exhibited iron-associated properties more consistent with prior studies, suggesting subtle strain differences. Vacuoles with functional V-ATPases appear unnecessary in W303 cells for iron to enter mitochondria and be used in ISC/heme biosynthesis; thus, there appears to be no direct or dedicated vacuole-to-mitochondria iron trafficking pathway. The vma2Δ phenotype may arise from alterations in trafficking of iron directly from cytosol to mitochondria.
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Affiliation(s)
- Joshua E Kim
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Shaik Waseem Vali
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Trang Q Nguyen
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Andrew Dancis
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA; Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, Texas, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
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12
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K JCB, Kapoor BS, Mandal K, Ghosh S, Mokhamatam RB, Manna SK, Mukhopadhyay SS. Loss of Mitochondrial Localization of Human FANCG Causes Defective FANCJ Helicase. Mol Cell Biol 2020; 40:e00306-20. [PMID: 32989015 PMCID: PMC7652403 DOI: 10.1128/mcb.00306-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/11/2020] [Accepted: 09/17/2020] [Indexed: 11/20/2022] Open
Abstract
Fanconi anemia (FA) is a unique DNA damage repair pathway. To date, 22 genes have been identified that are associated with the FA pathway. A defect in any of those genes causes genomic instability, and the patients bearing the mutation become susceptible to cancer. In our earlier work, we identified that Fanconi anemia protein G (FANCG) protects the mitochondria from oxidative stress. In this report, we have identified eight patients having a mutation (C.65G>C), which converts arginine at position 22 to proline (p.Arg22Pro) in the N terminus of FANCG. The mutant protein, hFANCGR22P, is able to repair the DNA and able to retain the monoubiquitination of FANCD2 in the FANCGR22P/FGR22P cell. However, it lost mitochondrial localization and failed to protect mitochondria from oxidative stress. Mitochondrial instability in the FANCGR22P cell causes the transcriptional downregulation of mitochondrial iron-sulfur cluster biogenesis protein frataxin (FXN) and the resulting iron deficiency of FA protein FANCJ, an iron-sulfur-containing helicase involved in DNA repair.
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Affiliation(s)
- Jagadeesh Chandra Bose K
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Bishwajit Singh Kapoor
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Kamal Mandal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Shubhrima Ghosh
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | | | - Sunil K Manna
- Center for DNA Finger Printing and Diagnostics, Hyderabad, India
| | - Sudit S Mukhopadhyay
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
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13
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Zulkifli M, Neff JK, Timbalia SA, Garza NM, Chen Y, Watrous JD, Murgia M, Trivedi PP, Anderson SK, Tomar D, Nilsson R, Madesh M, Jain M, Gohil VM. Yeast homologs of human MCUR1 regulate mitochondrial proline metabolism. Nat Commun 2020; 11:4866. [PMID: 32978391 PMCID: PMC7519068 DOI: 10.1038/s41467-020-18704-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 09/02/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria house evolutionarily conserved pathways of carbon and nitrogen metabolism that drive cellular energy production. Mitochondrial bioenergetics is regulated by calcium uptake through the mitochondrial calcium uniporter (MCU), a multi-protein complex whose assembly in the inner mitochondrial membrane is facilitated by the scaffold factor MCUR1. Intriguingly, many fungi that lack MCU contain MCUR1 homologs, suggesting alternate functions. Herein, we characterize Saccharomyces cerevisiae homologs Put6 and Put7 of MCUR1 as regulators of mitochondrial proline metabolism. Put6 and Put7 are tethered to the inner mitochondrial membrane in a large hetero-oligomeric complex, whose abundance is regulated by proline. Loss of this complex perturbs mitochondrial proline homeostasis and cellular redox balance. Yeast cells lacking either Put6 or Put7 exhibit a pronounced defect in proline utilization, which can be corrected by the heterologous expression of human MCUR1. Our work uncovers an unexpected role of MCUR1 homologs in mitochondrial proline metabolism.
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Affiliation(s)
- Mohammad Zulkifli
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - John K Neff
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Shrishiv A Timbalia
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Natalie M Garza
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Yingqi Chen
- Departments of Medicine and Pharmacology, University of California, San Diego, 9500 Gilman Avenue, La Jolla, CA, 92093, USA
| | - Jeramie D Watrous
- Departments of Medicine and Pharmacology, University of California, San Diego, 9500 Gilman Avenue, La Jolla, CA, 92093, USA
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, 35121, Padua, Italy
- Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
| | - Prachi P Trivedi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Steven K Anderson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Dhanendra Tomar
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Roland Nilsson
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
- Division of Cardiovascular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Muniswamy Madesh
- Department of Medicine, Cardiology Division, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California, San Diego, 9500 Gilman Avenue, La Jolla, CA, 92093, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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14
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Li Y, Lou W, Grevel A, Böttinger L, Liang Z, Ji J, Patil VA, Liu J, Ye C, Hüttemann M, Becker T, Greenberg ML. Cardiolipin-deficient cells have decreased levels of the iron-sulfur biogenesis protein frataxin. J Biol Chem 2020; 295:11928-11937. [PMID: 32636300 PMCID: PMC7450130 DOI: 10.1074/jbc.ra120.013960] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Cardiolipin (CL) is the signature phospholipid of mitochondrial membranes, where it is synthesized locally and plays an important role in mitochondrial bioenergetics. Previous studies in the yeast model have indicated that CL is required for optimal iron homeostasis, which is disrupted by a mechanism not yet determined in the yeast CL mutant, crd1Δ. This finding has implications for the severe genetic disorder, Barth syndrome (BTHS), in which CL metabolism is perturbed because of mutations in the CL-remodeling enzyme, tafazzin. Here, we investigate the effects of tafazzin deficiency on iron homeostasis in the mouse myoblast model of BTHS tafazzin knockout (TAZ-KO) cells. Similarly to CL-deficient yeast cells, TAZ-KO cells exhibited elevated sensitivity to iron, as well as to H2O2, which was alleviated by the iron chelator deferoxamine. TAZ-KO cells exhibited increased expression of the iron exporter ferroportin and decreased expression of the iron importer transferrin receptor, likely reflecting a regulatory response to elevated mitochondrial iron. Reduced activities of mitochondrial iron-sulfur cluster enzymes suggested that the mechanism underlying perturbation of iron homeostasis was defective iron-sulfur biogenesis. We observed decreased levels of Yfh1/frataxin, an essential component of the iron-sulfur biogenesis machinery, in mitochondria from TAZ-KO mouse cells and in CL-deleted yeast crd1Δ cells, indicating that the role of CL in iron-sulfur biogenesis is highly conserved. Yeast crd1Δ cells exhibited decreased processing of the Yfh1 precursor upon import, which likely contributes to the iron homeostasis defects. Implications for understanding the pathogenesis of BTHS are discussed.
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Affiliation(s)
- Yiran Li
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Wenjia Lou
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Alexander Grevel
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lena Böttinger
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Zhuqing Liang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jiajia Ji
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Vinay A Patil
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Cunqi Ye
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Thomas Becker
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
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15
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Hunsaker EW, Franz KJ. Candida albicans reprioritizes metal handling during fluconazole stress. Metallomics 2020; 11:2020-2032. [PMID: 31709426 DOI: 10.1039/c9mt00228f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Maintenance of metal homeostasis is critical to cell survival due to the multitude of cellular processes that depend on one or more metal cofactors. Here, we show that the opportunistic fungal pathogen Candida albicans extensively remodels its metal homeostasis networks to respond to treatment with the antifungal drug fluconazole. Disruption of the ergosterol biosynthetic pathway by fluconazole requires C. albicans adaptation, including increased Cu import and storage, increased retention of Fe, Mn, and Zn, altered utilization of Cu- and Mn-dependent enzymes, mobilization of Fe stores, and increased production of the heme prosthetic group utilized by the enzyme target of fluconazole. The findings offer a new perspective for thinking about fungal response to drug stress that pushes cells out of their metal homeostatic zones, leading them to enact metal-associated adaptation mechanisms to restore homeostasis to survive.
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Affiliation(s)
- Elizabeth W Hunsaker
- Department of Chemistry, Duke University, French Family Science Center, 124 Science Drive, Durham, North Carolina 27708, USA.
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16
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Patil VA, Li Y, Ji J, Greenberg ML. Loss of the mitochondrial lipid cardiolipin leads to decreased glutathione synthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158542. [PMID: 31672571 PMCID: PMC6980711 DOI: 10.1016/j.bbalip.2019.158542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
Abstract
Previous studies demonstrated that loss of CL in the yeast mutant crd1Δ leads to perturbation of mitochondrial iron‑sulfur (FeS) cluster biogenesis, resulting in decreased activity of mitochondrial and cytosolic Fe-S-requiring enzymes, including aconitase and sulfite reductase. In the current study, we show that crd1Δ cells exhibit decreased levels of glutamate and cysteine and are deficient in the essential antioxidant, glutathione, a tripeptide of glutamate, cysteine, and glycine. Glutathione is the most abundant non-protein thiol essential for maintaining intracellular redox potential in almost all eukaryotes, including yeast. Consistent with glutathione deficiency, the growth defect of crd1Δ cells at elevated temperature was rescued by supplementation of glutathione or glutamate and cysteine. Sensitivity to the oxidants iron (FeSO4) and hydrogen peroxide (H2O2), was rescued by supplementation of glutathione. The decreased intracellular glutathione concentration in crd1Δ was restored by supplementation of glutamate and cysteine, but not by overexpressing YAP1, an activator of expression of glutathione biosynthetic enzymes. These findings show for the first time that CL plays a critical role in regulating intracellular glutathione metabolism.
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Affiliation(s)
- Vinay A Patil
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Yiran Li
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Jiajia Ji
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
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17
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Wang Z, Ma T, Huang Y, Wang J, Chen Y, Kistler HC, Ma Z, Yin Y. A fungal ABC transporter FgAtm1 regulates iron homeostasis via the transcription factor cascade FgAreA-HapX. PLoS Pathog 2019; 15:e1007791. [PMID: 31545842 PMCID: PMC6788720 DOI: 10.1371/journal.ppat.1007791] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/11/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Iron homeostasis is important for growth, reproduction and other metabolic processes in all eukaryotes. However, the functions of ATP-binding cassette (ABC) transporters in iron homeostasis are largely unknown. Here, we found that one ABC transporter (named FgAtm1) is involved in regulating iron homeostasis, by screening sensitivity to iron stress for 60 ABC transporter mutants of Fusarium graminearum, a devastating fungal pathogen of small grain cereal crops worldwide. The lack of FgAtm1 reduces the activity of cytosolic Fe-S proteins nitrite reductase and xanthine dehydrogenase, which causes high expression of FgHapX via activating transcription factor FgAreA. FgHapX represses transcription of genes for iron-consuming proteins directly but activates genes for iron acquisition proteins by suppressing another iron regulator FgSreA. In addition, the transcriptional activity of FgHapX is regulated by the monothiol glutaredoxin FgGrx4. Furthermore, the phosphorylation of FgHapX, mediated by the Ser/Thr kinase FgYak1, is required for its functions in iron homeostasis. Taken together, this study uncovers a novel regulatory mechanism of iron homeostasis mediated by an ABC transporter in an important pathogenic fungus. Essential element iron plays important roles in many cellular processes in all organisms. The function of an ATP-binding cassette (ABC) transporter Atm1 in iron homeostasis has been characterized in Saccharomyces cerevisiae. Our study found that FgAtm1 regulates iron homeostasis via the transcription factor cascade FgAreA-HapX in F. graminearum and the function of FgHapX is dependent on its interaction with FgGrx4 and phosphorylation by the Ser/Thr kinase FgYak1. This study reveals a novel regulatory mechanism of iron homeostasis in an important plant pathogenic fungus, and advances our understanding in iron homeostasis and functions of ABC transporters in eukaryotes.
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Affiliation(s)
- Zhihui Wang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Tianling Ma
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yunyan Huang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Jing Wang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - H. Corby Kistler
- United States Department of Agriculture, Agricultural Research Service, St. Paul, Minnesota, United States of America
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- * E-mail: (ZM); (YY)
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- * E-mail: (ZM); (YY)
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18
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Ror S, Panwar SL. Sef1-Regulated Iron Regulon Responds to Mitochondria-Dependent Iron-Sulfur Cluster Biosynthesis in Candida albicans. Front Microbiol 2019; 10:1528. [PMID: 31354649 PMCID: PMC6630100 DOI: 10.3389/fmicb.2019.01528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/18/2019] [Indexed: 11/13/2022] Open
Abstract
Iron homeostasis mechanisms allow the prime commensal-pathogen Candida albicans to cope with the profound shift in iron levels in the mammalian host. The regulators, Sef1 and Sfu1 influence activation and repression of genes required for iron uptake and acquisition by inducing the expression of iron regulon genes in iron-deplete conditions and inactivating them in iron-replete condition. Our study for the first time shows that C. albicans coordinates the activation of the iron regulon with the mitochondrial use of iron for Fe–S cluster biosynthesis, a cellular process that is connected to cellular iron metabolism. We took advantage of a mutant defective in mitochondrial biogenesis (fzo1Δ/Δ) to assess the aforesaid link as this mutant exhibited sustained expression of the Sef1 iron regulon, signifying an iron-starved state in the mutant. Our analysis demonstrates that mitochondrion is pivotal for regulation of Fe–S cluster synthesis such that the disruption of this cellular process in fzo1Δ/Δ cells lead to excessive mitochondrial iron accumulation and reduced activity of the Fe–S cluster-containing enzyme aconitase. Sef1 responds to defective Fe–S cluster synthesis by regulated changes in its subcellular localization; it was retained in the nucleus resulting in the induced expression of the iron regulon. We predict that the mitochondrial Fe–S assembly generates a molecule that is critical for ensuring iron-responsive transcriptional activation of the Sef1 regulon. All told, our data marks Fe–S biogenesis as a mechanism that meshes cellular iron procurement with mitochondrial iron metabolism resulting in regulating the Sef1 regulon in C. albicans.
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Affiliation(s)
- Shivani Ror
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Panwar
- Yeast Molecular Genetics Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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19
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Jozwiakowski SK, Kummer S, Gari K. Human DNA polymerase delta requires an iron-sulfur cluster for high-fidelity DNA synthesis. Life Sci Alliance 2019; 2:2/4/e201900321. [PMID: 31278166 PMCID: PMC6613617 DOI: 10.26508/lsa.201900321] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023] Open
Abstract
The iron–sulfur cluster in human DNA polymerase delta has an impact on DNA polymerase and exonuclease activities and can hence influence the fidelity of DNA synthesis. Replication of eukaryotic genomes relies on the family B DNA polymerases Pol α, Pol δ, and Pol ε. All of these enzymes coordinate an iron–sulfur (FeS) cluster, but the function of this cofactor has remained largely unclear. Here, we show that the FeS cluster in the catalytic subunit of human Pol δ is coordinated by four invariant cysteines of the C-terminal CysB motif. FeS cluster loss causes a partial destabilisation of the four-subunit enzyme, a defect in double-stranded DNA binding, and compromised polymerase and exonuclease activities. Importantly, complex stability, DNA binding, and enzymatic activities are restored in the presence of proliferating cell nuclear antigen. We further show that also more subtle changes to the FeS cluster-binding pocket that do not abolish FeS cluster binding can have repercussions on the distant exonuclease domain and render the enzyme error-prone. Our data hence suggest that the FeS cluster in human Pol δ is an important co-factor that despite its C-terminal location has an impact on both DNA polymerase and exonuclease activities, and can influence the fidelity of DNA synthesis.
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Affiliation(s)
| | - Sandra Kummer
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Kerstin Gari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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20
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Grossman JD, Gay KA, Camire EJ, Walden WE, Perlstein DL. Coupling Nucleotide Binding and Hydrolysis to Iron-Sulfur Cluster Acquisition and Transfer Revealed through Genetic Dissection of the Nbp35 ATPase Site. Biochemistry 2019; 58:2017-2027. [PMID: 30865432 DOI: 10.1021/acs.biochem.8b00737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cytosolic iron-sulfur cluster assembly (CIA) scaffold, comprising Nbp35 and Cfd1 in yeast, assembles iron-sulfur (FeS) clusters destined for cytosolic and nuclear enzymes. ATP hydrolysis by the CIA scaffold plays an essential but poorly understood role in cluster biogenesis. Here we find that mutation of conserved residues in the four motifs comprising the ATPase site of Nbp35 diminished the scaffold's ability to both assemble and transfer its FeS cluster in vivo. The mutants fall into four phenotypic classes that can be understood by how each set of mutations affects ATP binding and hydrolysis. In vitro studies additionally revealed that occupancy of the bridging FeS cluster binding site decreases the scaffold's affinity for the nucleotide. On the basis of our findings, we propose that nucleotide binding and hydrolysis by the CIA scaffold drive a series of protein conformational changes that regulate association with other proteins in the pathway and with its newly formed FeS cluster. Our results provide insight into how the ATPase and cluster scaffolding activities are allosterically integrated.
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Affiliation(s)
- John D Grossman
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Kelly A Gay
- Department of Microbiology and Immunology , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Eric J Camire
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - William E Walden
- Department of Microbiology and Immunology , University of Illinois at Chicago , Chicago , Illinois 60612 , United States
| | - Deborah L Perlstein
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
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21
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Stegmaier K, Blinn CM, Bechtel DF, Greth C, Auerbach H, Müller CS, Jakob V, Reijerse EJ, Netz DJA, Schünemann V, Pierik AJ. Apd1 and Aim32 Are Prototypes of Bishistidinyl-Coordinated Non-Rieske [2Fe–2S] Proteins. J Am Chem Soc 2019; 141:5753-5765. [DOI: 10.1021/jacs.8b13274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Edward J. Reijerse
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
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22
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Depletion of thiol reducing capacity impairs cytosolic but not mitochondrial iron-sulfur protein assembly machineries. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:240-251. [DOI: 10.1016/j.bbamcr.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023]
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23
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Tonini ML, Peña-Diaz P, Haindrich AC, Basu S, Kriegová E, Pierik AJ, Lill R, MacNeill SA, Smith TK, Lukeš J. Branched late-steps of the cytosolic iron-sulphur cluster assembly machinery of Trypanosoma brucei. PLoS Pathog 2018; 14:e1007326. [PMID: 30346997 PMCID: PMC6211773 DOI: 10.1371/journal.ppat.1007326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 11/01/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
Fe-S clusters are ubiquitous cofactors of proteins involved in a variety of essential cellular processes. The biogenesis of Fe-S clusters in the cytosol and their insertion into proteins is accomplished through the cytosolic iron-sulphur protein assembly (CIA) machinery. The early- and middle-acting modules of the CIA pathway concerned with the assembly and trafficking of Fe-S clusters have been previously characterised in the parasitic protist Trypanosoma brucei. In this study, we applied proteomic and genetic approaches to gain insights into the network of protein-protein interactions of the late-acting CIA targeting complex in T. brucei. All components of the canonical CIA machinery are present in T. brucei including, as in humans, two distinct CIA2 homologues TbCIA2A and TbCIA2B. These two proteins are found interacting with TbCIA1, yet the interaction is mutually exclusive, as determined by mass spectrometry. Ablation of most of the components of the CIA targeting complex by RNAi led to impaired cell growth in vitro, with the exception of TbCIA2A in procyclic form (PCF) trypanosomes. Depletion of the CIA-targeting complex was accompanied by reduced levels of protein-bound cytosolic iron and decreased activity of an Fe-S dependent enzyme in PCF trypanosomes. We demonstrate that the C-terminal domain of TbMMS19 acts as a docking site for TbCIA2B and TbCIA1, forming a trimeric complex that also interacts with target Fe-S apo-proteins and the middle-acting CIA component TbNAR1. Cytosolic and nuclear proteins containing iron-sulphur clusters (Fe-S) are essential for the survival of every extant eukaryotic cell. The biogenesis of Fe-S clusters and their insertion into proteins is accomplished through the cytosolic iron-sulphur protein assembly (CIA) machinery. Recently, the CIA factors that generate cytosolic Fe-S clusters were characterised in T. brucei, a unicellular parasite that causes diseases in humans and animals. However, an outstanding question in this organism is the way by which the CIA machinery directs and inserts newly formed Fe-S clusters into proteins. We found that the T. brucei proteins TbCIA2B and TbCIA1 assemble at a region of the C-terminal domain of a third protein, TbMMS19, to form a complex labelled the CIA targeting complex (CTC). The CTC interacts with TbNAR1 and with Fe-S proteins, meaning that the complex assists in the transfer of Fe-S clusters from the upstream members of the pathway into target Fe-S proteins. T. brucei cells depleted of CTC had decreased levels of protein-bound cytosolic iron, and lower activities of cytosolic aconitase, an enzyme that depends upon Fe-S clusters to function.
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Affiliation(s)
- Maiko Luis Tonini
- Biomedical Sciences Research Complex (BSRC), University of St Andrews, St Andrews, Fife, United Kingdom
| | - Priscila Peña-Diaz
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Alexander C. Haindrich
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Somsuvro Basu
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Institut für Zytobiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Eva Kriegová
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Antonio J. Pierik
- Faculty of Chemistry–Biochemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Zentrum für synthetische Mikrobiologie, Marburg, Germany
| | - Stuart A. MacNeill
- Biomedical Sciences Research Complex (BSRC), University of St Andrews, St Andrews, Fife, United Kingdom
- * E-mail: (SAM); (TKS); (JL)
| | - Terry K. Smith
- Biomedical Sciences Research Complex (BSRC), University of St Andrews, St Andrews, Fife, United Kingdom
- * E-mail: (SAM); (TKS); (JL)
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
- * E-mail: (SAM); (TKS); (JL)
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24
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da Silva SM, Batista-Nascimento L, Gaspar-Cordeiro A, Vernis L, Pimentel C, Rodrigues-Pousada C. Transcriptional regulation of FeS biogenesis genes: A possible shield against arsenate toxicity activated by Yap1. Biochim Biophys Acta Gen Subj 2018; 1862:2152-2161. [PMID: 30025855 DOI: 10.1016/j.bbagen.2018.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/22/2018] [Accepted: 07/11/2018] [Indexed: 11/26/2022]
Abstract
In the eukaryotic model yeast Saccharomyces cerevisiae, arsenic (As) detoxification is regulated by two transcriptional factors, Yap8 and Yap1. Yap8 specifically controls As extrusion from the cell, whether Yap1 avoids arsenic-induced oxidative damages. Accordingly, cells lacking both Yap1 and Yap8 are more sensitive to arsenate than cells lacking each regulator individually. Strikingly enough, the same sensitivity pattern was observed under anoxia, suggesting that Yap1 role in As detoxification might not be restricted to the regulation of the oxidative stress response. This finding prompted us to study the transcriptomic profile of wild-type and yap1 mutant cells exposed to arsenate. Interestingly, we found that, under such conditions, several genes involved in the biogenesis of FeS proteins were upregulated in a Yap1-dependent way. In line with this observation, arsenate treatment decreases the activity of the mitochondrial aconitase, Aco1, an FeS cluster-containing enzyme, this effect being even more pronounced in the yap1 mutant. Reinforcing the relevance of FeS cluster biogenesis in arsenate detoxification, the overexpression of several ISC and CIA machinery genes alleviates the deleterious effect of arsenate caused by the absence of Yap1 and Yap8. Altogether our data suggest that the upregulation of FeS biogenesis genes regulated by Yap1 might work as a cellular shield against arsenate toxicity.
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Affiliation(s)
- Sofia M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Liliana Batista-Nascimento
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Institute of Molecular Biology, 55128 Mainz, Germany
| | - Ana Gaspar-Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Laurence Vernis
- CNRS UMR 3348, Centre Universitaire, 91405 Orsay, France; Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, 91405 Orsay, France
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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25
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Vo AT, Fleischman NM, Marquez MD, Camire EJ, Esonwune SU, Grossman JD, Gay KA, Cosman JA, Perlstein DL. Defining the domains of Cia2 required for its essential function in vivo and in vitro. Metallomics 2018; 9:1645-1654. [PMID: 29057997 DOI: 10.1039/c7mt00181a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The cytosolic iron-sulfur cluster assembly (CIA) system biosynthesizes iron-sulfur (FeS) cluster cofactors for cytosolic and nuclear proteins. The yeast Cia2 protein is the central component of the targeting complex which identifies apo-protein targets in the final step of the pathway. Herein, we determine that Cia2 contains five conserved motifs distributed between an intrinsically disordered N-terminal domain and a C-terminal domain of unknown function 59 (DUF59). The disordered domain is dispensible for binding the other subunits of the targeting complex, Met18 and Cia1, and the apo-target Rad3 in vitro. While in vivo assays reveal that the C-terminal domain is sufficient to support viability, several phenotypic assays indicate that deletion of the N-terminal domain negatively impacts CIA function. We additionally establish that Glu208, located within a conserved motif found only in eukaryotic DUF59 proteins, is important for the Cia1-Cia2 interaction in vitro. In vivo, E208A-Cia2 results in a diminished activity of the cytosolic iron sulfur cluster protein, Leu1 but only modest effects on hydroxyurea or methylmethane sulfonate sensitivity. Finally, we demonstrate that neither of the two highly conserved motifs of the DUF59 domain are vital for any of Cia2's interactions in vitro yet mutation of the DPE motif in the DUF59 domain results in a nonfunctional allele in vivo. Our observation that four of the five highly conserved motifs of Cia2 are dispensable for targeting complex formation and apo-target binding suggests that Cia2 is not simply a protein-protein interaction mediator but it likely possesses an additional, currently cryptic, function during the final cluster insertion step of CIA.
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Affiliation(s)
- Amanda T Vo
- Department of Chemistry, Boston University, Boston, MA, USA.
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26
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Gallagher PS, Larkin M, Thillainadesan G, Dhakshnamoorthy J, Balachandran V, Xiao H, Wellman C, Chatterjee R, Wheeler D, Grewal SIS. Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control. Nat Struct Mol Biol 2018; 25:372-383. [PMID: 29686279 PMCID: PMC5936480 DOI: 10.1038/s41594-018-0056-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/09/2018] [Indexed: 01/04/2023]
Abstract
Iron metabolism is critical for sustaining life and maintaining human health. Here, we find that iron homeostasis is linked to facultative heterochromatin assembly and regulation of gene expression during adaptive genome control. We show that the fission yeast Clr4/Suv39h histone methyltransferase is part of a rheostat-like mechanism in which transcriptional upregulation of mRNAs in response to environmental change provides feedback to prevent their uncontrolled expression through heterochromatin assembly. Interestingly, proper iron homeostasis is required, as iron depletion or downregulation of iron transporters causes defects in heterochromatin assembly and unrestrained upregulation of gene expression. Remarkably, an unbiased genetic screen revealed that restoration of iron homeostasis is sufficient to re-establish facultative heterochromatin and proper gene control genome-wide. These results establish a role for iron homeostasis in facultative heterochromatin assembly and reveal a dynamic mechanism for reprogramming the genome in response to environmental changes.
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Affiliation(s)
- Pamela S Gallagher
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Wellman
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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27
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Freibert SA, Weiler BD, Bill E, Pierik AJ, Mühlenhoff U, Lill R. Biochemical Reconstitution and Spectroscopic Analysis of Iron-Sulfur Proteins. Methods Enzymol 2018; 599:197-226. [PMID: 29746240 DOI: 10.1016/bs.mie.2017.11.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Iron-sulfur (Fe/S) proteins are involved in numerous key biological functions such as respiration, metabolic processes, protein translation, DNA synthesis, and DNA repair. The simplest types of Fe/S clusters include [2Fe-2S], [3Fe-4S], and [4Fe-4S] forms that sometimes are present in multiple copies. De novo assembly of Fe/S cofactors and their insertion into apoproteins in living cells requires complex proteinaceous machineries that are frequently highly conserved. In eukaryotes such as yeast and mammals, the mitochondrial iron-sulfur cluster assembly machinery and the cytosolic iron-sulfur protein assembly system consist of more than 30 components that cooperate in the generation of some 50 cellular Fe/S proteins. Both the mechanistic dissection of the intracellular Fe/S protein assembly pathways and the identification and characterization of Fe/S proteins rely on tool boxes of in vitro and in vivo methods. These cell biological, biochemical, and biophysical techniques help to determine the extent, stability, and type of bound Fe/S cluster. They also serve to distinguish bona fide Fe/S proteins from other metal-binding proteins containing similar cofactor coordination motifs. Here, we present a collection of in vitro methods that have proven useful for basic biochemical and biophysical characterization of Fe/S proteins. First, we describe the chemical assembly of [2Fe-2S] or [4Fe-4S] clusters on purified apoproteins. Then, we summarize a reconstitution system reproducing the de novo synthesis of a [2Fe-2S] cluster in mitochondria. Finally, we explain the use of UV-vis, CD, electron paramagnetic resonance, and Mössbauer spectroscopy for the routine characterization of Fe/S proteins.
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Affiliation(s)
| | | | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, Germany
| | - Antonio J Pierik
- Chemistry and Biochemistry, Technical University of Kaiserlautern, Kaiserlautern, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität, Marburg, Germany; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Marburg, Germany.
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28
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Ben-Shimon L, Paul VD, David-Kadoch G, Volpe M, Stümpfig M, Bill E, Mühlenhoff U, Lill R, Ben-Aroya S. Fe-S cluster coordination of the chromokinesin KIF4A alters its sub-cellular localization during mitosis. J Cell Sci 2018; 131:jcs.211433. [DOI: 10.1242/jcs.211433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/11/2018] [Indexed: 11/20/2022] Open
Abstract
Fe-S clusters act as co-factors of proteins with diverse functions, e.g. in DNA repair. Down-regulation of the cytosolic iron-sulfur protein assembly (CIA) machinery promotes genomic instability by the inactivation of multiple DNA repair pathways. Furthermore, CIA deficiencies are associated with so far unexplained mitotic defects. Here, we show that CIA2B and MMS19, constituents of the CIA targeting complex involved in facilitating Fe-S cluster insertion into cytosolic and nuclear target proteins, co-localize with components of the mitotic machinery. Down-regulation of CIA2B and MMS19 impairs the mitotic cycle. We identify the chromokinesin KIF4A as a mitotic component involved in these effects. KIF4A binds a Fe-S cluster in vitro through its conserved cysteine-rich domain. We demonstrate in vivo that this domain is required for the mitosis-related KIF4A localization and for the mitotic defects associated with KIF4A knockout. KIF4A is the first identified mitotic component carrying such a post-translational modification. These findings suggest that the lack of Fe-S clusters in KIF4A upon down-regulation of the CIA targeting complex contributes to the mitotic defects.
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Affiliation(s)
- Lilach Ben-Shimon
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Viktoria D. Paul
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Galit David-Kadoch
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Marina Volpe
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Martin Stümpfig
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim-Ruhr, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Shay Ben-Aroya
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
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29
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Stehling O, Paul VD, Bergmann J, Basu S, Lill R. Biochemical Analyses of Human Iron–Sulfur Protein Biogenesis and of Related Diseases. Methods Enzymol 2018; 599:227-263. [DOI: 10.1016/bs.mie.2017.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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30
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Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol 2017; 599:157-196. [PMID: 29746239 DOI: 10.1016/bs.mie.2017.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.
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Affiliation(s)
- Chi-Lin Tsai
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - John A Tainer
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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31
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Yu Q, Zhang B, Li J, Du T, Yi X, Li M, Chen W, Alvarez PJJ. Graphene oxide significantly inhibits cell growth at sublethal concentrations by causing extracellular iron deficiency. Nanotoxicology 2017; 11:1102-1114. [DOI: 10.1080/17435390.2017.1398357] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Bing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Jianrong Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Tingting Du
- College of Environmental Science and Engineering, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin, China
| | - Xiao Yi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Wei Chen
- College of Environmental Science and Engineering, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin, China
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
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32
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Boniecki MT, Freibert SA, Mühlenhoff U, Lill R, Cygler M. Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Nat Commun 2017; 8:1287. [PMID: 29097656 PMCID: PMC5668364 DOI: 10.1038/s41467-017-01497-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/21/2017] [Indexed: 01/25/2023] Open
Abstract
Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.
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Affiliation(s)
- Michal T Boniecki
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5
| | - Sven A Freibert
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany.
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043, Marburg, Germany.
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5.
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada, H3G 0B1.
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33
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Garcia-Santamarina S, Uzarska MA, Festa RA, Lill R, Thiele DJ. Cryptococcus neoformans Iron-Sulfur Protein Biogenesis Machinery Is a Novel Layer of Protection against Cu Stress. mBio 2017; 8:e01742-17. [PMID: 29089435 PMCID: PMC5666163 DOI: 10.1128/mbio.01742-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/03/2017] [Indexed: 11/20/2022] Open
Abstract
Copper (Cu) ions serve as catalytic cofactors to drive key biochemical processes, and yet Cu levels that exceed cellular homeostatic control capacity are toxic. The underlying mechanisms for Cu toxicity are poorly understood. During pulmonary infection by the fungal pathogen Cryptococcus neoformans, host alveolar macrophages compartmentalize Cu to the phagosome, and the ability to detoxify Cu is critical for its survival and virulence. Here, we report that iron-sulfur (Fe-S) clusters are critical targets of Cu toxicity in both Saccharomyces cerevisiae and C. neoformans in a manner that depends on the accessibility of Cu to the Fe-S cofactor. To respond to this Cu-dependent Fe-S stress, C. neoformans induces the transcription of mitochondrial ABC transporter Atm1, which functions in cytosolic-nuclear Fe-S protein biogenesis in response to Cu and in a manner dependent on the Cu metalloregulatory transcription factor Cuf1. As Atm1 functions in exporting an Fe-S precursor from the mitochondrial matrix to the cytosol, C. neoformans cells depleted for Atm1 are sensitive to Cu even while the Cu-detoxifying metallothionein proteins are highly expressed. We provide evidence for a previously unrecognized microbial defense mechanism to deal with Cu toxicity, and we highlight the importance for C. neoformans of having several distinct mechanisms for coping with Cu toxicity which together could contribute to the success of this microbe as an opportunistic human fungal pathogen.IMPORTANCEC. neoformans is an opportunistic pathogen that causes lethal meningitis in over 650,000 people annually. The severity of C. neoformans infections is further compounded by the use of toxic or poorly effective systemic antifungal agents as well as by the difficulty of diagnosis. Cu is a natural potent antimicrobial agent that is compartmentalized within the macrophage phagosome and used by innate immune cells to neutralize microbial pathogens. While the Cu detoxification machinery of C. neoformans is essential for virulence, little is known about the mechanisms by which Cu kills fungi. Here we report that Fe-S cluster-containing proteins, including members of the Fe-S protein biogenesis machinery itself, are critical targets of Cu toxicity and therefore that this biosynthetic process provides an important layer of defense against high Cu levels. Given the role of Cu ionophores as antimicrobials, understanding how Cu is toxic to microorganisms could lead to the development of effective, broad-spectrum antimicrobials. Moreover, understanding Cu toxicity could provide additional insights into the pathophysiology of human diseases of Cu overload such as Wilson's disease.
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Affiliation(s)
| | - Marta A Uzarska
- Institut für Zytobiologie & Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Richard A Festa
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Roland Lill
- Institut für Zytobiologie & Zytopathologie, Philipps-Universität, Marburg, Germany
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Marburg, Germany
| | - Dennis J Thiele
- Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pharmacology and Cancer Biology, Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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34
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Tripathi SK, Xu T, Feng Q, Avula B, Shi X, Pan X, Mask MM, Baerson SR, Jacob MR, Ravu RR, Khan SI, Li XC, Khan IA, Clark AM, Agarwal AK. Two plant-derived aporphinoid alkaloids exert their antifungal activity by disrupting mitochondrial iron-sulfur cluster biosynthesis. J Biol Chem 2017; 292:16578-16593. [PMID: 28821607 PMCID: PMC5633121 DOI: 10.1074/jbc.m117.781773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/15/2017] [Indexed: 11/06/2022] Open
Abstract
Eupolauridine and liriodenine are plant-derived aporphinoid alkaloids that exhibit potent inhibitory activity against the opportunistic fungal pathogens Candida albicans and Cryptococcus neoformans However, the molecular mechanism of this antifungal activity is unknown. In this study, we show that eupolauridine 9591 (E9591), a synthetic analog of eupolauridine, and liriodenine methiodide (LMT), a methiodide salt of liriodenine, mediate their antifungal activities by disrupting mitochondrial iron-sulfur (Fe-S) cluster synthesis. Several lines of evidence supported this conclusion. First, both E9591 and LMT elicited a transcriptional response indicative of iron imbalance, causing the induction of genes that are required for iron uptake and for the maintenance of cellular iron homeostasis. Second, a genome-wide fitness profile analysis showed that yeast mutants with deletions in iron homeostasis-related genes were hypersensitive to E9591 and LMT. Third, treatment of wild-type yeast cells with E9591 or LMT generated cellular defects that mimicked deficiencies in mitochondrial Fe-S cluster synthesis including an increase in mitochondrial iron levels, a decrease in the activities of Fe-S cluster enzymes, a decrease in respiratory function, and an increase in oxidative stress. Collectively, our results demonstrate that E9591 and LMT perturb mitochondrial Fe-S cluster biosynthesis; thus, these two compounds target a cellular pathway that is distinct from the pathways commonly targeted by clinically used antifungal drugs. Therefore, the identification of this pathway as a target for antifungal compounds has potential applications in the development of new antifungal therapies.
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Affiliation(s)
| | - Tao Xu
- From the National Center for Natural Products Research
| | - Qin Feng
- From the National Center for Natural Products Research
| | | | - Xiaomin Shi
- the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, and
| | - Xuewen Pan
- the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, and
| | - Melanie M Mask
- the United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677
| | - Scott R Baerson
- the United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677
| | | | | | - Shabana I Khan
- From the National Center for Natural Products Research
- the Divisions of Pharmacognosy and
| | - Xing-Cong Li
- From the National Center for Natural Products Research
- the Divisions of Pharmacognosy and
| | - Ikhlas A Khan
- From the National Center for Natural Products Research
- the Divisions of Pharmacognosy and
| | - Alice M Clark
- From the National Center for Natural Products Research
- the Divisions of Pharmacognosy and
| | - Ameeta K Agarwal
- From the National Center for Natural Products Research,
- Pharmacology, Department of Biomolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi 38677
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35
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Vallières C, Holland SL, Avery SV. Mitochondrial Ferredoxin Determines Vulnerability of Cells to Copper Excess. Cell Chem Biol 2017; 24:1228-1237.e3. [PMID: 28867595 PMCID: PMC5654725 DOI: 10.1016/j.chembiol.2017.08.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 03/02/2017] [Accepted: 08/01/2017] [Indexed: 01/17/2023]
Abstract
The essential micronutrient copper is tightly regulated in organisms, as environmental exposure or homeostasis defects can cause toxicity and neurodegenerative disease. The principal target(s) of copper toxicity have not been pinpointed, but one key effect is impaired supply of iron-sulfur (FeS) clusters to the essential protein Rli1 (ABCE1). Here, to find upstream FeS biosynthesis/delivery protein(s) responsible for this, we compared copper sensitivity of yeast-overexpressing candidate targets. Overexpression of the mitochondrial ferredoxin Yah1 produced copper hyper-resistance. 55Fe turnover assays revealed that FeS integrity of Yah1 was particularly vulnerable to copper among the test proteins. Furthermore, destabilization of the FeS domain of Yah1 produced copper hypersensitivity, and YAH1 overexpression rescued Rli1 dysfunction. This copper-resistance function was conserved in the human ferredoxin, Fdx2. The data indicate that the essential mitochondrial ferredoxin is an important copper target, determining a tipping point where plentiful copper supply becomes excessive. This knowledge could help in tackling copper-related diseases.
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Affiliation(s)
- Cindy Vallières
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Sara L Holland
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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36
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Li H, Stümpfig M, Zhang C, An X, Stubbe J, Lill R, Huang M. The diferric-tyrosyl radical cluster of ribonucleotide reductase and cytosolic iron-sulfur clusters have distinct and similar biogenesis requirements. J Biol Chem 2017; 292:11445-11451. [PMID: 28515324 DOI: 10.1074/jbc.m117.786178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/04/2017] [Indexed: 01/08/2023] Open
Abstract
How each metalloprotein assembles the correct metal at the proper binding site presents challenges to the cell. The di-iron enzyme ribonucleotide reductase (RNR) uses a diferric-tyrosyl radical (FeIII2-Y•) cofactor to initiate nucleotide reduction. Assembly of this cofactor requires O2, FeII, and a reducing equivalent. Recent studies show that RNR cofactor biosynthesis shares the same source of iron, in the form of [2Fe-2S]-GSH2 from the monothiol glutaredoxin Grx3/4, and the same electron source, in the form of the Dre2-Tah18 electron transfer chain, with the cytosolic iron-sulfur protein assembly (CIA) machinery required for maturation of [4Fe-4S] clusters in cytosolic and nuclear proteins. Here, we further investigated the interplay between the formation of the FeIII2-Y• cofactor in RNR and the cellular iron-sulfur (Fe-S) protein biogenesis pathways by examining both the iron loading into the RNR β subunit and the RNR catalytic activity in yeast mutants depleted of individual components of the mitochondrial iron-sulfur cluster assembly (ISC) and the CIA machineries. We found that both iron loading and cofactor assembly in RNR are dependent on the ISC machinery. We also found that Dre2 is required for RNR cofactor formation but appears to be dispensable for iron loading. None of the CIA components downstream of Dre2 was required for RNR cofactor formation. Thus, the pathways for RNR and Fe-S cluster biogenesis bifurcate after the Dre2-Tah18 step. We conclude that RNR cofactor biogenesis requires the ISC machinery to mature the Grx3/4 and Dre2 Fe-S proteins, which then function in iron and electron delivery to RNR, respectively.
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Affiliation(s)
- Haoran Li
- From the Departments of Chemistry and
| | - Martin Stümpfig
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany, and
| | - Caiguo Zhang
- the Departments of Dermatology and.,Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Xiuxiang An
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - JoAnne Stubbe
- From the Departments of Chemistry and.,Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany, and
| | - Mingxia Huang
- the Departments of Dermatology and .,Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
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37
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Fu DQ, Meng LH, Zhu BZ, Zhu HL, Yan HX, Luo YB. Silencing of the SlNAP7 gene influences plastid development and lycopene accumulation in tomato. Sci Rep 2016; 6:38664. [PMID: 27929131 PMCID: PMC5144135 DOI: 10.1038/srep38664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
Ripening is an important stage of fruit development. To screen the genes associated with pigment formation in tomato fruit, a suppression subtractive hybridization (SSH) cDNA library was constructed by using tomato fruit in the green ripe and break ripe stages, and 129 differential genes were obtained. Using redness as a screening marker, virus-induced gene silencing (VIGS) of the differential genes was performed with a sprout vacuum-infiltration system (SVI). The results showed that silencing the SlNAP7 gene affected the chloroplast development of tomato leaves, manifesting as a photo-bleaching phenotype, and silenced fruit significantly affected the accumulation of lycopene, manifested as a yellow phenotype. In our study, we found that silencing the SlNAP7 gene downregulates the expression of the POR and PORA genes and destroys the normal development of the chloroplast. The expression of related genes included in the lycopene biosynthesis pathway was not significantly changed, but lycopene accumulation was significantly reduced in tomato fruit. Perhaps it was caused by the destruction of the chromoplast, which leads to the oxidation of lycopene. The results show that the SlNAP7 gene influences chloroplast development and lycopene accumulation in tomato.
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Affiliation(s)
- Da-Qi Fu
- Laboratory of Fruit Biology, College of Food Science &Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Lan-Huan Meng
- Laboratory of Fruit Biology, College of Food Science &Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Ben-Zhong Zhu
- Laboratory of Fruit Biology, College of Food Science &Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hong-Liang Zhu
- Laboratory of Fruit Biology, College of Food Science &Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hua-Xue Yan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilisation, Ministry of Agriculture, Guangzhou 510640, China
| | - Yun-Bo Luo
- Laboratory of Fruit Biology, College of Food Science &Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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38
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Kirby J, Dietzel KL, Wichmann G, Chan R, Antipov E, Moss N, Baidoo EEK, Jackson P, Gaucher SP, Gottlieb S, LaBarge J, Mahatdejkul T, Hawkins KM, Muley S, Newman JD, Liu P, Keasling JD, Zhao L. Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae. Metab Eng 2016; 38:494-503. [PMID: 27989805 DOI: 10.1016/j.ymben.2016.10.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/19/2016] [Accepted: 10/25/2016] [Indexed: 01/28/2023]
Abstract
Isoprenoids are used in many commercial applications and much work has gone into engineering microbial hosts for their production. Isoprenoids are produced either from acetyl-CoA via the mevalonate pathway or from pyruvate and glyceraldehyde 3-phosphate via the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway. Saccharomyces cerevisiae exclusively utilizes the mevalonate pathway to synthesize native isoprenoids and in fact the alternative DXP pathway has never been found or successfully reconstructed in the eukaryotic cytosol. There are, however, several advantages to isoprenoid synthesis via the DXP pathway, such as a higher theoretical yield, and it has long been a goal to transplant the pathway into yeast. In this work, we investigate and address barriers to DXP pathway functionality in S. cerevisiae using a combination of synthetic biology, biochemistry and metabolomics. We report, for the first time, functional expression of the DXP pathway in S. cerevisiae. Under low aeration conditions, an engineered strain relying solely on the DXP pathway for isoprenoid biosynthesis achieved an endpoint biomass 80% of that of the same strain using the mevalonate pathway.
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Affiliation(s)
- James Kirby
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Kevin L Dietzel
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Gale Wichmann
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Rossana Chan
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Eugene Antipov
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Nathan Moss
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | | | - Peter Jackson
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Sara P Gaucher
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Shayin Gottlieb
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Jeremy LaBarge
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Tina Mahatdejkul
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Kristy M Hawkins
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Sheela Muley
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Jack D Newman
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Jay D Keasling
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94702, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94702, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé, DK2970 Hørsholm, Denmark
| | - Lishan Zhao
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
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39
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Uzarska MA, Nasta V, Weiler BD, Spantgar F, Ciofi-Baffoni S, Saviello MR, Gonnelli L, Mühlenhoff U, Banci L, Lill R. Mitochondrial Bol1 and Bol3 function as assembly factors for specific iron-sulfur proteins. eLife 2016; 5. [PMID: 27532772 PMCID: PMC5014550 DOI: 10.7554/elife.16673] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/08/2016] [Indexed: 01/01/2023] Open
Abstract
Assembly of mitochondrial iron-sulfur (Fe/S) proteins is a key process of cells, and defects cause many rare diseases. In the first phase of this pathway, ten Fe/S cluster (ISC) assembly components synthesize and insert [2Fe-2S] clusters. The second phase is dedicated to the assembly of [4Fe-4S] proteins, yet this part is poorly understood. Here, we characterize the BOLA family proteins Bol1 and Bol3 as specific mitochondrial ISC assembly factors that facilitate [4Fe-4S] cluster insertion into a subset of mitochondrial proteins such as lipoate synthase and succinate dehydrogenase. Bol1-Bol3 perform largely overlapping functions, yet cannot replace the ISC protein Nfu1 that also participates in this phase of Fe/S protein biogenesis. Bol1 and Bol3 form dimeric complexes with both monothiol glutaredoxin Grx5 and Nfu1. Complex formation differentially influences the stability of the Grx5-Bol-shared Fe/S clusters. Our findings provide the biochemical basis for explaining the pathological phenotypes of patients with mutations in BOLA3. DOI:http://dx.doi.org/10.7554/eLife.16673.001 Proteins perform almost all the tasks necessary for cells to survive. However, some proteins, especially enzymes involved in metabolism and energy production, need to contain extra molecules called co-factors to work properly. In human, yeast and other eukaryotic cells, co-factors called iron-sulfur clusters are made in compartments called mitochondria before being packaged into target proteins. Defects that affect the assembly of proteins with iron-sulfur clusters are associated with severe diseases that affect metabolism, the nervous system and the blood. Mitochondria contain at least 17 proteins involved in making iron-sulfur proteins, but there may be others that have not yet been identified. For example, a study on patients with a rare human genetic disease suggested that a protein called BOLA3 might also play a role in this process. BOLA3 is closely related to the BOLA1 proteins. Here, Uzarska, Nasta, Weiler et al. used yeast to test how these proteins contribute to the assembly of iron-sulfur proteins. Biochemical techniques showed that the yeast equivalents of BOLA1 and BOLA3 (known as Bol1 and Bol3) play specific roles in the assembly pathway. When both of these proteins were missing from yeast, some iron-sulfur proteins – including an important enzyme called lipoic acid synthase – did not assemble properly. The experiments suggest that yeast Bol1 and Bol3 play overlapping and critical roles during the last step of iron-sulfur protein assembly when the iron-sulfur cluster is inserted into the target protein. Lastly, Uzarska, Nasta, Weiler et al. used biophysical techniques to show how Bol1 and Bol3 interact with another mitochondrial protein that performs a more general role in iron-sulfur protein assembly. Defects in assembling iron-sulfur proteins are generally more harmful to human cells than yeast cells. Therefore, the next step is to investigate what exact roles BOLA1 and BOLA3 play in human cells and how similar this pathway is in different eukaryotes. DOI:http://dx.doi.org/10.7554/eLife.16673.002
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Affiliation(s)
- Marta A Uzarska
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Veronica Nasta
- Magnetic Resonance Center CERM, University of Florence, Florence, Italy
| | - Benjamin D Weiler
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Farah Spantgar
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Florence, Italy.,Department of Chemistry, University of Florence, Florence, Italy
| | - Maria Rosaria Saviello
- Magnetic Resonance Center CERM, University of Florence, Florence, Italy.,Department of Chemistry, University of Florence, Florence, Italy
| | - Leonardo Gonnelli
- Magnetic Resonance Center CERM, University of Florence, Florence, Italy.,Department of Chemistry, University of Florence, Florence, Italy
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Florence, Italy.,Department of Chemistry, University of Florence, Florence, Italy
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany.,LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Marburg, Germany
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40
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The conserved protein Dre2 uses essential [2Fe–2S] and [4Fe–4S] clusters for its function in cytosolic iron–sulfur protein assembly. Biochem J 2016; 473:2073-85. [DOI: 10.1042/bcj20160416] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/10/2016] [Indexed: 11/17/2022]
Abstract
The essential protein Dre2 uses iron–sulfur (Fe–S) clusters to transfer electrons for cytosolic Fe–S protein biogenesis. Biochemical, cell biological and spectroscopic approaches demonstrate that recombinant Dre2 binds oxygen-labile [2Fe–2S] and [4Fe–4S] clusters at two conserved C-terminal motifs with four cysteine residues each.
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41
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De Benedetti S, Lucchini G, Marocchi A, Penco S, Lunetta C, Iametti S, Gianazza E, Bonomi F. Serum metal evaluation in a small cohort of Amyotrophic Lateral Sclerosis patients reveals high levels of thiophylic species. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/ped-2015-0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractAmyotrophic Lateral Sclerosis (ALS) has often been associated with improper/altered metal metabolism. Analysis of thiophylic metals in serum from a small and geographically restricted cohort of ALS patients indicates contents of Pb and Ni much higher in patients than in controls (Ni, 5-fold; Pb, 2-fold). Se levels are also higher in the patients’ group, which has instead lower As levels than controls. Thiophylic metals may impair biogenesis of FeS clusters or substitute for iron, even in folded proteins; Se may non-functionally replace S. Thus, improper assembly/ function of FeS proteins could represent another possible issue to be considered in ALS pathogenesis.
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42
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Tanaka N, Kanazawa M, Tonosaki K, Yokoyama N, Kuzuyama T, Takahashi Y. Novel features of the ISC machinery revealed by characterization of Escherichia coli mutants that survive without iron-sulfur clusters. Mol Microbiol 2015; 99:835-48. [PMID: 26560204 DOI: 10.1111/mmi.13271] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 01/09/2023]
Abstract
Biological assembly of iron-sulfur (Fe-S) clusters is mediated by complex systems consisting of multiple proteins. Escherichia coli possesses two distinct systems called the ISC and SUF machineries encoded by iscSUA-hscBA-fdx-iscX and sufABCDSE respectively. Deletion of both pathways results in absence of the biosynthetic apparatus for Fe-S clusters, and consequent lethality, which has hampered detailed genetic studies. Here we report that modification of the isoprenoid biosynthetic pathway can offset the indispensability of the Fe-S cluster biosynthetic systems and show that the resulting Δisc Δsuf double mutants can grow without detectable Fe-S cluster-containing proteins. We also constructed a series of mutants in which each isc gene was disrupted in the deletion background of sufABCDSE. Phenotypic analysis of the mutants revealed that Fdx, an essential electron-transfer Fe-S protein in the ISC machinery, is dispensable under anaerobic conditions, which is similar to the situation with IscA. Furthermore, we found that several suppressor mutations in IscU, an Fe-S scaffold protein responsible for the de novo Fe-S cluster assembly, could bypass the essential role of the chaperone system HscA and HscB. These findings pave the way toward a detailed molecular analysis to understand the mechanisms involved in Fe-S cluster biosynthesis.
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Affiliation(s)
- Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Miaki Kanazawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Keitaro Tonosaki
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Nao Yokoyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
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43
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Saha PP, Srivastava S, Kumar S K P, Sinha D, D'Silva P. Mapping Key Residues of ISD11 Critical for NFS1-ISD11 Subcomplex Stability: IMPLICATIONS IN THE DEVELOPMENT OF MITOCHONDRIAL DISORDER, COXPD19. J Biol Chem 2015; 290:25876-90. [PMID: 26342079 DOI: 10.1074/jbc.m115.678508] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 11/06/2022] Open
Abstract
Biogenesis of the iron-sulfur (Fe-S) cluster is an indispensable process in living cells. In mammalian mitochondria, the initial step of the Fe-S cluster assembly process is assisted by the NFS1-ISD11 complex, which delivers sulfur to scaffold protein ISCU during Fe-S cluster synthesis. Although ISD11 is an essential protein, its cellular role in Fe-S cluster biogenesis is still not defined. Our study maps the important ISD11 amino acid residues belonging to putative helix 1 (Phe-40), helix 3 (Leu-63, Arg-68, Gln-69, Ile-72, Tyr-76), and C-terminal segment (Leu-81, Glu-84) are critical for in vivo Fe-S cluster biogenesis. Importantly, mutation of these conserved ISD11 residues into alanine leads to its compromised interaction with NFS1, resulting in reduced stability and enhanced aggregation of NFS1 in the mitochondria. Due to altered interaction with ISD11 mutants, the levels of NFS1 and Isu1 were significantly depleted, which affects Fe-S cluster biosynthesis, leading to reduced electron transport chain complex (ETC) activity and mitochondrial respiration. In humans, a clinically relevant ISD11 mutation (R68L) has been associated in the development of a mitochondrial genetic disorder, COXPD19. Our findings highlight that the ISD11 R68A/R68L mutation display reduced affinity to form a stable subcomplex with NFS1, and thereby fails to prevent NFS1 aggregation resulting in impairment of the Fe-S cluster biogenesis. The prime affected machinery is the ETC complex, which showed compromised redox properties, causing diminished mitochondrial respiration. Furthermore, the R68L ISD11 mutant displayed accumulation of mitochondrial iron and reactive oxygen species, leading to mitochondrial dysfunction, which correlates with the phenotype observed in COXPD19 patients.
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Affiliation(s)
- Prasenjit Prasad Saha
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
| | - Shubhi Srivastava
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
| | - Praveen Kumar S K
- the Department of Biochemistry, Karnatak University, Dharwad 580003, Karnataka, India
| | - Devanjan Sinha
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
| | - Patrick D'Silva
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka and
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44
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Tfp1 is required for ion homeostasis, fluconazole resistance and N-Acetylglucosamine utilization in Candida albicans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2731-44. [PMID: 26255859 DOI: 10.1016/j.bbamcr.2015.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 11/23/2022]
Abstract
The vacuolar-type H+-ATPase (V-ATPase) is crucial for the maintenance of ion homeostasis. Dysregulation of ion homeostasis affects various aspects of cellular processes. However, the importance of V-ATPase in Candida albicans is not totally clear. In this study, we demonstrated the essential roles of V-ATPase through Tfp1, a putative V-ATPase subunit. Deletion of TFP1 led to generation of an iron starvation signal and reduced total iron content, which was associated with mislocalization of Fet34p that was finally due to disorders in copper homeostasis. Furthermore, the tfp1∆/∆ mutant exhibited weaker growth and lower aconitase activity on nonfermentable carbon sources, and iron or copper addition partially rescued the growth defect. In addition, the tfp1∆/∆ mutant also showed elevated cytosolic calcium levels in normal or low calcium medium that were relevant to calcium release from vacuole. Kinetics of cytosolic calcium response to an alkaline pulse and VCX1 (VCX1 encodes a putative vacuolar Ca2+/H+ exchanger) overexpression assays indicated that the cytosolic calcium status was in relation to Vcx1 activity. Spot assay and concentration-kill curve demonstrated that the tfp1∆/∆ mutant was hypersensitive to fluconazole, which was attributed to reduced ergosterol biosynthesis and CDR1 efflux pump activity, and iron/calcium dysregulation. Interestingly, carbon source utilization tests found the tfp1∆/∆ mutant was defective for growth on N-Acetylglucosamine (GlcNAc) plate, which was associated with ATP depletion due to the decreased ability to catabolize GlcNAc. Taken together, our study gives new insights into functions of Tfp1, and provides the potential to better exploit V-ATPase as an antifungal target.
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Paul VD, Mühlenhoff U, Stümpfig M, Seebacher J, Kugler KG, Renicke C, Taxis C, Gavin AC, Pierik AJ, Lill R. The deca-GX3 proteins Yae1-Lto1 function as adaptors recruiting the ABC protein Rli1 for iron-sulfur cluster insertion. eLife 2015; 4:e08231. [PMID: 26182403 PMCID: PMC4523923 DOI: 10.7554/elife.08231] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/15/2015] [Indexed: 11/13/2022] Open
Abstract
Cytosolic and nuclear iron-sulfur (Fe-S) proteins are involved in many essential pathways including translation and DNA maintenance. Their maturation requires the cytosolic Fe-S protein assembly (CIA) machinery. To identify new CIA proteins we employed systematic protein interaction approaches and discovered the essential proteins Yae1 and Lto1 as binding partners of the CIA targeting complex. Depletion of Yae1 or Lto1 results in defective Fe-S maturation of the ribosome-associated ABC protein Rli1, but surprisingly no other tested targets. Yae1 and Lto1 facilitate Fe-S cluster assembly on Rli1 in a chain of binding events. Lto1 uses its conserved C-terminal tryptophan for binding the CIA targeting complex, the deca-GX3 motifs in both Yae1 and Lto1 facilitate their complex formation, and Yae1 recruits Rli1. Human YAE1D1 and the cancer-related ORAOV1 can replace their yeast counterparts demonstrating evolutionary conservation. Collectively, the Yae1-Lto1 complex functions as a target-specific adaptor that recruits apo-Rli1 to the generic CIA machinery. DOI:http://dx.doi.org/10.7554/eLife.08231.001 Many proteins depend on small molecules called cofactors to be able to perform their roles in cells. One class of proteins—the iron-sulfur proteins—contain cofactors that are made of clusters of iron and sulfide ions. In yeast, humans and other eukaryotes, the clusters are assembled and incorporated into their target proteins by a group of assembly factors called the CIA machinery. Several components of the CIA machinery have previously been identified and most of them appear to be core components that are needed to assemble many different proteins in cells. Since these iron-sulfur proteins are involved in important processes such as the production of proteins and the maintenance of DNA, losing of any of these CIA proteins tends to be lethal to the organism. Paul et al. used several ‘proteomic’ techniques to study the assembly of iron-sulfur proteins in yeast and identified two new proteins called Yae1 and Lto1 that are involved in this process. Unlike other CIA proteins, Yae1 and Lto1 are only required for the assembly of just one particular iron-sulfur protein called Rli1, which is essential for the production of proteins. Most newly made iron-sulfur proteins can bind directly to a group of CIA proteins called the CIA targeting complex, but Rli1 cannot. The experiments show that Lto1 binds to both the CIA targeting complex and to Yae1, which in turn recruits the Rli1 to the CIA complex. Paul et al. also show that humans have proteins that are very similar to Yae1 and Lto1. Inserting the human counterparts of Yae1 and Lto1 into yeast lacking these proteins could fully restore the assembly of iron-sulfur clusters into Rli1. This suggests that Yae1 and Lto1 proteins evolved in the common ancestors of fungi and humans and have changed little since. Taken together, Paul et al.'s findings reveal that Yae1 and Lto1 act as adaptors that link the rest of the CIA machinery to their specific target protein Rli1 in yeast and humans. A future challenge is to find out the three-dimensional structures of Yae1 and Lto1 to better understand how these proteins work and interact. DOI:http://dx.doi.org/10.7554/eLife.08231.002
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Affiliation(s)
- Viktoria Désirée Paul
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Martin Stümpfig
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Jan Seebacher
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karl G Kugler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Renicke
- Fachbereich Biologie/Genetik, Philipps-Universität Marburg, Marburg, Germany
| | - Christof Taxis
- Fachbereich Biologie/Genetik, Philipps-Universität Marburg, Marburg, Germany
| | - Anne-Claude Gavin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio J Pierik
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Marburg, Germany
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Lill R, Dutkiewicz R, Freibert SA, Heidenreich T, Mascarenhas J, Netz DJ, Paul VD, Pierik AJ, Richter N, Stümpfig M, Srinivasan V, Stehling O, Mühlenhoff U. The role of mitochondria and the CIA machinery in the maturation of cytosolic and nuclear iron–sulfur proteins. Eur J Cell Biol 2015; 94:280-91. [DOI: 10.1016/j.ejcb.2015.05.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Fox NG, Das D, Chakrabarti M, Lindahl PA, Barondeau DP. Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe-S Assembly Complex. Biochemistry 2015; 54:3880-9. [PMID: 26016518 PMCID: PMC4675465 DOI: 10.1021/bi5014497] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Iron-sulfur (Fe-S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe-S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe-S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe-S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe-S assembly complex. Here the kinetics of Fe-S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe-S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe-S assembly complex.
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Affiliation(s)
- Nicholas G. Fox
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Deepika Das
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Mrinmoy Chakrabarti
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Paul A. Lindahl
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States
| | - David P. Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
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Fox NG, Chakrabarti M, McCormick SP, Lindahl PA, Barondeau DP. The Human Iron-Sulfur Assembly Complex Catalyzes the Synthesis of [2Fe-2S] Clusters on ISCU2 That Can Be Transferred to Acceptor Molecules. Biochemistry 2015; 54:3871-9. [PMID: 26016389 PMCID: PMC4675461 DOI: 10.1021/bi5014485] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Iron-sulfur (Fe-S) clusters are essential protein cofactors for most life forms. In human mitochondria, the core Fe-S biosynthetic enzymatic complex (called SDUF) consists of NFS1, ISD11, ISCU2, and frataxin (FXN) protein components. Few mechanistic details about how this complex synthesizes Fe-S clusters and how these clusters are delivered to targets are known. Here circular dichroism and Mössbauer spectroscopies were used to reveal details of the Fe-S cluster assembly reaction on the SDUF complex. SDUF reactions generated [2Fe-2S] cluster intermediates that readily converted to stable [2Fe-2S] clusters bound to uncomplexed ISCU2. Similar reactions that included the apo Fe-S acceptor protein human ferredoxin (FDX1) resulted in formation of [2Fe-2S]-ISCU2 rather than [2Fe-2S]-FDX1. Subsequent addition of dithiothreitol (DTT) induced transfer of the cluster from ISCU2 to FDX1, suggesting that [2Fe-2S]-ISCU2 is an intermediate. Reactions that initially included DTT rapidly generated [2Fe-2S]-FDX1 and bypassed formation of [2Fe-2S]-ISCU2. In the absence of apo-FDX1, incubation of [2Fe-2S]-ISCU2 with DTT generated [4Fe-4S]-ISCU2 species. Together, these results conflict with a recent report of stable [4Fe-4S] cluster formation on the SDUF complex. Rather, they support a model in which SDUF builds transient [2Fe-2S] cluster intermediates that generate clusters on sulfur-containing molecules, including uncomplexed ISCU2. Additional small molecule or protein factors are required for the transfer of these clusters to Fe-S acceptor proteins or the synthesis of [4Fe-4S] clusters.
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Affiliation(s)
- Nicholas G. Fox
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Mrinmoy Chakrabarti
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Sean P. McCormick
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Paul A. Lindahl
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States
| | - David P. Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
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The Cytosolic Iron-Sulfur Cluster Assembly Protein MMS19 Regulates Transcriptional Gene Silencing, DNA Repair, and Flowering Time in Arabidopsis. PLoS One 2015; 10:e0129137. [PMID: 26053632 PMCID: PMC4459967 DOI: 10.1371/journal.pone.0129137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 05/05/2015] [Indexed: 11/19/2022] Open
Abstract
MMS19 is an essential component of the cytoplasmic iron-sulfur (Fe-S) cluster assembly complex in fungi and mammals; the mms19 null mutant alleles are lethal. Our study demonstrates that MMS19/MET18 in Arabidopsis thaliana interacts with the cytoplasmic Fe-S cluster assembly complex but is not an essential component of the complex. We find that MMS19 also interacts with the catalytic subunits of DNA polymerases, which have been demonstrated to be involved in transcriptional gene silencing (TGS), DNA repair, and flowering time regulation. Our results indicate that MMS19 has a similar biological function, suggesting a functional link between MMS19 and DNA polymerases. In the mms19 null mutant, the assembly of Fe-S clusters on the catalytic subunit of DNA polymerase α is reduced but not blocked, which is consistent with the viability of the mutant. Our study suggests that MMS19 assists the assembly of Fe-S clusters on DNA polymerases in the cytosol, thereby facilitating transcriptional gene silencing, DNA repair, and flowering time control.
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Substrate-induced radical formation in 4-hydroxybutyryl coenzyme A dehydratase from Clostridium aminobutyricum. Appl Environ Microbiol 2014; 81:1071-84. [PMID: 25452282 DOI: 10.1128/aem.03099-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
4-Hydroxybutyryl-coenzyme A (CoA) dehydratase (4HBD) from Clostridium aminobutyricum catalyzes the reversible dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA and the irreversible isomerization of vinylacetyl-CoA to crotonyl-CoA. 4HBD is an oxygen-sensitive homotetrameric enzyme with one [4Fe-4S](2+) cluster and one flavin adenine dinucleotide (FAD) in each subunit. Upon the addition of crotonyl-CoA or the analogues butyryl-CoA, acetyl-CoA, and CoA, UV-visible light and electron paramagnetic resonance (EPR) spectroscopy revealed an internal one-electron transfer to FAD and the [4Fe-4S](2+) cluster prior to hydration. We describe an active recombinant 4HBD and variants produced in Escherichia coli. The variants of the cluster ligands (H292C [histidine at position 292 is replaced by cysteine], H292E, C99A, C103A, and C299A) had no measurable dehydratase activity and were composed of monomers, dimers, and tetramers. Variants of other potential catalytic residues were composed only of tetramers and exhibited either no measurable (E257Q, E455Q, and Y296W) hydratase activity or <1% (Y296F and T190V) dehydratase activity. The E455Q variant but not the Y296F or E257Q variant displayed the same spectral changes as the wild-type enzyme after the addition of crotonyl-CoA but at a much lower rate. The results suggest that upon the addition of a substrate, Y296 is deprotonated by E455 and reduces FAD to FADH·, aided by protonation from E257 via T190. In contrast to FADH·, the tyrosyl radical could not be detected by EPR spectroscopy. FADH· appears to initiate the radical dehydration via an allylic ketyl radical that was proposed 19 years ago. The mode of radical generation in 4HBD is without precedent in anaerobic radical chemistry. It differs largely from that in enzymes, which use coenzyme B12, S-adenosylmethionine, ATP-driven electron transfer, or flavin-based electron bifurcation for this purpose.
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