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Querci L, Piccioli M, Ciofi-Baffoni S, Banci L. Structural aspects of iron‑sulfur protein biogenesis: An NMR view. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119786. [PMID: 38901495 DOI: 10.1016/j.bbamcr.2024.119786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/15/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
Over the last decade, structural aspects involving iron‑sulfur (Fe/S) protein biogenesis have played an increasingly important role in understanding the high mechanistic complexity of mitochondrial and cytosolic machineries maturing Fe/S proteins. In this respect, solution NMR has had a significant impact because of its ability to monitor transient protein-protein interactions, which are abundant in the networks of pathways leading to Fe/S cluster biosynthesis and transfer, as well as thanks to the developments of paramagnetic NMR in both terms of new methodologies and accurate data interpretation. Here, we review the use of solution NMR in characterizing the structural aspects of human Fe/S proteins and their interactions in the framework of Fe/S protein biogenesis. We will first present a summary of the recent advances that have been achieved by paramagnetic NMR and then we will focus our attention on the role of solution NMR in the field of human Fe/S protein biogenesis.
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Affiliation(s)
- Leonardo Querci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy.
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy.
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2
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Dancis A, Pandey AK, Pain D. Mitochondria function in cytoplasmic FeS protein biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119733. [PMID: 38641180 DOI: 10.1016/j.bbamcr.2024.119733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
Iron‑sulfur (FeS) clusters are cofactors of numerous proteins involved in essential cellular functions including respiration, protein translation, DNA synthesis and repair, ribosome maturation, anti-viral responses, and isopropylmalate isomerase activity. Novel FeS proteins are still being discovered due to the widespread use of cryogenic electron microscopy (cryo-EM) and elegant genetic screens targeted at protein discovery. A complex sequence of biochemical reactions mediated by a conserved machinery controls biosynthesis of FeS clusters. In eukaryotes, a remarkable epistasis has been observed: the mitochondrial machinery, termed ISC (Iron-Sulfur Cluster), lies upstream of the cytoplasmic machinery, termed CIA (Cytoplasmic Iron‑sulfur protein Assembly). The basis for this arrangement is the production of a hitherto uncharacterized intermediate, termed X-S or (Fe-S)int, produced in mitochondria by the ISC machinery, exported by the mitochondrial ABC transporter Atm1 (ABCB7 in humans), and then utilized by the CIA machinery for the cytoplasmic/nuclear FeS cluster assembly. Genetic and biochemical findings supporting this sequence of events are herein presented. New structural views of the Atm1 transport phases are reviewed. The key compartmental roles of glutathione in cellular FeS cluster biogenesis are highlighted. Finally, data are presented showing that every one of the ten core components of the mitochondrial ISC machinery and Atm1, when mutated or depleted, displays similar phenotypes: mitochondrial and cytoplasmic FeS clusters are both rendered deficient, consistent with the epistasis noted above.
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Affiliation(s)
- Andrew Dancis
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
| | - Ashutosh K Pandey
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Debkumar Pain
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
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3
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Botticelli S, La Penna G, Minicozzi V, Stellato F, Morante S, Rossi G, Faraloni C. Predicting the Structure of Enzymes with Metal Cofactors: The Example of [FeFe] Hydrogenases. Int J Mol Sci 2024; 25:3663. [PMID: 38612474 PMCID: PMC11011570 DOI: 10.3390/ijms25073663] [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: 01/19/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
The advent of deep learning algorithms for protein folding opened a new era in the ability of predicting and optimizing the function of proteins once the sequence is known. The task is more intricate when cofactors like metal ions or small ligands are essential to functioning. In this case, the combined use of traditional simulation methods based on interatomic force fields and deep learning predictions is mandatory. We use the example of [FeFe] hydrogenases, enzymes of unicellular algae promising for biotechnology applications to illustrate this situation. [FeFe] hydrogenase is an iron-sulfur protein that catalyzes the chemical reduction of protons dissolved in liquid water into molecular hydrogen as a gas. Hydrogen production efficiency and cell sensitivity to dioxygen are important parameters to optimize the industrial applications of biological hydrogen production. Both parameters are related to the organization of iron-sulfur clusters within protein domains. In this work, we propose possible three-dimensional structures of Chlorella vulgaris 211/11P [FeFe] hydrogenase, the sequence of which was extracted from the recently published genome of the given strain. Initial structural models are built using: (i) the deep learning algorithm AlphaFold; (ii) the homology modeling server SwissModel; (iii) a manual construction based on the best known bacterial crystal structure. Missing iron-sulfur clusters are included and microsecond-long molecular dynamics of initial structures embedded into the water solution environment were performed. Multiple-walkers metadynamics was also used to enhance the sampling of structures encompassing both functional and non-functional organizations of iron-sulfur clusters. The resulting structural model provided by deep learning is consistent with functional [FeFe] hydrogenase characterized by peculiar interactions between cofactors and the protein matrix.
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Affiliation(s)
- Simone Botticelli
- Department of Physics, University of Roma Tor Vergata, 00133 Rome, Italy; (S.B.); (V.M.); (F.S.); (S.M.); (G.R.)
- Section of Roma Tor Vergata, National Institute of Nuclear Physics, 00133 Rome, Italy
| | - Giovanni La Penna
- Section of Roma Tor Vergata, National Institute of Nuclear Physics, 00133 Rome, Italy
- Institute of Chemistry of Organometallic Compounds, National Research Council, 50019 Florence, Italy
| | - Velia Minicozzi
- Department of Physics, University of Roma Tor Vergata, 00133 Rome, Italy; (S.B.); (V.M.); (F.S.); (S.M.); (G.R.)
- Section of Roma Tor Vergata, National Institute of Nuclear Physics, 00133 Rome, Italy
| | - Francesco Stellato
- Department of Physics, University of Roma Tor Vergata, 00133 Rome, Italy; (S.B.); (V.M.); (F.S.); (S.M.); (G.R.)
- Section of Roma Tor Vergata, National Institute of Nuclear Physics, 00133 Rome, Italy
| | - Silvia Morante
- Department of Physics, University of Roma Tor Vergata, 00133 Rome, Italy; (S.B.); (V.M.); (F.S.); (S.M.); (G.R.)
- Section of Roma Tor Vergata, National Institute of Nuclear Physics, 00133 Rome, Italy
| | - Giancarlo Rossi
- Department of Physics, University of Roma Tor Vergata, 00133 Rome, Italy; (S.B.); (V.M.); (F.S.); (S.M.); (G.R.)
- Section of Roma Tor Vergata, National Institute of Nuclear Physics, 00133 Rome, Italy
- Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, 00184 Rome, Italy
| | - Cecilia Faraloni
- Institute of Bioeconomy, National Research Council, 50019 Florence, Italy
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Petronek MS, Allen BG. Maintenance of genome integrity by the late-acting cytoplasmic iron-sulfur assembly (CIA) complex. Front Genet 2023; 14:1152398. [PMID: 36968611 PMCID: PMC10031043 DOI: 10.3389/fgene.2023.1152398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability.
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Lindahl PA, Vali SW. Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei. Metallomics 2022; 14:mfac080. [PMID: 36214417 PMCID: PMC9624242 DOI: 10.1093/mtomcs/mfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX,USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX,USA
| | - Shaik Waseem Vali
- Department of Chemistry, Texas A&M University, College Station, TX,USA
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Fan X, Barshop WD, Vashisht AA, Pandey V, Leal S, Rayatpisheh S, Jami-Alahmadi Y, Sha J, Wohlschlegel JA. Iron-regulated assembly of the cytosolic iron-sulfur cluster biogenesis machinery. J Biol Chem 2022; 298:102094. [PMID: 35654137 PMCID: PMC9243173 DOI: 10.1016/j.jbc.2022.102094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 11/07/2022] Open
Abstract
The cytosolic iron–sulfur (Fe-S) cluster assembly (CIA) pathway delivers Fe-S clusters to nuclear and cytosolic Fe-S proteins involved in essential cellular functions. Although the delivery process is regulated by the availability of iron and oxygen, it remains unclear how CIA components orchestrate the cluster transfer under varying cellular environments. Here, we utilized a targeted proteomics assay for monitoring CIA factors and substrates to characterize the CIA machinery. We find that nucleotide-binding protein 1 (NUBP1/NBP35), cytosolic iron–sulfur assembly component 3 (CIAO3/NARFL), and CIA substrates associate with nucleotide-binding protein 2 (NUBP2/CFD1), a component of the CIA scaffold complex. NUBP2 also weakly associates with the CIA targeting complex (MMS19, CIAO1, and CIAO2B) indicating the possible existence of a higher order complex. Interactions between CIAO3 and the CIA scaffold complex are strengthened upon iron supplementation or low oxygen tension, while iron chelation and reactive oxygen species weaken CIAO3 interactions with CIA components. We further demonstrate that CIAO3 mutants defective in Fe-S cluster binding fail to integrate into the higher order complexes. However, these mutants exhibit stronger associations with CIA substrates under conditions in which the association with the CIA targeting complex is reduced suggesting that CIAO3 and CIA substrates may associate in complexes independently of the CIA targeting complex. Together, our data suggest that CIA components potentially form a metabolon whose assembly is regulated by environmental cues and requires Fe-S cluster incorporation in CIAO3. These findings provide additional evidence that the CIA pathway adapts to changes in cellular environment through complex reorganization.
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Affiliation(s)
- Xiaorui Fan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA; Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Vijaya Pandey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Stephanie Leal
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Shima Rayatpisheh
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jihui Sha
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA.
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7
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Petronek MS, Spitz DR, Allen BG. Iron-Sulfur Cluster Biogenesis as a Critical Target in Cancer. Antioxidants (Basel) 2021; 10:1458. [PMID: 34573089 PMCID: PMC8465902 DOI: 10.3390/antiox10091458] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Cancer cells preferentially accumulate iron (Fe) relative to non-malignant cells; however, the underlying rationale remains elusive. Iron-sulfur (Fe-S) clusters are critical cofactors that aid in a wide variety of cellular functions (e.g., DNA metabolism and electron transport). In this article, we theorize that a differential need for Fe-S biogenesis in tumor versus non-malignant cells underlies the Fe-dependent cell growth demand of cancer cells to promote cell division and survival by promoting genomic stability via Fe-S containing DNA metabolic enzymes. In this review, we outline the complex Fe-S biogenesis process and its potential upregulation in cancer. We also discuss three therapeutic strategies to target Fe-S biogenesis: (i) redox manipulation, (ii) Fe chelation, and (iii) Fe mimicry.
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Affiliation(s)
- Michael S. Petronek
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Douglas R. Spitz
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Bryan G. Allen
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
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Prusty NR, Camponeschi F, Ciofi-Baffoni S, Banci L. The human YAE1-ORAOV1 complex of the cytosolic iron-sulfur protein assembly machinery binds a [4Fe-4S] cluster. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Braymer JJ, Freibert SA, Rakwalska-Bange M, Lill R. Mechanistic concepts of iron-sulfur protein biogenesis in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118863. [PMID: 33007329 DOI: 10.1016/j.bbamcr.2020.118863] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.
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Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Sven A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany; SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
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10
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Daniel T, Faruq HM, Laura Magdalena J, Manuela G, Christopher Horst L. Role of GSH and Iron-Sulfur Glutaredoxins in Iron Metabolism-Review. Molecules 2020; 25:E3860. [PMID: 32854270 PMCID: PMC7503856 DOI: 10.3390/molecules25173860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/19/2020] [Accepted: 08/22/2020] [Indexed: 12/26/2022] Open
Abstract
Glutathione (GSH) was initially identified and characterized for its redox properties and later for its contributions to detoxification reactions. Over the past decade, however, the essential contributions of glutathione to cellular iron metabolism have come more and more into focus. GSH is indispensable in mitochondrial iron-sulfur (FeS) cluster biosynthesis, primarily by co-ligating FeS clusters as a cofactor of the CGFS-type (class II) glutaredoxins (Grxs). GSH is required for the export of the yet to be defined FeS precursor from the mitochondria to the cytosol. In the cytosol, it is an essential cofactor, again of the multi-domain CGFS-type Grxs, master players in cellular iron and FeS trafficking. In this review, we summarize the recent advances and progress in this field. The most urgent open questions are discussed, such as the role of GSH in the export of FeS precursors from mitochondria, the physiological roles of the CGFS-type Grx interactions with BolA-like proteins and the cluster transfer between Grxs and recipient proteins.
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Affiliation(s)
- Trnka Daniel
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, 17475 Greifswald, Germany; (T.D.); (H.M.F.); (J.L.M.); (G.M.)
| | - Hossain Md Faruq
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, 17475 Greifswald, Germany; (T.D.); (H.M.F.); (J.L.M.); (G.M.)
| | - Jordt Laura Magdalena
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, 17475 Greifswald, Germany; (T.D.); (H.M.F.); (J.L.M.); (G.M.)
| | - Gellert Manuela
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, 17475 Greifswald, Germany; (T.D.); (H.M.F.); (J.L.M.); (G.M.)
| | - Lillig Christopher Horst
- Christopher Horst Lillig, Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany
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Maione V, Grifagni D, Torricella F, Cantini F, Banci L. CIAO3 protein forms a stable ternary complex with two key players of the human cytosolic iron–sulfur cluster assembly machinery. J Biol Inorg Chem 2020; 25:501-508. [DOI: 10.1007/s00775-020-01778-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/16/2020] [Indexed: 11/24/2022]
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12
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Lindahl PA. A comprehensive mechanistic model of iron metabolism in Saccharomyces cerevisiae. Metallomics 2019; 11:1779-1799. [PMID: 31531508 DOI: 10.1039/c9mt00199a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ironome of budding yeast (circa 2019) consists of approximately 139 proteins and 5 nonproteinaceous species. These proteins were grouped according to location in the cell, type of iron center(s), and cellular function. The resulting 27 groups were used, along with an additional 13 nonprotein components, to develop a mesoscale mechanistic model that describes the import, trafficking, metallation, and regulation of iron within growing yeast cells. The model was designed to be simultaneously mutually autocatalytic and mutually autoinhibitory - a property called autocatinhibitory that should be most realistic for simulating cellular biochemical processes. The model was assessed at the systems' level. General conclusions are presented, including a new perspective on understanding regulatory mechanisms in cellular systems. Some unsettled issues are described. This model, once fully developed, has the potential to mimic the phenotype (at a coarse-grain level) of all iron-related genetic mutations in this simple and well-studied eukaryote.
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Affiliation(s)
- Paul A Lindahl
- Departments of Chemistry and of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-3255, USA.
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13
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Bai Y, Chen T, Happe T, Lu Y, Sawyer A. Iron-sulphur cluster biogenesis via the SUF pathway. Metallomics 2019; 10:1038-1052. [PMID: 30019043 DOI: 10.1039/c8mt00150b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Iron-sulphur (Fe-S) clusters are versatile cofactors, which are essential for key metabolic processes in cells, such as respiration and photosynthesis, and which may have also played a crucial role in establishing life on Earth. They can be found in almost all living organisms, from unicellular prokaryotes and archaea to multicellular animals and plants, and exist in diverse forms. This review focuses on the most ancient Fe-S cluster assembly system, the sulphur utilization factor (SUF) mechanism, which is crucial in bacteria for cell survival under stress conditions such as oxidation and iron starvation, and which is also present in the chloroplasts of green microalgae and plants, where it is responsible for plastidial Fe-S protein maturation. We explain the SUF Fe-S cluster assembly process, the proteins involved, their regulation and provide evolutionary insights. We specifically focus on examples from Fe-S cluster synthesis in the model organisms Escherichia coli and Arabidopsis thaliana and discuss in an in vivo context the assembly of the [FeFe]-hydrogenase H-cluster from Chlamydomonas reinhardtii.
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Affiliation(s)
- Y Bai
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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14
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Ciofi-Baffoni S, Nasta V, Banci L. Protein networks in the maturation of human iron-sulfur proteins. Metallomics 2019; 10:49-72. [PMID: 29219157 DOI: 10.1039/c7mt00269f] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The biogenesis of iron-sulfur (Fe-S) proteins in humans is a multistage process occurring in different cellular compartments. The mitochondrial iron-sulfur cluster (ISC) assembly machinery composed of at least 17 proteins assembles mitochondrial Fe-S proteins. A cytosolic iron-sulfur assembly (CIA) machinery composed of at least 13 proteins has been more recently identified and shown to be responsible for the Fe-S cluster incorporation into cytosolic and nuclear Fe-S proteins. Cytosolic and nuclear Fe-S protein maturation requires not only the CIA machinery, but also the components of the mitochondrial ISC assembly machinery. An ISC export machinery, composed of a protein transporter located in the mitochondrial inner membrane, has been proposed to act in mediating the export process of a still unknown component that is required for the CIA machinery. Several functional and molecular aspects of the protein networks operative in the three machineries are still largely obscure. This Review focuses on the Fe-S protein maturation processes in humans with the specific aim of providing a molecular picture of the currently known protein-protein interaction networks. The human ISC and CIA machineries are presented, and the ISC export machinery is discussed with respect to possible molecules being the substrates of the mitochondrial protein transporter.
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Affiliation(s)
- Simone Ciofi-Baffoni
- Magnetic Resonance Center-CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.
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Dikicioglu D, Oliver SG. Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements. Biotechnol Bioeng 2019; 116:610-621. [PMID: 30578666 PMCID: PMC6492170 DOI: 10.1002/bit.26905] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/21/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022]
Abstract
Metabolic networks adapt to changes in their environment by modulating the activity of their enzymes and transporters; often by changing their abundance. Understanding such quantitative changes can shed light onto how metabolic adaptation works, or how it can fail and lead to a metabolically dysfunctional state. We propose a strategy to quantify metabolic protein requirements for cofactor‐utilising enzymes and transporters through constraint‐based modelling. The first eukaryotic genome‐scale metabolic model to comprehensively represent iron metabolism was constructed, extending the most recent community model of the Saccharomyces cerevisiae metabolic network. Partial functional impairment of the genes involved in the maturation of iron‐sulphur (Fe‐S) proteins was investigated employing the model and the in silico analysis revealed extensive rewiring of the fluxes in response to this functional impairment, despite its marginal phenotypic effect. The optimal turnover rate of enzymes bearing ion cofactors can be determined via this novel approach; yeast metabolism, at steady state, was determined to employ a constant turnover of its iron‐recruiting enzyme at a rate of 3.02 × 10
−11 mmol·(g biomass)
−1·h
−1.
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Affiliation(s)
- Duygu Dikicioglu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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Function and crystal structure of the dimeric P-loop ATPase CFD1 coordinating an exposed [4Fe-4S] cluster for transfer to apoproteins. Proc Natl Acad Sci U S A 2018; 115:E9085-E9094. [PMID: 30201724 DOI: 10.1073/pnas.1807762115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Maturation of iron-sulfur (Fe-S) proteins in eukaryotes requires complex machineries in mitochondria and cytosol. Initially, Fe-S clusters are assembled on dedicated scaffold proteins and then are trafficked to target apoproteins. Within the cytosolic Fe-S protein assembly (CIA) machinery, the conserved P-loop nucleoside triphosphatase Nbp35 performs a scaffold function. In yeast, Nbp35 cooperates with the related Cfd1, which is evolutionary less conserved and is absent in plants. Here, we investigated the potential scaffold function of human CFD1 (NUBP2) in CFD1-depleted HeLa cells by measuring Fe-S enzyme activities or 55Fe incorporation into Fe-S target proteins. We show that CFD1, in complex with NBP35 (NUBP1), performs a crucial role in the maturation of all tested cytosolic and nuclear Fe-S proteins, including essential ones involved in protein translation and DNA maintenance. CFD1 also matures iron regulatory protein 1 and thus is critical for cellular iron homeostasis. To better understand the scaffold function of CFD1-NBP35, we resolved the crystal structure of Chaetomium thermophilum holo-Cfd1 (ctCfd1) at 2.6-Å resolution as a model Cfd1 protein. Importantly, two ctCfd1 monomers coordinate a bridging [4Fe-4S] cluster via two conserved cysteine residues. The surface-exposed topology of the cluster is ideally suited for both de novo assembly and facile transfer to Fe-S apoproteins mediated by other CIA factors. ctCfd1 specifically interacted with ATP, which presumably associates with a pocket near the Cfd1 dimer interface formed by the conserved Walker motif. In contrast, ctNbp35 preferentially bound GTP, implying differential regulation of the two fungal scaffold components during Fe-S cluster assembly and/or release.
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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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19
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20
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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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21
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Wang H, Nair VS, Holland AA, Capolicchio S, Jessen HJ, Johnson MK, Shears SB. Asp1 from Schizosaccharomyces pombe binds a [2Fe-2S](2+) cluster which inhibits inositol pyrophosphate 1-phosphatase activity. Biochemistry 2015; 54:6462-74. [PMID: 26422458 DOI: 10.1021/acs.biochem.5b00532] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-sulfur (Fe-S) clusters are widely distributed protein cofactors that are vital to cellular biochemistry and the maintenance of bioenergetic homeostasis, but to our knowledge, they have never been identified in any phosphatase. Here, we describe an iron-sulfur cluster in Asp1, a dual-function kinase/phosphatase that regulates cell morphogenesis in Schizosaccharomyces pombe. Full-length Asp1, and its phosphatase domain (Asp1(371-920)), were each heterologously expressed in Escherichia coli. The phosphatase activity is exquisitely specific: it hydrolyzes the 1-diphosphate from just two members of the inositol pyrophosphate (PP-InsP) signaling family, namely, 1-InsP7 and 1,5-InsP8. We demonstrate that Asp1 does not hydrolyze either InsP6, 2-InsP7, 3-InsP7, 4-InsP7, 5-InsP7, 6-InsP7, or 3,5-InsP8. We also recorded 1-phosphatase activity in a human homologue of Asp1, hPPIP5K1, which was heterologously expressed in Drosophila S3 cells with a biotinylated N-terminal tag, and then isolated from cell lysates with avidin beads. Purified, recombinant Asp1(371-920) contained iron and acid-labile sulfide, but the stoichiometry (0.8 atoms of each per protein molecule) indicates incomplete iron-sulfur cluster assembly. We reconstituted the Fe-S cluster in vitro under anaerobic conditions, which increased the stoichiometry to approximately 2 atoms of iron and acid-labile sulfide per Asp1 molecule. The presence of a [2Fe-2S](2+) cluster in Asp1(371-920) was demonstrated by UV-visible absorption, resonance Raman spectroscopy, and electron paramagnetic resonance spectroscopy. We determined that this [2Fe-2S](2+) cluster is unlikely to participate in redox chemistry, since it rapidly degraded upon reduction by dithionite. Biochemical and mutagenic studies demonstrated that the [2Fe-2S](2+) cluster substantially inhibits the phosphatase activity of Asp1, thereby increasing its net kinase activity.
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Affiliation(s)
- Huanchen Wang
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health , 101 T. W. Alexander Drive, Research Triangle Park, North Carolina 27709, United States
| | - Vasudha S Nair
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health , 101 T. W. Alexander Drive, Research Triangle Park, North Carolina 27709, United States
| | - Ashley A Holland
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602, United States
| | - Samanta Capolicchio
- Department of Chemistry, University of Zurich (UZH) , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Henning J Jessen
- Department of Chemistry, University of Zurich (UZH) , Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602, United States
| | - Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health , 101 T. W. Alexander Drive, Research Triangle Park, North Carolina 27709, United States
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22
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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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24
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Liu L, Huang M. Essential role of the iron-sulfur cluster binding domain of the primase regulatory subunit Pri2 in DNA replication initiation. Protein Cell 2015; 6:194-210. [PMID: 25645023 PMCID: PMC4348247 DOI: 10.1007/s13238-015-0134-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/04/2015] [Indexed: 11/26/2022] Open
Abstract
DNA primase catalyzes de novo synthesis of a short RNA primer that is further extended by replicative DNA polymerases during initiation of DNA replication. The eukaryotic primase is a heterodimeric enzyme comprising a catalytic subunit Pri1 and a regulatory subunit Pri2. Pri2 is responsible for facilitating optimal RNA primer synthesis by Pri1 and mediating interaction between Pri1 and DNA polymerase α for transition from RNA synthesis to DNA elongation. All eukaryotic Pri2 proteins contain a conserved C-terminal iron-sulfur (Fe-S) cluster-binding domain that is critical for primase catalytic activity in vitro. Here we show that mutations at conserved cysteine ligands for the Pri2 Fe-S cluster markedly decrease the protein stability, thereby causing S phase arrest at the restrictive temperature. Furthermore, Pri2 cysteine mutants are defective in loading of the entire DNA pol α-primase complex onto early replication origins resulting in defective initiation. Importantly, assembly of the Fe-S cluster in Pri2 is impaired not only by mutations at the conserved cysteine ligands but also by increased oxidative stress in the sod1Δ mutant lacking the Cu/Zn superoxide dismutase. Together these findings highlight the critical role of Pri2's Fe-S cluster domain in replication initiation in vivo and suggest a molecular basis for how DNA replication can be influenced by changes in cellular redox state.
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Affiliation(s)
- Lili Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Mingxia Huang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045 USA
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25
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Paul VD, Lill R. Biogenesis of cytosolic and nuclear iron-sulfur proteins and their role in genome stability. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1528-39. [PMID: 25583461 DOI: 10.1016/j.bbamcr.2014.12.018] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/08/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023]
Abstract
Iron-sulfur (Fe-S) clusters are versatile protein cofactors that require numerous components for their synthesis and insertion into apoproteins. In eukaryotes, maturation of cytosolic and nuclear Fe-S proteins is accomplished by cooperation of the mitochondrial iron-sulfur cluster (ISC) assembly and export machineries, and the cytosolic iron-sulfur protein assembly (CIA) system. Currently, nine CIA proteins are known to specifically assist the two major steps of the biogenesis reaction. They are essential for cell viability and conserved from yeast to man. The essential character of this biosynthetic process is explained by the involvement of Fe-S proteins in central processes of life, e.g., protein translation and numerous steps of nuclear DNA metabolism such as DNA replication and repair. Malfunctioning of these latter Fe-S enzymes leads to genome instability, a hallmark of cancer. This review is focused on the maturation and biological function of cytosolic and nuclear Fe-S proteins, a topic of central interest for both basic and medical research. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Viktoria Désirée Paul
- 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-Str., 35043 Marburg, Germany.
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Abstract
Iron is an essential element for all photosynthetic organisms. The biological use of this transition metal is as an enzyme cofactor, predominantly in electron transfer and catalysis. The main forms of iron cofactor are, in order of decreasing abundance, iron-sulfur clusters, heme, and di-iron or mononuclear iron, with a wide functional range. In plants and algae, iron-sulfur cluster assembly pathways of bacterial origin are localized in the mitochondria and plastids, where there is a high demand for these cofactors. A third iron-sulfur cluster assembly pathway is present in the cytosol that depends on the mitochondria but not on plastid assembly proteins. The biosynthesis of heme takes place mainly in the plastids. The importance of iron-sulfur cofactors beyond photosynthesis and respiration has become evident with recent discoveries of novel iron-sulfur proteins involved in epigenetics and DNA metabolism. In addition, increased understanding of intracellular iron trafficking is opening up research into how iron is distributed between iron cofactor assembly pathways and how this distribution is regulated.
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Affiliation(s)
- Janneke Balk
- John Innes Centre and University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom;
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27
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Netz DJA, Mascarenhas J, Stehling O, Pierik AJ, Lill R. Maturation of cytosolic and nuclear iron-sulfur proteins. Trends Cell Biol 2013; 24:303-12. [PMID: 24314740 DOI: 10.1016/j.tcb.2013.11.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 11/25/2022]
Abstract
Eukaryotic cells contain numerous cytosolic and nuclear iron-sulfur (Fe/S) proteins that perform key functions in metabolic catalysis, iron regulation, protein translation, DNA synthesis, and DNA repair. Synthesis of Fe/S clusters and their insertion into apoproteins are essential for viability and are conserved in eukaryotes. The process is catalyzed in two major steps by the CIA (cytosolic iron-sulfur protein assembly) machinery encompassing nine known proteins. First, a [4Fe-4S] cluster is assembled on a scaffold complex. This step requires a sulfur-containing compound from mitochondria and reducing equivalents from an electron transfer chain. Second, the Fe/S cluster is transferred from the scaffold to specific apoproteins by the CIA targeting complex. This review summarizes our molecular knowledge on CIA protein function during the assembly process.
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Affiliation(s)
- Daili J A Netz
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Judita Mascarenhas
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Oliver Stehling
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Antonio J Pierik
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany; Max-Planck-Institut für Terrestrische Mikrobiologie, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany; LOEWE (Landes-Offensive zur Entwicklung Wissenschaftlich-Ökonomischer Exzellenz) Zentrum für Synthetische Mikrobiologie (SynMikro), Hans-Meerwein-Strasse, 35043 Marburg, Germany.
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Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes. EUKARYOTIC CELL 2013; 13:143-53. [PMID: 24243793 DOI: 10.1128/ec.00158-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cytosolic iron/sulfur cluster assembly (CIA) machinery is responsible for the assembly of cytosolic and nuclear iron/sulfur clusters, cofactors that are vital for all living cells. This machinery is uniquely found in eukaryotes and consists of at least eight proteins in opisthokont lineages, such as animals and fungi. We sought to identify and characterize homologues of the CIA system proteins in the anaerobic stramenopile parasite Blastocystis sp. strain NandII. We identified transcripts encoding six of the components-Cia1, Cia2, MMS19, Nbp35, Nar1, and a putative Tah18-and showed using immunofluorescence microscopy, immunoelectron microscopy, and subcellular fractionation that the last three of them localized to the cytoplasm of the cell. We then used comparative genomic and phylogenetic approaches to investigate the evolutionary history of these proteins. While most Blastocystis homologues branch with their eukaryotic counterparts, the putative Blastocystis Tah18 seems to have a separate evolutionary origin and therefore possibly a different function. Furthermore, our phylogenomic analyses revealed that all eight CIA components described in opisthokonts originated before the diversification of extant eukaryotic lineages and were likely already present in the last eukaryotic common ancestor (LECA). The Nbp35, Nar1 Cia1, and Cia2 proteins have been conserved during the subsequent evolutionary diversification of eukaryotes and are present in virtually all extant lineages, whereas the other CIA proteins have patchy phylogenetic distributions. Cia2 appears to be homologous to SufT, a component of the prokaryotic sulfur utilization factors (SUF) system, making this the first reported evolutionary link between the CIA and any other Fe/S biogenesis pathway. All of our results suggest that the CIA machinery is an ubiquitous biosynthetic pathway in eukaryotes, but its apparent plasticity in composition raises questions regarding how it functions in nonmodel organisms and how it interfaces with various iron/sulfur cluster systems (i.e., the iron/sulfur cluster, nitrogen fixation, and/or SUF system) found in eukaryotic cells.
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Stehling O, Lill R. The role of mitochondria in cellular iron-sulfur protein biogenesis: mechanisms, connected processes, and diseases. Cold Spring Harb Perspect Biol 2013; 5:a011312. [PMID: 23906713 DOI: 10.1101/cshperspect.a011312] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Iron-sulfur (Fe/S) clusters belong to the most ancient protein cofactors in life, and fulfill functions in electron transport, enzyme catalysis, homeostatic regulation, and sulfur activation. The synthesis of Fe/S clusters and their insertion into apoproteins requires almost 30 proteins in the mitochondria and cytosol of eukaryotic cells. This review summarizes our current biochemical knowledge of mitochondrial Fe/S protein maturation. Because this pathway is essential for various extramitochondrial processes, we then explain how mitochondria contribute to the mechanism of cytosolic and nuclear Fe/S protein biogenesis, and to other connected processes including nuclear DNA replication and repair, telomere maintenance, and transcription. We next describe how the efficiency of mitochondria to assemble Fe/S proteins is used to regulate cellular iron homeostasis. Finally, we briefly summarize a number of mitochondrial "Fe/S diseases" in which various biogenesis components are functionally impaired owing to genetic mutations. The thorough understanding of the diverse biochemical disease phenotypes helps with testing the current working model for the molecular mechanism of Fe/S protein biogenesis and its connected processes.
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Affiliation(s)
- Oliver Stehling
- Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany
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Seki M, Takeda Y, Iwai K, Tanaka K. IOP1 protein is an external component of the human cytosolic iron-sulfur cluster assembly (CIA) machinery and functions in the MMS19 protein-dependent CIA pathway. J Biol Chem 2013; 288:16680-16689. [PMID: 23585563 DOI: 10.1074/jbc.m112.416602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The emerging link between iron metabolism and genome integrity is increasingly clear. Recent studies have revealed that MMS19 and cytosolic iron-sulfur cluster assembly (CIA) factors form a complex and have central roles in CIA pathway. However, the composition of the CIA complex, particularly the involvement of the Fe-S protein IOP1, is still unclear. The roles of each component are also largely unknown. Here, we show that MMS19, MIP18, and CIAO1 form a tight "core" complex and that IOP1 is an "external" component of this complex. Although IOP1 and the core complex form a complex both in vivo and in vitro, IOP1 behaves differently in vivo. A deficiency in any core component leads to down-regulation of all of the components. In contrast, IOP1 knockdown does not affect the level of any core component. In MMS19-overproducing cells, other core components are also up-regulated, but the protein level of IOP1 remains unchanged. IOP1 behaves like a target protein in the CIA reaction, like other Fe-S helicases, and the core complex may participate in the maturation process of IOP1. Alternatively, the core complex may catch and hold IOP1 when it becomes mature to prevent its degradation. In any case, IOP1 functions in the MMS19-dependent CIA pathway. We also reveal that MMS19 interacts with target proteins. MIP18 has a role to bridge MMS19 and CIAO1. CIAO1 also binds IOP1. Based on our in vivo and in vitro data, new models of the CIA machinery are proposed.
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Affiliation(s)
- Mineaki Seki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871.
| | - Yukiko Takeda
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871
| | - Kazuhiro Iwai
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871; Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kiyoji Tanaka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871.
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Couturier J, Touraine B, Briat JF, Gaymard F, Rouhier N. The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions. FRONTIERS IN PLANT SCIENCE 2013; 4:259. [PMID: 23898337 PMCID: PMC3721309 DOI: 10.3389/fpls.2013.00259] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/25/2013] [Indexed: 05/18/2023]
Abstract
Many metabolic pathways and cellular processes occurring in most sub-cellular compartments depend on the functioning of iron-sulfur (Fe-S) proteins, whose cofactors are assembled through dedicated protein machineries. Recent advances have been made in the knowledge of the functions of individual components through a combination of genetic, biochemical and structural approaches, primarily in prokaryotes and non-plant eukaryotes. Whereas most of the components of these machineries are conserved between kingdoms, their complexity is likely increased in plants owing to the presence of additional assembly proteins and to the existence of expanded families for several assembly proteins. This review focuses on the new actors discovered in the past few years, such as glutaredoxin, BOLA and NEET proteins as well as MIP18, MMS19, TAH18, DRE2 for the cytosolic machinery, which are integrated into a model for the plant Fe-S cluster biogenesis systems. It also discusses a few issues currently subjected to an intense debate such as the role of the mitochondrial frataxin and of glutaredoxins, the functional separation between scaffold, carrier and iron-delivery proteins and the crosstalk existing between different organelles.
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Affiliation(s)
- Jérémy Couturier
- Interactions Arbres/Micro-organismes, Faculté des Sciences, UMR1136 Université de Lorraine-INRAVandoeuvre, France
| | - Brigitte Touraine
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Jean-François Briat
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Frédéric Gaymard
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Nicolas Rouhier
- Interactions Arbres/Micro-organismes, Faculté des Sciences, UMR1136 Université de Lorraine-INRAVandoeuvre, France
- *Correspondence: Nicolas Rouhier, Université de Lorraine, UMR1136 Université de Lorraine-INRA, Interactions Arbres/Micro-organismes, Faculté des Sciences, Bd des aiguillettes, BP 239,54506 Vandoeuvre, France e-mail:
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Iron-sulphur clusters, their biosynthesis, and biological functions in protozoan parasites. ADVANCES IN PARASITOLOGY 2013; 83:1-92. [PMID: 23876871 DOI: 10.1016/b978-0-12-407705-8.00001-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fe-S clusters are ensembles of sulphide-linked di-, tri-, and tetra-iron centres of a variety of metalloproteins that play important roles in reduction and oxidation of mitochondrial electron transport, energy metabolism, regulation of gene expression, cell survival, nitrogen fixation, and numerous other metabolic pathways. The Fe-S clusters are assembled by one of four distinct systems: NIF, SUF, ISC, and CIA machineries. The ISC machinery is a house-keeping system conserved widely from prokaryotes to higher eukaryotes, while the other systems are present in a limited range of organisms and play supplementary roles under certain conditions such as stress. Fe-S cluster-containing proteins and the components required for Fe-S cluster biosynthesis are modulated under stress conditions, drug resistance, and developmental stages. It is also known that a defect in Fe-S proteins and Fe-S cluster biogenesis leads to many genetic disorders in humans, which indicates the importance of the systems. In this review, we describe the biological and physiological significance of Fe-S cluster-containing proteins and their biosynthesis in parasitic protozoa including Plasmodium, Trypanosoma, Leishmania, Giardia, Trichomonas, Entamoeba, Cryptosporidium, Blastocystis, and microsporidia. We also discuss the roles of Fe-S cluster biosynthesis in proliferation, differentiation, and stress response in protozoan parasites. The heterogeneity of the systems and the compartmentalization of Fe-S cluster biogenesis in the protozoan parasites likely reflect divergent evolution under highly diverse environmental niches, and influence their parasitic lifestyle and pathogenesis. Finally, both Fe-S cluster-containing proteins and their biosynthetic machinery in protozoan parasites are remarkably different from those in their mammalian hosts. Thus, they represent a rational target for the development of novel chemotherapeutic and prophylactic agents against protozoan infections.
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Zhang J, Kasciukovic T, White MF. The CRISPR associated protein Cas4 Is a 5' to 3' DNA exonuclease with an iron-sulfur cluster. PLoS One 2012; 7:e47232. [PMID: 23056615 PMCID: PMC3466216 DOI: 10.1371/journal.pone.0047232] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 09/10/2012] [Indexed: 11/26/2022] Open
Abstract
The Cas4 protein is one of the core CRISPR-associated (Cas) proteins implicated in the prokaryotic CRISPR system for antiviral defence. Cas4 is thought to play a role in the capture of new viral DNA sequences for incorporation into the host genome. No biochemical activity has been reported for Cas4, but it is predicted to include a RecB nuclease domain. We show here that Cas4 family proteins from the archaeon Sulfolobus solfataricus utilise four conserved cysteine residues to bind an iron-sulfur cluster in an arrangement reminiscent of the AddB nuclease of Bacillus subtilis. The Cas4 family protein Sso0001 is a 5′ to 3′ single stranded DNA exonuclease in vitro that is stalled by extrahelical DNA adducts. A role for Cas4 in DNA duplex strand resectioning to generate recombinogenic 3′ single stranded DNA overhangs is proposed. Comparison of the AddB structure with that of a related bacterial nuclease from Eubacterium rectales reveals that the iron-sulfur cluster can be replaced by a zinc ion without disrupting the protein structure, with implications for the evolution of iron-sulfur binding proteins.
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Affiliation(s)
- Jing Zhang
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Taciana Kasciukovic
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Malcolm F. White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, United Kingdom
- * E-mail:
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Netz DJA, Pierik AJ, Stümpfig M, Bill E, Sharma AK, Pallesen LJ, Walden WE, Lill R. A bridging [4Fe-4S] cluster and nucleotide binding are essential for function of the Cfd1-Nbp35 complex as a scaffold in iron-sulfur protein maturation. J Biol Chem 2012; 287:12365-78. [PMID: 22362766 DOI: 10.1074/jbc.m111.328914] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The essential P-loop NTPases Cfd1 and Nbp35 of the cytosolic iron-sulfur (Fe-S) protein assembly machinery perform a scaffold function for Fe-S cluster synthesis. Both proteins contain a nucleotide binding motif of unknown function and a C-terminal motif with four conserved cysteine residues. The latter motif defines the Mrp/Nbp35 subclass of P-loop NTPases and is suspected to be involved in transient Fe-S cluster binding. To elucidate the function of these two motifs, we first created cysteine mutant proteins of Cfd1 and Nbp35 and investigated the consequences of these mutations by genetic, cell biological, biochemical, and spectroscopic approaches. The two central cysteine residues (CPXC) of the C-terminal motif were found to be crucial for cell viability, protein function, coordination of a labile [4Fe-4S] cluster, and Cfd1-Nbp35 hetero-tetramer formation. Surprisingly, the two proximal cysteine residues were dispensable for all these functions, despite their strict evolutionary conservation. Several lines of evidence suggest that the C-terminal CPXC motifs of Cfd1-Nbp35 coordinate a bridging [4Fe-4S] cluster. Upon mutation of the nucleotide binding motifs Fe-S clusters could no longer be assembled on these proteins unless wild-type copies of Cfd1 and Nbp35 were present in trans. This result indicated that Fe-S cluster loading on these scaffold proteins is a nucleotide-dependent step. We propose that the bridging coordination of the C-terminal Fe-S cluster may be ideal for its facile assembly, labile binding, and efficient transfer to target Fe-S apoproteins, a step facilitated by the cytosolic iron-sulfur (Fe-S) protein assembly proteins Nar1 and Cia1 in vivo.
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Affiliation(s)
- Daili J A Netz
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Strasse 6, 35032 Marburg, Germany
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Netz DJA, Stith CM, Stümpfig M, Köpf G, Vogel D, Genau HM, Stodola JL, Lill R, Burgers PMJ, Pierik AJ. Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes. Nat Chem Biol 2011; 8:125-32. [PMID: 22119860 PMCID: PMC3241888 DOI: 10.1038/nchembio.721] [Citation(s) in RCA: 292] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 10/03/2011] [Indexed: 11/09/2022]
Abstract
The eukaryotic replicative DNA polymerases (Pol α, δ and ɛ) and the major DNA mutagenesis enzyme Pol ζ contain two conserved cysteine-rich metal-binding motifs (CysA and CysB) in the C-terminal domain (CTD) of their catalytic subunits. Here we demonstrate by in vivo and in vitro approaches the presence of an essential [4Fe-4S] cluster in the CysB motif of all four yeast B-family DNA polymerases. Loss of the [4Fe-4S] cofactor by cysteine ligand mutagenesis in Pol3 destabilized the CTD and abrogated interaction with the Pol31 and Pol32 subunits. Reciprocally, overexpression of accessory subunits increased the amount of the CTD-bound Fe-S cluster. This implies an important physiological role of the Fe-S cluster in polymerase complex stabilization. Further, we demonstrate that the Zn-binding CysA motif is required for PCNA-mediated Pol δ processivity. Together, our findings show that the function of eukaryotic replicative DNA polymerases crucially depends on different metallocenters for accessory subunit recruitment and replisome stability.
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Affiliation(s)
- Daili J A Netz
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
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36
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RNA silencing of hydrogenase(-like) genes and investigation of their physiological roles in the green alga Chlamydomonas reinhardtii. Biochem J 2010; 431:345-51. [DOI: 10.1042/bj20100932] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The genome of the green alga Chlamydomonas reinhardtii encodes two [FeFe]-hydrogenases, HydA1 and HydA2, and the hydrogenase-like protein HYD3. The unique combination of these proteins in one eukaryotic cell allows for direct comparison of their in vivo functions, which have not been established for HydA2 and HYD3. Using an artificial microRNA silencing method developed recently, the expression of HydA1, HydA2 and HYD3 was specifically down-regulated. Silencing of HydA1 resulted in 4-fold lower hydrogenase protein and activity under anaerobic conditions. In contrast, silencing of HydA2 or HYD3 did not affect hydrogen production. Cell lines with strongly (>90%) decreased HYD3 transcript levels grew more slowly than wild-type. The activity of aldehyde oxidase, a cytosolic Fe-S enzyme, was decreased in HYD3-knockdown lines, whereas Fe-S dependent activities in the chloroplast and mitochondria were unaffected. In addition, the HYD3-knockdown lines grew poorly on hypoxanthine, indicating impaired function of xanthine dehydrogenase, another cytosolic Fe-S enzyme. The expression levels of selected genes in response to hypoxia were unaltered upon HYD3 silencing. Together, our results clearly distinguish the cellular roles of HydA1 and HYD3, and indicate that HYD3, like its yeast and human homologues, has an evolutionary conserved role in the biogenesis or maintenance of cytosolic Fe-S proteins.
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Tah18 transfers electrons to Dre2 in cytosolic iron-sulfur protein biogenesis. Nat Chem Biol 2010; 6:758-65. [PMID: 20802492 DOI: 10.1038/nchembio.432] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 08/03/2010] [Indexed: 11/09/2022]
Abstract
Cytosolic and nuclear iron-sulfur (Fe-S) proteins play key roles in processes such as ribosome maturation, transcription and DNA repair-replication. For biosynthesis of their Fe-S clusters, a dedicated cytosolic Fe-S protein assembly (CIA) machinery is required. Here, we identify the essential flavoprotein Tah18 as a previously unrecognized CIA component and show by cell biological, biochemical and spectroscopic approaches that the complex of Tah18 and the CIA protein Dre2 is part of an electron transfer chain functioning in an early step of cytosolic Fe-S protein biogenesis. Electrons are transferred from NADPH via the FAD- and FMN-containing Tah18 to the Fe-S clusters of Dre2. This electron transfer chain is required for assembly of target but not scaffold Fe-S proteins, suggesting a need for reduction in the generation of stably inserted Fe-S clusters. The pathway is conserved in eukaryotes, as human Ndor1-Ciapin1 proteins can functionally replace yeast Tah18-Dre2.
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38
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Sharma AK, Pallesen LJ, Spang RJ, Walden WE. Cytosolic iron-sulfur cluster assembly (CIA) system: factors, mechanism, and relevance to cellular iron regulation. J Biol Chem 2010; 285:26745-26751. [PMID: 20522543 DOI: 10.1074/jbc.r110.122218] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FeS cluster biogenesis is an essential process in virtually all forms of life. Complex protein machineries that are conserved from bacteria through higher eukaryotes facilitate assembly of the FeS cofactor in proteins. In the last several years, significant strides have been made in our understanding of FeS cluster assembly and the functional overlap of this process with cellular iron homeostasis. This minireview summarizes the present understanding of the cytosolic iron-sulfur cluster assembly (CIA) system in eukaryotes, with a focus on information gained from studies in budding yeast and mammalian systems.
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Affiliation(s)
- Anil K Sharma
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois 60612
| | - Leif J Pallesen
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois 60612
| | - Robert J Spang
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois 60612
| | - William E Walden
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois 60612.
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