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Terenzi A, Pagani MA, Gomez-Casati DF, Busi MV. Structural and Functional Characterization of CreFH1, the Frataxin Homolog from Chlamydomonas reinhardtii. PLANTS 2022; 11:plants11151931. [PMID: 35893635 PMCID: PMC9331050 DOI: 10.3390/plants11151931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022]
Abstract
Frataxin plays a key role in cellular iron homeostasis of different organisms. It has been implicated in iron storage, detoxification, delivery for Fe-S cluster assembly and heme biosynthesis. However, its specific role in iron metabolism remains unclear, especially in photosynthetic organisms. To gain insight into the role and properties of frataxin in algae, we identified the gene CreFH1, which codes for the frataxin homolog from Chlamydomonas reinhardtii. We performed the cloning, expression and biochemical characterization of CreFH1. This protein has a predicted mitochondrial transit peptide and a significant structural similarity to other members of the frataxin family. In addition, CreFH1 was able to form a dimer in vitro, and this effect was increased by the addition of Cu2+ and also attenuated the Fenton reaction in the presence of a mixture of Fe2+ and H2O2. Bacterial cells with overexpression of CreFH1 showed increased growth in the presence of different metals, such as Fe, Cu, Zn and Ni and H2O2. Thus, results indicated that CreFH1 is a functional protein that shows some distinctive features compared to its more well-known counterparts, and would play an important role in response to oxidative stress in C. reinhardtii.
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Puglisi R, Karunanithy G, Hansen DF, Pastore A, Temussi PA. The anatomy of unfolding of Yfh1 is revealed by site-specific fold stability analysis measured by 2D NMR spectroscopy. Commun Chem 2021; 4:127. [PMID: 35243007 PMCID: PMC7612453 DOI: 10.1038/s42004-021-00566-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Most techniques allow detection of protein unfolding either by following the behaviour of single reporters or as an averaged all-or-none process. We recently added 2D NMR spectroscopy to the well-established techniques able to obtain information on the process of unfolding using resonances of residues in the hydrophobic core of a protein. Here, we questioned whether an analysis of the individual stability curves from each resonance could provide additional site-specific information. We used the Yfh1 protein that has the unique feature to undergo both cold and heat denaturation at temperatures above water freezing at low ionic strength. We show that stability curves inconsistent with the average NMR curve from hydrophobic core residues mainly comprise exposed outliers that do nevertheless provide precious information. By monitoring both cold and heat denaturation of individual residues we gain knowledge on the process of cold denaturation and convincingly demonstrate that the two unfolding processes are intrinsically different.
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Affiliation(s)
- Rita Puglisi
- grid.511435.7UK-DRI at King’s College London, The Wohl Institute, London, UK
| | - Gogulan Karunanithy
- grid.83440.3b0000000121901201Department of Structural Biology, Division of Biosciences, University College London, London, UK
| | - D. Flemming Hansen
- grid.83440.3b0000000121901201Department of Structural Biology, Division of Biosciences, University College London, London, UK
| | - Annalisa Pastore
- grid.511435.7UK-DRI at King’s College London, The Wohl Institute, London, UK ,grid.5398.70000 0004 0641 6373European Synchrotron Radiation Facility, Grenoble, France
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3
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Frataxins Emerge as New Players of the Intracellular Antioxidant Machinery. Antioxidants (Basel) 2021; 10:antiox10020315. [PMID: 33672495 PMCID: PMC7923443 DOI: 10.3390/antiox10020315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/30/2022] Open
Abstract
Frataxin is a mitochondrial protein which deficiency causes Friedreich's ataxia, a cardio-neurodegenerative disease. The lack of frataxin induces the dysregulation of mitochondrial iron homeostasis and oxidative stress, which finally causes the neuronal death. The mechanism through which frataxin regulates the oxidative stress balance is rather complex and poorly understood. While the absence of human (Hfra) and yeast (Yfh1) frataxins turn out cells sensitive to oxidative stress, this does not occur when the frataxin gene is knocked-out in E. coli. To better understand the biological roles of Hfra and Yfh1 as endogenous antioxidants, we have studied their ability to inhibit the formation of reactive oxygen species (ROS) from Cu2+- and Fe3+-catalyzed degradation of ascorbic acid. Both proteins drastically reduce the formation of ROS, and during this process they are not oxidized. In addition, we have also demonstrated that merely the presence of Yfh1 or Hfra is enough to protect a highly oxidation-prone protein such as α-synuclein. This unspecific intervention (without a direct binding) suggests that frataxins could act as a shield to prevent the oxidation of a broad set of intracellular proteins, and reinforces that idea that frataxin can be used to prevent neurological pathologies linked to an enhanced oxidative stress.
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Castro IH, Pignataro MF, Sewell KE, Espeche LD, Herrera MG, Noguera ME, Dain L, Nadra AD, Aran M, Smal C, Gallo M, Santos J. Frataxin Structure and Function. Subcell Biochem 2019; 93:393-438. [PMID: 31939159 DOI: 10.1007/978-3-030-28151-9_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian frataxin is a small mitochondrial protein involved in iron sulfur cluster assembly. Frataxin deficiency causes the neurodegenerative disease Friedreich's Ataxia. Valuable knowledge has been gained on the structural dynamics of frataxin, metal-ion-protein interactions, as well as on the effect of mutations on protein conformation, stability and internal motions. Additionally, laborious studies concerning the enzymatic reactions involved have allowed for understanding the capability of frataxin to modulate Fe-S cluster assembly function. Remarkably, frataxin biological function depends on its interaction with some proteins to form a supercomplex, among them NFS1 desulfurase and ISCU, the scaffolding protein. By combining multiple experimental tools including high resolution techniques like NMR and X-ray, but also SAXS, crosslinking and mass-spectrometry, it was possible to build a reliable model of the structure of the desulfurase supercomplex NFS1/ACP-ISD11/ISCU/frataxin. In this chapter, we explore these issues showing how the scientific view concerning frataxin structure-function relationships has evolved over the last years.
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Affiliation(s)
- Ignacio Hugo Castro
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - María Florencia Pignataro
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - Karl Ellioth Sewell
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - Lucía Daniela Espeche
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla"-A.N.L.I.S, Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina
| | - María Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Liliana Dain
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla"-A.N.L.I.S, Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina
| | - Alejandro Daniel Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Martín Aran
- Fundación Instituto Leloir E IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Clara Smal
- Fundación Instituto Leloir E IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Mariana Gallo
- IRBM Science Park S.p.A, Via Pontina km 30,600, 00071, Pomezia, RM, Italy
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina.
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina.
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5
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Guo L, Wang Q, Weng L, Hauser LA, Strawser CJ, Mesaros C, Lynch DR, Blair IA. Characterization of a new N-terminally acetylated extra-mitochondrial isoform of frataxin in human erythrocytes. Sci Rep 2018; 8:17043. [PMID: 30451920 PMCID: PMC6242848 DOI: 10.1038/s41598-018-35346-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/02/2018] [Indexed: 01/18/2023] Open
Abstract
Frataxin is a highly conserved protein encoded by the frataxin (FXN) gene. The full-length 210-amino acid form of protein frataxin (1-210; isoform A) expressed in the cytosol of cells rapidly translocates to the mitochondria, where it is converted to the mature form (81-210) by mitochondrial processing peptidase. Mature frataxin (81-210) is a critically important protein because it facilitates the assembly of mitochondrial iron-sulfur cluster protein complexes such as aconitase, lipoate synthase, and succinate dehydrogenases. Decreased expression of frataxin protein is responsible for the devastating rare genetic disease of Friedreich's ataxia. The mitochondrial form of frataxin has long been thought to be present in erythrocytes even though paradoxically, erythrocytes lack mitochondria. We have discovered that erythrocyte frataxin is in fact a novel isoform of frataxin (isoform E) with 135-amino acids and an N-terminally acetylated methionine residue. There is three times as much isoform E in erythrocytes (20.9 ± 6.4 ng/mL) from the whole blood of healthy volunteers (n = 10) when compared with the mature mitochondrial frataxin present in other blood cells (7.1 ± 1.0 ng/mL). Isoform E lacks a mitochondrial targeting sequence and so is distributed to both cytosol and the nucleus when expressed in cultured cells. When extra-mitochondrial frataxin isoform E is expressed in HEK 293 cells, it is converted to a shorter isoform identical to the mature frataxin found in mitochondria, which raises the possibility that it is involved in disease etiology. The ability to specifically quantify extra-mitochondrial and mitochondrial isoforms of frataxin in whole blood will make it possible to readily follow the natural history of diseases such as Friedreich's ataxia and monitor the efficacy of therapeutic interventions.
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Affiliation(s)
- Lili Guo
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Penn/CHOP Center of Excellence in Friedreich's ataxia, Philadelphia, PA, 19104, United States
| | - Qingqing Wang
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Penn/CHOP Center of Excellence in Friedreich's ataxia, Philadelphia, PA, 19104, United States
| | - Liwei Weng
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Lauren A Hauser
- Penn/CHOP Center of Excellence in Friedreich's ataxia, Philadelphia, PA, 19104, United States
- Departments of Pediatrics and Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States
- Departments of Pediatrics and Neurology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Cassandra J Strawser
- Penn/CHOP Center of Excellence in Friedreich's ataxia, Philadelphia, PA, 19104, United States
- Departments of Pediatrics and Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States
- Departments of Pediatrics and Neurology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Clementina Mesaros
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Penn/CHOP Center of Excellence in Friedreich's ataxia, Philadelphia, PA, 19104, United States
| | - David R Lynch
- Penn/CHOP Center of Excellence in Friedreich's ataxia, Philadelphia, PA, 19104, United States
- Departments of Pediatrics and Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States
- Departments of Pediatrics and Neurology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Ian A Blair
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States.
- Penn/CHOP Center of Excellence in Friedreich's ataxia, Philadelphia, PA, 19104, United States.
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6
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Rasheed M, Yan R, Kelly G, Pastore A. Chemical shift assignment of a thermophile frataxin. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:113-116. [PMID: 29090418 PMCID: PMC5869877 DOI: 10.1007/s12104-017-9790-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
Frataxin is the protein responsible for the genetically-inherited neurodegenerative disease Friedreich's ataxia caused by partial silencing of the protein and loss of function. Although the frataxin function is not yet entirely clear, it has been associated to the machine that builds iron-sulfur clusters, essential prosthetic groups involved in several processes and is strongly conserved in organisms from bacteria to humans. Two of its important molecular partners are the protein NFS1 (or IscS in bacteria), that is the desulfurase which converts cysteine to alanine and produces sulfur, and ISU (or IscU), the scaffold protein which transiently accepts the cluster. While bacterial frataxin has been extensively characterized, only few eukaryotic frataxins have been described. Here we report the 1H, 13C and 15N backbone and side-chain chemical shift assignments of frataxin from Chaetomium thermophilum, a thermophile increasingly used by virtue of its stability.
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Affiliation(s)
- Masooma Rasheed
- Maurice Wohl Institute, King's College London, 5 Cutcombe Rd, London, SE5 9RT, UK
| | - Robert Yan
- Maurice Wohl Institute, King's College London, 5 Cutcombe Rd, London, SE5 9RT, UK
| | - Geoff Kelly
- MRC-NMR Centre, The Crick Institute, London, NW7 1AT, UK
| | - Annalisa Pastore
- Maurice Wohl Institute, King's College London, 5 Cutcombe Rd, London, SE5 9RT, UK.
- Molecular Medicine Department, University of Pavia, Pavia, Italy.
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7
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Guo L, Wang Q, Weng L, Hauser LA, Strawser CJ, Rocha AG, Dancis A, Mesaros C, Lynch DR, Blair IA. Liquid Chromatography-High Resolution Mass Spectrometry Analysis of Platelet Frataxin as a Protein Biomarker for the Rare Disease Friedreich's Ataxia. Anal Chem 2018; 90:2216-2223. [PMID: 29272104 PMCID: PMC5817373 DOI: 10.1021/acs.analchem.7b04590] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Friedreich's ataxia (FA) is an autosomal recessive disease caused by an intronic GAA triplet expansion in the FXN gene, leading to reduced expression of the mitochondrial protein frataxin. FA is estimated to affect 1 in 50 000 with a mean age of death in the fourth decade of life. There are no approved treatments for FA, although experimental approaches, which involve up-regulation or replacement of frataxin protein, are being tested. Frataxin is undetectable in serum or plasma, and whole blood cannot be used because it is present in long-lived erythrocytes. Therefore, an assay was developed for analyzing frataxin in platelets, which have a half-life of 10 days. The assay is based on stable isotope dilution immunopurification two-dimensional nano-ultra high performance liquid chromatography/parallel reaction monitoring/mass spectrometry. The lower limit of quantification was 0.078 pg frataxin/μg protein, and the assay had 100% sensitivity and specificity for discriminating between controls and FA cases. The mean levels of control and FA platelet frataxin were 9.4 ± 2.6 and 2.4 ± 0.6 pg/μg protein, respectively. The assay should make it possible to rigorously monitor the effects of therapeutic interventions on frataxin expression in this devastating disease.
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Affiliation(s)
- Lili Guo
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, Pennsylvania 19104, United States
| | - Qingqing Wang
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, Pennsylvania 19104, United States
| | - Liwei Weng
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lauren A. Hauser
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, Pennsylvania 19104, United States
- Departments of Pediatrics and Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
- Departments of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Cassandra J. Strawser
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, Pennsylvania 19104, United States
- Departments of Pediatrics and Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
- Departments of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Agostinho G. Rocha
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Clementina Mesaros
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, Pennsylvania 19104, United States
| | - David R. Lynch
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, Pennsylvania 19104, United States
- Departments of Pediatrics and Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
- Departments of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ian A. Blair
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, Pennsylvania 19104, United States
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Ahlgren EC, Fekry M, Wiemann M, Söderberg CA, Bernfur K, Gakh O, Rasmussen M, Højrup P, Emanuelsson C, Isaya G, Al-Karadaghi S. Iron-induced oligomerization of human FXN81-210 and bacterial CyaY frataxin and the effect of iron chelators. PLoS One 2017; 12:e0188937. [PMID: 29200434 PMCID: PMC5714350 DOI: 10.1371/journal.pone.0188937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 11/15/2017] [Indexed: 12/12/2022] Open
Abstract
Patients suffering from the progressive neurodegenerative disease Friedreich's ataxia have reduced expression levels of the protein frataxin. Three major isoforms of human frataxin have been identified, FXN42-210, FXN56-210 and FXN81-210, of which FXN81-210 is considered to be the mature form. Both long forms, FXN42-210 and FXN56-210, have been shown to spontaneously form oligomeric particles stabilized by the extended N-terminal sequence. The short variant FXN81-210, on other hand, has only been observed in the monomeric state. However, a highly homologous E. coli frataxin CyaY, which also lacks an N-terminal extension, has been shown to oligomerize in the presence of iron. To explore the mechanisms of stabilization of short variant frataxin oligomers we compare here the effect of iron on the oligomerization of CyaY and FXN81-210. Using dynamic light scattering, small-angle X-ray scattering, electron microscopy (EM) and cross linking mass spectrometry (MS), we show that at aerobic conditions in the presence of iron both FXN81-210 and CyaY form oligomers. However, while CyaY oligomers are stable over time, FXN81-210 oligomers are unstable and dissociate into monomers after about 24 h. EM and MS studies suggest that within the oligomers FXN81-210 and CyaY monomers are packed in a head-to-tail fashion in ring-shaped structures with potential iron-binding sites located at the interface between monomers. The higher stability of CyaY oligomers can be explained by a higher number of acidic residues at the interface between monomers, which may result in a more stable iron binding. We also show that CyaY oligomers may be dissociated by ferric iron chelators deferiprone and DFO, as well as by the ferrous iron chelator BIPY. Surprisingly, deferiprone and DFO stimulate FXN81-210 oligomerization, while BIPY does not show any effect on oligomerization in this case. The results suggest that FXN81-210 oligomerization is primarily driven by ferric iron, while both ferric and ferrous iron participate in CyaY oligomer stabilization. Analysis of the amino acid sequences of bacterial and eukaryotic frataxins suggests that variations in the position of the acidic residues in helix 1, β-strand 1 and the loop between them may control the mode of frataxin oligomerization.
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Affiliation(s)
- Eva-Christina Ahlgren
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Mostafa Fekry
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Mathias Wiemann
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Christopher A. Söderberg
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Katja Bernfur
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Olex Gakh
- Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota, United States of America
| | - Morten Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Cecilia Emanuelsson
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Grazia Isaya
- Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota, United States of America
| | - Salam Al-Karadaghi
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
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9
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SAXS and stability studies of iron-induced oligomers of bacterial frataxin CyaY. PLoS One 2017; 12:e0184961. [PMID: 28931050 PMCID: PMC5607177 DOI: 10.1371/journal.pone.0184961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/04/2017] [Indexed: 01/19/2023] Open
Abstract
Frataxin is a highly conserved protein found in both prokaryotes and eukaryotes. It is involved in several central functions in cells, which include iron delivery to biochemical processes, such as heme synthesis, assembly of iron-sulfur clusters (ISC), storage of surplus iron in conditions of iron overload, and repair of ISC in aconitase. Frataxin from different organisms has been shown to undergo iron-dependent oligomerization. At least two different classes of oligomers, with different modes of oligomer packing and stabilization, have been identified. Here, we continue our efforts to explore the factors that control the oligomerization of frataxin from different organisms, and focus on E. coli frataxin CyaY. Using small-angle X-ray scattering (SAXS), we show that higher iron-to-protein ratios lead to larger oligomeric species, and that oligomerization proceeds in a linear fashion as a results of iron oxidation. Native mass spectrometry and online size-exclusion chromatography combined with SAXS show that a dimer is the most common form of CyaY in the presence of iron at atmospheric conditions. Modeling of the dimer using the SAXS data confirms the earlier proposed head-to-tail packing arrangement of monomers. This packing mode brings several conserved acidic residues into close proximity to each other, creating an environment for metal ion binding and possibly even mineralization. Together with negative-stain electron microscopy, the experiments also show that trimers, tetramers, pentamers, and presumably higher-order oligomers may exist in solution. Nano-differential scanning fluorimetry shows that the oligomers have limited stability and may easily dissociate at elevated temperatures. The factors affecting the possible oligomerization mode are discussed.
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10
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Gakh O, Ranatunga W, Galeano BK, Smith DS, Thompson JR, Isaya G. Defining the Architecture of the Core Machinery for the Assembly of Fe-S Clusters in Human Mitochondria. Methods Enzymol 2017; 595:107-160. [PMID: 28882199 DOI: 10.1016/bs.mie.2017.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although Fe-S clusters may assemble spontaneously from elemental iron and sulfur in protein-free systems, the potential toxicity of free Fe2+, Fe3+, and S2- ions in aerobic environments underscores the requirement for specialized proteins to oversee the safe assembly of Fe-S clusters in living cells. Prokaryotes first developed multiprotein systems for Fe-S cluster assembly, from which mitochondria later derived their own system and became the main Fe-S cluster suppliers for eukaryotic cells. Early studies in yeast and human mitochondria indicated that Fe-S cluster assembly in eukaryotes is centered around highly conserved Fe-S proteins (human ISCU) that serve as scaffolds upon which new Fe-S clusters are assembled from (i) elemental sulfur, provided by a pyridoxal phosphate-dependent cysteine desulfurase (human NFS1) and its stabilizing-binding partner (human ISD11), and (ii) elemental iron, provided by an iron-binding protein of the frataxin family (human FXN). Further studies revealed that all of these proteins could form stable complexes that could reach molecular masses of megadaltons. However, the protein-protein interaction surfaces, catalytic mechanisms, and overall architecture of these macromolecular machines remained undefined for quite some time. The delay was due to difficulties inherent in reconstituting these very large multiprotein complexes in vitro or isolating them from cells in sufficient quantities to enable biochemical and structural studies. Here, we describe approaches we developed to reconstitute the human Fe-S cluster assembly machinery in Escherichia coli and to define its remarkable architecture.
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Affiliation(s)
| | | | - Belinda K Galeano
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, United States
| | | | | | - Grazia Isaya
- Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, United States; Mayo Clinic Children's Research Center, Rochester, MN, United States.
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11
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Galeano BK, Ranatunga W, Gakh O, Smith DY, Thompson JR, Isaya G. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers. Metallomics 2017; 9:773-801. [PMID: 28548666 PMCID: PMC5552075 DOI: 10.1039/c7mt00089h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/02/2017] [Indexed: 02/06/2023]
Abstract
Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.
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Affiliation(s)
- B. K. Galeano
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Graduate School of Biomedical Sciences , Rochester , Minnesota , USA
| | - W. Ranatunga
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - O. Gakh
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - D. Y. Smith
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - J. R. Thompson
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
| | - G. Isaya
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
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12
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Uchida T, Kobayashi N, Muneta S, Ishimori K. The Iron Chaperone Protein CyaY from Vibrio cholerae Is a Heme-Binding Protein. Biochemistry 2017; 56:2425-2434. [DOI: 10.1021/acs.biochem.6b01304] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Takeshi Uchida
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Noriyuki Kobayashi
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Souichiro Muneta
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Koichiro Ishimori
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
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13
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Gakh O, Ranatunga W, Smith DY, Ahlgren EC, Al-Karadaghi S, Thompson JR, Isaya G. Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery. J Biol Chem 2016; 291:21296-21321. [PMID: 27519411 PMCID: PMC5076535 DOI: 10.1074/jbc.m116.738542] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/10/2016] [Indexed: 11/06/2022] Open
Abstract
Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN42-210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN42-210]24·[NFS1]24·[ISD11]24·[ISCU]24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN42-210]24·[ISCU]24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN42-210 trimer at each of its eight vertices. Binding of 12 [NFS1]2·[ISD11]2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN42-210 to ISCU.
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Affiliation(s)
- Oleksandr Gakh
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry Molecular Biology, Mayo Clinic Children's Research Center, and
| | - Wasantha Ranatunga
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry Molecular Biology, Mayo Clinic Children's Research Center, and
| | - Douglas Y Smith
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry Molecular Biology, Mayo Clinic Children's Research Center, and
| | - Eva-Christina Ahlgren
- the Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Salam Al-Karadaghi
- the Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - James R Thompson
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905 and
| | - Grazia Isaya
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry Molecular Biology, Mayo Clinic Children's Research Center, and
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14
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Söderberg C, Gillam ME, Ahlgren EC, Hunter GA, Gakh O, Isaya G, Ferreira GC, Al-Karadaghi S. The Structure of the Complex between Yeast Frataxin and Ferrochelatase: CHARACTERIZATION AND PRE-STEADY STATE REACTION OF FERROUS IRON DELIVERY AND HEME SYNTHESIS. J Biol Chem 2016; 291:11887-98. [PMID: 27026703 PMCID: PMC4882455 DOI: 10.1074/jbc.m115.701128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/11/2016] [Indexed: 01/08/2023] Open
Abstract
Frataxin is a mitochondrial iron-binding protein involved in iron storage, detoxification, and delivery for iron sulfur-cluster assembly and heme biosynthesis. The ability of frataxin from different organisms to populate multiple oligomeric states in the presence of metal ions, e.g. Fe(2+) and Co(2+), led to the suggestion that different oligomers contribute to the functions of frataxin. Here we report on the complex between yeast frataxin and ferrochelatase, the terminal enzyme of heme biosynthesis. Protein-protein docking and cross-linking in combination with mass spectroscopic analysis and single-particle reconstruction from negatively stained electron microscopic images were used to verify the Yfh1-ferrochelatase interactions. The model of the complex indicates that at the 2:1 Fe(2+)-to-protein ratio, when Yfh1 populates a trimeric state, there are two interaction interfaces between frataxin and the ferrochelatase dimer. Each interaction site involves one ferrochelatase monomer and one frataxin trimer, with conserved polar and charged amino acids of the two proteins positioned at hydrogen-bonding distances from each other. One of the subunits of the Yfh1 trimer interacts extensively with one subunit of the ferrochelatase dimer, contributing to the stability of the complex, whereas another trimer subunit is positioned for Fe(2+) delivery. Single-turnover stopped-flow kinetics experiments demonstrate that increased rates of heme production result from monomers, dimers, and trimers, indicating that these forms are most efficient in delivering Fe(2+) to ferrochelatase and sustaining porphyrin metalation. Furthermore, they support the proposal that frataxin-mediated delivery of this potentially toxic substrate overcomes formation of reactive oxygen species.
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Affiliation(s)
- Christopher Söderberg
- From the Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Mallory E Gillam
- Department of Molecular Medicine, Morsani College of Medicine and
| | - Eva-Christina Ahlgren
- From the Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Gregory A Hunter
- Department of Molecular Medicine, Morsani College of Medicine and
| | - Oleksandr Gakh
- the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota 55905
| | - Grazia Isaya
- the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota 55905
| | - Gloria C Ferreira
- Department of Molecular Medicine, Morsani College of Medicine and the Department of Chemistry, University of South Florida, Tampa, Florida 33612, and
| | - Salam Al-Karadaghi
- From the Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden,
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15
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Ranatunga W, Gakh O, Galeano BK, Smith DY, Söderberg CAG, Al-Karadaghi S, Thompson JR, Isaya G. Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: THE SUB-COMPLEX FORMED BY THE IRON DONOR, Yfh1 PROTEIN, AND THE SCAFFOLD, Isu1 PROTEIN. J Biol Chem 2016; 291:10378-98. [PMID: 26941001 PMCID: PMC4858984 DOI: 10.1074/jbc.m115.712414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/26/2016] [Indexed: 12/18/2022] Open
Abstract
The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24 Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of this complex at a resolution of ∼17 Å. In addition, via chemical cross-linking, limited proteolysis, and mass spectrometry, we identified protein-protein interaction surfaces within the complex. The data together reveal that [Yfh1]24·[Isu1]24 is a roughly cubic macromolecule consisting of one symmetric Isu1 trimer binding on top of one symmetric Yfh1 trimer at each of its eight vertices. Furthermore, molecular modeling suggests that two subunits of the cysteine desulfurase, Nfs1, may bind symmetrically on top of two adjacent Isu1 trimers in a manner that creates two putative [2Fe-2S] cluster assembly centers. In each center, conserved amino acids known to be involved in sulfur and iron donation by Nfs1 and Yfh1, respectively, are in close proximity to the Fe-S cluster-coordinating residues of Isu1. We suggest that this architecture is suitable to ensure concerted and protected transfer of potentially toxic iron and sulfur atoms to Isu1 during Fe-S cluster assembly.
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Affiliation(s)
- Wasantha Ranatunga
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, and the Mayo Clinic Children's Research Center, and
| | - Oleksandr Gakh
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, and the Mayo Clinic Children's Research Center, and
| | - Belinda K Galeano
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, and the Mayo Clinic Children's Research Center, and
| | - Douglas Y Smith
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, and the Mayo Clinic Children's Research Center, and
| | - Christopher A G Söderberg
- the Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Salam Al-Karadaghi
- the Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - James R Thompson
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905 and
| | - Grazia Isaya
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, and the Mayo Clinic Children's Research Center, and
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16
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Pica A, Graziano G. On the Effect of Sodium Chloride and Sodium Sulfate on Cold Denaturation. PLoS One 2015; 10:e0133550. [PMID: 26197394 PMCID: PMC4511003 DOI: 10.1371/journal.pone.0133550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 11/28/2022] Open
Abstract
Both sodium chloride and sodium sulfate are able to stabilize yeast frataxin, causing an overall increase of its thermodynamic stability curve, with a decrease in the cold denaturation temperature and an increase in the hot denaturation one. The influence of low concentrations of these two salts on yeast frataxin stability can be assessed by the application of a theoretical model based on scaled particle theory. First developed to figure out the mechanism underlying cold denaturation in water, this model is able to predict the stabilization of globular proteins provided by these two salts. The densities of the salt solutions and their temperature dependence play a fundamental role.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia – 80126 Napoli, Italy
- Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port’Arsa 11–82100 Benevento, Italy
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17
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Popovic M, Sanfelice D, Pastore C, Prischi F, Temussi PA, Pastore A. Selective observation of the disordered import signal of a globular protein by in-cell NMR: the example of frataxins. Protein Sci 2015; 24:996-1003. [PMID: 25772583 PMCID: PMC4456112 DOI: 10.1002/pro.2679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/08/2015] [Indexed: 01/16/2023]
Abstract
We have exploited the capability of in-cell NMR to selectively observe flexible regions within folded proteins to carry out a comparative study of two members of the highly conserved frataxin family which are found both in prokaryotes and in eukaryotes. They all contain a globular domain which shares more than 50% identity, which in eukaryotes is preceded by an N-terminal tail containing the mitochondrial import signal. We demonstrate that the NMR spectrum of the bacterial ortholog CyaY cannot be observed in the homologous E. coli system, although it becomes fully observable as soon as the cells are lysed. This behavior has been observed for several other compact globular proteins as seems to be the rule rather than the exception. The NMR spectrum of the yeast ortholog Yfh1 contains instead visible signals from the protein. We demonstrate that they correspond to the flexible N-terminal tail indicating that this is flexible and unfolded. This flexibility of the N-terminus agrees with previous studies of human frataxin, despite the extensive sequence diversity of this region in the two proteins. Interestingly, the residues that we observe in in-cell experiments are not visible in the crystal structure of a Yfh1 mutant designed to destabilize the first helix. More importantly, our results show that, in cell, the protein is predominantly present not as an aggregate but as a monomeric species.
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Affiliation(s)
- Matija Popovic
- National Institute for Medical Research, MRC, The RidgewayLondon, United Kingdom
| | - Domenico Sanfelice
- Department of Clinical Neuroscience, King's College London, Denmark Hill CampusLondon, United Kingdom
| | - Chiara Pastore
- Department of Life Sciences, Centre for Structural Biology, Sir Ernst Chain Building, Imperial College LondonLondon, SW7 2AZ, United Kingdom
| | - Filippo Prischi
- Department of Life Sciences, Centre for Structural Biology, Sir Ernst Chain Building, Imperial College LondonLondon, SW7 2AZ, United Kingdom
| | - Piero Andrea Temussi
- National Institute for Medical Research, MRC, The RidgewayLondon, United Kingdom
| | - Annalisa Pastore
- Department of Clinical Neuroscience, King's College London, Denmark Hill CampusLondon, United Kingdom
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18
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Noguera ME, Roman EA, Rigal JB, Cousido-Siah A, Mitschler A, Podjarny A, Santos J. Structural characterization of metal binding to a cold-adapted frataxin. J Biol Inorg Chem 2015; 20:653-64. [PMID: 25832196 DOI: 10.1007/s00775-015-1251-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 03/02/2015] [Indexed: 12/30/2022]
Abstract
Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.
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Affiliation(s)
- Martín E Noguera
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
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19
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Kim JH, Bothe JR, Alderson TR, Markley JL. Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1416-28. [PMID: 25450980 DOI: 10.1016/j.bbamcr.2014.11.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/18/2014] [Accepted: 11/13/2014] [Indexed: 12/26/2022]
Abstract
Proteins containing iron-sulfur (Fe-S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble Fe-S clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. To date, the best studied system is the iron-sulfur cluster (isc) operon of Escherichia coli, and the eight ISC proteins it encodes. Our investigations over the past five years have identified two functional conformational states for the scaffold protein (IscU) and have shown that the other ISC proteins that interact with IscU prefer to bind one conformational state or the other. From analyses of the NMR spectroscopy-derived network of interactions of ISC proteins, small-angle X-ray scattering (SAXS) data, chemical crosslinking experiments, and functional assays, we have constructed working models for Fe-S cluster assembly and delivery. Future work is needed to validate and refine what has been learned about the E. coli system and to extend these findings to the homologous Fe-S cluster biosynthetic machinery of yeast and human mitochondria. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Jin Hae Kim
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jameson R Bothe
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - T Reid Alderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
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20
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Gianni S, Camilloni C, Giri R, Toto A, Bonetti D, Morrone A, Sormanni P, Brunori M, Vendruscolo M. Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein. Proc Natl Acad Sci U S A 2014; 111:14141-6. [PMID: 25228761 PMCID: PMC4191818 DOI: 10.1073/pnas.1405233111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Folding and function may impose different requirements on the amino acid sequences of proteins, thus potentially giving rise to conflict. Such a conflict, or frustration, can result in the formation of partially misfolded intermediates that can compromise folding and promote aggregation. We investigate this phenomenon by studying frataxin, a protein whose normal function is to facilitate the formation of iron-sulfur clusters but whose mutations are associated with Friedreich's ataxia. To characterize the folding pathway of this protein we carry out a Φ-value analysis and use the resulting structural information to determine the structure of the folding transition state, which we then validate by a second round of rationally designed mutagenesis. The analysis of the transition-state structure reveals that the regions involved in the folding process are highly aggregation-prone. By contrast, the regions that are functionally important are partially misfolded in the transition state but highly resistant to aggregation. Taken together, these results indicate that in frataxin the competition between folding and function creates the possibility of misfolding, and that to prevent aggregation the amino acid sequence of this protein is optimized to be highly resistant to aggregation in the regions involved in misfolding.
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Affiliation(s)
- Stefano Gianni
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Università di Roma La Sapienza, 00185 Rome, Italy; and Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Rajanish Giri
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Università di Roma La Sapienza, 00185 Rome, Italy; and
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Università di Roma La Sapienza, 00185 Rome, Italy; and
| | - Daniela Bonetti
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Università di Roma La Sapienza, 00185 Rome, Italy; and
| | - Angela Morrone
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Università di Roma La Sapienza, 00185 Rome, Italy; and
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Università di Roma La Sapienza, 00185 Rome, Italy; and
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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21
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Vilanova B, Sanfelice D, Martorell G, Temussi PA, Pastore A. Trapping a salt-dependent unfolding intermediate of the marginally stable protein Yfh1. Front Mol Biosci 2014; 1:13. [PMID: 25988154 PMCID: PMC4428383 DOI: 10.3389/fmolb.2014.00013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/11/2014] [Indexed: 11/13/2022] Open
Abstract
Yfh1, the yeast ortholog of frataxin, is a protein of limited thermodynamic stability which undergoes cold denaturation at temperatures above the water freezing point. We have previously demonstrated that its stability is strongly dependent on ionic strength and that monovalent or divalent cations are able to considerably stabilize the fold. Here, we present a study of the folded state and of the structural determinants that lead to the strong salt dependence. We demonstrate by nuclear magnetic resonance that, at room temperature, Yfh1 exists as an equilibrium mixture of a folded species and a folding intermediate in slow exchange equilibrium. The equilibrium completely shifts in favor of the folded species by the addition of even small concentrations of salt. We demonstrate that Yfh1 is destabilized by a localized energetic frustration arising from an “electrostatic hinge” made of negatively charged residues mapped in the β-sheet. Salt interactions at this site have a “frustration-relieving” effect. We discuss the consequences of our findings for the function of Yfh1 and for our understanding of protein folding stability.
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Affiliation(s)
- Bartolomé Vilanova
- Departament de Química, Universitat de les Illes Balears Palma de Mallorca, Spain
| | - Domenico Sanfelice
- Molecular Structure Division, National Institute for Medical Research London, UK
| | - Gabriel Martorell
- Serveis Científico-Tècnics, Universitat de les Illes Balears Palma de Mallorca, Spain
| | - Piero A Temussi
- Department of Chemistry, Università di Napoli Federico II Napoli, Italy
| | - Annalisa Pastore
- Molecular Structure Division, National Institute for Medical Research London, UK
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22
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Puccio H, Anheim M, Tranchant C. Pathophysiogical and therapeutic progress in Friedreich ataxia. Rev Neurol (Paris) 2014; 170:355-65. [PMID: 24792433 DOI: 10.1016/j.neurol.2014.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 01/10/2023]
Abstract
Friedreich ataxia (FRDA) is the most common hereditary autosomal recessive ataxia, but is also a multisystemic condition with frequent presence of cardiomyopathy or diabetes. It has been linked to expansion of a GAA-triplet repeat in the first intron of the FXN gene, leading to a reduced level of frataxin, a mitochondrial protein which, by controlling both iron entry and/or sulfide production, is essential to properly assemble and protect the Fe-S cluster during the initial stage of biogenesis. Several data emphasize the role of oxidative damage in FRDA, but better understanding of pathophysiological consequences of FXN mutations has led to develop animal models. Conditional knockout models recapitulate important features of the human disease but lack the genetic context, GAA repeat expansion-based knock-in and transgenic models carry a GAA repeat expansion but they only show a very mild phenotype. Cells derived from FRDA patients constitute the most relevant frataxin-deficient cell model as they carry the complete frataxin locus together with GAA repeat expansions and regulatory sequences. Induced pluripotent stem cell (iPSC)-derived neurons present a maturation delay and lower mitochondrial membrane potential, while cardiomyocytes exhibit progressive mitochondrial degeneration, with frequent dark mitochondria and proliferation/accumulation of normal mitochondria. Efforts in developing therapeutic strategies can be divided into three categories: iron chelators, antioxidants and/or stimulants of mitochondrial biogenesis, and frataxin level modifiers. A promising therapeutic strategy that is currently the subject of intense research is to directly target the heterochromatin state of the GAA repeat expansion with histone deacytelase inhibitors (HDACi) to restore frataxin levels.
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Affiliation(s)
- H Puccio
- Translational medicine and neurogenetics, institut de génétique et de biologie moléculaire et cellulaire (IGBMC), 1, rue Laurent-Fries, BP 10142, 67404 Illkirch cedex, France; Inserm, U596, 1, rue Laurent-Fries, 67400 Illkirch Graffenstaden, France; CNRS, UMR7104, 1, rue Laurent-Fries, 67400 Illkirch Graffenstaden, France; Université de Strasbourg, 4, rue Blaise-Pascal, 67400 Strasbourg, France; Collège de France, chaire de génétique humaine, 1, rue Laurent-Fries, 67400 Illkirch Graffenstaden, France
| | - M Anheim
- Translational medicine and neurogenetics, institut de génétique et de biologie moléculaire et cellulaire (IGBMC), 1, rue Laurent-Fries, BP 10142, 67404 Illkirch cedex, France; Inserm, U596, 1, rue Laurent-Fries, 67400 Illkirch Graffenstaden, France; CNRS, UMR7104, 1, rue Laurent-Fries, 67400 Illkirch Graffenstaden, France; Université de Strasbourg, 4, rue Blaise-Pascal, 67400 Strasbourg, France; Service de neurologie, unité des pathologies du mouvement, hôpital de Hautepierre, hôpital universitaire, 1, place de l'Hôpital, 67000 Strasbourg, France
| | - C Tranchant
- Translational medicine and neurogenetics, institut de génétique et de biologie moléculaire et cellulaire (IGBMC), 1, rue Laurent-Fries, BP 10142, 67404 Illkirch cedex, France; Inserm, U596, 1, rue Laurent-Fries, 67400 Illkirch Graffenstaden, France; CNRS, UMR7104, 1, rue Laurent-Fries, 67400 Illkirch Graffenstaden, France; Université de Strasbourg, 4, rue Blaise-Pascal, 67400 Strasbourg, France; Service de neurologie, unité des pathologies du mouvement, hôpital de Hautepierre, hôpital universitaire, 1, place de l'Hôpital, 67000 Strasbourg, France.
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23
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Pastore A, Puccio H. Frataxin: a protein in search for a function. J Neurochem 2013; 126 Suppl 1:43-52. [PMID: 23859340 DOI: 10.1111/jnc.12220] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 01/18/2013] [Accepted: 01/23/2013] [Indexed: 01/01/2023]
Abstract
Reduced levels of the protein frataxin cause the neurodegenerative disease Friedreich's ataxia. Pathology is associated with disruption of iron-sulfur cluster biosynthesis, mitochondrial iron overload, and oxidative stress. Frataxin is a highly conserved iron-binding protein present in most organisms. Despite the intense interest generated since the determination of its pathology, identification of the cellular function of frataxin has so far remained elusive. In this review, we revisit the most significant milestones that have led us to our current understanding of frataxin and its functions. The picture that emerges is that frataxin is a crucial element of one of the most essential cellular machines specialized in iron-sulfur cluster biogenesis. Future developments, therefore, can be expected from further advancements in our comprehension of this machine.
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24
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The role of the N-terminal tail for the oligomerization, folding and stability of human frataxin. FEBS Open Bio 2013; 3:310-20. [PMID: 23951553 PMCID: PMC3741918 DOI: 10.1016/j.fob.2013.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 01/30/2023] Open
Abstract
The N-terminal stretch of human frataxin (hFXN) intermediate (residues 42–80) is not conserved throughout evolution and, under defined experimental conditions, behaves as a random-coil. Overexpression of hFXN56–210 in Escherichia coli yields a multimer, whereas the mature form of hFXN (hFXN81–210) is monomeric. Thus, cumulative experimental evidence points to the N-terminal moiety as an essential element for the assembly of a high molecular weight oligomer. The secondary structure propensity of peptide 56–81, the moiety putatively responsible for promoting protein–protein interactions, was also studied. Depending on the environment (TFE or SDS), this peptide adopts α-helical or β-strand structure. In this context, we explored the conformation and stability of hFXN56–210. The biophysical characterization by fluorescence, CD and SEC-FPLC shows that subunits are well folded, sharing similar stability to hFXN90–210. However, controlled proteolysis indicates that the N-terminal stretch is labile in the context of the multimer, whereas the FXN domain (residues 81–210) remains strongly resistant. In addition, guanidine hydrochloride at low concentration disrupts intermolecular interactions, shifting the ensemble toward the monomeric form. The conformational plasticity of the N-terminal tail might impart on hFXN the ability to act as a recognition signal as well as an oligomerization trigger. Understanding the fine-tuning of these activities and their resulting balance will bear direct relevance for ultimately comprehending hFXN function. hFXN56–210 is well-folded and shares similar stability to hFXN90–210. The oligomeric form of hFXN56–210 can be disassembled and reassembled in vitro. Proteolysis leads to the oligomer disassembly: subunits are abridged to hFXN81–210. Isolated peptide hFXN56–81 acquires structure in TFE and SDS solutions. The N-terminal tail is structurally malleable and triggers oligomerization.
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25
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Vaubel RA, Isaya G. Iron-sulfur cluster synthesis, iron homeostasis and oxidative stress in Friedreich ataxia. Mol Cell Neurosci 2013; 55:50-61. [PMID: 22917739 PMCID: PMC3530001 DOI: 10.1016/j.mcn.2012.08.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/01/2012] [Accepted: 08/05/2012] [Indexed: 12/21/2022] Open
Abstract
Friedreich ataxia (FRDA) is an autosomal recessive, multi-systemic degenerative disease that results from reduced synthesis of the mitochondrial protein frataxin. Frataxin has been intensely studied since its deficiency was linked to FRDA in 1996. The defining properties of frataxin - (i) the ability to bind iron, (ii) the ability to interact with, and donate iron to, other iron-binding proteins, and (iii) the ability to oligomerize, store iron and control iron redox chemistry - have been extensively characterized with different frataxin orthologs and their interacting protein partners. This very large body of biochemical and structural data [reviewed in (Bencze et al., 2006)] supports equally extensive biological evidence that frataxin is critical for mitochondrial iron metabolism and overall cellular iron homeostasis and antioxidant protection [reviewed in (Wilson, 2006)]. However, the precise biological role of frataxin remains a matter of debate. Here, we review seminal and recent data that strongly link frataxin to the synthesis of iron-sulfur cluster cofactors (ISC), as well as controversial data that nevertheless link frataxin to additional iron-related processes. Finally, we discuss how defects in ISC synthesis could be a major (although likely not unique) contributor to the pathophysiology of FRDA via (i) loss of ISC-dependent enzymes, (ii) mitochondrial and cellular iron dysregulation, and (iii) enhanced iron-mediated oxidative stress. This article is part of a Special Issue entitled 'Mitochondrial function and dysfunction in neurodegeneration'.
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Affiliation(s)
- Rachael A Vaubel
- Department of Pediatric & Adolescent Medicine and the Mayo Clinic Children's Center, Mayo Clinic, Rochester, MN 55905, USA
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26
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Söderberg CAG, Rajan S, Shkumatov AV, Gakh O, Schaefer S, Ahlgren EC, Svergun DI, Isaya G, Al-Karadaghi S. The molecular basis of iron-induced oligomerization of frataxin and the role of the ferroxidation reaction in oligomerization. J Biol Chem 2013; 288:8156-8167. [PMID: 23344952 PMCID: PMC3605634 DOI: 10.1074/jbc.m112.442285] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/22/2013] [Indexed: 11/06/2022] Open
Abstract
The role of the mitochondrial protein frataxin in iron storage and detoxification, iron delivery to iron-sulfur cluster biosynthesis, heme biosynthesis, and aconitase repair has been extensively studied during the last decade. However, still no general consensus exists on the details of the mechanism of frataxin function and oligomerization. Here, using small-angle x-ray scattering and x-ray crystallography, we describe the solution structure of the oligomers formed during the iron-dependent assembly of yeast (Yfh1) and Escherichia coli (CyaY) frataxin. At an iron-to-protein ratio of 2, the initially monomeric Yfh1 is converted to a trimeric form in solution. The trimer in turn serves as the assembly unit for higher order oligomers induced at higher iron-to-protein ratios. The x-ray crystallographic structure obtained from iron-soaked crystals demonstrates that iron binds at the trimer-trimer interaction sites, presumably contributing to oligomer stabilization. For the ferroxidation-deficient D79A/D82A variant of Yfh1, iron-dependent oligomerization may still take place, although >50% of the protein is found in the monomeric state at the highest iron-to-protein ratio used. This demonstrates that the ferroxidation reaction controls frataxin assembly and presumably the iron chaperone function of frataxin and its interactions with target proteins. For E. coli CyaY, the assembly unit of higher order oligomers is a tetramer, which could be an effect of the much shorter N-terminal region of this protein. The results show that understanding of the mechanistic features of frataxin function requires detailed knowledge of the interplay between the ferroxidation reaction, iron-induced oligomerization, and the structure of oligomers formed during assembly.
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Affiliation(s)
- Christopher A G Söderberg
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Sreekanth Rajan
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Alexander V Shkumatov
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Oleksandr Gakh
- Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota 55905
| | - Susanne Schaefer
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Eva-Christina Ahlgren
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Grazia Isaya
- Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota 55905.
| | - Salam Al-Karadaghi
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden.
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Amela I, Delicado P, Gómez A, Querol E, Cedano J. A dynamic model of the proteins that form the initial iron-sulfur cluster biogenesis machinery in yeast mitochondria. Protein J 2013; 32:183-96. [PMID: 23463383 DOI: 10.1007/s10930-013-9475-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The assembly of iron-sulfur clusters (ISCs) in eukaryotes involves the protein Frataxin. Deficits in this protein have been associated with iron inside the mitochondria and impair ISC biogenesis as it is postulated to act as the iron donor for ISCs assembly in this organelle. A pronounced lack of Frataxin causes Friedreich's Ataxia, which is a human neurodegenerative and hereditary disease mainly affecting the equilibrium, coordination, muscles and heart. Moreover, it is the most common autosomal recessive ataxia. High similarities between the human and yeast molecular mechanisms that involve Frataxin have been suggested making yeast a good model to study that process. In yeast, the protein complex that forms the central assembly platform for the initial step of ISC biogenesis is composed by yeast frataxin homolog, Nfs1-Isd11 and Isu. In general, it is commonly accepted that protein function involves interaction with other protein partners, but in this case not enough is known about the structure of the protein complex and, therefore, how it exactly functions. The objective of this work is to model the protein complex in order to gain insight into structural details that end up with its biological function. To achieve this goal several bioinformatics tools, modeling techniques and protein docking programs have been used. As a result, the structure of the protein complex and the dynamic behavior of its components, along with that of the iron and sulfur atoms required for the ISC assembly, have been modeled. This hypothesis will help to better understand the function and molecular properties of Frataxin as well as those of its ISC assembly protein partners.
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Affiliation(s)
- I Amela
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Parc de Recerca Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Catalonia, Spain
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28
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Li H, Gakh O, Smith DY, Ranatunga WK, Isaya G. Missense mutations linked to friedreich ataxia have different but synergistic effects on mitochondrial frataxin isoforms. J Biol Chem 2013; 288:4116-27. [PMID: 23269675 PMCID: PMC3567662 DOI: 10.1074/jbc.m112.435263] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/21/2012] [Indexed: 12/25/2022] Open
Abstract
Friedreich ataxia is an early-onset multisystemic disease linked to a variety of molecular defects in the nuclear gene FRDA. This gene normally encodes the iron-binding protein frataxin (FXN), which is critical for mitochondrial iron metabolism, global cellular iron homeostasis, and antioxidant protection. In most Friedreich ataxia patients, a large GAA-repeat expansion is present within the first intron of both FRDA alleles, that results in transcriptional silencing ultimately leading to insufficient levels of FXN protein in the mitochondrial matrix and probably other cellular compartments. The lack of FXN in turn impairs incorporation of iron into iron-sulfur cluster and heme cofactors, causing widespread enzymatic deficits and oxidative damage catalyzed by excess labile iron. In a minority of patients, a typical GAA expansion is present in only one FRDA allele, whereas a missense mutation is found in the other allele. Although it is known that the disease course for these patients can be as severe as for patients with two expanded FRDA alleles, the underlying pathophysiological mechanisms are not understood. Human cells normally contain two major mitochondrial isoforms of FXN (FXN(42-210) and FXN(81-210)) that have different biochemical properties and functional roles. Using cell-free systems and different cellular models, we show that two of the most clinically severe FXN point mutations, I154F and W155R, have unique direct and indirect effects on the stability, biogenesis, or catalytic activity of FXN(42-210) and FXN(81-210) under physiological conditions. Our data indicate that frataxin point mutations have complex biochemical effects that synergistically contribute to the pathophysiology of Friedreich ataxia.
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Affiliation(s)
- Hongqiao Li
- From the Department of Pediatric and Adolescent Medicine and the Department of Biochemistry and Molecular Biology and the Mayo Clinic Children's Center, Mayo Clinic, Rochester, Minnesota 55905
| | - Oleksandr Gakh
- From the Department of Pediatric and Adolescent Medicine and the Department of Biochemistry and Molecular Biology and the Mayo Clinic Children's Center, Mayo Clinic, Rochester, Minnesota 55905
| | - Douglas Y. Smith
- From the Department of Pediatric and Adolescent Medicine and the Department of Biochemistry and Molecular Biology and the Mayo Clinic Children's Center, Mayo Clinic, Rochester, Minnesota 55905
| | - Wasantha K. Ranatunga
- From the Department of Pediatric and Adolescent Medicine and the Department of Biochemistry and Molecular Biology and the Mayo Clinic Children's Center, Mayo Clinic, Rochester, Minnesota 55905
| | - Grazia Isaya
- From the Department of Pediatric and Adolescent Medicine and the Department of Biochemistry and Molecular Biology and the Mayo Clinic Children's Center, Mayo Clinic, Rochester, Minnesota 55905
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29
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Abstract
Friedreich ataxia is a rare disorder characterized by an autosomal recessive pattern of inheritance. The disease is noted for a constellation of clinical symptoms, notably loss of coordination and a variety of neurologic and cardiac complications. More recently, scientists have focused their research on an array of general investigations of the underlying cellular basis for the disease, including mitochondrial biogenesis, iron-sulfur cluster synthesis, iron metabolism, antioxidant responses, and mitophagy. Combined with investigations that have explored the pathogenesis of the disease and the function of the protein frataxin, these studies have led to insights that will be key to identifying new therapeutic strategies for treating the disease.
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Affiliation(s)
- Massimo Pandolfo
- Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium.
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30
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Abstract
Dps proteins are the structural relatives of bacterioferritins and ferritins ubiquitously present in the bacterial and archaeal kingdoms. The ball-shaped enzymes play important roles in the detoxification of ROS (reactive oxygen species), in iron scavenging to prevent Fenton reactions and in the mechanical protection of DNA. Detoxification of ROS and iron chaperoning represent the most archetypical functions of dodecameric Dps enzymes. Recent crystallographic studies of these dodecameric complexes have unravelled species-dependent mechanisms of iron uptake into the hollow spheres. Subsequent functions in iron oxidation at ferroxidase centres are highly conserved among bacteria. Final nucleation of iron as iron oxide nanoparticles has been demonstrated to originate at acidic residues located on the inner surface. Some Dps enzymes are also implicated in newly observed catalytic functions related to the formation of molecules playing roles in bacterium–host cell communication. Most recently, Dps complexes are attracting attention in semiconductor science as biomimetic tools for the technical production of the smallest metal-based quantum nanodots used in nanotechnological approaches, such as memory storage or solar cell development.
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31
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Adrover M, Martorell G, Martin SR, Urosev D, Konarev PV, Svergun DI, Daura X, Temussi P, Pastore A. The role of hydration in protein stability: comparison of the cold and heat unfolded states of Yfh1. J Mol Biol 2012; 417:413-24. [PMID: 22342930 DOI: 10.1016/j.jmb.2012.02.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/01/2012] [Indexed: 12/21/2022]
Abstract
Protein unfolding occurs at both low and high temperatures, although in most cases, only the high-temperature transition can be experimentally studied. A pressing question is how much the low- and high-temperature denatured states, although thermodynamically equivalent, are structurally and kinetically similar. We have combined experimental and computational approaches to compare the high- and low-temperature unfolded states of Yfh1, a natural protein that, at physiologic pH, undergoes cold and heat denaturation around 0 °C and 40 °C without the help of ad hoc destabilization. We observe that the two denatured states have similar but not identical residual secondary structures, different kinetics and compactness and a remarkably different degree of hydration. We use molecular dynamics simulations to rationalize the role of solvation and its effect on protein stability.
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Affiliation(s)
- Miquel Adrover
- National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
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32
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Söderberg CAG, Shkumatov AV, Rajan S, Gakh O, Svergun DI, Isaya G, Al-Karadaghi S. Oligomerization propensity and flexibility of yeast frataxin studied by X-ray crystallography and small-angle X-ray scattering. J Mol Biol 2011; 414:783-97. [PMID: 22051511 PMCID: PMC3332085 DOI: 10.1016/j.jmb.2011.10.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/29/2011] [Accepted: 10/19/2011] [Indexed: 02/04/2023]
Abstract
Frataxin is a mitochondrial protein with a central role in iron homeostasis. Defects in frataxin function lead to Friedreich's ataxia, a progressive neurodegenerative disease with childhood onset. The function of frataxin has been shown to be closely associated with its ability to form oligomeric species; however, the factors controlling oligomerization and the types of oligomers present in solution are a matter of debate. Using small-angle X-ray scattering, we found that Co(2+), glycerol, and a single amino acid substitution at the N-terminus, Y73A, facilitate oligomerization of yeast frataxin, resulting in a dynamic equilibrium between monomers, dimers, trimers, hexamers, and higher-order oligomers. Using X-ray crystallography, we found that Co(2+) binds inside the channel at the 3-fold axis of the trimer, which suggests that the metal has an oligomer-stabilizing role. The results reveal the types of oligomers present in solution and support our earlier suggestions that the trimer is the main building block of yeast frataxin oligomers. They also indicate that different mechanisms may control oligomer stability and oligomerization in vivo.
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Affiliation(s)
- Christopher AG Söderberg
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | | | - Sreekanth Rajan
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Oleksandr Gakh
- Department of Pediatric and Adolescent Medicine and Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | | | - Grazia Isaya
- Department of Pediatric and Adolescent Medicine and Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Salam Al-Karadaghi
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund, Sweden
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33
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Qi W, Cowan JA. Structural, Mechanistic and Coordination Chemistry of Relevance to the Biosynthesis of Iron-Sulfur and Related Iron Cofactors. Coord Chem Rev 2011; 255:688-699. [PMID: 21499539 DOI: 10.1016/j.ccr.2010.10.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Iron-sulfur clusters are an important class of protein-bound prosthetic center that find wide utility in nature. Roles include electron transfer, enzyme catalysis, protein structure stabilization, and regulation of gene expression as transcriptional and translational sensors. In eukaryotes their biosynthesis requires a complex molecular machinery that is located within the mitochondrion, while bacteria exhibit up to three independent cluster assembly pathways. All of these paths share common themes. This review summarizes some key structural and functional properties of three central proteins dedicated to the Fe-S cluster assembly process: namely, the sulfide donor (cysteine desulfurase); iron donor (frataxin), and the iron-sulfur cluster scaffold protein (IscU/ISU).
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Affiliation(s)
- Wenbin Qi
- Ohio State Biochemistry Program, The Ohio State University
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34
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Iron chaperones for mitochondrial Fe-S cluster biosynthesis and ferritin iron storage. Curr Opin Chem Biol 2011; 15:312-8. [PMID: 21288761 DOI: 10.1016/j.cbpa.2011.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 12/17/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
Abstract
Protein controlled iron homeostasis is essential for maintaining appropriate levels and availability of metal within cells. Recently, two iron chaperones have been discovered that direct metal within two unique pathways: (1) mitochondrial iron-sulfur (Fe-S) cluster assembly and (2) within the ferritin iron storage system. Although structural and functional details describing how these iron chaperones operate are emerging, both share similar iron binding affinities and metal-ligand site structures that enable them to bind and release Fe2+ to specific protein partners. Molecular details related to iron binding and delivery by these chaperones will be explored within this review.
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Schmucker S, Martelli A, Colin F, Page A, Wattenhofer-Donzé M, Reutenauer L, Puccio H. Mammalian frataxin: an essential function for cellular viability through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex. PLoS One 2011; 6:e16199. [PMID: 21298097 PMCID: PMC3027643 DOI: 10.1371/journal.pone.0016199] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/07/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Frataxin, the mitochondrial protein deficient in Friedreich ataxia, a rare autosomal recessive neurodegenerative disorder, is thought to be involved in multiple iron-dependent mitochondrial pathways. In particular, frataxin plays an important role in the formation of iron-sulfur (Fe-S) clusters biogenesis. METHODOLOGY/PRINCIPAL FINDINGS We present data providing new insights into the interactions of mammalian frataxin with the Fe-S assembly complex by combining in vitro and in vivo approaches. Through immunoprecipitation experiments, we show that the main endogenous interactors of a recombinant mature human frataxin are ISCU, NFS1 and ISD11, the components of the core Fe-S assembly complex. Furthermore, using a heterologous expression system, we demonstrate that mammalian frataxin interacts with the preformed core complex, rather than with the individual components. The quaternary complex can be isolated in a stable form and has a molecular mass of ≈190 kDa. Finally, we demonstrate that the mature human FXN(81-210) form of frataxin is the essential functional form in vivo. CONCLUSIONS/SIGNIFICANCE Our results suggest that the interaction of frataxin with the core ISCU/NFS1/ISD11 complex most likely defines the essential function of frataxin. Our results provide new elements important for further understanding the early steps of de novo Fe-S cluster biosynthesis.
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Affiliation(s)
- Stéphane Schmucker
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Inserm U596, Illkirch, France
- CNRS UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Alain Martelli
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Inserm U596, Illkirch, France
- CNRS UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Florent Colin
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Inserm U596, Illkirch, France
- CNRS UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Adeline Page
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Inserm U596, Illkirch, France
- CNRS UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Marie Wattenhofer-Donzé
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Inserm U596, Illkirch, France
- CNRS UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Laurence Reutenauer
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Inserm U596, Illkirch, France
- CNRS UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Hélène Puccio
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Inserm U596, Illkirch, France
- CNRS UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Chaire de Génétique Humaine, Collège de France, Illkirch, France
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Gakh O, Bedekovics T, Duncan SF, Smith DY, Berkholz DS, Isaya G. Normal and Friedreich ataxia cells express different isoforms of frataxin with complementary roles in iron-sulfur cluster assembly. J Biol Chem 2010; 285:38486-501. [PMID: 20889968 PMCID: PMC2992281 DOI: 10.1074/jbc.m110.145144] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 09/30/2010] [Indexed: 11/06/2022] Open
Abstract
Friedreich ataxia (FRDA) is an autosomal recessive degenerative disease caused by insufficient expression of frataxin (FXN), a mitochondrial iron-binding protein required for Fe-S cluster assembly. The development of treatments to increase FXN levels in FRDA requires elucidation of the steps involved in the biogenesis of functional FXN. The FXN mRNA is translated to a precursor polypeptide that is transported to the mitochondrial matrix and processed to at least two forms, FXN(42-210) and FXN(81-210). Previous reports suggested that FXN(42-210) is a transient processing intermediate, whereas FXN(81-210) represents the mature protein. However, we find that both FXN(42-210) and FXN(81-210) are present in control cell lines and tissues at steady-state, and that FXN(42-210) is consistently more depleted than FXN(81-210) in samples from FRDA patients. Moreover, FXN(42-210) and FXN(81-210) have strikingly different biochemical properties. A shorter N terminus correlates with monomeric configuration, labile iron binding, and dynamic contacts with components of the Fe-S cluster biosynthetic machinery, i.e. the sulfur donor complex NFS1·ISD11 and the scaffold ISCU. Conversely, a longer N terminus correlates with the ability to oligomerize, store iron, and form stable contacts with NFS1·ISD11 and ISCU. Monomeric FXN(81-210) donates Fe(2+) for Fe-S cluster assembly on ISCU, whereas oligomeric FXN(42-210) donates either Fe(2+) or Fe(3+). These functionally distinct FXN isoforms seem capable to ensure incremental rates of Fe-S cluster synthesis from different mitochondrial iron pools. We suggest that the levels of both isoforms are relevant to FRDA pathophysiology and that the FXN(81-210)/FXN(42-210) molar ratio should provide a useful parameter to optimize FXN augmentation and replacement therapies.
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Affiliation(s)
- Oleksandr Gakh
- From the Departments of Pediatric & Adolescent Medicine and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Tibor Bedekovics
- From the Departments of Pediatric & Adolescent Medicine and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Samantha F. Duncan
- From the Departments of Pediatric & Adolescent Medicine and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Douglas Y. Smith
- From the Departments of Pediatric & Adolescent Medicine and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Donald S. Berkholz
- From the Departments of Pediatric & Adolescent Medicine and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Grazia Isaya
- From the Departments of Pediatric & Adolescent Medicine and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
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Thierbach R, Drewes G, Fusser M, Voigt A, Kuhlow D, Blume U, Schulz TJ, Reiche C, Glatt H, Epe B, Steinberg P, Ristow M. The Friedreich's ataxia protein frataxin modulates DNA base excision repair in prokaryotes and mammals. Biochem J 2010; 432:165-72. [PMID: 20819074 PMCID: PMC2976068 DOI: 10.1042/bj20101116] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/25/2010] [Accepted: 09/06/2010] [Indexed: 11/23/2022]
Abstract
DNA-repair mechanisms enable cells to maintain their genetic information by protecting it from mutations that may cause malignant growth. Recent evidence suggests that specific DNA-repair enzymes contain ISCs (iron-sulfur clusters). The nuclearencoded protein frataxin is essential for the mitochondrial biosynthesis of ISCs. Frataxin deficiency causes a neurodegenerative disorder named Friedreich's ataxia in humans. Various types of cancer occurring at young age are associated with this disease, and hence with frataxin deficiency. Mice carrying a hepatocyte-specific disruption of the frataxin gene develop multiple liver tumours for unresolved reasons. In the present study, we show that frataxin deficiency in murine liver is associated with increased basal levels of oxidative DNA base damage. Accordingly, eukaryotic V79 fibroblasts overexpressing human frataxin show decreased basal levels of these modifications, while prokaryotic Salmonella enterica serotype Typhimurium TA104 strains transformed with human frataxin show decreased mutation rates. The repair rates of oxidative DNA base modifications in V79 cells overexpressing frataxin were significantly higher than in control cells. Lastly, cleavage activity related to the ISC-independent repair enzyme 8-oxoguanine glycosylase was found to be unaltered by frataxin overexpression. These findings indicate that frataxin modulates DNA-repair mechanisms probably due to its impact on ISC-dependent repair proteins, linking mitochondrial dysfunction to DNA repair and tumour initiation.
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Key Words
- dna base excision repair
- frataxin
- friedreich's ataxia
- iron–sulfur cluster
- oxidative stress
- tumorigenesis
- ber, base excision repair
- dmem, dulbecco's modified eagle's medium
- fpg, formamido-pyrimidine dna glycosylase
- frda, friedreich's ataxia
- hprt, hypoxanthine phosphoribosyltransferase
- isc, iron–sulfur cluster
- lb, luria–bertani
- mapk, mitogen-activated protein kinase
- mutyh, human muty homologue (escherichia coli)
- ogg1, 8-oxoguanine dna glycosylase 1
- 8-oxog, 7,8-dihydro-8-oxoguanine
- ros, reactive oxygen species
- ssb, dna single-strand break
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Affiliation(s)
- René Thierbach
- Department of Food Toxicology and Replacement/Complementary Methods to Animal Testing, University of Veterinary Medicine Hannover, Germany.
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Kell DB. Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. Arch Toxicol 2010; 84:825-89. [PMID: 20967426 PMCID: PMC2988997 DOI: 10.1007/s00204-010-0577-x] [Citation(s) in RCA: 286] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/14/2010] [Indexed: 12/11/2022]
Abstract
Exposure to a variety of toxins and/or infectious agents leads to disease, degeneration and death, often characterised by circumstances in which cells or tissues do not merely die and cease to function but may be more or less entirely obliterated. It is then legitimate to ask the question as to whether, despite the many kinds of agent involved, there may be at least some unifying mechanisms of such cell death and destruction. I summarise the evidence that in a great many cases, one underlying mechanism, providing major stresses of this type, entails continuing and autocatalytic production (based on positive feedback mechanisms) of hydroxyl radicals via Fenton chemistry involving poorly liganded iron, leading to cell death via apoptosis (probably including via pathways induced by changes in the NF-κB system). While every pathway is in some sense connected to every other one, I highlight the literature evidence suggesting that the degenerative effects of many diseases and toxicological insults converge on iron dysregulation. This highlights specifically the role of iron metabolism, and the detailed speciation of iron, in chemical and other toxicology, and has significant implications for the use of iron chelating substances (probably in partnership with appropriate anti-oxidants) as nutritional or therapeutic agents in inhibiting both the progression of these mainly degenerative diseases and the sequelae of both chronic and acute toxin exposure. The complexity of biochemical networks, especially those involving autocatalytic behaviour and positive feedbacks, means that multiple interventions (e.g. of iron chelators plus antioxidants) are likely to prove most effective. A variety of systems biology approaches, that I summarise, can predict both the mechanisms involved in these cell death pathways and the optimal sites of action for nutritional or pharmacological interventions.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and the Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK.
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Santos R, Lefevre S, Sliwa D, Seguin A, Camadro JM, Lesuisse E. Friedreich ataxia: molecular mechanisms, redox considerations, and therapeutic opportunities. Antioxid Redox Signal 2010; 13:651-90. [PMID: 20156111 PMCID: PMC2924788 DOI: 10.1089/ars.2009.3015] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 02/08/2010] [Accepted: 02/14/2010] [Indexed: 12/14/2022]
Abstract
Mitochondrial dysfunction and oxidative damage are at the origin of numerous neurodegenerative diseases like Friedreich ataxia and Alzheimer and Parkinson diseases. Friedreich ataxia (FRDA) is the most common hereditary ataxia, with one individual affected in 50,000. This disease is characterized by progressive degeneration of the central and peripheral nervous systems, cardiomyopathy, and increased incidence of diabetes mellitus. FRDA is caused by a dynamic mutation, a GAA trinucleotide repeat expansion, in the first intron of the FXN gene. Fewer than 5% of the patients are heterozygous and carry point mutations in the other allele. The molecular consequences of the GAA triplet expansion is transcription silencing and reduced expression of the encoded mitochondrial protein, frataxin. The precise cellular role of frataxin is not known; however, it is clear now that several mitochondrial functions are not performed correctly in patient cells. The affected functions include respiration, iron-sulfur cluster assembly, iron homeostasis, and maintenance of the redox status. This review highlights the molecular mechanisms that underlie the disease phenotypes and the different hypothesis about the function of frataxin. In addition, we present an overview of the most recent therapeutic approaches for this severe disease that actually has no efficient treatment.
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Affiliation(s)
- Renata Santos
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Sophie Lefevre
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
- University Pierre et Marie Curie, Paris, France
| | - Dominika Sliwa
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Alexandra Seguin
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Jean-Michel Camadro
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Emmanuel Lesuisse
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
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Torgovnick A, Schiavi A, Testi R, Ventura N. A role for p53 in mitochondrial stress response control of longevity in C. elegans. Exp Gerontol 2010; 45:550-7. [PMID: 20172019 DOI: 10.1016/j.exger.2010.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 01/29/2010] [Accepted: 02/12/2010] [Indexed: 11/24/2022]
Abstract
As in the case of aging, many degenerative disorders also result from progressive mitochondrial deterioration and cellular damage accumulation. Therefore, preventing damage accumulation may delay aging and help to prevent degenerative disorders, especially those associated with mitochondrial dysfunction. In the nematode Caenorhabditis elegans a mild mitochondrial dysfunction prolongs the lifespan. We previously proposed that, following a mild mitochondrial dysfunction, protective stress responses are activated in a hormetic-like fashion, and ultimately account for extended animal's lifespan. We recently showed that in C. elegans, lifespan extension induced by reduced expression of different mitochondrial proteins involved in electron transport chain functionality requires p53/cep-1. In this paper we find that reducing the expression of frataxin, the protein defective in patients with Friedreich's ataxia, triggers a complex stress response, and that the associated induction of the antioxidant glutathione-S-transferase is regulated by cep-1. Given the high percentage of homology between human and nematode genes and the conservation of fundamental intracellular pathways between the two species, identification of molecular mechanisms activated in response to frataxin suppression in C. elegans may suggest novel therapeutic approaches to prevent the accumulation of irreversible damage and the consequent appearance of symptoms in Friedreich's ataxia and possibly other human mitochondrial-associated diseases. The same pathways could be exploitable for delaying the aging process ascribed to mitochondrial degeneration.
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Affiliation(s)
- Alessandro Torgovnick
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
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Seguin A, Sutak R, Bulteau AL, Garcia-Serres R, Oddou JL, Lefevre S, Santos R, Dancis A, Camadro JM, Latour JM, Lesuisse E. Evidence that yeast frataxin is not an iron storage protein in vivo. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1802:531-8. [PMID: 20307653 DOI: 10.1016/j.bbadis.2010.03.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Revised: 03/14/2010] [Accepted: 03/16/2010] [Indexed: 11/29/2022]
Abstract
Yeast cells deficient in the yeast frataxin homolog (Yfh1p) accumulate iron in their mitochondria. Whether this iron is toxic, however, remains unclear. We showed that large excesses of iron in the growth medium did not inhibit growth and did not decrease cell viability. Increasing the ratio of mitochondrial iron-to-Yfh1p by decreasing the steady-state level of Yfh1p to less than 100 molecules per cell had very few deleterious effects on cell physiology, even though the mitochondrial iron concentration greatly exceeded the iron-binding capacity of Yfh1p in these conditions. Mössbauer spectroscopy and FPLC analyses of whole mitochondria or of isolated mitochondrial matrices showed that the chemical and biochemical forms of the accumulated iron in mitochondria of mutant yeast strains (Deltayfh1, Deltaggc1 and Deltassq1) displayed a nearly identical distribution. This was also the case for Deltaggc1 cells, in which Yfh1p was overproduced. In these mitochondria, most of the iron was insoluble, and the ratio of soluble-to-insoluble iron did not change when the amount of Yfh1p was increased up to 4500 molecules per cell. Our results do not privilege the hypothesis of Yfh1p being an iron storage protein in vivo.
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Affiliation(s)
- Alexandra Seguin
- Laboratoire Mitochondries, Métaux et Stress oxydant, Institut Jacques Monod, CNRS-Université Paris Diderot, France
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Schmucker S, Puccio H. Understanding the molecular mechanisms of Friedreich's ataxia to develop therapeutic approaches. Hum Mol Genet 2010; 19:R103-10. [PMID: 20413654 DOI: 10.1093/hmg/ddq165] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a neurodegenerative disease caused by reduced expression of the mitochondrial protein frataxin. The physiopathological consequences of frataxin deficiency are a severe disruption of iron-sulfur cluster biosynthesis, mitochondrial iron overload coupled to cellular iron dysregulation and an increased sensitivity to oxidative stress. Frataxin is a highly conserved protein, which has been suggested to participate in a variety of different roles associated with cellular iron homeostasis. The present review discusses recent advances that have made crucial contributions in understanding the molecular mechanisms underlying FRDA and in advancements toward potential novel therapeutic approaches. Owing to space constraints, this review will focus on the most commonly accepted and solid molecular and biochemical studies concerning the function of frataxin and the physiopathology of the disease. We invite the reader to read the following reviews to have a more exhaustive overview of the field [Pandolfo, M. and Pastore, A. (2009) The pathogenesis of Friedreich ataxia and the structure and function of frataxin. J. Neurol., 256 (Suppl. 1), 9-17; Gottesfeld, J.M. (2007) Small molecules affecting transcription in Friedreich ataxia. Pharmacol. Ther., 116, 236-248; Pandolfo, M. (2008) Drug insight: antioxidant therapy in inherited ataxias. Nat. Clin. Pract. Neurol., 4, 86-96; Puccio, H. (2009) Multicellular models of Friedreich ataxia. J. Neurol., 256 (Suppl. 1), 18-24].
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Affiliation(s)
- Stéphane Schmucker
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, BP10142, IllkirchF-67400, France
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Marmolino D, Manto M, Acquaviva F, Vergara P, Ravella A, Monticelli A, Pandolfo M. PGC-1alpha down-regulation affects the antioxidant response in Friedreich's ataxia. PLoS One 2010; 5:e10025. [PMID: 20383327 PMCID: PMC2850922 DOI: 10.1371/journal.pone.0010025] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Accepted: 03/16/2010] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cells from individuals with Friedreich's ataxia (FRDA) show reduced activities of antioxidant enzymes and cannot up-regulate their expression when exposed to oxidative stress. This blunted antioxidant response may play a central role in the pathogenesis. We previously reported that Peroxisome Proliferator Activated Receptor Gamma (PPARgamma) Coactivator 1-alpha (PGC-1alpha), a transcriptional master regulator of mitochondrial biogenesis and antioxidant responses, is down-regulated in most cell types from FRDA patients and animal models. METHODOLOGY/PRINCIPAL FINDINGS We used primary fibroblasts from FRDA patients and the knock in-knock out animal model for the disease (KIKO mouse) to determine basal superoxide dismutase 2 (SOD2) levels and the response to oxidative stress induced by the addition of hydrogen peroxide. We measured the same parameters after pharmacological stimulation of PGC-1alpha. Compared to control cells, PGC-1alpha and SOD2 levels were decreased in FRDA cells and did not change after addition of hydrogen peroxide. PGC-1alpha direct silencing with siRNA in control fibroblasts led to a similar loss of SOD2 response to oxidative stress as observed in FRDA fibroblasts. PGC-1alpha activation with the PPARgamma agonist (Pioglitazone) or with a cAMP-dependent protein kinase (AMPK) agonist (AICAR) restored normal SOD2 induction. Treatment of the KIKO mice with Pioglitazone significantly up-regulates SOD2 in cerebellum and spinal cord. CONCLUSIONS/SIGNIFICANCE PGC-1alpha down-regulation is likely to contribute to the blunted antioxidant response observed in cells from FRDA patients. This response can be restored by AMPK and PPARgamma agonists, suggesting a potential therapeutic approach for FRDA.
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Affiliation(s)
- Daniele Marmolino
- Laboratoire de Neurologie Expérimentale, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mario Manto
- Laboratoire de Neurologie Expérimentale, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Fonds National de la Recherche Scientifique (FNRS), Brussels, Belgium
| | - Fabio Acquaviva
- Department of Cellular and Molecular Biology, University of Naples “Federico II”, Naples, Italy
| | - Paola Vergara
- Department of Cellular and Molecular Biology, University of Naples “Federico II”, Naples, Italy
| | - Ajay Ravella
- Laboratoire de Neurologie Expérimentale, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Massimo Pandolfo
- Laboratoire de Neurologie Expérimentale, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Native and synthetic ferritins for nanobiomedical applications: recent advances and new perspectives. Future Med Chem 2010; 2:609-18. [DOI: 10.4155/fmc.09.171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ferritin is the protein whose function is to store iron that the cell does not require immediately for metabolic processes, thereby protecting against the toxic effects of free Fe2+. Ferritin therefore plays a crucial role in iron metabolism as well as in the development of some diseases, especially those related to the presence of free Fe2+ and toxic hydroxyl radicals. In addition, ferritin is itself a catalytic bionanoparticle. Its internal cavity can be used as a nanoreactor to produce non-native metallic nanoparticles. Moreover, its external protein shell can be chemically modified, allowing ferritin to be used as a precursor for a library of metallic nanoparticles, some which may have potential applications in biomedicine, especially as multimodal imaging probes. This article presents a brief overview of the evidence for the role of native ferritin in some diseases, as well as the potential of some synthetic ferritins – in which a non-native inorganic material has been introduced into the cavity and/or the external shell has been modified – in the field of nanobiomedicine.
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Kondapalli KC, Bencze KZ, Dizin E, Cowan JA, Stemmler TL. NMR assignments of a stable processing intermediate of human frataxin. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:61-4. [PMID: 20108066 PMCID: PMC3366117 DOI: 10.1007/s12104-010-9209-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 01/10/2010] [Indexed: 05/28/2023]
Abstract
Frataxin, a nuclear encoded protein targeted to the mitochondrial matrix, has recently been implicated as an iron chaperone that delivers Fe(II) to the iron-sulfur assembly enzyme ISU. During transport across the mitochondrial membrane, the N-terminal mitochondrial targeting sequence of frataxin is cleaved in a two-step process to produce the "mature" protein found within the matrix; however, N-terminally extended forms of the protein have also been observed in vivo as a result of processing deficiencies. Structural characterization studies of the mature human frataxin ortholog suggest the protein's N-terminus is predominately unfolded, in contrast to what has been observed for the yeast ortholog. Here we report the NMR assignments of a stable intermediate in the processing of human frataxin. These studies were completed to provide structural insight into editing events that lead to mature protein formation. This report also provides structural details of frataxin editing anomalies produced in vivo during altered protein processing events.
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Affiliation(s)
- Kalyan C. Kondapalli
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Krisztina Z. Bencze
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Eric Dizin
- Evans Laboratory of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - James A. Cowan
- Evans Laboratory of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Timothy L. Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Qi W, Cowan JA. A structural and functional homolog supports a general role for frataxin in cellular iron chemistry. Chem Commun (Camb) 2010; 46:719-21. [PMID: 20087498 DOI: 10.1039/b911975b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Bacillus subtilis YdhG lacks sequence homology, but demonstrates structural and functional similarity to the frataxin family, supporting a general cellular role for frataxin-type proteins in cellular iron homeostasis.
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Affiliation(s)
- Wenbin Qi
- Evans Laboratory of Chemistry, The Ohio State University, 100 West, 18th Avenue, Columbus, OH 43210, USA
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Leidgens S, De Smet S, Foury F. Frataxin interacts with Isu1 through a conserved tryptophan in its beta-sheet. Hum Mol Genet 2010; 19:276-86. [PMID: 19884169 DOI: 10.1093/hmg/ddp495] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Friedreich's ataxia is a neurodegenerative disease caused by the low expression of frataxin, a mitochondrial iron-binding protein which plays an important, but non-essential, role in the formation of iron-sulfur (Fe/S) clusters. It has been shown that Yfh1, the yeast frataxin homologue, interacts functionally and physically with Isu1, the scaffold protein on which the Fe/S clusters are assembled. The large beta-sheet platform of frataxin is a good ligand candidate for this interaction. We have generated 12 yeast mutants in conserved residues of the beta-sheet protruding at the surface or buried in the protein core. The Q129A, I130A, W131A(F) and R141A mutations, which reside in surface exposed residues of the fourth and fifth beta-strands, result in severe cell growth inhibition on high-iron media and low aconitase activity, indicating that Fe/S cluster biosynthesis is impaired. The null phenotype of the I130A mutant results from the high instability of the protein, pointing that this buried residue is essential for folding. In contrast, Gln-129, Trp-131 and Arg-141 residues which are spatially closely clustered define a patch important for protein function. Co-immunoprecipitation experiments using cell extracts show that W131A, unlike W131F, is the sole mutation that strongly decreases the interaction with Isu1. Therefore, Trp-131, which is the only strictly conserved frataxin residue in all sequenced species, appears as a major contributor to the interaction with Isu1 through its surface-exposed aromatic side chain.
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Affiliation(s)
- Sébastien Leidgens
- Unité de Biochimie Physiologique, Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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Prischi F, Giannini C, Adinolfi S, Pastore A. The N-terminus of mature human frataxin is intrinsically unfolded. FEBS J 2009; 276:6669-76. [PMID: 19843162 PMCID: PMC3430858 DOI: 10.1111/j.1742-4658.2009.07381.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/09/2009] [Accepted: 09/15/2009] [Indexed: 02/06/2023]
Abstract
Frataxin is a highly conserved nuclear-encoded mitochondrial protein whose deficiency is the primary cause of Friedreich's ataxia, an autosomal recessive neurodegenerative disease. The frataxin structure comprises a well-characterized globular domain that is present in all species and is preceded in eukaryotes by a non-conserved N-terminal tail that contains the mitochondrial import signal. Little is known about the structure and dynamic properties of the N-terminal tail. Here, we show that this region is flexible and intrinsically unfolded in human frataxin. It does not alter the iron-binding or self-aggregation properties of the globular domain. It is therefore very unlikely that this region could be important for the conserved functions of the protein.
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Affiliation(s)
- Filippo Prischi
- Dipartimento di Biologia Molecolare, University of Siena, Siena, Italy
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Berrisford JM, Sazanov LA. Structural basis for the mechanism of respiratory complex I. J Biol Chem 2009; 284:29773-83. [PMID: 19635800 PMCID: PMC2785608 DOI: 10.1074/jbc.m109.032144] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 07/15/2009] [Indexed: 11/06/2022] Open
Abstract
Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 A resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several alpha-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.
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Affiliation(s)
- John M. Berrisford
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | - Leonid A. Sazanov
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
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Affiliation(s)
- Aaron Atkinson
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84132
| | - Dennis R. Winge
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84132
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