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Da Conceição LMA, Cabral LM, Pereira GRC, De Mesquita JF. An In Silico Analysis of Genetic Variants and Structural Modeling of the Human Frataxin Protein in Friedreich's Ataxia. Int J Mol Sci 2024; 25:5796. [PMID: 38891993 PMCID: PMC11172458 DOI: 10.3390/ijms25115796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Friedreich's Ataxia (FRDA) stands out as the most prevalent form of hereditary ataxias, marked by progressive movement ataxia, loss of vibratory sensitivity, and skeletal deformities, severely affecting daily functioning. To date, the only medication available for treating FRDA is Omaveloxolone (Skyclarys®), recently approved by the FDA. Missense mutations within the human frataxin (FXN) gene, responsible for intracellular iron homeostasis regulation, are linked to FRDA development. These mutations induce FXN dysfunction, fostering mitochondrial iron accumulation and heightened oxidative stress, ultimately triggering neuronal cell death pathways. This study amalgamated 226 FXN genetic variants from the literature and database searches, with only 18 previously characterized. Predictive analyses revealed a notable prevalence of detrimental and destabilizing predictions for FXN mutations, predominantly impacting conserved residues crucial for protein function. Additionally, an accurate, comprehensive three-dimensional model of human FXN was constructed, serving as the basis for generating genetic variants I154F and W155R. These variants, selected for their severe clinical implications, underwent molecular dynamics (MD) simulations, unveiling flexibility and essential dynamic alterations in their N-terminal segments, encompassing FXN42, FXN56, and FXN78 domains pivotal for protein maturation. Thus, our findings indicate potential interaction profile disturbances in the FXN42, FXN56, and FXN78 domains induced by I154F and W155R mutations, aligning with the existing literature.
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Affiliation(s)
- Loiane Mendonça Abrantes Da Conceição
- Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Avenida Pasteur, 296, Urca, Rio de Janeiro 22290-250, Brazil (J.F.D.M.)
| | - Lucio Mendes Cabral
- Pharmaceutical Industrial Technology Laboratory, Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-590, Brazil
| | - Gabriel Rodrigues Coutinho Pereira
- Pharmaceutical Industrial Technology Laboratory, Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-590, Brazil
- Laboratory of Molecular Modeling & QSAR, Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-590, Brazil
| | - Joelma Freire De Mesquita
- Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Avenida Pasteur, 296, Urca, Rio de Janeiro 22290-250, Brazil (J.F.D.M.)
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2
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Doni D, Cavallari E, Noguera ME, Gentili HG, Cavion F, Parisi G, Fornasari MS, Sartori G, Santos J, Bellanda M, Carbonera D, Costantini P, Bortolus M. Searching for Frataxin Function: Exploring the Analogy with Nqo15, the Frataxin-like Protein of Respiratory Complex I from Thermus thermophilus. Int J Mol Sci 2024; 25:1912. [PMID: 38339189 PMCID: PMC10855754 DOI: 10.3390/ijms25031912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Nqo15 is a subunit of respiratory complex I of the bacterium Thermus thermophilus, with strong structural similarity to human frataxin (FXN), a protein involved in the mitochondrial disease Friedreich's ataxia (FRDA). Recently, we showed that the expression of recombinant Nqo15 can ameliorate the respiratory phenotype of FRDA patients' cells, and this prompted us to further characterize both the Nqo15 solution's behavior and its potential functional overlap with FXN, using a combination of in silico and in vitro techniques. We studied the analogy of Nqo15 and FXN by performing extensive database searches based on sequence and structure. Nqo15's folding and flexibility were investigated by combining nuclear magnetic resonance (NMR), circular dichroism, and coarse-grained molecular dynamics simulations. Nqo15's iron-binding properties were studied using NMR, fluorescence, and specific assays and its desulfurase activation by biochemical assays. We found that the recombinant Nqo15 isolated from complex I is monomeric, stable, folded in solution, and highly dynamic. Nqo15 does not share the iron-binding properties of FXN or its desulfurase activation function.
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Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Eva Cavallari
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
- Grenoble Alpes University, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Martin Ezequiel Noguera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
- Institute of Biological Chemistry and Physical Chemistry, Dr Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, Buenos Aires 1113AAD, Argentina
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Hernan Gustavo Gentili
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
| | - Federica Cavion
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Gustavo Parisi
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Maria Silvina Fornasari
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy;
| | - Javier Santos
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
| | - Massimo Bellanda
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
- Consiglio Nazionale delle Ricerche Institute of Biomolecular Chemistry, 35131 Padova, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
| | - Paola Costantini
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
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3
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Doni D, Cavion F, Bortolus M, Baschiera E, Muccioli S, Tombesi G, d'Ettorre F, Ottaviani D, Marchesan E, Leanza L, Greggio E, Ziviani E, Russo A, Bellin M, Sartori G, Carbonera D, Salviati L, Costantini P. Human frataxin, the Friedreich ataxia deficient protein, interacts with mitochondrial respiratory chain. Cell Death Dis 2023; 14:805. [PMID: 38062036 PMCID: PMC10703789 DOI: 10.1038/s41419-023-06320-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023]
Abstract
Friedreich ataxia (FRDA) is a rare, inherited neurodegenerative disease caused by an expanded GAA repeat in the first intron of the FXN gene, leading to transcriptional silencing and reduced expression of frataxin. Frataxin participates in the mitochondrial assembly of FeS clusters, redox cofactors of the respiratory complexes I, II and III. To date it is still unclear how frataxin deficiency culminates in the decrease of bioenergetics efficiency in FRDA patients' cells. We previously demonstrated that in healthy cells frataxin is closely attached to the mitochondrial cristae, which contain both the FeS cluster assembly machinery and the respiratory chain complexes, whereas in FRDA patients' cells with impaired respiration the residual frataxin is largely displaced in the matrix. To gain novel insights into the function of frataxin in the mitochondrial pathophysiology, and in the upstream metabolic defects leading to FRDA disease onset and progression, here we explored the potential interaction of frataxin with the FeS cluster-containing respiratory complexes I, II and III. Using healthy cells and different FRDA cellular models we found that frataxin interacts with these three respiratory complexes. Furthermore, by EPR spectroscopy, we observed that in mitochondria from FRDA patients' cells the decreased level of frataxin specifically affects the FeS cluster content of complex I. Remarkably, we also found that the frataxin-like protein Nqo15 from T. thermophilus complex I ameliorates the mitochondrial respiratory phenotype when expressed in FRDA patient's cells. Our data point to a structural and functional interaction of frataxin with complex I and open a perspective to explore therapeutic rationales for FRDA targeted to this respiratory complex.
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Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Federica Cavion
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, 35131, Padova, Italy
| | - Elisa Baschiera
- Clinical Genetics Unit, Department of Women's and Children Health, University of Padova, 35128, Padova, Italy
- Istituto di Ricerca Pediatrica (IRP) Città della Speranza, 35127, Padova, Italy
| | - Silvia Muccioli
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Giulia Tombesi
- Department of Biology, University of Padova, 35121, Padova, Italy
| | | | | | - Elena Marchesan
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Luigi Leanza
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Elisa Greggio
- Department of Biology, University of Padova, 35121, Padova, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
| | - Elena Ziviani
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Milena Bellin
- Department of Biology, University of Padova, 35121, Padova, Italy
- Veneto Institute of Molecular Medicine, 35129, Padova, Italy
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333, ZA, Leiden, The Netherlands
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, 35121, Padova, Italy
| | | | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women's and Children Health, University of Padova, 35128, Padova, Italy.
- Istituto di Ricerca Pediatrica (IRP) Città della Speranza, 35127, Padova, Italy.
| | - Paola Costantini
- Department of Biology, University of Padova, 35121, Padova, Italy.
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4
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Falb N, Patil G, Furtmüller PG, Gabler T, Hofbauer S. Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis. Comput Struct Biotechnol J 2023; 21:3933-3945. [PMID: 37593721 PMCID: PMC10427985 DOI: 10.1016/j.csbj.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
The coproporphyrin dependent heme biosynthesis pathway is almost exclusively utilized by Gram-positive bacteria. This fact makes it a worthwhile topic for basic research, since a fundamental understanding of a metabolic pathway is necessary to translate the focus towards medical biotechnology, which is very relevant in this specific case, considering the need for new antibiotic targets to counteract the pathogenicity of Gram-positive superbugs. Over the years a lot of structural data on the set of enzymes acting in Gram-positive heme biosynthesis has accumulated in the Protein Database (www.pdb.org). One major challenge is to filter and analyze all available structural information in sufficient detail in order to be helpful and to draw conclusions. Here we pursued to give a holistic overview of structural information on enzymes involved in the coproporphyrin dependent heme biosynthesis pathway. There are many aspects to be extracted from experimentally determined structures regarding the reaction mechanisms, where the smallest variation of the position of an amino acid residue might be important, but also on a larger level regarding protein-protein interactions, where the focus has to be on surface characteristics and subunit (secondary) structural elements and oligomerization. This review delivers a status quo, highlights still missing information, and formulates future research endeavors in order to better understand prokaryotic heme biosynthesis.
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Affiliation(s)
- Nikolaus Falb
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Gaurav Patil
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Thomas Gabler
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
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5
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Nobili G, Botticelli S, La Penna G, Morante S, Rossi G, Salina G. Probing protein stability: towards a computational atomistic, reliable, affordable, and improvable model. Front Mol Biosci 2023; 10:1122269. [PMID: 37325476 PMCID: PMC10267363 DOI: 10.3389/fmolb.2023.1122269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
We present an improved application of a recently proposed computational method designed to evaluate the change of free energy as a function of the average value of a suitably chosen collective variable in proteins. The method is based on a full atomistic description of the protein and its environment. The goal is to understand how the protein melting temperature changes upon single-point mutations, because the sign of the temperature variation will allow us to discriminate stabilizing vs. destabilizing mutations in protein sequences. In this refined application the method is based on altruistic well-tempered metadynamics, a variant of multiple-walkers metadynamics. The resulting metastatistics is then modulated by the maximal constrained entropy principle. The latter turns out to be especially helpful in free-energy calculations as it is able to alleviate the severe limitations of metadynamics in properly sampling folded and unfolded configurations. In this work we apply the computational strategy outlined above in the case of the bovine pancreatic trypsin inhibitor, a well-studied small protein, which is a reference for computer simulations since decades. We compute the variation of the melting temperature characterizing the folding-unfolding process between the wild-type protein and two of its single-point mutations that are seen to have opposite effect on the free energy changes. The same approach is used for free energy difference calculations between a truncated form of frataxin and a set of five of its variants. Simulation data are compared to in vitro experiments. In all cases the sign of the change of melting temperature is reproduced, under the further approximation of using an empirical effective mean-field to average out protein-solvent interactions.
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Affiliation(s)
- Germano Nobili
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Simone Botticelli
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Giovanni La Penna
- CNR-Istituto di Chimica Dei Composti Organometallici, Firenze, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Silvia Morante
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- CNR-Istituto di Chimica Dei Composti Organometallici, Firenze, Italy
| | - Giancarlo Rossi
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Roma, Italy
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6
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Kurt F, Filiz E, Yildiz K, Akbudak MA. Genome-Wide Identification, Characterization and Expression Profiling of Potato ( Solanum tuberosum) Frataxin ( FH) Gene. Genes (Basel) 2023; 14:468. [PMID: 36833395 PMCID: PMC9957314 DOI: 10.3390/genes14020468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Frataxin (FH) plays a crucial role in the biogenesis of mitochondria and the regulation of iron in the cells of various organisms. However, there has been very little research on FH in plants. In this study, the potato FH gene (StFH) was identified and characterized using a genome-wide approach, and its sequence was compared to those of FH genes from Arabidopsis, rice, and maize. The FH genes were found to have a lineage-specific distribution and were more conserved in monocots than in dicots. While multiple copies of FH genes have been reported in some species, including plants, only one isoform of FH was found in potato. The expression of StFH in leaves and roots was analyzed under two different abiotic stress conditions, and the results showed that StFH was upregulated more in leaves and that its expression levels increased with the severity of the stress. This is the first study to examine the expression of an FH gene under abiotic stress conditions.
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Affiliation(s)
- Firat Kurt
- Department of Plant Production and Technologies, Faculty of Applied Sciences, Mus Alparslan University, 49250 Mus, Turkey
| | - Ertugrul Filiz
- Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, Cilimli, 81750 Duzce, Turkey
| | - Kubra Yildiz
- Department of Agricultural Biotechnology, Akdeniz University, 07058 Antalya, Turkey
| | - M. Aydın Akbudak
- Department of Agricultural Biotechnology, Akdeniz University, 07058 Antalya, Turkey
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7
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Pignataro MF, Herrera MG, Fernández NB, Aran M, Gentili HG, Battaglini F, Santos J. Selection of synthetic proteins to modulate the human frataxin function. Biotechnol Bioeng 2023; 120:409-425. [PMID: 36225115 DOI: 10.1002/bit.28263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/13/2022] [Accepted: 10/09/2022] [Indexed: 01/13/2023]
Abstract
Frataxin is a kinetic activator of the mitochondrial supercomplex for iron-sulfur cluster assembly. Low frataxin expression or a decrease in its functionality results in Friedreich's Ataxia (FRDA). With the aim of creating new molecular tools to study this metabolic pathway, and ultimately, to explore new therapeutic strategies, we have investigated the possibility of obtaining small proteins exhibiting a high affinity for frataxin. In this study, we applied the ribosome display approach, using human frataxin as the target. We focused on Affi_224, one of the proteins that we were able to select after five rounds of selection. We have studied the interaction between both proteins and discussed some applications of this specific molecular tutor, concerning the modulation of the supercomplex activity. Affi_224 and frataxin showed a KD value in the nanomolar range, as judged by surface plasmon resonance analysis. Most likely, it binds to the frataxin acidic ridge, as suggested by the analysis of chemical shift perturbations (nuclear magnetic resonance) and computational simulations. Affi_224 was able to increase Cys NFS1 desulfurase activation exerted by the FRDA frataxin variant G130V. Importantly, Affi_224 interacts with frataxin in a human cellular model. Our results suggest quaternary addition may be a new tool to modulate frataxin function in vivo. Nevertheless, more functional experiments under physiological conditions should be carried out to evaluate Affi_224 effectiveness in FRDA cell models.
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Affiliation(s)
- María Florencia Pignataro
- Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Natalia Brenda Fernández
- Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Martín Aran
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina.,Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Hernán Gustavo Gentili
- Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando Battaglini
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), Buenos Aires, Argentina
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
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8
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Rodrigues AV, Batelu S, Hinton TV, Rotondo J, Thompson L, Brunzelle JS, Stemmler TL. Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions. Acta Crystallogr D Struct Biol 2023; 79:22-30. [PMID: 36601804 PMCID: PMC9815096 DOI: 10.1107/s2059798322011639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a hereditary cardiodegenerative and neurodegenerative disease that affects 1 in 50 000 Americans. FRDA arises from either a cellular inability to produce sufficient quantities or the production of a nonfunctional form of the protein frataxin, a key molecule associated with mitochondrial iron-sulfur cluster biosynthesis. Within the mitochondrial iron-sulfur cluster (ISC) assembly pathway, frataxin serves as an allosteric regulator for cysteine desulfurase, the enzyme that provides sulfur for [2Fe-2S] cluster assembly. Frataxin is a known iron-binding protein and is also linked to the delivery of ferrous ions to the scaffold protein, the ISC molecule responsible for the direct assembly of [2Fe-2S] clusters. The goal of this report is to provide structural details of the Drosophila melanogaster frataxin ortholog (Dfh), using both X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, in order to provide the foundational insight needed to understand the structure-function correlation of the protein. Additionally, NMR iron(II) titrations were used to provide metal contacts on the protein to better understand how it binds iron and aids its delivery to the ISC scaffold protein. Here, the structural and functional similarities of Dfh to its orthologs are also outlined. Structural data show that bacterial, yeast, human and Drosophila frataxins are structurally similar, apart from a structured C-terminus in Dfh that is likely to aid in protein stability. The iron-binding location on helix 1 and strand 1 of Dfh is also conserved across orthologs.
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Affiliation(s)
- Andria V Rodrigues
- Department of Biochemistry and Molecular Biology, Wayne State University, Detroit, Michigan, USA
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Tiara V Hinton
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - John Rotondo
- Department of Biochemistry and Molecular Biology, Wayne State University, Detroit, Michigan, USA
| | - Lindsey Thompson
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, Illinois, USA
| | - Timothy L Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University, Detroit, Michigan, USA
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9
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Iqbal S, Ge F, Li F, Akutsu T, Zheng Y, Gasser RB, Yu DJ, Webb GI, Song J. PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. J Chem Inf Model 2022; 62:4270-4282. [PMID: 35973091 DOI: 10.1021/acs.jcim.2c00799] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An essential step in engineering proteins and understanding disease-causing missense mutations is to accurately model protein stability changes when such mutations occur. Here, we developed a new sequence-based predictor for the protein stability (PROST) change (Gibb's free energy change, ΔΔG) upon a single-point missense mutation. PROST extracts multiple descriptors from the most promising sequence-based predictors, such as BoostDDG, SAAFEC-SEQ, and DDGun. RPOST also extracts descriptors from iFeature and AlphaFold2. The extracted descriptors include sequence-based features, physicochemical properties, evolutionary information, evolutionary-based physicochemical properties, and predicted structural features. The PROST predictor is a weighted average ensemble model based on extreme gradient boosting (XGBoost) decision trees and an extra-trees regressor; PROST is trained on both direct and hypothetical reverse mutations using the S5294 (S2647 direct mutations + S2647 inverse mutations). The parameters for the PROST model are optimized using grid searching with 5-fold cross-validation, and feature importance analysis unveils the most relevant features. The performance of PROST is evaluated in a blinded manner, employing nine distinct data sets and existing state-of-the-art sequence-based and structure-based predictors. This method consistently performs well on frataxin, S217, S349, Ssym, S669, Myoglobin, and CAGI5 data sets in blind tests and similarly to the state-of-the-art predictors for p53 and S276 data sets. When the performance of PROST is compared with the latest predictors such as BoostDDG, SAAFEC-SEQ, ACDC-NN-seq, and DDGun, PROST dominates these predictors. A case study of mutation scanning of the frataxin protein for nine wild-type residues demonstrates the utility of PROST. Taken together, these findings indicate that PROST is a well-suited predictor when no protein structural information is available. The source code of PROST, data sets, examples, and pretrained models along with how to use PROST are available at https://github.com/ShahidIqb/PROST and https://prost.erc.monash.edu/seq.
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Affiliation(s)
- Shahid Iqbal
- Department of Data Science and AI, Faculty of IT, Monash University, Clayton, Victoria 3800, Australia.,Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Monash Data Futures Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Fang Ge
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Fuyi Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Monash Data Futures Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Yuanting Zheng
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Geoffrey I Webb
- Department of Data Science and AI, Faculty of IT, Monash University, Clayton, Victoria 3800, Australia.,Monash Data Futures Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jiangning Song
- Department of Data Science and AI, Faculty of IT, Monash University, Clayton, Victoria 3800, Australia.,Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Monash Data Futures Institute, Monash University, Clayton, Victoria 3800, Australia
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10
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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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11
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Wang Q, Laboureur L, Weng L, Eskenazi NM, Hauser LA, Mesaros C, Lynch DR, Blair IA. Simultaneous Quantification of Mitochondrial Mature Frataxin and Extra-Mitochondrial Frataxin Isoform E in Friedreich’s Ataxia Blood. Front Neurosci 2022; 16:874768. [PMID: 35573317 PMCID: PMC9098139 DOI: 10.3389/fnins.2022.874768] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/22/2022] [Indexed: 11/25/2022] Open
Abstract
Friedreich’s ataxia (FRDA) is an autosomal recessive disease caused by an intronic guanine-adenine-adenine (GAA) triplet expansion in the frataxin (FXN) gene, which leads to reduced expression of full-length frataxin (1–210) also known as isoform 1. Full-length frataxin has a mitochondrial targeting sequence, which facilitates its translocation into mitochondria where it is processed through cleavage at G41-L42 and K80-S81 by mitochondrial processing (MPP) to release mitochondrial mature frataxin (81–210). Alternative splicing of FXN also leads to expression of N-terminally acetylated extra-mitochondrial frataxin (76–210) named isoform E because it was discovered in erythrocytes. Frataxin isoforms are undetectable in serum or plasma, and originally whole blood could not be used as a biomarker in brief therapeutic trials because it is present in erythrocytes, which have a half-life of 115-days and so frataxin levels would remain unaltered. Therefore, an assay was developed for analyzing frataxin in platelets, which have a half-life of only 10-days. However, our discovery that isoform E is only present in erythrocytes, whereas, mature frataxin is present primarily in short-lived peripheral blood mononuclear cells (PBMCs), granulocytes, and platelets, meant that both proteins could be quantified in whole blood samples. We now report a quantitative assay for frataxin proteoforms in whole blood from healthy controls and FRDA patients. The assay is based on stable isotope dilution coupled with immunoprecipitation (IP) and two-dimensional-nano-ultrahigh performance liquid chromatography/parallel reaction monitoring/high resolution mass spectrometry (2D-nano-UHPLC-PRM/HRMS). The lower limit of quantification was 0.5 ng/mL for each proteoform and the assays had 100% sensitivity and specificity for discriminating between healthy controls (n = 11) and FRDA cases (N = 100 in year-1, N = 22 in year-2,3). The mean levels of mature frataxin in whole blood from healthy controls and homozygous FRDA patients were significantly different (p < 0.0001) at 7.5 ± 1.5 ng/mL and 2.1 ± 1.2 ng/mL, respectively. The mean levels of isoform E in whole blood from healthy controls and homozygous FRDA patients were significantly different (p < 0.0001) at 26.8 ± 4.1 ng/mL and 4.7 ± 3.3 ng/mL, respectively. The mean levels of total frataxin in whole blood from healthy controls and homozygous FRDA patients were significantly different (p < 0.0001) at 34.2 ± 4.3 ng/mL and 6.8 ± 4.0 ng/mL, respectively. The assay will make it possible to rigorously monitor the natural history of the disease and explore the potential role of isoform E in etiology of the disease. It will also facilitate the assessment of therapeutic interventions (including gene therapy approaches) that attempt to increase frataxin protein expression as a treatment for this devastating disease.
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Affiliation(s)
- Qingqing Wang
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
| | - Laurent Laboureur
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
| | - Liwei Weng
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
| | - Nicolas M. Eskenazi
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
| | - Lauren A. Hauser
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
- Departments of Pediatrics and Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Departments of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Clementina Mesaros
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
| | - David R. Lynch
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
- Departments of Pediatrics and Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Departments of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ian A. Blair
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, Philadelphia, PA, United States
- *Correspondence: Ian A. Blair,
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12
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Botticelli S, La Penna G, Nobili G, Rossi G, Stellato F, Morante S. Modelling Protein Plasticity: The Example of Frataxin and Its Variants. Molecules 2022; 27:1955. [PMID: 35335316 PMCID: PMC8950120 DOI: 10.3390/molecules27061955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/07/2022] [Accepted: 03/13/2022] [Indexed: 12/20/2022] Open
Abstract
Frataxin (FXN) is a protein involved in storage and delivery of iron in the mitochondria. Single-point mutations in the FXN gene lead to reduced production of functional frataxin, with the consequent dyshomeostasis of iron. FXN variants are at the basis of neurological impairment (the Friedreich's ataxia) and several types of cancer. By using altruistic metadynamics in conjunction with the maximal constrained entropy principle, we estimate the change of free energy in the protein unfolding of frataxin and of some of its pathological mutants. The sampled configurations highlight differences between the wild-type and mutated sequences in the stability of the folded state. In partial agreement with thermodynamic experiments, where most of the analyzed variants are characterized by lower thermal stability compared to wild type, the D104G variant is found with a stability comparable to the wild-type sequence and a lower water-accessible surface area. These observations, obtained with the new approach we propose in our work, point to a functional switch, affected by single-point mutations, of frataxin from iron storage to iron release. The method is suitable to investigate wide structural changes in proteins in general, after a proper tuning of the chosen collective variable used to perform the transition.
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Affiliation(s)
- Simone Botticelli
- Dipartimento di Fisica, Università di Roma Tor Vergata and Sezione di Roma Tor Vergata, INFN, Via della Ricerca Scientifica 1, I-00133 Roma, Italy; (S.B.); (G.N.); (G.R.); (F.S.); (S.M.)
| | - Giovanni La Penna
- Dipartimento di Fisica, Università di Roma Tor Vergata and Sezione di Roma Tor Vergata, INFN, Via della Ricerca Scientifica 1, I-00133 Roma, Italy; (S.B.); (G.N.); (G.R.); (F.S.); (S.M.)
- Istituto di Chimica dei Composti Organometallici, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, I-50019 Firenze, Italy
| | - Germano Nobili
- Dipartimento di Fisica, Università di Roma Tor Vergata and Sezione di Roma Tor Vergata, INFN, Via della Ricerca Scientifica 1, I-00133 Roma, Italy; (S.B.); (G.N.); (G.R.); (F.S.); (S.M.)
| | - Giancarlo Rossi
- Dipartimento di Fisica, Università di Roma Tor Vergata and Sezione di Roma Tor Vergata, INFN, Via della Ricerca Scientifica 1, I-00133 Roma, Italy; (S.B.); (G.N.); (G.R.); (F.S.); (S.M.)
- Centro Fermi—Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, I-00184 Roma, Italy
| | - Francesco Stellato
- Dipartimento di Fisica, Università di Roma Tor Vergata and Sezione di Roma Tor Vergata, INFN, Via della Ricerca Scientifica 1, I-00133 Roma, Italy; (S.B.); (G.N.); (G.R.); (F.S.); (S.M.)
- Centro Fermi—Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, I-00184 Roma, Italy
| | - Silvia Morante
- Dipartimento di Fisica, Università di Roma Tor Vergata and Sezione di Roma Tor Vergata, INFN, Via della Ricerca Scientifica 1, I-00133 Roma, Italy; (S.B.); (G.N.); (G.R.); (F.S.); (S.M.)
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13
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Monfort B, Want K, Gervason S, D’Autréaux B. Recent Advances in the Elucidation of Frataxin Biochemical Function Open Novel Perspectives for the Treatment of Friedreich’s Ataxia. Front Neurosci 2022; 16:838335. [PMID: 35310092 PMCID: PMC8924461 DOI: 10.3389/fnins.2022.838335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 12/25/2022] Open
Abstract
Friedreich’s ataxia (FRDA) is the most prevalent autosomic recessive ataxia and is associated with a severe cardiac hypertrophy and less frequently diabetes. It is caused by mutations in the gene encoding frataxin (FXN), a small mitochondrial protein. The primary consequence is a defective expression of FXN, with basal protein levels decreased by 70–98%, which foremost affects the cerebellum, dorsal root ganglia, heart and liver. FXN is a mitochondrial protein involved in iron metabolism but its exact function has remained elusive and highly debated since its discovery. At the cellular level, FRDA is characterized by a general deficit in the biosynthesis of iron-sulfur (Fe-S) clusters and heme, iron accumulation and deposition in mitochondria, and sensitivity to oxidative stress. Based on these phenotypes and the proposed ability of FXN to bind iron, a role as an iron storage protein providing iron for Fe-S cluster and heme biosynthesis was initially proposed. However, this model was challenged by several other studies and it is now widely accepted that FXN functions primarily in Fe-S cluster biosynthesis, with iron accumulation, heme deficiency and oxidative stress sensitivity appearing later on as secondary defects. Nonetheless, the biochemical function of FXN in Fe-S cluster biosynthesis is still debated. Several roles have been proposed for FXN: iron chaperone, gate-keeper of detrimental Fe-S cluster biosynthesis, sulfide production stimulator and sulfur transfer accelerator. A picture is now emerging which points toward a unique function of FXN as an accelerator of a key step of sulfur transfer between two components of the Fe-S cluster biosynthetic complex. These findings should foster the development of new strategies for the treatment of FRDA. We will review here the latest discoveries on the biochemical function of frataxin and the implication for a potential therapeutic treatment of FRDA.
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14
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Puglisi R. Protein Mutations and Stability, a Link with Disease: The Case Study of Frataxin. Biomedicines 2022; 10:biomedicines10020425. [PMID: 35203634 PMCID: PMC8962269 DOI: 10.3390/biomedicines10020425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Protein mutations may lead to pathologies by causing protein misfunction or propensity to degradation. For this reason, several studies have been performed over the years to determine the capability of proteins to retain their native conformation under stress condition as well as factors to explain protein stabilization and the mechanisms behind unfolding. In this review, we explore the paradigmatic example of frataxin, an iron binding protein involved in Fe–S cluster biogenesis, and whose impairment causes a neurodegenerative disease called Friedreich’s Ataxia (FRDA). We summarize what is known about most common point mutations identified so far in heterozygous FRDA patients, their effects on frataxin structure and function and the consequences of its binding with partners.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, London SE59RT, UK
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15
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Doni D, Meggiolaro M, Santos J, Audran G, Marque SRA, Costantini P, Bortolus M, Carbonera D. A Combined Spectroscopic and In Silico Approach to Evaluate the Interaction of Human Frataxin with Mitochondrial Superoxide Dismutase. Biomedicines 2021; 9:biomedicines9121763. [PMID: 34944579 PMCID: PMC8698469 DOI: 10.3390/biomedicines9121763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022] Open
Abstract
Frataxin (FXN) is a highly conserved mitochondrial protein whose deficiency causes Friedreich’s ataxia, a neurodegenerative disease. The precise physiological function of FXN is still unclear; however, there is experimental evidence that the protein is involved in biosynthetic iron–sulfur cluster machinery, redox imbalance, and iron homeostasis. FXN is synthesized in the cytosol and imported into the mitochondria, where it is proteolytically cleaved to the mature form. Its involvement in the redox imbalance suggests that FXN could interact with mitochondrial superoxide dismutase (SOD2), a key enzyme in antioxidant cellular defense. In this work, we use site-directed spin labelling coupled to electron paramagnetic resonance spectroscopy (SDSL-EPR) and fluorescence quenching experiments to investigate the interaction between human FXN and SOD2 in vitro. Spectroscopic data are combined with rigid body protein–protein docking to assess the potential structure of the FXN-SOD2 complex, which leaves the metal binding region of FXN accessible to the solvent. We provide evidence that human FXN interacts with human SOD2 in vitro and that the complex is in fast exchange. This interaction could be relevant during the assembly of iron-sulfur (FeS) clusters and/or their incorporation in proteins when FeS clusters are potentially susceptible to attacks by reactive oxygen species.
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Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (D.D.); (M.M.); (P.C.)
| | - Marta Meggiolaro
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (D.D.); (M.M.); (P.C.)
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy;
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina;
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Gérard Audran
- Aix Marseille Universitè, CNRS, ICR, UMR 7273, case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.)
| | - Sylvain R. A. Marque
- Aix Marseille Universitè, CNRS, ICR, UMR 7273, case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.)
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (D.D.); (M.M.); (P.C.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy;
- Correspondence:
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy;
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16
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McCabe JW, Shirzadeh M, Walker TE, Lin CW, Jones BJ, Wysocki VH, Barondeau DP, Clemmer DE, Laganowsky A, Russell DH. Variable-Temperature Electrospray Ionization for Temperature-Dependent Folding/Refolding Reactions of Proteins and Ligand Binding. Anal Chem 2021; 93:6924-6931. [PMID: 33904705 DOI: 10.1021/acs.analchem.1c00870] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stabilities and structure(s) of proteins are directly coupled to their local environment or Gibbs free energy landscape as defined by solvent, temperature, pressure, and concentration. Solution pH, ionic strength, cofactors, chemical chaperones, and osmolytes perturb the chemical potential and induce further changes in structure, stability, and function. At present, no single analytical technique can monitor these effects in a single measurement. Mass spectrometry and ion mobility-mass spectrometry play increasingly essential roles in studies of proteins, protein complexes, and even membrane protein complexes; however, with few exceptions, the effects of the solution temperature on the stability and structure(s) of analytes have not been thoroughly investigated. Here, we describe a new variable-temperature electrospray ionization (vT-ESI) source that utilizes a thermoelectric chip to cool and heat the solution contained within the static ESI emitter. This design allows for solution temperatures to be varied from ∼5 to 98 °C with short equilibration times (<2 min) between precisely controlled temperature changes. The performance of the apparatus for vT-ESI-mass spectrometry and vT-ESI-ion mobility-mass spectrometry studies of cold- and heat-folding reactions is demonstrated using ubiquitin and frataxin. Instrument performance for studies on temperature-dependent ligand binding is shown using the chaperonin GroEL.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Benjamin J Jones
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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17
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Doni D, Rigoni G, Palumbo E, Baschiera E, Peruzzo R, De Rosa E, Caicci F, Passerini L, Bettio D, Russo A, Szabò I, Soriano ME, Salviati L, Costantini P. The displacement of frataxin from the mitochondrial cristae correlates with abnormal respiratory supercomplexes formation and bioenergetic defects in cells of Friedreich ataxia patients. FASEB J 2021; 35:e21362. [PMID: 33629768 DOI: 10.1096/fj.202000524rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022]
Abstract
Friedreich ataxia (FRDA) is a neurodegenerative disease resulting from a severe decrease of frataxin (FXN). Most patients carry a GAA repeat expansion in both alleles of the FXN gene, whereas a small fraction of them are compound heterozygous for the expansion and a point mutation in the other allele. FXN is involved in the mitochondrial biogenesis of the FeS-clusters. Distinctive feature of FRDA patient cells is an impaired cellular respiration, likely due to a deficit of key redox cofactors working as electrons shuttles through the respiratory chain. However, a definite relationship between FXN levels, FeS-clusters assembly dysregulation and bioenergetics failure has not been established. In this work, we performed a comparative analysis of the mitochondrial phenotype of cell lines from FRDA patients, either homozygous for the expansion or compound heterozygotes for the G130V mutation. We found that, in healthy cells, FXN and two key proteins of the FeS-cluster assembly machinery are enriched in mitochondrial cristae, the dynamic subcompartment housing the respiratory chain. On the contrary, FXN widely redistributes to the matrix in FRDA cells with defects in respiratory supercomplexes assembly and altered respiratory function. We propose that this could be relevant for the early mitochondrial defects afflicting FRDA cells and that perturbation of mitochondrial morphodynamics could in turn be critical in terms of disease mechanisms.
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Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, Padova, Italy
| | | | - Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Elisa Baschiera
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
- Istituto di Ricerca Pediatrica (IRP) Città della Speranza, Padova, Italy
| | | | - Edith De Rosa
- Department of Biology, University of Padova, Padova, Italy
| | | | | | - Daniela Bettio
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
- Istituto di Ricerca Pediatrica (IRP) Città della Speranza, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ildiko Szabò
- Department of Biology, University of Padova, Padova, Italy
| | | | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
- Istituto di Ricerca Pediatrica (IRP) Città della Speranza, Padova, Italy
- Myology Center, University of Padova, Padova, Italy
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18
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Gomez-Casati DF, Busi MV, Barchiesi J, Pagani MA, Marchetti-Acosta NS, Terenzi A. Fe-S Protein Synthesis in Green Algae Mitochondria. PLANTS 2021; 10:plants10020200. [PMID: 33494487 PMCID: PMC7911964 DOI: 10.3390/plants10020200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/28/2022]
Abstract
Iron and sulfur are two essential elements for all organisms. These elements form the Fe-S clusters that are present as cofactors in numerous proteins and protein complexes related to key processes in cells, such as respiration and photosynthesis, and participate in numerous enzymatic reactions. In photosynthetic organisms, the ISC and SUF Fe-S cluster synthesis pathways are located in organelles, mitochondria, and chloroplasts, respectively. There is also a third biosynthetic machinery in the cytosol (CIA) that is dependent on the mitochondria for its function. The genes and proteins that participate in these assembly pathways have been described mainly in bacteria, yeasts, humans, and recently in higher plants. However, little is known about the proteins that participate in these processes in algae. This review work is mainly focused on releasing the information on the existence of genes and proteins of green algae (chlorophytes) that could participate in the assembly process of Fe-S groups, especially in the mitochondrial ISC and CIA pathways.
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Affiliation(s)
- Diego F. Gomez-Casati
- Correspondence: (D.F.G.-C.); (M.V.B.); Tel.: +54-341-4391955 (ext. 113) (D.F.G.-C. & M.V.B.)
| | - Maria V. Busi
- Correspondence: (D.F.G.-C.); (M.V.B.); Tel.: +54-341-4391955 (ext. 113) (D.F.G.-C. & M.V.B.)
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19
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Doni D, Passerini L, Audran G, Marque SRA, Schulz M, Santos J, Costantini P, Bortolus M, Carbonera D. Effects of Fe 2+/Fe 3+ Binding to Human Frataxin and Its D122Y Variant, as Revealed by Site-Directed Spin Labeling (SDSL) EPR Complemented by Fluorescence and Circular Dichroism Spectroscopies. Int J Mol Sci 2020; 21:E9619. [PMID: 33348670 PMCID: PMC7766144 DOI: 10.3390/ijms21249619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022] Open
Abstract
Frataxin is a highly conserved protein whose deficiency results in the neurodegenerative disease Friederich's ataxia. Frataxin's actual physiological function has been debated for a long time without reaching a general agreement; however, it is commonly accepted that the protein is involved in the biosynthetic iron-sulphur cluster (ISC) machinery, and several authors have pointed out that it also participates in iron homeostasis. In this work, we use site-directed spin labeling coupled to electron paramagnetic resonance (SDSL EPR) to add new information on the effects of ferric and ferrous iron binding on the properties of human frataxin in vitro. Using SDSL EPR and relating the results to fluorescence experiments commonly performed to study iron binding to FXN, we produced evidence that ferric iron causes reversible aggregation without preferred interfaces in a concentration-dependent fashion, starting at relatively low concentrations (micromolar range), whereas ferrous iron binds without inducing aggregation. Moreover, our experiments show that the ferrous binding does not lead to changes of protein conformation. The data reported in this study reveal that the currently reported binding stoichiometries should be taken with caution. The use of a spin label resistant to reduction, as well as the comparison of the binding effect of Fe2+ in wild type and in the pathological D122Y variant of frataxin, allowed us to characterize the Fe2+ binding properties of different protein sites and highlight the effect of the D122Y substitution on the surrounding residues. We suggest that both Fe2+ and Fe3+ might play a relevant role in the context of the proposed FXN physiological functions.
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Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (D.D.); (P.C.)
| | - Leonardo Passerini
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; (L.P.); (D.C.)
| | - Gérard Audran
- Institut de Chimie Radicalaire, Aix Marseille Universitè, CNRS, ICR, UMR 7273, Case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.); (M.S.)
| | - Sylvain R. A. Marque
- Institut de Chimie Radicalaire, Aix Marseille Universitè, CNRS, ICR, UMR 7273, Case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.); (M.S.)
| | - Marvin Schulz
- Institut de Chimie Radicalaire, Aix Marseille Universitè, CNRS, ICR, UMR 7273, Case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.); (M.S.)
| | - Javier Santos
- Departamento de Química Biológica, Instituto de Biociencias, Biotecnología y Biomedicina (iB3-UBA), Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160—Ciudad Universitaria, 1428EGA CONICET, Godoy Cruz 2290, Buenos Aires C1425FQB, Argentina;
- Instituto de Química y Fisicoquímica Biológicas Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, Buenos Aires 1113AAD, Argentina
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (D.D.); (P.C.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; (L.P.); (D.C.)
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; (L.P.); (D.C.)
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20
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Smith FM, Kosman DJ. Molecular Defects in Friedreich's Ataxia: Convergence of Oxidative Stress and Cytoskeletal Abnormalities. Front Mol Biosci 2020; 7:569293. [PMID: 33263002 PMCID: PMC7686857 DOI: 10.3389/fmolb.2020.569293] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/10/2020] [Indexed: 01/18/2023] Open
Abstract
Friedreich’s ataxia (FRDA) is a multi-faceted disease characterized by progressive sensory–motor loss, neurodegeneration, brain iron accumulation, and eventual death by hypertrophic cardiomyopathy. FRDA follows loss of frataxin (FXN), a mitochondrial chaperone protein required for incorporation of iron into iron–sulfur cluster and heme precursors. After the discovery of the molecular basis of FRDA in 1996, over two decades of research have been dedicated to understanding the temporal manifestations of disease both at the whole body and molecular level. Early research indicated strong cellular iron dysregulation in both human and yeast models followed by onset of oxidative stress. Since then, the pathophysiology due to dysregulation of intracellular iron chaperoning has become central in FRDA relative to antioxidant defense and run-down in energy metabolism. At the same time, limited consideration has been given to changes in cytoskeletal organization, which was one of the first molecular defects noted. These alterations include both post-translational oxidative glutathionylation of actin monomers and differential DNA processing of a cytoskeletal regulator PIP5K1β. Currently unknown in respect to FRDA but well understood in the context of FXN-deficient cell physiology is the resulting impact on the cytoskeleton; this disassembly of actin filaments has a particularly profound effect on cell–cell junctions characteristic of barrier cells. With respect to a neurodegenerative disorder such as FRDA, this cytoskeletal and tight junction breakdown in the brain microvascular endothelial cells of the blood–brain barrier is likely a component of disease etiology. This review serves to outline a brief history of this research and hones in on pathway dysregulation downstream of iron-related pathology in FRDA related to actin dynamics. The review presented here was not written with the intent of being exhaustive, but to instead urge the reader to consider the essentiality of the cytoskeleton and appreciate the limited knowledge on FRDA-related cytoskeletal dysfunction as a result of oxidative stress. The review examines previous hypotheses of neurodegeneration with brain iron accumulation (NBIA) in FRDA with a specific biochemical focus.
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Affiliation(s)
- Frances M Smith
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Daniel J Kosman
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
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21
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Castro IH, Bringas M, Doni D, Noguera ME, Capece L, Aran M, Blaustein M, Costantini P, Santos J. Relationship between activity and stability: Design and characterization of stable variants of human frataxin. Arch Biochem Biophys 2020; 691:108491. [PMID: 32707090 DOI: 10.1016/j.abb.2020.108491] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 11/16/2022]
Abstract
The relationships between conformational dynamics, stability and protein function are not obvious. Frataxin (FXN) is an essential protein that forms part of a supercomplex dedicated to the iron-sulfur (Fe-S) cluster assembly within the mitochondrial matrix. In humans, the loss of FXN expression or a decrease in its functionality results in Friedreich's Ataxia, a cardio-neurodegenerative disease. Recently, the way in which FXN interacts with the rest of the subunits of the supercomplex was uncovered. This opens a window to explore relationships between structural dynamics and function. In this study, we prepared a set of FXN variants spanning a broad range of conformational stabilities. Variants S160I, S160M and A204R were more stable than the wild-type and showed similar biological activity. Additionally, we prepared SILCAR, a variant that combines S160I, L203C and A204R mutations. SILCAR was 2.4 kcal mol-1 more stable and equally active. Some of the variants were significantly more resistant to proteolysis than the wild-type FXN. SILCAR showed the highest resistance, suggesting a more rigid structure. It was corroborated by means of molecular dynamics simulations. Relaxation dispersion NMR experiments comparing SILCAR and wild-type variants suggested similar internal motions in the microsecond to millisecond timescale. Instead, variant S157I showed higher denaturation resistance but a significant lower function, similarly to that observed for the FRDA variant N146K. We concluded that the contribution of particular side chains to the conformational stability of FXN might be highly subordinated to their impact on both the protein function and the stability of the functional supercomplex.
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Affiliation(s)
- Ignacio Hugo Castro
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), C1428EGA, Buenos Aires, Argentina
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Martin Ezequiel Noguera
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), C1428EGA, Buenos Aires, Argentina
| | - Martín Aran
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Matías Blaustein
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina.
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22
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Olmos J, Pignataro MF, Benítez dos Santos AB, Bringas M, Klinke S, Kamenetzky L, Velazquez F, Santos J. A Highly Conserved Iron-Sulfur Cluster Assembly Machinery between Humans and Amoeba Dictyostelium discoideum: The Characterization of Frataxin. Int J Mol Sci 2020; 21:E6821. [PMID: 32957566 PMCID: PMC7554988 DOI: 10.3390/ijms21186821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Several biological activities depend on iron-sulfur clusters ([Fe-S]). Even though they are well-known in several organisms their function and metabolic pathway were poorly understood in the majority of the organisms. We propose to use the amoeba Dictyostelium discoideum, as a biological model to study the biosynthesis of [Fe-S] at the molecular, cellular and organism levels. First, we have explored the D. discoideum genome looking for genes corresponding to the subunits that constitute the molecular machinery for Fe-S cluster assembly and, based on the structure of the mammalian supercomplex and amino acid conservation profiles, we inferred the full functionality of the amoeba machinery. After that, we expressed the recombinant mature form of D. discoideum frataxin protein (DdFXN), the kinetic activator of this pathway. We characterized the protein and its conformational stability. DdFXN is monomeric and compact. The analysis of the secondary structure content, calculated using the far-UV CD spectra, was compatible with the data expected for the FXN fold, and near-UV CD spectra were compatible with the data corresponding to a folded protein. In addition, Tryptophan fluorescence indicated that the emission occurs from an apolar environment. However, the conformation of DdFXN is significantly less stable than that of the human FXN, (4.0 vs. 9.0 kcal mol-1, respectively). Based on a sequence analysis and structural models of DdFXN, we investigated key residues involved in the interaction of DdFXN with the supercomplex and the effect of point mutations on the energetics of the DdFXN tertiary structure. More than 10 residues involved in Friedreich's Ataxia are conserved between the human and DdFXN forms, and a good correlation between mutational effect on the energetics of both proteins were found, suggesting the existence of similar sequence/function/stability relationships. Finally, we integrated this information in an evolutionary context which highlights particular variation patterns between amoeba and humans that may reflect a functional importance of specific protein positions. Moreover, the complete pathway obtained forms a piece of evidence in favor of the hypothesis of a shared and highly conserved [Fe-S] assembly machinery between Human and D. discoideum.
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Affiliation(s)
- Justo Olmos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - María Florencia Pignataro
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - Ana Belén Benítez dos Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), Buenos Aires C1428EGA, Argentina;
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina;
| | - Laura Kamenetzky
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Francisco Velazquez
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)—(UBA/CONICET), Buenos Aires C1428EGA, Argentina
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, Buenos Aires C1033AAJ, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
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23
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Armas AM, Balparda M, Terenzi A, Busi MV, Pagani MA, Gomez-Casati DF. Iron-Sulfur Cluster Complex Assembly in the Mitochondria of Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091171. [PMID: 32917022 PMCID: PMC7570111 DOI: 10.3390/plants9091171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 05/02/2023]
Abstract
In plants, the cysteine desulfurase (AtNFS1) and frataxin (AtFH) are involved in the formation of Fe-S groups in mitochondria, specifically, in Fe and sulfur loading onto scaffold proteins, and the subsequent formation of the mature Fe-S cluster. We found that the small mitochondrial chaperone, AtISD11, and AtFH are positive regulators for AtNFS1 activity in Arabidopsis. Moreover, when the three proteins were incubated together, a stronger attenuation of the Fenton reaction was observed compared to that observed with AtFH alone. Using pull-down assays, we found that these three proteins physically interact, and sequence alignment and docking studies showed that several amino acid residues reported as critical for the interaction of their human homologous are conserved. Our results suggest that AtFH, AtNFS1 and AtISD11 form a multiprotein complex that could be involved in different stages of the iron-sulfur cluster (ISC) pathway in plant mitochondria.
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Affiliation(s)
- Alejandro M. Armas
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Rosario 2000, Argentina;
| | - Manuel Balparda
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario 2000, Argentina; (M.B.); (A.T.); (M.V.B.); (M.A.P.)
| | - Agustina Terenzi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario 2000, Argentina; (M.B.); (A.T.); (M.V.B.); (M.A.P.)
| | - Maria V. Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario 2000, Argentina; (M.B.); (A.T.); (M.V.B.); (M.A.P.)
| | - Maria A. Pagani
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario 2000, Argentina; (M.B.); (A.T.); (M.V.B.); (M.A.P.)
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario 2000, Argentina; (M.B.); (A.T.); (M.V.B.); (M.A.P.)
- Correspondence: ; Tel.: +54-341-4391955 (ext. 113)
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24
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Li Y, Lou W, Grevel A, Böttinger L, Liang Z, Ji J, Patil VA, Liu J, Ye C, Hüttemann M, Becker T, Greenberg ML. Cardiolipin-deficient cells have decreased levels of the iron-sulfur biogenesis protein frataxin. J Biol Chem 2020; 295:11928-11937. [PMID: 32636300 PMCID: PMC7450130 DOI: 10.1074/jbc.ra120.013960] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Cardiolipin (CL) is the signature phospholipid of mitochondrial membranes, where it is synthesized locally and plays an important role in mitochondrial bioenergetics. Previous studies in the yeast model have indicated that CL is required for optimal iron homeostasis, which is disrupted by a mechanism not yet determined in the yeast CL mutant, crd1Δ. This finding has implications for the severe genetic disorder, Barth syndrome (BTHS), in which CL metabolism is perturbed because of mutations in the CL-remodeling enzyme, tafazzin. Here, we investigate the effects of tafazzin deficiency on iron homeostasis in the mouse myoblast model of BTHS tafazzin knockout (TAZ-KO) cells. Similarly to CL-deficient yeast cells, TAZ-KO cells exhibited elevated sensitivity to iron, as well as to H2O2, which was alleviated by the iron chelator deferoxamine. TAZ-KO cells exhibited increased expression of the iron exporter ferroportin and decreased expression of the iron importer transferrin receptor, likely reflecting a regulatory response to elevated mitochondrial iron. Reduced activities of mitochondrial iron-sulfur cluster enzymes suggested that the mechanism underlying perturbation of iron homeostasis was defective iron-sulfur biogenesis. We observed decreased levels of Yfh1/frataxin, an essential component of the iron-sulfur biogenesis machinery, in mitochondria from TAZ-KO mouse cells and in CL-deleted yeast crd1Δ cells, indicating that the role of CL in iron-sulfur biogenesis is highly conserved. Yeast crd1Δ cells exhibited decreased processing of the Yfh1 precursor upon import, which likely contributes to the iron homeostasis defects. Implications for understanding the pathogenesis of BTHS are discussed.
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Affiliation(s)
- Yiran Li
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Wenjia Lou
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Alexander Grevel
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lena Böttinger
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Zhuqing Liang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jiajia Ji
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Vinay A Patil
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Cunqi Ye
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Thomas Becker
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
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25
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Fil D, Chacko BK, Conley R, Ouyang X, Zhang J, Darley-Usmar VM, Zuberi AR, Lutz CM, Napierala M, Napierala JS. Mitochondrial damage and senescence phenotype of cells derived from a novel frataxin G127V point mutation mouse model of Friedreich's ataxia. Dis Model Mech 2020; 13:dmm045229. [PMID: 32586831 PMCID: PMC7406325 DOI: 10.1242/dmm.045229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disease caused by reduced expression of the mitochondrial protein frataxin (FXN). Most FRDA patients are homozygous for large expansions of GAA repeat sequences in intron 1 of FXN, whereas a fraction of patients are compound heterozygotes, with a missense or nonsense mutation in one FXN allele and expanded GAAs in the other. A prevalent missense mutation among FRDA patients changes a glycine at position 130 to valine (G130V). Herein, we report generation of the first mouse model harboring an Fxn point mutation. Changing the evolutionarily conserved glycine 127 in mouse Fxn to valine results in a failure-to-thrive phenotype in homozygous animals and a substantially reduced number of offspring. Like G130V in FRDA, the G127V mutation results in a dramatic decrease of Fxn protein without affecting transcript synthesis or splicing. FxnG127V mouse embryonic fibroblasts exhibit significantly reduced proliferation and increased cell senescence. These defects are evident in early passage cells and are exacerbated at later passages. Furthermore, increased frequency of mitochondrial DNA lesions and fragmentation are accompanied by marked amplification of mitochondrial DNA in FxnG127V cells. Bioenergetics analyses demonstrate higher sensitivity and reduced cellular respiration of FxnG127V cells upon alteration of fatty acid availability. Importantly, substitution of FxnWT with FxnG127V is compatible with life, and cellular proliferation defects can be rescued by mitigation of oxidative stress via hypoxia or induction of the NRF2 pathway. We propose FxnG127V cells as a simple and robust model for testing therapeutic approaches for FRDA.
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Affiliation(s)
- Daniel Fil
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - Balu K Chacko
- Department of Pathology, University of Alabama at Birmingham, 901 19th Street South, Birmingham, AL 35294, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robbie Conley
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - Xiaosen Ouyang
- Department of Pathology, University of Alabama at Birmingham, 901 19th Street South, Birmingham, AL 35294, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Veteran Affairs Medical Center, Birmingham, AL 35294, USA
| | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, 901 19th Street South, Birmingham, AL 35294, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Veteran Affairs Medical Center, Birmingham, AL 35294, USA
| | - Victor M Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, 901 19th Street South, Birmingham, AL 35294, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aamir R Zuberi
- The Rare and Orphan Disease Center, JAX Center for Precision Genetics, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Cathleen M Lutz
- The Rare and Orphan Disease Center, JAX Center for Precision Genetics, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
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Baussier C, Fakroun S, Aubert C, Dubrac S, Mandin P, Py B, Barras F. Making iron-sulfur cluster: structure, regulation and evolution of the bacterial ISC system. Adv Microb Physiol 2020; 76:1-39. [PMID: 32408945 DOI: 10.1016/bs.ampbs.2020.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron sulfur (Fe-S) clusters rank among the most ancient and conserved prosthetic groups. Fe-S clusters containing proteins are present in most, if not all, organisms. Fe-S clusters containing proteins are involved in a wide range of cellular processes, from gene regulation to central metabolism, via gene expression, RNA modification or bioenergetics. Fe-S clusters are built by biogenesis machineries conserved throughout both prokaryotes and eukaryotes. We focus mostly on bacterial ISC machinery, but not exclusively, as we refer to eukaryotic ISC system when it brings significant complementary information. Besides covering the structural and regulatory aspects of Fe-S biogenesis, this review aims to highlight Fe-S biogenesis facets remaining matters of discussion, such as the role of frataxin, or the link between fatty acid metabolism and Fe-S homeostasis. Last, we discuss recent advances on strategies used by different species to make and use Fe-S clusters in changing redox environmental conditions.
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Affiliation(s)
- Corentin Baussier
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Soufyan Fakroun
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Sarah Dubrac
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
| | - Pierre Mandin
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Frédéric Barras
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
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27
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Wei X, Li ZC, Li SJ, Peng XB, Zhao Q. Protein structure determination using a Riemannian approach. FEBS Lett 2019; 594:1036-1051. [PMID: 31769509 DOI: 10.1002/1873-3468.13688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/31/2019] [Accepted: 11/14/2019] [Indexed: 11/05/2022]
Abstract
Protein NMR structure determination is one of the most extensively studied problems. Here, we adopt a novel method based on a matrix completion technique - the Riemannian approach - to rebuild the protein structure from the nuclear Overhauser effect distance restraints and the dihedral angle restraints. In comparison with the cyana method, the results generated via the Riemannian approach are more similar to the standard X-ray crystallographic structures as a result of the simple but powerful internal calculation processing function. In addition, our results demonstrate that the Riemannian approach has a comparable or even better performance than the cyana method on other structural assessment metrics, including the stereochemical quality and restraint violations. The Riemannian approach software is available at: https://github.com/xubiaopeng/Protein_Recon_MCRiemman.
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Affiliation(s)
- Xian Wei
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China.,Department of Science, Taiyuan Institute of Technology, China
| | - Zhi-Cheng Li
- Department of Physics, Taiyuan Normal University, China
| | - Shi-Jian Li
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China
| | - Xu-Biao Peng
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China
| | - Qing Zhao
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China
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28
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Bellanda M, Maso L, Doni D, Bortolus M, De Rosa E, Lunardi F, Alfonsi A, Noguera ME, Herrera MG, Santos J, Carbonera D, Costantini P. Exploring iron-binding to human frataxin and to selected Friedreich ataxia mutants by means of NMR and EPR spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2019; 1867:140254. [PMID: 31344531 DOI: 10.1016/j.bbapap.2019.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/12/2019] [Accepted: 07/18/2019] [Indexed: 11/23/2022]
Abstract
The neurodegenerative disease Friedreich ataxia results from a deficiency of frataxin, a mitochondrial protein. Most patients have a GAA expansion in the first intron of both alleles of frataxin gene, whereas a minority of them are heterozygous for the expansion and contain a mutation in the other allele. Frataxin has been claimed to participate in iron homeostasis and biosynthesis of FeS clusters, however its role in both pathways is not unequivocally defined. In this work we combined different advanced spectroscopic analyses to explore the iron-binding properties of human frataxin, as isolated and at the FeS clusters assembly machinery. For the first time we used EPR spectroscopy to address this key issue providing clear evidence of the formation of a complex with a low symmetry coordination of the metal ion. By 2D NMR, we confirmed that iron can be bound in both oxidation states, a controversial issue, and, in addition, we were able to point out a transient interaction of frataxin with a N-terminal 6his-tagged variant of ISCU, the scaffold protein of the FeS clusters assembly machinery. To obtain insights on structure/function relationships relevant to understand the disease molecular mechanism(s), we extended our studies to four clinical frataxin mutants. All variants showed a moderate to strong impairment in their ability to activate the FeS cluster assembly machinery in vitro, while keeping the same iron-binding features of the wild type protein. This supports the multifunctional nature of frataxin and the complex biochemical consequences of its mutations.
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Affiliation(s)
- Massimo Bellanda
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Lorenzo Maso
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Edith De Rosa
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Federica Lunardi
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Arianna Alfonsi
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), 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
| | - Maria Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), 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
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), 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
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
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29
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Petrosino M, Pasquo A, Novak L, Toto A, Gianni S, Mantuano E, Veneziano L, Minicozzi V, Pastore A, Puglisi R, Capriotti E, Chiaraluce R, Consalvi V. Characterization of human frataxin missense variants in cancer tissues. Hum Mutat 2019; 40:1400-1413. [PMID: 31074541 PMCID: PMC6744310 DOI: 10.1002/humu.23789] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 12/19/2022]
Abstract
Human frataxin is an iron-binding protein involved in the mitochondrial iron-sulfur (Fe-S) clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumor-initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study, we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function, and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions; however, some of the variants show a decreased stability and a decreased functional activity in comparison with that of the wild-type protein.
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Affiliation(s)
- Maria Petrosino
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Current address: IRCCS Istituto Neurologico Carlo Besta, Milano, Italia
- European Brain Research Institute-Fondazione Rita Levi Montalcini, Roma, Italia
| | - Alessandra Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory,FSN-TECFIS-DIM, Frascati, Italy
| | - Leonore Novak
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Elide Mantuano
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | | | - Velia Minicozzi
- INFN and Department of Physics, University of Rome Tor Vergata, Rome, Italy
| | - Annalisa Pastore
- The Wohl Institute, King’s College London, London, United Kingdom
| | - Rita Puglisi
- The Wohl Institute, King’s College London, London, United Kingdom
| | - Emidio Capriotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Roberta Chiaraluce
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
| | - Valerio Consalvi
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
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30
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Fox NG, Yu X, Feng X, Bailey HJ, Martelli A, Nabhan JF, Strain-Damerell C, Bulawa C, Yue WW, Han S. Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism. Nat Commun 2019; 10:2210. [PMID: 31101807 PMCID: PMC6525205 DOI: 10.1038/s41467-019-09989-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022] Open
Abstract
The core machinery for de novo biosynthesis of iron-sulfur clusters (ISC), located in the mitochondria matrix, is a five-protein complex containing the cysteine desulfurase NFS1 that is activated by frataxin (FXN), scaffold protein ISCU, accessory protein ISD11, and acyl-carrier protein ACP. Deficiency in FXN leads to the loss-of-function neurodegenerative disorder Friedreich's ataxia (FRDA). Here the 3.2 Å resolution cryo-electron microscopy structure of the FXN-bound active human complex, containing two copies of the NFS1-ISD11-ACP-ISCU-FXN hetero-pentamer, delineates the interactions of FXN with other component proteins of the complex. FXN binds at the interface of two NFS1 and one ISCU subunits, modifying the local environment of a bound zinc ion that would otherwise inhibit NFS1 activity in complexes without FXN. Our structure reveals how FXN facilitates ISC production through stabilizing key loop conformations of NFS1 and ISCU at the protein-protein interfaces, and suggests how FRDA clinical mutations affect complex formation and FXN activation.
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Affiliation(s)
- Nicholas G Fox
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Merck & Co, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Xiaodi Yu
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
- SMPS, Janssen Research and Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Xidong Feng
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
| | - Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alain Martelli
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Joseph F Nabhan
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Claire Strain-Damerell
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Christine Bulawa
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Seungil Han
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA.
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31
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Clark E, Strawser C, Schadt K, Lynch DR. Identification of a novel missense mutation in Friedreich's ataxia -FXN W 168R. Ann Clin Transl Neurol 2019; 6:812-816. [PMID: 31020006 PMCID: PMC6469249 DOI: 10.1002/acn3.728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/29/2018] [Accepted: 01/03/2019] [Indexed: 11/11/2022] Open
Abstract
Friedreich's ataxia, characterized by decreased expression of frataxin protein, is caused by GAA trinucleotide repeats within intron 1 in 98% of patients. Two percent of patients carry GAA repeats in conjunction with a point mutation. In this work, we find that frataxinW168R, a novel disease-causing missense mutation, is expressed predominantly as the intermediate frataxin42-210 form, with very little expression of mature frataxin81-210 form. Its localization to mitochondria is not impaired. Additionally, increasing frataxinW168R precursor levels do not lead to an increase in mature frataxin levels, suggesting these patients will require alternative approaches to repair frataxin processing in order to treat the disorder in a disease-modifying manner.
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Affiliation(s)
- Elisia Clark
- University of PennsylvaniaPhiladelphiaPennsylvania
- Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
| | - Cassandra Strawser
- Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
| | - Kimberly Schadt
- Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
| | - David R. Lynch
- University of PennsylvaniaPhiladelphiaPennsylvania
- Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
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32
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Llorens JV, Soriano S, Calap-Quintana P, Gonzalez-Cabo P, Moltó MD. The Role of Iron in Friedreich's Ataxia: Insights From Studies in Human Tissues and Cellular and Animal Models. Front Neurosci 2019; 13:75. [PMID: 30833885 PMCID: PMC6387962 DOI: 10.3389/fnins.2019.00075] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/23/2019] [Indexed: 12/12/2022] Open
Abstract
Friedreich’s ataxia (FRDA) is a rare early-onset degenerative disease that affects both the central and peripheral nervous systems, and other extraneural tissues, mainly the heart and endocrine pancreas. This disorder progresses as a mixed sensory and cerebellar ataxia, primarily disturbing the proprioceptive pathways in the spinal cord, peripheral nerves and nuclei of the cerebellum. FRDA is an inherited disease with an autosomal recessive pattern caused by an insufficient amount of the nuclear-encoded mitochondrial protein frataxin, which is an essential and highly evolutionary conserved protein whose deficit results in iron metabolism dysregulation and mitochondrial dysfunction. The first experimental evidence connecting frataxin with iron homeostasis came from Saccharomyces cerevisiae; iron accumulates in the mitochondria of yeast with deletion of the frataxin ortholog gene. This finding was soon linked to previous observations of iron deposits in the hearts of FRDA patients and was later reported in animal models of the disease. Despite advances made in the understanding of FRDA pathophysiology, the role of iron in this disease has not yet been completely clarified. Some of the questions still unresolved include the molecular mechanisms responsible for the iron accumulation and iron-mediated toxicity. Here, we review the contribution of the cellular and animal models of FRDA and relevance of the studies using FRDA patient samples to gain knowledge about these issues. Mechanisms of mitochondrial iron overload are discussed considering the potential roles of frataxin in the major mitochondrial metabolic pathways that use iron. We also analyzed the effect of iron toxicity on neuronal degeneration in FRDA by reactive oxygen species (ROS)-dependent and ROS-independent mechanisms. Finally, therapeutic strategies based on the control of iron toxicity are considered.
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Affiliation(s)
- José Vicente Llorens
- Department of Genetics, Faculty of Biological Sciences, University of Valencia, Valencia, Spain.,Unit for Psychiatry and Neurodegenerative Diseases, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Sirena Soriano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Pablo Calap-Quintana
- Department of Genetics, Faculty of Biological Sciences, University of Valencia, Valencia, Spain.,Unit for Psychiatry and Neurodegenerative Diseases, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Pilar Gonzalez-Cabo
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain.,Center of Biomedical Network Research on Rare Diseases CIBERER, Valencia, Spain.,Associated Unit for Rare Diseases INCLIVA-CIPF, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - María Dolores Moltó
- Department of Genetics, Faculty of Biological Sciences, University of Valencia, Valencia, Spain.,Unit for Psychiatry and Neurodegenerative Diseases, Biomedical Research Institute INCLIVA, Valencia, Spain.,Center of Biomedical Network Research on Mental Health CIBERSAM, Valencia, Spain
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33
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Faraj SE, Noguera ME, Delfino JM, Santos J. Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin. Sci Rep 2019; 9:1731. [PMID: 30742023 PMCID: PMC6370780 DOI: 10.1038/s41598-019-39429-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/18/2019] [Indexed: 12/28/2022] Open
Abstract
Local events that affect specific regions of proteins are of utmost relevance for stability and function. The aim of this study is to quantitatively assess the importance of locally-focused dynamics by means of a simple chemical modification procedure. Taking human Frataxin as a working model, we investigated local fluctuations of the C-terminal region (the last 16 residues of the protein) by means of three L → C replacement mutants: L98C, L200C and L203C. The conformation and thermodynamic stability of each variant was assessed. All the variants exhibited native features and high stabilities: 9.1 (wild type), 8.1 (L198C), 7.0 (L200C) and 10.0 kcal mol-1 (L203C). In addition, kinetic rates of Cys chemical modification by DTNB and DTDPy were measured, conformational dynamics data were extracted and free energy for the local unfolding of the C-terminal region was estimated. The analysis of these results indicates that the conformation of the C-terminal region fluctuates with partial independence from global unfolding events. Additionally, numerical fittings of the kinetic model of the process suggest that the local transition occurs in the seconds to minutes timescale. In fact, standard free energy differences for local unfolding were found to be significantly lower than those of the global unfolding reaction, showing that chemical modification results may not be explained in terms of the global unfolding reaction alone. These results provide unequivocal experimental evidence of local phenomena with global effects and contribute to understanding how global and local stability are linked to protein dynamics.
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Affiliation(s)
- Santiago E Faraj
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina
| | - Martín E Noguera
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina
| | - José María Delfino
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina
| | - Javier Santos
- Alejandro Paladini Institute of Biological Chemistry and Chemical Physics (UBA-CONICET), Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (C1113AAD), Buenos Aires, Argentina. .,Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires. Instituto de Biociencias, Biotecnología y Biomedicina (iB3). Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA, C.A.B.A., Argentina.
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Abstract
Friedreich's ataxia (FRDA) is a degenerative disease that affects both the central and the peripheral nervous systems and non-neural tissues including, mainly, heart, and endocrine pancreas. It is an autosomal recessive disease caused by a GAA triplet-repeat localized within an Alu sequence element in intron 1 of frataxin (FXN) gene, which encodes a mitochondrial protein FXN. This protein is essential for mitochondrial function by the involvement of iron-sulfur cluster biogenesis. The effects of its deficiency also include disruption of cellular, particularly mitochondrial, iron homeostasis, i.e., relatively more iron accumulated in mitochondria and less iron presented in cytosol. Though iron toxicity is commonly thought to be mediated via Fenton reaction, oxidative stress seems not to be the main problem to result in detrimental effects on cell survival, particularly neuron survival. Therefore, the basic research on FXN function is urgently demanded to understand the disease. This chapter focuses on the outcome of FXN expression, regulation, and function in cellular or animal models of FRDA and on iron pathophysiology in the affected tissues. Finally, therapeutic strategies based on the control of iron toxicity and iron cellular redistribution are considered. The combination of multiple therapeutic targets including iron, oxidative stress, mitochondrial function, and FXN regulation is also proposed.
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Affiliation(s)
- Kuanyu Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210093, People's Republic of China.
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35
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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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36
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Role of frataxin protein deficiency and metabolic dysfunction in Friedreich ataxia, an autosomal recessive mitochondrial disease. Neuronal Signal 2018; 2:NS20180060. [PMID: 32714592 PMCID: PMC7373238 DOI: 10.1042/ns20180060] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/04/2023] Open
Abstract
Friedreich ataxia (FRDA) is a progressive neurodegenerative disease with developmental features caused by a genetic deficiency of frataxin, a small, nuclear-encoded mitochondrial protein. Frataxin deficiency leads to impairment of iron–sulphur cluster synthesis, and consequently, ATP production abnormalities. Based on the involvement of such processes in FRDA, initial pathophysiological hypotheses focused on reactive oxygen species (ROS) production as a key component of the mechanism. With further study, a variety of other events appear to be involved, including abnormalities of mitochondrially related metabolism and dysfunction in mitochondrial biogenesis. Consequently, present therapies focus not only on free radical damage, but also on control of metabolic abnormalities and correction of mitochondrial biogenesis. Understanding the multitude of abnormalities in FRDA thus offers possibilities for treatment of this disorder.
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37
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Cai K, Frederick RO, Dashti H, Markley JL. Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering. Structure 2018; 26:1127-1136.e4. [PMID: 29983374 PMCID: PMC6082693 DOI: 10.1016/j.str.2018.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/16/2018] [Accepted: 05/24/2018] [Indexed: 11/19/2022]
Abstract
Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for assembling other components of the biosynthetic machinery, including ISCU, frataxin, and ferredoxin. The human mitochondrial cysteine desulfurase complex consists of two copies each of NFS1, ISD11, and acyl carrier protein. We describe results from chemical crosslinking coupled with tandem mass spectrometry and small-angle X-ray scattering studies that are consistent with a closed NFS1 dimer rather than an open one for both the cysteine desulfurase-ISCU and cysteine desulfurase-ISCU-frataxin complexes. We present a structural model for the cysteine desulfurase-ISCU-frataxin complex derived from chemical crosslinking restraints in conjunction with the recent crystal structure of the cysteine desulfurase-ISCU-zinc complex and distance constraints from nuclear magnetic resonance.
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Affiliation(s)
- Kai Cai
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Ronnie O Frederick
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Hesam Dashti
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
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38
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Monnier V, Llorens JV, Navarro JA. Impact of Drosophila Models in the Study and Treatment of Friedreich's Ataxia. Int J Mol Sci 2018; 19:E1989. [PMID: 29986523 PMCID: PMC6073496 DOI: 10.3390/ijms19071989] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/26/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023] Open
Abstract
Drosophila melanogaster has been for over a century the model of choice of several neurobiologists to decipher the formation and development of the nervous system as well as to mirror the pathophysiological conditions of many human neurodegenerative diseases. The rare disease Friedreich’s ataxia (FRDA) is not an exception. Since the isolation of the responsible gene more than two decades ago, the analysis of the fly orthologue has proven to be an excellent avenue to understand the development and progression of the disease, to unravel pivotal mechanisms underpinning the pathology and to identify genes and molecules that might well be either disease biomarkers or promising targets for therapeutic interventions. In this review, we aim to summarize the collection of findings provided by the Drosophila models but also to go one step beyond and propose the implications of these discoveries for the study and cure of this disorder. We will present the physiological, cellular and molecular phenotypes described in the fly, highlighting those that have given insight into the pathology and we will show how the ability of Drosophila to perform genetic and pharmacological screens has provided valuable information that is not easily within reach of other cellular or mammalian models.
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Affiliation(s)
- Véronique Monnier
- Unité de Biologie Fonctionnelle et Adaptative (BFA), Sorbonne Paris Cité, Université Paris Diderot, UMR8251 CNRS, 75013 Paris, France.
| | - Jose Vicente Llorens
- Department of Genetics, University of Valencia, Campus of Burjassot, 96100 Valencia, Spain.
| | - Juan Antonio Navarro
- Lehrstuhl für Entwicklungsbiologie, Universität Regensburg, 93040 Regensburg, Germany.
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39
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Cai K, Frederick RO, Tonelli M, Markley JL. Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly. J Inorg Biochem 2018; 183:107-116. [PMID: 29576242 PMCID: PMC5951399 DOI: 10.1016/j.jinorgbio.2018.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/15/2022]
Abstract
Frataxin (FXN) is involved in mitochondrial iron‑sulfur (Fe-S) cluster biogenesis and serves to accelerate Fe-S cluster formation. FXN deficiency is associated with Friedreich ataxia, a neurodegenerative disease. We have used a combination of isothermal titration calorimetry and multinuclear NMR spectroscopy to investigate interactions among the components of the biological machine that carries out the assembly of iron‑sulfur clusters in human mitochondria. Our results show that FXN tightly binds a single Fe2+ but not Fe3+. While FXN (with or without bound Fe2+) does not bind the scaffold protein ISCU directly, the two proteins interact mutually when each is bound to the cysteine desulfurase complex ([NFS1]2:[ISD11]2:[Acp]2), abbreviated as (NIA)2, where "N" represents the cysteine desulfurase (NFS1), "I" represents the accessory protein (ISD11), and "A" represents acyl carrier protein (Acp). FXN binds (NIA)2 weakly in the absence of ISCU but more strongly in its presence. Fe2+-FXN binds to the (NIA)2-ISCU2 complex without release of iron. However, upon the addition of both l-cysteine and a reductant (either reduced FDX2 or DTT), Fe2+ is released from FXN as consistent with Fe2+-FXN being the proximal source of iron for Fe-S cluster assembly.
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Affiliation(s)
- Kai Cai
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - Ronnie O Frederick
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - John L Markley
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States.
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40
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Télot L, Rousseau E, Lesuisse E, Garcia C, Morlet B, Léger T, Camadro JM, Serre V. Quantitative proteomics in Friedreich's ataxia B-lymphocytes: A valuable approach to decipher the biochemical events responsible for pathogenesis. Biochim Biophys Acta Mol Basis Dis 2018; 1864:997-1009. [DOI: 10.1016/j.bbadis.2018.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/19/2017] [Accepted: 01/08/2018] [Indexed: 11/29/2022]
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41
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Lupoli F, Vannocci T, Longo G, Niccolai N, Pastore A. The role of oxidative stress in Friedreich's ataxia. FEBS Lett 2018; 592:718-727. [PMID: 29197070 PMCID: PMC5887922 DOI: 10.1002/1873-3468.12928] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022]
Abstract
Oxidative stress and an increase in the levels of free radicals are important markers associated with several pathologies, including Alzheimer's disease, cancer and diabetes. Friedreich's ataxia (FRDA) is an excellent paradigmatic example of a disease in which oxidative stress plays an important, albeit incompletely understood, role. FRDA is a rare genetic neurodegenerative disease that involves the partial silencing of frataxin, a small mitochondrial protein that was completely overlooked before being linked to FRDA. More than 20 years later, we now know how important this protein is in terms of being an essential and vital part of the machinery that produces iron-sulfur clusters in the cell. In this review, we revisit the most important steps that have brought us to our current understanding of the function of frataxin and its role in disease. We discuss the current hypotheses on the role of oxidative stress in FRDA and review some of the existing animal and cellular models. We also evaluate new techniques that can assist in the study of the disease mechanisms, as well as in our understanding of the interplay between primary and secondary phenotypes.
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Affiliation(s)
- Federica Lupoli
- Department of Biotechnology, Chemistry and PharmacyUniversity of SienaItaly
| | - Tommaso Vannocci
- The Maurice Wohl InstituteDementia Research CentreKing's College LondonUK
| | | | - Neri Niccolai
- Department of Biotechnology, Chemistry and PharmacyUniversity of SienaItaly
| | - Annalisa Pastore
- The Maurice Wohl InstituteDementia Research CentreKing's College LondonUK
- Department of Molecular MedicineUniversity of PaviaItaly
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42
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Castro IH, Ferrari A, Herrera MG, Noguera ME, Maso L, Benini M, Rufini A, Testi R, Costantini P, Santos J. Biophysical characterisation of the recombinant human frataxin precursor. FEBS Open Bio 2018; 8:390-405. [PMID: 29511616 PMCID: PMC5832983 DOI: 10.1002/2211-5463.12376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/25/2017] [Accepted: 12/27/2017] [Indexed: 11/10/2022] Open
Abstract
Friedreich's ataxia is a disease caused by a decrease in the levels of expression or loss of functionality of the mitochondrial protein frataxin (FXN). The development of an active and stable recombinant variant of FXN is important for protein replacement therapy. Although valuable data about the mature form FXN81-210 has been collected, not enough information is available about the conformation of the frataxin precursor (FXN1-210). We investigated the conformation, stability and function of a recombinant precursor variant (His6-TAT-FXN1-210), which includes a TAT peptide in the N-terminal region to assist with transport across cell membranes. His6-TAT-FXN1-210 was expressed in Escherichia coli and conditions were found for purifying folded protein free of aggregation, oxidation or degradation, even after freezing and thawing. The protein was found to be stable and monomeric, with the N-terminal stretch (residues 1-89) mostly unstructured and the C-terminal domain properly folded. The experimental data suggest a complex picture for the folding process of full-length frataxin in vitro: the presence of the N-terminal region increased the tendency of FXN to aggregate at high temperatures but this could be avoided by the addition of low concentrations of GdmCl. The purified precursor was translocated through cell membranes. In addition, immune response against His6-TAT-FXN1-210 was measured, suggesting that the C-terminal fragment was not immunogenic at the assayed protein concentrations. Finally, the recognition of recombinant FXN by cellular proteins was studied to evaluate its functionality. In this regard, cysteine desulfurase NFS1/ISD11/ISCU was activated in vitro by His6-TAT-FXN1-210. Moreover, the results showed that His6-TAT-FXN1-210 can be ubiquitinated in vitro by the recently identified frataxin E3 ligase RNF126, in a similar way as the FXN1-210, suggesting that the His6-TAT extension does not interfere with the ubiquitination machinery.
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Affiliation(s)
- Ignacio Hugo Castro
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Alejandro Ferrari
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - María Georgina Herrera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Martín Ezequiel Noguera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Lorenzo Maso
- Department of Biology University of Padova Italy
| | - Monica Benini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Alessandra Rufini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Roberto Testi
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | | | - Javier Santos
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
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Noguera ME, Aran M, Smal C, Vazquez DS, Herrera MG, Roman EA, Alaimo N, Gallo M, Santos J. Insights on the conformational dynamics of human frataxin through modifications of loop-1. Arch Biochem Biophys 2017; 636:123-137. [PMID: 29097312 DOI: 10.1016/j.abb.2017.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/20/2017] [Accepted: 10/28/2017] [Indexed: 02/07/2023]
Abstract
Human frataxin (FXN) is a highly conserved mitochondrial protein involved in iron homeostasis and activation of the iron-sulfur cluster assembly. FXN deficiency causes the neurodegenerative disease Friedreich's Ataxia. Here, we investigated the effect of alterations in loop-1, a stretch presumably essential for FXN function, on the conformational stability and dynamics of the native state. We generated four loop-1 variants, carrying substitutions, insertions and deletions. All of them were stable and well-folded proteins. Fast local motions (ps-ns) and slower long-range conformational dynamics (μs-ms) were altered in some mutants as judged by NMR. Particularly, loop-1 modifications impact on the dynamics of a distant region that includes residues from the β-sheet, helix α1 and the C-terminal. Remarkably, all the mutants retain the ability to activate cysteine desulfurase, even when two of them exhibit a strong decrease in iron binding, revealing a differential sensitivity of these functional features to loop-1 perturbation. Consequently, we found that even for a small and relatively rigid protein, engineering a loop segment enables to alter conformational dynamics through a long-range effect, preserving the native-state structure and important aspects of function.
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Affiliation(s)
- Martín E Noguera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Martín Aran
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Clara Smal
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Diego S Vazquez
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - María Georgina Herrera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Ernesto A Roman
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Nadine Alaimo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy
| | - Mariana Gallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy; IRBM Science Park S.p.A., Via Pontina km 30,600., 00071 Pomezia (RM), Italy.
| | - Javier Santos
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina.
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44
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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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45
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Buchensky C, Sánchez M, Carrillo M, Palacios O, Capdevila M, Domínguez-Vera JM, Busi MV, Atrian S, Pagani MA, Gomez-Casati DF. Identification of two frataxin isoforms in Zea mays: Structural and functional studies. Biochimie 2017; 140:34-47. [PMID: 28630009 DOI: 10.1016/j.biochi.2017.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/15/2017] [Indexed: 11/19/2022]
Abstract
Frataxin is a ubiquitous protein that plays a role in Fe-S cluster biosynthesis and iron and heme metabolism, although its molecular functions are not entirely clear. In non-photosynthetic eukaryotes, frataxin is encoded by a single gene, and the protein localizes to mitochondria. Here we report the presence of two functional frataxin isoforms in Zea mays, ZmFH-1 and ZmFH-2. We confirmed our previous findings regarding plant frataxins: both proteins have dual localization in mitochondria and chloroplasts. Physiological, biochemical and biophysical studies show some differences in the expression pattern, protection against oxidants and in the aggregation state of both isoforms, suggesting that the two frataxin homologs would play similar but not identical roles in plant cell metabolism. In addition, two specific features of plant frataxins were evidenced: their ability to form dimers and their tendency to undergo conformational change under oxygen exposure.
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Affiliation(s)
- Celeste Buchensky
- CEFOBI - CONICET, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Manuel Sánchez
- Departamento de Química Inorgánica, Facultad de Ciencias. Instituto de Biotecnología, Universidad de Granada, 18071, Granada, Spain
| | - Martin Carrillo
- CEFOBI - CONICET, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Oscar Palacios
- Departament de Química, Facultat de Ciènces, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciènces, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Jose M Domínguez-Vera
- Departamento de Química Inorgánica, Facultad de Ciencias. Instituto de Biotecnología, Universidad de Granada, 18071, Granada, Spain
| | - Maria V Busi
- CEFOBI - CONICET, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Sílvia Atrian
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain
| | - Maria A Pagani
- CEFOBI - CONICET, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- CEFOBI - CONICET, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina.
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46
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Han THL, Camadro JM, Santos R, Lesuisse E, El Hage Chahine JM, Ha-Duong NT. Mechanisms of iron and copper-frataxin interactions. Metallomics 2017; 9:1073-1085. [PMID: 28573291 DOI: 10.1039/c7mt00031f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Frataxin is a mitochondrial protein whose deficiency is the cause of Friedreich's ataxia, a hereditary neurodegenerative disease. This protein plays a role in iron-sulfur cluster biosynthesis, protection against oxidative stress and iron metabolism. In an attempt to provide a better understanding of the role played by metals in its metabolic functions, the mechanisms of mitochondrial metal binding to frataxin in vitro have been investigated. A purified recombinant yeast frataxin homolog Yfh1 binds two Cu(ii) ions with a Kd1(CuII) of 1.3 × 10-7 M and a Kd2(CuII) of 3.1 × 10-4 M and a single Cu(i) ion with a higher affinity than for Cu(ii) (Kd(CuI) = 3.2 × 10-8 M). Mn(ii) forms two complexes with Yfh1 (Kd1(MnII) = 4.0 × 10-8 M; Kd2(MnII) = 4.0 × 10-7 M). Cu and Mn bind Yfh1 with higher affinities than Fe(ii). It is established for the first time that the mechanisms of the interaction of iron and copper with frataxin are comparable and involve three kinetic steps. The first step occurs in the 50-500 ms range and corresponds to a first metal uptake. This is followed by two other kinetic processes that are related to a second metal uptake and/or to a change in the conformation leading to thermodynamic equilibrium. Frataxin deficient Δyfh1 yeast cells exhibited a marked growth defect in the presence of exogenous Cu or Mn. Mitochondria from Δyfh1 strains also accumulated higher amounts of copper, suggesting a functional role of frataxin in vivo in copper homeostasis.
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Affiliation(s)
- T H L Han
- Université Paris Diderot, Sorbonne Paris Cité, "Interfaces, Traitements, Organisation et Dynamique des Systèmes", CNRS-UMR 7086, 15 rue Jean Antoine de Baïf, 75205 Paris Cedex 13, France.
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47
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Clark E, Butler JS, Isaacs CJ, Napierala M, Lynch DR. Selected missense mutations impair frataxin processing in Friedreich ataxia. Ann Clin Transl Neurol 2017; 4:575-584. [PMID: 28812047 PMCID: PMC5553228 DOI: 10.1002/acn3.433] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE Frataxin (FXN) is a highly conserved mitochondrial protein. Reduced FXN levels cause Friedreich ataxia, a recessive neurodegenerative disease. Typical patients carry GAA repeat expansions on both alleles, while a subgroup of patients carry a missense mutation on one allele and a GAA repeat expansion on the other. Here, we report that selected disease-related FXN missense mutations impair FXN localization, interaction with mitochondria processing peptidase, and processing. METHODS Immunocytochemical studies and subcellular fractionation were performed to study FXN import into the mitochondria and examine the mechanism by which mutations impair FXN processing. Coimmunoprecipitation was performed to study the interaction between FXN and mitochondrial processing peptidase. A proteasome inhibitor was used to model traditional therapeutic strategies. In addition, clinical profiles of subjects with and without point mutations were compared in a large natural history study. RESULTS FXNI154F and FXNG130V missense mutations decrease FXN 81-210 levels compared with FXNWT, FXNR165C, and FXNW155R, but do not block its association with mitochondria. FXNI154F and FXNG130V also impair FXN maturation and enhance the binding between FXN 42-210 and mitochondria processing peptidase. Furthermore, blocking proteosomal degradation does not increase FXN 81-210 levels. Additionally, impaired FXN processing also occurs in fibroblasts from patients with FXNG130V. Finally, clinical data from patients with FXNG130V and FXNI154F mutations demonstrates a lower severity compared with other individuals with Friedreich ataxia. INTERPRETATION These data suggest that the effects on processing associated with FXNG130V and FXNI154F mutations lead to higher levels of partially processed FXN, which may contribute to the milder clinical phenotypes in these patients.
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Affiliation(s)
- Elisia Clark
- University of Pennsylvania Philadelphia Pennsylvania.,Children's Hospital of Philadelphia Philadelphia Pennsylvania
| | - Jill S Butler
- University of Alabama at Birmingham Birmingham Alabama
| | | | | | - David R Lynch
- University of Pennsylvania Philadelphia Pennsylvania.,Children's Hospital of Philadelphia Philadelphia Pennsylvania
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48
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Blauenburg B, Mielcarek A, Altegoer F, Fage CD, Linne U, Bange G, Marahiel MA. Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU. PLoS One 2016; 11:e0158749. [PMID: 27382962 PMCID: PMC4934914 DOI: 10.1371/journal.pone.0158749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/21/2016] [Indexed: 12/31/2022] Open
Abstract
The biosynthesis of iron sulfur (Fe-S) clusters in Bacillus subtilis is mediated by a SUF-type gene cluster, consisting of the cysteine desulfurase SufS, the scaffold protein SufU, and the putative chaperone complex SufB/SufC/SufD. Here, we present the high-resolution crystal structure of the SufS homodimer in its product-bound state (i.e., in complex with pyrodoxal-5'-phosphate, alanine, Cys361-persulfide). By performing hydrogen/deuterium exchange (H/DX) experiments, we characterized the interaction of SufS with SufU and demonstrate that SufU induces an opening of the active site pocket of SufS. Recent data indicate that frataxin could be involved in Fe-S cluster biosynthesis by facilitating iron incorporation. H/DX experiments show that frataxin indeed interacts with the SufS/SufU complex at the active site. Our findings deepen the current understanding of Fe-S cluster biosynthesis, a complex yet essential process, in the model organism B. subtilis.
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Affiliation(s)
- Bastian Blauenburg
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Andreas Mielcarek
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Florian Altegoer
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Christopher D. Fage
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
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49
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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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50
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Galea CA, Huq A, Lockhart PJ, Tai G, Corben LA, Yiu EM, Gurrin LC, Lynch DR, Gelbard S, Durr A, Pousset F, Parkinson M, Labrum R, Giunti P, Perlman SL, Delatycki MB, Evans-Galea MV. Compound heterozygous FXN mutations and clinical outcome in friedreich ataxia. Ann Neurol 2016; 79:485-95. [PMID: 26704351 DOI: 10.1002/ana.24595] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Friedreich ataxia (FRDA) is an inherited neurodegenerative disease characterized by ataxia and cardiomyopathy. Homozygous GAA trinucleotide repeat expansions in the first intron of FXN occur in 96% of affected individuals and reduce frataxin expression. Remaining individuals are compound heterozygous for a GAA expansion and a FXN point/insertion/deletion mutation. We examined disease-causing mutations and the impact on frataxin structure/function and clinical outcome in FRDA. METHODS We compared clinical information from 111 compound heterozygotes and 131 individuals with homozygous expansions. Frataxin mutations were examined using structural modeling, stability analyses and systematic literature review, and categorized into four groups: (1) homozygous expansions, and three compound heterozygote groups; (2) null (no frataxin produced); (3) moderate/strong impact; and (4) minimal impact. Mean age of onset and the presence of cardiomyopathy and diabetes mellitus were compared using regression analyses. RESULTS Mutations in the hydrophobic core of frataxin affected stability whereas surface residue mutations affected interactions with iron sulfur cluster assembly and heme biosynthetic proteins. The null group of compound heterozygotes had significantly earlier age of onset and increased diabetes mellitus, compared to the homozygous expansion group. There were no significant differences in mean age of onset between homozygotes and the minimal and moderate/strong impact groups. INTERPRETATION In compound heterozygotes, expression of partially functional mutant frataxin delays age of onset and reduces diabetes mellitus, compared to those with no frataxin expression from the non-expanded allele. This integrated analysis of categorized frataxin mutations and their correlation with clinical outcome provide a definitive resource for investigating disease pathogenesis in FRDA.
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Affiliation(s)
- Charles A Galea
- Medicinal Chemistry and Drug Delivery, Disposition and Dynamics (D4), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Aamira Huq
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Geneieve Tai
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Louise A Corben
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
| | - Eppie M Yiu
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Neurology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Lyle C Gurrin
- Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - David R Lynch
- Departments of Neurology and Pediatrics, University of Pennsylvania School of Medicine and The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sarah Gelbard
- Departments of Neurology and Pediatrics, University of Pennsylvania School of Medicine and The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexandra Durr
- APHP, Department of Genetics and Cytogenetics, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle épinière (ICM), Pitié-Salpêtrière University Hospital, Paris, France
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Université Paris 06 UMR S_1127, ICM, F-75013, France
| | - Francoise Pousset
- APHP, Cardiology Department, AP-HP Pitie-Salpétrière Hospital, Paris, France
| | - Michael Parkinson
- Department of Molecular Neuroscience, University College London Institute of Neurology, London, United Kingdom
| | - Robyn Labrum
- Department of Neurogenetics, University College London Hospital, Institute of Neurology, London, United Kingdom
| | - Paola Giunti
- Department of Molecular Neuroscience, University College London Institute of Neurology, London, United Kingdom
- Department of Neurogenetics, University College London Hospital, Institute of Neurology, London, United Kingdom
| | - Susan L Perlman
- Ataxia Center and Huntington Disease Center of Excellence, Department of Neurology, David Geffen School of Medicine at the University of California at Los Angeles, CA
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- School of Psychological Sciences, Monash University, Clayton, Victoria, Australia
- Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Marguerite V Evans-Galea
- Bruce Lefroy Centre, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
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