1
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Shalash R, Levi-Ferber M, von Chrzanowski H, Atrash MK, Shav-Tal Y, Henis-Korenblit S. HLH-30/TFEB rewires the chaperone network to promote proteostasis under conditions of Coenzyme A and Iron-Sulfur Cluster Deficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597553. [PMID: 38895373 PMCID: PMC11185684 DOI: 10.1101/2024.06.05.597553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The maintenance of a properly folded proteome is critical for cellular function and organismal health, and its age-dependent collapse is associated with a wide range of diseases. Here, we find that despite the central role of Coenzyme A as a molecular cofactor in hundreds of cellular reactions, limiting Coenzyme A levels in C. elegans and in human cells, by inhibiting the conserved pantothenate kinase, promotes proteostasis. Impairment of the cytosolic iron-sulfur clusters formation pathway, which depends on Coenzyme A, similarly promotes proteostasis and acts in the same pathway. Proteostasis improvement by Coenzyme A/iron-sulfur cluster deficiencies are dependent on the conserved HLH-30/TFEB transcription factor. Strikingly, under these conditions, HLH-30 promotes proteostasis by potentiating the expression of select chaperone genes providing a chaperone-mediated proteostasis shield, rather than by its established role as an autophagy and lysosome biogenesis promoting factor. This reflects the versatile nature of this conserved transcription factor, that can transcriptionally activate a wide range of protein quality control mechanisms, including chaperones and stress response genes alongside autophagy and lysosome biogenesis genes. These results highlight TFEB as a key proteostasis-promoting transcription factor and underscore it and its upstream regulators as potential therapeutic targets in proteostasis-related diseases.
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Affiliation(s)
- Rewayd Shalash
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Mor Levi-Ferber
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Henrik von Chrzanowski
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Mohammad Khaled Atrash
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Sivan Henis-Korenblit
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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2
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Dancis A, Pandey AK, Pain D. Mitochondria function in cytoplasmic FeS protein biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119733. [PMID: 38641180 DOI: 10.1016/j.bbamcr.2024.119733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
Iron‑sulfur (FeS) clusters are cofactors of numerous proteins involved in essential cellular functions including respiration, protein translation, DNA synthesis and repair, ribosome maturation, anti-viral responses, and isopropylmalate isomerase activity. Novel FeS proteins are still being discovered due to the widespread use of cryogenic electron microscopy (cryo-EM) and elegant genetic screens targeted at protein discovery. A complex sequence of biochemical reactions mediated by a conserved machinery controls biosynthesis of FeS clusters. In eukaryotes, a remarkable epistasis has been observed: the mitochondrial machinery, termed ISC (Iron-Sulfur Cluster), lies upstream of the cytoplasmic machinery, termed CIA (Cytoplasmic Iron‑sulfur protein Assembly). The basis for this arrangement is the production of a hitherto uncharacterized intermediate, termed X-S or (Fe-S)int, produced in mitochondria by the ISC machinery, exported by the mitochondrial ABC transporter Atm1 (ABCB7 in humans), and then utilized by the CIA machinery for the cytoplasmic/nuclear FeS cluster assembly. Genetic and biochemical findings supporting this sequence of events are herein presented. New structural views of the Atm1 transport phases are reviewed. The key compartmental roles of glutathione in cellular FeS cluster biogenesis are highlighted. Finally, data are presented showing that every one of the ten core components of the mitochondrial ISC machinery and Atm1, when mutated or depleted, displays similar phenotypes: mitochondrial and cytoplasmic FeS clusters are both rendered deficient, consistent with the epistasis noted above.
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Affiliation(s)
- Andrew Dancis
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
| | - Ashutosh K Pandey
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Debkumar Pain
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
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3
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Dieckmann CL. A hub for regulation of mitochondrial metabolism: Fatty acid and lipoic acid biosynthesis. IUBMB Life 2024; 76:332-344. [PMID: 38088214 DOI: 10.1002/iub.2802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/21/2023] [Indexed: 05/28/2024]
Abstract
Having evolved from a prokaryotic origin, mitochondria retain pathways required for the catabolism of energy-rich molecules and for the biosynthesis of molecules that aid catabolism and/or participate in other cellular processes essential for life of the cell. Reviewed here are details of the mitochondrial fatty acid biosynthetic pathway (FAS II) and its role in building both the octanoic acid precursor for lipoic acid biosynthesis (LAS) and longer-chain fatty acids functioning in chaperoning the assembly of mitochondrial multisubunit complexes. Also covered are the details of mitochondrial lipoic acid biosynthesis, which is distinct from that of prokaryotes, and the attachment of lipoic acid to subunits of pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and glycine cleavage system complexes. Special emphasis has been placed on presenting what is currently known about the interconnected paths and loops linking the FAS II-LAS pathway and two other mitochondrial realms, the organellar translation machinery and Fe-S cluster biosynthesis and function.
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Affiliation(s)
- Carol L Dieckmann
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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4
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Kao YR, Chen J, Kumari R, Ng A, Zintiridou A, Tatiparthy M, Ma Y, Aivalioti MM, Moulik D, Sundaravel S, Sun D, Reisz JA, Grimm J, Martinez-Lopez N, Stransky S, Sidoli S, Steidl U, Singh R, D'Alessandro A, Will B. An iron rheostat controls hematopoietic stem cell fate. Cell Stem Cell 2024; 31:378-397.e12. [PMID: 38402617 PMCID: PMC10939794 DOI: 10.1016/j.stem.2024.01.011] [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: 05/25/2023] [Revised: 12/20/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Mechanisms governing the maintenance of blood-producing hematopoietic stem and multipotent progenitor cells (HSPCs) are incompletely understood, particularly those regulating fate, ensuring long-term maintenance, and preventing aging-associated stem cell dysfunction. We uncovered a role for transitory free cytoplasmic iron as a rheostat for adult stem cell fate control. We found that HSPCs harbor comparatively small amounts of free iron and show the activation of a conserved molecular response to limited iron-particularly during mitosis. To study the functional and molecular consequences of iron restriction, we developed models allowing for transient iron bioavailability limitation and combined single-molecule RNA quantification, metabolomics, and single-cell transcriptomic analyses with functional studies. Our data reveal that the activation of the limited iron response triggers coordinated metabolic and epigenetic events, establishing stemness-conferring gene regulation. Notably, we find that aging-associated cytoplasmic iron loading reversibly attenuates iron-dependent cell fate control, explicating intervention strategies for dysfunctional aged stem cells.
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Affiliation(s)
- Yun-Ruei Kao
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anita Ng
- Karches Center for Oncology Research, the Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Madhuri Tatiparthy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yuhong Ma
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Deeposree Moulik
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Daqian Sun
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juliane Grimm
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nuria Martinez-Lopez
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Ulrich Steidl
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rajat Singh
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Britta Will
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, USA.
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5
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Meisel JD, Miranda M, Skinner OS, Wiesenthal PP, Wellner SM, Jourdain AA, Ruvkun G, Mootha VK. Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism. Cell 2024; 187:659-675.e18. [PMID: 38215760 PMCID: PMC10919891 DOI: 10.1016/j.cell.2023.12.010] [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: 02/20/2023] [Revised: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/14/2024]
Abstract
The electron transport chain (ETC) of mitochondria, bacteria, and archaea couples electron flow to proton pumping and is adapted to diverse oxygen environments. Remarkably, in mice, neurological disease due to ETC complex I dysfunction is rescued by hypoxia through unknown mechanisms. Here, we show that hypoxia rescue and hyperoxia sensitivity of complex I deficiency are evolutionarily conserved to C. elegans and are specific to mutants that compromise the electron-conducting matrix arm. We show that hypoxia rescue does not involve the hypoxia-inducible factor pathway or attenuation of reactive oxygen species. To discover the mechanism, we use C. elegans genetic screens to identify suppressor mutations in the complex I accessory subunit NDUFA6/nuo-3 that phenocopy hypoxia rescue. We show that NDUFA6/nuo-3(G60D) or hypoxia directly restores complex I forward activity, with downstream rescue of ETC flux and, in some cases, complex I levels. Additional screens identify residues within the ubiquinone binding pocket as being required for the rescue by NDUFA6/nuo-3(G60D) or hypoxia. This reveals oxygen-sensitive coupling between an accessory subunit and the quinone binding pocket of complex I that can restore forward activity in the same manner as hypoxia.
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Affiliation(s)
- Joshua D Meisel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Maria Miranda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Presli P Wiesenthal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sandra M Wellner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexis A Jourdain
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
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6
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Wedan RJ, Longenecker JZ, Nowinski SM. Mitochondrial fatty acid synthesis is an emergent central regulator of mammalian oxidative metabolism. Cell Metab 2024; 36:36-47. [PMID: 38128528 PMCID: PMC10843818 DOI: 10.1016/j.cmet.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Contrary to their well-known functions in nutrient breakdown, mitochondria are also important biosynthetic hubs and express an evolutionarily conserved mitochondrial fatty acid synthesis (mtFAS) pathway. mtFAS builds lipoic acid and longer saturated fatty acids, but its exact products, their ultimate destination in cells, and the cellular significance of the pathway are all active research questions. Moreover, why mitochondria need mtFAS despite their well-defined ability to import fatty acids is still unclear. The identification of patients with inborn errors of metabolism in mtFAS genes has sparked fresh research interest in the pathway. New mammalian models have provided insights into how mtFAS coordinates many aspects of oxidative mitochondrial metabolism and raise questions about its role in diseases such as obesity, diabetes, and heart failure. In this review, we discuss the products of mtFAS, their function, and the consequences of mtFAS impairment across models and in metabolic disease.
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Affiliation(s)
- Riley J Wedan
- Department of Metabolism and Nutritional Programming, The Van Andel Institute, Grand Rapids, MI 49503, USA; College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jacob Z Longenecker
- Department of Metabolism and Nutritional Programming, The Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sara M Nowinski
- Department of Metabolism and Nutritional Programming, The Van Andel Institute, Grand Rapids, MI 49503, USA.
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7
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Dhembla C, Kumar A, Arya R, Kundu S, Sundd M. Mitochondrial Acyl Carrier Protein of Leishmania major Displays Features Distinct from the Canonical Type II ACP. Biochemistry 2023; 62:3347-3359. [PMID: 37967383 DOI: 10.1021/acs.biochem.3c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Prokaryotes synthesize fatty acids using a type II synthesis pathway (FAS). In this process, the central player, i.e., the acyl carrier protein (ACP), sequesters the growing acyl chain in its internal hydrophobic cavity. As the acyl chain length increases, the cavity expands in size, which is reflected in the NMR chemical shift perturbations and crystal structures of the acyl-ACP intermediates. A few eukaryotic organelles, such as plastids and mitochondria, also harbor type II fatty acid synthesis machinery. Plastid FAS from spinach and Plasmodium falciparum has been characterized at the molecular level, but the mitochondrial pathway remains unexplored. Here, we report NMR studies of the mitochondrial acyl-acyl carrier protein intermediates of Leishmania major (acyl-LmACP). Our studies show that LmACP experiences remarkably small conformational changes upon acylation, with perturbations confined to helices II and III only. CastP determined that the cavity size of apo-LmACP (PDB entry 5ZWT) is less than that of Escherichia coli ACP (PDB 1T8K). Thus, the small chemical shift perturbations observed in the LmACP intermediates, coupled with CastP results, suggest an unusually small cavity when fully expanded. The faster rate of C8-LmACP chain hydrolysis compared to E. coli ACP (EcACP) also supports these convictions. Structure comparison of LmACP with other type II ACP disclosed unique differences in the helix I and loop I conformations, as well as several residues present there. Numerous hydrophobic residues in helix I and loop I (conserved in all mitochondrial ACPs) are substituted with hydrophilic residues in the bacterial/plastid type II ACP. For instance, Phe and leucine at positions 14 and 34 in LmACP are substituted with a hydrophilic residue and Ala in bacterial/plastid type II ACP. Mutation of Leu 34 to Ala (corresponding residue in EcACP) resulted in a complete loss of structure, underscoring its importance in maintaining the ACP fold. Thus, our NMR studies, combined with insights from the crystal structure, highlight several unique features of LmACP, distinct from the prokaryote and plastid type II ACP. Given the high sequence identity, the features might be conserved in all mitochondrial ACPs.
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Affiliation(s)
- Chetna Dhembla
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Ambrish Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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8
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Zhong H, Janer A, Khalimonchuk O, Antonicka H, Shoubridge E, Barrientos A. BOLA3 and NFU1 link mitoribosome iron-sulfur cluster assembly to multiple mitochondrial dysfunctions syndrome. Nucleic Acids Res 2023; 51:11797-11812. [PMID: 37823603 PMCID: PMC10681725 DOI: 10.1093/nar/gkad842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
The human mitochondrial ribosome contains three [2Fe-2S] clusters whose assembly pathway, role, and implications for mitochondrial and metabolic diseases are unknown. Here, structure-function correlation studies show that the clusters play a structural role during mitoribosome assembly. To uncover the assembly pathway, we have examined the effect of silencing the expression of Fe-S cluster biosynthetic and delivery factors on mitoribosome stability. We find that the mitoribosome receives its [2Fe-2S] clusters from the GLRX5-BOLA3 node. Additionally, the assembly of the small subunit depends on the mitoribosome biogenesis factor METTL17, recently reported containing a [4Fe-4S] cluster, which we propose is inserted via the ISCA1-NFU1 node. Consistently, fibroblasts from subjects suffering from 'multiple mitochondrial dysfunction' syndrome due to mutations in BOLA3 or NFU1 display previously unrecognized attenuation of mitochondrial protein synthesis that contributes to their cellular and pathophysiological phenotypes. Finally, we report that, in addition to their structural role, one of the mitoribosomal [2Fe-2S] clusters and the [4Fe-4S] cluster in mitoribosome assembly factor METTL17 sense changes in the redox environment, thus providing a way to regulate organellar protein synthesis accordingly.
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Affiliation(s)
- Hui Zhong
- Department of Biochemistry and Molecular Biology. University of Miami Miller School of Medicine, 1600 NW 10Ave. Miami, FL 33136, USA
| | - Alexandre Janer
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Oleh Khalimonchuk
- Department of Biochemistry. University of Nebraska-Lincoln; 1901 Vine St. Beadle Center, Lincoln, NE 68588, USA
- Nebraska Redox Biology Center. University of Nebraska-Lincoln; 1901 Vine St. Beadle Center, Lincoln, NE 68588, USA
| | - Hana Antonicka
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Eric A Shoubridge
- The Neuro and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology. University of Miami Miller School of Medicine, 1600 NW 10Ave. Miami, FL 33136, USA
- Department of Neurology. University of Miami Miller School of Medicine; 1600 NW 10 Ave., Miami, FL 33136, USA
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9
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Motyčková A, Voleman L, Najdrová V, Arbonová L, Benda M, Dohnálek V, Janowicz N, Malych R, Šuťák R, Ettema TJG, Svärd S, Stairs CW, Doležal P. Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis. PLoS Pathog 2023; 19:e1010773. [PMID: 37792908 PMCID: PMC10578589 DOI: 10.1371/journal.ppat.1010773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/16/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023] Open
Abstract
Mitochondrial metabolism is entirely dependent on the biosynthesis of the [4Fe-4S] clusters, which are part of the subunits of the respiratory chain. The mitochondrial late ISC pathway mediates the formation of these clusters from simpler [2Fe-2S] molecules and transfers them to client proteins. Here, we characterized the late ISC pathway in one of the simplest mitochondria, mitosomes, of the anaerobic protist Giardia intestinalis that lost the respiratory chain and other hallmarks of mitochondria. In addition to IscA2, Nfu1 and Grx5 we identified a novel BolA1 homologue in G. intestinalis mitosomes. It specifically interacts with Grx5 and according to the high-affinity pulldown also with other core mitosomal components. Using CRISPR/Cas9 we were able to establish full bolA1 knock out, the first cell line lacking a mitosomal protein. Despite the ISC pathway being the only metabolic role of the mitosome no significant changes in the mitosome biology could be observed as neither the number of the mitosomes or their capability to form [2Fe-2S] clusters in vitro was affected. We failed to identify natural client proteins that would require the [2Fe-2S] or [4Fe-4S] cluster within the mitosomes, with the exception of [2Fe-2S] ferredoxin, which is itself part of the ISC pathway. The overall uptake of iron into the cellular proteins remained unchanged as also observed for the grx5 knock out cell line. The pull-downs of all late ISC components were used to build the interactome of the pathway showing specific position of IscA2 due to its interaction with the outer mitosomal membrane proteins. Finally, the comparative analysis across Metamonada species suggested that the adaptation of the late ISC pathway identified in G. intestinalis occurred early in the evolution of this supergroup of eukaryotes.
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Affiliation(s)
- Alžběta Motyčková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Vladimíra Najdrová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Lenka Arbonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Martin Benda
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Vít Dohnálek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Natalia Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Róbert Šuťák
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Biomedical Center (BMC), Uppsala University, Uppsala, Sweden
| | | | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
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10
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Álvarez-Córdoba M, Talaverón-Rey M, Povea-Cabello S, Cilleros-Holgado P, Gómez-Fernández D, Piñero-Pérez R, Reche-López D, Munuera-Cabeza M, Suárez-Carrillo A, Romero-González A, Romero-Domínguez JM, López-Cabrera A, Armengol JÁ, Sánchez-Alcázar JA. Patient-Derived Cellular Models for Polytarget Precision Medicine in Pantothenate Kinase-Associated Neurodegeneration. Pharmaceuticals (Basel) 2023; 16:1359. [PMID: 37895830 PMCID: PMC10609847 DOI: 10.3390/ph16101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The term neurodegeneration with brain iron accumulation (NBIA) brings together a broad set of progressive and disabling neurological genetic disorders in which iron is deposited preferentially in certain areas of the brain. Among NBIA disorders, the most frequent subtype is pantothenate kinase-associated neurodegeneration (PKAN) caused by pathologic variants in the PANK2 gene codifying the enzyme pantothenate kinase 2 (PANK2). To date, there are no effective treatments to stop the progression of these diseases. This review discusses the utility of patient-derived cell models as a valuable tool for the identification of pharmacological or natural compounds for implementing polytarget precision medicine in PKAN. Recently, several studies have described that PKAN patient-derived fibroblasts present the main pathological features associated with the disease including intracellular iron overload. Interestingly, treatment of mutant cell cultures with various supplements such as pantothenate, pantethine, vitamin E, omega 3, α-lipoic acid L-carnitine or thiamine, improved all pathophysiological alterations in PKAN fibroblasts with residual expression of the PANK2 enzyme. The information provided by pharmacological screenings in patient-derived cellular models can help optimize therapeutic strategies in individual PKAN patients.
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Affiliation(s)
- Mónica Álvarez-Córdoba
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Marta Talaverón-Rey
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Suleva Povea-Cabello
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Paula Cilleros-Holgado
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - David Gómez-Fernández
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Rocío Piñero-Pérez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Diana Reche-López
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Manuel Munuera-Cabeza
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra Suárez-Carrillo
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Ana Romero-González
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Jose Manuel Romero-Domínguez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra López-Cabrera
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - José Ángel Armengol
- Department of Physiology, Anatomy and Cellular Biology, Pablo de Olavide University, 41013 Seville, Spain;
| | - José Antonio Sánchez-Alcázar
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
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11
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Dutta D, Kanca O, Byeon SK, Marcogliese PC, Zuo Z, Shridharan RV, Park JH, Lin G, Ge M, Heimer G, Kohler JN, Wheeler MT, Kaipparettu BA, Pandey A, Bellen HJ. A defect in mitochondrial fatty acid synthesis impairs iron metabolism and causes elevated ceramide levels. Nat Metab 2023; 5:1595-1614. [PMID: 37653044 PMCID: PMC11151872 DOI: 10.1038/s42255-023-00873-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
In most eukaryotic cells, fatty acid synthesis (FAS) occurs in the cytoplasm and in mitochondria. However, the relative contribution of mitochondrial FAS (mtFAS) to the cellular lipidome is not well defined. Here we show that loss of function of Drosophila mitochondrial enoyl coenzyme A reductase (Mecr), which is the enzyme required for the last step of mtFAS, causes lethality, while neuronal loss of Mecr leads to progressive neurodegeneration. We observe a defect in Fe-S cluster biogenesis and increased iron levels in flies lacking mecr, leading to elevated ceramide levels. Reducing the levels of either iron or ceramide suppresses the neurodegenerative phenotypes, indicating an interplay between ceramide and iron metabolism. Mutations in human MECR cause pediatric-onset neurodegeneration, and we show that human-derived fibroblasts display similar elevated ceramide levels and impaired iron homeostasis. In summary, this study identifies a role of mecr/MECR in ceramide and iron metabolism, providing a mechanistic link between mtFAS and neurodegeneration.
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Affiliation(s)
- Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Seul Kee Byeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Rishi V Shridharan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Guang Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Ming Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Gali Heimer
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jennefer N Kohler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew T Wheeler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Benny A Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Manipal Academy of Higher Education, Manipal, India
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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12
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Pedroletti L, Moseler A, Meyer AJ. Assembly, transfer, and fate of mitochondrial iron-sulfur clusters. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3328-3344. [PMID: 36846908 DOI: 10.1093/jxb/erad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/13/2023] [Indexed: 06/08/2023]
Abstract
Since the discovery of an autonomous iron-sulfur cluster (Fe-S) assembly machinery in mitochondria, significant efforts to examine the nature of this process have been made. The assembly of Fe-S clusters occurs in two distinct steps with the initial synthesis of [2Fe-2S] clusters by a first machinery followed by a subsequent assembly into [4Fe-4S] clusters by a second machinery. Despite this knowledge, we still have only a rudimentary understanding of how Fe-S clusters are transferred and distributed among their respective apoproteins. In particular, demand created by continuous protein turnover and the sacrificial destruction of clusters for synthesis of biotin and lipoic acid reveal possible bottlenecks in the supply chain of Fe-S clusters. Taking available information from other species into consideration, this review explores the mitochondrial assembly machinery of Arabidopsis and provides current knowledge about the respective transfer steps to apoproteins. Furthermore, this review highlights biotin synthase and lipoyl synthase, which both utilize Fe-S clusters as a sulfur source. After extraction of sulfur atoms from these clusters, the remains of the clusters probably fall apart, releasing sulfide as a highly toxic by-product. Immediate refixation through local cysteine biosynthesis is therefore an essential salvage pathway and emphasizes the physiological need for cysteine biosynthesis in plant mitochondria.
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Affiliation(s)
- Luca Pedroletti
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Anna Moseler
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
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13
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Caubrière D, Moseler A, Rouhier N, Couturier J. Diversity and roles of cysteine desulfurases in photosynthetic organisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3345-3360. [PMID: 36861318 DOI: 10.1093/jxb/erad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/22/2023] [Indexed: 06/08/2023]
Abstract
As sulfur is part of many essential protein cofactors such as iron-sulfur clusters, molybdenum cofactors, or lipoic acid, its mobilization from cysteine represents a fundamental process. The abstraction of the sulfur atom from cysteine is catalysed by highly conserved pyridoxal 5'-phosphate-dependent enzymes called cysteine desulfurases. The desulfuration of cysteine leads to the formation of a persulfide group on a conserved catalytic cysteine and the concomitant release of alanine. Sulfur is then transferred from cysteine desulfurases to different targets. Numerous studies have focused on cysteine desulfurases as sulfur-extracting enzymes for iron-sulfur cluster synthesis in mitochondria and chloroplasts but also for molybdenum cofactor sulfuration in the cytosol. Despite this, knowledge about the involvement of cysteine desulfurases in other pathways is quite rudimentary, particularly in photosynthetic organisms. In this review, we summarize current understanding of the different groups of cysteine desulfurases and their characteristics in terms of primary sequence, protein domain architecture, and subcellular localization. In addition, we review the roles of cysteine desulfurases in different fundamental pathways and highlight the gaps in our knowledge to encourage future work on unresolved issues especially in photosynthetic organisms.
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Affiliation(s)
| | - Anna Moseler
- Institute of Crop Science and Resource Conservation (INRES) - Chemical Signalling, University of Bonn, 53113 Bonn, Germany
| | | | - Jérémy Couturier
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
- Institut Universitaire de France, F-75000, Paris, France
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14
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Berg JA, Zhou Y, Ouyang Y, Cluntun AA, Waller TC, Conway ME, Nowinski SM, Van Ry T, George I, Cox JE, Wang B, Rutter J. Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns. Nat Cell Biol 2023; 25:616-625. [PMID: 37012464 PMCID: PMC10104781 DOI: 10.1038/s41556-023-01117-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 02/24/2023] [Indexed: 04/05/2023]
Abstract
Metabolism is intertwined with various cellular processes, including controlling cell fate, influencing tumorigenesis, participating in stress responses and more. Metabolism is a complex, interdependent network, and local perturbations can have indirect effects that are pervasive across the metabolic network. Current analytical and technical limitations have long created a bottleneck in metabolic data interpretation. To address these shortcomings, we developed Metaboverse, a user-friendly tool to facilitate data exploration and hypothesis generation. Here we introduce algorithms that leverage the metabolic network to extract complex reaction patterns from data. To minimize the impact of missing measurements within the network, we introduce methods that enable pattern recognition across multiple reactions. Using Metaboverse, we identify a previously undescribed metabolite signature that correlated with survival outcomes in early stage lung adenocarcinoma patients. Using a yeast model, we identify metabolic responses suggesting an adaptive role of citrate homeostasis during mitochondrial dysfunction facilitated by the citrate transporter, Ctp1. We demonstrate that Metaboverse augments the user's ability to extract meaningful patterns from multi-omics datasets to develop actionable hypotheses.
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Affiliation(s)
- Jordan A Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Altos Labs, Redwood City, CA, USA.
| | - Youjia Zhou
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Yeyun Ouyang
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Altos Labs, Redwood City, CA, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - T Cameron Waller
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Megan E Conway
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sara M Nowinski
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Tyler Van Ry
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Metabolomics Core Facility, University of Utah, Salt Lake City, UT, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Ian George
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Metabolomics Core Facility, University of Utah, Salt Lake City, UT, USA
- Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA
| | - Bei Wang
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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15
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Moiseenok AG, Kanunnikova NP. Brain CoA and Acetyl CoA Metabolism in Mechanisms of Neurodegeneration. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:466-480. [PMID: 37080933 DOI: 10.1134/s000629792304003x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The processes of biotransformation of pantothenic acid (Pan) in the biosynthesis and hydrolysis of CoA, key role of pantothenate kinase (PANK) and CoA synthetase (CoASY) in the formation of the priority mitochondrial pool of CoA, with a high metabolic turnover of the coenzyme and limited transport of Pan across the blood-brain barrier are considered. The system of acetyl-CoA, a secondary messenger, which is the main substrate of acetylation processes including formation of N-acetyl aspartate and acetylcholine, post-translational modification of histones, predetermines protection of the neurons against degenerative signals and cholinergic neurotransmission. Biochemical mechanisms of neurodegenerative syndromes in the cases of PANK and CoASY defects, and the possibility of correcting of CoA biosynthesis in the models with knockouts of these enzymes have been described. The data of a post-mortem study of the brains from the patients with Huntington's and Alzheimer's diseases are presented, proving Pan deficiency in the CNS, which is especially pronounced in the pathognomonic neurostructures. In the frontal cortex of the patients with Parkinson's disease, combined immunofluorescence of anti-CoA- and anti-tau protein was detected, reflecting CoAlation during dimerization of the tau protein and its redox sensitivity. Redox activity and antioxidant properties of the precursors of CoA biosynthesis were confirmed in vitro with synaptosomal membranes and mitochondria during modeling of aluminum neurotoxicity accompanied by the decrease in the level of CoA in CNS. The ability of CoA biosynthesis precursors to stabilize glutathione pool in neurostructures, in particular, in the hippocampus, is considered as a pathogenetic protection mechanism during exposure to neurotoxins, development of neuroinflammation and neurodegeneration, and justifies the combined use of Pan derivatives (for example, D-panthenol) and glutathione precursors (N-acetylcysteine). Taking into account the discovery of new functions of CoA (redox-dependent processes of CoAlation of proteins, possible association of oxidative stress and deficiency of Pan (CoA) in neurodegenerative pathology), it seems promising to study bioavailability and biotransformation of Pan derivatives, in particular of D-panthenol, 4'-phospho-pantetheine, its acylated derivatives, and compositions with redox pharmacological compounds, are promising for their potential use as etiopathogenetic agents.
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Affiliation(s)
- Andrey G Moiseenok
- Institute of Biochemistry of Biologically Active Substances, National Academy of Sciences of Belarus, Grodno, 230023, Belarus.
| | - Nina P Kanunnikova
- Institute of Biochemistry of Biologically Active Substances, National Academy of Sciences of Belarus, Grodno, 230023, Belarus
- Yanka Kupala's Grodno State University, Grodno, 230023, Belarus
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16
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Asadi P, Milev MP, Saint-Dic D, Gamberi C, Sacher M. Vitamin B5, a coenzyme A precursor, rescues TANGO2 deficiency disease-associated defects in Drosophila and human cells. J Inherit Metab Dis 2023; 46:358-368. [PMID: 36502486 PMCID: PMC10464931 DOI: 10.1002/jimd.12579] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Mutations in the Transport and Golgi Organization 2 (TANGO2) gene are associated with intellectual deficit, neurodevelopmental delay and regression. Individuals can also present with an acute metabolic crisis that includes rhabdomyolysis, cardiomyopathy, and cardiac arrhythmias, the latter of which are potentially lethal. While preventing metabolic crises has the potential to reduce mortality, no treatments currently exist for this condition. The function of TANGO2 remains unknown but is suspected to be involved in some aspect of lipid metabolism. Here, we describe a model of TANGO2-related disease in the fruit fly Drosophila melanogaster that recapitulates crucial disease traits. Pairing a new fly model with human cells, we examined the effects of vitamin B5, a coenzyme A (CoA) precursor, on alleviating the cellular and organismal defects associated with TANGO2 deficiency. We demonstrate that vitamin B5 specifically improves multiple defects associated with TANGO2 loss-of-function in Drosophila and rescues membrane trafficking defects in human cells. We also observed a partial rescue of one of the fly defects by vitamin B3, though to a lesser extent than vitamin B5. Our data suggest that a B complex supplement containing vitamin B5/pantothenate may have therapeutic benefits in individuals with TANGO2-deficiency disease. Possible mechanisms for the rescue are discussed that may include restoration of lipid homeostasis.
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Affiliation(s)
- Paria Asadi
- Concordia University, Department of Biology, Montreal, Quebec, Canada, H4B1R6
| | - Miroslav P. Milev
- Concordia University, Department of Biology, Montreal, Quebec, Canada, H4B1R6
| | - Djenann Saint-Dic
- Concordia University, Department of Biology, Montreal, Quebec, Canada, H4B1R6
| | - Chiara Gamberi
- Coastal Carolina University, Department of Biology, Conway, South Carolina, USA, 29526
| | - Michael Sacher
- Concordia University, Department of Biology, Montreal, Quebec, Canada, H4B1R6
- McGill University, Department of Anatomy and Cell Biology, Montreal, Quebec, Canada, H3A0C7
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17
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Rahman MT, Koski MK, Panecka-Hofman J, Schmitz W, Kastaniotis AJ, Wade RC, Wierenga RK, Hiltunen JK, Autio KJ. An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration. Nat Commun 2023; 14:619. [PMID: 36739436 PMCID: PMC9899272 DOI: 10.1038/s41467-023-36358-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/25/2023] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial fatty acid synthesis (mtFAS) is essential for respiratory function. MtFAS generates the octanoic acid precursor for lipoic acid synthesis, but the role of longer fatty acid products has remained unclear. The structurally well-characterized component of mtFAS, human 2E-enoyl-ACP reductase (MECR) rescues respiratory growth and lipoylation defects of a Saccharomyces cerevisiae Δetr1 strain lacking native mtFAS enoyl reductase. To address the role of longer products of mtFAS, we employed in silico molecular simulations to design a MECR variant with a shortened substrate binding cavity. Our in vitro and in vivo analyses indicate that the MECR G165Q variant allows synthesis of octanoyl groups but not long chain fatty acids, confirming the validity of our computational approach to engineer substrate length specificity. Furthermore, our data imply that restoring lipoylation in mtFAS deficient yeast strains is not sufficient to support respiration and that long chain acyl-ACPs generated by mtFAS are required for mitochondrial function.
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Affiliation(s)
- M Tanvir Rahman
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Joanna Panecka-Hofman
- Faculty of Physics, University of Warsaw, Warsaw, Poland
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Werner Schmitz
- Faculty of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | | | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Zentrum für Molekulare Biologie (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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18
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Schulz V, Basu S, Freibert SA, Webert H, Boss L, Mühlenhoff U, Pierrel F, Essen LO, Warui DM, Booker SJ, Stehling O, Lill R. Functional spectrum and specificity of mitochondrial ferredoxins FDX1 and FDX2. Nat Chem Biol 2023; 19:206-217. [PMID: 36280795 PMCID: PMC10873809 DOI: 10.1038/s41589-022-01159-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/01/2022] [Indexed: 02/04/2023]
Abstract
Ferredoxins comprise a large family of iron-sulfur (Fe-S) proteins that shuttle electrons in diverse biological processes. Human mitochondria contain two isoforms of [2Fe-2S] ferredoxins, FDX1 (aka adrenodoxin) and FDX2, with known functions in cytochrome P450-dependent steroid transformations and Fe-S protein biogenesis. Here, we show that only FDX2, but not FDX1, is involved in Fe-S protein maturation. Vice versa, FDX1 is specific not only for steroidogenesis, but also for heme a and lipoyl cofactor biosyntheses. In the latter pathway, FDX1 provides electrons to kickstart the radical chain reaction catalyzed by lipoyl synthase. We also identified lipoylation as a target of the toxic antitumor copper ionophore elesclomol. Finally, the striking target specificity of each ferredoxin was assigned to small conserved sequence motifs. Swapping these motifs changed the target specificity of these electron donors. Together, our findings identify new biochemical tasks of mitochondrial ferredoxins and provide structural insights into their functional specificity.
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Affiliation(s)
- Vinzent Schulz
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Somsuvro Basu
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
- Freelance Medical Communications Consultant, Brno, Czech Republic
| | - Sven-A Freibert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Holger Webert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Linda Boss
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Fabien Pierrel
- Univ. of Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble, France
| | - Lars-O Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Douglas M Warui
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, USA
| | - Oliver Stehling
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
| | - Roland Lill
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
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19
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Selective colorimetric recognition of cysteine/Fe3+ ions using chalcone derived titanium nanocomposites in aqueous solution and human blood. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2022.121232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Berry TM, Moustafa AA. A novel treatment strategy to prevent Parkinson's disease: focus on iron regulatory protein 1 (IRP1). Int J Neurosci 2023; 133:67-76. [PMID: 33535005 DOI: 10.1080/00207454.2021.1885403] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We propose that neural damage in Parkinson's disease (PD) is due to dysregulation of iron utilization rather than to high iron levels per se. Iron deposits are associated with neuronal cell death in substantia nigra (SN) resulting in PD where high levels of iron in SNs are due to dysregulation of iron utilization. Cytosolic aconitase (ACO1) upon losing an iron-sulfur cluster becomes iron regulatory protein 1 (IRP1). Rotenone increases levels of IRP1 and induces PD in rats. An increase in iron leads to inactivation of IRP1. We propose a novel treatment strategy to prevent PD. Specifically in rats given rotenone by subcutaneous injections, iron, from iron carbonyl from which iron is slowly absorbed, given three times a day by gavage will keep iron levels constant in the gut whereby iron levels and iron utilization systematically can be tightly regulated. Rotenone adversely affects complex 1 iron-sulfur proteins. Iron supplementation will increase iron-sulfur cluster formation switching IRP1 to ACO1. With IRP1 levels kept constantly low, iron utilization will systematically be tightly regulated stopping dysregulation of complex 1 and the neural damage done by rotenone preventing PD.
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Affiliation(s)
- Thomas M Berry
- School of Psychology, Western Sydney University, Sydney, New South Wales, Australia
| | - Ahmed A Moustafa
- School of Psychology, Western Sydney University, Sydney, New South Wales, Australia.,Marcs Institute for Brain and Behaviour, Western Sydney University, Sydney, New South Wales, Australia.,Department of Human Anatomy and Physiology, the Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa
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21
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Hayflick SJ, Jeong SY, Sibon OCM. PKAN pathogenesis and treatment. Mol Genet Metab 2022; 137:283-291. [PMID: 36240582 PMCID: PMC9970616 DOI: 10.1016/j.ymgme.2022.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
Abstract
Studies aimed at supporting different treatment approaches for pantothenate kinase-associated neurodegeneration (PKAN) have revealed the complexity of coenzyme A (CoA) metabolism and the limits of our current knowledge about disease pathogenesis. Here we offer a foundation for critically evaluating the myriad approaches, argue for the importance of unbiased disease models, and highlight some of the outstanding questions that are central to our understanding and treating PKAN.
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Affiliation(s)
- Susan J Hayflick
- Departments of Molecular & Medical Genetics, Pediatrics, and Neurology, Oregon Health & Science University, Portland, OR 97239, USA.
| | - Suh Young Jeong
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ody C M Sibon
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, 9713 AV, the Netherlands
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22
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Camponeschi F, Ciofi-Baffoni S, Calderone V, Banci L. Molecular Basis of Rare Diseases Associated to the Maturation of Mitochondrial [4Fe-4S]-Containing Proteins. Biomolecules 2022; 12:biom12071009. [PMID: 35883565 PMCID: PMC9313013 DOI: 10.3390/biom12071009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
The importance of mitochondria in mammalian cells is widely known. Several biochemical reactions and pathways take place within mitochondria: among them, there are those involving the biogenesis of the iron–sulfur (Fe-S) clusters. The latter are evolutionarily conserved, ubiquitous inorganic cofactors, performing a variety of functions, such as electron transport, enzymatic catalysis, DNA maintenance, and gene expression regulation. The synthesis and distribution of Fe-S clusters are strictly controlled cellular processes that involve several mitochondrial proteins that specifically interact each other to form a complex machinery (Iron Sulfur Cluster assembly machinery, ISC machinery hereafter). This machinery ensures the correct assembly of both [2Fe-2S] and [4Fe-4S] clusters and their insertion in the mitochondrial target proteins. The present review provides a structural and molecular overview of the rare diseases associated with the genes encoding for the accessory proteins of the ISC machinery (i.e., GLRX5, ISCA1, ISCA2, IBA57, FDX2, BOLA3, IND1 and NFU1) involved in the assembly and insertion of [4Fe-4S] clusters in mitochondrial proteins. The disease-related missense mutations were mapped on the 3D structures of these accessory proteins or of their protein complexes, and the possible impact that these mutations have on their specific activity/function in the frame of the mitochondrial [4Fe-4S] protein biogenesis is described.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence: (S.C.-B.); (V.C.); Tel.: +39-055-4574192 (S.C.-B.); +39-055-4574276 (V.C.)
| | - Vito Calderone
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence: (S.C.-B.); (V.C.); Tel.: +39-055-4574192 (S.C.-B.); +39-055-4574276 (V.C.)
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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23
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Maio N, Rouault TA. Mammalian iron sulfur cluster biogenesis and human diseases. IUBMB Life 2022; 74:705-714. [PMID: 35098635 PMCID: PMC9247042 DOI: 10.1002/iub.2597] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 07/30/2023]
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
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24
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Tachezy J, Makki A, Hrdý I. The hydrogenosomes of Trichomonas vaginalis. J Eukaryot Microbiol 2022; 69:e12922. [PMID: 35567536 DOI: 10.1111/jeu.12922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.
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Affiliation(s)
- Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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25
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Mitochondrial De Novo Assembly of Iron–Sulfur Clusters in Mammals: Complex Matters in a Complex That Matters. INORGANICS 2022. [DOI: 10.3390/inorganics10030031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Iron–sulfur clusters (Fe–S or ISC) are essential cofactors that function in a wide range of biological pathways. In mammalian cells, Fe–S biosynthesis primarily relies on mitochondria and involves a concerted group of evolutionary-conserved proteins forming the ISC pathway. In the early stage of the ISC pathway, the Fe–S core complex is required for de novo assembly of Fe–S. In humans, the Fe–S core complex comprises the cysteine desulfurase NFS1, the scaffold protein ISCU2, frataxin (FXN), the ferredoxin FDX2, and regulatory/accessory proteins ISD11 and Acyl Carrier Protein (ACP). In recent years, the field has made significant advances in unraveling the structure of the Fe–S core complex and the mechanism underlying its function. Herein, we review the key recent findings related to the Fe–S core complex and its components. We highlight some of the unanswered questions and provide a model of the Fe–S assembly within the complex. In addition, we briefly touch on the genetic diseases associated with mutations in the Fe–S core complex components.
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26
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Santambrogio P, Ripamonti M, Cozzi A, Raimondi M, Cavestro C, Di Meo I, Rubio A, Taverna S, Tiranti V, Levi S. Massive iron accumulation in PKAN-derived neurons and astrocytes: light on the human pathological phenotype. Cell Death Dis 2022; 13:185. [PMID: 35217637 PMCID: PMC8881507 DOI: 10.1038/s41419-022-04626-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 12/11/2022]
Abstract
Neurodegeneration associated with defective pantothenate kinase-2 (PKAN) is an early-onset monogenic autosomal-recessive disorder. The hallmark of the disease is the massive accumulation of iron in the globus pallidus brain region of patients. PKAN is caused by mutations in the PANK2 gene encoding the mitochondrial enzyme pantothenate kinase-2, whose function is to catalyze the first reaction of the CoA biosynthetic pathway. To date, the way in which this alteration leads to brain iron accumulation has not been elucidated. Starting from previously obtained hiPS clones, we set up a differentiation protocol able to generate inhibitory neurons. We obtained striatal-like medium spiny neurons composed of approximately 70–80% GABAergic neurons and 10–20% glial cells. Within this mixed population, we detected iron deposition in both PKAN cell types, however, the viability of PKAN GABAergic neurons was strongly affected. CoA treatment was able to reduce cell death and, notably, iron overload. Further differentiation of hiPS clones in a pure population of astrocytes showed particularly evident iron accumulation, with approximately 50% of cells positive for Perls staining. The analysis of these PKAN astrocytes indicated alterations in iron metabolism, mitochondrial morphology, respiratory activity, and oxidative status. Moreover, PKAN astrocytes showed signs of ferroptosis and were prone to developing a stellate phenotype, thus gaining neurotoxic features. This characteristic was confirmed in iPS-derived astrocyte and glutamatergic neuron cocultures, in which PKAN glutamatergic neurons were less viable in the presence of PKAN astrocytes. This newly generated astrocyte model is the first in vitro disease model recapitulating the human phenotype and can be exploited to deeply clarify the pathogenetic mechanisms underlying the disease.
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Affiliation(s)
| | - Maddalena Ripamonti
- IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Anna Cozzi
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marzia Raimondi
- IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Chiara Cavestro
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Ivano Di Meo
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alicia Rubio
- IRCCS San Raffaele Scientific Institute, Milan, Italy.,Institute of Neuroscience, National Research Council, Milan, Italy
| | | | - Valeria Tiranti
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Sonia Levi
- IRCCS San Raffaele Scientific Institute, Milan, Italy. .,Vita-Salute San Raffaele University, Milan, Italy.
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27
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Uzarska MA, Grochowina I, Soldek J, Jelen M, Schilke B, Marszalek J, Craig EA, Dutkiewicz R. During FeS cluster biogenesis, ferredoxin and frataxin use overlapping binding sites on yeast cysteine desulfurase Nfs1. J Biol Chem 2022; 298:101570. [PMID: 35026224 PMCID: PMC8888459 DOI: 10.1016/j.jbc.2022.101570] [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: 12/02/2021] [Accepted: 01/04/2022] [Indexed: 01/30/2023] Open
Abstract
In mitochondria, cysteine desulfurase (Nfs1) plays a central role in the biosynthesis of iron-sulfur (FeS) clusters, cofactors critical for activity of many cellular proteins. Nfs1 functions both as a sulfur donor for cluster assembly and as a binding platform for other proteins functioning in the process. These include not only the dedicated scaffold protein (Isu1) on which FeS clusters are synthesized but also accessory FeS cluster biogenesis proteins frataxin (Yfh1) and ferredoxin (Yah1). Yfh1 has been shown to activate cysteine desulfurase enzymatic activity, whereas Yah1 supplies electrons for the persulfide reduction. While Yfh1 interaction with Nfs1 is well understood, the Yah1-Nfs1 interaction is not. Here, based on the results of biochemical experiments involving purified WT and variant proteins, we report that in Saccharomyces cerevisiae, Yah1 and Yfh1 share an evolutionary conserved interaction site on Nfs1. Consistent with this notion, Yah1 and Yfh1 can each displace the other from Nfs1 but are inefficient competitors when a variant with an altered interaction site is used. Thus, the binding mode of Yah1 and Yfh1 interacting with Nfs1 in mitochondria of S. cerevisiae resembles the mutually exclusive binding of ferredoxin and frataxin with cysteine desulfurase reported for the bacterial FeS cluster assembly system. Our findings are consistent with the generally accepted scenario that the mitochondrial FeS cluster assembly system was inherited from bacterial ancestors of mitochondria.
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Affiliation(s)
- Marta A Uzarska
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Igor Grochowina
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Joanna Soldek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Marcin Jelen
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Brenda Schilke
- Department of Biochemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland; Department of Biochemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin - Madison, Madison, Wisconsin, USA.
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
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28
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Maio N, Rouault TA. Mammalian iron sulfur cluster biogenesis: From assembly to delivery to recipient proteins with a focus on novel targets of the chaperone and co‐chaperone proteins. IUBMB Life 2022; 74:684-704. [PMID: 35080107 PMCID: PMC10118776 DOI: 10.1002/iub.2593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/05/2021] [Accepted: 12/23/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development Bethesda Maryland USA
| | - Tracey A. Rouault
- Molecular Medicine Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development Bethesda Maryland USA
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29
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Itoh Y, Singh V, Khawaja A, Naschberger A, Nguyen MD, Rorbach J, Amunts A. Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules. eLife 2022; 11:77460. [PMID: 36480258 PMCID: PMC9731571 DOI: 10.7554/elife.77460] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 10/27/2022] [Indexed: 12/13/2022] Open
Abstract
The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.
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Affiliation(s)
- Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Vivek Singh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Karolinska InstituteStockholmSweden,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska InstitutetStockholmSweden
| | - Andreas Naschberger
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Minh Duc Nguyen
- Department of Medical Biochemistry and Biophysics, Karolinska InstituteStockholmSweden,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska InstitutetStockholmSweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska InstituteStockholmSweden,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska InstitutetStockholmSweden
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
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30
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Fujishiro T, Nakamura R, Kunichika K, Takahashi Y. Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis. Biophys Physicobiol 2022; 19:1-18. [PMID: 35377584 PMCID: PMC8918507 DOI: 10.2142/biophysico.bppb-v19.0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ryosuke Nakamura
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Kouhei Kunichika
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Yasuhiro Takahashi
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
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31
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Rydz L, Wróbel M, Jurkowska H. Sulfur Administration in Fe-S Cluster Homeostasis. Antioxidants (Basel) 2021; 10:antiox10111738. [PMID: 34829609 PMCID: PMC8614886 DOI: 10.3390/antiox10111738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022] Open
Abstract
Mitochondria are the key organelles of Fe–S cluster synthesis. They contain the enzyme cysteine desulfurase, a scaffold protein, iron and electron donors, and specific chaperons all required for the formation of Fe–S clusters. The newly formed cluster can be utilized by mitochondrial Fe–S protein synthesis or undergo further transformation. Mitochondrial Fe–S cluster biogenesis components are required in the cytosolic iron–sulfur cluster assembly machinery for cytosolic and nuclear cluster supplies. Clusters that are the key components of Fe–S proteins are vulnerable and prone to degradation whenever exposed to oxidative stress. However, once degraded, the Fe–S cluster can be resynthesized or repaired. It has been proposed that sulfurtransferases, rhodanese, and 3-mercaptopyruvate sulfurtransferase, responsible for sulfur transfer from donor to nucleophilic acceptor, are involved in the Fe–S cluster formation, maturation, or reconstitution. In the present paper, we attempt to sum up our knowledge on the involvement of sulfurtransferases not only in sulfur administration but also in the Fe–S cluster formation in mammals and yeasts, and on reconstitution-damaged cluster or restoration of enzyme’s attenuated activity.
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Selvanathan A, Parayil Sankaran B. Mitochondrial iron-sulfur cluster biogenesis and neurological disorders. Mitochondrion 2021; 62:41-49. [PMID: 34687937 DOI: 10.1016/j.mito.2021.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/26/2021] [Accepted: 10/18/2021] [Indexed: 12/20/2022]
Abstract
Iron-sulfur clusters (ISCs) are highly conserved moieties embedded into numerous crucial proteins in almost all bacteria, plants and mammals. As such, ISC biosynthesis is critical to cellular function. The pathway was first characterized in bacteria by the late 1990s, and over the subsequent 20 years there has been increasing understanding of its components in humans. Defects in the ISC pathway are now associated with many different human disease states, such as Friedreich ataxia and ISCU myopathy. Whilst the disorders have variable clinical features, most involve neurological phenotypes. There are common biochemical signatures in most of these conditions, as a lack of ISCs causes deficiencies of target proteins including Complex I, II and III, aconitase and lipoic acid. This review focuses on the disorders of ISC biogenesis that have been described in the literature to-date. Key clinical, biochemical and neuroradiological features will be discussed, providing a reference point for clinicians diagnosing and managing these patients. Therapies are mostly supportive at this stage. However, the improved understanding of the pathophysiology of these conditions could pave the way for disease-modifying therapies in the near future.
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Affiliation(s)
- Arthavan Selvanathan
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, Australia
| | - Bindu Parayil Sankaran
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, Australia; Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Australia.
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Falekun S, Sepulveda J, Jami-Alahmadi Y, Park H, Wohlschlegel JA, Sigala PA. Divergent acyl carrier protein decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis in malaria parasites. eLife 2021; 10:71636. [PMID: 34612205 PMCID: PMC8547962 DOI: 10.7554/elife.71636] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Most eukaryotic cells retain a mitochondrial fatty acid synthesis (FASII) pathway whose acyl carrier protein (mACP) and 4-phosphopantetheine (Ppant) prosthetic group provide a soluble scaffold for acyl chain synthesis and biochemically couple FASII activity to mitochondrial electron transport chain (ETC) assembly and Fe-S cluster biogenesis. In contrast, the mitochondrion of Plasmodium falciparum malaria parasites lacks FASII enzymes yet curiously retains a divergent mACP lacking a Ppant group. We report that ligand-dependent knockdown of mACP is lethal to parasites, indicating an essential FASII-independent function. Decyl-ubiquinone rescues parasites temporarily from death, suggesting a dominant dysfunction of the mitochondrial ETC. Biochemical studies reveal that Plasmodium mACP binds and stabilizes the Isd11-Nfs1 complex required for Fe-S cluster biosynthesis, despite lacking the Ppant group required for this association in other eukaryotes, and knockdown of parasite mACP causes loss of Nfs1 and the Rieske Fe-S protein in ETC complex III. This work reveals that Plasmodium parasites have evolved to decouple mitochondrial Fe-S cluster biogenesis from FASII activity, and this adaptation is a shared metabolic feature of other apicomplexan pathogens, including Toxoplasma and Babesia. This discovery unveils an evolutionary driving force to retain interaction of mitochondrial Fe-S cluster biogenesis with ACP independent of its eponymous function in FASII.
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Affiliation(s)
- Seyi Falekun
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Jaime Sepulveda
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, United States
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Paul A Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
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Berry T, Abohamza E, Moustafa AA. Treatment-resistant schizophrenia: focus on the transsulfuration pathway. Rev Neurosci 2021; 31:219-232. [PMID: 31714892 DOI: 10.1515/revneuro-2019-0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022]
Abstract
Treatment-resistant schizophrenia (TRS) is a severe form of schizophrenia. The severity of illness is positively related to homocysteine levels, with high homocysteine levels due to the low activity of the transsulfuration pathway, which metabolizes homocysteine in synthesizing L-cysteine. Glutathione levels are low in schizophrenia, which indicates shortages of L-cysteine and low activity of the transsulfuration pathway. Hydrogen sulfide (H2S) levels are low in schizophrenia. H2S is synthesized by cystathionine β-synthase and cystathionine γ-lyase, which are the two enzymes in the transsulfuration pathway. Iron-sulfur proteins obtain sulfur from L-cysteine. The oxidative phosphorylation (OXPHOS) pathway has various iron-sulfur proteins. With low levels of L-cysteine, iron-sulfur cluster formation will be dysregulated leading to deficits in OXPHOS in schizophrenia. Molybdenum cofactor (MoCo) synthesis requires sulfur, which is obtained from L-cysteine. With low levels of MoCo synthesis, molybdenum-dependent sulfite oxidase (SUOX) will not be synthesized at appropriate levels. SUOX detoxifies sulfite from sulfur-containing amino acids. If sulfites are not detoxified, there can be sulfite toxicity. The transsulfuration pathway metabolizes selenomethionine, whereby selenium from selenomethionine can be used for selenoprotein synthesis. The low activity of the transsulfuration pathway decreases selenoprotein synthesis. Glutathione peroxidase (GPX), with various GPXs being selenoprotein, is low in schizophrenia. The dysregulations of selenoproteins would lead to oxidant stress, which would increase the methylation of genes and histones leading to epigenetic changes in TRS. An add-on treatment to mainline antipsychotics is proposed for TRS that targets the dysregulations of the transsulfuration pathway and the dysregulations of other pathways stemming from the transsulfuration pathway being dysregulated.
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Affiliation(s)
- Thomas Berry
- School of Social Sciences and Psychology, Western Sydney University, Sydney 2751, New South Wales, Australia
| | - Eid Abohamza
- Department of Social Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Ahmed A Moustafa
- School of Social Sciences and Psychology, Western Sydney University, Sydney 2751, New South Wales, Australia.,Marcs Institute for Brain and Behaviour, Western Sydney University, Sydney 2751, New South Wales, Australia
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Petronek MS, Spitz DR, Allen BG. Iron-Sulfur Cluster Biogenesis as a Critical Target in Cancer. Antioxidants (Basel) 2021; 10:1458. [PMID: 34573089 PMCID: PMC8465902 DOI: 10.3390/antiox10091458] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Cancer cells preferentially accumulate iron (Fe) relative to non-malignant cells; however, the underlying rationale remains elusive. Iron-sulfur (Fe-S) clusters are critical cofactors that aid in a wide variety of cellular functions (e.g., DNA metabolism and electron transport). In this article, we theorize that a differential need for Fe-S biogenesis in tumor versus non-malignant cells underlies the Fe-dependent cell growth demand of cancer cells to promote cell division and survival by promoting genomic stability via Fe-S containing DNA metabolic enzymes. In this review, we outline the complex Fe-S biogenesis process and its potential upregulation in cancer. We also discuss three therapeutic strategies to target Fe-S biogenesis: (i) redox manipulation, (ii) Fe chelation, and (iii) Fe mimicry.
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Affiliation(s)
- Michael S. Petronek
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Douglas R. Spitz
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Bryan G. Allen
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
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Jain A, Singh A, Maio N, Rouault TA. Assembly of the [4Fe-4S] cluster of NFU1 requires the coordinated donation of two [2Fe-2S] clusters from the scaffold proteins, ISCU2 and ISCA1. Hum Mol Genet 2021; 29:3165-3182. [PMID: 32776106 DOI: 10.1093/hmg/ddaa172] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/09/2020] [Accepted: 07/29/2020] [Indexed: 02/01/2023] Open
Abstract
NFU1, a late-acting iron-sulfur (Fe-S) cluster carrier protein, has a key role in the pathogenesis of the disease, multiple mitochondrial dysfunctions syndrome. In this work, using genetic and biochemical approaches, we identified the initial scaffold protein, mitochondrial ISCU (ISCU2) and the secondary carrier, ISCA1, as the direct donors of Fe-S clusters to mitochondrial NFU1, which appears to dimerize and reductively mediate the formation of a bridging [4Fe-4S] cluster, aided by ferredoxin 2. By monitoring the abundance of target proteins that acquire their Fe-S clusters from NFU1, we characterized the effects of several novel pathogenic NFU1 mutations. We observed that NFU1 directly interacts with each of the Fe-S cluster scaffold proteins known to ligate [2Fe-2S] clusters, ISCU2 and ISCA1, and we mapped the site of interaction to a conserved hydrophobic patch of residues situated at the end of the C-terminal alpha-helix of NFU1. Furthermore, we showed that NFU1 lost its ability to acquire its Fe-S cluster when mutagenized at the identified site of interaction with ISCU2 and ISCA1, which thereby adversely affected biochemical functions of proteins that are thought to acquire their Fe-S clusters directly from NFU1, such as lipoic acid synthase, which supports the Fe-S-dependent process of lipoylation of components of multiple key enzyme complexes, including pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase and the glycine cleavage complex.
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Affiliation(s)
- Anshika Jain
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anamika Singh
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nunziata Maio
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracey A Rouault
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Dietz JV, Fox JL, Khalimonchuk O. Down the Iron Path: Mitochondrial Iron Homeostasis and Beyond. Cells 2021; 10:cells10092198. [PMID: 34571846 PMCID: PMC8468894 DOI: 10.3390/cells10092198] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the processes of and components involved in mitochondrial iron trafficking and storage, as well as mitochondrial iron–sulfur cluster biogenesis and heme biosynthesis. Recent findings and the most pressing topics for future research are highlighted.
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Affiliation(s)
- Jonathan V. Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
| | - Jennifer L. Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA;
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
- Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE 68198, USA
- Correspondence:
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Coenzyme a Biochemistry: From Neurodevelopment to Neurodegeneration. Brain Sci 2021; 11:brainsci11081031. [PMID: 34439650 PMCID: PMC8392065 DOI: 10.3390/brainsci11081031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022] Open
Abstract
Coenzyme A (CoA) is an essential cofactor in all living organisms. It is involved in a large number of biochemical processes functioning either as an activator of molecules with carbonyl groups or as a carrier of acyl moieties. Together with its thioester derivatives, it plays a central role in cell metabolism, post-translational modification, and gene expression. Furthermore, recent studies revealed a role for CoA in the redox regulation by the S-thiolation of cysteine residues in cellular proteins. The intracellular concentration and distribution in different cellular compartments of CoA and its derivatives are controlled by several extracellular stimuli such as nutrients, hormones, metabolites, and cellular stresses. Perturbations of the biosynthesis and homeostasis of CoA and/or acyl-CoA are connected with several pathological conditions, including cancer, myopathies, and cardiomyopathies. In the most recent years, defects in genes involved in CoA production and distribution have been found in patients affected by rare forms of neurodegenerative and neurodevelopmental disorders. In this review, we will summarize the most relevant aspects of CoA cellular metabolism, their role in the pathogenesis of selected neurodevelopmental and neurodegenerative disorders, and recent advancements in the search for therapeutic approaches for such diseases.
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Campbell CJ, Pall AE, Naik AR, Thompson LN, Stemmler TL. Molecular Details of the Frataxin-Scaffold Interaction during Mitochondrial Fe-S Cluster Assembly. Int J Mol Sci 2021; 22:6006. [PMID: 34199378 PMCID: PMC8199681 DOI: 10.3390/ijms22116006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/23/2022] Open
Abstract
Iron-sulfur clusters are essential to almost every life form and utilized for their unique structural and redox-targeted activities within cells during many cellular pathways. Although there are three different Fe-S cluster assembly pathways in prokaryotes (the NIF, SUF and ISC pathways) and two in eukaryotes (CIA and ISC pathways), the iron-sulfur cluster (ISC) pathway serves as the central mechanism for providing 2Fe-2S clusters, directly and indirectly, throughout the entire cell in eukaryotes. Proteins central to the eukaryotic ISC cluster assembly complex include the cysteine desulfurase, a cysteine desulfurase accessory protein, the acyl carrier protein, the scaffold protein and frataxin (in humans, NFS1, ISD11, ACP, ISCU and FXN, respectively). Recent molecular details of this complex (labeled NIAUF from the first letter from each ISC protein outlined earlier), which exists as a dimeric pentamer, have provided real structural insight into how these partner proteins arrange themselves around the cysteine desulfurase, the core dimer of the (NIAUF)2 complex. In this review, we focus on both frataxin and the scaffold within the human, fly and yeast model systems to provide a better understanding of the biophysical characteristics of each protein alone and within the FXN/ISCU complex as it exists within the larger NIAUF construct. These details support a complex dynamic interaction between the FXN and ISCU proteins when both are part of the NIAUF complex and this provides additional insight into the coordinated mechanism of Fe-S cluster assembly.
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Affiliation(s)
| | | | | | | | - Timothy L. Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA; (C.J.C.); (A.E.P.); (A.R.N.); (L.N.T.)
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Álvarez-Córdoba M, Talaverón-Rey M, Villalón-García I, Povea-Cabello S, Suárez-Rivero JM, Suárez-Carrillo A, Munuera-Cabeza M, Salas JJ, Sánchez-Alcázar JA. Down regulation of the expression of mitochondrial phosphopantetheinyl-proteins in pantothenate kinase-associated neurodegeneration: pathophysiological consequences and therapeutic perspectives. Orphanet J Rare Dis 2021; 16:201. [PMID: 33952316 PMCID: PMC8101147 DOI: 10.1186/s13023-021-01823-3] [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: 12/24/2020] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background Neurodegeneration with brain iron accumulation (NBIA) is a group of genetic neurological disorders frequently associated with iron accumulation in the basal nuclei of the brain characterized by progressive spasticity, dystonia, muscle rigidity, neuropsychiatric symptoms, and retinal degeneration or optic nerve atrophy. Pantothenate kinase-associated neurodegeneration (PKAN) is the most widespread NBIA disorder. It is caused by mutations in the gene of pantothenate kinase 2 (PANK2) which catalyzes the first reaction of coenzyme A (CoA) biosynthesis. Thus, altered PANK2 activity is expected to induce CoA deficiency as well as low levels of essential metabolic intermediates such as 4′-phosphopantetheine which is a necessary cofactor for critical proteins involved in cytosolic and mitochondrial pathways such as fatty acid biosynthesis, mitochondrial respiratory complex I assembly and lysine and tetrahydrofolate metabolism, among other metabolic processes. Methods In this manuscript, we examined the effect of PANK2 mutations on the expression levels of proteins with phosphopantetheine cofactors in fibroblast derived from PKAN patients. These proteins include cytosolic acyl carrier protein (ACP), which is integrated within the multifunctional polypeptide chain of the fatty acid synthase involved in cytosolic fatty acid biosynthesis type I (FASI); mitochondrial ACP (mtACP) associated with mitocondrial fatty acid biosynthesis type II (FASII); mitochondrial alpha-aminoadipic semialdehyde synthase (AASS); and 10-formyltetrahydrofolate dehydrogenases (cytosolic, ALD1L1, and mitochondrial, ALD1L2). Results In PKAN fibroblasts the expression levels of cytosolic FAS and ALD1L1 were not affected while the expression levels of mtACP, AASS and ALD1L2 were markedly reduced, suggesting that 4′-phosphopantetheinylation of mitochondrial but no cytosolic proteins were markedly affected in PKAN patients. Furthermore, the correction of PANK2 expression levels by treatment with pantothenate in selected mutations with residual enzyme content was able to correct the expression levels of mitochondrial phosphopantetheinyl-proteins and restore the affected pathways. The positive effects of pantothenate in particular mutations were also corroborated in induced neurons obtained by direct reprograming of mutant PANK2 fibroblasts. Conclusions Our results suggest that the expression levels of mitochondrial phosphopantetheinyl-proteins are severely reduced in PKAN cells and that in selected mutations pantothenate increases the expression levels of both PANK2 and mitochondrial phosphopantetheinyl-proteins associated with remarkable improvement of cell pathophysiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01823-3.
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Affiliation(s)
- Mónica Álvarez-Córdoba
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Marta Talaverón-Rey
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Irene Villalón-García
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Suleva Povea-Cabello
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Juan M Suárez-Rivero
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Alejandra Suárez-Carrillo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Manuel Munuera-Cabeza
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Joaquín J Salas
- Departamento de Bioquímica Y Biología Molecular de Productos Vegetales, Instituto de La Grasa (CSIC), Sevilla, Spain
| | - José A Sánchez-Alcázar
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain. .,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain.
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Human Mitoribosome Biogenesis and Its Emerging Links to Disease. Int J Mol Sci 2021; 22:ijms22083827. [PMID: 33917098 PMCID: PMC8067846 DOI: 10.3390/ijms22083827] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022] Open
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) synthesize a small subset of proteins, which are essential components of the oxidative phosphorylation machinery. Therefore, their function is of fundamental importance to cellular metabolism. The assembly of mitoribosomes is a complex process that progresses through numerous maturation and protein-binding events coordinated by the actions of several assembly factors. Dysregulation of mitoribosome production is increasingly recognized as a contributor to metabolic and neurodegenerative diseases. In recent years, mutations in multiple components of the mitoribosome assembly machinery have been associated with a range of human pathologies, highlighting their importance to cell function and health. Here, we provide a review of our current understanding of mitoribosome biogenesis, highlighting the key factors involved in this process and the growing number of mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors that lead to human disease.
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42
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Zeng M, Xu J, Zhang Z, Zou X, Wang X, Cao K, Lv W, Cui Y, Long J, Feng Z, Liu J. Htd2 deficiency-associated suppression of α-lipoic acid production provokes mitochondrial dysfunction and insulin resistance in adipocytes. Redox Biol 2021; 41:101948. [PMID: 33774475 PMCID: PMC8027779 DOI: 10.1016/j.redox.2021.101948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondria harbor a unique fatty acid synthesis pathway (mtFAS) with mysterious functions gaining increasing interest, while its involvement in metabolic regulation is essentially unknown. Here we show that 3-Hydroxyacyl-ACP dehydratase (HTD2), a key enzyme in mtFAS pathway was primarily downregulated in adipocytes of mice under metabolic disorders, accompanied by decreased de novo production of lipoic acid, which is the byproduct of mtFAS pathway. Knockdown of Htd2 in 3T3-L1 preadipocytes or differentiated 3T3-L1 mature adipocytes impaired mitochondrial function via suppression of complex I activity, resulting in enhanced oxidative stress and impaired insulin sensitivity, which were all attenuated by supplement of lipoic acid. Moreover, lipidomic study revealed limited lipid alterations in mtFAS deficient cells which primarily presenting accumulation of triglycerides, attributed to mitochondrial dysfunction. Collectively, the present study highlighted the pivotal role of mtFAS pathway in regulating mitochondrial function and adipocytes insulin sensitivity, demonstrating supportive evidence for lipoic acid being potential effective nutrient for improving insulin resistance and related metabolic disorders. 3-Hydroxyacyl-ACP dehydratase is decreased in adipocytes under diabetic condition. Deficient of 3-Hydroxyacyl-ACP dehydratase (HTD2) triggers mitochondrial dysfunction. Deficient of HTD2 promotes insulin resistance in adipocytes. Supplement of lipoic acid ameliorates deleterious effects of HTD2 deficiency.
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Affiliation(s)
- Mengqi Zeng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Jie Xu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Zhengyi Zhang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Xuan Zou
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, 710004, China
| | - Xueqiang Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Ke Cao
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Weiqiang Lv
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Yuting Cui
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Zhihui Feng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China; Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China; National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, 710004, China; Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
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Przybyla-Toscano J, Christ L, Keech O, Rouhier N. Iron-sulfur proteins in plant mitochondria: roles and maturation. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2014-2044. [PMID: 33301571 DOI: 10.1093/jxb/eraa578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/05/2020] [Indexed: 05/22/2023]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe-S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe-S proteins. Several other proteins or complexes present in the matrix require Fe-S clusters as well, or depend either on Fe-S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe-S proteins. In this review, we have listed and discussed the Fe-S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe-S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe-S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.
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Affiliation(s)
- Jonathan Przybyla-Toscano
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Loïck Christ
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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Tobiasson V, Gahura O, Aibara S, Baradaran R, Zíková A, Amunts A. Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit. EMBO J 2021; 40:e106292. [PMID: 33576519 PMCID: PMC7957421 DOI: 10.15252/embj.2020106292] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022] Open
Abstract
Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt‐EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl‐carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.
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Affiliation(s)
- Victor Tobiasson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Shintaro Aibara
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Rozbeh Baradaran
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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45
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Kotabova E, Malych R, Pierella Karlusich JJ, Kazamia E, Eichner M, Mach J, Lesuisse E, Bowler C, Prášil O, Sutak R. Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability. mSystems 2021; 6:e00738-20. [PMID: 33563784 PMCID: PMC7883536 DOI: 10.1128/msystems.00738-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022] Open
Abstract
The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model marine chlorarachniophyte Bigelowiella natans varies across regions with different iron concentrations. We performed a comprehensive proteomics analysis of the molecular mechanisms underpinning the adaptation of B. natans to iron scarcity and report on the temporal response of cells to iron enrichment. Our results highlight the role of phytotransferrin in iron homeostasis and indicate the involvement of CREG1 protein in the response to iron availability. Analysis of the Tara Oceans metagenomes and metatranscriptomes also points to a similar role for CREG1, which is found to be widely distributed among marine plankton but to show a strong bias in gene and transcript abundance toward iron-deficient regions. Our analyses allowed us to define a new subfamily of the CobW domain-containing COG0523 putative metal chaperones which are involved in iron metabolism and are restricted to only a few phytoplankton lineages in addition to B. natans At the physiological level, we elucidated the mechanisms allowing a fast recovery of PSII photochemistry after resupply of iron. Collectively, our study demonstrates that B. natans is well adapted to dynamically respond to a changing iron environment and suggests that CREG1 and COG0523 are important components of iron homeostasis in B. natans and other phytoplankton.IMPORTANCE Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes. In the present work, we focused on the model chlorarachniophyte Bigelowiella natans, integrating physiological and proteomic analyses in culture conditions with the mining of omics data generated by the Tara Oceans expedition. We provide unique insight into the complex responses of B. natans to iron availability, including novel links to iron metabolism conserved in other phytoplankton lineages.
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Affiliation(s)
- Eva Kotabova
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Juan José Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Elena Kazamia
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Meri Eichner
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Emmanuel Lesuisse
- Jacques Monod Institute, UMR7592 CNRS, Paris Diderot University, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ondřej Prášil
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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Ren K, Feng L, Sun S, Zhuang X. Plant Mitophagy in Comparison to Mammals: What Is Still Missing? Int J Mol Sci 2021; 22:1236. [PMID: 33513816 PMCID: PMC7865480 DOI: 10.3390/ijms22031236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial homeostasis refers to the balance of mitochondrial number and quality in a cell. It is maintained by mitochondrial biogenesis, mitochondrial fusion/fission, and the clearance of unwanted/damaged mitochondria. Mitophagy represents a selective form of autophagy by sequestration of the potentially harmful mitochondrial materials into a double-membrane autophagosome, thus preventing the release of death inducers, which can trigger programmed cell death (PCD). Recent advances have also unveiled a close interconnection between mitophagy and mitochondrial dynamics, as well as PCD in both mammalian and plant cells. In this review, we will summarize and discuss recent findings on the interplay between mitophagy and mitochondrial dynamics, with a focus on the molecular evidence for mitophagy crosstalk with mitochondrial dynamics and PCD.
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Affiliation(s)
| | | | | | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (K.R.); (L.F.); (S.S.)
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47
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Chen N, Wang C. Chemical Labeling of Protein 4'-Phosphopantetheinylation. Chembiochem 2021; 22:1357-1367. [PMID: 33289264 DOI: 10.1002/cbic.202000747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Indexed: 11/11/2022]
Abstract
Nature uses a diverse array of protein post-translational modifications (PTMs) to regulate protein structure, activity, localization, and function. Among them, protein 4'-phosphopantetheinylation derived from coenzyme A (CoA) is an essential PTM for the biosynthesis of fatty acids, polyketides, and nonribosomal peptides in prokaryotes and eukaryotes. To explore its functions, various chemical probes mimicking the natural structure of 4'-phosphopantetheinylation have been developed. In this minireview, we summarize these chemical probes and describe their applications in direct and metabolic labeling of proteins in bacterial and mammalian cells.
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Affiliation(s)
- Nan Chen
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Chu Wang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, Peking University, Beijing, 100871, P. R. China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
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48
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Pietikäinen LP, Rahman MT, Hiltunen JK, Dieckmann CL, Kastaniotis AJ. Genetic dissection of the mitochondrial lipoylation pathway in yeast. BMC Biol 2021; 19:14. [PMID: 33487163 PMCID: PMC7831266 DOI: 10.1186/s12915-021-00951-3] [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: 07/23/2020] [Accepted: 01/06/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lipoylation of 2-ketoacid dehydrogenases is essential for mitochondrial function in eukaryotes. While the basic principles of the lipoylation processes have been worked out, we still lack a thorough understanding of the details of this important post-translational modification pathway. Here we used yeast as a model organism to characterize substrate usage by the highly conserved eukaryotic octanoyl/lipoyl transferases in vivo and queried how amenable the lipoylation system is to supplementation with exogenous substrate. RESULTS We show that the requirement for mitochondrial fatty acid synthesis to provide substrates for lipoylation of the 2-ketoacid dehydrogenases can be bypassed by supplying the cells with free lipoic acid (LA) or octanoic acid (C8) and a mitochondrially targeted fatty acyl/lipoyl activating enzyme. We also provide evidence that the S. cerevisiae lipoyl transferase Lip3, in addition to transferring LA from the glycine cleavage system H protein to the pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase (KGD) E2 subunits, can transfer this cofactor from the PDH complex to the KGD complex. In support of yeast as a model system for human metabolism, we demonstrate that the human octanoyl/lipoyl transferases can substitute for their counterparts in yeast to support respiratory growth and protein lipoylation. Like the wild-type yeast enzyme, the human lipoyl transferase LIPT1 responds to LA supplementation in the presence of the activating enzyme LplA. CONCLUSIONS In the yeast model system, the eukaryotic lipoylation pathway can use free LA and C8 as substrates when fatty/lipoic acid activating enzymes are targeted to mitochondria. Lip3 LA transferase has a wider substrate specificity than previously recognized. We show that these features of the lipoylation mechanism in yeast are conserved in mammalian mitochondria. Our findings have important implications for the development of effective therapies for the treatment of LA or mtFAS deficiency-related disorders.
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Affiliation(s)
- Laura P Pietikäinen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland
| | - M Tanvir Rahman
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland
| | - Carol L Dieckmann
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland.
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Azam T, Przybyla-Toscano J, Vignols F, Couturier J, Rouhier N, Johnson MK. [4Fe-4S] cluster trafficking mediated by Arabidopsis mitochondrial ISCA and NFU proteins. J Biol Chem 2020; 295:18367-18378. [PMID: 33122194 PMCID: PMC7939391 DOI: 10.1074/jbc.ra120.015726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/12/2020] [Indexed: 12/17/2022] Open
Abstract
Numerous iron-sulfur (Fe-S) proteins with diverse functions are present in the matrix and respiratory chain complexes of mitochondria. Although [4Fe-4S] clusters are the most common type of Fe-S cluster in mitochondria, the molecular mechanism of [4Fe-4S] cluster assembly and insertion into target proteins by the mitochondrial iron-sulfur cluster (ISC) maturation system is not well-understood. Here we report a detailed characterization of two late-acting Fe-S cluster-carrier proteins from Arabidopsis thaliana, NFU4 and NFU5. Yeast two-hybrid and bimolecular fluorescence complementation studies demonstrated interaction of both the NFU4 and NFU5 proteins with the ISCA class of Fe-S carrier proteins. Recombinant NFU4 and NFU5 were purified as apo-proteins after expression in Escherichia coliIn vitro Fe-S cluster reconstitution led to the insertion of one [4Fe-4S]2+ cluster per homodimer as determined by UV-visible absorption/CD, resonance Raman and EPR spectroscopy, and analytical studies. Cluster transfer reactions, monitored by UV-visible absorption and CD spectroscopy, showed that a [4Fe-4S]2+ cluster-bound ISCA1a/2 heterodimer is effective in transferring [4Fe-4S]2+ clusters to both NFU4 and NFU5 with negligible back reaction. In addition, [4Fe-4S]2+ cluster-bound ISCA1a/2, NFU4, and NFU5 were all found to be effective [4Fe-4S]2+ cluster donors for maturation of the mitochondrial apo-aconitase 2 as assessed by enzyme activity measurements. The results demonstrate rapid, unidirectional, and quantitative [4Fe-4S]2+ cluster transfer from ISCA1a/2 to NFU4 or NFU5 that further delineates their respective positions in the plant ISC machinery and their contributions to the maturation of client [4Fe-4S] cluster-containing proteins.
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Affiliation(s)
- Tamanna Azam
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA
| | | | - Florence Vignols
- BPMP, Université de Montpellier, INRAE, CNRS, SupAgro, Montpellier, France
| | | | | | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA.
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50
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Aw YTV, Seidi A, Hayward JA, Lee J, Makota FV, Rug M, van Dooren GG. A key cytosolic iron-sulfur cluster synthesis protein localizes to the mitochondrion of Toxoplasma gondii. Mol Microbiol 2020; 115:968-985. [PMID: 33222310 DOI: 10.1111/mmi.14651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups on proteins that function in a range of enzymatic and electron transfer reactions. Fe-S cluster synthesis is essential for the survival of all eukaryotes. Independent Fe-S cluster biosynthesis pathways occur in the mitochondrion, plastid, and cytosolic compartments of eukaryotic cells. Little is known about the cytosolic Fe-S cluster biosynthesis in apicomplexan parasites, the causative agents of diseases such as malaria and toxoplasmosis. NBP35 serves as a key scaffold protein on which cytosolic Fe-S clusters assemble, and has a cytosolic localization in most eukaryotes studied thus far. Unexpectedly, we found that the NBP35 homolog of the apicomplexan Toxoplasma gondii (TgNBP35) localizes to the outer mitochondrial membrane, with mitochondrial targeting mediated by an N-terminal transmembrane domain. We demonstrate that TgNBP35 is critical for parasite proliferation, but that, despite its mitochondrial localization, it is not required for Fe-S cluster synthesis in the mitochondrion. Instead, we establish that TgNBP35 is important for the biogenesis of cytosolic Fe-S proteins. Our data are consistent with TgNBP35 playing a central and specific role in cytosolic Fe-S cluster biosynthesis, and imply that the assembly of cytosolic Fe-S clusters occurs on the cytosolic face of the outer mitochondrial membrane in these parasites.
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Affiliation(s)
- Yi Tong Vincent Aw
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Azadeh Seidi
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jenni A Hayward
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jiwon Lee
- Centre for Advanced Microscopy, Australian National University, Canberra, ACT, Australia
| | - F Victor Makota
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Melanie Rug
- Centre for Advanced Microscopy, Australian National University, Canberra, ACT, Australia
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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