1
|
Strefeler A, Blanco-Fernandez J, Jourdain AA. Nucleosides are overlooked fuels in central carbon metabolism. Trends Endocrinol Metab 2024; 35:290-299. [PMID: 38423899 DOI: 10.1016/j.tem.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024]
Abstract
From our daily nutrition and synthesis within cells, nucleosides enter the bloodstream and circulate throughout the body and tissues. Nucleosides and nucleotides are classically viewed as precursors of nucleic acids, but recently they have emerged as a novel energy source for central carbon metabolism. Through catabolism by nucleoside phosphorylases, the ribose sugar group is released and can provide substrates for lower steps in glycolysis. In environments with limited glucose, such as at sites of infection or in the tumor microenvironment (TME), cells can use, and may even require, this alternative energy source. Here, we discuss the implications of these new findings in health and disease and speculate on the potential new roles of nucleosides and nucleic acids in energy metabolism.
Collapse
Affiliation(s)
- Abigail Strefeler
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, CP51, 1066 Epalinges, Switzerland
| | - Joan Blanco-Fernandez
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, CP51, 1066 Epalinges, Switzerland
| | - Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Ch. des Boveresses 155, CP51, 1066 Epalinges, Switzerland.
| |
Collapse
|
2
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
3
|
Lewis SC, Jourdain AA, Schulman BA, Vousden KH, Fabius JM, Liu H. Recovering from the stress of the COVID-19 pandemic. Mol Cell 2024; 84:8-11. [PMID: 38181764 DOI: 10.1016/j.molcel.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
For our special issue on stress, we asked scientists about recovering from the stress of the pandemic, including some who shared insights with us in mid-2020. They discuss the importance of teamwork, reassessing priorities, and the added stresses of the cost-of-living crisis, funding cuts, and retaining scientists in academia.
Collapse
|
4
|
Affiliation(s)
- Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| | - Feilong Wang
- Shanghai East Hospital, Tongji University, Shanghai, China.
| |
Collapse
|
5
|
Gobelli D, Serrano-Lorenzo P, Esteban-Amo MJ, Serna J, Pérez-García MT, Orduña A, Jourdain AA, Martín-Casanueva MÁ, Á. de la Fuente M, Simarro M. The mitochondrial succinate dehydrogenase complex controls the STAT3-IL-10 pathway in inflammatory macrophages. iScience 2023; 26:107473. [PMID: 37575201 PMCID: PMC10416071 DOI: 10.1016/j.isci.2023.107473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/17/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023] Open
Abstract
The functions of macrophages are tightly regulated by their metabolic state. However, the role of the mitochondrial electron transport chain (ETC) in macrophage functions remains understudied. Here, we provide evidence that the succinate dehydrogenase (SDH)/complex II (CII) is required for respiration and plays a role in controlling effector responses in macrophages. We find that the absence of the catalytic subunits Sdha and Sdhb in macrophages impairs their ability to effectively stabilize HIF-1α and produce the pro-inflammatory cytokine IL-1β in response to LPS stimulation. We also arrive at the novel result that both subunits are essential for the LPS-driven production of IL-10, a potent negative feedback regulator of the macrophage inflammatory response. This phenomenon is explained by the fact that the absence of Sdha and Sdhb leads to the inhibition of Stat3 tyrosine phosphorylation, caused partially by the excessive accumulation of mitochondrial reactive oxygen species (mitoROS) in the knockout cells.
Collapse
Affiliation(s)
- Dino Gobelli
- Department of Cell Biology, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
| | - Pablo Serrano-Lorenzo
- Hospital 12 de Octubre Research Institute (imas12), 28041 Madrid, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Mitochondrial Disorders Laboratory, Clinical Biochemistry Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - María J. Esteban-Amo
- Department of Cell Biology, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
| | - Julia Serna
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain
| | - M. Teresa Pérez-García
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain
| | - Antonio Orduña
- Division of Microbiology, Hospital Clínico of Valladolid, 47003 Valladolid, Spain
- Department of Microbiology, University of Valladolid, 47005 Valladolid, Spain
| | - Alexis A. Jourdain
- Department of Immunobiology, Faculty of Biology and Medicine, University of Lausanne, 1011 Lausanne, Switzerland
| | - Miguel Á. Martín-Casanueva
- Hospital 12 de Octubre Research Institute (imas12), 28041 Madrid, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Mitochondrial Disorders Laboratory, Clinical Biochemistry Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Miguel Á. de la Fuente
- Department of Cell Biology, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
| | - María Simarro
- Department of Cell Biology, Histology and Pharmacology, Faculty of Medicine, University of Valladolid, 47005 Valladolid, Spain
- Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Spanish National Research Council (CSIC), 47003 Valladolid, Spain
| |
Collapse
|
6
|
Blanco-Fernandez J, Jourdain AA. Two-Step Tag-Free Isolation of Mitochondria for Improved Protein Discovery and Quantification. J Vis Exp 2023. [PMID: 37335104 DOI: 10.3791/65252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Most physiological and disease processes, from central metabolism to immune response to neurodegeneration, involve mitochondria. The mitochondrial proteome is composed of more than 1,000 proteins, and the abundance of each can vary dynamically in response to external stimuli or during disease progression. Here, we describe a protocol for isolating high-quality mitochondria from primary cells and tissues. The two-step procedure comprises (1) mechanical homogenization and differential centrifugation to isolate crude mitochondria, and (2) tag-free immune capture of mitochondria to isolate pure organelles and eliminate contaminants. Mitochondrial proteins from each purification stage are analyzed by quantitative mass spectrometry, and enrichment yields are calculated, allowing the discovery of novel mitochondrial proteins by subtractive proteomics. Our protocol provides a sensitive and comprehensive approach to studying mitochondrial content in cell lines, primary cells, and tissues.
Collapse
|
7
|
Skinner OS, Blanco-Fernández J, Goodman RP, Kawakami A, Shen H, Kemény LV, Joesch-Cohen L, Rees MG, Roth JA, Fisher DE, Mootha VK, Jourdain AA. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nat Metab 2023; 5:765-776. [PMID: 37198474 PMCID: PMC10229423 DOI: 10.1038/s42255-023-00774-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/03/2023] [Indexed: 05/19/2023]
Abstract
Glucose is vital for life, serving as both a source of energy and carbon building block for growth. When glucose is limiting, alternative nutrients must be harnessed. To identify mechanisms by which cells can tolerate complete loss of glucose, we performed nutrient-sensitized genome-wide genetic screens and a PRISM growth assay across 482 cancer cell lines. We report that catabolism of uridine from the medium enables the growth of cells in the complete absence of glucose. While previous studies have shown that uridine can be salvaged to support pyrimidine synthesis in the setting of mitochondrial oxidative phosphorylation deficiency1, our work demonstrates that the ribose moiety of uridine or RNA can be salvaged to fulfil energy requirements via a pathway based on: (1) the phosphorylytic cleavage of uridine by uridine phosphorylase UPP1/UPP2 into uracil and ribose-1-phosphate (R1P), (2) the conversion of uridine-derived R1P into fructose-6-P and glyceraldehyde-3-P by the non-oxidative branch of the pentose phosphate pathway and (3) their glycolytic utilization to fuel ATP production, biosynthesis and gluconeogenesis. Capacity for glycolysis from uridine-derived ribose appears widespread, and we confirm its activity in cancer lineages, primary macrophages and mice in vivo. An interesting property of this pathway is that R1P enters downstream of the initial, highly regulated steps of glucose transport and upper glycolysis. We anticipate that 'uridine bypass' of upper glycolysis could be important in the context of disease and even exploited for therapeutic purposes.
Collapse
Affiliation(s)
- Owen S Skinner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Russell P Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Hongying Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
- Yale Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Lajos V Kemény
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Department of Dermatology, Venereology and Dermatooncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | | | | | | | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| |
Collapse
|
8
|
Blanco-Fernandez J, Jourdain AA. Dead-Seq: Discovering Synthetic Lethal Interactions from Dead Cells Genomics. Methods Mol Biol 2023; 2661:329-342. [PMID: 37166646 DOI: 10.1007/978-1-0716-3171-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pooled genetic screens have revolutionized the field of functional genomics, yet perturbations that decrease fitness, such as those leading to synthetic lethality, have remained difficult to quantify at the genomic level. We and colleagues previously developed "death screening," a protocol based on the purification of dead cells in genetic screens, and used it to identify a set of genes necessary for mitochondrial gene expression, translation, and oxidative phosphorylation (OXPHOS), thus offering new possibilities for the diagnosis of mitochondrial disorders. Here, we describe Dead-Seq, a refined protocol for death screening that is compatible with most pooled screening protocols, including genome-wide CRISPR/Cas9 screening. Dead-Seq converts negative-selection screens into positive-selection screens and generates high-quality data directly from dead cells, at limited sequencing costs.
Collapse
Affiliation(s)
| | - Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| |
Collapse
|
9
|
Jourdain AA, Begg BE, Mick E, Shah H, Calvo SE, Skinner OS, Sharma R, Blue SM, Yeo GW, Burge CB, Mootha VK. Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS. Mol Cell 2021; 81:1905-1919.e12. [PMID: 33852893 DOI: 10.1016/j.molcel.2021.02.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022]
Abstract
Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the full set of molecular mechanisms governing the relative expression and balance of these two pathways is unknown. Here, we focus on genes whose loss leads to an increase in OXPHOS activity. Unexpectedly, this class of genes is enriched for components of the pre-mRNA splicing machinery, in particular for subunits of the U1 snRNP. Among them, we show that LUC7L2 represses OXPHOS and promotes glycolysis by multiple mechanisms, including (1) splicing of the glycolytic enzyme PFKM to suppress glycogen synthesis, (2) splicing of the cystine/glutamate antiporter SLC7A11 (xCT) to suppress glutamate oxidation, and (3) secondary repression of mitochondrial respiratory supercomplex formation. Our results connect LUC7L2 expression and, more generally, the U1 snRNP to cellular energy metabolism.
Collapse
Affiliation(s)
- Alexis A Jourdain
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Eran Mick
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hardik Shah
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Owen S Skinner
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rohit Sharma
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
10
|
Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW, Joshi PR, Jourdain AA, Kim SH, Kotrys AV, Lam SS, McCoy JG, Meisel JD, Miranda M, Panda A, Patgiri A, Rogers R, Sadre S, Shah H, Skinner OS, To TL, Walker M, Wang H, Ward PS, Wengrod J, Yuan CC, Calvo SE, Mootha VK. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res 2020; 49:D1541-D1547. [PMID: 33174596 PMCID: PMC7778944 DOI: 10.1093/nar/gkaa1011] [Citation(s) in RCA: 603] [Impact Index Per Article: 150.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 02/04/2023] Open
Abstract
The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). We previously developed MitoCarta, a catalogue of over 1000 genes encoding the mammalian mitochondrial proteome. This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. Here, we introduce MitoCarta3.0. Beginning with the MitoCarta2.0 inventory, we performed manual review to remove 100 genes and introduce 78 additional genes, arriving at an updated inventory of 1136 human genes. We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical 'MitoPathways' spanning seven broad functional categories relevant to mitochondria. MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine.
Collapse
Affiliation(s)
| | | | | | - Tslil Ast
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Connie Chan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy J Durham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Russell P Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zenon Grabarek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mary E Haas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wendy H W Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Pallavi R Joshi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexis A Jourdain
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon H Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anna V Kotrys
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie S Lam
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason G McCoy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua D Meisel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Maria Miranda
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Apekshya Panda
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anupam Patgiri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Rogers
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shayan Sadre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hardik Shah
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Owen S Skinner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tsz-Leung To
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Melissa A Walker
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hong Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick S Ward
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jordan Wengrod
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Ching Yuan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah E Calvo
- Correspondence may also be addressed to Sarah E. Calvo.
| | - Vamsi K Mootha
- To whom correspondence should be addressed. Tel: +1 617 643 3059;
| |
Collapse
|
11
|
Mick E, Titov DV, Skinner OS, Sharma R, Jourdain AA, Mootha VK. Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell. eLife 2020; 9:49178. [PMID: 32463360 PMCID: PMC7255802 DOI: 10.7554/elife.49178] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dysfunction is associated with activation of the integrated stress response (ISR) but the underlying triggers remain unclear. We systematically combined acute mitochondrial inhibitors with genetic tools for compartment-specific NADH oxidation to trace mechanisms linking different forms of mitochondrial dysfunction to the ISR in proliferating mouse myoblasts and in differentiated myotubes. In myoblasts, we find that impaired NADH oxidation upon electron transport chain (ETC) inhibition depletes asparagine, activating the ISR via the eIF2α kinase GCN2. In myotubes, however, impaired NADH oxidation following ETC inhibition neither depletes asparagine nor activates the ISR, reflecting an altered metabolic state. ATP synthase inhibition in myotubes triggers the ISR via a distinct mechanism related to mitochondrial inner-membrane hyperpolarization. Our work dispels the notion of a universal path linking mitochondrial dysfunction to the ISR, instead revealing multiple paths that depend both on the nature of the mitochondrial defect and on the metabolic state of the cell.
Collapse
Affiliation(s)
- Eran Mick
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Broad Institute, Cambridge, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Denis V Titov
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Broad Institute, Cambridge, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Owen S Skinner
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Broad Institute, Cambridge, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Rohit Sharma
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Broad Institute, Cambridge, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Alexis A Jourdain
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Broad Institute, Cambridge, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Broad Institute, Cambridge, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States
| |
Collapse
|
12
|
Guièze R, Liu VM, Rosebrock D, Jourdain AA, Hernández-Sánchez M, Martinez Zurita A, Sun J, Ten Hacken E, Baranowski K, Thompson PA, Heo JM, Cartun Z, Aygün O, Iorgulescu JB, Zhang W, Notarangelo G, Livitz D, Li S, Davids MS, Biran A, Fernandes SM, Brown JR, Lako A, Ciantra ZB, Lawlor MA, Keskin DB, Udeshi ND, Wierda WG, Livak KJ, Letai AG, Neuberg D, Harper JW, Carr SA, Piccioni F, Ott CJ, Leshchiner I, Johannessen CM, Doench J, Mootha VK, Getz G, Wu CJ. Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. Cancer Cell 2019; 36:369-384.e13. [PMID: 31543463 PMCID: PMC6801112 DOI: 10.1016/j.ccell.2019.08.005] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/04/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022]
Abstract
Mitochondrial apoptosis can be effectively targeted in lymphoid malignancies with the FDA-approved B cell lymphoma 2 (BCL-2) inhibitor venetoclax, but resistance to this agent is emerging. We show that venetoclax resistance in chronic lymphocytic leukemia is associated with complex clonal shifts. To identify determinants of resistance, we conducted parallel genome-scale screens of the BCL-2-driven OCI-Ly1 lymphoma cell line after venetoclax exposure along with integrated expression profiling and functional characterization of drug-resistant and engineered cell lines. We identified regulators of lymphoid transcription and cellular energy metabolism as drivers of venetoclax resistance in addition to the known involvement by BCL-2 family members, which were confirmed in patient samples. Our data support the implementation of combinatorial therapy with metabolic modulators to address venetoclax resistance.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Apoptosis/drug effects
- Apoptosis/genetics
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Cell Line, Tumor
- Clonal Evolution/drug effects
- Disease Progression
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Energy Metabolism/drug effects
- Energy Metabolism/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Middle Aged
- Mitochondria/drug effects
- Mitochondria/pathology
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Oxidative Phosphorylation/drug effects
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Sulfonamides/pharmacology
- Sulfonamides/therapeutic use
- Treatment Outcome
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Romain Guièze
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; CHU de Clermont-Ferrand, 63000 Clermont-Ferrand, France; Université Clermont Auvergne, EA7453 CHELTER, 63000 Clermont-Ferrand, France
| | - Vivian M Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA
| | | | - Alexis A Jourdain
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - María Hernández-Sánchez
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Instituto de Investigación Biomédica de Salamanca, Centro de Investigación del Cáncer-IBMCC, Universidad de Salamanca, 37007 Salamanca, Spain; Servicio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | | | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Kaitlyn Baranowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Philip A Thompson
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Zachary Cartun
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Ozan Aygün
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Giulia Notarangelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Dimitri Livitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Anat Biran
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Ana Lako
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zoe B Ciantra
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew A Lawlor
- Harvard Medical School, Boston, MA 02215, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02214, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | | | - William G Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Donna Neuberg
- Harvard Medical School, Boston, MA 02215, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Christopher J Ott
- Harvard Medical School, Boston, MA 02215, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02214, USA
| | | | | | - John Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02214, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA.
| |
Collapse
|
13
|
Silva J, Aivio S, Knobel PA, Bailey LJ, Casali A, Vinaixa M, Garcia-Cao I, Coyaud É, Jourdain AA, Pérez-Ferreros P, Rojas AM, Antolin-Fontes A, Samino-Gené S, Raught B, González-Reyes A, Ribas de Pouplana L, Doherty AJ, Yanes O, Stracker TH. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nat Cell Biol 2018; 20:162-174. [PMID: 29335528 DOI: 10.1038/s41556-017-0016-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/27/2017] [Indexed: 02/08/2023]
Abstract
Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3'-5' domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome. Loss of EXD2 results in defective mitochondrial translation, impaired respiration, reduced ATP production, increased reactive oxygen species and widespread metabolic abnormalities. Depletion of the Drosophila melanogaster EXD2 orthologue (CG6744) causes developmental delays and premature female germline stem cell attrition, reduced fecundity and a dramatic extension of lifespan that is reversed with an antioxidant diet. Our results define a conserved role for EXD2 in mitochondrial translation that influences development and ageing.
Collapse
Affiliation(s)
- Joana Silva
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Suvi Aivio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department for Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Andreu Casali
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maria Vinaixa
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Isabel Garcia-Cao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexis A Jourdain
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pablo Pérez-Ferreros
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,EMBL Australia, University of New South Wales, Lowy Cancer Research Center, Single Molecule Science Node, Sydney and Arc Center of Excellence in Advance Molecular Imaging, Sydney, New South Wales, Australia
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville (IBIS/CSIC/US/JA), Campus Hospital Universitario Virgen del Rocio, Seville, Spain
| | - Albert Antolin-Fontes
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sara Samino-Gené
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Acaimo González-Reyes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Seville, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| |
Collapse
|
14
|
Jourdain AA, Popow J, de la Fuente MA, Martinou JC, Anderson P, Simarro M. The FASTK family of proteins: emerging regulators of mitochondrial RNA biology. Nucleic Acids Res 2017; 45:10941-10947. [PMID: 29036396 PMCID: PMC5737537 DOI: 10.1093/nar/gkx772] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022] Open
Abstract
The FASTK family proteins have recently emerged as key post-transcriptional regulators of mitochondrial gene expression. FASTK, the founding member and its homologs FASTKD1-5 are architecturally related RNA-binding proteins, each having a different function in the regulation of mitochondrial RNA biology, from mRNA processing and maturation to ribosome assembly and translation. In this review, we outline the structure, evolution and function of these FASTK proteins and discuss the individual role that each has in mitochondrial RNA biology. In addition, we highlight the aspects of FASTK research that still require more attention.
Collapse
Affiliation(s)
- Alexis A Jourdain
- Department of Cell Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Johannes Popow
- Department of Cancer Cell Signalling, Boehringer-Ingelheim Regional Center Vienna, 1121 Vienna, Austria
| | - Miguel A de la Fuente
- Departamento de Biología, Histología y Farmacología, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
| | | | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Maria Simarro
- Departamento de Enfermería, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
| |
Collapse
|
15
|
Feichtinger RG, Oláhová M, Kishita Y, Garone C, Kremer LS, Yagi M, Uchiumi T, Jourdain AA, Thompson K, D'Souza AR, Kopajtich R, Alston CL, Koch J, Sperl W, Mastantuono E, Strom TM, Wortmann SB, Meitinger T, Pierre G, Chinnery PF, Chrzanowska-Lightowlers ZM, Lightowlers RN, DiMauro S, Calvo SE, Mootha VK, Moggio M, Sciacco M, Comi GP, Ronchi D, Murayama K, Ohtake A, Rebelo-Guiomar P, Kohda M, Kang D, Mayr JA, Taylor RW, Okazaki Y, Minczuk M, Prokisch H. Biallelic C1QBP Mutations Cause Severe Neonatal-, Childhood-, or Later-Onset Cardiomyopathy Associated with Combined Respiratory-Chain Deficiencies. Am J Hum Genet 2017; 101:525-538. [PMID: 28942965 PMCID: PMC5630164 DOI: 10.1016/j.ajhg.2017.08.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022] Open
Abstract
Complement component 1 Q subcomponent-binding protein (C1QBP; also known as p32) is a multi-compartmental protein whose precise function remains unknown. It is an evolutionary conserved multifunctional protein localized primarily in the mitochondrial matrix and has roles in inflammation and infection processes, mitochondrial ribosome biogenesis, and regulation of apoptosis and nuclear transcription. It has an N-terminal mitochondrial targeting peptide that is proteolytically processed after import into the mitochondrial matrix, where it forms a homotrimeric complex organized in a doughnut-shaped structure. Although C1QBP has been reported to exert pleiotropic effects on many cellular processes, we report here four individuals from unrelated families where biallelic mutations in C1QBP cause a defect in mitochondrial energy metabolism. Infants presented with cardiomyopathy accompanied by multisystemic involvement (liver, kidney, and brain), and children and adults presented with myopathy and progressive external ophthalmoplegia. Multiple mitochondrial respiratory-chain defects, associated with the accumulation of multiple deletions of mitochondrial DNA in the later-onset myopathic cases, were identified in all affected individuals. Steady-state C1QBP levels were decreased in all individuals' samples, leading to combined respiratory-chain enzyme deficiency of complexes I, III, and IV. C1qbp-/- mouse embryonic fibroblasts (MEFs) resembled the human disease phenotype by showing multiple defects in oxidative phosphorylation (OXPHOS). Complementation with wild-type, but not mutagenized, C1qbp restored OXPHOS protein levels and mitochondrial enzyme activities in C1qbp-/- MEFs. C1QBP deficiency represents an important mitochondrial disorder associated with a clinical spectrum ranging from infantile lactic acidosis to childhood (cardio)myopathy and late-onset progressive external ophthalmoplegia.
Collapse
Affiliation(s)
- René G Feichtinger
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Yoshihito Kishita
- Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Caterina Garone
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK; Department of Neurology, Columbia University Medical Center, New York, NY 10032-3784, USA
| | - Laura S Kremer
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Mikako Yagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Alexis A Jourdain
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Genome Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Aaron R D'Souza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK
| | - Robert Kopajtich
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johannes Koch
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Wolfgang Sperl
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Elisa Mastantuono
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saskia B Wortmann
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Germaine Pierre
- South West Regional Metabolic Department, Bristol Royal Hospital for Children, Bristol BS1 3NU, UK
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK
| | - Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, NY 10032-3784, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Genome Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Genome Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maurizio Moggio
- Neuromuscular Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Monica Sciacco
- Neuromuscular Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giacomo P Comi
- Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, IRCCS Foundation Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Dario Ronchi
- Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, IRCCS Foundation Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba 266-0007, Japan
| | - Akira Ohtake
- Department of Pediatrics, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK; Graduate Program in Areas of Basic and Applied Biology, University of Porto, 4099-002 Porto, Portugal
| | - Masakazu Kohda
- Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Johannes A Mayr
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience and Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Yasushi Okazaki
- Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan; Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust, MRC Building, Cambridge CB2 0XY, UK
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
| |
Collapse
|
16
|
Boehm E, Zaganelli S, Maundrell K, Jourdain AA, Thore S, Martinou JC. FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain. Nucleic Acids Res 2017; 45:6135-6146. [PMID: 28335001 PMCID: PMC5449608 DOI: 10.1093/nar/gkx164] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/28/2017] [Indexed: 11/14/2022] Open
Abstract
FASTK family proteins have been identified as regulators of mitochondrial RNA homeostasis linked to mitochondrial diseases, but much remains unknown about these proteins. We show that CRISPR-mediated disruption of FASTKD1 increases ND3 mRNA level, while disruption of FASTKD4 reduces the level of ND3 and of other mature mRNAs including ND5 and CYB, and causes accumulation of ND5-CYB precursor RNA. Disrupting both FASTKD1 and FASTKD4 in the same cell results in decreased ND3 mRNA similar to the effect of depleting FASTKD4 alone, indicating that FASTKD4 loss is epistatic. Interestingly, very low levels of FASTKD4 are sufficient to prevent ND3 loss and ND5-CYB precursor accumulation, suggesting that FASTKD4 may act catalytically. Furthermore, structural modeling predicts that each RAP domain of FASTK proteins contains a nuclease fold with a conserved aspartate residue at the putative active site. Accordingly, mutation of this residue in FASTKD4 abolishes its function. Experiments with FASTK chimeras indicate that the RAP domain is essential for the function of the FASTK proteins, while the region upstream determines RNA targeting and protein localization. In conclusion, this paper identifies new aspects of FASTK protein biology and suggests that the RAP domain function depends on an intrinsic nucleolytic activity.
Collapse
Affiliation(s)
- Erik Boehm
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Sofia Zaganelli
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Kinsey Maundrell
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Alexis A Jourdain
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Stéphane Thore
- INSERM U-1212, CNRS UMR 5320, Université de Bordeaux, ARNA Laboratory, Bordeaux 33000, France
| | | |
Collapse
|
17
|
Li Y, Jourdain AA, Calvo SE, Liu JS, Mootha VK. CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PLoS Comput Biol 2017; 13:e1005653. [PMID: 28719601 PMCID: PMC5546725 DOI: 10.1371/journal.pcbi.1005653] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 08/07/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022] Open
Abstract
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression. CLIC accepts as input a pathway consisting of two or more genes. It then uses a Bayesian partition model to simultaneously partition the input gene set into coherent co-expressed modules (CEMs), while assigning the posterior probability for each dataset in support of each CEM. CLIC then expands each CEM by scanning the transcriptome for additional co-expressed genes, quantified by an integrated log-likelihood ratio (LLR) score weighted for each dataset. As a byproduct, CLIC automatically learns the conditions (datasets) within which a CEM is operative. We implemented CLIC using a compendium of 1774 mouse microarray datasets (28628 microarrays) or 1887 human microarray datasets (45158 microarrays). CLIC analysis reveals that of 910 canonical biological pathways, 30% consist of strongly co-expressed gene modules for which new members are predicted. For example, CLIC predicts a functional connection between protein C7orf55 (FMC1) and the mitochondrial ATP synthase complex that we have experimentally validated. CLIC is freely available at www.gene-clic.org. We anticipate that CLIC will be valuable both for revealing new components of biological pathways as well as the conditions in which they are active.
Collapse
Affiliation(s)
- Yang Li
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Department of Statistics, Harvard University, Cambridge, MA, United States of America
| | - Alexis A. Jourdain
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Broad Institute, Cambridge, MA, United States of America
| | - Sarah E. Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Broad Institute, Cambridge, MA, United States of America
- * E-mail: (SEC); (JSL); (VKM)
| | - Jun S. Liu
- Department of Statistics, Harvard University, Cambridge, MA, United States of America
- * E-mail: (SEC); (JSL); (VKM)
| | - Vamsi K. Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology and the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States of America and Department of Systems Biology, Harvard Medical School, Boston, MA United States of America
- Broad Institute, Cambridge, MA, United States of America
- * E-mail: (SEC); (JSL); (VKM)
| |
Collapse
|
18
|
Zaganelli S, Rebelo-Guiomar P, Maundrell K, Rozanska A, Pierredon S, Powell CA, Jourdain AA, Hulo N, Lightowlers RN, Chrzanowska-Lightowlers ZM, Minczuk M, Martinou JC. The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules. J Biol Chem 2017; 292:4519-4532. [PMID: 28082677 PMCID: PMC5377769 DOI: 10.1074/jbc.m116.771105] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/11/2017] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial gene expression is a fundamental process that is largely dependent on nuclear-encoded proteins. Several steps of mitochondrial RNA processing and maturation, including RNA post-transcriptional modification, appear to be spatially organized into distinct foci, which we have previously termed mitochondrial RNA granules (MRGs). Although an increasing number of proteins have been localized to MRGs, a comprehensive analysis of the proteome of these structures is still lacking. Here, we have applied a microscopy-based approach that has allowed us to identify novel components of the MRG proteome. Among these, we have focused our attention on RPUSD4, an uncharacterized mitochondrial putative pseudouridine synthase. We show that RPUSD4 depletion leads to a severe reduction of the steady-state level of the 16S mitochondrial (mt) rRNA with defects in the biogenesis of the mitoribosome large subunit and consequently in mitochondrial translation. We report that RPUSD4 binds 16S mt-rRNA, mt-tRNAMet, and mt-tRNAPhe, and we demonstrate that it is responsible for pseudouridylation of the latter. These data provide new insights into the relevance of RNA pseudouridylation in mitochondrial gene expression.
Collapse
Affiliation(s)
- Sofia Zaganelli
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom.,Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto 4200-135, Portugal
| | - Kinsey Maundrell
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Agata Rozanska
- Wellcome Trust Centre for Mitochondrial Research, Institute of Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom, and
| | - Sandra Pierredon
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Alexis A Jourdain
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Nicolas Hulo
- Institute of Genetics and Genomics of Geneva, Université de Genève, 1211 Genève 4, Switzerland
| | - Robert N Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute of Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom, and
| | - Zofia M Chrzanowska-Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute of Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom, and
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Jean-Claude Martinou
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland,
| |
Collapse
|
19
|
Arroyo JD, Jourdain AA, Calvo SE, Ballarano CA, Doench JG, Root DE, Mootha VK. A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation. Cell Metab 2016; 24:875-885. [PMID: 27667664 PMCID: PMC5474757 DOI: 10.1016/j.cmet.2016.08.017] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022]
Abstract
Oxidative phosphorylation (OXPHOS) is the major pathway for ATP production in humans. Deficiencies in OXPHOS can arise from mutations in either mitochondrial or nuclear genomes and comprise the largest collection of inborn errors of metabolism. At present we lack a complete catalog of human genes and pathways essential for OXPHOS. Here we introduce a genome-wide CRISPR "death screen" that actively selects dying cells to reveal human genes required for OXPHOS, inspired by the classic observation that human cells deficient in OXPHOS survive in glucose but die in galactose. We report 191 high-confidence hits essential for OXPHOS, including 72 underlying known OXPHOS diseases. Our screen reveals a functional module consisting of NGRN, WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2 that regulates the mitochondrial 16S rRNA and intra-mitochondrial translation. Our work yields a rich catalog of genes required for OXPHOS and, more generally, demonstrates the power of death screening for functional genomic analysis.
Collapse
Affiliation(s)
- Jason D Arroyo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexis A Jourdain
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carmine A Ballarano
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
20
|
Boehm E, Zornoza M, Jourdain AA, Delmiro Magdalena A, García-Consuegra I, Torres Merino R, Orduña A, Martín MA, Martinou JC, De la Fuente MA, Simarro M. Role of FAST Kinase Domains 3 (FASTKD3) in Post-transcriptional Regulation of Mitochondrial Gene Expression. J Biol Chem 2016; 291:25877-25887. [PMID: 27789713 DOI: 10.1074/jbc.m116.730291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 09/30/2016] [Indexed: 11/06/2022] Open
Abstract
The Fas-activated serine/threonine kinase (FASTK) family of proteins has recently emerged as a central regulator of mitochondrial gene expression through the function of an unusual RNA-binding domain named RAP (for RNA-binding domain abundant in Apicomplexans), shared by all six members of the family. Here we describe the role of one of the less characterized members, FASTKD3, in mitochondrial RNA metabolism. First, we show that, in contrast to FASTK, FASTKD2, and FASTKD5, FASTKD3 does not localize in mitochondrial RNA granules, which are sites of processing and maturation of mtRNAs and ribosome biogenesis. Second, we generated FASTKD3 homozygous knock-out cell lines by homologous recombination and observed that the absence of FASTKD3 resulted in increased steady-state levels and half-lives of a subset of mature mitochondrial mRNAs: ND2, ND3, CYTB, COX2, and ATP8/6. No aberrant processing of RNA precursors was observed. Rescue experiments demonstrated that RAP domain is required for FASTKD3 function in mRNA stability. Besides, we describe that FASTKD3 is required for efficient COX1 mRNA translation without altering mRNA levels, which results in a decrease in the steady-state levels of COX1 protein. This finding is associated with reduced mitochondrial complex IV assembly and activity. Our observations suggest that the function of this family of proteins goes beyond RNA processing and ribosome assembly and includes RNA stability and translation regulation within mitochondria.
Collapse
Affiliation(s)
- Erik Boehm
- From the Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - María Zornoza
- the Departamento de Biología, Histología y Farmacología, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
| | - Alexis A Jourdain
- From the Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Aitor Delmiro Magdalena
- Instituto de Investigación, Hospital Universitario 12 de Octubre (i+12), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid 28041, Spain
| | - Inés García-Consuegra
- Instituto de Investigación, Hospital Universitario 12 de Octubre (i+12), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid 28041, Spain
| | - Rebeca Torres Merino
- the Departamento de Biología, Histología y Farmacología, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
| | - Antonio Orduña
- the Departamento de Microbiología, Facultad de Medicina, Edificio de Ciencias de la Salud, Valladolid 47005, Spain, and
| | - Miguel A Martín
- Instituto de Investigación, Hospital Universitario 12 de Octubre (i+12), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid 28041, Spain
| | - Jean-Claude Martinou
- From the Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Miguel A De la Fuente
- the Departamento de Biología, Histología y Farmacología, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
| | - María Simarro
- the Departamento de Microbiología, Facultad de Medicina, Edificio de Ciencias de la Salud, Valladolid 47005, Spain, and .,the Departamento de Enfermería, Facultad de Enfermería, Edificio de Ciencias de la Salud, Avda Ramón y Cajal 7, Valladolid 47005, Spain
| |
Collapse
|
21
|
Jourdain AA, Boehm E, Maundrell K, Martinou JC. Mitochondrial RNA granules: Compartmentalizing mitochondrial gene expression. J Cell Biol 2016; 212:611-4. [PMID: 26953349 PMCID: PMC4792075 DOI: 10.1083/jcb.201507125] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/11/2016] [Indexed: 11/25/2022] Open
Abstract
In mitochondria, DNA replication, gene expression, and RNA degradation machineries coexist within a common nondelimited space, raising the question of how functional compartmentalization of gene expression is achieved. Here, we discuss the recently characterized “mitochondrial RNA granules,” mitochondrial subdomains with an emerging role in the regulation of gene expression.
Collapse
Affiliation(s)
- Alexis A Jourdain
- Department of Cell Biology, University of Geneva, 1211 Genève, Switzerland
| | - Erik Boehm
- Department of Cell Biology, University of Geneva, 1211 Genève, Switzerland
| | - Kinsey Maundrell
- Department of Cell Biology, University of Geneva, 1211 Genève, Switzerland
| | | |
Collapse
|
22
|
Brun T, Li N, Jourdain AA, Gaudet P, Duhamel D, Meyer J, Bosco D, Maechler P. Diabetogenic milieus induce specific changes in mitochondrial transcriptome and differentiation of human pancreatic islets. Hum Mol Genet 2015; 24:5270-84. [PMID: 26123492 DOI: 10.1093/hmg/ddv247] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/23/2015] [Indexed: 01/09/2023] Open
Abstract
In pancreatic β-cells, mitochondria play a central role in coupling glucose metabolism to insulin secretion. Chronic exposure of β-cells to metabolic stresses impairs their function and potentially induces apoptosis. Little is known on mitochondrial adaptation to metabolic stresses, i.e. high glucose, fatty acids or oxidative stress; being all highlighted in the pathogenesis of type 2 diabetes. Here, human islets were exposed for 3 days to 25 mm glucose, 0.4 mm palmitate, 0.4 mm oleate and transiently to H2O2. Culture at physiological 5.6 mm glucose served as no-stress control. Expression of mitochondrion-associated genes was quantified, including the transcriptome of mitochondrial inner membrane carriers. Targets of interest were further evaluated at the protein level. Three days after acute oxidative stress, no significant alteration in β-cell function or apoptosis was detected in human islets. Palmitate specifically increased expression of the pyruvate carriers MPC1 and MPC2, whereas the glutamate carrier GC1 and the aspartate/glutamate carrier AGC1 were down-regulated by palmitate and oleate, respectively. High glucose decreased mRNA levels of key transcription factors (HNF4A, IPF1, PPARA and TFAM) and energy-sensor SIRT1. High glucose also reduced expression of 11 mtDNA-encoded respiratory chain subunits. Interestingly, transcript levels of the carriers for aspartate/glutamate AGC2, malate DIC and malate/oxaloacetate/aspartate UCP2 were increased by high glucose, a profile suggesting important mitochondrial anaplerotic/cataplerotic activities and NADPH-generating shuttles. Chronic exposure to high glucose impaired glucose-stimulated insulin secretion, decreased insulin content, promoted caspase-3 cleavage and cell death, revealing glucotoxicity. Overall, expression profile of mitochondrion-associated genes was selectively modified by glucose, delineating a glucotoxic-specific signature.
Collapse
Affiliation(s)
- Thierry Brun
- Department of Cell Physiology and Metabolism, University of Geneva, Medical Center, Geneva, Switzerland,
| | - Ning Li
- Department of Cell Physiology and Metabolism, University of Geneva, Medical Center, Geneva, Switzerland
| | - Alexis A Jourdain
- Department of Cell Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - Pascale Gaudet
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland, University of Geneva, Medical Center, Geneva, Switzerland and
| | - Dominique Duhamel
- Department of Cell Physiology and Metabolism, University of Geneva, Medical Center, Geneva, Switzerland
| | - Jérémy Meyer
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva University Hospital, Geneva, Switzerland
| | - Domenico Bosco
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva University Hospital, Geneva, Switzerland
| | - Pierre Maechler
- Department of Cell Physiology and Metabolism, University of Geneva, Medical Center, Geneva, Switzerland,
| |
Collapse
|
23
|
Wilson WC, Hornig-Do HT, Bruni F, Chang JH, Jourdain AA, Martinou JC, Falkenberg M, Spåhr H, Larsson NG, Lewis RJ, Hewitt L, Baslé A, Cross HE, Tong L, Lebel RR, Crosby AH, Chrzanowska-Lightowlers ZMA, Lightowlers RN. A human mitochondrial poly(A) polymerase mutation reveals the complexities of post-transcriptional mitochondrial gene expression. Hum Mol Genet 2014; 23:6345-55. [PMID: 25008111 PMCID: PMC4222368 DOI: 10.1093/hmg/ddu352] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The p.N478D missense mutation in human mitochondrial poly(A) polymerase (mtPAP) has previously been implicated in a form of spastic ataxia with optic atrophy. In this study, we have investigated fibroblast cell lines established from family members. The homozygous mutation resulted in the loss of polyadenylation of all mitochondrial transcripts assessed; however, oligoadenylation was retained. Interestingly, this had differential effects on transcript stability that were dependent on the particular species of transcript. These changes were accompanied by a severe loss of oxidative phosphorylation complexes I and IV, and perturbation of de novo mitochondrial protein synthesis. Decreases in transcript polyadenylation and in respiratory chain complexes were effectively rescued by overexpression of wild-type mtPAP. Both mutated and wild-type mtPAP localized to the mitochondrial RNA-processing granules thereby eliminating mislocalization as a cause of defective polyadenylation. In vitro polyadenylation assays revealed severely compromised activity by the mutated protein, which generated only short oligo(A) extensions on RNA substrates, irrespective of RNA secondary structure. The addition of LRPPRC/SLIRP, a mitochondrial RNA-binding complex, enhanced activity of the wild-type mtPAP resulting in increased overall tail length. The LRPPRC/SLIRP effect although present was less marked with mutated mtPAP, independent of RNA secondary structure. We conclude that (i) the polymerase activity of mtPAP can be modulated by the presence of LRPPRC/SLIRP, (ii) N478D mtPAP mutation decreases polymerase activity and (iii) the alteration in poly(A) length is sufficient to cause dysregulation of post-transcriptional expression and the pathogenic lack of respiratory chain complexes.
Collapse
Affiliation(s)
- William C Wilson
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health
| | - Hue-Tran Hornig-Do
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health
| | - Francesco Bruni
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health
| | - Jeong Ho Chang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Alexis A Jourdain
- Department of Cell Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Jean-Claude Martinou
- Department of Cell Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Maria Falkenberg
- Department of Biochemistry and Cell Biology, University of Göteborg, Box 440, 40530 Göteborg, Sweden
| | - Henrik Spåhr
- Max Planck Institute for Biology of Ageing, Gleueler Strasse 50a, D-50931 Cologne, Germany
| | - Nils-Göran Larsson
- Max Planck Institute for Biology of Ageing, Gleueler Strasse 50a, D-50931 Cologne, Germany
| | | | | | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences and
| | - Harold E Cross
- Department of Ophthalmology, University of Arizona School of Medicine, Tucson, AZ 85711, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Robert R Lebel
- Center for Behavior, Development, and Genetics, Medical Genetics, SUNY Upstate Medical University, Syracuse, NY 13210, USA and
| | - Andrew H Crosby
- Molecular Genetics, University of Exeter Medical School, Royal Devon and Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Zofia M A Chrzanowska-Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Newcastle upon Tyne NE2 4HH, UK,
| | - Robert N Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Newcastle upon Tyne NE2 4HH, UK,
| |
Collapse
|