1
|
Zhang B, Mullmann J, Ludewig AH, Fernandez IR, Bales TR, Weiss RS, Schroeder FC. Acylspermidines are conserved mitochondrial sirtuin-dependent metabolites. Nat Chem Biol 2024; 20:812-822. [PMID: 38167917 DOI: 10.1038/s41589-023-01511-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024]
Abstract
Sirtuins are nicotinamide adenine dinucleotide (NAD+)-dependent protein lysine deacylases regulating metabolism and stress responses; however, characterization of the removed acyl groups and their downstream metabolic fates remains incomplete. Here we employed untargeted comparative metabolomics to reinvestigate mitochondrial sirtuin biochemistry. First, we identified N-glutarylspermidines as metabolites downstream of the mitochondrial sirtuin SIR-2.3 in Caenorhabditis elegans and demonstrated that SIR-2.3 functions as a lysine deglutarylase and that N-glutarylspermidines can be derived from O-glutaryl-ADP-ribose. Subsequent targeted analysis of C. elegans, mouse and human metabolomes revealed a chemically diverse range of N-acylspermidines, and formation of N-succinylspermidines and/or N-glutarylspermidines was observed downstream of mammalian mitochondrial sirtuin SIRT5 in two cell lines, consistent with annotated functions of SIRT5. Finally, N-glutarylspermidines were found to adversely affect C. elegans lifespan and mammalian cell proliferation. Our results indicate that N-acylspermidines are conserved metabolites downstream of mitochondrial sirtuins that facilitate annotation of sirtuin enzymatic activities in vivo and may contribute to sirtuin-dependent phenotypes.
Collapse
Affiliation(s)
- Bingsen Zhang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - James Mullmann
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
- Department of Molecular Medicine, Cornell University, Ithaca, NY, USA
| | | | - Irma R Fernandez
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Tyler R Bales
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA.
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
2
|
Mailloux RJ. The emerging importance of the α-keto acid dehydrogenase complexes in serving as intracellular and intercellular signaling platforms for the regulation of metabolism. Redox Biol 2024; 72:103155. [PMID: 38615490 PMCID: PMC11021975 DOI: 10.1016/j.redox.2024.103155] [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: 03/12/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024] Open
Abstract
The α-keto acid dehydrogenase complex (KDHc) class of mitochondrial enzymes is composed of four members: pyruvate dehydrogenase (PDHc), α-ketoglutarate dehydrogenase (KGDHc), branched-chain keto acid dehydrogenase (BCKDHc), and 2-oxoadipate dehydrogenase (OADHc). These enzyme complexes occupy critical metabolic intersections that connect monosaccharide, amino acid, and fatty acid metabolism to Krebs cycle flux and oxidative phosphorylation (OxPhos). This feature also imbues KDHc enzymes with the heightened capacity to serve as platforms for propagation of intracellular and intercellular signaling. KDHc enzymes serve as a source and sink for mitochondrial hydrogen peroxide (mtH2O2), a vital second messenger used to trigger oxidative eustress pathways. Notably, deactivation of KDHc enzymes through reversible oxidation by mtH2O2 and other electrophiles modulates the availability of several Krebs cycle intermediates and related metabolites which serve as powerful intracellular and intercellular messengers. The KDHc enzymes also play important roles in the modulation of mitochondrial metabolism and epigenetic programming in the nucleus through the provision of various acyl-CoAs, which are used to acylate proteinaceous lysine residues. Intriguingly, nucleosomal control by acylation is also achieved through PDHc and KGDHc localization to the nuclear lumen. In this review, I discuss emerging concepts in the signaling roles fulfilled by the KDHc complexes. I highlight their vital function in serving as mitochondrial redox sensors and how this function can be used by cells to regulate the availability of critical metabolites required in cell signaling. Coupled with this, I describe in detail how defects in KDHc function can cause disease states through the disruption of cell redox homeodynamics and the deregulation of metabolic signaling. Finally, I propose that the intracellular and intercellular signaling functions of the KDHc enzymes are controlled through the reversible redox modification of the vicinal lipoic acid thiols in the E2 subunit of the complexes.
Collapse
Affiliation(s)
- Ryan J Mailloux
- School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.
| |
Collapse
|
3
|
Minogue E, Cunha PP, Wadsworth BJ, Grice GL, Sah-Teli SK, Hughes R, Bargiela D, Quaranta A, Zurita J, Antrobus R, Velica P, Barbieri L, Wheelock CE, Koivunen P, Nathan JA, Foskolou IP, Johnson RS. Glutarate regulates T cell metabolism and anti-tumour immunity. Nat Metab 2023; 5:1747-1764. [PMID: 37605057 PMCID: PMC10590756 DOI: 10.1038/s42255-023-00855-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/03/2023] [Indexed: 08/23/2023]
Abstract
T cell function and fate can be influenced by several metabolites: in some cases, acting through enzymatic inhibition of α-ketoglutarate-dependent dioxygenases, in others, through post-translational modification of lysines in important targets. We show here that glutarate, a product of amino acid catabolism, has the capacity to do both, and has potent effects on T cell function and differentiation. We found that glutarate exerts those effects both through α-ketoglutarate-dependent dioxygenase inhibition, and through direct regulation of T cell metabolism via glutarylation of the pyruvate dehydrogenase E2 subunit. Administration of diethyl glutarate, a cell-permeable form of glutarate, alters CD8+ T cell differentiation and increases cytotoxicity against target cells. In vivo administration of the compound is correlated with increased levels of both peripheral and intratumoural cytotoxic CD8+ T cells. These results demonstrate that glutarate is an important regulator of T cell metabolism and differentiation with a potential role in the improvement of T cell immunotherapy.
Collapse
Affiliation(s)
- Eleanor Minogue
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Pedro P Cunha
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Brennan J Wadsworth
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Guinevere L Grice
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Shiv K Sah-Teli
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - Rob Hughes
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - David Bargiela
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Alessandro Quaranta
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Javier Zurita
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Pedro Velica
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Barbieri
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Iosifina P Foskolou
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Randall S Johnson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
4
|
Scumaci D, Zheng Q. Epigenetic meets metabolism: novel vulnerabilities to fight cancer. Cell Commun Signal 2023; 21:249. [PMID: 37735413 PMCID: PMC10512595 DOI: 10.1186/s12964-023-01253-7] [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: 06/24/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
Histones undergo a plethora of post-translational modifications (PTMs) that regulate nucleosome and chromatin dynamics and thus dictate cell fate. Several evidences suggest that the accumulation of epigenetic alterations is one of the key driving forces triggering aberrant cellular proliferation, invasion, metastasis and chemoresistance pathways. Recently a novel class of histone "non-enzymatic covalent modifications" (NECMs), correlating epigenome landscape and metabolic rewiring, have been described. These modifications are tightly related to cell metabolic fitness and are able to impair chromatin architecture. During metabolic reprogramming, the high metabolic flux induces the accumulation of metabolic intermediate and/or by-products able to react with histone tails altering epigenome homeostasis. The accumulation of histone NECMs is a damaging condition that cancer cells counteracts by overexpressing peculiar "eraser" enzymes capable of removing these modifications preserving histones architecture. In this review we explored the well-established NECMs, emphasizing the role of their corresponding eraser enzymes. Additionally, we provide a parterre of drugs aiming to target those eraser enzymes with the intent to propose novel routes of personalized medicine based on the identification of epi-biomarkers which might be selectively targeted for therapy. Video Abstract.
Collapse
Affiliation(s)
- Domenica Scumaci
- Research Center On Advanced Biochemistry and Molecular Biology, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
5
|
Pokrovsky VS, Abo Qoura L, Morozova E, Bunik VI. Predictive markers for efficiency of the amino-acid deprivation therapies in cancer. Front Med (Lausanne) 2022; 9:1035356. [PMID: 36405587 PMCID: PMC9669297 DOI: 10.3389/fmed.2022.1035356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Amino acid deprivation therapy (AADT) is a promising strategy for developing novel anticancer treatments, based on variations in metabolism of healthy and malignant cells. L-asparaginase was the first amino acid-degrading enzyme that received FDA approval for the treatment of acute lymphoblastic leukemia (ALL). Arginase and arginine deiminase were effective in clinical trials for the treatment of metastatic melanomas and hepatocellular carcinomas. Essential dependence of certain cancer cells on methionine explains the anticancer efficacy of methionine-g-lyase. Along with significant progress in identification of metabolic vulnerabilities of cancer cells, new amino acid-cleaving enzymes appear as promising agents for cancer treatment: lysine oxidase, tyrosine phenol-lyase, cysteinase, and phenylalanine ammonia-lyase. However, sensitivity of specific cancer cell types to these enzymes differs. Hence, search for prognostic and predictive markers for AADT and introduction of the markers into clinical practice are of great importance for translational medicine. As specific metabolic pathways in cancer cells are determined by the enzyme expression, some of these enzymes may define the sensitivity to AADT. This review considers the known predictors for efficiency of AADT, emphasizing the importance of knowledge on cancer-specific amino acid significance for such predictions.
Collapse
Affiliation(s)
- Vadim S. Pokrovsky
- Laboratory of Experimental Oncology, Research Institute of Molecular and Cellular Medicine, People’s Friendship University of Russia (RUDN University), Moscow, Russia
- Laboratory of Combined Treatment, N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of Russian Federation, Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
- *Correspondence: Vadim S. Pokrovsky,
| | - Louay Abo Qoura
- Laboratory of Experimental Oncology, Research Institute of Molecular and Cellular Medicine, People’s Friendship University of Russia (RUDN University), Moscow, Russia
| | - Elena Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Victoria I. Bunik
- A.N. Belozersky Institute of Physicochemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Department of Biological Chemistry, Sechenov First Moscow State Medical University, Moscow, Russia
| |
Collapse
|
6
|
McGinnis CD, Jennings EQ, Harris PS, Galligan JJ, Fritz KS. Biochemical Mechanisms of Sirtuin-Directed Protein Acylation in Hepatic Pathologies of Mitochondrial Dysfunction. Cells 2022; 11:cells11132045. [PMID: 35805129 PMCID: PMC9266223 DOI: 10.3390/cells11132045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial protein acetylation is associated with a host of diseases including cancer, Alzheimer’s, and metabolic syndrome. Deciphering the mechanisms regarding how protein acetylation contributes to disease pathologies remains difficult due to the complex diversity of pathways targeted by lysine acetylation. Specifically, protein acetylation is thought to direct feedback from metabolism, whereby nutritional status influences mitochondrial pathways including beta-oxidation, the citric acid cycle, and the electron transport chain. Acetylation provides a crucial connection between hepatic metabolism and mitochondrial function. Dysregulation of protein acetylation throughout the cell can alter mitochondrial function and is associated with numerous liver diseases, including non-alcoholic and alcoholic fatty liver disease, steatohepatitis, and hepatocellular carcinoma. This review introduces biochemical mechanisms of protein acetylation in the regulation of mitochondrial function and hepatic diseases and offers a viewpoint on the potential for targeted therapies.
Collapse
Affiliation(s)
- Courtney D. McGinnis
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (C.D.M.); (P.S.H.)
| | - Erin Q. Jennings
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA; (E.Q.J.); (J.J.G.)
| | - Peter S. Harris
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (C.D.M.); (P.S.H.)
| | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA; (E.Q.J.); (J.J.G.)
| | - Kristofer S. Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (C.D.M.); (P.S.H.)
- Correspondence:
| |
Collapse
|