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WDR76 is a RAS binding protein that functions as a tumor suppressor via RAS degradation. Nat Commun 2019; 10:295. [PMID: 30655611 PMCID: PMC6336889 DOI: 10.1038/s41467-018-08230-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/19/2018] [Indexed: 12/15/2022] Open
Abstract
Stability regulation of RAS that can affect its activity, in addition to the oncogenic mutations, occurs in human cancer. However, the mechanisms for stability regulation of RAS involved in their activity and its roles in tumorigenesis are poorly explored. Here, we identify WD40-repeat protein 76 (WDR76) as one of the HRAS binding proteins using proteomic analyses of hepatocellular carcinomas (HCC) tissue. WDR76 plays a role as an E3 linker protein and mediates the polyubiquitination-dependent degradation of RAS. WDR76-mediated RAS destabilization results in the inhibition of proliferation, transformation, and invasion of liver cancer cells. WDR76-/- mice are more susceptible to diethylnitrosamine-induced liver carcinogenesis. Liver-specific WDR76 induction destabilizes Ras and markedly reduces tumorigenesis in HRasG12V mouse livers. The clinical relevance of RAS regulation by WDR76 is indicated by the inverse correlation of their expressions in HCC tissues. Our study demonstrates that WDR76 functions as a tumor suppressor via RAS degradation.
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Hwang IW, Makishima Y, Suzuki T, Kato T, Park S, Terzic A, Chung SK, Park EY. Phosphorylation of Ser-204 and Tyr-405 in human malonyl-CoA decarboxylase expressed in silkworm Bombyx mori regulates catalytic decarboxylase activity. Appl Microbiol Biotechnol 2015; 99:8977-86. [PMID: 26004805 DOI: 10.1007/s00253-015-6687-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/13/2015] [Accepted: 05/08/2015] [Indexed: 11/26/2022]
Abstract
Decarboxylation of malonyl-CoA to acetyl-CoA by malonyl-CoA decarboxylase (MCD; EC 4.1.1.9) is a vital catalytic reaction of lipid metabolism. While it is established that phosphorylation of MCD modulates the enzymatic activity, the specific phosphorylation sites associated with the catalytic function have not been documented due to lack of sufficient production of MCD with proper post-translational modifications. Here, we used the silkworm-based Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid system to express human MCD (hMCD) and mapped phosphorylation effects on enzymatic function. Purified MCD from silkworm displayed post-translational phosphorylation and demonstrated coherent enzymatic activity with high yield (-200 μg/silkworm). Point mutations in putative phosphorylation sites, Ser-204 or Tyr-405 of hMCD, identified by bioinformatics and proteomics analyses reduced the catalytic activity, underscoring the functional significance of phosphorylation in modulating decarboxylase-based catalysis. Identified phosphorylated residues are distinct from the decarboxylation catalytic site, implicating a phosphorylation-induced global conformational change of MCD as responsible in altering catalytic function. We conclude that phosphorylation of Ser-204 and Tyr-405 regulates the decarboxylase function of hMCD leveraging the silkworm-based BmNPV bacmid expression system that offers a fail-safe eukaryotic production platform implementing proper post-translational modification such as phosphorylation.
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Affiliation(s)
- In-Wook Hwang
- Laboratory of Biotechnology, Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Yu Makishima
- Laboratory of Biotechnology, Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Tomohiro Suzuki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Tatsuya Kato
- Laboratory of Biotechnology, Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Sungjo Park
- Center for Regenerative Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Marriott Heart Disease Research Program, Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Medical Genetics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Andre Terzic
- Center for Regenerative Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Marriott Heart Disease Research Program, Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Medical Genetics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Shin-Kyo Chung
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 702-701, Republic of Korea.
| | - Enoch Y Park
- Laboratory of Biotechnology, Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Laboratory of Biotechnology, Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka, 422-8529, Japan.
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Laurent G, German NJ, Saha AK, de Boer VCJ, Davies M, Koves TR, Dephoure N, Fischer F, Boanca G, Vaitheesvaran B, Lovitch SB, Sharpe AH, Kurland IJ, Steegborn C, Gygi SP, Muoio DM, Ruderman NB, Haigis MC. SIRT4 coordinates the balance between lipid synthesis and catabolism by repressing malonyl CoA decarboxylase. Mol Cell 2013; 50:686-98. [PMID: 23746352 DOI: 10.1016/j.molcel.2013.05.012] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/22/2013] [Accepted: 05/02/2013] [Indexed: 12/01/2022]
Abstract
Lipid metabolism is tightly controlled by the nutritional state of the organism. Nutrient-rich conditions increase lipogenesis, whereas nutrient deprivation promotes fat oxidation. In this study, we identify the mitochondrial sirtuin, SIRT4, as a regulator of lipid homeostasis. SIRT4 is active in nutrient-replete conditions to repress fatty acid oxidation while promoting lipid anabolism. SIRT4 deacetylates and inhibits malonyl CoA decarboxylase (MCD), an enzyme that produces acetyl CoA from malonyl CoA. Malonyl CoA provides the carbon skeleton for lipogenesis and also inhibits fat oxidation. Mice lacking SIRT4 display elevated MCD activity and decreased malonyl CoA in skeletal muscle and white adipose tissue. Consequently, SIRT4 KO mice display deregulated lipid metabolism, leading to increased exercise tolerance and protection against diet-induced obesity. In sum, this work elucidates SIRT4 as an important regulator of lipid homeostasis, identifies MCD as a SIRT4 target, and deepens our understanding of the malonyl CoA regulatory axis.
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Affiliation(s)
- Gaëlle Laurent
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Froese DS, Forouhar F, Tran TH, Vollmar M, Kim YS, Lew S, Neely H, Seetharaman J, Shen Y, Xiao R, Acton TB, Everett JK, Cannone G, Puranik S, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Montelione GT, Oppermann U, Yue WW, Tong L. Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations. Structure 2013; 21:1182-92. [PMID: 23791943 PMCID: PMC3701320 DOI: 10.1016/j.str.2013.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 01/17/2023]
Abstract
Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design. Structures of human and bacterial MCDs were determined at up to 2.3 Å resolution Distinct tetrameric and dimeric MCD oligomerizations were observed Unexpected homology to the GNAT superfamily gives insights into catalytic mechanism The structures provide the molecular basis for the disease-causing mutations in MCD
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Affiliation(s)
- D Sean Froese
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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Reisner HM, Lundblad RL. Identifying residues in antigenic determinants by chemical modification. Methods Mol Biol 2009; 524:103-117. [PMID: 19377940 DOI: 10.1007/978-1-59745-450-6_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemical modification of the side chains of amino acid residues was one of the first methods developed to investigate epitopes in protein antigens. The principle of the method is that alteration of the structure of a key residue of an epitope by a chemical modification will alter reactivity with antibody by affecting either specificity or avidity or both. Chemical modification has the advantage that it can be applied to discontinuous as well as continuous epitopes and may be of value in identifying cryptic epitopes. We consider here the several recent studies that have applied site-specific chemical modification to the identification of epitopes on antigens, including the use of formaldehyde, glutaraldehyde, and acid anhydrides, to produce allergoids where determinants important to reaction with IgE are modified but the ability to elicit an IgG response is retained. It is noteworthy that modification of amino groups with charge reversal appears to be the most useful approach. The approach to the use of site-specific chemical modification as a tool for the study of protein function is discussed, and emphasis is placed on the necessity to (1) validate the specificity of modification and (2) assess potential conformational change that may occur secondary to modification. Finally, a list of chemical reagents used for protein modification is presented, together with properties and references to use.
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Affiliation(s)
- Howard M Reisner
- Department of Pathology and Laboratory Medicine, University of North Carolina, PO Box 16695, Chapel Hill, NC 27516, USA
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