Lysine Malonylation Is Elevated in Type 2 Diabetic Mouse Models and Enriched in Metabolic Associated Proteins*

Protein lysine malonylation, a newly identified protein post-translational modification (PTM), has been proved to be evolutionarily conserved and is present in both eukaryotic and prokaryotic cells. However, its potential roles associated with human diseases remain largely unknown. In the present study, we observed an elevated lysine malonylation in a screening of seven lysine acylations in liver tissues of db/db mice, which is a typical model of type 2 diabetes. We also detected an elevated lysine malonylation in ob/ob mice, which is another model of type 2 diabetes. We then performed affinity enrichment coupled with proteomic analysis on liver tissues of both wild-type (wt) and db/db mice and identified a total of 573 malonylated lysine sites from 268 proteins. There were more malonylated lysine sites and proteins in db/db than in wt mice. Five proteins with elevated malonylation were verified by immunoprecipitation coupled with Western blot analysis. Bioinformatic analysis of the proteomic results revealed the enrichment of malonylated proteins in metabolic pathways, especially those involved in glucose and fatty acid metabolism. In addition, the biological role of lysine malonylation was validated in an enzyme of the glycolysis pathway. Together, our findings support a potential role of protein lysine malonylation in type 2 diabetes with possible implications for its therapy in the future.

[1]  Yixue Li,et al.  Regulation of Cellular Metabolism by Protein Lysine Acetylation , 2010, Science.

[2]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[3]  D. Coleman Obesity syndromes in mice. , 1981 .

[4]  C. Ahn,et al.  Rosiglitazone and fenofibrate improve insulin sensitivity of pre-diabetic OLETF rats by reducing malonyl-CoA levels in the liver and skeletal muscle. , 2009, Life sciences.

[5]  J. Clore,et al.  Glucose-6-phosphatase flux in vitro is increased in type 2 diabetes. , 2000, Diabetes.

[6]  Kim A Connelly,et al.  Diabetes Induces Lysine Acetylation of Intermediary Metabolism Enzymes in the Kidney , 2014, Diabetes.

[7]  Gary D. Bader,et al.  An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.

[8]  Shasha Wei,et al.  Chronic high glucose induced INS‐1β cell mitochondrial dysfunction: A comparative mitochondrial proteome with SILAC , 2013, Proteomics.

[9]  G. R. Wagner,et al.  Widespread and Enzyme-independent Nϵ-Acetylation and Nϵ-Succinylation of Proteins in the Chemical Conditions of the Mitochondrial Matrix*♦ , 2013, The Journal of Biological Chemistry.

[10]  Anushya Muruganujan,et al.  Large-scale gene function analysis with the PANTHER classification system , 2013, Nature Protocols.

[11]  J. Auwerx,et al.  Metabolic Characterization of a Sirt5 deficient mouse model , 2013, Scientific Reports.

[12]  F M Matschinsky,et al.  Familial hyperinsulinism caused by an activating glucokinase mutation. , 1998, The New England journal of medicine.

[13]  L. Vitagliano,et al.  Functional and molecular modelling studies of two hereditary fructose intolerance-causing mutations at arginine 303 in human liver aldolase. , 2000, The Biochemical journal.

[14]  Yingming Zhao,et al.  SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. , 2013, Molecular cell.

[15]  R. Nussinov,et al.  Allosteric post-translational modification codes. , 2012, Trends in biochemical sciences.

[16]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[17]  Huadong Liu,et al.  Molecular Characterization of Propionyllysines in Non-histone Proteins *S , 2009, Molecular & Cellular Proteomics.

[18]  David Millington,et al.  Hepatic expression of malonyl-CoA decarboxylase reverses muscle, liver and whole-animal insulin resistance , 2004, Nature Medicine.

[19]  Zhihong Zhang,et al.  Identification of lysine succinylation as a new post-translational modification. , 2011, Nature chemical biology.

[20]  M. Vorgerd,et al.  Deficiency of phosphofructo-1-kinase/muscle subtype in humans impairs insulin secretion and causes insulin resistance. , 1997, The Journal of clinical investigation.

[21]  Xiang David Li,et al.  A chemical probe for lysine malonylation. , 2013, Angewandte Chemie.

[22]  D. Danley,et al.  Discovery of a human liver glycogen phosphorylase inhibitor that lowers blood glucose in vivo. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[23]  D. Coleman Diabetes-Obesity Syndromes in Mice , 1982, Diabetes.

[24]  T. Wei,et al.  Hydrogen peroxide impairs autophagic flux in a cell model of nonalcoholic fatty liver disease. , 2013, Biochemical and biophysical research communications.

[25]  G. R. Wagner,et al.  WIDESPREAD AND ENZYMEINDEPENDENT N EPSILON-ACETYLATION AND N?-SUCCINYLATION OF PROTEINS IN THE CHEMICAL CONDITIONS OF THE MITOCHONDRIAL MATRIX , 2013 .

[26]  Christodoulos A. Floudas,et al.  Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database , 2011, Scientific reports.

[27]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[28]  Sylvie Garneau-Tsodikova,et al.  Protein posttranslational modifications: the chemistry of proteome diversifications. , 2005, Angewandte Chemie.

[29]  J. Olefsky,et al.  Increased Malonyl-CoA Levels in Muscle From Obese and Type 2 Diabetic Subjects Lead to Decreased Fatty Acid Oxidation and Increased Lipogenesis; Thiazolidinedione Treatment Reverses These Defects , 2006, Diabetes.

[30]  Zhike Lu,et al.  Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification , 2011, Cell.

[31]  Functional and molecular modelling studies of two hereditary fructose intolerance-causing mutations at arginine 303 in human liver aldolase. , 2000 .

[32]  N. Barzilai,et al.  Induction of Hepatic Glucose-6-Phosphatase Gene Expression by Lipid Infusion , 1997, Diabetes.

[33]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[34]  Hsien-Da Huang,et al.  dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications , 2012, Nucleic Acids Res..

[35]  Yingming Zhao,et al.  Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. , 2014, Cell metabolism.

[36]  Yi Tang,et al.  Lysine Propionylation and Butyrylation Are Novel Post-translational Modifications in Histones*S , 2007, Molecular & Cellular Proteomics.

[37]  J. Beckmann,et al.  Close linkage of glucokinase locus on chromosome 7p to early-onset non-insulin-dependent diabetes mellitus , 1992, Nature.

[38]  Yi Zhang,et al.  The First Identification of Lysine Malonylation Substrates and Its Regulatory Enzyme* , 2011, Molecular & Cellular Proteomics.