First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L.

Protein acetylation and succinylation are the most crucial protein post-translational modifications (PTMs) involved in the regulation of plant growth and development. In this study, we present the first lysine-acetylation and lysine-succinylation proteome analysis of seedling leaves in Brachypodium distachyon L (Bd). Using high accuracy nano LC-MS/MS combined with affinity purification, we identified a total of 636 lysine-acetylated sites in 353 proteins and 605 lysine-succinylated sites in 262 proteins. These proteins participated in many biology processes, with various molecular functions. In particular, 119 proteins and 115 sites were found to be both acetylated and succinylated, simultaneously. Among the 353 acetylated proteins, 148 had acetylation orthologs in Oryza sativa L., Arabidopsis thaliana, Synechocystis sp. PCC 6803, and Glycine max L. Among the 262 succinylated proteins, 170 of them were found to have homologous proteins in Oryza sativa L., Escherichia coli, Sacchayromyces cerevisiae, or Homo sapiens. Motif-X analysis of the acetylated and succinylated sites identified two new acetylated motifs (K---K and K-I-K) and twelve significantly enriched succinylated motifs for the first time, which could serve as possible binding loci for future studies in plants. Our comprehensive dataset provides a promising starting point for further functional analysis of acetylation and succinylation in Bd and other plant species.

[1]  Robert D. Finn,et al.  Making your database available through Wikipedia: the pros and cons , 2011, Nucleic Acids Res..

[2]  Mingkun Yang,et al.  Acetylome analysis reveals the involvement of lysine acetylation in photosynthesis and carbon metabolism in the model cyanobacterium Synechocystis sp. PCC 6803. , 2015, Journal of proteome research.

[3]  M. Mann,et al.  Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.

[4]  J. Thelen,et al.  Initial description of the developing soybean seed protein Lys-N(ε)-acetylome. , 2014, Journal of proteomics.

[5]  P. Boyer.  The ATP synthase--a splendid molecular machine. , 1997, Annual review of biochemistry.

[6]  V. Allfrey,et al.  Chemical studies of histone acetylation. The occurrence of epsilon-N-acetyllysine in the f2a1 histone. , 1968, The Journal of biological chemistry.

[7]  Pierre Thibault,et al.  Large-scale analysis of lysine SUMOylation by SUMO remnant immunoaffinity profiling , 2014, Nature Communications.

[8]  M. Mann,et al.  Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions , 2009, Science.

[9]  Wei Liu,et al.  First succinyl-proteome profiling of extensively drug-resistant Mycobacterium tuberculosis revealed involvement of succinylation in cellular physiology. , 2015, Journal of proteome research.

[10]  Masasuke Yoshida,et al.  ATP synthase — a marvellous rotary engine of the cell , 2001, Nature Reviews Molecular Cell Biology.

[11]  D. Lv,et al.  Integrative network analysis of the signaling cascades in seedling leaves of bread wheat by large-scale phosphoproteomic profiling. , 2014, Journal of proteome research.

[12]  V. Vogel.  Journal club , 2010, Nature.

[13]  A. Wolfe,et al.  Bacterial protein acetylation: the dawning of a new age , 2010, Molecular microbiology.

[14]  J. Vogel,et al.  High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3 , 2008, Plant Cell Reports.

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

[16]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[17]  Zhongyi Cheng,et al.  Global analysis of lysine acetylation in strawberry leaves , 2015, Front. Plant Sci..

[18]  J. Thelen,et al.  Is Lys-Nɛ-acetylation the next big thing in post-translational modifications? , 2014, Trends in plant science.

[19]  Weibo Jin,et al.  Proteome-Wide Identification of Lysine Succinylation in the Proteins of Tomato (Solanum lycopersicum) , 2016, PloS one.

[20]  Zhongyi Cheng,et al.  Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed. , 2016, Journal of proteome research.

[21]  G. Mulliert,et al.  Involvement of two positively charged residues of Chlamydomonas reinhardtii glyceraldehyde-3-phosphate dehydrogenase in the assembly process of a bi-enzyme complex involved in CO2 assimilation. , 2004, European journal of biochemistry.

[22]  Sebastian A. Wagner,et al.  Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. , 2013, Cell reports.

[23]  Sang J. Chung,et al.  Acetylation of malate dehydrogenase 1 promotes adipogenic differentiation via activating its enzymatic activity , 2012, Journal of Lipid Research.

[24]  J. Seemann,et al.  The allocation of protein nitrogen in the photosynthetic apparatus: costs, consequences, and control. , 1989 .

[25]  Sai Guna Ranjan Gurazada,et al.  Genome sequencing and analysis of the model grass Brachypodium distachyon , 2010, Nature.

[26]  Yu Xue,et al.  CPLA 1.0: an integrated database of protein lysine acetylation , 2010, Nucleic Acids Res..

[27]  Michael L. Creech,et al.  Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.

[28]  V. Allfrey,et al.  Chemical Studies of Histone Acetylation THE OCCURRENCE OF ε-N-ACETYLLYSINE IN THE f2a1 HISTONE , 1968 .

[29]  Cyrus Martin,et al.  The diverse functions of histone lysine methylation , 2005, Nature Reviews Molecular Cell Biology.

[30]  V. Eijsink,et al.  Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface. , 2004, Journal of molecular biology.

[31]  L. Willmitzer,et al.  Reduction of the chloroplastic fructose‐1,6‐bisphosphatase in transgenic potato plants impairs photosynthesis and plant growth , 1994 .

[32]  S. Gygi,et al.  An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets , 2005, Nature Biotechnology.

[33]  T. Hunter.  The age of crosstalk: phosphorylation, ubiquitination, and beyond. , 2007, Molecular cell.

[34]  Zhongyi Cheng,et al.  Succinylome Analysis Reveals the Involvement of Lysine Succinylation in Metabolism in Pathogenic Mycobacterium tuberculosis* , 2015, Molecular & Cellular Proteomics.

[35]  S. Jaffrey,et al.  Profiling lysine ubiquitination by selective enrichment of ubiquitin remnant-containing peptides. , 2014, Methods in molecular biology.

[36]  J. Minagawa.  State transitions--the molecular remodeling of photosynthetic supercomplexes that controls energy flow in the chloroplast. , 2011, Biochimica et biophysica acta.

[37]  F. Tan,et al.  Global Analysis of Lysine Acetylation Suggests the Involvement of Protein Acetylation in Diverse Biological Processes in Rice (Oryza sativa) , 2014, PloS one.

[38]  J. Thelen,et al.  In silico analysis of protein Lys-N𝜀-acetylation in plants , 2014, Front. Plant Sci..

[39]  D. Lv,et al.  N-linked glycoproteome profiling of seedling leaf in Brachypodium distachyon L. , 2015, Journal of proteome research.

[40]  F. Carrari,et al.  Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport. , 2004, Current opinion in plant biology.

[41]  Matthew J. Rardin,et al.  SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. , 2013, Cell metabolism.

[42]  Wafa Skalli,et al.  Dynamic Three-Dimensional Shoulder Mri during Active Motion for Investigation of Rotator Cuff Diseases , 2016, PloS one.

[43]  J. Berry,et al.  A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species , 1980, Planta.

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

[45]  Paul Horton,et al.  Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .

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

[47]  Jianyi Pan,et al.  Global Analysis of Protein Lysine Succinylation Profiles and Their Overlap with Lysine Acetylation in the Marine Bacterium Vibrio parahemolyticus. , 2015, Journal of proteome research.

[48]  D J Nicholls,et al.  Malate dehydrogenase: A model for structure, evolution, and catalysis , 1994, Protein science : a publication of the Protein Society.

[49]  R. Appels,et al.  Proteome and Phosphoproteome Characterization Reveals New Response and Defense Mechanisms of Brachypodium distachyon Leaves under Salt Stress , 2013, Molecular & Cellular Proteomics.

[50]  L. Miguet,et al.  Proteins of Diverse Function and Subcellular Location Are Lysine Acetylated in Arabidopsis1[W][OA] , 2011, Plant Physiology.

[51]  Mayandi Sivaguru,et al.  Lysine Acetylation Is a Widespread Protein Modification for Diverse Proteins in Arabidopsis1[C][W][OA] , 2011, Plant Physiology.

[52]  Eberhard Backus,et al.  Unanswered Questions. , 2017, Deutsches Arzteblatt international.

[53]  Jenn-Kang Hwang,et al.  Prediction of protein subcellular localization , 2006, Proteins.

[54]  Y. Poirier,et al.  The protein acetylome and the regulation of metabolism. , 2012, Trends in plant science.

[55]  Jay J Thelen,et al.  Modulation of Protein Phosphorylation, N-Glycosylation and Lys-Acetylation in Grape (Vitis vinifera) Mesocarp and Exocarp Owing to Lobesia botrana Infection* , 2012, Molecular & Cellular Proteomics.

[56]  Guo-Ping Zhao,et al.  Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux , 2010, Science.

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

[58]  Hening Lin,et al.  Identification of Lysine Succinylation Substrates and the Succinylation Regulatory Enzyme CobB in Escherichia coli* , 2013, Molecular & Cellular Proteomics.

[59]  R. Houtz,et al.  Co- and post-translational modifications in Rubisco: unanswered questions. , 2007, Journal of experimental botany.

[60]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[61]  J. Draper,et al.  Brachypodium distachyon. A new model system for functional genomics in grasses. , 2001, Plant physiology.

[62]  Joshua D. Jones,et al.  Protein acetylation in prokaryotes , 2011, Proteomics.

[63]  M. Baly.  Dawning of a new age. , 1998, Nursing Standard.

[64]  S. Shiu,et al.  Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. , 2012, The Plant journal : for cell and molecular biology.

[65]  L. A. Kane,et al.  Post-translational modifications of ATP synthase in the heart: biology and function , 2009, Journal of bioenergetics and biomembranes.