title: A comprehensive catalog of the lysine-acetylation targets in rice (Oryza sativa) based on proteomic analyses.
abstract: Lysine acetylation is a dynamic and reversible post-translational modification that plays an important role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation (Kac) sites and Kac proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings. About 42% of the sites were predicted to be localized in the chloroplast. Seven putative acetylation motifs were detected. Phenylalanine, located in both the upstream and downstream of the Kac sites, is the most conserved amino acid surrounding the regions. In addition, protein interaction network analysis revealed that a variety of signaling pathways are modulated by protein acetylation. KEGG pathway category enrichment analysis indicated that glyoxylate and dicarboxylate metabolism, carbon metabolism, and photosynthesis pathways are significantly enriched. Our results provide an in-depth understanding of the acetylome in rice seedlings, and the method described here will facilitate the systematic study of how Kac functions in growth, development, and abiotic and biotic stress responses in rice and other plants.
  
  
  CONCLUSIONS
  Rice is one of the most important crops consumption and is a model monocot for research. In this study, we combined a highly sensitive immune-affinity purification method (used pan anti-acetyl-lysine antibody conjugated agarose for immunoaffinity acetylated peptide enrichment) with high-resolution LC-MS/MS. In total, we identified 1337 Kac sites on 716 Kac proteins in rice cells. Bioinformatic analysis of the acetylome revealed that the acetylated proteins are involved in a variety of cellular functions and have diverse subcellular localizations. We also identified seven putative acetylation motifs in the acetylated proteins of rice. In addition, protein interaction network analysis revealed that a variety of signaling pathways were modulated by protein acetylation. KEGG pathway category enrichment analysis indicated that glyoxylate and dicarboxylate metabolism, carbon metabolism, and photosynthesis pathways were significantly enriched. To our knowledge, the number of Kac sites we identified was 23-times greater and the number of Kac proteins was 16-times greater than in a previous report. Our results provide an in-depth understanding of the acetylome in rice seedlings, and the method described here will facilitate the systematic study of how Kac functions in growth, development and responses to abiotic and biotic stresses in rice or other plants.
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Yehui
authors.initials: Y
authors.lastname: Xiong
authors.affiliation: Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Peng
authors.affiliation: Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China.
authors.forename: Zhongyi
authors.initials: Z
authors.lastname: Cheng
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: liuwende@caas.cn.
authors.forename: Wende
authors.initials: W
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA. Electronic address: wang.620@osu.edu.
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Wang
mesh_terms: D000107:Acetylation; D008239:Lysine / Q000378:metabolism; D012275:Oryza / Q000378:metabolism*; D010940:Plant Proteins / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics
chemical_list: D010940:Plant Proteins; D020543:Proteome; D008239:Lysine