Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds

• Published in: Scientific reports Vol. 7; no. 1; pp. 17486 - 11
• Main Authors: Meng, Xiaoxi, Xing, Shihai, Perez, Loida M., Peng, Xiaojun, Zhao, Qingyong, Redoña, Edilberto D., Wang, Cailin, Peng, Zhaohua
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13.12.2017; Nature Publishing Group
• Subjects: 631/337/458; 631/449/1659; 631/45/475; 82; 82/1; 82/58; 82/81; Biosynthesis; Deoxyribonucleic acid; DNA; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gluconeogenesis; Glycolysis; High-performance liquid chromatography; Humanities and Social Sciences; Lipid metabolism; Liquid chromatography; Lysine; Lysine - analogs & derivatives; Lysine - metabolism; multidisciplinary; Oryza - genetics; Oryza - growth & development; Oryza - metabolism; Oryza sativa; Peptides; Plant Proteins - genetics; Plant Proteins - metabolism; Post-translation; Protein biosynthesis; Protein Processing, Post-Translational; Protein turnover; Proteins; Proteome; Proteomes; Proteomics; Science; Science (multidisciplinary); Seeds; Seeds - genetics; Seeds - growth & development; Seeds - metabolism; Starch; Tricarboxylic acid cycle
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-17756-6

Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants. Functional annotation analyses indicated that a wide variety of vital biological processes were preferably targeted by lysine 2-hydroxyisobutyrylation, including glycolysis/gluconeogenesis, TCA cycle, starch biosynthesis, lipid metabolism, protein biosynthesis and processing. Our finding showed that 2-hydroxyisobutyrylated histone sites were conserved across plants, human, and mouse. A number of 2-hydroxyisobutyryl sites were shared with other lysine acylations in both histone and non-histone proteins. Comprehensive analysis of the lysine 2-hydroxyisobutyrylation sites illustrated that the modification sites were highly sequence specific with distinct motifs, and they had less surface accessibility than other lysine residues in the protein. Overall, our study provides the first systematic analysis of lysine 2-hydroxyisobutyrylation proteome in plants, and it serves as an important resource for future investigations of the regulatory mechanisms and functions of lysine 2-hydroxyisobutyrylation.