title: Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed.
abstract: Regulation of rice seed germination has been shown to mainly occur at post-transcriptional levels, of which the changes on proteome status is a major one. Lysine acetylation and succinylation are two prevalent protein post-translational modifications (PTMs) involved in multiple biological processes, especially for metabolism regulation. To investigate the potential mechanism controlling metabolism regulation in rice seed germination, we performed the lysine acetylation and succinylation analyses simultaneously. Using high-accuracy nano-LC-MS/MS in combination with the enrichment of lysine acetylated or succinylated peptides from digested embryonic proteins of 24 h after imbibition (HAI) rice seed, a total of 699 acetylated sites from 389 proteins and 665 succinylated sites from 261 proteins were identified. Among these modified lysine sites, 133 sites on 78 proteins were commonly modified by two PTMs. The overlapped PTM sites were more likely to be in polar acidic/basic amino acid regions and exposed on the protein surface. Both of the acetylated and succinylated proteins cover nearly all aspects of cellular functions. Ribosome complex and glycolysis/gluconeogenesis-related proteins were significantly enriched in both acetylated and succinylated protein profiles through KEGG enrichment and protein-protein interaction network analyses. The acetyl-CoA and succinyl-CoA metabolism-related enzymes were found to be extensively modified by both modifications, implying the functional interaction between the two PTMs. This study provides a rich resource to examine the modulation of the two PTMs on the metabolism pathway and other biological processes in germinating rice seed.
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.
authors.forename: Dongli
authors.initials: D
authors.lastname: He
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.|University of Chinese Academy of Sciences , Beijing 100049, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.|University of Chinese Academy of Sciences , Beijing 100049, China.
authors.forename: Rebecca Njeri
authors.initials: RN
authors.lastname: Damaris
authors.affiliation: Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China.
authors.forename: Xingling
authors.initials: X
authors.lastname: Yi
authors.affiliation: Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China.
authors.forename: Zhongyi
authors.initials: Z
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.
authors.forename: Pingfang
authors.initials: P
authors.lastname: Yang
mesh_terms: D000107:Acetylation; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D063990:Gene Ontology; D018525:Germination; D008239:Lysine / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D012275:Oryza / Q000378:metabolism*; D010940:Plant Proteins / Q000378:metabolism*; D060066:Protein Interaction Maps; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000378:metabolism*; D036226:Seedlings / Q000378:metabolism; D012639:Seeds / Q000378:metabolism*; D019802:Succinic Acid / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D020543:Proteome; D019802:Succinic Acid; D008239:Lysine
keywords: acetyllysine; metabolism; post-translational modification; rice; seed germination; succinyllysine