Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed

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.