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.
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- Authors
- He, D., Wang, Q., Li, M., Damaris, R. N., Yi, X., Cheng, Z., & Yang, P.
- Affiliations
- Chinese Academy of Sciences (CN)
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd., Hangzhou 310018, China
- Corresponding author
- Yang, Pingfang
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2016-01-28
- Volume
- 15
- Issue
- 3
- Pages
- 879-890
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2235305215
- Cited by
- 124
- References
- 58
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 7 · 2023: 4 · 2022: 17 · 2021: 14 · 2020: 12 · 2019: 18 · 2018: 12 · 2017: 22 · 2016: 9
- FWCI
- 23.81
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (31101213, 31271805)
- Chinese Academy of Sciences
- Central People's Government of the People's Republic of China (SAJC201324)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Seed Germination and Physiology
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Keywords
- lysine acetylation, lysine succinylation, post-translational modification, rice seed germination, seed embryo, metabolic regulation, acetyl-CoA metabolism, glycolysis/gluconeogenesis
- MeSH terms
- Acetylation, Amino Acid Sequence, Lysine, Plant Proteins, Protein Processing, Post-Translational, Oryza, Seeds, Germination, Succinic Acid, Proteome, Amino Acid Motifs, Seedlings, Metabolic Networks and Pathways, Protein Interaction Maps, Gene Ontology
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