Abstract
BackgroundLysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed.ResultsIn this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalk of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms.ConclusionsIn summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.
Highlights
Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals
Through the crosstalk of the 2-hydroxyisobutyrylome, crotonylome, and acetylome in rice leaves, we found that these acylations have overlapping modified proteins and sites to participate in regulatory metabolisms, and have significant distinctions to execute diverse protein functions
Proteome-Wide Analyses Revealed a Large Lysine 2Hydroxyisobutyrylome in Rice Khib has been proved to be involved in diverse biological processes in eukaryotes and prokaryotes (Yu et al 2017; Tan et al 2011; Dai et al 2014; Dong et al 2018)
Summary
Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. Lysine 2-hydroxyisobutyrylation (Khib) is a novel PTM first identified in human and mouse proteins as a widely distributed active histone mark (Dai et al 2014) In this pioneering study, histone Khib was shown to have a different genomic distribution from those of histone Kac or Kcr during male germ cell differentiation. Khib in non-histones has been involved in diverse biological processes, including the tricarboxylic acid cycle, glycolysis/gluconeogenesis, and especially enriched in mitochondrial proteins within energy metabolic networks (Huang et al 2018a; Wu et al 2018; Huang et al 2018b) These findings indicate that Khib has regulatory functions on cellular processes and gene transcriptional activity. The regulatory mechanisms of this new PTM in diverse biological processes are not well understood for both eukaryotes and prokaryotes
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