ABSTRACT
BACKGROUND: Lysine 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. RESULTS: In 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. CONCLUSIONS: In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.
ABSTRACT
BACKGROUND: Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice. MAIN BODY: In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) analyses, the result showed that major enrichment of histone Kbu located in genebody regions of rice genome, especially in exons. The enrichment level of Kbu histone modification is positively correlated with gene expression. Furthermore, we compared Kbu with DNase-seq and other histone modifications in rice. We found that 60.06% Kub enriched region co-located with DHSs in intergenic regions. The similar profiles were detected among Kbu and several acetylation modifications such as H3K4ac, H3K9ac, and H3K23ac, indicating that Kbu modification is an active signal of transcription. Genes with both histone Kbu and one other acetylation also had significantly increased expression compared with genes with only one acetylation. Gene Ontology (GO) enrichment analysis revealed that these genes with histone Kbu can regulate multiple metabolic process in different rice varieties. CONCLUSION: Our study showed that the lysine butyrylation modificaiton may promote gene expression as histone acetylation and will provide resources for futher studies on histone Kbu and other epigenetic modifications in plants.
ABSTRACT
The maize Ac/Ds transposable elements are members of the hAT transposon superfamily, and have stable transpositional activity in transgenic rice plants. Ac/Ds transposable elements are considered to transpose via a conservative non-replicative "cut and paste" model, though their transposition mechanism is not completely understood. Previous studies have shown that Ds preferentially transposes to genetically linked sites after being excised from its original site in the presence of Ac-transposase. In this study, genomic sequences flanking Ds insertions from a Ds-tagged rice mutant and its rever- tant were determined by TAIL-PCR. The Ds insertion site, the excision footprint and the re-insertion sites in the mutant were identified using bioinformatics tool. The results showed that Ds element excised from its original insertion site on chromosome 3 by leaving an 8 bp footprint (CATCATGA), which resulted in exon changes in tagged gene. After the excision, Ds element was re-inserted into the coding sequences of two genes on chromosome 2 and chromosome 6, which encode a nicotianamine aminotransferase and a senescence-associated protein, respectively. The transposition behavior of Ds element in this study could not be fully explained by the "cut and paste" mechanism, while it is likely to transpose in a "cut and copy and paste" way.
