Integrated multi-omics analysis provide insights into the importance of acetylation modification in flavonoid biosynthesis of Ginkgo biloba (PRJCA017404)

Flavonoids are important medicinal active ingredients in Ginkgo biloba. However, the contribution of protein post-translational modification (PTM) in flavonoid biosynthesis has not been studied. Acetylation of lysine residues is a reversible protein PTM, which plays a key regulatory role in metabolism. To fully understand the molecular mechanism of flavonoid biosynthesis, the transcriptome, metabolome, proteome and lysine acetylome of different tissues of G. biloba were comprehensively analyzed. A total of 11,788 Kac sites were identified on 4,324 acetylated proteins, including 23 histones with 89 Kac sites. And 128 kinds of flavonoids accumulated differentially among tissues were identified, and a data set of differentially expressed genes related to flavonoid biosynthesis pathway was constructed. Twelve (CHI, C3H1, ANR, DFR, CCoAOMT1, F3H1, F3H2, CCoAOMT2, C3H2, HCT, F3'5'H and FG2) acetylated proteins that might be involved in flavonoid biosynthesis were identified. Further verified that C3H1, CCoAOMT1 and F3'5'H were all different in multi-omics data, and the mRNA and protein levels were highly correlated, and all of them were positively correlated with some differentially accumulation flavonoids. Among them, the modification level of CCoAOMT1 and F3'5'H sites was consistent with the change trend of catalytic products homoerodictyol and dihydromyricetin, respectively. Lysine deacetylases inhibitors affected the content of total flavonoids in different tissues and increased the content of flavonoids in roots of G. biloba. Collectively, these findings reveal for the first time the important role of acetylation in flavonoid biosynthesis.