Landscape of the regulatory elements for lysine 2-hydroxyisobutyrylation pathway

• Published in: Cell research Vol. 28; no. 1; pp. 111 - 125
• Main Authors: Huang, He, Luo, Zhouqing, Qi, Shankang, Huang, Jing, Xu, Peng, Wang, Xiuxuan, Gao, Li, Li, Fangyi, Wang, Jian, Zhao, Wenhui, Gu, Wei, Chen, Zhucheng, Dai, Lunzhi, Dai, Junbiao, Zhao, Yingming
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.01.2018; Nature Publishing Group
• Subjects: 631/443/319; 631/80/458; 631/80/86; Acetyltransferases - metabolism; Acylation; Biomedical and Life Sciences; Cell Biology; Fatty acids; Gene expression; HDAC2 protein; HEK293 Cells; HeLa Cells; Histone deacetylase; Histone Deacetylase 2 - metabolism; Histone Deacetylases - metabolism; Homology; Humans; Hydroxybutyrates - metabolism; Life Sciences; Lysine; Lysine - analogs & derivatives; Lysine - metabolism; Lysine Acetyltransferase 5 - metabolism; Mammalian cells; Metabolic pathways; Metabolites; Original; original-article; Post-translation; Protein Processing, Post-Translational; Proteins; Proteomes; Regulatory sequences; Saccharomyces cerevisiae Proteins - metabolism; Substrates; Translation; Yeast; Yeasts; lysine 2-hydroxyisobutyrylation; regulatory element; post-translational modification; deacylase; substrate; acyltransferase
• ISSN: 1001-0602; 1748-7838
• DOI: 10.1038/cr.2017.149

Short-chain fatty acids and their corresponding acyl-CoAs sit at the crossroads of metabolic pathways and play important roles in diverse cellular processes. They are also precursors for protein post-translational lysine acylation modifications. A noteworthy example is the newly identified lysine 2-hydroxyisobutyrylation （Khib） that is derived from 2-hydroxyisobutyrate and 2-hydroxyisobutyryl-CoA. Histone Khib has been shown to be associated with active gene expression in spermatogenic cells. However, the key elements that regulate this post-translational lysine acyla- tion pathway remain unknown. This has hindered characterization of the mechanisms by which this modification exerts its biological functions. Here we show that Esalp in budding yeast and its homologue Tip60 in human could add Khib to substrate proteins both in vitro and in vivo. In addition, we have identified HDAC2 and HDAC3 as the major enzymes to remove Khmb. Moreover, we report the first global profiling of Khib proteome in mammalian cells, identifying 6 548 Khb sites on 1 725 substrate proteins. Our study has thus discovered both the ＂writers＂ and ＂erasers＂ for histone Kh~b marks, and major Khib protein substrates. These results not only illustrate the landscape of this new lysine acylation pathway, but also open new avenues for studying diverse functions of cellular metabolites associated with this pathway.