Identification of SIRT3 as an eraser of H4K16la

Zhuming Fan; Zhiyang Liu; Nan Zhang; Wenyu Wei; Ke Cheng; Hongyan Sun; Quan Hao

doi:10.1016/j.isci.2023.107757

Identification of SIRT3 as an eraser of H4K16la

iScience. 2023 Aug 28;26(10):107757. doi: 10.1016/j.isci.2023.107757. eCollection 2023 Oct 20.

Authors

Zhuming Fan^{1

2

3}, Zhiyang Liu⁴, Nan Zhang³, Wenyu Wei⁴, Ke Cheng⁴, Hongyan Sun⁴, Quan Hao^{1

2

3}

Affiliations

¹ Institute of High Energy Physics, CAS, Beijing 100000, China.
² Spallation Neutron Source Science Center, CAS, Dongguan, Guangdong 523000, China.
³ School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.
⁴ Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China.

Abstract

Lysine lactylation (Kla) is a novel histone post-translational modification discovered in late 2019. Later, HDAC1-3, were identified as the robust Kla erasers. While the Sirtuin family proteins showed weak eraser activities toward Kla, as reported. However, the catalytic mechanisms and physiological functions of HDACs and Sirtuins are not identical. In this study, we observed that SIRT3 exhibits a higher eraser activity against the H4K16la site than the other human Sirtuins. Crystal structures revealed the detailed binding mechanisms between lactyl-lysine peptides and SIRT3. Furthermore, a chemical probe, p-H4K16laAlk, was developed to capture potential Kla erasers from cell lysates. SIRT3 was captured by this probe and detected via proteomic analysis. And another chemical probe, p-H4K16la-NBD, was developed to detect the eraser-Kla delactylation processes directly via fluorescence indication. Our findings and chemical probes provide new directions for further investigating Kla and its roles in gene transcription regulation.

Keywords: Enzymology; Molecular interaction; Protein; Structural biology.