Global profiling of regulatory elements in the histone benzoylation pathway

Duo Wang, Fuxiang Yan, Ping Wu, Kexue Ge, Muchun Li, Tingting Li, Ying Gao, Chao Peng () and Yong Chen ()
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Duo Wang: Chinese Academy of Sciences
Fuxiang Yan: Chinese Academy of Sciences
Ping Wu: Chinese Academy of Science
Kexue Ge: Chinese Academy of Sciences
Muchun Li: Chinese Academy of Sciences
Tingting Li: Chinese Academy of Sciences
Ying Gao: Chinese Academy of Sciences
Chao Peng: Chinese Academy of Science
Yong Chen: Chinese Academy of Sciences

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract Lysine benzoylation (Kbz) is a recently discovered post-translational modification associated with active transcription. However, the proteins for maintaining and interpreting Kbz and the physiological roles of Kbz remain elusive. Here, we systematically characterize writer, eraser, and reader proteins of histone Kbz in S. cerevisiae using proteomic, biochemical, and structural approaches. Our study identifies 27 Kbz sites on yeast histones that can be regulated by cellular metabolic states. The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex and NAD+-dependent histone deacetylase Hst2 could function as the writer and eraser of histone Kbz, respectively. Crystal structures of Hst2 complexes reveal the molecular basis for Kbz recognition and catalysis by Hst2. In addition, we demonstrate that a subset of YEATS domains and bromodomains serve as Kbz readers, and structural analyses reveal how YEATS and bromodomains recognize Kbz marks. Moreover, the proteome-wide screening of Kbz-modified proteins identifies 207 Kbz sites on 149 non-histone proteins enriched in ribosome biogenesis, glycolysis/gluconeogenesis, and rRNA processing pathways. Our studies identify regulatory elements for the Kbz pathway and provide a framework for dissecting the biological functions of lysine benzoylation.

Date: 2022
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DOI: 10.1038/s41467-022-29057-2

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