Small-sample learning reveals propionylation in determining global protein homeostasis

Ke Shui, Chenwei Wang, Xuedi Zhang, Shanshan Ma, Qinyu Li, Wanshan Ning, Weizhi Zhang, Miaomiao Chen, Di Peng, Hui Hu, Zheng Fang, Anyuan Guo, Guanjun Gao, Mingliang Ye, Luoying Zhang () and Yu Xue ()
Additional contact information
Ke Shui: Huazhong University of Science and Technology
Chenwei Wang: Huazhong University of Science and Technology
Xuedi Zhang: ShanghaiTech University
Shanshan Ma: Huazhong University of Science and Technology
Qinyu Li: Huazhong University of Science and Technology
Wanshan Ning: Huazhong University of Science and Technology
Weizhi Zhang: Huazhong University of Science and Technology
Miaomiao Chen: Huazhong University of Science and Technology
Di Peng: Huazhong University of Science and Technology
Hui Hu: Huazhong University of Science and Technology
Zheng Fang: Dalian Institute of Chemical Physics, Chinese Academy of Sciences
Anyuan Guo: Huazhong University of Science and Technology
Guanjun Gao: ShanghaiTech University
Mingliang Ye: Dalian Institute of Chemical Physics, Chinese Academy of Sciences
Luoying Zhang: Huazhong University of Science and Technology
Yu Xue: Huazhong University of Science and Technology

Nature Communications, 2023, vol. 14, issue 1, 1-23

Abstract: Abstract Proteostasis is fundamental for maintaining organismal health. However, the mechanisms underlying its dynamic regulation and how its disruptions lead to diseases are largely unclear. Here, we conduct in-depth propionylomic profiling in Drosophila, and develop a small-sample learning framework to prioritize the propionylation at lysine 17 of H2B (H2BK17pr) to be functionally important. Mutating H2BK17 which eliminates propionylation leads to elevated total protein level in vivo. Further analyses reveal that H2BK17pr modulates the expression of 14.7–16.3% of genes in the proteostasis network, and determines global protein level by regulating the expression of genes involved in the ubiquitin-proteasome system. In addition, H2BK17pr exhibits daily oscillation, mediating the influences of feeding/fasting cycles to drive rhythmic expression of proteasomal genes. Our study not only reveals a role of lysine propionylation in regulating proteostasis, but also implements a generally applicable method which can be extended to other issues with little prior knowledge.

Date: 2023
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DOI: 10.1038/s41467-023-38414-8

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