Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains

Lining Lu (), Xiaoguo Zhai, Xiaolong Li, Shuansuo Wang, Lijun Zhang, Luyang Wang, Xi Jin, Lujun Liang, Zhiheng Deng, Zichen Li, Yanfeng Wang, Xiangdong Fu, Honggang Hu, Jiawei Wang, Ziqing Mei (), Zhengguo He () and Feng Wang ()
Additional contact information
Lining Lu: Guangxi University
Xiaoguo Zhai: Guangxi University
Xiaolong Li: Beijing Institute of Technology
Shuansuo Wang: Shanxi Agricultural University
Lijun Zhang: Guangxi University
Luyang Wang: Guangxi University
Xi Jin: Guangxi University
Lujun Liang: Tsinghua University
Zhiheng Deng: Tsinghua University
Zichen Li: Tsinghua University
Yanfeng Wang: Beijing Institute of Technology
Xiangdong Fu: Chinese Academy of Sciences
Honggang Hu: Tsinghua University
Jiawei Wang: Tsinghua University
Ziqing Mei: University of Science and Technology Beijing
Zhengguo He: Guangxi University
Feng Wang: Beijing Institute of Technology

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract Linear (Met1-linked) ubiquitination is involved inflammatory and innate immune signaling. Previous studies have characterized enzymes regulating the addition and removal of this modification in mammalian systems. However, only a few plant-derived deubiquitinases targeting Met1-linked ubiquitin chains have been reported and their mechanism of action remains elusive. Here, using a dehydroalanine-bearing Met1-diubiquitin suicide probe, we discover OTUB1 from Oryza sativa (OsOTUB1) as a Met1-linked ubiquitin chain-targeting deubiquitinase. By solving crystal structures of apo OsOTUB1 and an OsOTUB1/Met1-diubiquitin complex, we find that Met1 activity is conferred by Met1-specific motifs in the S1’ pocket of OsOTUB1. Large-scale sequence alignments and hydrolysis experiments provide evidence that these motifs are a general determinant of Met1 activity in the OTUB subfamily across species. Analysis of the species distribution of OTUBs capable of hydrolysing Met1-linked ubiquitin chains shows that this activity is conserved in green plants (Viridiplantae) and does not exist in metazoans, providing insights into the evolutionary differentiation between primitive plants and animals.

Date: 2022
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DOI: 10.1038/s41467-022-32364-3

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