Crystal structures and insights into precursor tRNA 5’-end processing by prokaryotic minimal protein-only RNase P

Yangyang Li, Shichen Su, Yanqing Gao, Guoliang Lu, Hehua Liu, Xi Chen, Zhiwei Shao, Yixi Zhang, Qiyuan Shao, Xin Zhao, Jie Yang, Chulei Cao, Jinzhong Lin, Jinbiao Ma and Jianhua Gan ()
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Yangyang Li: Fudan University
Shichen Su: Fudan University
Yanqing Gao: Fudan University
Guoliang Lu: Fudan University
Hehua Liu: Fudan University
Xi Chen: Fudan University
Zhiwei Shao: Fudan University
Yixi Zhang: Fudan University
Qiyuan Shao: Fudan University
Xin Zhao: Fudan University
Jie Yang: Fudan University
Chulei Cao: Fudan University
Jinzhong Lin: Fudan University
Jinbiao Ma: Fudan University
Jianhua Gan: Fudan University

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

Abstract: Abstract Besides the canonical RNA-based RNase P, pre-tRNA 5’-end processing can also be catalyzed by protein-only RNase P (PRORP). To date, various PRORPs have been discovered, but the basis underlying substrate binding and cleavage by HARPs (homolog of Aquifex RNase P) remains elusive. Here, we report structural and biochemical studies of HARPs. Comparison of the apo- and pre-tRNA-complexed structures showed that HARP is able to undergo large conformational changes that facilitate pre-tRNA binding and catalytic site formation. Planctomycetes bacterium HARP exists as dimer in vitro, but gel filtration and electron microscopy analysis confirmed that HARPs from Thermococcus celer, Thermocrinis minervae and Thermocrinis ruber can assemble into larger oligomers. Structural analysis, mutagenesis and in vitro biochemical studies all supported one cooperative pre-tRNA processing mode, in which one HARP dimer binds pre-tRNA at the elbow region whereas 5’-end removal is catalyzed by the partner dimer. Our studies significantly advance our understanding on pre-tRNA processing by PRORPs.

Date: 2022
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DOI: 10.1038/s41467-022-30072-6

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