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

Author

Listed:
  • 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)

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.

Suggested Citation

  • 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 & Jianhua Gan, 2022. "Crystal structures and insights into precursor tRNA 5’-end processing by prokaryotic minimal protein-only RNase P," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30072-6
    DOI: 10.1038/s41467-022-30072-6
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    References listed on IDEAS

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    1. Nicholas J. Reiter & Amy Osterman & Alfredo Torres-Larios & Kerren K. Swinger & Tao Pan & Alfonso Mondragón, 2010. "Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA," Nature, Nature, vol. 468(7325), pages 784-789, December.
    2. Johannes Popow & Jennifer Jurkin & Alexander Schleiffer & Javier Martinez, 2014. "Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors," Nature, Nature, vol. 511(7507), pages 104-107, July.
    3. Futang Wan & Qianmin Wang & Jing Tan & Ming Tan & Juan Chen & Shaohua Shi & Pengfei Lan & Jian Wu & Ming Lei, 2019. "Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
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