Structure and mechanistic features of the prokaryotic minimal RNase P

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Abstract

Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by RNase P is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various Eukarya (there termed PRORPs) and in some bacteria (Aquifex aeolicus and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of Aquifex RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here we solved the structure of the bacterial HARP from Halorhodospira halophila by cryo-EM revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5'-end in close proximity to the active site of the neighboring dimer. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system.

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Coordinates and structure factors have been deposited within the protein data bank (PDB) and the electron microscopy data bank (EMDB) under accession codes: 7OG5 and EMD-12878. The authors declare that all other data supporting the findings of this study are available within the article and its supplementary information files.

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Rebecca Feyh

Institute of Pharmaceutical Chemistry, Philipps-University Marburg,, Marburg, Germany

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The authors declare that no competing interests exist.
Nadine Bianca Waeber

Institute of Pharmaceutical Chemistry, Philipps-University Marburg,, Marburg, Germany

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Simone Prinz

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany

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Pietro Ivan Giammarinaro

Chemistry, Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany

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"This ORCID iD identifies the author of this article:" 0000-0002-0356-8481
Gert Bange

Max Planck Institute of Biophysics, Marburg, Germany

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Georg Hochberg

Max Planck Institute of Biophysics, Marburg, Germany

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Roland Karl Hartmann

Philipps-Universitaet Marburg, Marburg, Germany

For correspondence
roland.hartmann@staff.uni-marburg.de

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The authors declare that no competing interests exist.
Florian Altegoer

Chemistry, Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany

For correspondence
altegoer@uni-marburg.de

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The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6012-9047

Funding

Deutsche Forschungsgemeinschaft (HA 1672/19-1)

Roland Karl Hartmann

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.