tRNA recognition, processing, and disease: Hypotheses around an unorthodox type of RNase P in human mitochondria

Abstract Pentatricopeptide repeat (PPR) motifs are α-helical structures known for their modular recognition of single-stranded RNA sequences with each motif in a tandem array binding to a single nucleotide. Protein-only RNase P 1 (PRORP1) in Arabidopsis thaliana is an endoribonuclease that uses its PPR domain to recognize precursor tRNAs (pre-tRNAs) as it catalyzes removal of the 5′-leader sequence from pre-tRNAs with its NYN metallonuclease domain. To gain insight into the mechanism by which PRORP1 recognizes tRNA, we determined a crystal structure of the PPR domain in complex with yeast tRNAPhe at 2.85 Å resolution. The PPR domain of PRORP1 bound to the structurally conserved elbow of tRNA and recognized conserved structural features of tRNAs using mechanisms that are different from the established single-stranded RNA recognition mode of PPR motifs. The PRORP1 PPR domain-tRNAPhe structure revealed a conformational change of the PPR domain upon tRNA binding and moreover demonstrated the need for pronounced overall flexibility in the PRORP1 enzyme conformation for substrate recognition and catalysis. The PRORP1 PPR motifs have evolved strategies for protein-tRNA interaction analogous to tRNA recognition by the RNA component of ribonucleoprotein RNase P and other catalytic RNAs, indicating convergence on a common solution for tRNA substrate recognition.

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Role of the D arm and the anticodon arm in tRNA recognition by eubacterial and eukaryotic RNase P enzymes

Biochemistry ◽

10.1021/bi00211a014 ◽

1993 ◽

Vol 32 (48) ◽

pp. 13046-13053 ◽

Cited By ~ 37

Author(s):

Wolf Dietrich Hardt ◽

Judith Schlegl ◽

Volker A. Erdmann ◽

Roland K. Hartmann

Keyword(s):

Rnase P ◽

Trna Recognition

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C2′-endo nucleotides as molecular timers suggested by the folding of an RNA domain

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0901319106 ◽

2009 ◽

Vol 106 (37) ◽

pp. 15622-15627 ◽

Cited By ~ 30

Author(s):

Stefanie A. Mortimer ◽

Kevin M. Weeks

Keyword(s):

Conformational Dynamics ◽

Rnase P ◽

Single Nucleotide ◽

Trna Recognition ◽

Rate Determining Step ◽

Global Fold ◽

Evolutionarily Conserved ◽

Order Of Magnitude ◽

Rate Limiting ◽

Specificity Domain

A striking and widespread observation is that higher-order folding for many RNAs is very slow, often requiring minutes. In some cases, slow folding reflects the need to disrupt stable, but incorrect, interactions. However, a molecular explanation for slow folding in most RNAs is unknown. The specificity domain of the Bacillus subtilis RNase P ribozyme undergoes a rate-limiting folding step on the minute time-scale. This RNA also contains a C2′-endo nucleotide at A130 that exhibits extremely slow local conformational dynamics. This nucleotide is evolutionarily conserved and essential for tRNA recognition by RNase P. Here we show that deleting this single nucleotide accelerates folding by an order of magnitude even though this mutation does not change the global fold of the RNA. These results demonstrate that formation of a single stacking interaction at a C2′-endo nucleotide comprises the rate-determining step for folding an entire 154 nucleotide RNA. C2′-endo nucleotides exhibit slow local dynamics in structures spanning isolated helices to complex tertiary interactions. Because the motif is both simple and ubiquitous, C2′-endo nucleotides may function as molecular timers in many RNA folding and ligand recognition reactions.

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Faculty Opinions recommendation of Life without RNase P.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1108271.565133 ◽

2008 ◽

Author(s):

Judy Wall

Keyword(s):

Rnase P

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Faculty Opinions recommendation of RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1141875.598973 ◽

2009 ◽

Author(s):

Burckhard Seelig

Keyword(s):

Rnase P ◽

Mitochondrial Trna ◽

Trna Processing ◽

Processing Enzyme

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Faculty Opinions recommendation of In vitro reconstitution and analysis of eukaryotic RNase P RNPs.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733164313.793554514 ◽

2018 ◽

Author(s):

Venkat Gopalan ◽

Lien Lai ◽

Walter Zahurancik

Keyword(s):

Rnase P ◽

In Vitro Reconstitution

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Faculty Opinions recommendation of Endoribonucleolytic Cleavage of m6A-Containing RNAs by RNase P/MRP Complex.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.735404862.793575746 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sabine Müller

Keyword(s):

Rnase P

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Towards plant resistance to viruses using protein-only RNase P

Nature Communications ◽

10.1038/s41467-021-21338-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Anthony Gobert ◽

Yifat Quan ◽

Mathilde Arrivé ◽

Florent Waltz ◽

Nathalie Da Silva ◽

...

Keyword(s):

Mosaic Virus ◽

Virus Replication ◽

Yield Loss ◽

Rnase P ◽

Plant Viruses ◽

Yellow Mosaic Virus ◽

Resistance To Viruses ◽

Target Plant

AbstractPlant viruses cause massive crop yield loss worldwide. Most plant viruses are RNA viruses, many of which contain a functional tRNA-like structure. RNase P has the enzymatic activity to catalyze the 5′ maturation of precursor tRNAs. It is also able to cleave tRNA-like structures. However, RNase P enzymes only accumulate in the nucleus, mitochondria, and chloroplasts rather than cytosol where virus replication takes place. Here, we report a biotechnology strategy based on the re-localization of plant protein-only RNase P to the cytosol (CytoRP) to target plant viruses tRNA-like structures and thus hamper virus replication. We demonstrate the cytosol localization of protein-only RNase P in Arabidopsis protoplasts. In addition, we provide in vitro evidences for CytoRP to cleave turnip yellow mosaic virus and oilseed rape mosaic virus. However, we observe varied in vivo results. The possible reasons have been discussed. Overall, the results provided here show the potential of using CytoRP for combating some plant viral diseases.

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