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Bacterial RNase P: a new view of an ancient enzyme

Key Points

  • Ribonuclease P (RNase P) is a ribonucleoprotein particle that catalyses maturation of the 5′ end of transfer RNA (tRNA) by cleavage of precursor-specific sequences. RNase P is found in cells from all three domains of life: the Bacteria, Eukarya and Archaea. It contains a highly conserved catalytic RNA component — a unique, natural ribozyme that conducts multiple turnovers with a broad substrate specificity.

  • RNase P RNA is a metalloenzyme that catalyses hydrolysis of a specific internucleotide phosphodiester bond through an SN2-like nucleophilic substitution mechanism. Divalent metal ions participate directly in the reaction through a variation of a two-metal-ion mechanism that is typical of the large ribozymes such as group-I introns and many protein-based phosphoryl-transfer enzymes.

  • Early perspectives into the structure of the RNase P RNA came from phylogenetic comparative studies, complemented by photo-affinity crosslinking and computer modelling. Recent crystallographic studies of bacterial RNase P RNA corroborate the results of early structural, biochemical and biophysical studies, and provide a new and detailed view of the overall structural organization of the ribozyme, its substrate-binding interface and the proposed chemically active site.

  • Based on the newly available structural information, the functional complexes of the bacterial RNase P RNA with its protein cofactor and with the product tRNA have been modelled. Considering the relatively low resolution of the available crystal structures, many details of the RNA interaction with the protein component and with the substrate are still uncertain, and the atomic details of how the RNA participates in catalysis remain to be elucidated.

Abstract

Ribonuclease P (RNase P) is a ubiquitous endonuclease that catalyses the maturation of the 5′ end of transfer RNA (tRNA). Although it carries out a biochemically simple reaction, RNase P is a complex ribonucleoprotein particle composed of a single large RNA and at least one protein component. In bacteria and some archaea, the RNA component of RNase P can catalyse tRNA maturation in vitro in the absence of proteins. The discovery of the catalytic activity of the bacterial RNase P RNA triggered numerous mechanistic and biochemical studies of the reactions catalysed by the RNA alone and by the holoenzyme and, in recent years, structures of individual components of the RNase P holoenzyme have been determined. The goal of the present review is to summarize what is known about the bacterial RNase P, and to bring together the recent structural results with extensive earlier biochemical and phylogenetic findings.

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Figure 1: RNase P catalyses maturation of the 5′ end of tRNA.
Figure 2: Phylogenetic variation and nucleotide conservation among bacterial RNase P RNAs.
Figure 3: Comparison of the crystal structures of the A-type and B-type RNase P RNAs.
Figure 4: Conserved nucleotides in the bacterial RNase P RNA and reconstruction of the RNase P RNA complex.
Figure 5: Modelling of the bacterial RNase P holoenzyme structure and its complex with tRNA.

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Acknowledgements

The authors' research is supported by a grant from the National Institutes of Health.

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Correspondence to Norman R. Pace.

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DATABASES

Entrez Genome Project

Bacillus stearothermophilus

Bacillus subtilis

Thermotoga maritima

Thermus thermophilus

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Glossary

Ribozyme

An enzyme that has an RNA as the catalytic component. RNase P belongs to the large ribozyme class, which also includes the self-splicing group-I and group-II introns.

4.5S RNA

In bacteria, the signal-recognition particle comprises 4.5S RNA and the Ffh protein.

Transfer messenger RNA

(Tm RNA). Also known as SsrA. Involved in a trans-translation process that adds a C-terminal peptide tag to unfinished proteins at stalled ribosomes that targets the unfinished proteins for proteolysis.

Riboswitch

A regulatory structure in an mRNA molecule that undergoes a conformational change induced by the binding of a small metabolite, and which results in activation or inactivation of the mRNA.

SN2 nucleophilic reaction

A bimolecular nucleophilic substitution reaction that involves displacement of a leaving group by an attacking nucleophile. An SN2 reaction that involves phosphate esters (for example, an internucleotide phosphodiester) proceeds through the formation of a trigonal bipyramidal transition state.

Quench-flow technique

A technique that allows the analysis of chemical reactions at the millisecond time scale.

Hill analysis

A common technique that analyses cooperative binding of ligands to biomacromolecules (proteins and nucleic acids). Either equilibrium binding (for example, extent of saturation) or the rate of the ligand-dependent enzymatic reaction is followed as a function of the concentration of the ligand. Mathematical analysis of the binding function yields the number of cooperatively bound ligands as well as the affinity constant.

Phosphorothioate substitution

A common chemical modification that substitutes a sulphur atom for one of the non-bridging oxygens in the phosphodiester linkage.

Thiophilic

Having a high affinity for sulphur.

Kinetic isotope-effect study

A kinetic isotope effect is a change in the rate of a chemical reaction owing to a substitution of a participating chemical group with an analogue that contains a different isotope of one of the constituent atoms. As kinetic isotope effects reflect changes in the vibration energy of the transition state of the reaction caused by substitution, they are a useful tool for studying the mechanism of chemical reactions.

RNase H

An endoribonuclease that specifically hydrolyses the phosphodiester bonds of RNA that are hybridized to DNA. Does not digest single-stranded or double-stranded DNA.

Homing endonucleases

A large class of endonuclease that recognize a specific sequence that flanks the homing endonuclease-encoding gene, but only when the homing endonuclease-encoding gene itself does not interrupt this sequence.

A-minor interaction

A common long-range interaction in structured RNA molecules achieved by docking of a bulged nucleotide (usually adenine) into a minor groove of a double-stranded helical structure. Four types of A-minor interactions are known; not all are specific for adenine. A-minor interactions are considered to be a subclass of ribose-zipper interactions.

Tetraloop

A four-base loop that caps a hairpin helix. Tetraloops often dock into other structural elements of RNA to provide long-range structural stability.

Ribose zipper

An element of RNA structure that is characterized by consecutive hydrogen-bonding interactions between ribose 2′-hydroxyls from different regions of an RNA chain or between RNA chains.

Dinucleotide platform

A structural feature in which folding of the RNA chain results in an in-plane, side-by-side positioning of consecutive bases.

Nucleotide analogue interference mapping

(NAIM). A technique that involves random, but sequence-specific, incorporation of chemical modifications into a pool of RNA molecules (usually achieved by in vitro transcription in the presence of nucleotide analogues) that is followed by a selection for a certain property (for example, folding, catalytic activity or ligand binding). Biochemical analysis of the distribution of such modifications reveals sites in RNA where the chemical modification interferes with the RNA property of interest.

S5 superfamily

A protein structural family that includes proteins and protein domains with a similar α–β-sandwich-like fold. The family is named after one of its members, a small subunit ribosomal protein S5.

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Kazantsev, A., Pace, N. Bacterial RNase P: a new view of an ancient enzyme. Nat Rev Microbiol 4, 729–740 (2006). https://doi.org/10.1038/nrmicro1491

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