Ribonuclease P (EC3.1.26.5,RNase P) is a type ofribonuclease which cleavesRNA. RNase P is unique from other RNases in that it is aribozyme – a ribonucleic acid that acts as acatalyst in the same way that aprotein-based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA ontRNA molecules. Further, RNase P is one of two known multiple turnover ribozymes in nature (the other being theribosome), the discovery of which earnedSidney Altman andThomas Cech theNobel Prize in Chemistry in 1989: in the 1970s, Altman discovered the existence of precursor tRNA with flanking sequences and was the first to characterize RNase P and its activity in processing of the5' leader sequence of precursor tRNA.[1]
Its best characterisedenzyme activity is the generation of mature 5′-ends oftRNAs by cleaving the 5′-leader elements of precursor-tRNAs. Cellular RNase Ps areribonucleoproteins. TheRNA from bacterial RNase P retains its catalytic activity in the absence of the protein subunit, i.e. it is aribozyme. Similarly, archaeal RNase P RNA has been shown to be weakly catalytically active in the absence of its respective protein cofactors.[2] Isolated eukaryotic RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of theholoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all three lineages arehomologous—the helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet there is considerable sequence variation, particularly among the eukaryotic RNAs.
Bacterial RNase P has two components: an RNA chain, called M1 RNA, and apolypeptide chain, or protein, called C5 protein.[3][4]In vivo, both components are necessary for the ribozyme to function properly, butin vitro, the M1 RNA can act alone as a catalyst.[1] The primary role of the C5 protein is to enhance the substrate binding affinity and the catalytic rate of the M1 RNA enzyme probably by increasing the metal ion affinity in the active site. The crystal structure of a bacterial RNase P holoenzyme with tRNA has been recently resolved, showing how the large, coaxially stacked helical domains of the RNase P RNA engage in shape selective recognition of the pre-tRNA target. This crystal structure confirms earlier models of substrate recognition and catalysis, identifies the location of the active site, and shows how the protein component increases RNase P functionality.[5][6]
Ribonuclease P (RNase P) is a ubiquitousendoribonuclease, found in archaea, bacteria and eukarya as well aschloroplasts andmitochondria. Its best characterised activity is the generation of mature 5'-ends of tRNAs by cleaving the 5'-leader elements of precursor-tRNAs. Cellular RNase Ps areribonucleoproteins (RNP). RNA from bacterial RNase Ps retains its catalytic activity in the absence of theprotein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the eubacterial ones, the RNA cores from all the three lineages are homologous—helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
RNA family
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Inarchaea, RNase Pribonucleoproteins consist of 4–5 protein subunits that are associated with RNA. As revealed byin vitro reconstitution experiments these protein subunits are individually dispensable for tRNA processing that is essentially mediated by the RNA component.[7][8][9] The structures of protein subunits of archaeal RNase P have been resolved byx-raycrystallography andNMR, thus revealing new protein domains and folding fundamental for function.
Usingcomparative genomics and improved computational methods, a radically minimized form of the RNase P RNA, dubbed "Type T", has been found in all complete genomes in the crenarchaeal phylogenetic familyThermoproteaceae, including species in the generaPyrobaculum, Caldivirga andVulcanisaeta.[10] All retain a conventional catalytic domain, but lack a recognizable specificity domain. 5′ tRNA processing activity of the RNA alone was experimentally confirmed. The Pyrobaculum andCaldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans-acting ribozymes.[10] Loss of the specificity domain in these RNAs suggests potential altered substrate specificity.
It has recently been argued that the archaebacteriumNanoarchaeum equitans does not possess RNase P. Computational and experimental studies failed to find evidence for its existence. In this organism the tRNA promoter is close to the tRNA gene and it is thought that transcription starts at the first base of the tRNA thus removing the requirement for RNase P.[11]
RNA family
| RNA family
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| Nuclear RNase P | |
|---|---|
 Predictedsecondary structure andsequence conservation of RNaseP_nuc | |
| Identifiers | |
| Symbol | RNaseP_nuc |
| Rfam | RF00009 |
| Other data | |
| RNA type | Gene;ribozyme |
| Domain(s) | Eukaryota;Bacteria;Archaea |
| GO | GO:0008033GO:0004526GO:0030677 |
| SO | SO:0000386 |
| PDB structures | PDBe |
Ineukaryotes, such as humans andyeast,[12] most RNase P consists of an RNA chain that is structurally similar to that found in bacteria[13] as well as nine to ten associated proteins (as opposed to the single bacterial RNase P protein, C5).[14][15] Five of these protein subunits exhibit homology to archaeal counterparts.
Recent (2007) findings also reveal that eukaryotic RNase P has a new function:[14] It has been shown that human nuclear RNase P is required for the normal and efficient transcription of varioussmall noncoding RNAs, such as tRNA,5S rRNA,SRP RNA andU6 snRNA genes,[16] which are transcribed byRNA polymerase III, one of three major nuclear RNA polymerases in human cells.
RNase P from eukaryotes was only recently (2007) demonstrated to be a ribozyme.[17] Accordingly, the numerous protein subunits of eukaryotic RNase P have a minor contribution to tRNA processing per se,[18] while they seem to be essential for the function of RNase P and RNase MRP in other biological settings, such as gene transcription and thecell cycle.[16][19]
| Subunit | Function/interaction (in tRNA processing) |
|---|---|
| RPP14 | RNA binding |
| RPP20 | ATPase, helicase/Hsp27, SMN, Rpp25 |
| RPP21 | RNA binding, activityg/Rpp29 |
| RPP25 | RNA binding/Rpp20 |
| RPP29 | tRNA binding, activity/Rpp21 |
| RPP30 | RNA binding, activity/Pop5 |
| RPP38 | RNA binding, activity |
| RPP40 | |
| hPop1 | |
| hPop5 | RNA binding, activity/Rpp30 |
| H1 RNA | Activity/Rpp21, Rpp29, Rpp30, Rpp38 |
Protein subunits of RNase P are shared withRNase MRP,[15][20][21] an evolutionarily related catalytic ribonucleoprotein involved in processing of ribosomal RNA in thenucleolus and[22] DNA replication in the mitochondrion.[23]
Most eukaryotes havemitochondria, an organelle derived from proteobacteria, or a reduced version. Some also havechloroplasts, an organelle derived from cyanobacteria. These organelles have their own genome and machinery for transcription and translation. They make their own tRNAs, which requires maturation by RNase P.
As expected for the endosymbiotic theory – and similarly to other organellar genes – RNase P RNA genes (Rpm1 in yeast nomenclature orrnpB in bacterial nomenclature) have in the mitochondrial genome of the baker's yeast and most of its relatives in Saccharomycetales. These RNAs are extremely minimized ("crippled" according to Rossmanith) and do not work alonein vitro. They also show high divergence even among related yeasts. The baker's yeast version has one identified protein partnerRpm2, the only protein partner to mitochondrial RNase P RNA a known as of 2012. The identification ofrnpB in the broader category of fungi remains patchy.[24]
AmongArchaeplastida ("broader plants": plants, green algae, red algae), only two early-branchingprasinophytes have a mtRNase P RNA gene. The secondary structure resembles α-proteobacterial RNase P RNA, but they do not work alonein vitro. It is unknown what the required protein partner is.[24] The glaucophytes, red algae, and some prasinophytes have a bacterial type A RNase P RNA in their chloroplast genomes. Other plants use the protein-only system described below.[24]
The situation among so-calledprotists is less clear due to the lack of data. The jakobidReclinomonas americana is notable for having a mtRNase P RNA believed to be the closest to the version in theproto-mitochondrion, though it also does not work alonein vitro.[24] (Mixing and matching parts from this RNA with theE. coli P-RNA does produce an RNA that is active alone.)[25]
No mitochondrial mtRNase P RNA has been found among animals as of 2012. Most of them have a copy of the protein-only system identified.[24]
| Protein-only RNase P, C-terminal catalytic | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | PRORP_C | ||||||||
| Pfam | PF16953 | ||||||||
| InterPro | IPR031595 | ||||||||
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The alternative to a RNA-based RNase P in animals and plants is theprotein-only RNase P (PRORP). Most PRORPs consist of a C-terminal metallonucleasePIN domain and an N-terminalpentatricopeptide repeat (PPR) domain,[26] but variations exist.[27]
The PRORP was originally discovered in plants, specifically inSpinachchloroplasts.[28] The model plantArabidopsis thaliana has three protein-only RNase P genes: PRORP1, PRORP2, PRORP3. PRORP1 goes to the mitochondria and chloroplasts while PRORP2 and PRORP3 stays in the nucleus. All can cleave tRNAin vitro. The plant version has all functionalities in one chain of protein.[29]
Human mitochondrial RNase P is a trimericprotein and does not containRNA. It consists ofTRMT10C,HSD17B10, and the catalyticPRORP.[30] Its structure has been solved. The PPR domain in human PRORP does not perform base recognition, unlike in plant single-protein PRORPs.[31] Other animals have a similar setup. Evennematodes have a divergent version of this trimeric system.[24]
Thekinetoplastids also have PRORP.[24]
| RNA-free ribonuclease P / PINc domain ribonuclease | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | PIN_5 | ||||||||
| Pfam | PF08745 | ||||||||
| InterPro | IPR014856 | ||||||||
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Some prokrayotes (bacteria and archaea) have a single-protein RNase P quite different from the eukaryotic PRORP. They are called HARP (Homologs ofAquifex RNase P). They are tiny proteins of up to 23 kDa. They only share sequence similarity with eukaryotic PRORP in one region, the metallonucleasePIN domain. Some of them form high-order oligomers.[32]
HARP does not carry out the functions of RNase P very efficiently. Many organisms that have HARP also have a typical RNase P. This hints at a different function. In 2025, it was found that HARP has a tendency to appear with theRNA ligase protein. A new theory backed by immunodepletion is that it acts with RNA ligase to mature and circularizeC/D box snoRNAs.[33]
RNase P is now being studied as a potential therapy for diseases such asherpes simplex virus,[34]cytomegalovirus,[34][35]influenza and other respiratory infections,[36] HIV-1[37] and cancer caused by fusion geneBCR-ABL.[34][38] External guide sequences (EGSs) are formed withcomplementarity to viral or oncogenic mRNA and structures that mimic the T loop and acceptor stem oftRNA.[36] These structures allow RNase P to recognize the EGS and cleave the target mRNA. EGS therapies have shown to be effective in culture and in live mice.[39]
