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RPRs from O. tauri mitochondria and chloroplasts. a Secondary structure models of RPRs from O. tauri mitochondria (mt; left) and chloroplast (cp; right). Paired regions (helices) are labeled as P1, P2, etc., consecutively from 5 to 3 following the nomenclature used for bacterial RPRs. The preWx L refers to loops capping paired regions. Universally conserved nucleotides (Chen and Pace 1997; Brown 1999; Marquez et al. 2005; Gopalan 2007) are highlighted with a black circle. Solid lines show long-distance interactions that generate pseudoknots P4 and P6, as well as other tertiary interactions . b Expression of organellar RPRs in O. tauri. Detection of the cDNAs corresponding to the RPR from O. tauri mitochondria (left; 255 bp) and chloroplast (right; 304 bp) by RT-PCR (+) but not by PCR alone (¡) in total RNA isolated from O. tauri cells
Source publication
RNase P catalyzes 5'-maturation of tRNAs. While bacterial RNase P comprises an RNA catalyst and a protein cofactor, the eukaryotic (nuclear) variant contains an RNA and up to ten proteins, all unrelated to the bacterial protein. Unexpectedly, a nuclear-encoded bacterial RNase P protein (RPP) homolog is found in several prasinophyte algae including...
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... an RPR gene has already been annotated in the sequenced O. tauri mitochondrial genome (Fig. 6), we successfully identiWed a bacterial RPR-like gene in the chloroplast genome ( Fig. 6; accession number CR954199, complementary strand positions 4,980 to 5,307). These Wndings are not surprising since genes coding for bacterial- like RPRs have been previously identiWed in the organellar genomes of Nephroselmis olivacea, another ...
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... an RPR gene has already been annotated in the sequenced O. tauri mitochondrial genome (Fig. 6), we successfully identiWed a bacterial RPR-like gene in the chloroplast genome ( Fig. 6; accession number CR954199, complementary strand positions 4,980 to 5,307). These Wndings are not surprising since genes coding for bacterial- like RPRs have been previously identiWed in the organellar genomes of Nephroselmis olivacea, another prasinophyte alga (Turmel et al. 1999a, b). Moreover, the organellar genomes in O. tauri and ...
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... O. tauri mitochondrial RPR is 269 nts long and has a 37% GC content, while the plastid RPR is 327 nts long with 29% GC content (Fig. 6a). The predicted secondary structures of these O. tauri RPRs (Fig. 6a) agree with the bacterial consensus and contain all the universally con- served nucleotides (Chen and Pace 1997;Brown 1999;Marquez et al. 2005;Gopalan 2007). However, the second- ary structure of these AU-rich O. tauri organellar RPRs, when compared to bacterial ...
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... O. tauri mitochondrial RPR is 269 nts long and has a 37% GC content, while the plastid RPR is 327 nts long with 29% GC content (Fig. 6a). The predicted secondary structures of these O. tauri RPRs (Fig. 6a) agree with the bacterial consensus and contain all the universally con- served nucleotides (Chen and Pace 1997;Brown 1999;Marquez et al. 2005;Gopalan 2007). However, the second- ary structure of these AU-rich O. tauri organellar RPRs, when compared to bacterial prototypes, show notable diVerences that likely account for the absence of ...
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... to embarking on biochemical studies, we inquired if the putative O. tauri organellar RPRs are expressed in vivo. RT-PCR using gene-speciWc oligonucleotides and total RNA as the template revealed that these two non-cod- ing RNAs are indeed expressed in O. tauri (Fig. 6b). DNA sequencing of these RT-PCR products, which encompass most of the predicted RPR sequences, conWrmed their iden- tity. We assayed these O. tauri organellar RPRs under a number of diVerent conditions (including diVerent pre- tRNA substrates, temperature, pH, and range of divalent/ monovalent ion concentrations) but have been unable ...
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... 5), arguing against the presence of a cleavable transit peptide for import into organelles. It is not possible, however, to rule out aberrant migration arising from post-translational modiWcations of a shorter version. Second, the O. tauri mitochondrial and chloroplast genomes each encode a bac- terial RPR-like RNA, which is expressed in vivo (Fig. 6). Schematic summarizing the RNase P components encoded by each of the three O. tauri genomes. They were identiWed based on sequence homology However, the exact functions of these RPRs remain to be determined. Third, we have now demonstrated that a recombinant version of O. tauri PRORP supports pre-tRNA 5-processing in vitro (Fig. 7), ...
Citations
... However, the RNase P status of Ostreococcus tauri, another unicellular green algal species belonging to the Chlorophyta division, seems more complex. The nuclear genome of O. tauri solely encodes the Pop5 and Rpp30 protein subunits instead of a full set of the protein components required for a putative eukaryotic RNP RNase P. In addition, it encodes a bacterial RPP-like protein that was shown to be functional in vitro upon reconstitution with bacterial RPR (Lai et al., 2011) and a OtPRORP, homologous to AtPRORP1, that is functionally active in vitro, possibly localizing to organelles. Interestingly, the O. tauri organellar genome also encodes a bacterial RPR-like RNA of unknown functional significance (Lai et al., 2011). ...
... The nuclear genome of O. tauri solely encodes the Pop5 and Rpp30 protein subunits instead of a full set of the protein components required for a putative eukaryotic RNP RNase P. In addition, it encodes a bacterial RPP-like protein that was shown to be functional in vitro upon reconstitution with bacterial RPR (Lai et al., 2011) and a OtPRORP, homologous to AtPRORP1, that is functionally active in vitro, possibly localizing to organelles. Interestingly, the O. tauri organellar genome also encodes a bacterial RPR-like RNA of unknown functional significance (Lai et al., 2011). The CrPRORP and OtPRORP await further structural characterization. ...
... The suitably altered archaeal RPR C-domain could functionally replace the E. coli RPR C-domain (Li et al., 2011), indicating that common structural elements conserved across organisms are key to achieve RNase P functionality. The RNase P protein subunit encoded in the nucleus of O. tauri could effectively be reconstituted with bacterial RPRs but not with its own organellar RPRs (Lai et al., 2011). RNase P activity could also be achieved by the reconstitution of plastid RPR and bacterial RPP (Li et al., 2007;Pascual & Vioque, 1999). ...
The precursor transfer RNAs (pre‐tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5′‐processing, 3′‐processing, modifications at specific sites, if any, and 3′‐CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre‐tRNA sequences at the 5′ end by the removal of phosphodiester linkages between nucleotides at position −1 and +1. Except for an archaeal species: Nanoarchaeum equitan s where tRNAs are transcribed from leaderless‐position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion‐mediated conserved catalytic reaction. While the canonical RNA‐based ribonucleoprotein RNase P has been well‐known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA‐free protein‐only RNase P in eukaryotes and RNA‐free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA‐based and RNA‐free RNase P holoenzymes towards harnessing critical RNA–protein and protein–protein interactions in achieving conserved pre‐tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications.
This article is categorized under: RNA Processing > tRNA Processing
RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution
RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes
... In the eukaryal domain, the RNase P family encompasses ribonucleoproteins of various le v els of complexity, as well as a class of comparati v ely 'simple', 2 Nucleic Acids Research, 2023 monomeric 60-kDa protein enzymes called pro teinaceous R Nase P (PR ORP) ( 10 , 11 ). PR ORP proteins function as RNase P in the nucleus, mitochondria, and / or plastids of land plants , algae , trypanosomes , and probab ly se v eral other eukaryal groups (12)(13)(14)(15)(16)(17)(18). Also, human mtRNase P comprises a PRORP protein (also known as MRPP3) as endonuclease, but it r equir es two additional essential protein subunits that have further functions, unrelated to their role as RNase P subunits ( 9 , 19 ): short-chain dehydro genase / reductase famil y 5C member 1 (SDR5C1, also MRPP2 or HSD17B10) catalyzes the penultimate step in the -oxidation of short branched-chain fatty and amino acids ( 20 ), and tRNA methyltr ansfer ase 10C (TRMT10C, also MRPP1) forms a stable subcomplex with SDR5C1 that constitutes the methyltr ansfer ase responsible for N 1methylation of purines at position 9 of mitochondrial tRNAs ( 19 ). ...
... With the identification of the subunits of human mtRNase P, we originally found all three proteins to be r equir ed for the r econstitution of the pr e-tRNAcleavage acti vity ( 9 ). Howe v er, the recombinant forms of various PRORP homologs later identified in plants or protists were found to have RNase P activity on their own, without the involvement of additional proteins (12)(13)(14)(15)(16)(17). The ar chitectur e of human PRORP mor eover shows all the defining features generally found in PRORP homologs ( 18 ), i.e. a characteristic C-terminal NYN metallonuclease domain, an N-terminal ␣-super helical domain containing penta tricopeptide repea t (PPR) motifs, and a bipartite zincbinding module connecting these two domains, in a largely identical three-dimensional arrangement ( 22 ). ...
RNase P is the endonuclease responsible for the 5′ processing of precursor tRNAs (pre-tRNAs). Unlike the single-subunit protein-only RNase P (PRORP) found in plants or protists, human mitochondrial RNase P is a multi-enzyme assembly that in addition to the homologous PRORP subunit comprises a methyltransferase (TRMT10C) and a dehydrogenase (SDR5C1) subunit; these proteins, but not their enzymatic activities, are required for efficient pre-tRNA cleavage. Here we report a kinetic analysis of the cleavage reaction by human PRORP and its interplay with TRMT10C-SDR5C1 including 12 different mitochondrial pre-tRNAs. Surprisingly, we found that PRORP alone binds pre-tRNAs with nanomolar affinity and can even cleave some of them at reduced efficiency without the other subunits. Thus, the ancient binding mode, involving the tRNA elbow and PRORP’s PPR domain, appears basically retained by human PRORP, and its metallonuclease domain is in principle correctly folded and functional. Our findings support a model according to which the main function of TRMT10C-SDR5C1 is to direct PRORP’s nuclease domain to the cleavage site, thereby increasing the rate and accuracy of cleavage. This functional dependence of human PRORP on an extra tRNA-binding protein complex likely reflects an evolutionary adaptation to the erosion of canonical structural features in mitochondrial tRNAs.
... This is true for several fungal lineages, basal Chlorophyta algae and jakobids [7]. The protein moiety is often encoded in the nucleus and imported from the cytosol [35][36][37]. The RNA moieties in these organisms can be very similar to the bacterial counterpart, but still to date no functional proof of activity was obtained in vitro with solely these RNAs supplemented or not with their proper protein subunits. ...
... The RNP RNase P in mitochondria seems to be replaced over evolution by another type of RNase P with a single protein component: PRORP. Indeed, even if discovered as a protein complex in human mitochondria [38], there is no doubt that in the remaining phyla PRORP is active without any helpers [32,36,39,40]. PRORP has "invaded" various phyla and is present in metazoan mitochondria solely, streptophytes and most of the Chlorophyta algae mitochondria, the TSAR group contains mainly organisms with PRORP enzymes that are predicted to be localized in mitochondria, and finally the euglenozoan mitochondria (Trypanosoma) [7]. ...
... Still, in most cases, we can imagine a bacterial-like enzyme with probably addition of one or more protein partners. Indeed, as explained earlier, no RNase P activity could be obtained with only the two classical components for mitochondrial RNase P [36,37]. ...
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
... How 5 pre-tRNA processing was carried out in the apparent absence of RNP RNase P in plant cells and organelles in eukaryotic cells was a mystery until the discovery of PRORP in 2008. PRORP was initially found in human mitochondria (12,13) and subsequently found in the organelles and nuclei of the model plant A. thaliana (14,15), the alga Ostreococcus tauri (16), the protozoan Trypanosoma brucei (17) and the moss Physcomitrella patens (18). A recent bioinformatics analysis described that PRORP proteins are widely present in four out of the five main eukaryotic supergroups (apparently absent in Amoebozoa), and that the occurrence of RNP RNase P and PRORP proteins seems mutually exclusive in genetic compartments of modern Eukarya (19). ...
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.
... Andalucia mtDNA encodes a bacterial-type RNase P RNA [30], and we retrieved a mitochondrion-targeted ortholog of RnpA, the protein component of bacterial RNase P. The putative Andalucia protein is highly diverged compared to its bacterial counterparts but it does display the specific RnpA domain (COG0594) that contains most of the conserved residues that have been implicated in RnpA function [96]. Bacterial-type RnpA orthologs have previously been reported in several prasinophyte algae [97], although their subcellular localization (mitochondrion or plastid) has not been established. ...
Background:
Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date.
Results:
In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids.
Conclusions:
As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.
... Protein-based RNase P, the focus of this study, falls into two broad classes: HARP (Homologs of Aquifex RNase P), a ~23 kDa protein found thus far in bacteria and archaea (7); PRORP (PRotein-Only RNase P), a ~60 kDa protein present in four of the five eukaryal supergroups (Amoebozoa being the exception) (12). Single-polypeptide recombinant HARP from bacteria/archaea and PRORPs from algae, plants, and protists are active in vitro, and cleave a variety of pre-tRNA and non-tRNA substrates (7,(13)(14)(15)(16)(17)(18). In Arabidopsis thaliana (At), a dicot plant, three PRORP isoenzymes are present; AtPRORPs1, AtPRORPs2, and AtPRORPs3 (13). ...
RNase P catalyzes removal of the 5′ leader from precursor tRNAs (pre-tRNAs) in all three domains of life. Some eukaryotic cells contain multiple forms of the protein-only RNase P (PRORP) variant, prompting efforts to unravel this seeming redundancy. Previous studies concluded that there were only modest differences in the processing of typical pre-tRNAs by the three isoforms in Arabidopsis thaliana [AtPRORP1 (organellar), AtPRORP2 and AtPRORP3 (nuclear)]. Here, we investigated if different physical attributes of the three isoforms might engender payoffs under specific conditions. Our temperature–activity profiling studies revealed that AtPRORPs display substrate-identity dependent behavior at elevated temperatures (37–45 °C), with the organellar variant outperforming the nuclear counterparts. Echoing these findings, molecular dynamics simulations revealed that AtPRORP2 relative to AtPRORP1 samples a wider conformational ensemble that deviates from the crystal structure. Results from our biochemical studies and molecular dynamics simulations support the idea that AtPRORPs have overlapping but not necessarily redundant attributes and inspire new perspectives on the suitability of each variant to perform its function(s) in a specific cellular locale.
... In many eukaryotic species, including protists, algae, land plants, and metazoans, protein-only RNase Ps (PRORPs) have been identified (Holzmann et al. 2008;Gobert et al. 2010;Lai et al. 2011;Taschner et al. 2012). Human mitochondrial RNase P (mtRNase P) was the first PRORP described and it requires two additional protein subunits for activity (Holzmann et al. 2008). ...
... In contrast to the metazoan PRORP, the PRORPs from algae, protists, and plants do not require additional subunits for efficient catalysis in vitro (Gobert et al. 2010;Lai et al. 2011;Gutmann et al. 2012;Taschner et al. 2012;Sugita et al. 2014;Howard et al. 2015;Bonnard et al. 2016), suggesting differences in substrate recognition. The three PRORPs from Arabidopsis thaliana are designated PRORP1-3. ...
Protein-only ribonuclease P (PRORP) is an enzyme responsible for catalyzing the 5' end maturation of precursor transfer ribonucleic acids (pre-tRNAs) encoded by various cellular compartments in many eukaryotes. PRORPs from plants act as single-subunit enzymes and have been used as a model system for analyzing the function of the metazoan PRORP nuclease subunit, which requires two additional proteins for efficient catalysis. There are currently few molecular details known about the PRORP-pre-tRNA complex. Here, we characterize the determinants of substrate recognition by the single subunit Arabidopsis thaliana PRORP1 and PRORP2 using kinetic and thermodynamic experiments. The salt dependence of binding affinity suggests 4-5 contacts with backbone phosphodiester bonds on substrates, including a single phosphodiester contact with the pre-tRNA 5' leader, consistent with prior reports of short leader requirements. PRORPs contain an N-terminal pentatricopeptide repeat (PPR) domain, truncation of which results in > 30-fold decrease in substrate affinity. While most PPR-containing proteins have been implicated in single-stranded sequence specific RNA recognition, we find that the PPR motifs of PRORPs recognize pre-tRNA substrates differently. Notably, the PPR domain residues most important for substrate binding in PRORPs do not correspond to positions involved in base recognition in other PPR proteins. Several of these residues are highly conserved in PRORPs from algae, plants, and metazoans, suggesting a conserved strategy for substrate recognition by the PRORP PPR domain. Furthermore, there is no evidence for sequence specific interactions. This work clarifies molecular determinants of PRORP-substrate recognition and provides a new predictive model for the PRORP-substrate complex.
... However, no rnpB gene was found in the mitochondrial genomes of all glaucophytes and red alga sequenced to date. Furthermore, the functionality of the aforementioned P RNAs is questionable, as the mitochondrial or plastidial P RNAs of Ostreococcus tauri, Micromonas RCC299 and Pycnococcus provasoli (basal green algae), the mt-or pt-P RNA, and the pt-P RNA from various red algae, did not show any RNase P activity (either alone or in complex with their putative protein partners) (Lai et al. 2011;Bernal-Bayard et al. 2014). ...
... Similarly, the search for RNase P proteins in Cyanidioschizon merola and Galdieria sulphuraria nuclear genome databases did not identify clear candidates when either green algae, cyanobacterial or -proteobacterial rnpA sequences were used as queries (Matsuzaki et al. 2004;Barbier et al. 2005). In contrast, in Mammiellophyceae of the Chlorophyta lineage, rnpA-like genes are encoded in several nuclear genomes (e.g. in Ostreoccocus, Micromonas and Bathycoccus) (Lai et al. 2011); they are predicted to localize to mitochondria and plastids (supplementary table. S2). ...
... The function of these extensions is unknown, but might be involved in specific contacts with algae organellar P RNAs or with other yet unidentified proteins. The RnpA homologue of O. tauri was shown to be functional in association with E. coli P RNA, but not with the endogenous P RNA encoded in the mitochondrial and chloroplast genomes (Lai et al. 2011). Thus, supplementary protein cofactors are most likely required in vivo if the P RNA candidate of O. tauri indeed serves as a genuine component of a functional organellar RNP RNase P. ...
... PRORP proteins were initially described in human mitochondria and in the organelles and nucleus of the model plant Arabidopsis thaliana [20][21][22][23]. They were also characterized in Trypanosoma brucei nucleus and mitochondria [24], and in other species of the green lineage, i.e., Ostreococcus tauri [25], the moss Physcomitrella patens [26], and the model green algae Chlamydomonas reinhardtii [27]. Interestingly, while separate RNase P enzymes were always found in the nucleus and organelles of eukaryotes (either multiple RNPs, multiple PRORPs or a combination of both), Chlamydomonas utilizes a single PRORP protein for RNase P activity in the nucleus, mitochondria and the chloroplast, thus making the most compact and versatile RNase P machinery described to date in both prokaryotes and eukaryotes [27]. ...
RNase P, the essential activity that performs the 5' maturation of tRNA precursors, can be achieved either by ribonucleoproteins containing a ribozyme present in the three domains of life or by protein-only enzymes called protein-only RNase P (PRORP) that occur in eukaryote nuclei and organelles. A fast growing list of studies has investigated three-dimensional structures and mode of action of PRORP proteins. Results suggest that similar to ribozymes, PRORP proteins have two main domains. A clear functional analogy can be drawn between the specificity domain of the RNase P ribozyme and PRORP pentatricopeptide repeat domain, and between the ribozyme catalytic domain and PRORP N4BP1, YacP-like Nuclease domain. Moreover, both types of enzymes appear to dock with the acceptor arm of tRNA precursors and make specific contacts with the corner of pre-tRNAs. While some clear differences can still be delineated between PRORP and ribonucleoprotein (RNP) RNase P, the two types of enzymes seem to use, fundamentally, the same catalytic mechanism involving two metal ions. The occurrence of PRORP and RNP RNase P represents a remarkable example of convergent evolution. It might be the unique witness of an ongoing replacement of catalytic RNAs by proteins for enzymatic activities.
... The alga Ostreococcus tauri encodes RNase P RNAs in its mitochondrial and plastid genomes, but not in the nuclear genome, which instead encodes a PRORP [62]. The RNase P RNAs associate with a nuclear-encoded bacterial-like P protein and catalyze pre-tRNA cleavage in vitro [62]. ...
... The alga Ostreococcus tauri encodes RNase P RNAs in its mitochondrial and plastid genomes, but not in the nuclear genome, which instead encodes a PRORP [62]. The RNase P RNAs associate with a nuclear-encoded bacterial-like P protein and catalyze pre-tRNA cleavage in vitro [62]. Further, the O. tauri RNA-based RNase P protein complements growth of E. coli that encode a bacterial P protein with a temperature-sensitive mutation at the restrictive temperature [62]. ...
... The RNase P RNAs associate with a nuclear-encoded bacterial-like P protein and catalyze pre-tRNA cleavage in vitro [62]. Further, the O. tauri RNA-based RNase P protein complements growth of E. coli that encode a bacterial P protein with a temperature-sensitive mutation at the restrictive temperature [62]. The retention of organelle-encoded P RNAs in Fungi and some algae indicate that these enzymes were present in basal eukaryotic lineages, but have been replaced by PRORP in clades as diverse as land plants and mammals. ...
Ribonuclease P (RNase P) is an essential endonuclease responsible for catalyzing 5’ end maturation in precursor transfer RNAs. Since its discovery in the 1970s, RNase P enzymes have been identified and studied throughout the three domains of life. Interestingly, RNase P is either RNA-based, with a catalytic RNA subunit, or a protein-only (PRORP) enzyme with differential evolutionary distribution. The available structural data, including the active site data, provides insight into catalysis and substrate recognition. The hydrolytic and kinetic mechanisms of the two forms of RNase P enzymes are similar, yet features unique to the RNA-based and PRORP enzymes are consistent with different evolutionary origins. The various RNase P enzymes, in addition to their primary role in tRNA 5’ maturation, catalyze cleavage of a variety of alternative substrates, indicating a diversification of RNase P function in vivo. The review concludes with a discussion of recent advances and interesting research directions in the field.
