Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae

Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA.
RNA (Impact Factor: 4.94). 06/2011; 17(8):1441-50. DOI: 10.1261/rna.2737511
Source: PubMed


Ribonuclease P (RNase P) is an essential endoribonuclease that catalyzes the cleavage of the 5' leader of pre-tRNAs. In addition, a growing number of non-tRNA substrates have been identified in various organisms. RNase P varies in composition, as bacterial RNase P contains a catalytic RNA core and one protein subunit, while eukaryotic nuclear RNase P retains the catalytic RNA but has at least nine protein subunits. The additional eukaryotic protein subunits most likely provide additional functionality to RNase P, with one possibility being additional RNA recognition capabilities. To investigate the possible range of additional RNase P substrates in vivo, a strand-specific, high-density microarray was used to analyze what RNA accumulates with a mutation in the catalytic RNA subunit of nuclear RNase P in Saccharomyces cerevisiae. A wide variety of noncoding RNAs were shown to accumulate, suggesting that nuclear RNase P participates in the turnover of normally unstable nuclear RNAs. In some cases, the accumulated noncoding RNAs were shown to be antisense to transcripts that commensurately decreased in abundance. Pre-mRNAs containing introns also accumulated broadly, consistent with either compromised splicing or failure to efficiently turn over pre-mRNAs that do not enter the splicing pathway. Taken together with the high complexity of the nuclear RNase P holoenzyme and its relatively nonspecific capacity to bind and cleave mixed sequence RNAs, these data suggest that nuclear RNase P facilitates turnover of nuclear RNAs in addition to its role in pre-tRNA biogenesis.

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Available from: Lars M Steinmetz, May 29, 2014
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    • "Although RNase MRP is structurally and evolutionarily related to RNase P, the substrate specificities of the two enzymes differ (20,24–26,49,50,65–67). The recognition of the ‘canonical’ RNase P substrate, pre-tRNA, involves interactions between the T- and D-loops of the substrate and the specificity (S-) domain of the RNA component (40,42,48). "
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    ABSTRACT: Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.
    Full-text · Article · May 2013 · Nucleic Acids Research
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    • "RNA-based RNase P is a ribonucleoprotein complex found in practically all organisms (Altman 2010). RNase P is universally responsible for the maturation of the 59 end of tRNA and is involved in the metabolism of a variety of other RNA molecules (Coughlin et al. 2008; Altman 2010; Marvin et al. 2011a); in addition, human RNase P was suggested to play a role in transcription (Reiner et al. 2006, 2008). The well-conserved RNA component of RNase P (Chen and Pace 1997) is the catalytic subunit of the enzyme in all domains of life (Guerrier-Takada et al. 1983; Pannucci et al. 1999; Thomas et al. 2000; Kikovska et al. 2007; Li et al. 2009). "
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    ABSTRACT: Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA-protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes.
    Preview · Article · Feb 2012 · RNA
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    • "Bacterial RNase P processes precursors to 4.5S RNA and tmRNA, select viral RNAs, C4 antisense RNA from bacteriophage P1 and P7, and some mRNAs, not all of which have a tRNA-like motif (44–49). Recently, human and yeast RNase P have been implicated in processing certain short-lived non-coding (nc) RNAs and mRNAs, and shown to even cleave single-stranded (ss) RNAs (50–56); intriguingly, common recognition determinants (tRNA-like or otherwise) in these substrates are not apparent. While the biological significance of processing these non-tRNA substrates by human/yeast RNase P remains to be uncovered, these findings reveal an unexpected expansion in the repertoire of substrates of eukaryotic RNase P and provide a possible basis for the association of the eukaryotic (and archaeal) RPR with multiple RPPs. "
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    ABSTRACT: RNase P, which catalyzes tRNA 5′-maturation, typically comprises a catalytic RNase P RNA (RPR) and a varying number of RNase P proteins (RPPs): 1 in bacteria, at least 4 in archaea and 9 in eukarya. The four archaeal RPPs have eukaryotic homologs and function as heterodimers (POP5•RPP30 and RPP21•RPP29). By studying the archaeal Methanocaldococcus jannaschii RPR's cis cleavage of precursor tRNAGln (pre-tRNAGln), which lacks certain consensus structures/sequences needed for substrate recognition, we demonstrate that RPP21•RPP29 and POP5•RPP30 can rescue the RPR's mis-cleavage tendency independently by 4-fold and together by 25-fold, suggesting that they operate by distinct mechanisms. This synergistic and preferential shift toward correct cleavage results from the ability of archaeal RPPs to selectively increase the RPR's apparent rate of correct cleavage by 11 140-fold, compared to only 480-fold for mis-cleavage. Moreover, POP5•RPP30, like the bacterial RPP, helps normalize the RPR's rates of cleavage of non-consensus and consensus pre-tRNAs. We also show that archaeal and eukaryal RNase P, compared to their bacterial relatives, exhibit higher fidelity of 5′-maturation of pre-tRNAGln and some of its mutant derivatives. Our results suggest that protein-rich RNase P variants might have evolved to support flexibility in substrate recognition while catalyzing efficient, high-fidelity 5′-processing.
    Full-text · Article · Jan 2012 · Nucleic Acids Research
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