RNase P RNA

Proteins that bind to the RNA may influence the folding. As a consequence, patterns of sequence co-variations that have evolved for RNAs that are functional in complexes with proteins (e. g., rRNA, RNAse P-RNA) might not conform very well with predicted folding for the isolated RNA. 

Chen, J.-L., Nolan, J. M., Harris, M. E., and Pace, N. R. (1998). Comparative photocrosslinking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNAse P RNAs. EMBOJ. 17, 1515-1525. 

RNase P, which removes the 5 leader from tRNA transcripts, contains an RNA moiety in bacteria, eucarya, and archaea. The enzyme from Haloferax volcanii has been purified and the 345-nucleotide RNA portion used to generate a probe for cloning of the corresponding gene [123]. The sequence can be folded into a structure similar to that of bacterial RNase P RNAs. SI nuclease and primer extension localize the 5 end of the transcript adjacent to four potential archaeal promotor sequences. An in vitro transcript corresponding to the native RNA plus twenty 5 and nine 3 flanking nucleotides did not by itself exhibit RNase P activity (as bacterial RNase P RNAs do), under a variety of conditions. It was, however, able to reconstitute an active enzyme in combination with the protein moiety from Bacillus subtilis. This indicates that in Haloferax volcanii the RNase P RNA is the catalytic part of the enzyme but it may require some structural help [123]. 

RNase P cleaves a specific phosphodiester bond of tRNA precursors to form the mature 5 -end of tRNA. Bacterial RNase P is a natural occurring ribozyme composed of a catalytic RNA subunit and one or more proteins. Each bacterial RNAse P holoenzyme also consists of a small basic protein that stabilizes the folded structure of the RNA under physiological conditions. It may also help to discriminate pre-tRNA substrate from tRNA product and to mediate RNAse P dimerization. The three domains of life bacteria, Archaea, and Eukarya have similar structurally related RNAse P RNAs but different protein subunits this indicates that RNAse P is very ancient... 

Figure 2. Structure of the mouse PARP-2 gene and comparison with the mouse PARP-1 exon organization. The gene strucmre is shown with length in bp, as deduct from Southern blot analysis with PARP-2 cDNA oligonudeotide probes. PARP-2 exons (1-16) as well as RNase P RNA (HI RNA, GenBank accession number L08802) are represented as dosed boxes. Mouse PARP-1 protein and its intron-exon organization has been aligned with the mPARP-2 protein.lVLS, nudear localization signal. (Taken from Am et al, with permission).

Ame JC, Schreiber V, Frauiob V et al. A bidirectional promoter connects the poly(ADP-tibose) polymerase 2 (PARP-2) gene to the gene for RNase P RNA. structure and expression of the mouse PARP-2 gene. J Biol Chem 2001 276(14) 11092-9. 

One of the most striking evidence for the existence of modularity in RNA structure is the possibility of swapping one structural motif for another. Loop-loop interaction and -GNRA- elix contact have been successfully exchanged experimentally in group I introns (12,28,43 53). Very recently, phylogenetic evidence has shown that a similar swap occurs in bacterial RNase P RNAs (12,28,43,54). 

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