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Ribonuclease P is the ubiquitous endonuclease that generates the mature 5′-ends of precursor tRNAs. In bacteria, the enzyme is composed of a catalytic RNA (∼400 nucleotides) and a small essential protein subunit (∼13 kDa). Most bacterial RNase P RNAs (P RNAs) belong to the architectural type A; type B RNase P RNA is confined to the low-G+C Gram-positive bacteria. Here we demonstrate that the L5.1-L15.1 intradomain contact in the catalytic domain of the prototypic type B RNase P RNA of  Bacillus subtilis  is crucial for adopting a compact functional conformation: Disruption of the L5.1-L15.1 contact by antisense oligonucleotides or mutation reduced P RNA-alone and holoenzyme activity by one to two orders of magnitude in vitro, largely retarded gel mobility of the RNA and further affected the structure of regions P7/P8/P10.1, P15 and L15.2, and abolished the ability of  B. subtilis  P RNA to complement a P RNA-deficient  Escherichia coli  strain. We also provide mutational evidence that an L9-P1 tertiary contact, as found in some  Mycoplasma  type B RNAs, is not formed in canonical type B RNAs as represented by  B. subtilis  P RNA. We finally explored the P5.1 and P15 stem–loop structures as targets for LNA-modified antisense oligonucleotides. Oligonucleotides targeting P15, but not those directed against P5.1, were found to efficiently anneal to P RNA and to inhibit activity (IC 50  of ∼2 nM) when incubated with preassembled  B. subtilis  RNase P holoenzymes.

Bacterial type B RNase P: functional characterization of the L5.1-L15.1 tertiary contact and antisense inhibition