We investigated the catalytic efficiency and the
specificity of the Bacillus subtilis RNase P holoenzyme
reaction with substrates that contain a single strand,
a hairpin loop, or a tRNA 3′ to the cleavage site.
At a saturating ribozyme concentration, RNase P can cleave
a single-stranded RNA at ∼0.6 min−1
at pH 7.8. Replacing the single-stranded RNA 3′ to
the cleavage site by a hairpin loop or by the yeast tRNAPhe
increases the cleavage rate by up to ∼600-fold and
∼3,200-fold, respectively. These results show that
compared to a single-stranded RNA substrate, the cleavage
rate for the holoenzyme reaction is primarily enhanced
by an acceptor-stem-like helix. Substrate binding, ∼7–10
μM for a single-stranded RNA, improves by ∼1,000-fold
upon the addition of the tRNA. The efficiency of the RNase
P holoenzyme cleaving a single-stranded RNA is sufficiently
high to consider autolytic processing of the RNase P RNA
(denoted P RNA) transcript in the cell. The addition of
the RNase P protein to a precursor form of the P RNA in
vitro results in autolytic processing of the 5′ and
the 3′ end of this precursor in a matter of minutes.
Autolytic processing produces the reported 5′ end
of the mature P RNA. The precise 3′ end generated
by autolytic processing is different over the course of
the reaction and the final product is 4 nt shorter than
the reported 3′ end of the B. subtilis P
RNA. The observed 3′ end in vitro is consistent with
the property of the holoenzyme reaction with single-stranded
RNA substrates. The discrepancy with the reported 3′
end may be due to other processing events in vivo or inaccurate
determination of the mature 3′ end of the P RNA isolated
from the cell. We propose that the mature B. subtilis
P RNA is generated at least in part by autolytic processing
upon the binding of the RNase P protein to the precursor P RNA.