Substrate recognition by human RNase P: identification of small, model substrates for the enzyme.

RNase P from HeLa cells can efficiently cleave tRNA precursor molecules in vitro but cannot cleave potential substrates from which the D, anticodon and variable loops and stems of the tRNA moiety have all been removed. However, molecules from which the latter subdomains have been removed individually do serve as substrates. We show here that molecules that contain only a 5' leader sequence, the acceptor stem and the T stem and loop of the tRNA domain, and a bulge as small as one nucleotide downstream from nucleotide 7 in the tRNA sequence at the junction of the two stems, can serve as substrates for human RNase P. The identity of the nucleotide in the bulge is important in determining both the efficiency of the cleavage and the conformation of the substrate and/or the enzyme-substrate complex. We also show that the human enzyme locates the appropriate site for cleavage of its substrates in part by 'measuring' the length of the helices in the acceptor and T stems in both model and natural substrates.