Role of base G-2 of pre-tRNAfMet in cleavage site selection by Escherichia coli RNase P in vitro

In this study, a protocol for the purification of fully active Escherichia coli RNase P holoenzyme from a strain overproducing both the C5 protein and the M1 RNA components is described. A total of 0.8 mg of homogeneous enzyme, with a 1:1 protein/RNA subunit stoichiometry, was recovered from a 1 L bacterial culture. In addition, a convenient and reliable method based on capillary gel electrophoresis was developed to measure initial rates of pre-tRNA maturation by RNase P. Using these tools, the kinetic parameters of cleavage by RNase P of various mutants of pre-tRNA(fMet) showing maturation defects in vivo [Meinnel and Blanquet (1995) J. Biol. Chem. 270, 15906-15914] were investigated in vitro and the locations of cleavage sites were determined from the length of the various products of the reaction. The nucleotide at position -2 of pre-tRNA(fMet) is shown to be important only in the selection of the cleavage site, whereas it has no role in the efficiency of the reaction. It is concluded that base G(-2) acts as an antideterminant by preventing an alternative cleavage by RNase P. In addition, the presence of G(-2) alone is enough to fully compensate for the lack of a G at position +1 of pre-tRNA(fMet).