Metal ion and substrate structure dependence of the processing of tRNA precursors by RNase P and M1 RNA

A synthetic tRNA precursor analog containing the structural elements of Escherichia coli tRNA(Phe) was characterized as a substrate for E. coli ribonuclease P and for M1 RNA, the catalytic RNA subunit. Processing of the synthetic precursor exhibited a Mg²⁺ dependence quite similar to that of natural tRNA precursors such as E. coli tRNA(Tyr) precursor. It was found that Sr²⁺, Ca²⁺, and Ba²⁺ ions promoted processing of the dimeric precursor at Mg²⁺ concentrations otherwise insufficient to support processing; very similar behavior was noted for E. coli tRNA(Tyr). As noted previously for natural tRNA precursors, the absence of the 3'-terminal CA sequence in the synthetic precursor diminished the facility of processing of this substrate by RNase P and M1 RNA. A study of the Mg²⁺ dependence of processing of the synthetic tRNA dimeric substrate radiolabeled between C⁷⁵ and A⁷⁶ provided unequivocal evidence for an alteration in the actual site of processing by E. coli RNase P as a function of Mg²⁺ concentration. This property was subsequently demonstrated to obtain (Carter, B.J., Vold, B.S., and Hecht, S.M. (1990) J. Biol. Chem. 265, 7100-7103) for a mutant Bacillus subtilis tRNA(His) precursor containing a potential A-C base pair at the end of the acceptor stem.