Differential evolution of substrates for an RNA enzyme in the presence and absence of its protein cofactor.

Selection of substrates for an RNA enzyme, the catalytic subunit of RNAase P from E. coli, has been carried out by simulation of evolution in vitro in the presence and absence of the protein cofactor of the enzyme. In the presence of the protein, substrates resembling precursor tRNAs, which were readily cleaved by the catalytic RNA, were selected in addition to others, with different sequences and structures (one of which resembled the precursor to 4.5S RNA) that were not readily cleaved by the catalytic RNA alone. The ribonucleoprotein enzyme is more versatile than the RNA enzyme, and our results suggest that it and 4.5S RNA may have evolved after ancestral tRNAs.