Archaeal-bacterial chimeric RNase P RNAs: towards understanding RNA's architecture, function and evolution.

ABSTRACT

The higher protein content of archaeal RNase P (1 RNA+4 proteins) compared to the bacterial homologue (1 RNA+1 protein) correlates with a large loss of RNA-alone activity (i.e., in the absence of protein cofactors). Here we show, for the first time, that a catalytic (C) domain of an archaeal RNase P RNA (P RNA) can functionally replace the Escherichia coli C domain in a chimeric P RNA, to provide the essential RNase P function in E. coli cells. This adaptation was achieved by 1) three minor alterations in the archaeal C domain, 2) restoration of the L9-P1 interdomain contact that is found in bacterial and archaeal type A RNAs, and 3) installation of another interdomain contact (L18-P8) that is present in bacterial but absent in archaeal P RNAs. We conclude 1) that the C domains of bacterial and archaeal P RNAs of type A have been largely conserved since the evolutionary separation of bacteria and archaea, and 2) that the L18-P8 RNA-RNA contact has been replaced with protein-protein contacts in archaeal RNase P. Function of the chimeric P RNA in E. coli required overexpression of the E. coli RNase P protein to increase the RNA's reduced cellular levels; this was attributed to enhanced degradation of the chimeric P RNA.