Selective decay of Escherichia coli dnaG messenger RNA is initiated by RNase E.

The rpsU-dnaG-rpoD operon messenger RNA that encodes S21, primase, and sigma-70 is cleaved under normal physiological conditions. The dnaG coding portion of the mRNA is then rapidly degraded. An endonuclease activity has been isolated from wild type Escherichia coli cells that cleaves dnaG mRNA. This activity has been identified as RNase E, and the identity confirmed by the accumulation of the unprocessed operon polycistronic mRNA in RNase E mutants, rne-3071 and ams-1, when incubated at nonpermissive temperatures. Extracts prepared from RNase E mutant strains failed to cleave dnaG mRNA in vitro. The dnaG mRNA RNase E cleavage site (5'-AAGUGAUUUA-3') is only 50% homologous to the ribosomal RNA RNase E cleavage site. By using computer programs predicting secondary structure, the dnaG RNase E cleavage site appears to be in a single stranded RNA loop.