Maturatio of 5‐S rRNA: Ribonuclease E Cleavages and Their Dependence on Precursor Sequences

Abstract

9‐S RNA is a processing intermediate that accumulates in an RNase E⁻ strain of Escherichia coli. It spans from the RNase III cleavage site, after 23‐S rRNA, to the 3′ end of the transcript and is derived from rRNA genes which do not contain tRNAs distal to 5‐S rRNA. Here, we have studied the processing of 9‐S RNA with ribonuclease E. RNase E cleaves 9‐S RNA in two sites: one of these is three nucleotides upstream from the 5′ end of 5‐S rRNA, the other downstream from its 3′ end. Both cleavages are probably introduced by the same enzyme, since both cleavages are thermolabile when an extract of a temperature‐sensitive RNase E mutant was used for processing in vitro. In order to asses the role of 5′ and 3′ end precursor‐specific sequences in the RNase E reaction, we isolated the molecules lacking nucleotides at the 5′ or 3′ end. Molecules having the 5′ end of 9‐S RNA but missing nucleotides from the 3′ end (called 8‐S RNA) were as good a substrate for RNase E as 9‐S, RNA itself. However, molecules having the 3′ end of 9‐S RNA but the 5′ end of p5 (called 7‐S RNA), were less efficient substrates for RNase E. Finally, the removal of as little as seven nucleotides from the 5′ end of 8‐S RNA rendered it almost completely unstuitable as a substrate for RNase E.