Stability of "spacer" sequences of pre-ribosomal RNA in Escherichia coli.

"SPACER" SEQUENCES OF AN RRNA gene transcript were detected with high efficiency by hybridization with DNA of the specilized transducing phase phi80rrn. Hybridization-competition studies revealed that 20 to 23% of the 30S precursor rRNA, obtained from E. coli mutant strain AB301/105, consist of "spacer" sequences. The "spacer" sequences formed hybrids with E. coli DNA, but not with Vibrio DNA. Experiments with RNA labeling in the presence of rifampicin showed that more than 80% of the spacer sequences arrive in full-length 30S pre rRNA chains before any cleavage of the RNA occurs. The hybridization assays also permitted the detection of "spacer" sequences in pulse-labeled rRNA of wild-type cells, in which the 30S pre-rRNA is already cleaved during its synthesis. Many of these "spacer" sequences degraded to alcohol-soluble materials with a half-life time of 1.2 min. The half-life was not lengthened by the treatment of cells with chloramphenicol, which stabilizes bulk mRNA. However, unstable "spacer" sequences transcribed in cells deficient in RNase III exhibited slower degradation, with a half-life time of about 9 min, whereas the cleavage of 30S pre-rRNA to smaller RNA species occurred with a half-life of about 3 min. These results are consistent with the notion that a rate-limiting action of RNase III in the initial attack leads to degradation of "spacer" sequences in rRNA gene transcript; and that degradation is not at all connected with ribosome translocation.