Small Ribonucleic Acids of Escherichia coli: II. NONCOORDINATE ACCUMULATION DURING STRINGENT CONTROL

Abstract

Abstract The accumulation of small RNAs (4 to 6 S) in Escherichia coli during amino acid starvation has been studied by 10% polyacrylamide gel electrophoresis and two-dimensional fingerprint analysis. In CP78, a stringent (rel+) strain, RNA labeled with 32PO43- during amino acid starvation has a gel electrophoresis pattern that is very different from that of nonstarved cells. However, in CP79, a relaxed (rel-) mutant, RNA labeled during starvation has a gel pattern similar to normal. During starvation of the stringent strain, 32PO43- labeling of 5 S RNA, 4.5 S RNA, and most tRNAs is reduced to about 5% normal. The accumulation of an unstable molecule containing dihydrouracil, with an electrophoretic mobility similar to that of 6 S RNA, is also reduced. In contrast, 6 S RNA (which is stable) and an unstable molecule with GTP at its 5' end are much less severely reduced, if at all. Thus the accumulation of these molecules during stringent control is noncoordinate and the inhibition of accumulation is not necessarily correlated with metabolic stability. When cells of the stringent strain are treated with the antibiotic trimethoprim, an undermethylated form of tRNALeu1 appears as the most highly labeled single species of the small RNAs. Trimethoprim treatment reduces both the level of bulk tRNA labeling and the extent of tRNA methylation. These effects of trimethoprim are inhibited by the addition of methionine to the medium. The various RNA molecules are labeled with different kinetics. In short labeling periods the GTP-starting unstable molecule is one of the most highly labeled species. From radioactivity pulse-chase experiments under normal and starvation conditions it was found that amino acid starvation does not seem to affect the stability of the RNAs.