The ribonuclease-III-processing site near the 5′ end of an RNA precursor of bacteriophage T4 and its effect on termination

Abstract

Infection of RNase III− (rnc) Escherichia coli cells with bacteriophage T4Δ27, a deletion mutant missing seven out of the ten genes in the tRNA transciption unit, results in the accumulation of tRNA precursor (10.5‐SRNA) that contains the sequence of tRNAGln, tRNALeu and species 1 RNA [Pragai and Apirion (1981) J. Mol. Biol. 153, 619–630]. In vitro studies, using partially purified RNase III or cell extracts and 10.5‐S RNA as substrate, have revealed a cleavage site at the 5′ side of the molecule. A computerized secondry structure suggests that the RNase III cleavage site can be placed in a small bulge which could be part of a duplex structure and is adjacent to A‐A‐G and its complementry sequence U‐U‐U in the same relative relationship found for most RNase III cleavage sites were the adjacent sequences are (A‐A‐G/U‐U‐C). Under normal processing conditions (presence of RNase III) the 3′ end of the processed intermediate precursors, 10.1‐S and p2Sp1 RNAs, is C‐U‐U‐(U1–2)‐UOH, which is determined by a stem and loop structure that could serve as a rho‐independent termination single site. However, in the absence of RNase III, the accumulated 10.5‐S precursor RNA does not terminate at the same site and its 3′ end is shifted a few nucleotides downstream. Thus, RNase III, besides playing a role in processing of 10.5‐S RNA, also affects the termination of that molecule, even though both sites, the RNase III cleavage site and the termination site, are about 390 nucleotides apart.