Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5′ and 3′ extremeties of the primary transcript

Abstract The degradation process of the rpsO mRNA is one of the best characterised in E coli . Two independent degradation pathways have been identified. The first one is initiated by an RNase E endonucleolytic cleavage which allows access to the transcript by polynucleotide phosphorylase and RNase II. Cleavage by RNase E-gives rise to an rpsO message lacking the stabilising hairpin of the primary transcript, this truncated mRNA is then degraded exonucleolytically from its 3′ terminus. This pathway might be coupled to the translation of the message. The second pathway allows degradation of polyadenylated rpsO mRNA independently of RNase II, PNPase and RNase E. The ribonucleases responsible for degradation of poly(A) mRNAs under these conditions are not known. Poly(A) tails have been proposed to facilitate the degradation of structured RNA by polynucleotide phosphorylase. In contrast, we believe that removal of poly(A) by RNase II stabilises the rpsO mRNA harbouring a 3′ hairpin. In addition to these two pathways, we have identified endonucleolytic cleavages which occur only in strains deficient for both RNase E and RNase III suggesting that these two endonucleases protect the 5′ leader of the mRNA from the attack of unidentified ribonuclease(s). Looping of the rpsO mRNA might explain how RNase E bound at the 5′ end can cleave at a site located just upstream the hairpin of the transcription terminator.