Poly(A)- and poly(U)-specific RNA 3′ tail shortening by E. coli ribonuclease E

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Ribonuclease (RNase) E is an extensively studied enzyme from Escherichia coli whose site-specific endoribonuclease activity on single-stranded RNA has a central role in the processing of ribosomal RNA, the degradation of messenger RNA and the control of replication of ColE1-type plasmids (for recent reviews, see 13). Here we report a previously undetected activity of RNase E: the ability to shorten 3′ poly(A)- and poly(U)-homopolymer tails on RNA molecules. This activity, which leaves a 6-nucleotide adenylate or a 1-nucleotide uridylate remnant on primary transcripts, resides in the amino-terminal region of RNase E and does not require other protein cofactors. Addition of a 3′-terminal phosphate group prevents both removal of the poly(A) tail and endonucleolytic cleavage within primary transcripts, but has no effect on the cleavage of transcripts with tails that have already been truncated. The ability of RNase E to shorten poly(A) tails, together with the effect of tail length on endonucleolytic cleavage within primary transcripts, suggests a mechanism by which RNase E may exercise overall control over RNA decay.

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Figure 1: Purification of RNase E.
Figure 2: Poly(A)- and poly(U)-specific exonucleolytic activity of purified RNase E.
Figure 3: Elimination of both poly(A)-tail removal and endonucleolytic activity of N-Rne by 3′ terminal addition of [32P]AP to RNAI-40A.


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These studies were supported by a grant for mthe US NIH. We thank Y. Feng for his-tagged PAP I constructs, and J. Belasco, R. Lehman and C. Higgins for comments on this manuscript.

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Correspondence to Stanley, N. Cohen.

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