Polyadenylation promotes degradation of 3′-structured RNA by the Escherichia coli RNA degradosome in vitro

University of Oxford, Oxford, England, United Kingdom
Journal of Biological Chemistry (Impact Factor: 4.57). 03/1999; 274(7):4009-16. DOI: 10.1074/jbc.274.7.4009
Source: PubMed


Polyadenylation contributes to the destabilization of bacterial mRNA. We have investigated the role of polyadenylation in the degradation of RNA by the purified Escherichia coli degradosome in vitro. RNA molecules with 3'-ends incorporated into a stable stem-loop structure could not readily be degraded by purified polynucleotide phosphorylase or by the degradosome, even though the degradosome contains active RhlB helicase which normally facilitates degradation of structured RNA. The exoribonucleolytic activity of the degradosome was due to polynucleotide phosphorylase, rather than the recently reported exonucleolytic activity exhibited by a purified fragment of RNase E (Huang, H., Liao, J., and Cohen, S. N. (1998) Nature 391, 99-102). Addition of a 3'-poly(A) tail stimulated degradation by the degradosome. As few as 5 adenosine residues were sufficient to achieve this stimulation, and generic sequences were equally effective. The data show that the degradosome requires a single-stranded "toehold" 3' to a secondary structure to recognize and degrade the RNA molecule efficiently; polyadenylation can provide this single-stranded 3'-end. Significantly, oligo(G) and oligo(U) tails were unable to stimulate degradation; for oligo(G), at least, this is probably due to the formation of a G quartet structure which makes the 3'-end inaccessible. The inaccessibility of 3'-oligo(U) sequences is likely to have a role in stabilization of RNA molecules generated by Rho-independent terminators.

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    • "The 5 0 region of AsxR is complementary to the single-stranded loop of the FnrS Rho-independent terminator. FnrS was destabilized by AsxR, consistent with AsxR hybridization unfolding the terminator stem that protects the 3 0 end from exonucleolytic attack (Blum et al., 1999; Cisneros et al., 1996; Figueroa-Bossi et al., 2009). A similar mechanism of sRNA destabilization has been proposed for ChiX (MicM), an sRNA that is destabilized by an intercistronic region of the chbBC transcript with complementarity to the terminator stem of ChiX (Figueroa-Bossi et al., 2009). "
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