The RNA Degradosome of Escherichia coli: An mRNA-Degrading Machine Assembled on RNase E

Abstract

The RNA degradosome of Escherichia coli is a multiprotein complex involved in the degradation of mRNA. The principal components are RNase E, PNPase, RhlB, and enolase. RNase E is a large multidomain protein with an N-terminal catalytic region and a C-terminal noncatalytic region that is mostly natively unstructured protein. The noncatalytic region contains sites for binding RNA and for protein-protein interactions with other components of the RNA degradosome. Several recent studies suggest that there are alternative forms of the RNA degradosome depending on growth conditions or other factors. These alternative forms appear to modulate RNase E activity in the degradation of mRNA. RNA degradosome-like complexes appear to be conserved throughout the Proteobacteria, but there is a surprising variability in composition that might contribute to the adaptation of these bacteria to the enormously wide variety of niches in which they live.

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

“…RNase E is considered the rate-limiting enzyme for the degradation of many mRNAs 48 and for rRNA decay during carbon starvation and quality control. 24 It is also a major endoribonuclease in tRNA 49 and rRNA 50 maturation.…”

“…24 It is also a major endoribonuclease in tRNA 49 and rRNA 50 maturation. Furthermore, RNase E is a core member of the degradosome which is a multiprotein complex involved in RNA degradation 48 assembled on RNase E through PNPase, RhlB, and enolase binding to the C-terminal half of RNase E. 51-53 The degradosome is effective in structured RNA decay from duplex unwinding by the helicase RhIB. 54 For these reasons, we investigated whether RNase E may be involved in tRNA degradation after amino acid starvation.…”

DEAD-Box RNA Helicases in Gram-Positive RNA Decay

“…Recently, it was shown that a dominant-negative mutation in motif VI of dbpA results in a ribosome biogenesis defect (Elles and Uhlenbeck, 2008). While the above proteins are involved in ribosome biogenesis, the RhlB protein is part of the degradosome, a multicomponent complex involved in the targeted degradation of a large subset of mRNAs (Carpousis, 2007;Py et al, 1996). The RNA helicase in this complex is associated on the scaffold protein RNase E and is generally assumed to assist the degradosome on structured RNAs.…”

Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

“…Moreover, Hfq protects poly(A) tails from degradation by the exoribonucleases RNase II and polynucleotide phosphorylase (PNPase), and the endoribonuclease RNase E (28). The latter two enzymes are members of the degradosome, a multicomponent assembly that is responsible for RNA decay in bacteria (32). Hfq has been shown to interact with polynucleotide phosphorylase (PNPase), which adds AG-rich polynucleotide tails to the 3Ј ends of mRNAs that are terminated in a Rho-independent fashion, and RNase E, the key endoribonuclease involved in RNA destruction (27)(28)(29)-both presumably via protein-RNA-protein interactions (33).…”