Analysis of the natively unstructured RNA/protein-recognition core in the Escherichia coli RNA degradosome and its interactions with regulatory RNA/Hfq complexes

Abstract

The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We have structurally characterized a subassembly of the degradosome–comprising a 248-residue segment of the natively unstructured part of RNase E, the DEAD-box helicase RhlB and the glycolytic enzyme enolase, and provide evidence that it serves as a flexible recognition centre that can co-recruit small regulatory RNA and the RNA chaperone Hfq. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition centre, facilitates pairing to cognate transcripts and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.

Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas

“…In fact, there are no experimental evidences yet of which are the direct or indirect proteins interactors of members of the CsrA superfamily. Because of its major role in posttranscriptional control of mRNAs, most efforts have been directed to reveal the RNA interactome of CsrA proteins, but it may be expected that accessory proteins would be recruited to the CsrA-RNA ribonucleoprotein complex, like Hfq and the degradosome (Sorger-Domenigg et al, 2007 ; De Lay et al, 2013 ; Bruce et al, 2018 ).…”

Omnipresent Maxwell's demons orchestrate information management in living cells

“…SrmB is tethered to nascent ribosome through interactions with L4, L24 and the region from domain I of 23S rRNA that binds them (Proux et al ., ). Besides SrmB, several related helicases are present in E. coli : DeaD (Jain, ), DbpA [RhlC, (Lopez de Victoria et al ., )], RhlB [also MmrA, (Bruce et al ., )] and RhlE (Cartier et al ., ). The two‐first ones are involved in ribosome biogenesis while the two latter are involved in RNA degradation.…”

Effects of individual base-pairs onin vivotarget search and destruction kinetics of small RNA

“…The co-degradation of the SgrS-ptsG complex is brought about by the degradosome, in which RNase E is a key component. Hfq copurifies with RNase E and SgrS 57 , and at least one sRNA (MicC) has been shown to mediate the interaction between Hfq and the C-terminal part of RNase E in vitro 58 and in vivo 59 . It has been hypothesized that the sRNA-Hfq-RNase E complex forms first and subsequently the complementary mRNA binds to this complex, aided by Hfq, followed by a coupled or sequential degradation of the RNA pair 58 .…”

“…Hfq copurifies with RNase E and SgrS 57 , and at least one sRNA (MicC) has been shown to mediate the interaction between Hfq and the C-terminal part of RNase E in vitro 58 and in vivo 59 . It has been hypothesized that the sRNA-Hfq-RNase E complex forms first and subsequently the complementary mRNA binds to this complex, aided by Hfq, followed by a coupled or sequential degradation of the RNA pair 58 . The changes in kon and koff in our study account for the disruption of the SgrS-ptsG mRNA annealing, but once a stable complex with all four components forms, the co-degradation occurs at the same rate irrespective of the SgrS mutations.…”