A natively unstructured RNA/protein-recognition core in the E. coli RNA degradosome facilitates riboregulation

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. The core of the assembly is provided by the endoribonuclease RNase E, one of the largest E. coli proteins. The C-terminal half of RNase E is predicted to be predominantly unstructured and is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We demonstrate that a subassembly of the degradosome - comprising a 248-residue segment of the C-terminal part of RNase E, the DEAD-box helicase RhlB, and the glycolytic enzyme enolase - serves as a flexible recognition centre that can co-recruit small regulatory RNA (sRNA) molecules and the RNA chaperone Hfq into an effector complex. The association of enolase with the degradosome impacts on carbon utilisation pathways under changing metabolic conditions, most likely by facilitating recruitment and the activity of sRNAs. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition core, facilitates pairing to cognate transcripts, and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing. In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed. Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5-fold change expression cut-off for ratio experiments was applied together with anti-correlation of color-swapped ratio profiles was applied, rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.