TheEscherichia coliRNA processing and degradation machinery is compartmentalized within an organized cellular network

Abstract

Bacterial RNA processing and degradation involves the co-ordinated action of a large number of RNases, RNA helicases and other proteins. It is not known how this functional network is organized within the cell nor how it is co-ordinated or regulated. In the present study, we show that multiple components of the RNA degradation and processing network of Escherichia coli are localized within extended cellular structures that appear to coil around the periphery of the cell. These include Orn, Hfq, PAP I, RNase III, RppH, RraA and RraB in addition to the previously reported proteins RNase II and RNaseE. Double-label localization studies of several of the proteins showed co-localization of the proteins within the observed structures. Assembly of the proteins into the structures was independent of the MreBCD or MinCDE cytoskeletal systems, RNA synthesis, or nucleoid positioning within the cell. Our results indicate that the components of the RNA processing and degradation network are compartmentalized within the cell rather than diffusely distributed in the cytoplasm. This sequestration provides the cell with a possible mechanism to control access to RNA substrates and to functionally co-ordinate the multiple players of the RNA processing and degradation pathways.

Supramolecular membrane-associated assemblies of RNA metabolic proteins in Escherichia coli

“…The channelled tRNA cycle concept was later extended to the nucleus, on the basis of the finding of EF-1α in nuclear tRNA-containing fractions and aminoacylation of tRNAs before nuclear export [13,14]. The findings of Taghbalout et al [4] are consistent with the idea that similar RNA channelling principles are also implemented in bacterial cells. The reader is further referred to a recent review by George Mackie [15] where the author proposes a model of RNA channelling in bacteria: RNAs are transcribed in the nucleoid in the centre of the cell, from where they diffuse into a thin shell of ribosome-rich cytosol surrounding the nucleoid; if bound by ribosomes (and not, for example, by small non-coding RNAs and Hfq), mRNAs will have a certain dwell time there depending on how intensely they are translated before they are channelled to the RNA-degrading machinery at the inner membrane.…”

“…Taghbalout et al [4] in the current issue offer two potential and intertwined explanations: "The sequestration of the machinery could provide the cell a mechanism to control access to RNA substrates and to co-ordinate the coupled or overlapping biochemical functions of the different components of the network". Indeed, if RNA substrates are channelled to the supramolecular machinery, this saves its individual protein components from 'searching' their RNA substrates within the heavily crowded cytoplasm, simultaneously preventing unwanted degradation of RNAs encountered by the enzymes during their odyssey through the cytoplasm.…”

“…However, the research activities of the Taghbalout and Arluison groups (see the paper in the current issue of the Biochemical Journal [4]) now come into play: the authors drilled deeper and investigated the cellular localization of an expanded spectrum of E. coli proteins involved in RNA metabolism. This was addressed by elegant immunofluorescence microscopy experiments, employing a series of E. coli mutant strains with respective gene deletions/truncations and replacements of endogenous genes with variants encoding HA (haemagglutinin)-, FLAG-or YFP-tagged versions.…”

“…Studies such as the one by Taghbalout et al [4] in the current issue of the Biochemical Journal deepen our understanding on how bacterial cells organize and apparently orchestrate their RNA metabolic activities. It becomes evident that supramolecular assemblies compartmentalize cellular activities also in bacteria that lack compartments spatially separated by membranes.…”

“…Taghbalout et al [4] then scrutinized whether the E. coli RNA degradosome (RNaseE, RhlB, PNPase and enolase) might serve as a platform to organize the other components of the RNA degradation and processing network. It has been known that RNaseE and RhlB can assemble into membrane-associated supramolecular structures independent of each other, whereas attachment of PNPase requires the membrane contacts of RNaseE or RhlB [5].…”