The Escherichia coli RNA 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.