Isolation and Partial Characterization of Novel, Structurally Uniform (Hfq6)n≥8 Assemblies Carrying Accessory Transcription and Translation Factors

Abstract

In growing E. coli cells, the transcription–translation complexes (TTCs) form characteristic foci; however, the exact molecular composition of these superstructures is not known with certainty. Herein, we report that, during our recently developed “fast” procedures for purification of E. coli RNA polymerase (RP), a fraction of the RP’s α/RpoA subunits is displaced from the core RP complexes and copurifies with multiprotein superstructures carrying the nucleic acid-binding protein Hfq and the ribosomal protein S6. We show that the main components of these large multiprotein assemblies are fixed protein copy-number (Hfq₆)_n≥8 complexes; these complexes have a high level of structural uniformity and are distinctly unlike the previously described (Hfq₆)_n “head-to-tail” polymers. We describe purification of these novel, structurally uniform (Hfq₆)_n≥8 complexes to near homogeneity and show that they also contain small nonprotein molecules and accessory S6. We demonstrate that Hfq, S6, and RP have similar solubility profiles and present evidence pointing to a role of the Hfq C-termini in superstructure formation. Taken together, our data offer new insights into the composition of the macromolecular assemblies likely acting as scaffolds for transcription complexes and ribosomes during bacterial cells’ active growth.