Remodeling of the Bacterial RNA Polymerase Supramolecular Complex in Response to Environmental Conditions

Directed binding of RNA polymerase to distinct promoter elements controls transcription and promotes adaptive responses to changing environmental conditions. To identify proteins that modulate transcription, we have expressed a tagged α-subunit of RNA polymerase in Shewanella oneidensis under controlled growth conditions, isolated the protein complex using newly developed multiuse affinity probes, and used LC−MS/MS to identify proteins in the complex. Complementary fluorescence correlation spectroscopy measurements were used to determine the average size of the RNA polymerase complex in cellular lysates. We find that RNA polymerase exists as a large supramolecular complex with an apparent mass in excess of 1.4 MDa, whose protein composition substantially changes in response to growth conditions. Enzymes that copurify with RNA polymerase include those associated with tRNA processing, nucleotide metabolism, and energy biosynthesis, which we propose to be necessary for optimal transcriptional rates.