Every cellular RNA polymerase (RNAP), from bacteria to humans, contains a small subunit called ω. This protein is thought to function as a dedicated chaperone of the largest β’ subunit that contains the active site, assisting the β’ folding under some adverse conditions. Our recent data challenge this view.
We found that ω is essential for Escherichia coli resistance to acid stress. Our recent results show that non-productive interactions between β’ and ω may lock RNAP in an inactive conformation. Structures reveal that ω interacts with the universally conserved regions of β’, which harbor two essential catalytic elements, the Asp triad and the trigger loop. We hypothesize that ω modulates stress responses and silencing of horizontally-transferred genes through direct contacts to RNAP, which allosterically control catalysis in the active site. Accessory proteins that bind to ω and β’ and alter their structural dynamics may control RNAP activity in response to specific environmental cues.
We will elucidate the contribution of ω to regulation of RNA synthesis in E. coli. We will identify cellular factors that interact with ω using genetics and proteomics, characterize ω-induced changes in transcription complexes using cryo-EM analysis (in collaboration with Markus Wahl), and investigate ω effects on in vitro RNA synthesis. Our findings will shed light on the role of ω and its eukaryotic ortholog RPB6 in the basic function and regulation of RNAP.