Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain

Abstract

The Carboxy-Terminal Domain (CTD) of the RNA polymerase II (Pol II) large subunit cycles through multiple phosphorylation states that correlate with progression through the transcription cycle and regulate nascent mRNA processing. Structural analyses of yeast and mammalian CTD have been hampered by their repetitive sequences. Here we identify a region of the Drosophila melanogaster CTD that is essential for Pol II function in vivo and capitalize on natural sequence variations within it to facilitate structural analysis. Mass spectrometry and NMR spectroscopy reveal that hyper-Ser5 phosphorylation transforms the local structure of this essential region via proline isomerization. The sequence context of this switch tunes the apparent activity of the CTD phosphatase Ssu72, suggesting a mechanism for the selective recruitment of cis-proline specific regulatory factors that may synergize with CTD phosphorylation to augment gene regulation in developmentally complex organisms.