PT - JOURNAL ARTICLE AU - Chenxi Qiu AU - Olivia C. Erinne AU - Jui Dave AU - Ping Cui AU - Huiyan Jin AU - Nandhini Muthukrishnan AU - Leung K. Tang AU - Sabareesh Ganesh Babu AU - Kenny C. Lam AU - Paul J. Vandeventer AU - Ralf Strohner AU - Jan Van den Brulle AU - Sing-Hoi Sze AU - Craig D. Kaplan TI - High-resolution phenotypic landscape of the RNA Polymerase II trigger loop AID - 10.1101/068726 DP - 2016 Jan 01 TA - bioRxiv PG - 068726 4099 - http://biorxiv.org/content/early/2016/08/14/068726.short 4100 - http://biorxiv.org/content/early/2016/08/14/068726.full AB - The active site of multicellular RNA polymerases have a “trigger loop” (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three major mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis. Furthermore, allele-specific genetic interactions among TL and TL-proximal domain residues support the contribution of the funnel and bridge helices (BH) to TL dynamics. Our structural genetics approach incorporates structural and phenotypic data for high-resolution dissection of transcription mechanisms and their evolution, and is readily applicable to other essential yeast proteins.