Open AccessHigh-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop
Author(s) -
Chenxi Qiu,
Olivia C. Erinne,
Jui M. Dave,
Ping Cui,
Hailing Jin,
Nandhini Muthukrishnan,
Leung K. Tang,
Sabareesh Ganesh Babu,
Kenny C. Lam,
Paul J. Vandeventer,
Ralf Strohner,
Jan Brülle,
SingHoi Sze,
Craig D. Kaplan
Publication year - 2016
Publication title -
plos genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.587
H-Index - 233
eISSN - 1553-7404
pISSN - 1553-7390
DOI - 10.1371/journal.pgen.1006321
Subject(s) - biology , saccharomyces cerevisiae , phenotype , genetics , polymerase , transcription (linguistics) , mutant , rna , rna polymerase , rna polymerase ii , yeast , microbiology and biotechnology , biophysics , gene , gene expression , linguistics , philosophy , promoter
The active sites of multisubunit 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 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.