Title
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
Date Issued
24 September 2013
Access level
open access
Resource Type
journal article
Author(s)
Dangkulwanich M.
Ishibashi T.
Liu S.
Kireeva M.L.
Lubkowska L.
Kashlev M.
University of California
Publisher(s)
eLife Sciences Publications
Abstract
During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme. By challenging individual yeast RNA polymerase II with a nucleosomal barrier, we separately measured the forward and reverse translocation rates. Surprisingly, we found that the forward translocation rate is comparable to the catalysis rate. This finding reveals a linear, non-branched ratchet mechanism for the nucleotide addition cycle in which translocation is one of the rate-limiting steps. We further determined all the major on- and off-pathway kinetic parameters in the elongation cycle. The resulting translocation energy landscape shows that the off-pathway states are favored thermodynamically but not kinetically over the on-pathway states, conferring the enzyme its propensity to pause and furnishing the physical basis for transcriptional regulation.
Volume
2013
Issue
2
Language
English
OCDE Knowledge area
Métodos de investigación bioquÃmica
BiologÃa
Scopus EID
2-s2.0-84884682805
PubMed ID
Source
eLife
ISSN of the container
2050-084X
Sponsor(s)
Howard Hughes Medical Institute
National Institutes of Health R01-GM032543
U.S. Department of Energy DE-AC02-05CH11231
National Cancer Institute ZIABC010795 NCI
Sources of information:
Directorio de Producción CientÃfica
Scopus