Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; Kireeva, Maria L.; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos J.

doi:10.7554/eLife.00971

Title: Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

Journal Article · Tue Sep 24 00:00:00 EDT 2013 · eLife

DOI:https://doi.org/10.7554/eLife.00971· OSTI ID:1197625

Dangkulwanich, Manchuta ^[1]; Ishibashi, Toyotaka ^[2]; Liu, Shixin ^[3]; Kireeva, Maria L. ^[4]; Lubkowska, Lucyna ^[4]; Kashlev, Mikhail ^[4]; Bustamante, Carlos J. ^[5]

Jason L Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, United States, Department of Chemistry, University of California, Berkeley, Berkeley, United States
Jason L Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, United States, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
Jason L Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, United States, Department of Physics, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research–National Cancer Institute, Frederick, United States
Jason L Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, United States, Department of Chemistry, University of California, Berkeley, Berkeley, United States, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States, Department of Physics, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1197625

Alternate ID(s):: OSTI ID: 1197626; OSTI ID: 1628801

Journal Information:: eLife, Journal Name: eLife Vol. 2; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 89 works

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