Translocation and fidelity of Escherichia coli RNA polymerase
Exonuclease (exo) III was used as a probe of the Escherichia coli RNA polymerase (RNAP) ternary elongation complex (TEC) downstream border. In the absence of NTPs, RNAP appears to stall primarily in a post-translocated state and to return slowly to a pre-translocated state. Exo III mapping, therefor...
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| Format: | Online |
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Landes Bioscience
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4042587/ |
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pubmed-40425872014-06-04 Translocation and fidelity of Escherichia coli RNA polymerase Nedialkov, Yuri A. Burton, Zachary F. Research Paper Exonuclease (exo) III was used as a probe of the Escherichia coli RNA polymerase (RNAP) ternary elongation complex (TEC) downstream border. In the absence of NTPs, RNAP appears to stall primarily in a post-translocated state and to return slowly to a pre-translocated state. Exo III mapping, therefore, appears inconsistent with an unrestrained thermal ratchet model for translocation, in which RNAP freely and rapidly oscillates between pre- and post-translocated positions. The forward translocation state is made more stable by lowering the pH and/or by elevating the salt concentration, indicating a probable role of protonated histidine(s) in regulating accurate NTP loading and translocation. Because the post-translocated TEC can be strongly stabilized by NTP addition, NTP analogs were ranked for their ability to preserve the post-translocation state, giving insight into RNAP fidelity. Effects of NTPs (and analogs) and analysis of chemically modified RNA 3′ ends demonstrate that patterns of exo III mapping arise from intrinsic and subtle alterations at the RNAP active site, far from the site of exo III action. Landes Bioscience 2013-05-01 2013-07-11 /pmc/articles/PMC4042587/ /pubmed/23863783 http://dx.doi.org/10.4161/trns.25527 Text en Copyright © 2013 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Nedialkov, Yuri A. Burton, Zachary F. |
| spellingShingle |
Nedialkov, Yuri A. Burton, Zachary F. Translocation and fidelity of Escherichia coli RNA polymerase |
| author_facet |
Nedialkov, Yuri A. Burton, Zachary F. |
| author_sort |
Nedialkov, Yuri A. |
| title |
Translocation and fidelity of Escherichia coli RNA polymerase |
| title_short |
Translocation and fidelity of Escherichia coli RNA polymerase |
| title_full |
Translocation and fidelity of Escherichia coli RNA polymerase |
| title_fullStr |
Translocation and fidelity of Escherichia coli RNA polymerase |
| title_full_unstemmed |
Translocation and fidelity of Escherichia coli RNA polymerase |
| title_sort |
translocation and fidelity of escherichia coli rna polymerase |
| description |
Exonuclease (exo) III was used as a probe of the Escherichia coli RNA polymerase (RNAP) ternary elongation complex (TEC) downstream border. In the absence of NTPs, RNAP appears to stall primarily in a post-translocated state and to return slowly to a pre-translocated state. Exo III mapping, therefore, appears inconsistent with an unrestrained thermal ratchet model for translocation, in which RNAP freely and rapidly oscillates between pre- and post-translocated positions. The forward translocation state is made more stable by lowering the pH and/or by elevating the salt concentration, indicating a probable role of protonated histidine(s) in regulating accurate NTP loading and translocation. Because the post-translocated TEC can be strongly stabilized by NTP addition, NTP analogs were ranked for their ability to preserve the post-translocation state, giving insight into RNAP fidelity. Effects of NTPs (and analogs) and analysis of chemically modified RNA 3′ ends demonstrate that patterns of exo III mapping arise from intrinsic and subtle alterations at the RNAP active site, far from the site of exo III action. |
| publisher |
Landes Bioscience |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4042587/ |
| _version_ |
1612095766817406976 |