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A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting
Programmed ribosomal frameshifting (PRF) is a process by which ribosomes produce two different polypeptides from the same mRNA. In this study, we propose three different kinetic models of +1 PRF, incorporating the effects of the ribosomal E-, P- and A-sites toward promoting efficient +1 frameshiftin...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377451/ https://www.ncbi.nlm.nih.gov/pubmed/18344525 http://dx.doi.org/10.1093/nar/gkn100 |
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author | Liao, Pei-Yu Gupta, Prateek Petrov, Alexey N. Dinman, Jonathan D. Lee, Kelvin H. |
author_facet | Liao, Pei-Yu Gupta, Prateek Petrov, Alexey N. Dinman, Jonathan D. Lee, Kelvin H. |
author_sort | Liao, Pei-Yu |
collection | PubMed |
description | Programmed ribosomal frameshifting (PRF) is a process by which ribosomes produce two different polypeptides from the same mRNA. In this study, we propose three different kinetic models of +1 PRF, incorporating the effects of the ribosomal E-, P- and A-sites toward promoting efficient +1 frameshifting in Escherichia coli. Specifically, the timing of E-site tRNA dissociation is discussed within the context of the kinetic proofreading mechanism of aminoacylated tRNA (aa-tRNA) selection. Mathematical modeling using previously determined kinetic rate constants reveals that destabilization of deacylated tRNA in the E-site, rearrangement of peptidyl-tRNA in the P-site, and availability of cognate aa-tRNA corresponding to the A-site act synergistically to promote efficient +1 PRF. The effect of E-site codon:anticodon interactions on +1 PRF was also experimentally examined with a dual fluorescence reporter construct. The combination of predictive modeling and empirical testing allowed the rate constant for P-site tRNA slippage (k(s)) to be estimated as k(s) ≈1.9 s(−1) for the release factor 2 (RF2) frameshifting sequence. These analyses suggest that P-site tRNA slippage is the driving force for +1 ribosomal frameshifting while the presence of a ‘hungry codon’ in the A-site and destabilization in the E-site further enhance +1 PRF in E. coli. |
format | Text |
id | pubmed-2377451 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-23774512008-05-14 A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting Liao, Pei-Yu Gupta, Prateek Petrov, Alexey N. Dinman, Jonathan D. Lee, Kelvin H. Nucleic Acids Res RNA Programmed ribosomal frameshifting (PRF) is a process by which ribosomes produce two different polypeptides from the same mRNA. In this study, we propose three different kinetic models of +1 PRF, incorporating the effects of the ribosomal E-, P- and A-sites toward promoting efficient +1 frameshifting in Escherichia coli. Specifically, the timing of E-site tRNA dissociation is discussed within the context of the kinetic proofreading mechanism of aminoacylated tRNA (aa-tRNA) selection. Mathematical modeling using previously determined kinetic rate constants reveals that destabilization of deacylated tRNA in the E-site, rearrangement of peptidyl-tRNA in the P-site, and availability of cognate aa-tRNA corresponding to the A-site act synergistically to promote efficient +1 PRF. The effect of E-site codon:anticodon interactions on +1 PRF was also experimentally examined with a dual fluorescence reporter construct. The combination of predictive modeling and empirical testing allowed the rate constant for P-site tRNA slippage (k(s)) to be estimated as k(s) ≈1.9 s(−1) for the release factor 2 (RF2) frameshifting sequence. These analyses suggest that P-site tRNA slippage is the driving force for +1 ribosomal frameshifting while the presence of a ‘hungry codon’ in the A-site and destabilization in the E-site further enhance +1 PRF in E. coli. Oxford University Press 2008-05 2008-03-15 /pmc/articles/PMC2377451/ /pubmed/18344525 http://dx.doi.org/10.1093/nar/gkn100 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | RNA Liao, Pei-Yu Gupta, Prateek Petrov, Alexey N. Dinman, Jonathan D. Lee, Kelvin H. A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting |
title | A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting |
title_full | A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting |
title_fullStr | A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting |
title_full_unstemmed | A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting |
title_short | A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting |
title_sort | new kinetic model reveals the synergistic effect of e-, p- and a-sites on +1 ribosomal frameshifting |
topic | RNA |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377451/ https://www.ncbi.nlm.nih.gov/pubmed/18344525 http://dx.doi.org/10.1093/nar/gkn100 |
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