Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization. / Mitarai, Namiko; Sneppen, Kim; Pedersen, Steen.

In: Journal of Molecular Biology, Vol. 382, No. 1, 2008, p. 236-245.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Mitarai, N, Sneppen, K & Pedersen, S 2008, 'Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization', Journal of Molecular Biology, vol. 382, no. 1, pp. 236-245. https://doi.org/10.1016/j.jmb.2008.06.068

APA

Mitarai, N., Sneppen, K., & Pedersen, S. (2008). Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization. Journal of Molecular Biology, 382(1), 236-245. https://doi.org/10.1016/j.jmb.2008.06.068

Vancouver

Mitarai N, Sneppen K, Pedersen S. Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization. Journal of Molecular Biology. 2008;382(1):236-245. https://doi.org/10.1016/j.jmb.2008.06.068

Author

Mitarai, Namiko ; Sneppen, Kim ; Pedersen, Steen. / Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization. In: Journal of Molecular Biology. 2008 ; Vol. 382, No. 1. pp. 236-245.

Bibtex

@article{fc3776f0dbe511dd9473000ea68e967b,
title = "Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization",
abstract = "Individual mRNAs are translated by multiple ribosomes that initiate translation with an interval of a few seconds. The ribosome speed is codon dependent, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modeling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations/s) and the time (1 s) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of mRNA breakdown is offset by the concomitant increase in translation efficiency.",
author = "Namiko Mitarai and Kim Sneppen and Steen Pedersen",
note = "Keywords: Codon; Conserved Sequence; Escherichia coli; Genetic Code; Kinetics; Models, Biological; Protein Biosynthesis; RNA Stability; RNA, Messenger; Ribosomes; Time Factors; beta-Galactosidase",
year = "2008",
doi = "10.1016/j.jmb.2008.06.068",
language = "English",
volume = "382",
pages = "236--245",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press",
number = "1",

}

RIS

TY - JOUR

T1 - Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization

AU - Mitarai, Namiko

AU - Sneppen, Kim

AU - Pedersen, Steen

N1 - Keywords: Codon; Conserved Sequence; Escherichia coli; Genetic Code; Kinetics; Models, Biological; Protein Biosynthesis; RNA Stability; RNA, Messenger; Ribosomes; Time Factors; beta-Galactosidase

PY - 2008

Y1 - 2008

N2 - Individual mRNAs are translated by multiple ribosomes that initiate translation with an interval of a few seconds. The ribosome speed is codon dependent, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modeling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations/s) and the time (1 s) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of mRNA breakdown is offset by the concomitant increase in translation efficiency.

AB - Individual mRNAs are translated by multiple ribosomes that initiate translation with an interval of a few seconds. The ribosome speed is codon dependent, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modeling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations/s) and the time (1 s) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of mRNA breakdown is offset by the concomitant increase in translation efficiency.

U2 - 10.1016/j.jmb.2008.06.068

DO - 10.1016/j.jmb.2008.06.068

M3 - Journal article

C2 - 18619977

VL - 382

SP - 236

EP - 245

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 1

ER -

ID: 9536237