Charting the dynamics of translation.

Article English OPEN
Chu, Dominique ; Thompson, James ; von der Haar, Tobias (2014)

Codon usage bias (CUB) is the well-known phenomenon that the frequency of synonymous codons is unequal. This is presumably the result of adaptive pressures favouring some codons over others. The underlying reason for this pressure is unknown, although a large number of possible driver mechanisms have been proposed. According to one hypothesis, the decoding time could be such a driver. A tacit assumption of this hypothesis is that faster codons lead to a higher translation rate which in turn is more resource efficient. While it is generally assumed that there is such a link, there are no rigorous studies to establish under which conditions the link between translation speed and rate actually exists. Using a computational simulation model and explicitly calculated codon decoding times, this contribution maps the entire range of dynamical regimes of translation. These simulations make it possible to understand precisely under which conditions translation speed and rate are linked.
  • References (37)
    37 references, page 1 of 4

    Aitken, J.L.C., 2012. A mechanistic overview of translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 6, 568-576,

    Bentele, K., Saffert, P., Rauscher, R., Ignatova, Z., Bluthgen, N., 2013. Efficient translation initiation dictates codon usage at gene start. Mol. Syst. Biol. 9, 675,

    Blythe, R., Evans, M., 2007. Nonequilibrium steady states of matrixproduct form: a solver's guide. J. Phys. A: Math. Theor. 40 (46), R333

    Charneski, C., Hurst, L., 2013. Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol. 11 (3), e1001508,

    Chu, D., von der Haar, T., 2012. The architecture of eukaryotic translation. Nucleic Acids Res. 40 (20), 10098-10106.,

    Chu, D., Barnes, D., von der Haar, T., 2011. The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae. Nucleic Acids Res. 39 (15), 6705-6714,

    Chu, D., Zabet, N., von der Haar, T., 2012. A novel and versatile computational tool to model translation. Bioinformatics 28 (2), 292-293,

    Chu, D., Kazana, E., Bellanger, N., Singh, T., Tuite, M., von der Haar, T., 2013. Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO J. 33 (1), 21-34,, arXiv:,

    Ciandrini, L., Stansfield, I., Romano, M., 2010. Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation. Phys. Rev. E81 (5 Pt 1), 051904.

    Coghlan, A., Wolfe, K.H., 2000. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16 (12), 1131-1145;2-F

  • Related Research Results (4)
  • Metrics
    views in OpenAIRE
    views in local repository
    downloads in local repository

    The information is available from the following content providers:

    From Number Of Views Number Of Downloads
    Kent Academic Repository - IRUS-UK 0 39
Share - Bookmark