title: Charting the dynamics of translation.
abstract: 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.
authors.affiliation: School of Computing, University of Kent, CT2 7NF Canterbury, UK. Electronic address: d.f.chu@kent.ac.uk.
authors.forename: Dominique
authors.initials: D
authors.lastname: Chu
authors.affiliation: School of Computing, University of Kent, CT2 7NF Canterbury, UK.
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.affiliation: School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK.
authors.forename: Tobias
authors.initials: T
authors.lastname: von der Haar
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D003198:Computer Simulation; D007700:Kinetics; D008957:Models, Genetic; D014176:Protein Biosynthesis / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D013997:Time Factors
chemical_list: D003062:Codon; D012333:RNA, Messenger
keywords: Codon usage bias; Modelling; Translation