THEORETICAL ANALYSIS OF POSSIBLE EVOLUTIONARY TRENDS IN THE DISTRIBUTION OF CODONS ALONG MRNA
Likhoshvay V. A., Matushkin Yu. G.
Science and Research Institute of Molecular Biology, "Vector", Koltsovo, Novosibirsk region;; 2 Institute of Cytology and Genetics, 630090, Novosibirsk, 10, pr.Lavrentyeva; E-mail: likho@bionet.nsc.ru
This work is concerned with analysis of the evolutionary features of
the distribution of the synonymous codons as part of translated mRNA as
following from the commonnest principles of the structure of the translation
apparatus. A mathematical model has been developed which depends on: a)
translation initiation; b) elongation with an account of isoacceptor tRNA;
c) mutual disposition of the codons; d) the distance that the A-sites of
two ribosomes cannot get closer than while the translation of an mRNA molecule
is in progress; e) sterical blocking of the translation initiation start
by the ribosome at the earlier stages of protein synthesis; f) translation
termination; g) synthesis and degradation of individual mRNA, tRNA and
ribosomes. Because long-running evolutionary processes have been modelled,
no regulation of the functioning of the translation apparatus was assumed
under the model, nor its interaction with other cellular systems within
one cycle of propagation. The dependence of the cell cycle duration, of
the rate of incorporation of amino acid residues into the growing polypeptides,
of the gross incorporation of amino acids into proteins within one cell
cycle, the economical functioning of the translation system, of the averaged
elongation rate and of some other functionals on the model parameters has
been subject to numerical analysis.
Some inferences can be made from present evidence on the likely trends
in the evolution of the codon content of mRNA.
- There is a long-term tendency to increase the average elongation rate
and to improve the economical capability of the translation system in the
course of evolution, although locally
- the parameters may take on lower values.
- Elevated elongation rates are advantageous for the organism within
a wide range of parameter values. The farther away the selection codon
from the translation initiation start, the higher the relative value of
the acquisition.
- At a higher translation initiation rate it becomes advantageous for
a fixed codon close to the translation start to elongate at a lower rate.
The higher the translation initiation rate, the farther away from the initiation
start the codon can be.
- No matter which initial conditions, the general trend in synonymous
codon selection is reaching for the state at which "faster" codons
are located closer to the end of the translation frame. The more actively
translated mRNA, the more it is observed.