MSc Thesis Proposal

Simulation Models of Prebiotic Evolution of Genetic Coding

Common to all life on Earth are the mechanisms of genetic encoding, in which specific trinucleotide sequences in DNA and RNA map to specific amino acids in synthesized proteins. This thesis project investigates feasible models of the evolution of genetic encoding from an initially random population of proteins. The focus of the research is on developing an abstract framework that does not make explicit the molecular details while demonstrating a plausible mechanism of self-organisation.

Wills [1] developed a model in which the proteins responsible for the genetic encoding, the translatases, catalyse their own synthesis, resulting in the self-organisation of a stable translation system.

Füchslin and McCaskill [2] extended the model to include gene replication with mutational errors, catalysed by replicase proteins. Their model used one translatase enzyme to catalyse the synthesis of an entire protein, a simplification of Wills’ model of one enzyme for each codon to amino acid assignment. They demonstrated self-organisation in a system with diffusion on a three-dimensional lattice.

This project seeks to extend prior work by investigating a model in which there is a separate enzyme for each possible codon-to-amino-acid assignment. Reactions will be modelled as taking place in homogeneous compartments with limited diffusion between compartments. The initial model will be simplified by using a binary coding, in which there are only two classes of codons.

The research will be conducted by writing computer programs to implement simulation models and running them to gather data on the self-organising behaviour of the models.

If parameters can be found for which the initial model demonstrates self-organisation to a stable configuration, the model will be expanded to more closely represent biological genetic coding by increasing the number of codons.

If the model does not self-organise, it will be modified to be more like the Füchslin/McCaskill model, for example by utilising a three dimensional lattice of compartments. Another possibility is to explicitly model molecular interactions in the compartments with small numbers of molecules.

In either case, the goal will be to explore the characteristics of the model and the ranges of parameter space that support self-organisation using somewhat more biologically plausible models than have been used in prior research.

References

[1] Wills, P. R. 1993. Self-organisation of genetic coding.
J. Theor. Biol. 162:267-287

[2] Füchslin, R. M. and McCaskill, J. S. 2001.
Evolutionary self-organisation of cell-free genetic coding.
PNAS 98:9185-9190