Evolution of default genetic control mechanisms

TL;DR

This study models the evolution of gene control mechanisms, revealing that genome complexity influences default gene activity states, with implications for understanding eukaryotic genome evolution.

Contribution

It introduces a computational model simulating the evolution of gene control logic under environmental constraints, highlighting factors influencing default gene activity modes.

Findings

Genomes with higher complexity tend to evolve 'default on' control logic.

Less active gene fractions correlate with 'default off' control logic.

Control logic evolution is not significantly affected by environmental complexity.

Abstract

We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell as well as the environment to control expression of a coding region. Control and coding regions evolve to maximize a fitness function between expressed coding sequences and the environment. 118 runs of the model run to an average of 1.4 x 10^6 `generations' each with a range of starting parameters probed the conditions under which genomes evolved a `default style' of control. Unexpectedly, the control logic that evolved was not significantly correlated to the complexity of the environment. Genetic logic was strongly correlated with genome complexity and with the fraction of genes active in the cell at any one time. More complex genomes correlated with the evolution of genetic controls in which genes were active (`default on'), and a low fraction of genes being expressed correlated with a genetic logic in which genes were biased to being inactive unless positively activated (`default off' logic). We discuss how this might relate to the evolution of the complex eukaryotic genome, which operates in a `default off' mode.