In this simulation, the aim was to study evolution when enzyme function was fixed. Instead, all evolution could work with was the amount of enzyme present in a cell. This could be altered by modifying the rate at which proteins degraded and the rate at which there were expressed (transcription and translation were combined).
LEGEND Enz: enzyme; Op: operator: TF: transcription factor
Each of the five reactions described in the previous post is catalysed by an enzyme that is associated with four parameters. These parameters could be randomly mutated between generations, so act like genes in the simulation. The four genes determine the stability of an enzyme, and the strength of the operator region for three transcription factors.
The first gene for each enzyme determined its stability. The function of these genes is relatively straightforward: they have a value between 0 and 0.96, and during every unit of time, the amount of each enzyme is multiplied by this value. This number represents either the inherent stability of the enzyme or the rate at which it is bound and degraded by a peptidase. Since this value is always less than 1, the amount of enzyme decreases every time unit and cells constantly have to fight protein degradation in order to survive.
A small change in a stability gene can have quite a large effect on the amount of enzyme that can accumulate. If 1 unit of enzyme is produced every time unit, then with a stability of 0.9, the enzyme will accumulate to 10 units, while with a stability of 0.96, the enzyme will accumulate to 25 units.
The stability genes are also crucial for gene regulation because degradation is the only way the cell can reduce the amount of an enzyme in this simulation. This greatly limited how cells could regulate reactions, especially since heterocyst formation requires the quick removal of Photosystem II (reaction 1). Adding enzyme regulation by, for example, phosphorylation, would make cell much more effective, but is complex to implement. In this simulation the lack of other means to reduce the rate of reaction created a regulatory problem for evolution to overcome.
The amount of an enzyme was increased by transcription of the gene by transcription factors (the rate of translation was assumed to be constant). There were three transcription factors in the simulation, because that's the fewest I thought I could get away with. If I were to rerun the simulation, I might add a fourth just to see if it could be made useful.
In addition to the five enzymes, there were three transcription factors. The properties of each transcription factor was controlled by five genes. These genes determined which metabolite the transcription factor responded and how the amount of that signal metabolite affected the transcription factors activity.