Analysis of stability genes


March 11, 2010

The first group of genes I've analysed are the stability genes. These genes determine how stable each protein is. The smaller the number, the less stable (the more a protein is degraded each time unit).

The graph shows the value of the five stability genes in the top organism after four separate runs of evolution. The horizontal line indicates the value of the gene in the ancestor organism. The colour of the bar gives an indication of the fitness of the top organism relative to the other runs of evolution (the darker the bar, the faster the filament of bacteria grew).

Analysis of stability genes

I'm part way through looking at detail at these genes and have been developing a way to visualise how genes change in the population over time, which I'll add to this analysis later.

Photosystem II

The stability of Photosystem II in the ancestral organism was much lower than the stability of the other enzymes. There were two reasons for this. First, the amount of Photosystem II was capped at 2.7 units, representing the amount of enzyme that could fit in the plastid membranes. Second, the reaction catalysed by Photosystem II produces oxygen, so it is vital that is enzyme is quickly removed from cells that are transforming into heterocysts. If the protein has a low stability, then it will be remove almost as soon as its expression is halted.

Nitrogenase

The evolution of the nitrogenase stability gene is simplest to understand. In all four runs of evolution, the fastest organism has a mutation that increases the stability of nitrogenase to the maximum value of 0.96. In each case, this mutation appeared early on in evolution and quickly spread through the population. This is because the availability of fixed nitrogen is the limiting factor for cell growth, so the more that can be produced, the faster a filament of cells will grow.

Catabolism

The stability of the catabolism enzyme is also the same in all four runs of evolution, however, in this case, the optimum value appears to be the original value of 0.9. At first glance, this is surprising, since the rate of catabolism directly controls the rate of cell growth, so we might predict that the more enzyme the better.

I think the reason that a higher stability enzyme wasn't selected for is that this enzyme uses up fixed carbon and nitrogen. More enzyme will therefore reduce the amount of fixed carbon available to heterocysts to produce energy. In addition, the more stable the catabolism enzyme, the greater the chance that a heterocyst will replicate, which will result in two heterocysts next to one another, which is inefficient for filament growth. It is still surprising that the optimum value exactly 0.9, the value in the ancestral organism.

Anabolism

This gene either increases or stays at its original value. It increases to the maximum value in the runs of evolution that gave rise to the fittest organisms. This makes sense, since fitness is measured as the speed at which the cells grow, and cell growth is directly determined by protein, which this enzyme produces. The only reason not to maximise this enzyme would be because it uses up fixed carbon, which could also be burnt to use up oxygen.

Rubisco

This is the hardest gene to understand. In two runs of evolution, its value was unchanged; in one, its value increases; and in one - the run that gave rise to the fittest cell - it was significantly reduced. This suggests that that organisms is working in a fundamentally different way from the others. I love to know what's it's doing, but I don't have access to the simulation at the moment.

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