29 May 2009
Brookhaven National Lab
It has been reported  that the number of transcription factors in a prokaryotic genome scales approximately quadratically with the total number of its genes. As a consequence the fraction of transcriptional regulators among all genes in small bacterial genomes (< 500 genes) is less than 0.5%, while in large genomes (~10,000 genes) it reaches as high as 10%.
We recently proposed  a conceptual explanation of this empirical scaling law and illustrated it using a simple evolutionary model. In this model prokaryotic organisms master new functional tasks by the virtue of horizontal gene transfer of entire co-regulated metabolic pathways from a shared gene pool (the "universal metabolic network") This process can be compared to constantly buying tool sets from a hardware store (hence our "Home Depot" metaphor) and later returning duplicate or unnecessary items.
Our model faithfully reproduces the empirically observed  quadratic scaling law. Furthermore, the distribution of lengths of co-regulated pathways in our model agrees with that in real-life metabolic network of E coli. Thus, as an unexpected bonus our model offers a conceptual explanation for the broad distribution of regulon sizes observed in prokaryotes.
I will then describe several possible regulatory network architectures ensuring proper coordination of activity of metabolic pathways with each other. They are all consistent with our "Home Depot" scenario and it remains to be determined which of them (if any) are realized in real-life prokaryotes.
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