Genome resource utilization during prokaryotic development.

Abstract

The distributions of synthesis rates of expressed proteins in a liquid batch culture of the prokaryote S. coelicolor during 3 days' growth have been analyzed by using a law governing the relation between the synthesis rates and the corresponding ranks in a list of rates (the so-called simplified canonical law, scl), which we have found previously to characterize the distribution of prokaryotic protein expression. The scl remains valid throughout development and the two parameters of the distribution, q and r, evolve in a highly characteristic and revealing way. q is a measure of the degree to which available genomic resources are used, in the sense of exploiting their potential diversity. The passage from one developmental phase to another is marked by a sharp peak in q, as these resources are fully mobilized to deal with a crisis (i.e., exhaustion of the habitual food supply). This is followed by an even more pronounced trough, as the organism briefly focuses its resources on synthesizing just those proteins most essential for survival, especially those hitherto unavailable and needed for metabolizing the new nutrient source. The parameter r indicates redundancy among the most abundantly expressed proteins: higher r corresponds to more diversity; i.e., less duplication of function, hence less robustness. This parameter is relatively steady throughout the development of the culture, except for a pronounced peak during the developmental phase transition. This corresponds to the "emergency mode" characterized by extremely low q, during which a minimum repertoire of proteins is expressed.