mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle

The dynamical regulation due to mRNA stability is found to be an important aspect of the genome-wide coordination of the long-period yeast metabolic cycle. It is shown that for periodic genes, arranged in classes according either to expression profile or to function, the pulses of mRNA abundance have phase and width which are directly proportional to the corresponding turnover rates.The cascade of events occurring during the yeast metabolic cycle (and their correlation with mRNA turnover) reflects to a large extent the gene expression program observable in other dynamical contexts such as the response to stresses/stimuli.Ultradian self-sustaining energy-metabolic oscillations arising spontaneously in high density Saccharomyces cerevisiae continuous cultures exposed to glucose-limited growth have been known and studied for decades [1,2], and have more recently been observed to induce genome-wide periodic patterns in different series of microarray experiments [3,4], although with widely different periodicities, ~40 min for [3] and ~300 min for [4].Many studies aim at understanding the mechanisms inducing these sustained oscillations and the rigorous temporal compartmentalization they induce, see [5,6] for surveys. Suggested causes range from a single critical pathway (like the feedback effect of cysteine on the sulfur assimilation pathway [7]) to the alternation of aerobic and anaerobic respiratory modes (as deduced by the fluctuations in the concentration of dissolved O2 and of other observed metabolites [4]), from the interaction with cell cycle [8,9] to the mutual incompatibility of different redox biochemical processes [10,11].The scope of this work is to emphasize a different aspect, intrinsically dynamical and post-transcriptional, which is likely to play an important role in the coordination of the "slower" yeast metabolic cycle (YMC) of [4], namely mRNA stability. We will show that there is a roughly linear relationship between the average half life (HL) of th