Abstract
BackgroundIn yeast, genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short (approx. 40 min) and long (approx. 300 min) periods.ResultsThe 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.ConclusionThe 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.
Highlights
In yeast, genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short and long periods
The cascade of events occurring during the yeast metabolic cycle 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 genomewide periodic patterns in different series of microarray experiments [3,4], with widely different periodicities, ~40 min for [3] and ~300 min for [4]
Summary
Genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short (approx. 40 min) and long (approx. 300 min) periods. Genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short 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 genomewide periodic patterns in different series of microarray experiments [3,4], with widely different periodicities, ~40 min for [3] and ~300 min for [4]. 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. There seems to be a strong correlation between HL and the shape of the pulses of gene (page number not for citation purposes) expression: genes with short HL have short and sharp (almost impulsive in the time scale considered) pulses, while genes with long HL have pulses that are delayed and broader and with more gentle slopes
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