Activity Motifs Reveal Principles of Timing in Transcriptional Control of the Yeast Metabolic Network
Venue
Nature Biotechnology, vol. 26 (11) (2008), pp. 1251-1259
Publication Year
2008
Authors
Gal Chechik, Eugene Oh, Oliver Rando, Jonathan Weissman, Aviv Regev, Daphne Koller
BibTeX
Abstract
Significant insight about biological networks arises from the study of network
motifs—overly abundant network subgraphs, but such wiring patterns do not specify
when and how potential routes within a cellular network are used. To address this
limitation, we introduce activity motifs, which capture patterns in the dynamic use
of a network. Using this framework to analyze transcription in Saccharomyces
cerevisiae metabolism, we find that cells use different timing activity motifs to
optimize transcription timing in response to changing conditions: forward
activation to produce metabolic compounds efficiently, backward shutoff to rapidly
stop production of a detrimental product and synchronized activation for
co-production of metabolites required for the same reaction. Measuring protein
abundance over a time course reveals that mRNA timing motifs also occur at the
protein level. Timing motifs significantly overlap with binding activity motifs,
where genes in a linear chain have ordered binding affinity to a transcription
factor, suggesting a mechanism for ordered transcription. Finely timed
transcriptional regulation is therefore abundant in yeast metabolism, optimizing
the organism's adaptation to new environmental conditions.
