期刊
NATURE BIOTECHNOLOGY
卷 26, 期 11, 页码 1251-1259出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.1499
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资金
- National Science Foundation [BDI-0345474]
- Burroughs Wellcome Fund
- NIGMS
- Howard Hughes Medical Institute
Significant insight about biological networks arises from the study of network motifs-overly abundant network subgraphs(1,2)-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.
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