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Papers In Press, published online ahead of print February 10, 2005
J. Biol. Chem, 10.1074/jbc.M414050200
Submitted on December 14, 2004
Revised on January 26, 2005
Accepted on February 10, 2005
University of Wisconsin-Madison, Madison
Corresponding Author: fred{at}genome.wisc.edu
By exploring global gene expression of E. coli growing on six different carbon sources, we discovered a striking genome transcription pattern: as carbon substrate quality declines, cells systematically increase the number of genes expressed. Gene induction occurs in a hierarchical manner and includes many factors for uptake and metabolism of better but currently unavailable carbon sources. Concomitantly, cells also increase their motility. Thus, as the growth potential of the environment decreases, cells appear to devote progressively more energy on the mere possibility of improving conditions. This adaptation is not what would be predicated by classic regulatory models alone. We also observe an inverse correlation between gene activation and ribosomal RNA (rRNA) synthesis suggesting that reapportioning RNA polymerase (RNAP) contributes to the expanded genome activation. Significant differences in RNAP distribution in vivo, monitored using an RNAP-GFP fusion, from energy-rich and energy–poor carbon source cultures support this hypothesis. Together, these findings represent the integration of both substrate-specific and global regulatory systems, and may be a bacterial approximation to metazoan risk-prone foraging behaviour.
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