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Originally published In Press as doi:10.1074/jbc.M301981200 on April 3, 2003

J. Biol. Chem., Vol. 278, Issue 28, 26146-26158, July 11, 2003
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Multiple Pathways Are Co-regulated by the Protein Kinase Snf1 and the Transcription Factors Adr1 and Cat8*,

Elton T. Young {ddagger} §, Kenneth M. Dombek §, Chris Tachibana and Trey Ideker ¶

From the Department of Biochemistry, the University of Washington, Seattle, Washington 98195-7350

ADR1 and CAT8 encode carbon source-responsive transcriptional regulators that cooperatively control expression of genes involved in ethanol utilization. These transcription factors are active only after the diauxic transition, when glucose is depleted and energy-generating metabolism has shifted to the aerobic oxidation of non-fermentable carbon sources. The Snf1 protein kinase complex is required for activation of their downstream target genes described previously. Using DNA microarrays, we determined the extent to which these three factors collaborate in regulating the expression of the yeast genome after glucose depletion. The expression of 108 genes is significantly decreased in the absence of ADR1. The importance of ADR1 during the diauxic transition is illustrated by the observation that expression of almost one-half of the 40 most highly glucose-repressed genes is ADR1-dependent. ADR1-dependent genes fall into a variety of functional classes with carbon metabolism containing the largest number of members. Most of the genes in this class are involved in the oxidation of different non-fermentable carbon sources. These microarray data show that ADR1 coordinates the biochemical pathways that generate acetyl-CoA and NADH from non-fermentable substrates. Only a small number of ADR1-dependent genes are also CAT8-dependent. However, nearly one-half of the ADR1-dependent genes are also dependent on the Snf1 protein kinase for derepression. Many more genes are SNF1-dependent than are either ADR1- or CAT8-dependent suggesting that SNF1 plays a broader role in gene expression than either ADR1 or CAT8. The largest class of SNF1-dependent genes encodes regulatory proteins that could extend SNF1 dependence to additional pathways.


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  		TABLE I
S. cerevisiae strains used in this study

 

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  		TABLE II
Primers used for PCR analysis of Adr1 ChIP DNA

 

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  		TABLE III
Functional classification of ADR1-dependent genes

 

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  		TABLE IV
Expression ratios of the 40 most highly glucose repressed genes Expression ratios in boldface type indicate a significantly higher level of expression based on a {lambda} statistic that is above the significance threshold.

 

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  		TABLE V
ADR1-dependent expression of IME1/lacZ in haploid and diploid

Haploid strains TYY201 and TYY202, ADR1 and adr1{Delta}1::LEU2, respectively, with pWL21 (IME1/lacZ, URA3) and diploid strains TGY25 and TGY27, adr1{Delta}1::LEU2/adr1{Delta}1::LEU2 and adr1{Delta}1::LEU2/ADR1, respectively, with pWL21 (IME1/lacZ, URA3), were grown in selective media (ura-) with 5% glucose (R) to about 2 x 107 cells/ml. A portion of the culture was assayed for {beta}-galactosidase activity (R) as described under "Experimental Procedures," and cells from another portion were collected by centrifugation and resuspended in selective media plus 0.05% glucose (DR) or 0.1% potassium acetate (SPM) and grown for 18 h at 30°C. A portion of each culture was removed and assayed for {beta}-galactosidase activity (DR and SPM, respectively). The {beta}-galactosidase activities are Miller units, and the standard deviations of the assays were about 20%.

 

Received for publication, February 25, 2003 , and in revised form, March 31, 2003.

* This work was supported by NIGMS Research Grant GM26079 from the National Institutes of Health (to E. T. Y.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains Tables I II III IV V and additional data.

§ Both authors contributed equally to this work.

Present address: Whitehead Institute, Nine Cambridge Center, Cambridge, MA 02142-1479.

{ddagger} To whom correspondence should be addressed: Dept. of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350. Tel.: 206-543-6517; Fax: 206-685-1792; E-mail: ety{at}u.washington.edu.


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