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Journal of Bacteriology, January 2002, p. 250-265, Vol. 184, No. 1
0021-9193/01/$04.00+0     DOI: 10.1128/JB.184.1.250-265.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Genomic Analyses of Anaerobically Induced Genes in Saccharomyces cerevisiae: Functional Roles of Rox1 and Other Factors in Mediating the Anoxic Response

Kurt E. Kwast,1* Liang-Chuan Lai,1 Nina Menda,1 David T. James, III,1 Susanne Aref,2 and Patricia V. Burke1

Department of Molecular & Integrative Physiology,1 Department of Statistics, University of Illinois, Urbana, Illinois 618012

Received 7 August 2001/ Accepted 3 October 2001

DNA arrays were used to investigate the functional role of Rox1 in mediating acclimatization to anaerobic conditions in Saccharomyces cerevisiae. Multiple growth conditions for wild-type and rox1 null strains were used to identify open reading frames with a statistically robust response to this repressor. These results were compared to those obtained for a wild-type strain in response to oxygen availability. Transcripts of nearly one-sixth of the genome were differentially expressed (P < 0.05) with respect to oxygen availability, the majority (>65%) being down-regulated under anoxia. Of the anaerobically induced genes, about one-third (106) contain putative Rox1-binding sites in their promoters and were significantly (P < 0.05) up-regulated in the rox1 null strains under aerobiosis. Additional promoter searches revealed that nearly one-third of the anaerobically induced genes contain an AR1 site(s) for the Upc2 transcription factor, suggesting that Upc2 and Rox1 regulate the majority of anaerobically induced genes in S. cerevisiae. Functional analyses indicate that a large fraction of the anaerobically induced genes are involved in cell stress (~1/3), cell wall maintenance (~1/8), carbohydrate metabolism (~1/10), and lipid metabolism (~1/12), with both Rox1 and Upc2 predominating in the regulation of this latter group and Upc2 predominating in cell wall maintenance. Mapping the changes in expression of functional regulons onto metabolic pathways has provided novel insight into the role of Rox1 and other trans-acting factors in mediating the physiological response of S. cerevisiae to anaerobic conditions.

* Corresponding author. Mailing address: Department of Molecular & Integrative Physiology, University of Illinois, 524 Burrill Hall, 407 S. Goodwin Ave., Urbana, IL 61801. Phone: (217) 244-3122. Fax: (217) 333-1133. E-mail: kwast{at}uiuc.edu.

Journal of Bacteriology, January 2002, p. 250-265, Vol. 184, No. 1
0021-9193/01/$04.00+0     DOI: 10.1128/JB.184.1.250-265.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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