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Molecular and Cellular Biology, April 2007, p. 3065-3086, Vol. 27, No. 8
0270-7306/07/$08.00+0     doi:10.1128/MCB.01084-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast Saccharomyces cerevisiae{triangledown} ,{dagger}

Patrice Godard,1 Antonio Urrestarazu,1 Stéphan Vissers,1 Kevin Kontos,3 Gianluca Bontempi,3 Jacques van Helden,2 and Bruno André1*

Physiologie Moléculaire de la Cellule, IBMM, Université Libre de Bruxelles (ULB), Rue des Pr. Jeener et Brachet 12, 6041 Gosselies, Belgium,1 Conformation des Macromolécules Biologiques, ULB, CP 263, Boulevard du Triomphe, 1050 Bruxelles, Belgium,2 Machine Learning Group, ULB, CP 212, Boulevard du Triomphe, 1050 Bruxelles, Belgium3

Received 16 June 2006/ Returned for modification 24 July 2006/ Accepted 16 January 2007

We compared the transcriptomes of Saccharomyces cerevisiae cells growing under steady-state conditions on 21 unique sources of nitrogen. We found 506 genes differentially regulated by nitrogen and estimated the activation degrees of all identified nitrogen-responding transcriptional controls according to the nitrogen source. One main group of nitrogenous compounds supports fast growth and a highly active nitrogen catabolite repression (NCR) control. Catabolism of these compounds typically yields carbon derivatives directly assimilable by a cell's metabolism. Another group of nitrogen compounds supports slower growth, is associated with excretion by cells of nonmetabolizable carbon compounds such as fusel oils, and is characterized by activation of the general control of amino acid biosynthesis (GAAC). Furthermore, NCR and GAAC appear interlinked, since expression of the GCN4 gene encoding the transcription factor that mediates GAAC is subject to NCR. We also observed that several transcriptional-regulation systems are active under a wider range of nitrogen supply conditions than anticipated. Other transcriptional-regulation systems acting on genes not involved in nitrogen metabolism, e.g., the pleiotropic-drug resistance and the unfolded-protein response systems, also respond to nitrogen. We have completed the lists of target genes of several nitrogen-sensitive regulons and have used sequence comparison tools to propose functions for about 20 orphan genes. Similar studies conducted for other nutrients should provide a more complete view of alternative metabolic pathways in yeast and contribute to the attribution of functions to many other orphan genes.

* Corresponding author. Mailing address: Physiologie Moléculaire de la Cellule, IBMM, Université Libre de Bruxelles, Rue des Pr. Jeener et Brachet 12, 6041 Gosselies, Belgium. Phone: 32 2 650 99 58. Fax: 32 2 650 99 50. E-mail: bran{at}ulb.ac.be

{triangledown} Published ahead of print on 16 February 2007.

{dagger} Supplemental material for this article may be found at http://mcb.asm.org/.

Molecular and Cellular Biology, April 2007, p. 3065-3086, Vol. 27, No. 8
0270-7306/07/$08.00+0     doi:10.1128/MCB.01084-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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