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Microbiology 153 (2007), 877-886; DOI  10.1099/mic.0.2006/002873-0
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Microbiology 153 (2007), 877-886; DOI  10.1099/mic.0.2006/002873-0
© 2007 Society for General Microbiology

Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae

Siew Leng Tai1, Ishtar Snoek2, Marijke A. H. Luttik1, Marinka J. H. Almering1, Michael C. Walsh3, Jack T. Pronk1 and Jean-Marc Daran1

1 Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
2 Institute of Biology Leiden, Leiden University, Leiden, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
3 Heineken Supply Chain, Research and Innovation, Burgemeester Smeetsweg 1, 2380 BB Zoeterwoude, The Netherlands

Correspondence
Jean-Marc Daran
j.m.daran{at}tnw.tudelft.nl

The applicability of transcriptomics for functional genome analysis rests on the assumption that global information on gene function can be inferred from transcriptional regulation patterns. This study investigated whether Saccharomyces cerevisiae genes that show a consistently higher transcript level under anaerobic than aerobic conditions do indeed contribute to fitness in the absence of oxygen. Tagged deletion mutants were constructed in 27 S. cerevisiae genes that showed a strong and consistent transcriptional upregulation under anaerobic conditions, irrespective of the nature of the growth-limiting nutrient (glucose, ammonia, sulfate or phosphate). Competitive anaerobic chemostat cultivation showed that only five out of the 27 mutants (eug1{Delta}, izh2{Delta}, plb2{Delta}, ylr413w{Delta} and yor012w{Delta}) conferred a significant disadvantage relative to a tagged reference strain. The implications of this study are that: (i) transcriptome analysis has a very limited predictive value for the contribution of individual genes to fitness under specific environmental conditions, and (ii) competitive chemostat cultivation of tagged deletion strains offers an efficient approach to select relevant leads for functional analysis studies.

Abbreviations: qrtPCR, quantitative real-time PCR

Primers used in this study and expression data of YGR059W and ACT1 over different chemostat culture conditions are available as supplementary data with the online version of this paper.






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