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Genome‐wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism
Author(s) -
Bro Christoffer,
Regenberg Birgitte,
Nielsen Jens
Publication year - 2003
Publication title -
biotechnology and bioengineering
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.136
H-Index - 189
eISSN - 1097-0290
pISSN - 0006-3592
DOI - 10.1002/bit.10899
Subject(s) - gene , orfs , biology , saccharomyces cerevisiae , genetics , genome , alcohol dehydrogenase , transcription (linguistics) , enzyme , biochemistry , open reading frame , peptide sequence , linguistics , philosophy
The genome‐wide transcriptional response of a Saccharomyces cerevisiae strain deleted in GDH1 that encodes a NADP + ‐dependent glutamate dehydrogenase was compared to a wild‐type strain under anaerobic steady‐state conditions. The GDH1 ‐deleted strain has a significantly reduced NADPH requirement, and therefore, an altered redox metabolism. Identification of genes with significantly changed expression using a t ‐test and a Bonferroni correction yielded only 16 transcripts when accepting two false‐positives, and 7 of these were Open Reading Frames (ORFs) with unknown function. Among the 16 transcripts the only one with a direct link to redox metabolism was GND1 , encoding phosphogluconate dehydrogenase. To extract additional information we analyzed the transcription data for a gene subset consisting of all known genes encoding metabolic enzymes that use NAD + or NADP + . The subset was analyzed for genes with significantly changed expression again with a t ‐test and correction for multiple testing. This approach was found to enrich the analysis since GND1 , ZWF1 and ALD6 , encoding the most important enzymes for regeneration of NADPH under anaerobic conditions, were down‐regulated together with eight other genes encoding NADP(H)‐dependent enzymes. This indicates a possible common redox‐dependent regulation of these genes. Furthermore, we showed that it might be necessary to analyze the expression of a subset of genes to extract all available information from global transcription analysis. © 2004 Wiley Periodicals, Inc.