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Papers In Press, published online ahead of print October 19, 2004
Bioinformatics, Institute of Biochemistry and Biophysics PAS, Warszawa 02-106
Corresponding Author: andrzejk{at}ibb.waw.pl
The Crt1 (RFX1) protein in Saccharomyces cerevisiae is an effector of the DNA-damage checkpoint pathway. It recognizes a 13 bp cis-regulatory element in the 5’ untranslated region (5’UTR) of the ribonucleotide reductase genes RNR2, RNR3, RNR4, the HUG1 gene and itself. We calculated the weight matrix representing the Crt1p binding site motif according to analysis of the 5’UTR sequences of the genes that are under its regulation. We subsequently searched the 5’UTR sequences of all the genes in the yeast genome for the occurrence of this motif. The motif was found in regulatory regions of 30 genes. A statistical analysis shows that it is unlikely that a random gene cluster contains the motif conserved as well as the Crt1p binding site. Analysis of microarray data provides supporting evidence for five putative Crt1p targets: FSH3, YLR345W, UBC5, NDE2 and NTH2. We have used reverse transcription PCR to compare the expression levels of these genes in wild-type and crt1 strains. Our results indicate that FSH3, YLR345W and NTH2 are indeed under the regulation of Crt1p. Sequence analysis of the FSH3p indicates that this protein may be involved in folate metabolism, either by carrying serine hydrolase activity required for the novel metabolic pathway involving dihydrofolate reductase (DHFR), or by directly interacting with the DHFR enzyme. We postulate that Crt1p may influence deoxyribonucleotide synthesis not only by regulating expression of the RNR genes but also by modulating DHFR activity. FSH3p shares significant sequence similarity with the product of the human tumor supressor gene OVCA2. YLR345Wp and NTH2p are enzymes involved in the central metabolism under stress conditions.
J. Biol. Chem, 10.1074/jbc.M404669200
Submitted on April 27, 2004
Revised on October 13, 2004
Accepted on October 18, 2004
Identification of new genes regulated by the Crt1 transcription factor, an effector of DNA-damage checkpoint pathway in saccharomyces cerevisiae
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