Livas et al. BMC Genomics 2011, 12:405 http://www.biomedcentral.com/1471-2164/12/405 Page 5 of 12 Figure 3 Consequences of the lack of PKA in the repression by glucose of some representative genes. Yeast strains TPK1 TPK2 TPK3, tpk1 tpk2 tpk3 msn2 msn4, and tpk1 tpk2 tpk3 yak1 were grown on ethanol and samples were taken before the addition of glucose to the medium and 30 min after, as described in Methods. mRNA levels were measured using Affymetrix microarrays. Biological duplicates were performed. Expression data from biological replicates generally differed from the average by less than 25%. The repression factor is the quotient of the values measured in samples grown in the absence of glucose and in those incubated in the presence of glucose. Repression is considered “total” when the repression factor is no less than 70% of that measured in the reference strain in at least one of the strains lacking PKA. the reference strain) in strains without a functional PKA, others were partially repressed, and still others not repressed at all in the PKA-negative strains. Representa- tive expression profiles for each of these groups are shown in Figure 3. Many of the genes required for growth on non-fer- mentable carbon sources were repressed by glucose in at least one of the two yeast strains without a functional PKA, either fully (ACS1, ADY2, CIT2, CIT3, DLD1, FBP1, ICL1, MDH2, MLS1, PCK1, SFC1) or partially (ACH1, ACO1, ADH2, CIT1, COX7, CYB2, CYT1, FUM1, GUT2, IDH1, IDP2, JEN1, KGD1, KGD2, LSC1, MDH1, MDH3) (Figure 3 and results not shown). Besides, genes encoding proteins that control carbon metabolism were repressed by glucose in the absence of PKA, with some showing full (CAT8, MAL33, REG2, SIP4, SNF3) and others partial (ADR1, HAP4, RGT1) repression. Several genes encoding proteins with a variety of other functions were also strongly repressed by glucose in the absence of PKA. Their functions included glucose meta- bolism (HXK1, YIG1), lipid metabolism (CRC1, INO1, YAT1, YAT2), nitrogen metabolism (ATO3, PUT1, PUT4), phosphate metabolism (PHO89), and tolerance