Livas et al. BMC Genomics 2011, 12:405 http://www.biomedcentral.com/1471-2164/12/405 catalytic subunits and thereby activates them. In a yeast strain harbouring a RAS2Val19 gene, encoding a constitu- tively active form of Ras2, under the control of the GAL1 promoter, an increase in internal cAMP levels may be achieved in the absence of glucose through the addition of galactose. Even when galactose metabolism in such a strain is blocked by disruption of the GAL1 gene (encod- ing galactokinase), the increase in cAMP levels that fol- lows galactose addition causes many of the effects on transcription that are elicited by glucose [5]. The same authors also report that in a bcy1 strain, where PKA activity is independent of cAMP levels, transcription of many genes still responds to the presence of glucose. This last observation suggests that there are additional, and possibly redundant, glucose signalling pathway(s) independent of changes in PKA activity triggered by cAMP [5]. This does not, however, discard the possibility that the alternative pathway(s) require a basal activity of PKA, even if they do not depend on its activation by cAMP. The goal of the present study was to investigate the occurrence of PKA-independent glucose signalling in S. cerevisiae. To this end, we have used global tran- scription analysis to study the effects of glucose on yeast strains completely devoid of PKA activity. In S. cerevisiae three genes TPK1, TPK2, and TPK3 encode catalytic subunits of PKA. While strains expressing only one of these genes grow normally, a triple mutant (tpk1 tpk2 tpk3) is not viable [13]. Characteri- zation of different mutations able to suppress the growth defect of the triple mutant [14-16] has enabled identification of the crucial function of PKA. As shown Page 2 of 12 in Figure 1, PKA is needed to counteract the negative effect of the protein kinase Yak1 on yeast growth [17,18]. In the presence of PKA the protein kinase Rim15 [15] and the transcription factors Msn2 and Msn4 [19] can be phosphorylated and exported to the cytoplasm. As a consequence, transcription of Msn2/ Msn4 activated genes, among them YAK1 [16], is reduced, Yak1 levels remain low and growth is not hindered. In the absence of PKA, Rim15 remains in the nucleus where it can activate Msn2/Msn4 [20] that turn on YAK1 transcription. Yak1 then blocks growth by mechanisms that may include the phosphorylation and activation of Msn2/Msn4 [21]. This explains why strains lacking Rim15, Msn2/Msn4 or Yak1 no longer require PKA for growth. In this work we have used two isogenic strains lacking PKA and carrying the sup- pressor mutations msn2 msn4 or yak1. Two different suppressor mutants were used with the aim to enable a dissection of effects of the lack of PKA and effects of the suppressor mutations themselves. We found that glucose induction of genes related with glucose metabolism or glucose repression of genes involved in the utilization of carbon sources alternative to glucose can proceed in the absence of PKA. We noted, however, that genes related with similar types of pro- cesses, such as biosynthesis of amino acids or transport of drugs, may respond differently to the lack of PKA. Results Genes induced by glucose When ethanol-grown cultures of the TPK1 TPK2 TPK3 reference strain were exposed to glucose over 700 Figure 1 Relationships between Tpk1, 2, 3, Rim15, Msn2/4 and Yak1. Activated Tpks can phosphorylate Msn2/4 and Rim15 leading to their export to the cytoplasm, thus reducing the transcription rate of YAK1 and allowing growth. In the absence of Tpks, Rim15 and Msn2/4 are not phosphorylated and remain in the nucleus, in an active or potentially active form. Rim15 activates Msn2/4, Msn2/4 activate the transcription of YAK1 and Yak1 blocks cellular growth.