Livas et al. BMC Genomics 2011, 12:405 http://www.biomedcentral.com/1471-2164/12/405 Another important group of glucose-induced genes encodes proteins involved in the biogenesis of ribosomes and is subject to a very complex combinatorial control. Binding, through Rap1, of the transcription factor Fhl1 together with the coactivator Ifh1 to the corresponding promoters activates the transcription of these genes, while other factors, Cfr1, Dot6 and Tod6, Stb3, contri- bute to repress their transcription. Glucose modifies the intracellular localization of these factors: it promotes a cytoplasmic location for Cfr1 [34], Dot6 and Tod6 [35], and Stb3 [36] and the nuclear localization of Fhl1 and Ifh1 [37]. While PKA can phosphorylate Dot6 and Tod6 and this is likely to direct them to the cytoplasm, export from the nucleus of Stb3 depends on Tor activity but not on PKA. Glucose also promotes the phosphorylation by PKA of the global transcriptional regulator Sfp1, responsible for the nuclear relocalization of Fhl1 and Ifh1. However, phosphorylation by PKA of Sfp1, in the absence of glucose, is not sufficient to direct Sfp1 to the nucleus [37]. This indicates that an alternative signalling pathway is involved in the process; it may be Tor- dependent, since there is already evidence for activation by glucose of the Tor signalling pathway [36,38,39]. However, the molecular mechanism responsible for this effect of glucose on Tor has not been yet established. With respect to genes encoding glycolytic enzymes, they depend on the transcription factors Gcr1 and Gcr2 [40,41] but there is no information on the regulation of these factors by glucose. Most of the genes repressed by glucose depend for their transcription on the activity of the protein kinase Snf1 and/or on the transcription factors Hap1, Hap4, Cat8 and Adr1 [27]. There is no evidence that Hap1 itself is regulated by glucose; repression by glucose of genes activated by Hap1 depends on its control of other transcription factors such as Hap4 or Adr1 [42]. Tran- scription of HAP4 and ADR1 is repressed by glucose and we have found that the degree of repression decreases in the absence of PKA, but the intimate mechanism of the repression of transcription is unknown. Snf1 is not required for the induction of ADR1 [43] or of HAP4 [27], that takes place in the absence of glucose, but a Snf1-dependent pathway is responsible for the activation of the transcription factor Adr1 in these conditions [44]. Snf1 is also necessary both for the transcription of CAT8 and for the tran- scriptional activation of Cat8 [45]. We have observed that glucose represses SNF1 transcription about 2-fold, in addition to its well-known role in decreasing Snf1 activity [33]. Although the mechanism for this decrease is not established, it has been proposed that the b subu- nit of the Snf1 complex is important to maintain Snf1 in an inactive state [46]. Specifically, the glycogen-bind- ing domain of the b subunit Gal83 would mediate the Page 9 of 12 recruitment of the Reg1-Glc7 complex, responsible for the dephosphorylation and subsequent inactivation of Snf1. It should be stressed that, even in cases where PKA has been shown to play an important role in the control of gene transcription by glucose, the target for PKA has not been generally identified. A possible approach for clarifying the role of PKA could be to check whether selected proteins identified as potential PKA substrates participate in the glucose response. Surprisingly, among the many proteins interacting with Tpk1, Tpk2 or Tpk3 and characterized as possible substrates [47,48] few good candidates appeared. The proteins Msn2/Msn4 are an interesting exception. For the genes under control of Msn2/Msn4, PKA operates directly through the phos- phorylation of the transcription factors, allowing their export to the cytoplasm, and thus precluding transcrip- tion. As shown in table 5, expression of the relevant genes is already low in the absence of glucose in the strain lacking Msn2/Msn4 and the effect of glucose is modest. In the tpk1 tpk2 tpk3 yak1 strain expression is similar to that of the wild-type strain under gluconeo- genic conditions but it is much less sensitive to the addition of glucose, as the transcriptional activators remain in the nucleus. New strategies would have to be devised to identify additional protein substrates of PKA that may play a role in the response to glucose. Conclusions This study shows that, although PKA is frequently involved in the control of transcription by glucose, there are many instances in which PKA activity is dispensable. We have also observed that for genes regulated exclu- sively through PKA the effect of glucose on transcrip- tion may be transient. It may be concluded that the role of cAMP/PKA in transcription, which was first identi- fied a couple of decades ago, still represents many chal- lenges and that one of the goals of systems biology, the Table 5 Genes activated by Msn2/Msn4 and depending on PKA for glucose repression Relevant genotype tpk1 tpk2 tpk3 msn2 msn4 tpk1 tpk2 tpk3 yak1 Gene GPX1 GSY2 HPF1 MSC1 TSL1 TPK1 TPK2 TPK3 Et 100 100 100 100 100 + Glu 6 13 41 4 8 Et 15 23 21 9 16 + Glu 8 15 42 6 9 Et 73 80 94 45 90 + Glu 45 62 108 39 92 A wild-type strain and two strains lacking PKA were grown on ethanol, samples taken before (Et) and 30 min after the addition of glucose (+Glu), and mRNA levels measured (see Methods for details). Expression is given as percent of the value in the wild-type strain growing on ethanol.