BMC Genomics 2008, 9:627 http://www.biomedcentral.com/1471-2164/9/627 Background Previous studies with Saccharomyces cerevisiae have found that a common transcriptomic program is initiated in response to a diverse array of environmental challenges. These include temperature shock, osmotic or oxidative stress, low pH, DNA damaging agents, nutrient starvation, a switch to lower quality carbon sources, and oxygen dep- rivation under catabolite non-repressed conditions [1-6]. This program has been called the "environmental stress response" (ESR) [2] or "common environmental response" (CER) [4], but the factors responsible for initi- ating the response and the function of its various compo- nents remain unclear. Our previous gene network analyses of an ESR/CER-like response elicited by anaero- biosis [5,6] suggest it is involved in rebalancing energy supply and demand in response to an abrupt change in cellular energy status while concomitantly coordinating growth rate and entry into the cell cycle. Although not measured in most studies, acute yet transient changes in the cellular energetics would be expected to occur in response to any perturbations that disrupt catabolic path- ways for producing energy (e.g., anaerobiosis, glucose starvation, or a switch to a lower quality energy source) or when survival depends on rapidly up-regulating energeti- cally costly programs for combating specific stressors (e.g., temperature shock, osmotic or oxidative stress, DNA dam- aging agents, etc.). Thus, a common metabolic conse- quence that would be predicted to result from any of these environmental challenges is an abrupt, although transi- tory, decrease in energy that would require compensatory actions for survival. Further support comes from the fact that the acute with- drawal of oxygen does not elicit such a response under cat- abolite-repressed conditions (glucose) but does under non-repressed conditions (galactose) [5,6]. A fundamen- tal difference in the metabolism of these sugars that may explain this difference is the fact that oxygen deprivation does not substantially affect the overall yield or rate of ATP formation from glucose dissimilation but does severely limit both during galactose dissimilation. Thus, when cells are grown in glucose the aerobic-to-anaerobic transition proceeds without a change in growth rate [5,6], but in galactose the rapid withdrawal of oxygen results in the abrupt decrease in energy production and slowing of growth to a rate that is nearly half of that supported by mixed respiro-fermentative metabolism [5,6]. Although several recent studies have suggested that the ESR is evoked by growth rate differences [7], if this were true it is difficult to reconcile the fact these networks are not differ- entially expressed between the much faster respiro-fer- mentative growth phase in galactose and the slower fermentative growth phase but rather only transiently respond during the change [8,9]. An alternative explana- tion is that it is the abrupt decrease in cellular energy stores that elicits the ESR/CER under these conditions, not the withdrawal of oxygen. In other words, that it is the abrupt inhibition of oxidative phosphorylation and asso- ciated changes in cellular energetics that triggers this ESR/ CER-like response, not changes in growth rate per se. Further support comes from functional and gene network analyses of the anaerobic response in galactose [5,6]. Using a novel clustering approach for recovering active gene networks, as well as knockouts of selected transcrip- tion factors [5], we revealed the ESR/CER-like response is comprised of the transient up-regulation of Msn2/4-regu- lated networks involved in both hexose import/dissimila- tion and reserve energy regulation as well as the transient down-regulation of Fhl1 and PAC/RRPE-associated net- works involved in energetically costly programs for ribos- omal biogenesis and protein synthesis. In addition, MBF- and SBF-regulated networks involved in the G1/S transi- tion of the cell cycle are also transiently down-regulated, resulting in a delay of its progression as mass (e.g., glyco- gen and trehalose stores) and energy are assessed before committing to another round of the cycle. Given their function, these results suggest that transient changes in the activity of these gene networks are required for balanc- ing energy supply and demand and coordinating growth with progression through the cell cycle during the abrupt switch to strictly fermentative growth. Additional support comes from a study that found that treatment with the cytochrome bc1 inhibitor myxothiazol under normoxia in galactose grown cells also elicits a transient response in many of the genes that comprise the ESR/CER [10]. To further investigate the regulatory factors involved and distinguish between networks that respond to oxygen deprivation and those that respond to the abrupt cessa- tion of respiration, we poisoned the respiratory chain with the cytochrome bc1 inhibitor antimycin A and conducted a temporal analysis of the transcriptomic response over three generations of aerobiosis followed by three genera- tions of anaerobiosis. This treatment served several pur- poses. First, poisoning respiration under normoxic conditions mimics the loss of respiratory-dependent energy production that occurs during the shift to anaero- biosis, independent of a change in oxygen availability. Given that changes in the activity of more chronically responding gene networks are observed within three gen- erations of anaerobic growth [6], assaying gene expression over this period should allow us to differentiate between networks that respond to the cessation of respiration and any that may respond to the chronic loss of respiratory capacity, independent of a change in oxygen availability. Moreover, by then shifting the respiratory incompetent cells to anaerobiosis and assaying gene expression over three additional generations of growth, we should be able to distinguish between any networks that acutely respond Page 2 of 14 (page number not for citation purposes)