BMC Genomics 2008, 9:627 http://www.biomedcentral.com/1471-2164/9/627 with their estimated half-lives. Predictable yet less dra- matic differences in the expression of these, as well as most other genes that comprise the common stress response, have been shown to result from simply varying the growth rate [7], providing further evidence that their expression is in step with the physiological status of the cell. In nearly all conditions examined except nutrient starva- tion [2], the stress response has shown to be transitory, with maximal transcriptional changes frequently observed between 15 and 30 min and a diminishing response after 60 min. Although, multiple interpretations have been provided (e.g., see discussions in [2,4,43]), a simple hypothesis that fits with the transcriptomic data is that all of these environmental challenges, whether per- turbations that temporally disrupt catabolic pathways or ones that require rapidly up-regulating costly programs for combating a specific stressor, require the immediate expenditure of sufficient energy as to require the suspen- sion of other cellular operations, such as general protein synthesis. Obviously, such a hypothesis needs to be cor- roborated with careful measurements of cellular energet- ics, measurements that are the focus of ongoing studies in the laboratory. After the initial energetic drain, it would appear that a new balance is quickly achieved and cells resume their normal activities given these genes do not continue to be differentially expressed except under nutri- ent starvation conditions. Moreover, such an interpreta- tion suggests the response is graded according to the degree to which the energetic status of the cell is per- turbed, a hypothesis that is directly testable and the sub- ject of additional ongoing experiments in our laboratory. Finally, several recent studies have suggested that many of the genes that have been previously characterized as "stress responsive" are perhaps more appropriately labeled "growth-rate responsive" [7-9]. In a serious of ele- gant, nutrient-limited chemostat studies, these authors have shown the expression of most of the genes compris- ing the ESR is in-step with steady-state growth rate. Thus, rather than responding to the stress directly, perhaps they are responding to a change in growth rate secondary to the stress [8,9]. To determine if the genes we identified are correlated with growth rate, we divide the clustered expression profiles of the anaerobic dataset into groups of transiently and chronically responding ones and then fur- ther into repressed and induced sets. Using the online util- ity http://growthrate.princeton.edu developed by Brauer et al. 2008 [9] we plotted the distribution of growth-rate slopes for these sets. As shown in Additional file 7, those that are transiently expressed are highly correlated with growth rate whereas those that were more chronically expressed are not. Given this, it is also possible to infer the instantaneous growth rate using these transiently expressed genes [9], which in our datasets suggests a max- imal slowing of growth between 0.13 and 0.19 genera- tions (ca. 30 min) in response to N2 and antimycin A treatment in air and complete recovery by about 0.5 gen- erations (ca. 2 h). If changes in the expression of these genes are a direct result of differences in growth rate, what is puzzling here is the fact they are not differentially expressed between the strictly fermentative phase, in which the mass doubling time is 4 h, and the respiro-fer- mentative phase, in which the mass doubling time is 2.4 h. Rather the response is strictly transitory. What's more is that inhibiting galactose-dependent respiration limits the rate at which ATP can be generated (QATP) and, thus, it is hard to see how acute changes in cellular energetics can- not be at the core of this response. In other words, that it is the acute change in cellular energetics that initiates the response resulting in the change in growth rate, a hypoth- esis that is being tested with on-going experiments in our laboratory. In summary, all eukaryotic cells have necessarily evolved mechanisms for effectively dealing with fluctuations in physical, chemical, and physiological parameters. Even within the relatively protected confines of multicellular organisms, cells experience fluctuations in osmolarity, oxygen and reactive oxygen species as well as various nutrients and noxious substances. Comparative studies have shown that many of the factors important for regu- lating the stress response, including both signaling path- ways (e.g., MAPK) and transcription factors (e.g., AP-1), are conserved from yeast to humans. Understanding the factors that influence this response has important implica- tions for pathophysiological conditions, such as heart dis- ease, tumorigenesis, various metabolic syndromes, and aging, all of which contribute to stress at the cellular level. Here we set forth a hypothesis that at its core is the regu- lation of cellular energetics via an as yet unidentified met- abolic signal. Such internal signals are being actively studied in bacteria [44] but comparatively little work has been done in eukaryotes. Two, partially redundant, ser- ine/threonine kinases containing PAS domains, Psk1 andPsk2, which coordinately regulate protein synthesis and carbohydrate metabolism in response to nutritional status of the cell, have been implicated in signaling in yeast. Although a small molecule/metabolite is presumed to trigger this response by interacting with the PAS domain, it has not been identified [45,46]. Variants of this system are found from yeast to mammals [47-49]. Thus, future studies with such factors will be of great interest to unravel both the sensing and signaling aspects of this con- served stress response program. Methods Media and growth conditions The S. cerevisiae strain JM43 (MAT leu2-3,112 his4-580 trp1-289 ura3-52 [ +])[50] was used. Liquid pre-cultures were grown in a semi-synthetic galactose medium con- Page 10 of 14 (page number not for citation purposes)