BMC Genomics 2008, 9:627 http://www.biomedcentral.com/1471-2164/9/627 Is the acute response to respiratory inhibition an "envi- ronmental stress response"? While it is common practice to look for congruence in lists of differentially expressed genes among various treatments to answer this question, such comparisons are more meaningful and robust when comparing functional groups and transcriptional units defined by common cis-regulatory sequences statistically enriched in the clustered genes. Even when identical experimental treatments are compared, differences in strain backgrounds, media, time courses, expression plat- forms, statistical criteria, and experimental variation can result in frighteningly little congruence among gene sets. For example, when we compare our transiently respond- ing genes to those that comprise the ESR [2], there is only modest (40%) overlap. However, after performing SOM clustering of the ESR data and calculating FCS and CS as we did for our data sets, we recovered eight clusters of transiently up-regulated genes and four clusters of tran- siently down-regulated genes in which the predominant cis-regulatory sequences and functional categories were nearly the same as in our study. These include rapidly repressed networks involved in aminoacyl-tRNA synthesis and protein synthesis that are enriched for SCB, Swi6 and Abf1 binding sites, and several clusters of transiently repressed genes involved in ribosomal biogenesis, rRNA transcription/processing and/or protein synthesis that are significantly enriched for Fhl1, Rap1, PAC, RRPE, and/or Abf1 sites. Those that were transiently induced are pre- dominated by Msn2/4 and/or Nrg1 sites and enriched for categories of rescue and defense, the stress response, metabolism of energy reserves and peroxisome function. Thus, from a network comparison it is clear that the same or similar gene networks respond to respiratory inhibition as they do to a large number of other environmental chal- lenges. Functional Attributes of the General Stress Response The general stress response was first postulated to explain the phenomenon of cross-protection, wherein exposure to a non-lethal dose of one stress protects against a poten- tially lethal dose of another, often seemingly unrelated, stress [20-25]. It is now clear that this cross protection is afforded by the transcriptional up-regulation of a com- mon set of general stress-responsive genes involved in diverse cellular functions, including reserve energy regula- tion, carbohydrate metabolism, protein folding and deg- radation, oxidative stress defense, autophagy, cytoskeletal reorganization, DNA-damage repair, and other processes [2,4]. However, the degree of cross-protection varies depending on the stresses and it is not always reciprocal, indicating that stress-specific responses are required for full protection from a specific stressor. Stress resistance has also been shown to occur following nutrient depriva- tion and stationary phase [2,26-28]. A number of different signaling pathways acting in response to specific stressors have been shown to control these stress-responsive genes. Signaling pathways implicated in coordinating the response include the protein kinase C (PKC)-mitogen- activated protein (MAP) kinase pathway following secre- tion defects and cell wall damage [29-32], the MEC1 path- way following DNA damage [33], and the Ssk1/Ste11- dependent pathways and high osmolarity glycerol (HOG)-MAP kinase cascade following osmotic stress [1,34]. Pathways involved in suppressing the response include the target of rapamycin (TOR) pathway [35], the Snf1 protein kinase pathway [36], and the PKA-MAP kinase pathway [37-39]. Although seemingly complex, such a multiplex of signaling cascades is likely required for dictating specificity in the cellular response to an environ- ment in which a multitude of different parameters (e.g., temperature, osmolarity, pH, O2 and other nutrients) can change simultaneously. From functional analyses of the response, it is clear that a rapid change in steady-state conditions (environmental or physiological) prepares the cell to meet a myriad of unforeseen challenges. From a systems level viewpoint, the cell must coordinate energy metabolism with growth rate, the cell cycle, and any specific requirements dictated by the environmental conditions. Given the gene net- works that respond, it would appear that at its core is the sparing of energetic demand by rapidly down-regulating the expression of a large set of genes (~600) involved in energy consuming pathways. Simultaneously, supplies may be bolstered by up-regulating key genes involved in import/utilization of primary and secondary carbon sub- strates and presumably recycling cellular components through autophagy. More complex changes are observed for genes involved in reserve energy stores (trehalose and glycogen), which presumably reflect appropriate parsing of supplies for cell-cycle function and stress mitigation while preserving a modicum of reserve capacity. In addi- tion to changes in gene expression, many of these latter genes are regulated post-transcriptionally. In terms of potential energetic sparing measures, more than 70% of the characterized genes [40,41] whose expression is down-regulated in the ESR are involved in protein synthesis, including genes required for ribosome synthesis and processing, RNA polymerase I- and III- dependent transcription, and protein translation. Thus, it should be of no surprise that these include some of the most abundant and shortest-lived mRNAs, namely genes for ribosomal proteins (RP genes) and rRNA transcrip- tion. RP genes alone account for about 60% of all tran- scription-initiation events in rapidly growing yeast cells [42] and a remarkable 90% of all mRNA splicing events. Temporal analyses suggest rapid transcriptional deactiva- tion or silencing of these genes followed by mRNA decay given that the decline in their transcript levels tracks well Page 9 of 14 (page number not for citation purposes)