Background: Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.

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Using competition experiments in continuous cultures grown in different nutrient environments (glucose limited, ammonium limited, phosphate limited and white grape juice), we identified genes that show haploinsufficiency phenotypes (reduced growth rate when hemizygous) or haploproficiency phenotypes (increased growth rate when hemizygous). Haploproficient genes (815, 1,194, 733 and 654 in glucose-limited, ammonium-limited, phosphate-limited and white grape juice environments, respectively) frequently show that phenotype in a specific environmental context. For instance, genes encoding components of the ubiquitination pathway or the proteasome show haploproficiency in nitrogen-limited conditions where protein conservation may be beneficial. Haploinsufficiency is more likely to be observed in all environments, as is the case with genes determining polar growth of the cell. Haploproficient genes seem randomly distributed in the genome, whereas haploinsufficient genes (685, 765, 1,277 and 217 in glucose-limited, ammonium-limited, phosphate-limited and white grape juice environments, respectively) are over-represented on chromosome III. This chromosome determines a yeast's mating type, and the concentration of haploinsufficient genes there may be a mechanism to prevent its loss.

Members of the ternary complex factor (TCF) subfamily of the ETS-domain transcription factors are activated through phosphorylation by mitogen-activated protein kinases (MAPKs) in response to a variety of mitogenic and stress stimuli. The TCFs bind and activate serum response elements (SREs) in the promoters of target genes in a ternary complex with a second transcription factor, serum response factor (SRF). The association of TCFs with SREs within immediate-early gene promoters is suggestive of a role for the ternary TCF-SRF complex in promoting cell cycle entry and proliferation in response to mitogenic signaling. Here we have investigated the downstream gene regulatory and phenotypic effects of inhibiting the activity of genes regulated by TCFs by expressing a dominantly acting repressive form of the TCF, Elk-1. Inhibition of ternary complex activity leads to the downregulation of several immediate-early genes. Furthermore, blocking TCFmediated gene expression leads to growth arrest and triggers apoptosis. By using mutant Elk-1 alleles, we demonstrated that these effects are via an SRF-dependent mechanism. The antiapoptotic gene Mcl-1 is identified as a key target for the TCF-SRF complex in this system. Thus, our data confirm a role for TCF-SRF-regulated gene activity in regulating proliferation and provide further evidence to indicate a role in protecting cells from apoptotic cell death.Elk-1 is a member of the ternary complex factor (TCF) subfamily of ETS-domain transcription factors (reviewed in references 46 and 50). In mammals there are two other TCFs, SAP-1 and SAP-2/ERP/Net. These proteins are characterized by their ability to form ternary complexes on target promoters in conjunction with the MADS-box protein serum response factor (SRF). The TCFs share four domains, the ETS DNAbinding domain, the B-box, the D-domain, and the C-domain. SAP-2/Net contains additional regions that impart repressive properties (9, 29). The D-and C-domains constitute the regulatory part of Elk-1 and other TCFs. The D-domain acts as a docking site for mitogen-activated protein kinases (MAPKs) (reviewed in references 15 and 49). These docked kinases can then phosphorylate residues in the C-domain, which constitutes the transcriptional activation domain (TAD). Phosphorylation of the TAD leads to elevation of the transactivation potential of the TCFs and also enhances ternary complex formation (reviewed in references 46, 50, 54, and 58). The TCFs can be phosphorylated by members of all three of the major MAPK pathways present in mammals: ERK, JNK, and p38 (reviewed in references 46, 50, and 58). The ERK MAPK pathway predominantly transmits mitogenic and differentiation stimuli, whereas the JNK and p38 MAPK pathways primarily transduce stress and cytokine stimuli to the nucleus (reviewed in reference 41). The TCFs therefore play a pivotal role in transducing extracellular stimuli into alterations in gene expression in the nucleus.The B-box of the TCFs is required for ternary complex formation (11,23,55) and mediates protein-prote...

Global gene expression in yeast was examined in five different nutrient-limited steady states and in their corresponding starvationinduced stationary phases. The use of chemostats, with their ability to generate defined and reproducible physiological conditions, permitted the exclusion of the confounding variables that frequently complicate transcriptome analyses. This approach allowed us to dissect out effects on gene expression that are specific to particular physiological states. Thus, we discovered that a large number of ORFs involved in protein synthesis were activated under ammonium limitation, whereas the expression of ORFs concerned with energy and metabolism was enhanced by carbon limitation. Elevated transcription of genes in high-affinity glucose uptake, the trichloroacetic acid cycle, and oxidative phosphorylation were observed in glucoselimiting, but not glucose-abundant, conditions. In contrast, genes involved in gluconeogenesis and, interestingly, genes subject to nitrogen catabolite repression increased their transcription when ethanol was the carbon source, even though ammonium was in excess. This result suggests that up-regulation of genes sensitive to nitrogen catabolite repression may contribute anapleurotic intermediates in ethanol-grown cells. The different starvation conditions produced two general types of transcription profiles, with carbonstarved cells transcribing far fewer genes than cells starved for any of the other macronutrients. Nonetheless, each starvation condition induced its own peculiar set of genes, and only 17 genes were induced >5-fold by all five starvations. In all cases, analysis of the upstream sequences of clusters of coregulated genes identified motifs that may be recognized by transcription factors specific for controlling gene expression in each of the physiological conditions examined.chemostat culture ͉ global gene expression ͉ nutrient limitation ͉ nutrient starvation