Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response - PubMed (original) (raw)
Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response
Kurt E Kwast et al. J Bacteriol. 2002 Jan.
Abstract
DNA arrays were used to investigate the functional role of Rox1 in mediating acclimatization to anaerobic conditions in Saccharomyces cerevisiae. Multiple growth conditions for wild-type and rox1 null strains were used to identify open reading frames with a statistically robust response to this repressor. These results were compared to those obtained for a wild-type strain in response to oxygen availability. Transcripts of nearly one-sixth of the genome were differentially expressed (P < 0.05) with respect to oxygen availability, the majority (>65%) being down-regulated under anoxia. Of the anaerobically induced genes, about one-third (106) contain putative Rox1-binding sites in their promoters and were significantly (P < 0.05) up-regulated in the rox1 null strains under aerobiosis. Additional promoter searches revealed that nearly one-third of the anaerobically induced genes contain an AR1 site(s) for the Upc2 transcription factor, suggesting that Upc2 and Rox1 regulate the majority of anaerobically induced genes in S. cerevisiae. Functional analyses indicate that a large fraction of the anaerobically induced genes are involved in cell stress (approximately 1/3), cell wall maintenance (approximately 1/8), carbohydrate metabolism (approximately 1/10), and lipid metabolism (approximately 1/12), with both Rox1 and Upc2 predominating in the regulation of this latter group and Upc2 predominating in cell wall maintenance. Mapping the changes in expression of functional regulons onto metabolic pathways has provided novel insight into the role of Rox1 and other trans-acting factors in mediating the physiological response of S. cerevisiae to anaerobic conditions.
Figures
FIG. 1.
Mean transcript levels of 6,150 yeast ORFs from wild-type and rox1 null strains. Batch cultures of strains JM43, KKY6 (JM43Δ_rox1_), RZ53-6, and RZ53-6Δ_rox1_ were aerobically grown in SSG-TEA and YPGal media. [33P]dATP-labeled cDNA probes were reverse transcribed from 10 μg of total RNA and hybridized to GeneFilter arrays. Each point represents the mean mRNA abundance for the rox1 null strains compared to that from the wild-type strains (n = 12 for each strain). The diagonal lines indicate ratios of the rox1 and wild-type transcript levels.
FIG. 2.
Mean transcript levels of 6,150 yeast ORFs from aerobic and anaerobic batch cultures. Batch cultures of strain JM43 were grown in SSG-TEA medium under aerobic or anaerobic conditions. Probe generation and hybridization were as described in the legend to Fig. 1. Each point represents the mean mRNA abundance for anaerobic cultures (n = 4) compared to aerobic cultures (n = 8). The diagonal lines indicate ratios of anaerobic to aerobic transcript levels.
FIG. 3.
Functional classification of anaerobically induced genes. The 346 genes that were significantly (P < 0.05) up-regulated under anaerobiosis were grouped into major functional categories using both YPD and MIPS classifications. The ORFs are listed in alphabetical order except those appearing in specific functional groups for which gene names are provided. The ANOVA results (P values) and expression ratios (rox1/wild-type [WT] and anaerobic/aerobic [N2/air]) are shown for both comparisons and are represented by different colors, as indicated in the key. The 35 genes listed under “Cell Stress” are those left after overlap with the other functional categories had been eliminated.
FIG. 4.
Schematic representation of oxygen-responsive and Rox1-regulated genes involved in reserve carbohydrate metabolism, glycolysis, redox balance, and mitochondrial function. The yeast genes encoding proteins involved in each step of the metabolic pathways are identified by name in the boxes, with bold lettering indicating significant (P < 0.05) induction in the rox1 strains and italics indicating significant repression. Red boxes indicate genes significantly up-regulated under anaerobiosis, red and yellow indicate those marginally up-regulated, green indicates those significantly up-regulated under aerobiosis, and white indicates those not affected. The magnitude of induction or repression with respect to oxygen availability is indicated to the left of each box, and the P value is shown to the right. The inferred metabolic reprogramming in the upper portion of the figure is indicated by the broad gray arrows. The direction of the arrows connecting reversible enzymatic steps indicates the inferred direction of the flow based upon expression levels with respect to oxygen availability. Abbreviations: UDP-glc, UDP glucose; Glc-1-P, glucose 1-phosphate, Glc-6-P, glucose 6-phosphate; Fru-6-P, fructose 6-phosphate; Fru-1,6-P, fructose 1,6-bisphosphate; DHAP, dihydroxyacetone phosphate; Gly-3-P, glycerol 3-phosphate; GA-3-P, glyceraldehyde 3-phosphate; 1,3-BPG, 1,3-bisphosphoglycerate; 3-PG, 3-phosphoglycerate; 2-PG, 2-phosphoglycerate; PEP, phosphoenolpyruvate; Q, ubiquinone.
FIG. 5.
Schematic representation of oxygen-responsive and Rox1-regulated genes involved in sterol and phospholipid biosynthesis. The yeast genes encoding proteins involved in sterol and phospholipid biosynthesis are identified by name in the boxes using the color and numbering scheme described in the legend to Fig. 4. Only key metabolic intermediates are shown. Abbreviations: HMG CoA, hydroxy-methylglutaryl coenzyme A; MVA, mevalonic acid; IPP, isopentynyl pyrophosphate; GPP, geranylpyrophosphate; FPP, farnesyl-pyrophosphate; C16:0-CoA, palmitic coenzyme A; CDP-C, CDP-choline; CDP-DAG, CDP-diacylglycerol; Cho, choline; Cho-P, cholinephosphate; CL, cardiolipin; DAG, diacylglycerol; DHS-1-P, dihydrosphingosine-1-phosphate; Etn, ethanolamine; Etn-P, ethanolaminephosphate; FA-CoA, fatty acid-CoA; G-6-P, glucose-6-phosphate; Gly-3-P, glycerol-3-phosphate; I, inositol; I-1-P, inositol-1-phosphate; IPC, inositol phosphorylceramide; MIPC, mannose-inositol-P-ceramide; M(IP)2C, phosphoinositol-mannose-inositol-P-ceramide; PA, phosphatidic acid; PtC, phosphatidylcholine; PtE, phosphatidylethanolamine; PtI, phosphatidylinositol; PtS, phosphatidylserine; PhytoCer, phytoceramide; PhytoS-1-P, phytosphingosine-1-phosphate; Ser, serine.
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