Glucose represses transcription of Saccharomyces cerevisiae nuclear genes that encode mitochondrial components

Reactive oxygen species-mediated control of mitochondrial biogenesis

Mitochondrial biogenesis is a complex process. It necessitates the contribution of both the nuclear and the mitochondrial genomes and therefore crosstalk between the nucleus and mitochondria. It is now well established that cellular mitochondrial content can vary according to a number of stimuli and physiological states in eukaryotes. The knowledge of the actors and signals regulating the mitochondrial biogenesis is thus of high importance. The cellular redox state has been considered for a long time as a key element in the regulation of various processes. In this paper, we report the involvement of the oxidative stress in the regulation of some actors of mitochondrial biogenesis.

PAS kinase: integrating nutrient sensing with nutrient partitioning

Recent data suggests that PAS kinase acts as a signal integrator to adjust metabolic behavior in response to nutrient conditions. Specifically, PAS kinase controls the partitioning of nutrient resources between the myriad of possible fates. In this capacity, PAS kinase elicits a pro-growth program, which includes both signaling and metabolic control, both in yeast and in mammals. We propose that, like other kinases possessing these properties-AMPK and TOR, PAS kinase might be target for therapy of diabetes, obesity and cancer.

Increased iron supplied through Fet3p results in replicative life span extension of Saccharomyces cerevisiae under conditions requiring respiratory metabolism

We have previously shown that copper supplementation extends the replicative life span of Saccharomyces cerevisiae when grown under conditions forcing cells to respire. We now show that copper's effect on life span is through Fet3p, a copper containing enzyme responsible for high affinity transport of iron into yeast cells. Life span extensions can also be obtained by supplementing the growth medium with 1mM ferric chloride. Extension by high iron levels is still dependent on the presence of Fet3p. Life span extension by iron or copper requires growth on media containing glycerol as the sole carbon source, which forces yeast to respire. Yeast grown on glucose containing media supplemented with iron show no extension of life span. The iron associated with cells grown in media supplemented with copper or iron is 1.4-1.8 times that of cells grown without copper or iron supplementation. As with copper supplementation, iron supplementation partially rescues the life span of superoxide dismutase mutants. Cells grown with copper supplementation display decreased production of superoxide as measured by dihydroethidium staining.

Interorganelle signaling is a determinant of longevity in Saccharomyces cerevisiae

Replicative capacity, which is the number of times an individual cell divides, is the measure of longevity in the yeast Saccharomyces cerevisiae. In this study, a process that involves signaling from the mitochondrion to the nucleus, called retrograde regulation, is shown to determine yeast longevity, and its induction resulted in postponed senescence. Activation of retrograde regulation, by genetic and environmental means, correlated with increased replicative capacity in four different S. cerevisiae strains. Deletion of a gene required for the retrograde response, RTG2, eliminated the increased replicative capacity. RAS2, a gene previously shown to influence longevity in yeast, interacts with retrograde regulation in setting yeast longevity. The molecular mechanism of aging elucidated here parallels the results of genetic studies of aging in nematodes and fruit flies, as well as the caloric restriction paradigm in mammals, and it underscores the importance of metabolic regulation in aging, suggesting a general applicability.

The control of mitochondrial respiration in yeast: a possible role of the outer mitochondrial membrane

Mitochondrial respiration in yeast (S. cerevisiae) is regulated by the level of glucose in the medium. Glucose is known to inhibit respiration by repressing key enzymes in the respiratory chain. We present evidence that the early events in this inhibition include the closure of VDAC channels, the primary pathway for metabolite flow across the outer membrane. Aluminum hydroxide is known to inhibit the closure of VDAC. Addition of aluminum acetylacetonate to yeast cells, which should elevate the aluminum hydroxide concentrations in the cytoplasm, caused the inhibition of cell respiration by glucose to be delayed for up to 100 min. No significant effect of aluminum was observed in cells grown on glycerol. Yeast cells lacking the VDAC gene were also unresponsive to the addition of aluminum salt in the presence of glucose. Therefore, the closure of VDAC channels may be an early step in the inhibition of the respiration of yeast by glucose.

Genetic analysis of glucose regulation in saccharomyces cerevisiae: control of transcription versus mRNA turnover

A major determinant of the steady-state level of the mRNA encoding the iron protein (Ip) subunit of succinate dehydrogenase of yeast is its rate of turnover. This mRNA is significantly more stable in glycerol than in glucose media. Many other genes, for example, SUC2, that are repressed in the presence of glucose are believed to be controlled at the level of transcription. The present study elucidates differences in the regulatory mechanisms by which glucose controls the transcription and turnover of the SUC2 and Ip mRNAs. The signaling pathway for glucose repression at the transcriptional level has been associated with a number of gene products linking glucose uptake with nuclear events. We have investigated whether the same genes are involved in the control of Ip mRNA stability. Phosphorylation of glucose or fructose is critical in triggering the transcript's degradation, but any hexokinase will do. Of the other known genes examined, most, with the exception of REG1, are not involved in determining the differential stability of the Ip transcript. Finally, our results indicate that differential stability on different carbon sources also plays a role in determining the steady-state level of the SUC2 mRNA. Thus, glucose repression includes both transcriptional and post-transcriptional mechanisms.

Strain-dependent variation in carbon source regulation of nucleus-encoded mitochondrial proteins of Saccharomyces cerevisiae

Nuclear genes encoding mitochondrial proteins are regulated by carbon source with significant heterogeneity among four Saccharomyces cerevisiae strains. This strain-dependent variation is seen both in respiratory capacity of the cells and in the expression of beta-galactosidase reporter fusions to the promoters of CYB2, CYC1, CYC3, MnSOD, and RPO41.

Apparent functional independence of the mitochondrial and nuclear transcription systems in cultured human cells

We have constructed a series of reporter constructs which test the effects of sequence elements from the control region of human mitochondrial DNA on expression in the nucleus, as assayed by transient expression in cultured human cells. The mitochondrial heavy-strand promoter (HSP) was unable to function as a promoter in nuclear DNA. Neither the HSP, nor the binding region for the mitochondrial transcription factor mtTF1 from the light-strand promoter, had any significant or systematic modulatory effects upon transcription from strong or weak RNA polymerase II (pol II) promoters, in three different human cell lines. The same finding held true regardless of orientation with respect to the start site of transcription. Similar results were obtained with a rho 0 derivative of one of these lines, indicating that mitochondrial promoter sequences in the nucleus cannot modulate transcription in response to altered mtDNA copy number. These results support the view that the nuclear and mitochondrial transcription systems in human cells are functionally independent, and do not communicate through factors recognizing shared sequence elements, as suggested by studies in yeast.

Increased expression of F1ATP synthase subunits in yeast strains carrying point mutations which destabilize the beta subunit

In yeast strains (S. cerevisiae) carrying a point mutation of the ATP2 gene, which destabilizes the beta subunit of F1 ATP synthase in vitro, the growth rate was reduced significantly, demonstrating that the mutation is also deleterious in vivo. Immunoblots showed that levels of the mutated beta, but also of the wild-type alpha subunit were increased in the mutated strains, together with levels of the corresponding mRNAs (approximately 1.6-fold). Northern analysis showed that this was due to both the appearance of new transcript species as well as upregulation of the cognate transcripts, strongly indicating that the increase was probably due to activation of transcription. Levels of other mitochondrial proteins, e.g. cytochrome c oxidase, were unaffected. We conclude that a specific signal communicates the actual performance of the ATP synthase inside the mitochondria to the nuclear genes encoding its subunits.

Catabolite repression of the H(+)-translocating ATPase in Vibrio parahaemolyticus

Cells of Vibrio parahaemolyticus grown in the presence of glucose showed reduced (by about 40%) oxidative phosphorylation. With this observation as a basis, we examined the effect of glucose on the level of H(+)-translocating ATPase. The addition of glucose to the growth medium reduced the specific activity and the amount of the H(+)-translocating ATPase in membrane vesicles of V. parahaemolyticus. These reductions were reversed by adding cyclic AMP (cAMP) to the growth medium. We cloned some parts of the unc genes encoding subunits of the H(+)-translocating ATPase of V. parahaemolyticus by means of the polymerase chain reaction. Using an amplified DNA fragment, we carried out Northern (RNA) blot analysis and found that glucose reduced the mRNA level of the H(+)-translocating ATPase gene by about 40% and that cAMP restored it. We determined the DNA sequence of the unc promoter region of V. parahaemolyticus and found a consensus sequence for the cAMP receptor protein-cAMP-binding site. Such a sequence was also found in the promoter region of the unc operon of Vibrio alginolyticus but not in its counterpart in Escherichia coli. We observed a similar reduction in the level of ATPase due to glucose in V. alginolyticus. In E. coli, however, reductions in the ATPase and the unc mRNA levels were not observed. Thus, the unc operon is controlled by cAMP-regulated catabolite repression in V. parahaemolyticus and V. alginolyticus but not in E. coli. Catabolite repression of the unc operon in V. parahaemolyticus is not severe.

MOL1, a Saccharomyces cerevisiae gene that is highly expressed in early stationary phase during growth on molasses

We have isolated a new Saccharomyces cerevisiae gene, MOL1, that is transiently expressed at high levels in the early stationary phase of batch cultures growing on industrial molasses medium. The DNA sequence of the MOL1 gene (for MOLasses-inducible) with its flanking regions was determined (EMBL accession number X61669). It encodes a polypeptide of M(r) 35 kDa that is closely related to stress-inducible proteins of similar size from two Fusarium species. Unlike ST135 of Fusarium, MOL1 is not induced by ethanol or heat shock. MOL1 expression is absent in rich (YP) medium, and only very low levels of expression are detectable in minimal (YNB) medium. The gene is not essential, and a MOL1 disruption strain showed no apparent phenotype under a variety of growth conditions. The 5' region of MOL1 contains the complete sequence previously determined for the SUF4 locus, encoding a tRNA-gly (UCC) gene, which has been mapped to chromosome VII.

Hsp60/chaperonin gene expression and differentiation of human colon adenocarcinoma and multipotent leukaemic cells

Elevated mitochondrial gene expression is an early event in the switch from proliferation to differentiation of the human colon adenocarcinoma cell line, HT29, promoted by trehalose replacement of exogenous glucose. Here we report the isolation and elevated expression of hsp60, the gene encoding chaperonin, a mitochondrial protein required for assembly of mitochondrial and cellular proteins. In contrast to HT29, leukaemic cells (HL60 and K562) neither differentiated nor altered their mitochondrial gene expression after treatment with trehalose. However, differentiation of these cells, as promoted by 12-O-tetradecanoylphorbol-13-acetate actually resulted in decreased levels of hsp60 mRNA expression as well as mitochondrial RNA expression, suggesting significant differences in involvement of mitochondria in the differentiation of these cell lineages.

Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae

Functional TATA elements in the 5' untranslated region of the CYC1 gene in the yeast Saccharomyces cerevisiae have been defined by transcriptional analysis of site-directed mutations. Five sites previously suggested to contain functional TATA elements were altered individually and in all possible combinations. The results indicated that only two elements are required for transcription at the normal level and the normal start sites. The two functional TATA elements are located at sites -178 and -123, where the A of the ATG start codon is assigned nucleotide position +1. They direct initiation within windows encompassing -70 to -46 and -46 to -28, respectively. Only when both of the upstream TATA sites were rendered nonfunctional were the third and fourth downstream TATA-like sequences activated, as indicated by the presence of low levels of transcription starting at -28. The two upstream functional TATA elements differed in sequence. The sequence of the most 5' one at site 1, denoted beta-type, was ATATATATAT, whereas that of the second one at site 2, denoted alpha-type, was TATATAAAA. The following rearrangements of the beta-type and alpha-type elements at two sites (1 and 2) were examined: site1 beta-site2 alpha; site 1 alpha-site 2 beta; site1 alpha-site2 alpha; and site1 beta-site2 beta. When different types were at different sites (site1 beta-site2 alpha and site1 alpha-site2 beta), both were used equally. In contrast, when the same type was present at both sites (site1 alpha-site2 alpha and site1 beta-site2 beta), only the upstream element was used. We suggest that the two TATA elements are recognized by different factors of the transcription apparatus.

Effects of ethidium bromide treatment of mouse cells on expression and assembly of nuclear-coded subunits of complexes involved in the oxidative phosphorylation

Using mouse cell lines 5P and 5PEr (ethidium bromide-resistant derivative of 5P), we examined the influence of blocking expression of mitochondrial-gene products with ethidium bromide on the expression and assemblies of nuclear-coded subunits of the complexes involved in the oxidative phosphorylation. The results suggest that in the absence of mitochondrial-coded products, the expressions of subunit VIc of complex IV and beta-subunit of F1-ATPase are not affected, but that most nuclear-coded subunits other than alpha- and beta-subunits of F1-ATPase cannot be assembled nor inserted into the inner membrane.

Regulation of mitochondrial ATP synthesis in mammalian cells by transcriptional control

1. Mitochondrial ATP synthesis (oxidative phosphorylation) is mainly regulated by the membrane potential (respiratory control) and protein synthesis (transcriptional control). 2. According to the current view, genes for enzymes of oxidative phosphorylation are classified as housekeeping genes that are transcribed constitutively. These genes have been sequenced. 3. Four complexes of oxidative phosphorylation (complexes I, III and IV, and ATP synthase) are exceptional oligomers that contain subunits encoded by mitochondrial DNA. The remaining subunits of these complexes, as well as thousands of other mammalian enzymes are encoded by nuclear DNA. 4. It is proposed that ATP synthase (F0F1) and these oligomers supplying energy to F0F1, though they are housekeeping, are under some coordinated transcriptional control. Not transcription, but translation of mitochondrial DNA is mainly regulated. 5. Recently, studies on cloned human genes for the FoF1 beta subunit and 7 enzymes related to ATP synthesis revealed coordinated transcription. Moreover, a novel common cis-element (enhancer) was discovered in the 5'-upstream region of genes for the F1 beta subunit, cytochrome c1 and pyruvate dehydrogenase E1 alpha subunit. 6. In contrast to heme control and catabolite repression of yeast via trans-acting elements such as HAP and GP, signal transduction and coordinated transcription of human oxidative phosphorylation is not directed by CP1 (a HAP homolog), but may be closely related to cell differentiation.

Isolation and expression analysis of two yeast regulatory genes involved in the derepression of glucose-repressible enzymes

Yeast strains carrying one of the two regulatory mutations cat1 and cat3 are defective in derepression of several glucose-repressible enzymes that are necessary for utilizing non-fermentable carbon sources. Hence, these strains fail to grow on ethanol, glycerol or acetate. The synthesis of isocitrate lyase, malate synthase, malate dehydrogenase and fructose-1,6-bisphosphatase is strongly affected in cat1 and cat3 strains. Genes CAT1 and CAT3 have been isolated by complementation of the cognate mutations after transformation with an episomal plasmid gene library. The restriction map of CAT1 proved its allelism to the earlier isolated SNF1 gene. Both genes appear to exist as single-copy genes per haploid genome as indicated by Southern hybridization. Northern analysis has shown that the 1.35 kb CAT3 mRNA is constitutively expressed, independent of the carbon source in the medium. Derepression studies with CAT3 transformants using a multi-copy plasmid showed over-expression of glyoxylate cycle enzymes. This result would be consistent with a direct effector function for the CAT3 gene product.

Unusually high-level expression of a foreign gene (hepatitis B virus core antigen) in Saccharomyces cerevisiae

As a model system for the study of factors affecting gene expression, hepatitis B virus core antigen (HBcAg) has been expressed in the yeast Saccharomyces cerevisiae. The singularly high levels of expression achieved are approx. 40% of the soluble yeast protein. The HBcAg polypeptides are present as 28-nm particles which are morphologically indistinguishable from HBcAg particles in human plasma and are highly immunogenic in mice. The plasmid construction employed to achieve these very high levels of expression utilizes the constitutively active yeast promoter from the GAP491 gene which is fused in a way that all non-translated sequences flanking the HBcAg coding region are yeast-derived. Hybrid constructions containing 3'-nontranslated viral DNA (yeast 5') or 5'-nontranslated viral DNA (yeast 3') as well as a construction with both 5'- and 3'-nontranslated viral DNA also have been made. A comparison of these constructions for levels of HBcAg expression indicates that the strongest contributor to the high levels of protein is the presence of 5'-flanking sequences which are yeast-derived; secondarily, a significant improvement can be achieved if the 3'-flanking sequences also are yeast-derived. The high abundance of HBcAg in the highest producer is explicable in part on the basis of the very high stability in yeast cells of HBcAg polypeptides. Analysis of the HBcAg coding sequence reveals a very low index of codon bias for S. cerevisiae, largely discounting codon usage as a contributor to the high level of protein obtained.