Cyclic AMP can decrease expression of genes subject to catabolite repression in Saccharomyces cerevisiae

Biological roles of cAMP: variations on a theme in the different kingdoms of life

Cyclic AMP (cAMP) plays a key regulatory role in most types of cells; however, the pathways controlled by cAMP may present important differences between organisms and between tissues within a specific organism. Changes in cAMP levels are caused by multiple triggers, most affecting adenylyl cyclases, the enzymes that synthesize cAMP. Adenylyl cyclases form a large and diverse family including soluble forms and others with one or more transmembrane domains. Regulatory mechanisms for the soluble adenylyl cyclases involve either interaction with diverse proteins, as happens in Escherichia coli or yeasts, or with calcium or bicarbonate ions, as occurs in mammalian cells. The transmembrane cyclases can be regulated by a variety of proteins, among which the α subunit and the βγ complex from G proteins coupled to membrane receptors are prominent. cAMP levels also are controlled by the activity of phosphodiesterases, enzymes that hydrolyze cAMP. Phosphodiesterases can be regulated by cAMP, cGMP or calcium-calmodulin or by phosphorylation by different protein kinases. Regulation through cAMP depends on its binding to diverse proteins, its proximal targets, this in turn causing changes in a variety of distal targets. Specifically, binding of cAMP to regulatory subunits of cAMP-dependent protein kinases (PKAs) affects the activity of substrates of PKA, binding to exchange proteins directly activated by cAMP (Epac) regulates small GTPases, binding to transcription factors such as the cAMP receptor protein (CRP) or the virulence factor regulator (Vfr) modifies the rate of transcription of certain genes, while cAMP binding to ion channels modulates their activity directly. Further studies on cAMP signalling will have important implications, not only for advancing fundamental knowledge but also for identifying targets for the development of new therapeutic agents.

Regulation of mitochondrial biogenesis in eukaryotic cells

Mitochondria amount within a cell is modulated in response to energy demand. This involves a tight regulation of mitochondrial biogenesis and the coordinated expression of hundreds of genes, both at the nuclear and at the mitochondrial level. This review will focus on two aspects of mitochondrial biogenesis regulation: (i) In mammalian cells, physiological effectors, and the regulatory proteins that control the expression of the respiratory apparatus, will be considered, and different kinds of tissue will be addressed. (ii) In yeast, the regulation of mitochondrial biogenesis in response to growth conditions as well as the signaling pathway involved will be considered.

Transcriptional responses to glucose in Saccharomyces cerevisiae strains lacking a functional protein kinase A

Background

The pattern of gene transcripts in the yeast Saccharomyces cerevisiae is strongly affected by the presence of glucose. An increased activity of protein kinase A (PKA), triggered by a rise in the intracellular concentration of cAMP, can account for many of the effects of glucose on transcription. In S. cerevisiae three genes, TPK1, TPK2, and TPK3, encode catalytic subunits of PKA. The lack of viability of tpk1 tpk2 tpk3 triple mutants may be suppressed by mutations such as yak1 or msn2/msn4. To investigate the requirement for PKA in glucose control of gene expression, we have compared the effects of glucose on global transcription in a wild-type strain and in two strains devoid of PKA activity, tpk1 tpk2 tpk3 yak1 and tpk1 tpk2 tpk3 msn2 msn4.

Results

We have identified different classes of genes that can be induced -or repressed- by glucose in the absence of PKA. Representative examples are genes required for glucose utilization and genes involved in the metabolism of other carbon sources, respectively. Among the genes responding to glucose in strains devoid of PKA some are also controlled by a redundant signalling pathway involving PKA activation, while others are not affected when PKA is activated through an increase in cAMP concentration. On the other hand, among genes that do not respond to glucose in the absence of PKA, some give a full response to increased cAMP levels, even in the absence of glucose, while others appear to require the cooperation of different signalling pathways. We show also that, for a number of genes controlled by glucose through a PKA-dependent pathway, the changes in mRNA levels are transient. We found that, in cells grown in gluconeogenic conditions, expression of a small number of genes, mainly connected with the response to stress, is reduced in the strains lacking PKA.

Conclusions

In S. cerevisiae, the transcriptional responses to glucose are triggered by a variety of pathways, alone or in combination, in which PKA is often involved. Redundant signalling pathways confer a greater robustness to the response to glucose, while cooperative pathways provide a greater flexibility.

Differential glucose repression in common yeast strains in response to HXK2 deletion

Under aerobic, high glucose conditions, Saccharomyces cerevisiae exhibits glucose repression and thus a predominantly fermentative metabolism. Here, we show that two commonly used prototrophic representatives of the CEN.PK and S288C strain families respond differently to deletion of the hexokinase 2 (HXK2) - a key player in glucose repression: In CEN.PK, growth rate collapses and derepression occurs on the physiological level, while the S288C descendant FY4 Deltahxk2 still grows like the parent strain and shows a fully repressed metabolism. A CEN.PK Deltahxk2 strain with a repaired adenylate cyclase gene CYR1 maintains repression but not growth rate. A comparison of the parent strain's physiology, metabolome, and proteome revealed higher metabolic rates, identical biomass, and byproduct yields, suggesting a lower Snf1 activity and a higher protein kinase A (PKA) activity in CEN.PK. This study highlights the importance of the genetic background in the processes of glucose signaling and regulation, contributes novel evidence on the overlap between the classical glucose repression pathway and the cAMP/PKA signaling pathway, and might have the potential to resolve some of the conflicting findings existing in the field.

The early steps of glucose signalling in yeast

In the presence of glucose, yeast undergoes an important remodelling of its metabolism. There are changes in the concentration of intracellular metabolites and in the stability of proteins and mRNAs; modifications occur in the activity of enzymes as well as in the rate of transcription of a large number of genes, some of the genes being induced while others are repressed. Diverse combinations of input signals are required for glucose regulation of gene expression and of other cellular processes. This review focuses on the early elements in glucose signalling and discusses their relevance for the regulation of specific processes. Glucose sensing involves the plasma membrane proteins Snf3, Rgt2 and Gpr1 and the glucose-phosphorylating enzyme Hxk2, as well as other regulatory elements whose functions are still incompletely understood. The similarities and differences in the way in which yeasts and mammalian cells respond to glucose are also examined. It is shown that in Saccharomyces cerevisiae, sensing systems for other nutrients share some of the characteristics of the glucose-sensing pathways.

Glucose controls multiple processes inSaccharomyces cerevisiaethrough diverse combinations of signaling pathways

We have studied how the lack of glucose sensors in the plasma membrane, or of the enzymes Hxk1, Hxk2, Glk1, which catalyze the first intracellular step in glucose metabolism, affect the different responses of Saccharomyces cerevisiae to glucose. Lack of the G-protein-coupled receptor Gpr1 or of Snf3/Rgt2 did not affect glucose repression of different genes or activation by glucose of plasma membrane ATPase, whereas lack of Gpr1 decreased, in an additive manner with lack of Mth1, the degradation of fructose 1,6-bisphosphatase that takes place in the presence of glucose. In an hxk1 hxk2 glk1 strain, unable to phosphorylate glucose, all of these responses to the sugar were suppressed or strongly reduced. In the absence of Hxk2 (or Hxk1 and Hxk2), glucose repression of SUC2, GAL1 and GDH2 was relieved, but that of FBP1 and ICL1 was maintained. Hxk1 or Hxk2 were needed for activation of plasma membrane ATPase but not for degradation of FbPase.

CO2 sensing at ocean surface mediated by cAMP in a marine diatom

Marine diatoms are known to be responsible for about a quarter of global primary production and their photosynthesis is sustained by inorganic carbon-concentrating mechanisms and/or C(4) metabolism. Activities of the inorganic carbon-concentrating mechanism are attenuated under enriched [CO(2)]; however, impacts of this factor on primary productivity and the molecular mechanisms of CO(2) responses in marine diatoms are unknown. In this study, transgenic cells were generated of the marine diatom Phaeodactylum tricornutum by the introduction of a beta-glucuronidase reporter gene under the control of an intrinsic CO(2)-responsive promoter, which is the sequence between -80 to +61 relative to the transcription start site of a chloroplastic-carbonic anhydrase gene, ptca1, obtained from P. tricornutum. The activity of the ptca1 promoter was effectively repressed in air-level CO(2) by treating cells with a 1.0 mm cAMP analog, dibutyryl cAMP, or a cAMP phosphodiesterase inhibitor, 3-isobutyl-1-methylxanthine. Deletion of the intrinsic cAMP-response element from the ptca1 promoter caused a lack of repression of the reporter gene uidA, even under elevated [CO(2)] and a null phenotype to the strong repressive effects of dibutyryl cAMP and 3-isobutyl-1-methylxanthine on the ptca1 promoter. Deletion of the cAMP-response element was also shown to cause derepression of the uidA reporter gene in the dark. These results indicate that the cytosolic cAMP level increases under elevated [CO(2)] and represses the ptca1 promoter. This strongly suggests the participation of cAMP metabolism, presumably at the cytosolic level, in controlling CO(2)-acquisition systems under elevated [CO(2)] at the ocean surface in a marine diatom.

Mechanisms of mitochondrial response to variations in energy demand in eukaryotic cells

This review focuses on the different mechanisms involved in the adjustment of mitochondrial ATP production to cellular energy demand. The oxidative phosphorylation steady state at constant mitochondrial enzyme content can vary in response to energy demand. However, such an adaptation is tightly linked to a modification in both oxidative phosphorylation yield and phosphate potential and is obviously very limited in eukaryotic cells. We describe the three main mechanisms involved in mitochondrial response to energy demand. In heart cells, a short-term adjustment can be reached mainly through metabolic signaling via phosphotransfer networks by the compartmentalized energy transfer and signal transmission. In such a complex regulatory mechanism, Ca(2+) signaling participates in activation of matricial dehydrogenases as well as mitochondrial ATP synthase. These processes allow a large increase in ATP production rate without an important modification in thermodynamic forces. For a long-term adaptation, two main mechanisms are involved: modulation of the mitochondrial enzyme content as a function of energy demand and/or kinetic regulation by covalent modifications (phosphorylations) of some respiratory chain complex subunits. Regardless of the mechanism involved (kinetic regulation by covalent modification or adjustment of mitochondrial enzyme content), the cAMP signaling pathway plays a major role in molecular signaling, leading to the mitochondrial response. We discuss the energetic advantages of these mechanisms.

Degradation of the gluconeogenic enzymes fructose-1,6-bisphosphatase and malate dehydrogenase is mediated by distinct proteolytic pathways and signaling events

The key gluconeogenic enzyme fructose-1,6-bisphosphatase (FBPase) is subjected to catabolite inactivation and degradation when glucose-starved cells are replenished with fresh glucose. In various studies, the proteasome and the vacuole have each been reported to be the major site of FBPase degradation. Because different growth conditions were used in these studies, we examined whether variations in growth conditions could alter the site of FBPase degradation. Here, we demonstrated that FBPase was degraded outside the vacuole (most likely in the proteasome), when glucose was added to cells that were grown in low glucose media for a short period of time. By contrast, cells that were grown in the same low glucose media for longer periods of time degraded FBPase in the vacuole in response to glucose. Another gluconeogenic enzyme malate dehydrogenase (MDH2) showed the same degradation characteristics as FBPase in that the short term starvation of cells led to a non-vacuolar degradation, whereas long term starvation resulted in the vacuolar degradation of this protein. The N-terminal proline is required for the degradation of FBPase and MDH2 for both the vacuolar and non-vacuolar proteolytic pathways. The cAMP signaling pathway and the phosphorylation of glucose were needed for the vacuolar-dependent degradation of FBPase and MDH2. By contrast, the cAMP-dependent signaling pathway was not involved in the non-vacuolar degradation of these proteins, although the phosphorylation of glucose was required.

cAMP-induced modulation of the growth yield of Saccharomyces cerevisiae during respiratory and respiro-fermentative metabolism

The aim of this study was to investigate the effects of an overactivation of the cAMP/protein kinase A signaling pathway on the energetic metabolism of growing yeast. By using a cAMP-permeant mutant strain, we show that the rise in intracellular cAMP activates both anabolic and catabolic pathways. Indeed, different physiological patterns were observed with respect to the growth condition: (i) When cells were grown with a limiting amount of lactate, cAMP addition markedly increased the growth rate, whereas it only slightly increased the mitochondrial and cellular protein content. In parallel, the respiratory rate increased and the growth yield, as assessed by direct microcalorimetry, was not significantly modified by cAMP. (ii) Under conditions where the growth rate was already optimal (high lactate concentration), exogenous cAMP led to a proliferation of well-coupled mitochondria within cells and to an accumulation of cellular and mitochondrial proteins. This phenomenon was associated with a rise in the respiratory activity, thus leading to a drop in the growth yield. (iii) Under conditions of catabolic repression (high glucose concentration), cAMP addition markedly increased the fermentation rate and decreased the growth yield. It is concluded that overactivation of the cAMP/PKA pathway leads to uncoupling between biomass synthesis and catabolism, under conditions where an optimal growth rate is sustained by either a fermentative or a respiratory metabolism.

Activation of Ras cascade increases the mitochondrial enzyme content of respiratory competent yeast

We investigated the effects of genetic and physiological modulations of the cAMP-protein kinase A pathway on mitochondrial biogenesis of yeast cells grown on lactate. Yeast mutants with over-activated Ras/adenylate cyclase pathway (i.e., Ras2(val19), ira1Delta(ira2)Delta) or with a constitutive downstream activation of protein kinases A (i.e., bcyDelta) showed an increase in the mitochondrial enzyme content. In contrast, loss of Ras activity (i.e., Ras2 mutant) resulted in a slight decrease. The treatment by cAMP of a responsive mutant increased the oxidative phosphorylation capacity of cells and increased the transcript level of nuclear genes encoding for mitochondrial proteins. In contrast, the transcript level of mitochondrial DNA genes was unchanged. It is concluded that the Ras/cAMP/protein kinase A pathway is part of the regulatory circuit controlling biogenesis of the oxidative phosphorylation complexes in yeast cells.

Elements from the cAMP signaling pathway are involved in the control of expression of the yeast gluconeogenic gene FBP1

cAMP represses the transcription of some Saccharomyces cerevisiae genes sensitive to catabolite repression. The effect of cAMP on the expression of FBP1, encoding fructose-1,6-bisphosphatase (FbPase), has been further investigated. In yeast cells shifted to a derepressing medium, synthesis of FbPase was delayed if the strong decrease in intracellular cAMP, which occurs during the shift, was prevented. A similar delay occurred in a RAS2val19 strain, while in a tpk1w strain, with weak protein kinase A activity, induction of FbPase occurred earlier than in a TPK1 strain. In the tpk1w strain, proteins which bind the UAS1 element of FBP1 were present during growth on glucose but they were only weakly operative. Expression of CAT8 and SIP4, encoding proteins which bind the UAS2 element, was blocked by a high concentration of cAMP, but catabolite repression of these genes was not much relieved in a tpk1w strain. We conclude that in S. cerevisiae, as reported for Schizosaccharomyces pombe, control of FBP1 requires both cAMP-dependent and independent pathways; however, the mechanisms operating in the two yeasts are different.

Regulatory elements in the FBP1 promoter respond differently to glucose-dependent signals in Saccharomyces cerevisiae

In Saccharomyces cerevisiae expression of the fructose-1,6-bisphosphatase-encoding gene, FBP1, is controlled by glucose through the upstream activating sequences UAS1 and UAS2 and the upstream repressing sequence URS1 in its promoter. We have studied the regulation of the proteins that could bind to these elements. We have investigated the role of the putative transcription factors Cat8 and Sip4 in the formation of specific DNA-protein complexes with UAS1 and UAS2, and in the expression of UAS1-lacZ and UAS2-lacZ. The expression of CAT8-lacZ and SIP4-lacZ has been also measured in mig1, tup1 or hxk2 mutants, partially refractory to catabolite repression. We conclude that there is no strict correlation between Cat8 and Sip4 expression or in vitro formation of DNA-protein complexes and expression of UAS1-lacZ and UAS2-lacZ. The URS1 element binds the regulatory protein Mig1, which blocks transcription by recruiting the proteins Cyc8 and Tup1. The pattern of complexes of URS1 with nuclear extracts was dependent on the carbon source and on Cyc8, but not on Tup1; it was also affected by the protein kinase Snf1 and by the exportin Msn5. The repression caused by URS1 in a fusion gene was dependent on Mig1, Cyc8 and Tup1, and on the carbon source in the medium; in a snf1 strain the repression observed was independent of the carbon source. Expression of Mig1 could occur in the absence of Snf1 and was moderately sensitive to glucose. We present data showing that different elements of the regulatory system controlling FBP1 responded differently to the concentration of glucose in the medium.

Carbohydrate and energy-yielding metabolism in non-conventional yeasts

Sugars are excellent carbon sources for all yeasts. Since a vast amount of information is available on the components of the pathways of sugar utilization in Saccharomyces cerevisiae it has been tacitly assumed that other yeasts use sugars in the same way. However, although the pathways of sugar utilization follow the same theme in all yeasts, important biochemical and genetic variations on it exist. Basically, in most non-conventional yeasts, in contrast to S. cerevisiae, respiration in the presence of oxygen is prominent for the use of sugars. This review provides comparative information on the different steps of the fundamental pathways of sugar utilization in non-conventional yeasts: glycolysis, fermentation, tricarboxylic acid cycle, pentose phosphate pathway and respiration. We consider also gluconeogenesis and, briefly, catabolite repression. We have centered our attention in the genera Kluyveromyces, Candida, Pichia, Yarrowia and Schizosaccharomyces, although occasional reference to other genera is made. The review shows that basic knowledge is missing on many components of these pathways and also that studies on regulation of critical steps are scarce. Information on these points would be important to generate genetically engineered yeast strains for certain industrial uses.

Mth1 receives the signal given by the glucose sensors Snf3 and Rgt2 in Saccharomyces cerevisiae

We have determined that the mutant genes DGT1-1 and BPC1-1, which impair glucose transport and catabolite repression in Saccharomyces cerevisiae, are allelic forms of MTH1. Deletion of MTH1 had only slight effects on the expression of HXT1 or SNF3, but increased expression of HXT2 in the absence of glucose. A two-hybrid screen revealed that the Mth1 protein interacts with the cytoplasmic tails of the glucose sensors Snf3 and Rgt2. This interaction was affected by mutations in Mth1 and by the concentration of glucose in the medium. A double mutant, snf3 rgt2, recovered sensitivity to glucose when MTH1 was deleted, thus showing that glucose signalling may occur independently of Snf3 and Rgt2. A model for the possible mode of action of Snf3 and Rgt2 is presented.