PDC2, a yeast gene essential for synthesis of pyruvate decarboxylase, encodes a novel transcription factor

Thiamine: a key nutrient for yeasts during wine alcoholic fermentation

Alcoholic fermentation is a crucial step of winemaking, during which yeasts convert sugars to alcohol and also produce or biotransform numerous flavour compounds. In this context, nutrients are essential compounds to support yeast growth and ultimately ensure complete fermentation, as well as optimized production of flavour compounds over that of off-flavour compounds. In particular, the vitamin thiamine not only plays an essential cofactor role for several enzymes involved in various metabolic pathways, including those leading to the production of wine-relevant flavour compounds, but also aids yeast survival via thiamine-dependent stress protection functions. Most yeast species are able to both assimilate exogenous thiamine into the cell and synthesize thiamine de novo. However, the mechanism and level of thiamine accumulation depend on several factors. This review provides an in-depth overview of thiamine utilization and metabolism in the model yeast species Saccharomyces cerevisiae, as well as the current knowledge on (1) the intracellular functions of thiamine, (2) the balance between and regulation of uptake and synthesis of thiamine and (3) the multitude of factors influencing thiamine availability and utilization. For the latter, a particular emphasis is placed on conditions occurring during wine fermentation. The adequacy of thiamine concentration in grape must to ensure successful fermentation is discussed together with the effect of thiamine concentration on fermentation kinetics and on wine sensory properties. This knowledge may serve as a resource to optimise thiamine concentrations for optimal industrial application of yeasts. KEY POINTS: • Thiamine uptake is preferred over biosynthesis and is transcriptionally repressed. • Multiple factors affect thiamine synthesis, availability and uptake for wine yeast. • Thiamine availability impacts fermentation kinetics and wine's sensory properties.

Deciphering regulatory variation of THI genes in alcoholic fermentation indicate an impact of Thi3p on PDC1 expression

BACKGROUND

Thiamine availability is involved in glycolytic flux and fermentation efficiency. A deficiency of this vitamin may be responsible for sluggish fermentations in wine making. Therefore, both thiamine uptake and de novo synthesis could have key roles in fermentation processes. Thiamine biosynthesis is regulated in response to thiamine availability and is coordinated by the thiamine sensor Thi3p, which activates Pdc2p and Thi2p. We used a genetic approach to identify quantitative trait loci (QTLs) in wine yeast and we discovered that a set of thiamine genes displayed expression-QTL on a common locus, which contains the thiamine regulator THI3.

RESULTS

We deciphered here the source of these regulatory variations of the THI and PDC genes. We showed that alteration of THI3 results in reduced expression of the genes involved in thiamine biosynthesis (THI11/12/13 and THI74) and increased expression of the pyruvate decarboxylase gene PDC1. Functional analysis of the allelic effect of THI3 confirmed the control of the THI and PDC1 genes. We observed, however, only a small effect of the THI3 on fermentation kinetics. We demonstrated that the expression levels of several THI genes are correlated with fermentation rate, suggesting that decarboxylation activity could drive gene expression through a modulation of thiamine content. Our data also reveals a new role of Thi3p in the regulation of the main pyruvate decarboxylase gene, PDC1.

CONCLUSIONS

This highlights a switch from PDC1 to PDC5 gene expression during thiamine deficiency, which may improve the thiamine affinity or conservation during the enzymatic reaction. In addition, we observed that the lab allele of THI3 and of the thiamin transporter THI7 have diverged from the original alleles, consistent with an adaptation of lab strains to rich media containing an excess of thiamine.

Regulation of primary carbon metabolism in Kluyveromyces lactis

In the recent past, through advances in development of genetic tools, the budding yeast Kluyveromyces lactis has become a model system for studies on molecular physiology of so-called "Nonconventional Yeasts." The regulation of primary carbon metabolism in K. lactis differs markedly from Saccharomyces cerevisiae and reflects the dominance of respiration over fermentation typical for the majority of yeasts. The absence of aerobic ethanol formation in this class of yeasts represents a major advantage for the "cell factory" concept and large-scale production of heterologous proteins in K. lactis cells is being applied successfully. First insight into the molecular basis for the different regulatory strategies is beginning to emerge from comparative studies on S. cerevisiae and K. lactis. The absence of glucose repression of respiration, a high capacity of respiratory enzymes and a tight regulation of glucose uptake in K. lactis are key factors determining physiological differences to S. cerevisiae. A striking discrepancy exists between the conservation of regulatory factors and the lack of evidence for their functional significance in K. lactis. On the other hand, structurally conserved factors were identified in K. lactis in a new regulatory context. It seems that different physiological responses result from modified interactions of similar molecular modules.

Identification of a gene encoding the pyruvate decarboxylase gene regulator CaPdc2p from Candida albicans

In a screen for Candida albicans genes encoding transactivating proteins, a pyruvate decarboxylase (EC 4.1.1.1.) regulator gene was isolated. An open reading frame (ORF) of 2511 bp was identified encoding a predicted protein of 836 amino acids with a molecular weight of 94.4 kDa. The protein showed glutamine- and proline-rich stretches typical for transcriptional activators. The amino acid sequence comparisons between CaPdc2p of C. albicans and both Pdc2p of Saccharomyces cerevisiae and Rag3p of Kluyveromyces lactis, revealed similarities of 40% and 39%, respectively. The CaPDC2 gene was localized on chromosome 1. Southern blot analysis indicated that CaPDC2 might be a single copy gene. The growth defect of a S. cerevisiae pdc2 delta mutant on glucose was compensated by transformation of the C. albicans CaPDC2 gene.

Regulation of the expression of the Kluyveromyces lactis PDC1 gene: carbon source-responsive elements and autoregulation

The yeast Kluyveromyces lactis has a single structural gene coding for pyruvate decarboxylase (KIPDC1). In order to study the regulation of the expression of KIPDC1, we have sequenced (EMBL Accession No. Y15435) its promoter and have fused the promoter to the reporter gene lacZ from E. coli. Transcription analysis in a Klpdc1 delta strain showed that KIPDC1 expression is subject to autoregulation. The PDC1 gene from Saccharomyces cerevisiae was able to complement the Rag- phenotype of the Klpdc1 delta mutant strain and it could also repress transcription of the KIPDC1-lacZ fusion on glucose. A deletion analysis of the promoter region was performed to study carbon source-dependent regulation and revealed that at least two cis-acting regions are necessary for full induction of gene expression on glucose. Other cis-elements mediate repression on ethanol.

The RAG3 gene of Kluyveromyces lactis is involved in the transcriptional regulation of genes coding for enzymes implicated in pyruvate utilization and genes of the biosynthesis of thiamine pyrophosphate

The RAG3 gene of Kluyveromyces lactis, a homolog of PDC2 of Saccharomyces cerevisiae, is known to be a regulator of the pyruvate decarboxylase gene KlPDC1. We have identified new target genes for Rag3p. The RAG3 gene product was found to be required for the transcription of two genes of the biosynthetic pathway of thiamine (a cofactor of pyruvate decarboxylase). Conversely, the RAG3 gene product partially repressed the expression of the pyruvate dehydrogenase gene KlPDA1. Therefore, RAG3 may act as a general regulator in the balance of the two alternative pathways of pyruvate metabolism in yeast.

Thiamin metabolism and thiamin diphosphate-dependent enzymes in the yeast Saccharomyces cerevisiae: genetic regulation

The yeast Saccharomyces cerevisiae utilises external thiamin for the production of thiamin diphosphate (ThDP) or can synthesise the cofactor itself. Prior to uptake into the cell thiamin phosphates are first hydrolysed and thiamin is taken up as free vitamin which is then pyrophosphorylated by a pyrophosphokinase. Synthesis of ThDP starts with the production of hydroxyethylthiazole and hydroxymethylpyrimidine. Those are linked to yield thiamin phosphate which is hydrolysed to thiamin and subsequently pyrophosphorylated. The THI genes encoding the enzymes of these final steps of ThDP production and of thiamin utilisation have been identified. Their expression is controlled by the level of thiamin and a number of regulatory proteins involved in regulated expression of the THI genes are known. However, the molecular details of the regulatory circuits need to be deciphered. Since the nucleotide sequence of the entire yeast genome is known we can predict the number of ThDP-dependent enzymes in S. cerevisiae. Eleven such proteins have been found: pyruvate decarboxylase (Pdc, three isoforms), acetolactate synthase, a putative alpha-ketoisocaproate decarboxylase with a regulatory role in ThDP synthesis and two proteins of unknown function form the group of Pdc related enzymes. In addition there are two isoforms for transketolase as well as the E1 subunits of pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase. Expression of most of these genes is either induced or repressed by glucose. Surprisingly, it has been found recently that expression of one of the genes for Pdc is repressed by thiamin. In addition, the regulatory protein Pdc2p was shown to be required for high level expression of both the THI and the PDC genes. Apparently, the production of ThDP and of the enzymes using this cofactor is coordinately regulated. Future research will focus on the elucidation of the molecular mechanisms of this novel type of regulation.

Pyruvate decarboxylase and anaerobic survival in Aspergillus nidulans

The presence of pyruvate decarboxylase activity has been demonstrated in Aspergillus nidulans, and a gene encoding a pyruvate decarboxylase has been isolated from this organism and physically characterized. The isolation of the pdcA gene in A. nidulans confirms the existence of the alcoholic fermentation pathway in this fungus, despite it being an obligate aerobic organism. Southern analysis showed that it is most probably a single copy gene. Several potential binding sites for a GATAR-binding protein were identified in the sequence just prior to the start point of transcription, and mutant alleles of the GATAR-binding protein-encoding gene, areA, affected pdcA mRNA levels in a manner that suggested that it influences pdcA expression in nitrogen repressing conditions. Other previously reported cases of AREA action are in nitrogen-limiting conditions. Interestingly, the production of ethanol was affected in a similar way by the same areA alleles, suggesting that changes in pdcA mRNA level are reflected in the changes in the level of ethanol production. The experiments presented here confirm that PDC levels are a major determinant of ethanol production under these conditions.

RAG3 gene and transcriptional regulation of the pyruvate decarboxylase gene in Kluyveromyces lactis

The RAG3 gene has been cloned from a Kluyveromyces lactis genomic library by complementation of the rag3 mutation, which shows impaired fermentative growth on glucose in the presence of respiratory inhibitors. From the nucleotide sequence of the cloned DNA, which contained an open reading frame of 765 codons, the predicted protein is 49.5% identical to the Pdc2 protein of Saccharomyces cerevisiae, a regulator of pyruvate decarboxylase in this yeast. Measurement of the pyruvate decarboxylase activity in the original rag3-1 mutant and in the null mutant confirmed that the RAG3 gene is involved in pyruvate decarboxylase synthesis in K. lactis. The effect is exerted at the mRNA level of the pyruvate decarboxylase structural gene KIPDCA. Despite analogies between the RAG3 gene of K. lactis and the PDC2 gene of S. cerevisiae, these genes were unable to reciprocally complement.