Specific gene probes as tools in yeast taxonomy

The phosphoglycerate mutases

The phosphoglycerate mutase family is generally very well documented with respect to structure, evolution, and mode of action. However, a few individuals in the family remain relatively poorly characterized and will clearly require more detailed study. Furthermore, certain aspects of the detailed behavior of these enzymes are, as yet, incompletely understood and require further investigation. Cofactor-dependent monophosphoglycerate mutase and bisphosphoglycerate mutase are undoubtedly very closely related. Their amino acid sequences are strongly similar, they can form active heterodimers, and they catalyze the same three reactions, albeit at substantially different relative rates. Both enzymes catalyze a ping-pong type of reaction with a phosphohistidine intermediate. The presence of an additional phospho ligand at the active site of monophosphoglycerate mutase helps to explain why this enzyme is better at retaining the 2,3-bisphosphoglycerate intermediate and why it is thus more efficient (by a factor of about 10(3)) at catalyzing the interconversion of 3- and 2-phosphoglycerates. The reason why 1,3-bisphosphoglycerate is a better substrate for bisphosphoglycerate mutase than for monophosphoglycerate mutase (by a factor of about 30) is not yet apparent but presumably relates to the relative positioning of the two phospho-binding sites. Both enzymes are equally good as phosphatases when the reaction is activated by 2-phosphoglycollate. Available evidence indicates that these mutases are similar in many respects to the much smaller, cofactor-dependent monophosphoglycerate mutase from Schizosaccharomyces pombe, but further information is required to define the relationship more precisely. Cofactor-independent monophosphoglycerate mutase belongs to a quite distinct branch of the phosphoglycerate mutase family. It is not known at present whether this branch is related divergently or convergently to the cofactor-dependent monophosphoglycerate mutase/bisphosphoglycerate mutase branch. Existing evidence can be argued both ways. For example, the kinetic evidence shows a ping-pong type of reaction and would be consistent with a phosphohistidine intermediate as encountered in the other mutases. Thus the cofactor-independent enzyme may also have arisen by gene duplication--but, in this case, yielding an enzyme of about twice the size, with slightly different residues at the active site and C-terminal tail. An alternative possibility, of course, is that the two branches of the phosphoglycerate mutase family are quite unrelated in a divergent sense and are little more similar structurally than is, for example, the catalytically similar enzyme phosphoglucomutase.(ABSTRACT TRUNCATED AT 400 WORDS)

Characterization of a glucose-repressed pyruvate kinase (Pyk2p) in Saccharomyces cerevisiae that is catalytically insensitive to fructose-1,6-bisphosphate

We have characterized the gene YOR347c of Saccharomyces cerevisiae and shown that it encodes a second functional pyruvate kinase isoenzyme, Pyk2p. Overexpression of the YOR347c/PYK2 gene on a multicopy vector restored growth on glucose of a yeast pyruvate kinase 1 (pyk1) mutant strain and could completely substitute for the PYK1-encoded enzymatic activity. PYK2 gene expression is subject to glucose repression. A pyk2 deletion mutant had no obvious growth phenotypes under various conditions, but the growth defects of a pyk1 pyk2 double-deletion strain were even more pronounced than those of a pyk1 single-mutation strain. Pyk2p is active without fructose-1,6-bisphosphate. However, overexpression of PYK2 during growth on ethanol did not cause any of the deleterious effects expected from a futile cycling between pyruvate and phosphoenolpyruvate. The results indicate that the PYK2-encoded pyruvate kinase may be used under conditions of very low glycolytic flux.

The nucleotide sequence and initial characterization of pyruvate decarboxylase from the yeast Hanseniaspora uvarum

We have isolated a pyruvate decarboxylase (PDC) gene from the yeast Hanseniaspora uvarum using the Saccharomyces cerevisiae PDC1 gene as a probe. The nucleotide sequence of this gene was determined and compared to PDC genes from yeast and other organisms. The H. uvarum PDC gene is more than 70% identical to the S. cerevisiae PDC isozymes and possesses a putative thiamine diphosphate binding site. The PDC enzyme was purified and partially characterized. The H. uvarum PDC was very similar to other known PDCs; the Km for pyruvate was 0.75 mM, and the enzyme is a homotetramer with subunits of M(r) = 57,000.

Induction of pyruvate decarboxylase in glycolysis mutants of Saccharomyces cerevisiae correlates with the concentrations of three-carbon glycolytic metabolites

Pyruvate decarboxylase, PDCase, activity in wild-type yeast cells growing on ethanol is quite low but increases up to tenfold upon addition of glucose, less with galactose and only slightly with glycerol. PDCase levels in glycolysis mutant strains growing on ethanol or acetate were higher than in the wild-type strain. These levels correlated with the sum of the concentrations of three-carbon glycolytic metabolites. The highest accumulation was observed in a fructose bisphosphate aldolase deletion mutant concomitant with the highest PDCase activity ever observed under gluconeogenic conditions. Glucose addition induced an increase in PDCase activity in all mutants. However, the enzyme activities never reached wild-type level. On the other hand, the PDCase levels in the different mutants again correlated with the sum of the concentrations of the three-carbon glycolytic metabolites. This was interpreted to mean that full induction of PDCase activity requires the accumulation of hexose- and triosephosphates.

Molecular genetics of phosphofructokinase in the yeast Kluyveromyces lactis

We have undertaken a study of phosphofructokinase (PFK; E.C. 2.7.1.11) in the yeast Kluyveromyces lactis. Like other eukaryotic PFKs, the K. lactis enzyme is activated by the allosteric effectors AMP and fructose-2,6-bisphosphate. PFK activity is induced in cells grown on glucose as compared to ethanol-grown cells, in contrast to the constitutive expression of PFK in Saccharomyces cerevisiae. We show here that phosphofructokinase of the yeast K. lactis is composed of two non-identical types of subunits, encoded by the genes KIPFK1 and KIPFK2. We have cloned and sequenced both genes. KIPFK1 and KIPFK2 encode the alpha- and the beta-PFK subunits with deduced molecular weights of 109.336 Da and 104.074 Da, respectively. Sequence analysis indicates that the genes evolved from a double duplication event. Null mutants in either of the genes lack detectable PFK activity in vitro and the respective subunits cannot be detected on Western blots. In contrast to the situation in S. cerevisiae, Klpfk1 Klpfk2 double mutants retain the ability to grow on glucose. However, Klpfk2 mutants and the double mutants do not grow on glucose, when respiration is blocked. These data suggest that the pentose phosphate pathway and respiration play a substantial role in glucose utilization by K. lactis. The K. lactis PFK genes can be expressed independently in S. cerevisiae and each of them complements the glucose-negative phenotype of pfk1 pfk2 double deletion mutants in this yeast. Expression of both K. lactis PFK genes simultaneously in S. cerevisiae pfk double deletion mutants complements for PFK activity. However, expression of a combination of PFK genes from K. lactis and S. cerevisiae does not lead to the production of a functional enzyme.

Genomic comparisons among parental and fusant strains of Candida shehatae and Pichia stipitis

DNA-DNA binding experiments on selected fusants of Candida shehatae and Pichia stipitis showed that the nucleus of these strains was composed predominantly of Pichia DNA. Electrophoretic karyotyping revealed that the fusants contained four chromosomes, similar to those found in the Pichia parental strain. In addition, the fusants showed only marginal increases in cell DNA content when compared with the parents. Karyogamy was confirmed, however, by the isolation of recombinant phenotypic segregants, induced by meiotic and mitotic segregation. The results suggest that the fusion led to integration of Candida genes, rather than whole chromosomes, with the entire genome of P. stipitis.

Phylogenetic relationships among wine yeast strains based on electrophoretic whole-cell protein patterns

In the present work, a phylogenetic study based on protein electrophoretic profiles of Saccharomyces strains isolated from different Spanish wine regions has been carried out. Qualitative differences between the protein electrophoregrams were found at inter- and intraspecific level, but not between electrophoregrams of strains isolated at the same ecosystem. The numerical analysis of these results allowed us to conclude that intraspecific relationships are determined by ecological factors, as well as human influences (dispersion and artificial selection). A correlation between ecological and/or geographical origin and the relationships among strains was observed.

A method for taxonomic determination of Candida albicans with DNA probes

Determination of Candida species represents an important problem derived from the clinical implications of the species belonging to this genus. DNA probes have already been used for the epidemiology of Candida albicans, as well as for taxonomic analysis of Candida and other genera, although these probes are based on non-species-specific DNA sequences. In this work we carried out a 48-h assay, allowing the identification of C. albicans from clinical isolates, using DNA probes based on C. albicans LEU2 and URA3 genes. Another probe related to C. albicans SEC18 gene was shown not to be C. albicans specific.

Genetic homology between Saccharomyces cerevisiae and its sibling species S. paradoxus and S. bayanus: electrophoretic karyotypes

Chromosomal DNAs of many monosporic strains of the biological species Saccharomyces cerevisiae, S. paradoxus and S. bayanus were analysed using contour-clamped homogeneous electric field electrophoresis. Southern blot hybridization with eight cloned S. cerevisiae genes (ADC1, CUP1, GAL4, LEU2, rDNA, SUC2, TRP1 and URA3) assigned to different chromosomes was used to study homology and chromosomal location of the genes in the three sibling species. A comparative study of Ty1, Ty2 and telomere-associated Y' sequences having multiple chromosomal location was also done. Chromosome length polymorphism was found in cultured strains of S. cerevisiae. Wild S. cerevisiae and S. paradoxus strains yielded chromosome banding patterns very similar to each other. The karyotype pattern of S. bayanus was readily distinguishable from that of S. cerevisiae and S. paradoxus. Southern blot analysis revealed a low degree of homology between the S. cerevisiae genes studied and the corresponding S. paradoxus and S. bayanus genes. The number of chromosomes appears to be 16 in all three species.

The value of electrophoretic fingerprinting and karyotyping in wine yeast breeding programmes

Electrophoretic banding patterns of total soluble cell proteins, DNA restriction fragments and chromosomal DNA were used to characterise ten strains of Saccharomyces cerevisiae used for commercial production of wine. These fingerprinting procedures provided unique profiles for all the different yeast strains and can therefore be used to identify and control industrial strains. Furthermore, the protein profiles, restriction fragments banding patterns and electrophoretic karyotyping by contour clamped homogeneous electric field electrophoresis (CHEF), were valuable to differentiate hybrid and parental strains in yeast breeding programmes. Hybrid strains, with desirable oenological properties, were obtained by mass spore-cell mating between a heterothallic killer yeast and two homothallic sensitive strains and all were shown to have unique DNA fingerprints and electrophoretic karyotypes.

Sequence and localization of the gene encoding yeast phosphoglycerate mutase

In this study we report on the complete nucleotide sequence of the yeast phosphoglycerate mutase gene (GPM1) and its essential 5' and 3' non-coding regions. The transcriptional start points were determined by S1-mapping and sequencing of a cDNA clone. Several sequences identified as important for transcriptional regulation in yeast promoters are present upstream of the transcription start point. 3' to the coding region we sequenced a composite repetitive element which, apparently, originated from a recombination between a delta- and a tau-element. Finally, we mapped the GPM1 gene 13 cM distal to fas1 on chromosome XI.

Autoregulation may control the expression of yeast pyruvate decarboxylase structural genes PDC1 and PDC5

Recently we deleted the pyruvate decarboxylase structural gene PDC1 from the genome of the yeast Saccharomyces cerevisiae. The pdc1 deletion mutants had pyruvate decarboxylase activity due to the presence of a second structural gene [Schaaff, I., Green, J. B. A., Gozalbo, D. & Hohmann, S. (1989) Curr. Genet. 15, 75-81]. We cloned and sequenced this gene which we call PDC5. The predicted amino acid sequences of PDC1 and PDC5 are 88% identical. Deletion of PDC5 did not cause any decrease in the specific pyruvate decarboxylase activity while pdc1 deletion mutants had 80% of the wild-type activity. Deletion mutants lacking both PDC1 and PDC5 did not show any detectable pyruvate decarboxylase activity in vitro and were unable to ferment glucose. This indicates that PDC1 and PDC5 are the only structural genes for pyruvate decarboxylase in yeast. The PDC5 isoenzyme showed a slightly higher Km value for its substrate pyruvate than the PDC1 product (PDC5: Km = 8 mM; PDC1: Km = 5 mM), as measured in crude extract of pdc1 and pdc5 deletion mutants, respectively. PDC5 is only expressed in pdc1 deletion mutants. No mRNA transcribed from PDC5 could be detected in wild-type cells. Thus, in addition to the control by glucose induction, pyruvate decarboxylase activity seems to be subject to autoregulation. Similar phenomena have been described previously for tubulin, histones and a ribosomal protein but not for metabolic enzymes.

pdc1(0) mutants of Saccharomyces cerevisiae give evidence for an additional structural PDC gene: cloning of PDC5, a gene homologous to PDC1

The PDC1 gene coding for a pyruvate decarboxylase (PDC; EC 4.1.1.1) was deleted from the Saccharomyces cerevisiae genome. The resulting pdc1(0) mutants were able to grow on glucose and still contained 60 to 70% of the wild-type PDC activity. Two DNA fragments with sequences homologous to that of the PDC1 gene were cloned from the yeast genome. One of the cloned genes (PDC5) was expressed at high rates predominantly in pdc1(0) strains and probably encodes the remaining PDC activity in these strains. Expression from the PDC1 promoter in PDC1 wild-type and pdc1(0) strains was examined by the use of two reporter genes. Deletion of PDC1 led to increased expression of the two reporter genes regardless of whether the fusions were integrated into the genome or present on autonomously replicating plasmids. The results suggested that this effect was due to feedback regulation of the PDC1 promoter-driven expression in S. cerevisiae pdc1(0) strains. The yeast PDC1 gene was expressed in Escherichia coli, leading to an active PDC. This result shows that the PDC1-encoded subunit alone can form an active tetramer without yeast-specific processing steps.

Overproduction of glycolytic enzymes in yeast

Eight different enzymes for glycolysis and alcoholic fermentation were overproduced in a common Saccharomyces cerevisiae strain by placing their genes on multicopy vectors. The specific enzyme activities were increased between 3.7- and 13.9-fold above the wild-type level. The overproduction of the different glycolytic enzymes had no effect on the rate of ethanol formation, even with those enzymes that catalyse irreversible steps: hexokinase, phosphofructokinase and pyruvate kinase. Also the simultaneous increase in the activities of pairs of enzymes such as pyruvate kinase and phosphofructokinase or pyruvate decarboxylase and alcohol dehydrogenase, did not increase the rate of ethanol production. The levels of key glycolytic metabolites were also normal, compared to the reference strain.

A deletion of the PDC1 gene for pyruvate decarboxylase of yeast causes a different phenotype than previously isolated point mutations

We deleted most of the pyruvate decarboxylase structural gene PDC1 from the genome of Saccharomyces cerevisiae. Surprisingly, mutants carrying this deletion allele showed a completely different phenotype than previously described point mutations. They were able to ferment glucose and their specific pyruvate decarboxylase activity was only reduced to 45% of the wild type level. Northern blot analysis revealed that a sequence in the yeast genome homologous to PDC1 and formerly designated as a possible pseudogene is expressed and may code for a different but closely related pyruvate decarboxylase. The products of the two PDC genes seem to form hybrid oligomers, however both homooligomers have enzyme activity. Thus, the product of the PDC1 gene is not absolutely necessary for glucose fermentation in yeast.

Molecular characterization of yeast regulatory gene CAT3 necessary for glucose derepression and nuclear localization of its product

The yeast regulatory gene CAT3 has an essential function for the depression of several glucose-repressible enzymes. Therefore, cat3 mutants are unable to grow on maltose or on non-fermentable carbon sources. Unlike the point mutants isolated previously, cat3 null allele strains also failed to utilize raffinose or galactose as sole carbon sources. Sequencing of an 1.6-kb HindIII-BglII fragment complementing cat3 mutations revealed an open reading frame of 322 codons, size of which is in good agreement with the 1.3-kb size of mRNA. No significant similarities with previously sequenced genes could be detected. CAT3-lacZ fusions confirmed the proposed reading frame. A CAT3-lacZ fusion encoding 307 amino acids of CAT3 was able to complement the growth defects of cat3 point mutants and null allele strains. Assay of beta-galactosidase activity under different growth conditions indicated a constitutive expression of the CAT3 gene product. Cellular fractionation studies showed the nuclear localization of the CAT3 protein.

Isolation of a DNA fragment which complements glutamine synthetase deficient strains of S. pombe

From a gene bank of S. pombe DNA, a 5.6 kb clone was isolated which complemented mutants defective in glutamine synthetase (GS) activity. Sub-cloning fragments of this 5.6 kb clone showed that the complementing activity was localised in a 1.6 kb HindIII-AvaI fragment and a partial DNA sequence revealed an open reading frame preceded by TATA sequences and a TGACTA sequence. Plasmid constructs carrying up to 3.4 kb of DNA used to transform gln- strains gave transformants which showed a wide range of GS activity, in some cases 100 times the wild-type level. These constructs identify DNA sequences lying downstream from the putative coding sequence which have effects on the total amount of enzyme activity, but do not affect the control imposed by the nitrogen source on which the cells are grown.

Isolation of the yeast phosphoglyceromutase gene and construction of deletion mutants

The PGM1 gene (also called GPM; Fraenkel 1982) coding for phosphoglyceromutase was isolated by functional complementation. When present on a multicopy vector and introduced into yeast cells it led to an about eightfold increase in specific enzymatic activity. This apparent overproduction was confirmed by SDS-polyacrylamide gel electrophoresis of crude extracts and at the transcriptional level by Northern analysis. By subcloning of the yeast DNA insertions of the plasmids originally isolated the PGM1 coding region was located within a 1.3 kb SalI-HindIII fragment. Integration at the chromosomal locus confirmed that the PGM1 gene had indeed been isolated. Southern analysis of genomic digests showed the same restriction patterns as the cloned sequences. However, a BamHI restriction polymorphism was observed. Furthermore, a repetitive element was found in the PGM1 flanking region. Finally, the chromosomal copy of the gene was deleted by replacement with a URA3 marker. The deletion mutants showed that the gene is not essential for yeast growing in the presence of a combination of glycerol and ethanol. However, growth was inhibited by glucose and neither glycerol nor ethanol alone were sufficient to support growth.