Cloning of maltase regulatory genes in Saccharomyces cerevisiae: I. Isolation of the MAL2-8c regulatory gene

Trans-regulation and localization of orthologous maltose transporters in the interspecies lager yeast hybrid

In the interspecies lager yeast hybrid there are MAL loci involved in maltose and maltotriose utilization derived from each parent (Saccharomyces cerevisiae and Saccharomyces eubayanus). We show that trans-regulation across hybrid subgenomes occurs for MAL genes. However, gene expression is less efficient with non-native activators (trans-activation) compared to native activators (cis-activation). MAL genes were induced by maltose and repressed by glucose irrespective of host. Despite the strong expression of S. cerevisiae-type genes in the S. eubayanus host, a very low amount of transporter protein was actually observed in cells. This suggests that proper formation and configuration of the S. cerevisiae transporters is not efficient in S. eubayanus. The S. eubayanus-type Malx1 transporter was present in the plasma membrane in high amounts in all hosts (S. cerevisiae, S. eubayanus and Saccharomyces pastorianus) at all times. However, the S. cerevisiae-type transporters appeared sequentially in the plasma membrane; scMalx1 was localized in the plasma membrane during early to late linear growth and subsequently withdrawn to intracellular compartments. In contrast, the scAgt1 transporter was found in the plasma membrane mainly in the stationary phase of growth. Different localization patterns may explain why certain transporter orthologues in natural S. pastorianus strains were lost to mutation.

Characterization and functional analysis of the MAL and MPH Loci for maltose utilization in some ale and lager yeast strains

Maltose and maltotriose are the major sugars in brewer's wort. Brewer's yeasts contain multiple genes for maltose transporters. It is not known which of these express functional transporters. We correlated maltose transport kinetics with the genotypes of some ale and lager yeasts. Maltose transport by two ale strains was strongly inhibited by other alpha-glucosides, suggesting the use of broad substrate specificity transporters, such as Agt1p. Maltose transport by three lager strains was weakly inhibited by other alpha-glucosides, suggesting the use of narrow substrate specificity transporters. Hybridization studies showed that all five strains contained complete MAL1, MAL2, MAL3, and MAL4 loci, except for one ale strain, which lacked a MAL2 locus. All five strains also contained both AGT1 (coding a broad specificity alpha-glucoside transporter) and MAL11 alleles. MPH genes (maltose permease homologues) were present in the lager but not in the ale strains. During growth on maltose, the lager strains expressed AGT1 at low levels and MALx1 genes at high levels, whereas the ale strains expressed AGT1 at high levels and MALx1 genes at low levels. MPHx expression was negligible in all strains. The AGT1 sequences from the ale strains encoded full-length (616 amino acid) polypeptides, but those from both sequenced lager strains encoded truncated (394 amino acid) polypeptides that are unlikely to be functional transporters. Thus, despite the apparently similar genotypes of these ale and lager strains revealed by hybridization, maltose is predominantly carried by AGT1-encoded transporters in the ale strains and by MALx1-encoded transporters in the lager strains.

Genomic stability of Saccharomyces cerevisiae baker's yeasts

The objective of this study has been to gather data on genomic stability of baker's yeast strains during long-term mitotic growth under restrictive conditions so that comparisons could be made to other studies indicating genomic instability during meiosis. The work describes the analysis of mitotic stability of the nuclear and mitochondrial genomes in the baker's yeast strain V1 during incubation in continuous culture for 190 generations (300 days). The cells were cultured in complete medium containing 2% glucose and 8 to 12% ethanol, as a mutagenic agent specific for mtDNA. The high concentration of ethanol severely limited the growth rate of the cells. DNA samples were monitored for chromosomal pattern, polymorphisms in selected nuclear genes (SUC2, MALIT, ADH1) and mobile genetic elements (Ty1 and Y'), and for RFLPs in mtDNA. The results show that both the nuclear and mitochondrial genomes of grande cells were very stable. However, the frequency of petite mutants in the population varied dramatically during the course of the experiment, reaching as high as 87% petite during the first 27 days of the experiment and declining to 5.8% petite at the end. This decline can be attributed to selection against petite mutants in media containing high concentrations of ethanol. Moreover, when samples and the parental strain were compared at the end of the experiment, no change could be observed in parameters such as their growth rate in different media, capacity to leave doughs, viability in ethanol or frequency of petite mutants. Results therefore indicated that the majority of the cells in the population were very similar to the parental throughout the experiments, with no apparent molecular or phenotypical changes.

Genetic evidence that high noninduced maltase and maltose permease activities, governed by MALx3-encoded transcriptional regulators, determine efficiency of gas production by baker's yeast in unsugared dough

Strain selection and improvement in the baker's yeast industry have aimed to increase the speed of maltose fermentation in order to increase the leavening activity of industrial baking yeast. We identified two groups of baker's strains of Saccharomyces cerevisiae that can be distinguished by the mode of regulation of maltose utilization. One group (nonlagging strains), characterized by rapid maltose fermentation, had at least 12-fold more maltase and 130-fold-higher maltose permease activities than maltose-lagging strains in the absence of inducing sugar (maltose) and repressing sugar (glucose). Increasing the noninduced maltase activity of a lagging strain 13-fold led to an increase in CO2 production in unsugared dough. This increase in CO2 production also was seen when the maltose permease activity was increased 55-fold. Only when maltase and maltose permease activities were increased in concert was CO2 production by a lagging strain similar to that of a nonlagging strain. The noninduced activities of maltase and maltose permease constitute the largest determinant of whether a strain displays a nonlagging or a lagging phenotype and are dependent upon the MALx3 allele. Previous strategies for strain improvement have targeted glucose derepression of maltase and maltose permease expression. Our results suggest that increasing noninduced maltase and maltose permease levels is an important target for improved maltose metabolism in unsugared dough.

A flow cytometric method for rapid selection of novel industrial yeast hybrids

We rapidly produced and isolated novel yeast hybrids by using two-color flow cytometric cell sorting. We labeled one parent strain with a fluorescent green stain and the other parent with a fluorescent orange stain, and hybrids were selected based on their dual orange and green fluorescence. When this technique was applied to the production of hybrids by traditional mating procedures, more than 96% of the isolates were hybrids. When it was applied to rare mating, three hybrids were identified among 50 isolates enriched from a population containing 2 x 10(6) cells. This technology is not dependent on genetic markers and has applications in the development of improved industrial yeast strains.

A two-reporter gene system for the analysis of bi-directional transcription from the divergent MAL6T-MAL6S promoter in Saccharomyces cerevisiae

Many sets of genes in Saccharomyces cerevisiae are divergently transcribed, but at present there are no vectors generally available for the simultaneous analysis of divergent transcription from these promoters. In the present study MEL1 and lacZ were used to construct a vector capable of measuring the divergent expression initiated by the MAL6T-MAL6S bi-directional promoter. Our observations demonstrate that the expression of both reporter genes was regulated in a similar fashion to the native MAL6T and MAL6S genes, and that induction was dependent upon the presence of a functional MALR activator gene. The results confirmed that the MAL6T-MAL6S promoter was co-ordinately regulated, repressed by glucose, induced by maltose, and that basal expression was more active in the MAL6S direction than in the MAL6T direction.

ACR1, a gene encoding a protein related to mitochondrial carriers, is essential for acetyl-CoA synthetase activity in Saccharomyces cerevisiae

The utilization of ethanol via acetate by the yeast Saccharomyces cerevisiae requires the presence of the enzyme acetyl-coenzyme A synthetase (acetyl-CoA synthetase), which catalyzes the activation of acetate to acetyl-coenzyme A (acetyl-CoA). We have isolated a mutant, termed acr1, defective for this activity by screening for mutants unable to utilize ethanol as a sole carbon source. Genetic and biochemical characterization show that, in this mutant, the structural gene for acetyl-CoA synthetase is not affected. Cloning and sequencing demonstrated that the ACR1 gene encodes a protein of 321 amino acids with a molecular mass of 35370 Da. Computer analysis suggested that the ACR1 gene product (ACR1) is an integral membrane protein related to the family of mitochondrial carriers. The expression of the gene is induced by growing yeast cells in media containing ethanol or acetate as sole carbon sources and is repressed by glucose. ACR1 is essential for the utilization of ethanol and acetate since a mutant carrying a disruption in this gene is unable to grow on these compounds.

Transcriptional regulation of the isocitrate lyase encoding gene in Saccharomyces cerevisiae

In this work, we studied the transcriptional regulation of isocitrate lyase synthesis. In Northern blot analyses we first showed that the steady-state ICL1 mRNA levels depend on the carbon source used for growth. In addition, we determined the kinetics of transcriptional repression upon a shift of ethanol-grown cells to glucose and of the induction when cells were transferred from glucose to ethanol. By deletion analyses as well as by studying the influence on expression of different fragments cloned into the heterologous CYC1 promoter lacking its own UAS sequences, we defined UAS and URS elements in the ICL1 promoter. A region mediating the control by CAT3, a gene also involved in the control of expression of other genes subject to carbon catabolite repression, was found to overlap with one of these UAS elements.

The ICL1 gene from Saccharomyces cerevisiae

The glyoxylate cycle is essential for the utilization of C2 compounds by the yeast Saccharomyces cerevisiae. Within this cycle, isocitrate lyase catalyzes one of the key reactions. We obtained mutants lacking detectable isocitrate lyase activity, screening for their inability to grow on ethanol. Genetic and biochemical analysis suggested that they carried a defect in the structural gene, ICL1. The mutants were used for the isolation of this gene and it was located on a 3.1-kb BglII-SphI DNA fragment. We then constructed a deletion-substitution mutant in the haploid yeast genome. It did not have any isocitrate lyase activity and lacked the ability to grow on ethanol as the sole carbon source. Both strands of a DNA fragment carrying the gene and its flanking regions were sequenced. An open reading frame of 1671 bp was detected, encoding a protein of 557 amino acids with a calculated molecular mass of 62515 Da. The deduced amino acid sequence shows extensive similarities to genes encoding isocitrate lyases from various organisms. Two putative cAMP-dependent protein-kinase phosphorylation sites may explain the susceptibility of the enzyme to carbon catabolite inactivation.

Structure of the multigene family of MAL loci in Saccharomyces

Multigene families are a ubiquitous feature of eukaryotes; however, their presence in Saccharomyces is more limited. The MAL multigene family is comprised of five unlinked loci, MAL1, MAL2, MAL3, MAL4 and MAL6, any one of which is sufficient for yeast to metabolize maltose. A cloned MAL6 locus was used as a probe to facilitate the cloning of the other four functional loci as well as two partially active alleles of MAL1. Each locus could be characterized as a cluster of three genes, MALR (regulatory), MALT (maltose transport or permease) and MALS (structural or maltase), encoded by a total of about 7 kb of DNA; however, homologous sequences at each locus extend beyond the coding regions. Our results indicate that there is extensive homology among the MAL loci, especially within their maltase genes. The greatest sequence diversity occurs in their regulatory gene regions. Southern cross analyses of the cloned MAL loci indicate a single duplication of the MAL6R-homologous sequences upstream of the MAL6R gene as well as an extensive duplication of more than 10 kb at the MAL3 locus. The large repeat at the MAL3 locus results in the presence of four copies of MAL3R-homologous sequences and two copies of MAL3T-homologous sequences at that locus. Two naturally occurring inactive alleles of MAL1 show a deletion or divergence of their MALR sequences. The significance of these repeats in the evolution of the MAL multigene family is discussed.

Cloning and characterization of baker's yeast alpha-glucosidase: over-expression in a yeast strain devoid of vacuolar proteinases

Two alpha-glucosidase (maltase) genes, designated GLUCPI and GLUCPII, have been cloned from an industrial strain of baker's yeast (Saccharomyces cerevisiae) by complementation of a maltase-negative mutant strain. The different genes were identified according to their alternatively expressed isoenzymes PI and PII in transformants after isoelectric focusing and activity staining in separated cell lysates. The gene encoding alpha-glucosidase PI (GLUCPI), which was not present in laboratory strains of S. carlsbergensis with a defined MAL1, 2, 3, 4 or 6 locus, was sequenced and compared with the recently published MAL6S gene. This comparison revealed single amino acid deviations at three positions in the predicted polypeptide sequence. In addition, the divergent promoter region of GLUCPI differed from MAL6S by a triple repeated 147-bp DNA segment. Maltose induction and glucose repression of alpha-glucosidase PI were not affected by the deletion of the repeated DNA segment. However, the absolute expression of alpha-glucosidase PI increased two- to four-fold. In addition, a two-fold increase in the maltase synthesis occurred when the cloned positive regulator gene MAL2-8ep was on the same plasmid. Furthermore, stability of the alpha-glucosidase in cultures in the stationary growth phase was greatly enhanced using a host strain lacking the proteinases A and B and the carboxypeptidases Y and S. Promoter trimming, MAL2-8cp stimulation and the use of a host strain deficient in four vacuolar proteinases resulted in alpha-glucosidase PI expression of about 13% of the soluble protein.

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.

Insertion of non-homologous DNA sequences into a regulatory gene cause a constitutive maltase synthesis in yeast

Two maltase constitutive alleles MAL1-1c and MAL1-2c were obtained as revertants from a defective mall-1 mutant allele not promoting maltose fermentation. Classical genetical analysis showed that the mutations were linked or allelic to the MAL1 locus. Dominance relations were established by testing alpha-glucosidase activities in diploids containing various allele combinations. The maltose regulatory genes belonging to the MAL1, MAL1-1c and MAL1-2c alleles were cloned. Differences in restriction sites were found between the wild type MAL1 and the derived MAL1-constitutive alleles. The MAL1 regulatory gene was located in a 1.15 kb EcoRI fragment (Rodicio and Zimmermann 1985a, b). An EcoRI fragment of this size was found in plasmids containing the MAL1 regulatory wild type allele but was absent from plasmids carrying the constitutive alleles. The genomic organization of the MAL loci in the constitutive mutants was confirmed by Southern analysis. Various fragments containing sequences of the different MAL1 alleles were used to probe genomic digests of MAL1, MAL1-1c and MAL1-2c strains. The results obtained support the conclusion that the constitutive mutations had arisen by a rearrangement between the original mal1-1 mutant allele and sequences with different location in the genome.

Trehalose and maltose metabolism in yeast transformed by a MAL4 regulatory gene cloned from a constitutive donor strain

A 6.8 kb fragment of DNA containing the regulatory sequence MAL4p has been cloned from a genomic library prepared from Saccharomyces cerevisiae strain 1403-7A which ferments maltose constitutively. The library was prepared by ligation of 5-20 kb Sau3AI restriction fragments of total yeast DNA into the BamH1 restriction site of shuttle vector YEp13. A restriction map of the cloned fragment indicates that it encompasses a 2.6 kb segment which closely resembles the regulatory MAL6 gene previously identified (Needleman et al. 1984). The hybrid plasmid, p(MAL4p)4, could transform maltose-nonfermenting strains which contain cryptic alpha-glucosidase and maltose permease genes (malp MALg), but could not transform strains containing a functional regulatory sequence and a defective maltase-permease region (MAlp malg). A correlated absence of maltase and permease DNA from the cloned fragment was indicated by the restriction map. Although the cloned DNA fragment was derived from a constitutive strain, maltose fermentation and alpha-glucosidase formation by yeast transformed with p(MAL4p)4 was largely inducible by maltose and sensitive to catabolite repression. Moreover, the active trehalose accumulation pattern (TAC(+) phenotype) linked to the complete MAL4 locus in strain 1403-7A and other constitutive MAL strains (Oliveira et al. 1981b) was not found in p(MAL4p)4 transformants. It may be concluded that constitutivity of maltose fermentation and the associated active trehalose accumulation are not merely consequences of a cis-dominant mutation causing constitutive formation of the MALp regulatory product. Moreover, constitutivity may not be caused solely by a mutation within the structural region of the MALp gene.

Control of cell growth and division in Saccharomyces cerevisiae

Considerable advances have been made in recent years in our understanding of the biochemistry of protein and nucleic acid synthesis and, particularly, the molecular biology of gene expression in eukaryotes. The yeast Saccharomyces cerevisiae, and to a lesser extent Schizosaccharomyces pombe, has had a preeminent role as a focus for these studies, principally because of the facility with which these organisms can be experimentally manipulated biochemically and genetically. This review will be designed to critically examine and integrate recent advances in several vital areas of regulatory control of enzyme synthesis in yeast: structure and organization of DNA, transcriptional regulation, post-transcriptional modification, control of translation, post-translational modification and secretion, and cell-cycle modulation. It will attempt to emphasize and illustrate, where detailed information is available, principal underlying molecular mechanisms, and it will attempt to make relevant comparisons of this material to inferred and demonstrated facets of regulatory control of enzyme and protein synthesis in higher eukaryotes.