Constitutive expression of the maltose fermentative enzymes in Saccharomyces carlsbergensis is dependent upon the mutational activation of a nonessential homolog of MAL63

MAL73, a novel regulator of maltose fermentation, is functionally impaired by single nucleotide polymorphism in sake brewing yeast

For maltose fermentation, budding yeast Saccharomyces cerevisiae operates a mechanism that involves transporters (MALT), maltases (MALS) and regulators (MALR) collectively known as MAL genes. However, functional relevance of MAL genes during sake brewing process remains largely elusive, since sake yeast is cultured under glucose-rich condition achieved by the co-culture partner Aspergillus spp.. Here we isolated an ethyl methane sulfonate (EMS)-mutagenized sake yeast strain exhibiting enhanced maltose fermentation compared to the parental strain. The mutant carried a single nucleotide insertion that leads to the extension of the C-terminal region of a previously uncharacterized MALR gene YPR196W-2, which was renamed as MAL73. Introduction of the mutant allele MAL73L with extended C-terminal region into the parental or other sake yeast strains enhanced the growth rate when fed with maltose as the sole carbon source. In contrast, disruption of endogenous MAL73 in the sake yeasts decreased the maltose fermentation ability of sake yeast, confirming that the original MAL73 functions as a MALR. Importantly, the MAL73L-expressing strain fermented more maltose in practical condition compared to the parental strain during sake brewing process. Our data show that MAL73(L) is a novel MALR gene that regulates maltose fermentation, and has been functionally attenuated in sake yeast by single nucleotide deletion during breeding history. Since the MAL73L-expressing strain showed enhanced ability of maltose fermentation, MAL73L might also be a valuable tool for enhancing maltose fermentation in yeast in general.

Clustered-charge to alanine scanning mutagenesis of the Mal63 MAL-activator C-terminal regulatory domain

The MAL-activator genes of Saccharomyces cerevisiae encode regulatory proteins required for the expression of the structural genes encoding maltose permease and maltase. Residues within the C-terminal region of the Mal63 protein required for negative regulation were previously identified. Evidence suggested that the C-terminal domain is also involved in positive regulatory functions, such as inducer responsiveness and transactivation in the context of a full-length protein. Charged-cluster to alanine scanning mutagenesis of the regulatory domain of MAL63 and the constitutive MAL43-C were undertaken to identify distinct regions within Mal63p involved in positive functions and to define their roles in induction. Mutations that affect the ability to activate transcription in the inducible MAL63 but have no effect in the constitutive MAL43-C define regions that function in induction. Those that affect both the inducible and constitutive alleles define regions involved in activation more generally. Mutations in MAL63 fell into three classes, those that have little or no impact on activity, those that decrease activity, and those that enhance function. Mutations from these classes mapped to distinct regions of the protein, identifying a region of approximately 90 residues (residues 331-423) involved in maltose sensing and an approximately 50-residue region at the extreme C-terminus (residues 420-470) required for activation, such as the formation and/or maintenance of an active state. These studies support a model for MAL-activator function which involves complex protein-protein interactions and overlapping negative and positive regulatory regions.

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.

Characterization of the glucose-induced inactivation of maltose permease in Saccharomyces cerevisiae

The addition of glucose to maltose-fermenting Saccharomyces cerevisiae cells causes a rapid and irreversible loss of the ability to transport maltose, resulting both from the repression of transcription of the maltose permease gene and from the inactivation of maltose permease. The latter is referred to as glucose-induced inactivation or catabolite inactivation. We describe an analysis of this process in a maltose-fermenting strain expressing a hemagglutinin (HA)-tagged allele of MAL61, encoding maltose permease. The transfer of maltose-induced cells expressing the Mal61/HA protein to rich medium containing glucose produces a decrease in maltose transport rates which is paralleled by a decrease in Mal61/HA maltose permease protein levels. In nitrogen starvation medium, glucose produces a biphasic inactivation, i.e., an initial, rapid loss in transport activity (inhibition) followed by a slower decrease in transport activity, which correlates with a decrease in the amount of maltose permease protein (proteolysis). The inactivation in both rich and nitrogen-starved media results from a decrease in Vmax with no apparent change in Km. Using strains carrying mutations in END3, REN1(VPS2), PEP4, and PRE1 PRE2, we demonstrate that the proteolysis of Mal61/HAp is dependent on endocytosis and vacuolar proteolysis and is independent of the proteosome. Moreover, we show that the Mal61/HA maltose permease is present in differentially phosphorylated forms.

Removal of Mig1p binding site converts a MAL63 constitutive mutant derived by interchromosomal gene conversion to glucose insensitivity

Maltose fermenting strains of Saccharomyces cerevisiae have one or more complex loci called MAL. Each locus comprises at least three genes: MALx1 encodes maltose permease, MALx2 encodes maltase, and MALx3 encodes an activator of MALx1 and MALx2 (x denotes one of five MAL loci, with x = 1, 2, 3, 4, or 6). The MAL43c allele is constitutive and relatively insensitive to glucose repression. To understand better this unique phenotype of MAL43c, we have isolated several MAL63c constitutive mutants from a MAL6 strain. All constitutive mutants remain glucose repressible, and all have multiple amino acid substitutions in the C-terminal region, now making this region of Mal63cp similar to that of Mal43cp. These changes have been generated by gene conversion, which transfers DNA from the telomeres of chromosome II and chromosome III or XVI to chromosome VIII (MAL6). The removal of a Mig1p binding site from the MAL63c promoter leads to a loss of glucose repression, imitating the phenotype of MAL43c. Conversely, addition of a Mig1p binding site to the promoter of MAL43c converts it to glucose sensitivity. Mig1p modulation of Mal63p and Mal43p expression therefore plays a substantial role in glucose repression of the MAL genes.

The UAS(MAL) is a bidirectional promotor element required for the expression of both the MAL61 and MAL62 genes of the Saccharomyces MAL6 locus

Maltose fermentation in Saccharomyces yeasts requires one of five unlinked MAL loci: MAL1, 2, 3, 4, or 6. Each locus consists of three genes encoding maltose permease, maltase and the MAL activator. At MAL6 the genes are called MAL61, MAL62 and MAL63, respectively. Transcription of MAL61 and MAL62 is coordinately induced by maltose and repressed by glucose and this regulation is mediated by the MAL activator. By deletion analysis of the MAL61-MAL62 intergenic region, we show that a 68-basepair region, from base pairs -515 to -582 upstream of the MAL61 start codon, contains a sequence necessary for the maltose-induced expression of MAL61 and MAL62, the UAS(MAL). This sequence contains two copies of an 11-basepair dyad which may be the active elements of the UAS(MAL). Using heterologous gene plasmid constructs, we demonstrate that the UAS(MAL) sequence is sufficient for maltose inducibility of MAL62 and that this regulated expression requires a functional MAL activator. Our results suggest that the MAL61-MAL62 intergenic region contains additional distinct elements which function to precisely regulate MAL61 and/or MAL62 expression. Among these are repressing sequences, including a glucose-responsive element located between base pairs -583 and -638, which is partially responsible for mediating glucose-repression of MAL62 expression.

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.

The MAL63 gene of Saccharomyces encodes a cysteine-zinc finger protein

Inducible maltose fermentation by Saccharomyces carlesbergensis requires the product of the MAL63 gene of the MAL6 locus. It has been suggested that this gene product is an activator protein controlling the expression of the structural genes encoding the maltose fermentative enzymes perhaps by binding to DNA sequences upstream of these genes. We report the sequence of the MAL63 gene. A single open reading frame is seen capable of encoding a protein of 470 amino acid residues. The deduced sequence of this protein indicates that it is a cysteine-zinc finger protein supporting the hypothesis that the MAL63 gene product is a DNA binding protein.