The constitutive, glucose-repression-insensitive mutation of the yeast MAL4 locus is an alteration of the MAL43 gene

Hsp90 cochaperone Aha1 is a negative regulator of the Saccharomyces MAL activator and acts early in the chaperone activation pathway

Aha1 is a ubiquitous cochaperone of the Hsp90/Hsp70 chaperone machine. It binds the middle domain of Hsp90 and stimulates ATPase activity, suggesting a function late in the chaperone pathway. Saccharomyces Mal63 MAL activator is a DNA-binding transcription factor and Hsp90 client protein. This study utilizes several MAL activator mutants to investigate Aha1 function in vivo. Deletion of AHA1 enhances induced Mal63-dependent maltase activity levels 2-fold, whereas overproduction of Aha1 represses expression. Maltase expression in strains carrying constitutive and super-inducible mutant activators with alterations near the C terminus (particularly residues 433-463) is unaffected by either aha1Delta or Aha1 overproduction. However, another constitutive activator with alterations outside of this C-terminal region is sensitive to Aha1 regulation. Previously, we showed that in the absence of inducer, Mal63 forms a stable intermediate complex with Hsp70, Hsp90, and Sti1, whereas noninducible mutant activators bind only with Hsp70 in an apparent early complex. Here, we find that triple Myc-tagged Aha1/Myc3 copurifies with all noninducible Mal63 mutant activators tested. Aha1/Myc3 association with inducible Mal63 is observed only in a sti1Delta strain, in which Hsp90 binding and intermediate complex formation are defective. Constitutive and super-inducible mutant activators with C-terminal alterations do not bind Aha1 even in a sti1Delta strain. Mal63 binding to Hsp90 and Hsp70 is enhanced 3-fold by loss of Aha1. These results suggest an interaction between Aha1 and residues near the C terminus of Mal63 thereby regulating Hsp90 association. A novel mechanism for the negative regulation of the MAL activator by Aha1 cochaperone is proposed.

Flocculation in Saccharomyces cerevisiae is repressed by the COMPASS methylation complex during high-gravity fermentation

The significance of COMPASS on silencing of the FLO and MAL genes, located close to telomeres, was studied in different Saccharomyces cerevisiae strains that fermented high concentrations of maltose (20%) with different efficiency. In one particular fast maltose-fermenting yeast strain, with constitutive expression of FLO11, the expression of FLO1, FLO5 and FLO9 was induced during fermentation of high concentrations of maltose or glucose. In another strain the expression of mainly FLO1 was induced. Mutants of these strains with a defective COMPASS, however, formed very large aggregates of cells earlier in the fermentation and more pronounced than the wild-type. The formation of the large flocs was dependent on calcium ions and was inhibited by mannose. The flocculation displayed by mutants defective in COMPASS was due to increased amounts of FLO1, FLO5 and FLO9 transcripts. COMPASS-mediated silencing of the MAL genes was detected at the later stages of fermentation in strains that fermented high concentrations of maltose slowly and incompletely, while silencing was not detectable in strains that fermented maltose fast. Thus, COMPASS, in addition to the MAL genes, is also involved in silencing the expression of the FLO1, FLO5 and FLO9 genes.

Hsp90/Hsp70 chaperone machine regulation of the Saccharomyces MAL-activator as determined in vivo using noninducible and constitutive mutant alleles

The Hsp90/Hsp70 chaperone machine is an essential regulator of cell growth and division. It is required for activation of select client proteins, chiefly protein kinases and transcription activators and thus plays a major role in regulating intracellular signaling and gene expression. This report demonstrates, in vivo, the association of the Saccharomyces cerevisiae maltose-responsive transcription activator Mal63 (MAL-activator) with the yeast Hsp70 (Ssa1), Hsp90 (Hsp82), and Hop (Sti1) homologs, using a collection of inducible, constitutive, and noninducible alleles. Each class of mutant activator forms a distinctly different stable multichaperone complex in the absence of maltose. Inducible Mal63p associates with Ssa1, Hsp82, and Sti1 and is released in the presence of maltose. Noninducible mal63 mutant proteins bind to Ssa1 alone and do not stably associate with Hsp82 or Sti1. Constitutive MAL-activators bind well to Hsp82 and poorly to Ssa1 and Sti1, but deletion of STI1 restores Ssa1 binding. Taken together, Mal63p regulation requires the formation of Hsp90/Hsp70 subcomplexes comparable to, yet distinct from those observed with previously characterized Hsp90 clients including glucocorticoid receptor and yeast Hap1p. Thus, comparative studies of different client proteins highlight functional diversity in the operation of the Hsp90/Hsp70 chaperone machine.

Inactivation of maltose permease and maltase in sporulating Saccharomyces cerevisiae

Maltose transport and maltase activities were inactivated during sporulation of a MAL constitutive yeast strain harboring different MAL loci. Both activities were reduced to almost zero after 5 h of incubation in sporulation medium. The inactivation of maltase and maltose permease seems to be related to optimal sporulation conditions such as a suitable supply of oxygen and cell concentration in the sporulating cultures, and occurs in the fully derepressed conditions of incubation in the sporulation acetate medium. The inactivation of maltase and maltose permease under sporulation conditions in MAL constitutive strains suggests an alternative mechanism for the regulation of the MAL gene expression during the sporulation process.

Analysis of the mechanism by which glucose inhibits maltose induction of MAL gene expression in Saccharomyces

Expression of the MAL genes required for maltose fermentation in Saccharomyces cerevisiae is induced by maltose and repressed by glucose. Maltose-inducible regulation requires maltose permease and the MAL-activator protein, a DNA-binding transcription factor encoded by MAL63 and its homologues at the other MAL loci. Previously, we showed that the Mig1 repressor mediates glucose repression of MAL gene expression. Glucose also blocks MAL-activator-mediated maltose induction through a Mig1p-independent mechanism that we refer to as glucose inhibition. Here we report the characterization of this process. Our results indicate that glucose inhibition is also Mig2p independent. Moreover, we show that neither overexpression of the MAL-activator nor elimination of inducer exclusion is sufficient to relieve glucose inhibition, suggesting that glucose acts to inhibit induction by affecting maltose sensing and/or signaling. The glucose inhibition pathway requires HXK2, REG1, and GSF1 and appears to overlap upstream with the glucose repression pathway. The likely target of glucose inhibition is Snf1 protein kinase. Evidence is presented indicating that, in addition to its role in the inactivation of Mig1p, Snf1p is required post-transcriptionally for the synthesis of maltose permease whose function is essential for maltose induction.

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.

Tandemly repeated 147 bp elements cause structural and functional variation in divergent MAL promoters of Saccharomyces cerevisiae

We have studied four novel MAL promoters isolated from a single strain of bakers' yeast. Within these promoters we have identified up to five tandem 147 bp repeats located between the MAL UAS region and the MALT TATA box. These repeats strongly reduce MALT (maltose permease) gene expression but only weakly reduce MALS (maltase) gene expression. Insertion of the 147 bp elements into the heterologous CYC1 promoter reduced expression when located between the CYC1 UAS and the TATA box, but not when located upstream of the UAS. We propose that these naturally occurring repeats have evolved as a mechanism to lower the level of MALT expression relative of MALS expression, thus avoiding possible toxic effects associated with over-expression from multiple copies of the permease gene.

Constitutive mutations of the Saccharomyces cerevisiae MAL-activator genes MAL23, MAL43, MAL63, and mal64

We report the sequence of several MAL-activator genes, including inducible, constitutive, and noninducible alleles of MAL23, MAL43, MAL63, and mal64. Constitutive alleles of MAL23 and MAL43 vary considerably from inducible alleles in their C-terminal domain, with many of the alterations clustered and common to both alleles. The 27 alterations from residues 238-461 of Mal43-C protein are sufficient for constitutivity, but the minimal number of alterations needed for the constitutive phenotype could not be determined. The sequence of mal64, a nonfunctional homologue of MAL63, revealed that Mal64p is 85% identical to Mal63p. Two mutations that activate mal64 and cause constitutivity are nonsense mutations resulting in truncated proteins of 306 and 282 residues. We conclude that the C-terminal region of the MAL-activator, from residues 283-470, contains a maltose-responsive negative regulatory domain, and that extensive mutation or deletion of the entire region causes loss of the negative regulatory function. Additionally, certain sequence elements in the region appear to be necessary for efficient induction of the full-length Mal63 activator protein. These studies highlight the role of ectopic recombination as an important mechanism of mutagenesis of the telomere-associated family of MAL loci.

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.

MIG1-dependent and MIG1-independent glucose regulation of MAL gene expression in Saccharomyces cerevisiae

Glucose repression is a global regulatory system in Saccharomyces cerevisiae controlling carbon-source utilization, mitochondrial biogenesis, gluconeogenesis and other metabolic pathways. Mig1p, a zinc-finger class of DNA-binding protein, is a transcriptional repressor regulating GAL and SUC gene expression in response to glucose. This report demonstrates that Mig1 protein represses transcription of the MAL61 and MAL62 structural genes and also the MAL63 gene, which encodes the Mal-activator. Mig1p DNA-binding sites were identified upstream of all three MAL genes. Both of the Mig1p-binding sites found in the bidirectional MAL61-MAL62 promoter were shown to function in the Mig1p-dependent glucose repression. Studies using constitutive Mal-activator alleles suggest that glucose regulation of inducer availability is a second major contributing factor in glucose repression of MAL gene expression and is even stronger than the Mig1p-dependent component of repression. Moreover, our results also suggest the contribution of other minor mechanisms in glucose regulation of MAL gene expression.

Accumulation of trehalose in Saccharomyces cerevisiae growing on maltose is dependent on the TPS1 gene encoding the UDPglucose-linked trehalose synthase

When yeast strains were cultivated on maltose, the synthesis of trehalose already started in the exponential phase of growth, well before exhaustion of the sugar from the medium. This active pattern of trehalose accumulation was also observed in a maltose constitutive mutant strain growing on glucose. However, this accumulation was completely prevented by deletion of the TPS1 gene coding for the catalytic subunit of the UDPglucose-linked trehalose-6-phosphate synthase, indicating that no alternative pathway for trehalose synthesis exists in yeast. The active pattern of trehalose accumulation seems to be consistent with the finding that trehalose-6-phosphate synthase is more active in strains growing on maltose than on glucose.

Genetic mapping and biochemical analysis of mutants in the maltose regulatory gene of the MAL1 locus of Saccharomyces cerevisiae

The MAL1 locus of Saccharomyces cerevisiae comprises three genes necessary for maltose utilization: a regulatory (MALR), a maltose transport (MALT) and a maltase gene (MALS). A fine structure genetic map of the MAL1R gene was constructed and the order of mutations was confirmed by plasmid-mediated chromosomal recombination. The mutations cluster non-randomly within the 5' half of the gene, where the putative DNA binding domain of the encoded protein is located. Only mutations mal1R-22 and MAL1R-72 map in the 3' terminal half of the gene; these mutations cause a different pattern of transcriptional regulation of plasmid-borne MAL6T genes. Experiments supporting a direct involvement of the MALR-encoded protein in carbon catabolite repression of MAL gene expression are reported.

The maltose permease encoded by the MAL61 gene of Saccharomyces cerevisiae exhibits both sequence and structural homology to other sugar transporters

The MAL61 gene of Saccharomyces cerevisiae encodes maltose permease, a protein required for the transport of maltose across the plasma membrane. Here we report the nucleotide sequence of the cloned MAL61 gene. A single 1842 bp open reading frame is present within this region encoding the 614 residue putative MAL61 protein. Hydropathy analysis suggests that the secondary structure consists of two blocks of six transmembrane domains separated by an approximately 71 residue intracellular region. The N-terminal and C-terminal domains of 100 and 67 residues in length, respectively, also appear to be intracellular. Significant sequence and structural homology is seen between the MAL61 protein and the Saccharomyces high-affinity glucose transporter encoded by the SNF3 gene, the Kluyveromyces lactis lactose permease encoded by the LAC12 gene, the human HepG2 glucose transporter and the Escherichia coli xylose and arabinose transporters encoded by the xylE and araE genes, indicating that all are members of a family of sugar transporters and are related either functionally or evolutionarily. A mechanism for glucose-induced inactivation of maltose transport activity is discussed.

Genetic Analysis of Haploids from Industrial Strains of Baker's Yeast

Strains of baker's yeast conventionally used by the baking industry in Japan were tested for the ability to sporulate and produce viable haploid spores. Three isolates which possessed the properties of baker's yeasts were obtained from single spores. Each strain was a haploid, and one of these strains, YOY34, was characterized. YOY34 fermented maltose and sucrose, but did not utilize galactose, unlike its parental strain. Genetic analysis showed that YOY34 carried two MAL genes, one functional and one cryptic; two SUC genes; and one defective gal gene. The genotype of YOY34 was identified as MAT α MAL1 MAL3g SUC2 SUC4 gall. The MAL1 gene from this haploid was constitutively expressed, was dominant over other wild-type MAL tester genes, and gave a weak sucrose fermentation. YOY34 was suitable for both bakery products, like conventional baker's yeasts, and for genetic analysis, like laboratory strains.

Molecular evolution of the telomere-associated MAL loci of Saccharomyces

The MAL gene family of Saccharomyces consists of five multigene complexes (MAL1, MAL2, MAL3, MAL4, and MAL6) each of which encodes maltose permease (GENE 1), maltase (GENE 2) and the trans-acting MAL-activator (GENE 3). Four of these loci have been mapped and each is located at or near the telomere of a different chromosome. We compare the physical structure of the MAL loci and their flanking sequences. The MAL loci were shown to be both structurally and functionally homologous throughout an approximately 9.0-kb region. The orientation of the MAL loci was determined to be: CENTROMERE . . . GENE 3-GENE 1-GENE 2 . . . TELOMERE. Telomere-adjacent sequences were found flanking GENE 2 of the MAL1, MAL3 and MAL6 loci. No common repeated elements were found on the centromere-proximal side of all the MAL1, loci. These results suggest that, during the evolution of this polygenic family, the MAL loci translocated to different chromosomes via a mechanism that involved the rearrangement(s) of chromosome termini.

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.

The naturally occurring alleles of MAL1 in Saccharomyces species evolved by various mutagenic processes including chromosomal rearrangement

In order for a yeast strain to ferment maltose it must contain any one of the five dominant MAL loci. Each dominant MAL locus thus far analyzed contains three genes: GENE 1, encoding maltose permease, GENE 2 encoding maltase and GENE 3 encoding a positive trans-acting regulatory protein. In addition to these dominant MAL loci, several naturally occurring, partially functional alleles of MAL1 and MAL3 have been identified. Here, we present genetic and molecular analysis of the three partially functional alleles of MAL1: the MAL1p allele which can express only the MAL activator; the MAL1 g allele which can express both a maltose permease and maltase; and the mal1(0) allele which can express only maltase. Based on our results, we propose that the MAL1p, MAL1g and mal1(0) alleles evolved from the dominant MAL1 locus by a series of rearrangements and/or deletions of this yeast telomere-associated locus as well as by other mutagenic processes of gene inactivation. One surprising finding is that the MAL1g-encoded maltose permease exhibits little sequence homology to the MAL1-encoded maltose permease though they appear to be functionally homologous.

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

Maltose fermentation in Saccharomyces carlsbergensis is dependent upon the MAL6 locus. This complex locus is composed of the MAL61 and MAL62 genes, which encode maltose permease and maltase, respectively, and a third gene, MAL63, which codes for a trans-acting positive regulatory product. In wild-type strains, expression of the MAL61 and MAL62 mRNAs and proteins is induced by maltose and induction is dependent upon the MAL63 gene. Mutants constitutively expressing the MAL61 and MAL62 gene products have been isolated in mal63 backgrounds, and the mutations which have been analyzed map to a fourth MAL6-linked gene, MAL64. Cloning and characterization of this new gene are described in this report. The results revealed that the MAL64-C alleles present in constitutive strains encode a trans-acting positive function required for constitutive expression of the MAL61 and MAL62 gene products. In inducible strains, the MAL64 gene is dispensable, as deletion of the gene had no effect on maltose fermentation or maltose-regulated induction. MAL64 encoded transcripts of 2.0 and 1.4 kilobase pairs. While both MAL64 mRNAs were constitutively expressed in constitutive strains, they were maltose inducible in wild-type strains and induction was dependent upon the MAL63 gene. The MAL63 and MAL64 genes are at least partially structurally homologous, suggesting that they control MAL61 and MAL62 transcript accumulation by similar mechanisms.