Disruption of regulatory gene GAL80 in Saccharomyces cerevisiae: effects on carbon-controlled regulation of the galactose/melibiose pathway genes

Computational study on ratio-sensing in yeast galactose utilization pathway

Metabolic networks undergo gene expression regulation in response to external nutrient signals. In microbes, the synthesis of enzymes that are used to transport and catabolize less preferred carbon sources is repressed in the presence of a preferred carbon source. For most microbes, glucose is a preferred carbon source, and it has long been believed that as long as glucose is present in the environment, the expression of genes related to the metabolism of alternative carbon sources is shut down, due to catabolite repression. However, recent studies have shown that the induction of the galactose (GAL) metabolic network does not solely depend on the exhaustion of glucose. Instead, the GAL genes respond to the external concentration ratio of galactose to glucose, a phenomenon of unknown mechanism that we termed ratio-sensing. Using mathematical modeling, we found that ratio-sensing is a general phenomenon that can arise from competition between two carbon sources for shared transporters, between transcription factors for binding to communal regulatory sequences of the target genes, or a combination of the aforementioned two levels of competition. We analyzed how the parameters describing the competitive interaction influenced ratio-sensing behaviors in each scenario and found that the concatenation of both layers of signal integration could expand the dynamical range of ratio-sensing. Finally, we investigated the influence of circuit topology on ratio-sensing and found that incorporating negative auto-regulation and/or coherent feedforward loop motifs to the basic signal integration unit could tune the sensitivity of the response to the external nutrient signals. Our study not only deepened our understanding of how ratio-sensing is achieved in yeast GAL metabolic regulation, but also elucidated design principles for ratio-sensing signal processing that can be used in other biological settings, such as being introduced into circuit designs for synthetic biology applications.

Microbes make sophisticated choices about the uptake and metabolism of nutrients depending on the variety of nutrient choices available to them in their environment. In the well-studied yeast galactose utilization network, a recent study has shown that galactose metabolic genes respond to the external concentration ratio of galactose to glucose. Using computational models, we showed that this type of phenomenon could arise from a competition between galactose and glucose for transporters, a competition between transcription factors for promoters, or a combination of these two mechanisms. We further revealed the controlling parameters that determined the system sensitivity towards competing input signals and that determined the concentration ratio required to induce the metabolic network in each scenario. Combining competition inhibition at both the transporter level and the transcriptional level can enlarge the ratio-sensing regime, resulting a robust signal integration module. We suspect that modules of this kind may be common in many areas of biology.

Chromatin regulatory genes differentially interact in networks to facilitate distinct GAL1 activity and noise profiles

Controlling chromatin state constitutes a major regulatory step in gene expression regulation across eukaryotes. While global cellular features or processes are naturally impacted by chromatin state alterations, little is known about how chromatin regulatory genes interact in networks to dictate downstream phenotypes. Using the activity of the canonical galactose network in yeast as a model, here, we measured the impact of the disruption of key chromatin regulatory genes on downstream gene expression, genetic noise and fitness. Using Trichostatin A and nicotinamide, we characterized how drug-based modulation of global histone deacetylase activity affected these phenotypes. Performing epistasis analysis, we discovered phenotype-specific genetic interaction networks of chromatin regulators. Our work provides comprehensive insights into how the galactose network activity is affected by protein interaction networks formed by chromatin regulators.

Laboratory evolution of a glucose-phosphorylation-deficient, arabinose-fermenting S. cerevisiae strain reveals mutations in GAL2 that enable glucose-insensitive l-arabinose uptake

Cas9-assisted genome editing was used to construct an engineered glucose-phosphorylation-negative S. cerevisiae strain, expressing the Lactobacillus plantaruml-arabinose pathway and the Penicillium chrysogenum transporter PcAraT. This strain, which showed a growth rate of 0.26 h⁻¹ on l-arabinose in aerobic batch cultures, was subsequently evolved for anaerobic growth on l-arabinose in the presence of d-glucose and d-xylose. In four strains isolated from two independent evolution experiments the galactose-transporter gene GAL2 had been duplicated, with all alleles encoding Gal2^N376T or Gal2^N376I substitutions. In one strain, a single GAL2 allele additionally encoded a Gal2^T89I substitution, which was subsequently also detected in the independently evolved strain IMS0010. In ¹⁴C-sugar-transport assays, Gal2^N376S, Gal2^N376T and Gal2^N376I substitutions showed a much lower glucose sensitivity of l-arabinose transport and a much higher K_m for d-glucose transport than wild-type Gal2. Introduction of the Gal2^N376I substitution in a non-evolved strain enabled growth on l-arabinose in the presence of d-glucose. Gal2^{N376T, T89I} and Gal2^T89I variants showed a lower K_m for l-arabinose and a higher K_m for d-glucose than wild-type Gal2, while reverting Gal2^{N376T, T89I} to Gal2^N376 in an evolved strain negatively affected anaerobic growth on l-arabinose. This study indicates that optimal conversion of mixed-sugar feedstocks may require complex ‘transporter landscapes’, consisting of sugar transporters with complementary kinetic and regulatory properties.

Systematic Engineering for Improved Carbon Economy in the Biosynthesis of Polyhydroxyalkanoates and Isoprenoids

With the rapid development of synthetic biology and metabolic engineering, a broad range of biochemicals can be biosynthesized, which include polyhydroxyalkanoates and isoprenoids. However, some of the bio-approaches in chemical synthesis have just started to be applied outside of laboratory settings, and many require considerable efforts to achieve economies of scale. One of the often-seen barriers is the low yield and productivity, which leads to higher unit cost and unit capital investment for the bioconversion process. In general, higher carbon economy (less carbon wastes during conversion process from biomass to objective bio-based chemicals) will result in higher bioconversion yield, which results in less waste being generated during the process. To achieve this goal, diversified strategies have been applied; matured strategies include pathway engineering to block competitive pathways, enzyme engineering to enhance the activities of enzymes, and process optimization to improve biomass/carbon yield. In this review, we analyze the impact of carbon sources from different types of biomass on the yield of bio-based chemicals (especially for polyhydroxyalkanoates and isoprenoids). Moreover, we summarize the traditional strategies for improving carbon economy during the bioconversion process and introduce the updated techniques in building up non-natural carbon pathways, which demonstrate higher carbon economies than their natural counterparts.

The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae

BACKGROUND

l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these feedstocks by engineered pentose-metabolizing S. cerevisiae strains.

RESULTS

Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least threefold higher in l-arabinose-limited cultures than in d-glucose-limited and ethanol-limited cultures. Of five genes, that encoded putative transport proteins and showed an over 30-fold higher transcript level in l-arabinose-grown cultures compared to d-glucose-grown cultures, only one (Pc20g01790) restored growth on l-arabinose upon expression in an engineered l-arabinose-fermenting S. cerevisiae strain in which the endogenous l-arabinose transporter, GAL2, had been deleted. Sugar transport assays indicated that this fungal transporter, designated as PcAraT, is a high-affinity (K_m = 0.13 mM), high-specificity l-arabinose-proton symporter that does not transport d-xylose or d-glucose. An l-arabinose-metabolizing S. cerevisiae strain in which GAL2 was replaced by PcaraT showed 450-fold lower residual substrate concentrations in l-arabinose-limited chemostat cultures than a congenic strain in which l-arabinose import depended on Gal2 (4.2 × 10^-3 and 1.8 g L^-1, respectively). Inhibition of l-arabinose transport by the most abundant sugars in hydrolysates, d-glucose and d-xylose was far less pronounced than observed with Gal2. Expression of PcAraT in a hexose-phosphorylation-deficient, l-arabinose-metabolizing S. cerevisiae strain enabled growth in media supplemented with both 20 g L^-1 l-arabinose and 20 g L^-1 d-glucose, which completely inhibited growth of a congenic strain in the same condition that depended on l-arabinose transport via Gal2.

CONCLUSION

Its high affinity and specificity for l-arabinose, combined with limited sensitivity to inhibition by d-glucose and d-xylose, make PcAraT a valuable transporter for application in metabolic engineering strategies aimed at engineering S. cerevisiae strains for efficient conversion of lignocellulosic hydrolysates.

Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeast

BACKGROUND

Assembly of heterologous metabolic pathways is commonly required to generate microbial cell factories for industrial production of both commodity chemicals (including biofuels) and high-value chemicals. Promoter-mediated transcriptional regulation coordinates the expression of the individual components of these heterologous pathways. Expression patterns vary during culture as conditions change, and this can influence yeast physiology and productivity in both positive and negative ways. Well-characterized strategies are required for matching transcriptional regulation with desired output across changing culture conditions.

RESULTS

Here, constitutive and inducible regulatory mechanisms were examined to optimize synthetic isoprenoid metabolic pathway modules for production of trans-nerolidol, an acyclic sesquiterpene alcohol, in yeast. The choice of regulatory system significantly affected physiological features (growth and productivity) over batch cultivation. Use of constitutive promoters resulted in poor growth during the exponential phase. Delaying expression of the assembled metabolic modules using the copper-inducible CUP1 promoter resulted in a 1.6-fold increase in the exponential-phase growth rate and a twofold increase in productivity in the post-exponential phase. However, repeated use of the CUP1 promoter in multiple expression cassettes resulted in genetic instability. A diauxie-inducible expression system, based on an engineered GAL regulatory circuit and a set of four different GAL promoters, was characterized and employed to assemble nerolidol synthetic metabolic modules. Nerolidol production was further improved by 60% to 392 mg L^-1 using this approach. Various carbon source systems were investigated in batch/fed-batch cultivation to regulate induction through the GAL system; final nerolidol titres of 4-5.5 g L^-1 were achieved, depending on the conditions.

CONCLUSION

Direct comparison of different transcriptional regulatory mechanisms clearly demonstrated that coupling the output strength to the fermentation stage is important to optimize the growth fitness and overall productivities of engineered cells in industrially relevant processes. Applying different well-characterized promoters with the same induction behaviour mitigates against the risks of homologous sequence-mediated genetic instability. Using these approaches, we significantly improved sesquiterpene production in yeast.

Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network

The evolutionary mechanisms leading to duplicate gene retention are well understood, but the long-term impacts of paralog differentiation on the regulation of metabolism remain underappreciated. Here we experimentally dissect the functions of two pairs of ancient paralogs of the GALactose sugar utilization network in two yeast species. We show that the Saccharomyces uvarum network is more active, even as over-induction is prevented by a second co-repressor that the model yeast Saccharomyces cerevisiae lacks. Surprisingly, removal of this repression system leads to a strong growth arrest, likely due to overly rapid galactose catabolism and metabolic overload. Alternative sugars, such as fructose, circumvent metabolic control systems and exacerbate this phenotype. We further show that S. cerevisiae experiences homologous metabolic constraints that are subtler due to how the paralogs have diversified. These results show how the functional differentiation of paralogs continues to shape regulatory network architectures and metabolic strategies long after initial preservation.

Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression

Evolutionary changes in transcription networks are an important source of diversity across species, yet the quantitative consequences of network evolution have rarely been studied. Here we consider the transcriptional 'rewiring' of the three GAL genes that encode the enzymes needed for cells to convert galactose to glucose. In Saccharomyces cerevisiae, the transcriptional regulator Gal4 binds and activates these genes. In the human pathogen Candida albicans (which last shared a common ancestor with S. cerevisiae some 300 million years ago), we show that different regulators, Rtg1 and Rtg3, activate the three GAL genes. Using single-cell dynamics and RNA-sequencing, we demonstrate that although the overall logic of regulation is the same in both species-the GAL genes are induced by galactose-there are major differences in both the quantitative response of these genes to galactose and in the position of these genes in the overall transcription network structure of the two species.

Perturbation of the interaction between Gal4p and Gal80p of the Saccharomyces cerevisiae GAL switch results in altered responses to galactose and glucose

In S. cerevisiae, following the Whole Genome Duplication (WGD), GAL1-encoded galactokinase retained its signal transduction function but lost basal expression. On the other hand, its paralogue GAL3, lost kinase activity but retained its signalling function and basal expression, thus making it indispensable for the rapid induction of the S. cerevisiae GAL switch. However, a gal3Δ strain exhibits delayed growth kinetics due to the redundant signalling function of GAL1. The subfunctionalization between the paralogues GAL1 and GAL3 is due to expression divergence and is proposed to be due to the alteration in the Upstream Activating Sequences (UASG ). We demonstrate that the GAL switch becomes independent of GAL3 by altering the interaction between Gal4p and Gal80p without altering the configuration of UASG . In addition to the above, the altered switch of S. cerevisiae loses ultrasensitivity and stringent glucose repression. These changes caused an increase in fitness in the disaccharide melibiose at the expense of a decrease in fitness in galactose. The above altered features of the ScGAL switch are similar to the features of the GAL switch of K. lactis that diverged from S. cerevisiae before the WGD.

GAL regulon of Saccharomyces cerevisiae performs optimally to maximize growth on galactose

The GAL regulon in Saccharomyces cerevisiae is a well-characterized genetic network that is utilized for the metabolism of galactose as an energy source. The network contains a transcriptional activator, Gal4p, which binds to its cognate-binding site to express GAL genes. Further, Gal80p and Gal3p are the repressor and galactose sensor, respectively, which are also under the regulation of GAL regulon. It is shown that the wild-type strain produces only about 80% of the maximum expression feasible from the regulon, which is observed in a mutant strain lacking Gal80p. This raises a fundamental question regarding the optimality of expression from the GAL regulon in S. cerevisiae. To address this issue, we evaluated the burden on growth due to the synthesis of GAL proteins in S. cerevisiae. The analysis demonstrated that both the media type and the extent of enzyme synthesized play a role in determining the burden on growth. We show that the burden can be quantified by relating to a parameter, β, the ratio of enzyme activity to the initial substrate concentration. The analysis demonstrated that the GAL regulon of the wild-type strain performed effectively to optimize growth on galactose.

Multiple genomic changes associated with reorganization of gene regulation and adaptation in yeast

Frequently during evolution, new phenotypes evolved due to novelty in gene regulation, such as that caused by genome rewiring. This has been demonstrated by comparing common regulatory sequences among species and by identifying single regulatory mutations that are associated with new phenotypes. However, while a single mutation changes a single element, gene regulation is accomplished by a regulatory network involving multiple interactive elements. Therefore, to better understand regulatory evolution, we have studied how mutations contributed to the adaptation of cells to a regulatory challenge. We created a synthetic genome rewiring in yeast cells, challenged their gene regulation, and studied their adaptation. HIS3, an essential enzyme for histidine biosynthesis, was placed exclusively under a GAL promoter, which is induced by galactose and strongly repressed in glucose. Such rewired cells were faced with significant regulatory challenges in a repressive glucose medium. We identified several independent mutations in elements of the GAL system associated with the rapid adaptation of cells, such as the repressor GAL80 and the binding sites of the activator GAL4. Consistent with the extraordinarily high rate of cell adaptation, new regulation emerged during adaptation via multiple trajectories, including those involving mutations in elements of the GAL system. The new regulation of HIS3 tuned its expression according to histidine requirements with or without these significant mutations, indicating that additional factors participated in this regulation and that the regulatory network could reorganize in multiple ways to accommodate different mutations. This study, therefore, stresses network plasticity as an important property for regulatory adaptation and evolution.

Galactose-Inducible promoters in Cryptococcus neoformans var. grubii

Inducible promoters are invaluable tools for modulating gene expression (turning transcription on or off) and have been a key approach for ascertaining gene essentiality in Cryptococcus neoformans. Galactose-inducible promoters have been successfully used in Saccharomyces cerevisiae to manipulate heterologous gene expression. Utilizing S. cerevisiae galactose-inducible genes in a BLAST search of the sequenced C. neoformans var. grubii genome, we found three potential galactose-inducible promoters, P(GAL1), P(GAL7), and P(UGE2) that are induced by galactose and repressed by glucose in this variety. This chapter describes how to make a fusion of these promoters with heterologous genes, how to insert the fused gene back into the genome, and how to induce expression during asexual and sexual growth in C. neoformans var. grubii.

New insights into galactose metabolism by Schizosaccharomyces pombe: isolation and characterization of a galactose-assimilating mutant

The fission yeast Schizosaccharomyces pombe cannot use galactose as a carbon or energy source, and little is known about galactose metabolism in this species. Here we report isolation of a galactose-assimilating mutant that grows on a medium containing galactose as a sole carbon source through use of a proofreading-deficient DNA polymerase δ variant encoded by cdc6-1. Based on comparative analysis of gene expression profiles in the wild-type and the mutant (FG2-8), we found that SPBPB2B2.10c (gal7+), SPBPB2B2.12c (gal10+) and SPBPB2B2.13 (gal1+), homologous to Saccharomyces cerevisiae GAL7, GAL10 and GAL1, respectively, and SPBPB2B2.08, SPBPB2B2.09c, and SPBPB2B2.11 that localize close to the gal genes, were highly expressed and dramatically induced by addition of galactose. The gal7Δ strain, carrying an integrated ura4+ marker at the gal7+ locus, grew on 5-fluoroorotic acid (5-FOA)-containing medium. In contrast, the FG2-8 gal7Δ strain could not grow on 5-FOA medium. In addition, expression of gal7+, SPBPB2B2.13, gal10+ and gal1+ genes increased in the wild-type strain when carried on a vector, and these transformants grew on galactose medium. We suggest that gal7+, gal10+, and gal1+ are localized close to a chromosomal terminal repressed by gene silencing in S. pombe. In contrast, gene silencing was defective in the FG2-8 strain making galactose assimilation possible.

Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: modeling and experiments reveal hierarchy in glucose repression

Background

Transcriptional regulation involves protein-DNA and protein-protein interactions. Protein-DNA interactions involve reactants that are present in low concentrations, leading to stochastic behavior. In addition, multiple regulatory mechanisms are typically involved in transcriptional regulation. In the GAL regulatory system of Saccharomyces cerevisiae, the inhibition of glucose is accomplished through two regulatory mechanisms: one through the transcriptional repressor Mig1p, and the other through regulating the amount of transcriptional activator Gal4p. However, the impact of stochasticity in gene expression and hierarchy in regulatory mechanisms on the phenotypic level is not clearly understood.

Results

We address the question of quantifying the effect of stochasticity inherent in these regulatory mechanisms on the performance of various genes under the regulation of Mig1p and Gal4p using a dynamic stochastic model. The stochastic analysis reveals the importance of both the mechanisms of regulation for tight expression of genes in the GAL network. The mechanism involving Gal4p is the dominant mechanism, yielding low variability in the expression of GAL genes. The mechanism involving Mig1p is necessary to maintain the switch-like response of certain GAL genes. The number of binding sites for Mig1p and Gal4p further influences the expression of the genes, with extra binding sites lowering the variability of expression. Our experiments involving growth on various substrates show that the trends predicted in mean expression and its variability are transmitted to the phenotypic level.

Conclusion

The mechanisms involved in the transcriptional regulation and their variability set up a hierarchy in the phenotypic response to growth on various substrates. Structural motifs, such as the number of binding sites and the mechanism of regulation, determine the level of stochasticity and eventually, the phenotypic response.

Yeast chromatin structure and regulation of GAL gene expression

Yeast genomic DNA is covered by nucleosome cores spaced by short, discrete length linkers. The short linkers, reinforced by novel histone properties, create a number of unique and dynamic nucleosome structural features in vivo: permanent unpeeling of DNA from the ends of the core, an inability to bind even full 147 bp core DNA lengths, and facility to undergo a conformational transition that resembles the changes found in active chromatin. These features probably explain how yeast can maintain most of its genome in a transcribable state and avoid large-scale packaging away of inactive genes. The GAL genes provide a closely regulated system in which to study gene-specific chromatin structure. GAL structural genes are inactive without galactose but are highly transcribed in its presence; the expression patterns of the regulatory genes can account for many of the features of GAL structural gene control. In the inactive state, GAL genes demonstrate a characteristic promoter chromosomal organization; the major upstream activation sequence (UASG) elements lie in open, hypersensitive regions, whereas the TATA and transcription start sites are in nucleosomes. This organization helps implement gene regulation in this state and may benefit the organism. Induction of GAL expression triggers Gal4p-dependent upstream nucleosome disruption. Disruption is transient and can readily be reversed by a Gal80p-dependent nucleosome deposition process. Both are sensitive to the metabolic state of the cell. Induction triggers different kinds of nucleosome changes on the coding sequences, perhaps reflecting the differing roles of nucleosomes on coding versus promoter regions. GAL gene activation is a complex process involving multiple Gal4p activities, numerous positive and negative cofactors, and the histone tails. DNA bending and chromosomal architecture of the promoter regions may also play a role in GAL regulation. Regulator-mediated competition between nucleosomes and the TATA binding protein complex for the TATA region is probably a central aspect of GAL regulation and a focal point for the numerous factors and processes that contribute to it.

Disruption of galactokinase signature sequence in gal3p of Saccharomyces cerevisiae does not lead to loss of signal transduction function

Gal3p of Saccharomyces cerevisiae is a 520-amino-acid residue protein, which activates the GAL genes in the presence of galactose by relieving the repression of Gal80p. It shows significant amino acid sequence homology to galactokinases but does not possess galactokinase activity. Deletion mutants of Gal3p were generated to identify the role of N-terminal amino acid residues required for function. The mutant versions of Gal3p could be detected on a Western blot. The Gal3p mutant lacking N-terminal 50-amino-acid residues which is disrupted for galactokinase signature sequence was found to be functional. These results suggest that the evolutionarily conserved galactokinase signature sequence present in known galactokinases may not have a role in Gal3p function.

Vectors allowing amplified expression of the Saccharomyces cerevisiae Gal3p-Gal80p-Gal4p transcription switch: applications to galactose-regulated high-level production of proteins

The Gal4, Gal80, and Gal3 proteins of Saccharomyces cerevisiae constitute a galactose-responsive regulatory switch for GAL gene promoters. The low cellular levels of these proteins have hampered mechanistic studies and limit the utility of the GAL gene promoters for high-yield production of endogenous and exogenous proteins. We have constructed two new vectors, pMEGA2 and pMEGA2-DeltaURA3, that increase the level of the Gal4p-Gal80p-Gal3p switch proteins under conditions that preserve the Gal3p-Gal80p-Gal4p stoichiometries required for normal switch function. Cells carrying pMEGA2 show 15- to 20-fold more Gal4p and 30- to 40-fold more Gal3p and Gal80p than cells lacking pMEGA2. These high levels of Gal4p, Gal80p, and Gal3p do not perturb the integrity of galactose-inducible regulation. Cells that carry pMEGA2 exhibit normal galactose-induction kinetics for the chromosomal MEL1 gene expression and normal, albeit slower, log-phase growth. Insertion of the MEL1 gene into pMEGA2 provides a 24- to 30-fold increase in the Mel1 protein. Cells carrying a 2-microm-based URA3-selectable plasmid containing a GAL1pro:lacZ reporter gene and a second plasmid, pMEGA2-DeltaURA3, produce 12-fold more beta-galactosidase than cells carrying only the GAL1pro:lacZ reporter plasmid. The performance of the MEGA plasmids in providing amplified production of the Gal3, Gal80, and Gal4 proteins should prove useful in investigations of the mechanistic aspects of these transcription switch proteins and in work aimed at achieving high-level, galactose-regulatable production of proteins in yeast.

Effect of ethanol on the production of carboxypeptidase Y using the GAL10 promoter in a Saccharomyces cerevisiae gal80 mutant

In the course of studying carboxypeptidase Y (CPY) production, we found that the expression level of the gene, which is under the control of the GAL10 promoter, increased in a Saccharomyces cerevisiae gal80 mutant grown in a medium containing ethanol as the sole carbon source. In the cultivation of the gal80 mutant KS58-2D/pCY303 carrying a multicopy plasmid, which contains the PRC1 gene fused to the GAL10 promoter, CPY production continued after the consumption of galactose. In this phase, the cells utilized ethanol as the carbon source. To increase the CPY production level, we examined the effect of carbon source feeding in a fed-batch culture. The production level in the fed-batch culture using ethanol was 1.3-fold higher than that in a batch culture and 1.6-fold higher than that in a fed-batch culture using galactose. By 5'-deletion analysis of the GAL10 promoter, the region between -256 and -232 was found to be important for the promoter activity in the gal80 mutant growing in the presence of ethanol.

Expression of human inositol monophosphatase suppresses galactose toxicity in Saccharomyces cerevisiae: possible implications in galactosemia

A suppressor of galactose toxicity in a gal7 yeast strain (lacking galactose 1-phosphate uridyl transferase) has been isolated from a HeLa cell cDNA library. Analysis of the plasmid clone indicated that the insert has an ORF identical to that of hIMPase (human myo-inositol monophosphatase). The ability of hIMPase to suppress galactose toxicity is sensitive to the presence of Li(+) in the medium. A gal7 yeast strain harboring a plasmid containing cloned hIMPase grows on galactose as a sole carbon source. hIMPase mediated galactose metabolism is dependent on the functionality of GAL1 as well as GAL10 encoded galactokinase and epimerase respectively. These results predicted that the UDP-glucose/galactose pyrophosphorylase mediated pathway may be responsible for the relief of galactose toxicity. Experiments conducted to test this prediction revealed that expression of UGP1 encoded UDP-glucose pyrophosphorylase can indeed overcome the relief of galactose toxicity. Moreover, expression of UGP1 allows a gal7 strain to grow on galactose as a sole carbon source. Unlike the hIMPase mediated relief of galactose toxicity, UGP1 mediated relief of galactose toxicity is lithium insensitive. Based on our results and on the basis of available information on galactose toxicity, we suggest an alternative explanation for the molecular mechanism of galactose toxicity.

Glucose signaling in yeast is partially mimicked by galactose and does not require the Tps1 protein

Glucose produces multiple effects in Saccharomyces cerevisiae, as it controls the expression of many genes and the activity of various enzymes. However, the elements involved in glucose signaling are not well characterized. In this work the capacity of galactose to bring about the same effects than glucose has been assessed. Galactose mimics glucose only partially; it is suggested that it does not interact with a "sensor" in the plasma membrane and that it produces a weaker intracellular signal than glucose. To examine whether trehalose-6P synthase (Tps1) is required to transduce the glucose signal, we have constructed a tps1 hxk2/tps1 HXK2 strain which, at difference of a tps1 strain, grows on glucose, and, at difference of a tps1 hxk2 strain, still possess the Hxk2 protein, possibly involved in glucose repression. From the response of this strain to glucose, we conclude that Tps1 does not play a prominent role in glucose signaling.

The cysteine-peptidase bleomycin hydrolase is a member of the galactose regulon in yeast

Bleomycin hydrolase is a cysteine peptidase discovered through its ability to detoxify the anti-cancer glycopeptide, bleomycin. Although found in all tissues in mammals and in both eukaryotes and prokaryotes, the normal cellular function of this peptidase is not known. We had previously reported the purification of bleomycin hydrolase from yeast based on its unexpected ability to bind DNA. Recently we collaborated in solving the crystal structure of this protein, revealing a hexameric ring organization. We now report that the molecular characterization of the gene encoding yeast bleomycin hydrolase is also surprising. The transcription of the gene is regulated by galactose. Furthermore, this regulation is conveyed by a binding site for the Gal4 regulatory protein in its promoter, prompting the designation of this gene as GAL6. Gal6p also appears to have a negative effect on the GAL system as a deletion of the gene leads to a 2-5-fold higher expression of the GAL1, GAL2, GAL7, and MEL1 genes. The GAL6 deletion does not affect the expression of another inducible gene, HSP26. Neither the peptidase nor the nucleic acid binding activity of Gal6p as assayed is apparently required to convey this regulation, implying yet another function for this new member of the GAL regulon.

Meiotic inheritance of functional Gal80S gene product in Saccharomyces cerevisiae

Transcription factors inherited during meiosis play a crucial role directing subsequent gene activity. Factors of maternal origin have been shown to influence the pattern of early zygotic transcription during Drosophila and Xenopus embryogenesis. Nevertheless, little is known regarding the meiotic inheritance of the vast majority of transcription factors. In the case of yeast meiosis, for example, it is not yet known whether any of the multitude of transcription factors expressed in the diploid are transmitted to haploid spores in functional form. Here we use a GAL1-STE4 reporter whose activity is detectable in single living cells to identify a transcription factor inherited during sporulation in Saccharomyces cerevisiae. We show that functional Gal80S repressor is meiotically inherited at levels reflecting its expression in the diploid parent.

GAL4/GAL80-dependent nucleosome disruption/deposition on the upstream regions of the yeast GAL1-10 and GAL80 genes

Metabolic reactivation (incubating spheroplasts with galactose and casamino acids) causes disruption of nucleosomes from the upstream regions of the yeast GAL1, GAL10, and GAL80 genes. The disruption is specific. It depends on the transcription activator Gal4; it only occurs in galactose-reactivated chromatin from galactose-grown cells; it only affects upstream region, gene-proximal nucleosomes. Due to this specificity and because some of the same regions have shown induction-dependent changes by in vivo analyses, we suggest that the nucleosome-disrupted structure produced by reactivation is the authentic chromatin structure for these regions under conditions of galactose-induced GAL1-10 and GAL80 expression. It is necessary to carry out a spheroplast reactivation treatment in order to observe this disrupted structure in nuclear chromatin because nucleosomes are redeposited onto these regions during the preliminary steps of nuclear isolation (cell harvest/spheroplast preparation) probably in response to the nonphysiological conditions associated with these steps. However, during the same isolation procedures in cells lacking Gal80 protein, there is no nucleosome deposition on these regions, and the in vivo disrupted structure remains present in the nuclear chromatin. Therefore, the nucleosome deposition process that operates in wild-type cells is dependent on Gal80 protein, defining another activity of this negative regulator.

S-phase-promoting cyclin-dependent kinases prevent re-replication by inhibiting the transition of replication origins to a pre-replicative state

BACKGROUND

DNA replication and mitosis are triggered by activation of kinase complexes, each made up of a cyclin and a cyclin-dependent kinase (Cdk). It had seemed possible that the association of Cdks with different classes of cyclins specifies whether S phase (replication) or M phase (mitosis) will occur. The recent finding that individual B-type cyclins (encoded by the genes CLB1-CLB6) can have functions in both processes in the budding yeast Saccharomyces cerevisiae casts doubt on this notion.

RESULTS

S. cerevisiae strains lacking C1b1-C1b4 undergo DNA replication once but fail to enter mitosis. We have isolated mutations in two genes, SIM1 and SIM2 (SIM2 is identical to SEC72), which allow such cells to undergo an extra round of DNA replication without mitosis. The Clb5 kinase, which promotes S phase, remains active during the G2-phase arrest of cells of the parental strain, but its activity declines rapidly in sim mutants. Increased expression of the CLB5 gene prevents re-replication. Thus, a cyclin B-kinase that promotes DNA replication in G1-phase cells can prevent re-replication in G2-phase cells. Inactivation of C1b kinases by expression of the specific C1b-Cdk1 inhibitor p40SIC1 is sufficient to induce a prereplicative state at origins of replication in cells blocked in G2/M phase by nocodazole. Re-activation of C1b-Cdk1 kinases induces a second round of DNA replication.

CONCLUSIONS

We propose that S-phase-promoting cyclin B--Cdk complexes prevent re-replication during S, G2 and M phases by inhibiting the transition of replication origins to a pre-replicative state. This model can explain both why origins 'fire' only once per S phase and why S phase is dependent on completion of the preceding M phase.

Requirement for RGR1 and SIN4 in RME1-dependent repression in Saccharomyces cerevisiae

RME1 is a zinc-finger protein homolog that functions as a repressor of the meiotic activator IME1. RME1 is unusual among yeast repressors in two respects: it acts over a considerable distance (2 kbp) and it can activate transcription from a binding site separated from its natural flanking region. To identify genes required for RME1 to exert repression, we have selected mutants with improved RME1-dependent activation. One rare mutant was defective in RME1-dependent repression of an artificial reporter gene as well as the native IME1 gene. The mutation permits sporulation of a/a diploids, which express RME1 from its natural promoter, and of a/alpha diploids constructed to express RME1 from the GAL1 promoter. The mutation also causes temperature-sensitive growth and a methionine or cysteine requirement. Analysis of a complementing genomic clone indicates that the mutation lies in a known essential gene, RGR1. Prior studies have indicated a functional relationship between RGR1 and SIN4 (also called TSF3); we have found that a sin4 null mutation also causes a defect in RME1-dependent repression and a methionine or cysteine requirement. The rgr1 and sin4 mutations do not cause a reduction of RME1 polypeptide levels. The defect in RME1-dependent repression may result from effects of sin4 and, presumably, rgr1 on chromatin structure.

Fermentation of lactose by yeast cells secreting recombinant fungal lactase

Strains of Saccharomyces cerevisiae transformed with a yeast multicopy expression vector carrying the cDNA for Aspergillus niger secretory beta-galactosidase under the control of ADH1 promoter and terminator were studied for their fermentation properties on lactose (V. Kumar, S. Ramakrishnan, T. T. Teeri, J. K. C. Knowles, and B. S. Hartley, Biotechnology 10:82-85, 1992). Lactose was hydrolyzed extracellularly into glucose and galactose, and both sugars were utilized simultaneously. Diauxic growth patterns were not observed. However, a typical biphasic growth was observed on a mixture of glucose and galactose under aerobic and anaerobic conditions with transformants of a haploid S. cerevisiae strain, GRF167. Polyploid distiller's yeast (Mauri) transformants were selected simply on the basis of the cloned gene expression on X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside) plates. Rapid and complete lactose hydrolysis and higher ethanol (0.31 g/g of sugar) and biomass (0.24 g/g of sugar) production were observed with distiller's yeast grown under aerobic conditions. A constant proportion (10%) of the population retained the plasmid throughout the fermentation period (48 h). Nearly theoretical yields of ethanol were obtained under anaerobic conditions on lactose, glucose, galactose, and whey permeate media. However, the rate and the amount of lactose hydrolysis were lower under anaerobic than aerobic conditions. All lactose-grown cells expressed partial galactokinase activity.

HTS1 encodes both the cytoplasmic and mitochondrial histidyl-tRNA synthetase of Saccharomyces cerevisiae: mutations alter the specificity of compartmentation

Genetic and biochemical evidence shows that a single nuclear gene HTS1 encodes both the mitochondrial and cytoplasmic histidyl-tRNA synthetases (Hts). The gene specifies two messages, one with two in-frame ATGs (-60 and +1) and another with only the downstream ATG (+1). We have made a new set of mutations that enables us to express only the mitochondrial or the cytoplasmic form and compared the subcellular distribution of the Hts1 protein in these mutants and wild type, using an antibody that interacts with both the mitochondrial and cytoplasmic Hts1 as well as Hts1::LacZ fusions. Mutations in the upstream ATG (-60) or frameshift mutations in the presequence affect only the mitochondrial enzyme and not the cytoplasmic enzyme. Mutations in the downstream ATG (+1 ATG to ATC) destroy the function of the cytosolic enzyme, but do not affect the function of the mitochondrial enzyme. Overexpression of this construct restores cytoplasmic function. Cells expressing a truncated form of Hts containing a deletion of the first 20 amino-terminal residues (Htsc) produce a functional cytoplasmic enzyme, which does not provide mitochondrial function. Overexpression of this truncated cytoplasmic protein provides mitochondrial function and produces detectable levels of the synthetase in the mitochondrion. These experiments suggest that Hts1 contains two domains that together allow efficient localization of Htsm to the mitochondrion: an amino-terminal presequence in the mitochondrial precursor that is likely cleaved upon delivery to the mitochondrion and a second amino-terminal sequence (residues 21-53) present in both the precursor and the cytoplasmic form. Neither one by itself is sufficient to act as an efficient mitochondrial targeting signal. Using our antibody we have been able to detect a protein of increased molecular mass that corresponds to that of the predicted precursor. Taken together these studies show that the specificity of compartmentation of the Hts protein depends upon both the primary sequence and the concentration of the protein in the cell.

Inhibition of cell proliferation in Saccharomyces cerevisiae by expression of human NAD+ ADP-ribosyltransferase requires the DNA binding domain ("zinc fingers")

Constitutive expression of human nuclear NAD+: protein ADP-ribosyltransferase (polymerizing) [pADPRT; poly(ADP-ribose)polymerase; EC 2.4.2.30] as an active enzyme in Saccharomyces cerevisiae, under the control of the alcohol dehydrogenase promoter, was only possible with simultaneous inhibition of ADP-ribosylation by 3-methoxybenzamide. Induction of fully active pADPRT from the inducible galactose epimerase promoter resulted in inhibition of cell division and morphological changes reminiscent of cell cycle mutants. Expression of a pADPRT cDNA truncated at its 5' end had no influence on cell proliferation at all. Obviously the amino-terminal part of the DNA binding domain containing the first "zinc finger", which is essential for inducibility of pADPRT activity by DNA breaks, is also required for inhibition of cell growth on expression in yeast. Full-length as well as truncated pADPRT molecules were directed to the cell nucleus where the fully active enzyme produced large amounts of poly(ADP-ribose) by automodification. Since pADPRT turned out to be the only target for ADP-ribosylation in these cells, elevated levels of poly(ADP-ribose) were the most likely cause of inhibition of cell division, presumably resulting from interaction with chromosomal proteins.

Cloning of the Schwanniomyces occidentalis glucoamylase gene (GAM1) and its expression in Saccharomyces cerevisiae

The Schwanniomyces occidentalis glucoamylase (GAM)-encoding gene (GAM1) was isolated from a lambda Charon4A genomic library using synthetic oligodeoxynucleotides as probes. GAM1 contains an ORF of 2874 nucleotides (nt) coding for 958 amino acids. S1 mapping revealed that the transcript has only a very short 5'-untranslated leader of 8-12 nt. Disruption and displacement of the GAM1 gene in Sc. occidentalis resulted in loss of the ability to grow on starch efficiently. The gam1 strains still exhibit low GAM activity suggesting that at least a second weakly expressed GAM-encoding gene (GAM2) is present in Sc. occidentalis. Expression of the Sc. occidentalis GAM1 gene in Saccharomyces cerevisiae was achieved after promoter exchange. S. cerevisiae cells transformed with centromere plasmids carrying the GAM1 gene fused to promoters of different S. cerevisiae genes, namely GAL1, PDC1 and ADH1, efficiently secrete GAM and are able to grow with soluble starch as a sole carbon source. The essential enzymatic properties of the GAMs secreted from S. cerevisiae and Sc. occidentalis are identical, although the modifications of the proteins are different.

A new family of polymorphic genes in Saccharomyces cerevisiae: alpha-galactosidase genes MEL1-MEL7

Using genetic hybridization analysis we identified seven polymorphic genes for the fermentation of melibiose in different Mel+ strains of Saccharomyces cerevisiae. Four laboratory strains (1453-3A, 303-49, N2, C.B.11) contained only the MEL1 gene and a wild strain (VKM Y-1830) had only the MEL2 gene. Another wild strain (CBS 4411) contained five genes: MEL3, MEL4, MEL5, MEL6 and MEL7. MEL3-MEL7 were isolated and identified by backcrosses with Mel- parents (X2180-1A, S288C). A cloned MEL1 gene was used as a probe to investigate the physical structure and chromosomal location of the MEL gene family and to check the segregation of MEL genes from CBS 4411 in six complete tetrads. Restriction and Southern hybridization analyses showed that all seven genes are physically very similar. By electrokaryotyping we found that all seven genes are located on different chromosomes: MEL1 on chromosome II as shown previously by Voll-rath et al. (1988), MEL2 on VII, MEL3 on XVI, MEL4 on XI, MEL5 on IV. MEL6 on XIII, and MEL7 on VI. Molecular analysis of the segregation of MEL genes from strain CBS 4411 gave results identical to those from the genetic analyses. The homology in the physical structure of this MEL gene family suggests that the MEL loci have evolved by transposition of an ancestral gene to specific locations within the genome.

Analysis of the GAL3 signal transduction pathway activating GAL4 protein-dependent transcription in Saccharomyces cerevisiae

The Saccharomyces cerevisiae GAL/MEL regulon genes are normally induced within minutes of galactose addition, but gal3 mutants exhibit a 3-5-day induction lag. We have discovered that this long-term adaptation (LTA) phenotype conferred by gal3 is complemented by multiple copies of the GAL1 gene. Based on this result and the striking similarity between the GAL3 and GAL1 protein sequences we attempted to detect galactokinase activity that might be associated with the GAL3 protein. By both in vivo and in vitro tests the GAL3 gene product does not appear to catalyze a galactokinase-like reaction. In complementary experiments, Escherichia coli galactokinase expressed in yeast was shown to complement the gal1 but not the gal3 mutation. Thus, the complementation activity provided by GAL1 is not likely due to galactokinase activity, but rather due to a distinct GAL3-like activity. Overall, the results indicate that GAL1 encodes a bifunctional protein. In related experiments we tested for function of the LTA induction pathway in gal3 cells deficient for other gene functions. It has been known for some time that gal3gal1, gal3gal7, gal3gal10, and gal3 rho- are incapable of induction. We constructed isogenic haploid strains bearing the gal3 mutation in combination with either gal15 or pgi1 mutations: the gal15 and pgi1 blocks are not specific for the galactose pathway in contrast to the gal1, gal7 and gal10 blocks. The gal3gal5 and gal3pgi1 double mutants were not inducible, whereas both the gal5 and pgi1 single mutants were inducible. We conclude that, in addition to the GAL3-like activity of GAL1, functions beyond the galactose-specific GAL1, GAL7 and GAL10 enzymes are required for the LTA induction pathway.

Transcriptional control by galactose of a yeast gene encoding a protein homologous to mammalian aldo/keto reductases

Expression of the S. cerevisiae gene, GCY, encoding a 35-kDa protein with striking homology to mammalian aldo/keto reductases, is under the control of galactose: the intracellular concentration of the respective mRNA (about 1300 nt in length) varies strongly with the carbon source. It is particularly high when galactose is the sole energy source but is low as soon as glucose is present. Lactate, glycerol and raffinose lead to intermediate expression. Both Northern blot analyses and lacZ fusion data indicate a 20- to 50-fold increase in the steady state concentrations of mRNA and beta Gal activity, respectively, when grown on galactose as compared to glucose. The gene is derepressed after cultivation on glycerol in the wt and in a gal80 mutant background but remains uninducible by galactose in strains carrying either a gal2 or a gal4 mutation, affecting galactose permease and the GAL gene trans-activator, respectively. Analysis of GCY expression in gal regulatory mutants reveals epistasis interactions of the gal4 and the gal80 mutations as expected if GCY is regulated by the Gal control system. Repression of GCY transcription by glucose is observed in all three above gal mutant strains. The results suggest that the gene is both positively controlled by galactose and negatively by glucose. Analysis of a set of upstream deletions identifies a single UAS matching the consensus for GAL gene upstream regulation sites. By contrast to other genes regulated by galactose, disruption mutants of GCY exhibit no obvious phenotype, and in particular do not lose the ability to grow on and adapt to galactose. Enzyme tests with AKR-specific substrates suggest that GCY encodes a carbonyl reductase.

The genetic control of direct-repeat recombination in Saccharomyces: the effect of rad52 and rad1 on mitotic recombination at GAL10, a transcriptionally regulated gene

We have previously shown direct-repeat recombination events leading to loss of a plasmid integrated at the GAL10 locus in Saccharomyces cerevisiae are stimulated by transcription of the region. We have examined the role of two recombination- and repair-defective mutations, rad1 and rad52, on direct repeat recombination in transcriptionally active and inactive sequences. We show that the RAD52 gene is required for transcription-stimulated recombination events leading to loss of the integrated plasmid. Similarly, Gal+ events between the duplicated repeats that retain the integrated plasmid DNA (Gal+ Ura+ replacement events) are reduced 20-fold in the rad52 mutant in sequences that are constitutively expressed. In contrast, in sequences that are not expressed, the rad52 mutation reduces plasmid loss events by only twofold and Gal+ Ura+ replacements by fourfold. We also observe an increase in disome-associated plasmid loss events in the rad52 mutant, indicative of chromosome gain. This event is not affected by expression of the region. Plasmid loss events in rad1 mutant strains are reduced only twofold in transcriptionally active sequences and are not affected in sequences that are repressed. However, the rad1 and rad52 double mutant shows a decrease in plasmid loss events greater than the sum of the decreases in the rates of this event displayed by either single mutant in both constitutive and repressed DNA, indicating a synergistic interaction between these two genes. The synergism is limited to recombination since the rad1 rad52 double mutant is no more sensitive when compared with either single mutant in its ability to survive radiation damage. Finally, the recombination pathway that remains in the double mutant is positively affected by transcription of the region.

Elevated recombination rates in transcriptionally active DNA

We have examined the effect of RNA polymerase II-dependent transcription on recombination between directly repeated sequences of the GAL10 gene in S. cerevisiae. Direct repeat recombination leading either to plasmid loss or conversion was examined in isogenic strains containing null mutations in the positive activator, GAL4, or the repressor, GAL80. A 15-fold increase in the rate of plasmid loss is observed in cells constitutively expressing the construct compared with cells that are not. Conversion events that retain the integrated plasmid are not stimulated by expression of the repeats. Northern analysis of strains containing plasmid inserts with various promoter mutations suggests that the stimulation in recombination is mediated by events initiating within the integrated plasmid sequences.

Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast

Arrays of nucleosomes were positioned with respect to the GAL1-GAL10 intergenic region inserted into Saccharomyces cerevisiae minichromosomes. Deletions of DNA flanking the upstream activation sequence left the array unaltered, showing that nucleosome positioning was not a consequence of sequence-specific histone-DNA interactions but depended on proximity to the galactose-responsive upstream activation sequence (UASG). Replacement of the upstream activation sequence by synthetic oligonucleotides with different protein-binding properties identified a short sequence within this region that is responsible for the ordered array. This sequence overlaps a binding site for GAL4 protein, a positive regulator of transcription, but exerts its effect on chromatin structure independently of GAL4, probably through binding a novel factor that is not GAL-specific.

A new class of yeast transcriptional activators

We describe yeast transcriptional activators encoded by E. coli genomic DNA fragments fused to the coding sequence of the DNA-binding portion of GAL4. All of the new activating sequences that we have analyzed, like those of GAL4 and GCN4, are acidic; most of these sequences show no obvious sequence homology when compared with the identified activating regions of GAL4 and GCN4 or among themselves. We also describe a fusion protein that contains no yeast protein sequence but activates transcription in yeast.

The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80

In wild-type yeast the action of the transcriptional activator GAL4 is inhibited by GAL80, and galactose relieves this inhibition. We show that deletion mutants of GAL4 lacking 30 amino acids of the carboxyl terminus activate transcription constitutively, whereas other deletion mutants bearing the carboxy-terminal 30 amino acids are inhibited by GAL80. Moreover, GAL4 fragments bearing these 30 amino acids, when expressed from a strong promoter on multicopy plasmids, free the endogenous GAL4 from inhibition by GAL80. These and other results suggest that GAL80 recognizes the carboxy-terminal 30 amino acids of GAL4, forming a complex that, though bound to DNA, does not activate transcription.

Interaction of positive and negative regulatory proteins in the galactose regulon of yeast

Transcriptional regulation in the galactose regulon of yeast is determined by an interplay between a positive regulatory protein, GAL4, and a negative regulatory protein, GAL80. We show that derivatives of GAL4 missing as few as 28 carboxy-terminal amino acids are not responsive to GAL80 regulation, implying that the carboxyl terminus of GAL4 is required for interaction with GAL80. Furthermore, a lesion in GAL4 that genetically defines the GAL80-interactive region maps to the 3' end of the gene. Since the carboxyl terminus of GAL4 has also been implicated in interaction with a transcriptional factor, we propose a model for negative regulation in which GAL80 and this factor compete for binding a common region of GAL4, and the on/off state of transcription is determined by the relative affinities of the negative regulator and the transcriptional factor for this region.

Transcription of multiple copies of the yeast GAL7 gene is limited by specific factors in addition to GAL4

High levels of the GAL7 gene in the yeast cell appear to titrate regulatory factors and to impair transcription of related sequences. To investigate the role that the GAL regulatory factors GAL4 and GAL80 have in this process we have compared the accumulation of mRNA transcribed from single-copy (plasmid-borne GAL7 and chromosomal GAL10) and high-copy (plasmid-borne GAL7) genes in several GAL regulatory mutants. Our results show that functional GAL4 gene product is required for induction of transcription from the single- and high-copy genes. In a strain containing the GAL4 gene fused to the high expression ADH1 promoter, glucose can replace galactose to induce high levels of transcription of GAL7 and GAL10 genes, although the kinetics of accumulation induced by the two sugars are distinctly different. In the presence of high levels of GAL4, maximum accumulation of mRNA from single and high copy genes is elevated two-fold; disruption of the gal80 gene in combination with high levels of GAL4 results in a further two-fold increase in transcription. In this genetic background, galactose-induced transcription of the high copy GAL7 gene results in a greater than 50-fold increase in the levels of GAL7 mRNA, representing 30%-50% of the total cellular mRNA. Our results are consistent with a cooperative effect of saturation of multiple GAL4 DNA binding sites and with a limiting factor, in addition to GAL4, that is required for transcription of the GAL genes.

Cell cycle regulation of SW15 is required for mother-cell-specific HO transcription in yeast

In haploid homothallic yeast, cell division gives rise to a mother cell that transiently transcribes the HO gene (as it undergoes START) and a daughter cell that does not. Consequently, only mother cells switch their mating types. Here, we test the proposition that a transcription factor called SWI5 is the "determinant" of mother-cell-specific HO transcription; that is, that SWI5 is the only factor missing in daughter cells. We show that SWI5 RNAs are cell-cycle regulated so that they are only produced after the post-START window of HO transcription. This regulation is vital for mother-cell specificity since constitutive transcription of SWI5 causes daughter cells to switch their mating types. We propose that SWI5 gene products are partitioned asymmetrically at cell division.

Autogenous regulation of the Saccharomyces cerevisiae regulatory gene GAL80

We have suggested previously from Northern blot analysis that transcription of the negative regulatory gene GAL80 was controlled positively by another regulatory gene GAL4, and negatively by GAL80 itself, in similar way to GAL1, GAL7 and GAL10 genes encoding galactose-metabolizing enzymes in Saccharomyces cerevisiae. To study further the controlled expression of GAL80, we have exploited the gene fusion technique. We constructed gene fusions consisting of 5' fragments of GAL80 and a 5' truncated lacZ of Escherichia coli, and introduced the GAL80'-'lacZ fusions into wild-type yeast or various GAL4 or GAL80 mutants using multiple-copy or single-copy plasmid vectors. We then studied beta-galactosidase activity in the resultant transformants under uninduced, induced or glucose-repressed conditions. Expression of the GAL80'-'lacZ fusions was clearly under the control of Gal4/Gal80. Next we constructed GAL7'-'lacZ fusions, whose upstream activating sequence (UAS) from GAL7 was replaced with a GAL80 fragment containing a UAS-like sequence located in the 5' flanking region of GAL80. Synthesis of beta-galactosidase directed by the hybrid genes was inducible by galactose exactly like the original GAL7'-'lacZ fusion with a UAS from GAL7. Finally we constructed a GAL7-GAL80 hybrid gene, in which the entire 5' flanking region was derived from GAL7. When the chromosomal GAL80 gene in wild-type yeast was replaced with the hybrid gene, the uninduced level, but not the induced level, of the GAL10-encoded enzyme (uridine diphosphoglucose-4-epimerase) was significantly increased.

Regulated overproduction of the GAL4 gene product greatly increases expression from galactose-inducible promoters on multi-copy expression vectors in yeast

High-level, galactose-inducible expression originating from GAL promoters in Saccharomyces cerevisiae is mediated by highly specific interactions between the GAL4-coded protein and nucleotide sequences. The potential utility of recombinant GAL promoter/foreign gene constructions for the regulatable and high-level expression of foreign proteins in yeast is well recognized. However, the utility of this system is limited severely in the case of multiple copies of such constructions due to the very low level of the GAL4-coded protein and to the loss of inducibility which occurs if levels of the GAL4 protein are amplified constitutively. To surmount these limitations, we have constructed a novel yeast strain which overproduces the GAL4 protein in a regulated fashion. This 'integrant' strain contains an integrated copy of a hybrid gene consisting of the galactose-inducible GAL10 promoter fused to the GAL4 structural gene. In the absence of galactose, the integrant strain and the isogenic 'non-integrant' parental strain show only a basal level of transcription from the constitutively active chromosomal GAL4 gene. However, following the addition of galactose to the culture medium, the 'integrant' strain synthesizes at least 20-fold more GAL4 mRNA and substantially more GAL4 protein than the 'non-integrant' strain. A high-copy-number expression vector containing the GAL10 promoter and alpha mating factor pre-pro leader fused to the structural gene for Epstein-Barr virus gp350 was introduced into both types of cells. The resulting transformed 'integrant' cells produced approximately five-fold more gp350 mRNA and ten-fold more gp350-related proteins than the transformed 'non-integrant' cells following galactose induction. This 'integrant' strain should prove generally useful for the maximal, regulated expression in yeast of structural genes driven by a galactose-inducible promoter.