Three aromatic amino acid residues critical for galactose transport in yeast Gal2 transporter

Identification of key residues for efficient glucose transport by the hexose transporter CgHxt4 in high sugar fermentation yeast Candida glycerinogenes

Efficient hexose transporters are essential for the development of industrial yeast strains with high fermentation performance. We previously identified a hexose transporter, CgHxt4, with excellent sugar uptake performance at ultra-high glucose concentrations (200 g/L) in the high sugar fermenting yeast C. glycerinogenes. To understand the working mechanism of this transporter, we constructed 87 mutants and examined their glucose uptake performance. The results revealed that five residues (N321, N322, F325, G426, and P427) are essential for the efficient glucose transport of CgHxt4. Subsequently, we focused our analysis on the roles of N321 and P427. Specifically, N321 and P427 are likely to play a role in glucose coordination and conformational flexibility, respectively. Our results help to expand the application potential of this transporter and provide insights into the working mechanism of yeast hexose transporter. KEY POINTS: • Five residues, transmembrane segments 7 and 10, were found to be essential for CgHxt4. • N321 and P427 are likely to play a role in glucose coordination and conformational flexibility, respectively. • Chimeric CgHxt5.4TM7 significantly enhanced the performance of CgHxt5.

Glucose regulation of the paralogous glucose sensing receptors Rgt2 and Snf3 of the yeast Saccharomyces cerevisiae

BACKGROUND

The yeast Saccharomyces cerevisiae senses extracellular glucose levels through the two paralogous glucose sensing receptors Rgt2 and Snf3, which appear to sense high and low levels of glucose, respectively.

METHODS

Western blotting and qRT-PCR were used to determine expression levels of the glucose sensing receptors.

RESULTS

Rgt2 and Snf3 are expressed at different levels in response to different glucose concentrations. SNF3 expression is repressed by high glucose, whereas Rgt2 is turned over in response to glucose starvation. As a result, Rgt2 is predominant in cells grown on high glucose, whereas Snf3 is more abundant of the two paralogs in cells grown on low glucose. When expressed from a constitutive promoter, however, Snf3 behaves like Rgt2, being able to transduce the high glucose signal that induces HXT1 expression. Of note, constitutively active Rgt2 does not undergo glucose starvation-induced endocytic downregulation, whereas signaling defective Rgt2 is constitutively targeted for vacuolar degradation. These results suggest that glucose protects Rgt2 from endocytic degradation and reveal a previously unknown function of glucose as a signaling molecule that regulates the stability of its receptor.

CONCLUSION

Expression of Rgt2 and Snf3 is regulated by different mechanisms: Rgt2 expression is highly regulated at the level of protein stability; Snf3 expression is mainly regulated at the level of transcription.

GENERAL SIGNIFICANCE

The difference in the roles of Rgt2 and Snf3 in glucose sensing is a consequence of their cell surface abundance rather than a result of the two paralogous proteins having different functions.

Reverse Evolution of a Classic Gene Network in Yeast Offers a Competitive Advantage

Glucose repression is a central regulatory system in yeast that ensures the utilization of carbon sources in a highly economical manner. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that a Saccharomyces cerevisiae (S. cerevisiae) lineage in spontaneously fermented milk has swapped all its structural GAL genes (GAL2 and the GAL7-10-1 cluster) with early diverged versions through introgression. The rewired GAL network has abolished glucose repression and conversed from a strictly inducible to a constitutive system through polygenic changes in the regulatory components of the network, including a thymine (T) to cytosine (C) and a guanine (G) to adenine (A) transition in the upstream repressing sequence (URS) sites of GAL1 and GAL4, respectively, which impair Mig1p-mediated repression, loss of function of the repressor Gal80p through a T146I substitution in the protein, and subsequent futility of GAL3. Furthermore, the milk lineage of S. cerevisiae has achieved galactose-utilization rate elevation and galactose-over-glucose preference switch through the duplication of the introgressed GAL2 and the loss of function of the main glucose transporter genes HXT6 and HXT7. In addition, we demonstrate that GAL2 requires GAL7 or GAL10 for its expression, and Gal2p likely requires Gal1p for its transportation function in the milk lineage of S. cerevisiae. We show a clear case of reverse evolution of a classic gene network for ecological adaptation and provide new insights into the regulatory model of the canonical GAL network.

Expansion and Diversification of MFS Transporters in Kluyveromyces marxianus

In yeasts, proteins of the Major Superfamily Transporter selectively bind and allow the uptake of sugars to permit growth on varied substrates. The genome of brewer’s yeast, Saccharomyces cerevisiae, encodes multiple hexose transporters (Hxt) to transport glucose and other MFS proteins for maltose, galactose, and other monomers. For sugar uptake, the dairy yeast, Kluyveromyces lactis, uses Rag1p for glucose, Hgt1 for glucose and galactose, and Lac12 for lactose. In the related industrial species Kluyveromyces marxianus, there are four genes encoding Lac12-like proteins but only one of them, Lac12, can transport lactose. In this study, which initiated with efforts to investigate possible functions encoded by the additional LAC12 genes in K. marxianus, a genome-wide survey of putative MFS sugar transporters was performed. Unexpectedly, it was found that the KHT and the HGT genes are present as tandem arrays of five to six copies, with the precise number varying between isolates. Heterologous expression of individual genes in S. cerevisiae and mutagenesis of single and multiple genes in K. marxianus was performed to establish possible substrates for these transporters. The focus was on the sugar galactose since it was already reported in K. lactis that this hexose was a substrate for both Lac12 and Hgt1. It emerged that three of the four copies of Lac12, four Hgt-like proteins and one Kht-like protein have some capacity to transport galactose when expressed in S. cerevisiae and inactivation of all eight genes was required to completely abolish galactose uptake in K. marxianus. Analysis of the amino acid sequence of all known yeast galactose transporters failed to identify common residues that explain the selectivity for galactose. Instead, the capacity to transport galactose has arisen three different times in K. marxianus via polymorphisms in proteins that are probably ancestral glucose transporters. Although, this is analogous to S. cerevisiae, in which Gal2 is related to glucose transporters, there are not conserved amino acid changes, either with Gal2, or among the K. marxianus galactose transporters. The data highlight how gene duplication and functional diversification has provided K. marxianus with versatile capacity to utilise sugars for growth.

RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium

Calcium (Ca) is required for normal growth and is involved in cellular physiology, signal transduction, and bone mineralization. In humans, inadequate Ca intake causes hypocalcaemia, and excessive Ca intake causes hypercalcemia. In chicken, Ca is also required for body weight gain and eggshell formation. However, transcriptomic responses to low/high Ca intake, and mechanisms affecting body weight have not been explored. In this study, we performed comparative RNA sequencing (RNA-seq) using the kidney of broiler chickens fed diets containing 0.8, 1.0, and 1.2% Ca. Annotation of RNA-seq data revealed a significant number of differentially expressed genes (DEGs) in the kidney via pairwise comparison using Cufflinks and edgeR. Using edgeR, we identified 12 DEGs; seven overlapped with those found by cufflinks. Seven DEGs were validated by real-time quantitative-PCR (qRT-PCR) in Ca-supplemented kidneys, and the results correlated with the RNA-seq data. DEGs identified by cufflinks/edgeR were subjected to pathway enrichment, protein/protein interaction, and co-occurrence analyses to determine their involvement in disease. The National Research Council (NRC) recommended Ca intake for 21-day post-hatch broilers is about 1.0%. Our findings suggest that higher-than-recommended Ca intake (1.2%) could reduce body weight gain in broilers, and that affected DEGs are related to stress-induced diseases, such as hypertension.

Identification of Important Amino Acids in Gal2p for Improving the L-arabinose Transport and Metabolism in Saccharomyces cerevisiae

Efficient and cost-effective bioethanol production from lignocellulosic materials requires co-fermentation of the main hydrolyzed sugars, including glucose, xylose, and L-arabinose. Saccharomyces cerevisiae is a glucose-fermenting yeast that is traditionally used for ethanol production. Fermentation of L-arabinose is also possible after metabolic engineering. Transport into the cell is the first and rate-limiting step for L-arabinose metabolism. The galactose permease, Gal2p, is a non-specific, endogenous monosaccharide transporter that has been shown to transport L-arabinose. However, Gal2p-mediated transport of L-arabinose occurs at a low efficiency. In this study, homologous modeling and L-arabinose docking were used to predict amino acids in Gal2p that are crucial for L-arabinose transport. Nine amino acid residues in Gal2p were identified and were the focus for site-directed mutagenesis. In the Gal2p transport-deficient chassis cells, the capacity for L-arabinose transport of the different Gal2p mutants was compared by testing growth rates using L-arabinose as the sole carbon source. Almost all the tested mutations affected L-arabinose transport capacity. Among them, F85 is a unique site. The F85S, F85G, F85C, and F85T point mutations significantly increased L-arabinose transport activities, while, the F85E and F85R mutations decreased L-arabinose transport activities compared to the Gal2p-expressing wild-type strain. These results verified F85 as a key residue in L-arabinose transport. The F85S mutation, having the most significant effect, elevated the exponential growth rate by 40%. The F85S mutation also improved xylose transport efficiency and weakened the glucose transport preference. Overall, enhancing the L-arabinose transport capacity further improved the L-arabinose metabolism of engineered S. cerevisiae.

Endocytosis and vacuolar degradation of the yeast cell surface glucose sensors Rgt2 and Snf3

Sensing and signaling the presence of extracellular glucose is crucial for the yeast Saccharomyces cerevisiae because of its fermentative metabolism, characterized by high glucose flux through glycolysis. The yeast senses glucose through the cell surface glucose sensors Rgt2 and Snf3, which serve as glucose receptors that generate the signal for induction of genes involved in glucose uptake and metabolism. Rgt2 and Snf3 detect high and low glucose concentrations, respectively, perhaps because of their different affinities for glucose. Here, we provide evidence that cell surface levels of glucose sensors are regulated by ubiquitination and degradation. The glucose sensors are removed from the plasma membrane through endocytosis and targeted to the vacuole for degradation upon glucose depletion. The turnover of the glucose sensors is inhibited in endocytosis defective mutants, and the sensor proteins with a mutation at their putative ubiquitin-acceptor lysine residues are resistant to degradation. Of note, the low affinity glucose sensor Rgt2 remains stable only in high glucose grown cells, and the high affinity glucose sensor Snf3 is stable only in cells grown in low glucose. In addition, constitutively active, signaling forms of glucose sensors do not undergo endocytosis, whereas signaling defective sensors are constitutively targeted for degradation, suggesting that the stability of the glucose sensors may be associated with their ability to sense glucose. Therefore, our findings demonstrate that the amount of glucose available dictates the cell surface levels of the glucose sensors and that the regulation of glucose sensors by glucose concentration may enable yeast cells to maintain glucose sensing activity at the cell surface over a wide range of glucose concentrations.

Ght2⁺ is required for UDP-galactose synthesis from extracellular galactose by Schizosaccharomyces pombe

Schizosaccharomyces pombe has eight hexose transporter genes, ght1 (+) to ght8 (+). Here we report that ght2 (+), which is highly expressed in the presence of glucose, is essential for UDP-galactose synthesis from extracellular galactose when cells grow on glucose. The galactosylation defect of a uge1Δ mutant defective in synthesis of UDP-galactose from glucose was suppressed in galactose-containing medium, but disruption of ght2 (+) in the uge1Δ mutant reversed suppression of the galactosylation defect. Expression of Saccharomyces cerevisiae GAL2 in uge1Δght2Δ cells suppressed the defective galactosylation phenotype in galactose-containing medium. These results indicate that galactose is transported from the medium to the cytosol in a Ght2-dependent manner, and is then converted into UDP-galactose.

Identification by Comprehensive Chimeric Analysis of a Key Residue Responsible for High Affinity Glucose Transport by Yeast HXT2

Hxt2 and Hxt1 are, respectively, high affinity and low affinity facilitative glucose transporter paralogs of Saccharomyces cerevisiae. We have previously investigated which amino acid residues of Hxt2 are important for high affinity transport activity. Studies with all the possible combinations of 12 transmembrane segments (TMs) of Hxt2 and Hxt1 revealed that TMs 1, 5, 7, and 8 of Hxt2 are necessary for high affinity transport. Systematic shuffling of the 20 amino acid residues that differ between Hxt2 and Hxt1 in these TMs subsequently identified 5 residues as important for such activity: Leu(59) and Leu(61) (TM1), Leu(201) (TM5), Asn(331) (TM7), and Phe(366) (TM8). We have now studied the relative importance of these 5 residues by individually replacing them with each of the other 19 residues. Replacement of Asn(331) yielded transporters with various affinities, with those of the Ile(331), Val(331), and Cys(331) mutants being higher than that of the wild type. Replacement of the Hxt2 residues at the other four sites yielded transporters with affinities similar to that of the wild type but with various capacities. A working homology model of the chimeric transporters containing Asn(331) or its 19 replacement residues indicated that those residues at this site that yield high affinity transporters (Ile(331), Val(331), Cys(331)) face the central cavity and are within van der Waals distances of Phe(208) (TM5), Leu(357) (TM8), and Tyr(427) (TM10). Interactions via these residues of the four TMs, which compose a half of the central pore, may thus play a pivotal role in formation of a core structure for high affinity transport.

An integrated model of glucose and galactose metabolism regulated by the GAL genetic switch

Glucose and galactose are two alternative carbon sources in yeast for energy production, producing CO2 and alcohol. The yeast needs to switch from glucose to galactose metabolism as required, by transcriptional regulation of the respective metabolic enzymes. This regulation is achieved mainly through the GAL genetic switch, in addition to glucose repression mechanism. This study integrates the two metabolic pathways with the genetic regulatory circuit using the GEPASI 3.30 simulation environment, and investigates the model behavior under various nutrient conditions. Our system is successful in achieving transcriptional upregulation of the galactose metabolizing enzymes as required. Under high glucose and high galactose concentrations, the in silico yeast chooses to metabolize glucose first, after which it resorts to using the galactose available. We also show what the preferred storage macromolecules are in different metabolic pathways.

Eight amino acid residues in transmembrane segments of yeast glucose transporter Hxt2 are required for high affinity transport

Hxt2 and Hxt1 are high affinity and low affinity facilitative glucose transporter paralogs of Saccharomyces cerevisiae, respectively, that differ at 75 amino acid positions in their 12 transmembrane segments (TMs). Comprehensive analysis of chimeras of these two proteins has previously revealed that TMs 1, 5, 7, and 8 of Hxt2 are required for high affinity glucose transport activity and that leucine 201 in TM5 is the most important in this regard of the 20 amino acid residues in these regions that differ between Hxt2 and Hxt1. To evaluate the importance of the remaining residues, we systematically shuffled the amino acids at these positions and screened the resulting proteins for high affinity and high capacity glucose transport activity. In addition to leucine 201 (TM5), four residues of Hxt2 (leucine 59 and leucine 61 in TM1, asparagine 331 in TM7, and phenylalanine 366 in TM8) were found to be important for such activity. Furthermore, phenylalanine 198 (TM5), alanine 363 (TM8), and either valine 316 (TM7) or alanine 368 (TM8) were found to be supportive of maximal activity. Construction of a homology model suggested that asparagine 331 interacts directly with the substrate and that the other identified residues may contribute to maintenance of protein conformation.

Comprehensive Chimeric Analysis of Amino Acid Residues Critical for High Affinity Glucose Transport by Hxt2 of Saccharomyces cerevisiae

Chimeras of Hxt2 and Hxt1, high affinity and low affinity glucose transporters, respectively, of Saccharomyces cerevisiae, were previously constructed by random replacement of each of the 12 transmembrane segments (TMs) of Hxt2 with the corresponding region of Hxt1. Characterization of these chimeras revealed that at least TMs 1, 5, 7, and 8 of Hxt2 are required for high affinity transport activity. To determine which amino acid residues in these TMs are important for high affinity glucose transport, we systematically shuffled all of the 20 residues in these regions that differ between Hxt2 and Hxt1. Analysis of 60 independent mutant strains identified as expressing high affinity and high capacity glucose transport activity by selection on glucose-limited agar plates revealed that Leu-201 in TM5 of Hxt2 is most important for such activity and that either Cys-195 or Phe-198 is also required for maximal activity.

Transmembrane segments 1, 5, 7 and 8 are required for high-affinity glucose transport by Saccharomyces cerevisiae Hxt2 transporter

Hxt2 is a high-affinity facilitative glucose transporter of Saccharomyces cerevisiae and belongs to the major facilitator superfamily. Hxt1 shares approximately 70% amino acid identity with Hxt2 in its transmembrane segments (TMs) and inter-TM loops, but transports D-glucose with an affinity about one-tenth of that of Hxt2. To determine which TMs of Hxt2 are important for high-affinity glucose transport, we constructed chimaeras of Hxt2 and Hxt1 by randomly replacing each of the 12 TMs of Hxt2 with the corresponding segment of Hxt1, for a total of 4096 different transporters. Among > 20000 yeast transformants screened, 39 different clones were selected by plate assays of high-affinity glucose-transport activity and sequenced. With only two exceptions, the selected chimaeras contained Hxt2 TMs 1, 5, 7 and 8. We then constructed chimaeras corresponding to all 16 possible combinations of Hxt2 TMs 1, 5, 7 and 8. Only one chimaera, namely that containing all four Hxt2 TMs, exhibited transport activity comparable with that of Hxt2. The K (m) and V (max) values for D-glucose transport, and the substrate specificity of this chimaera were almost identical with those of Hxt2. These results indicate that TMs 1, 5, 7 and 8 are necessary for exhibiting high-affinity glucose-transport activity of Hxt2.

Interaction between the critical aromatic amino acid residues Tyr(352) and Phe(504) in the yeast Gal2 transporter

Three critical aromatic sites have been identified in the yeast galactose transporter Gal2: Tyr(352) at the extracellular boundary of putative transmembrane segment (TM) 7, Tyr(446) in the middle of TM10 and Phe(504) in the middle of TM12. The relationship between these sites was investigated by random mutagenesis of each combination of two of the three residues. Galactose transport-positive clones selected by plate assays encoded Tyr(446) and specific combinations of aromatic residues at sites 352 and 504. Double-site mutants containing aromatic residues at these latter two positions showed either essentially full galactose transport activity (Phe(352)Trp(504) and Trp(352)Trp(504)) or no significant activity (Phe(352)Tyr(504) and Trp(352)Tyr(504)), whereas single-site mutants showed markedly reduced activity. These results are indicative of a specific interaction between sites 352 and 504 of Gal2.