Cloning and biochemical characterization of hexokinase from the methylotrophic yeast Hansenula polymorpha

Cloning and screening of the putative hexokinase genes from Rhizopus oryzae and their heterologous expression in Saccharomyces cerevisiae

BACKGROUND

A filamentous fungus, Rhizopus oryzae (R. oryzae) is one of the ideal candidates for ethanol and lactic acid production due to its ability to grow on renewable carbon sources.

METHODS AND RESULTS

In this study, the nucleotide sequence of hexokinases and glucokinase from S. cerevisiae was found on the NCBI site ( http://www.ncbi.nlm.nih.gov/blast/Blast.cgi ) were used. With these nucleotide sequences, a blast search was done on the R. oryzae genome database ( http://www.broad.mit.edu/annotation/genome/rhizopus_oryzae/Home.html ) and ten probable genes were obtained. cDNA was synthesized from the total RNA and PCR products of the seven of these putative genes were determined using the primers designed for them.

CONCLUSION

The results of the sequences and the complementation studies revealed that three of these seven putative genes were expressed in R. oryzae and the growth was observed on selective media.

Increased flux in acetyl-CoA synthetic pathway and TCA cycle of Kluyveromyces marxianus under respiratory conditions

Yeasts are extremely useful, not only for fermentation but also for a wide spectrum of fuel and chemical productions. We analyzed the overall metabolic turnover and transcript dynamics in glycolysis and the TCA cycle, revealing the difference in adaptive pyruvate metabolic response between a Crabtree-negative species, Kluyveromyces marxianus, and a Crabtree-positive species, Saccharomyces cerevisiae, during aerobic growth. Pyruvate metabolism was inclined toward ethanol production under aerobic conditions in S. cerevisiae, while increased transcript abundances of the genes involved in ethanol metabolism and those encoding pyruvate dehydrogenase were seen in K. marxianus, indicating the augmentation of acetyl-CoA synthesis. Furthermore, different metabolic turnover in the TCA cycle was observed in the two species: malate and fumarate production in S. cerevisiae was higher than in K. marxianus, irrespective of aeration; however, fluxes of both the reductive and oxidative TCA cycles were enhanced in K. marxianus by aeration, implying both the cycles contribute to efficient electron flux without producing ethanol. Additionally, decreased hexokinase activity under aerobic conditions is expected to be important for maintenance of suitable carbon flux. These findings demonstrate differences in the key metabolic trait of yeasts employing respiration or fermentation, and provide important insight into the metabolic engineering of yeasts.

Genome Mining of Non-Conventional Yeasts: Search and Analysis of MAL Clusters and Proteins

Genomic clustering of functionally related genes is rare in yeasts and other eukaryotes with only few examples available. Here, we summarize our data on a nontelomeric MAL cluster of a non-conventional methylotrophic yeast Ogataea (Hansenula) polymorpha containing genes for α-glucosidase MAL1, α-glucoside permease MAL2 and two hypothetical transcriptional activators. Using genome mining, we detected MAL clusters of varied number, position and composition in many other maltose-assimilating non-conventional yeasts from different phylogenetic groups. The highest number of MAL clusters was detected in Lipomyces starkeyi while no MAL clusters were found in Schizosaccharomyces pombe and Blastobotrys adeninivorans. Phylograms of α-glucosidases and α-glucoside transporters of yeasts agreed with phylogenesis of the respective yeast species. Substrate specificity of unstudied α-glucosidases was predicted from protein sequence analysis. Specific activities of Scheffersomycesstipitis α-glucosidases MAL7, MAL8, and MAL9 heterologously expressed in Escherichia coli confirmed the correctness of the prediction-these proteins were verified promiscuous maltase-isomaltases. α-Glucosidases of earlier diverged yeasts L. starkeyi, B. adeninivorans and S. pombe showed sequence relatedness with α-glucosidases of filamentous fungi and bacilli.

Kinase Screening in Pichia pastoris Identified Promising Targets Involved in Cell Growth and Alcohol Oxidase 1 Promoter (PAOX1) Regulation

As one of the most commonly used eukaryotic recombinant protein expression systems, P. pastoris relies heavily on the AOX1 promoter (PAOX1), which is strongly induced by methanol but strictly repressed by glycerol and glucose. However, the complicated signaling pathways involved in PAOX1 regulation when supplemented with different carbon sources are poorly understood. Here we constructed a kinase deletion library in P. pastoris and identified 27 mutants which showed peculiar phenotypes in cell growth or PAOX1 regulation. We analyzed both annotations and possible functions of these 27 targets, and then focused on the MAP kinase Hog1. In order to locate its potential downstream components, we performed the phosphoproteome analysis on glycerol cultured WT and Δhog1 strains and identified 157 differentially phosphorylated proteins. Our results identified important kinases involved in P. pastoris cell growth and PAOX1 regulation, which could serve as valuable targets for further mechanistic studies.

Repression vs. activation of MOX, FMD, MPP1 and MAL1 promoters by sugars in Hansenula polymorpha: the outcome depends on cell's ability to phosphorylate sugar

A high-throughput approach was used to assess the effect of mono- and disaccharides on MOX, FMD, MPP1 and MAL1 promoters in Hansenula polymorpha. Site-specifically designed strains deficient for (1) hexokinase, (2) hexokinase and glucokinase, (3) maltose permease or (4) maltase were used as hosts for reporter plasmids in which β-glucuronidase (Gus) expression was controlled by these promoters. The reporter strains were grown on agar plates containing varied carbon sources and Gus activity was measured in permeabilized cells on microtitre plates. We report that monosaccharides (glucose, fructose) repress studied promoters only if phosphorylated in the cell. Glucose-6-phosphate was proposed as a sugar repression signalling metabolite for H. polymorpha. Intriguingly, glucose and fructose strongly activated expression from these promoters in strains lacking both hexokinase and glucokinase, indicating that unphosphorylated monosaccharides have promoter-derepressing effect. We also show that maltose and sucrose must be internalized and split into monosaccharides to exert repression on MOX promoter. We demonstrate that at yeast growth on glucose-containing agar medium, glucose-limitation is rapidly created that promotes derepression of methanol-specific promoters and that derepression is specifically enhanced in hexokinase-negative strain. We recommend double kinase-negative and hexokinase-negative mutants as hosts for heterologous protein production from MOX and FMD promoters.

The early steps of glucose signalling in yeast

In the presence of glucose, yeast undergoes an important remodelling of its metabolism. There are changes in the concentration of intracellular metabolites and in the stability of proteins and mRNAs; modifications occur in the activity of enzymes as well as in the rate of transcription of a large number of genes, some of the genes being induced while others are repressed. Diverse combinations of input signals are required for glucose regulation of gene expression and of other cellular processes. This review focuses on the early elements in glucose signalling and discusses their relevance for the regulation of specific processes. Glucose sensing involves the plasma membrane proteins Snf3, Rgt2 and Gpr1 and the glucose-phosphorylating enzyme Hxk2, as well as other regulatory elements whose functions are still incompletely understood. The similarities and differences in the way in which yeasts and mammalian cells respond to glucose are also examined. It is shown that in Saccharomyces cerevisiae, sensing systems for other nutrients share some of the characteristics of the glucose-sensing pathways.

Regulation of methanol utilisation pathway genes in yeasts

Methylotrophic yeasts such as Candida boidinii, Hansenula polymorpha, Pichia methanolica and Pichia pastoris are an emerging group of eukaryotic hosts for recombinant protein production with an ever increasing number of applications during the last 30 years. Their applications are linked to the use of strong methanol-inducible promoters derived from genes of the methanol utilisation pathway. These promoters are tightly regulated, highly repressed in presence of non-limiting concentrations of glucose in the medium and strongly induced if methanol is used as carbon source. Several factors involved in this tight control and their regulatory effects have been described so far. This review summarises available data about the regulation of promoters from methanol utilisation pathway genes. Furthermore, the role of cis and trans acting factors (e.g. transcription factors, glucose processing enzymes) in the expression of methanol utilisation pathway genes is reviewed both in the context of the native cell environment as well as in heterologous hosts.

The significance of peroxisomes in methanol metabolism in methylotrophic yeast

The capacity to use methanol as sole source of carbon and energy is restricted to relatively few yeast species. This may be related to the low efficiency of methanol metabolism in yeast, relative to that of prokaryotes. This contribution describes the details of methanol metabolism in yeast and focuses on the significance of compartmentalization of this metabolic pathway in peroxisomes.

Alcohol oxidase: a complex peroxisomal, oligomeric flavoprotein

Alcohol oxidase (AO) is the key enzyme of methanol metabolism in methylotrophic yeast species. It catalyses the first step of methanol catabolism, namely its oxidation to formaldehyde with concomitant production of hydrogen peroxide. In its mature active form, AO is a molecule of high molecular mass (600 kDa) that consists of eight identical subunits, each of which carry one non-covalently bound flavin adenine nucleotide (FAD) molecule as the prosthetic group. In vivo, the protein is compartmentalized into special cell organelles, termed peroxisomes. AO is an abundant protein and its synthesis is strictly regulated by repression/derepression and induction mechanisms that occur at the transcriptional level. Various aspects of its sorting and assembly/activation render AO a unique protein. Recent developments of AO synthesis, sorting and assembly/activation are highlighted in this paper.

Clustering of MAL genes in Hansenula polymorpha: cloning of the maltose permease gene and expression from the divergent intergenic region between the maltose permease and maltase genes

Hansenula polymorpha uses maltase to grow on maltose and sucrose. Inspection of genomic clones of H. polymorpha showed that the maltase gene HPMAL1 is clustered with genes corresponding to Saccharomyces cerevisiae maltose permeases and MAL activator genes orthologues. We sequenced the H. polymorpha maltose permease gene HPMAL2 of the cluster. The protein (582 amino acids) deduced from the HPMAL2 gene is predicted to have eleven transmembrane domains and shows 39-57% identity with yeast maltose permeases. The identity of the protein is highest with maltose permeases of Debaryomyces hansenii and Candida albicans. Expression of the HPMAL2 in a S. cerevisiae maltose permease-negative mutant CMY1050 proved functionality of the permease protein encoded by the gene. HPMAL1 and HPMAL2 genes are divergently positioned similarly to maltase and maltose permease genes in many yeasts. A two-reporter assay of the expression from the HPMAL1-HPMAL2 intergenic region showed that expression of both genes is coordinately regulated, repressed by glucose, induced by maltose, and that basal expression is higher in the direction of the permease gene.