Cloning of glycerol-3-phosphate dehydrogenase genes (ZrGPD1 and ZrGPD2) and glycerol dehydrogenase genes (ZrGCY1 and ZrGCY2) from the salt-tolerant yeast Zygosaccharomyces rouxii

Reviewing the Source, Physiological Characteristics, and Aroma Production Mechanisms of Aroma-Producing Yeasts

Flavor is an essential element of food quality. Flavor can be improved by adding flavoring substances or via microbial fermentation to impart aroma. Aroma-producing yeasts are a group of microorganisms that can produce aroma compounds, providing a strong aroma to foods and thus playing a great role in the modern fermentation industry. The physiological characteristics of aroma-producing yeast, including alcohol tolerance, acid tolerance, and salt tolerance, are introduced in this article, beginning with their origins and biological properties. The main mechanism of aroma-producing yeast is then analyzed based on its physiological roles in the fermentation process. Functional enzymes such as proteases, lipases, and glycosidase are released by yeast during the fermentation process. Sugars, fats, and proteins in the environment can be degraded by these enzymes via pathways such as glycolysis, methoxylation, the Ehrlich pathway, and esterification, resulting in the production of various aromatic esters (such as ethyl acetate and ethyl caproate), alcohols (such as phenethyl alcohol), and terpenes (such as monoterpenes, sesquiterpenes, and squalene). Furthermore, yeast cells can serve as cell synthesis factories, wherein specific synthesis pathways can be introduced into cells using synthetic biology techniques to achieve high-throughput production. In addition, the applications of aroma yeast in the food, pharmaceutical, and cosmetic industries are summarized, and the future development trends of aroma yeasts are discussed to provide a theoretical basis for their application in the food fermentation industry.

Recent developments in the biology and biotechnological applications of halotolerant yeasts

Natural hypersaline environments are inhabited by an abundance of prokaryotic and eukaryotic microorganisms capable of thriving under extreme saline conditions. Yeasts represent a substantial fraction of halotolerant eukaryotic microbiomes and are frequently isolated as food contaminants and from solar salterns. During the last years, a handful of new species has been discovered in moderate saline environments, including estuarine and deep-sea waters. Although Saccharomyces cerevisiae is considered the primary osmoadaptation model system for studies of hyperosmotic stress conditions, our increasing understanding of the physiology and molecular biology of halotolerant yeasts provides new insights into their distinct metabolic traits and provides novel and innovative opportunities for genome mining of biotechnologically relevant genes. Yeast species such as Debaryomyces hansenii, Zygosaccharomyces rouxii, Hortaea werneckii and Wallemia ichthyophaga show unique properties, which make them attractive for biotechnological applications. Select halotolerant yeasts are used in food processing and contribute to aromas and taste, while certain gene clusters are used in second generation biofuel production. Finally, both pharmaceutical and chemical industries benefit from applications of halotolerant yeasts as biocatalysts. This comprehensive review summarizes the most recent findings related to the biology of industrially-important halotolerant yeasts and provides a detailed and up-to-date description of modern halotolerant yeast-based biotechnological applications.

The revenge of Zygosaccharomyces yeasts in food biotechnology and applied microbiology

Non-conventional yeasts refer to a huge and still poorly explored group of species alternative to the well-known model organism Saccharomyces cerevisiae. Among them, Zygosaccharomyces rouxii and the sister species Zygosaccharomyces bailii are infamous for spoiling food and beverages even in presence of several food preservatives. On the other hand, their capability to cope with a wide range of process conditions makes these yeasts very attractive factories (the so-called "ZygoFactories") for bio-converting substrates poorly permissive for the growth of other species. In balsamic vinegar Z. rouxii is the main yeast responsible for converting highly concentrated sugars into ethanol, with a preference for fructose over glucose (a trait called fructophily). Z. rouxii has also attracted much attention for the ability to release important flavor compounds, such as fusel alcohols and the derivatives of 4-hydroxyfuranone, which markedly contribute to fragrant and smoky aroma in soy sauce. While Z. rouxii was successfully proposed in brewing for producing low ethanol beer, Z. bailii is promising for lactic acid and bioethanol production. Recently, several research efforts exploited omics tools to pinpoint the genetic bases of distinctive traits in "ZygoFactories", like fructophily, tolerance to high concentrations of sugars, lactic acid and salt. Here, I provided an overview of Zygosaccharomyces industrially relevant phenotypes and summarized the most recent findings in disclosing their genetic bases. I suggest that the increasing number of genomes available for Z. rouxii and other Zygosaccharomyces relatives, combined with recently developed genetic engineering toolkits, will boost the applications of these yeasts in biotechnology and applied microbiology.

Genomic Insights Into Sugar Adaptation in an Extremophile Yeast Zygosaccharomyces rouxii

The osmotolerant Zygosaccharomyces rouxii is known for its trait to survive in extreme high sugar environments. This ability determines its role in the fermentation process and leads to yeast spoilage in the food industry. However, our knowledge of the gene expression in response to high sugar stress remains limited. Here, we conducted RNA-sequencing (RNA-seq) under different sugar concentrations of the spoilage yeast, Z. rouxii, which exhibit extremely high tolerance to sugar stress. The obtained differentially expressed genes (DEGs) are significantly different to that of the Saccharomyces cerevisiae, which is sensitive to extreme high sugar stress. Most of the DEGs participated in the “glucan synthesis,” “transmembrane transport,” “ribosome,” etc. In this work, we also demonstrated that the gene ZYRO0B03476g (ZrKAR2) encoding Kar2p can significantly affect the growth of Z. rouxii under high sugar stress. In addition, we combined with a previous study on the genome sequence of Z. rouxii, indicating that several gene families contain significantly more gene copies in the Z. rouxii lineage, which involved in tolerance to sugar stress. Our results provide a gene insight for understanding the high sugar tolerance trait, which may impact food and biotechnological industries and improve the osmotolerance in other organisms.

Two glycerol 3-phosphate dehydrogenase isogenes from Candida versatilis SN-18 play an important role in glycerol biosynthesis under osmotic stress

Two isogenes of glycerol 3-phosphate dehydrogenase (GPD) from Candida versatilis SN-18 were cloned and sequenced. These intronless genes (Cagpd1 and Cagpd2) were both predicted to encode a 378 amino acid polypeptide, and the deduced amino acid sequences mutually showed 76% identity. Interestingly, Cagpd1 and Cagpd2 were located tandemly in a locus of genomic DNA within a 262 bp interval. To our knowledge, this represents a novel instance of isogenic genes relating to glucose metabolism. The stress response element (STRE) was found respectively at -93 to -89 bp upstream of the 5'end of Cagpd1 and -707 to -703 bp upstream of Cagpd2, indicating that these genes are involved in osmotic stress response. In heterologous expression using a gpd1Δgpd2Δ double deletion mutant of Saccharomyces cerevisiae, Cagpd1 and Cagpd2 transformants complemented the function of GPD, with Cagpd2 being much more effective than Cagpd1 in promoting growth and glycerol synthesis. Phylogenetic analysis of the amino acid sequences suggested that Cagpd1p and Cagpd2p are NADP(+)-dependent GPDs (EC 1.1.1.94). However, crude enzyme extract from Cagpd1 and Cagpd2 transformants showed GPD activity with only NAD(+) as cofactor. Hence, both Cagpd1p and Cagpd2p are likely NAD(+)-dependent GPDs (EC 1.1.1.8), similar to GPDs from S. cerevisiae and Candida magnoliae.

Cloning and characterization of a glycerol-3-phosphate dehydrogenase (NAD+) gene from the halotolerant yeast Pichia farinosa

In this study, a novel glycerol-3-phosphate dehydrogenase (NAD(+)) (EC1.1.1.8) gene (PfGPD) was cloned from halotolerant yeast Pichia farinosa, using degenerate reverse transcription (RT)-PCR and rapid amplification of cDNA ends (RACE) methods. The full-length cDNA of the PfGPD gene is 1403 bp, which has an open reading frame (ORF) encoding 370 amino acids. PfGPD is conserved with other glycerol-3-phosphate dehydrogenase genes and presents a single copy in the P. farinosa genome. Transcriptional analysis revealed that PfGPD gene expression level was high after 2 h induction in a hyperosmotic environment containing 2 M NaCl and returned to normal within 6 h. These results suggest that the PfGPD gene is induced by salt stress. Yeast complementation experiment indicated that PfGPD complements gpd1 mutation in S. cerevisiae. The Accession No. for PfGPD in GenBank is EF601986.

Genome size and ploidy level: new insights for elucidating relationships in Zygosaccharomyces species

Ploidy is a fundamental genetic trait with important physiological and genomic implications. We applied complementary molecular tools to highlight differences in genome size and ploidy between Zygosaccharomyces rouxii strain CBS 732T and other related wild strains (ATCC 42981, ABT 301, and ABT 601). The cell cycle analysis by flow cytometry revealed a genome size of 12.7+/-0.2 Mb for strain CBS 732T, 21.9+/-0.2 Mb for ATCC 42981, 28.1+/-1.3 Mb for ABT 301, and 39.00+/-0.3 Mb for ABT 601. Moreover, karyotyping analysis showed a high variability, with wild strains having a higher number of chromosomal bands than CBS 732T. The ploidy level was assessed comparing genome size from flow cytometry with the average haploid size from electrophoretic karyotyping. Strain CBS 732T showed an haploid DNA content, whereas the wild strains a diploid DNA content. In addition gene probe-chromosome hybridization targeted to ZSOD genes showed that wild strains with a diploid DNA content have two ZSOD copies located on different chromosomes.

[Cloning of the gene encoding a key enzyme involved in production of glycerol in Candida glycerinogenes]

Candida glycerinogenes WL2002-5, an excellent glycerol producer, has been used for industrial scale fermentation of glycerol by an aerobic process. However, our knowledge about glycerol biosynthesis at the molecular level and genetic background of this yeast species lags far behind those of model yeasts such as Saccharomyces cerevisiae et al. In this report, inverse primers, in conjunction with degenerated primers, were used to amplify the NAD+-dependent glycerol 3-phosphate dehydrogenase (GPD) encoding gene from C. glycerinogenes. The completed nucleotide sequence of the coding, as well as flanking genomic regions was determined (GenBank accession No. EU186536). DNA sequence analysis revealed the present of the open reading frame (ORF) of 1,167 bp, encoding a polypeptide with 388-amino-acid with a molecular mass of 42,695 Da. The CgGPD did not exhibit significant sequence similarity with others described in other eukaryotic systems by comparative analysis. However, it consisted of two typical functional domains which belong to almost all eukaryotic GPDs: a co-enzyme binding domain in the N-terminal, and a catalytic domain. Moreover, some relevant features involved in initiation, regulation and stress response element of gene transcription were observed in the nucleotide sequence of the 5'-non-coding regions. Heterologous expression of CgGPD gene in S. cerevisiae improved its glycerol production significantly. In conclusion, the functional CgGPD has been cloned and identified successfully from C. glycerinogenes genome.

Expression of glycerol 3-phosphate dehydrogenase gene (CvGPD1) in salt-tolerant yeastCandida versatilis is stimulated by high concentrations of NaCl

We cloned the glycerol 3-phosphate dehydrogenase (GPDH) gene (CvGPD1) from salt-tolerant yeast Candida versatilis. When CvGPD1 was expressed in glycerol synthesis-deficient Saccharomyces cerevisiae cells, the salt tolerance of the recombinant strain was enhanced, and NADP(+)-dependent GPDH (EC 1.1.1.94), Cvgpd1p synthesis and recovery of glycerol synthesis were confirmed. The transcription of CvGPD1 in C. versatilis cells was stimulated by high concentrations of NaCl. The relationship between expression of CvGPD1 and growth of C. versatilis cells in the mash of Japanese seasonings (miso- and shoyu-moromi) is also discussed.

Identification of the genes GPD1 and GPD2 of Pichia jadinii

Two genes coding for proteins with a high degree of sequence similarity to glycerol-3-phosphate dehydrogenases have been isolated from the yeast Pichiajadinii. Fragments of the genes were PCR-amplified with degenerated primers from genomic DNA of P. jadinii. Clones containing the full-length genes PjGPDI and PjGPD2 were isolated by screening genomic libraries. DNA sequencing revealed open reading frames (ORFs) of 1182 bp and 1185 bp for PjGpdlp and PjGpd2p, respectively. In a complementation study PjGPD1 rescued the growth defect of a Saccharomyces cerevisiae Agpdl mutant strain under osmotic stress, while complementation by PjGPD2 is temperature sensitive. The sequences of the PjGPD1 and PjGPD2 ORFs have been submitted to the EMBL Nucleotide Sequence Database under Accession No. AJ632339 and AJ632340, the sequences of the corresponding genomic DNA fragments under Accession No. AJ632341 and AJ635370, respectively.

Osmoresistant yeastZygosaccharomyces rouxii: the two most studied wild-type strains (ATCC 2623 and ATCC 42981) differ in osmotolerance and glycerol metabolism

The yeast Zygosaccharomyces rouxii is known for its high tolerance to osmotic stress, which is thought to be caused by sets of specific genes. Relatively few Z. rouxii genes have been identified so far, all of them having homologues in Saccharomyces cerevisiae; none of them was Z. rouxii-specific. Most of the known Z. rouxii genes were isolated from two wild-type strains, ATCC 2623 and ATCC 42981. In this study, we compared these two strains with regard to some of their morphological, physiological and genomic properties. Important differences were found in their salt tolerance and assimilation of glycerol and karyotype; slight differences were also present in their cell morphology. The ATCC 42981 strain showed a higher resistance to salts, higher glycerol production and, unlike ATCC 2623, was able to assimilate glycerol. Under conditions of osmotic stress, the glycerol production in both Z. rouxii strains was much lower than in a S. cerevisiae S288c culture, which suggested the presence of a system that efficiently retains glycerol inside Z. rouxii cells. The karyotype analysis revealed that ATCC 42981 cells contain more chromosomes and have a bigger genome size than those of ATCC 2623.

Co-expression of the Na/H-antiporter and H-ATPase genes of the salt-tolerant yeast in

We cloned two genes from the salt-tolerant yeast Zygosaccharomyces rouxii: ZrSOD2 for the cell membrane Na(+)/H(+)-antiporter and ZrPMA1 for the cell membrane H(+)-ATPase. The products of these genes play cooperative roles in the salt-tolerance of Z. rouxii, and the function of the ZrPMA1 product is regulated at the transcription level. We constructed a yeast expression vector that is able to co-express the ZrSOD2 and ZrPMA1 genes. Single expression of ZrSOD2 was effective in conferring salt-tolerance, and although a slight synergic effect was observed with co-expression of ZrSOD2 and ZrPMA1, the usefulness of this co-expression is likely to be minimal with regard to salt-tolerance.

Purification and characterization of NADPH-dependent aldo?keto reductase specific for ?-keto esters from Penicillium citrinum, and production of methyl (S)-4-bromo-3-hydroxybutyrate

A novel beta-keto ester reductase (KER) was purified to homogeneity from recombinant Escherichia coli (pTrcKER) cells, which efficiently expressed the ker gene cloned from Penicillium citrinum IFO4631. The enzyme was monomeric and had a molecular mass of 37 kDa. It catalyzed the reduction of some beta-keto esters, especially alkyl 4-halo-3-oxobutyrates. However, it did not catalyze the reverse reaction, the dehydrogenation of alkyl 4-halo-3-hydroxybutyrates and other alcohols. The enzyme required NADPH as a cofactor and showed no activity with NADH. Therefore, it was defined as a NADPH-dependent aldo-keto reductase (AKR3E1), belonging to the AKR superfamily. The enzyme stereospecifically produced methyl (S)-4-bromo-3-hydroxybutyrate from its keto derivative with high stereospecificity (97.9% enantiomer excess). E. coli cells expressing KER and glucose dehydrogenase in the water/butyl acetate two-phase system achieved a high productivity of (S)-4-bromo-3-hydroxybutyrate (277 mM, 54 mg/ml) in the organic solvent layer.

Heterologous expression of glycerol 3-phosphate dehydrogenase gene () and glycerol dehydrogenase gene () in

We examined the effects of heterologous expression of the open reading frames (ORF) of two genes on salt tolerance and glycerol production in a Saccharomyces cerevisiae strain deficient in glycerol synthesis (gpd1Deltagpd2Delta). When the ORF of the Zygosaccharomyces rouxii glycerol 3-phosphate dehydrogenase gene (ZrGPD1) was expressed under the control of the GAL10 promoter, salt tolerance and glycerol production increased; when the ORF of the glycerol dehydrogenase gene (ZrGCY1) was expressed under the control of the GAL1 promoter, no such changes were observed. Zrgcy1p had a weak effect on glycerol production. These results suggest that Zrgpd1p is the primary enzyme involved in Z. rouxii glycerol production, following a mechanism similar to that of S. cerevisiae (Gpd1p). When the ORFs of the S. cerevisiae glycerol 3-phosphatase gene (GPP2) and ZrGPD1 were simultaneously expressed, glycerol production increased, compared with that in yeast expressing only ZrGPD1.

Glycerol dehydrogenase, encoded by gldB is essential for osmotolerance in Aspergillus nidulans

We have characterized the Aspergillus nidulans gldB gene encoding a NADP+-dependent glycerol dehydrogenase. A basal expression level was observed for gldB, which increased significantly under conditions of hyper-osmotic shock (1 M NaCl). Growth of strains in which gldB was disrupted was severely reduced on plates containing 1% glucose and 1 M NaCl, but these strains were able to grow on plates containing 1 M NaCl and 1% glycerol, arabitol, mannitol or erythritol. Uptake of these polyols compensated for the inability of the gldB disruptants to produce glycerol. Presence of 1% glucose in these plates prevented growth restoration by all the polyols tested with the exemption of glycerol, indicating that uptake of mannitol, arabitol and erythritol is subject to glucose repression, whereas uptake of glycerol is significantly less or not repressed. No intracellular glycerol dehydrogenase activity could be detected in the gldB disruption strains. Intracellular glycerol levels in these strains were strongly decreased compared to wild type, whereas intracellular mannitol, erythritol and arabitol levels were increased. Conidia of the gldB disruption strain did not accumulate glycerol upon germination in glucose media with or without 1 M NaCl and germ tube emergence was significantly delayed in this strain in the presence of 1 M NaCl in comparison to the wild type. These data indicate that gldB is essential for osmotolerance in A. nidulans and that the pathways for glycerol biosynthesis under osmotic stress differ between yeast and filamentous fungi.

Cloning, sequencing and characterization of a gene encoding dihydroxyacetone kinase from Zygosaccharomyces rouxii NRRL2547

The dihydroxyacetone pathway, an alternative pathway for the dissimilation of glycerol via reduction by glycerol dehydrogenase and subsequent phosphorylation by dihydroxyacetone (DHA) kinase, is activated in the yeasts Saccharomyces cerevisiae and Zygosaccharomyces rouxii during osmotic stress. In experiments aimed at investigating the physiological function of the DHA pathway in Z. rouxii, a typical osmotolerant yeast, we cloned and characterized a DAK gene encoding dihydroxyacetone kinase from Z. rouxii NRRL 2547. Sequence analysis revealed a 1761 bp open reading frame, encoding a peptide composed of 587 deduced amino acids with the predicted molecular weight of 61 664 Da. As the amino acid sequence was most closely homologous (68% identity) to the S. cerevisiae Dak1p, we named the gene and protein ZrDAK1 and ZrDak1p, respectively. A putative ATP binding site was also found but no consensus element associated with osmoregulation was found in the upstream region of the ZrDAK1 gene. The ZrDAK1 gene complemented a S. cerevisiae W303-1A dak1delta dak2 delta strain by improving the growth of the mutant on 50 mmol/l dihydroxyacetone and by increasing the tolerance to dihydroxyacetone in a medium containing 5% sodium chloride, suggesting that it is a functional homologue of the S. cerevisiae DAK1. However, expression of the ZrDAK1 gene in the S. cerevisiae dak1delta dak2 delta strain had no significant effect on glycerol levels during osmotic stress. The ZrDAK1 sequence has been deposited in the public data bases under Accession No. AJ294719; regions upstream and downstream of ZrDAK1are deposited as Accession Nos AJ294739 and AJ294720, respectively.

Identification of salt-induced genes of Zygosaccharomyces rouxii by using Saccharomyces cerevisiae GeneFilters

Yeast GeneFilters containing all Saccharomyces cerevisiae open reading frame (ORF) sequences were used to elucidate gene activity in the osmotolerant yeast Zygosaccharomyces rouxii. Labelled cDNA derived from Z. rouxii was targeted to spotted S. cerevisiae ORFs. Approximately 90-100% homology of Z. rouxii genes with those of S. cerevisiae was required for definitive identification of the cDNAs hybridised to GeneFilter. Hybridised labelled cDNAs were visualised as small spots on the microarray, providing simultaneous information on homologous genes present in Z. rouxii and on their level of gene activity. Cross-hybridisation of the GeneFilters displayed 155 as yet unidentified genes of Z. rouxii hybridising to S. cerevisiae ORFs. From those 155 genes, the activity of 86 genes was influenced as a result of NaCl stress. In comparison with S. cerevisiae 24% of Z. rouxii genes revealed a different transcription behaviour following NaCl stress. All of these genes had no previously defined function in osmotic-stress response in Z. rouxii. Therefore, cross-hybridisation of GeneFilters proves to be an appropriate and straightforward method for screening transcripts in Z. rouxii, which provides an extension of the knowledge of genes present in a yeast genus other than S. cerevisiae.