Mutants of the methylotrophic yeast Pichia pinus defective in C2 metabolism

A collection of mutants of Pichia pinus which are unable to grow on ethanol but retain the ability to grow on glucose and methanol, was obtained. Genetic and biochemical analysis of these strains revealed mutations in seven nuclear genes affecting activities of isocitrate lyase (icl1), malate synthase (mls1), phosphoenolpyruvate carboxykinase (pck1), ‘malic’ enzyme (mdd1) and acetyl-CoA synthetase (acs1, acs2 and acs3). All mutations except acs1-acs3 have no effect on the activities of other enzymes involved in C₂ metabolism. Mutations acs1, acs2 and acs3 have a pleiotropic action, leading to partial reduction in activities of isocitrate lyase and malate synthase. Ethanol-induced repression of the synthesis of the methanol oxidative enzymes, alcohol oxidase and catalase, is not impaired in these seven mutant classes. On the other hand, C₂ compound-induced inactivation of alcohol oxidase and catalase is impaired in mutants acs1, acs2, acs3 and icl1. It was suggested that glyoxylate and acetate (or acetate precursors) act as low molecular weight effectors, ‘switching on’ inactivation and repression, respectively, of alcohol oxidase and catalase in the medium containing ethanol or acetate.     

Pichia stipitis木糖醇脱氢酶基因XYL2在酿酒酵母中的表达

通过PCR方法克隆得到树干毕赤氏酵母木糖醇脱氢酶(XDH)基因XYL2.将该基因连入酵母表达载体pYX212的强启动子磷酸丙糖异构酶(TPI)启动子下,得到融合表达载体pYX-XYL2.通过电转化方法将pYX-XYL2转入酿酒酵母Saccharomyces cerevisiae W303-1A中,酶活测定表明在酿酒酵母中树干毕赤氏酵母木糖醇脱氢酶基因XYL2得到活性表达,酿酒酵母转化子粗酶液中木糖醇脱氢酶比活为每毫克蛋白0.6 U左右,约为供体菌的2.4倍.与基因供体菌不同,木糖醇脱氢酶基因在酿酒酵母中表达不需木糖诱导,为组成型表达.     

I. Yeast sequencing reports. Isolation and characterization of the LEU2 gene of Hansenula polymorpha

A DNA fragment carrying the LEU2 gene of methylotrophic yeast Hansenula polymorpha was isolated by complementation of the leuB mutation of Escherichia coli. The nucleotide sequence of the isolated DNA fragment contains an open reading frame of 363 codons, coding for a protein 80% identical to the LEU2 gene product of Saccharomyces cerevisiae. Further downstream, there is a partial reading frame with no obvious similarity to known proteins. The LEU2 gene of H. polymorpha cannot complement the leu2 mutation of S. cerevisiae. The sequence has been entered in the EMBL data library under the Accession Number U00889.     

Influence of the codon following the initiation codon on the expression of the lacZ gene in Saccharomyces cerevisiae

A set of 32 different codons were introduced in a lacZ expression vector (pPTK400) immediately 3' from the AUG initiation codon. Expression of the lacZ gene was determined in Saccharomyces cerevisiae by measuring the amount of beta-galactosidase fusion protein using immuno-gel electrophoresis. A 5.3-fold difference in expression was found among the various constructs. It was found that there was no preference for a certain nucleotide in any position of the second codon and there was no distinct correlation between the level of tRNA corresponding to any particular second codon and expression. No correlation could be found between the local secondary structure and expression. When the overall codon usage in yeast and the codon usage in the second position of the mRNA is compared, there is no obvious significant difference in preference. This indicates that in yeast, in contrast to Escherichia coli, the codon choice at the beginning of the mRNA does not deviate from the one further downstream and is determined by the requirements for optimal translation elongation. Important determinants of the optimal context for an initiation codon in yeast therefore must be located mainly 5' from this codon.     

Linear DNA plasmid pPK2 of Pichia kluyveri: distinction between cytoplasmic and mitochondrial linear plasmids in yeasts

The linear plasmids frequently found in plants and filamentous fungi are associated with mitochondria or chloroplasts. In contrast, all the linear plasmids known in yeasts are cytoplasmic elements. From a strain of the yeast Pichia kluyveri, we have isolated a new linear plasmid, pPK2, which was found to be associated with mitochondria. This 7·1 kilobase pairs‐long DNA contained only two genes, which code for DNA and RNA polymerases, as judged from their nucleotide sequences translated by a mitochondrial genetic code. When we examined several recently isolated yeast plasmids for their subcellular localization, we found that two linear plasmids, pPH1 from Pichia heedii, as well as pPK1 from another strain of P. kluyveri, were also localized in mitochondria. These plasmids are the first examples of mitochondria‐associated linear plasmids in yeast. All other linear plasmids we examined were of cytoplasmic origin. Whilst the cytoplasmic type linear plasmids were efficiently eliminated by ultraviolet irradiation of host cells, the mitochondria‐associated plasmids were highly resistant. The mitochondrial pPK2 plasmid was rapidly lost by treatment of the host cells with ethidum bromide. Copyright © 1999 John Wiley & Sons, Ltd.     

Genome-wide effect of tetracycline,doxycycline and 4-epidoxycycline on gene expression in Saccharomyces cerevisiae

Tetracycline (Tet) and derivative chemicals (e.g., doxycycline or Dox) have gained widespread recognition for their antibiotic properties since their introduction in the late 1970s, but recent work with these chemicals in the lab has shifted to include multiple techniques in all genetic model systems for the precise control of gene expression. The most widely used Tet-modulated methodology is the Tet-On/Tet-Off gene expression system. Tet is generally considered to have effects specific to bacteria; therefore, it should have few off-target effects when used in eukaryotic systems, and a previous study in the yeast Saccharomyces cerevisiae found that Dox had no effect on genome-wide gene expression as measured by microarray. In contrast, another study found that the use of Dox in common cell lines and several model organisms led to mitonuclear protein imbalance, suggesting an inhibitory role of Dox in eukaryotic mitochondria. Recently, a new Dox derivative, 4-epidoxycycline (4-ED) was developed that was shown to have less off-target consequences on mitochondrial health. To determine the best tetracycline family chemical to use for gene expression control in S. cerevisiae, we performed RNA sequencing (RNA-seq) on yeast grown on standard medium compared with growth on media supplemented with Tet, Dox or 4-ED. We found each caused dozens of genes to change expression, with Dox eliciting the greatest expression responses, suggesting that the specific tetracycline used in experiments should be tailored to the specific gene(s) of interest when using the Tet-On/Tet-Off system to reduce the consequences of confounding off-target responses.     

Expression and in vivo determination of firefly luciferase as gene reporter in Saccharomyces cerevisiae

The LUC gene coding for Photinus pyralis firefly luciferase was cloned in different yeast episomal plasmids in order to assess its possibilities as an in vivo reporter gene. Activity of the enzyme in transformed cells in vivo was measured by following light emission and assay conditions optimized in intact cells, with regard to oxygen concentration, temperature, cell concentration in assay mixtures and external ATP concentration. Among the factors tested, light emission was drastically influenced by the external pH in the assay (which resulted in a ten-fold amplification signal) and by substrate permeability. The growth phase of the cells was also important for the level of activity detected. Cloning of firefly luciferase gene under the control of different yeast-regulated promoters (ADH1, GAL1–10) enabled us to measure their strength which correlated well with previously described data. We conclude that firefly luciferase is an adequate gene reporter for the in vivo sensitive determination of gene expression and promoter strength in yeast.     

Cloning and sequence analysis of the TRP1 gene encoding the phosphoribosyl anthranilate isomerase from Pichia anomala (strain K)

Pichia anomala (strain K) is an efficient biocontrol agent against post-harvest diseases affecting apples. To study the role of strain K genes in biocontrol activity, it is useful to identify selectable markers on which to base a gene disruption strategy. The Pichia anomala TRP1 gene (PaTRP1) was isolated by complementation of the multi-auxotrophic S. cerevisiae strain FY-1679-18b. DNA sequence analysis revealed the presence of a 699 bp ORF encoding a 233 amino acid protein showing the typical conserved structure of proteins of the phosphoribosyl anthranilate isomerase (PRAI) family. Codon analysis revealed a high number of unused codons. Downstream from PaTRP1 was found the 3' extremity of a gene highly similar to the IPP1 gene (coding for the inorganic pyrophosphatase).     

A novel mechanism regulates H(2) S and SO(2) production in Saccharomyces cerevisiae

Sulfite (SO(2) ) plays an important role in flavour stability in alcoholic beverages, whereas hydrogen sulfide (H(2) S) has an undesirable aroma. To discover the cellular processes that control SO(2) and H(2) S production, we screened a library of Saccharomyces cerevisiae deletion mutants. Deletion of 12 genes led to increased H(2) S productivity. Ten of these genes are known to be involved in sulfur-containing amino acid metabolism, whereas UBI4 functions in the ubiquitin-proteasome system and SKP2 encodes an F-box-containing protein whose function is unknown. We found that the skp2 mutant accumulated H(2) S and SO(2) , because the adenosylphophosulfate kinase Met14p is a substrate of SCF(Skp2) and more stable in the skp2 mutant than in the wild-type strain. Furthermore, the skp2 mutant grew more slowly than the wild-type strain under nutrient-limited conditions. Metabolome analysis showed that the concentration of intracellular cysteine is lower in the skp2 mutant than in the wild-type strain. The slow growth of the skp2 mutant was due to a lower concentration of intracellular cysteine, because the addition of cysteine suppressed the slow growth. In the skp2 mutant, the cysteine biosynthesis proteins Str2p, Str3p and Str4p are more stable than in the wild-type strain. Moreover, supplementation with methionine, S-adenosylmethionine, S-adenosylhomocysteine and homocysteine also suppressed the slow growth. Overexpression of STR1 or STR4 caused a more severe defect in the skp2 mutant. These results suggest that the balance of methionine and cysteine biosynthesis is important for yeast cell growth. Thus, Skp2p is one of the key components regulating this balance and H(2) S/SO(2) production.     

The identification of the Saccharomyces cerevisiae gene AYT1(ORF-YLL063c) encoding an acetyltransferase

The recent isolation and characterization of Tri101 in Fusarium sporotrichioides has led to the functional identification of the yeast open reading frame (ORF) YLL063c, located on chromosome XII of Saccharomyces cerevisiae. The sequence of YLL063c predicts a protein of 474 residues that has 45% identity and 70% similarity to FsTri101. FsTri101 encodes a trichothecene 3-O-acetyltransferase that functions in trichothecene biosynthesis. Feeding studies indicated low levels of C3-OH acetylation in cultures of the laboratory yeast strain, RW2802. No similar activity was found in RW2802 transformed with an integrative plasmid carrying a disrupted YLL063c gene. Based on these results, which show structural and functional similarities between YLL063c and FsTri101, we propose that YLL063c encodes an acetyltransferase capable of trichothecene 3-O-acetylation and have named this gene AYT1. Published in 2002 by John Wiley & Sons, Ltd.     

Fermentation properties of a wine yeast over-expressing the Saccharomyces cerevisiae glycerol 3-phosphate dehydrogenase gene (GPD2)

Wine yeasts efficiently convert sugar into ethanol. The possibility of diverting some of the sugar into compounds other than ethanol by using molecular genetic methods was tested. Over-expression of the yeast glycerol 3-phosphate dehydrogenase gene ( GPD2 ) in a laboratory strain of Saccharomyces cerevisiae led to an approximate two-fold increase in the extracellular glycerol concentration. In the medium fermented with the modified strain, acetic acid concentration also increased approximately two-fold when respiration was blocked. A strain deleted for the GPD2 gene had the opposite phenotype, producing lower amounts of glycerol and acetic acid, with the latter compound only reduced during non-respiratory growth. A commercial wine yeast over-expressing GPD2 produced 16.5 g/L glycerol in a wine fermentation, compared to 7.9 g/L obtained with the parent strain. As seen for the laboratory strain, acetic acid concentrations were also increased when using the genetically modified wine yeast. A panel of wine judges confirmed the increase in volatile acidity of these wines. The altered glycerol biosynthetic pathway sequestered carbon from glycolysis and reduced the production of ethanol by 6 g/L.     

Genome comparison and evolutionary analysis of different industrial lager yeasts (Saccharomyces pastorianus)

Fermented beverages, especially beer, have accompanied human civilizations throughout our history. The yeast strains used for lager beer fermentation have long been recognized as hybrids between two Saccharomyces species. For hundreds of years, lager yeast (Saccharomyces pastorianus) has been subjected to multiple rounds of domestication owing to artificial selection during beer production. As a result, this species comprises a genetically diverse collection of strains that are used in different breweries. However, the scope of genetic diversity captured during the domesticated evolution of this species remains to be determined. To begin to address this, we collected the genome information of the only four lager strains that had been whole‐genome sequenced. For the first time, genome comparison was conducted between lager yeasts and clear signatures were found that defined each industrial yeast strain. The genetic variation comprises both single nucleotide polymorphisms and insertions and deletions. In addition, the core–pan genome was introduced for the first time to the genomic analysis of lager yeasts, detecting numerous strain‐specific and species‐shared genes. Furthermore, phylogenetic tree and synteny analysis results obtained in this study revealed information regarding the evolutionary relationship and group differentiation of studied strains. Genome comparison of the lager strains will, therefore, enable the characterization of the overall genetic diversity of this species, assist in the identification of genomic loci that play important roles in regulating key industrial phenotypes, and highlight the understanding of the hybrid nature and evolutionary details. Copyright © 2016 The Institute of Brewing & Distilling     

Nutritional and toxicological evaluation of yeast (Saccharomyces cerevisiae) biomass and a yeast protein concentrate

Brewer's yeast was prepared by alkaline treatment for debittering, cell wall rupture and dehydration by spray drying. Yeast protein concentrate was prepared by centrifugation of the ruptured cell suspension, treatment of the supernatant with sodium perchlorate, precipitation of the protein at isoelectric pH (4.2) and neutralisation of the isoelectric protein to pH 6.5 with sodium hydroxide, prior to lyophylisation. Chemical characterisation was performed on the biomass and protein concentrate. Amino acid scores were 98.1 and 87.2% for the whole biomass and protein concentrate respectively, based on available lysine and compared with the FAO/WHO/UNU reference standard. The growth‐promoting property of the yeast biomass protein was roughly 85% of casein and was significantly better than for the yeast protein concentrate. No difference in growth was found between 15 and 30% dietary protein for all three sources, ie casein, whole yeast biomass and yeast protein concentrate. When tested for subchronical toxicity at 15 and 30% protein concentration, no evidence of toxicity was found for the whole yeast biomass, compared with casein, after 45 and 90 days of feeding. Retarded growth and discrete liver steatosis were observed in rats fed the yeast protein concentrate at both dietary levels. © 2000 Society of Chemical Industry     

The HTL1 gene (YCR020W-b) of Saccharomyces cerevisiae is necessary for growth at 37 degrees C, and for the conservation of chromosome stability and fertility

A small 78 codon ORF, named HTL1 (Chen et al., unpublished results), situated between loci MAK31 and HSP30 on chromosome III of Saccharomyces cerevisiae, is required for growth at 37 degrees C. In this communication, we characterize the ORF and show that disruption of HTL1, besides preventing growth at 37 degrees C, causes genetic and/or epigenetic instability at 26 degrees C: ploidy increases in about 10% of cells grown from individual disruptants and a fraction of disruptant clones are predestined to a rapid and progressive loss of fertility during growth at 26 degrees C.     

Identification and characterization of calcium and manganese transporting ATPase (PMR1) gene of Pichia pastoris

A gene homologous to Saccharomyces cerevisiae PMR1 has been cloned in the methylotrophic yeast Pichia pastoris. The entire P. pastoris PMR1 gene (PpPMR1) codes a protein of 924 amino acids. Sequence analysis of the PpPMR1 cDNA and the genomic DNA revealed that there is no intron in the coding region. The putative gene product contains all of the conserved regions observed in P-type ATPases and exhibits 66.2%, 60.3% and 50.6% identity to Pichia angusta (Hansenula polymorpha), Saccharomyces cerevisiae PMR1 and human ATP2C1 gene products, respectively. A pmr1 null mutant strain of P. pastoris exhibited growth defects in media with the addition of EGTA, but with supplementation of Ca2+ to a calcium-deficient media reversed the growth defects of the mutant strain. Manganese reversed the growth defects of the mutant strain; however, the cell growth was not as profound as the Ca2+ -supplemented media. The results demonstrated that the P. pastoris gene encodes the functional homologue of the S. cerevisiae PMR1 gene product, a P-type Ca2+/Mn2+ -ATPase. The DNA sequence of the P. pastoris PMR1 gene has been submitted to GenBank under Accession No. DQ239958.     

Human pancreatic glucokinase (GlkB) complements the glucose signalling defect of Saccharomyces cerevisiae hxk2 mutants

Human pancreatic glucokinase (GlkB, hexokinase IV) has been expressed in Saccharomyces cerevisiae. The recombinant protein showed similar enzyme kinetics to those described for the original enzyme. When expressed in hxk2 yeast mutants, GlkB complemented both the glucose induction and the glucose repression defects present in the mutant. It was also functional in regulating the activity of the Snf1 kinase complex in response to glucose, participating in the regulation of the Reg1/Glc7 phosphatase complex, as its yeast counterpart.     

Cloning of CDC33: a gene essential for growth and sporulation which does not interfere with cAMP production in Saccharomyces cerevisiae

The CDC33 gene of Saccharomyces cerevisiae belongs to the class II 'START' genes. Its product is required for the initiation of a new cell division cycle (Hartwell, 1974). Many results suggest that the cAMP signalling pathway is one of the major controlling elements of 'START'. Components of this pathway are encoded by class II 'START' genes. The aim of the present study is to determine whether or not the CDC33 gene interferes with the cAMP signalling pathway. We report here the molecular cloning of the CDC33 gene by complementation of the cdc33-1 thermosensitive mutant. The identity of the cloned gene is confirmed by site-specific reintegration and segregation analysis. This gene is transcribed into a 900-nucleotides mRNA and appears to be relatively abundant in the cell. We also show that the CDC33 gene product is essential for sporulation. cdc33-1 mutant cells are able to enter into the resting state. The cAMP intracellular pool is not modified when the cdc33-1 mutant is shifted to the restrictive temperature. The cdc33-1 mutation is not suppressed by other known elements of the cAMP cascade. All these results suggest that the CDC33 'START' gene does not interfere with the cAMP signalling pathway which controls cell division.     

The Branched-Chain Amino Acid Permease Gene of Saccharomyces cerevisiae,BAP2, Encodes the High-Affinity Leucine Permease (S1)

The amino acid leucine has been shown previously to be transported into a yeast cell by at least three permeases: the general amino acid permease, a high-affinity permease (S1) and a low-affinity permease (S2). We isolated the gene BAP2 as a multicopy suppressor of the YPD⁻ phenotype of aat1leu2 yeast. BAP2 has been identified previously as encoding an amino acid permease which transports branched-chain amino acids. In order to align the genetic and biochemical studies of leucine uptake we completed a detailed kinetic analysis of yeast strains in which the BAP2 gene was disrupted and compared this to the kinetics of uptake of the parental strain. We demonstrate that BAP2 encodes the high-affinity leucine permease previously called S1. © 1997 John Wiley & Sons, Ltd.