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[Organic acid production by the yeast Yarrowia lipolytica (a review)].

The review sums up the results of studies of (1) physiological growth characteristics of the yeast Yarrowia lipolytica, cultured in the presence of diverse carbon sources (n-alkanes, glucose, and glycerol), and (2) superhigh synthesis of organic acids, which were performed at the Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences. Microbiological processes of obtaining alpha-ketoglutaric, pyruvic, isocitric, and citric acids are discussed.

Alkanes↗

[Tolerance of the yeast Yarrowia lipolytica to oxidative stress].

The adaptive response of the yeast Yarrowia lipolytica to the oxidative stress induced by the oxidants hydrogen peroxide, menadione, and juglone has been studied. H2O2, menadione, and juglone completely inhibited yeast growth at concentrations higher than 120, 0.5, and 0.03 mM, respectively. The stationary-phase yeast cells were found to be more resistant to the oxidants than the exponential-phase cells. The 60-min pre-treatment of logarithmic-phase cells with nonlethal concentrations of H2O2 (0.3 mM), menadione (0.05 mM), and juglone (0.005 mM) made the cells more resistant to high concentrations of these oxidants. The adaptation of yeast cells to H2O2, menadione, and juglone was associated with an increase in the activity of cellular catalase, superoxide dismutase, glucose-6-phosphate dehydrogenase, and glutathione reductase, the main enzymes involved in cell defense against oxidative stress.

Adaptation, Psychological↗

[Range of substrates and steroid bioconversion reactions performed by recombinant microorganisms Saccharomyces cerevisiae and Yarrowia lipolytica expressing cytochrome P450c17].

The relationship between 17alpha-hydroxylation and 20-oxidation-reduction of progesterone and some of its derivatives was studied in yeast strains Saccharomyces cerevisiae YEp51alpha, Yarrowia lipolytica E129A15, and expressing cytochrome P450c17. The key metabolites were found to be 17alpha-hydroxyprogesterone and 17alpha,20(alpha,beta)-dihydroxypregn-4-ene-3-ones. The bioconversion pathways of pregn-4-ene-20(alpha,beta)-ol-3-ones were determined. They included cycles of 20-oxidation, 17alpha-hydroxylation, and stereospecific 20-reduction. The efficiency and kinetic parameters of steroid bioconversion by the recombinant strains were determined. The role of yeast analogs of mammalian steroid dehydrogenases is discussed. It was found that any of the desired derivatives, 17alpha-hydroxyprogesterone or progesterone 17alpha,20(alpha,beta)-diols, could be obtained from progesterone.

Gene Expression↗

Yarrowia lipolytica SRP54 homolog and translocation of Kar2p.

To investigate the role of Srp54p in protein translocation, the Yarrowia lipolytica SRP54 homolog was cloned. Sequencing revealed an open reading frame of 536 amino acids coding for a 57.2 kilodalton polypeptide with 55 to 57% sequence identity to Srp54ps of Saccharomyces cerevisiae, Schizosaccharomyces pombe, and mouse. Like these Srp54ps, Y. lipolytica Srp54p has an N-terminal domain with a highly conserved GTP-binding site and a methionine-rich C-terminal domain. Differing results regarding the essentiality of SRP subunits were obtained. SRP54 is important but not essential for growth, but it was reconfirmed that at least one SRP RNA gene is essential. Cells with SRP54 deleted grow about six times more slowly than wild type; faster-growing colonies, still growing much slower than wild type, appeared quite frequently. In srp54 delta cells, no untranslocated alkaline extracellular protease precursor was detected. Therefore, to develop another reporter molecule the Y. lipolytica KAR2 homolog was cloned and Kar2p antibodies were produced. For Kar2p an untranslocated precursor was detected in srp54 delta but not in wild-type cells, suggesting that its translocation was defective in the srp54 delta cells. These results confirm an in vivo rule for SRP in protein translocation in Y. lipolytica, suggest that SRP RNA or an SRP core-particle has functions not shared by Srp54p, and show that, as in S. cerevisiae and Sz. pombe, reporter molecules differ in their dependency on SRP for translocation.

Amino Acid Sequence↗

Secretion and pH-dependent self-processing of the pro-form of the Yarrowia lipolytica acid extracellular protease.

The secretion and maturation of the acid extracellular protease (AXP) of the yeast Yarrowia lipolytica have been characterized using antiserum raised against this enzyme. A 42 kDa pro-enzyme form of AXP was identified from lysates of radiolabelled Y. lipolytica cells and found to contain no N-linked carbohydrate moieties. Using pulse-chase immune precipitation it was demonstrated that the AXP precursor was secreted into the extracellular medium where, under conditions of low pH, it underwent autocatalytic activation forming the mature enzyme. Conversion of the AXP pro-form in the presence of the protease inhibitor pepstatin indicated that an intramolecularly-catalysed reaction mechanism was involved in AXP maturation. Further evidence supporting the role of autocatalytic processing came from the side-chain specificity of mature AXP towards the oxidized B-chain of insulin.

Amino Acid Sequence↗

Cloning and characterization of the peroxisomal acyl CoA oxidase ACO3 gene from the alkane-utilizing yeast Yarrowia lipolytica.

The ACO3 gene, which encodes one of the acyl-CoA oxidase isoenzymes, was isolated from the alkane-utilizing yeast Yarrowia lipolytica as a 10 kb genomic fragment. It was sequenced and found to encode a 701-amino acid protein very similar to other ACOs, 67.5% identical to Y. lipolytica Aco1p and about 40% identical to S. cerevisiae Pox1p. Haploid strains with a disrupted allele were able to grow on fatty acids. The levels of acyl-CoA oxidase activity in the ACO3 deleted strain, in an ACO1 deleted strain and in the wild-type strain, suggested that ACO3 encodes a short chain acyl-CoA oxidase isoenzyme. This narrow substrate spectrum was confirmed by expression of Aco3p in E. coli.

Acyl-CoA Oxidase↗

Cloning and characterization of an n-alkane-inducible cytochrome P450 gene essential for n-decane assimilation by Yarrowia lipolytica.

A gene encoding cytochrome P450 involved in n-alkane utilization was cloned from an n-alkane assimilating yeast, Yarrowia lipolytica CX161-1B. The RT-PCR was performed on the mRNA prepared from the cells grown on n-alkane as a template using degenerated PCR primers designed for the conserved amino acid sequences of the CYP52 family. The RT-PCR amplified fragment was then used as a probe to isolate genes coding for P450 of the CYP52 family from the genomic DNA library of the strain CX161-1B. The nucleotide sequence of one of the positive clones was determined. An open reading frame which had the same nucleotide sequence as the RT-PCR-amplified fragment was identified. It was of 523 amino acid residues, 60.2 kDa in molecular mass, and had 30-45% sequence identity with the other members of the CYP52 family of Candida species so far analysed. The expression of the P450 gene that was named as YlALK1 was induced by n-tetradecane and repressed by glycerol. A YlALK1 gene disruptant did not grow well on n-decane, but grew on longer-chain n-alkanes such as hexadecane as a sole carbon source. Introduction of YlALK1 on a plasmid to the disruptant restored the decane assimilation. These results suggest that the YlALK1 gene product is the major P450A1k to metabolize short-chain n-alkanes such as decane and dodecane in Y. lipolytica.

Alkanes↗

Distribution of the actin cytoskeleton during the cell cycle of Yarrowia lipolytica and the visualization of the tubulin cytoskeleton by immunofluorescence.

Actin distribution was examined during the cell cycle of the dimorphic yeast Yarrowia lipolytica, showing the correlation between bud growth, nuclear migration and rearrangement of the actin cytoskeleton. The results correspond with observations made in cells of Saccharomyces cerevisiae, S. uvarum and Candida albicans. Localization of actin was also determined in hyphal cells, where actin is stained predominantly in the tip and also at the septum of hyphae. The standard methods used for tubulin immunostaining in S. cerevisiae and C. albicans cells were adapted for application in Y. lipolytica.

Actins↗

Sequence analysis of SLA2 of the dimorphic yeasts Candida albicans and Yarrowia lipolytica.

We report the complete nucleotide sequence of SLA2 of the dimorphic yeasts Candida albicans and Yarrowia lipolytica. In Saccharomyces cerevisiae, SLA2 codes for an actin binding protein. The deduced amino acid (aa) sequences of C. albicans CaSla2p and Y. lipolytica YlSla2p consist of 1063 and 1054 aa, respectively. The alignment of the deduced proteins of Saccharomyces cerevisiae, Y. lipolytica and C. albicans shows regions of identity in the N-terminal part of the proteins, which are essential for growth at 37 degrees C, endocytosis and actin organization in S. cerevisiae. The Sla2p proteins have also several conserved regions in the C-terminal moiety, the I/LWEQ boxes, displaying homology to the talin protein of mouse, Dictyostelium discoideum, Caenorhabditis elegans and to human huntingtin interacting protein (Hip 1p). The sequence data of C. albicans SLA2 are registered in the EMBL database (AJ009556), and for the Y. lipolytica gene in GenBank (U65409).

Amino Acid Sequence↗

Molecular cloning and characterization of the gene HXK1 encoding the hexokinase from Yarrowia lipolytica.

We have cloned the gene HXK1 from the dimorphic yeast Yarrowia lipolytica that encodes the unique hexokinase of this yeast. The gene has an intron located 39 base pairs after the A of the first ATG. The putative protein contains a sequence of 40 amino acids which is absent from other known hexokinase sequences. Y. lipolytica strains devoid of hexokinase grew in glucose slower than wild-type. This growth was due to the existence of a glucokinase. The hexokinase from Y. lipolytica substituted effectively for hexokinase II from S. cerevisiae in catabolite repression of invertase. The hexokinases from Schizosaccharomyces pombe or Kluyveromyces lactis were much less effective in this role. The K(m) for glucose and fructose of hexokinase was 0.38 mM and 3.56 mM, respectively. The K(m) of glucokinase for glucose was 0.17 mM. While the hexokinase was strongly inhibited by trehalose-6-phosphate (K(i)=3.6 microM), glucokinase was not affected by this compound.

Amino Acid Sequence↗

Cloning and characterization of the EXG1 gene from the yeast Yarrowia lipolytica.

The YlEXG1 gene of Yarrowia lipolytica, encoding an exo-1, 3-beta-glucanase, was isolated by screening a genomic library with a DNA probe obtained by PCR amplification, using oligonucleotides designed according to conserved regions in the EXG1, EXG2 and SSG1 genes from Saccharomyces cerevisiae. YlEXG1 consists of a 1263 bp open reading frame encoding a protein of 421 amino acids with a calculated molecular weight of 48 209 Da. Northern blot analysis revealed a unique YlEXG1-specific transcript, 1.4 kb long. A putative pre(signal)-peptide of 15 amino acids is proposed at the N-terminal domain of the primary translation product. The deduced amino acid sequence shares a high degree of homology with exo-1, 3-beta-glucanases from other yeast species, including S. cerevisiae, Kluyveromyces lactis, Pichia angusta and Debaryomyces occidentalis. YlExg1p contains the invariant amino acid positions which have been shown to be important in the catalytic function of family 5 glycosyl hydrolases. Chromoblot analysis indicated that YlEXG1 is located on chromosome VI. Disruption of YlEXG1 did not result in a phenotype under laboratory conditions and did not prevent the yeast-hypha transition. The sequence data reported in this paper have been assigned EMBL Accession No. Z46872.

Amino Acid Sequence↗

trans-dominant mutations in the GPR1 gene cause high sensitivity to acetic acid and ethanol in the yeast Yarrowia lipolytica.

Acetate non-utilizing strains harbouring trans-dominant mutations in the GPR1 gene (GPR1(d)) of the dimorphic yeast Yarrowia lipolytica have been selected and characterized. These mutants are highly sensitive to low concentrations of acetic acid and ethanol, even in presence of glucose. The toxic effect of acetic acid is pH-dependent and has the strongest effect at low pH. In contrast, the action of ethanol is pH-independent. One GPR1(d) mutant has been detected that was highly sensitive to acetic acid but could still grow on ethanol, which indicates putative differences in the function of the GPR1 gene product in the sensitivity to acetic acid and ethanol. The GPR1(d) mutants exhibit a complex pleiotropic phenotype. The mutations cause changed colony morphology as well as dimorphism of cells, and induce early cell death during growth on glucose, even without the presence of dicarbon compounds. Composition of intracellular membranes, as well as morphology of vacuole and mitochondria, were strongly changed. Back-crosses with wild-type strains and analysis of recombinant strains have shown that the expression of the pleiotropic phenotype depends on the site of mutation in the GPR1 gene, as well as on the genetic background of the strain harbouring the responsive mutation. Our data suggest that Gpr1p is involved in a general response of cells to the toxic action of dicarbon compounds like acetic acid and ethanol.

Acetic Acid↗

Cloning and characterization of the Yarrowia lipolytica squalene synthase (SQS1) gene and functional complementation of the Saccharomyces cerevisiae erg9 mutation.

The squalene synthase (SQS) gene encodes a key regulatory enzyme, farnesyl-diphosphate farnesyltransferase (EC 2.5.1.21), in sterol biosynthesis. The SQS1 gene was isolated from a subgenomic library of the industrially important yeast Yarrowia lipolytica, using PCR-generated probes. Probes were based on conserved regions of homologues from different organisms. The complete nucleotide sequence of the coding region and the corresponding amino acid sequence were determined. The sequences showed extensive homologies with squalene synthase genes and enzymes from a number of other organisms and extreme amino acid conservation within the binding and catalytic domains. Direct cloning of a 4.3 kb genomic Y. lipolytica fragment, also comprising its own promoter and terminator sequences, into autonomously replicating plasmid YEp352 and subsequent transformation of a Saccharomyces cerevisiae mutant strain with relevant erg9: ura3-1 markers, resulted in functional complementation of these deficiencies, although Northern blot analyses did not reveal a unique full-length messenger. The availability of the Y. lipolytica SQS1 gene (GenBank Accession No. AF092497) offers prospects for metabolic engineering of the isoprenoid and sterol biosynthetic pathways.

Amino Acid Sequence↗

Transformations of membrane-bound organelles in sec 14 mutants of the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica.

BACKGROUND: In early descriptions of ultrastructural alterations of secretory (sec) mutants of the yeast Saccharomyces cerevisiae, two mutants, sec7 and sec14, were shown to produce cell structures, the so-called Berkeley bodies thought at first to correspond to Golgi structures. In sec7 mutants grown at restrictive temperature, secretion granules soon dis-appeared, whereas networks of Golgi tubules increased in size and transformed into stacks of seven to eight flattened elements. At these time intervals, structures resembling Berkeley bodies appeared to be extensions of the endoplasmic reticulum (Rambourg et al., 1993). It is the purpose of the present study to examine by electron microscopy S. cerevisiae sec14 mutants and to compare the modifications along their secretory pathway with those occurring in a homologous mutant of Yarrowia lipolytica. METHODS: S. cerevisiae sec 14 mutant cells coming from exponentially growing cultures were examined either at 24 degrees C or after shifting at 37 degrees C for 0, 2, 5, 10, 15, 20, 30, 45, 60, 90, and 120 min. Y. lipolytica mutant cells were first cultured in YNB in 5000 medium and then transferred for 0, 6, 8, 12, 20, and 24 hr, in a phosphate-buffered YPD medium, which allows wild cells to differentiate from yeast to mycelian form. In both cases, cells were fixed in 2% glutaraldehyde, treated for 15 min in 1% sodium metaperiodate, post-fixed in reduced osmium, and embedded in Epon. To visualize the three-dimensional configuration of cell organelles, stereopairs were prepared from section stained with lead citrate and tilted at +/- 15 degrees from the 0 degree position of the goniometric stage of the electron microscope. RESULTS: In S. cerevisiae mutant cells shifted for 2 min at the restrictive temperature, faintly stained networks of thin anastomosed tubules were located at close proximity and often continuous with faintly stained ER cisternae. More intensely stained tubular networks with nodular dilations having the size of secretion granules were dispersed throughout the cytoplasm. Later on, the faintly stained ER elements and related tubular networks decreased in number, whereas the intensely stained nodular tubular networks increased in frequency. The incidence of secretion granules also increased and were distributed at random throughout the cytoplasm. Widemeshed, intensely stained fenestrated spheres were often encountered and increased in number, in parallel to the increase in the number of nodular tubular networks. At late time intervals, the fenestrated spheres decreased in number as they seemingly transformed into spherical bodies identical to vacuoles. In contrast to what occurred in S. cerevisiae sec14 mutant, the main ultrastructural modification observed in Y. lipolytica transferred to the YPD medium was the formation of deep plasma membrane invaginations. CONCLUSIONS: It appears that two functionally homologous PI/PC transfer proteins (Sec14psc and Sec14pyl) control distinct physiological processes in the two sec14 mutants examined. Such differences are perhaps related to the regulatory role of these proteins in different target organelles, i.e., the Golgi apparatus in S. cerevisiae or the plasma membrane in Y. lipolytica.

Carrier Proteins↗

Improvement of heterologous protein productivity using recombinant Yarrowia lipolytica and cyclic fed-batch process strategy.

A cyclic fed-batch bioprocess is designed and a significant improvement of rice alpha-amylase productivity of recombinant Yarrowia lipolytica is illustrated. A bioprocess control strategy developed and reported here entails use of a genetically stable recombinant cloned for heterologous protein, use of optimized media for cell growth and enzyme production phases, and process control strategy enabling high cell-density culture and high alpha-amylase productivity. This process control can be achieved through maintaining a constant optimal specific cell growth rate at a predetermined value (i.e., 0.1 h-1), controlling medium feed rate commensurate with the cell growth rate, and maintaining a high cell-density culture (i.e., 60-70 g/L) for high productivity of cloned heterologous protein. The volumetric enzyme productivity (1, 960 units/L. h) achieved from the cyclic fed-batch process was about 3-fold higher than that of the fed-batch culture process (630 units/L. h).

Bioreactors↗

The cytochrome P450ALK multigene family of an n-alkane-assimilating yeast, Yarrowia lipolytica: cloning and characterization of genes coding for new CYP52 family members.

Genes encoding cytochromes P450 of the CYP52 family in the n-alkane-assimilating yeast Yarrowia lipolytica have been cloned and analyzed. Degenerate PCR primers which were designed for the conserved amino acid sequences of cytochromes P450ALK of Candida species were used for amplification and isolation of genes encoding P450ALK from a genomic DNA library of Y. lipolytica CX161-1B. Seven new genes (YlALK2-YlALK8) were isolated. Five of the seven YlALK genes were induced by n-alkane under the culture conditions used in this study, whereas their expression was strictly repressed by glycerol but not by glucose, similar to the case of YlALK1, reported previously. Disruption of YlALK2, YlALK3, YlALK4 or YlALK6 did not change the growth of Y. lipolytica on medium containing n-alkanes of various chain lengths. A mutant with disruptions in both YlALK1 and YlALK2 did not grow well on n-hexadecane, whereas one with disruptions in both YlALK1 and YlALK3, which has the same phenotype as the YlALK1 singly disrupted mutant, grew well on n-hexadecane. These results suggest that the presence of multiple P450ALK species is a rather common phenomenon among the n-alkane-assimilating yeasts and that in the n-alkane assimilation of Y. lipolytica, YlALK1 functions to assimilate n-decane and longer molecules, whereas YlALK2 is involved in the assimilation of molecules longer than n-dodecane; other YlALKs are not significantly involved in the assimilation of C10-C16 n-alkanes.

Alkanes↗

Current awareness on yeast.

In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on yeasts. Each bibliography is divided into 10 sections. 1 Books, Reviews & Symposia; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (3 weeks journals - search completed 21st June 2000)

Yeasts↗

Natural zeolite clinoptilolite increases the concentrations of sphingoid bases in the yeast Yarrowia lipolytica.

In the present paper, we studied the effect of natural zeolite clinoptilolite on sphingolipid metabolism in the yeast Yarrowia lipolytica. We also investigated if zeolite addition had any impact on cell shape and size, as well as on the pH alterations during the culture growth. High performance liquid chromatography analysis of sphingoid bases obtained by acid hydrolysis of complex sphingolipids from Y. lipolytica showed that their concentrations markedly rose upon the zeolite addition. The largest increase among the identified molecular species of sphingoid bases was seen in C18 phytosphingosine, whose levels rose 6.2-fold and 22.3-fold after culturing cells for 24 and 36 hours respectively in the presence of finely ground zeolite. pH measurements of the culture medium showed a similarity between pH profiles of control and zeolite-supplemented cells, suggesting that ion-exchange capacity was not probably responsible for the observed change in sphingolipid metabolism. Scanning electron microscopy revealed that zeolite affected cell size and shape. Y. lipolytica cells grown in the absence of zeolite were oval-shaped with an average cell size of 0.7-2.7 microns, whereas when cultured with zeolite, they were round-shaped and larger, having an average cell size of 1.3-2.9 microns.

Culture Media↗