Cloning,nucleotide sequence and functions of XPR6, which codes for a dibasic processing endoprotease from the yeast Yarrowia lipolytica

Yarrowia lipolytica DO613, carrying the xpr6-13 mutation, secretes an inactive precursor of alkaline extracellular protease that has not been cleaved after the Lys-Arg at the end of the pro-region. Compared to wild type, DO613 membrane preparations had significantly reduced ability to cleave after Lys-Arg of an artificial substrate. The XPR6 gene was cloned by complementation by screening for restoration of production of alkaline protease activity. Sequencing of a 3735 base pair SalI-SphI XPR6 fragment revealed a large open reading frame with a coding capacity of 976 amino acids (molecular weight, 110 016). The deduced amino acid sequence had significant homology to Saccharomyces cerevisiae Kex2p, a processing endoprotease that cleaves after pairs of basic amino acids. Disruption of the XPR6 gene was not lethal, but it resulted in several phenotypic changes. First, essentially no mature alkaline extracellular protease was produced indicating that the low levels produced by strains carrying previously isolated xpr6 alleles were due to leaky mutations. Second, mating type B strains carrying the disrupted XPR6 gene did not mate, but mating type A strains did. Third, the XPR6 disruption strains grew poorly on rich media at pH 5·5 and above. Cells remained physically attached after budding and continued to bud forming large dog balloon-like structures. In addition, these structures aggregated forming visible clumps in liquid culture. These growth aberrations were largely eliminated by growing cells in medium at pH 4. Fourth, no mycelial forms were observed regardless of the pH.     

Overexpression of diacylglycerol acetyltransferase from Euonymus europaeus in Yarrowia lipolytica leads to the production of single-cell oil enriched with 3-acetyl-1,2-diacylglycerols

The 3-acetyl-1,2-diacylglycerols (acTAGs) are the molecules that are structurally similar to triacylglycerols (TAGs). They are naturally produced by plants of the family Celastraceae and animals such as Cervus nippon and Eurosta solidaginis. The presence of acetate in the sn–3 position of the glycerol backbone confers advantages to these compounds, for example, lower viscosity and calorific value compared to classical TAGs. In this work, the gene EeDAcT, which encodes diacylglycerol acetyltransferase in a species of bush (Euonymus europaeus), was overexpressed in strains Po1d (capable of accumulating storage lipids) and JMY1877 (incapable of accumulating storage lipids) of Yarrowia lipolytica, to test the activity of the gene EeDAcT and the production of acTAGs in oleaginous and nonoleaginous genetic backgrounds. It was observed that both the strains containing the gene EeDAcT (YL33 and YL35 for Po1d and JMY1877 strains, respectively) produced acTAGs. The strain YL33 accumulated up to 20% intracellular lipids, 20% of which was acTAGs, and 40% was TAGs. On the other hand, the strain YL35, which showed interrupted TAGs accumulation, produced up to 10% acTAGs as the only storage lipid. Unfortunately, the quantity of acTAGs produced in YL35 was insignificant, as the overall lipid accumulated in the strain was not more than 4% of the biomass. The fatty acid profile of acTAGs produced by the YL33 strain was remarkably similar to TAGs, and both of these structures were rich in oleic (45%) and palmitic (25%) acids.     

尼罗红荧光光谱法快速测定解脂耶氏酵母油脂含量的研究

为了建立快速简便检测解脂耶氏酵母油脂含量的方法,探讨了尼罗红-光谱法测定解脂耶氏酵母油脂含量的检测条件。通过研究解脂耶氏酵母最佳发射光波长、细胞密度、尼罗红染液用量、染色时间、不同助溶剂效能及最佳体积分数对荧光强度的影响,确定了最佳检测条件,得到细胞油脂含量与荧光强度的线性关系。解脂耶氏酵母在激发光560 nm、发射光650 nm处有最高荧光值,每毫升菌液加入质量分数为0.1 mg/m L的尼罗红染液20μL,加入体积分数为15%的异丙醇,黑暗染色5 min,在细胞OD600=0¹.3的范围内,菌液的油脂含量（X）与荧光值（Y）呈较好的线性关系,线性关系式为Y=6.3651X+10.097,R2=0.9902,灵敏度达0.0001 g。该方法能够准确地反映出解脂耶氏酵母胞内油脂含量。尼罗红-荧光法可成为一种快速检测解脂耶氏酵母胞内油脂含量的新方法。      

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. © 1998 John Wiley & Sons, Ltd.     

共轭亚油酸合成相关基因在耶氏解脂酵母中异源表达及活性研究

为了探究植物乳杆菌(Lactobacillus plantarum)中与共轭亚油酸(CLA)生物合成相关的3个基因:(亚)油酸水合酶基因(mcra)、短链脱氢酶/氧化还原酶基因(dh)、乙酰乙酸脱羧酶基因(dc)在耶氏解脂酵母(Yarrowia lipolytica,Y.lipolytica)中异源表达后能否具有活性,利用两个耶氏解脂酵母整合表达质粒(p INA 1269和p INA 1312),将3个基因分别导入耶氏解脂酵母营养缺陷型宿主菌Polf(Ura~-,Leu~-)中,构建了重组菌株。在不同重组菌中添加相应的底物:亚油酸(LA)和10-羟基-顺12-十八碳烯酸(10-HOE),然后对反应体系进行脂肪酸检测,得到基因对应的不同产物:10-HOE和10-氧代-反11-十八碳烯酸(10-oxo-trans 11-octadecenoic acid),证明mcra、dh、dc在耶氏解脂酵母中进行了异源表达并且具有活性。     

解脂耶氏酵母作为微生物细胞工厂的应用研究进展

解脂耶氏酵母（Yarrowia lipolytica）是一种重要的工业微生物菌种,被公认为食品级安全微生物。近年来,随着合成生物学和基因编辑技术的快速发展,科学家们利用合成生物学及基因编辑技术已经成功构建出了能够生产生物化学品、生物燃料、香料、药物、工业酶和药用蛋白等多种高附加值工业产品的解脂耶氏酵母细胞工厂,使得该酵母在食品、药品和生化能源等领域均具有巨大的应用潜力。本文将重点介绍解脂耶氏酵母表达系统、合成生物学元件和基因编辑方法的最新研究进展和应用情况,并对近年来以解脂耶氏酵母作为微生物细胞工厂生产高附加值产品的应用实例进行总结,希望为研究人员进一步利用解脂耶氏酵母进行底盘细胞设计、构建和优化相关合成途径并最终实现目的产物的高效合成提供有用的信息。     

Screening a genomic library for genes involved in propionate tolerance in Yarrowia lipolytica

Microbial oils are regarded as promising alternatives to fossil fuels. For bio-oil production to be sustainable over the long term, utilizing low-cost substrates like volatile fatty acids (VFAs) is crucial. Increasing attention is being paid to one of the most common VFAs: propionate, a substrate that could be used to produce the odd-chain FAs of industrial interest. However, little is known about microbial responses to propionate-induced stress and the genes involved. Using genomic library screening, we identified two genes involved in propionate tolerance in Yarrowia lipolytica—MFS1 and RTS1. Strains containing each of the genes displayed enhanced tolerance to propionate even when the genes were expressed in truncated form via a replicative plasmid. Compared with the control strain, the strain overexpressing MFS1 under a constitutive promoter displayed greater tolerance to propionate: It had a shorter lag phase and higher growth rate in propionate medium (0.047 hr⁻¹ versus 0.030 hr⁻¹ for the control in 40 g/L propionate); it also accumulated more total lipids and more odd-chain lipids (10% and 3.3%, respectively) than the control. The strain overexpressing RTS1 showed less tolerance for propionate than the strains harboring the truncated form (0.057 hr⁻¹ versus 0.065 hr⁻¹ in 40 g/L propionate medium) but still had higher tolerance than the control strain. Furthermore, the overexpression of RTS1 seemed to confer tolerance to other weak acids such as lactate, formic acid, malic acid, and succinic acid. This work provides a basis for better understanding the response to propionate-induced stress in Y. lipolytica.     

Optimization of cyclopropane fatty acids production in Yarrowia lipolytica

Cyclopropane fatty acids, which can be simply converted to methylated fatty acids, are good unusual fatty acid candidates for long-term resistance to oxidization and low-temperature fluidity useful for oleochemistry and biofuels. Cyclopropane fatty acids are present in low amounts in plants or bacteria. In order to develop a process for large-scale biolipid production, we expressed 10 cyclopropane fatty acid synthases from various organisms in the oleaginous yeast Yarrowia lipolytica, a model yeast for lipid metabolism and naturally capable of producing large amounts of lipids. The Escherichia coli cyclopropane fatty acid synthase expression in Y. lipolytica allows the production of two classes of cyclopropane fatty acids, a C17:0 cyclopropanated form and a C19:0 cyclopropanated form, whereas others produce only the C17:0 form. Expression optimization and fed-batch fermentation set-up enable us to reach a specific productivity of 0.032 g·L⁻¹·hr⁻¹ with a genetically modified strain containing cyclopropane fatty acid up to 45% of the total lipid content corresponding to a titre of 2.3 ± 0.2 g/L and a yield of 56.2 ± 4.4 mg/g.     

The use of Yarrowia lipolytica for the expression of human cytochrome P450 CYP1A1

Cytochromes P450 constitute a superfamily of haem-thiolate mono-oxygenases that are involved in the oxidative metabolism of lipophilic subtrates. These enzymes require association with cytochrome P450 reductase (CPR) to achieve optimal activities. We have expressed human cytochrome P450 CYP1A1 under the POX2 promoter (pPOX2-CYP1A1) in Y. lipolytica, with or without overproduction of Y. lipolytica CPR expressed under the ICL promoter (pICL-CPR) or the POX2 promoter (pPOX2-CPR). Activity of cytochrome CYP1A1 was analysed by conversion of hydroxyresorufin to resorufin. Strain JMY330 and JMY330-CPR present no activity, the monocopy cytochrome CYP1A1 integrant JMY331 and JMY331-CPR derivatives present an average activity of 32.0 pM/min/dw and 48.3 and 64.6 pM/min/dw for pICL-CPR and pPOX2-CPR, respectively. Increase of CPR expression resulted in about two-fold higher activity. The multicopy 1A1 integrant JMY339 and JMY339-CPR derivatives present an activity of 129 pM/min/dw and 815-1845 pM/min/dw, respectively. Increase of CPR expression resulted in 6.3-12.8-fold higher activity, depending on the CPR transformant. We observed a 50-fold increase of activity between the monocopy integrant JMY331 as compared to the multicopies integrant JMY339-CPR in which CPR was overexpressed.     

Isolation of the MNN9 gene of Yarrowia lipolytica (YlMNN9) and phenotype analysis of a mutant ylmnn9 Delta strain

In this work we describe the isolation of the Yarrowia lipolytica homologue of Saccharomyces cerevisiae MNN9 gene, which we have named YlMNN9, and the phenotype analysis of a Y. lipolytica strain containing the disrupted YlMNN9 allele. YlMNN9 was cloned using degenerate consensus oligonucleotides to generate specific probes that were in turn used to screen mini-gene libraries. The gene is defined by a 1014 bp ORF predicted to encode a protein 337 amino acids long that shares significant homology with the Mnn9ps of S. cerevisiae, Candida albicans and Hansenula polymorpha, including a putative N-terminal transmembrane domain. Disruption of YlMNN9 leads to phenotypes such as resistance to sodium orthovanadate and sensitivity to hygromycin B, compatible with a glycosylation defect, and hypersensitivity to Calcofluor white, Congo red or zymolyase, characteristic of cell wall defects. Analysis of cell wall proteins present in beta-mercaptoethanol and zymolyase extracts showed significant differences between the parental and the ylmnn9 Delta strain. These results suggest that, as has been the case with the mnn9 strain of S. cerevisiae, the ylmnn9 Delta strain we present in this work, could be used to study the cell wall proteins of Y. lipolytica and how they are organized into the cell wall.     

Characterization of mutants of the yeast Yarrowia lipolytica defective in acetyl-coenzyme A synthetase.

The expression of the glyoxylate cycle enzymes is required for growth of the yeast Yarrowia lipolytica on acetate or fatty acids as sole carbon source. Acetyl-coenzyme A, which is produced by acetyl-coenzyme A synthetase (ACS) from acetate, is needed for induction of this expression. Acetate-non-utilizing mutants of this yeast were investigated in order to identify mutants which express no or strongly reduced activity of this enzyme. Mutations in gene ICL2 exhibited the strongest effects on the activity. In icl2 mutants, lack of ACS activity resulted in a non-induced glyoxylate cycle on acetate; however, induction on fatty acids was not affected. Gene ICL2 was identified as the structural gene encoding the monomer of ACS. It is shown that a high level of ACS activity is necessary for full expression of the glyoxylate cycle enzymes. Mutations in gene ICL1, which encodes isocitrate lyase, resulted in overproduction of ACS without any growth on acetate. A new gene (GPR1 = glyoxylate pathway regulation) was detected in which trans-dominant mutations inhibit expression of ACS and the glyoxylate cycle on acetate as carbon source.     

Evaluation of the ability of Yarrowia lipolytica to impart strain-dependent characteristics to cheese when used as a ripening adjunct

Four Yarrowia lipolytica strains were tested as cheese-ripening adjuncts with milk culture in cheese production to evaluate their effects on the microbiological and biochemical features of the cheeses. The Y. lipolytica strains were able to overcome the other naturally occurring yeasts and were compatible with lactic acid bacteria (LAB). Fourier transform infrared (FTIR) profiles and analysis of free fatty acids (FFAs) released during ripening showed that the strains induced a marked lipolysis and gave rise to different FFAs accumulation over time with respect to the control. Strain-dependent protein breakdown patterns were identified and these biochemical differences resulted in different cheese organoleptic characteristics.     

Experimental Design as a Tool for the Development of Citric Acid Production by Yarrowia lipolytica Using Glycerol as a Feedstock

Due to the scarcity of fossil fuels in the world, there is increasing interest in the commercial production of biodiesel, which leads to obtaining large amounts of glycerol as a byproduct. If not disposed of properly, glycerol can generate environmental impact. One of the promises, the application of the crude glycerol is the production of citric acid by microbial fermentation. Citric acid is industrially produced by a submerged fermentation process with Aspergillus niger, using sucrose as carbon source, but due to increased demand for citric acid, alternative processes using renewable sources or waste materials as substrates and the cultivation of yeast strains are being studied. The aim of the study was to determine the best culture condition for maximum citric acid synthesis and lower isocitric acid production from crude glycerol through experimental design tool. For this purpose, the yeast strain Yarrowia lipolytica IMUFRJ-50682 was cultivated in nitrogen-limited glycerol-based media. Therefore, glycerol and yeast extract concentrations and agitation speed were evaluated as independent variables. With pure glycerol, the highest citric acid production achieved was 16.5 g/L with an isocitric acid production of 7.7% （in relation to citric acid）. With crude glycerol, citric acid production reduced to 6.7 g/L because of higher biomass yield. Therefore, an increase in the initial carbon to nitrogen molar ratio from 714 to 1,561 was necessary to increase citric acid production to 9.2 g/L, reducing isocitric acid production and to achieve a yield of 0.41 g of citric acid per glycerol consumed. In this condition, less nitrogen source was used, reducing production costs.     

Isolation and characterization of the TRP1 gene from the yeast Yarrowia lipolytica and multiple gene disruption using a TRP blaster

The TRP1 gene encoding N-(5'-phosphoribosyl)-anthranilate isomerase was isolated from the yeast Yarrowia lipolytica, in which only a few genetic marker genes are available. The Y. lipolytica TRP1 gene (YlTRP1) cloned by complementation of Y. lipolytica trp1 mutation was found to be a functional homologue of Saccharomyces cerevisiae TRP1. Since YlTRP1 could be used for counterselection in medium containing 5-fluoroanthranilic acid (5-FAA), we constructed TRP blasters that contained YlTRP1 flanked by a direct repeat of a sequence and allowed the recycling of the YlTRP1 marker. Using the TRP blasters the sequential disruption of target genes could be carried out within the same strain of Y. lipolytica. The nucleotide sequence of the YlTRP1 gene has been deposited at GenBank under Accession No. AF420590.     

RHO1 (YlRHO1) is a non-essential gene in Yarrowia lipolytica and complements rho1Delta lethality in Saccharomyces cerevisiae

The synthesis of beta-1,3-glucan, the structural component of the yeast cell wall that gives shape to the cell, occurs at the plasma membrane and is the result of the activity of at least a two-component complex. Fks1p is the catalytic subunit directly responsible for the synthesis of beta-1,3-glucan, whilst the second subunit, Rho1p, has a GTP-dependent regulatory role (Yamochi et al., 1994). RHO1 has been characterized in Saccharomyces cerevisiae (Yamochi et al., 1994), and in several other fungal species. In this work, we have used degenerate oligonucleotides derived from the conserved regions of Rho1ps to isolate the RHO1 gene of Yarrowia lipolytica. The gene isolated in this way, which we have named YlRHO1, encodes a 204 amino acid protein that shows a high degree of homology with other Rho1ps. However, unlike S. cerevisiae, the ylrho1Delta disruptant strain in Y. lipolytica is viable, although it exhibits an increased sensitivity to Calcofluor white and Congo red. Also, YlRHO1 complements rho1 lethality in S. cerevisiae at both 28 degrees C and 37 degrees C. The complete sequence of YlRHO1 can be obtained from GenBank under Accession No. AF279915.     

Soluble forms of YlCrh1p and YlCrh2p, cell wall proteins of Yarrowia lipolytica, have beta-1,3-glycosidase activity

Crh1p and Crh2p of Saccharomyces cerevisiae are cell wall proteins covalently attached to cell wall glucan and are thought to be putative glycosidases involved in cell wall remodelling. We investigated whether YlCrh1p and YlCrh2p, the Yarrowia lipolytica proteins homologous to ScCrh1p and ScCrh2p, had the required glycosidase activity for cell wall biosynthesis and maintenance. Ylcrh1Delta and Ylcrh2Delta mutants showed sensitivity to compounds that interfere with cell wall construction. Soluble forms of YlCrh1p and YlCrh2p that lacked the C-terminal consensus sequence for GPI anchoring showed glycosidase activity on laminarin, a substrate carrying beta-1,3-glycosidic linkage. Our study suggests that the YlCrh1p and YlCrh2p may participate in cell wall biosynthesis and remodelling through their beta-1,3-glycosidase activity.     

Gene order in a 10 275 bp fragment of Yarrowia lipolytica, including adjacent YlURA5 and YlSEC65 genes conserved in four yeast species.

We have determined the sequence of a 10275 bp DNA segment of Yarrowia lipolytica located on chromosome VI. The sequence contains six complete open reading frames (ORFs) longer than 100 amino acids and two more partial ORFs at both ends. Two of the ORFs encode for the well-characterized genes YlURA5 (orotate phosphoribosyltransferase) and YlSEC65 (encoding a subunit of the signal recognition particle). These two genes show an identical organization-located on opposite strands and in opposite orientations-in four yeast species: Saccharomyces cerevisiae, Kluyveromyces lactis, Candida albicans and Y. lipolytica. One ORF and the two partial ORFs code for putative proteins showing significant homology with proteins from other organisms. YlVI-108w (partial) and YlVI-103w show 39% and 54% identity, respectively, with YDR430c and YHR088w from S. cerevisiae. YlVI-102c (partial) shows significant homology with a matrix protein, lustrin A from Haliotis rufescens, and with the PGRS subfamily (Gly-rich proteins) of Mycobacterium tuberculosis. The three remaining ORFs show weak or non-significant homology with previously sequenced genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AI006754.