Construction of a Quadruple Auxotrophic Mutant of an Industrial Polyploid Saccharomyces cerevisiae Strain by Using RNA-Guided Cas9 Nuclease

Industrial polyploid yeast strains harbor numerous beneficial traits but suffer from a lack of available auxotrophic markers for genetic manipulation. Here we demonstrated a quick and efficient strategy to generate auxotrophic markers in industrial polyploid yeast strains with the RNA-guided Cas9 nuclease. We successfully constructed a quadruple auxotrophic mutant of a popular industrial polyploid yeast strain, Saccharomyces cerevisiae ATCC 4124, with ura3, trp1, leu2, and his3 auxotrophies through RNA-guided Cas9 nuclease. Even though multiple alleles of auxotrophic marker genes had to be disrupted simultaneously, we observed knockouts in up to 60% of the positive colonies after targeted gene disruption. In addition, growth-based spotting assays and fermentation experiments showed that the auxotrophic mutants inherited the beneficial traits of the parental strain, such as tolerance of major fermentation inhibitors and high temperature. Moreover, the auxotrophic mutants could be transformed with plasmids containing selection marker genes. These results indicate that precise gene disruptions based on the RNA-guided Cas9 nuclease now enable metabolic engineering of polyploid S. cerevisiae strains that have been widely used in the wine, beer, and fermentation industries.     

利用可重复使用的URA3标记基因建立热带假丝酵母基因敲除系统

热带假丝酵母(Candida tropicalis)在发酵工业中具有重要的应用潜力,但二倍体遗传结构和较低的遗传转化效率限制了其代谢工程育种技术的应用。建立可靠的遗传转化技术并高效的删除目的基因是代谢工程改造热带假丝酵母的重要前提。文章以C. tropicalis ATCC 20336为出发菌株,通过化学诱变筛选获得了尿嘧啶缺陷型突变株C. tropicalis XZX(ura3/ura3)。以丙酮酸脱羧酶(Pyruvate decarboxylase,PDC)基因作为靶基因构建了两端包含同源臂并在选择性标记C. tropicalis URA3(Orotidine-5′-phosphate decarboxylase,乳清酸核苷-5-磷酸脱羧酶)基因两侧同向插入源于沙门氏菌(Salmonella typhimurium)的hisG序列的基因敲除盒PDC1-hisG-URA3-hisG- PDC1(PHUHP),并转化宿主菌株C. tropicalis XZX,筛选获得PHUHP片段正确整合到染色体的PDC基因位点的转化子XZX02。在此基础上,将转化子XZX02涂布于5-FOA(5-氟乳清酸)选择培养基上,筛选得到URA3基因从PHUHP片段中丢失的营养缺陷型菌株XZX03。进一步构建了第2个PDC等位基因的删除表达盒PDCm- URA3-PDCm,并转化C. tropicalis XZX03菌株,获得转化子C. tropicalis XZX04。经PCR和DNA测序确认转化子C. tropicalis XZX04细胞染色体上的两个PDC等位基因被成功敲除。文章建立了一种营养缺陷型标记可重复使用的热带假丝酵母遗传转化技术,利用该技术成功敲除了细胞的PDC基因,为进一步利用代谢工程改造热带假丝酵母奠定了基础。     

通过替代失活的方法分析核酸片段在肺炎链球菌毒力中的作用

目的鉴定基因spd—ABC、spd-1672、sp-1673和长间隔序列spd—J在肺炎链球菌（Streptococcus pneumoniae,S．pn）毒力中的作用。方法采用长臂同源聚合酶链反应（LFH—PCR）的方法分别构建这4个序列的红霉素抗性基因（erm）替代缺失突变体,通过PCR和测序鉴定是否构建成功;通过绘制生长曲线观察基因对细菌生长繁殖的影响,通过小鼠毒力实验观察基因对细菌致病性的影响。结果所构建缺陷菌目的基因由eFm基因完全替代;spd—ABC、spd-1673和长间隔序列spd—J3个片段缺陷菌的生长趋势与野生菌没有明显差异,生长大约5hA值均可达到峰值,而spd-1672缺陷菌出现明显的延迟现象,生长8h后其4值才达到最高值;野生菌与缺失spd—ABC、spd-1673和长间隔序列spd—J的缺陷菌感染小鼠各组半数死亡时间分别为19、22、24和24h,差异无统计学意义,而spd-1672缺陷菌感染小鼠的半数死亡时间在75h左右,显著长于野生菌感染小鼠组（P〈0．05）。结论在构建的4个单个基因缺失突变体中,spd-1672缺陷后．S．pn生长明显延迟,毒力显著下降,提示spd-1672是s-Pn的一个新的毒力因子。     

Aspartate kinase-independent lysine synthesis in an extremely thermophilic bacterium, Thermus thermophilus: lysine is synthesized via alpha-aminoadipic acid not via diaminopimelic acid

An aspartate kinase-deficient mutant of Thermus thermophilus, AK001, was constructed. The mutant strain did not grow in a minimal medium, suggesting that T. thermophilus contains a single aspartate kinase. Growth of the mutant strain was restored by addition of both threonine and methionine, while addition of lysine had no detectable effect on growth. To further elucidate the lysine biosynthetic pathway in T. thermophilus, lysine auxotrophic mutants of T. thermophilus were obtained by chemical mutagenesis. For all lysine auxotrophic mutants, growth in a minimal medium was not restored by addition of diaminopimelic acid, whereas growth of two mutants was restored by addition of alpha-aminoadipic acid, a precursor of lysine in biosynthetic pathways of yeast and fungi. A BamHI fragment of 4.34 kb which complemented the lysine auxotrophy of a mutant was cloned. Determination of the nucleotide sequence suggested the presence of homoaconitate hydratase genes, termed hacA and hacB, which could encode large and small subunits of homoaconitate hydratase, in the cloned fragment. Disruption of the chromosomal copy of hacA yielded mutants showing lysine auxotrophy which was restored by addition of alpha-aminoadipic acid or alpha-ketoadipic acid. All of these results indicated that in T. thermophilus, lysine was not synthesized via the diaminopimelic acid pathway, believed to be common to all bacteria, but via a pathway using alpha-aminoadipic acid as a biosynthetic intermediate.     

Development of a novel quadruple auxotrophic host transformation system by argB gene disruption using adeA gene and exploiting adenine auxotrophy in Aspergillus oryzae

We previously designed a triple auxotrophic host-vector system in Aspergillus oryzae by isolating red-colored adenine auxotrophic mutants upon UV mutagenesis of a double auxotrophic host (niaD-sC-). In the present study an effort to exploit this system and construct a novel quadruple auxotrophic host was made by disrupting the argB gene involved in arginine biosynthesis. The argB gene-disruption cassette was generated by fusion PCR, which required only two steps of PCR to insert the selectable marker, adeA, into the target argB gene. The chimeric DNA fragment was transformed into the triple auxotrophic strain (niaD-sC-adeA-) and the argB disruptants were obtained with a high rate of efficiency (approximately 40%). The argB disruptants were characterized by normal colony color and reversal of arginine auxotrophy by introduction of the wild-type argB gene. Quadruple auxotrophic strains (niaD-sC-DeltaargB adeA- or niaD-sC-DeltaargB adeB-) were subsequently isolated upon UV mutagenesis of the triple auxotrophic strain (niaD-sC-DeltaargB) followed by screening of red-colored colonies for adenine auxotrophy. The results obtained showed that the adeA gene served as an efficient selection marker in developing a novel host-vector system with quadruple auxotrophy in A. oryzae, thus providing a powerful tool to breed multiple auxotrophic mutants from a deuteromycete wherein sexual crossing is impossible.     

A new mutation protocol for obtaining auxotrophic mutants of the yeastPhaffia rhodozyma

Summary A new mutation strategy, which involves -irradiation of cells followed by a selective enzymatic enrichment step, was worked out to obtain auxotrophic mutants from the astaxanthin-producing yeast P. rhodozyma. Under the optimized conditions described, different mutants suitable for strain improvement were isolated.     

Arginase plays a pivotal role in polyamine precursor metabolism in Leishmania. Characterization of gene deletion mutants

The polyamine pathway of protozoan parasites has been successfully targeted in anti-parasitic therapies and is significantly different from that of the mammalian host. To gain knowledge into the metabolic routes by which parasites synthesize polyamines and their precursors, the arginase gene was cloned from Leishmania mexicana, and Deltaarg null mutants were created by double targeted gene replacement and characterized. The ARG sequence exhibited significant homology to ARG proteins from other organisms and predicted a peroxisomal targeting signal (PTS-1) that steers proteins to the glycosome, an organelle unique to Leishmania and related parasites. ARG was subsequently demonstrated to be present in the glycosome, whereas the polyamine biosynthetic enzymes, in contrast, were shown to be cytosolic. The Deltaarg knockouts expressed no ARG activity, lacked an intracellular ornithine pool, and were auxotrophic for ornithine or polyamines. The ability of the Deltaarg null mutants to proliferate could be restored by pharmacological supplementation, either with low putrescine or high ornithine or spermidine concentrations, or by complementation with an arginase episome. Transfection of an arg construct lacking the PTS-1 directed the synthesis of an arg that mislocalized to the cytosol and notably also complemented the genetic lesion and restored polyamine prototrophy to the Deltaarg parasites. This molecular, biochemical, and genetic dissection of ARG function in L. mexicana promastigotes establishes: (i) that the enzyme is essential for parasite viability; (ii) that Leishmania, unlike mammalian cells, expresses only one ARG activity; (iii) that the sole vital function of ARG is to provide polyamine precursors for the parasite; and (iv) that ARG is present in the glycosome, but this subcellular milieu is not essential for its role in polyamine biosynthesis.     

vMIP-II-TfN融合蛋白在毕赤酵母中的表达和纯化

目的:构建pPIC-vMIP-II-TfN酵母表达载体,表达纯化vMIP-II-TfN融合蛋白。方法:利用PCR方法扩增编码人转铁蛋白N端半分子的基因片段,通过酶切、连接、转化等分子克隆方法构建pPIC-vMIP-II-TfN酵母表达载体;电击法转化X33酵母菌;用甲醇诱导重组酵母菌表达融合蛋白,利用硫酸铵沉淀、透析、Ni-NTA层析等技术进行蛋白纯化,SDS-PAGE和Western blot检测蛋白表达和纯化情况,利用趋化实验进行纯化蛋白活性检测。结果:经过两次PCR扩增了一个长约1.1kb的包含Xba I酶切位点的IgG3-TfN基因片段,插入pPIC-vMIP-II的Xba I酶切位点,经菌液PCR鉴定获得重组子,测序结果表明构建载体pPIC-vMIP-II-TfN的表达框正确无误,转化X33酵母菌,用甲醇诱导表达出48kDa的vMIP-II-TfN融合蛋白,经硫酸铵沉淀、透析、Ni-NTA纯化后得到纯度约为95%的vMIP-II-TfN融合蛋白。Western印迹结果表明融合蛋白能与转铁蛋白抗体特异性结合。活性检测表明经过诱导表达的vMIP-II-TfN融合蛋白具有趋化抑制活性。结论:成功构建pPIC-vMIP-II-TfN酵母表达载体,重组酵母工程菌经甲醇诱导成功表达出vMIP-II-TfN融合蛋白,纯化后的vMIP-II-TfN融合蛋白具有趋化抑制活性。     

植酸酶基因的多点突变及在毕赤酵母中的高效表达

根据毕赤酵母基因的密码子选择偏爱性,不改变其编码氨基酸序列,对来源于黑曲霉N25植酸酶phyA基因,进行了突变,构建了含有正确突变的酵母表达载体pPIC9k-phyAm-4,电击转化毕赤酵母,获得优化了密码子的重组酵母转化子。经PCR鉴定表明,植酸酶基因已整合到酵母基因组中; 表达产物的SDS-PAGE分析表明,酶蛋白分子大小为70.15KD。Southern blotting结果表明,phyA基因整合到酵母染色体DNA中;转化子酶活测定结果表明,经密码子优化的重组酵母PP-NPm-4-2酶活可达136900U/ml,比Arg没有优化的PP-NPm-8 (47600 Uoml-1)酶活高约2.8倍。     

香蕉乙二醛酶基因增强酿酒酵母对非生物胁迫抵抗能力的研究

从香蕉cDNA文库中克隆到了一个香蕉(Musa acuminata AAA subgroup)乙二醛酶(glyoxalase,GLO)基因(MaGLO14)。构建了带有MaGLO14的酵母表达载体PYES2-MaGLO14,转化酿酒酵母(Saccharomyces cerevisiae)尿嘧啶营养缺陷型菌株INVSC1,挑取转化子进行PCR和酶切鉴定,证实获得了转基因菌株。通过比较转基因菌株和非转基因菌株在NaCl、高温、低温、干旱、UV胁迫下的生长状况,证明转基因菌株在以上非生物胁迫条件下的存活菌落数均高于非转基因菌株。利用酿酒酵母初步证明MaGLO14具有增强酵母菌对非生物胁迫抵抗力的功能。     

植酸酶基因中稀有密码子的改造提高其在毕赤酵母中的表达量

对来源于黑曲霉N2 5(AspergillusnigerChinaStrain)的植酸酶基因phyA进行PCR介导的定点突变 ,不改变其所编码氨基酸 ,选用毕赤酵母偏爱的密码子对该基因保守序列中第 81位和第 85位的Arg密码子进行同义突变 .构建了含正确突变的克隆载体pUC18 phyAm 和酵母表达载体pPIC9k phyAm,电击转化毕赤酵母 ,经MM、MD平板筛选和产物的酶活性测定 ,筛选出突变与未突变高酶活酵母转化子各 2株 .这 4株转化子的Southern印迹结果表明 ,phyA基因以单交换方式单拷贝整合到酵母染色体DNA中 .表达产物的SDS PAGE分析表明 ,重组酵母中的植酸酶能有效分泌和表达 ,蛋白质分子大小为 70 15kD .转化子酶活测定结果表明 ,经密码子优化的突变重组酵母酶活力明显高于未进行优化的重组酵母转化子 .经密码子优化的突变重组酵母株PP NPm 8于麦芽汁培养基中诱导 36h后酶活力可达 4 76 0 0U/ml,其活力比未优化重组酵母株PP NP 2 (2 36 6 7U/ml)提高了约 1倍 ,且重组转化子遗传稳定性良好 .     

Mechanized systems for media dispensing, inoculation, and replication of microorganisms

Two instruments were developed to mechanize the handling of anaerobic microorganisms for microbial mutant isolation. The instruments automatically dispense liquid or agar medium to large and small 96-well platesand petridishes. Protocols were developed for inoculating different microorganisms, and calibration curves of number of areas or wells inoculated versus cell concentration were prepared for bacteria, yeast and fungi (spores). Experiments with yeast auxotrophic mutants and fungal spores showed that microbe inoculation follows Poisson statistics in distributing a single microorganism per inoculation point. The isolation and identification of Yarrowia lipolytica auxotrophic, morphological, and temperature-sensitive or tolerant mutants demonstrated the use of the instruments for microbial screening.     

Industrial Application of Artificially Induced Diploid Strains of Torulaspora delbrueckii

Diploid strains of Torulaspora delbrueckii were tested for industrial application. Because the cell volume of the diploid strain was three times as large as that of the parental haploid strain, collection and subsequent dehydration to make compressed yeast cakes were greatly improved with the diploid YL3. The time required for dehydration of the diploid strain was shortened to 1/2.5 that of the parent strain under conventional conditions. Moreover, for the diploid cells frequent filter changes for dehydration were not required, which was the case with parental cells. Fermentation activity and tolerance to freeze-thawing in dough were succesfully inherited by the diploid strains. The diploid YL3 showed nearly the same activity as the diploid F31 in bread making. However, the endurance period of yeast cakes when stored at 30°C without softening to lead to liquefaction was much longer in YL3 (199 h) than in F31 (132 h). This superiority was ascribed to the fact that YL3 was induced through direct diploidization and had no genetic defect on chromosomes because the wild-type strain was employed as the parent, whereas F31 was obtained through protoplast fusion from two auxotrophic mutants and carried at least two mutagenized genes that were masked by heterolallelism.     

Auxotrophic mutants in the selection of the rubomycin producer, Actinomyces coeruleorubidus

A total of 351 auxotrophic mutants with different antibiotic activity, including several mutants with activity higher than that of the parent prototrophic strains were obtained under the effect of gamma-rays from 3 prototrophic strains of Act. coeruleorubidus. It was shown that most of the auxotrophic mutants did not preserve the property of biochemical insufficiency on passages on complete media. A mutant strain 1059-32 with activity 2 times higher than that of the prototrophic strain 2-39 and the parent auxotrophic culture was obtained from the revertants. Requirements in 29 growth factors including 17 amino acids, 4 nitrous bases, 8 vitamins and coenzymes were determined in 46 stable auxotrophic mutants isolated. The effect of the specific and non-specific growth factors on the culture antibiotic production was studied.     

UHRF2结构域突变体的原核表达与纯化

目的构建UHRF2各个以结构域为基础的突变体原核表达载体,在大肠埃希菌中表达并对融合蛋白进行纯化和鉴定。方法以pCMV-3xFlag—UHRF2为模板,PCR扩增UHRF2的各个结构域基因片段,各PCR产物经酶切后连接到pGEX-4T-1载体上;将重组载体转化大肠埃希菌（BL21菌株）,IPTG诱导表达各GST融合蛋白,超声波破碎细菌,离心收获蛋白并经谷胱甘肽琼脂糖凝胶4B（glutathione sepharose 4B）亲合纯化;纯化的蛋白经SDS-PAGE电泳后用考马斯亮蓝染色或免疫印记实验鉴定各蛋白表达情况。结果成功构建了UHRF2结构域突变体的原核表达载体,各突变体蛋白表达正确。结论UHRF2各结构域突变体的成功构建便于用GST pull—down实验研究UHRF2参与与其它蛋白相互作用的结构域,为了解UHRF2功能打下了基础。     

Construction of an Arxula adeninivorans host-vector system based on trp1 complementation

A host/vector expression system based on an Arxula adeninivorans Delta atrp1 gene disruption mutant has been constructed. For this purpose the ATRP1 gene encoding a phosphoribosyl anthranilate isomerase was isolated from the yeast A. adeninivorans and its genome locus was characterized. The Delta atrp1 mutant was generated applying an amplified DNA fragment containing the ALEU2m gene flanked by ATRP1 gene sequences of some 750 bp. The generated auxotrophic host strain was transformed with the plasmid pAL-ATRP1-amyA, which contains the ATRP1 gene as selection marker and the 25S rDNA for targeting. For expression assessment, the plasmid was equipped with an expression cassette consisting of the Bacillus amyloliquefaciens-derived amyA gene fused to the constitutive A. adeninivorans-derived TEF1 promoter and Saccharomyces cerevisiae-derived PHO5 terminator. Transformants contained a single chromosomal copy of the heterologous DNA and were found to be mitotically stable. In initial fermentation trials on a 200 ml shake flask scale maximal alpha-amylase product levels of ca. 300 nkat ml(-1) were observed after 72 h of cultivation with more than 95% of the recombinant alpha-amylase accumulated in the culture medium.     

毛霉△6-脂肪酸脱氢酶随机突变文库的构建与分析

毛霉Mucor sp.EIM-10△6-脂肪酸脱氢酶是γ-亚麻酸合成途径的关键酶。为提高脂肪酸脱氢酶的活性以及研究该酶一级结构对酶活性的影响,利用易错PCR对毛霉△6-脂肪酸脱氢酶基因(mcd6)进行随机突变,将PCR产物与大肠杆菌-酿酒酵母穿梭表达载体PYMD6PMCD6连接,获得随机突变质粒PYTBMCD6,转化酿酒酵母Saccharomyces cerevisiae,构建了原始库容为4.6×104 CFU的△6-脂肪酸脱氢酶的随机突变表达文库。随机突变表达文库的构建与分析为定点突变等酶蛋白的理性设计奠定基础。     

L-Phenylalanine production by double auxotrophic analogue resistant mutants of Arthrobacter globiformis

A number of tryptophan plus tyrosine double auxotrophic mutants isolated by the NTG treatment of a glutamate producing strain of Arthrobacter globiformis were found to excrete phenylalanine in a mineral salt medium. By controlling the pH of the medium to near neutrality, the active growth period could be extended up to 72 h and more phenylalanine was accumulated compared to the unregulated culture where the growth period took up to 48 h. Under optimum culture conditions, the best double auxotroph (TT-39) produced 3 g phenylalanine/l. Further improvement of phenylalanine production has been achieved by the step-by-step isolation of a mutant resistant to the phenylalanine analogues p-fluorophenylalanine (PFP) and β-2-thienylalanine (TA) from the TT-39 strain. Under optimum culture conditions, the best double auxotrophic analogue resistant mutant TT-39 PT^r-21 yielded 8.7 g/l phenylalanine.     

Construction of two new vectors for transformation of laboratory,natural and industrial<Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> strains to trifluoroleucine and G418 resistance

Two new plasmids, pEC3 and pECkan, were constructed and their use in yeast transformation described. Both plasmids are derivative of the pRS416 vector, in which the URA3 auxotrophic marker was replaced by the LEU4* gene (pEC3) or the kanMX4 gene (pECkan). pEC3 and pECkan plasmids transformed natural and commercial Saccharomyces cerevisiae strains to 5,5,5-trifluoro-DL-leucine and G418 (aminoglycoside related to gentamicin) resistance, respectively, with efficiency ranging from 10(-5) to 10(-7) transformants per number of viable cells. pEC3 transformed the Leu- laboratory strain, carrying the mutations leu4 leu9, to leucine prototrophy with efficiency of approximately 10(-4).