CUP1为筛选标记的酿酒酵母整合型多基因表达载体的构建

为了赋予工业酿酒酵母对淀粉和纤维素的降解活性,提高酿酒酵母对粗木薯粉进行酒精发酵时的酒精产率;另一方面,为了解决工业酿酒酵母不适于使用营养缺陷型筛选标记对转化子进行筛选的问题,以及避免引入抗药性标记基因带来的安全性问题,构建了以抗铜蛋白基因CUP1为筛选标记的酿酒酵母整合型多基因表达载体.以载体pYES2-PMF-rDNA为基础,以新的筛选标记基因CUP1替换原有的尿嘧啶Ura-基因,得到载体pYES2M.再顺序插入葡聚糖内切酶基因eg3、葡萄糖淀糖酶基因gal和β-葡萄糖苷酶基因bgl1,构建得到以CUP1为筛选标记的酵母整合型三价表达载体pYES2M-eg3-ga1 -bgl1,其中每个基因都具有独立而完整的表达盒,包括启动子、信号肽和终止子,从而实现多基因单表达载体一次转化.     

Yeast genome evolution in the post-genome era.

The Saccharomyces cerevisiae genome sequence, augmented by new data on gene expression and function, continues to yield new findings about eukaryote genome evolution. Analysis of the duplicate gene pairs formed by whole-genome duplication indicates that selection for increased levels of gene expression was a significant factor determining which genes were retained as duplicates and which were returned to a single-copy state, possibly in addition to selection for novel gene functions. Proteome comparisons between worm and yeast show that genes for core metabolic processes are shared among eukaryotes and unchanging in function, while comparisons between different yeast species identify 'orphan' genes as the most rapidly evolving fraction of the proteome. Natural hybridisation among yeast species is frequent, but its long-term evolutionary significance is unknown.     

Differentiated Gene Expression in Cells within Yeast Colonies

Yeast cells growing on solid media organize themselves into multicellular structures, colonies, exhibiting patterns specific for particular yeast strains. With the aim of identifying genes involved in regulations of the colony formation, we applied a new approach enabling the extensive screening of Saccharomyces cerevisiae genes, the expression of which is changed during colony development. We used the library of S. cerevisiae DNA fragments inserted in front of the lacZ gene lacking its own promoter. Colonies of transformants with a blue/white patterned morphotype, implying that the expression of the lacZ gene from the inserted yeast promoter is switched on and off during the colony formation, were isolated. We identified several genes with variable expression during colony morphogenesis, including CCR4, PAM1, MEP3, ADE5,7 and CAT2. S. cerevisiae strain deleted in the CCR4 gene forms colonies with less organized morphology when compared with the isogenic parental strain. The synchronization of the expression patterns of some of the isolated genes in neighboring colonies was observed.     

酵母基因中断技术

酵母基因中断技术是研究酵母基因功能的重要手段，自80年代初诞生以来经历了不断的改进和发展.PCR介导的酵母基因中断技术，大大简化了操作，实现了酵母基因的精确缺失；酵母基因的多重中断技术，可在酵母内实现多个基因的中断；可进行大规模基因中断和功能分析的酵母基因中断技术，适应了在酵母全基因组测序完成的情况下进行功能基因组学研究的要求.酵母基因中断技术对人类基因功能研究也有很大启示作用.     

非常规酵母基因工程表达系统

非常规酵母系指除了酿酒酵母与粟裂殖酵母之外的酵母曹。非常规酵母可利用其自主复制序列构建载体,但整合载体是进行外源基因导入的主要方式。非常规酵母的转化有一定的宿主范围,可采用与酿酒酵母相同的方法,最常用的仍为化学法。高效表达元件可利用酿酒酵母的强启动子,也可以根据非常规酵母菌的代谢特点寻找强启动子．本文综述了近年来应用非常规酵母基因表达系统表达外源基因的一些实例。     

The primary structure of the alcohol dehydrogenase gene from the fission yeast Schizosaccharomyces pombe

We have cloned and sequenced the alcohol dehydrogenase gene of the fission yeast Schizosaccharomyces pombe. The gene was isolated by transformation and complementation of a Saccharomyces cerevisiae strain which lacked functional alcohol dehydrogenase with an S. pombe gene bank constructed in the autonomously replicating yeast plasmid YEp13. Southern hybridization analysis indicates that S. pombe contains only one alcohol dehydrogenase gene. The structural region of the gene is 50% homologous to the alcohol dehydrogenase encoding genes of the budding yeast S. cerevisiae. The gene exhibits a very strong codon usage bias; with the set of predominantly used codons generally resembling that which S. cerevisiae employs preferentially. All of the differences in codon usage bias between S. pombe and S. cerevisiae are in the direction of greater G + C content in S. pombe codons. It is argued that this observation supports the hypothesis that selection toward uniform codon-anticodon binding energies contributes to codon usage bias and that the optimum binding energy is, on the average, higher in S. pombe than S. cerevisiae.     

Genome-wide expression profile of sake brewing yeast under shaking and static conditions

To identify the genes responsible for characteristics, that are different as between sake brewing yeasts and laboratory yeast strains, we used a DNA microarray to compare the genome-wide gene expression profiles of a sake yeast, Saccharomyces cerevisiae K-9 (kyokai 9), and a laboratory yeast, S. cerevisiae X2180-1A, under shaking and static conditions.The genes overexpressed in K-9 more than in X2180-1A were related to C-metabolism, including the HXT, ATP, and COX genes, ergosterol biosynthesis, ERG genes, and thiamine metabolism, THI genes. These genes may contribute to higher growth rates and fermentation ability and the ethanol tolerance of sake yeast.The genes underexpressed in K-9 more than in X2180-1A were CUP1-1 and CUP1-2, PHO genes, which may explain the low copper tolerance and low acid phosphatase activity of sake yeast. These underexpressed genes agree with the features and the alteration of the genome structure of sake yeast.     

An inducible expression vector for both fission and budding yeast

We have developed a vector system for inducible gene expression in both fission yeast (Schizosaccharomyces pombe) and budding yeast (Saccharomyces cerevisiae). The autonomously replicating expression vector contains multiple glucocorticoid response elements, rendering a linked promoter inducible 20-70-fold by glucocorticoid hormones in the presence of the mammalian glucocorticoid receptor. A polylinker with several unique cloning sites allows insertion of cDNAs of interest. Glucocorticoids are gratuitous signalling molecules in yeast, exerting little or no effect on the expression of genes other than those fused to the regulated promoter.     

酿酒酵母中双链RNA介导基因沉默技术研究GRE3基因表达抑制

RNA沉默技术作为探索基因功能的实验手段应用于多种生物.以编码酿酒酵母NADPH依赖型醛糖还原酶的GRE3基因为对象,检测酿酒酵母双链RNA介导的基因沉默效应.以pESC-LEU为骨架,构建重组质粒psiLENT-GRE3并用于转化酿酒酵母YPH499.用RT-PCR检测到诱导1 kb RNA双螺旋和136 bp loop结构引起的GRE3基因表达下调.结果表明,双链RNA介导的基因沉默技术,能够用作降低酿酒酵母某一特定基因表达水平的工具.并有助于理解芽殖酵母的RNA干扰现象.     

Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis

During industrial production process using yeast, cells are exposed to the stress due to the accumulation of ethanol, which affects the cell growth activity and productivity of target products, thus, the ethanol stress-tolerant yeast strains are highly desired. To identify the target gene(s) for constructing ethanol stress tolerant yeast strains, we obtained the gene expression profiles of two strains of Saccharomyces cerevisiae, namely, a laboratory strain and a strain used for brewing Japanese rice wine (sake), in the presence of 5% (v/v) ethanol, using DNA microarray. For the selection of target genes for breeding ethanol stress tolerant strains, clustering of DNA microarray data was performed. For further selection, the ethanol sensitivity of the knockout mutants in each of which the gene selected by DNA microarray analysis is deleted, was also investigated. The integration of the DNA microarray data and the ethanol sensitivity data of knockout strains suggests that the enhancement of expression of genes related to tryptophan biosynthesis might confer the ethanol stress tolerance to yeast cells. Indeed, the strains overexpressing tryptophan biosynthesis genes showed a stress tolerance to 5% ethanol. Moreover, the addition of tryptophan to the culture medium and overexpression of tryptophan permease gene conferred ethanol stress tolerance to yeast cells. These results indicate that overexpression of the genes for trypophan biosynthesis increases the ethanol stress tolerance. Tryptophan supplementation to culture and overexpression of the tryptophan permease gene are also effective for the increase in ethanol stress tolerance. Our methodology for the selection of target genes for constructing ethanol stress tolerant strains, based on the data of DNA microarray analysis and phenotypes of knockout mutants, was validated.     

Significant impact of protein dispensability on the instantaneous rate of protein evolution

The neutral theory of molecular evolution predicts that important proteins evolve more slowly than unimportant ones. High-throughput gene-knockout experiments in model organisms have provided information on the dispensability, and therefore importance, of thousands of proteins in a genome. However, previous studies of the correlation between protein dispensability and evolutionary rate were equivocal, and it has been proposed that the observed correlation is due to the covariation with the level of gene expression or is limited to duplicate genes. We here analyzed the gene dispensability data of the yeast Saccharomyces cerevisiae and estimated protein evolutionary rates by comparing S. cerevisiae with nine species of varying degrees of divergence from S. cerevisiae. The correlation between gene dispensability and evolutionary rate, although low, is highly significant, even when the gene expression level is controlled for or when duplicate genes are excluded. Our results thus support the hypothesis of lower evolution rates for more important proteins, a widely used principle in the daily practice of molecular biology. When the evolutionary rate is estimated from closely related species, the ratio between the mean rate of nonessential proteins to that of essential proteins is 1.4. This ratio declines to 1.1 when the evolutionary rate is estimated from distantly related species, suggesting that the importance of a protein may change in evolution, so the dispensability data obtained from a model organism only predicts a short-term rate of protein evolution. A comparison of the fitness contributions of orthologous genes in yeast and nematode supports this conclusion.     

Design, total synthesis, and functional overexpression of the Candida rugosa lip1 gene coding for a major industrial lipase.

The dimorphic yeast Candida rugosa has an unusual codon usage that hampers the functional expression of genes derived from this yeast in a conventional heterologous host. Commercial samples of C. rugosa lipase (CRL) are widely used in industry, but contain several different isoforms encoded by the lip gene family, among which the isoform encoded by the gene lip1 is the most prominent. In a first laborious attempt, the lip1 gene was systematically modified by site-directed mutagenesis to gain functional expression in Saccharomyces cerevisiae. As alternative approach, the gene (1647 bp) was completely synthesized with an optimized nucleotide sequence in terms of heterologous expression in yeast and simplified genetic manipulation. The synthetic gene was functionally expressed in both hosts S. cerevisiae and Pichia pastoris, and the effect of heterologous leader sequences on expression and secretion was investigated. In particular, using P. pastoris cells, the synthetic gene was functionally overexpressed, allowing for the first time to produce recombinant Lipl of high purity at a level of 150 U/mL culture medium. The physicochemical and catalytic properties of the recombinant lipase were compared with those of a commercial, nonrecombinant C. rugosa lipase preparation containing lipase isoforms.     

高SO2产量啤酒酵母工业菌株的构建

二氧化硫在啤酒中具有抗氧化的重要功能,而在其形成过程中APS激酶(MET14编码)起着非常重要的作用。以二氧化硫产量较高的青岛啤酒酵母(Saccharomyces cerevisiae)YSF-5的总DNA为模板,用PCR方法克隆得到MET14基因。为使目的基因在酿酒酵母中表达,以大肠杆菌-酿酒酵母穿梭质粒YEp352为载体,以PGK1强启动子为调控元件,构建了重组表达质粒pPM,并转化酿酒酵母YS58。转化子在YNB添加亮氨酸、组氨酸和色氨酸的选择性培养基上筛选鉴定,盐酸副玫瑰苯胺法测得转化子的SO2产量是受体菌的2倍左右。在重组表达质粒pPM的基础上添加铜抗性标记基因构建了重组表达质粒pCPM,并转化青岛啤酒工业酵母菌株YSF-38,转化子在YEPD 4mmol/L CuSO4的选择性培养基上筛选鉴定,实验室条件下培养后,测得转化子YSF-38(pCPM)的SO2产量是受体菌的3.2倍。用该转化子在青岛啤酒厂进行小型发酵实验,结果表明在发酵结束时,YSF-38(pCPM)转化子的SO2产量是受体菌的1.4倍。因此,MET14基因的有效表达可以提高啤酒工业酵母的SO2产量。     

A new transformation system of Saccharomyces cerevisiae with blasticidin S deaminase gene

A new method for transformation of Saccharomyces cerevisiae that allows selection was developed. As the frequency of spontaneous blasticidin S resistant mutants from diploid type yeast strain (X-2180AB) was 5.2×10^–6, which was a thousandfold less than that from haploid type yeast strain (X-2180B), it was considered that the mechanism of spontaneous blasticidin S resistant mutations was related to recessive gene. Industrial yeasts, which were diploid, were transformed with blasticidin S deaminase gene from Aspergillus terreus to blasticidin S resistance. Expression of blasticidin S deaminase gene allowed selection of transformants from industrial yeasts.     

Population genetic variation in genome-wide gene expression

Evolutionary biologists seek to understand which traits display variation, are heritable, and influence differential reproduction, because such traits respond to natural selection and underlie organic evolution. Selection acts upon individual differences within a population. Whether individual differences within a natural population include variation in gene expression levels has not yet been addressed on a genome-wide scale. Here we use DNA microarray technology for measuring comparative gene expression and a refined statistical analysis for the purpose of comparing gene expression levels in natural isolates of the wine yeast Saccharomyces cerevisiae. A method for the Bayesian analysis of gene expression levels is used to compare four natural isolates of S. cerevisiae from Montalcino, Italy. Widespread variation in amino acid metabolism, sulfur assimilation and processing, and protein degradation-primarily consisting of differences in expression level smaller than a factor of 2-is demonstrated. Genetic variation in gene expression among isolates from a natural population is present on a genomic scale. It remains to be determined what role differential gene expression may play in adaptation to new or changing environments.     

Cytoplasmic ribosomal protein genes of the fission yeast Schizosaccharomyces pombe display a unique promoter type: a suggestion for nomenclature of cytoplasmic ribosomal proteins in databases.

We identified 34 new ribosomal protein genes in the Schizosaccharomyces pombe database at the Sanger Centre coding for 30 different ribosomal proteins. All contain the Homol D-box in their promoter. We have shown that Homol D is, in this promoter type, the TATA-analogue. Many promoters contain the Homol E-box, which serves as a proximal activation sequence. Furthermore, comparative sequence analysis revealed a ribosomal protein gene encoding a protein which is the equivalent of the mammalian ribosomal protein L28. The budding yeast Saccharomyces cerevisiae has no L28 equivalent. Over the past 10 years we have isolated and characterized nine ribosomal protein (rp) genes from the fission yeast S.pombe . This endeavor yielded promoters which we have used to investigate the regulation of rp genes. Since eukaryotic ribosomal proteins are remarkably conserved and several rp genes of the budding yeast S.cerevisiae were sequenced in 1985, we probed DNA fragments encoding S.cerevisiae ribosomal proteins with genomic libraries of S.pombe . The deduced amino acid sequence of the different isolated rp genes of fission yeast share between 65 and 85% identical amino acids with their counterparts of budding yeast.