Characterisation of genes encoding key enzymes involved in sugar metabolism of apple fruit in controlled atmosphere storage

Sugars are essential contributors to fruit flavour. Controlled atmosphere (CA) storage has been proved to be beneficial for maintaining harvested fruit quality. To explore regulatory mechanism of sugar metabolism in fruit stored in CA condition, we cloned several genes, encoding key enzymes, involved in sugar metabolism in apple fruit, and analyzed sugar contents, along with gene expression and enzyme activities in fruits stored in air and CA. The results indicated that CA could maintain higher contents of sugars, including sucrose, fructose and glucose. Expression levels of key genes, such as sucrose synthase (SS), sucrose phosphate synthase (SPS), fructokinase (FK) and hexokinase (HK), were shown to be correlated with the corresponding enzyme activities. We found that activities of neutral invertase (NI), vacuolar invertase (VI), FK and HK were inhibited, but SPS activity was promoted in apple fruit stored in CA, suggesting that CA storage could enhance sucrose synthesis and delay hydrolysis of sucrose and hexose. These findings provided molecular evidence to explain why higher sugar levels in harvested fruit are maintained under CA storage.     

Gene expression in wheat beer yeast strains and the synthesis of acetate esters

The synthesis of aroma compounds represents one of the most important parameters in beer production. Although it has been a historical topic of research, exactly how aroma components are formed has yet to be fully explained. Moreover, all of the research that has been published on yeast strains is focused on lagers and ales. Wheat beer yeast strains have not been the focus of aroma and flavour research. In this study, five different wheat beer yeasts were analysed to determine their capacity for producing acetate esters. In this study, the most commonly used wheat beer yeast strains for the production of German‐style wheat beer were analysed. This involved measuring the level of expression of the alcohol acetyl transferase genes ATF1, ATF2 and IAH1 over a period of 4 days (during primary fermentation) and plotting the data to observe the development of expression of the genes over time. Results confirmed their capacity to form acetate esters and showed a distinct correlation with increasing expression of the gene ATF1. However, the findings also indicated that gene expression in different yeast strains can vary considerably during fermentation. Copyright © 2016 The Institute of Brewing & Distilling     

Discovery of genes involved in mitosis,cell division,cell wall integrity and chromosome segregation through construction of Schizosaccharomyces pombe deletion strains

The fission yeast model system Schizosaccharomyces pombe is used to study fundamental biological processes. To continue to fill gaps in the Sz. pombe gene deletion collection, we constructed a set of 90 haploid gene deletion strains covering many previously uncharacterized genes. To begin to understand the function of these genes, we exposed this collection of strains to a battery of stress conditions. Using this information in combination with microscopy, proteomics and mini‐chromosome loss assays, we identified genes involved in cell wall integrity, cytokinesis, chromosome segregation and DNA metabolism. This subset of non‐essential gene deletions will add to the toolkits available for the study of biological processes in Sz. pombe. Copyright © 2016 John Wiley & Sons, Ltd.     

Galactose-inducible Expression Systems in Candida maltosa using Promoters of Newly-isolated GAL1 and GAL10 Genes

The GAL1 and GAL10 gene cluster encoding the enzymes of galactose utilization was isolated from an asporogenic yeast, Candida maltosa. The structure of the gene cluster in which both genes were divergently transcribed from the central promoter region resembled those of some other yeasts. The expression of both genes was strongly induced by galactose and repressed by glucose in the medium. Galactose-inducible expression vectors in C. maltosa were constructed on low- and high-copy number plasmids using the promoter regions of both genes. With these vectors and the β-galactosidase gene from Kluyveromyces lactis as a reporter, galactose-inducible expression was confirmed. Homologous overexpression of members of the cytochrome P-450 gene family in C. maltosa was also successful by using a high-copy-number vector under the control of these promoters. © 1997 by John Wiley & Sons, Ltd.     

Improvement of Ethanol Production by an Industrial Yeast Strain via Multiple Gene Deletions

The genetic engineering of yeasts used in commercial processes can be both time-consuming and laborious. This is because industrial yeasts possess largely uncharacterised genomes, which frequently carry at least two copies of any gene. Such strains are usually devoid of auxotrophic or other genetic markers and this requires the incorporation of positively selectable (and often heterologous) genes into plasmids or other transforming DNA molecules. In this paper, we demonstrate that multiple gene deletions may be readily performed in industrial yeasts. Using a specially designed loxPkanMX4 gene replacement cassette, we deleted the two PET191 alleles essential to respiration in the diploid, high alcohol-producing, wine yeast, K1. The two integrated deletion cassettes, which rendered the respiratory-deficient mutant, K1 Δpet191ab, resistant to the antibiotic geneticin were then excised from the genome following the expression of a cre recombinase gene harboured on the multi-copy plasmid YEP351-cre-cyh. This plasmid was maintained in the mutant under the selective pressure of the antibiotic cycloheximide and then removed when both genes had been successfully deleted. Batch fermentations were performed in homebrew style for strains K1 and K1Δpet191ab and revealed a 40% higher volumetric ethanol production rate and a 9% higher ethanol ceiling for the mutant. This demonstrates that, because of their respiratory deficiency, nuclear petites are not subject to the Pasteur effect and so exhibit higher rates of fermentation. Furthermore, nuclear petites cannot metabolise the product of fermentation, ethanol, allowing higher ethanol titres to be achieved. We believe that the method of strain manipulation demonstrated here will be of interest to scientists in the alcoholic beverages industry, who wish to delete genes in production yeast strains, while simultaneously ensuring the removal of all foreign coding sequences.     

Application of the FLP/FRT system for conditional gene deletion in yeast Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae has proved to be an excellent model organism to study the function of proteins. One of the many advantages of yeast is the many genetic tools available to manipulate gene expression, but there are still limitations. To complement the many methods used to control gene expression in yeast, we have established a conditional gene deletion system by using the FLP/FRT system on yeast vectors to conditionally delete specific yeast genes. Expression of Flp recombinase, which is under the control of the GAL1 promoter, was induced by galactose, which in turn excised FRT sites flanked genes. The efficacy of this system was examined using the FRT site-flanked genes HSP104, URA3 and GFP. The pre-excision frequency of this system, which might be caused by the basal activity of the GAL1 promoter or by spontaneous recombination between FRT sites, was detected ca. 2% under the non-selecting condition. After inducing expression of Flp recombinase, the deletion efficiency achieved ca. 96% of cells in a population within 9 h. After conditional deletion of the specific gene, protein degradation and cell division then diluted out protein that was expressed from this gene prior to its excision. Most importantly, the specific protein to be deleted could be expressed under its own promoter, so that endogenous levels of protein expression were maintained prior to excision by the Flp recombinase. Therefore, this system provides a useful tool for the conditional deletion of genes in yeast.     

Characterization of the cytochrome c gene from the starch-fermenting yeast Schwanniomyces occidentalis and its expression in Baker's yeast

A cytochrome c protein gene, CYC10, of the dextran- and starch-fermenting yeast, Schwanniomyces occidentalis was cloned and characterized. The DNA sequence was determined, and the predicted amino acid sequence of the protein-coding region shares close homologies to the cytochrome c genes. A S. occidentalis strain with a disruption of the gene revealed that CYC10 was the only functional cytochrome c protein-encoding gene in S. occidentalis, unlike the two cytochrome c protein genes (CYC1 and CYC7) in Saccharomyces cerevisiae. The CYC10 gene was oxygen-induced but not subject to catabolite repression. The expression of the CYC10 gene was studied in the heterologous yeast S. cerevisiae. The oxygen induction of the gene was found to be identical to that of the CYC1 gene, indicating that these two genes share similar or closely related cis- and trans-acting oxygen regulatory elements. However, the CYC10 gene was glucose repressed in S. cerevisiae strains; a phenomenon which was not observed in the native S. occidentalis cells. Search in the 5' untranslated region of the CYC10 gene revealed some homologies at -425 to -405 to UAS1 of the S. cerevisiae CYC1 gene. A deletion of a segment of upstream region including this sequence abolished expression in S. cerevisiae. Finally the phylogenetic relationships of different yeasts and fungi were determined based upon the amino acid sequences of the cytochrome c proteins. These relationships do not completely agree with classical divisions.     

Partial 26S rDNA restriction analysis as a tool to characterise non-Saccharomyces yeasts present during red wine fermentations

Restriction patterns of amplified regions of ribosomal large subunit RNA encoding genes (26S rDNA) were evaluated as a routine methodology to examine yeast species diversity during red wine fermentation. The results were confirmed by sequencing of D1/D2 region of 26S rDNA. Red wine production was carried out using a yeast starter culture together with different commercial products, namely enzymes, fermentation activators and tannins and their influence on the non-Saccharomyces yeast population was studied. Yeast strains were isolated using lysine agar as a selective medium for non-Saccharomyces yeasts, after morphological characterisation of colonies. Amplification of 26S rDNA followed by digestion with three restriction enzymes applied to the 121 isolates, generated 19 profiles and a very high correlation with sequencing results was achieved. Although a starter yeast culture was added, results showed that several yeast species were present during all stages of fermentation, independent of the conditions tested, emphasizing the diversity of microorganisms associated with winemaking. On the other hand commercial additives did not significantly influence the diversity of yeast population during the fermentation process. For non-Saccharomyces strains, restriction patterns of a PCR amplified 26S rDNA region proved to be an adequate tool for clustering strains at species level and enabled the monitoring of yeast population dynamics during red wine fermentation.     

CHARACTERIZATION OF BREWING YEAST STRAINS BY NUMERICAL ANALYSIS OF TOTAL SOLUBLE CELL PROTEIN PATTERNS

Total soluble cell proteins from 33 yeast strains from the brewing industry were extracted and subjected to polyacrylamide gel electrophoresis. Yeast strains were grouped by computerized numerical analysis of protein banding patterns. Three clusters were obtained at r>0.90. Cluster I contained 21 Saccharomyces cerevisiae lager beer strains. Cluster II comprised two strains isolated from beer with a phenolic off flavour and a third strain used for lager beer brewing. Cluster III consisted of two bottom ale yeasts. Protein patterns of yeast strains within each cluster corresponded closely or were identical. However, the intensity of certain bands often varied and the number of peaks recorded was not identical. These minor differences were reproducible and regarded as characteristic for the specific strains. Protein patterns can therefore be used to characterize or fingerprint individual yeast strains.     

Yeasts isolated from three varieties of grapes cultivated in different locations of the Dolenjska vine-growing region, Slovenia

The number and diversity of yeasts on grape berry surfaces are influenced by several factors, such as grape variety, degree of grape maturity at harvest, climatological conditions, geographic location, physical damage of grapes, the intensity of pest management etc. Cvicek is a typical Slovene wine, which has obtained a special protection under the Slovene Wine Law for its geographical origin. This blended red wine is produced from different grape varieties (Vitis vinifera L.), mostly from red grapes of Zametovka and Modra frankinja and from white grapes of Kraljevina. The aim of this study was to evaluate the impact of geographical locations in the Dolenjska vine-growing region and to obtain precise information about the influence of different grape varieties on the composition of yeast community on grape berries. The restriction fragment length polymorphism of PCR-amplified fragments from the rDNA gene cluster (PCR RFLP of rDNA) has been used for the differentiation of yeast species. The standard identification procedure has been performed on representative strains that shared identical RFLP profiles. The number of yeasts and yeast species isolated varied according to different grape varieties, Zametovka, Modra frankinja and Kraljevina (V. vinifera L.) and according to different sampling location. On the surface of grape berries 13 different yeast species have been identified. Saccharomyces cerevisiae has not been found.     

High expression of unsaturated fatty acid synthesis gene OLE 1 in sake yeasts

Gene Filters and Northern blot analysis revealed that the sake yeast strain Kyokai no. 7 (K 7) showed a higher expression level of OLE 1, which encodes a Delta-9 fatty acid desaturase gene, compared with the laboratory yeast strain X 2180-1A. Other sake yeasts also showed a high expression level of OLE 1. Unsaturated fatty acid concentrations in strain K 7 are higher than that in strain X 2180-1A, suggesting that the higher expression level of OLE 1 in sake yeasts increases the unsaturated fatty acid content in the cell membrane. Experiments using OLE 1 promoter:lacZ fusion reporter genes revealed that both the cis element of the OLE 1 promoter and trans factors are involved in the increased expression of OLE 1 in sake yeasts.     

Polymorphism of Saccharomyces cerevisiae aquaporins

Aquaporin water channels facilitate the transmembrane diffusion of water and higher organisms possess a large number of isoforms. The genome of the yeast Saccharomyces cerevisiae contains two highly similar aquaporin genes, AQY1 and AQY2. AQY1 has been shown to encode a functional water channel but only in certain laboratory strains. Here we show that the AQY2 gene is interrupted by an 11 bp deletion in 23 of the 27 laboratory strains tested, with the exception of strains from the sigma 1278b background, which also exhibit a functional Aqy1p. However, although the AQY2 gene from sigma 1278b is highly homologous to functional aquaporins, we did not observe Aqy2p-mediated water transport in Xenopus oocytes. A survey of 52 yeast strains revealed that all industrial and wild yeasts carry the allele encoding a functional Aqy1p, while none of these strains appear to have a functional Aqy2p. We conclude that natural and industrial conditions provide selective pressure to maintain AQY1 but apparently not AQY2.     

Study of the counts,species and characteristics of the yeast population during the manufacture of dry-cured “lacón”. Effect of salt level

The aim of this work was to study the yeast population during the manufacture of dry-cured “lacón” (a Spanish traditional meat product) and the effect of the salting time. For this study, six batches of “lacón” were manufactured with three different salting times (LS (3 days of salting), MS (4 days of salting) and HS (5 days of salting)). Yeast counts increased significantly (P < 0.001) during the whole process from 2.60 to 6.37 log cfu/g. An increased length of salting time did not affect yeast counts throughout the manufacture of dry-cured “lacón”, although the highest yeast counts were obtained from LS batches. A total of 226 isolates were obtained from dry-cured “lacón” during drying-ripening stage, of which 151 were yeasts and were identified at the species level using molecular techniques. The total of 151 identified yeasts belonged to 4 different genera: Debaryomyces, Candida, Cryptococcus and Rhodotorula. Debaryomyces hansenii was the most abundant species isolated throughout the whole process as much in the interior as in the exterior of the pieces of three salt levels of “lacón” studied, while Candida zeylanoides was only isolated from the interior of MS and HS batches and from the exterior of LS and HS groups, but at lesser proportion than D. hansenii.     

Systematic analysis of yeast strains with possible defects in lipid metabolism

Lipids are essential components of all living cells because they are obligate components of biological membranes, and serve as energy reserves and second messengers. Many but not all genes encoding enzymes involved in fatty acid, phospholipid, sterol or sphingolipid biosynthesis of the yeast Saccharomyces cerevisiae have been cloned and gene products have been functionally characterized. Less information is available about genes and gene products governing the transport of lipids between organelles and within membranes or the turnover and degradation of complex lipids. To obtain more insight into lipid metabolism, regulation of lipid biosynthesis and the role of lipids in organellar membranes, a group of five European laboratories established methods suitable to screen for novel genes of the yeast Saccharomyces cerevisiae involved in these processes. These investigations were performed within EUROFAN (European Function Analysis Network), a European initiative to identify the functions of unassigned open reading frames that had been detected during the Yeast Genome Sequencing Project. First, the methods required for the complete lipid analysis of yeast cells based on chromatographic techniques were established and standardized. The reliability of these methods was demonstrated using tester strains with established defects in lipid metabolism. During these investigations it was demonstrated that different wild‐type strains, among them FY1679, CEN.PK2‐1C and W303, exhibit marked differences in lipid content and lipid composition. Second, several candidate genes which were assumed to encode proteins involved in lipid metabolism were selected, based on their homology to genes of known function. Finally, lipid composition of mutant strains deleted of the respective open reading frames was determined. For some genes we found evidence suggesting a possible role in lipid metabolism. Copyright © 1999 John Wiley & Sons, Ltd.     

不同来源植物乳杆菌基因组的比较分析

目的 对分离自母乳、婴儿肠道的植物乳杆菌进行全基因组测序,分析菌株间亲缘关系和细菌素合成相关基因。方法 本研究采用Illumina高通量测序平台对不同来源的植物乳杆菌进行全基因组测序,质控过滤后的数据经Unicycler组装获得基因组精细图,通过比对COG、CAZy数据库对功能基因进注释,并借助BAGEL4等生物信息学分析工具鉴别植物乳杆菌素合成相关的基因簇,分析不同来源植物乳杆菌的益生潜力。结果 本研究5株植物乳杆菌基因组平均GC含量为44 %,母乳源植物乳杆菌基因数量多于婴儿肠道源菌株。进化树和ANI分析结果显示,分离所得菌株具有较高的同源性,相同来源的菌株更倾向于聚类到一个分支。功能注释结果显示,母乳源菌株与肠道源菌株相比拥有更多编码碳水化合物代谢的基因,且拥有完整的产植物乳杆菌素基因簇。结论 植物乳杆菌基因组GC含量、功能基因数目及产细菌素基因簇结构等与分离源有一定的关联,母乳源植物乳杆菌更适于作为潜在益生菌的候选菌株,本研究为益生菌的益生潜力研究提供了遗传学基础。     

普通烟草SWEET基因家族的鉴定与表达分析

  目的  为挖掘参与烟草糖代谢的SWEET（sugar will eventually be exported transported）基因家族成员。  方法  以拟南芥SWEET蛋白为参考,利用生物信息学方法,对栽培烟草的SWEET蛋白家族进行鉴定,分析蛋白理化性质、系统进化、染色体定位、基因结构和顺式作用元件,对其在不同组织和不同胁迫处理的表达模式进行检测。  结果  从普通烟草中鉴定到70个可能的SWEET基因,系统发育树将其划分为4个亚家族,大多数烟草SWEET基因在进化过程中经历纯化选择。不同烟草组织的表达模式分析显示,一些烟草SWEET基因具有组织表达特异性。不同胁迫处理的表达模式分析显示,部分烟草SWEET基因在葡萄糖、蔗糖、低温、干旱或者是盐胁迫处理下表达量变化明显。  结论  Ntab0097340和Ntab0727890是烟草植株重要的响应干旱与低温胁迫的基因,本研究为深入研究烟草SWEET基因功能提供有价值的参考信息。