A high-throughput system for two-hybrid screening based on growth curve analysis in microtiter plates

The yeast two-hybrid system is a powerful tool for identifying novel protein-protein interactions. In general, biochemical marker genes such as lacZ are exploited for indirect quantification of the interaction, and commonly involve the conduct of rather laborious beta-galactosidase assays. This paper describes a simple alternative method based on growth curve analysis of yeast cultures that is amenable to microtiter plate format, and therefore allows the quantification of large numbers of yeast two-hybrid combinations. The analyzed results of yeast cultures grown in microtiter plates were compared with those obtained from the classical beta-galactosidase assay. We conclude that the method presented here is reproducible, of equal or greater sensitivity than the beta-galactosidase assay, and can be further adapted for application to the conduct of large-scale, automated yeast two-hybrid experiments.     

Chromium accumulation by living yeast at various environmental conditions

Yeast tolerance to Cr (III) and Cr (VI) as well as chromium accumulation potential were shown to depend on treatment time, metal concentration, biomass density and the phase of growth. Kinetic studies as exemplified by Pichia guilliermondii ATCC 201911 revealed a biphasic mode of Cr (III) uptake: a rapid sorption phase was followed by a slow process of accumulation, in which the contribution of the cell-bound Cr fraction increased, while the total cellular Cr level remained constant. Cr (VI) uptake was characterized by a time-dependent increase of total Cr and by a constant fractional contribution of the cell-adsorbed chromium, which suggests that the amount of cell-accumulated Cr also tended to increase over time. The resistance to Cr and metal accumulation levels were substantially elevated for a given strain when cultures were treated at high initial biomass densities (1 mg dry weight/ml) of exponentially proliferating cells. Maximum accumulation capabilities ranged between 4.0 and 13 mg Cr (III)/g dry weight and 2-6.7 mg Cr (VI)/g dry weight. The total cell-accumulated Cr contained 29.3% and 52.3% of organically bound chromium for the treatment of P. guilliermondii with Cr (III) and Cr (VI), respectively. Selected yeast strains, under specified physiological conditions, can be applied for bioremediation of environmental Cr contamination, and might be useful too for attempts to obtain chromium-enriched biomass containing biostabilized and nontoxic Cr forms for nutritional applications.     

Saccharomyces cerevisiae CSM1 gene encoding a protein influencing chromosome segregation in meiosis I interacts with elements of the DNA replication complex

We present the characteristics of the Csm1 (Spo86) protein of Saccharomyces cerevisiae that are important for meiotic division. The level of Csm1p does not change throughout the cell cycle, but this protein is absent in mature spores. Deletion of CSM1 causes incorrect spore formation and meiotic chromosome missegregation together with increased sensitivity of vegetative cells to benomyl and manganese. In a two-hybrid analysis with Csm1p as bait, we detected interactions with three members of the Mcm2-7 family of proteins involved in the initiation of DNA replication, and with Clf1p also implicated in replication. The Csm1p-Mcm3, Mcm5 and Mcm7p interactions were confirmed by co-immunoprecipitation. Three other interacting proteins, Mgs1p, Ulp2, and Plp2, participate in chromosome assembling and segregation, whereas the function of two others has not been established. Genetic experiments showed that the two-hybrid isolates MGS1, CLF1, MCM3, 5, 7 (CDC47), and YDL089w, when overexpressed, partially suppress the csm1Delta/csm1Delta sporulation defect. We propose that, besides its other functions, Csm1p may be involved in premeiotic DNA replication.     

Estrogenic activity of triterpene glycosides in yeast two-hybrid assay

Estrogenic potency of six triterpene glycosides, Holothurin A, Holotoxin A₁, Frondoside A, Cucumarioside A₂-2 and Cauloside C, that are natural products and semi-synthesized Ginsenoside-Rh₂, were examined with yeast two-hybrid system, including expressed genes of human estrogen receptor, hER, the co-activator TIF2 and lacZ as a reporter gene. Only Ginsenoside-Rh₂ exhibited significant moderate estrogenic activity in the concentration range of 10⁻⁷ to 10⁻⁶ M. Its effect was approximately 30% of the activity of 17β-estradiol applied at half-effective concentration. This indicates Ginsenosides-Rh₂ is a weak phytoestrogen. The sea cucumber triterpene glycosides, Holothurin A, Holotoxin A₁, Cucumarioside A₂-2 and Frondoside A, and plant glycoside Cauloside C had no appreciable estrogenic activity. Data obtained by yeast two-hybrid assay reflect structure–activity relationship between tested compounds and 17β-estradiol. Only Ginsenoside-Rh₂ has some similarity in chemical structure with 17β-estradiol that might explain affinity of this glycoside to the hER receptor.     

酵母双杂交相关方法的改良及应用

对酵母双杂交实验过程中较为耗时的阳性克隆鉴定过程进行改进,以期建立一种快速有效的鉴定方法。分别采用液氮冻融法、超声破碎法、渗透压破壁法以及煮沸裂解法裂解酵母细胞,获得质粒作为PCR模板,直接测序鉴定筛选到的相互作用蛋白。以液氮冻融法和超声破碎法裂解细胞获得的质粒为模板进行PCR,得到特异的产物,测序鉴定结果明确,与经典的鉴定方法相比效果相当,但更加经济快捷;而渗透压破壁法和煮沸裂解法则效果不好。说明前两种方法可代替常规方法用于阳性克隆的鉴定,从而加快酵母双杂交实验中大量阳性克隆的筛查工作。     

Self-association of the hepatitis B virus X protein in the yeast two-hybrid system

Self-association of the transactivator HBx protein of hepatitis B virus was investigated using the yeast two-hybrid system. Expression vectors for the full-length HBx (X0) and its truncated mutants (X15 and X16) were constructed by separately ligating the DNA-binding (BD) and transactivation domains (AD) of Gal4. Co-transformants of the BD and AD constructs of HBx were selected using defined minimal medium and analyzed for the reconstitution of beta-galactosidase activity. No two-hybrid interaction was observed either between the full-length HBx molecules or its highly truncated mutant X16. However, a strong functional interaction between X0 and X15, X0 and X16, and X15 and X16 suggested that HBx could self-associate in a cellular environment through its carboxy-terminal region.     

神经病靶标酯酶调控结构域结合蛋白筛选及其在COS-7细胞中的表达

本研究采用酵母双杂交系统探寻与神经病靶标酯酶（NTE）调控结构域相互作用的蛋白因子,揭示与NTE信号转导相关的可能机制。通过构建含有NTE调控结构域的诱饵蛋白载体筛选胎脑文库,并将筛选得到的阳性克隆在酵母中进行了验证,随后在哺乳动物细胞中表达了该蛋白。生物信息学分析显示：该阳性克隆为前列腺素受体结合蛋白54（ARA54）,具有泛素连接酶活性,提示细胞可能存在依赖于细胞周期的NTE活性调节机制,为阐明NTE生理功能创造了条件[动物学报51（5）：840—844,2005]。     

Species specificity in avian sperm:perivitelline interaction

The interaction of chicken spermatozoa with the inner perivitelline layer from different avian species in vitro during a 5 min co-incubation was measured as the number of points of hydrolysis produced per unit area of inner perivitelline layer. The average degree of interaction, as a proportion of that between chicken spermatozoa and their homologous inner perivitelline layer, was: equal to or greater than 100% within Galliformes (chicken, turkey, quail, pheasant, peafowl and guineafowl); 44% within Anseriformes (goose, duck); and less than 30% in Passeriformes (Zebra Finch) and Columbiformes (collared-dove). The homologue of the putative chicken sperm-binding proteins, chicken ZP1 and ZP3, were identified by Western blotting with anti-chicken ZP1/ZP3 antibody in the perivitelline layers of all species. The functional cross-reactivity between chicken spermatozoa and heterologous inner perivitelline layer appeared to be linked to known phylogenetic distance between the species, although it was not related to the relative affinity of the different ZP3 homologues for anti-chicken ZP3. This work demonstrates that sperm interaction with the egg investment does not represent such a stringent species-specific barrier in birds as it does in mammals and marine invertebrates. This may be a factor in the frequency of hybrid production in birds.     

A new recombinant protein expression system for high-throughput screening in the yeast Yarrowia lipolytica

Development of a high-throughput eukaryotic screening procedure is important to increase success in obtaining improved enzymes through directed enzyme evolution. This procedure was developed for the yeast Yarrowia lipolytica which becomes the second eukaryotic host for this purpose. The extracellular lipase Lip2 was used as expressed enzyme but this system will be easily adjusted for other enzymes. We adapted and optimized the protocol for protein expression by Y. lipolytica in 96-well microplates. Yeast transformation efficiency and expression cassette insertion were increased by constructing a strain containing a zeta docking platform for targeted integration into the genome. The coefficient of variance of the full process was reduced from 36.3% to 18.9%. The main part of the variability (11.7%) arises from the specific lipase enzyme assay whereas the coefficient of variance concerning transformation, growth and expression steps represents only 7.2%. The rate of clone with no activity was reduced from 5.8% to 0.2%. Both transformation efficiency and variability are then compatible with high-throughput screening in the yeast Y. lipolytica.     

清香型白酒发酵过程中酵母群落结构及其与尿素代谢的关系

【目的】探索清香型白酒发酵过程中酵母群落结构及演变,分析潜在的关键尿素代谢酵母及其环境调控因素,为降低发酵过程中氨基甲酸乙酯的含量提供理论依据。【方法】通过相关性分析明确发酵过程中氨基甲酸乙酯主要前体物质及其代谢微生物类群,利用高通量测序技术解析酵母群落结构组成,并结合偏最小二乘回归分析寻找潜在的关键尿素代谢酵母。采用冗余分析评价发酵过程中环境因素对酵母群落结构的影响。【结果】尿素是清香型白酒发酵过程中氨基甲酸乙酯的主要前体物质,酵母是尿素代谢的主要微生物。高通量测序结果显示,在97%的相似度下进行操作分类单元聚类后,共鉴定出22个酵母种。其中,嗜高压有孢汉生酵母(Hanseniaspora osmophila)、发酵毕赤酵母(Pichia fermentans)和酿酒酵母(Saccharomyces cerevisiae)与尿素合成存在正相关性,库德毕赤酵母(Pichia kudriavzevii)与尿素降解存在正相关性。酒醅含水量、p H、乙醇和精氨酸是影响发酵过程中酵母群落演替的重要环境因素。【结论】环境因素影响潜在的关键尿素代谢酵母,为降低发酵过程中尿素与氨基甲酸乙酯含量提供理论依据。     

Yeast nuclear pore complexes have a cytoplasmic ring and internal filaments

The nuclear pore complex (NPC) controls transport of macromolecules across the nuclear envelope. It is large and complex but appears to consist of only approximately 30 different proteins despite its mass of > 60MDa. Vertebrate NPC structure has been analyzed by several methods giving a comprehensive architectural model. Despite our knowledge of yeast nucleoporins, structural data is more limited and suggests the basic organization is similar to vertebrates, but may lack some peripheral and other components. Using field emission scanning electron microscopy to probe NPC structure we found that the yeast, like higher eukaryotic, NPCs contain similar peripheral components. We can detect cytoplasmic rings and evidence of nucleoplasmic rings in yeasts. A filamentous basket is present on the nucleoplasmic face and evidence for cytoplasmic filaments is shown. We observed a central structure, possibly the transporter, that which may be linked to the cytoplasmic ring by internal filaments. Immuno-gold labeling suggested that Nup159p may be attached to the cytoplasmic ring, whereas Nup116p may be associated, partly, with the cytoplasmic filaments. Analysis of a Nup57p mutant suggested a role in maintaining the stability of cytoplasmic components of the NPC. We conclude that peripheral NPC components appear similar in yeasts compared to higher organisms and present a revised model for yeast NPC structural composition.     

Correlations of amino acids in proteins

A correlation analysis among 20 amino acids is performed for four protein structural classes (, β, /β, and +β) in a total of 204 proteins. The correlation relationships among amino acids can be classified into the following four types: (1) strong positive correlation, (2) strong negative correlation, (3) weak correlation, and (4) no correlation. The correlation relationships are different for different proteins and are correlated with the features of their structural classes. The amino acids with the weak correlation relationship can be treated as the independent basis functions for the space where proteins are defined. The amino acids with large correlation coefficients are linear correlative with each other and they are not independent. The strong correlation among amino acids reflects their mutual constrained relationship, as exhibited by their relevant structural features. The information obtained through the correlation analysis is used for predicting protein structural classes and a better prediction quality is obtained than that by the simple geometry distance methods without taking into account the correlation effects.     

Substrate specificity of inner membrane peptidase in yeast mitochondria

The inner membrane protease (IMP) cleaves intra-organelle sorting peptides from precursor proteins in mitochondria of the yeast Saccharomyces cerevisiae. An unusual feature of the IMP is the presence of two catalytic subunits, Imp1p and Imp2p, which recognize distinct substrate sets even though both enzymes belong to the same protease family. This nonoverlapping substrate specificity was hypothesized to result from the recognition of distinct residues at the P′₁ position (also termed +1 position) in the protease substrates. Here, we constructed an extensive series of mutations to obtain a profile of the critical cleavage site residues in IMP substrates and conclude that Imp1p, and not Imp2p, recognizes specific P′₁ residues. In addition to its specificity for P′₁ residues, Imp1p also shows substrate specificity for the P₃ (−3) position. In contrast, Imp2p recognizes the P₁ (−1) position and the P₃ position. Based on this new understanding of IMP substrate specificity, we conducted a survey for candidate IMP substrates in mammalian mitochondria and found consensus Imp2p cleavage sites in mammalian precursors to cytochrome c₁ and glycerol-3-phosphate (G-3-P) dehydrogenase. Presence of a putative Imp2p cleavage site in G-3-P dehydrogenase was surprising, as its yeast ortholog contains an Imp1p cleavage site. To address this issue experimentally, we performed the first co-expression of mammalian IMP with proposed mammalian IMP precursors in yeast and show that murine precursors to cytochrome c₁ and G-3-P dehydrogenase are cleaved by murine Imp2p. These results suggest, surprisingly, G-3-P dehydrogenase has switched from Imp1p in yeast to Imp2p in mammals.     

Effect of F-2 and T-2 fusariotoxins on experimental Cryptosporidium baileyi infection in chickens

The course of Cryptosporidium baileyi infection in chickens fed with different doses of fusariotoxins was compared with that of control groups. F-2 toxin levels of 0.187–1.5 mg kg⁻¹ and T-2 toxin levels of 0.187–6.0 mg kg⁻¹ were investigated. The experimental amimals were orally infected with 6 × 10⁵ C. baileyi oocysts at 1 week of age. Total daily oocyst output was monitored by a quantitative method. Acquired immunity was tested at the age of 4 weeks, by ELISA and by a challenge infection with an equal number of oocysts, upon recovery from the primary infection. The results show that in chickens kept on the lower doses of F-2 and T-2 toxins, the parasite infection ran a similar course to that in the control groups, and the animals became resistant to re-infection. However, when higher doses (2.0–6.0 mg kg⁻¹) of T-2 toxin were used, a depression of weight gain was observed with some other physiological parameters (PCV, weight of bursa, weight of thymus, skin thickness in PHA-P skin test) also indicating toxic effect and, simultaneously, the oocyst output decreased significantly and the patent period was slightly prolonged. Although certain modifications of the immune response could be revealed, the chickens became resistant to re-infection. Only early (1 week of age) parasite infection and 6 mg kg⁻¹ T-2 toxin in the feed significantly depressed body weight gain and immunity.     

Itraconazole and leishmaniasis: A randomised double-blind trial in cutaneous disease

Cutaneous leishmaniasis (CL) is a vector-borne parasitic disease of the skin. Previous open controlled studies with oral itraconazole suggest that it was effective for CL in India. Twenty patients with localised CL participated in this trial. Patients were allocated randomly to receive capsule itraconazole and matching placebo for 6 weeks. No topical medicines were used. Demonstration of Leishmania by slit smear was mandatory. Prior to, periodically during and 3 months after completion of therapy an overall clinical assessment, liver function tests and urinalysis were performed. On decoding, out of the 10 cases receiving drug itraconazole, 7 were declared cured by clinical and parasitological criteria. No major side-effects were noted. Spontaneous remission was observed in 1 case in the placebo group at 3 months follow up. Oral itraconazole has a promising antileishmanial potential and may thus secure CL patient from the hazards of antimonials.     

Extracellular alpha 6 integrin cleavage by urokinase-type plasminogen activator in human prostate cancer

During human prostate cancer progression, the integrin alpha6beta1 (laminin receptor) is expressed on the cancer cell surface during invasion and in lymph node metastases. We previously identified a novel structural variant of the alpha6 integrin called alpha6p. This variant was produced on the cell surface and was missing the beta-barrel extracellular domain. Using several different concentrations of amiloride, aminobenzamidine and PAI-1 and the urokinase-type plasminogen activator (uPA) function-blocking antibody (3689), we showed that uPA, acting as a protease, is responsible for production of alpha6p. We also showed that addition of uPA in the culture media of cells that do not produce alpha6p, resulted in a dose-dependent alpha6p production. In contrast, the addition of uPA did not result in the cleavage of other integrins. Using alpha2-antiplasmin and plasmin depleted media, we observed that uPA cleaves the alpha6 integrin directly. Further, 12-o-tetradecanoyl-phorbol-13-acetate (TPA) induced the production of alpha6p, and this induction was abolished by PAI-1 but not alpha2-antiplasmin. Finally, the alpha6p integrin variant was detected in invasive human prostate carcinoma tissue indicating that this is not a tissue culture phenomenon. These data, taken together, suggest that this is a novel function of uPA, that is, to remove the beta-barrel ligand-binding domain of the integrin while preserving its heterodimer association.     

Tectal responses to potassium loads and subsequent visual stimuli in the toad, Bufo bufo

Calling male toads were tested behaviourally for their prey catching responses to wormlike stimuli and assigned to groups of non-hungry and hungry depending on their prey catching motivation before being prepared for visual unit, massed unit and slow potential shift (SPS) recording from the optic tectum. Control recordings to visual stimuli were made before recording the effects of application of isotonic solutions containing concentrations of 0-41 mM K(+). Application of solution was followed by presentation of the visual stimulus while the solution still bathed the tectum. The best tectal responses were made to large square visual stimuli in the non-hungry toads, perhaps because recordings were made in the breeding season. Responses of the tectum to solution addition were significant in the concentration range of 7-17 mM K(+). Hungry toads showed an earlier, smaller response than non-hungry (sexually motivated) animals. When the visual stimulus was presented, there were unit and massed unit responses at all bathing solution concentrations, which were larger in non-hungry animals. These experiments revealed that toads motivated to feed respond earlier than non-hungry toads to application of artificial CSF to the tectum, though non-hungry toads responded best to the subsequent visual stimulus.