Identification and classification of genes required for tolerance to freeze-thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains

Yeasts used in bread making are exposed to freeze-thaw stress during frozen-dough baking. To clarify the genes required for freeze-thaw tolerance, genome-wide screening was performed using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 58 gene deletions that conferred freeze-thaw sensitivity. These genes were then classified based on their cellular function and on the localization of their products. The results showed that the genes required for freeze-thaw tolerance were frequently involved in vacuole functions and cell wall biogenesis. The highest numbers of gene products were components of vacuolar H(+)-ATPase. Next, the cross-sensitivity of the freeze-thaw-sensitive mutants to oxidative stress and to cell wall stress was studied; both of these are environmental stresses closely related to freeze-thaw stress. The results showed that defects in the functions of vacuolar H(+)-ATPase conferred sensitivity to oxidative stress and to cell wall stress. In contrast, defects in gene products involved in cell wall assembly conferred sensitivity to cell wall stress but not to oxidative stress. Our results suggest the presence of at least two different mechanisms of freeze-thaw injury: oxidative stress generated during the freeze-thaw process, and defects in cell wall assembly.     

Fermentative capacity of baker's yeast exposed to hyperbaric stress

Baker's yeast suspensions were incubated at different pressures (from 1 bar to 6 bar) and different gases [air, O(2) and a mixture of 8% (v/v) CO(2), 21% O(2) and N(2)]. Raising the air pressure from 1 bar to 6 bar stimulated cell growth but had no effect on leavening ability or viability of the cells. A 50% reduction of the CO(2) produced in dough occurred with 6 bar O(2) which also stopped growth. The fermentative capacity of the cells was stimulated by the cells exposure to increased CO(2) partial pressure up to 0.48 bar.     

On the Beneficial Role of Silicon to Organisms: A Case Study on the Importance of Silicon Chemistry to Metal Accumulation in Yeast

Silicon is involved in numerous important structural and functional roles in a wide range of organisms, including diatoms, plants, and humans, but clear mechanisms have been discovered only in diatoms and sponges. Silicate availability influences metal concentrations within various cell- and tissue-types, but a mechanism has not been discovered so far. In an earlier study on Baker’s yeast Saccharomyces cerevisiae it was proposed that a chemical mechanism, rather than a biological one, is important. In the present study, the interaction of silicon with Baker’s yeast is further investigated by studying the influence of zinc and magnesium on Si accumulation both at a low and a high silicate concentration in the medium. Si accumulation fitted well with Freundlich adsorption and Si release followed depolymerization kinetics, indicating that silicate adsorbs to the surface of the cell rather than being transported over the cell membrane. Subsequently, adsorbed silicate interacts with metal ions and, therefore, alters the cell’s affinity for these ions. Since several metals are nutritional, these Si interactions can significantly change the growth and viability of organisms. In conclusion, the results show that chemistry is important in Si and metal accumulation in Baker’s yeast, and suggest that similar mechanisms should be studied in detail in other organisms to unravel essential roles of Si.     

Thermodynamic analysis of the nondenaturational conformational change of baker's yeast phosphoglycerate kinase at 24 degrees C

A plot of the Gibbs free energy of unfolding vs. temperature is calculated for baker’s yeast phosphoglycerate kinase in 150 mM sodium phosphate (pH = 7.0) from a combination of reversible differential scanning calorimetry measurements and isothermal guanidine hydrochloride titrations. The stability curve reveals the existence of two stable, folded conformers with an abrupt conformational transition occurring at 24 °C. The transition state thermodynamics for the low- to high-temperature conformational change are calculated from slow-scan-rate differential scanning calorimetry measurements where it is found that the free energy barrier for the conversion is 90 kJ/mol and the transition state possesses a significant unfolding quality. This analysis also confirms a nondenaturational conformational transition at 24 °C. The data therefore suggest that X-ray structures obtained from crystals grown below this temperature may differ considerably from the physiological structure and that the two conformers are not readily interconverted.     

Crossflow filtration of baker's yeast with periodical stopping of permeation flow and bubbling

The periodical stopping of permeation flow was applied to increase the permeation flux in crossflow filtration of commercially available baker's yeast cell suspension. The permeation flux after 3 h filtration in the crossflow filtration increased to 8 x 10(-5) m(3) /m(2) s (290 L/m(2) h) from 2 x 10(-5) m(3)/m(2) s (72 L/m(2) h) by applying the periodical stopping of permeation. Introduction of air bubbles during the stopping period of permeation further increased the flux.(c) John Wiley & Sons, Inc.     

A preliminary study of chromium distribution in chromium-rich brewer's yeast cell by NAA

The purpose of this study was to assess the chromium (Cr) distribution in chromium-rich brewer’s yeast cell. The chromium concentrations in the cell wall and protoplast fractions of the chromium-rich yeast were determined by neutron activation analysis (NAA). Moreover, the combined state of chromium and amino acid content in the Cr-rich brewer’s yeasts was analyzed and measured. The experimental results indicate that the introduction of water-soluble chromium (III) salt as a component of the culture medium for yeasts results in a substantial amount of chromium absorbed through the cell wall by the yeast, among which 80.9% are accumulated in the protoplast. It implies that, under optimal conditions, yeasts are capable of accumulating large amounts of chromium and incorporating chromium into organic compounds.     

Acetophenone tolerance, chemical adaptation, and residual bioreductive capacity of non-fermenting baker’s yeast (Saccharomyces cerevisiae) during sequential reactor cycles

Bioreduction of acetophenone (ACP) to phenethyl alcohol (PEA) by baker’s yeast (Saccharomyces cerevisiae), which is highly enantioselective, can be carried out entirely in a resting state using stored carbohydrate, suggesting that a high degree of chemical tolerance might be possible. However, viability and catalytic activity of precultured cells decline steeply within 24 h at initial ACP concentrations >0.2% (17 mM). Viability of cells at 0.4% ACP was 1/4 the viability at 0.2% ACP as determined by vital staining, and <1% based on colony-forming ability. this sensitivity was observed in suspensions with a cell content of nearly 30% (w/v). longterm pea production is strongly dependent on viability, indicating that the cumulative yield per batch of cells is maximized by maintaining a very low concentration of substrate (0.2%). however, nonviable cells (cfu ml⁻¹ <1% cells ml⁻¹) can achieve PEA yields up to 1/3 the maximum, an amount representing initial absorption of ACP without further uptake. Regarding population adaptability, when cells surviving the most selective (toxic) concentration of ACP (0.6%) were subcultured in an ACP-free medium and re-reacted, the 24-h percent viabilities (vital staining) and colony-forming frequencies exceeded those of non-selected cells. However, the surviving cells represented only a small fraction (1%) of the recultured progeny. Even at ACP concentrations as low as 0.25% (w/v), surviving cells were unreliable in transmitting and maintaining ACP-tolerance. In addition, there was no evidence that the chemical yield of recultured ACP-tolerant cells (amount of PEA relative to initial amount of ACP) can consistently exceed the maximum yield of an equivalent density of previously unreacted (non-selected) cells. These results indicate that over a broad range of substrate concentrations, rapid replacement of cells may be more cost-effective than maintenance or reuse of viable cells. Received 18 December 1997/ Accepted in revised form 22 January 1999     

Effect of ionic liquid [BMIM][PF<Subscript>6</Subscript>] on asymmetric reduction of ethyl 2-oxo-4-phenylbutyrate by <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

The effect of ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF₆]) on the asymmetric reduction of ethyl 2-oxo-4-phenylbutyrate (EOPB) to synthesize optical active ethyl 2-hydroxy-4-phenylbutyrate (EHPB) catalyzed by Saccharomyces cerevisiae was investigated. (R)-EHPB [70.4%, e.e.(R)] is obtained using ethyl ether or benzene as the solvent. The main product is (S)-EHPB [27.7%, e.e.(S)] in [BMIM][PF₆]. However, in ionic liquid-water (10:1, v/v) biphasic system, the enantioselectivity of the reduction is shifted towards (R)-side, and e.e.(R) is increased from 6.6 to 82.5% with the addition of ethanol (1%, v/v). The effect of the use of [BMIM][PF₆] as an additive in relatively small amounts on the reduction was also studied. We find that there is a decline in the enantioselectivity of the reduction in benzene. In addition, a decrease in the conversion of EOPB and the yield of EHPB with increasing [BMIM][PF₆] concentrations occurs in either organic solvent–water biphasic systems or benzene.     

Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae

Yeasts used in bread making are exposed to high concentrations of sucrose during sweet dough fermentation. Despite its importance, tolerance to high-sucrose stress is poorly understood at the gene level. To clarify the genes required for tolerance to high-sucrose stress, genome-wide screening was undertaken using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 273 deletions that yielded high sucrose sensitivity, approximately 20 of which were previously uncharacterized. These 273 deleted genes were classified based on their cellular function and localization of their gene products. Cross-sensitivity of the high-sucrose-sensitive mutants to high concentrations of NaCl and sorbitol was studied. Among the 273 sucrose-sensitive deletion mutants, 269 showed cross-sensitivities to sorbitol or NaCl, and four (i.e. ade5,7, ade6, ade8, and pde2) were specifically sensitive to high sucrose. The general stress response pathways via high-osmolarity glycerol and stress response element pathways and the function of the invertase in the ade mutants were similar to those in the wild-type strain. In the presence of high-sucrose stress, intracellular contents of ATP in ade mutants were at least twofold lower than that of the wild-type cells, suggesting that depletion of ATP is a factor in sensitivity to high-sucrose stress. The genes identified in this study might be important for tolerance to high-sucrose stress, and therefore should be target genes in future research into molecular modification for breeding of yeast tolerant to high-sucrose stress.     

Stereoselective bioreduction of 1-(5-phenylfuran-2-yl)-ethanones mediated by baker's yeast

Abstract

Baker's yeast mediated reduction of various phenylfuran-2-yl-ethanones has been studied. The influence of the reaction conditions, the type and position of the substituents, as well the presence of various additives on the enantiomeric composition of the products and the reaction yield are discussed. The absolute configuration of the reaction products was established using a retrosynthetic procedure.     

Hydrogen transfer pathways of the asymmetric reduction of alpha,beta-unsaturated ketone mediated by baker's yeast

The hydrogen transfer mechanism of cofactor reduction and recycling processes in the yeast reduction of alpha,beta-unsaturated ketone was studied by using quantitative isotope tracing close to natural abundance measured by (2)H NMR. In the reaction, the active cofactor is NADPH. The cofactor-transferred hydride attacks the beta sp(2) carbon of the enone carbonyl while water hydrogen is transferred to the alpha position. The reductant involved in the reaction depends on the quantity of yeast. When the amount of yeast is very large, the enzymes use preferentially certain unidentified substance stored in the yeast cells rather than the added glucose as electron donor. In this case, the hydrogen transferred by the cofactor is mainly of water origin. When the yeast amount is low, the added glucose is more efficiently used by the enzymes as electron donor and its hydrogen atoms bound to C-1 and C-3 are delivered to the substrate.     

Induction of renal oxidative stress and cell proliferation response by ferric nitrilotriacetate (Fe-NTA): diminution by soy isoflavones

Ferric nitrilotriacetate (Fe-NTA) is a known potent nephrotoxic agent. In this communication, we report the chemopreventive effect of soy isoflavones on renal oxidative stress, toxicity and cell proliferation response in Wistar rats. Fe-NTA (9 mg Fe/kg body weight, intraperitoneally) enhances gamma-glutamyl transpeptidase, renal lipid peroxidation, xanthine oxidase and hydrogen peroxide (H2O2) generation with reduction in renal glutathione content, antioxidant enzymes, viz., glutathione peroxidase, glutathione reductase, catalase, glucose-6-phosphate dehydrogenase and phase-II metabolising enzymes such as glutathione-S-transferase and quinone reductase. Fe-NTA treatment also induced tumor promotion markers, viz., ornithine decarboxylase (ODC) activity and thymidine [3H] incorporation into renal DNA. A sharp elevation in the levels of blood urea nitrogen and serum creatinine has also been observed. Treatment of rats orally with soy isoflavones (5 mg/kg body weight and 10 mg/kg body weight) resulted in significant decreases in gamma-glutamyl transpeptidase, lipid peroxidation, xanthine oxidase, H2O2 generation, blood urea nitrogen, serum creatinine, renal ODC activity and DNA synthesis (P < 0.001). Renal glutathione content (P < 0.01), glutathione metabolizing enzymes (P < 0.001) and antioxidant enzymes were also returned to normal levels (P < 0.001). Thus, our data suggest that soy isoflavones may be used as an effective chemopreventive agent against Fe-NTA-mediated renal oxidative stress, toxicity and cell proliferation response in Wistar rats.     

A method for simple identification of signature peptides derived from polyUb-K48 and K63 by MALDI-TOF MS and chemically assisted MS/MS fragmentation

Summary. A simple method is described to identify signature peptides derived from polyubiquitin (polyUb) chains. The method is based on MALDI-TOF MS/MS analysis after chemically assisted fragmentation, and works on peptides isolated from polyacrylamide gels. PolyUb chains branched at K48 and K63 were chosen as models for Ub-protein conjugates. They were resolved by SDS-PAGE, and their tryptic peptides (in-gel-trypsinolysis) derivatized with 3-sulfopropinic acid NHSester to obtain chemically assisted fragmentation during the MS/MS analysis. PolyUb-K63 produced a single peptide identified as ⁵⁵TLSDYNIQK⁶³ (GG)ESTLHLVLR⁷². PolyUb-K48 produced two branched signature peptides identified as ⁴³LIFAGK⁴⁸(GG)QLEDGR⁵⁴ and ⁴³LIFAGK⁴⁸(LRGG)QLEDGR⁵⁴. The recovery of signature peptide with LRGG as branched chain underscores the need to take limited proteolysis into account in the search for detection of ubiquitinated peptides in proteomics studies. In conclusion, a simple method has been described allowing the identification of signature peptides, which are diagnostic markers of the majority of polyUb-conjugated proteins. In principle, the method should be applicable also for other more rare signature peptides.     

Transgenic tobacco plants overexpressing the Met25 gene of Saccharomyces cerevisiae exhibit enhanced levels of cysteine and glutathione and increased tolerance to oxidative stress

Summary. The cysteine biosynthesis pathway differs between plants and the yeast Saccharomyces cerevisiae. The yeast MET25 gene encoded to O-acetylhomoserine sulfhydrylase (AHS) catalyzed the reaction that form homocysteine, which later can be converted into cystiene. In vitro studies show that this enzyme possesses also the activity of O-acetyl(thiol)lyase (OASTL) that catalyzes synthesis of cysteine in plants. In this study, we generated transgenic tobacco plants expressing the yeast MET25 gene under the control of a constitutive promoter and targeted the yeast protein to the cytosol or to the chloroplasts. Both sets of transgenic plants were taller and greener than wild-type plants. Addition of SO₂, the substrate of the yeast enzyme caused a significant elevation of the glutathione content in representative plants from each of the two sets of transgenic plants expressing the yeast gene. Determination of non-protein thiol content indicated up to four-folds higher cysteine and 2.5-fold glutathione levels in these plants. In addition, the leaf discs of the transgenic plants were more tolerant to toxic levels of sulphite, and to paraquat, an herbicide generating active oxygen species.     

Using pseudo amino acid composition to predict protein subnuclear location with improved hybrid approach

Summary. The subnuclear localization of nuclear protein is very important for in-depth understanding of the construction and function of the nucleus. Based on the amino acid and pseudo amino acid composition (PseAA) as originally introduced by K. C. Chou can incorporate much more information of a protein sequence than the classical amino acid composition so as to significantly enhance the power of using a discrete model to predict various attributes of a protein, an algorithm of increment of diversity combined with the improved quadratic discriminant analysis is proposed to predict the protein subnuclear location. The overall predictive success rates and correlation coefficient are 75.4% and 0.629 for 504 single localization proteins in jackknife test, and 80.4% for an independent set of 92 multi-localization proteins, respectively. For 406 single localization nuclear proteins with ≤25% sequence identity, the results of jackknife test show that the overall accuracy of prediction is 77.1%. Authors’ address: Qian-Zhong Li, Laboratory of Theoretical Biophysics, Department of Physics, College of Sciences and Technology, Inner Mongolia University, Hohhot 010021, China     

Inactivation of genes encoding superoxide dismutase modifies yeast response to S-nitrosoglutathione-induced stress

Antioxidant enzymes can modify cell response to nitrosative stress induced, for example, by nitric oxide or compounds decomposing with its formation. Therefore, we investigated the effects of S-nitrosoglutathione (GSNO) on cell survival, activity of antioxidant enzymes, and concentrations of reduced and oxidized glutathione in parental and isogenic strains defective in Cu,Zn- or Mn-superoxide dismutases (Cu,Zn-SOD and Mn-SOD, respectively), or in both of them. Stress was induced by incubation of the yeast with 1–20 mM GSNO. The strains used demonstrated different sensitivity to GSNO. A Cu,Zn-SOD-defective strain survived the stress better than the parental strain, while the double mutant was the most sensitive to GSNO. The ^·NO-donor at low concentrations (1–5 mM) increased SOD activity, but its high concentrations (10 and 20 mM) decreased it. The activity of catalase in all strains was enhanced by GSNO. Inhibition of protein synthesis by cycloheximide did not prevent the activation of SOD, but it prevented the activation of catalase. These facts suggest that SOD was activated at a posttranslational level and catalase activity was enhanced via de novo synthesis. A GSNO-induced increase in oxidized glutathione level in the studied yeast strains might account for cell killing by GSNO due to the development of oxidative/nitrosative stress. Published in Russian in Biokhimiya, 2009, Vol. 74, No. 4, pp. 550–557.     

Study of the oxygen transfer in a disposable flexible bioreactor with surface aeration in vibrated medium

The oxygen mass transfer is a critical design parameter for most bioreactors. It can be described and analyzed by means of the volumetric mass transfer coefficient K _L a. This coefficient is affected by many factors such as geometrical and operational characteristics of the vessels, type, media composition, rheology and microorganism’s morphology and concentration. In this study, we aim to develop and characterize a new culture system based on the surface aeration of a flexible, single-used bioreactor fixed on a vibrating table. In this context, the K _L a was evaluated using a large domain of operating variables such as vibration frequency of the table, overpressure inside the pouch and viscosity of the liquid. A novel method for K _L a determination based on the equilibrium state between oxygen uptake rate and oxygen transfer rate of the system at given conditions was also developed using resting cells of baker’s fresh yeast with a measured oxygen uptake rate of 21 mg g⁻¹ h⁻¹ (at 30°C). The effect of the vibration frequency on the oxygen transfer performance was studied for frequencies ranging from 15 to 30 Hz, and a maximal K _L a of 80 h⁻¹ was recorded at 30 Hz. A rheological study of the medium added with carboxymethylcellulose at different concentrations and the effect of the liquid viscosity on K _L a were determined. Finally, the mixing time of the system was also measured using the pH method.