Person: TOKSOY ÖNER, EBRU
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TOKSOY ÖNER
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Publication Metadata only The Stimulatory Effect of Mannitol on Levan Biosynthesis: Lessons from Metabolic Systems Analysis of Halomonas smyrnensis AAD6(T)(WILEY, 2013) TOKSOY ÖNER, EBRU; Ates, Ozlem; Arga, Kazim Y.; Oner, Ebru ToksoyHalomonas smyrnensis AAD(T) is a halophilic, gram-negative bacterium that can efficiently produce levan from sucrose as carbon source via levansucrase activity. However, systems-based approaches are required to further enhance its metabolic performance for industrial application. As an important step toward this goal, the genome-scale metabolic network of Chromohalobacter salexigens DSM3043, which is considered a model organism for halophilic bacteria, has been reconstructed based on its genome annotation, physiological information, and biochemical information. In the present work, the genome-scale metabolic network of C. salexigens was recruited, and refined via integration of the available biochemical, physiological, and phenotypic features of H. smyrnensis AAD6(T). The generic metabolic model, which comprises 1,393 metabolites and 1,108 reactions, was then systematically analyzed in silico using constraints-based simulations. To elucidate the relationship between levan biosynthesis and other metabolic processes, an enzyme-graph representation of the metabolic network and a graph decomposition technique were employed. Using the concept of control effective fluxes, significant links between several metabolic processes and levan biosynthesis were estimated. The major finding was the elucidation of the stimulatory effect of mannitol on levan biosynthesis, which was further verified experimentally via supplementation of mannitol to the fermentation medium. The optimal concentration of 30 g/L mannitol supplemented to the 50 g/L sucrose-based medium resulted in a twofold increase in levan production in parallel with increased sucrose hydrolysis rate, accumulated extracellular glucose, and decreased fructose uptake rate. (c) 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1386-1397, 2013Publication Metadata only Evaluation of industrial Saccharomyces cerevisiae strains for ethanol production from biomass(PERGAMON-ELSEVIER SCIENCE LTD, 2012) KASAVİ, CEYDA; Kasavi, Ceyda; Finore, Ilaria; Lama, Licia; Nicolaus, Barbara; Oliver, Stephen G.; Oner, Ebru Toksoy; Kirdar, BetulFive industrial Saccharomyces cerevisiae strains were evaluated for their suitability for strain improvement for future use in ethanol production processes. Principal components analysis of growth-related and production-related fermentation parameters of the 5 strains grown on glucose demonstrated the superiority of the Y9 strain in terms of its rapid growth and highest ethanol yields on both biomass and glucose. The growth and ethanol production performances of these strains on various agro-industrial wastes (including sugar beet pulp, starch and sugar beet molasses) and biological residues (including carrot, tomato and potato peel) were also determined. Ethanol tolerance studies, using both solid and liquid cultures, revealed the remarkable abilities of the BC187 and Y9 strains to survive and grow at high ethanol concentrations. Suspension cultures were found to be highly tolerant to 78.80 g L-1 ethanol however their growth ability showed a distinct decrease with increasing ethanol concentration such that only (1-2)% of the control growth was observed in media containing 118.20 g L-1 ethanol. The importance of choosing the appropriate S. cerevisiae strain to be used in ethanol production was clearly established with this study. Fermentation performances of the cultures under different cultivation conditions pointed to the fact that the choice of strain will not only depend on the ethanol tolerance but also on the preferential utilization of the carbon resources of biological residues. (c) 2012 Elsevier Ltd. All rights reserved.Publication Metadata only Levan promotes antiproliferative and pro-apoptotic effects in MCF-7 breast cancer cells mediated by oxidative stress(ELSEVIER, 2017) TOKSOY ÖNER, EBRU; Queiroz, Eveline A. I. F.; Fortes, Zuleica B.; da Cunha, Mario A. A.; Sarilmiser, Hande Kazak; Dekker, Aneli M. Barbosa; Oner, Ebru Toksoy; Dekker, Robert F. H.; Khaper, NeelamExopolysaccharides are high-valued bio-products produced by various microbial species and have been described to possess biological response modifying activities. These bio-products have been effective as therapeutic agents in various human disease conditions. The objective of this study was to examine the effects of levan (a (2 -> 6)-beta-D-fructan) produced on sucrose by the halophilic bacterium, Halomonas smyrnensis AAD6(T), in human breast cancer MCF-7 cells. MCF-7 cells were exposed to levan for 24 and 48 h. The antiproliferative activity was analyzed by the MTF assay. Oxidative stress was measured by the CM-H(2)DCFDA assay, and cell apoptosis was analyzed by the caspase-3/7 assay. Cell cycle was analyzed by flow cytometry and gene expression was determined by RT-PCR. Levan showed a time- and concentration-dependent antiproliferative activity, and this effect was associated with an increase in cell apoptosis and oxidative stress. In addition, levan increased the gene expression of p53 and p27. Here we demonstrated that levan exhibited an antiproliferative effect that was mediated by an increase in apoptosis and oxidative stress. (C) 2017 Elsevier B.V. All rights reserved.Publication Metadata only An integrative analysis of transcriptomic response of ethanol tolerant strains to ethanol in Saccharomyces cerevisiae(ROYAL SOC CHEMISTRY, 2016) KASAVİ, CEYDA; Kasavi, Ceyda; Eraslan, Serpil; Oner, Ebru Toksoy; Kirdar, BetulThe accumulation of ethanol is one of the main environmental stresses that Saccharomyces cerevisiae cells are exposed to in industrial alcoholic beverage and bioethanol production processes. Despite the known impacts of ethanol, the molecular mechanisms underlying ethanol tolerance are still not fully understood. Novel gene targets leading to ethanol tolerance were previously identified via a network approach and the investigations of the deletions of these genes resulted in the improved ethanol tolerance of pmt7 Delta/pmt7 Delta and yhl042w Delta/yhl042w Delta strains. In the present study, an integrative system based approach was used to investigate the global transcriptional changes in these two ethanol tolerant strains in response to ethanol and hence to elucidate the mechanisms leading to the observed tolerant phenotypes. In addition to strain specific biological processes, a number of common and already reported biological processes were found to be affected in the reference and both ethanol tolerant strains. However, the integrative analysis of the transcriptome with the transcriptional regulatory network and the ethanol tolerance network revealed that each ethanol tolerant strain had a specific organization of the transcriptomic response. Transcription factors around which most important changes occur were determined and active subnetworks in response to ethanol and functional clusters were identified in all strains.Publication Open Access A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris(SPRINGER, 2019-04) TOKSOY ÖNER, EBRU; Ozcan, Emrah; Selvi, S. Selvin; Nikerel, Emrah; Teusink, Bas; Oner, Ebru Toksoy; Cakir, TunahanLeuconostoc mesenteroides subsp. cremoris is an obligate heterolactic fermentative lactic acid bacterium that is mostly used in industrial dairy fermentations. The phosphoketolase pathway (PKP) is a unique feature of the obligate heterolactic fermentation, which leads to the production of lactate, ethanol, and/or acetate, and the final product profile of PKP highly depends on the energetics and redox state of the organism. Another characteristic of the L. mesenteroides subsp. cremoris is the production of aroma compounds in dairy fermentation, such as in cheese production, through the utilization of citrate. Considering its importance in dairy fermentation, a detailed metabolic characterization of the organism is necessary for its more efficient use in the industry. To this aim, a genome-scale metabolic model of dairy-origin L. mesenteroides subsp. cremoris ATCC 19254 (iLM.c559) was reconstructed to explain the energetics and redox state mechanisms of the organism in full detail. The model includes 559 genes governing 1088 reactions between 1129 metabolites, and the reactions cover citrate utilization and citrate-related flavor metabolism. The model was validated by simulating co-metabolism of glucose and citrate and comparing the in silico results to our experimental results. Model simulations further showed that, in co-metabolism of citrate and glucose, no flavor compounds were produced when citrate could stimulate the formation of biomass. Significant amounts of flavor metabolites (e.g., diacetyl and acetoin) were only produced when citrate could not enhance growth, which suggests that flavor formation only occurs under carbon and ATP excess. The effects of aerobic conditions and different carbon sources on product profiles and growth were also investigated using the reconstructed model. The analyses provided further insights for the growth stimulation and flavor formation mechanisms of the organism.Publication Open Access Optimization of ethanol production using newly isolated ethanologenic yeasts(ELSEVIER, 2021-03) TOKSOY ÖNER, EBRU; Tesfaw, Asmamaw; Oner, Ebru Toksoy; Assefa, FassilYeasts are important microorganisms used for ethanol production; however, they are not equally efficient in the amount of ethanol production under different environmental conditions. It is, therefore, necessary to screen for elite strains to utilize them for commercial production of these commodities. In this study, yeasts were isolated from different Ethiopian traditional fermented alcoholic beverages (teji, tella, shamiata and areqe tinisis), milk and ergo, teff and maize dough, soil and compost, flowers, and fruits to evaluate their potential use for ethanol fermentation process. Isolates were screened for efficient ethanol production and the selected ones were identified using phenotypic and genetic characters using D1/D2 region of LSU rDNA sequence analysis. The yeast isolates were evaluated based on their growth and fermentation of different carbon sources. Response surface methodology (RSM) was applied to optimize temperature, pH and incubation time using central composite design (CCD) in Design-Expert 7.0.0. A total of 211 yeasts colonies were isolated of which 60% were ethanologenic yeasts (ethanol producers) and 40% were non-ethanol producers. The yeast population detected from various sources was in the range of 10(5) CFU from traditional foods and beverages to that of 10(3) CFU from fruits and soil samples. The data also showed that the number of colony types (diversity) did not correlate with population density. The highly fermentative isolates were taxonomically characterized into four genera, of which 65% of the isolates (ETP37, ETP50; ETP53, ETP89, ETP94) were categorized under Saccharomyces cerevisiae, and the remaining were Pichia fermentans ETP22, Kluyveromyces marxianus ETP87, and Candida humilis ETP122. The S. cerevisiae isolates produced ethanol (7.6-9.0 g/L) similar with K. marxianus ETP87 producing 7.97 g/L; comparable to the ethanol produced from commercial baker's yeast (8.43 g/L) from 20 g/L dextrose; whereas C. humilis ETP122 and P. fermentans ETP22 produced 5.37 g/L and 6.43 g/L ethanol, respectively. S. cerevisiae ETP53, K. marxianus ETP87, P. fermentans ETP22 and C. humilis ETP122 tolerated 10% extraneous ethanol but the percentage of ethanol tolerance considerably decreased upon 15%. S. cerevisiae ETP53 produced ethanol optimally at pH 5.0, 60 h, and 34 degrees C. pH 4.8, temperature 36 degrees C, and 65 h of time were optimal growth conditions of ethanol fermentation by K. marxianus ETP87. The ethanol fermentation conditions of P. fermentans ETP22 was similar to S. cerevisiae ETP53 though the ethanol titer of S. cerevisiae ETP53 was higher than P. fermentans ETP22. Therefore, S. cerevisiae ETP53, K. marxianus and P. fermentans ETP22 are good candidates for ethanol production.Publication Open Access A system based network approach to ethanol tolerance in Saccharomyces cerevisiae(BMC, 2014-12) KASAVİ, CEYDA; Kasavi, Ceyda; Eraslan, Serpil; Arga, Kazim Yalcin; Oner, Ebru Toksoy; Kirdar, BetulBackground: Saccharomyces cerevisiae has been widely used for bio-ethanol production and development of rational genetic engineering strategies leading both to the improvement of productivity and ethanol tolerance is very important for cost-effective bio-ethanol production. Studies on the identification of the genes that are up-or down-regulated in the presence of ethanol indicated that the genes may be involved to protect the cells against ethanol stress, but not necessarily required for ethanol tolerance. Results: In the present study, a novel network based approach was developed to identify candidate genes involved in ethanol tolerance. Protein-protein interaction (PPI) network associated with ethanol tolerance (tETN) was reconstructed by integrating PPI data with Gene Ontology (GO) terms. Modular analysis of the constructed networks revealed genes with no previously reported experimental evidence related to ethanol tolerance and resulted in the identification of 17 genes with previously unknown biological functions. We have randomly selected four of these genes and deletion strains of two genes (YDR307W and YHL042W) were found to exhibit improved tolerance to ethanol when compared to wild type strain. The genome-wide transcriptomic response of yeast cells to the deletions of YDR307W and YHL042W in the absence of ethanol revealed that the deletion of YDR307W and YHL042W genes resulted in the transcriptional re-programming of the metabolism resulting from a mis-perception of the nutritional environment. Yeast cells perceived an excess amount of glucose and a deficiency of methionine or sulfur in the absence of YDR307W and YHL042W, respectively, possibly resulting from a defect in the nutritional sensing and signaling or transport mechanisms. Mutations leading to an increase in ribosome biogenesis were found to be important for the improvement of ethanol tolerance. Modulations of chronological life span were also identified to contribute to ethanol tolerance in yeast. Conclusions: The system based network approach developed allows the identification of novel gene targets for improved ethanol tolerance and supports the highly complex nature of ethanol tolerance in yeast.Publication Metadata only Optimization of ethanol production from starch by an amylolytic nuclear petite Saccharomyces cerevisiae strain(WILEY, 2006) TOKSOY ÖNER, EBRU; Oner, Ebru ToksoyEthanol fermentation characteristics of the 100% respiratory-deficient nuclear petite amylolytic Saccharomyces cerevisiae NPB-G strain was investigated in both shake-flask and controlled bioreactor cultivation conditions, and comparison with the earlier reported results revealed 54.6% increase in ethanol yield. Efforts to improve the starch utilization rate by increasing the selection pressure or supplying the fermentation medium with glucose did not prevent the observed decrease in time-dependent amylolytic activity. Response surface methodology (RSM) was then used as a statistical tool to optimize the initial yeast extract and starch contents of the medium, which resulted in a substantial increase in the stability of the expression plasmid in both the respiratory-deficient NPB-G and the parental respiratory-sufficient WTPB-G strains, with concomitant improvement in their amylolytic potentials. High ethanol yields on substrate values of the bioreactor cultures, which were very close to the theoretical yield, indicated that the amylolytic respiratory-deficient NPB-G strain was effective in the direct fermentation of starch into ethanol. Copyright (c) 2006 John Wiley & Sons, Ltd.Publication Open Access Evaluating crude whey for bioethanol production using non-Saccharomyces yeast, Kluyveromyces marxianus(SPRINGER INTERNATIONAL PUBLISHING AG, 2021-01) TOKSOY ÖNER, EBRU; Tesfaw, Asmamaw; Oner, Ebru Toksoy; Assefa, FassilEthanol production from non-food substrate is strongly recommended to avoid competition with food production. Whey, which is rich in nutrients, is one of the non-food substrate for ethanol production by Kluyveromyces spp. The purpose of this study was to optimize ethanol from different crude (non-deproteinized, non-pH adjusted, and non-diluted) whey using K. marxianus ETP87 which was isolated from traditional yoghurt. The sterilized and non-sterilized whey were employed for K. marxianus ETP87 substrate to evaluate the yeast competition potential with lactic acid and other microflora in whey. The effect of pH and temperature on ethanol productivity from whey was also investigated. Peptone, yeast extract, ammonium sulfate ((NH4)(2)SO4), and urea were supplemented to whey in order to investigate the requirement of additional nutrient for ethanol optimization. The ethanol obtained from non-sterilized whey was slightly and statistically lower than sterilized whey. The whey storage at 4 degrees C didn't guarantee the constant lactose presence at longer preservation time. Significantly high amount of ethanol was attained from whey without pH adjustment (3.9) even if it was lower than pH controlled (5.0) whey. The thermophilic yeast, K. marxianus ETP87, yielded high ethanol between 30 and 35 degrees C, and the yeast was able to produce high ethanol until 45 degrees C, and significantly lower ethanol was recorded at 50 degrees C. The ammonium sulfate and peptone enhanced ethanol productivity, whereas yeast extract and urea depressed the yeast ethanol fermentation capability. The K. marxianus ETP87, the yeast isolated from traditional yoghurt, is capable of producing ethanol from non-sterilized and non-deproteinized substrates.