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TOKSOY ÖNER, EBRU

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Mühendislik Fakültesi

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TOKSOY ÖNER

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Open Access
Levansucrase from Halomonas smyrnensis AAD6(T): first halophilic GH-J clan enzyme recombinantly expressed, purified, and characterized
(SPRINGER, 2018-11) TOKSOY ÖNER, EBRU; Kirtel, Onur; Menendez, Carmen; Versluys, Maxime; Van den Ende, Wim; Hernandez, Lazaro; Oner, Ebru Toksoy
Fructans, homopolymers of fructose produced by fructosyltransferases (FTs), are emerging as intriguing components in halophiles since they are thought to be associated with osmotic stress tolerance and overall fitness of microorganisms and plants under high-salinity conditions. Here, we report on the full characterization of the first halophilic FT, a levansucrase from Halomonas smyrnensis AAD6(T) (HsLsc; EC 2.4.1.10). The encoding gene (lsc) was cloned into a vector with a 6xHis Tag at its C-terminus, then expressed in Escherichia coli. The purified recombinant enzyme (47.3kDa) produces levan and a wide variety of fructooligosaccharides from sucrose, but only in the presence of high salt concentrations (>1.5M NaCl). HsLsc showed Hill kinetics and pH and temperature optima of 5.9 and 37 degrees C, respectively. Interestingly, HsLsc was still very active at salt concentrations close to saturation (4.5M NaCl) and was selectively inhibited by divalent cations. The enzyme showed high potential in producing novel saccharides derived from raffinose as both fructosyl donor and acceptor and cellobiose, lactose, galactose, and -arabinose as fructosyl acceptors. With its unique biochemical characteristics, HsLsc is an important enzyme for future research and potential industrial applications in a world faced with drought and diminishing freshwater supplies.
Open Access
Evaluation of the Potential Use of Levan Polysaccharide in Paper Conservation
(WILEY-HINDAWI, 2020-08-10) TOKSOY ÖNER, EBRU; Saglam, Rumeysa Ozen; Genc, Seval; Oner, Ebru Toksoy
Conservation of paper-based materials, namely, manuscripts, includes repair of tears, gap filling, consolidation, and fixation, which requires the use of adhesives. The adhesive in use for these purposes should be compatible with the chemical and physical properties of paper and should present good aging characteristics. In this study, we conducted a set of experiments with paper samples on which fructan-based biopolymer Halomonas levan (Hlevan) was applied for the first time and compared with glucan-based adhesive starch. Adhesive-applied samples were initially prepared by the application of different historical recipes of sizing and ink. Then, they underwent accelerated thermal aging. Chemical and physical changes of paper samples (crystallinity, pH, and color) were analyzed. Finally, Principal Component Analysis was performed to identify dominating factors affecting sample behavior with applied adhesives. This study demonstrates the aging characteristics of Hlevan on cellulose-based materials. The results showed that there is a color shift from blue to yellow for all samples after aging, but it is more pronounced for some samples with Hlevan. In addition, Hlevan is slightly less acidic than starch in all cases and acted as a plasticizer for a specific kind of sizing material. The methodology of this research is also efficacious in terms of understanding the interaction of paper media with the adhesives and their effects on aging.
Open Access
Synthesis and characterization of interpenetrating network (IPN) based levan-polyacrylamide hydrogels and their application in conservation of cultural heritage
(2023-11-01) ÜNAL YILDIRIM, SEMRA; OKTAR, FAİK NÜZHET; GENÇ, SEVAL; TOKSOY ÖNER, EBRU; Özen Sağlam R., Ünal Yıldırım S., Oktar F. N., Genç S., Erdem G., Toksoy Öner E.
In this study, an IPN based enzymatic levan-polyacrylamide hydrogel (EL-PA) was developed and characterized for its structural, morphological, rheological properties and swelling kinetics to underline hydrogel properties and its potential use in paper conservation. The addition of levan also led to changes in the viscoelastic behavior of the hydrogels, with the complex viscosity of EL-PA samples showing pronounced dependence on shear rate. The swelling and the overall surface area of the hydrogels were increased with the addition of levan into the polymer network. Source associated structural differences were found to be negligible such that both microbially produced linear and enzymatically produced branched forms of levan performed equally well. Solvent loaded hydrogels were then applied on an artifact, a 19th century book of Namık Kemal, and investigated using FTIR, SEM, XRD and colorimetric analysis. Old adhesive layers were successfully removed, and hydrogels showed good compatibility and ease of application. This study has shown that levan has improved hydrogel properties and levan based systems bear high potential in conservation science.
Open Access
Extremophilic Natrinema versiforme Against Pseudomonas aeruginosa Quorum Sensing and Biofilm
(FRONTIERS MEDIA SA, 2020-02-06) TOKSOY ÖNER, EBRU; Basaran, Tunahan Irmak; Berber, Didem; Gokalsin, Baris; Tramice, Annabella; Tommonaro, Giuseppina; Abbamondi, Gennaro Roberto; Erginer Haskoylu, Merve; Toksoy oner, Ebru; Iodice, Carmine; Sesal, Nuzhet Cenk
Pseudomonas aeruginosa is an opportunistic pathogen that causes high morbidity and mortality rates due to its biofilm form. Biofilm formation is regulated via quorum sensing (QS) mechanism and provides up to 1000 times more resistance against conventional antibiotics. QS related genes are expressed according to bacterial population density via signal molecules. QS inhibitors (QSIs) from natural sources are widely studied evaluating various extracts from extreme environments. It is suggested that extremely halophilic Archaea may also produce QSI compounds. For this purpose, we tested QS inhibitory potentials of ethyl acetate extracts from cell free supernatants and cells of Natrinema versiforme against QS and biofilm formation of P. aeruginosa. To observe QS inhibition, all extracts were tested on P. aeruginosa lasB-gfp, rhlA-gfp, and pqsA-gfp biosensor strains and biofilm inhibition was studied using P. aeruginosa PAO1. According to our results, QS inhibition ratios of cell free supernatant extract (CFSE) were higher than cell extract (CE) on las system, whereas CE was more effective on rhl system. In addition, anti-biofilm effect of CFSE was higher than CE. Structural analysis revealed that the most abundant compound in the extracts was trans 4-(2-carboxy-vinyl) benzoic acid.
Open Access
Fructans Prime ROS Dynamics and Botrytis cinerea Resistance in Arabidopsis
(MDPI, 2020-09-01) TOKSOY ÖNER, EBRU; Janse van Rensburg, Henry Christopher; Takacs, Zoltan; Freynschlag, Florentina; Toksoy Oner, Ebru; Jonak, Claudia; Van den Ende, Wim
Naturally derived molecules can be used as priming or defense stimulatory agents to protect against biotic stress. Fructans have gained strong interest due to their ability to induce resistance in a number of crop species. In this study, we set out to establish the role of fructan-induced immunity against the fungal pathogen Botrytis cinerea in Arabidopsis thaliana. We show that both inulin- and levan-type fructans from different sources can enhance Arabidopsis resistance against B. cinerea. We found that inulin from chicory roots and levan oligosaccharides from the exopolysaccharide-producing bacterium Halomonas smyrnensis primed the NADPH-oxidase-mediated reactive oxygen species (ROS) burst in response to the elicitors flg22, derived from the bacterial flagellum, and oligogalacturonides (OGs), derived from the host cell wall. Neither induced a direct ROS burst typical of elicitors. We also found a primed response after infection with B. cinerea for H2O2 accumulation and the activities of ascorbate peroxidase and catalase. Sucrose accumulated as a consequence of fructan priming, and glucose and sucrose levels increased in fructan-treated plants after infection with B. cinerea. This study shows that levan-type fructans, specifically from bacterial origin, can prime plant defenses and that both inulin and levan oligosaccharide-mediated priming is associated with changes in ROS dynamics and sugar metabolism. Establishing fructan-induced immunity in Arabidopsis is an important step to further study the underlying mechanisms since a broad range of biological resources are available for Arabidopsis.
Open Access
High bioreactor production and emulsifying activity of an unusual exopolymer by Chromohalobacter canadensis 28
(WILEY, 2020-08) TOKSOY ÖNER, EBRU; Radchenkova, Nadja; Boyadzhieva, Ivanka; Haskoylu, Merve Erginer; Atanasova, Nikolina; Yildiz, Songul Yasar; Kuncheva, Margarita J.; Panchev, Ivan; Kisov, Hristo; Vassilev, Spasen; Oner, Ebru Toksoy; Kambourova, Margarita S.
Unusual composition of an exopolymer (EP) from an obligate halophilic bacterium Chromohalobacter canadensis 28 has triggered an interest in development of an effective bioreactor process for its production. Its synthesis was investigated in 2-L bioreactor at agitation speeds at interval 600-1000 rpm, at a constant air flow rate of 0.5 vvm; aeration rates of 0.5, 1.0, and 1.5 vvm were tested at constant agitation rate of 900 rpm. EP production was affected by both, agitation and aeration. As a result twofold increase of EP yield was observed and additionally increased up to 3.08 mg/mL in a presence of surfactants. For effective scale-up of bioreactors mass transfer parameters were estimated and lowest values of K(L)a obtained for the highest productivity fermentation was established. Emulsification activity of EP exceeded that of trade hydrocolloids xanthan, guar gum, and cellulose. A good synergism between EP and commercial cellulose proved its potential exploration as an enhancer of emulsifying properties of trade emulsions. A pronounced lipophilic effect of EP was established toward olive oil and liquid paraffin. Cultivation of human keratinocyte cells (HaCaT) with crude EP and purified gamma-polyglutamic acid (PGA) showed higher viability than control group.
Open Access
Effect of temperature on the hydrolysis of levan treated with compressed hot water fluids
(WILEY, 2020-04) TOKSOY ÖNER, EBRU; Shimizu, Naoto; Abea, Andres; Ushiyama, Tetsuya; Oner, Ebru
The hydrolysis of levan using compressed hot water for the production of functional fructooligosaccharides (FOSs) was investigated. Levans from Erwinia herbicola (EH) and Halomonas smyrnensis (HS) were characterized using scanning electron microscopy and light scattering techniques, and hydrolyzed using compressed hot water at four temperatures (120, 140, 160, and 180 degrees C). The hydrolysates were analyzed using high-performance liquid chromatography and electrospray ionization-mass spectrometry. Levan HS showed a crystalline morphology, whereas levan EH showed an aggregated structure. Both levans had molar masses on the order of 10(6) g/mol, but levan EH had a smaller radius of gyration, hydrodynamic radius, and intrinsic viscosity. Levan EH hydrolyzed into FOSs at approximately 120 degrees C, whereas levan HS required a temperature of at least 160 degrees C, possibly because of differences in the degree of branching of the two levans. Both samples were degraded to fructose when treated at 180 degrees C.
Open Access
Biosynthesis of Levan by Halomonas elongata 153B: Optimization for Enhanced Production and Potential Biological Activities for Pharmaceutical Field
(2022-01-01) TOKSOY ÖNER, EBRU; Erdal Altıntaş Ö., TOKSOY ÖNER E., ÇABUK A., AYTAR ÇELİK P.
Halophilic organisms are a novel attractive option as cell factories for the production of industrially valuable bioproducts. Halomonas elongata is the cell factory of choice for ectoine production, but its levan production has not been well researched. Based on this scientifc motivation, in this study, we evaluated the chemical and biological properties of levan produced by the halophilic extremophile Halomonas elongata 153B (HeL). First, the central composite design was used to determine the optimal process variables for maximum levan biosynthesis. Then, the levan produced from HeL was purifed, quantifed, and chemically characterized with FTIR, 1 H-NMR, and GPC analyses. This was followed by antioxidant, anti-infammatory, antibioflm, and antimicrobial activity tests to assess its biological activities as well as a cytotoxcity assay. Maximum levan yields of 5.13±0.38 g/L were achieved after dialysis at the optimum levels of process variables. The 1 H-NMR spectrum of HeL revealed characteristic signals. It showed a strong antioxidant activity of 67.88% and the best radical scavenger. At a concentration of 400 µg/mL, HeL showed the most anti-infammatory efcacy. Also, at all indicated concentrations (250, 500, 750, and 1000 μg/mL) HeL, acted against bioflms formed by Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 6538, Pseudomonas aeruginosa ATCC 11778, Candida albicans ATCC 10231. Furthermore, HeL displayed antimicrobial activities against all strains tested. Finally, HeL showed high Cell viability in all dosages and no cytotoxicity was observed. In light of these results, HeL may have high potential in the medical, pharmaceutical and dermo-cosmetics industries.
Open Access
Dynamic co-culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures
(WILEY, 2021-01) TOKSOY ÖNER, EBRU; Ozcan, Emrah; Seven, Merve; Sirin, Burcu; Cakir, Tunahan; Nikerel, Emrah; Teusink, Bas; Toksoy Oner, Ebru
In this study, we have investigated the cheese starter culture as a microbial community through a question: can the metabolic behaviour of a co-culture be explained by the characterized individual organism that constituted the co-culture? To address this question, the dairy-origin lactic acid bacteriaLactococcus lactissubsp.cremoris,Lactococcus lactissubsp.lactis,Streptococcus thermophilus andLeuconostoc mesenteroides, commonly used in cheese starter cultures, were grown in pure and four different co-cultures. We used a dynamic metabolic modelling approach based on the integration of the genome-scale metabolic networks of the involved organisms to simulate the co-cultures. The strain-specific kinetic parameters of dynamic models were estimated using the pure culture experiments and they were subsequently applied to co-culture models. Biomass, carbon source, lactic acid and most of the amino acid concentration profiles simulated by the co-culture models fit closely to the experimental results and the co-culture models explained the mechanisms behind the dynamic microbial abundance. We then applied the co-culture models to estimate further information on the co-cultures that could not be obtained by the experimental method used. This includes estimation of the profile of various metabolites in the co-culture medium such as flavour compounds produced and the individual organism level metabolic exchange flux profiles, which revealed the potential metabolic interactions between organisms in the co-cultures.
Open Access
Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043
(BIOMED CENTRAL LTD, 2011-12) TOKSOY ÖNER, EBRU; Ates, Ozlem; Oner, Ebru Toksoy; Arga, Kazim Y.
Background: Chromohalobacter salexigens (formerly Halomonas elongata DSM 3043) is a halophilic extremophile with a very broad salinity range and is used as a model organism to elucidate prokaryotic osmoadaptation due to its strong euryhaline phenotype. Results: C. salexigens DSM 3043's metabolism was reconstructed based on genomic, biochemical and physiological information via a non-automated but iterative process. This manually-curated reconstruction accounts for 584 genes, 1386 reactions, and 1411 metabolites. By using flux balance analysis, the model was extensively validated against literature data on the C. salexigens phenotypic features, the transport and use of different substrates for growth as well as against experimental observations on the uptake and accumulation of industrially important organic osmolytes, ectoine, betaine, and its precursor choline, which play important roles in the adaptive response to osmotic stress. Conclusions: This work presents the first comprehensive genome-scale metabolic model of a halophilic bacterium. Being a useful guide for identification and filling of knowledge gaps, the reconstructed metabolic network iOA584 will accelerate the research on halophilic bacteria towards application of systems biology approaches and design of metabolic engineering strategies.