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Analysis and prediction of the physiological effects of altered coenzyme specificity in xylose reductase and xylitol dehydrogenase during xylose fermentation by Saccharomyces cerevisiae.
J Biotechnol. 2012 Apr 30; 158(4):192-202.JB

Abstract

An advanced strategy of Saccharomyces cerevisiae strain development for fermentation of xylose applies tailored enzymes in the process of metabolic engineering. The coenzyme specificities of the NADPH-preferring xylose reductase (XR) and the NAD⁺-dependent xylitol dehydrogenase (XDH) have been targeted in previous studies by protein design or evolution with the aim of improving the recycling of NADH or NADPH in their two-step pathway, converting xylose to xylulose. Yeast strains expressing variant pairs of XR and XDH that according to in vitro kinetic data were suggested to be much better matched in coenzyme usage than the corresponding pair of wild-type enzymes, exhibit widely varying capabilities for xylose fermentation. To achieve coherence between enzyme properties and the observed strain performance during fermentation, we explored the published kinetic parameters for wild-type and engineered forms of XR and XDH as possible predictors of xylitol by-product formation (Y(xylitol)) in yeast physiology. We found that the ratio of enzymatic reaction rates using NADP(H) and NAD(H) that was calculated by applying intracellular reactant concentrations to rate equations derived from bi-substrate kinetic analysis, succeeded in giving a statistically reliable forecast of the trend effect on Y(xylitol). Prediction based solely on catalytic efficiencies with or without binding affinities for NADP(H) and NAD(H) were not dependable, and we define a minimum demand on the enzyme kinetic characterization to be performed for this purpose. An immediate explanation is provided for the typically lower Y(xylitol) in the current strains harboring XR engineered for utilization of NADH as compared to strains harboring XDH engineered for utilization of NADP⁺. The known XDH enzymes all exhibit a relatively high K(m) for NADP⁺ so that physiological boundary conditions are somewhat unfavorable for xylitol oxidation by NADP⁺. A criterion of physiological fitness is developed for engineered XR working together with wild-type XDH.

Authors+Show Affiliations

Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/I, A-8010 Graz, Austria.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21903144

Citation

Krahulec, Stefan, et al. "Analysis and Prediction of the Physiological Effects of Altered Coenzyme Specificity in Xylose Reductase and Xylitol Dehydrogenase During Xylose Fermentation By Saccharomyces Cerevisiae." Journal of Biotechnology, vol. 158, no. 4, 2012, pp. 192-202.
Krahulec S, Klimacek M, Nidetzky B. Analysis and prediction of the physiological effects of altered coenzyme specificity in xylose reductase and xylitol dehydrogenase during xylose fermentation by Saccharomyces cerevisiae. J Biotechnol. 2012;158(4):192-202.
Krahulec, S., Klimacek, M., & Nidetzky, B. (2012). Analysis and prediction of the physiological effects of altered coenzyme specificity in xylose reductase and xylitol dehydrogenase during xylose fermentation by Saccharomyces cerevisiae. Journal of Biotechnology, 158(4), 192-202. https://doi.org/10.1016/j.jbiotec.2011.08.026
Krahulec S, Klimacek M, Nidetzky B. Analysis and Prediction of the Physiological Effects of Altered Coenzyme Specificity in Xylose Reductase and Xylitol Dehydrogenase During Xylose Fermentation By Saccharomyces Cerevisiae. J Biotechnol. 2012 Apr 30;158(4):192-202. PubMed PMID: 21903144.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis and prediction of the physiological effects of altered coenzyme specificity in xylose reductase and xylitol dehydrogenase during xylose fermentation by Saccharomyces cerevisiae. AU - Krahulec,Stefan, AU - Klimacek,Mario, AU - Nidetzky,Bernd, Y1 - 2011/08/25/ PY - 2011/04/16/received PY - 2011/07/21/revised PY - 2011/08/18/accepted PY - 2011/9/10/entrez PY - 2011/9/10/pubmed PY - 2012/10/17/medline SP - 192 EP - 202 JF - Journal of biotechnology JO - J. Biotechnol. VL - 158 IS - 4 N2 - An advanced strategy of Saccharomyces cerevisiae strain development for fermentation of xylose applies tailored enzymes in the process of metabolic engineering. The coenzyme specificities of the NADPH-preferring xylose reductase (XR) and the NAD⁺-dependent xylitol dehydrogenase (XDH) have been targeted in previous studies by protein design or evolution with the aim of improving the recycling of NADH or NADPH in their two-step pathway, converting xylose to xylulose. Yeast strains expressing variant pairs of XR and XDH that according to in vitro kinetic data were suggested to be much better matched in coenzyme usage than the corresponding pair of wild-type enzymes, exhibit widely varying capabilities for xylose fermentation. To achieve coherence between enzyme properties and the observed strain performance during fermentation, we explored the published kinetic parameters for wild-type and engineered forms of XR and XDH as possible predictors of xylitol by-product formation (Y(xylitol)) in yeast physiology. We found that the ratio of enzymatic reaction rates using NADP(H) and NAD(H) that was calculated by applying intracellular reactant concentrations to rate equations derived from bi-substrate kinetic analysis, succeeded in giving a statistically reliable forecast of the trend effect on Y(xylitol). Prediction based solely on catalytic efficiencies with or without binding affinities for NADP(H) and NAD(H) were not dependable, and we define a minimum demand on the enzyme kinetic characterization to be performed for this purpose. An immediate explanation is provided for the typically lower Y(xylitol) in the current strains harboring XR engineered for utilization of NADH as compared to strains harboring XDH engineered for utilization of NADP⁺. The known XDH enzymes all exhibit a relatively high K(m) for NADP⁺ so that physiological boundary conditions are somewhat unfavorable for xylitol oxidation by NADP⁺. A criterion of physiological fitness is developed for engineered XR working together with wild-type XDH. SN - 1873-4863 UR - https://www.unboundmedicine.com/medline/citation/21903144/Analysis_and_prediction_of_the_physiological_effects_of_altered_coenzyme_specificity_in_xylose_reductase_and_xylitol_dehydrogenase_during_xylose_fermentation_by_Saccharomyces_cerevisiae_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0168-1656(11)00496-2 DB - PRIME DP - Unbound Medicine ER -