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Article
Open AccessSubstrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods
In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated a...
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Article
Open Access2D Assignment and quantitative analysis of cellulose and oxidized celluloses using solution-state NMR spectroscopy
The limited access to fast and facile general analytical methods for cellulosic and/or biocomposite materials currently stands as one of the main barriers for the progress of these disciplines. To that end, a ...
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Article
Open AccessProduction and characterization of Aspergillus niger GH29 family α-fucosidase and production of a novel non-reducing 1-fucosyllactose
Fucosylated oligosaccharides are interesting molecules due to their bioactive properties. In particular, their application as active ingredient in milk powders is attractive for dairy industries. The objective...
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Article
Open AccessIn vitro reconstitution and characterisation of the oxidative d-xylose pathway for production of organic acids and alcohols
The oxidative d-xylose pathway, i.e. Dahms pathway, can be utilised to produce from cheap biomass raw material useful chemical intermediates. In vitro metabolic pathways offer a fast way to study the rate-limitin...
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Article
Enzymatic synthesis of fucose-containing galacto-oligosaccharides using β-galactosidase and identification of novel disaccharide structures
Fucosylated oligosaccharides have an important role in maintaining a healthy immune system and homeostatic gut microflora. This study employed a commercial β-galactosidase in the production of fucose-containin...
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Article
Open AccessNew insight on the structural features of the cytotoxic auristatins MMAE and MMAF revealed by combined NMR spectroscopy and quantum chemical modelling
Antibody-drug conjugates (ADCs) are emerging as a promising class of selective drug delivery systems in the battle against cancer and other diseases. The auristatins monomethyl auristatin E (MMAE) and monometh...
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Article
Open AccessThe introduction of the fungal d-galacturonate pathway enables the consumption of d-galacturonic acid by Saccharomyces cerevisiae
Pectin-rich wastes, such as citrus pulp and sugar beet pulp, are produced in considerable amounts by the juice and sugar industry and could be used as raw materials for biorefineries. One possible process in s...
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Article
Characterization of a unique Caulobacter crescentus aldose-aldose oxidoreductase having dual activities
We describe here the characterization of a novel enzyme called aldose-aldose oxidoreductase (Cc AAOR; EC 1.1.99) from Caulobacter crescentus. The Cc AAOR exists in solution as a dimer, belongs to the Gfo/Idh/MocA...
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Article
l-Arabinose/d-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of l-arabinose to l-arabonate with Saccharomyces cerevisiae
Four potential dehydrogenases identified through literature and bioinformatic searches were tested for l-arabonate production from l-arabinose in the yeast Saccharomyces cerevisiae. The most efficient enzyme, ann...
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Protocol
Labelling Analysis for 13C MFA Using NMR Spectroscopy
NMR spectroscopy is an efficient method for analyzing 13C labelling of cellular metabolites. The strength of it is especially the ability to provide direct quantitative positional information on the 13C labelling...
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Article
Open AccessMetabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures
The methylotrophic yeast Pichia pastoris has emerged as one of the most promising yeast hosts for the production of heterologous proteins. Mixed feeds of methanol and a multicarbon source instead of methanol as s...
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Article
Open AccessA multi-level study of recombinant Pichia pastoris in different oxygen conditions
Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive...
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Article
Identification in Agrobacterium tumefaciens of the d-galacturonic acid dehydrogenase gene
There are at least three different pathways for the catabolism of d-galacturonate in microorganisms. In the oxidative pathway, which was described in some prokaryotic species, d-galacturonate is first oxidised to...
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Article
Enhancing the flux of D-glucose to the pentose phosphate pathway in Saccharomyces cerevisiae for the production of D-ribose and ribitol
Phosphoglucose isomerase-deficient (pgi1) strains of Saccharomyces cerevisiae were studied for the production of D-ribose and ribitol from D-glucose via the intermediates of the pentose phosphate pathway. Overexp...
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Article
Open Access13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose
The filamentous fungus Trichoderma reesei is an important host organism for industrial enzyme production. It is adapted to nutrient poor environments where it is capable of producing large amounts of hydrolytic e...
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Article
Open AccessOxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A
The yeast Saccharomyces cerevisiae is able to adjust to external oxygen availability by utilizing both respirative and fermentative metabolic modes. Adjusting the metabolic mode involves alteration of the intrace...
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Article
Open AccessAn analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Metabolic fluxes provide invaluable insight on the integrated response of a cell to environmental stimuli or genetic modifications. Current computational methods for estimating the metabolic fluxes from 13C isoto...
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Chapter and Conference Paper
Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation
The most accurate estimates of the activity of metabolic pathways are obtained by conducting isotopomer tracer experiments. The success of this method, however, is intimately dependent on the quality and amoun...
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Chapter and Conference Paper
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information
Metabolic flux estimation—the problem of finding out the rates of reactions in metabolic pathways—is an important problem area in the study of metabolism.The most accurate technique for this task today is the ...
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Article
Bi-antennary oligo-(N-acetyllactosamino)glycans of I-type are galactosylated preferentially at the GlcNAcβ1-6Gal linked arms by α1,3-galactosyltransferase of bovine thymus
α1,3-Galactosylation of radiolabelled bi-antennary acceptors Galβ1-4GlcNAcβ1-3(Galβ1-4GlcNAcβ1-6)Gal-R (R=1-OH, β1-4GlcNAc or β1-4Glc) with bovine thymus α1,3-galactosyltransferase was studied. At all stages of t...
