Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Optimization of the dilute maleic acid pretreatment of wheat straw
Kootstra, A.M.J. ; Beeftink, H.H. ; Scott, E.L. ; Sanders, J.P.M. - \ 2009
Biotechnology for Biofuels 2 (2009). - ISSN 1754-6834 - p. 31 - 31.
cellulose hydrolysis - enzymatic-hydrolysis - ethanologenic yeast - high-temperature - organic-acids - corn stover - pig diets - d-xylose - biomass - degradation
Background - In this study, the dilute maleic acid pretreatment of wheat straw is optimized, using pretreatment time, temperature and maleic acid concentration as design variables. A central composite design was applied to the experimental set up. The response factors used in this study are: (1) glucose benefits from improved enzymatic digestibility of wheat straw solids; (2) xylose benefits from the solubilization of xylan to the liquid phase during the pretreatment; (3) maleic acid replenishment costs; (4) neutralization costs of pretreated material; (5) costs due to furfural production; and (6) heating costs of the input materials. For each response factor, experimental data were fitted mathematically. After data translation to €/Mg dry straw, determining the relative contribution of each response factor, an economic optimization was calculated within the limits of the design variables. Results - When costs are disregarded, an almost complete glucan conversion to glucose can be reached (90% from solids, 7%-10% in liquid), after enzymatic hydrolysis. During the pretreatment, up to 90% of all xylan is converted to monomeric xylose. Taking cost factors into account, the optimal process conditions are: 50 min at 170°C, with 46 mM maleic acid, resulting in a yield of 65 €/Mg (megagram = metric ton) dry straw, consisting of 68 €/Mg glucose benefits (from solids: 85% of all glucan), 17 €/Mg xylose benefits (from liquid: 80% of all xylan), 17 €/Mg maleic acid costs, 2.0 €/Mg heating costs and 0.68 €/Mg NaOH costs. In all but the most severe of the studied conditions, furfural formation was so limited that associated costs are considered negligible. Conclusions - After the dilute maleic acid pretreatment and subsequent enzymatic hydrolysis, almost complete conversion of wheat straw glucan and xylan is possible. Taking maleic acid replenishment, heating, neutralization and furfural formation into account, the optimum in the dilute maleic acid pretreatment of wheat straw in this study is 65 €/Mg dry feedstock. This is reached when process conditions are: 50 min at 170°C, with a maleic acid concentration of 46 mM. Maleic acid replenishment is the most important of the studied cost factors
Comparison of dilute mineral and organic acid pretreatment for enzymatic hydrolysis of wheat straw
Kootstra, A.M.J. ; Beeftink, H.H. ; Scott, E.L. ; Sanders, J.P.M. - \ 2009
Biochemical Engineering Journal 46 (2009)2. - ISSN 1369-703X - p. 126 - 131.
corn stover - hemicellulose hydrolysis - cellulose hydrolysis - high-temperature - sulfuric-acid - pig diets - d-xylose - ethanol - degradation - inhibitors
The efficiencies of fumaric, maleic, and sulfuric acid in wheat straw pretreatment were compared. As a measure for pretreatment efficiency, enzymatic digestibility of the lignocellulose was determined. Monomeric glucose and xylose concentrations were measured after subsequent enzymatic hydrolysis, as were levels of sugar degradation products furfural and hydroxymethylfurfural after pretreatment. The influence of pretreatment temperature and of wheat straw loading was studied. It is shown that, at 150 °C and 20–30% (w/w) dry wheat straw, the pretreatment with dilute fumaric or maleic acid can be a serious alternative to dilute sulfuric acid pretreatment
Differential effects of mineral and organic acids on the kinetics of arabinose degradation under lignocellulose pretreatment conditions
Kootstra, A.M.J. ; Mosier, N.S. ; Scott, E.L. ; Beeftink, H.H. ; Sanders, J.P.M. - \ 2009
Biochemical Engineering Journal 43 (2009)1. - ISSN 1369-703X - p. 92 - 97.
saccharomyces-cerevisiae - high-temperature - fumaric-acid - cellulose hydrolysis - enzymatic-hydrolysis - rhizopus-oryzae - corn stover - pig diets - d-xylose - ethanol
Sugar degradation occurs during acid-catalyzed pretreatment of lignocellulosic biomass at elevated temperatures, resulting in degradation products that inhibit microbial fermentation in the ethanol production process. Arabinose, the second most abundant pentose in grasses like corn stover and wheat straw, degrades into furfural. This paper focuses on the first-order rate constants of arabinose (5 g/L) degradation to furfural at 150 and 170 °C in the presence of sulfuric, fumaric, and maleic acid and water alone. The calculated degradation rate constants (kd) showed a correlation with the acid dissociation constant (pKa), meaning that the stronger the acid, the higher the arabinose degradation rate. However, de-ionized water alone showed a catalytic power exceeding that of 50 mM fumaric acid and equaling that of 50 mM maleic acid. This cannot be explained by specific acid catalysis and the shift in pKw of water at elevated temperatures. These results suggest application of maleic and fumaric acid in the pretreatment of lignocellulosic plant biomass may be preferred over sulfuric acid. Lastly, the degradation rate constants found in this study suggest that arabinose is somewhat more stable than its stereoisomer xylose under the tested conditions
Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily
Brouns, S.J.J. ; Barends, T.R.M. ; Worm, P. ; Akerboom, J. ; Turnbull, A.P. ; Salmon, L. ; Oost, J. van der - \ 2008
Journal of Molecular Biology 379 (2008)2. - ISSN 0022-2836 - p. 357 - 371.
l-arabinose metabolism - alpha-ketoglutaric semialdehyde - fumarylacetoacetate hydrolase - crystal-structure - escherichia-coli - caulobacter-crescentus - alternative pathway - l-2-keto-3-deoxyarabonate dehydratase - evolutionary insight - d-xylose
The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.
Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei)
Stricker, A.R. ; Mach, R.L. ; Graaff, L.H. de - \ 2008
Applied Microbiology and Biotechnology 78 (2008)2. - ISSN 0175-7598 - p. 211 - 220.
ccaat-binding complex - activator xlnr - beta-glucosidase - dna recognition - xylanase genes - d-xylose - expression - induction - degradation - proteins
The filamentous fungi Aspergillus niger and Hypocrea jecorina (Trichoderma reesei) have been the subject of many studies investigating the mechanism of transcriptional regulation of hemicellulase- and cellulase-encoding genes. The transcriptional regulator XlnR that was initially identified in A. niger as the transcriptional regulator of xylanase-encoding genes controls the transcription of about 20¿30 genes encoding hemicellulases and cellulases. The orthologous xyr1 (xylanase regulator 1-encoding) gene product of H. jecorina has a similar function as XlnR, although at points, the mechanisms seems to be different. Specifically in H. jecorina, the interaction of Xyr1 and the co-regulators Ace1 and Ace2 in the regulation of transcription of xylanases and cellulases has been studied. This paper describes the similarities and differences in the transcriptional regulation of expression of hemicellulases and cellulases in A. niger and H. jecorina.
Regulation of pentose catabolic pathway genes of Aspergillus niger
Groot, M.J.L. de; Dool, C. van den; Wosten, H.A.B. ; Levisson, M. ; vanKuyk, P.A. ; Ruijter, G.J.G. ; Vries, R.P. de - \ 2007
Food Technology and Biotechnology 45 (2007)2. - ISSN 1330-9862 - p. 134 - 138.
transcriptional activator xlnr - d-xylose - l-arabinose - alpha-glucuronidase - degrading enzymes - kinase gene - expression - nidulans - polysaccharides - degradation
The aim of this study was to obtain a better understanding of the pentose catabolism in Aspergillus niger and the regulatory systems that affect it. To this end, we have cloned and characterised the genes encoding A. niger L-arabitol dehydrogenase (ladA) and xylitol dehydrogenase (xdhA), and compared the regulation of these genes to other genes of the pentose catabolic pathway. This demonstrated that activation of the pathway depends on two transcriptional regulators, the xylanolytic activator (XlnR) and an unidentified L-arabinose specific regulator (AraR). These two regulators affect those genes of the pentose catabolic pathway that are related to catabolic conversion of their corresponding inducers (D-xylose and L-arabinose, respectively).
Metabolic control analysis of Aspergillus niger L-arabinose catabolism
Groot, M.J.L. de; Prathumpai, W. ; Visser, J. ; Ruijter, G.J.G. - \ 2005
Biotechnology Progress 21 (2005)6. - ISSN 8756-7938 - p. 1610 - 1616.
alpha-l-arabinofuranosidase - enzyme-catalyzed reactions - d-xylose - extracellular arabinases - degrading enzymes - gene-expression - pichia-stipitis - reductase gene - nidulans - purification
A mathematical model of the L-arabinose/D-xylose catabolic pathway of Aspergillus niger was constructed based on the kinetic properties of the enzymes. For this purpose L-arabinose reductase, L-arabitol dehydrogenase and D-xylose reductase were purified using dye-affinity chromatography, and their kinetic properties were characterized. For the other enzymes of the pathway the kinetic data were available from the literature. The metabolic model was used to analyze flux and metabolite concentration control of the L-arabinose catabolic pathway. The model demonstrated that flux control does not reside at the enzyme following the intermediate with the highest concentration, L-arabitol, but is distributed over the first three steps in the pathway, preceding and following L-arabitol. Flux control appeared to be strongly dependent on the intracellular L-arabinose concentration. At 5 mM intracellular L-arabinose, a level that resulted in realistic intermediate concentrations in the model, flux control coefficients for L-arabinose reductase, L-arabitol dehydrogenase and L-xylulose reductase were 0.68, 0.17 and 0.14, respectively. The analysis can be used as a guide to identify targets for metabolic engineering aiming at either flux or metabolite level optimization of the L-arabinose catabolic pathway of A. niger. Faster L-arabinose utilization may enhance utilization of readily available organic waste containing hemicelluloses to be converted into industrially interesting metabolites or valuable enzymes or proteins.
Functional analysis of the transcriptional activator XlnR from Aspergillus niger
Hasper, A.A. ; Trindade, L.M. ; Veen, D. van der; Ooyen, A.J.J. van; Graaff, L.H. de - \ 2004
Microbiology 150 (2004). - ISSN 1350-0872 - p. 1367 - 1375.
saccharomyces-cerevisiae - utilization pathway - importin beta - d-xylose - sequence - protein - regulator - gene - expression - nidulans
The transcriptional activator XlnR from Aspergillus niger is a zinc binuclear cluster transcription factor that belongs to the GAL4 superfamily. Several putative structural domains in XInR were predicted using database and protein sequence analysis. Thus far, only the functionality of the N-terminal DNA-binding domain has been determined experimentally. Deletion mutants of the xInR gene were constructed to localize the functional regions of the protein. The results showed that a putative C-terminal coiled-coil region is involved in nuclear import of XInR. After deletion of the C-terminus, including the coiled-coil region, XInR was found in the cytoplasm, while deletion of the C-terminus downstream of the coiled-coil region resulted in nuclear import of XlnR. The latter mutant also showed increased xylanase activity, indicating the presence of a region with an inhibitory function in XInR-controlled transcription. Previous findings had already shown that a mutation in the XlnR C-terminal region resulted in transcription of the structural genes under non-inducing conditions. A regulatory model of XInR is presented in which the C-terminus responds to repressing signals, resulting in an inactive state of the protein.
Isolation and characterization of two specific regulatory Aspergillus niger mutants shows antagonistic regulation of arabinan and xylan metabolism
Groot, M.J.L. de; Vondervoort, P.J.I. van de; Vries, R.P. de; Kuyk, P.A. van; Ruijter, G.J.G. ; Visser, J. - \ 2003
Microbiology 149 (2003). - ISSN 1350-0872 - p. 1183 - 1191.
alpha-l-arabinofuranosidase - transcriptional activator xlnr - gene-expression - d-xylose - degrading enzymes - degradation - induction - nidulans - cloning - construction
This paper describes two Aspergillus niger mutants (araA and araB) specifically disturbed in the regulation of the arabinanase system in response to the presence of L-arabinose. Expression of the three known L-arabinose-induced arabinanolytic genes, abfA, abfB and abnA, was substantially decreased or absent in the araA and araB strains compared to the wild-type when incubated in the presence of L-arabinose or L-arabitol. In addition, the intracellular activities Of L-arabitol dehydrogenase and L-arabinose reductase, involved in L-arabinose catabolism, were decreased in the araA and araB strains. Finally, the data show that the gene encoding D-xylulose kinase, xkiA, is also under control of the arabinanolytic regulatory system. L-Arabitol, most likely the true inducer of the arabinanolytic and L-arabinose catabolic genes, accumulated to a high intracellular concentration in the araA and araB mutants. This indicates that the decrease of expression of the arabinanolytic genes was not due to lack of inducer accumulation. Therefore, it is proposed that the araA and araB mutations are localized in positive-acting components of the regulatory system involved in the expression of the arabinanase-encoding genes and the genes encoding the L-arabinose catabolic pathway.
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