Advantages of isothermal titration calorimetry for xylanase kinetics in comparison to chemical-reducing-end assays.
Baumann, M. J., Murphy, L., Lei, N., Krogh, K. B. R. M., Borch, K. & Westh, P. (2011). Analytical Biochemistry, 410(1), 19-26.
In lignocellulosic raw materials for biomass conversion, hemicelluloses constitute a substantial fraction, with xylan being the primary part. Although many pretreatments reduce the amount or change the distribution of xylan, it is important to degrade residual xylan so as to improve the overall yield. Typically, xylanase reaction rates are measured in stopped assays by chemical quantification of the reducing ends. With isothermal titration calorimetry (ITC), the heat flow of the hydrolysis can be measured in continuous fashion, with the reaction rate being directly proportional to the heat flow. Reaction enthalpies for carbohydrate hydrolysis are typically below 5 kJ/mol, which is the limiting factor for straight forward calorimetric quantification of enzymatic reaction rates using current ITC technology. To increase the apparent reaction enthalpy, we employed a subsequent oxidation of hydrolysis products by carbohydrate oxidase and catalase. Here we show that the coupled assay with carbohydrate oxidase and catalase can be used to measure enzyme kinetics of a GH10 xylanase from Aspergillus aculeatus on birch xylan and wheat arabinoxylan. Results are discussed in the light of a critical analysis of the sensitivity of four chemical-reducing-end quantification methods using well-characterized substrates.
Insight into the distribution of arabinoxylans, endoxylanases, and endoxylanase inhibitors in industrial wheat roller mill streams.
Dornez, E., Gebruers, K., Wiame, S., Delcour, J. A. & Courtin, C. M. (2006). Journal of Agricultural and Food Chemistry, 54(22), 8521-8529.
To gain insight into the distribution of arabinoxylans (AX), endoxylanases, and endoxylanase inhibitors in industrial wheat roller milling, all streams, that is, 54 flour fractions, 4 bran fractions, and the germ, were analyzed for ash, starch, and protein contents, α-amylase activity levels, total (TOT-AX) and water-extractable arabinoxylan (WE-AX) contents, endoxylanase activity levels, and endoxylanase inhibitor (TAXI and XIP) contents. In general, bran fractions were significantly richer in TOT-AX and WE-AX contents, endoxylanase activity levels, and endoxylanase inhibitor contents than germ and, even more so, than flour fractions. In the 54 different flour fractions, minimal and maximal values for TOT-AX and WE-AX contents differed by ca. 2-fold, whereas they differed by ca. 15-fold for endoxylanase activity levels. The latter were positively correlated with ash and negatively correlated with starch content, suggesting that the endoxylanase activity in flour is strongly influenced by the level of bran contamination. TAXI contents in the flour fractions varied ca. 4-fold and were strongly correlated with bran-related parameters such as ash content and enzyme activity levels, whereas XIP contents varied ca. 3-fold and were not correlated with any of the parameters measured in this study. The results can be valuable in blending and optimizing wheat flour fractions to obtain flours with specific technological and nutritional benefits.
Purification and characterisation of two extremely halotolerant xylanases from a novel halophilic bacterium.
Wejse, P. L., Ingvorsen, K. & Mortensen, K. K. (2003). Extremophiles, 7(5), 423-431.
The present work reports for the first time the purification and characterisation of two extremely halotolerant endo-xylanases from a novel halophilic bacterium, strain CL8. Purification of the two xylanases, Xyl 1 and 2, was achieved by anion exchange and hydrophobic interaction chromatography. The enzymes had relative molecular masses of 43 kDa and 62 kDa and pI of 5.0 and 3.4 respectively. Stimulation of activity by Ca+2, Mn+2, Mg+2, Ba+2, Li+2, NaN3, and isopropanol was observed. The K m and V max values determined for Xyl 1 with 4-O-methyl-D-glucuronoxylan are 5 mg/ml and 125,000 nkat/mg respectively. The corresponding values for Xyl 2 were 1 mg/ml and 143,000 nkat/mg protein. Xylobiose and xylotriose were the major end products for both endoxylanases. The xylanases were stable at pH 4–11 showing pH optima around pH 6. Xyl 1 shows maximal activity at 60°C, Xyl 2 at 65°C (at 4 M NaCl). The xylanases showed high temperature stability with half-lives at 60°C of 97 min and 192 min respectively. Both xylanases showed optimal activity at 1 M NaCl, but substantial activity remained for both enzymes at 5 M NaCl.
Plant cell wall degradation with a powerful Fusarium graminearum enzymatic arsenal.
Phalip, V., Goubet, F., Carapito, R. & Jeltsch, J. M. (2009). J Microbiol Biotechnol, 19(6), 573-581.
The complex enzyme pool secreted by the phytopathogenic fungus Fusarium graminearum in response to glucose or hop cell wall material as sole carbon sources was analyzed. The biochemical characterization of the enzymes present in the supernatant of fungal cultures in the glucose medium revealed only 5 different glycosyl hydrolase activities; by contrast, when analyzing cultures in the cell wall medium, 17 different activities were detected. This dramatic increase reflects the adaptation of the fungus by the synthesis of enzymes targeting all layers of the cell wall. When the enzymes secreted in the presence of plant cell wall were used to hydrolyze pretreated crude plant material, high levels of monosaccharides were measured with yields approaching 50% of total sugars released by an acid hydrolysis process. This report is the first biochemical characterization of numerous cellulases, hemicellulases, and pectinases secreted by F. graminearum and demonstrates the usefulness of the described protein cocktail for efficient enzymatic degradation of plant cell wall.
Development of an improved variant of GH51 α-L-arabinofuranosidase from Pleurotus ostreatus by directed evolution.
Giacobbe, S., Vincent, F. & Faraco, V. (2014). New Biotechnology, 31(3), 230-236.
In this study, the α-L-arabinofuranosidase from Pleurotus ostreatus was subjected to directed evolution by expressing a library of around 7000 randomly mutated variants by error prone Polymerase Chain Reaction. High-throughput screening of the library for the most active variants was performed by assaying activity towards p-nitrophenyl α-L-arabinofuranoside, and a variant with higher activity than the wild type was selected, purified and characterised. It exhibited a Kcat of 7.3 × 103 ± 0.3 min-1, around 3-fold higher than that of the wild type (2.2 × 103 ± 0.2 min-1), and a KM (0.54 ± 0.06 mM) 30% lower than that of the wild type (0.70 ± 0.05 mM) towards this substrate. The mutant also showed improved catalytic properties towards pNP-β-D-glucopyranoside (Kcat of 50.85 ± 0.21 min−1 versus 11.0 ± 0.6 min-1) and it was shown able to hydrolyse larch arabinogalactan which is not recognised by the wild type. The mutant was also more active than the wild type towards arabinoxylan and was able to hydrolyse arabinan, which was not transformed by the wild type. The ability of rPoAbf F435Y/Y446F to hydrolyse these insoluble substrates expands its potential for application also to hemicelluloses, which in some types of pretreatment are recovered in solid fractions.
Onsite enzyme production during bioethanol production from biomass: screening for suitable fungal strains.
Sørensen, A., Teller, P. J., Lübeck, P. S. & Ahring, B. K. (2011). Applied Biochemistry and Biotechnology, 164(7), 1058-1070.
Cellulosic ethanol production from biomass raw materials involves process steps such as pre-treatment, enzymatic hydrolysis, fermentation, and distillation. Use of streams within cellulosic ethanol production was explored for onsite enzyme production as part of a biorefinery concept. Sixty-four fungal isolates were in plate assays screened for lignocellulolytic activities to discover the most suitable fungal strain with efficient hydrolytic enzymes for lignocellulose conversion. Twenty-five were selected for further enzyme activity studies using a stream derived from the bioethanol process. The filter cake left after hydrolysis and fermentation was chosen as substrate for enzyme production. Five of the 25 isolates were further selected for synergy studies with commercial enzymes, Celluclast 1.5L and Novozym 188. Finally, IBT25747 (Aspergillus niger) and strain AP (CBS 127449, Aspergillus saccharolyticus) were found as promising candidates for onsite enzyme production where the filter cake was inoculated with the respective fungus and in combination with Celluclast 1.5L used for hydrolysis of pre-treated biomass.
Evaluation of cellulolytic and hemicellulolytic abilities of fungi isolated from coffee residue and sawdust composts.
Eida, M. F., Nagaoka, T., Wasaki, J. & Kouno, K. (2011). Microbes Environ, 26(3), 220-227.
This study focused on the evaluation of cellulolytic and hemicellulolytic fungi isolated from sawdust compost (SDC) and coffee residue compost (CRC). To identify fungal isolates, the ITS region of fungal rRNA was amplified and sequenced. To evaluate enzyme production, isolates were inoculated onto wheat bran agar plates, and enzymes were extracted and tested for cellulase, xylanase, β-glucanase, mannanase, and protease activities using different azurine cross-linked (AZCL) substrates. In total, 18 isolates from SDC and 29 isolates from CRC were identified and evaluated. Four genera (Aspergillus, Galactomyces, Mucor, and Penicillium) and five genera (Aspergillus, Coniochaeta, Fusarium, Penicillium, and Trichoderma/Hypocrea) were dominant in SDC and CRC, respectively. Penicillium sp., Trichoderma sp., and Aspergillus sp. displayed high cellulolytic and hemicellulolytic activities, while Mucor isolates exhibited the highest β-glucanase and mannanase activities. The enzyme analyses revealed that Penicillium, Aspergillus, and Mucor isolates significantly contributed to the degradation of SDC, whereas Penicillium, Aspergillus, and Trichoderma isolates had a dominant role in the degradation of CRC. Notably, isolates SDCF5 (P. crustosum), CRCF6 (P. verruculosum), and CRCF2 and CRCF16 (T. harzianum/H. lixii) displayed high activity regarding cellulose and hemicellulose degradation, which indicates that these species could be beneficial for the improvement of biodegradation processes involving lignocellulosic materials.
The Carbohydrate Metabolism Signature of Lactococcus lactis Strain A12 Reveals Its Sourdough Ecosystem Origin.
Passerini, D., Coddeville, M., Le Bourgeois, P., Loubière, P., Ritzenthaler, P., Fontagné-Faucher, C., Daveran-Mingot, M. L. & Cocaign-Bousquet, M. (2013). Applied and Environmental Microbiology, 79(19), 5844-5852.
Lactococcus lactis subsp. lactis strain A12 was isolated from sourdough. Combined genomic, transcriptomic, and phenotypic analyses were performed to understand its survival capacity in the complex sourdough ecosystem and its role in the microbial community. The genome sequence comparison of strain A12 with strain IL1403 (a derivative of an industrial dairy strain) revealed 78 strain-specific regions representing 23% of the total genome size. Most of the strain-specific genes were involved in carbohydrate metabolism and are potentially required for its persistence in sourdough. Phenotype microarray, growth tests, and analysis of glycoside hydrolase content showed that strain A12 fermented plant-derived carbohydrates, such as arabinose and α-galactosides. Strain A12 exhibited specific growth rates on raffinose that were as high as they were on glucose and was able to release sucrose and galactose outside the cell, providing soluble carbohydrates for sourdough microflora. Transcriptomic analysis identified genes specifically induced during growth on raffinose and arabinose and reveals an alternative pathway for raffinose assimilation to that used by other lactococci.
Expanding the feruloyl esterase gene family of Aspergillus niger by characterization of a feruloyl esterase, FaeC.
Dilokpimol, A., Mäkelä, M. R., Mansouri, S., Belova, O., Waterstraat, M., Bunzel, M., de Vries, R. P. & Hildén, K. S. (2017). New Biotechnology, 37, 200-209.
A feruloyl esterase (FAE) from Aspergillus niger N402, FaeC was heterologously produced in Pichia pastoris X-33 in a yield of 10 mg/L. FaeC was most active at pH 7.0 and 50°C, and showed broad substrate specificity and catalyzed the hydrolysis of methyl 3,4-dimethoxycinnamate, ethyl ferulate, methyl ferulate, methyl p-coumarate, ethyl coumarate, methyl sinapate, and methyl caffeate. The enzyme released both ferulic acid and p-coumaric acid from wheat arabinoxylan and sugar beet pectin (up to 3 mg/g polysaccharide), and acted synergistically with a commercial xylanase increasing the release of ferulic acid up to six-fold. The expression of faeC increased over time in the presence of feruloylated polysaccharides. Cinnamic, syringic, caffeic, vanillic and ferulic acid induced the expression of faeC. Overall expression of faeC was very low in all tested conditions, compared to two other A. niger FAE encoding genes, faeA and faeB. Our data showed that the fae genes responded differently towards the feruloylated polysaccharides and tested monomeric phenolic compounds suggesting that the corresponding FAE isoenzymes may target different substrates in a complementary manner. This may increase the efficiency of the degradation of diverse plant biomass.
Aspergillus hancockii sp. nov., a biosynthetically talented fungus endemic to southeastern Australian soils.
Pitt, J. I., Lange, L., Lacey, A. E., Vuong, D., Midgley, D. J., Greenfield, P., Bradbury, M. I., Lacey, E., Busk, P. K., Pilgaard, B., Chooi, Y. H. & Piggott, A. M. (2017). PloS One, 12(4), e0170254.
Aspergillus hancockii sp. nov., classified in Aspergillus subgenus Circumdati section Flavi, was originally isolated from soil in peanut fields near Kumbia, in the South Burnett region of southeast Queensland, Australia, and has since been found occasionally from other substrates and locations in southeast Australia. It is phylogenetically and phenotypically related most closely to A. leporis States and M. Chr., but differs in conidial colour, other minor features and particularly in metabolite profile. When cultivated on rice as an optimal substrate, A. hancockii produced an extensive array of 69 secondary metabolites. Eleven of the 15 most abundant secondary metabolites, constituting 90% of the total area under the curve of the HPLC trace of the crude extract, were novel. The genome of A. hancockii, approximately 40 Mbp, was sequenced and mined for genes encoding carbohydrate degrading enzymes identified the presence of more than 370 genes in 114 gene clusters, demonstrating that A. hancockii has the capacity to degrade cellulose, hemicellulose, lignin, pectin, starch, chitin, cutin and fructan as nutrient sources. Like most Aspergillus species, A. hancockii exhibited a diverse secondary metabolite gene profile, encoding 26 polyketide synthase, 16 nonribosomal peptide synthase and 15 nonribosomal peptide synthase-like enzymes.
Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge.
Wilkens, C., Busk, P. K., Pilgaard, B., Zhang, W. J., Nielsen, K. L., Nielsen, P. H. & Lange, L. (2017). Biotechnology for Biofuels, 10(1), 158.
Background: Improved carbohydrate-active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals, and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs a unique niche to look for CAZymes that can potentiate the enzyme blends currently used in industry. Results: Enzymatic assays showed that functional CAZymes were secreted into the AD environments in four full-scale mesophilic Danish ADs fed with primary and surplus sludge from municipal wastewater treatment plants. Metagenomes from the ADs were mined for CAZymes with Homology to Peptide Patterns (HotPep). 19,335 CAZymes were identified of which 30% showed 50% or lower identity to known proteins demonstrating that ADs make up a promising pool for discovery of novel CAZymes. A function was assigned to 54% of all CAZymes identified by HotPep. Many different α-glucan-acting CAZymes were identified in the four metagenomes, and the most abundant family was glycoside hydrolase family 13, which contains α-glucan-acting CAZymes. Cellulytic and xylanolytic CAZymes were also abundant in the four metagenomes. The cellulytic enzymes were limited almost to endoglucanases and β-glucosidases, which reflect the large amount of partly degraded cellulose in the sludge. No dockerin domains were identified suggesting that the cellulytic enzymes in the ADs studied operate independently. Of xylanolytic CAZymes, especially xylanases and β-xylosidase, but also a battery of accessory enzymes, were present in the four ADs. Conclusions: Our findings suggest that the ADs are a good place to look for novel plant biomass degrading and modifying enzymes that can potentiate biological processes and provide basis for production of a range of added-value products from biorefineries.
Biochemical and structural analyses of two cryptic esterases in Bacteroides intestinalis and their synergistic activities with cognate xylanases.
Wefers, D., Cavalcante, J. J., Schendel, R. R., Deveryshetty, J., Wang, K., Wawrzak, Z., Mackie, R. I., Korotkin, N. M. & Cann, I. (2017). Journal of Molecular Biology, 429(16), 2509-2527.
Arabinoxylans are constituents of the human diet. Although not utilizable by the human host, they can be fermented by colonic bacteria. The arabinoxylan backbone is decorated with arabinose side chains that may be substituted with ferulic acid, thus limiting depolymerization to fermentable sugars. We investigated the polypeptides encoded by two genes upregulated during growth of the colonic bacterium Bacteroides intestinalis on wheat arabinoxylan. The recombinant proteins, designated BiFae1A and BiFae1B, were functionally assigned esterase activities. Both enzymes were active on acetylated substrates, although each showed a higher ferulic acid esterase activity on methyl-ferulate. BiFae1A showed a catalytic efficiency of 12 mM s-1 on para-nitrophenyl-acetate, and on methyl-ferulate, the value was 27 times higher. BiFae1B showed low catalytic efficiencies for both substrates. Furthermore, the two enzymes released ferulic acid from various structural elements, and NMR spectroscopy indicated complete de-esterification of arabinoxylan oligosaccharides from wheat bran. BiFae1A is a tetramer based on the crystal structure, whereas BiFae1B is a dimer in solution based on size exclusion chromatography. The structure of BiFae1A was solved to 1.98 Å resolution, and two tetramers were observed in the asymmetric unit. A flexible loop that may act as a hinge over the active site and likely coordinates critical interactions with the substrate was prominent in BiFae1A. Sequence alignments of the esterase domains in BiFae1B with the feruloyl esterase from Clostridium thermocellum suggest that both domains lack the flexible hinge in BiFae1A, an observation that may partly provide a molecular basis for the differences in activities in the two esterases.