Novel substrates for the automated and manual assay of endo-1,4-β-xylanase.
Mangan, D., Cornaggia, C., Liadova, A., McCormack, N., Ivory, R., McKie, V. A., Ormerod, A. & McCleary, D. V. (2017). Carbohydrate Research, 445, 14-22.
endo-1,4-β-Xylanase (EC 188.8.131.52) is employed across a broad range of industries including animal feed, brewing, baking, biofuels, detergents and pulp (paper). Despite its importance, a rapid, reliable, reproducible, automatable assay for this enzyme that is based on the use of a chemically defined substrate has not been described to date. Reported herein is a new enzyme coupled assay procedure, termed the XylX6 assay, that employs a novel substrate, namely 4,6-O-(3-ketobutylidene)-4-nitrophenyl-β-45-O-glucosyl-xylopentaoside. The development of the substrate and associated assay is discussed here and the relationship between the activity values obtained with the XylX6 assay versus traditional reducing sugar assays and its specificity and reproducibility were thoroughly investigated.
Comparison of endolytic hydrolases that depolymerise 1,4-β-D-mannan, 1,5-α-L-arabinan and 1,4-β-D-galactan.
McCleary, B. V. (1991). “Enzymes in Biomass Conversion”, (M. E. Himmel and G. F. Leatham, Eds.), ACS Symposium Series 460, Chapter 34, pp. 437-449. American Chemical Society, Washington.
Hydrolysis of mannan-type polysaccharides by β-mannanase is dependent on substitution on and within the main-chain as well as the source of the β-mannanase employed. Characterisation of reaction products can be used to define the sub-site binding requirements of the enzymes as well as the fine-structures of the polysaccharides. Action of endo-arabinanase and endo-galactanase on arabinans and arabinogalactans is described. Specific assays for endo-arabinanase and arabinan (in fruit-juice concentrates) are reported.
Measurement of endo-1,4-β-D-xylanase.
McCleary, B. V. (1992). “Xylans and Xylanases”, (J. Visser, G. Beldman, M. A. Kusters-van Someron and A. G. J. Voragen, Eds.), Progress in Biotechnology Vol. 7, Elsevier, Science Publishers B. V., pp. 161-169.
Various procedures for the measurement of xylanase in fermentation broths, commercial enzyme mixtures, bread improver mixtures and feed samples are described. Problems associated with the routine use of reducing-sugar based methods axe highlighted and the advantages and limitations of viscometric and dye-labelled substrate procedures for measurement of trace levels of activity in feed samples are discussed.
Measurement of polysaccharide degrading enzymes using chromogenic and colorimetric substrates.
McCleary, B. V. (1991). Chemistry in Australia, 58, 398-401.
Enzymic degradation of carbohydrates is of major significance in the industrial processing of cereals and fruits. In the production of beer, barley is germinated under well defined conditions (malting) to induce maximum enzyme synthesis with minimum respiration of reserve carbohydrates. The grains are dried and then extracted with water under controlled conditions. The amylolytic enzymes synthesized during malting, as well as those present in the original barley, convert the starch reserves to fermentable sugars. Other enzymes act on the cell wall polysaccharides, mixed-linkage β-glucan and arabinoxylan, reducing the viscosity and thus aiding filtration, and reducing the possibility of subsequent precipitation of polymeric material. In baking, β-amylase and α-amylase give controlled degradation of starch to fermentable sugars so as to sustain yeast growth and gas production. Excess quantities of α-amylase in the flour result in excessive degradation of starch during baking which in turn gives a sticky crumb texture and subsequent problems with bread slicing. Juice yield from fruit pulp is significantly improved if cell-wall degrading enzymes are used to destroy the three-dimensional structure and water binding capacity of the pectic polysaccharide components of the cell walls. Problems of routine and reliable assay of carbohydrate degrading enzymes in the presence of high levels of sugar compounds are experienced with such industrial process.
Optimising the response.
Acamovic, T. & McCleary, B. V. (1996). Feed Mix, 4, 14-19.
A fine balance exists between enzyme activity and the adverse effects associated with feed processing. Accurate estimation of enzyme activity in the feed is a pre-requisite to optimising the response.
Non starch polysaccharide hydrolyzing enzymes as feed additives: detection of enzyme activities and problems encountered with quantitative determination in complex samples.
Vahjen, W., Gläser, K., Froeck, M. & Simon, O. (1997). Archives of Animal Nutrition, 50(4), 331-345.
Chromogenic substrates, an agar diffusion assay and viscosity reduction were used to estimate β-glu‐canase and xylanase activities in water soluble extracts of different feedstuffs and digesta supernatants. The dinitrosalicylic acid reducing sugar method was employed to calibrate results from different methods based on international units (IU, glucose equivalents). The detection of dye release from chromogenic substrates was a suitable method, allowing the detection of 0.05 IU of enzyme activity per ml of extract, although measurements in digesta supernatants were limited in linearity (0.1–0.5 IU/ml supernatant). With the agar diffusion assay the detection of enzyme activity was possible over a wider concentration range (extracts: 0.05–1 IU/ml, digesta supernatants: 0.1–1 IU/ml), but visual evaluation led to inaccurate measurement. Accuracy can be improved by computer based evaluation of digital images. The use of viscosity reduction produced linear standard curves from 0.01 to 0.5 IU/ml in feed extracts, but reliability of measurements depended on modification of substrates. Quantification of enzyme activities was influenced by matrix effects of complex samples. Cereal dependant differences were found in various extracts of feed mixtures and cereal extracts. Digesta supernatants partly inhibited enzyme activity, depending on the origin of the sample. Interaction of substrates with digesta components varied between methods. The sensitivity of the methods is comparable, however, all methods require specific calibrations to account for matrix‐ and enzyme specific effects.
aguA, the gene encoding an extracellular α-glucuronidase from Aspergillus tubingensis, is specifically induced on xylose and not on glucuronic acid.
de Vries, R. P., Poulsen, C. H., Madrid, S. & Visser, J. (1998). Journal of Bacteriology, 180(2), 243-249.
An extracellular α-glucuronidase was purified and characterized from a commercial Aspergillus preparation and from culture filtrate of Aspergillus tubingensis. The enzyme has a molecular mass of 107 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 112 kDa as determined by mass spectrometry, has a determined pI just below 5.2, and is stable at pH 6.0 for prolonged times. The pH optimum for the enzyme is between 4.5 and 6.0, and the temperature optimum is 70°C. The α-glucuronidase is active mainly on small substituted xylo-oligomers but is also able to release a small amount of 4-O-methylglucuronic acid from birchwood xylan. The enzyme acts synergistically with endoxylanases and β-xylosidase in the hydrolysis of xylan. The enzyme is N glycosylated and contains 14 putative N-glycosylation sites. The gene encoding this α-glucuronidase (aguA) was cloned from A. tubingensis. It consists of an open reading frame of 2,523 bp and contains no introns. The gene codes for a protein of 841 amino acids, containing a eukaryotic signal sequence of 20 amino acids. The mature protein has a predicted molecular mass of 91,790 Da and a calculated pI of 5.13. Multiple copies of the gene were introduced in A. tubingensis, and expression was studied in a highly overproducing transformant. The aguA gene was expressed on xylose, xylobiose, and xylan, similarly to genes encoding endoxylanases, suggesting a coordinate regulation of expression of xylanases and α-glucuronidase. Glucuronic acid did not induce the expression of aguA and also did not modulate the expression on xylose. Addition of glucose prevented expression of aguA on xylan but only reduced the expression on xylose.
Crystallization and preliminary crystallographic analysis of endo-1,4-beta-xyalanase I from Aspergillus niger.
Krengel, U., Rozeboom, H. J., Kalk, K. H. & Dijkstra, B. W. (1996). Biological Crystallography, 52(3), 571-576.
A family G xylanase from Aspergillus niger has been crystallized using the vapor-diffusion method. Several crystal forms could be obtained using various sodium salts as precipitants. Three of the crystal forms belong to space groups P21, P212121 and P43 and have cell parameters of approximately a = b = 85.1, c = 113.6 Å and α = β = γ = 90°. These crystal forms can be converted into one another by flash freezing or macroseeding. A fourth crystal form is cubic (space group P213) with unit-cell axes of a = b = c = 112.3 Å. Data sets for three of the four crystal forms have been collected, extending to a maximum resolution of 2.4 Å. The structures of the monoclinic and orthorhombic crystals have been solved by molecular replacement by combining the crystallographic information of the different crystal forms. Refinement of the orthorhombic crystal form is now in progress.
Disruption of the L‐arabitol dehydrogenase encoding gene in Aspergillus tubingensis results in increased xylanase production.
Nikolaev, I., Farmer Hansen, S., Madrid, S. & de Vries, R. P. (2013). Biotechnology Journal, 8(8), 905-911.
Fungal xylanases are of major importance to many industrial sectors, such as food and feed, paper and pulp, and biofuels. Improving their production is therefore highly relevant. We determined the molecular basis of an improved xylanase-producing strain of Aspergillus tubingensis that was generated by UV mutagenesis in an industrial strain improvement program. Using enzyme assays, gene expression, sequencing of the ladA locus in the parent and mutant, and complementation of the mutation, we were able to show that improved xylanase production was mainly caused by a chromosomal translocation that occurred between a subtilisin-like protease pepD gene and the L-arabitol dehydrogenase encoding gene (ladA), which is part of the L-arabinose catabolic pathway. This genomic rearrangement resulted in disruption of both genes and, as a consequence, the inability of the mutant to use L-arabinose as a carbon source, while growth on D-xylose was unaffected. Complementation with constitutively expressed ladA confirmed that the xylanase overproducing phenotype was mainly caused by loss of ladA function, while a knockout of xlnR in the UV mutant demonstrated that improved xylanase production was mediated by XlnR. This study demonstrates the potential of metabolic manipulation for increased production of fungal enzymes.
Mapping of residues involved in the interaction between the Bacillus subtilis xylanase A and proteinaceous wheat xylanase inhibitors.
Sørensen, J. F. & Sibbesen, O. (2006). Protein Engineering Design & Selection, 19(5), 205-210.
The Bacillus subtilis xylanase A was subjected to site-directed mutagenesis, aimed at changing the interaction with Triticum aestivum xylanase inhibitor, the only wheat endogenous proteinaceous xylanase inhibitor interacting with this xylanase. The published structure of Bacillus circulans XynA was used to target amino acids surrounding the active site cleft of B.subtilis XynA for mutation. Twenty-two residues were mutated, resulting in 62 different variants. The catalytic activity of active mutants ranged from 563 to 5635 XU/mg and the interaction with T.aestivum xylanase inhibitor showed a similar variation. The results indicate that T.aestivum xylanase inhibitor interacts with several amino acid residues surrounding the active site of the enzyme. Three different amino acid substitutions in one particular residue (D11) completely abolished the interaction between T.aestivum xylanase inhibitor and B.subtilis xylanase A.
Safety evaluation of a xylanase expressed in Bacillus subtilis.
Harbak, L. & Thygesen, H. V. (2002). Food and Chemical Toxicology, 40(1), 1-8.
A programme of studies was conducted to establish the safety of a xylanase expressed in a self-cloned strain of Bacillus subtilis to be used as a processing aid in the baking industry. To assess acute and subchronic oral toxicity, rat feeding studies were conducted. In addition, the potential of the enzyme to cause mutagenicity and chromosomal aberrations was assessed in microbial and tissue culture in vitro studies. Acute and subchronic oral toxicity was not detected at the highest dose recommended by OECD guidelines. There was no evidence of mutagenic potential or chromosomal aberrations. Furthermore, the organism used for production of the xylanase is already accepted as safe by several major national regulatory agencies.