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Azo-Xylan (Birchwood) (Powder)

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00:02   Principle of the Assay Procedure
00:34    Substrate & Kit Description
01:02    Dissolution of Azo-CM-Cellulose
03:10    Precipitant Solution
04:59    Preparation of Buffer Solution
05:10    Assay Procedure
08:49    Calculation

Product code: S-AXBP

3 g

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Content: 3 g
Shipping Temperature: Ambient
Storage Temperature: Ambient
Physical Form: Powder
Stability: > 2 years under recommended storage conditions
Substrate For (Enzyme): endo-1,4-β-Xylanase
Assay Format: Spectrophotometer, Petri-dish (Qualitative)
Detection Method: Absorbance
Wavelength (nm): 590
Reproducibility (%): ~ 7%

High purity dyed, soluble Azo-Xylan (Birchwood) for the measurement of enzyme activity, for research, biochemical enzyme assays and in vitro diagnostic analysis.

Substrate for the specific assay of endo-1,4-β-D-xylanase.

Please note the video above shows the protocol for assay of endo-cellulase using Azo-CM cellulose. The procedure for the assay of endo-1,4-β-xylanase using Azo-Xylan (Birchwood) (Powder) is equivalent to this.

View other related products for more enzyme substrates.

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Megazyme publication
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 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.

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Production Of Cellulosic Enzymes By Aspergillus Niger And Hydrolysis Of Cellulosic Materials.

Bakare, V., Abdulsalami, M. S., Ndibe, T. O., Ejuama, C. K. & Effiong, T. (2022). Global Journal of Pure and Applied Sciences, 28(2), 121-129.

Microorganisms such as fungi can fragment carbon compounds by hydrolytic enzymes. The filamentous fungus, Aspergillus niger is now mostly considered because of its ubiquitous nature, non-fastidious nutritional requirements and it is classified generally as safe. This study was aimed at the production of cellulosic enzymes by A. niger and hydrolytic degradation of cellulosic materials by these enzymes. Standard methods were employed in soil samples collection, isolation of A. niger from the soils and their screening for enzyme production. Results showed that the A. niger isolates exhibited considerable activities of degrading and hydrolyzing cellulose in the agar media. The highest FPase, cellulase and xylanase activities were obtained from white saw dust with concentrations of 0.4059 U/ml, 0.7695U/ml and 1.3488 U/ml respectively. Also, results showed high enzyme activity at pH 6 (0.52U/ml) and temperature of 30ºC (0.72U/ml). Acid hydrolysis of the cellulosic substrates resulted to the release of 6.5% total sugar from white sawdust. The findings of this study revealed that the enzymes produced by A. niger hydrolyzed cellulosic materials but acid is more efficient than the enzymes in the hydrolysis and release of total sugar from cellulosic materials. This study recommends that cellulolytic enzymes used in the industries should be produced locally using filamentous fungus such as Aspergillus niger and cellulosic materials as carbon source.

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PACER: a novel 3D plant cell wall model for the analysis of non-catalytic and enzymatic responses.

Monschein, M., Jurak, E., Paasela, T., Koitto, T., Lambauer, V., Pavicic, M., Enjalbert, T., Dumon, C. & Master, E. R. (2022). Biotechnology for Biofuels and Bioproducts, 15(1), 1-11.

Background: Substrate accessibility remains a key limitation to the efficient enzymatic deconstruction of lignocellulosic biomass. Limited substrate accessibility is often addressed by increasing enzyme loading, which increases process and product costs. Alternatively, considerable efforts are underway world-wide to identify amorphogenesis-inducing proteins and protein domains that increase the accessibility of carbohydrate-active enzymes to targeted lignocellulose components. Results: We established a three-dimensional assay, PACER (plant cell wall model for the analysis of non-catalytic and enzymatic responses), that enables analysis of enzyme migration through defined lignocellulose composites. A cellulose/azo-xylan composite was made to demonstrate the PACER concept and then used to test the migration and activity of multiple xylanolytic enzymes. In addition to non-catalytic domains of xylanases, the potential of loosenin-like proteins to boost xylanase migration through cellulose/azo-xylan composites was observed. Conclusions: The PACER assay is inexpensive and parallelizable, suitable for screening proteins for ability to increase enzyme accessibility to lignocellulose substrates. Using the PACER assay, we visualized the impact of xylan-binding modules and loosenin-like proteins on xylanase mobility and access to targeted substrates. Given the flexibility to use different composite materials, the PACER assay presents a versatile platform to study impacts of lignocellulose components on enzyme access to targeted substrates.

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Development of an Efficient C-to-T Base-Editing System and Its Application to Cellulase Transcription Factor Precise Engineering in Thermophilic Fungus Myceliophthora thermophila.

Zhang, C., Li, N., Rao, L., Li, J., Liu, Q. & Tian, C. (2022). Microbiology Spectrum, e02321-21.

Myceliophthora thermophila is a thermophilic fungus with great potential in biorefineries and biotechnology. The base editor is an upgraded version of the clustered regularly interspaced short palindromic repeats (CRISPR)-dependent genome-editing tool that introduces precise point mutations without causing DNA double-strand breaks (DSBs) and has been used in various organisms but rarely in filamentous fungi, especially thermophilic filamentous fungi. Here, for the first time, we constructed three cytosine base editors (CBEs) in M. thermophila, namely, evolved apolipoprotein B mRNA-editing enzyme catalytic subunit 1 (APOBEC1) cytosine base editor 4 max (Mtevo-BE4max), bacteriophage Mu Gam protein cytosine base editor 4 max (MtGAM-BE4max), and evolved CDA1 deaminase cytosine base editor (Mtevo-CDA1), and efficiently inactivated genes by precisely converting three codons (CAA, CAG, and CGA) into stop codons without DSB formation. The Mtevo-CDA1 editor with up to 92.6% editing efficiency is a more suitable tool for cytosine base editing in thermophilic fungi. To investigate the function of each motif of the cellulase transcription factor M. thermophila CLR-2 (MtCLR-2), we used the Mtevo-CDA1 editor. The fungal-specific motif of MtCLR-2 was found to be strongly involved in cellulase secretion, conidium formation, hyphal branching, and colony formation. Mutation of the fungus-specific motif caused significant defects in these characteristics. Thus, we developed an efficient thermophilic fungus-compatible base-editing system that could also be used for genetic engineering in other relevant filamentous fungi.

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The chimeric GaaR-XlnR transcription factor induces pectinolytic activities in the presence of D-xylose in Aspergillus niger.

Kun, R. S., Garrigues, S., Di Falco, M., Tsang, A. & de Vries, R. P. (2021). Applied Microbiology and Biotechnology, 105(13), 5553-5564.

Aspergillus niger is a filamentous fungus well known for its ability to produce a wide variety of pectinolytic enzymes, which have many applications in the industry. The transcriptional activator GaaR is induced by 2-keto-3-deoxy-L-galactonate, a compound derived from D-galacturonic acid, and plays a major role in the regulation of pectinolytic genes. The requirement for inducer molecules can be a limiting factor for the production of enzymes. Therefore, the generation of chimeric transcription factors able to activate the expression of pectinolytic genes by using underutilized agricultural residues would be highly valuable for industrial applications. In this study, we used the CRISPR/Cas9 system to generate three chimeric GaaR-XlnR transcription factors expressed by the xlnR promoter by swapping the N-terminal region of the xylanolytic regulator XlnR to that of the GaaR in A. niger. As a test case, we constructed a PpgaX-hph reporter strain to evaluate the alteration of transcription factor specificity in the chimeric mutants. Our results showed that the chimeric GaaR-XlnR transcription factor was induced in the presence of D-xylose. Additionally, we generated a constitutively active GaaR-XlnR V756F version of the most efficient chimeric transcription factor to better assess its activity. Proteomics analysis confirmed the production of several pectinolytic enzymes by ΔgaaR mutants carrying the chimeric transcription factor. This correlates with the improved release of D-galacturonic acid from pectin by the GaaR-XlnR V756F mutant, as well as by the increased L-arabinose release from the pectin side chains by both chimeric mutants under inducing condition, which is required for efficient degradation of pectin.

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Effect of ammonia fiber expansion-treated wheat straw and a recombinant fibrolytic enzyme on rumen microbiota and fermentation parameters, total tract digestibility, and performance of lambs.

Ribeiro, G. O., Gruninger, R. J., Jones, D. R., Beauchemin, K. A., Yang, W. Z., Wang, Y., Abbott, D. W., Tsang, A. & McAllister, T. A. (2020). Journal of Animal Science, 98(5), skaa116.

The objective of this study was to evaluate the effect of ammonia fiber expansion (AFEX)-treated wheat straw pellets and a recombinant fibrolytic enzyme on the rumen microbiome, rumen fermentation parameters, total tract diet digestibility, and performance of lambs. Eight rumen cannulated wethers and 60 lambs (n = 15 per diet, 8 rams and 7 ewes) were used in a replicated 4 × 4 Latin square design digestibility study and a complete randomized growth performance study, respectively. Four treatment diets were arranged in a 2 × 2 factorial structure with AFEX wheat straw (0% or 30% AFEX straw pellets on a dietary DM basis replacing alfalfa hay pellets) and fibrolytic enzyme (with or without XYL10C, a β-1,4-xylanase, from Aspergillus niger) as main factors. Enzyme was applied at 100 mg/kg of diet DM, 22 h before feeding. Rumen bacteria diversity Pielou evenness decreased (P = 0.05) with AFEX compared with the control diet and increased (P < 0.01) with enzyme. Enzyme increased (P ≤ 0.02) the relative abundancies of Prevotellaceae UCG-004, Christensenellaceae R-7 group, Saccharofermentans, and uncultured Kiritimatiellaeota. Total protozoa counts were greater (P ≤ 0.04) in the rumen of lambs fed AFEX compared with control, with enzyme reducing (P ≤ 0.05) protozoa counts for both diets. Digestibility of DM did not differ (P > 0.10) among diets, but digestibility of CP was reduced (P = 0.001), and digestibility of NDF and ADF increased (P < 0.05) as AFEX replaced alfalfa. Compared with control, AFEX promoted greater DMI (P = 0.003) and improved ADG up to 42 d on feed (P = 0.03), but not (P = 0.51) over the full ~94-d experiment. Consequently, overall G:F was reduced (P = 0.04) for AFEX when compared with control (0.188 vs. 0.199), but days on feed were lower (P = 0.04) for AFEX (97 vs. 91 d). Enzyme improved DMI of AFEX up to day 70 (P = 0.01), but did not affect DMI of the control diet. Enzyme addition improved ADG of lambs fed both diets in the first 28 d (P = 0.02), but not over the entire feeding period (P ≥ 10). As a result, G:F was improved with enzyme for the first 28 d (P = 0.04), but not overall (P = 0.45). This study shows that AFEX-treated wheat straw can replace alfalfa hay with no loss in lamb growth performance. Additionally, the enzyme XYL10C altered the rumen microbiome and improved G:F in the first month of the feeding.

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Innovative microscale workflow from fungi cultures to Cell Wall‐Degrading Enzyme screening.

Raulo, R., Heuson, E., Siah, A., Phalip, V. & Froidevaux, R. (2019). Microbial Biotechnology, 12(6), 1286-1292.

This study aimed at developing a complete miniaturized high‐throughput screening workflow for the evaluation of the Cell Wall‐Degrading Enzyme (CWDE) activities produced by any fungal strain directly cultivated on raw feedstock in a submerged manner. In this study, wheat straw was selected as model substrate as it represents an important carbon source but yet poorly valorised to yield high added value products. Fungi were grown in a microbioreactor in a high‐throughput (HT) way to replace the fastidious shaking flask cultivations. Both approaches were compared in order to validate our new methodology. The range of CWDE activities produced from the cultures was assayed using AZO‐died and pNP‐linked substrates in an SBS plate format using a Biomek FXp pipetting platform. As highlighted in this study, it was shown that the CWDE activities gathered from the microbioreactor cultivations were similar or higher to those obtained from shake flasks cultures, with a lower standard deviation on the measured values, making this new method much faster than the traditional one and suitable for HT CWDE production thanks to its pipetting platform compatibility. Also, the results showed that the enzymatic activities measured were the same when doing the assay manually or using the automated method.

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Enzymatic potential and biosurfactant production by endophytic fungi from mangrove forest in Southeastern Brazil.

Martinho, V., dos Santos Lima, L. M., Barros, C. A., Ferrari, V. B., Passarini, M. R. Z., Santos, L. A., de Souza Debastianes, F. L., Lacava, P. T. & de Vasconcellos, S. P. (2019). AMB Express, 9(1), 1-8.

Microbial activity is the main route for cycling mangrove nutrients. In general, microorganisms have abilities to degrade lignocellulosic compounds. Among the biotechnological potential of the microbiota from mangroves, it is noteworthy about endophytic fungi, which can be considered as effective sources of different bioactive compounds. In this sense, thirty (30) endophytic fungi were isolated from mangrove forest sampling Cananeia, SP, Brazil. These microorganisms were analyzed about their enzymatic activities including: lignin peroxidase EC, manganese peroxidase EC and laccase EC, as well endo-cellulase EC and endo-xylanase EC Besides that, production of bioactive secondary metabolites like biosurfactant and/or bioemulsifier was also investigated. As results, nineteen (19) isolates were selected about their ligninolytic abilities, nine (9) of them about cellulase activity and thirteen (13) showed xylanase abilities. The fungal isolate named as 3(3), characterized as Fusarium sambucinum, showed a prominent lignin peroxidase (42.4 U L−1) and manganese peroxidase (23.6 U L−1) activities. The isolate 63.1, also related to Fusarium sp. genera, was selected about its laccase activity (41.5 U L−1). From all the investigated fungi, the isolate 47(4) Trichoderma camerunense was selected about its cellulolytic and xylanolytic activities, showing 45.23 and 26.09 U mL−1, respectively. The same fungi also showed biosurfactant ability demonstrated by superficial tension decreasing to 38 mN/m. In addition, fifteen (15) fungi exhibited bioemulsifier activity, with E24 values up to 62.8%.

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Mechanisms of utilisation of arabinoxylans by a porcine faecal inoculum: competition and co-operation.

Feng, G., Flanagan, B. M., Mikkelsen, D., Williams, B. A., Yu, W., Gilbert, R. G. & Gidley, M. J. (2018). Scientific Reports, 8(1), 4546.

Recent studies show that a single or small number of intestinal microbes can completely degrade complex carbohydrates. This suggests a drive towards competitive utilisation of dietary complex carbohydrates resulting in limited microbial diversity, at odds with the health benefits associated with a diverse microbiome. This study investigates the enzymatic metabolism of wheat and rye arabinoxylans (AX) using in vitro fermentation, with a porcine faecal inoculum. Through studying the activity of AX-degrading enzymes and the structural changes of residual AX during fermentation, we show that the AX-degrading enzymes are mainly cell-associated, which enables the microbes to utilise the AX competitively. However, potential for cross-feeding is also demonstrated to occur by two distinct mechanisms: (1) release of AX after partial degradation by cell-associated enzymes, and (2) release of enzymes during biomass turnover, indicative of co-operative AX degradation. This study provides a model for the combined competitive-co-operative utilisation of complex dietary carbohydrates by gut microorganisms.

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Optimization of Xylanase Production from Fermentation of Water Hyacinth (Eichhornia crassipes) using Trichoderma species.

Udeh, C. B., Ameh, J. B., Ado, S. A. & Okoduwa, S. I. R. (2017). Journal of Biotechnology Research, 3(3), 15-24.

Background: In the present study, optimized cultural conditions for enhanced production of xylanase from local soil isolate of Trichoderma species, using water hyacinth as a substrate in submerged culture fermentation is presented. Method: The Megazyme assay method was used for endo 1, 4-β-xylanase using Azo-xylan (Birchwood). Results: A continuous increase in xylanase production was observed with increasing level of substrate concentration in the medium and highest production was obtained with water hyacinth at 6% w/v level. Maximum xylanase production was achieved with a pH 5.0, incubation temperature of 30°C and agitation rate of 150 rpm. The highest production was achieved on day five of fermentation at optimum parameters under study. Conclusion: The study showed that production of xylanase can be cost effective using water hyacinth and can be implored on large scale for industrial applications.

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Functional characterization of a xylose transporter in Aspergillus nidulans.

Colabardini, A. C., Ries, L. N. A., Brown, N. A., dos Reis, T. F., Savoldi, M., Goldman, M. H. S., Menino, J. F., Rodrigues, F. & Goldman, G. H. (2014). Biotechnology for Biofuels, 7(1), 46.

Background: The production of bioethanol from lignocellulosic feedstocks will only become economically feasible when the majority of cellulosic and hemicellulosic biopolymers can be efficiently converted into bioethanol. The main component of cellulose is glucose, whereas hemicelluloses mainly consist of pentose sugars such as D-xylose and L-arabinose. The genomes of filamentous fungi such as A. nidulans encode a multiplicity of sugar transporters with broad affinities for hexose and pentose sugars. Saccharomyces cerevisiae, which has a long history of use in industrial fermentation processes, is not able to efficiently transport or metabolize pentose sugars (e.g. xylose). Subsequently, the aim of this study was to identify xylose-transporters from A. nidulans, as potential candidates for introduction into S. cerevisiae in order to improve xylose utilization. Results: In this study, we identified the A. nidulans xtrD (xylose transporter) gene, which encodes a Major Facilitator Superfamily (MFS) transporter, and which was specifically induced at the transcriptional level by xylose in a XlnR-dependent manner, while being partially repressed by glucose in a CreA-dependent manner. We evaluated the ability of xtrD to functionally complement the S. cerevisiae EBY.VW4000 strain which is unable to grow on glucose, fructose, mannose or galactose as single carbon source. In S. cerevisiae, XtrD was targeted to the plasma membrane and its expression was able to restore growth on xylose, glucose, galactose, and mannose as single carbon sources, indicating that this transporter accepts multiple sugars as a substrate. XtrD has a high affinity for xylose, and may be a high affinity xylose transporter. We were able to select a S. cerevisiae mutant strain that had increased xylose transport when expressing the xtrD gene. Conclusions: This study characterized the regulation and substrate specificity of an A. nidulans transporter that represents a good candidate for further directed mutagenesis. Investigation into the area of sugar transport in fungi presents a crucial step for improving the S. cerevisiae xylose metabolism. Moreover, we have demonstrated that the introduction of adaptive mutations beyond the introduced xylose utilization genes is able to improve S. cerevisiae xylose metabolism.

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Biochemical characterization of an endoxylanase from Pseudozyma brasiliensis sp. nov strain GHG001 isolated from the intestinal tract of Chrysomelidae larvae associated to sugarcane roots.

Borges, T. A., De Souza, A. T., Squina, F. M., Riaño-Pachón, D. M., Dos Santos, R. A. C., Machado, E., Oliveira, J. R. L. D. C., Damásio, A. R. L. & Goldman, G. H. (2014). Process Biochemistry, 49(1), 77-83.

Endo-xylanases play a key role in the hydrolysis of xylan and recently they have attracted much attention due to their potential applications on the biofuel and paper industries. We isolated a Pseudozyma brasiliensis sp. nov. strain from the intestinal tract of Chrysomelidae larvae that parasitize sugarcane roots. This basidiomycetous yeast produces a xylanase designated PbXynA which was purified and characterized. The molecular weight of PbXynA is 24 kDa, it belongs to the GH11 family and its optimum pH and optimum temperature are 4.0 and 55°C, respectively. PbXynA has as secondary structure predominantly β-sheets and sigmoidal kinetic behavior with elevated speed conversion from substrate-to-products (Vmax = 2792.0 μmol product/min/mg protein). It is highly activated by bivalent cations such as Ca2+, however in the presence of Cu2+ xylanase activity was inhibited. It has a high specific activity and produces xylooligosaccharides that have a variety of industrial applications, indicating PbXynA has a great biotechnological potential.

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Generation of doubled haploid transgenic wheat lines by microspore transformation.

Brew-Appiah, R. A. T., Ankrah, N., Liu, W., Konzak, C. F., Wettstein, D. V. & Rustgi, S. (2013). PLoS One, 8(11), e80155.

Microspores can be induced to develop homozygous doubled haploid plants in a single generation. In the present experiments androgenic microspores of wheat have been genetically transformed and developed into mature homozygous transgenic plants. Two different transformation techniques were investigated, one employing electroporation and the other co-cultivation with Agrobacterium tumefaciens. Different tissue culture and transfection conditions were tested on nine different wheat cultivars using four different constructs. A total of 19 fertile transformants in five genotypes from four market classes of common wheat were recovered by the two procedures. PCR followed by DNA sequencing of the products, Southern blot analyses and bio/histo-chemical and histological assays of the recombinant enzymes confirmed the presence of the transgenes in the To transformants and their stable inheritance in homozygous T1:2 doubled haploid progenies. Several decisive factors determining the transformation and regeneration efficiency with the two procedures were determined: (i) pretreatment of immature spikes with CuSO4 solution (500 mg/L) at 4°C for 10 days; (ii) electroporation of plasmid DNA in enlarged microspores by a single pulse of ~375 V; (iii) induction of microspores after transfection at 28°C in NPB-99 medium and regeneration at 26°C in MMS5 medium; (iv) co-cultivation with Agrobacterium AGL-1 cells for transfer of plasmid T-DNA into microspores at day 0 for <24 hours; and (v) elimination of AGL-1 cells after co-cultivation with timentin (200-400 mg/L).

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Influence of high temperature and ethanol on thermostable lignocellulolytic enzymes.

Skovgaard, P. A. & Jørgensen, H. (2013). Journal of Industrial Microbiology & Biotechnology, 40(5), 447-456.

Lignocellulolytic enzymes are among the most costly part in production of bioethanol. Therefore, recycling of enzymes is interesting as a concept for reduction of process costs. However, stability of the enzymes during the process is critical. In this work, focus has been on investigating the influence of temperature and ethanol on enzyme activity and stability in the distillation step, where most enzymes are inactivated due to high temperatures. Two enzyme mixtures, a mesophilic and a thermostable mixture, were exposed to typical process conditions [temperatures from 55 to 65°C and up to 5 % ethanol (w/v)] followed by specific enzyme activity analyses and SDS-PAGE. The thermostable and mesophilic mixture remained active at up to 65 and 55°C, respectively. When the enzyme mixtures reached their maximum temperature limit, ethanol had a remarkable influence on enzyme activity, e.g., the more ethanol, the faster the inactivation. The reason could be the hydrophobic interaction of ethanol on the tertiary structure of the enzyme protein. The thermostable mixture was more tolerant to temperature and ethanol and could therefore be a potential candidate for recycling after distillation.

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Diversity of termitomyces associated with fungus-farming termites assessed by cultural and culture-independent methods.

Makonde, H. M., Boga, H. I., Osiemo, Z., Mwirichia, R., Stielow, J. B., Göker, M. & Klenk, H. P. (2013). PLoS One, 8(2), e56464.

Background: Fungus-cultivating termites make use of an obligate mutualism with fungi from the genus Termitomyces, which are acquired through either vertical transmission via reproductive alates or horizontally transmitted during the formation of new mounds. Termitomyces taxonomy, and thus estimating diversity and host specificity of these fungi, is challenging because fruiting bodies are rarely found. Molecular techniques can be applied but need not necessarily yield the same outcome than morphological identification. Methodology: Culture-dependent and culture-independent methods were used to comprehensively assess host specificity and gut fungal diversity. Termites were identified using mitochondrial cytochrome oxidase II (COII) genes. Twenty-three Termitomyces cultures were isolated from fungal combs. Internal transcribed spacer (ITS) clone libraries were constructed from termite guts. Presence of Termitomyces was confirmed using specific and universal primers. Termitomyces species boundaries were estimated by cross-comparison of macromorphological and sequence features, and ITS clustering parameters accordingly optimized. The overall trends in coverage of Termitomyces diversity and host associations were estimated using Genbank data. Results and Conclusion: Results indicate a monoculture of Termitomyces in the guts as well as the isolation sources (fungal combs). However, cases of more than one Termitomyces strains per mound were observed since mounds can contain different termite colonies. The newly found cultures, as well as the clustering analysis of GenBank data indicate that there are on average between one and two host genera per Termitomyces species. Saturation does not appear to have been reached, neither for the total number of known Termitomyces species nor for the number of Termitomyces species per host taxon, nor for the number of known hosts per Termitomyces species. Considering the rarity of Termitomyces fruiting bodies, it is suggested to base the future taxonomy of the group mainly on well-characterized and publicly accessible cultures.

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Novel modular endo-β-1,4-xylanase with transglycosylation activity from Cellulosimicrobium sp. strain HY-13 that is homologous to inverting GH family 6 enzymes.

Kim, D. Y., Ham, S. J., Kim, H. J., Kim, J., Lee, M. H., Cho, H. Y., Shin, D. H., Rhee, Y. H., Son, K. H. & Park, H. Y. (2012). Bioresource Technology, 107, 25-32.

The gene (2304-bp) encoding a novel xylanolytic enzyme (XylK2) with a catalytic domain, which is 70% identical to that of Cellulomonas flavigena DSM 20109 GH6 β-1,4-cellobiohydrolase, was identified from an earthworm (Eisenia fetida)-symbiotic bacterium, Cellulosimicrobium sp. strain HY-13. The enzyme consisted of an N-terminal catalytic GH6-like domain, a fibronectin type 3 (Fn3) domain, and a C-terminal carbohydrate-binding module 2 (CBM 2). XylK2δFn3-CBM 2 displayed high transferase activity (788.3 IU mg-1) toward p-nitrophenyl (PNP) cellobioside, but did not degrade xylobiose, glucose-based materials, or other PNP-sugar derivatives. Birchwood xylan was degraded by XylK2δFn3-CBM 2 to xylobiose (59.2%) and xylotriose (40.8%). The transglycosylation activity of the enzyme, which enabled the formation of xylobiose (33.6%) and xylotriose (66.4%) from the hydrolysis of xylotriose, indicates that it is not an inverting enzyme but a retaining enzyme. The endo-β-1,4-xylanase activity of XylK2δFn3-CBM 2 increased significantly by approximately 2.0-fold in the presence of 50 mM xylobiose.

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Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa.

Sun, J., Tian, C., Diamond, S. & Glass, N. L. (2012). Eukaryotic Cell, 11(4), 482-493.

Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential substrate for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). Neurospora crassa, a model filamentous fungus, expresses and secretes enzymes required for plant cell wall deconstruction. To better understand genes specifically associated with degradation of hemicellulose, we applied secretome and transcriptome analysis to N. crassa grown on beechwood xylan. We identified 34 secreted proteins and 353 genes with elevated transcription on xylan. The xylanolytic phenotype of strains with deletions in genes identified from the secretome and transcriptome analysis of the wild type was assessed, revealing functions for known and unknown proteins associated with hemicellulose degradation. By evaluating phenotypes of strains containing deletions of predicted TF genes in N. crassa, we identified a TF (XLR-1; xylan degradation regulator 1) essential for hemicellulose degradation that is an ortholog to XlnR/XYR1 in Aspergillus and Trichoderma species, respectively, a major transcriptional regulator of genes encoding both cellulases and hemicellulases. Deletion of xlr-1 in N. crassa abolished growth on xylan and xylose, but growth on cellulose and cellulolytic activity were only slightly affected. To determine the regulatory mechanisms for hemicellulose degradation, we explored the transcriptional regulon of XLR-1 under xylose, xylanolytic, and cellulolytic conditions. XLR-1 regulated only some predicted hemicellulase genes in N. crassa and was required for a full induction of several cellulase genes. Hemicellulase gene expression was induced by a combination of release from carbon catabolite repression (CCR) and induction. This systematic analysis illustrates the similarities and differences in regulation of hemicellulose degradation among filamentous fungi.

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Isolation and characterization of a Bacillus licheniformis strain capable of degrading zearalenone.

Yi, P. J., Pai, C. K., & Liu, J. R. (2011). World Journal of Microbiology and Biotechnology, 27(5), 1035-1043.

The worldwide contamination of cereals, oilseeds, and other crops by mycotoxin-producing moulds is a significant problem. Mycotoxins have adverse effects on humans and animals that result in illnesses and economic losses. Reduction or elimination of mycotoxin contamination in food and feed is an important issue. This study aimed to screen soil bacteria for degradation of zearalenone (ZEN). A pure culture of strain CK1 isolated from soil samples showed most capable of degradation of ZEN. Using physiological, biochemical, and 16S rRNA gene sequence analysis methods, CK1 was identified as Bacillus licheniformis. Addition of 2 ppm of ZEN in Luria–Bertani (LB) medium, B. licheniformis CK1 decreased 95.8% of ZEN after 36 h of incubation. In ZEN-contaminated corn meal medium, B. licheniformis CK1 decreased more than 98% of ZEN after 36 h of incubation. In addition, B. licheniformis CK1 was non-hemolytic, non-enterotoxin producing, and displayed high levels of extracellular xylanase, cellulase, and protease activities. These findings suggest that B. licheniformis CK1 could be used to reduce the concentrations of ZEN and improve the digestibility of nutrients in feedstuffs simultaneously.

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Engineering hyperthermostability into a GH11 xylanase is mediated by subtle changes to protein structure.

Dumon, C., Varvak, A., Wall, M. A., Flint, J. E., Lewis, R. J., Lakey, J. H., Morland, C., Luginbühl, P., Healey, S., Todaro, T., DeSantis, G., Sun, M., Parra-Gessert, L., Tan, X., Weiner, D. P. & Gilbert, H. J. (2008). Journal of Biological Chemistry, 283(33), 22557-22564.

Understanding the structural basis for protein thermostability is of considerable biological and biotechnological importance as exemplified by the industrial use of xylanases at elevated temperatures in the paper pulp and animal feed sectors. Here we have used directed protein evolution to generate hyperthermostable variants of a thermophilic GH11 xylanase, EvXyn11. The Gene Site Saturation MutagenesisTM (GSSM) methodology employed assesses the influence on thermostability of all possible amino acid substitutions at each position in the primary structure of the target protein. The 15 most thermostable mutants, which generally clustered in the N-terminal region of the enzyme, had melting temperatures (Tm) 1–8°C higher than the parent protein. Screening of a combinatorial library of the single mutants identified a hyperthermostable variant, EvXyn11TS, containing seven mutations. EvXyn11TS had a Tm ~ 25°C higher than the parent enzyme while displaying catalytic properties that were similar to EvXyn11. The crystal structures of EvXyn11 and EvXyn11TS revealed an absence of substantial changes to identifiable intramolecular interactions. The only explicable mutations are T13F, which increases hydrophobic interactions, and S9P that apparently locks the conformation of a surface loop. This report shows that the molecular basis for the increased thermostability is extraordinarily subtle and points to the requirement for new tools to interrogate protein folding at non-ambient temperatures.

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CreA mediates repression of the regulatory gene xlnR which controls the production of xylanolytic enzymes in Aspergillus nidulans.

Tamayo, E. N., Villanueva, A., Hasper, A. A., De Graaff, L. H., Ramón, D. & Orejas, M. (2008). Fungal Genetics and Biology, 45(6), 984-993.

The Aspergillus nidulans xlnR gene encodes a Zn2 Cys6 transcription activator necessary for the synthesis of the main xylanolytic enzymes, i.e. endo-xylanases X22, X24 and X34, and β-xilosidase XlnD. Expression of xlnR is not sufficient for induction of genes encoding the xylanolytic complex, the presence of xylose is absolutely required. It has been established previously that the wide-domain carbon catabolite repressor CreA indirectly represses xlnA (encodes X22) and xlnB (encodes X24) genes as well as exerting direct repression on xlnA. This work provides evidence that CreA-mediated indirect repression occurs through repression of xlnR: (i) the xlnR gene promoter is repressed by glucose and this repression is abolished increAd30 mutant strains and (ii) deregulated expression of xlnR completely relieves glucose repression of xlnA and xlnB. Thus, CreA and XlnR form a transcriptional cascade regulating A. nidulans xylanolytic genes.

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