Role of hydrogen bonding in the interaction between a xylan binding module and xylan

NMR studies of the internal family 2b carbohydrate binding module (CBM2b-1) of Cellulomonas fimi xylanase 11A have identified six polar residues and two aromatic residues that interact with its target ligand, xylan. To investigate the importance of the various interactions, free energy and enthalpy changes have been measured for the binding of xylan to native and mutant forms of CBM2b-1. The data show that the two aromatic residues, Trp 259 and Trp 291, play a critical role in the binding, and similarly that mutants N264A and T316A have no affinity for the xylose polymer. Interestingly, mutations E257A, Q288A, N292A, E257A/Q288A, E257A/N292A, and E257A/N292A/Q288A do not significantly diminish the affinity of CBM2b-1 for the xylose polymers, but do influence the thermodynamics driving the protein-carbohydrate interactions. These thermodynamic parameters have been interpreted in light of a fresh understanding of enthalpy-entropy compensation and show the following. (1) For proteins whose ligands are bound on an exposed surface, hydrogen bonding confers little specificity or affinity. It also displays little cooperativity. Most specificity and affinity derive from binding between the face of sugar rings and aromatic rings. (2) Loss of hydrogen bonding interactions leads to a redistribution of the remaining bonding interactions such that the entropic mobility of the ligand is maximized, at the expense (if necessary) of enthalpically favorable bonds. (3) Changes in entropy and enthalpy in the binding between polysaccharide and a range of mutants can be interpreted by considering changes in binding and flexibility, without any need to consider solvent reorganization.     

Citric acid production from xylan and xylan hydrolysate by semi-solid culture of Aspergillus niger

Citric acid production from xylan and xylan hydrolysate was done by Aspergillus niger Yang no. 2 cultivated in a semi-solid culture using bagasse as a carrier. Yang no. 2 produced 72.4 g/l and 52.6 g/l of citric acid in 5 d from 140 g/l of xylose and arabinose, respectively. Yang no. 2 produced 51.6 g/l of citric acid in 3 d from a concentrated xylan hydrolysate prepared by cellulase treatment, containing 100 g/l of reducing sugars. Moreover, Yang no. 2 directly produced 39.6 g/l of citric acid maximally in 3 d from 140 g/l of xylan.     

Biosynthesis of pure araban and xylan

A crude particulate enzyme preparation from mung bean shoots partially freed from sugar transferases synthesized pure araban from UDP-l-¹⁴C-arabinose. The preparation thus allowed to study some properties of the UDP-arabinose transferase which was shown to require 7 mM Mn²⁺ and pH 6–6·5 for optimal activity. Pure xylan was synthesized from UDP-d-¹⁴C-xylose if a mixture of 0·06% Triton X100 and 35 mM EDTA was added to the crude enzyme preparation. In contrast to the UDP-arabinose transferase the UDP-xylose transferase does not require bivalent metal ions.     

Chemical structure of kenaf xylan

Methylation and partial acid hydrolysis of xylans from the bast and core of kenaf (Hibiscus cannabinus) showed that the main chain of these xylans consists of (1 → 4)-linked β-d-xylopyranosyl (Xylp) residues, some of which carry a -1,2-linked 4-O-methyl-glucopyranosyluronic acid (Me-GlcAp) and glucopyranosyluronic acid (GlcAp) residues as side chains. Partial hydrolysis of kenaf xylans afforded two series of aldouronic acids from aldobio- to aldotetraouronic acids. The acids of the first series composed of 4-O-Me-d-GlcAp and d-Xylp residues: 4-O-Me-GlcA-Xyl₃, 4-O-Me-GlcA-Xyl₂ and 4-O-Me-GlcA-Xyl. The second series composed of d-GlcAp and d-Xylp: GlcA-Xyl₃, GlcA-Xyl₂ and GlcA-Xyl.

In addition to these acids, another aldobiouronic acid, 4-O-(-d-GalAp)-d-Xyl was found to be present in the partial hydrolysate.

The molar ratio of GalA, GlcA, 4-O-Me-GlcA, and Xyl residues was calculated to be 1.0:2.0:9.4:119 for the bast xylan and 1.0:1.3:7.9:99.4 for the core xylan.     

Polarized-light-stimulated enzymatic hydrolysis of xylan

The 1- to 2-h illumination of xylanase with visible polarized light (PL) prior to the action of that enzyme upon beechwood xylan significantly increased its activity. The activity only negligibly decreased on 3 months storage. The hydrolysis of xylan proceeded in three well-distinguished stages. In the first and fastest stage the effect of illumination was only slightly positive. The effect of the stimulation was noted in the second, slower stage. Enzyme stimulated with PL, preferably by means of the 2-h illumination, performed better than enzyme stimulated with nonpolarized light and non-stimulated enzyme. In the last, the slowest stage, the rates of the reaction were nearly the same using either stimulated or non-stimulated enzyme.     

Hyperthermostable acetyl xylan esterase

An esterase which is encoded within a Thermotoga maritima chromosomal gene cluster for xylan degradation and utilization was characterized after heterologous expression of the corresponding gene in Escherichia coli and purification of the enzyme. The enzyme, designated AxeA, shares amino acid sequence similarity and its broad substrate specificity with the acetyl xylan esterase from Bacillus pumilus, the cephalosporin C deacetylase from Bacillus subtilis, and other (putative) esterases, allowing its classification as a member of carbohydrate esterase family 7. The recombinant enzyme displayed activity with p-nitrophenyl-acetate as well as with various acetylated sugar substrates such as glucose penta-acetate, acetylated oat spelts xylan and DMSO (dimethyl sulfoxide)-extracted beechwood xylan, and with cephalosporin C. Thermotoga maritima AxeA represents the most thermostable acetyl xylan esterase known to date. In a 10 min assay at its optimum pH of 6.5 the enzyme's activity peaked at 90°C. The inactivation half-life of AxeA at a protein concentration of 0.3 µg µl⁻¹ in the absence of substrate was about 13 h at 98°C and about 67 h at 90°C. Differential scanning calorimetry analysis of the thermal stability of AxeA corroborated its extreme heat resistance. A multi-phasic unfolding behaviour was found, with two apparent exothermic peaks at approximately 100–104°C and 107.5°C. In accordance with the crystal structure, gel filtration analysis at ambient temperature revealed that the enzyme has as a homohexameric oligomerization state, but a dimeric form was also found.     

Studies on xylan hydrolases from different strains ofStreptomyces and their mutual influences in the breakdown of xylan

A good proportion ofStreptomyces isolates from natural sources produced extracellular xylan hydrolase. Nineteen isolated showing high activity were able to completely or partially degrade wheat bran in the growth medium. Chromatographic analysis of commercial xylan degradation products suggested that the isolates produced either endo-or exo-xylan hydrolases or their mixtures. Mixed additions of culture fluids showed a highly synergistic effect, up to an increase by 200 %. In a few cases antagonism was seen which, however, could be removed by dialysis of the culture fluid.     

Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis

Previous studies using co-expression analysis have identified a large number of genes likely to be involved in secondary cell-wall formation. However, the function of very few of these genes is known. We have studied the cell-wall phenotype of irx7, irx8 and irx9, three previously described irregular xylem (irx) mutants, and irx14 and parvus-3, which we now show also to be secondary cell-wall mutants. All five mutants, which have mutations in genes encoding putative glycosyltransferases, exhibited large decreases in xylan. In addition, all five mutants were found to have the same specific defect in xylan structure, retaining MeGlcUA but lacking GlcUA side branches. Polysaccharide analysis by carbohydrate gel electrophoresis (PACE) was used to determine the xylan structure in Arabidopsis, and revealed that side branches are added to approximately one in every eight xylose residues. Interestingly, this ratio is constant in all the lines analysed despite the wide variation in xylan content and the absence of GlcUA branches. Xylanase digestion of xylan from wild-type plants released a short oligosaccharide sequence at the reducing end of the xylan chain. MALDI-TOF MS analysis indicated that this sequence of sugars was absent in xylan from irx7, irx8 and parvus-3 mutants, but was present in irx9 and irx14. This is consistent with previous NMR analysis of xylan from irx7, irx8 and irx9, and suggests that PARVUS may be involved in the synthesis of a xylan primer whereas IRX14 may be required to synthesize the xylan backbone. This hypothesis is supported by assays showing that irx9 and irx14 are both defective in incorporation of radiolabel from UDP (14)C-xylose. This study has important implications for both our understanding of xylan biosynthesis and the functional analysis of cell-wall biosynthesis genes.     

Relationships between activities of xylanases and xylan structures

Structures of five water-soluble xylans have been determined. Four purified xylanase enzymes have been studied for the hydrolysis of the xylans. Different xylanases have different activities against various xylan structures. The key factors that influence the rate of xylan hydrolysis are chain length and degree of substitution. Two family 11 xylanases, Orpinomyces pc2 xylanase and Trichoderma longibrachiatum xylanase, can rapidly hydrolyze xylans that have a chain length greater than 8 xylose residues, and their hydrolytic rates are not sensitive to substituents on the xylan backbone. A family 11 xylanase from Aureobasidium pullulans is most effective on xylans that have a long chain (greater than 19 xylose residues), and also is effective against substituent groups. Although Thermatoga maritima xylanase is also more active on a long xylan chain (greater than 19 xylose residues), its hydrolytic rate is greatly reduced by substituents on xylan backbones.     

Distinct roles of carbohydrate esterase family CE16 acetyl esterases and polymer-acting acetyl xylan esterases in xylan deacetylation

Mass spectrometric analysis was used to compare the roles of two acetyl esterases (AE, carbohydrate esterase family CE16) and three acetyl xylan esterases (AXE, families CE1 and CE5) in deacetylation of natural substrates, neutral (linear) and 4-O-methyl glucuronic acid (MeGlcA) substituted xylooligosaccharides (XOS). AEs were similarly restricted in their action and apparently removed in most cases only one acetyl group from the non-reducing end of XOS, acting as exo-deacetylases. In contrast, AXEs completely deacetylated longer neutral XOS but had difficulties with the shorter ones. Complete deacetylation of neutral XOS was obtained after the combined action of AEs and AXEs. MeGlcA substituents partially restricted the action of both types of esterases and the remaining acidic XOS were mainly substituted with one MeGlcA and one acetyl group, supposedly on the same xylopyranosyl residue. These resisting structures were degraded to great extent only after inclusion of α-glucuronidase, which acted with the esterases in a synergistic manner. When used together with xylan backbone degrading endoxylanase and β-xylosidase, both AE and AXE enhanced the hydrolysis of complex XOS equally.     

Cellulose and xylan degrading enzymes of Fusarium avenaceum

It was found that crude preparation obtained from the culture medium of Fusarium avenaceum degraded cellulose and xylan. After chromatography on CM-Sepharose CL-6B of this preparation six fraction were obtained. The eluted fractions II and V showed xylanase activity, fraction IV — cellulase activity and fraction III — xylanase and cellulase activity. The end products of xylan hydrolysis by all xylanase fractions (II, III, V) were xylobiose, xylose, xylotriose and xylotetrose. The end products of cellulose hydrolysis by fractions III and IV was cellobiose, glucose and cellotriose. The data from gel filtration on Sephacryl S-200 indicated a molecular weight of more than 250,000 for both cellulase IV and xylanase V. After gel filtration in the presence of urea disaggregation of those high molecular xylanase and cellulase particles was observed. Xylanase II in difference from the other fractions contained higher amount of sugar. Digestion of fraction II with cellulase-hemicellulase preparation from Phoma hibernica decreased the content of sugar from 17% to 8%, but did not change its enzymatic properties. Cellulase IV as well as xylanase V were inactivated by N-bromosuccinimide, 2-hydroxy-5-nitrobenzyl bromide and tetranitromethane, hence it is suggested that tryptophan and tyrosine are the essential for the activity of these enzymes.     

X-Ray and stereochemical studies on xylan diacetate

By means of x-ray fiber diffraction, it has been found that xylan diacetate crystallizes with two chains or four residues in a monoclinic cell (space group P2₁): a = 7.64, b = 12.44, c (fiber axis) = 10.31 Å, and γ = 85°. Pairs of residues are related by a twofold screw axis in the c direction. Based on the observed fiber repeat and chain symmetry, the probable conformation of a pair of xylose diacetate residues joined via a β-1,4′ linkage has been obtained by energy minimization methods. The conformations corresponding to a threefold screw axis and a twofold screw axis along the chain have been compared and the reason why xylan diacetate assumes a twofold screw axis seems to be due to intermolecular packing effects rather than intramolecular non-bonded interactions.     

Green synthesis of xylan hemicellulose esters

The esterification of xylan type hemicelluloses, isolated from birchwood, was carried out firstly in homogeneous conditions using N,N-dimethylformamide (DMF) and lithium chloride (LiCl) in the presence of 4-dimethylaminipyridine (DMAP). The degree of substitution (DS) of xylan acetates ranged between 0.9 and 2.0 as a function of experimental conditions. Due to the problems of toxicity and recycling of DMF, an alternative method of esterification is reported in the second part of this work, performing in the absence of organic solvent and using DMAP or methanesulfonic acid (MSA) as catalysts. Acetylation reaction catalyzed by MSA was developed through an experimental design in order to achieve the highest DS under the mildest conditions. The significant factors and their interactions were identified. The optimization of reaction parameters allowed to obtain a high DS (1.6) and maximal yield (85%). Moreover, the reactivity of propionic and hexanoic anhydrides was evaluated and hydrophobic xylan esters with low degrees of substitution were obtained.     

Arabidopsis family GT43 members are xylan xylosyltransferases required for the elongation of the xylan backbone

Xylan is the second most abundant polysaccharide in plant biomass targeted for biofuel production. Therefore, it is imperative to understand the biochemical mechanism underlying xylan biosynthesis. Although previous genetic studies have identified several genes implicated in xylan biosynthesis, biochemical proof of any of their encoded proteins as a xylan xylosyltransferase (XylT) responsible for xylan backbone biosynthesis is still lacking. In this study, we investigated the enzymatic activities of two Arabidopsis thaliana GT43 members, IRX9 (Irregular Xylem9) and IRX14, which have been genetically shown to be non-redundantly involved in the elongation of the xylan backbone. IRX9 and IRX14, alone or simultaneously, were heterologously expressed in tobacco BY2 cells, and microsomes isolated from the transgenic BY2 cells were tested for XylT activity using xylotetraose (Xyl(4)) as an acceptor and UDP-[(14)C]xylose as a donor. It was found that although microsomes with expression of IRX9 or IRX14 alone exhibited little incorporation of radiolabeled xylose, a high level of incorporation of radiolabeled xylose onto Xyl(4) was conferred by microsomes with co-expression of IRX9 and IRX14. Further analysis using fluorescent anthranilic acid-labeled xylotetraose (Xyl(4)-AA) as an acceptor revealed that up to five β-(1,4)-linked xylosyl residues were able to be transferred onto Xyl(4)-AA by microsomes with co-expression of IRX9 and IRX14. Furthermore, it was shown that xylooligomers ranging from Xyl(3)-AA to Xyl(6)-AA could all be used as acceptors for the xylosyl transfer by microsomes with co-expression of IRX9 and IRX14. Together, these findings provide the first biochemical evidence that IRX9 and IRX14 are xylosyltransferases that operate cooperatively in the elongation of the xylan backbone.     

Hydrolysis of xylan and fermentation of xylose to ethanol

The focus in the development of pulping processes has usually been exclusively on cellulose. However, hemicellulose could serve as a valuable source of hexose and pentose sugars. Consequently, it should not be destroyed in a process designed for very high cellulose fibre yields. Novel procedures developed for production of ethanol by the fermentation of pentoses as well as hexoses provide new possibilities of hemicellulose utilization.

Many fungi produce extracellular hemicellulases. In the present work the production of xylanase and β-xylosidase with strains of Aspergillus and Trichoderma was studied. The enzymes were used for the hydrolysis of xylan. Xylose was fermented to ethanol by the mold Fusarium oxysporum.     

Xylanase and acetyl xylan esterase activities of XynA,a key subunit of the Clostridium cellulovorans cellulosome for xylan degradation

The Clostridium cellulovorans xynA gene encodes the cellulosomal endo-1,4-beta-xylanase XynA, which consists of a family 11 glycoside hydrolase catalytic domain (CD), a dockerin domain, and a NodB domain. The recombinant acetyl xylan esterase (rNodB) encoded by the NodB domain exhibited broad substrate specificity and released acetate not only from acetylated xylan but also from other acetylated substrates. rNodB acted synergistically with the xylanase CD of XynA for hydrolysis of acetylated xylan. Immunological analyses revealed that XynA corresponds to a major xylanase in the cellulosomal fraction. These results indicate that XynA is a key enzymatic subunit for xylan degradation in C. cellulovorans.