Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.

Although many xylanases have been studied, many of the characteristics of xylanases toward branches in xylan remain unclear. In this study, the substrate specificity of a GH11 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn11B) was elucidated based on its three-dimensional structure. Subsite mapping suggests that SoXyn11B has seven subsites (four subsites on the - side and three subsites on the + side), and it is one longer than the GH10 xylanase from S. olivaceoviridis (SoXyn10A). SoXyn11B has no affinity for the subsites at either end of the scissile glycosidic bond, and the sugar-binding energy at subsite - 2 was the highest, followed by subsite + 2. These properties were very similar to those of SoXyn10A. In contrast, SoXyn11B produced different branched oligosaccharides from bagasse compared with those of SoXyn10A. These branched oligosaccharides were identified as O-ß-D-xylopyranosyl-(1→4)-[O-α-L-arabinofuranosyl-(1→3)]-O-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranose (Ara3Xyl4) and O-ß-D-xylopyranosyl-(1→4)-[O-4-O-methyl-α-D-glucuronopyranosyl-(l→2)]-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranose (MeGlcA3Xyl4) by nuclear magnetic resonance (NMR) and electrospray ionization mass spectrometry (ESI-MS) and confirmed by crystal structure analysis of SoXyn11B in complex with these branched xylooligosaccharides. SoXyn11B has a ß-jerryroll fold structure, and the catalytic cleft is located on the inner ß-sheet of the fold. The ligand-binding structures revealed seven subsites of SoXyn11B. The 2- and 3-hydroxy groups of xylose at the subsites + 3, + 2, and - 3 face outwards, and an arabinose or a glucuronic acid side chain can be linked to these positions. These subsite structures appear to cause the limited substrate specificity of SoXyn11B for branched xylooligosaccharides. KEY POINTS: • Crystal structure of family 11 ß-xylanase from Streptomyces olivaceoviridis was determined. • Topology of substrate-binding cleft of family 11 ß-xylanase from Streptomyces olivaceoviridis was characterized. • Mode of action of family 11 ß-xylanase from Streptomyces olivaceoviridis for substitutions in xylan was elucidated.

Molecular and biochemical characteristics of inulosucrase InuBK from Alkalihalobacillus krulwichiae JCM 11691.

Information about the inulosucrase of nonlactic acid bacteria is scarce. We found a gene encoding inulosucrase (inuBK) in the genome of the Gram-positive bacterium Alkalihalobacillus krulwichiae JCM 11691. The inuBK open reading frame encoded a protein comprising 456 amino acids. We expressed His-tagged InuBK in culture medium using a Brevibacillus system. The optimal pH and temperature of purified InuBK were 7.0-9.0 and 50-55 °C, respectively. The findings of high-performance anion-exchange chromatography, nuclear magnetic resonance spectroscopy, and high-performance size-exclusion chromatography with multiangle laser light scattering showed that the polysaccharide produced by InuBK was an inulin with a molecular weight of 3806, a polydispersity index (PI) of 1.047, and fructosyl chain lengths with 3-27 degrees of polymerization. The size of InuBK was smaller than commercial inulins, and the PI of the inulin that it produced was lower.

Microorganisms Capable of Producing Polysaccharides from D-Xylose.

In recent years, the importance of biomass utilization has increased, but it has not been effectively exploited. In particular, it is difficult to use hemicellulose, the second most abundant biopolymer of biomass. Therefore, in order to promote the utilization of hemicellulose, we screened for microorganisms capable of producing polysaccharides from D-xylose. The following four strains were selected from samples collected from various regions of Okinawa Prefecture: Kosakonia sp. (SO_001), Papiliotrema terrestris (SO_005), Pseudarthrobacter sp. (SO_006), and Williamsia sp. (SO_009). Observation with a scanning electron microscope (SEM) confirmed that each bacterium produced polysaccharides with different shapes. In addition, the molecular weight and sugar composition of the polysaccharides produced by each bacterium were distinct. The selected microorganisms include closely related species known to promote plant growth and known to suppress postharvest pathogens. Since these microorganisms may be used not only in known fields but also in new fields, the results of this research are expected to greatly expand the uses of hemicellulose.

Substrate Specificities of GH8, GH39, and GH52 ß-xylosidases from Bacillus halodurans C-125 Toward Substituted Xylooligosaccharides.

Substrate specificities of glycoside hydrolase families 8 (Rex), 39 (BhXyl39), and 52 (BhXyl52) ß-xylosidases from Bacillus halodurans C-125 were investigated. BhXyl39 hydrolyzed xylotriose most efficiently among the linear xylooligosaccharides. The activity decreased in the order of xylohexaose > xylopentaose > xylotetraose and it had little effect on xylobiose. In contrast, BhXyl52 hydrolyzed xylobiose and xylotriose most efficiently, and its activity decreased when the main chain became longer as follows: xylotetraose > xylopentaose > xylohexaose. Rex produced O-ß-D-xylopyranosyl-(1 → 4)-[O-α-L-arabinofuranosyl-(1 → 3)]-O-ß-D-xylopyranosyl-(1 → 4)-ß-D-xylopyranose (Ara2Xyl3) and O-ß-D-xylopyranosyl-(1 → 4)-[O-4-O-methyl-α-D-glucuronopyranosyl-(l → 2)]-ß-D-xylopyranosyl-(1 → 4)-ß-D-xylopyranose (MeGlcA2Xyl3), which lost a xylose residue from the reducing end of O-ß-D-xylopyranosyl-(1 → 4)-[O-α-L-arabinofuranosyl-(1 → 3)]-O-ß-D-xylopyranosyl-(1 → 4)-ß-D-xylopyranosyl-(1 → 4)-ß-D-xylopyranose (Ara3Xyl4) and O-ß-D-xylopyranosyl-(1 → 4)-[O-4-O-methyl-α-D-glucuronopyranosyl-(1 → 2)]-ß-D-xylopyranosyl-(1 → 4)-ß-D-xylopyranosyl-(1 → 4)-ß-D-xylopyranose (MeGlcA3Xyl4). It was considered that there is no space to accommodate side chains at subsite -1. BhXyl39 rapidly hydrolyzes the non-reducing-end xylose linkages of MeGlcA3Xyl4, while the arabinose branch does not significantly affect the enzyme activity because it degrades Ara3Xyl4 as rapidly as unmodified xylotetraose. The model structure suggested that BhXyl39 enhanced the activity for MeGlcA3Xyl4 by forming a hydrogen bond between glucuronic acid and Lys265. BhXyl52 did not hydrolyze Ara3Xyl4 and MeGlcA3Xyl4 because it has a narrow substrate binding pocket and 2- and 3-hydroxyl groups of xylose at subsite +1 hydrogen bond to the enzyme.

Evaluation of Ammonia Pretreatment for Enzymatic Hydrolysis of Sugarcane Bagasse to Recover Xylooligosaccharides.

Sugarcane bagasse is a useful biomass resource. In the present study, we examined the efficacy of ammonia pretreatment for selective release of hemicellulose from bagasse. Pretreatment of bagasse with aqueous ammonia resulted in significant loss of xylan. In contrast, pretreatment of bagasse with anhydrous ammonia resulted in almost no xylan loss. Aqueous ammonia or anhydrous ammonia-pretreated bagasse was then subjected to enzymatic digestion with a xylanase from the glycoside hydrolase (GH) family 10 or a xylanase from the GH family 11. The hydrolysis rate of xylan in bagasse pretreated with aqueous ammonia was approximately 50 %. In contrast, in the anhydrous ammonia-treated bagasse, xylan hydrolysis was > 80 %. These results suggested that anhydrous ammonia pretreatment would be an effective method for preparation of sugarcane bagasse for enzymatic hydrolysis to recover xylooligosaccharides.

Functional Characterization of the GH10 and GH11 Xylanases from Streptomyces olivaceoviridis E-86 Provide Insights into the Advantage of GH11 Xylanase in Catalyzing Biomass Degradation.

We functionally characterized the GH10 xylanase (SoXyn10A) and the GH11 xylanase (SoXyn11B) derived from the actinomycete Streptomyces olivaceoviridis E-86. Each enzyme exhibited differences in the produced reducing power upon degradation of xylan substrates. SoXyn10A produced higher reducing power than SoXyn11B. Gel filtration of the hydrolysates generated by both enzymes revealed that the original substrate was completely decomposed. Enzyme mixtures of SoXyn10A and SoXyn11B produced the same level of reducing power as SoXyn10A alone. These observations were in good agreement with the composition of the hydrolysis products. The hydrolysis products derived from the incubation of soluble birchwood xylan with a mixture of SoXyn10A and SoXyn11B produced the same products as SoXyn10A alone with similar compositions. Furthermore, the addition of SoXyn10A following SoXyn11B-mediated digestion of xylan produced the same products as SoXyn10A alone with similar compositions. Thus, it was hypothesized that SoXyn10A could degrade xylans to a smaller size than SoXyn11B. In contrast to the soluble xylans as the substrate, the produced reducing power generated by both enzymes was not significantly different when pretreated milled bagasses were used as substrates. Quantification of the pentose content in the milled bagasse residues after the enzyme digestions revealed that SoXyn11B hydrolyzed xylans in pretreated milled bagasses much more efficiently than SoXyn10A. These data suggested that the GH10 xylanases can degrade soluble xylans smaller than the GH11 xylanases. However, the GH11 xylanases may be more efficient at catalyzing xylan degradation in natural environments (e.g. biomass) where xylans interact with celluloses and lignins.