Tomoko Maehara

Crystal Structure of an Exo-1,5-α-l-arabinofuranosidase from Streptomyces avermitilis Provides Insights into the Mechanism of Substrate Discrimination between Exo- and Endo-type Enzymes in Glycoside Hydrolase Family 43

Exo-1,5-α-l-arabinofuranosidases belonging to glycoside hydrolase family 43 have strict substrate specificity. These enzymes hydrolyze only the α-1,5-linkages of linear arabinan and arabino-oligosaccharides in an exo-acting manner. The enzyme from Streptomyces avermitilis contains a core catalytic domain belonging to glycoside hydrolase family 43 and a C-terminal arabinan binding module belonging to carbohydrate binding module family 42. We determined the crystal structure of intact exo-1,5-α-l-arabinofuranosidase. The catalytic module is composed of a 5-bladed β-propeller topologically identical to the other family 43 enzymes. The arabinan binding module had three similar subdomains assembled against one another around a pseudo-3-fold axis, forming a β-trefoil-fold. A sugar complex structure with α-1,5-l-arabinofuranotriose revealed three subsites in the catalytic domain, and a sugar complex structure with α-l-arabinofuranosyl azide revealed three arabinose-binding sites in the carbohydrate binding module. A mutagenesis study revealed that substrate specificity was regulated by residues Asn-159, Tyr-192, and Leu-289 located at the aglycon side of the substrate-binding pocket. The exo-acting manner of the enzyme was attributed to the strict pocket structure of subsite −1, formed by the flexible loop region Tyr-281–Arg-294 and the side chain of Tyr-40, which occupied the positions corresponding to the catalytic glycon cleft of GH43 endo-acting enzymes.

Use of whole crop sorghums as a raw material in consolidated bioprocessing bioethanol production using Flammulina velutipes.

The possibility of using two kinds of sorghum as raw materials in consolidated bioprocessing bioethanol production using Flammulina velutipes was investigated. Enzymatic saccharification of sweet sorghum was not as high as in brown mid-rib (bmr) mutated sorghum, but the amount of ethanol production was higher. Ethanol production from bmr mutated sorghum significantly increased when saccharification enzymes were added to the culture.

The Structure of a Streptomyces avermitilis α-l-Rhamnosidase Reveals a Novel Carbohydrate-binding Module CBM67 within the Six-domain Arrangement

Background: α-l-Rhamnosidase hydrolyzes α-linked l-rhamnose from rhamnoglycosides or polysaccharides. Results: The crystal structure of Streptomyces avermitilis α-l-rhamnosidase belonging to glycoside hydrolase family 78 was determined. Conclusion: The l-rhamnose complexed structure revealed the catalytic mechanism of the enzyme and a calcium-dependent carbohydrate-binding module. Significance: Efficient catalysis of an exo-rhamnosidase requires a novel carbohydrate-binding module that binds terminal l-rhamnose sugars. α-l-Rhamnosidases hydrolyze α-linked l-rhamnosides from oligosaccharides or polysaccharides. We determined the crystal structure of the glycoside hydrolase family 78 Streptomyces avermitilis α-l-rhamnosidase (SaRha78A) in its free and l-rhamnose complexed forms, which revealed the presence of six domains N, D, E, F, A, and C. In the ligand complex, l-rhamnose was bound in the proposed active site of the catalytic module, revealing the likely catalytic mechanism of SaRha78A. Glu636 is predicted to donate protons to the glycosidic oxygen, and Glu895 is the likely catalytic general base, activating the nucleophilic water, indicating that the enzyme operates through an inverting mechanism. Replacement of Glu636 and Glu895 resulted in significant loss of α-rhamnosidase activity. Domain D also bound l-rhamnose in a calcium-dependent manner, with a KD of 135 μm. Domain D is thus a non-catalytic carbohydrate binding module (designated SaCBM67). Mutagenesis and structural data identified the amino acids in SaCBM67 that target the features of l-rhamnose that distinguishes it from the other major sugars present in plant cell walls. Inactivation of SaCBM67 caused a substantial reduction in the activity of SaRha78A against the polysaccharide composite gum arabic, but not against aryl rhamnosides, indicating that SaCBM67 contributes to enzyme function against insoluble substrates.

Ethanol production from high cellulose concentration by the basidiomycete fungus Flammulina velutipes

Ethanol production by Flammulina velutipes from high substrate concentrations was evaluated. F. velutipes produces approximately 40-60 g l(-1) ethanol from 15% (w/v) D-glucose, D-fructose, D-mannose, sucrose, maltose, and cellobiose, with the highest conversion rate of 83% observed using cellobiose as a carbon source. We also attempted to assess direct ethanol fermentation from sugarcane bagasse cellulose (SCBC) by F. velutipes. The hydrolysis rate of 15% (w/v) SCBC with commercial cellulase was approximately 20%. In contrast, F. velutipes was able to produce a significant amount of ethanol from 15% SCBC with the production of β-glucosidase, cellobohydrolase, and cellulase, although the addition of a small amount of commercial cellulase to the culture was required for the conversion. When 9 mg g(-1) biomass of commercial cellulase was added to cultures, 0.36 g of ethanol was produced from 1 g of cellulose, corresponding to an ethanol conversion rate of 69.6%. These results indicate that F. velutipes would be useful for consolidated bioprocessing of lignocellulosic biomass to bioethanol.

Crystal structure and characterization of the glycoside hydrolase family 62 α-L-arabinofuranosidase from Streptomyces coelicolor

Background: Glycoside hydrolase family 62 α-l-arabinofuranosidases specifically release l-arabinose from arabinoxylan. Results: The crystal structure of glycoside hydrolase family 62 α-l-arabinofuranosidase from Streptomyces coelicolor was determined. Conclusion: l-Arabinose and xylohexaose complexed structures revealed the mechanism of substrate specificity of this enzyme. Significance: Efficient catalysis by glycoside hydrolase family 62 α-l-arabinofuranosidase requires its binding to terminal xylose sugars at the substrate-binding cleft. α-l-Arabinofuranosidase, which belongs to the glycoside hydrolase family 62 (GH62), hydrolyzes arabinoxylan but not arabinan or arabinogalactan. The crystal structures of several α-l-arabinofuranosidases have been determined, although the structures, catalytic mechanisms, and substrate specificities of GH62 enzymes remain unclear. To evaluate the substrate specificity of a GH62 enzyme, we determined the crystal structure of α-l-arabinofuranosidase, which comprises a carbohydrate-binding module family 13 domain at its N terminus and a catalytic domain at its C terminus, from Streptomyces coelicolor. The catalytic domain was a five-bladed β-propeller consisting of five radially oriented anti-parallel β-sheets. Sugar complex structures with l-arabinose, xylotriose, and xylohexaose revealed five subsites in the catalytic cleft and an l-arabinose-binding pocket at the bottom of the cleft. The entire structure of this GH62 family enzyme was very similar to that of glycoside hydrolase 43 family enzymes, and the catalytically important acidic residues found in family 43 enzymes were conserved in GH62. Mutagenesis studies revealed that Asp202 and Glu361 were catalytic residues, and Trp270, Tyr461, and Asn462 were involved in the substrate-binding site for discriminating the substrate structures. In particular, hydrogen bonding between Asn462 and xylose at the nonreducing end subsite +2 was important for the higher activity of substituted arabinofuranosyl residues than that for terminal arabinofuranoses.

Properties of Ethanol Fermentation by Flammulina velutipes

Basidiomycetes have the ability to degrade lignocellulosic biomass, and some basidiomycetes produce alcohol dehydrogenase. These characteristics may be useful in the direct production of ethanol from lignocellulose. Ethanol fermentation by basidiomycetes was investigated to examine the possibility of ethanol production by consolidated bioprocessing (CBP) using Flammulina velutipes. F. velutipes converted D-glucose to ethanol with a high efficiency (a theoretical ethanol recovery rate of 88%), but ethanol production from pentose was not observed. These properties of F. velutipes are similar to those of Saccharomyces cerevisiae, but the basidiomycete converted not only sucrose, but also maltose, cellobiose, cellotriose, and cellotetraose to ethanol, with almost the same efficiency as that for D-glucose. From these results, we concluded that F. velutipes possesses advantageous characteristics for use in CBP.

Development of a gene transfer system for the mycelia of Flammulina velutipes Fv-1 strain.

To develop a gene transformation method for Flammulina velutipes, we constructed a vector with hph gene under control of the trp1 gene promoter. The vector was integrated into protoplast derived from mycelia by the calcium-polyethylene glycol method, as it has not been reported for F. velutipes. Transformation efficiency was much improved when transformation was performed by the restriction enzyme mediated integration method.

Effect of lime pretreatment of brown midrib sorghums.

The effect of lime pretreatment of brown midrib sorghums on enzymatic saccharification was investigated. Under most of the pretreatment conditions, the saccharification yields of bmrs were higher than those of the normal counterparts. This result suggests that bmr is useful to reduce pretreatment costs, because the amount of lime necessary for the pretreatment of biomass can reduced by using bmr mutants.

Improvement of the transformation efficiency of Flammulina velutipes Fv-1 using the glyceraldehyde-3-phosphate dehydrogenase gene promoter.

To improve the expression level of heterologous genes in Flammulina velutipes Fv-1, we constructed new vectors having glyceraldehydes-3-phosphate dehydrogenase (gpd) gene promoter to control the expression of target genes. When the hygromycin B phosphotransferase (hph) gene from Escherichia coli was controlled by the gpd promoter, transformation efficiency was 3-fold higher than the case of that controlled by the tryptophan synthetase gene (trp1) promoter.

Expression of Arabidopsis thaliana xylose isomerase gene and its effect on ethanol production in Flammulina velutipes

To improve the pentose fermentation rate in Flammulina velutipes, the putative xylose isomerase (XI) gene from Arabidopsis thaliana was cloned and introduced into F. velutipes and the gene expression was evaluated in transformants. mRNA expression of the putative XI gene and XI activity were observed in two transformants, indicating that the putative gene from A. thaliana was successfully expressed in F. velutipes as a xylose isomerase. In addition, ethanol production from xylose was increased in the recombinant strains. This is the first report demonstrating the possibility of using plant genes as candidates for improving the characteristics of F. velutipes.