Isolated fungal cellulose terminal domains and a synthetic minimum analogue bind to cellulose

Trichoderma reesei Dehydrogenase, a Pyrroloquinoline Quinone-Dependent Member of Auxiliary Activity Family 12 of the Carbohydrate-Active Enzymes Database: Functional and Structural Characterization

Pyrroloquinoline quinone (PQQ) is an ortho-quinone cofactor of several prokaryotic oxidases. Widely available in the diet and necessary for the correct growth of mice, PQQ has been suspected to be a vitamin for eukaryotes. However, no PQQ-dependent eukaryotic enzyme had been identified to use the PQQ until 2014, when a basidiomycete enzyme catalyzing saccharide dehydrogenation using PQQ as a cofactor was characterized and served to define auxiliary activity family 12 (AA12). Here we report the biochemical characterization of the AA12 enzyme encoded by the genome of the ascomycete Trichoderma reesei (TrAA12). Surprisingly, only weak activity against uncommon carbohydrates like l-fucose or d-arabinose was measured. The three-dimensional structure of TrAA12 reveals important similarities with bacterial soluble glucose dehydrogenases (sGDH). The enzymatic characterization and the structure solved in the presence of calcium confirm the importance of this ion in catalysis, as observed for sGDH. The structural characterization of TrAA12 was completed by modeling PQQ and l-fucose in the enzyme active site. Based on these results, the AA12 family of enzymes is likely to have a catalytic mechanism close to that of bacterial sGDH.IMPORTANCE Pyrroloquinoline quinone (PQQ) is an important cofactor synthesized by prokaryotes and involved in enzymatic alcohol and sugar oxidation. In eukaryotes, the benefit of PQQ as a vitamin has been suggested but never proved. Recently, the first eukaryotic enzyme using PQQ was characterized in the basidiomycete Coprinopsis cinerea, demonstrating that fungi are able to use PQQ as an enzyme cofactor. This discovery led to the classification of the fungal PQQ-dependent enzymes in auxiliary activity family 12 (AA12) of the Carbohydrate-Active Enzymes (CAZy) database (www.cazy.org) classification. In the present paper, we report on the characterization of the ascomycete AA12 enzyme from Trichoderma reesei (TrAA12). Our enzymatic and phylogenetic results show divergence with the only other member of the family characterized, that from the basidiomycete Coprinopsis cinerea The crystallographic structure of TrAA12 shows similarities to the global active-site architecture of bacterial glucose dehydrogenases, suggesting a common evolution between the two families.

Molecular-scale features that govern the effects of O-glycosylation on a carbohydrate-binding module

Protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. Going forward, this study suggests the possibility of designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.

Specificity of O-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules

The majority of biological turnover of lignocellulosic biomass in nature is conducted by fungi, which commonly use Family 1 carbohydrate-binding modules (CBMs) for targeting enzymes to cellulose. Family 1 CBMs are glycosylated, but the effects of glycosylation on CBM function remain unknown. Here, the effects of O-mannosylation are examined on the Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase at three glycosylation sites. To enable this work, a procedure to synthesize glycosylated Family 1 CBMs was developed. Subsequently, a library of 20 CBMs was synthesized with mono-, di-, or trisaccharides at each site for comparison of binding affinity, proteolytic stability, and thermostability. The results show that, although CBM mannosylation does not induce major conformational changes, it can increase the thermolysin cleavage resistance up to 50-fold depending on the number of mannose units on the CBM and the attachment site. O-Mannosylation also increases the thermostability of CBM glycoforms up to 16 °C, and a mannose disaccharide at Ser3 seems to have the largest themostabilizing effect. Interestingly, the glycoforms with small glycans at each site displayed higher binding affinities for crystalline cellulose, and the glycoform with a single mannose at each of three positions conferred the highest affinity enhancement of 7.4-fold. Overall, by combining chemical glycoprotein synthesis and functional studies, we show that specific glycosylation events confer multiple beneficial properties on Family 1 CBMs.

Effects of sulfate groups on the adsorption and activity of cellulases on cellulose substrates

Pretreatment of lignocellulosic biomass with sulfuric acid may leave sulfate groups on its surface that may hinder its biochemical conversion. This study investigates the effects of sulfate groups on cellulase adsorption onto cellulose substrates and the enzymatic hydrolysis of these substrates. Substrates with different sulfate group densities were prepared from H2SO4- and HCl-hydrolyzed and partially and fully desulfated cellulose nanocrystals. Adsorption onto and hydrolysis of the substrates was analyzed by quartz crystal microbalance with dissipation monitoring (QCM-D). The surface roughness of the substrates, measured by atomic force microscopy, increased with decreasing sulfate group density, but their surface accessibilities, measured by QCM-D H2O/D2O exchange experiments, were similar. The adsorption of cellulose binding domains onto sulfated substrates decreased with increasing sulfate group density, but the adsorption of cellulases increased. The rate of hydrolysis of sulfated substrates decreased with increasing sulfate group density. The results indicated an inhibitory effect of sulfate groups on the enzymatic hydrolysis of cellulose, possibly due to nonproductive binding of the cellulases onto the substrates through electrostatic interactions instead of their cellulose binding domains.

Visualization of cellobiohydrolase I from Trichoderma reesei moving on crystalline cellulose using high-speed atomic force microscopy

Cellulases hydrolyze β-1,4-glucosidic linkages of insoluble cellulose at the solid/liquid interface, generating soluble cellooligosaccharides. We describe here our method for real-time observation of the behavior of cellulase molecules on the substrate, using high-speed atomic force microscopy (HS-AFM). When glycoside hydrolase family 7 cellobiohydrolase from Trichoderma reesei (TrCel7A) was incubated with crystalline cellulose, many enzyme molecules were observed to move unidirectionally on the surface of the substrate by HS-AFM. The velocity of the moving molecules of TrCel7A on cellulose I crystals was estimated by means of image analysis.

Activation of crystalline cellulose to cellulose IIII results in efficient hydrolysis by cellobiohydrolase

The crystalline polymorphic form of cellulose (cellulose I(alpha)-rich) of the green alga, Cladophora, was converted into cellulose III(I) and I(beta) by supercritical ammonium and hydrothermal treatments, respectively, and the hydrolytic rate and the adsorption of Trichoderma viride cellobiohydrolase I (Cel7A) on these products were evaluated by a novel analysis based on the surface density of the enzyme. Cellobiose production from cellulose III(I) was more than 5 times higher than that from cellulose I. However, the amount of enzyme adsorbed on cellulose III(I) was less than twice that on cellulose I, and the specific activity of the adsorbed enzyme for cellulose III(I) was more than 3 times higher than that for cellulose I. When cellulose III(I) was converted into cellulose I(beta) by hydrothermal treatment, cellobiose production was dramatically decreased, although no significant change was observed in enzyme adsorption. This clearly indicates that the enhanced hydrolysis of cellulose III(I) is related to the structure of the crystalline polymorph. Thus, supercritical ammonium treatment activates crystalline cellulose for hydrolysis by cellobiohydrolase.

Surface density of cellobiohydrolase on crystalline celluloses

The enzymatic kinetics of glycoside hydrolase family 7 cellobiohydrolase (Cel7A) towards highly crystalline celluloses at the solid-liquid interface was evaluated by applying the novel concept of surface density (rho) of the enzyme, which is defined as the amount of adsorbed enzyme divided by the maximum amount of adsorbed enzyme. When the adsorption levels of Trichoderma viride Cel7A on cellulose I(alpha) from Cladophora and cellulose I(beta) from Halocynthia were compared, the maximum adsorption of the enzyme on cellulose I(beta) was approximately 1.5 times higher than that on cellulose I(alpha), although the rate of cellobiose production from cellulose I(beta) was lower than that from cellulose I(alpha). This indicates that the specific activity (k) of Cel7A adsorbed on cellulose I(alpha) is higher than that of Cel7A adsorbed on cellulose I(beta). When k was plotted versus rho, a dramatic decrease of the specific activity was observed with the increase of surface density (rho-value), suggesting that overcrowding of enzyme molecules on a cellulose surface lowers their activity. An apparent difference of the specific activity was observed between crystalline polymorphs, i.e. the specific activity for cellulose I(alpha) was almost twice that for cellulose I(beta). When cellulose I(alpha) was converted to cellulose I(beta) by hydrothermal treatment, the specific activity of Cel7A decreased and became similar to that of native cellulose I(beta) at the same rho-value. These results indicate that the hydrolytic activity (rate) of bound Cel7A depends on the nature of the crystalline cellulose polymorph, and an analysis that takes surface density into account is an effective means to evaluate cellulase kinetics at a solid-liquid interface.

The active component in the flax-retting system of the zygomycete Rhizopus oryzae sb is a family 28 polygalacturonase

The zygomycete Rhizopus oryzae sb is a very efficient organism for retting of flax, the initial microbiological step in the process of making linen. An extracellular polygalacturonase, when isolated could perform retting, and therefore probably is the key component in the retting system of R. oryzae. This was purified and characterized. The purified enzyme has a molecular mass of 37,436 Da from mass spectrometric determination, an isoelectric point of 8.4, and has non-methylated polygalacturonic acid as its preferred substrate. Peptide sequences indicate that the enzyme belongs to family 28, in similarity with other polygalacturonases (EC. 3.2.1.15). It contains, however an N-terminal sequence absent in other fungal pectinases, but present in an enzyme from the phytopathogenic bacterium Ralstonia solanacearum. The biochemical background for the superior retting efficiency of R. oryzae sb is discussed.

Recent developments on cellulases and carbohydrate-binding modules with cellulose affinity

This review concerns basic research on cellulases and cellulose-specific carbohydrate-binding modules (CBMs). As a background, glycosyl hydrolases are also briefly reviewed. The nomenclature of cellulases and CBMs is discussed. The main cellulase-producing organisms and their cellulases are described. Synergy, enantioseparation, cellulases in plants, cellulosomes, cellulases and CBMs as analytical tools and cellulase-like enzymes are also briefly reviewed.

Monocomponent endoglucanase treatment increases the reactivity of softwood sulphite dissolving pulp

Softwood dissolving pulp was treated with a commercial monocomponent fungal endocellulase. The reactivity of the pulp for the production of rayon and cellulose derivatives as determined with the Fock method increased drastically with relatively low amounts of enzyme, and the yield loss and decrease of viscosity were moderate. The mechanism behind the increased reactivity is discussed.

Cloning and Characterization of the Xyn11A Gene from Lentinula edodes

Hemicellulose represents a rich source of biomass that can be converted into useful chemical feedstocks. One of the main components of hemicellulose is xylan, a polymer of xylose residues. Xylanase enzymes that hydrolyze xylan are therefore of great commercial interest. We have cloned a gene (xyn11A) that encodes a 283-amino acid xylanase enzyme from the fungus Lentinula edodes. The enzyme has a pI of 4.6 and belongs to the highly conserved glycosyl hydrolase family 11. The xylanase gene was cloned into a Pichia pastoris expression vector that secretes active enzyme into both solid and liquid media. The optimal reaction conditions were at pH 4.5 and 50 degrees C. The enzyme had a Km of 1.5 mg/ml and a Vmax of 2.1 mmol/min/mg. Xyn11A produced primarily xylobiose, xylotriose, and xylotetraose from a birchwood xylan substrate. This is the first report on the cloning of a hemicellulase gene from L. edodes.

Isolation, characterization and manipulation of cellulase genes

The complete hydrolysis of cellulose requires a number of different enzymes including endoglucanase, exoglucanase and beta-glucosidase. These enzymes function in concert as part of a 'cellulase'complex called a cellulosome. In order (i) to develop a better understanding of the biochemical nature of the cellulase complex as well as the genetic regulation of its integral components and (ii) to utilize cellulases either as purified enzymes or as part of an engineered organism for a variety of purposes, researchers have, as a first step, used recombinant DNA technology to isolate the genes for these enzymes from a variety of organisms. This review provides some perspective on the current status of the isolation, characterization and manipulation of cellulase genes and specifically discusses (i) strategies for the isolation of endoglucanase, exoglucanase and beta-glucosidase genes; (ii) DNA sequence characterization of the cellulase genes and their accompanying regulatory elements; (iii) the expression of cellulase genes in heterologous host organisms and (iv) some of the proposed uses for isolated cellulase genes.

Cloning and characterization of two cellulase genes from Lentinula edodes

Lentinula edodes has traditionally been grown on fallen logs. It produces a wide array of enzymes to digest the lignocellulolytic substrate for nutrients. Thus, this organism represents a rich source of potentially potent lignocellulolytic enzymes that can be harnessed for conversion of biomass to simple sugars. These sugars can then be used as feedstock for ethanol production or other chemical syntheses. We have cloned two cellulase genes from L. edodes grown on a wood substrate without the use of genomic or cDNA libraries by using a PCR-based strategy employing degenerate primers directed at the cellulose-binding domain. cel7A encoded a 516-amino acid protein that belonged to glycosyl hydrolase family 7 and had sequence similarities to cbhI genes from other fungi. cel6B encoded a 444-amino acid protein that belonged to glycosyl hydrolase family 6 and had sequence similarities to cbhII genes from other fungi. We demonstrated that cel7A and cel6B transcript levels were positively correlated to L. edodes growth in the presence of crystalline cellulose.

Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 A resolution and homology models of the isozymes

Cellobiohydrolase 58 (Cel7D) is the major cellulase produced by the white-rot fungus Phanerochaete chrysosporium, constituting approximately 10 % of the total secreted protein in liquid culture on cellulose. The enzyme is classified into family 7 of the glycosyl hydrolases, together with cellobiohydrolase I (Cel7A) and endoglucanase I (Cel7B) from Trichoderma reesei. Like those enzymes, it catalyses cellulose hydrolysis with net retention of the anomeric carbon configuration. The structure of the catalytic module (431 residues) of Cel7D was determined at 3.0 A resolution using the structure of Cel7A from T. reesei as a search model in molecular replacement, and ultimately refined at 1.32 A resolution. The core structure is a beta-sandwich composed of two large and mainly antiparallel beta-sheets packed onto each other. A long cellulose-binding groove is formed by loops on one face of the sandwich. The catalytic residues are conserved and the mechanism is expected to be the same as for other family members. The Phanerochaete Cel7D binding site is more open than that of the T. reesei cellobiohydrolase, as a result of deletions and other changes in the loop regions, which may explain observed differences in catalytic properties. The binding site is not, however, as open as the groove of the corresponding endoglucanase. A tyrosine residue at the entrance of the tunnel may be part of an additional subsite not present in the T. reesei cellobiohydrolase. The Cel7D structure was used to model the products of the five other family 7 genes found in P. chrysosporium. The results suggest that at least two of these will have differences in specificity and possibly catalytic mechanism, thus offering some explanation for the presence of Cel7 isozymes in this species, which are differentially expressed in response to various growth conditions.

Mechanism of substrate inhibition in cellulose synergistic degradation

A comprehensive experimental study of substrate inhibition in cellulose hydrolysis based on a well defined system is presented. The hydrolysis of bacterial cellulose by synergistically operating binary mixtures of cellobiohydrolase I from Trichoderma reesei and five different endoglucanases as well as their catalytic domains displays a characteristic substrate inhibition. This inhibition phenomenon is shown to require the two-domain structure of an intact cellobiohydrolase. The experimental data were in accordance with a mechanism where cellobiohydrolases previously bound to the cellulose by means of their cellulose binding domains are able to find chain ends by lateral diffusion. An increased substrate concentration at a fixed enzyme load will also increase the average diffusion distance/time needed for cellobiohydrolases to reach new chain ends created by endoglucanases, resulting in an apparent substrate inhibition of the synergistic action. The connection between the binding properties and the substrate inhibition is encouraging with respect to molecular engineering of the binding domain for optimal performance in biotechnological processes.

Cellulose-binding modules from extracellular matrix proteins of Dictyostelium discoideum stalk and sheath

Cellulose-binding modules (CBMs) of two extracellular matrix proteins, St15 and ShD, from the slime mold Dictyostelium discoideum were expressed in Escherichia coli. The expressed proteins were purified to > 98% purity by extracting inclusion bodies at pH 11.5 and refolding proteins at pH 7.5. The two refolded CBMs bound tightly to amorphous phosphoric acid swollen cellulose (PASC), but had a low affinity toward xylan. Neither protein exhibited cellulase activity. St15, the stalk-specific protein, had fourfold higher binding affinity toward microcrystalline cellulose (Avicel) than the sheath-specific ShD CBM. St15 is unusual in that it consists of a solitary CBM homologous to family IIa CBMs. Sequence analysis of ShD reveals three putative domains containing: (a) a C-terminal CBM homologous to family IIb CBMs; (b) a Pro/Thr-rich linker domain; and (c) a N-terminal Cys-rich domain. The biological functions and potential role of St15 and ShD in building extracellular matrices during D. discoideum development are discussed.

Solution structure and conformational changes of the Streptomyces chitin-binding protein (CHB1)

The shape and overall dimensions of the recently discovered Streptomyces alpha-chitin-binding protein, CHB1, were investigated by synchrotron radiation X-ray solution scattering. The radius of gyration and the maximum size of CHB1 were determined to be 1.75 +/- 0.03 nm and 6.0 +/- 0.2 nm, respectively. Using two independent ab initio approaches the low-resolution shape of the protein was found to consist of two domains, an elongated main globule with a length of about 4 nm and a foot-like domain of about 2 nm width. The structural and functional properties of CHB1 depend strongly on the presence of disulfide bonds; upon their reduction, the protein loses its affinity to chitin.

Endoglucanase 28 (Cel12A), a new Phanerochaete chrysosporium cellulase

A 28-kDa endoglucanase was isolated from the culture filtrate of Phanerochaete chrysosporium strain K3 and named EG 28. It degrades carboxymethylated cellulose and amorphous cellulose, and to a lesser degree xylan and mannan but not microcrystalline cellulose (Avicel). EG 28 is unusual among cellulases from aerobic fungi, in that it appears to lack a cellulose-binding domain and does not bind to crystalline cellulose. The enzyme is efficient at releasing short fibres from filter paper and mechanical pulp, and acts synergistically with cellobiohydrolases. Its mode of degrading filter paper appears to be different to that of endoglucanase I from Trichoderma reesei. Furthermore, EG 28 releases colour from stained cellulose beads faster than any other enzyme tested. Peptide mapping suggests that it is not a fragment of another known endoglucanases from P. chrysosporium and peptide sequences indicate that it belongs to family 12 of the glycosyl hydrolases. EG 28 is glycosylated. The biological function of the enzyme is discussed, and it is hypothesized that it is homologous to EG III in Trichoderma reesei and the role of the enzyme is to make the cellulose in wood more accessible to other cellulases.

Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage

Knottins are a group of small, disulphide-bonded proteins that bind with high specificity to their target molecules. These proteins appear to use different faces of the protein for their interactions with different targets. Here, we attempted to create knottins with novel binding activities based on the cellulose-binding domain of the fungal enzyme cellobiohydrolase I. Variation was introduced to the face of the protein that binds cellulose. Seven residues, which are located in two regions of the polypeptide chain and form a patch of about 400 A2 on the protein surface, were simultaneously varied by random mutation of the gene. The repertoire was cloned for display on filamentous bacteriophage (5.5 x 10(8) clones), and selected for binding to cellulose or to one of three enzymes (alpha-amylase, alkaline phosphatase and beta-glucuronidase). We thereby isolated variant knottins against cellulose (differing in sequence from the parent knottin) and also against alkaline phosphatase. The binding to (glycosylated) alkaline phosphatase was highly specific with an affinity of about 10 microM, required the presence of disulphide bonds and was mediated through protein (rather than carbohydrate) contacts. Knottin scaffolds therefore appear to be a promising architecture for the creation of small folded proteins with binding activities, with the potential for improvement of binding affinities by mutation, or of using other faces of the protein to provide greater structural diversity in the primary repertoire.

Detection of cellulose with improved specificity using laser-based instruments

Specific detection of cellulose has not been possible using laser based instruments such as laser scanning confocal microscopes (LSCM) and fluorescently activated cell sorters (FACS). Common cellulose dyes are nonspecific and/or nonexcitable with common lasers. Furthermore, many lasers emit wavelengths that overlap with autofluorescence from chlorophyll and other plant molecules. We demonstrate that a cellulase and an isolated bacterial cellulose binding domain (CBD) conjugated to fluorescent dyes can be used for laser detection of cellulose with improved specificity. Cell walls of differentiating tracheary elements and spores of Dictyostelium discoideum were tested in this study. For double labeling, autofluorescence interfering with the rhodamine signal was eliminated by collecting each excitation channel separately followed by computer recombination or by using a narrow band pass barrier filter allowing simultaneous channel collection. Using these methods, cellulose and microtubules tagged with a monoclonal antibody to alpha-tubulin were effectively colocalized in chlorophyll-containing tracheary elements using a LSCM. Also, Dictyostelium discoideum spores labeled or unlabeled with CBD-FITC were separated into two populations by FACS indicating that this tag should be useful in future mutagenesis experiments. Therefore, the presence or absence of cellulose can now be analyzed using common lasers.

Characterization of a double cellulose-binding domain. Synergistic high affinity binding to crystalline cellulose

Most cellulose-degrading enzymes have a two-domain structure that consists of a catalytic and a cellulose-binding domain (CBD) connected by a linker region. The linkage and the interactions of the two domains represent one of the key questions for the understanding of the function of these enzymes. The CBDs of fungal cellulases are small peptides folding into a rigid, disulfide-stabilized structure that has a distinct cellulose binding face. Here we describe properties of a recombinant double CBD, constructed by fusing the CBDs of two Trichoderma reesei cellobiohydrolases via a linker peptide similar to the natural cellulase linkers. After expression in Escherichia coli, the protein was purified from the culture medium by reversed phase chromatography and the individual domains obtained by trypsin digestion. Binding of the double CBD and its single CBD components was investigated on different types of cellulose substrates as well as chitin. Under saturating conditions, nearly 20 micromol/g of the double CBD was bound onto microcrystalline cellulose. The double CBD exhibited much higher affinity on cellulose than either of the single CBDs, indicating an interplay between the two components. A two-step model is proposed to explain the binding behavior of the double CBD. A similar interplay between the domains in the native enzyme is suggested for its binding to cellulase.

The difference in affinity between two fungal cellulose-binding domains is dominated by a single amino acid substitution

Cellulose-binding domains (CBDs) form distinct functional units of most cellulolytic enzymes. We have compared the cellulose-binding affinities of the CBDs of cellobiohydrolase I (CBHI) and endoglucanase I (EGI) from the fungus Trichoderma reesei. The CBD of EGI had significantly higher affinity than that of CBHI. Four variants of the CBHI CBD were made in order to identify the residues responsible for the increased affinity in EGI. Most of the difference could be ascribed to a replacement of a tyrosine by a tryptophan on the flat cellulose-binding face.

Identification of functionally important amino acids in the cellulose-binding domain of Trichoderma reesei cellobiohydrolase I

Cellobiohydrolase I (CBHI) of Trichoderma reesei has two functional domains, a catalytic core domain and a cellulose binding domain (CBD). The structure of the CBD reveals two distinct faces, one of which is flat and the other rough. Several other fungal cellulolytic enzymes have similar two-domain structures, in which the CBDs show a conserved primary structure. Here we have evaluated the contributions of conserved amino acids in CBHI CBD to its binding to cellulose. Binding isotherms were determined for a set of six synthetic analogues in which conserved amino acids were substituted. Two-dimensional NMR spectroscopy was used to assess the structural effects of the substitutions by comparing chemical shifts, coupling constants, and NOEs of the backbone protons between the wild-type CBD and the analogues. In general, the structural effects of the substitutions were minor, although in some cases decreased binding could clearly be ascribed to conformational perturbations. We found that at least two tyrosine residues and a glutamine residue on the flat face were essential for tight binding of the CBD to cellulose. A change on the rough face had only a small effect on the binding and it is unlikely that this face interacts with cellulose directly.

Induced circular dichroism study of the aqueous solution complexation of cello-oligosaccharides and related polysaccharides with aromatic dyes

Acetobacter xylinum, grown in the presence of low levels of the water-soluble dye Calcofluor White ST produces a pellicle of cellulose that has no detectable crystallinity. Biological factors of this sort are probably more important than physical factors in controlling the higher order structures of celluloses. Circular dichroism (CD) is induced by complexes that are formed by specific interactions between chiral oligosaccharides and dye molecules. Using CD, equilibrium constants were measured for the association reactions between various dyes with a series of cello-oligosaccharides (n = 2-6), methylcellulose, hydroxypropylcellulose (HPC), amylose, cyclomalto-oligosaccharides (cyclodextrins), and the linear malto-oligosaccharides (n = 3-7). Possible structural features of the complexes are discussed. Dyes that are capable of binding to the higher cello-oligomers in aqueous solutions are the same dyes that modify the solid structure of bacterial cellulose. An analogy between the binding of water-soluble dyes to cello-oligosaccharides and the binding of the cellulose-degrading enzyme, cellobiohydrolase I, to cellulose is discussed.

Domain structure and multiplicity of raw-starch-digesting amylase from Bacillus circulans: extensive proteolysis with proteinase K, endopeptidase Glu-C and thermolysin

Raw-starch-digesting amylase (RSDA) is a key extracellular enzyme of mesophilic Bacillus circulans F-2 which uses raw starch granules as a carbon source. Previous work has demonstrated that there are two domains of the enzyme during digestion with subtilisin, and that RSDA activity is selectively inactivated by limited proteolysis with subtilisin, which cleaves the enzyme between these hydrolytic and adsorption domains (Kim, C.-H., Kwon, S.-T., Taniguchi, H. and Lee, D.-S. (1992) Biochim. Biophys. Acta 1122, 243-250). In this work we show that a similar phenomenon is observed during limited proteinase K, thermolysin and endopeptidase Glu-C proteolysis of the enzyme. Fragments resulting from proteolysis were characterized by immunoblotting with anti-RSDA. The proteolytic patterns resulting from proteinase K and subtilisin were the same, producing 63 and 30-kDa fragments. Similar patterns were obtained with endopeptidase Glu-C or thermolysin. All proteolytic digests contained a common, major 63-kDa fragment. Inactivation of RSDA activity results from splitting off the C-terminal domain. Hence, it seems probable that the proteinase-sensitive locus is in a hinge region susceptible to cleavage. Extracellular enzymes immunoreactive towards anti-RSDA were detected through whole bacterial cultivation. 93, 75, 63, 55, 38 and 31-kDa proteins were immunologically identical to RSDA. Of these, the 75-kDa and 63-kDa proteins correspond to the major products of proteolysis with Glu-C and thermolysin. These results suggest that enzyme heterogeneity of the raw-starch hydrolysis system might arise from the endogenous proteolytic activity of the bacterium.

Real-time kinetic analysis of limited proteolysis by ion-exchange chromatography using compressed, non-porous agarose beads

In biotechnology there is a great need for methods that can be used for kinetic studies of ongoing processes, such as limited proteolysis. Ion-exchange chromatography on a nonporous, compressed agarose matrix was used in the study presented in this paper to monitor papain cleavage of fungal cellulases. This non-porous matrix allows completion of a chromatographic analysis, with baseline resolution, within 30-60 s. Utilizing this very fast chromatographic method one can monitor a proteolysis 'continuously' by repeated chromatographic analysis of the incubation mixture and, if desired, terminate it at the optimal moment. Fractions were also collected for identification by activity assays and analytical SDS-PAGE.

Investigation of the function of mutated cellulose-binding domains of Trichoderma reesei cellobiohydrolase I

The function of the cellulose-binding domain (CBD) of the cellobiohydrolase I of Trichoderma reesei was studied by site-directed mutagenesis of two amino acid residues identified by analyzing the 3D structure of this domain. The mutant enzymes were produced in yeast and tested for binding and activity on crystalline cellulose. Mutagenesis of the tyrosine residue (Y492) located at the tip of the wedge-shaped domain to alanine or aspartate reduced the binding and activity on crystalline cellulose to the level of the core protein lacking the CBD. However, there was no effect on the activity toward small oligosaccharide (4-methylumbelliferyl beta-D-lactoside). The mutation tyrosine to histidine (Y492H) lowered but did not destroy the cellulose binding, suggesting that the interaction of the pyranose ring of the substrate with an aromatic side chain is important. However, the catalytic activity of this mutant on crystalline cellulose was identical to the other two mutants. The mutation P477R on the edge of the other face of the domain reduces both binding and activity of CBHI. These results support the hypothesis that both surfaces of the CBD are involved in the interaction of the binding domain with crystalline cellulose.

Genomic organization of a cellulase gene family in Phanerochaete chrysosporium

Southern blot and nucleotide sequence analysis of Phanerochaete chrysosporium BKM-F-1767 genomic clones indicate that this wood-degrading fungus contains at least six genes with significant homology to the Trichoderma reesei cellobiohydrolase I gene (cbh1). Using pulsed-field gel electrophoresis to separate P. chrysosporium chromosomes, the six cellulase genes were found to hybridize to at least three different chromosomes, one of which is dimorphic. The organization of these genes was similar in another P. chrysosporium strain, ME 446. It is clear that, unlike T. reesei, the most well-studied cellulolytic fungus, P. chrysosporium contains a complex, cbh1-like gene family.

Structure, organization, and transcription of a cellobiohydrolase gene cluster from Phanerochaete chrysosporium

Restriction mapping and sequence analysis of cosmid clones revealed a cluster of three cellobiohydrolase genes in Phanerochaete chrysosporium. P. chrysosporium cbh1-1 and cbh1-2 are separated by only 750 bp and are located approximately 14 kb upstream from a cellulase gene previously cloned from P. chrysosporium (P. Sims, C. James, and P. Broda, Gene 74:411-422, 1988). Within a well-conserved region, the deduced amino acid sequences of P. chrysosporium cbh1-1 and cbh1-2 are, respectively, 80 and 69% homologous to that of the Trichoderma reesei cellobiohydrolase I gene. The conserved cellulose-binding domain typical of microbial cellulases is absent from cbh1-1. Transcript levels of the three P. chrysosporium genes varied substantially, depending on culture conditions. cbh1-1 and cbh1-2 were not induced in the presence of cellulose, nor did they appear to be subject to glucose repression. Therefore, aspects of the chromosomal organization, structure, and transcription of these genes are unlike those of any previously described cellulase genes.

The 1,4-beta-D-glucan glucanohydrolases from Phanerochaete chrysosporium. Re-assessment of their significance in cellulose degradation mechanisms

A physico-chemical, functional and structural characterization, including partial sequence data, of three major 1,4-beta-D-glucan glucanohydrolases (EC. 3.2.1.4) isolated from the culture filtrate of the white-rot fungus Phanerochaete chrysosporium, shows that all three enzymes belong to a single family of cellulases. EG44, pI 4.3, (named after its apparent molecular mass in kDa), shows a clear homology with Schizopyllum commune Endoglucanase I (EGI); whereas EG38, pI 4.9, (named in the same manner) is related more closely to Trichoderma reesei (Trichoderma longibrachiatum) Endoglucanase III (EGIII). EG36, pI 5.6-5.7, is probably an EG38 protein lacking its cellulose binding domain. Strong synergistic action is induced by the enzymes acting in concert with cellobiohydrolases (CBHI and CBHII) from the same organism, indicating a highly effective enzymatic system for cellulose degradation. Controlled proteolysis with papain has allowed a so far unique cleavage of endoglucanases EG44 and EG38 into two domains: a core protein, which virtually lacks the capacity to absorb onto microcrystal-line cellulose but retains full catalytic activity against carboxymethyl cellulose and low molecular weight soluble substrates; and a peptide fragment corresponding to the cellulose binding domain. The latter appears to be of paramount significance in the mechanisms involved in the hydrolysis of microcrystalline cellulose.

Monoclonal antibodies against core and cellulose-binding domains of Trichoderma reesei cellobiohydrolases I and II and endoglucanase I

Cellulases from Trichoderma reesei form an enzyme group with a common structural organization. Each cellulase enzyme is composed of two functional domains, the core region containing the active site and the cellulose-binding domain (CBD). To facilitate the specific detection of each domain, monoclonal antibodies (mAb) against cellobiohydrolase I (CBHI), cellobiohydrolase II (CBHII) and endoglucanase I (EGI) were produced. Five mAb were obtained against CBHI, ten against CBHII and eight against EGI. The location of the antigenic epitope for each antibody was mapped by allowing the antibodies to react with truncated cellulases, synthesized from deleted cDNA in Saccharomyces cerevisiae. Proteolytic fragments of Trichoderma cellulases, obtained by papain digestion, were used to confirm the results. Specific antibodies were detected against the core and the CBD epitopes for all three cellulases. Using the truncated enzymes, it was possible to locate the epitopes to a reasonably short region within the protein. To obtain a quantitative assay for each enzyme, a specific mAb against each antigen was chosen, based on the affinity to the corresponding antigen on Western-blot staining and on filter blots of the cellulolytic yeasts. The mAb were used to quantitative the corresponding enzymes in T. reesei culture medium. Specific quantitation of each cellulase enzyme has not been possible by biochemical assays or using polyclonal antibodies, due to their cross-reactions. Now, these mAb can be specifically used to recognize and quantitate different domains of these three important cellulolytic enzymes.

Purification of synthetic peptides. Immobilized metal ion affinity chromatography (IMAC)

Immobilized metal ion affinity chromatography (IMAC) is a useful method for purification of synthetic peptides with an N-terminal metal-binding amino acid such as His, Trp, or Cys, especially when such residues are not present in other parts of the molecule. In solid phase peptide synthesis (SPPS), capping with acetic anhydride will, in principle, produce truncated peptides as the only side-products due to incomplete couplings. Consequently, only the desired product will carry the affinity label. Most of the impurities, therefore, can be removed by a single passage through an IMAC column. Some representative examples are presented, where fairly large peptides (30-40 amino acid residues) were efficiently purified by this approach.

The 1,4-beta-D-glucan cellobiohydrolases from Phanerochaete chrysosporium. I. A system of synergistically acting enzymes homologous to Trichoderma reesei

A physico-chemical and structural characterization of three 1,4-beta-D-glucan cellobiohydrolases (EC. 3.2.1.91), isolated from a culture filtrate of the white-rot fungus Phanerochaete chrysosporium, reveals that the cellulolytic enzyme secretion pattern and thus the general degradation strategy for P. chrysosporium is similar to that of Trichoderma reesei. Partial sequence data show that two of the isolated enzymes, i.e., CBHI, pI 3.82 and CBH62, pI 4.85, are homologous with CBHI and EGI from T. reesei; while, the third, i.e., CBH50, pI 4.87, is homologous to T. reesei CBHII. Limited proteolysis with papain cleaved each of the three enzymes into two domains: a core protein which retained full catalytic activity against low molecular weight substrates and a peptide fragment corresponding to the cellulose binding domain, in striking similarity to the structural organization of T. reesei. CBHI and CBH62 have their binding domain located at the C-terminus, whereas in CBH50 it is located at the N-terminus. It is evident that synergistically acting cellobiohydrolases is a general requirement for efficient hydrolysis of crystalline cellulose by cellulolytic fungi.

Production and purification of a granular-starch-binding domain of glucoamylase 1 from Aspergillus niger

A domain of glucoamylase 1 from Aspergillus niger which binds to granular starch was produced by proteolytic digestion and purified to apparent homogeneity by extraction with corn starch followed by anion-exchange chromatography and gel filtration. The peptide has a molecular weight of 25,100, contains approximately 38% carbohydrate (w/w) and corresponds to residues 471-616 at the C-terminus of glucoamylase 1. The peptide bound to granular corn starch maximally at 1.08 nmol/mg starch. It inhibited the hydrolysis of granular starch by glucoamylase 1 but had no effect on the hydrolysis of starch in solution.