Studies of the cellulolytic system of Trichoderma reesei QM 9414. Analysis of domain function in two cellobiohydrolases by limited proteolysis

Cellobiohydrolase I from Trichoderma reesei: identification of an active-site nucleophile and additional information on sequence including the glycosylation pattern of the core protein

(R,S)-3,4-Epoxybutyl beta-cellobioside, but not the corresponding propyl and pentyl derivatives, inactivates specifically and irreversibly cellobiohydrolase I from Trichoderma reesei by covalent modification of Glu212, the putative active-site nucleophile. The position and identity of the modified amino acid residue were determined using a combination of comparative liquid chromatography coupled on-line to electrospray ionization mass spectrometry, tandem mass spectrometry and microsequencing. It was found that the core protein corresponds to the N-terminal sequence pyrGlu1-Gly434 (Gly435) of intact cellobiohydrolase I. In the particular enzyme samples investigated, the asparagine residues in positions 45, 270 and 384 are each linked to a single 2-acetamido-2-deoxy-D-glucopyranose residue.

Structure and function of poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis T1

Poly(3-hydroxybutyrate) (PHB) depolymerase from Alcaligenes faecalis T1 is composed of three domains: the catalytic (C) domain, the fibronectin type III-like (F) domain, and the substrate-binding (S) domain. We constructed domain deletion, inversion, chimera, and extra-F-domain mutants and examined their enzyme activity and PHB-binding ability. In addition, we performed substitution of 214Asp and 273His with glycine and aspartate, respectively, to examine their participation in a catalytic triad together with 139Ser. The mutant with both the F and S domains deleted and the trypsin-digested enzyme showed no PHB-hydrolyzing activity and less PHB-binding ability than that of the wild-type enzyme but retained D-(-)-3-hydroxybutyrate trimer-hydrolyzing activity at a level similar to that of the wild-type enzyme. The mutant with the F domain deleted and the mutant which had the order of the F and S domains inverted retained PHB-binding ability and trimer-hydrolyzing activity at levels similar to those of the wild-type enzyme but lost PHB-hydrolyzing activity. The chimera mutant, in which the F domain was substituted with a Thr-rich domain of PHB depolymerase A from Pseudomonas lemoignei, and the extra-F-domain mutant, with an additional F domain, retained trimer- and PHB-hydrolyzing activities and PHB-binding ability at levels similar to those of the wild-type enzyme. Two mutants (D214G and H273D) showed no enzymatic activity toward trimer and PHB, and they were not labeled with [3H]diisopropylfluorophosphate.

The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 A resolution, and a comparison with related enzymes

Cellulose is the most abundant polymer in the biosphere. Although generally resistant to degradation, it may be hydrolysed by cellulolytic organisms that have evolved a variety of structurally distinct enzymes, cellobiohydrolases and endoglucanases, for this purpose. Endoglucanase I (EG I) is the major endoglucanase produced by the cellulolytic fungus Trichoderma reesei, accounting for 5 to 10% of the total amount of cellulases produced by this organism. Together with EG I from Humicola insolens and T. reesei cellobiohydrolase I (CBH I), the enzyme is classified into family 7 of the glycosyl hydrolases, and it catalyses hydrolysis with a net retention of the anomeric configuration. The structure of the catalytic core domain (residues 1 to 371) of EG I from T. reesei has been determined at 3.6 A resolution by the molecular replacement method using the structures of T. reesei CBH I and H. insolens EG I as search models. By employing the 2-fold non-crystallographic symmetry (NCS), the structure was refined successfully, despite the limited resolution. The final model has an R-factor of 0.201 (Rfree 0.258). The structure of EG I reveals an extended, open substrate-binding cleft, rather than a tunnel as found in the homologous cellobiohydrolase CBH I. This confirms the earlier proposal that the tunnel-forming loops in CBH I have been deleted in EG I, which has resulted in an open active site in EG I, enabling it to function as an endoglucanase. Comparison of the structure of EG I with several related enzymes reveals structural similarities, and differences that relate to their biological function in degrading particular substrates. A possible structural explanation of the drastically different pH profiles of T. reesei and H. insolens EG I is proposed.

Trichoderma reesei cellobiohydrolase I with an endoglucanase cellulose-binding domain: action on bacterial microcrystalline cellulose

Cellulolytic enzymes consist of distinct catalytic and cellulose-binding domains (CBDs). The presence of a CBD improves the binding and activity of cellulases on insoluble substrates but has no influence on their activities on soluble substrates. Structural and biochemical studies of a fungal CBD from Trichoderma reesei cellobiohydrolase I have revealed a wedge shaped structure with a flat cellulose binding surface containing three essential tyrosine residues. The face of the wedge is strictly conserved in all fungal CBDs while many differences occur on the other face of the wedge. Here we have studied the importance of these differences on the function of the T. reesei CBHI by replacing its CBD by a homologous CBD from the endoglucanase, EGI. Our data shows that, apart from slightly improved affinity of the hybrid enzyme, the domain exchange does not significantly influence the function of CBHI.

Cellulose binding domains and linker sequences potentiate the activity of hemicellulases against complex substrates

To evaluate the role of the CBDs and linker sequences in Pseudomonas xylanase A (XYLA) and arabinofuranosidase C (XYLC), the catalytic activity of derivatives of these enzymes, lacking either the linker sequences or CBDs, was assessed. Removal of the CBDs or linker sequences did not affect the activity of either XYLA or XYLC against soluble arabinoxylan, while derivatives of XYLA, in which either the CBD or interdomain regions had been deleted, exhibited decreased activity against the xylan component of cellulose/hemicellulose complexes. Although a truncated derivative of XYLC (XYLC"'), lacking its CBD, was less active than the full-length enzyme against plant cell wall material containing highly substituted arabinoxylan, XYLC"' was more active than XYLC on complex substrates where the degree of substitution of arabinoxylan was very low. These data indicate that CBDs and linker sequences play an important role in the activity of hemicellulases against plant cell walls and other cellulose/hemicellulose complexes.

Interaction between Clostridium thermocellum endoglucanase CelD and polypeptides derived from the cellulosome-integrating protein CipA: stoichiometry and cellulolytic activity of the complexes

Four mini-scaffoldins were constructed from modules derived from the Clostridium thermocellum cellulosome-integrating protein CipA. Cip7 and Cip6 contained one and two cohesin modules respectively. Cip14 and Cip16, also containing one and two cohesin modules respectively, were flanked by a cellulose-binding domain. Endoglucanase CelD formed stable complexes with all mini-scaffoldins. Analytical ultracentrifugation of the complexes showed that 1 mol of CelD bound per mol of Cip14, and 2 mol of CelD bound per mol of Cip16. Under the conditions used for assaying cellulase activity, 96% of CelD alone bound to Avicel. Association with Cip14 or Cip16 increased the cellulose binding of CelD to 99%, while association with Cip7 or Cip6 decreased binding to 79 and 75% respectively. The hydrolytic activity of CelD against Avicel was increased 3-fold in complexes with Cip14 and Cip16, but remained substantially the same in complexes with Cip6 and Cip7. Addition of whole CipA also enhanced the efficiency of Avicel hydrolysis by CelD. However, even at an optimal ratio of the components, CelD-CipA complexes were somewhat less active than complexes of CelD with Cip14 or Cip16. These results suggest that the synergism observed between CelD and Cip14 or Cip16 is mostly due to the presence of the cellulose-binding domain, which promotes productive binding of the enzyme.

Studies of cellulose binding by cellobiose dehydrogenase and a comparison with cellobiohydrolase 1

The binding isotherm to cellulose of cellobiose dehydrogenase (CDH) from Phanerochaete chrysosporium has been compared with that of cellobiohydrolase 1 (CBH 1) from Trichoderma reesei. CDH binds more strongly but more sparsely to cellulose than does CBH 1. In a classical Scatchard analysis, a better fit to a one-site binding model was obtained for CDH than for CBH 1. The binding of both enzymes decreased in the presence of ethylene glycol, increased in the presence of ammonium sulphate and was unaffected by sodium chloride. Attempts to localize the cellulose-binding site on CDH have also been made by exposing enzymically digested CDH to cellulose and isolating the cellulose-bound peptides. The results suggest that the cellulose-binding site is located internally in the amino acid sequence of CDH.

Interaction between cellohexaose and cellulose binding domains from Trichoderma reesei cellulases

Most Trichoderma reesei cellulases consist of a catalytic and a cellulose binding domain (CBD) joined by a linker. We have used cellohexaose as a model compound for the glucose chain to investigate the interaction between the soluble enzyme and cellulose. The binding of cellohexaose to family I CBDs was studied by NMR spectroscopy. CBDs cause line broadening effects and decreasing T2 relaxation times for certain cellohexaose resonances, whereas there are no effects in the presence of a mutant which binds weakly to cellulose. Yet it remains uncertain how well the soluble cellooligosaccharide mimics the binding of CBD to the cellulose.

Role of scaffolding protein CipC of Clostridium cellulolyticum in cellulose degradation

The role of a miniscaffolding protein, miniCipC1, forming part of Clostridium cellulolyticum scaffolding protein CipC in insoluble cellulose degradation was investigated. The parameters of the binding of miniCipC1, which contains a family III cellulose-binding domain (CBD), a hydrophilic domain, and a cohesin domain, to four insoluble celluloses were determined. At saturating concentrations, about 8.2 micromol of protein was bound per g of bacterial microcrystalline cellulose, while Avicel, colloidal Avicel, and phosphoric acid-swollen cellulose bound 0.28, 0.38, and 0.55 micromol of miniCipC1 per g, respectively. The dissociation constants measured varied between 1.3 x 10(-7) and 1.5 x 10(-8) M. These results are discussed with regard to the properties of the various substrates. The synergistic action of miniCipC1 and two forms of endoglucanase CelA (with and without the dockerin domain [CelA2 and CelA3, respectively]) in cellulose degradation was also studied. Although only CelA2 interacted with miniCipC1 (K(d), 7 x 10(-9) M), nonhydrolytic miniCipC1 enhanced the activities of endoglucanases CelA2 and CelA3 with all of the insoluble substrates tested. This finding shows that miniCipC1 plays two roles: it increases the enzyme concentration on the cellulose surface and enhances the accessibility of the enzyme to the substrate by modifying the structure of the cellulose, leading to an increased available cellulose surface area. In addition, the data obtained with a hybrid protein, CelA3-CBD(CipC), which was more active towards all of the insoluble substrates tested confirm that the CBD of the scaffolding protein plays an essential role in cellulose degradation.

Expression of a fungal cellobiohydrolase in insect cells

The gene for Trichoderma reesei cellobiohydrolase I (CBHI) was expressed with a recombinant baculovirus and high levels of secreted protein were produced in Spodoptera frugiperda and Trichoplusia ni insect cells. Electrophoretic analysis indicated that the recombinant CBHI (rCBHI) was similar in apparent molecular weight to the native form and immunoblotting with anti-CBHI monoclonal antibodies confirmed its identity. The rCBHI was easily purified by affinity and hydrophobic interaction chromatography and demonstrated enzymatic activity on soluble substrate.

Isotherms for adsorption of cellobiohydrolase I and II from Trichoderma reesei on microcrystalline cellulose

Adsorption to microcrystalline cellulose (Avicel) of pure cellobiohydrolase I and II (CBH I and CBH II) from Trichoderma reesei has been studied. Adsorption isotherms of the enzymes were measured at 4 degrees C using CBH I and CBH II alone and in reconstituted equimolar mixtures. Several models (Langmuir, Freundlich, Temkin, Jovanovic) were tested to describe the experimental adsorption isotherms. The isotherms did not follow the basic (one site) Langmuir equation that has often been used to describe adsorption isotherms of cellulases; correlation coefficients (R2) were only 0.926 and 0.947, for CBH I and II, respectively. The experimental isotherms were best described by a model of Langmuir type with two adsorption sites and by a combined Langmuir-Freundlich model (analogous to the Hill equation); using these models the correlation coefficients were in most cases higher than 0.995. Apparent binding parameters derived from the two sites Langmuir model indicated stronger binding of CBH II compared to CBH I; the distribution coefficients were 20.7 and 3.7 L/g for the two enzymes, respectively. The binding capacity, on the other hand, was higher for CBH I, 1.0 mumol (67 mg) per gram Avicel, compared to 0.57 mumol/g (30 mg/g) for CBH II. The isotherms when analyzed with the combined Langmuir-Freundlich model indicated presence of unequal binding sites on cellulose and/or negative cooperatively in the binding of the enzyme molecules.

Substrate specificity of endoglucanases: what determines xyloglucanase activity?

Endoglucanases from Trichoderma viride differ in their activity and mode of action towards xyloglucans. In order to explain the basis for their different behavior, the number of substrate-binding sites of three endoglucanases (endoI, endoIV, and endoV) were determined using bond cleavage frequencies of both normal and reduced cellodextrins and Ko/K(m). EndoIV differed from other endoglucanases described so far, in having at least nine putative binding sites. The specificities of the three endoglucanases towards various xyloglucans derived from apple fruit and potato were determined. Also, the release of oligosaccharides from these substrates in time was monitored. It was concluded that the endoglucanases prefer to bind unbranched glucosyl residues. Because most xyloglucans are composed of XXXG-type of building units, distant subsites are needed to bind xyloglucan. Having at least nine substrate-binding sites, endoIV seems to be well equipped to degrade xyloglucans which was confirmed by its high xyloglucanase activity.

Cel1, probably encoding a cellobiohydrolase lacking the substrate binding domain, is expressed in the initial infection phase of Claviceps purpurea on Secale cereale

At the host-pathogen interface of hyphae penetrating host cell walls in the rye ovary, a lack of cellulase-gold labeling of beta-1, 4-glucan in host cell walls indicates that enzymatic degradation of cellulose might be an important factor during the infection of rye by Claviceps purpurea. Using cbh1 from Trichoderma reesei as a probe, a putative cellulase gene (cel1) was isolated from a genomic library of the C. purpurea strain T5. The coding region of 1,616 bp contains two introns and a putative signal peptidase cleavage site, leaving a coding capacity of 437 amino acids for the mature protein. The derived amino acid sequence shares significant homology with other fungal cellobiohydrolases and lacks the substrate binding domain. Expression analysis using reverse transcriptase-polymerase chain reaction (RT-PCR) shows that cel1 is induced during the first days of infection of rye by C. purpurea. It may be involved in the penetration and degradation of host cell walls by depolymerizing plant beta-1, 4-glucan and, therefore, play a role in the infection process.

Three-dimensional structures of three engineered cellulose-binding domains of cellobiohydrolase I from Trichoderma reesei

Three-dimensional solution structures for three engineered, synthetic CBDs (Y5A, Y31A, and Y32A) of cellobiohydrolase I (CBHI) from Trichoderma reesei were studied with nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. According to CD measurements the antiparallel beta-sheet structure of the CBD fold was preserved in all engineered peptides. The three-dimensional NMR-based structures of Y31A and Y32A revealed only small local changes due to mutations in the flat face of CBD, which is expected to bind to crystalline cellulose. Therefore, the structural roles of Y31 and Y32 are minor, but their functional importance is obvious because these mutants do not bind strongly to cellulose. In the case of Y5A, the disruption of the structural framework at the N-terminus and the complete loss of binding affinity implies that Y5 has both structural and functional significance. The number of aromatic residues and their precise spatial arrangement in the flat face of the type I CBD fold appears to be critical for specific binding. A model for the CBD binding in which the three aligned aromatic rings stack onto every other glucose ring of the cellulose polymer is discussed.

Domain structure and conformation of a cellobiohydrolase from Trichoderma pseudokiningii S-38

A cellobiohydrolase (CBH) with a molecular mass of 66 kD was purified from Trichoderma pseudokiningii S-38. Papain digestion produced a 59- to 60-kD core domain with 54% of intact activity on crystalline cellulose and with full activity against soluble substrates. Digestion products also included two small peptides with molecular mass of about 3-4 kD, which are heavily glycosylated and difficult to purify; the mixed peptides displayed the capacity to disorganize the cellulose fiber. The sequencing results indicated that the intact enzyme had a blocked N-terminal and there was a 10-amino-acid sequence in the N-terminal of the core protein of Ser-Gly-Thr-Ala-Val-Thr-Cys-Leu-Ala-Asp. Fluorescence and circular dichroism properties indicated that the core protein has an independent conformation and is conformationally similar to intact enzyme, suggesting that the spectroscopic properties of the intact enzyme come from the core protein.

Interaction of polysaccharides with the N-terminal cellulose-binding domain of Cellulomonas fimi CenC. 1. Binding specificity and calorimetric analysis

The carbohydrate-binding specificity of the N-terminal cellulose-binding domain (CBDN1) from Cellulomonas fimi beta-1,4-glucanase C (CenC) was investigated using affinity electrophoresis, binding assays and microcalorimetry in parallel with NMR and difference ultraviolet absorbance spectroscopy [Johnson, P.E., Tomme, P., Joshi, M.D., & McIntosh, I., P. (1996) Biochemistry 35, 13895-13906]. Binding of CBDN1 on insoluble cellulose is distinctly different from other cellulose-binding domains. CBDN1 binds amorphous cellulose (phosphoric acid-swollen) with high affinity (Kr = 5.1 L g-1), binds Avicel weakly and does not bind highly crystalline bacterial or tunicin cellulose. Moreover, CBDN1 binds soluble cellooligosaccharides and beta-1,4-linked oligomers of glucose such as hydroxyethycellulose, soluble beta-1,3-1,4-glucans from barley and oat, but has no affinity for alpha-1,4-, beta-1,3-, or beta-1,6-polymers of glucose. This is the first report of a cellulose-binding domain with strong and specific affinity for soluble glycans. The thermodynamics for binding of CBDN1 to oligosaccharides, soluble glycans, and phosphoric acid-swollen cellulose were investigated by titration microcalorimetry. At least four beta-1,4-linked glucopyranosides are required to detect binding. For larger glucans, with five or more glucopyranoside units, the binding constants and standard free energy changes are virtually independent of the glucan chain length, indicating that cellopentaose completely fills the binding site. Binding is moderately strong with binding constants ranging from 3,200 +/- 500 M-1 for cellotetraose, to 25,000 +/- 3,000 M-1 for the larger sugars. The reactions are controlled by favorable standard free enthalpy changes which are compensated in a linear fashion by a significant decrease in entropy. A predominance of polar interactions such as hydrogen bonding together with van der Waals interactions provide the major driving forces for the binding event.

Cloning, sequencing, and expression of a Thermomonospora fusca protease gene in Streptomyces lividans

The major Thermomonospora fusca YX extracellular protease gene (tfpA) was cloned into Escherichia coli and Streptomyces lividans and was sequenced. The open reading frame encoded 375 residues, including a 31-residue potential signal sequence, an N-terminal prosequence containing 150 residues, and the 194-residue mature protease that belongs to the chymotrypsin family. The protease was secreted by S. lividans, but evidence suggested that it was bound to an extracellular protease inhibitor. An inhibitor-deficient mutant was selected to produce protease for purification.

The cellulose-binding domain of the major cellobiohydrolase of Trichoderma reesei exhibits true reversibility and a high exchange rate on crystalline cellulose

Cellulose-binding domains (CBDs) bind specifically to cellulose, and form distinct domains of most cellulose degrading enzymes. The CBD-mediated binding of the enzyme has a fundamental role in the hydrolysis of the solid cellulose substrate. In this work we have investigated the reversibility and kinetics of the binding of the CBD from Trichoderma reesei cellobiohydrolase I on microcrystalline cellulose. The CBD was produced in Escherichia coli, purified, and radioactively labeled by reductive alkylation with 3H. Sensitive detection of the labeled CBD allowed more detailed analysis of its behavior than has been possible before, and important novel features were resolved. Binding of the CBD was found to be temperature sensitive, with an increased affinity at lower temperatures. The interaction of the CBD with cellulose was shown to be fully reversible and the CBD could be eluted from cellulose by simple dilution. The rate of exchange measured for the CBD-cellulose interaction compares well with the hydrolysis rate of cellobiohydrolase I, which is consistent with its proposed mode of action as a processive exoglucanase.

Evidence that linker sequences and cellulose-binding domains enhance the activity of hemicellulases against complex substrates

Xylanase A (XYLA) and arabinofuranosidase C (XYLC) from Pseudomonas fluorescens subsp. cellulosa are modular enzymes consisting of discrete cellulose-binding domains (CBDs) and catalytic domains joined by serine-rich linker sequences. To evaluate the role of the CBDs and interdomain regions, the capacity of full-length and truncated derivatives of the two enzymes, lacking either the linker sequences or CBDs, to hydrolyse a range of substrates, and bind to cellulose, was determined. Removal of the CBDs did not affect either the activity of XYLA or XYLC against soluble arabinoxylan. Similarly, deletion of the linker sequences did not alter the affinity of the enzymes for cellulose or their activity against soluble substrates, even when bound to cellulose via the CBDs. Truncated derivatives of XYLA lacking either the linker sequences or the CBD were less active against xylan contained in cellulose-hemicellulose complexes, compared with the full-length xylanase. Similarly, removal of the CBD from XYLC diminished the activity of the enzyme (XYLC''') against plant-cell-wall material containing highly substituted arabinoxylan. The role of CBDs and linker sequences in the catalytic activity of hemicellulases against the plant cell wall is discussed.

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.

The active sites of cellulases are involved in chiral recognition: a comparison of cellobiohydrolase 1 and endoglucanase 1

The cellulases cellobiohydrolase 1 (CBH 1) and endoglucanase 1 (EG 1) from the fungus Trichoderma reesei are closely related with 40% sequence identity and very similar in structure. In CBH 1 the active site is enclosed by long loops and some antiparallel beta-strands forming a 40 A long tunnel, whereas in EG 1 part of those loops are missing so that the enzyme has a more common active site groove. Both enzymes were immobilized on silica and these materials were used as chiral stationary phases for chromatographic separation of the enantiomers of two chiral drugs, propranolol and alprenolol. The CBH 1 phase showed much better resolution than did the EG 1 phase, suggesting that the tunnel structure of the protein may play an important role in the chiral separation. The chiral compounds were found to be competitive inhibitors of both enzymes when p-nitrophenyl lactoside (pNPL) was used as substrate. (S)-enantiomers showed stronger inhibitory effects and also longer retention time on the stationary phases than the (R)-enantiomers. The consistency between kinetic data and retention on the stationary phases clearly shows that the enzymatically active sites of CBH 1 and EG 1 are involved in chiral recognition.

The cellulosome: an exocellular, multiprotein complex specialized in cellulose degradation

Clostridium thermocellum produces a highly active cellulase system that consists of a high-M(r) multienzyme complex termed cellulosome. Hydrolytic components of the cellulosome are organized around a large, noncatalytic glycoprotein termed CipA that acts both as a scaffolding component and a cellulose-binding factor. Catalytic subunits of the cellulosome bear conserved, noncatalytic subdomains, termed dockerin domains, which bind to receptor domains of CipA, termed cohesin domains. CipA includes nine cohesin domains, a cellulose-binding domain, and a specialized dockerin domain. Proteins of the cell envelope carrying cohesin domains that specifically bind the dockerin domain of CipA have been identified. These proteins may mediate anchoring of the cellulosomes to the cell surface. Cellulase complexes similar to the cellulosome of C. thermocellum are produced by several cellulolytic clostridia. High-M(r) multienzyme complexes have also been identified in anaerobic rumen fungi. The architecture of the fungal complexes also seems to rely on the interaction of conserved, noncatalytic docking domains with a scaffolding component. However, the sequence of the fungal docking domains bears no resemblance to the clostridial dockerin domains, suggesting that the fungal and clostridial complexes arose independently.

Characterization of a Neocallimastix patriciarum cellulase cDNA (celA) homologous to Trichoderma reesei cellobiohydrolase II

The nucleotide sequence of a cellulase cDNA (celA) from the rumen fungus Neocallimastix patriciarum and the primary structure of the protein which it encodes were characterized. The celA cDNA was 1.95 kb long and had an open reading frame of 1,284 bp, which encoded a polypeptide having 428 amino acid residues. A sequence alignment showed that cellulase A (CELA) exhibited substantial homology with family B cellulases (family 6 glycosyl hydrolases), particularly cellobiohydrolase II from the aerobic fungus Trichoderma reesei. In contrast to previously characterized N. patriciarum glycosyl hydrolases, CELA did not exhibit homology with any other rumen microbial cellulases described previously. Primary structure and function studies in which deletion analysis and a sequence comparison with other well-characterized cellulases were used revealed that CELA consisted of a cellulose-binding domain at the N terminus and a catalytic domain at the C terminus. These two domains were separated by an extremely Asn-rich linker. Deletion of the cellulose-binding domain resulted in a marked decrease in the cellulose-binding ability and activity toward crystalline cellulose. When CELA was expressed in Escherichia coli, it was located predominantly in the periplasmic space, indicating that the signal sequence of CELA was functional in E.coli. Enzymatic studies showed that CELA had an optimal pH of 5.0 and an optimal temperature of 40 degrees C. The specific activity of immunoaffinity-purified CELA against Avicel was 9.7 U/mg of protein, and CELA appeared to be a relatively active cellobiohydrolase compared with the specific activities reported for other cellobiohydrolases, such as T. reesei cellobiohydrolases I and II.

The synthesis of the Streptomyces reticuli cellulase (avicelase) is regulated by both activation and repression mechanisms

The Streptomyces reticuli cellulase (Cell, Avicelase) hydrolyzes crystalline cellulose (Avicel) efficiently to cellobiose. The synthesis of the enzyme is induced by Avicel and repressed by glucose. DNA-binding proteins were purified from induced S. reticuli mycelia by affinity chromatography using the upstream region of the cell gene linked to Sepharose. The enriched protein(s) provoked a gel electrophoresis mobility shift of the upstream region, irrespective of the presence or absence of a 14-bp palindromic sequence, and enhanced the transcription of the cell gene by the S. reticuli RNA polymerase in vitro. The binding site (GTGACTGAGCGCCG) for the protein(s) was located in the vicinity of a DNA bend upstream of the transcriptional start site. Results of physiological studies, deletion and gel-shift analyses lead to the conclusion that a 14-bp palindrome (TGGGAGCGCTCCCA)--situated between the transcriptional start site and the structure gene--is the operator for a repressor protein. The data presented suggest that the two identified cis-acting elements, in cooperation with an activator and a repressor, mediate regulation of cell transcription.

Acetyl xylan esterase from Trichoderma reesei contains an active-site serine residue and a cellulose-binding domain

The axe1 gene encoding acetyl xylan esterase was isolated from an expression library of the filamentous fungus Trichoderma reesei using antibodies raised against the purified enzyme. Apparently axe1 codes for the two forms, pI 7 and pI 6.8, of acetyl xylan esterase previously characterized. The axe1 encodes 302 amino acids including a signal sequence and a putative propeptide. The catalytic domain has no amino acid similarity with the reported acetyl xylan esterases but has a clear similarity, especially in the active site, with fungal cutinases which are serine esterases. Similarly to serine esterases, the axe1 product was inactivated with phenylmethylsulfonyl fluoride. At its C-terminus it carries a cellulose binding domain of fungal type, which is separated from the catalytic domain by a region rich in serine, glycine, threonine and proline. The binding domain can be separated from the catalytic domain by limited proteolysis without affecting the activity of the enzyme towards acetylated xylan, but abolishing its capability to bind cellulose.

Induction of a Cryphonectria parasitica cellobiohydrolase I gene is suppressed by hypovirus infection and regulated by a GTP-binding-protein-linked signaling pathway involved in fungal pathogenesis

Extracellular cellulase activity is readily induced when the chestnut blight fungus Cryphonectria parasitica is grown on cellulose substrate as the sole carbon source. However, an isogenic C. parasitica strain rendered hypovirulent due to hypovirus infection failed to secrete detectable cellulase activity when grown under parallel conditions. Efforts to identify C. parasitica cellulase-encoding genes resulted in the cloning of a cellobiohydrolase (exoglucanase, EC 3.2.1.91) gene designated chb-1. Northern blot analysis revealed an increase in cbh-1 transcript accumulation in a virus-free virulent C. parasitica strain concomitant with the induction of extracellular cellulase activity. In contrast, induction of cbh-1 transcript accumulation was suppressed in an isogenic hypovirus-infected strain. Significantly, virus-free C. parasitica strains rendered hypovirulent by transgenic cosuppression of a GTP-binding protein alpha subunit were also found to be deficient in the induction of cbh-1 transcript accumulation.

Dynamic light scattering study of the two-domain structure of Humicola insolens endoglucanase V

Endoglucanase V (EG V) of HUmicola insolens is composed of a catalytic domain and of a cellulose-binding domain linked by a 33 amino acid long peptide rich in Ser, Thr and Pro residues. This work describes the dynamic behavior of the two-domain structure of EG V as revealed by quasi-elastic light scattering experiments. For both the full-length and the isolated catalytic domain, the autocorrelation function is essentially described by a single relaxation mode. The equivalent hydrodynamic radius of the catalytic domain was found to correspond precisely to the dimensions measured from the previously determined three-dimensional structure. The results obtained with the full-length protein allow a description of the two domain structure of EG V similar to that resulting from earlier studies using small angle X-ray scattering on cellulases from Trichoderma reesei. The hydrodynamic dimensions of the entire enzyme can be approximated as an ellipsoid with dimensions of 42 x 133.6 A.

Characterization of a bifunctional cellulase and its structural gene. The cell gene of Bacillus sp. D04 has exo- and endoglucanase activity

Bacillus sp. D04 secreted a bifunctional cellulase that had a molecular weight of 35,000. This cellulase degraded Cm-cellulose, cellotetraose, cellopentaose, p-nitrophenyl-beta-D-cellobioside, and avicel PH101. Based on the high performance liquid chromatography analysis of the degradation products, this cellulase randomly cleaved internal beta-1, 4-glycosidic bonds in cellotetraose and cellopentaose as an endoglucanase. It also hydrolyzed the aglycosidic bond in p-nitrophenyl-beta-D-cellobioside and cleaved avicel to cellobiose as an exoglucanase. Cellobiose competitively inhibited the p-nitrophenyl-beta-D-cellobioside degrading activity but not Cm-cellulose degrading activity. Ten mM p-chloromercuribenzoate inhibited p-nitrophenyl-beta-D-cellobioside degrading activity completely, but Cm-cellulose degrading activity incompletely. Cm-cellulose increased p-nitrophenyl-beta-D-cellobioside degrading activity, and vice versa, whereas methylumbelliferyl-beta-D-cellobiose strongly inhibited p-nitrophenyl-beta-D-cellobioside degrading activity. The cellulase gene (cel gene), 1461 base pairs, of Bacillus sp. D04 was cloned. The nucleotide sequence of the cel gene was highly homologous to those of Bacillus subtilis DLG and B. subtilis BSE616. The cel gene was overexpressed in Escherichia coli, and its product was purified. The substrate specificity and substrate competition pattern of the purified recombinant cellulase were the same as those of the purified cellulase from Bacillus sp. D04. These results suggest that a single polypeptide cellulase had both endo- and exoglucanase activities and each activity exists in a separate site.

Filament-specific expression of a cellulase gene in the dimorphic fungus Ustilago maydis

The phytopathogenic fungus Ustilago maydis exists in a yeast-like haploid form and as a filamentous dikaryon. Only the dikaryon can infect corn plants. We have isolated a gene, egl1, that is not expressed in haploid cells but strongly induced in the filament. Molecular and biochemical analyses revealed that egl1 encodes a cellulase. By immunogold labelling, secreted protein could be detected at the hyphal tip. Mutants deleted for egl1 are viable and are affected neither in filament formation nor in pathogenic development under the conditions tested.

The anchorage function of CipA (CelL), a scaffolding protein of the Clostridium thermocellum cellulosome

Enzymatic cellulose degradation is a heterogeneous reaction requiring binding of soluble cellulase molecules to the solid substrate. Based on our studies of the cellulase complex of Clostridium thermocellum (the cellulosome), we have previously proposed that such binding can be brought about by a special "anchorage subunit." In this "anchor-enzyme" model, CipA (a major subunit of the cellulosome) enhances the activity of CelS (the most abundant catalytic subunit of the cellulosome) by anchoring it to the cellulose surface. We have subsequently reported that CelS contains a conserved duplicated sequence at its C terminus and that CipA contains nine repeated sequences with a cellulose binding domain (CBD) in between the second and third repeats. In this work, we reexamined the anchor-enzyme mechanism by using recombinant CelS (rCelS) and various CipA domains, CBD, R3 (the repeat next to CBD), and CBD/R3, expressed in Escherichia coli. As analyzed by non-denaturing gel electrophoresis, rCelS, through its conserved duplicated sequence, formed a stable complex with R3 or CBD/R3 but not with CBD. Although R3 or CBD alone did not affect the binding of rCelS to cellulose, such binding was dependent on CBD/R3, indicating the anchorage role of CBD/R3. Such anchorage apparently increased the rCelS activity toward crystalline cellulose. These results substantiate the proposed anchor-enzyme model and the expected roles of individual CipA domains and the conserved duplicated sequence of CelS.

Comparison of a fungal (family I) and bacterial (family II) cellulose-binding domain

A family II cellulose-binding domain (CBD) of an exoglucanase/xylanase (Cex) from the bacterium Cellulomonas fimi was replaced with the family I CBD of cellobiohydrolase I (CbhI) from the fungus Trichoderma reesei. Expression of the hybrid gene in Escherichia coli yielded up to 50 mg of the hybrid protein, CexCBDCbhI, per liter of culture supernatant. The hybrid was purified to homogeneity by affinity chromatography on cellulose. The relative association constants (Kr) for the binding of Cex, CexCBDCbhI, the catalytic domain of Cex (p33), and CbhI to bacterial microcrystalline cellulose (BMCC) were 14.9, 7.8, 0.8, and 10.6 liters g-1, respectively. Cex and CexCBDCbhI had similar substrate specificities and similar activities on crystalline and amorphous cellulose. Both released predominantly cellobiose and cellotriose from amorphous cellulose. CexCBDCbhI was two to three times less active than Cex on BMCC, but significantly more active than Cex on soluble cellulose and on xylan. Unlike Cex, the hybrid protein neither bound to alpha-chitin nor released small particles from dewaxed cotton fibers.

Effects of pH and high ionic strength on the adsorption and activity of native and mutated cellobiohydrolase I from Trichoderma reesei

Cellobiohydrolase I (CBHI) is the major cellulase of Trichoderma reesei. The enzyme contains a discrete cellulose-binding domain (CBD), which increases its binding and activity on crystalline cellulose. We studied cellulase-cellulose interactions using site-directed mutagenesis on the basis of the three-dimensional structure of the CBD of CBHI. Three mutant proteins which have earlier been produced in Saccharomyces cerevisiae were expressed in the native host organism. The data presented here support the hypothesis that a conserved tyrosine (Y492) located on the flat and more hydrophilic surface of the CBD is essential for the functionality. The data also suggest that the more hydrophobic surface is not directly involved in the CBD function. The pH dependence of the adsorption revealed that electrostatic repulsion between the bound proteins may also control the adsorption. The binding of CBHI to cellulose was significantly affected by high ionic strength suggesting that the interaction with cellulose includes a hydrophobic effect. High ionic strength increased the activity of the isolated core and of mutant proteins on crystalline cellulose, indicating that once productively bound, the enzymes are capable of solubilizing cellulose even with a mutagenized or with no CBD.

The non-catalytic cellulose-binding domain of a novel cellulase from Pseudomonas fluorescens subsp. cellulosa is important for the efficient hydrolysis of Avicel

A genomic library of Pseudomonas fluorescens subsp. cellulosa DNA, constructed in lambda ZAPII, was screened for carboxymethyl-cellulase activity. The pseudomonad insert from a recombinant phage which displayed elevated cellulase activity in comparison with other cellulase-positive clones present in the library, was excised into pBluescript SK- to generate the plasmid pC48. The nucleotide sequence of the cellulase gene, designated celE, revealed a single open reading frame of 1710 bp that encoded a polypeptide, defined as endoglucanase E (CelE), of M(r) 59663. The deduced primary structure of CelE revealed an N-terminal signal peptide followed by a 300-amino-acid sequence that exhibited significant identity with the catalytic domains of cellulases belonging to glycosyl hydrolase Family 5. Adjacent to the catalytic domain was a 40-residue region that exhibited strong sequence identity to non-catalytic domains located in two other endoglucanases and a xylanase from P. fluorescens. The C-terminal 100 residues of CelE were similar to Type-I cellulose-binding domains (CBDs). The three domains of the cellulase were joined by linker sequences rich in serine residues. Analysis of the biochemical properties of full-length and truncated derivatives of CelE confirmed that the enzyme comprised an N-terminal catalytic domain and a C-terminal CBD. Analysis of purified CelE revealed that the enzyme had an M(r) of 56000 and an experimentally determined N-terminal sequence identical to residues 40-54 of the deduced primary structure of full-length CelE. The enzyme exhibited an endo mode of action in hydrolysing a range of cellulosic substrates including Avicel and acid-swollen cellulose, but did not attack xylan or any other hemicelluloses. A truncated form of the enzyme, which lacked the C-terminal CBD, displayed the same activity as full-length CelE against soluble cellulose and acid-swollen cellulose, but exhibited substantially lower activity than the full-length cellulase against Avicel. The significance of these data in relation to the role of the CBD is discussed.

Progress-curve analysis shows that glucose inhibits the cellotriose hydrolysis catalysed by cellobiohydrolase II from Trichoderma reesei

NMR spectroscopy and HPLC were used to investigate the hydrolysis of cellotriose by cellobiohydrolase II from Trichoderma reesei. Substrate and product concentrations were followed as a function of time. Progress curves were calculated by forward numerical integration of the full kinetic equations and were fitted to the experimental data. Binding and rate constants were obtained from this fit, whereby no initial slope or Michaelis-Menten approximation was used. The progress curves from a single experiment sufficed to produce agreement with the Michaelis-Menten model (eight experiments). The absence of a kinetic isotope effect was proven. The progress-curve analysis showed that a simple degradation model cannot describe the experimental time-courses at substrate concentrations greater than 1 mM. A model containing competitive inhibition from cellobiose as well as non-competitive inhibition from glucose was developed. This four-parameter model accurately reproduces about 1000 experimental data points covering five orders of magnitude in oligosaccharide concentrations. Glucose binding to the enzyme/cellotriose complex retards, in a non-competitive fashion, cellotriose hydrolysis by at least a factor of 30. A structural model for the non-competitive inhibition is discussed. The NMR experiment also produced individual progress curves for the alpha and beta anomers. The beta anomer of cellotriose was degraded 2.5-times faster than the alpha anomer.

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.

Binding and substrate specificities of a Streptomyces olivaceoviridis chitinase in comparison with its proteolytically processed form

Streptomyces olivaceoviridis is an efficient chitin degrader. One of its genes encoding an exochitinase (exo-ChiO1) was previously characterized. The transcription was found to be inducible by chitin, but not by glucose. The transcriptional start site is situated 38 bp upstream of the start codon. S. olivaceoviridis as well as transformants of S. vinaceus and S. lividans carrying the exo-chiO1 gene on a multicopy vector secrete a 59-kDa chitinase which adheres strongly and under most conditions irreversibly to the substrate chitin. After having released the enzyme from the crystalline substrate in the presence of high concentrations of guanidine hydrochloride, it was purified to homogeneity by consecutive chitin- and immunoaffinity chromatographies. Immunofluorescence microscopy revealed that the enzyme specifically binds to crystalline alpha-chitin within fungi and other organisms as well as to beta-chitin, but not to colloidal chitin, chitosan, various types of cellulose, or other polysaccharides. The amino acids deduced from the highly specific binding domain (12 kDa) of this enzyme do not share significant similarity with any known region interacting with chitin or another substrate. During cultivation with chitin, the 59-kDa enzyme is proteolytically processed to a 47-kDa truncated chitinase lacking the chitin-binding domain. The 47-kDa enzyme hydrolyses crystalline chitin considerably less efficiently than the 59-kDa enzyme, whereas colloidal chitin and low-molecular-mass substrates are quite equally degraded by both enzymes at identical optimal pH (7.3) and temperature (45-55 degrees C) values. Thus a strong adhesion of the enzyme to its crystalline substrate via its binding domain is a prerequisite for efficient hydrolysis.

Characterization of a Thermomonospora fusca exocellulase

The exocellulase E3 gene was cloned on a 7.1 kb NotI fragment from Thermomonospora fusca genomic DNA into Escherichia coli and expressed in Streptomyces lividans. The E3 gene was sequenced and encoded a 596 residue peptide. The molecular masses of the native and cloned E3s were determined by mass spectrometry, and the value for E. coli E3, 59,797 Da, agreed well with that predicted from the DNA sequence, 59,646 Da. The value of 61,200 Da for T. fusca E3 is consistent with E3 being a glycoprotein. E3 is thermostable, retaining full activity after 16 h at 55 degrees C. It also has a broad pH optimum around 7-8, retaining 90% of its maximal activity between pH 6 and 10. The cloned E3s were identical to the native enzyme in their activity, cellulose binding, and thermostability. Papain digestion produced a 45.7 kDa catalytic domain with 77% of the native activity on amorphous cellulose and 33% on crystalline cellulose. E3 belongs to cellulase family B and retains the residues that have been identified to be crucial for catalytic activity in Trichoderma reesei cellobiohydrolase II and T. fusca E2. The E3 gene contains a 14 bp inverted repeat regulatory sequence 212 bp before the translational start codon instead of the 30-70 bp found for the other T. fusca cellulase genes. An additional copy of this sequence with one base changed is 314 bp before the translational start codon. The transcriptional start site of the E3 gene was shown to be between these two inverted repeats.

Studies of Streptomyces reticuli cel-1 (cellulase) gene expression in Streptomyces strains, Escherichia coli, and Bacillus subtilis

Various streptomyces strains [Streptomyces lividans 66, Streptomyces vinaceus, and Strepotmyces coelicolor A3 (2)] acquired the ability to utilize crystalline cellulose (Avicel) after transformation with a multicopy vector containing the cel-1 gene from Streptomyces reticuli. The expression level in these hosts was two to three times lower than in S. reticuli, indicating the absence of positive regulatory elements. Like S. reticuli, they processed the Avicelase to its catalytic domain and to an enzymatically inactive part. The cel-1 gene with its original upstream region was not expressed within Escherichia coli. When cel-1 had been fused in phase with the lacZ gene, large quantities of the fusion protein were produced in E. coli. However, this protein was enzymatically inactive and proteolytically degraded to a series of truncated forms. As the cellulase (Avicelase) synthesized by S. reticuli is not cleaved by the E. coli proteases, its posttranslational modification is proposed. With Bacillus subtilis as host, the cel-1 gene was expressed neither under its own promoter nor under the control of a strong Bacillus promoter.