Two structurally discrete GH7-cellobiohydrolases compete for the same cellulosic substrate fiber

Background: Cellulose consisting of arrays of linear beta-1,4 linked glucans, is the most abundant carbon-containing polymer present in biomass. Recalcitrance of crystalline cellulose towards enzymatic degradation is widely reported and is the result of intra-and inter-molecular hydrogen bonds within and among the linear glucans. Cellobiohydrolases are enzymes that attack crystalline cellulose. Here we report on two forms of glycosyl hydrolase family 7 cellobiohydrolases common to all Aspergillii that attack Avicel, cotton cellulose and other forms of crystalline cellulose. Results: Cellobiohydrolases Cbh1 and CelD have similar catalytic domains but only Cbh1 contains a carbohydrate-binding domain (CBD) that binds to cellulose. Structural superpositioning of Cbh1 and CelD on the Talaromyces emersonii Cel7A 3-dimensional structure, identifies the typical tunnel-like catalytic active site while Cbh1 shows an additional loop that partially obstructs the substrate-fitting channel. CelD does not have a CBD and shows a four amino acid residue deletion on the tunnel-obstructing loop providing a continuous opening in the absence of a CBD. Cbh1 and CelD are catalytically functional and while specific activity against Avicel is 7.7 and 0.5 U. mg prot-1, respectively specific activity on pNPC is virtually identical. Cbh1 is slightly more stable to thermal inactivation compared to CelD and is much less sensitive to glucose inhibition suggesting that an open tunnel configuration, or absence of a CBD, alters the way the catalytic domain interacts with the substrate. Cbh1 and CelD enzyme mixtures on crystalline cellulosic substrates show a strong combinatorial effort response for mixtures where Cbh1 is present in 2: 1 or 4: 1 molar excess. When CelD was overrepresented the combinatorial effort could only be partially overcome. CelD appears to bind and hydrolyze only loose cellulosic chains while Cbh1 is capable of opening new cellulosic substrate molecules away from the cellulosic fiber. Conclusion: Cellobiohydrolases both with and without a CBD occur in most fungal genomes where both enzymes are secreted, and likely participate in cellulose degradation. The fact that only Cbh1 binds to the substrate and in combination with CelD exhibits strong synergy only when Cbh1 is present in excess, suggests that Cbh1 unties enough chains from cellulose fibers, thus enabling processive access of CelD.

Purification, crystallization and preliminary crystallographic analysis of the catalytic domain of the extracellular cellulase CBHI from Trichoderma harzianum

The filamentous fungus Trichoderma harzianum has a considerable cellulolytic activity that is mediated by a complex of enzymes which are essential for the hydrolysis of microcrystalline cellulose. These enzymes were produced by the induction of T. harzianum with microcrystalline cellulose (Avicel) under submerged fermentation in a bioreactor. The catalytic core domain (CCD) of cellobiohydrolase I (CBHI) was purified from the extracellular extracts and submitted to robotic crystallization. Diffraction-quality CBHI CCD crystals were grown and an X-ray diffraction data set was collected under cryogenic conditions using a synchrotron-radiation source.

Technological advances and mechanistic basis for fungal biopulping

Biopulping fundamentals, technology and mechanisms are reviewed in this article. Mill evaluation of Eucalyptus grandis wood chips biotreated by Ceriporiopsis subvermispora on a 50-tonne pilot-plant demonstrated that equivalent energy savings can be obtained in lab- and mill-scale biopulping. Some drawbacks concerning limited improvements in pulp strength and contamination of the chip pile with opportunist fungi have been observed. The use of pre-cultured wood chips as inoculum seed for the biotreatment process minimized contamination problems related to the use of blended mycelium and corn-steep liquor in the inoculation step. Alkaline wash restored part of the brightness in biopulps and marketable brightness values were obtained by one-stage bleaching with 5% H2O2 when bio-TMP pulps were under evaluation. Considering the current scenario, the understanding of biopulping mechanisms has gained renewed attention because more resistant and competitive fungal species could be selected with basis on a function-directed screening project. A series of studies aimed to elucidate structural changes in lignin during wood biodegradation by C. subvermispora had indicated that lignin depolymerization occurs during initial stages of wood biotreatment. Aromatic hydroxyls did not increase with the split of aryl-ether linkages, suggesting that the ether-cleavage-products remain as quitione-type structures. On the other hand, cellulose is more resistant to the attack by C subvermispora. MnP-initiated lipid peroxidation reactions have been proposed to explain degradation of non-phenolic lignin substructures by C subvermispora, while the lack of cellobiohydrolases and the occurrence of systems able to suppress Fenton`s reaction in the cultures have explained non-efficient cellulose degradation by this biopulping fungus. (C) 2007 Elsevier Inc. All rights reserved.

β-glucosidases from Aspergillus unguis NII 08123: Molecular characterization, properties and applications

Lignocellulosic biomass is probably the best alternative resource for biofuel production and it is composed mainly of cellulose, hemicelluloses and lignin. Cellulose is the most abundant among the three and conversion of cellulose to glucose is catalyzed by the enzyme cellulase. Cellulases are groups of enzymes act synergistically upon cellulose to produce glucose and comprise of endoglucanase, cellobiohydrolase and β-glucosidase. β -glucosidase assumes great importance due to the fact that it is the rate limiting enzyme. Endoglucanases (EG) produces nicks in the cellulose polymer exposing reducing and non reducing ends, cellobiohydrolases (CBH) acts upon the reducing or non reducing ends to liberate cellobiose units, and β - glucosidases (BGL) cleaves the cellobiose to liberate glucose completing the hydrolysis. . β -glucosidases undergo feedback inhibition by their own product- β glucose, and cellobiose which is their substrate. Few filamentous fungi produce glucose tolerant β - glucosidases which can overcome this inhibition by tolerating the product concentration to a particular threshold. The present study had targeted a filamentous fungus producing glucose tolerant β - glucosidase which was identified by morphological as well as molecular method. The fungus showed 99% similarity to Aspergillus unguis strain which comes under the Aspergillus nidulans group where most of the glucose tolerant β -glucosidase belongs. The culture was designated the strain number NII 08123 and was deposited in the NII culture collection at CSIR-NIIST. β -glucosidase multiplicity is a common occurrence in fungal world and in A.unguis this was demonstrated using zymogram analysis. A total 5 extracellular isoforms were detected in fungus and the expression levels of these five isoforms varied based on the carbon source available in the medium. Three of these 5 isoforms were expressed in higher levels as identified by the increased fluorescence (due to larger amounts of MUG breakdown by enzyme action) and was speculated to contribute significantly to the total _- β glucosidase activity. These isoforms were named as BGL 1, BGL3 and BGL 5. Among the three, BGL5 was demonstrated to be the glucose tolerant β -glucosidase and this was a low molecular weight protein. Major fraction was a high molecular weight protein but with lesser tolerance to glucose. BGL 3 was between the two in both activity and glucose tolerance.121 Glucose tolerant .β -glucosidase was purified and characterized and kinetic analysis showed that the glucose inhibition constant (Ki) of the protein is 800mM and Km and Vmax of the enzyme was found to be 4.854 mM and 2.946 mol min-1mg protein-1respectively. The optimumtemperature was 60°C and pH 6.0. The molecular weight of the purified protein was ~10kDa in both SDS as well as Native PAGE indicating that the glucose tolerant BGL is a monomeric protein.The major β -glucosidase, BGL1 had a pH and temperature optima of 5.0 and 60 °C respectively. The apparent molecular weight of the Native protein is 240kDa. The Vmax and Km was 78.8 mol min-1mg protein-1 and 0.326mM respectively. Degenerate primers were designed for glycosyl hydrolase families 1, 3 and 5 and the BGL genes were amplified from genomic DNA of Aspergillus unguis. The sequence analyses performed on the amplicons results confirmed the presence of all the three genes. Amplicon with a size of ~500bp was sequenced and which matched to a GH1 –BGL from Aspergillus oryzae. GH3 degenerate primers producing amplicons were sequenced and the sequences matched to β - glucosidase of GH3 family from Aspergillus nidulans and Aspergillus acculateus. GH5 degenerate primers also gave amplification and sequencing results indicated the presence of GH5 family BGL gene in the Aspergillus unguis genomic DNA.From the partial gene sequencing results, specific as well as degenerate primers were designed for TAIL PCR. Sequencing results of the 1.0 Kb amplicon matched Aspergillus nidulans β -glucosidase gene which belongs to the GH1 family. The sequence mainly covered the N-Terminal region of the matching peptide. All the three BGL proteins ie. BGL1, BGL3 and BGL5 were purified by chromatography an electro elution from Native PAGE gels and were subjected to MALDI-TOF mass spectrometric analysis. The results showed that BGL1 peptide mass matched to . β -glucosidase-I of Aspergillus flavus which is a 92kDa protein with 69% protein coverage. The glucose tolerant β -glucosidase BGL5 mass matched to the catalytic C-terminal domain of β -glucosidase-F from Emericella nidulans, but the protein coverage was very low compared to the size of the Emericella nidulans protein. While comparing the size of BGL5 from Aspergillus unguis, the protein sequence coverage is more than 80%. BGL F is a glycosyl hydrolase family 3 protein.The properties of BGL5 seem to be very unique, in that it is a GH3 β -glucosidase with a very low molecular weight of ~10kDa and at the same time having catalytic activity and glucose 122 tolerance which is as yet un-described in GH β -glucosidases. The occurrence of a fully functional 10kDA protein with glucose tolerant BGL activity has tremendous implications both from the points of understanding the structure function relationships as well as for applications of BGL enzymes. BGL-3 showed similarity to BGL1 of Aspergillus aculateus which was another GH3 β -glucosidase. It may be noted that though PCR could detect GH1, GH3 and GH5 β-glucosidases in the fungus, the major isoforms BGL1 BGL3 and BGL5 were all GH3 family enzymes. This would imply that β-glucosidases belonging to other families may also co-exist in the fungus and the other minor isoforms detected in zymograms may account for them. In biomass hydrolysis, GT-BGL containing BGL enzyme was supplemented to cellulase and the performances of blends were compared with a cocktail where commercial β- glucosidase was supplemented to the biomass hydrolyzing enzyme preparation. The cocktail supplemented with A unguis BGL preparation yielded 555mg/g sugar in 12h compared to the commercial enzyme preparation which gave only 333mg/g in the same period and the maximum sugar yield of 858 mg/g was attained in 36h by the cocktail containing A. unguis BGL. While the commercial enzyme achieved almost similar sugar yield in 24h, there was rapid drop in sugar concentration after that, indicating probably the conversion of glucose back to di-or oligosaccharides by the transglycosylation activity of the BGl in that preparation. Compared this, the A.unguis enzyme containing preparation supported peak yields for longer duration (upto 48h) which is important for biomass conversion to other products since the hydrolysate has to undergo certain unit operations before it goes into the next stage ie – fermentation in any bioprocesses for production of either fuels or chemicals.. Most importantly the Aspergillus unguis BGL preparation yields approximately 1.6 fold increase in the sugar release compared to the commercial BGL within 12h of time interval and 2.25 fold increase in the sugar release compared to the control ie. Cellulase without BGL supplementation. The current study therefore leads to the identification of a potent new isolate producing glucose tolerant β - glucosidase. The organism identified as Aspergillus unguis comes under the Aspergillus nidulans group where most of the GT-BGL producers belong and the detailed studies showed that the glucose tolerant β -glucosidase was a very low molecular weight protein which probably belongs to the glycosyl hydrolase family 3. Inhibition kinetic studies helped to understand the Ki and it is the second highest among the nidulans group of Aspergilli. This has promoted us for a detailed study regarding the mechanism of glucose tolerance. The proteomic 123 analyses clearly indicate the presence of GH3 catalytic domain in the protein. Since the size of the protein is very low and still its active and showed glucose tolerance it is speculated that this could be an entirely new protein or the modification of the existing β -glucosidase with only the catalytic domain present in it. Hydrolysis experiments also qualify this BGL, a suitable candidate for the enzyme cocktail development for biomass hydrolysis

Small-angle X-ray scattering and structural modeling of full-length: Cellobiohydrolase I from Trichoderma harzianum

Cellobiohydrolases hydrolyze cellulose releasing cellobiose units. They are very important for a number of biotechnological applications, such as, for example, production of cellulosic ethanol and cotton fiber processing. The Trichoderma cellobiohydrolase I (CBH1 or Cel7A) is an industrially important exocellulase. It exhibits a typical two domain architecture, with a small C-terminal cellulose-binding domain and a large N-terminal catalytic core domain, connected by an O-glycosylated linker peptide. The mechanism by which the linker mediates the concerted action of the two domains remains a conundrum. Here, we probe the protein shape and domain organization of the CBH1 of Trichoderma harzianum (ThCel7A) by small angle X-ray scattering (SAXS) and structural modeling. Our SAXS data shows that ThCel7A linker is partially-extended in solution. Structural modeling suggests that this linker conformation is stabilized by inter- and intra-molecular interactions involving the linker peptide and its O-glycosylations. © 2013 Springer Science+Business Media Dordrecht.

Aspergillus niger beta-Glucosidase Has a Cellulase-like Tadpole Molecular Shape INSIGHTS INTO GLYCOSIDE HYDROLASE FAMILY 3 (GH3) beta-GLUCOSIDASE STRUCTURE AND FUNCTION

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cellulose-binding domains promote hydrolysis of different sites on crystalline cellulose

The cohesin-dockerin interaction in Clostridium thermocellum cellulosome mediates the tight binding of cellulolytic enzymes to the cellulosome-integrating protein CipA. Here, this interaction was used to study the effect of different cellulose-binding domains (CBDs) on the enzymatic activity of C. thermocellum endoglucanase CelD (1,4-β-d endoglucanase, EC3.2.1.4) toward various cellulosic substrates. The seventh cohesin domain of CipA was fused to CBDs originating from the Trichoderma reesei cellobiohydrolases I and II (CBDCBH1 and CBDCBH2) (1,4-β-d glucan-cellobiohydrolase, EC3.2.1.91), from the Cellulomonas fimi xylanase/exoglucanase Cex (CBDCex) (β-1,4-d glucanase, EC3.2.1.8), and from C. thermocellum CipA (CBDCipA). The CBD-cohesin hybrids interacted with the dockerin domain of CelD, leading to the formation of CelD-CBD complexes. Each of the CBDs increased the fraction of cellulose accessible to hydrolysis by CelD in the order CBDCBH1 < CBDCBH2 ≈ CBDCex < CBDCipA. In all cases, the extent of hydrolysis was limited by the disappearance of sites accessible to CelD. Addition of a batch of fresh cellulose after completion of the reaction resulted in a new burst of activity, proving the reversible binding of the intact complexes despite the apparent binding irreversibility of some CBDs. Furthermore, burst of activity also was observed upon adding new batches of CelD–CBD complexes that contained a CBD differing from the first one. This complementation between different CBDs suggests that the sites made available for hydrolysis by each of the CBDs are at least partially nonoverlapping. The only exception was CBDCipA, whose sites appeared to overlap all of the other sites.