The use of carbohydrate binding modules (CBMs) to monitor changes in fragmentation and cellulose fiber surface morphology during cellulase- and Swollenin-induced deconstruction of lignocellulosic substrates

Chemical mapping of xyloglucan distribution and cellulose crystallinity in cotton textiles reveals novel enzymatic targets to improve clothing longevity

Pilling is a form of textile mechanical damage, forming fibrous bobbles on the surface of garments, resulting in premature disposal of clothing by consumers. However, our understanding on how the structural properties of the cellulosic matrix compliment the three-dimensional shape of cotton pills remains limited. This knowledge gap has hindered the development of effective 'pillase' technologies over the past 20 years due to challenges in balancing depilling efficacy with fabric integrity preservation. Therefore, the main focus here was characterising the role of cellulose and the hemicellulose components in cotton textiles to elucidate subtle differences between the chemistry of pills and fibre regions involved in structural integrity. State-of-the-art bioimaging using carbohydrate binding modules, monoclonal antibodies, and Leica SP8 and a Nikon A1R confocal microscopes, revealed the biophysical structure of cotton pills for the first time. Identifying regions of increased crystalline cellulose in the base of anchor fibres and weaker amorphous cellulose at dislocations in their centres, enhancing our understanding of current enzyme specificity. Surprisingly, pills contained a 7-fold increase in the concentration of xyloglucan compared to the main textile. Therefore, xyloglucan offers a previously undescribed target for overcoming this benefit-to-risk paradigm, suggesting a role for xyloglucanase enzymes in future pillase systems.

An aptamer highly specific to cellulose enables the analysis of the association of cellulose with matrix cell wall polymers in vitro and in muro

The current toolbox of cell wall-directed molecular probes has been pivotal for advancing basic and application-oriented plant carbohydrate research; however, it still exhibits limitations regarding target diversity and specificity. Scarcity of probes targeting intramolecular associations between cell wall polymers particularly hinders our understanding of the cell wall microstructure and affects the development of effective means for its efficient deconstruction for bioconversion. Here we report a detailed characterization of a cellulose-binding DNA aptamer CELAPT MINI using a combination of various in vitro biochemical, biophysical, and molecular biology techniques. Our results show evidence for its high specificity towards long non-substituted β-(1-4)-glucan chains in both crystalline and amorphous forms. Fluorescent conjugates of CELAPT MINI are applicable as in situ cellulose probes and are well suited for various microscopy techniques, including super-resolution imaging. Compatibility of fluorescent CELAPT MINI variants with immunodetection of cell wall matrix polymers enabled them simultaneously to resolve the fibrillar organization of complex cellulose-enriched pulp material and to quantify the level of cellulose masking by xyloglucan and xylan. Using enzymatically, chemically, or genetically modulated Brachypodium internode sections we showed the diversity in cell wall packing among various cell types and even cell wall microdomains. We showed that xylan is the most prominent, but not the only, cellulose-masking agent in Brachypodium internode tissues. These results collectively highlight the hitherto unexplored potential to expand the cell wall probing toolbox with highly specific and versatile in vitro generated polynucleotide probes.

Preparation of cellulose microfibril (CMF) from Gelidium amansii and feasibility of CMF as a cosmetic ingredient

Cellulose microfibrils (CMF) were successfully isolated from the red alga, Gelidium amansii. G. amansii was processed in two stages, microwave digestion and high-speed blending to remove agar and extract microfibrils, respectively. After pretreatment at 180 °C for 10 min, G. amansii containing 40.1 % glucan was microfibrillated through homogenization. Morphological analysis by SEM and FTIR, and analysis of the degree of fibrillation with water retention, sedimentation, and CtCBD3 protein binding of G. amansii-derived CMF were investigated. Functional analysis of CMF showed suppression of cyclooxygenase-2 expression in both in vitro and in vivo experiments. Additionally, suppression was evident in the: i) epidermal thickness of mice skin; ii) presence of proinflammatory cytokines; and iii) inhibition of JNK1/2 and p38 phosphorylation in human keratinocyte HaCaT cells. Such activity demonstrates its anti-inflammatory properties. The results in this study showed the possibility of using CMF derived from a red alga as an anti-inflammation material.

Expansin Engineering Database: A navigation and classification tool for expansins and homologues

Expansins have the remarkable ability to loosen plant cell walls and cellulose material without showing catalytic activity and therefore have potential applications in biomass degradation. To support the study of sequence-structure-function relationships and the search for novel expansins, the Expansin Engineering Database (ExED, https://exed.biocatnet.de) collected sequence and structure data on expansins from Bacteria, Fungi, and Viridiplantae, and expansin-like homologues such as carbohydrate binding modules, glycoside hydrolases, loosenins, swollenins, cerato-platanins, and EXPNs. Based on global sequence alignment and protein sequence network analysis, the sequences are highly diverse. However, many similarities were found between the expansin domains. Newly created profile hidden Markov models of the two expansin domains enable standard numbering schemes, comprehensive conservation analyses, and genome annotation. Conserved key amino acids in the expansin domains were identified, a refined classification of expansins and carbohydrate binding modules was proposed, and new sequence motifs facilitate the search of novel candidate genes and the engineering of expansins.

Elucidation of Changes in Cellulose Ultrastructure and Accessibility in Hardwood Fractionation Processes with Carbohydrate Binding Modules

We have recently presented a sequential treatment method, in which steam explosion (STEX) was followed by hydrotropic extraction (HEX), to selectively fractionate cellulose, hemicellulose, and lignin in hardwood into separate process streams. However, above a treatment severity threshold, the structural alterations in the cellulose-enriched fraction appeared to restrict the enzymatic hydrolyzability and delignification efficiency. To better understand the ultrastructural changes in the cellulose, hardwood chips were treated by single (STEX or HEX) and combined treatments (STEX and HEX), and the cellulose accessibility quantified with carbohydrate-binding modules (CBMs) that bind preferentially to crystalline (CBM2a) and paracrystalline cellulose (CBM17). Fluorescent-tagged versions of the CBMs were used to map the spatial distribution of cellulose substructures with confocal laser scanning microscopy. With increasing severities, STEX increased the apparent crystallinity (CBM2a/CBM17-ratio) and overall accessibility (CBM2aH6 + CBM17) of the cellulose, whereas HEX demonstrated the opposite trend. The respective effects could also be discerned in the combined treatments where increasing severities further resulted in higher hemicellulose dissolution and, although initially beneficial, in stagnating accessibility and hydrolyzability. This study suggests that balancing the severities in the two treatments is required to maximize the fractionation and simultaneously achieve a reactive and accessible cellulose that is readily hydrolyzable.

Quantifying cellulose accessibility during enzyme-mediated deconstruction using 2 fluorescence-tagged carbohydrate-binding modules

Two fluorescence-tagged carbohydrate-binding modules (CBMs), which specifically bind to crystalline (CBM2a-RRedX) and paracrystalline (CBM17-FITC) cellulose, were used to differentiate the supramolecular cellulose structures in bleached softwood Kraft fibers during enzyme-mediated hydrolysis. Differences in CBM adsorption were elucidated using confocal laser scanning microscopy (CLSM), and the structural changes occurring during enzyme-mediated deconstruction were quantified via the relative fluorescence intensities of the respective probes. It was apparent that a high degree of order (i.e., crystalline cellulose) occurred at the cellulose fiber surface, which was interspersed by zones of lower structural organization and increased cellulose accessibility. Quantitative image analysis, supported by 13C NMR, scanning electron microscopy (SEM) imaging, and fiber length distribution analysis, showed that enzymatic degradation predominates at these zones during the initial phase of the reaction, resulting in rapid fiber fragmentation and an increase in cellulose surface crystallinity. By applying this method to elucidate the differences in the enzyme-mediated deconstruction mechanisms, this work further demonstrated that drying decreased the accessibility of enzymes to these disorganized zones, resulting in a delayed onset of degradation and fragmentation. The use of fluorescence-tagged CBMs with specific recognition sites provided a quantitative way to elucidate supramolecular substructures of cellulose and their impact on enzyme accessibility. By designing a quantitative method to analyze the cellulose ultrastructure and accessibility, this study gives insights into the degradation mechanism of cellulosic substrates.

Combined in situ Physical and ex-situ Biochemical Approaches to Investigate in vitro Deconstruction of Destarched Wheat Bran by Enzymes Cocktail Used in Animal Nutrition

Wheat bran is a foodstuff containing more than 40% of non-starch polysaccharides (NSPs) that are hardly digestible by monogastric animals. Therefore, cocktails enriched of hydrolytic enzymes (termed NSPases) are commonly provided as feed additives in animal nutrition. However, how these enzymes cocktails contribute to NSPs deconstruction remains largely unknown. This question was addressed by employing an original methodology that makes use of a multi-instrumented bioreactor that allows to dynamically monitor enzymes in action and to extract in-situ physical and ex-situ biochemical data from this monitoring. We report here that the deconstruction of destarched wheat bran by an industrial enzymes cocktail termed Rovabio® was entailed by two concurrent events: a particles fragmentation that caused in <2 h a 70% drop of the suspension viscosity and a solubilization that released <30 % of the wheat bran NSPs. Upon longer exposure, the fragmentation of particles continued at a very slow rate without any further solubilization. Contrary to this cocktail, xylanase C alone caused a moderate 25% drop of viscosity and a very weak fragmentation. However, the amount of xylose and arabinose from solubilized sugars after 6 h treatment with this enzyme was similar to that obtained after 2 h with Rovabio®. Altogether, this multi-scale analysis supported the synergistic action of enzymes mixture to readily solubilize complex polysaccharides, and revealed that in spite of the richness and diversity of hydrolytic enzymes in the cocktail, the deconstruction of NSPs in wheat bran was largely incomplete.

Binding and hydrolysis properties of engineered cellobiohydrolases and endoglucanases

Because cellulase was the main enzyme used in bioconversion of lignocellulose, it was a valid way to reduce the hydrolysis cost by increasing the adsorption and hydrolysis efficiency of cellulase. In this study, modified cellobiohydrolases (CBHs) and endoglucanases (EGs) were constructed. Two engineered cellulases CBH-TrCBM^{V27E,P30D,Link1} and EG-TrCBM^{V27E,P30D,Link1} well-performed during hydrolysis. Compared to wild-type enzymes, EG-TrCBM^{V27E,P30D,Link1} had relatively less adsorption ability to lignin and greater affinity to cellulose, especially Avicel. However, for CBH-TrCBM^{V27E,P30D,Link1}, the hydrolysis manner was changed and in favor to hydrolysis process, although the adsorption properties were unexpected. It suggested that various binding conformations of polysaccharide on CBMs hypothetically resulted in different functions of CBMs, including binding ability, processive and digestive properties on fiber surface. Fusion of T. r-CBM^{V27E,P30D,Link1} to cellulase, both CBH and EG, gave the destruction ability of enzyme and increased the accessible surface of substrate to cellulase, enhanced the adsorption and hydrolysis efficiency of cellulase.

Comparison of catalytically non-productive adsorption of fungal proteins to lignins and pseudo-lignin using isobaric mass tagging

Catalytically non-productive adsorption of fungal enzymes to pseudo-lignin (PL) was compared to adsorption to lignin preparations derived from different sources (SL, spruce; BL, birch; OL, beech) using different methods [steam pretreatment/enzymatic saccharification (SL, BL) and organosolv processing (OL)]. The protein adsorption to the SL was more extensive than the adsorption to the hardwood lignins, which was relatively similar to the adsorption to the PL. The adsorption patterns of 13 individual proteins were studied using isobaric mass tagging with TMTsixplex reagent and LC-MS/MS analysis. The results suggest that, on an average, adsorption of proteins equipped with carbohydrate-binding modules, such as the cellulases CBHI, EGII, and EGIV, was less dependent on the quality of the lignin/PL than adsorption of other proteins, such as β-Xyl, Xyn-1, and Xyn-2, which are involved in xylan degradation.

Monitoring Polysaccharide Dynamics in the Plant Cell Wall

New technologies reveal the deposition and remodeling of plant cell wall polysaccharides and their impact on plant development.

Pichia pastoris is a Suitable Host for the Heterologous Expression of Predicted Class I and Class II Hydrophobins for Discovery, Study, and Application in Biotechnology

The heterologous expression of proteins is often a crucial first step in not only investigating their function, but also in their industrial application. The functional assembly and aggregation of hydrophobins offers intriguing biotechnological applications from surface modification to drug delivery, yet make developing systems for their heterologous expression challenging. In this article, we describe the development of Pichia pastoris KM71H strains capable of solubly producing the full set of predicted Cordyceps militaris hydrophobins CMil1 (Class IA), CMil2 (Class II), and CMil3 (IM) at mg/L yields with the use of 6His-tags not only for purification but for their detection. This result further demonstrates the feasibility of using P. pastoris as a host organism for the production of hydrophobins from all Ascomycota Class I subdivisions (a classification our previous work defined) as well as Class II. We highlight the specific challenges related to the production of hydrophobins, notably the challenge in detecting the protein that will be described, in particular during the screening of transformants. Together with the literature, our results continue to show that P. pastoris is a suitable host for the soluble heterologous expression of hydrophobins with a wide range of properties.

Determination of optimal biomass pretreatment strategies for biofuel production: investigation of relationships between surface-exposed polysaccharides and their enzymatic conversion using carbohydrate-binding modules

BACKGROUND

Pretreatment of lignocellulosic biomass (LCB) is a key step for its efficient bioconversion into ethanol. Determining the best pretreatment and its parameters requires monitoring its impacts on the biomass material. Here, we used fluorescent protein-tagged carbohydrate-binding modules method (FTCM)-depletion assay to study the relationship between surface-exposed polysaccharides and enzymatic hydrolysis of LCB.

RESULTS

Our results indicated that alkali extrusion pretreatment led to the highest hydrolysis rates for alfalfa stover, cattail stems and flax shives, despite its lower lignin removal efficiency compared to alkali pretreatment. Corn crop residues were more sensitive to alkali pretreatments, leading to higher hydrolysis rates. A clear relationship was consistently observed between total surface-exposed cellulose detected by the FTCM-depletion assay and biomass enzymatic hydrolysis. Comparison of bioconversion yield and total composition analysis (by NREL/TP-510-42618) of LCB prior to or after pretreatments did not show any close relationship. Lignin removal efficiency and total cellulose content (by NREL/TP-510-42618) led to an unreliable prediction of enzymatic polysaccharide hydrolysis.

CONCLUSIONS

Fluorescent protein-tagged carbohydrate-binding modules method (FTCM)-depletion assay provided direct evidence that cellulose exposure is the key determinant of hydrolysis yield. The clear and robust relationships that were observed between the cellulose accessibility by FTCM probes and enzymatic hydrolysis rates change could be evolved into a powerful prediction tool that might help develop optimal biomass pretreatment strategies for biofuel production.

Predicting the most appropriate wood biomass for selected industrial applications: comparison of wood, pulping, and enzymatic treatments using fluorescent-tagged carbohydrate-binding modules

BACKGROUND

Lignocellulosic biomass will progressively become the main source of carbon for a number of products as the Earth's oil reservoirs disappear. Technology for conversion of wood fiber into bioproducts (wood biorefining) continues to flourish, and access to reliable methods for monitoring modification of such fibers is becoming an important issue. Recently, we developed a simple, rapid approach for detecting four different types of polymer on the surface of wood fibers. Named fluorescent-tagged carbohydrate-binding module (FTCM), this method is based on the fluorescence signal from carbohydrate-binding modules-based probes designed to recognize specific polymers such as crystalline cellulose, amorphous cellulose, xylan, and mannan.

RESULTS

Here we used FTCM to characterize pulps made from softwood and hardwood that were prepared using Kraft or chemical-thermo-mechanical pulping. Comparison of chemical analysis (NREL protocol) and FTCM revealed that FTCM results were consistent with chemical analysis of the hemicellulose composition of both hardwood and softwood samples. Kraft pulping increased the difference between softwood and hardwood surface mannans, and increased xylan exposure. This suggests that Kraft pulping leads to exposure of xylan after removal of both lignin and mannan. Impact of enzyme cocktails from Trichoderma reesei (Celluclast 1.5L) and from Aspergillus sp. (Carezyme 1000L) was investigated by analysis of hydrolyzed sugars and by FTCM. Both enzymes preparations released cellobiose and glucose from pulps, with the cocktail from Trichoderma being the most efficient. Enzymatic treatments were not as effective at converting chemical-thermomechanical pulps to simple sugars, regardless of wood type. FTCM revealed that amorphous cellulose was the primary target of either enzyme preparation, which resulted in a higher proportion of crystalline cellulose on the surface after enzymatic treatment. FTCM confirmed that enzymes from Aspergillus had little impact on exposed hemicelluloses, but that enzymes from the more aggressive Trichoderma cocktail reduced hemicelluloses at the surface.

CONCLUSIONS

Overall, this study indicates that treatment with enzymes from Trichoderma is appropriate for generating crystalline cellulose at fiber surface. Applications such as nanocellulose or composites requiring chemical resistance would benefit from this enzymatic treatment. The milder enzyme mixture from Aspergillus allowed for removal of amorphous cellulose while preserving hemicelluloses at fiber surface, which makes this treatment appropriate for new paper products where surface chemical responsiveness is required.

Hydrolytic potential of five fungal supernatants to enhance a commercial enzyme cocktail

Objectives

To evaluate the potential of enzyme cocktails produced by five filamentous fungi to supplement the industrial cellulase cocktail, Celluclast 1.5L, in order to improve the efficiency of saccharification.

Results

The fungi were cultivated on wheat bran and the resulting supernatants were combined with Celluclast in enzymatic hydrolysis experiments to test their ability to hydrolyze wheat bran and five cellulose-rich substrates. The supernatant showing the best performance was that from an Aspergillus niger cellulase mutant. The addition of β-glucosidase only to the Celluclast cocktail was not as beneficial.

Conclusion

Supplementing commercial cocktails with enzymes from carefully selected fungi may result in significantly more efficient saccharification of lignocellulosic materials. Furthermore, such an approach could lead to the identification of novel enzyme activities crucial for saccharification.

Functional characterization of the native swollenin from Trichoderma reesei: study of its possible role as C1 factor of enzymatic lignocellulose conversion

BACKGROUND

Through binding to cellulose, expansin-like proteins are thought to loosen the structural order of crystalline surface material, thus making it more accessible for degradation by hydrolytic enzymes. Swollenin SWO1 is the major expansin-like protein from the fungus Trichoderma reesei. Here, we have performed a detailed characterization of a recombinant native form of SWO1 with respect to its possible auxiliary role in the enzymatic saccharification of lignocellulosic substrates.

RESULTS

The swo1 gene was overexpressed in T. reesei QM9414 Δxyr1 mutant, featuring downregulated cellulase production, and the protein was purified from culture supernatant. SWO1 was N-glycosylated and its circular dichroism spectrum suggested a folded protein. Adsorption isotherms (25 °C, pH 5.0, 1.0 mg substrate/mL) revealed SWO1 to be 120- and 20-fold more specific for binding to birchwood xylan and kraft lignin, respectively, than for binding to Avicel PH-101. The SWO1 binding capacity on lignin (25 µmol/g) exceeded 12-fold that on Avicel PH-101 (2.1 µmol/g). On xylan, not only the binding capacity (22 µmol/g) but also the affinity of SWO1 (K d = 0.08 µM) was enhanced compared to Avicel PH-101 (K d = 0.89 µM). SWO1 caused rapid release of a tiny amount of reducing sugars (<1 % of total) from different substrates (Avicel PH-101, nanocrystalline cellulose, steam-pretreated wheat straw, barley β-glucan, cellotetraose) but did not promote continued saccharification. Atomic force microscopy revealed that amorphous cellulose films were not affected by SWO1. Also with AFM, binding of SWO1 to cellulose nanocrystallites was demonstrated at the single-molecule level, but adsorption did not affect this cellulose. SWO1 exhibited no synergy with T. reesei cellulases in the hydrolysis of the different celluloses. However, SWO1 boosted slightly (1.5-fold) the reducing sugar release from a native grass substrate.

CONCLUSIONS

SWO1 is a strongly glycosylated protein, which has implications for producing it in heterologous hosts. Although SWO1 binds to crystalline cellulose, its adsorption to xylan is much stronger. SWO1 is not an auxiliary factor of the enzymatic degradation of a variety of cellulosic substrates. Effect of SWO1 on sugar release from intact plant cell walls might be exploitable with certain (e.g., mildly pretreated) lignocellulosic feedstocks.

Understanding the structure and function of bacterial expansins: a prerequisite towards practical applications for the bioenergy and agricultural industries

Since the publication of a landmark article on the structure of EXLX1 from Bacillus subtilis in 2011, our knowledge of bacterial expansins has steadily increased and our view and understanding of these enigmatic proteins has advanced with relation to their structure, phylogenetic relationships and substrate interaction, although the molecular basis for their mechanism of action remains to be determined. Lignocellulosic material represents a source of fermentable sugars for the production of biofuels, and cell‐wall degrading activities are essential to efficiently release such sugars from their polymeric structures. Because expansins from fungi and bacteria seem to be required to properly colonize or cause disease to plant tissues, and because they share some characteristics with their plant counterparts for loosening the cell wall they have been seen as a promising tool to overcome the recalcitrance of these materials. However, microbial expansins activity is at best, very low compared with plant expansins activity. This revision analyses recent work on bacterial expansins structure, function and biological role, emphasizing our need to focus on their mechanism of action as a means to design better strategies for their use, in both in the energy and agricultural industries.

The binding of cellulase variants to dislocations: a semi-quantitative analysis based on CLSM (confocal laser scanning microscopy) images

Binding of enzymes to the substrate is the first step in enzymatic hydrolysis of lignocellulose, a key process within biorefining. During this process elongated plant cells such as fibers and tracheids have been found to break into segments at irregular cell wall regions known as dislocations or slip planes. Here we study whether cellulases bind to dislocations to a higher extent than to the surrounding cell wall. The binding of fluorescently labelled cellobiohydrolases and endoglucanases to filter paper fibers was investigated using confocal laser scanning microscopy and a ratiometric method was developed to assess and quantify the abundance of the binding of cellulases to dislocations as compared to the surrounding cell wall. Only Humicola insolens EGV was found to have stronger binding preference to dislocations than to the surrounding cell wall, while no difference in binding affinity was seen for any of the other cellulose variants included in the study (H. insolens EGV variants, Trichoderma reesei CBHI, CBHII and EGII). This result favours the hypothesis that fibers break at dislocations during the initial phase of hydrolysis mostly due to mechanical failure rather than as a result of faster degradation at these locations.

Bacterial expansins and related proteins from the world of microbes

The discovery of microbial expansins emerged from studies of the mechanism of plant cell growth and the molecular basis of plant cell wall extensibility. Expansins are wall-loosening proteins that are universal in the plant kingdom and are also found in a small set of phylogenetically diverse bacteria, fungi, and other organisms, most of which colonize plant surfaces. They loosen plant cell walls without detectable lytic activity. Bacterial expansins have attracted considerable attention recently for their potential use in cellulosic biomass conversion for biofuel production, as a means to disaggregate cellulosic structures by nonlytic means ("amorphogenesis"). Evolutionary analysis indicates that microbial expansins originated by multiple horizontal gene transfers from plants. Crystallographic analysis of BsEXLX1, the expansin from Bacillus subtilis, shows that microbial expansins consist of two tightly packed domains: the N-terminal domain D1 has a double-ψ β-barrel fold similar to glycosyl hydrolase family-45 enzymes but lacks catalytic residues usually required for hydrolysis; the C-terminal domain D2 has a unique β-sandwich fold with three co-linear aromatic residues that bind β-1,4-glucans by hydrophobic interactions. Genetic deletion of expansin in Bacillus and Clavibacter cripples their ability to colonize plant tissues. We assess reports that expansin addition enhances cellulose breakdown by cellulase and compare expansins with distantly related proteins named swollenin, cerato-platanin, and loosenin. We end in a speculative vein about the biological roles of microbial expansins and their potential applications. Advances in this field will be aided by a deeper understanding of how these proteins modify cellulosic structures.