The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism o
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Mahoney, Brendan J.↗
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Lignin-enzyme interaction: A roadblock for efficient enzymatic hydrolysis of lignocellulosics
Efficiently producing second-generation biofuels from biomass is of strategic significance and meets sustainability targets, but it remains a long-term challenge due to the existence of biomass recalcitrance. Lignin contributes significantly to biomass recalcitrance by physically limiting the access of enzymes to carbohydrates, and this could be partially overcome by applying a pretreatment step to directly target lignin. However, lignin typically cannot be completely removed, and its structure is also significantly altered during the pretreatment. As a result, lignin residue in the pretreated materials still significantly hindered a complete conversion of carbohydrate to its monosugars by interacting with cellulase enzymes. The non-productive adsorption driven by hydrophobic, electrostatic, and/or hydrogen bonding interactions is widely considered as the major mechanism of action governing the unfavored lignin-enzyme interaction. One could argue this type of interaction between lignin residue and the activated enzymes is the major roadblock for efficient enzymatic hydrolysis of pretreated lignocellulosics. To alleviate the negative effects of lignin on enzyme performance, a deep understanding of lignin structural transformation upon different types of pretreatments as well as how and where does lignin bind to enzymes are prerequisites. In the last decade, the progress toward a fundamental understanding of lignin-enzyme interaction, structural characterization of lignin during pretreatment and/or conformation change of enzyme during hydrolysis is resulting in advances in the development of methodologies to mitigate the negative effect of lignin. Here in this review, the lignin structural transformation upon different types of pretreatments and the inhibition mechanism of lignin in the bioconversion of lignocellulose to bioethanol are summarized. Some technologies to minimize the adverse impact of lignin on the enzymatic hydrolysis, including chemical modification of lignin, adding blocking additives, and post-treatment to remove lignin were also introduced. The production of liquid biofuels from lignocellulosic biomass has shown great environmental benefits such as reducing greenhouse gas emissions and mitigate climate change. By addressing the root causes of lignin-enzyme interaction and how to retard this interaction, it is our hope that this comprehensive review will pave the way for significantly reducing the high cost associated with the enzymatic hydrolysis process, and ultimately achieving a cost-effective and sustainable biorefinery system.
09 BIOMASS FUELS↗
A Swollenin From Talaromyces leycettanus JCM12802 Enhances Cellulase Hydrolysis Toward Various Substrates
Swollenins exist within some fungal species and are candidate accessory proteins for the biodegradation of cellulosic substrates. Here, we describe the identification of a swollenin gene, Tlswo , in Talaromyces leycettanus JCM12802. Tlswo was successfully expressed in both Trichoderma reesei and Pichia pastoris . Assay results indicate that Tl SWO is capable of releasing reducing sugars from lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin. The specific activity of Tl SWO toward lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin is 9.0 ± 0.100, 8.9 ± 0.100, 2.3 ± 0.002 and 0.79 ± 0.002 U/mg, respectively. Additionally, Tl SWO had disruptive activity on Avicel and a synergistic effect with cellobiohydrolases, increasing the activity on pretreated corn stover by up to 72.2%. The functional diversity of Tl SWO broadens its applicability in experimental settings, and indicating that it may be a promising candidate for future industrial applications.
59 BASIC BIOLOGICAL SCIENCES↗
Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non‐productive binding: insights from crystal structures and MD simulation
Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) ( EC3.2.1.176 ) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p‐ nitrophenyl‐β‐ d ‐cellobioside (pNPC), p‐ nitrophenyl‐β‐ d ‐lactoside (pNPL) and methylumbelliferyl‐β‐ d ‐cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o‐nitrophenyl‐β‐ d ‐cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium . Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non‐productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non‐productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates ( k cat ) than TrCel7A, but higher Michaelis–Menten ( K M ) constants as well. Furthermore, oNPC turned out to be useful as an active‐site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.
59 BASIC BIOLOGICAL SCIENCES↗
Uncovering Sequence and Structural Characteristics of Fungal Expansin‐Related Proteins With Potential to Drive Substrate Targeting
Expansins loosen plant cell wall networks through disrupting non-covalent bonds between cellulose microfibrils and matrix polysaccharides. Whereas expansins were first discovered in plants, expansin-related proteins have since been identified in bacteria and fungi. The biological function of microbial expansins remains unclear; however, several studies have shown distinct binding preferences toward different structural polysaccharides. Earlier studies of bacterial expansin-related proteins uncovered sequence and structural features that correlate to substrate binding. Herein, 20 fungal expansin-related sequences were recombinantly produced in Komagataella phaffii, and the purified proteins were compared in terms of substrate binding to cellulosic and chitinous substrates. The impact of pH on the zeta potential of prioritized substrates was also measured, and Principal Component Analysis was performed to uncover correlations between protein characteristics (e.g., pI, hydrophobicity, surface charge distribution) and measured substrate binding preferences. Whereas acidic proteins with a predicted pI less than 5.0 preferentially bound to chitin, basic proteins with pI greater than 8.0 preferentially bound to xylan and xylan-containing fiber. Similar to many cellulases, binding to cellulose was correlated to relatively high aromatic amino acid content in the protein sequence and presence of a carbohydrate binding module (CBM), which in the case of expansins is a C-terminal CBM63. Whereas overall sequence characteristics could be correlated to substrate binding preference, the identity of amino acids occupying conserved positions that impact protein activity was better correlated with loosenin versus expansin classifications.
chitin↗
Substrate-Dependent Cellulose Saccharification Efficiency and LPMO Activity of Cellic CTec2 and a Cellulolytic Secretome from Thermoascus aurantiacus and the Impact of H 2 O 2 -Producing Glucose Oxidase
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Effect of Dilute Acetic Acid Hydrolysis on Xylooligosaccharide Production and the Inhibitory Effect of Cellulolytic Enzyme Lignin from Poplar
Acetic acid (AC) hydrolysis has been reported to prepare xylooligosaccharides (XOS) from poplar. However, the influence of AC hydrolysis on the lignin structure changes is not clear, which is important for the following enzymatic hydrolysis of poplar. Herein, AC was used to produce XOS, and cellulase adsorption on cellulolytic enzyme lignin (CEL) from AC-hydrolyzed poplar and its inhibitory effect on two commercial cellulase preparations were investigated. AC hydrolysis gave a XOS yield of 39.8% from poplar. After AC hydrolysis at 170 °C, the hydrophobicity and ζ-potential of CEL decreased to 2.3 L/g and 14.8 mV, respectively. The adsorption strength of CTec2 on CEL samples did not increase by AC hydrolysis, and the inhibitory effect of CEL on Celluclast 1.5L and β-glucosidase was observed, but not on CTec2. CEL samples improved the lytic polysaccharide monooxygenase (LPMO) activity of the enzymatic hydrolysis by CTec2. After CEL samples were added in enzymatic hydrolysis, the free filter paper activity of Celluclast 1.5L and β-G retained in the enzymatic hydrolysate decreased from 60.5 to 29.3–42.9%. The addition of CEL samples in enzymatic hydrolysis could not decrease the free filter paper activity of CTec2 retained in the enzymatic hydrolysate. In the enzymatic hydrolysis with CEL samples, higher glucose yields were obtained by CTec2 than those by Celluclast 1.5L and β-glucosidase. This work will help to understand the structure and inhibitory effects of AC-CELs and guide the development of AC hydrolysis for the production of XOS and monosaccharides from poplar.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cellulolytic enzymes production guided by morphology engineering
Not provided.
Biotechnology & Applied Microbiology↗
Protective effects of non–catalytic proteins on endoglucanase activity at air and lignin interfaces
The manner in which added non-catalytic proteins during enzymatic hydrolysis of lignocellulosic substrates enhances hydrolysis mechanisms is not completely understood. Prior research has indicated that a reduction in the non-specific adsorption of enzymes on lignin, and deactivation of enzymes exposed to air–liquid interface provide rationale. This work investigated root causes including effects of the air–liquid interface on non-catalytic proteins, and effects of lignin on endoglucanase. Three different experimental designs and three variables (air–liquid interfacial area, the types of lignin (acid or enzymatic lignin), and the presence of non-enzymatic protein (bovine serum albumin [BSA] or soy proteins ) were used. The results showed that acid isolated lignin adsorbed almost all endoglucanase activity initially present in supernatant, independent of air interface conditions (25 or 250 ml flasks) with the presence of BSA preventing this effect. Endoglucanase lost 30%–50% of its activity due to an air–liquid interface in the presence of lignin while addition of non-enzymatic protein helped to preserve this enzyme's activity. Langmuir and Freundlich models applied to experimental data indicated that the adsorption increases with increasing temperature for both endoglucanase and BSA. Adsorption of the enzyme and protein were endothermic with an increase in entropy. Finally, these results, combined, show that hydrophobicity plays a strong role in the adsorption of both endoglucanase and BSA on lignin.
59 BASIC BIOLOGICAL SCIENCES↗
Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei : a Molecular Dynamics Approach
Trichoderma reesei is a ‘workhorse’ fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on two side-chain hemicellulases, a-L-arabinofuranosidases and a-D-galactosidases, which are important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render these enzymes inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D-protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of proteins when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized proteins. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized proteins, implying a less favorable reaction pathway. These results reveal the basis for loss of function in these carbohydrate active enzymes (CAZYs) in T. reesei.
60 APPLIED LIFE SCIENCES↗
A genomic analysis reveals the diversity of cellulosome displaying bacteria
Introduction Several species of cellulolytic bacteria display cellulosomes, massive multi-cellulase containing complexes that degrade lignocellulosic plant biomass (LCB). A greater understanding of cellulosome structure and enzyme content could facilitate the development of new microbial-based methods to produce renewable chemicals and materials. Methods To identify novel cellulosome-displaying microbes we searched 305,693 sequenced bacterial genomes for genes encoding cellulosome proteins; dockerin-fused glycohydrolases (DocGHs) and cohesin domain containing scaffoldins. Results and discussion This analysis identified 33 bacterial species with the genomic capacity to produce cellulosomes, including 10 species not previously reported to produce these complexes, such asAcetivibrio mesophilus. Cellulosome-producing bacteria primarily originate from theAcetivibrio, Ruminococcus, Ruminiclostridium, andClostridiumgenera. A rigorous analysis of their enzyme, scaffoldin, dockerin, and cohesin content reveals phylogenetically conserved features. Based on the presence of a high number of genes encoding both scaffoldins and dockerin-fused GHs, the cellulosomes inAcetivibrioandRuminococcusbacteria possess complex architectures that are populated with a large number of distinct LCB degrading GH enzymes. Their complex cellulosomes are distinguishable by their mechanism of attachment to the cell wall, the structures of their primary scaffoldins, and by how they are transcriptionally regulated. In contrast, bacteria in theRuminiclostridiumandClostridiumgenera produce ‘simple’ cellulosomes that are constructed from only a few types of scaffoldins that based on their distinct complement of GH enzymes are predicted to exhibit high and low cellulolytic activity, respectively. Collectively, the results of this study reveal conserved and divergent architectural features in bacterial cellulosomes that could be useful in guiding ongoing efforts to harness their cellulolytic activities for bio-based chemical and materials production.
Microbiology↗