Patricia Bubner

Cellulose surface degradation by a lytic polysaccharide monooxygenase and its effect on cellulase hydrolytic efficiency

Background: Lytic polysaccharide monooxygenase (LPMO) has recently been discovered to depolymerize cellulose. Results: Dynamic imaging was applied to reveal the effects of LPMO and cellulase activity on solid cellulose surface. Conclusion: Critical features of surface morphology for LPMO synergy with cellulases are recognized. Significance: Direct insights into cellulose deconstruction by LPMO alone and in synergy with cellulases are obtained. Lytic polysaccharide monooxygenase (LPMO) represents a unique principle of oxidative degradation of recalcitrant insoluble polysaccharides. Used in combination with hydrolytic enzymes, LPMO appears to constitute a significant factor of the efficiency of enzymatic biomass depolymerization. LPMO activity on different cellulose substrates has been shown from the slow release of oxidized oligosaccharides into solution, but an immediate and direct demonstration of the enzyme action on the cellulose surface is lacking. Specificity of LPMO for degrading ordered crystalline and unordered amorphous cellulose material of the substrate surface is also unknown. We show by fluorescence dye adsorption analyzed with confocal laser scanning microscopy that a LPMO (from Neurospora crassa) introduces carboxyl groups primarily in surface-exposed crystalline areas of the cellulosic substrate. Using time-resolved in situ atomic force microscopy we further demonstrate that cellulose nano-fibrils exposed on the surface are degraded into shorter and thinner insoluble fragments. Also using atomic force microscopy, we show that prior action of LPMO enables cellulases to attack otherwise highly resistant crystalline substrate areas and that it promotes an overall faster and more complete surface degradation. Overall, this study reveals key characteristics of LPMO action on the cellulose surface and suggests the effects of substrate morphology on the synergy between LPMO and hydrolytic enzymes in cellulose depolymerization.

Dissecting and reconstructing synergism - in situ visualization of cooperativity among cellulases

Background: Synergistic interplay of cellulases is key for efficiency of cellulose hydrolysis. Results: In situ observation of individual and synergistic action of endo- and exo-cellulases on a polymorphic cellulose substrate reveals specificity of individual enzyme components for crystalline or amorphous regions. Conclusion: Cellulase synergism is governed by mesoscopic morphological characteristics of the cellulose substrate. Significance: Advanced knowledge basis for rational optimization of cellulose saccharification. Cellulose is the most abundant biopolymer and a major reservoir of fixed carbon on earth. Comprehension of the elusive mechanism of its enzymatic degradation represents a fundamental problem at the interface of biology, biotechnology, and materials science. The interdependence of cellulose disintegration and hydrolysis and the synergistic interplay among cellulases is yet poorly understood. Here we report evidence from in situ atomic force microscopy (AFM) that delineates degradation of a polymorphic cellulose substrate as a dynamic cycle of alternating exposure and removal of crystalline fibers. Direct observation shows that chain-end-cleaving cellobiohydrolases (CBH I, CBH II) and an internally chain-cleaving endoglucanase (EG), the major components of cellulase systems, take on distinct roles: EG and CBH II make the cellulose surface accessible for CBH I by removing amorphous-unordered substrate areas, thus exposing otherwise embedded crystalline-ordered nanofibrils of the cellulose. Subsequently, these fibrils are degraded efficiently by CBH I, thereby uncovering new amorphous areas. Without prior action of EG and CBH II, CBH I was poorly active on the cellulosic substrate. This leads to the conclusion that synergism among cellulases is morphology-dependent and governed by the cooperativity between enzymes degrading amorphous regions and those targeting primarily crystalline regions. The surface-disrupting activity of cellulases therefore strongly depends on mesoscopic structural features of the substrate: size and packing of crystalline fibers are key determinants of the overall efficiency of cellulose degradation.

Visualizing cellulase activity

Commercial exploitation of lignocellulose for biotechnological production of fuels and commodity chemicals requires efficient—usually enzymatic—saccharification of the highly recalcitrant insoluble substrate. A key characteristic of cellulose conversion is that the actual hydrolysis of the polysaccharide chains is intrinsically entangled with physical disruption of substrate morphology and structure. This “substrate deconstruction” by cellulase activity is a slow, yet markedly dynamic process that occurs at different length scales from and above the nanometer range. Little is currently known about the role of progressive substrate deconstruction on hydrolysis efficiency. Application of advanced visualization techniques to the characterization of enzymatic degradation of different celluloses has provided important new insights, at the requisite nano‐scale resolution and down to the level of single enzyme molecules, into cellulase activity on the cellulose surface. Using true in situ imaging, dynamic features of enzyme action and substrate deconstruction were portrayed at different morphological levels of the cellulose, thus providing new suggestions and interpretations of rate‐determining factors. Here, we review the milestones achieved through visualization, the methods which significantly promoted the field, compare suitable (model) substrates, and identify limiting factors, challenges and future tasks. Biotechnol. Bioeng. 2013; 110: 1529–1549.

Cellulases Dig Deep IN SITU OBSERVATION OF THE MESOSCOPIC STRUCTURAL DYNAMICS OF ENZYMATIC CELLULOSE DEGRADATION

Background: The exact mechanism by which cellulases degrade cellulose is still elusive. Results: An empirical model of the structural dynamics of cellulose degradation is shown. Conclusion: Enzymatic cellulose hydrolysis is subjected to deceleration and acceleration caused by periodically emerging internal limitations and overcoming them. Significance: Understanding structural dynamics of enzymatic cellulose disintegration is pivotal for making biofuel production from lignocellulosic feedstock economic. Enzymatic hydrolysis of cellulose is key for the production of second generation biofuels, which represent a long-standing leading area in the field of sustainable energy. Despite the wealth of knowledge about cellulase structure and function, the elusive mechanism by which these enzymes disintegrate the complex structure of their insoluble substrate, which is the gist of cellulose saccharification, is still unclear. We herein present a time-resolved structural characterization of the action of cellulases on a nano-flat cellulose preparation, which enabled us to overcome previous limitations, using atomic force microscopy (AFM). As a first step in substrate disintegration, elongated fissures emerge which develop into coniform cracks as disintegration continues. Detailed data analysis allowed tracing the surface evolution back to the dynamics of crack morphology. This, in turn, reflects the interplay between surface degradation inside and outside of the crack. We observed how small cracks evolved and initially increased in size. At a certain point, the crack diameter stagnated and then started decreasing again. Stagnation corresponds with a decrease in the total amount of surface which is fissured and thus leads to the conclusion that the surface hydrolysis “around” the cracks is proceeding more rapidly than inside the cracks. The mesoscopic view presented here is in good agreement with various mechanistic proposals from the past and allows a novel insight into the structural dynamics occurring on the cellulosic substrate through cellulase action.

Surface structural dynamics of enzymatic cellulose degradation, revealed by combined kinetic and atomic force microscopy studies

Highly heterogeneous and usually weakly defined substrate morphologies complicate the study of enzymatic cellulose hydrolysis. The cellulose surface has a non‐uniform shape in particular, with consequent impacts on cellulase adsorption and activity. We have therefore prepared a cellulosic model substrate which is shown by atomic force microscopy (AFM) to display a completely smooth surface, the residual squared mean roughness being 10 nm or lower, and applied it for kinetic analysis of cellulase action. The substrate consists of an amorphous cellulose matrix into which variably sized crystalline fibers are distributed in apparently irregular fashion. Its conversion into soluble sugars by Trichoderma sp. cellulase at 50 °C proceeded without apparent limitation up to 70% completion and was paralleled by a steady increase in cellulase adsorption to the cellulose. Individual cellulase components (CBH I, CBH II, EG) also showed strongly enhanced adsorption with progressing cellulose conversion, irrespective of their preference for degrading the amorphous or crystalline substrate parts as revealed by AFM. The specific activity of the adsorbed cellulases, however, decreased concomitantly. Cellulose surface morphologies evolving as a consequence of cellulase action were visualized by AFM. Three‐dimensional surface degradation by the cellulases resulted in a large increase in cellulose surface area for enzyme adsorption. However, the decline in enzyme specific activity during conversion was caused by factors other than surface ablation and disruption. Based on kinetic evidence for enzymatic hydrolyses of the smooth‐surface model substrate and microcrystalline cellulose (Avicel), we hypothesize that, due to gradual loss of productive dynamics in their interactions with the cellulose surface, individual cellulases get progressively confined to substrate parts where they are no longer optimally active. This eventually leads to an overall slow‐down of hydrolysis.

Structure-guided engineering of the coenzyme specificity of Pseudomonas fluorescens mannitol 2-dehydrogenase to enable efficient utilization of NAD(H) and NADP(H)

The structure of Pseudomonas fluorescens mannitol 2‐dehydrogenase with bound NAD+ leads to the suggestion that the carboxylate group of Asp69 forms a bifurcated hydrogen bond with the 2′ and 3′ hydroxyl groups of the adenosine of NAD+ and contributes to the 400‐fold preference of the enzyme for NAD+ as compared to NADP+. Accordingly, the enzyme with the Asp69 → Ala substitution was found to use NADP(H) almost as well as wild‐type enzyme uses NAD(H). The Glu68 → Lys substitution was expected to enhance the electrostatic interaction of the enzyme with the 2′‐phosphate of NADP+. The Glu68 → Lys:Asp69 → Ala doubly mutated enzyme showed about a 10‐fold preference for NADP(H) over NAD(H), accompanied by a small decrease in catalytic efficiency for NAD(H)‐dependent reactions as compared to wild‐type enzyme.

Polyol-specific long-chain dehydrogenases/reductases of mannitol metabolism in Aspergillus fumigatus: biochemical characterization and pH studies of mannitol 2-dehydrogenase and mannitol-1-phosphate 5-dehydrogenase.

Functional genomics data suggests that the metabolism of mannitol in the human pathogen Aspergillus fumigatus involves the action of two polyol-specific long-chain dehydrogenases/reductases, mannitol-1-phosphate 5-dehydrogenase (M1PDH) and mannitol 2-dehydrogenase (M2DH). The gene encoding the putative M2DH was expressed in Escherichia coli, and the purified recombinant protein was characterized biochemically. The predicted enzymatic function of a NAD(+)-dependent M2DH was confirmed. The enzyme is a monomer of 58kDa in solution and does not require metals for activity. pH profiles for M2DH and the previously isolated M1PDH were recorded in the pH range 6.0-10.0 for the oxidative and reductive direction of the reactions under conditions where substrate was limiting (k(cat)/K) or saturating (k(cat)). The pH-dependence of logk(cat) was usually different from that of log(k(cat)/K), suggesting that more than one step of the enzymatic mechanism was affected by changes in pH. The greater complexity of the pH profiles of log(k(cat)/K) for the fungal enzymes as compared to the analogous pH profiles for M2DH from Pseudomonas fluorescens may reflect sequence changes in vicinity of the conserved catalytic lysine.