Cellulases dig deep: in situ observation of the mesoscopic structural dynamics of enzymatic cellulose degradation

Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils

Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin-cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.

Advances and perspectives on mass transfer and enzymatic hydrolysis in the enzyme-mediated lignocellulosic biorefinery: A review

Enzymatic hydrolysis is a critical process for the cellulase-mediated lignocellulosic biorefinery to produce sugar syrups that can be converted into a whole range of biofuels and biochemicals. Such a process operating at high-solid loadings (i.e., scarcely any free water or roughly ≥ 15% solids, w/w) is considered more economically feasible, as it can generate a high sugar concentration at low operation and capital costs. However, this approach remains restricted and incurs "high-solid effects", ultimately causing the lower hydrolysis yields with increasing solid loadings. The lack of available water leads to a highly viscous system with impaired mixing that exhibits strong transfer resistance and reaction limitation imposed on enzyme action. Evidently, high-solid enzymatic hydrolysis involves multi-scale mass transfer and multi-phase enzyme reaction, and thus requires a synergistic perspective of transfer and biotransformation to assess the interactions among water, biomass components, and cellulase enzymes. Porous particle characteristics of biomass and its interface properties determine the water form and distribution state surrounding the particles, which are summarized in this review aiming to identify the water-driven multi-scale/multi-phase bioprocesses. Further aided by the cognition of rheological behavior of biomass slurry, solute transfer theories, and enzyme kinetics, the coupling effects of flow-transfer-reaction are revealed under high-solid conditions. Based on the above basic features, this review lucidly explains the causes of high-solid hydrolysis hindrances, highlights the mismatched issues between transfer and reaction, and more importantly, presents the advanced strategies for transfer and reaction enhancements from the viewpoint of process optimization, reactor design, as well as enzyme/auxiliary additive customization.

Cellulase Immobilization on Nanostructured Supports for Biomass Waste Processing

Nanobiocatalysts, i.e., enzymes immobilized on nanostructured supports, received considerable attention because they are potential remedies to overcome shortcomings of traditional biocatalysts, such as low efficiency of mass transfer, instability during catalytic reactions, and possible deactivation. In this short review, we will analyze major aspects of immobilization of cellulase-an enzyme for cellulosic biomass waste processing-on nanostructured supports. Such supports provide high surface areas, increased enzyme loading, and a beneficial environment to enhance cellulase performance and its stability, leading to nanobiocatalysts for obtaining biofuels and value-added chemicals. Here, we will discuss such nanostructured supports as carbon nanotubes, polymer nanoparticles (NPs), nanohydrogels, nanofibers, silica NPs, hierarchical porous materials, magnetic NPs and their nanohybrids, based on publications of the last five years. The use of magnetic NPs is especially favorable due to easy separation and the nanobiocatalyst recovery for a repeated use. This review will discuss methods for cellulase immobilization, morphology of nanostructured supports, multienzyme systems as well as factors influencing the enzyme activity to achieve the highest conversion of cellulosic biowaste into fermentable sugars. We believe this review will allow for an enhanced understanding of such nanobiocatalysts and processes, allowing for the best solutions to major problems of sustainable biorefinery.

Real-time imaging of enzymatic degradation of pretreated maize internodes reveals different cell types have different profiles

This work presents a dynamic view of the enzymatic degradation of maize cell walls, and sheds new light on the recalcitrance of hot water pretreated maize stem internodes. Infra-red microspectrometry, mass spectrometry, fluorescence recovery after photobleaching and fluorescence imaging were combined to investigate enzymatic hydrolysis at the cell scale. Depending on their polymer composition and organisation, cell types exhibits different extent and rate of enzymatic degradation. Enzymes act sequentially from the cell walls rich in accessible cellulose to the most recalcitrant cells. This phenomenon can be linked to the heterogeneous distribution of enzymes in the liquid medium and the adsorption/desorption mechanisms that differ with the type of cell.

Investigating the role of mechanics in lignocellulosic biomass degradation during hydrolysis: Part II

Lignocellulose breakdown in biorefineries is facilitated by enzymes and physical forces. Enzymes degrade and solubilize accessible lignocellulosic polymers, primarily on fiber surfaces, and make fibers physically weaker. Meanwhile physical forces acting during mechanical agitation induce tearing and cause rupture and attrition of the fibers, leading to liquefaction, that is, a less viscous hydrolysate that can be further processed in industrial settings. This study aims at understanding how mechanical agitation during enzymatic saccharification can be used to promote fiber attrition. The effects of reaction conditions, such as substrate and enzyme concentration on fiber attrition rate and hydrolysis yield were investigated. To gain insight into the fiber attrition mechanism, enzymatic hydrolysis was compared to hydrolysis by use of hydrochloric acid. Results show that fiber attrition depends on several factors concerning reactor design and operation including drum diameter, rotational speed, mixing schedule, and concentrations of fibers and enzymes. Surprisingly, different fiber attrition patterns during enzymatic and acid hydrolysis were found for similar mixing schedules. Specifically, for tumbling mixing, slow continuous mixing appears to function better than faster, intermittent mixing even for the same total number of drum revolutions. The findings indicate that reactor design and operation as well as hydrolysis conditions are key to process optimization and that detailed insights are needed to obtain fast liquefaction without sacrificing saccharification yields.

Sugar production from bioenergy sorghum by using pilot scale continuous hydrothermal pretreatment combined with disk refining

Chemical-free pretreatments are attracting increased interest because they generate less inhibitor in hydrolysates. In this study, pilot-scaled continuous hydrothermal (PCH) pretreatment followed by disk refining was evaluated and compared to laboratory-scale batch hot water (LHW) pretreatment. Bioenergy sorghum bagasse (BSB) was pretreated at 160-190 °C for 10 min with and without subsequent disk milling. Hydrothermal pretreatment and disk milling synergistically improved glucose and xylose release by 10-20% compared to hydrothermal pretreatment alone. Maximum yields of glucose and xylose of 82.55% and 70.78%, respectively were achieved, when BSB was pretreated at 190 °C and 180 °C followed by disk milling. LHW pretreated BSB had 5-15% higher sugar yields compared to PCH for all pretreatment conditions. The surface area improvement was also performed. PCH pretreatment combined with disk milling increased BSB surface area by 31.80-106.93%, which was greater than observed using LHW pretreatment.

Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization

Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks.

Enzymatic hydrolysis of biomimetic bacterial cellulose-hemicellulose composites

The production of biofuels and other chemicals from lignocellulosic biomass is limited by the inefficiency of enzymatic hydrolysis. Here a biomimetic composite material consisting of bacterial cellulose and wood-based hemicelluloses was used to study the effects of hemicelluloses on the enzymatic hydrolysis with a commercial cellulase mixture. Bacterial cellulose synthesized in the presence of hemicelluloses, especially xylan, was found to be more susceptible to enzymatic hydrolysis than hemicellulose-free bacterial cellulose. The reason for the easier hydrolysis could be related to the nanoscale structure of the substrate, particularly the packing of cellulose microfibrils into ribbons or bundles. In addition, small-angle X-ray scattering was used to show that the average nanoscale morphology of bacterial cellulose remained unchanged during the enzymatic hydrolysis. The reported easier enzymatic hydrolysis of bacterial cellulose produced in the presence of wood-based xylan offers new insights to overcome biomass recalcitrance through genetic engineering.

Visualising recalcitrance by colocalisation of cellulase, lignin and cellulose in pretreated pine biomass using fluorescence microscopy

Mapping the location of bound cellulase enzymes provides information on the micro-scale distribution of amenable and recalcitrant sites in pretreated woody biomass for biofuel applications. The interaction of a fluorescently labelled cellulase enzyme cocktail with steam-exploded pine (SEW) was quantified using confocal microscopy. The spatial distribution of Dylight labelled cellulase was quantified relative to lignin (autofluorescence) and cellulose (Congo red staining) by measuring their colocalisation using Pearson correlations. Correlations were greater in cellulose-rich secondary cell walls compared to lignin-rich middle lamella but with significant variations among individual biomass particles. The distribution of cellulose in the pretreated biomass accounted for 30% of the variation in the distribution of enzyme after correcting for the correlation between lignin and cellulose. For the first time, colocalisation analysis was able to quantify the spatial distribution of amenable and recalcitrant sites in relation to the histochemistry of cellulose and lignin. This study will contribute to understanding the role of pretreatment in enzymatic hydrolysis of recalcitrant softwood biomass.

Direct-Write Fabrication of Cellulose Nano-Structures via Focused Electron Beam Induced Nanosynthesis

In many areas of science and technology, patterned films and surfaces play a key role in engineering and development of advanced materials. Here, we introduce a new generic technique for the fabrication of polysaccharide nano-structures via focused electron beam induced conversion (FEBIC). For the proof of principle, organosoluble trimethylsilyl-cellulose (TMSC) thin films have been deposited by spin coating on SiO2 / Si and exposed to a nano-sized electron beam. It turns out that in the exposed areas an electron induced desilylation reaction takes place converting soluble TMSC to rather insoluble cellulose. After removal of the unexposed TMSC areas, structured cellulose patterns remain on the surface with FWHM line widths down to 70 nm. Systematic FEBIC parameter sweeps reveal a generally electron dose dependent behavior with three working regimes: incomplete conversion, ideal doses and over exposure. Direct (FT-IR) and indirect chemical analyses (enzymatic degradation) confirmed the cellulosic character of ideally converted areas. These investigations are complemented by a theoretical model which suggests a two-step reaction process by means of TMSC → cellulose and cellulose → non-cellulose material conversion in excellent agreement with experimental data. The extracted, individual reaction rates allowed the derivation of design rules for FEBIC parameters towards highest conversion efficiencies and highest lateral resolution.

Nanoscale Engineering of Designer Cellulosomes

Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.

Real-time single molecular study of a pretreated cellulose hydrolysis mode and individual enzyme movement

BACKGROUND

The main challenges of large-scale biochemical conversion involve the high costs of cellulolytic enzymes and the inefficiency in enzymatic deconstruction of polysaccharides embedded in the complex structure of the plant cell wall, leading to ongoing interests in studying the predominant mode of enzymatic hydrolysis. In this study, complete enzymatic hydrolysis of pretreated biomass substrates was visualized in situ and in real time by atomic force microscopy (AFM) topography and recognition imaging. Throughout the entire hydrolytic process, a hydrolysis mode for exoglucanase (CBH I) consisting of a peeling action, wherein cellulose microfibrils are peeled from sites on the pretreated cellulose substrate that have cracks sufficiently large for CBH I to immobilize.

RESULTS

We quantitatively monitored the complete hydrolytic process on pretreated cellulose. The synergetic effect among the different enzymes can accelerate the cellulose hydrolysis rate dramatically. However, the combination of CBH I and β-glucosidases (β-G) exhibited a similar degradation capacity as did whole enzyme (contains the cellobiohydrolases and endoglucanase as its major enzyme components). We developed a comprehensive dynamic analysis for individual cellulase acting on single pretreated cellulose through use of functional AFM topography and recognition imaging. The single crystalline cellulose was divided into different regions based on the cracks on the substrate surface and was observed to either depolymerize or to peel away by the jammed enzyme molecules. After the exfoliation of one region, new cracks were produced for the enzyme molecules to immobilize. The fiber width may have a relationship with the peeling mode of the fibers. We performed a statistical height measure of the generated peaks of the peeled fibers. The height values range from 11 to 24 nm. We assume that the CBH I enzymes stop progressing along the cellulose microfibril when the peeled microfibril height exceeds 11 nm.

CONCLUSION

The combination of CBH I and β-G can achieve an effective hydrolysis of the pretreated biomass substrates. The single-molecule study of the complete hydrolytic process indicates that the hydrolytic mode involves the peeling of the microfibrils and progressive depolymerization, which depend on the size of the cracks on the surface of the pretreated cellulose microfibrils.

A critical review on analysis in pretreatment of lignocelluloses: Degree of polymerization, adsorption/desorption, and accessibility

The pretreatment of lignocelluloses results in changes in the different properties of these materials. In a recent review (Karimi and Taherzadeh, 2016), the details of compositional, imaging, and crystallinity analyses of lignocelluloses were reviewed and critically discussed. Changes in the cellulose degree of polymerization, accessibility, and enzyme adsorption/desorption by pretreatments are also among the effective parameters. This paper deals with the measurement techniques, modifications, and relation to bioconversions, as well as the challenges of these three properties. These analyses are very helpful to investigate the pretreatment processes; however, the pretreatments are very complicated and challenging processes. It is not easily possible to study the effects of only one of these parameters and even to find which one is the dominant one. Moreover, it is not possible to accurately predict the changes in the bioconversion yield using these methods.

Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution

BACKGROUND

Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field.

RESULTS

We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate.

CONCLUSIONS

Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.

Effect of pretreatment severity in continuous steam explosion on enzymatic conversion of wheat straw: Evidence from kinetic analysis of hydrolysis time courses

Focusing on continuous steam explosion, the influence of pretreatment severity due to varied acid loading on hydrolysis of wheat straw by Trichoderma reesei cellulases was investigated based on kinetic evaluation of the saccharification of each pretreated substrate. Using semi-empirical descriptors of the hydrolysis time course, key characteristics of saccharification efficiency were captured in a quantifiable fashion. Not only hydrolysis rates per se, but also the transition point of their bi-phasic decline was crucial for high saccharification degree. After 48h the highest saccharification was achieved for substrate pretreated at relatively low severity (1.2% acid). Higher severity increased enzyme binding to wheat straw, but reduced the specific hydrolysis rates. Higher affinity of the lignocellulosic material for cellulases does not necessarily result in increased saccharification, probably because of lignin modifications occurring at high pretreatment severities. At comparable severity, continuous pretreatment produced a substrate more susceptible to enzymatic hydrolysis than the batch process.

Chemical and structural analysis of alkali pretreated pinewood for efficient ethanol production

Improvement of enzymatic hydrolysis and ethanol production from softwood pine was conducted by pretreatment with 8% (w/v) NaOH at different temperatures of 0, 25, and 80 °C for 2 h.

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

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 the effect of chemical additives on the enzymatic hydrolysis of pretreated wheat straw

Chemical additives were examined for ability to increase the enzymatic hydrolysis of thermo-acidically pretreated wheat straw by Trichoderma reesei cellulase at 50 °C. Semi-empirical descriptors derived from the hydrolysis time courses were applied to compare influence of these additives on lignocellulose bioconversion on a kinetic level, presenting a novel view on their mechanism of action. Focus was on rate retardation during hydrolysis, substrate conversion and enzyme adsorption. PEG 8000 enabled a reduction of enzyme loading by 50% while retaining the same conversion of 67% after 24h. For the first time, a beneficial effect of urea is reported, increasing the final substrate conversion after 48 h by 16%. The cationic surfactant cetyl-trimethylammonium bromide (CTAB) enhanced the hydrolysis rate at extended reaction time (rlim) by 34% and reduced reaction time by 28%. A combination of PEG 8000 and urea increased sugar release more than additives used individually.

Redox-initiated hydrogel system for detection and real-time imaging of cellulolytic enzyme activity

Understanding the process of biomass degradation by cellulolytic enzymes is of urgent importance for biofuel and chemical production. Optimizing pretreatment conditions and improving enzyme formulations both require assays to quantify saccharification products on solid substrates. Typically, such assays are performed using freely diffusing fluorophores or dyes that measure reducing polysaccharide chain ends. These methods have thus far not allowed spatial localization of hydrolysis activity to specific substrate locations with identifiable morphological features. Here we describe a hydrogel reagent signaling (HyReS) system that amplifies saccharification products and initiates crosslinking of a hydrogel that localizes to locations of cellulose hydrolysis, allowing for imaging of the degradation process in real time. Optical detection of the gel in a rapid parallel format on synthetic and natural pretreated solid substrates was used to quantify activity of T. emersonii and T. reesei enzyme cocktails. When combined with total internal reflection fluorescence microscopy and AFM imaging, the reagent system provided a means to visualize enzyme activity in real-time with high spatial resolution (<2 μm). These results demonstrate the versatility of the HyReS system in detecting cellulolytic enzyme activity and suggest new opportunities in real-time chemical imaging of biomass depolymerization.

Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused.

BACKGROUND

Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported.

RESULTS

In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family.

CONCLUSIONS

Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

BACKGROUND

Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported.

RESULTS

In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family.

CONCLUSIONS

Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.

Enzymatic hydrolysis of microcrystalline cellulose and pretreated wheat straw: a detailed comparison using convenient kinetic analysis

Marked slow-down of soluble sugar production at low degree of substrate conversion limits the space-time yield of enzymatic hydrolysis of ligno-cellulosic materials. A simple set of kinetic descriptors was developed to compare reducing sugar release from pure crystalline cellulose (Avicel) and pretreated wheat straw by Trichoderma reesei cellulase at 50 °C. The focus was on the rate-retarding effect of maximum hydrolysis rate at reaction start (r(max)), limiting hydrolysis rate (r(lim)) at extended reaction time (24h), and substrate conversion, marking the transition between the r(max) and r(lim) kinetic regimes (C(trans)). At apparent saturation of substrate (12.2g cellulose/L) with enzyme, r(max) for pretreated wheat straw (~9.6g/L/h) surpassed that for Avicel by about 1.7-fold whereas their r(lim) were almost identical (~0.15 g/L/h). C(trans) roughly doubled as enzyme/substrate loading was increased from 3.8 to 75FPU/g, suggesting C(trans) to be a complex manifestation of cellulase-cellulose interaction, not an intrinsic substrate property. A low-temperature adsorption step preceding hydrolysis at 50 °C resulted in enhanced cellulase binding at reaction start without increasing r(max). C(trans) was higher for pretreated wheat straw (~30%) than for Avicel (~20%) under these conditions.

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

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.

Form and function of Clostridium thermocellum biofilms

The importance of bacterial adherence has been acknowledged in microbial lignocellulose conversion studies; however, few reports have described the function and structure of biofilms supported by cellulosic substrates. We investigated the organization, dynamic formation, and carbon flow associated with biofilms of the obligately anaerobic cellulolytic bacterium Clostridium thermocellum 27405. Using noninvasive, in situ fluorescence imaging, we showed biofilms capable of near complete substrate conversion with a characteristic monolayered cell structure without an extracellular polymeric matrix typically seen in biofilms. Cell division at the interface and terminal endospores appeared throughout all stages of biofilm growth. Using continuous-flow reactors with a rate of dilution (2 h(-1)) 12-fold higher than the bacterium's maximum growth rate, we compared biofilm activity under low (44 g/liter) and high (202 g/liter) initial cellulose loading. The average hydrolysis rate was over 3-fold higher in the latter case, while the proportions of oligomeric cellulose hydrolysis products lost from the biofilm were 13.7% and 29.1% of the total substrate carbon hydrolyzed, respectively. Fermentative catabolism was comparable between the two cellulose loadings, with ca. 4% of metabolized sugar carbon being utilized for cell production, while 75.4% and 66.7% of the two cellulose loadings, respectively, were converted to primary carbon metabolites (ethanol, acetic acid, lactic acid, carbon dioxide). However, there was a notable difference in the ethanol-to-acetic acid ratio (g/g), measured to be 0.91 for the low cellulose loading and 0.41 for the high cellulose loading. The results suggest that substrate availability for cell attachment rather than biofilm colonization rates govern the efficiency of cellulose conversion.