Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.
Nature protocols
Designing a reliable computational methodology to calculate protein:ligand standard binding free energies is extremely challenging. The large change in configurational enthalpy and entropy that accompanies the association of ligand and protein is notoriously difficult to capture in naive brute-force simulations. Addressing this issue, the present protocol rests upon a rigorous statistical mechanical framework for the determination of protein:ligand binding affinities together with the comprehensive Binding Free-Energy Estimator 2 (BFEE2) application software. With the knowledge of the bound state, available from experiments or docking, application of the BFEE2 protocol with a reliable force field supplies in a matter of days standard binding free energies within chemical accuracy, for a broad range of protein:ligand complexes. Limiting undesirable human intervention, BFEE2 assists the end user in preparing all the necessary input files and performing the post-treatment of the simulations towards the final estimate of the binding affinity.
10.1038/s41596-021-00676-1
Nanoscale dynamics of cellulose digestion by the cellobiohydrolase TrCel7A.
Haviland Zachary K,Nong Daguan,Vasquez Kuntz Kate L,Starr Thomas J,Ma Dengbo,Tien Ming,Anderson Charles T,Hancock William O
The Journal of biological chemistry
Understanding the mechanism by which cellulases from bacteria, fungi, and protozoans catalyze the digestion of lignocellulose is important for developing cost-effective strategies for bioethanol production. Cel7A from the fungus Trichoderma reesei is a model exoglucanase that degrades cellulose strands from their reducing ends by processively cleaving individual cellobiose units. Despite being one of the most studied cellulases, the binding and hydrolysis mechanisms of Cel7A are still debated. Here, we used single-molecule tracking to analyze the dynamics of 11,116 quantum dot-labeled TrCel7A molecules binding to and moving processively along immobilized cellulose. Individual enzyme molecules were localized with a spatial precision of a few nanometers and followed for hundreds of seconds. Most enzyme molecules bound to cellulose in a static state and dissociated without detectable movement, whereas a minority of molecules moved processively for an average distance of 39 nm at an average speed of 3.2 nm/s. These data were integrated into a three-state model in which TrCel7A molecules can bind from solution into either static or processive states and can reversibly switch between states before dissociating. From these results, we conclude that the rate-limiting step for cellulose degradation by Cel7A is the transition out of the static state, either by dissociation from the cellulose surface or by initiation of a processive run. Thus, accelerating the transition of Cel7A out of its static state is a potential avenue for improving cellulase efficiency.
10.1016/j.jbc.2021.101029
Cellulolytic systems in insects.
Watanabe Hirofumi,Tokuda Gaku
Annual review of entomology
Despite the presence of many carbohydrolytic activities in insects, their cellulolytic mechanisms are poorly understood. Whereas cellulase genes are absent from the genomes of Drosophila melanogaster or Bombyx mori, other insects such as termites produce their own cellulases. Recent studies using molecular biological techniques have brought new insights into the mechanisms by which the insects and their microbial symbionts digest cellulose in the small intestine. DNA sequences of cellulase and associated genes, as well as physiological and morphological information about the digestive systems of cellulase-producing insects, may allow the efficient use of cellulosic biomass as a sustainable energy source.
10.1146/annurev-ento-112408-085319
Reactor design for minimizing product inhibition during enzymatic lignocellulose hydrolysis: I. Significance and mechanism of cellobiose and glucose inhibition on cellulolytic enzymes.
Andrić Pavle,Meyer Anne S,Jensen Peter A,Dam-Johansen Kim
Biotechnology advances
Achievement of efficient enzymatic degradation of cellulose to glucose is one of the main prerequisites and one of the main challenges in the biological conversion of lignocellulosic biomass to liquid fuels and other valuable products. The specific inhibitory interferences by cellobiose and glucose on enzyme-catalyzed cellulose hydrolysis reactions impose significant limitations on the efficiency of lignocellulose conversion - especially at high-biomass dry matter conditions. To provide the base for selecting the optimal reactor conditions, this paper reviews the reaction kinetics, mechanisms, and significance of this product inhibition, notably the cellobiose and glucose inhibition, on enzymatic cellulose hydrolysis. Particular emphasis is put on the distinct complexity of cellulose as a substrate, the multi-enzymatic nature of the cellulolytic degradation, and the particular features of cellulase inhibition mechanisms and kinetics. The data show that new strategies that place the bioreactor design at the center stage are required to alleviate the product inhibition and in turn to enhance the efficiency of enzymatic cellulose hydrolysis. Accomplishment of the enzymatic hydrolysis at medium substrate concentration in separate hydrolysis reactors that allow continuous glucose removal is proposed to be the way forward for obtaining feasible enzymatic degradation in lignocellulose processing.
10.1016/j.biotechadv.2010.01.003
Effect of phosphoric acid pretreatment on enzymatic hydrolysis of microcrystalline cellulose.
Zhang Juanhua,Zhang Beixiao,Zhang Jingqiang,Lin Lu,Liu Shijie,Ouyang Pingkai
Biotechnology advances
Microcrystalline cellulose (MCC) was pretreated with phosphoric acid at 323K for 10h. X-ray diffraction (XRD) and Atomic Force Microscope (AFM) analyses revealed that the fiber surface morphology of pretreated MCC (P-MCC) were uneven and rough with the crystalline diffraction peaks of P-MCC decreased to a distinct range. The X-ray Photoelectron Spectroscopy (XPS) analysis showed that the uneven and rough surface of P-MCC could enhance the adsorption of cellulose to the molecular surface of cellulose, which is one of the key factors affecting enzymatic hydrolysis of cellulose. A reversible first order kinetics was employed to describe the adsorption kinetics of cellulase to MCC and P-MCC, and the adsorption rate constants of MCC and P-MCC were found to be 0.016, 0.024, 0.041, and 0.095, 0.149, 0.218min(-1), respectively at 278K, 293K and 308K. The activation energies of MCC and P-MCC hydrolysis reactions were found to be 22.257 and 19.721kJ mol(-1). The major hydrolysis products of MCC and P-MCC were cellobiose and glucose. Hydrolysis of MCC for 120h resulted in yields of glucose (7.21%), cellobiose (13.16%) and total sugars (20.37%). However, after the pretreatment with phosphoric acid, the corresponding sugar yields resulted from enzymatic hydrolysis of P-MCC were increased to 24.10%, 41.42%, and 65.52%; respectively, which were 3.34, 3.15, and 3.22 times of the sugars yields from enzymatic hydrolysis of MCC.
10.1016/j.biotechadv.2010.05.010
Cellodextrin transport in yeast for improved biofuel production.
Galazka Jonathan M,Tian Chaoguang,Beeson William T,Martinez Bruno,Glass N Louise,Cate Jamie H D
Science (New York, N.Y.)
Fungal degradation of plant biomass may provide insights for improving cellulosic biofuel production. We show that the model cellulolytic fungus Neurospora crassa relies on a high-affinity cellodextrin transport system for rapid growth on cellulose. Reconstitution of the N. crassa cellodextrin transport system in Saccharomyces cerevisiae promotes efficient growth of this yeast on cellodextrins. In simultaneous saccharification and fermentation experiments, the engineered yeast strains more rapidly convert cellulose to ethanol when compared with yeast lacking this system.
10.1126/science.1192838
Alternatives to Trichoderma reesei in biofuel production.
Gusakov Alexander V
Trends in biotechnology
Mutant strains of Trichoderma reesei are considered indisputable champions in cellulase production among biomass-degrading fungi. So, it is not surprising that most R&D projects on bioethanol production from lignocellulosics have been based on using T. reesei cellulases. The present review focuses on whether any serious alternatives to T. reesei enzymes in cellulose hydrolysis exist. Although not widely accepted, more and more data have been accumulated that demonstrate that fungi belonging to the genera Penicillium, Acremonium and Chrysosporium might represent such alternatives because they are competitive to T. reesei on some important parameters, such as protein production level, cellulase hydrolytic performance per unit of activity or milligram of protein.
10.1016/j.tibtech.2011.04.004
How does plant cell wall nanoscale architecture correlate with enzymatic digestibility?
Ding Shi-You,Liu Yu-San,Zeng Yining,Himmel Michael E,Baker John O,Bayer Edward A
Science (New York, N.Y.)
Greater understanding of the mechanisms contributing to chemical and enzymatic solubilization of plant cell walls is critical for enabling cost-effective industrial conversion of cellulosic biomass to biofuels. Here, we report the use of correlative imaging in real time to assess the impact of pretreatment, as well as the resulting nanometer-scale changes in cell wall structure, upon subsequent digestion by two commercially relevant cellulase systems. We demonstrate that the small, noncomplexed fungal cellulases deconstruct cell walls using mechanisms that differ considerably from those of the larger, multienzyme complexes (cellulosomes). Furthermore, high-resolution measurement of the microfibrillar architecture of cell walls suggests that digestion is primarily facilitated by enabling enzyme access to the hydrophobic cellulose face. The data support the conclusion that ideal pretreatments should maximize lignin removal and minimize polysaccharide modification, thereby retaining the essentially native microfibrillar structure.
10.1126/science.1227491
Lignocellulose-degrading enzymes from termites and their symbiotic microbiota.
Ni Jinfeng,Tokuda Gaku
Biotechnology advances
Lignocellulose-the dry matter of plants, or "plant biomass"-digestion is of increasing interest in organismal metabolism research, specifically the conversion of biomass into biofuels. Termites efficiently decompose lignocelluloses, and studies on lignocellulolytic systems may elucidate mechanisms of efficient lignocellulose degradation in termites as well as offer novel enzyme sources, findings which have significant potential industrial applications. Recent progress in metagenomic and metatranscriptomic research has illuminated the diversity of lignocellulolytic enzymes within the termite gut. Here, we review state-of-the-art research on lignocellulose-degrading systems in termites, specifically cellulases, xylanases, and lignin modification enzymes produced by termites and their symbiotic microbiota. We also discuss recent investigations into heterologous overexpression of lignocellulolytic enzymes from termites and their symbionts.
10.1016/j.biotechadv.2013.04.005
Genomics review of holocellulose deconstruction by aspergilli.
Segato Fernando,Damásio André R L,de Lucas Rosymar C,Squina Fabio M,Prade Rolf A
Microbiology and molecular biology reviews : MMBR
SUMMARY:Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
10.1128/MMBR.00019-14
Restructuring the crystalline cellulose hydrogen bond network enhances its depolymerization rate.
Chundawat Shishir P S,Bellesia Giovanni,Uppugundla Nirmal,da Costa Sousa Leonardo,Gao Dahai,Cheh Albert M,Agarwal Umesh P,Bianchetti Christopher M,Phillips George N,Langan Paul,Balan Venkatesh,Gnanakaran S,Dale Bruce E
Journal of the American Chemical Society
Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils. We provide a molecular-scale explanation of these phenomena through molecular dynamics (MD) simulations and enzymatic assays. Ammonia transformed the naturally occurring crystalline allomorph I(β) to III(I), which led to a decrease in the number of cellulose intrasheet hydrogen bonds and an increase in the number of intersheet hydrogen bonds. This rearrangement of the hydrogen bond network within cellulose III(I), which increased the number of solvent-exposed glucan chain hydrogen bonds with water by ~50%, was accompanied by enhanced saccharification rates by up to 5-fold (closest to amorphous cellulose) and 60-70% lower maximum surface-bound cellulase capacity. The enhancement in apparent cellulase activity was attributed to the "amorphous-like" nature of the cellulose III(I) fibril surface that facilitated easier glucan chain extraction. Unrestricted substrate accessibility to active-site clefts of certain endocellulase families further accelerated deconstruction of cellulose III(I). Structural and dynamical features of cellulose III(I), revealed by MD simulations, gave additional insights into the role of cellulose crystal structure on fibril surface hydration that influences interfacial enzyme binding. Subtle alterations within the cellulose hydrogen bond network provide an attractive way to enhance its deconstruction and offer unique insight into the nature of cellulose recalcitrance. This approach can lead to unconventional pathways for development of novel pretreatments and engineered cellulases for cost-effective biofuels production.
10.1021/ja2011115
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system.
Lian Jiazhang,HamediRad Mohammad,Hu Sumeng,Zhao Huimin
Nature communications
Designing an optimal microbial cell factory often requires overexpression, knock-down, and knock-out of multiple gene targets. Unfortunately, such rewiring of cellular metabolism is often carried out sequentially and with low throughput. Here, we report a combinatorial metabolic engineering strategy based on an orthogonal tri-functional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae. This strategy enables perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. We demonstrate the application of CRISPR-AID not only to increase the production of β-carotene by 3-fold in a single step, but also to achieve 2.5-fold improvement in the display of an endoglucanase on the yeast surface by optimizing multiple metabolic engineering targets in a combinatorial manner.
10.1038/s41467-017-01695-x
Cell surface engineering of industrial microorganisms for biorefining applications.
Tanaka Tsutomu,Kondo Akihiko
Biotechnology advances
In order to decrease carbon emissions and negative environmental impacts of various pollutants, biofuel/biochemical production should be promoted for replacing fossil-based industrial processes. Utilization of abundant lignocellulosic biomass as a feedstock has recently become an attractive option. In this review, we focus on recent efforts of cell surface display using industrial microorganisms such as Escherichia coli and yeast. Cell surface display is used primarily for endowing cellulolytic activity on the host cells, and enables direct fermentation to generate useful fuels and chemicals from lignocellulosic biomass. Cell surface display systems are systematically summarized, and the drawbacks/perspectives as well as successful application of surface display for industrial biotechnology are discussed.
10.1016/j.biotechadv.2015.06.002
The Enigmatic Universe of the Herbivore Gut.
Glass N Louise
Trends in biochemical sciences
The herbivore gut is a fascinating ecosystem exquisitely adapted to plant biomass degradation. Within this ecosystem, anaerobic fungi invade biomass and secrete hydrolytic enzymes. In a recent study, Solomon et al. characterized three anaerobic fungi by transcriptomics, proteomics, and functional analyses to identify novel components essential for plant biomass deconstruction.
10.1016/j.tibs.2016.05.007
Ionic Liquids as Tool to Improve Enzymatic Organic Synthesis.
Itoh Toshiyuki
Chemical reviews
Ionic liquids (ILs) have now been acknowledged as reaction media for biotransformations. The first three examples were reported in this field in 2000, and since then, numerous applications have been reported for biocatalytic reactions using ILs. Two topics using ILs for enzymatic reactions have been reviewed from the standpoint of biocatalyst mediating organic synthesis; the first is "Biocatalysis in Ionic Liquids" which includes various types of biocatalytic reactions in ILs (section 2): (1) recent examples of lipase-mediated reactions using ILs as reaction media for biodiesel oil production and for sugar ester production, (2) oxidase-catalyzed reactions in ILs, (3) laccase-catalyzed reactions, (4) peroxidase-catalyzed reactions, (4) cytochrome-mediated reactions, (5) microbe-mediated hydrations, (6) protease-catalyzed reactions, (8) whole cell mediated asymmetric reduction of ketones, (10) acylase-catalyzed reactions, (11) glycosylation or cellulase-mediated hydrolysis of polysaccharides, (12) hydroxynitrile lyase-catalyzed reaction, (13) fluorinase or haloalkane dehydrogenase-catalyzed reaction, (14) luciferase-catalyzed reactions, and (15) biocatalytic promiscuity of enzymatic reactions for organic synthesis using ILs. The second is "Enzymes Activated by Ionic Liquids for Organic Synthesis", particularly describing the finding story of activation of lipases by the coating with a PEG-substituted IL (section 3). The author's opinion toward "Future Perspectives of Using ILs for Enzymatic Reactions" has also been discussed in section 4.
10.1021/acs.chemrev.7b00158
Production, characterization and gene cloning of the extracellular enzymes from the marine-derived yeasts and their potential applications.
Chi Zhenming,Chi Zhe,Zhang Tong,Liu Guanglei,Li Jing,Wang Xianghong
Biotechnology advances
In this review article, the extracellular enzymes production, their properties and cloning of the genes encoding the enzymes from marine yeasts are overviewed. Several yeast strains which could produce different kinds of extracellular enzymes were selected from the culture collection of marine yeasts available in this laboratory. The strains selected belong to different genera such as Yarrowia, Aureobasidium, Pichia, Metschnikowia and Cryptococcus. The extracellular enzymes include cellulase, alkaline protease, aspartic protease, amylase, inulinase, lipase and phytase, as well as killer toxin. The conditions and media for the enzyme production by the marine yeasts have been optimized and the enzymes have been purified and characterized. Some genes encoding the extracellular enzymes from the marine yeast strains have been cloned, sequenced and expressed. It was found that some properties of the enzymes from the marine yeasts are unique compared to those of the homologous enzymes from terrestrial yeasts and the genes encoding the enzymes in marine yeasts are different from those in terrestrial yeasts. Therefore, it is of very importance to further study the enzymes and their genes from the marine yeasts. This is the first review on the extracellular enzymes and their genes from the marine yeasts.
10.1016/j.biotechadv.2009.01.002
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Hess Matthias,Sczyrba Alexander,Egan Rob,Kim Tae-Wan,Chokhawala Harshal,Schroth Gary,Luo Shujun,Clark Douglas S,Chen Feng,Zhang Tao,Mackie Roderick I,Pennacchio Len A,Tringe Susannah G,Visel Axel,Woyke Tanja,Wang Zhong,Rubin Edward M
Science (New York, N.Y.)
The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.
10.1126/science.1200387
Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface.
Igarashi Kiyohiko,Uchihashi Takayuki,Koivula Anu,Wada Masahisa,Kimura Satoshi,Okamoto Tetsuaki,Penttilä Merja,Ando Toshio,Samejima Masahiro
Science (New York, N.Y.)
A deeper mechanistic understanding of the saccharification of cellulosic biomass could enhance the efficiency of biofuels development. We report here the real-time visualization of crystalline cellulose degradation by individual cellulase enzymes through use of an advanced version of high-speed atomic force microscopy. Trichoderma reesei cellobiohydrolase I (TrCel7A) molecules were observed to slide unidirectionally along the crystalline cellulose surface but at one point exhibited collective halting analogous to a traffic jam. Changing the crystalline polymorphic form of cellulose by means of an ammonia treatment increased the apparent number of accessible lanes on the crystalline surface and consequently the number of moving cellulase molecules. Treatment of this bulky crystalline cellulose simultaneously or separately with T. reesei cellobiohydrolase II (TrCel6A) resulted in a remarkable increase in the proportion of mobile enzyme molecules on the surface. Cellulose was completely degraded by the synergistic action between the two enzymes.
10.1126/science.1208386
Protein allostery at the solid-liquid interface: endoglucanase attachment to cellulose affects glucan clenching in the binding cleft.
Lin Yuchun,Silvestre-Ryan Jordi,Himmel Michael E,Crowley Michael F,Beckham Gregg T,Chu Jhih-Wei
Journal of the American Chemical Society
At phase boundaries, physical activities of enzymes such as substrate complexation play critical roles in driving biocatalysis. A prominent example is the cellulase cocktails secreted by fungi and bacteria for deconstructing crystalline cellulose in biomass into soluble sugars. At interfaces, molecular mechanisms of the physical steps in biocatalysis remain elusive due to the difficulties of characterizing protein action with high temporal and spatial resolution. Here, we focus on endoglucanase I (Cel7B) from the fungus Trichoderma reesei that hydrolyzes glycosidic bonds on cellulose randomly. We employ all-atom molecular dynamics (MD) simulations to elucidate the interactions of the catalytic domain (CD) of Cel7B with a cellulose microfibril before and after complexing a glucan chain in the binding cleft. The calculated mechanical coupling networks in Cel7B-glucan and Cel7B-microfibril complexes reveal a previously unresolved allosteric coupling at the solid-liquid interface: attachment of the Cel7B CD to the cellulose surface affects glucan chain clenching in the binding cleft. Alternative loop segments of the Cel7B CD were found to affix to intact or defective surface structures on the microfibril, depending on the complexation state. From a multiple sequence alignment, residues in surface-affixing segments show strong conservation, highlighting the functional importance of the physical activities that they facilitate. Surface-affixing residues also demonstrate significant sequence correlation with active-site residues, revealing the functional connection between complexation and hydrolysis. Analysis of the Cel7B CD exemplifies that the mechanical coupling networks calculated from atomistic MD simulations can be used to capture the conservation and correlation in sequence alignment.
10.1021/ja206692g
Genome analyses highlight the different biological roles of cellulases.
Mba Medie Felix,Davies Gideon J,Drancourt Michel,Henrissat Bernard
Nature reviews. Microbiology
Cellulolytic enzymes have been the subject of renewed interest owing to their potential role in the conversion of plant lignocellulose to sustainable biofuels. An analysis of ∼1,500 complete bacterial genomes, presented here, reveals that ∼40% of the genomes of sequenced bacteria encode at least one cellulase gene. Most of the bacteria that encode cellulases are soil and marine saprophytes, many of which encode a range of enzymes for cellulose hydrolysis and also for the breakdown of the other constituents of plant cell walls (hemicelluloses and pectins). Intriguingly, cellulases are present in organisms that are usually considered as non-saprophytic, such as Mycobacterium tuberculosis, Legionella pneumophila, Yersinia pestis and even Escherichia coli. We also discuss newly emerging roles of cellulases in such non-saprophytic organisms.
10.1038/nrmicro2729
Cellulosome-based, Clostridium-derived multi-functional enzyme complexes for advanced biotechnology tool development: advances and applications.
Biotechnology advances
The cellulosome is one of nature's most elegant and elaborate nanomachines and a key biological and biotechnological macromolecule that can be used as a multi-functional protein complex tool. Each protein module in the cellulosome system is potentially useful in an advanced biotechnology application. The high-affinity interactions between the cohesin and dockerin domains can be used in protein-based biosensors to improve both sensitivity and selectivity. The scaffolding protein includes a carbohydrate-binding module (CBM) that attaches strongly to cellulose substrates and facilitates the purification of proteins fused with the dockerin module through a one-step CBM purification method. Although the surface layer homology (SLH) domain of CbpA is not present in other strains, replacement of the cell surface anchoring domain allows a foreign protein to be displayed on the surface of other strains. The development of a hydrolysis enzyme complex is a useful strategy for consolidated bioprocessing (CBP), enabling microorganisms with biomass hydrolysis activity. Thus, the development of various configurations of multi-functional protein complexes for use as tools in whole-cell biocatalyst systems has drawn considerable attention as an attractive strategy for bioprocess applications. This review provides a detailed summary of the current achievements in Clostridium-derived multi-functional complex development and the impact of these complexes in various areas of biotechnology.
10.1016/j.biotechadv.2013.03.009
Multifunctional Cellulolytic Enzymes Outperform Processive Fungal Cellulases for Coproduction of Nanocellulose and Biofuels.
Yarbrough John M,Zhang Ruoran,Mittal Ashutosh,Vander Wall Todd,Bomble Yannick J,Decker Stephen R,Himmel Michael E,Ciesielski Peter N
ACS nano
Producing fuels, chemicals, and materials from renewable resources to meet societal demands remains an important step in the transition to a sustainable, clean energy economy. The use of cellulolytic enzymes for the production of nanocellulose enables the coproduction of sugars for biofuels production in a format that is largely compatible with the process design employed by modern lignocellulosic (second generation) biorefineries. However, yields of enzymatically produced nanocellulose are typically much lower than those achieved by mineral acid production methods. In this study, we compare the capacity for coproduction of nanocellulose and fermentable sugars using two vastly different cellulase systems: the classical "free enzyme" system of the saprophytic fungus, Trichoderma reesei (T. reesei) and the complexed, multifunctional enzymes produced by the hot springs resident, Caldicellulosiruptor bescii (C. bescii). We demonstrate by comparative digestions that the C. bescii system outperforms the fungal enzyme system in terms of total cellulose conversion, sugar production, and nanocellulose production. In addition, we show by multimodal imaging and dynamic light scattering that the nanocellulose produced by the C. bescii cellulase system is substantially more uniform than that produced by the T. reesei system. These disparities in the yields and characteristics of the nanocellulose produced by these disparate systems can be attributed to the dramatic differences in the mechanisms of action of the dominant enzymes in each system.
10.1021/acsnano.7b00086
Modeling cellulase kinetics on lignocellulosic substrates.
Bansal Prabuddha,Hall Mélanie,Realff Matthew J,Lee Jay H,Bommarius Andreas S
Biotechnology advances
The enzymatic hydrolysis of cellulose to glucose by cellulases is one of the major steps involved in the conversion of lignocellulosic biomass to yield biofuel. This hydrolysis by cellulases, a heterogeneous reaction, currently suffers from some major limitations, most importantly a dramatic rate slowdown at high degrees of conversion. To render the process economically viable, increases in hydrolysis rates and yields are necessary and require improvement both in enzymes (via protein engineering) and processing, i.e. optimization of reaction conditions, reactor design, enzyme and substrate cocktail compositions, enzyme recycling and recovery strategies. Advances in both areas in turn strongly depend on the progress in the accurate quantification of substrate-enzyme interactions and causes for the rate slowdown. The past five years have seen a significant increase in the number of studies on the kinetics of the enzymatic hydrolysis of cellulose. This review provides an overview of the models published thus far, classifies and tabulates these models, and presents an analysis of their basic assumptions. While the exact mechanism of cellulases on lignocellulosic biomass is not completely understood yet, models in the literature have elucidated various factors affecting the enzymatic rates and activities. Different assumptions regarding rate-limiting factors and basic substrate-enzyme interactions were employed to develop and validate these models. However, the models need to be further tested against additional experimental data to validate or disprove any underlying hypothesis. It should also provide better insight on additional parameters required in the case that more substrate and enzyme properties are to be included in a model.
10.1016/j.biotechadv.2009.06.005
Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment.
Graham Joel E,Clark Melinda E,Nadler Dana C,Huffer Sarah,Chokhawala Harshal A,Rowland Sara E,Blanch Harvey W,Clark Douglas S,Robb Frank T
Nature communications
Despite extensive studies on microbial and enzymatic lignocellulose degradation, relatively few Archaea are known to deconstruct crystalline cellulose. Here we describe a consortium of three hyperthermophilic archaea enriched from a continental geothermal source by growth at 90 °C on crystalline cellulose, representing the first instance of Archaea able to deconstruct lignocellulose optimally above 90 °C. Following metagenomic studies on the consortium, a 90 kDa, multidomain cellulase, annotated as a member of the TIM barrel glycosyl hydrolase superfamily, was characterized. The multidomain architecture of this protein is uncommon for hyperthermophilic endoglucanases, and two of the four domains of the enzyme have no characterized homologues. The recombinant enzyme has optimal activity at 109 °C, a half-life of 5 h at 100 °C, and resists denaturation in strong detergents, high-salt concentrations, and ionic liquids. Cellulases active above 100 °C may assist in biofuel production from lignocellulosic feedstocks by hydrolysing cellulose under conditions typically employed in biomass pretreatment.
10.1038/ncomms1373
Endowing non-cellulolytic microorganisms with cellulolytic activity aiming for consolidated bioprocessing.
Yamada Ryosuke,Hasunuma Tomohisa,Kondo Akihiko
Biotechnology advances
With the exhaustion of fossil fuels and with the environmental issues they pose, utilization of abundant lignocellulosic biomass as a feedstock for biofuels and bio-based chemicals has recently become an attractive option. Lignocellulosic biomass is primarily composed of cellulose, hemicellulose, and lignin and has a very rigid and complex structure. It is accordingly much more expensive to process than starchy grains because of the need for extensive pretreatment and relatively large amounts of cellulases for efficient hydrolysis. Efficient and cost-effective methods for the production of biofuels and chemicals from lignocellulose are required. A consolidated bioprocess (CBP), which integrates all biological steps consisting of enzyme production, saccharification, and fermentation, is considered a promising strategy for reducing production costs. Establishing an efficient CBP using lignocellulosic biomass requires both lignocellulose degradation into glucose and efficient production of biofuels or chemicals from glucose. With this aim, many researchers are attempting to endow selected microorganisms with lignocellulose-assimilating ability. In this review, we focus on studies aimed at conferring lignocellulose-assimilating ability not only to yeast strains but also to bacterial strains by recombinant technology. Recent developments in improvement of enzyme productivity by microorganisms and in improvement of the specific activity of cellulase are emphasized.
10.1016/j.biotechadv.2013.02.007
Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era.
Liu Guodong,Qin Yuqi,Li Zhonghai,Qu Yinbo
Biotechnology advances
The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.
10.1016/j.biotechadv.2013.03.001
A single-molecule analysis reveals morphological targets for cellulase synergy.
Fox Jerome M,Jess Phillip,Jambusaria Rakesh B,Moo Genny M,Liphardt Jan,Clark Douglas S,Blanch Harvey W
Nature chemical biology
The mechanisms of enzyme activity on solid substrates are not well understood. Unlike enzyme catalysis in aqueous solutions, enzyme activity on surfaces is complicated by adsorption steps and structural heterogeneities that make enzyme-substrate interactions difficult to characterize. Cellulase enzymes, which catalyze the depolymerization of cellulose, show binding specificities for different cellulose surface morphologies, but the influence of these specificities on the activity of multienzyme mixtures has remained unclear. We developed a metric to quantify binding-target arrangements determined by photoactivated localization microscopy, and we used that metric to show that combinations of cellulases designed to bind within similar but nonidentical morphologies can have synergistic activity. This phenomenon cannot be explained with the binary crystalline or amorphous classifications commonly used to characterize cellulase-binding targets. Our results reveal a strategy for improving the activity of cellulolytic mixtures and demonstrate a versatile method for investigating protein organization on heterogeneous surfaces.
10.1038/nchembio.1227
Cellulases for biomass degradation: comparing recombinant cellulase expression platforms.
Garvey Megan,Klose Holger,Fischer Rainer,Lambertz Camilla,Commandeur Ulrich
Trends in biotechnology
Improvement of cellulase expression has the potential to change the nature of the biofuel industry. Increasing the economic feasibility of cellulase systems would significantly broaden the range of practicable biomass conversion, lowering the environmental impact of our civilisations' fuel needs. Cellulases are derived from certain fungi and bacteria, which are often difficult to culture on an industrial scale. Accordingly, methods to recombinantly express important cellulases and other glycosyl hydrolase (GH) enzymes are under serious investigation. Herein, we examine the latest developments in bacterial, yeast, plant, and fungal expression systems. We discuss current strategies for producing cellulases, and evaluate the benefits and drawbacks in yield, stability, and activity of enzymes from each system, and the overall progress in the field.
10.1016/j.tibtech.2013.06.006
Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA.
Brunecky Roman,Alahuhta Markus,Xu Qi,Donohoe Bryon S,Crowley Michael F,Kataeva Irina A,Yang Sung-Jae,Resch Michael G,Adams Michael W W,Lunin Vladimir V,Himmel Michael E,Bomble Yannick J
Science (New York, N.Y.)
Most fungi and bacteria degrade plant cell walls by secreting free, complementary enzymes that hydrolyze cellulose; however, some bacteria use large enzymatic assemblies called cellulosomes, which recruit complementary enzymes to protein scaffolds. The thermophilic bacterium Caldicellulosiruptor bescii uses an intermediate strategy, secreting many free cellulases that contain multiple catalytic domains. One of these, CelA, comprises a glycoside hydrolase family 9 and a family 48 catalytic domain, as well as three type III cellulose-binding modules. In the saccharification of a common cellulose standard, Avicel, CelA outperforms mixtures of commercially relevant exo- and endoglucanases. From transmission electron microscopy studies of cellulose after incubation with CelA, we report morphological features that suggest that CelA not only exploits the common surface ablation mechanism driven by general cellulase processivity, but also excavates extensive cavities into the surface of the substrate. These results suggest that nature's repertoire of cellulose digestion paradigms remain only partially discovered and understood.
10.1126/science.1244273
Response to Comment on "Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA".
Brunecky Roman,Alahuhta Markus,Xu Qi,Donohoe Bryon S,Crowley Michael F,Kataeva Irina A,Yang Sung-Jae,Resch Michael G,Adams Michael W W,Lunin Vladimir V,Himmel Michael E,Bomble Yannick J
Science (New York, N.Y.)
Gusakov critiques our methodology for comparing the cellulolytic activity of the bacterial cellulase CelA with the fungal cellulase Cel7A. We address his concerns by clarifying some misconceptions, carefully referencing the literature, and justifying our approach to point out that the results from our study still stand.
10.1126/science.1251701
Heterologous protein expression in Hypocrea jecorina: a historical perspective and new developments.
Singh Arjun,Taylor Larry E,Vander Wall Todd A,Linger Jeffrey,Himmel Michael E,Podkaminer Kara,Adney William S,Decker Stephen R
Biotechnology advances
Hypocrea jecorina, the sexual teleomorph of Trichoderma reesei, has long been favored as an industrial cellulase producer, first utilizing its native cellulase system and later augmented by the introduction of heterologous enzymatic activities or improved variants of native enzymes. Expression of heterologous proteins in H. jecorina was once considered difficult when the target was an improved variant of a native cellulase. Developments over the past nearly 30 years have produced strains, vectors, and selection mechanisms that have continued to simplify and streamline heterologous protein expression in this fungus. More recent developments in fungal molecular biology have pointed the way toward a fundamental transformation in the ease and efficiency of heterologous protein expression in this important industrial host. Here, 1) we provide a historical perspective on advances in H. jecorina molecular biology, 2) outline host strain engineering, transformation, selection, and expression strategies, 3) detail potential pitfalls when working with this organism, and 4) provide consolidated examples of successful cellulase expression outcomes from our laboratory.
10.1016/j.biotechadv.2014.11.009
Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities.
Xu Qi,Resch Michael G,Podkaminer Kara,Yang Shihui,Baker John O,Donohoe Bryon S,Wilson Charlotte,Klingeman Dawn M,Olson Daniel G,Decker Stephen R,Giannone Richard J,Hettich Robert L,Brown Steven D,Lynd Lee R,Bayer Edward A,Himmel Michael E,Bomble Yannick J
Science advances
Clostridium thermocellum is the most efficient microorganism for solubilizing lignocellulosic biomass known to date. Its high cellulose digestion capability is attributed to efficient cellulases consisting of both a free-enzyme system and a tethered cellulosomal system wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins to generate large protein complexes attached to the bacterial cell wall. This study demonstrates that C. thermocellum also uses a type of cellulosomal system not bound to the bacterial cell wall, called the "cell-free" cellulosomal system. The cell-free cellulosome complex can be seen as a "long range cellulosome" because it can diffuse away from the cell and degrade polysaccharide substrates remotely from the bacterial cell. The contribution of these two types of cellulosomal systems in C. thermocellum was elucidated by characterization of mutants with different combinations of scaffoldin gene deletions. The primary scaffoldin, CipA, was found to play the most important role in cellulose degradation by C. thermocellum, whereas the secondary scaffoldins have less important roles. Additionally, the distinct and efficient mode of action of the C. thermocellum exoproteome, wherein the cellulosomes splay or divide biomass particles, changes when either the primary or secondary scaffolds are removed, showing that the intact wild-type cellulosomal system is necessary for this essential mode of action. This new transcriptional and proteomic evidence shows that a functional primary scaffoldin plays a more important role compared to secondary scaffoldins in the proper regulation of CAZyme genes, cellodextrin transport, and other cellular functions.
10.1126/sciadv.1501254
Single-molecule study of oxidative enzymatic deconstruction of cellulose.
Eibinger Manuel,Sattelkow Jürgen,Ganner Thomas,Plank Harald,Nidetzky Bernd
Nature communications
LPMO (lytic polysaccharide monooxygenase) represents a unique paradigm of cellulosic biomass degradation by an oxidative mechanism. Understanding the role of LPMO in deconstructing crystalline cellulose is fundamental to the enzyme's biological function and will help to specify the use of LPMO in biorefinery applications. Here we show with real-time atomic force microscopy that C1 and C4 oxidizing types of LPMO from Neurospora crassa (NcLPMO9F, NcLPMO9C) bind to nanocrystalline cellulose with high preference for the very same substrate surfaces that are also used by a processive cellulase (Trichoderma reesei CBH I) to move along during hydrolytic cellulose degradation. The bound LPMOs, however, are immobile during their adsorbed residence time ( ~ 1.0 min for NcLPMO9F) on cellulose. Treatment with LPMO resulted in fibrillation of crystalline cellulose and strongly ( ≥ 2-fold) enhanced the cellulase adsorption. It also increased enzyme turnover on the cellulose surface, thus boosting the hydrolytic conversion.Understanding the role of enzymes in biomass depolymerization is essential for the development of more efficient biorefineries. Here, the authors show by atomic force microscopy the real-time mechanism of cellulose deconstruction by lytic polysaccharide monooxygenases.
10.1038/s41467-017-01028-y
A bacterial pioneer produces cellulase complexes that persist through community succession.
Kolinko Sebastian,Wu Yu-Wei,Tachea Firehiwot,Denzel Evelyn,Hiras Jennifer,Gabriel Raphael,Bäcker Nora,Chan Leanne Jade G,Eichorst Stephanie A,Frey Dario,Chen Qiushi,Azadi Parastoo,Adams Paul D,Pray Todd R,Tanjore Deepti,Petzold Christopher J,Gladden John M,Simmons Blake A,Singer Steven W
Nature microbiology
Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.
10.1038/s41564-017-0052-z
Engineering of filamentous fungi for efficient conversion of lignocellulose: Tools, recent advances and prospects.
Liu Guodong,Qu Yinbo
Biotechnology advances
Filamentous fungi, as the main producers of lignocellulolytic enzymes in industry, need to be engineered to improve the economy of large-scale lignocellulose conversion. Investigation of the cellular processes involved in lignocellulolytic enzyme production, as well as optimization of enzyme mixtures for higher hydrolysis efficiency, have provided effective targets for the engineering of lignocellulolytic fungi. Recently, the development of efficient genetic manipulation systems in several lignocellulolytic fungi opens up the possibility of systems engineering of these strains. Here, we review the recent progresses made in the engineering of lignocellulolytic fungi and highlight the research gaps in this area.
10.1016/j.biotechadv.2018.12.004