Publications

Authors: Parthasarathi R, Bellesia G, Chundawat SPS, Dale BE, Langan P, Gnanakaran S

Media Coverage: New insights into hydrogen-bonding and stacking interactions in cellulose (Cover article for Journal of Physical Chemistry-A)

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Abstract: In this quantum chemical study, we explore hydrogen bonding (H-bonding) and stacking interactions in different crystalline cellulose allomorphs; namely, cellulose Iβ and cellulose IIII. We consider a model system representing a cellulose crystalline core made from six cellobiose units arranged in three layers with two chains per layer. We calculate the contributions of intrasheet and intersheet interactions to the structure and stability in both cellulose Iβ and cellulose IIII crystalline cores. Reference structures for this study were generated from molecular dynamics simulations of water-solvated cellulose Iβ and IIII fibrils. A systematic analysis of various conformations describing different mutual orientations of cellobiose units is performed using the hybrid density functional theory with the M06-2X with 6-31+G(d,p) basis sets. We dissect the nature of the forces that stabilize the cellulose Iβ and cellulose IIII crystalline cores and quantify the relative strength of H-bonding and stacking interactions. Our calculations demonstrate that individual H-bonding interactions are stronger in cellulose Iβ than in cellulose IIII; however, the total H-bonding contribution to stabilization is larger in cellulose IIII because of the highly cooperative nature of the H-bonding network. In addition, we observe a significant contribution from cooperative stacking interactions to the stabilization of cellulose Iβ. The theory of atoms-in-molecules (AIM) has been employed to characterize and quantify these intermolecular interactions. AIM analyses highlight the role of nonconventional CH···O H-bonding in the cellulose assemblies. Finally, we calculate molecular electrostatic potential maps for the cellulose allomorphs that capture the differences in chemical reactivity of the systems considered in our study.

Authors: Bellesia G, Chundawat SPS, Langan P, Dale BE, Gnanakaran S

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Abstract: Various chemicals are being explored for catalyzing efficient lignocellulose deconstruction. In particular, when liquid ammonia is used to convert the naturally occurring cellulose crystalline phase Iβ, to cellulose IIII, the rearrangement of the hydrogen bond network in cellulose IIII results in enhanced hydrolysis yields. We use molecular dynamics simulations to analyze the interaction between a cellulose Iβ fibril and ammonia. Our simulations reveal that early structural changes in the fibril are driven by the rapid formation of an extended hydrogen bond network between the solvent-exposed surface chains and ammonia that precedes ammonia penetration into the fibril. The emergence of this hydrogen bond network causes relative shifting of the cellulose layers within the fibril that in turn leads to the formation of channels orthogonal to the (100) and (−100) fibril surfaces. The channels allow ammonia molecules to penetrate into the cellulose fibril. These findings provide avenues for improving existing chemical pretreatments to make them more effective and economical.

Authors: Chundawat SPS*, Lipton M*, Purvine S, Uppugundla N, Gao D, Balan V, Dale BE

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Abstract: Efficient deconstruction of cellulosic biomass to fermentable sugars for fuel and chemical production is accomplished by a complex mixture of cellulases, hemicellulases, and accessory enzymes (e.g., >50 extracellular proteins). Cellulolytic enzyme mixtures, produced industrially mostly using fungi like Trichoderma reesei, are poorly characterized in terms of their protein composition and its correlation to hydrolytic activity on cellulosic biomass. The secretomes of commercial glycosyl hydrolase-producing microbes was explored using a proteomics approach with high-throughput quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we show that proteomics-based spectral counting approach is a reasonably accurate and rapid analytical technique that can be used to determine protein composition of complex glycosyl hydrolase mixtures that also correlates with the specific activity of individual enzymes present within the mixture. For example, a strong linear correlation was seen between Avicelase activity and total cellobiohydrolase content. Reliable, quantitative and cheaper analytical methods that provide insight into the cellulosic biomass degrading fungal and bacterial secretomes would lead to further improvements toward commercialization of plant biomass-derived fuels and chemicals.

Authors: Chundawat SPS*, Bellesia G, Uppugundla N, Sousa L, Gao D, Cheh A, Agarwal U, Bianchetti C, Phillips G, Langan P, Balan V, Gnanakaran S*, Dale BE

Media Coverage: Researchers find potential key for unlocking biomass energy using ammonia (Michigan State University, Materials Research Society Bulletin 360 Energy Focus, AICHE Chemical & Engineering Progress (September 2011, Vol. 107, No. 9)

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Abstract: 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 Iβ to IIII, 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 IIII, 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 IIII fibril surface that facilitated easier glucan chain extraction. Unrestricted substrate accessibility to active-site clefts of certain endocellulase families further accelerated deconstruction of cellulose IIII. Structural and dynamical features of cellulose IIII, 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.

Authors: Park S-H, Ransom C, Mei C, Sabzikar R, Qi C, Chundawat SPS, Dale BE, Sticklen M

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Abstract: BACKGROUND: Production of cellulosic ethanol is still expensive compared with corn (maize) grain ethanol due to the high costs of bulk production of microbial cellulases. At least three cellulases including endo-cellulase, exo-cellulase and cellobiase are needed to convert cellulosic biomass into fermentable sugars. All these cellulases could be self-produced within cells of transgenic bio-energy crops. The production of heterologous Acidothermus cellulolyticus (E1) endo-cellulase in endoplasmic reticulum and mitochondria of green tissues of transgenic corn plants was recently reported, and it was confirmed that the heterologous E1 converts cellulose into fermentable sugars. RESULTS: Biologically active A. cellulolyticus E1, Trichoderma reesei 1,4-β-cellobiohydrolases I (CBH I) exo-cellulase and bovine rumen Butyrivibrio fibrisolvens cellobiase were expressed in corn plant endoplasmic reticulum (ER), apoplast (cell wall areas) and vacuole respectively. Results show that the ratio 1:4:1 (E1:CBH I:cellobiase) of crude heterologous cellulases is ideal for converting ammonia fiber explosion (AFEX) pretreated corn stover into fermentable sugars. CONCLUSIONS: Corn plants that express all three biologically active heterologous cellulases within their cellulosic biomass to facilitate conversion of pretreated corn stover into fermentable sugars is a step forward in the quest for alternatives to the present microbial cellulase mix production for cellulosic biofuels.

Authors: Li C, Cheng G, Balan V, Kent MS, Ong M, Chundawat SPS, Sousa L, Melnichenko YB, Dale BE, Simmons BA, Singh S*

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Abstract: Ionic liquid (IL) and ammonia fiber expansion (AFEX) pretreatments were studied to develop the first direct side-by-side comparative assessment on their respective impacts on biomass structure, composition, process mass balance, and enzymatic saccharification efficiency. AFEX pretreatment completely preserves plant carbohydrates, whereas IL pretreatment extracts 76% of hemicellulose. In contrast to AFEX, the native crystal structure of the recovered corn stover from IL pretreatment was significantly disrupted. For both techniques, more than 70% of the theoretical sugar yield was attained after 48 h of hydrolysis using commercial enzyme cocktails. IL pretreatment requires less enzyme loading and a shorter hydrolysis time to reach 90% yields. Hemicellulase addition led to significant improvements in the yields of glucose and xylose for AFEX pretreated corn stover, but not for IL pretreated stover. These results provide new insights into the mechanisms of IL and AFEX pretreatment, as well as the advantages and disadvantages of each.

Authors: Gao D*, Chundawat SPS, Uppugundla N, Balan V, Dale BE

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Abstract: Studying the binding properties of cellulases to lignocellulosic substrates is critical to achieving a fundamental understanding of plant cell wall saccharification. Lignin auto-fluorescence and degradation products formed during pretreatment impede accurate quantification of individual glycosyl hydrolases (GH) binding to pretreated cell walls. A high-throughput fast protein liquid chromatography (HT-FPLC)-based method has been developed to quantify cellobiohydrolase I (CBH I or Cel7A), cellobiohydrolase II (CBH II or Cel6A), and endoglucanase I (EG I or Cel7B) present in hydrolyzates of untreated, ammonia fiber expansion (AFEX), and dilute-acid pretreated corn stover (CS). This method can accurately quantify individual enzymes present in complex binary and ternary protein mixtures without interference from plant cell wall-derived components. The binding isotherms for CBH I, CBH II, and EG I were obtained after incubation for 2 h at 4 °C. Both AFEX and dilute acid pretreatment resulted in increased cellulase binding compared with untreated CS. Cooperative binding of CBH I and/or CBH II in the presence of EG I was observed only for AFEX treated CS. Competitive binding between enzymes was found for certain other enzyme-substrate combinations over the protein loading range tested (i.e., 25-450 mg/g glucan). Langmuir single-site adsorption model was fitted to the binding isotherm data to estimate total available binding sites E(bm) (mg/g glucan) and association constant K(a) (L/mg). Our results clearly demonstrate that the characteristics of cellulase binding depend not only on the enzyme GH family but also on the type of pretreatment method employed.

Authors: Humpula J*, Chundawat SPS, Vismeh R, Jones AD, Balan V, Dale BE

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Abstract:Accurate quantification of reaction products formed during thermochemical pretreatment of lignocellulosic biomass would lead to a better understanding of plant cell wall deconstruction for production of cellulosic biofuels and biochemicals. However, quantification of some process byproducts, most notably acetamide, acetic acid and furfural, present several analytical challenges using conventional liquid chromatography methods. Therefore, we have developed a high-throughput gas chromatography based mass spectrometric (GC–MS) method in order to quantify relevant compounds without requiring time-consuming sample derivatization prior to analysis. Solvent extracts of untreated, ammonia fiber expansion (AFEX) treated and dilute-acid treated corn stover were analyzed by this method. Biomass samples were extracted with acetone using an automated solvent extractor, serially diluted and directly analyzed using the proposed GC–MS method. Acetone was the only solvent amongst water, methanol and acetonitrile that did not contain detectable background levels of the target compounds or facilitate a buildup of plant-derived residues in the GC injector, which decreased analytical reproducibility. Quantitative results were based on the method of standard addition and external standard calibration curves.

Authors: Gao D*, Uppugundla N, Chundawat SPS, Yu X, Hermanson S, Gowda K, Brumm P, Balan V, Dale BE

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Abstract: High enzyme loading is a major economic bottleneck for the commercial processing of pretreated lignocellulosic biomass to produce fermentable sugars. Optimizing the enzyme cocktail for specific types of pretreated biomass allows for a significant reduction in enzyme loading without sacrificing hydrolysis yield. This is especially important for alkaline pretreatments such as Ammonia fiber expansion (AFEX) pretreated corn stover. Hence, a diverse set of hemicellulases supplemented along with cellulases is necessary for high recovery of monosaccharides.

Authors: Chundawat SPS*, Donohoe B, Sousa LdC, Elder T, Agarwal U, Lu F, Ralph J, Himmel M, Balan V, Dale BE

Media Coverage: Improving chemical pre-treatments for better biomass conversion (Royal Society of Chemistry, Great Lakes Bioenergy Research Center)

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Abstract: Deconstruction of lignocellulosic plant cell walls to fermentable sugars by thermochemical and/or biological means is impeded by several poorly understood ultrastructural and chemical barriers. A promising thermochemical pretreatment called ammonia fiber expansion (AFEX) overcomes the native recalcitrance of cell walls through subtle morphological and physicochemical changes that enhance cellulase accessibility without extracting lignin and hemicelluloses into separate liquid streams. Multi-scale visualization and characterization of Zea mays (i.e., corn stover) cell walls were carried out by laser scanning confocal fluorescence microscopy (LSCM), Raman spectroscopy, atomic force microscopy (AFM), electron microscopy (SEM, TEM), nuclear magnetic resonance (NMR), and electron spectroscopy for chemical analysis (ESCA) to elucidate the mechanism of AFEX pretreatment. AFEX first dissolves, then extracts and, as the ammonia evaporates, redeposits cell wall decomposition products (e.g., amides, arabinoxylan oligomers, lignin-based phenolics) on outer cell wall surfaces. As a result, nanoporous tunnel-like networks, as visualized by 3D-electron tomography, are formed within the cell walls. We propose that this highly porous structure greatly enhances enzyme accessibility to embedded cellulosic microfibrils. The shape, size (10 to 1000 nm), and spatial distribution of the pores depended on their location within the cell wall and the pretreatment conditions used. Exposed pore surface area per unit AFEX pretreated cell wall volume, estimated via TEM-tomogram image analysis, ranged between 0.005 and 0.05 nm2 per nm3. AFEX results in ultrastructural and physicochemical modifications within the cell wall that enhance enzymatic hydrolysis yield by 4–5 fold over that of untreated cell walls.

Authors: Shao Q, Chundawat SPS, Krishnan C, Bals B, Sousa LdC, Thelen K, Dale B, Balan V

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Abstract: Corn grain is an important renewable source for bioethanol production in the USA. Corn ethanol is currently produced by steam liquefaction of starch-rich grains followed by enzymatic saccharification and fermentation. Corn stover (the non-grain parts of the plant) is a potential feedstock to produce cellulosic ethanol in second-generation biorefineries. At present, corn grain is harvested by removing the grain from the living plant while leaving the stover behind on the field. Alternatively, whole corn plants can be harvested to cohydrolyze both starch and cellulose after a suitable thermochemical pretreatment to produce fermentable monomeric sugars. In this study, we used physiologically immature corn silage (CS) and matured whole corn plants (WCP) as feedstocks to produce ethanol using ammonia fiber expansion (AFEX) pretreatment followed by enzymatic hydrolysis (at low enzyme loadings) and cofermentation (for both glucose and xylose) using a cellulase-amylase-based cocktail and a recombinant Saccharomyces cerevisiae 424A (LNH-ST) strain, respectively. The effect on hydrolysis yields of AFEX pretreatment conditions and a starch/cellulose-degrading enzyme addition sequence for both substrates was also studied.

Authors: Chundawat SPS*, Vismeh R, Sharma L, Humpula J, Sousa L, Chambliss CK, Jones AD, Balan V, Dale BE

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Abstract: Decomposition products formed/released during ammonia fiber expansion (AFEX) and dilute acid (DA) pretreatment of corn stover (CS) were quantified using robust mass spectrometry based analytical platforms. Ammonolytic cleavage of cell wall ester linkages during AFEX resulted in the formation of acetamide (25 mg/g AFEX CS) and various phenolic amides (15 mg/g AFEX CS) that are effective nutrients for downstream fermentation. After ammonolysis, Maillard reactions with carbonyl-containing intermediates represent the second largest sink for ammonia during AFEX. On the other hand, several carboxylic acids were formed (e.g. 35 mg acetic acid/g DA CS) during DA pretreatment. Formation of furans was 36-fold lower for AFEX compared to DA treatment; while carboxylic acids (e.g. lactic and succinic acids) yield was 100–1000-fold lower during AFEX compared to previous reports using sodium hydroxide as pretreatment reagent.

Authors: Gao D*, Chundawat SPS, Liu T, Hermanson S, Gowda K, Brumm P, Dale BE, Balan V

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Abstract: A rational four-step strategy to identify novel bacterial glycosyl hydrolases (GH), in combination with various fungal enzymes, was applied in order to develop tailored enzyme cocktails to efficiently hydrolyze pretreated lignocellulosic biomass. The fungal cellulases include cellobiohydrolase I (CBH I; GH family 7A), cellobiohydrolase II (CBH II; GH family 6A), endoglucanase I (EG I; GH family 7B), and β-glucosidase (βG; GH family 3). Bacterial endocellulases (LC1 and LC2; GH family 5), β-glucosidase (LβG; GH family 1), endoxylanases (LX1 and LX2; GH family 10), and β-xylosidase (LβX; GH family 52) from multiple sources were cloned, expressed, and purified. Enzymatic hydrolysis for varying enzyme combinations was carried out on ammonia fiber expansion (AFEX)-treated corn stover at three total protein loadings (i.e., 33, 16.5, and 11 mg enzyme/g glucan). The optimal mass ratio of enzymes necessary to maximize both glucan and xylan yields was determined using a suitable design of experiments. The optimal hybrid enzyme mixtures contained fungal cellulases (78% of total protein loading), which included CBH I (loading ranging between 9-51% of total enzyme), CBH II (9-51%), EG I (10-50%), and bacterial hemicellulases (22% of total protein loading) comprising of LX1 (13%) and LβX (9%). The hybrid mixture was effective at 50°C, pH 4.5 to maximize saccharification of AFEX-treated corn stover resulting in 95% glucan and 65% xylan conversion. This strategy of screening novel enzyme mixtures on pretreated lignocellulose would ultimately lead to the development of tailored enzyme cocktails that can hydrolyze plant cell walls efficiently and economically to produce cellulosic ethanol.

Authors: Gao D*, Chundawat SPS, Krishnan C, Balan V, Dale BE

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Abstract: In this work, six core glycosyl hydrolases (GH) were isolated and purified from various sources to help rationally optimize an enzyme cocktail to digest ammonia fiber expansion (AFEX) treated corn stover. The four core cellulases were endoglucanase I (EG I, GH family 7B), cellobiohydrolase I (CBH I, GH family 7A), cellobiohydrolase II (CBH II, GH family 6A) and beta-glucosidase (betaG, GH family 3). The two core hemicellulases were an endo-xylanase (EX, GH family 11) and a beta-xylosidase (betaX, GH family 3). Enzyme family and purity were confirmed by proteomics. Synergistic interactions among the six core enzymes for varying relative and total protein loading (8.25, 16.5 and 33 mg/g glucan) during hydrolysis of AFEX-treated corn stover was studied using a high-throughput microplate based protocol. The optimal composition (based on% protein mass loading) of the cocktail mixture was CBH I (28.4%): CBH II (18.0%): EG I (31.0%): EX (14.1%): betaG (4.7%): betaX (3.8%). These results demonstrate a rational strategy for the development of a minimal, synergistic enzymes cocktail that could reduce enzyme usage and maximize the fermentable sugar yields from pretreated lignocellulosics.

Authors: Balan V*, Sousa L, Chundawat SPS, Marshall D, Sharma L, Chambliss C, Dale BE

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Abstract: There is a growing need to find alternatives to crude oil as the primary feed stock for the chemicals and fuel industry and ethanol has been demonstrated to be a viable alternative. Among the various feed stocks for producing ethanol, poplar (Populus nigra x Populus maximowiczii) is considered to have great potential as a biorefinery feedstock in the United States, due to their widespread availability and good productivity in several parts of the country. We have optimized AFEX pretreatment conditions (180 degrees C, 2:1 ammonia to biomass loading, 233% moisture, 30 minutes residence time) and by using various combinations of enzymes (commercical celluloses and xylanases) to achieve high glucan and xylan conversion (93 and 65%, respectively). We have also identified and quantified several important degradation products formed during AFEX using liquid chromatography followed by mass spectrometry (LC-MS/MS). As a part of degradation product analysis, we have also quantified oligosaccharides in the AFEX water wash extracts by acid hydrolysis. It is interesting to note that corn stover (C4 grass) can be pretreated effectively using mild AFEX pretreatment conditions, while on the other hand hardwood poplar requires much harsher AFEX conditions to obtain equivalent sugar yields upon enzymatic hydrolysis. Comparing corn stover and poplar, we conclude that pretreatment severity and enzymatic hydrolysis efficiency are dictated to a large extent by lignin carbohydrate complexes and arabinoxylan cross-linkages for AFEX.

Authors: Balan V*, Rogers C, Chundawat SPS, da Costa Sousa L, Slininger P, Gupta R, Dale BE

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Abstract: We have come up with a novel, integrated approach for making biodiesel by in-house producion of ethanol after fermentation of hexane extracted edible oil cake fiber. In addition, we have demonstrated how ethanol could be manufactured from commonly available oil cakes (such as canola, sunflower, sesame, soy, peanut) and dried distiller’s grains with solubles (DDGS). The edible oil cakes and DDGS were hexane extracted, ammonia fiber expansion pretreated, enzymatically hydrolysed and fermented to produce ethanol. From all the oil cakes tested in this work, DDGS and peanut oil cake showed the most promising results giving more than 180 g of glucose/kg of oil cake. These two feedstock’s were hydrolyzed at 15% solids loading and fermented by a native strain of Pichia stipitis. Most sugars were consumed during the first 24 h, with no pronounced inhibition of P. stipitis by the degradation products in the hydrolysate. Xylose consumption was more effective for peanut cake hydrolyzate compared to DDGS.

Authors: Garlock R*, Chundawat SPS, Balan V, Dale B

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Abstract: Corn stover composition changes considerably throughout the growing season and also varies between the various fractions of the plant. These differences can impact optimal pretreatment conditions, enzymatic digestibility and maximum achievable sugar yields in the process of converting lignocellulosics to ethanol. The goal of this project was to determine which combination of corn stover fractions provides the most benefit to the biorefinery in terms of sugar yields and to determine the preferential order in which fractions should be harvested. Ammonia fiber expansion (AFEX) pretreatment, followed by enzymatic hydrolysis, was performed on early and late harvest corn stover fractions (stem, leaf, husk and cob). Sugar yields were used to optimize scenarios for the selective harvest of corn stover assuming 70% or 30% collection of the total available stover.