Pushing the boundaries of phosphorylase cascade reaction for cellobiose production II: Model-based multiobjective optimization

The inherent complexity of coupled biocatalytic reactions presents a major challenge for process development with one-pot multienzyme cascade transformations. Kinetic models are powerful engineering tools to guide the optimization of cascade reactions towards a performance suitable for scale up to an actual production. Here, we report kinetic model-based window of operation analysis for cellobiose production (≥100 g/L) from sucrose and glucose by indirect transglycosylation via glucose 1-phosphate as intermediate. The two-step cascade transformation is catalyzed by sucrose and cellobiose phosphorylase in the presence of substoichiometric amounts of phosphate (≤27 mol% of substrate). Kinetic modeling was instrumental to uncover the hidden effect of bulk microviscosity due to high sugar concentrations on decreasing the rate of cellobiose phosphorylase specifically. The mechanistic-empirical hybrid model thus developed gives a comprehensive description of the cascade reaction at industrially relevant substrate conditions. Model simulations serve to unravel opposed relationships between efficient utilization of the enzymes and maximized concentration (or yield) of the product within a given process time, in dependence of the initial concentrations of substrate and phosphate used. Optimum balance of these competing key metrics of process performance is suggested from the model-calculated window of operation and is verified experimentally. The evidence shown highlights the important use of kinetic modeling for the characterization and optimization of cascade reactions in ways that appear to be inaccessible to purely data-driven approaches.

Pushing the boundaries of phosphorylase cascade reaction for cellobiose production I: Kinetic model development

One-pot cascade reactions of coupled disaccharide phosphorylases enable an efficient transglycosylation via intermediary α-d-glucose 1-phosphate (G1P). Such transformations have promising applications in the production of carbohydrate commodities, including the disaccharide cellobiose for food and feed use. Several studies have shown sucrose and cellobiose phosphorylase for cellobiose synthesis from sucrose, but the boundaries on transformation efficiency that result from kinetic and thermodynamic characteristics of the individual enzyme reactions are not known. Here, we assessed in a step-by-step systematic fashion the practical requirements of a kinetic model to describe cellobiose production at industrially relevant substrate concentrations of up to 600 mM sucrose and glucose each. Mechanistic initial-rate models of the two-substrate reactions of sucrose phosphorylase (sucrose + phosphate → G1P + fructose) and cellobiose phosphorylase (G1P + glucose → cellobiose + phosphate) were needed and additionally required expansion by terms of glucose inhibition, in particular a distinctive two-site glucose substrate inhibition of the cellobiose phosphorylase (from Cellulumonas uda). Combined with mass action terms accounting for the approach to equilibrium, the kinetic model gave an excellent fit and a robust prediction of the full reaction time courses for a wide range of enzyme activities as well as substrate concentrations, including the variable substoichiometric concentration of phosphate. The model thus provides the essential engineering tool to disentangle the highly interrelated factors of conversion efficiency in the coupled enzyme reaction; and it establishes the necessary basis of window of operation calculations for targeted optimizations toward different process tasks.

Transcriptional regulation of cellobiose utilization by PRD-domain containing Sigma54-dependent transcriptional activator (CelR) and catabolite control protein A (CcpA) in Bacillus thuringiensis

Cellobiose, a β-1,4-linked glucose dimer, is a major cellodextrin resulting from the enzymatic hydrolysis of cellulose. It is a major source of carbon for soil bacteria. In bacteria, the phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS), encoded by the cel operon, is responsible for the transport and utilization of cellobiose. In this study, we analyzed the transcription and regulation of the cel operon in Bacillus thuringiensis (Bt). The cel operon is composed of five genes forming one transcription unit. β-Galactosidase assays revealed that cel operon transcription is induced by cellobiose, controlled by Sigma54, and positively regulated by CelR. The HTH-AAA+ domain of CelR recognized and specifically bound to three possible binding sites in the celA promoter region. CelR contains two PTS regulation domains (PRD1 and PRD2), which are separated by two PTS-like domains-the mannose transporter enzyme IIA component domain (EIIAMan) and the galactitol transporter enzyme IIB component domain (EIIBGat). Mutations of His-546 on the EIIAMan domain and Cys-682 on the EIIBGat domain resulted in decreased transcription of the cel operon, and mutations of His-839 on PRD2 increased transcription of the cel operon. Glucose repressed the transcription of the cel operon and catabolite control protein A (CcpA) positively regulated this process by binding the cel promoter. In the celABCDE and celR mutants, PTS activities were decreased, and cellobiose utilization was abolished, suggesting that the cel operon is essential for cellobiose utilization. Bt has been widely used as a biological pesticide. The metabolic properties of Bt are critical for fermentation. Nutrient utilization is also essential for the environmental adaptation of Bt. Glucose is the preferred energy source for many bacteria, and the presence of the phosphotransferase system allows bacteria to utilize other sugars in addition to glucose. Cellobiose utilization pathways have been of particular interest owing to their potential for developing alternative energy sources for bacteria. The data presented in this study improve our understanding of the transcription patterns of cel gene clusters. This will further help us to better understand how cellobiose is utilized for bacterial growth.

Efficient and Economic Utilization of Cellobiose for Glycosylation Modification by Regulating Carbon Source Supply and Metabolic Pathway In Vivo

Glycosylation, one of the most common and significant modifications in nature, has prompted the development of a cellobiose phosphorolysis route for glycosylation in vivo. However, the process of glycosylation is hampered by the notably low conversion rate of cellobiose. In this work, regulation of the carbon source supply by changing the ratio of glucose to cellobiose improved the conversion rate of cellobiose, resulting in enhancing the efficiency of glycosylation and the production of vitexin. Moreover, three genes (pgm, agp, and ushA) involved in the degradation of UDP-glucose were knocked out to relieve the degradation and diversion of the cellobiose phosphorolysis route. Finally, through the optimization of conversion conditions, we observed a continuous enhancement in cellobiose conversion rate and vitexin production in BL21ΔushAΔagp-TcCGT-CepA, corresponding to an increased concentration of added glucose. The maximum production of vitexin reached 2228 mg/L with the addition of 2 g/L cellobiose and 6 g/L glucose, which was 312% of that in BL21-TcCGT-CepA with the addition of 2 g/L cellobiose. The conversion rate of cellobiose in BL21ΔushAΔagp-TcCGT-CepA reached 88%, which was the highest conversion rate of cellobiose to date. Therefore, this study presents a cost-effective and efficient method to enhance the conversion rate of cellobiose during the glycosylation process.

Engineering of Ogataea polymorpha strains with ability for high-temperature alcoholic fermentation of cellobiose

Successful conversion of cellulosic biomass into biofuels requires organisms capable of efficiently utilizing xylose as well as cellodextrins and glucose. Ogataea (Hansenula) polymorpha is the natural xylose-metabolizing organism and is one of the most thermotolerant yeasts known, with a maximum growth temperature above 50°C. Cellobiose-fermenting strains, derivatives of an improved ethanol producer from xylose O. polymorpha BEP/cat8∆, were constructed in this work by the introduction of heterologous genes encoding cellodextrin transporters (CDTs) and intracellular enzymes (β-glucosidase or cellobiose phosphorylase) that hydrolyze cellobiose. For this purpose, the genes gh1-1 of β-glucosidase, CDT-1m and CDT-2m of cellodextrin transporters from Neurospora crassa and the CBP gene coding for cellobiose phosphorylase from Saccharophagus degradans, were successfully expressed in O. polymorpha. Through metabolic engineering and mutagenesis, strains BEP/cat8∆/gh1-1/CDT-1m and BEP/cat8∆/CBP-1/CDT-2mAM were developed, showing improved parameters for high-temperature alcoholic fermentation of cellobiose. The study highlights the need for further optimization to enhance ethanol yields and elucidate cellobiose metabolism intricacies in O. polymorpha yeast. This is the first report of the successful development of stable methylotrophic thermotolerant strains of O. polymorpha capable of coutilizing cellobiose, glucose, and xylose under high-temperature alcoholic fermentation conditions at 45°C.

Plant structural and storage glucans trigger distinct transcriptional responses that modulate the motility of Xanthomonas pathogens

IMPORTANCE

Pathogenic Xanthomonas bacteria can affect a variety of economically relevant crops causing losses in productivity, limiting commercialization and requiring phytosanitary measures. These plant pathogens exhibit high level of host and tissue specificity through multiple molecular strategies including several secretion systems, effector proteins, and a broad repertoire of carbohydrate-active enzymes (CAZymes). Many of these CAZymes act on the plant cell wall and storage carbohydrates, such as cellulose and starch, releasing products used as nutrients and modulators of transcriptional responses to support host colonization by mechanisms yet poorly understood. Here, we reveal that structural and storage β-glucans from the plant cell function as spatial markers, providing distinct chemical stimuli that modulate the transition between higher and lower motility states in Xanthomonas citri, a key virulence trait for many bacterial pathogens.

Role of the Solute-Binding Protein CuaD in the Signaling and Regulating Pathway of Cellobiose and Cellulose Utilization in Ruminiclostridium cellulolyticum

In Ruminiclostridium cellulolyticum, cellobiose is imported by the CuaABC ATP-binding cassette transporter containing the solute-binding protein (SBP) CuaA and is further degraded in the cytosol by the cellobiose phosphorylase CbpA. The genes encoding these proteins have been shown to be essential for cellobiose and cellulose utilization. Here, we show that a second SBP (CuaD), whose gene is adjacent to two genes encoding a putative two-component regulation system (CuaSR), forms a three-component system with CuaS and CuaR. Studies of mutant and recombinant strains of R. cellulolyticum have indicated that cuaD is important for the growth of strains on cellobiose and cellulose. Furthermore, the results of our RT-qPCR experiments suggest that both the three (CuaDSR)- and the two (CuaSR)-component systems are able to perceive the cellobiose signal. However, the strain producing the three-component system is more efficient in its cellobiose and cellulose utilization. As CuaD binds to CuaS, we propose an in-silico model of the complex made up of two extracellular domains of CuaS and two of CuaD. CuaD allows microorganisms to detect very low concentrations of cellobiose due to its high affinity and specificity for this disaccharide, and together with CuaSR, it triggers the expression of the cuaABC-cbpA genes involved in cellodextrins uptake.

Cellobiose elicits immunity in lettuce conferring resistance to Botrytis cinerea

Cellobiose is the primary product of cellulose hydrolysis and is expected to function as a type of pathogen/damage-associated molecular pattern in evoking plant innate immunity. In this study, cellobiose was demonstrated to be a positive regulator in the immune response of lettuce, but halted autoimmunity when lettuce was exposed to concentrations of cellobiose >60 mg l-1. When lettuce plants were infected by Botrytis cinerea, cellobiose endowed plants with enhanced pre-invasion resistance by activating high β-1,3-glucanase and antioxidative enzyme activities at the initial stage of pathogen infection. Cellobiose-activated core regulatory factors such as EDS1, PTI6, and WRKY70, as well as salicylic acid signaling, played an indispensable role in modulating plant growth-defense trade-offs. Transcriptomics data further suggested that the cellobiose-activated plant-pathogen pathways are involved in microbe/pathogen-associated molecular pattern-triggered immune responses. Genes encoding receptor-like kinases, transcription factors, and redox homeostasis, phytohormone signal transduction, and pathogenesis-related proteins were also up- or down-regulated by cellobiose. Taken together, the findings of this study demonstrated that cellobiose serves as an elicitor to directly activate disease-resistance-related cellular functions. In addition, multiple genes have been identified as potential modulators of the cellobiose-induced immune response, which could aid understanding of underlying molecular events.

Glucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiae

Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metabolize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endogenous PDCs will eliminate ethanol production, but the resulting strain suffers from C₂ auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product without the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae expressing the Rhizopus oryzae lactic acid dehydrogenase (LdhA). While the membrane glucose sensors Snf3 and Rgt2 did not play any direct role in the option of predominant product, the sugar assimilation rate was strongly correlated to the partition of flux at pyruvate: fast sugar assimilation favors ethanol production while slow sugar assimilation favors lactic acid. Applying this knowledge, we created an engineered yeast capable of simultaneously converting glucose and xylose into lactic acid, increasing lactic acid production to approximately 17 g L^-1 from the 12 g L^-1 observed during sequential consumption of sugars. This work elucidates the carbon source-dependent effects on product selection in engineered yeast.

Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium

The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation.

The claim of primacy of human gut Bacteroides ovatus in dietary cellobiose degradation

A demonstration of cellulose degrading bacterium from human gut changed our view that human cannot degrade the cellulose. However, investigation of cellulose degradation by human gut microbiota on molecular level has not been completed so far. We showed here, using cellobiose as a model that promoted the growth of human gut key members, such as Bacteroides ovatus (BO), to clarify the molecular mechanism. Our results showed that a new polysaccharide utilization locus (PUL) from BO was involved in the cellobiose capturing and degradation. Further, two new cellulases BACOVA_02626^GH5 and BACOVA_02630^GH5 on the cell surface performed the degradation of cellobiose into glucose were determined. The predicted structures of BACOVA_02626^GH5 and BACOVA_02630^GH5 were highly homologous with the cellulase from soil bacteria, and the catalytic residues were highly conservative with two glutamate residues. In murine experiment, we observed cellobiose reshaped the composition of gut microbiota and probably modified the metabolic function of bacteria. Taken together, our findings further highlight the evidence of cellulose can be degraded by human gut microbes and provide new insight in the field of investigation on cellulose.

Comprehensive Characterization of Mutant Pichia stipitis Co-Fermenting Cellobiose and Xylose through Genomic and Transcriptomic Analyses

The development of a yeast strain capable of fermenting mixed sugars efficiently is crucial for producing biofuels and value-added materials from cellulosic biomass. Previously, a mutant Pichia stipitis YN14 strain capable of co-fermenting xylose and cellobiose was developed through evolutionary engineering of the wild-type P. stipitis CBS6054 strain, which was incapable of cofermenting xylose and cellobiose. In this study, through genomic and transcriptomic analyses, we sought to investigate the reasons for the improved sugar metabolic performance of the mutant YN14 strain in comparison with the parental CBS6054 strain. Unfortunately, comparative wholegenome sequencing (WGS) showed no mutation in any of the genes involved in the cellobiose metabolism between the two strains. However, comparative RNA sequencing (RNA-seq) revealed that the YN14 strain had 101.2 times and 5.9 times higher expression levels of HXT2.3 and BGL2 genes involved in cellobiose metabolism, and 6.9 times and 75.9 times lower expression levels of COX17 and SOD2.2 genes involved in respiration, respectively, compared with the CBS6054 strain. This may explain how the YN14 strain enhanced cellobiose metabolic performance and shifted the direction of cellobiose metabolic flux from respiration to fermentation in the presence of cellobiose compared with the CBS6054 strain.

Mechanism Analysis of Ethanol Production from Cellulosic Insulating Paper Based on Reaction Molecular Dynamics

The paper/oil system is the main component of transformer insulation. Indicator plays a vital role in assessing the aging condition of local hot spots of transformer insulation paper. The cellulosic insulating paper is mainly composed of cellobiose. This study uses the molecular dynamics method based on reactive force field (ReaxFF) to pyrolyze the insulating paper. Various production paths of ethanol were studied at the atomic level through ReaxFF simulations. A model consisting of 40 cellobioses was established for repeated simulation at 500 K-3000 K. Besides, to explore the relationship between the intermediate products and ethanol, the combination model of intermediate products (levoglucosan, acetaldehyde, 2,2-dihydroxyacetaldehyde) was established for repeated simulation. The simulation results showed that the increase in temperature can accelerate the production of ethanol from insulating paper and its pyrolysis intermediate products, which matched the related experimental results. This study can provide an effective reference for the use of ethanol as an indicator to assess the aging condition of the local hot spots of transformers.

Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design

Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower K_m values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.

Characterization of an operon required for growth on cellobiose in Clostridioides difficile

Cellobiose metabolism is linked to the virulence properties in numerous bacterial pathogens. Here, we characterized a putative cellobiose PTS operon of Clostridiodes difficile to investigate the role of cellobiose metabolism in C. difficile pathogenesis. Our gene knockout experiments demonstrated that the putative cellobiose operon enables uptake of cellobiose into C. difficile and allows growth when cellobiose is provided as the sole carbon source in minimal medium. Additionally, using reporter gene fusion assays and DNA pulldown experiments, we show that its transcription is regulated by CelR, a novel transcriptional repressor protein, which directly binds to the upstream region of the cellobiose operon to control its expression. We have also identified cellobiose metabolism to play a significant role in C. difficile physiology as observed by the reduction of sporulation efficiency when cellobiose uptake was compromised in the mutant strain. In corroboration to in vitro study findings, our in vivo hamster challenge experiment showed a significant reduction of pathogenicity by the cellobiose mutant strain in both the primary and the recurrent infection model - substantiating the role of cellobiose metabolism in C. difficile pathogenesis.

Synthetic Cellobiose-Inducible Regulatory Systems Allow Tight and Dynamic Controls of Gene Expression in Streptomyces

Precise control of microbial gene expression is crucial for synthetic biotechnological applications. This is particularly true for the bacterial genus Streptomyces, major producers of diverse natural products including many antibiotics. Although a plethora of genetic tools have been developed for Streptomyces, there is still an urgent need for effective gene induction systems. We herein created two novel cellobiose-inducible regulatory systems referred to as Cel-RS1 and Cel-RS2. The regulatory systems are based upon the well-characterized repressor/operator pair CebR/cebO from Streptomyces scabies and the well-defined constitutive kasO* promoter. Both Cel-RS1 and Cel-RS2 exhibit a high level of induced reporter activity and virtually no leaky expression in three model Streptomyces species, which are commonly used as surrogate hosts for expression of natural product biosynthetic gene clusters. Cel-RS2 has been proven successful for programmable control of gene expression and controllable production of specialized metabolites in multiple Streptomyces species. The strategy can be used to expand the toolkit of inducible regulatory systems that will be broadly applicable to various Streptomyces.

Structural aspects of β-glucosidase of Myceliophthora thermophila (MtBgl3c) by homology modelling and molecular docking

Cellulases are the enzymes with diverse range of industrial applications. Cellulases degrade cellulose into monomeric glucose units by hydrolysing β-1,4-glycosidic bonds. There are three components of cellulases: a) endoglucanase, b) exoglucanase and c) β-glucosidase which act synergistically in cellulose bioconversion. The cellulases are the third largest industrial enzymes with a great potential in bioethanol production. In this investigation, a β-glucosidase of a thermophilic fungus Myceliophthora thermophila (MtBgl3c) was analysed for its structural characterization using in silico approaches. The protein structure of MtBgl3c is unknown, therefore an attempt has been made to model 3D structure using Modeller 9.23 software. The MtBgl3c protein model generated was validated from Verify 3D and ERRAT scores of 89.37% and 71.25%, respectively derived from SAVES. Using RAMPAGE the Ramachandran plot was generated, which predicted the accuracy of the 3D model with 91.5% amino acid residues in the favored region. The ion binding and N-glycosylation sites were also predicted. The generated model was docked with cellobiose to predict the most favorable binding sites of MtBgl3c. The key amino acid residues involved in cellobiose bonding are Val88, Asp106, Asp287, Tyr255, Arg170, Glu514. The catalytic conserved amino residues of MtBgl3c were identified. The dock score of cellobiose with MtBgl3c is much lower (-6.46 kcal/mol) than that of glucose (-5.61 kcal/mol), suggesting its high affinity for cellobiose. The docking data of MtBgl3c with glucose illustrate its tolerance to glucose. The present study provides insight into structural characteristics of the MtBgl3c which can be further validated by experimental data. Highlights3D structure of β-glucosidase (MtBgl3c) of Myceliophthora thermophila is being proposed based on computational analysesThe amino acid residues Asp106, Asp287, Tyr255, Arg170 and Glu514 have been identified to play catalytically important role in substrate bindingDocking and interaction of MtBgl3c with cellobiose and glucose has been confirmedDocking analysis of MtBgl3c with glucose suggested its glucose toleranceThe data would be useful in engineering enzymes for attaining higher catalytic efficiencyCommunicated by Ramaswamy H. Sarma.

Gentiobiose and cellobiose content in fresh and fermenting cucumbers and utilization of such disaccharides by lactic acid bacteria in fermented cucumber juice medium

The content of cellobiose and gentiobiose, cellulose-derived dissacharides, in fresh and fermented cucumber was evaluated along with the ability of Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus buchneri and Lactobacillus brevis to utilize them during and after fermentation. The disaccharide content in fresh and fermenting cucumbers was below the detection level (10 µM) using HPLC for analysis. Utilization of cellobiose and gentiobiose by lactic acid bacteria (LAB) was tested in fermented cucumber juice medium (FCJM), a model system for the bioconversion and postfermentation lacking glucose and fructose. Changes in the fermentation metabolites were followed using HPLC and pH measurements as a function of time. The disaccharides were utilized by L. plantarum, L. pentosus, and L. buchneri in FCJM at pH 4.7 ± 0.1, representative of the active fermentation period, and converted to lactic acid. The disaccharides were not utilized in FCJM at pH 3.7 ± 0.1, representative of the end of fermentation. While L. brevis was unable to utilize cellobiose efficiently in FCJM, they were able to remove gentiobiose at pH 4.7 ± 0.1. Some strain level differences in cellobiose utilization were observed. It is concluded that the disaccharides are absent in the fresh cucumber and the typical fermentation. The LAB prevalent in the bioconversion utilizes cellobiose and gentiobiose, if available, at pH 4.7 ± 0.1. The LAB would not remove the disaccharides, which could become available from cellulose degradation by the acid resistant indigenous microbiota, after the pH is reduced to 3.7 ± 0.1.

Metabolic Engineering of Shikimic Acid-Producing Corynebacterium glutamicum From Glucose and Cellobiose Retaining Its Phosphotransferase System Function and Pyruvate Kinase Activities

The production of aromatic compounds by microbial production is a promising and sustainable approach for producing biomolecules for various applications. We describe the metabolic engineering of Corynebacterium glutamicum to increase its production of shikimic acid. Shikimic acid and its precursor-consuming pathways were blocked by the deletion of the shikimate kinase, 3-dehydroshikimate dehydratase, shikimate dehydratase, and dihydroxyacetone phosphate phosphatase genes. Plasmid-based expression of shikimate pathway genes revealed that 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, encoded by aroG, and DHQ synthase, encoded by aroB, are key enzymes for shikimic acid production in C. glutamicum. We constructed a C. glutamicum strain with aroG, aroB and aroE3 integrated. This strain produced 13.1 g/L of shikimic acid from 50 g/L of glucose, a yield of 0.26 g-shikimic acid/g-glucose, and retained both its phosphotransferase system and its pyruvate kinase activity. We also endowed β-glucosidase secreting ability to this strain. When cellobiose was used as a carbon source, the strain produced shikimic acid at 13.8 g/L with the yield of 0.25 g-shikimic acid/g-glucose (1 g of cellobiose corresponds to 1.1 g of glucose). These results demonstrate the feasibility of producing shikimic acid and its derivatives using an engineered C. glutamicum strain from cellobiose as well as glucose.

Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus

Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. This integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.

Cross-utilization of β-galactosides and cellobiose in Geobacillus stearothermophilus

Strains of the Gram-positive, thermophilic bacterium Geobacillus stearothermophilus possess elaborate systems for the utilization of hemicellulolytic polysaccharides, including xylan, arabinan, and galactan. These systems have been studied extensively in strains T-1 and T-6, representing microbial models for the utilization of soil polysaccharides, and many of their components have been characterized both biochemically and structurally. Here, we characterized routes by which G. stearothermophilus utilizes mono- and disaccharides such as galactose, cellobiose, lactose, and galactosyl-glycerol. The G. stearothermophilus genome encodes a phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) for cellobiose. We found that the cellobiose-PTS system is induced by cellobiose and characterized the corresponding GH1 6-phospho-β-glucosidase, Cel1A. The bacterium also possesses two transport systems for galactose, a galactose-PTS system and an ABC galactose transporter. The ABC galactose transport system is regulated by a three-component sensing system. We observed that both systems, the sensor and the transporter, utilize galactose-binding proteins that also bind glucose with the same affinity. We hypothesize that this allows the cell to control the flux of galactose into the cell in the presence of glucose. Unexpectedly, we discovered that G. stearothermophilus T-1 can also utilize lactose and galactosyl-glycerol via the cellobiose-PTS system together with a bifunctional 6-phospho-β-gal/glucosidase, Gan1D. Growth curves of strain T-1 growing in the presence of cellobiose, with either lactose or galactosyl-glycerol, revealed initially logarithmic growth on cellobiose and then linear growth supported by the additional sugars. We conclude that Gan1D allows the cell to utilize residual galactose-containing disaccharides, taking advantage of the promiscuity of the cellobiose-PTS system.

Quantitative Proteome Profiling Reveals Cellobiose-Dependent Protein Processing and Export Pathways for the Lignocellulolytic Response in Neurospora crassa

Filamentous fungi are intensively used for producing industrial enzymes, including lignocellulases. Employing insoluble cellulose to induce the production of lignocellulases causes some drawbacks, e.g., a complex fermentation operation, which can be overcome by using soluble inducers such as cellobiose. Here, a triple β-glucosidase mutant of Neurospora crassa, which prevents rapid turnover of cellobiose and thus allows the disaccharide to induce lignocellulases, was applied to profile the proteome responses to cellobiose and cellulose (Avicel). Our results revealed a shared proteomic response to cellobiose and Avicel, whose elements included lignocellulases and cellulolytic product transporters. While the cellulolytic proteins showed a correlated increase in protein and mRNA levels, only a moderate correlation was observed on a proteomic scale between protein and mRNA levels (R ² = 0.31). Ribosome biogenesis and rRNA processing were significantly overrepresented in the protein set with increased protein but unchanged mRNA abundances in response to Avicel. Ribosome biogenesis, as well as protein processing and protein export, was also enriched in the protein set that showed increased abundance in response to cellobiose. NCU05895, a homolog of yeast CWH43, is potentially involved in transferring a glycosylphosphatidylinositol (GPI) anchor to nascent proteins. This protein showed increased abundance but no significant change in mRNA levels. Disruption of CWH43 resulted in a significant decrease in cellulase activities and secreted protein levels in cultures grown on Avicel, suggesting a positive regulatory role for CWH43 in cellulase production. The findings should have an impact on a systems engineering approach for strain improvement for the production of lignocellulases.IMPORTANCE Lignocellulases are important industrial enzymes for sustainable production of biofuels and bio-products. Insoluble cellulose has been commonly used to induce the production of lignocellulases in filamentous fungi, which causes a difficult fermentation operation and enzyme loss due to adsorption to cellulose. The disadvantages can be overcome by using soluble inducers, such as the disaccharide cellobiose. Quantitative proteome profiling of the model filamentous fungus Neurospora crassa revealed cellobiose-dependent pathways for cellulase production, including protein processing and export. A protein (CWH43) potentially involved in protein processing was found to be a positive regulator of lignocellulase production. The cellobiose-dependent mechanisms provide new opportunities to improve the production of lignocellulases in filamentous fungi.

Neither 1G nor 2G fuel ethanol: setting the ground for a sugarcane-based biorefinery using an iSUCCELL yeast platform

First-generation (1G) fuel ethanol production in sugarcane-based biorefineries is an established economic enterprise in Brazil. Second-generation (2G) fuel ethanol from lignocellulosic materials, though extensively investigated, is currently facing severe difficulties to become economically viable. Some of the challenges inherent to these processes could be resolved by efficiently separating and partially hydrolysing the cellulosic fraction of the lignocellulosic materials into the disaccharide cellobiose. Here, we propose an alternative biorefinery, where the sucrose-rich stream from the 1G process is mixed with a cellobiose-rich stream in the fermentation step. The advantages of mixing are 3-fold: (i) decreased concentrations of metabolic inhibitors that are typically produced during pretreatment and hydrolysis of lignocellulosic materials; (ii) decreased cooling times after enzymatic hydrolysis prior to fermentation; and (iii) decreased availability of free glucose for contaminating microorganisms and undesired glucose repression effects. The iSUCCELL platform will be built upon the robust Saccharomyces cerevisiae strains currently present in 1G biorefineries, which offer competitive advantage in non-aseptic environments, and into which intracellular hydrolyses of sucrose and cellobiose will be engineered. It is expected that high yields of ethanol can be achieved in a process with cell recycling, lower contamination levels and decreased antibiotic use, when compared to current 2G technologies.

Highly Efficient and Recyclable Catalysts for Cellobiose Hydrolysis: Systematic Comparison of Carbon Nanomaterials Functionalized With Benzyl Sulfonic Acids

Carbon materials such as activated coal, nanotubes, nanofibers, or graphene nanoplatelets were functionalized with sulfonic acid moieties by a diazonium coupling strategy. High acidity was obtained for the majority of the carbon solids except for the carbon nanofibers. The activity of these acidic catalysts for the hydrolysis of cellobiose, as model molecule for cellulose, into glucose in neutral water medium was studied. The conversion of cellobiose is increasing with the acidity of the catalyst. We found that a minimum threshold amount of acidic functions is required for triggering the hydrolysis. The selectivity toward glucose is very high as soon as sulfonic functions are present on the catalyst. The robustness of the sulfonic functions grafted on the carbons has been highlighted by successful recyclability over six runs.

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.

Identification and Characterization of a Cellodextrin Transporter in Aspergillus niger

Aspergillus niger produces a wide spectrum of extracellular polysaccharide hydrolases that hydrolyze cellulose into soluble glucose and cellodextrins. Transporters are essential for sugar uptake, yet it is not clear whether cellodextrin transporters exist in A. niger. Here, one cellulose inducible cellodextrin transporter CtA was identified in A. niger B2. It was found that CtA not only could transport cellobiose, but also cellotriose, cellotetraose, and cellopentaose. The yeast strain YPβG-CtA, expressing cellodextrin transporter CtA and an intracellular β-glucosidase, grew on cellobiose with the cell growth rate of 0.0830 ± 0.0113 h^–1 under aerobic condition. Furthermore, the engineered yeast could produce 1.1 g/L ethanol anaerobically on cellobiose in 2 days. The identification of CtA provides evidence that the cellodextrin uptake is a complementary strategy of cellulose utilization in A. niger, and the CtA could be a strong transporter candidate for constructing engineered cellodextrin-utilizing microorganisms.

Targeted Deletion of Hepatocyte Abca1 Increases Plasma HDL (High-Density Lipoprotein) Reverse Cholesterol Transport via the LDL (Low-Density Lipoprotein) Receptor

OBJECTIVE

The role of hepatocyte Abca1 (ATP binding cassette transporter A1) in trafficking hepatic free cholesterol (FC) into plasma versus bile for reverse cholesterol transport (RCT) is poorly understood. We hypothesized that hepatocyte Abca1 recycles plasma HDL-C (high-density lipoprotein cholesterol) taken up by the liver back into plasma, maintaining the plasma HDL-C pool, and decreasing HDL-mediated RCT into feces. Approach and Results: Chow-fed hepatocyte-specific Abca1 knockout (HSKO) and control mice were injected with human HDL radiolabeled with ¹²⁵I-tyramine cellobiose (¹²⁵I-TC; protein) and ³H-cholesteryl oleate (³H-CO). ¹²⁵I-TC and ³H-CO plasma decay, plasma HDL ³H-CO selective clearance (ie, ³H-¹²⁵I fractional catabolic rate), liver radiolabel uptake, and fecal ³H-sterol were significantly greater in HSKO versus control mice, supporting increased plasma HDL RCT. Twenty-four hours after ³H-CO-HDL injection, HSKO mice had reduced total hepatic ³H-FC (ie, ³H-CO hydrolyzed to ³H-FC in liver) resecretion into plasma, demonstrating Abca1 recycled HDL-derived hepatic ³H-FC back into plasma. Despite similar liver LDLr (low-density lipoprotein receptor) expression between genotypes, HSKO mice treated with LDLr-targeting versus control antisense oligonucleotide had slower plasma ³H-CO-HDL decay, reduced selective ³H-CO clearance, and decreased fecal ³H-sterol excretion that was indistinguishable from control mice. Increased RCT in HSKO mice was selective for ³H-CO-HDL, since macrophage RCT was similar between genotypes.

CONCLUSIONS

Hepatocyte Abca1 deletion unmasks a novel and selective FC trafficking pathway that requires LDLr expression, accelerating plasma HDL-selective CE uptake by the liver and promoting HDL RCT into feces, consequently reducing HDL-derived hepatic FC recycling into plasma.

A Short-Term Response of Soil Microbial Communities to Cadmium and Organic Substrate Amendment in Long-Term Contaminated Soil by Toxic Elements

Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria but influenced their community composition. Namely, numbers of Actinobacteria determined by phylum specific qPCR increased and also the proportion of Actinobacteria and Chloroflexi increased in Illumina sequence libraries in the more contaminated soil. In the experiment, secondary disturbance by supplemented cadmium (doses from double to 100-fold the concentration in the original soil) and organic substrates (cellobiose or straw) increased bacterial diversity in the less contaminated soil and decreased it in the more contaminated soil. Respiration in the experiment was higher in the more contaminated soil in all treatments and correlated with bacterial numbers. Considering the most significant changes in bacterial community, it seemed that particularly Actinobacteria withstand contamination by toxic elements. The results proved higher resistance to secondary disturbance in terms of both, respiration and bacterial community structure in the less contaminated soil.

Multiplexed CRISPR Activation of Cryptic Sugar Metabolism Enables Yarrowia Lipolytica Growth on Cellobiose

The yeast Yarrowia lipolytica has been widely studied for its ability to synthesize and accumulate intracellular lipids to high levels. Recent studies have identified native genes that enable growth on biomass-derived sugars, but these genes are not sufficiently expressed to facilitate robust metabolism. In this work, a CRISPR-dCas9 activation (CRISPRa) system in Y. lipolytica is developed and is used it to activate native β-glucosidase expression to support growth on cellobiose. A series of different transcriptional activators are compared for their effectiveness in Y. lipolytica, with the synthetic tripartite activator VPR yielding the highest activation. A VPR-dCas9 fusion is then targeted to various locations in a synthetic promoter driving hrGFP expression, and activation is achieved. Subsequently, the CRISPRa system is used to activate transcription of two different native β-glucosidase genes, facilitating enhanced growth on cellobiose as the sole carbon source. This work expands the synthetic biology toolbox for metabolic engineering in Y. lipolytica and demonstrates how the programmability of the CRISPR-Cas9 system can enable facile investigation of transcriptionally silent regions of the genome.

Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens

Fungi can decompose plant biomass into small oligo- and monosaccharides to be used as carbon sources. Some of these small molecules may induce metabolic pathways and the production of extracellular enzymes targeted for degradation of plant cell wall polymers. Despite extensive studies in ascomycete fungi, little is known about the nature of inducers for the lignocellulolytic systems of basidiomycetes. In this study, we analyzed six sugars known to induce the expression of lignocellulolytic genes in ascomycetes for their role as inducers in the basidiomycete white-rot fungus Dichomitus squalens using a transcriptomic approach. This identified cellobiose and l-rhamnose as the main inducers of cellulolytic and pectinolytic genes, respectively, of D. squalens Our results also identified differences in gene expression patterns between dikaryotic and monokaryotic strains of D. squalens cultivated on plant biomass-derived monosaccharides and the disaccharide cellobiose. This suggests that despite conservation of the induction between these two genetic forms of D. squalens, the fine-tuning in the gene regulation of lignocellulose conversion is differently organized in these strains.IMPORTANCE Wood-decomposing basidiomycete fungi have a major role in the global carbon cycle and are promising candidates for lignocellulosic biorefinery applications. However, information on which components trigger enzyme production is currently lacking, which is crucial for the efficient use of these fungi in biotechnology. In this study, transcriptomes of the white-rot fungus Dichomitus squalens from plant biomass-derived monosaccharide and cellobiose cultures were studied to identify compounds that induce the expression of genes involved in plant biomass degradation.

Fine-Tuned Enzymatic Hydrolysis of Organosolv Pretreated Forest Materials for the Efficient Production of Cellobiose

Non-digestible oligosaccharides (NDOs) are likely prebiotic candidates that have been related to the prevention of intestinal infections and other disorders for both humans and animals. Lignocellulosic biomass is the largest carbon source in the biosphere, therefore cello-oligosacharides (COS), especially cellobiose, are potentially the most widely available choice of NDOs. Production of COS and cellobiose with enzymes offers numerous benefits over acid-catalyzed processes, as it is milder, environmentally friendly and produces fewer by-products. Cellobiohydrolases (CBHs) and a class of endoglucanases (EGs), namely processive EGs, are key enzymes for the production of COS, as they have higher preference toward glycosidic bonds near the end of cellulose chains and are able to release soluble products. In this work, we describe the heterologous expression and characterization of two CBHs from the filamentous fungus Thermothelomyces thermophila, as well as their synergism with proccessive EGs for cellobiose release from organosolv pretreated spruce and birch. The properties, inhibition kinetics and substrate specific activities for each enzyme are described in detail. The results show that a combination of EGs belonging to Glycosyl hydrolase families 5, 6, and 9, with a CBHI and CBHII in appropriate proportions, can enhance the production of COS from forest materials, underpinning the potential of these biocatalysts in the production of NDOs.

Transcriptome and Zymogram Analyses Reveal a Cellobiose-Dose Related Reciprocal Regulatory Effect on Cellulase Synthesis in Cellulosilyticum ruminicola H1

The rumen bacterium Cellulosilyticum ruminicola H1 efficiently hydrolyzes cellulose. To gain insights into the regulatory mechanisms of cellulase synthesis, comparative transcriptome analysis was conducted for cultures grown on 2% filter paper, 0.5 and 0.05% cellobiose, and 0.5% birchwood xylan. It was found that cellulose induced a majority of (hemi)cellulases, including 33 cellulases and a cellulosomal scaffoldin (1.3- to 22.7-fold); seven endoxylanases, two mannanases, and two pectatelyases (2- to 16-fold); and pyruvate formate-lyase (PFL, 1.5- to 7-fold). Noticeably, 3- and 2.5-fold increased transcription of a cellobiohydrolase and the cellulosomal scaffoldin precursor were detected in 0.05% than in 0.5% cellobiose. Consistently, 9- and 4-fold higher specific cellobiohydrolase activities were detected in the filter paper and 0.05% cellobiose culture. SDS- and native-PAGE zymograms of cellulose-enriched proteins from the filter paper culture displayed cellulase activities, and cellulolytic “complexes” were enriched from the filter paper- and 0.05% cellobiose-cultures, but not from the 0.5% cellobiose culture. LC-MS/MS identified the cellulosomal scaffoldin precursor in the “complexes” in addition to cellulase, hemicellulase, and PFL proteins. The addition of 0.5% cellobiose, but not 0.05% cellobiose remarkably inhibited strain H1 to degrade filter paper. Therefore, this work reveals a cellobiose-dose related regulatory mechanism of cellulase synthesis by lower for induction and higher for repression, which has extended our understanding of the regulation of microbial cellulase synthesis.

Disruption of a Transcriptional Repressor by an Insertion Sequence Element Integration Leads to Activation of a Novel Silent Cellobiose Transporter in Lactococcus lactis MG1363

Lactococcus lactis subsp. cremoris strains typically carry many dairy niche-specific adaptations. During adaptation to the milk environment these former plant strains have acquired various pseudogenes and insertion sequence elements indicative of ongoing genome decay and frequent transposition events in their genomes. Here we describe the reactivation of a silenced plant sugar utilization cluster in an L. lactis MG1363 derivative lacking the two main cellobiose transporters, PtcBA-CelB and PtcBAC, upon applying selection pressure to utilize cellobiose. A disruption of the transcriptional repressor gene llmg_1239 by an insertion sequence (IS) element allows expression of the otherwise silent novel cellobiose transporter Llmg_1244 and leads to growth of mutant strains on cellobiose. Llmg_1239 was labeled CclR, for cellobiose cluster repressor.IMPORTANCE Insertion sequences (ISs) play an important role in the evolution of lactococci and other bacteria. They facilitate DNA rearrangements and are responsible for creation of new genetic variants with selective advantages under certain environmental conditions. L. lactis MG1363 possesses 71 copies in a total of 11 different types of IS elements. This study describes yet another example of an IS-mediated adaptive evolution. An integration of IS981 or IS905 into a gene coding for a transcriptional repressor led to activation of the repressed gene cluster coding for a plant sugar utilization pathway. The expression of the gene cluster allowed assembly of a novel cellobiose-specific transporter and led to cell growth on cellobiose.

Metabolic Profile of the Cellulolytic Industrial Actinomycete Thermobifida fusca

Actinomycetes have a long history of being the source of numerous valuable natural products and medicinals. To expedite product discovery and optimization of biochemical production, high-throughput technologies can now be used to screen the library of compounds present (or produced) at a given time in an organism. This not only facilitates chemical product screening, but also provides a comprehensive methodology to the study cellular metabolic networks to inform cellular engineering. Here, we present some of the first metabolomic data of the industrial cellulolytic actinomycete Thermobifida fusca generated using LC-MS/MS. The underlying objective of conducting global metabolite profiling was to gain better insight on the innate capabilities of T. fusca, with a long-term goal of facilitating T. fusca-based bioprocesses. The T. fusca metabolome was characterized for growth on two cellulose-relevant carbon sources, cellobiose and Avicel. Furthermore, the comprehensive list of measured metabolites was computationally integrated into a metabolic model of T. fusca, to study metabolic shifts in the network flux associated with carbohydrate and amino acid metabolism.

Cellobiose Consumption Uncouples Extracellular Glucose Sensing and Glucose Metabolism in Saccharomyces cerevisiae

Glycolysis is central to energy metabolism in most organisms and is highly regulated to enable optimal growth. In the yeast Saccharomyces cerevisiae, feedback mechanisms that control flux through glycolysis span transcriptional control to metabolite levels in the cell. Using a cellobiose consumption pathway, we decoupled glucose sensing from carbon utilization, revealing new modular layers of control that induce ATP consumption to drive rapid carbon fermentation. Alterations of the beta subunit of phosphofructokinase-1 (PFK2), H⁺-plasma membrane ATPase (PMA1), and glucose sensors (SNF3 and RGT2) revealed the importance of coupling extracellular glucose sensing to manage ATP levels in the cell. Controlling the upper bound of cellular ATP levels may be a general mechanism used to regulate energy levels in cells, via a regulatory network that can be uncoupled from ATP concentrations under perceived starvation conditions.

Living cells are fine-tuned through evolution to thrive in their native environments. Genome alterations to create organisms for specific biotechnological applications may result in unexpected and undesired phenotypes. We used a minimal synthetic biological system in the yeast Saccharomyces cerevisiae as a platform to reveal novel connections between carbon sensing, starvation conditions, and energy homeostasis.

Relief of Xylose Binding to Cellobiose Phosphorylase by a Single Distal Mutation

Cellobiose phosphorylase (CBP) cleaves cellobiose-abundant in plant biomass-to glucose and glucose 1-phosphate. However, the pentose sugar xylose, also abundant in plant biomass, acts as a mixed-inhibitor and a substrate for the reverse reaction, limiting the industrial potential of CBP. Preventing xylose, which lacks only a single hydroxymethyl group relative to glucose, from binding to the CBP active site poses a spatial challenge for protein engineering, since simple steric occlusion cannot be used to block xylose binding without also preventing glucose binding. Using CRISPR-based chromosomal library selection, we identified a distal mutation in CBP, Y47H, responsible for improved cellobiose consumption in the presence of xylose. In silico analysis suggests this mutation may alter the conformation of the cellobiose phosphorylase dimer complex to reduce xylose binding to the active site. These results may aid in engineering carbohydrate phosphorylases for improved specificity in biofuel production, and also in the production of industrially important oligosaccharides.

Functional Studies of β-Glucosidases of Cytophaga hutchinsonii and Their Effects on Cellulose Degradation

Cytophaga hutchinsonii can rapidly digest crystalline cellulose without free cellulases or cellulosomes. Its cell-contact cellulose degradation mechanism is unknown. In this study, the four β-glucosidase (bgl) genes in C. hutchinsonii were singly and multiply deleted, and the functions of these β-glucosidases in cellobiose and cellulose degradation were investigated. We found that the constitutively expressed BglB played a key role in cellobiose utilization, while BglA which was induced by cellobiose could partially make up for the deletion of bglB. The double deletion mutant ΔbglA/bglB lost the ability to digest cellobiose and could not thrive in cellulose medium, indicating that β-glucosidases were important for cellulose degradation. When cultured in cellulose medium, a small amount of glucose accumulated in the medium in the initial stage of growth for the wild type, while almost no glucose accumulated for ΔbglA/bglB. When supplemented with a small amount of glucose, ΔbglA/bglB started to degrade cellulose and grew in cellulose medium. We inferred that glucose might be essential for initiating cellulose degradation, and with additional glucose, C. hutchinsonii could partially utilize cellulose without β-glucosidases. We also found that there were both cellulose binding cells and free cells when cultured in cellulose. Since direct contact between C. hutchinsonii cells and cellulose is necessary for cellulose degradation, we deduced that the free cells which were convenient to explore new territory in the environment might be fed by the adherent cells which could produce cello-oligosaccharide and glucose into the environment. This study enriched our knowledge of the cellulolytic pathway of C. hutchinsonii.

A New Way to Produce Cellobiose Carbonates Using Green Chemistry

The preparation of cellulose derivatives using green (i.e., environmentally friendly) reagents would improve sustainability and reduce concerns arising from the use of non-green reagents. The objective of this work was to prepare cellobiose carbonate using a green reagent, dimethyl carbonate. The carbonation reaction was carried out in the presence of ethanolic potassium hydroxide solution and dimethyl carbonate for 6 h at a range of temperatures (25-70 °C). A cellobiose derivative was successfully prepared with a recovered yield of more than 70 % and characterized by FTIR and NMR spectroscopy techniques. The presence of a grafted disaccharide with a degree of substitution higher than 2 was determined by (13) C NMR analysis. The spectra of the prepared cellobiose carbonate exhibited peaks that were associated with cellulose molecules (C1 -C6 ) and corresponded to carbonate functions at around 159.4 ppm.

Alleviating product inhibition in cellulase enzyme Cel7A

Enzymes that degrade cellulose into glucose are one of the most expensive components of processes for converting cellulosic biomass to fuels and chemicals. Cellulase enzyme Cel7A is the most abundant enzyme naturally employed by fungi to depolymerize cellulose, and like other cellulases is inhibited by its product, cellobiose. There is thus great economic incentive for minimizing the detrimental effects of product inhibition on Cel7A. In this work, we experimentally generated 10 previously proposed site-directed mutant Cel7A enzymes expected to have reduced cellobiose binding energies (the majority of mutations were to alanine). We then tested their resilience to cellobiose as well as their hydrolytic activities on microcrystalline cellulose. Although every mutation tested conferred reduced product inhibition (and abolished it for some), our results confirm a trade-off between Cel7A tolerance to cellobiose and enzymatic activity: Reduced product inhibition was accompanied by lower overall enzymatic activity on crystalline cellulose for the mutants tested. The tempering effect of mutations on inhibition was nearly constant despite relatively large differences in activities of the mutants. Our work identifies an amino acid in the Cel7A product binding site of interest for further mutational studies, and highlights both the challenge and the opportunity of enzyme engineering toward improving product tolerance in Cel7A.

Simultaneous utilization of cellobiose, xylose, and acetic acid from lignocellulosic biomass for biofuel production by an engineered yeast platform

The inability of fermenting microorganisms to use mixed carbon components derived from lignocellulosic biomass is a major technical barrier that hinders the development of economically viable cellulosic biofuel production. In this study, we integrated the fermentation pathways of both hexose and pentose sugars and an acetic acid reduction pathway into one Saccharomyces cerevisiae strain for the first time using synthetic biology and metabolic engineering approaches. The engineered strain coutilized cellobiose, xylose, and acetic acid to produce ethanol with a substantially higher yield and productivity than the control strains, and the results showed the unique synergistic effects of pathway coexpression. The mixed substrate coutilization strategy is important for making complete and efficient use of cellulosic carbon and will contribute to the development of consolidated bioprocessing for cellulosic biofuel. The study also presents an innovative metabolic engineering approach whereby multiple substrate consumption pathways can be integrated in a synergistic way for enhanced bioconversion.

First Glycoside Hydrolase Family 2 Enzymes from Thermus antranikianii and Thermus brockianus with β-Glucosidase Activity

Two glycoside hydrolase encoding genes (tagh2 and tbgh2) were identified from different Thermus species using functional screening. Based on amino acid similarities, the enzymes were predicted to belong to glycoside hydrolase (GH) family 2. Surprisingly, both enzymes (TaGH2 and TbGH2) showed twofold higher activities for the hydrolysis of nitrophenol-linked β-D-glucopyranoside than of -galactopyranoside. Specific activities of 3,966 U/mg for TaGH2 and 660 U/mg for TbGH2 were observed. In accordance, K_m values for both enzymes were significantly lower when β-D-glucopyranoside was used as substrate. Furthermore, TaGH2 was able to hydrolyze cellobiose. TaGH2 and TbGH2 exhibited highest activity at 95 and 90°C at pH 6.5. Both enzymes were extremely thermostable and showed thermal activation up to 250% relative activity at temperatures of 50 and 60°C. Especially, TaGH2 displayed high tolerance toward numerous metal ions (Cu²⁺, Co²⁺, Zn²⁺), which are known as glycoside hydrolase inhibitors. In this study, the first thermoactive GH family 2 enzymes with β-glucosidase activity have been identified and characterized. The hydrolysis of cellobiose is a unique property of TaGH2 when compared to other enzymes of GH family 2. Our work contributes to a broader knowledge of substrate specificities in GH family 2.

Structural insights into the inhibition of cellobiohydrolase Cel7A by xylo-oligosaccharides

The filamentous fungus Hypocrea jecorina (anamorph of Trichoderma reesei) is the predominant source of enzymes for industrial saccharification of lignocellulose biomass. The major enzyme, cellobiohydrolase Cel7A, constitutes nearly half of the total protein in the secretome. The performance of such enzymes is susceptible to inhibition by compounds liberated by physico-chemical pre-treatment if the biomass is kept unwashed. Xylan and xylo-oligosaccharides (XOS) have been proposed to play a key role in inhibition of cellobiohydrolases of glycoside hydrolase family 7. To elucidate the mechanism behind this inhibition at a molecular level, we used X-ray crystallography to determine structures of H. jecorina Cel7A in complex with XOS. Structures with xylotriose, xylotetraose and xylopentaose revealed a predominant binding mode at the entrance of the substrate-binding tunnel of the enzyme, in which each xylose residue is shifted ~ 2.4 Å towards the catalytic center compared with binding of cello-oligosaccharides. Furthermore, partial occupancy of two consecutive xylose residues at subsites -2 and -1 suggests an alternative binding mode for XOS in the vicinity of the catalytic center. Interestingly, the -1 xylosyl unit exhibits an open aldehyde conformation in one of the structures and a ring-closed pyranoside in another complex. Complementary inhibition studies with p-nitrophenyl lactoside as substrate indicate mixed inhibition rather than pure competitive inhibition.

DATABASE

The atomic coordinates and structure factors are available in the Protein Data Bank under accession number 4D5I (H. jecorina Cel7A E212Q variant, complex with xylotriose), 4D5J (H. jecorina Cel7A E217Q variant, complex with xylotriose), 4D5O (H. jecorina Cel7A E212Q variant, complex with xylopentaose), 4D5P (H. jecorina Cel7A E217Q variant, complex with xylopentaose), 4D5Q (wild-type H. jecorina Cel7A, complex with xylopentaose) and 4D5V (H. jecorina Cel7A E217Q variant, complex with xylotetraose).

A paradigm shift in biomass technology from complete to partial cellulose hydrolysis: lessons learned from nature

A key characteristic of current biomass technology is the requirement for complete hydrolysis of cellulose and hemicellulose, which stems from the inability of microbial strains to use partially hydrolyzed cellulose, or cellodextrin. The complete hydrolysis paradigm has been practiced over the past 4 decades with major enzyme companies perfecting their cellulase mix for maximal yield of monosaccharides, with corresponding efforts in strain development focus almost solely on the conversion of monosaccharides, not cellodextrin, to products. While still in its nascent infancy, a new paradigm requiring only partial hydrolysis has begun to take hold, promising a shift in the biomass technology at its fundamental core. The new paradigm has the potential to reduce the requirement for cellulase enzymes in the hydrolysis step and provides new strategies for metabolic engineers, synthetic biologists and alike in engineering fermenting organisms. Several recent publications reveal that microorganisms engineered to metabolize cellodextrins, rather than monomer glucose, can reap significant energy gains in both uptake and subsequent phosphorylation. These energetic benefits can in turn be directed for enhanced robustness and increased productivity of a bioprocess. Furthermore, the new cellodextrin metabolism endows the biocatalyst the ability to evade catabolite repression, a cellular regulatory mechanism that is hampering rapid conversion of biomass sugars to products. Together, the new paradigm offers significant advantages over the old and promises to overcome several critical barriers in biomass technology. More research, however, is needed to realize these promises, especially in discovery and engineering of cellodextrin transporters, in developing a cost-effective method for cellodextrin generation, and in better integration of cellodextrin metabolism to endogenous glycolysis.

Authenticity analysis of pear juice employing chromatographic fingerprinting

Pear juice is predominately composed of carbohydrates/polyols (>95% of the total soluble solids), making it susceptible to adulteration by the addition of less expensive commercial sweeteners. In this research, the major carbohydrate and polyol (fructose, glucose, sucrose, and sorbitol) content of 32 pure pear juices representing five world producing regions and three years of production was determined. Additionally, methods employing oligosaccharide profiling to detect the debasing of these samples with four commercial sweeteners (HFCS 55 and 90, TIS, and HIS) were developed using capillary gas chromatography with flame ionization detection (CGC-FID) and high-performance liquid chromatography with pulsed amperometric detection (HPAE-PAD). Detection limits for the four commercial sweeteners ranged from 0.5 to 5.0% (v/v). In addition, the developed CGC-FID method could be used to (a) detect the addition of pear to apple juice via arbutin detection and (b) determine if a pear juice was produced using enzymatic liquefaction via the presence of O-β-d-glucopyranosyl-(1→4)-d-glucopyranose (cellobiose), all within a single chromatographic analysis.

Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq

The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism.

β-Glucosidase activities of lactic acid bacteria: mechanisms, impact on fermented food and human health

Through the hydrolysis of plant metabolite glucoconjugates, β-glucosidase activities of lactic acid bacteria (LAB) make a significant contribution to the dietary and sensory attributes of fermented food. Deglucosylation can release attractive flavour compounds from glucosylated precursors and increases the bioavailability of health-promoting plant metabolites as well as that of dietary toxins. This review brings the current literature on LAB β-glucosidases into context by providing an overview of the nutritional implications of LAB β-glucosidase activities. Based on biochemical and genomic information, the mechanisms that are currently considered to be critical for the hydrolysis of β-glucosides by intestinal and food-fermenting LAB will also be reviewed.

The electronic nature of the 1,4-β-glycosidic bond and its chemical environment: DFT insights into cellulose chemistry

The molecular understanding of the chemistry of 1,4-β-glucans is essential for designing new approaches to the conversion of cellulose into platform chemicals and biofuels. In this endeavor, much attention has been paid to the role of hydrogen bonding occurring in the cellulose structure. So far, however, there has been little discussion about the implications of the electronic nature of the 1,4-β-glycosidic bond and its chemical environment for the activation of 1,4-β-glucans toward acid-catalyzed hydrolysis. This report sheds light on these central issues and addresses their influence on the acid hydrolysis of cellobiose and, by analogy, cellulose. The electronic structure of cellobiose was explored by DFT at the BB1 K/6-31++G(d,p) level. Natural bond orbital (NBO) analysis was performed to grasp the key bonding concepts. Conformations, protonation sites, and hydrolysis mechanisms were examined. The results for cellobiose indicate that cellulose is protected against hydrolysis not only by its supramolecular structure, as currently accepted, but also by its electronic structure, in which the anomeric effect plays a key role.

Molecular docking study of Beta-glucosidase with cellobiose, cellotetraose and cellotetriose

Beta-glucosidase (3.2.1.21) plays an essential role in the removal of non-reducing terminal glucosyl residues from glycosides. Recently, beta-glucosidase has been of interest for biomass conversion that acts in synergy with two other enzymes, endoglucanase and exo-glucanase. However, there is not much information available on the catalytic interactions of beta-glucosidase with its substrates. Thus, this study reports on the binding modes between beta-glucosidase from glycoside hydrolase family 1 namely BglB with cellobiose, cellotetraose and cellotetriose via molecular docking simulation. From the results, the binding affinities of BglB-cellobiose, BglB-cellotetraose, and BglB-cellotetriose complexes were reported to be -6.2kJ/mol , -5.68 kJ/mol and -5.63 kJ/mol, respectively. The detail interactions were also been investigated that revealed the key residues involved in forming hydrogen bonds (h-bond) with the substrates. These findings may provide valuable insigths in designing beta-glucosidase with higher cellobiose-hydrolyzing efficiency.

Product inhibition of cellulases studied with 14C-labeled cellulose substrates

BACKGROUND

As a green alternative for the production of transportation fuels, the enzymatic hydrolysis of lignocellulose and subsequent fermentation to ethanol are being intensively researched. To be economically feasible, the hydrolysis of lignocellulose must be conducted at a high concentration of solids, which results in high concentrations of hydrolysis end-products, cellobiose and glucose, making the relief of product inhibition of cellulases a major challenge in the process. However, little quantitative information on the product inhibition of individual cellulases acting on cellulose substrates is available because it is experimentally difficult to assess the hydrolysis of the heterogeneous polymeric substrate in the high background of added products.

RESULTS

The cellobiose and glucose inhibition of thermostable cellulases from Acremonium thermophilum, Thermoascus aurantiacus, and Chaetomium thermophilum acting on uniformly 14C-labeled bacterial cellulose and its derivatives, 14C-bacterial microcrystalline cellulose and 14C-amorphous cellulose, was studied. Cellulases from Trichoderma reesei were used for comparison. The enzymes most sensitive to cellobiose inhibition were glycoside hydrolase (GH) family 7 cellobiohydrolases (CBHs), followed by family 6 CBHs and endoglucanases (EGs). The strength of glucose inhibition followed the same order. The product inhibition of all enzymes was relieved at higher temperatures. The inhibition strength measured for GH7 CBHs with low molecular-weight model substrates did not correlate with that measured with 14C-cellulose substrates.

CONCLUSIONS

GH7 CBHs are the primary targets for product inhibition of the synergistic hydrolysis of cellulose. The inhibition must be studied on cellulose substrates instead of on low molecular-weight model substrates when selecting enzymes for lignocellulose hydrolysis. The advantages of using higher temperatures are an increase in the catalytic efficiency of enzymes and the relief of product inhibition.

Selecting β-glucosidases to support cellulases in cellulose saccharification

BACKGROUND

Enzyme end-product inhibition is a major challenge in the hydrolysis of lignocellulose at a high dry matter consistency. β-glucosidases (BGs) hydrolyze cellobiose into two molecules of glucose, thereby relieving the product inhibition of cellobiohydrolases (CBHs). However, BG inhibition by glucose will eventually lead to the accumulation of cellobiose and the inhibition of CBHs. Therefore, the kinetic properties of candidate BGs must meet the requirements determined by both the kinetic properties of CBHs and the set-up of the hydrolysis process.

RESULTS

The kinetics of cellobiose hydrolysis and glucose inhibition of thermostable BGs from Acremonium thermophilum (AtBG3) and Thermoascus aurantiacus (TaBG3) was studied and compared to Aspergillus sp. BG purified from Novozyme®188 (N188BG). The most efficient cellobiose hydrolysis was achieved with TaBG3, followed by AtBG3 and N188BG, whereas the enzyme most sensitive to glucose inhibition was AtBG3, followed by TaBG3 and N188BG. The use of higher temperatures had an advantage in both increasing the catalytic efficiency and relieving the product inhibition of the enzymes. Our data, together with data from a literature survey, revealed a trade-off between the strength of glucose inhibition and the affinity for cellobiose; therefore, glucose-tolerant BGs tend to have low specificity constants for cellobiose hydrolysis. However, although a high specificity constant is always an advantage, in separate hydrolysis and fermentation, the priority may be given to a higher tolerance to glucose inhibition.

CONCLUSIONS

The specificity constant for cellobiose hydrolysis and the inhibition constant for glucose are the most important kinetic parameters in selecting BGs to support cellulases in cellulose hydrolysis.