Thermostable enzymes as biocatalysts in the biofuel industry

PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications

Protein language models (PLMs) play a dominant role in protein representation learning. Most existing PLMs regard proteins as sequences of 20 natural amino acids. The problem with this representation method is that it simply divides the protein sequence into sequences of individual amino acids, ignoring the fact that certain residues often occur together. Therefore, it is inappropriate to view amino acids as isolated tokens. Instead, the PLMs should recognize the frequently occurring combinations of amino acids as a single token. In this study, we use the byte-pair-encoding algorithm and unigram to construct advanced residue vocabularies for protein sequence tokenization, and we have shown that PLMs pre-trained using these advanced vocabularies exhibit superior performance on downstream tasks when compared to those trained with simple vocabularies. Furthermore, we introduce PETA, a comprehensive benchmark for systematically evaluating PLMs. We find that vocabularies comprising 50 and 200 elements achieve optimal performance. Our code, model weights, and datasets are available at https://github.com/ginnm/ProteinPretraining . SCIENTIFIC CONTRIBUTION: This study introduces advanced protein sequence tokenization analysis, leveraging the byte-pair-encoding algorithm and unigram. By recognizing frequently occurring combinations of amino acids as single tokens, our proposed method enhances the performance of PLMs on downstream tasks. Additionally, we present PETA, a new comprehensive benchmark for the systematic evaluation of PLMs, demonstrating that vocabularies of 50 and 200 elements offer optimal performance.

A Stochastic Landscape Approach for Protein Folding State Classification

Protein folding is a critical process that determines the functional state of proteins. Proper folding is essential for proteins to acquire their functional three-dimensional structures and execute their biological role, whereas misfolded proteins can lead to various diseases, including neurodegenerative disorders like Alzheimer's and Parkinson's. Therefore, a deeper understanding of protein folding is vital for understanding disease mechanisms and developing therapeutic strategies. This study introduces the Stochastic Landscape Classification (SLC), an innovative, automated, nonlearning algorithm that quantitatively analyzes protein folding dynamics. Focusing on collective variables (CVs) - low-dimensional representations of complex dynamical systems like molecular dynamics (MD) of macromolecules - the SLC approach segments the CVs into distinct macrostates, revealing the protein folding pathway explored by MD simulations. The segmentation is achieved by analyzing changes in CV trends and clustering these segments using a standard density-based spatial clustering of applications with noise (DBSCAN) scheme. Applied to the MD-based CV trajectories of Chignolin and Trp-Cage proteins, the SLC demonstrates apposite accuracy, validated by comparing standard classification metrics against ground-truth data. These metrics affirm the efficacy of the SLC in capturing intricate protein dynamics and offer a method to evaluate and select the most informative CVs. The practical application of this technique lies in its ability to provide a detailed, quantitative description of protein folding processes, with significant implications for understanding and manipulating protein behavior in industrial and pharmaceutical contexts.

Trends in the development and current perspective of thermostable bacterial hemicellulases with their industrial endeavors: A review

Hemicellulases are enzymes that hydrolyze hemicelluloses, common polysaccharides in nature. Thermophilic hemicellulases, derived from microbial strains, are extensively studied as natural biofuel sources due to the complex structure of hemicelluloses. Recent research aims to elucidate the catalytic principles, mechanisms and specificity of hemicellulases through investigations into their high-temperature stability and structural features, which have applications in biotechnology and industry. This review article targets to serve as a comprehensive resource, highlighting the significant progress in the field and emphasizing the vital role of thermophilic hemicellulases in eco-friendly catalysis. The primary goal is to improve the reliability of hemicellulase enzymes obtained from thermophilic bacterial strains. Additionally, with their ability to break down lignocellulosic materials, hemicellulases hold immense potential for biofuel production. Despite their potential, the commercial viability is hindered by their high enzyme costs, necessitating the development of efficient bioprocesses involving waste pretreatment with microbial consortia to overcome this challenge.

A Recombinant Thermophilic and Glucose-Tolerant GH1 β-Glucosidase Derived from Hehua Hot Spring

As a crucial enzyme for cellulose degradation, β-glucosidase finds extensive applications in food, feed, and bioethanol production; however, its potential is often limited by inadequate thermal stability and glucose tolerance. In this study, a functional gene (lq-bg5) for a GH1 family β-glucosidase was obtained from the metagenomic DNA of a hot spring sediment sample and heterologously expressed in E. coli and the recombinant enzyme was purified and characterized. The optimal temperature and pH of LQ-BG5 were 55 °C and 4.6, respectively. The relative residual activity of LQ-BG5 exceeded 90% at 55 °C for 9 h and 60 °C for 6 h and remained above 100% after incubation at pH 5.0-10.0 for 12 h. More importantly, LQ-BG5 demonstrated exceptional glucose tolerance with more than 40% activity remaining even at high glucose concentrations of 3000 mM. Thus, LQ-BG5 represents a thermophilic β-glucosidase exhibiting excellent thermal stability and remarkable glucose tolerance, making it highly promising for lignocellulose development and utilization.

Establishing an itaconic acid production process with Ustilago species on the low-cost substrate starch

Ustilago maydis and Ustilago cynodontis are natural producers of a broad range of valuable molecules including itaconate, malate, glycolipids, and triacylglycerols. Both Ustilago species are insensitive toward medium impurities, and have previously been engineered for efficient itaconate production and stabilized yeast-like growth. Due to these features, these strains were already successfully used for the production of itaconate from different alternative feedstocks such as molasses, thick juice, and crude glycerol. Here, we analyzed the amylolytic capabilities of Ustilago species for metabolization of starch, a highly abundant and low-cost polymeric carbohydrate widely utilized as a substrate in several biotechnological processes. Ustilago cynodontis was found to utilize gelatinized potato starch for both growth and itaconate production, confirming the presence of extracellular amylolytic enzymes in Ustilago species. Starch was rapidly degraded by U. cynodontis, even though no α-amylase was detected. Further experiments indicate that starch hydrolysis is caused by the synergistic action of glucoamylase and α-glucosidase enzymes. The enzymes showed a maximum activity of around 0.5 U ml-1 at the fifth day after inoculation, and also released glucose from additional substrates, highlighting potential broader applications. In contrast to U. cynodontis, U. maydis showed no growth on starch accompanied with no detectable amylolytic activity.

Unlocking Flavor Potential Using Microbial β-Glucosidases in Food Processing

Aroma is among of the most important criteria that indicate the quality of food and beverage products. Aroma compounds can be found as free molecules or glycosides. Notably, a significant portion of aroma precursors accumulates in numerous food products as nonvolatile and flavorless glycoconjugates, termed glycosidic aroma precursors. When subjected to enzymatic hydrolysis, these seemingly inert, nonvolatile glycosides undergo transformation into fragrant volatiles or volatiles that can generate odor-active compounds during food processing. In this context, microbial β-glucosidases play a pivotal role in enhancing or compromising the development of flavors during food and beverage processing. β-glucosidases derived from bacteria and yeast can be utilized to modulate the concentration of particular aroma and taste compounds, such as bitterness, which can be decreased through hydrolysis by glycosidases. Furthermore, oral microbiota can influence flavor perception by releasing volatile compounds that can enhance or alter the perception of food products. In this review, considering the glycosidic flavor precursors present in diverse food and beverage products, we underscore the significance of glycosidases with various origins. Subsequently, we delve into emerging insights regarding the release of aroma within the human oral cavity due to the activity of oral microbial glycosidases.

Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data

Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.

Biochemical characteristics of Myceliophthora thermophila recombinant β-glucosidase (MtBgl3c) applicable in cellulose bioconversion

The GH3 β-glucosidase gene of Myceliophthora thermophila (MtBgl3c) has been cloned and heterologously expressed in E. coli for the first time. This study highlights the important characteristics of recombinant MtBgl3c (rMtBgl3c) which make it a promising candidate in industrial applications. Optimization of the production of rMtBgl3c led to 28,000 U L-1. On purification, it has a molecular mass of ∼100 kDa. It is a broad substrate specific thermostable enzyme that exhibits pH and temperature optima at 5.0 and 55 °C, respectively. The amino acid residues Asp287 and Glu514 act as nucleophile and catalytic acid/base, respectively in the enzyme catalysis. Its low Km value (1.28 mM) indicates a high substrate affinity as compared to those previously reported. The rMtBgl3c displays a synergistic action with the commercial enzyme cocktail in the saccharification of sugarcane bagasse suggesting its utility in the cellulose bioconversion. Tolerance to solvents, detergents as well as glucose make this enzyme applicable in wine, detergent, paper and textile industries too.

The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition

The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.

Evolving Robust and Interpretable Enzymes for the Bioethanol Industry

Obtaining a robust and applicable enzyme for bioethanol production is a dream for biorefinery engineers. Herein, we describe a general method to evolve an all-round and interpretable enzyme that can be directly employed in the bioethanol industry. By integrating the transferable protein evolution strategy InSiReP 2.0 (In Silico guided Recombination Process), enzymatic characterization for actual production, and computational molecular understanding, the model cellulase PvCel5A (endoglucanase II Cel5A from Penicillium verruculosum) was successfully evolved to overcome the remaining challenges of low ethanol and temperature tolerance, which primarily limited biomass transformation and bioethanol yield. Remarkably, application of the PvCel5A variants in both first- and second-generation bioethanol production processes (i. Conventional corn ethanol fermentation combined with the in situ pretreatment process; ii. cellulosic ethanol fermentation process) resulted in a 5.7-10.1 % increase in the ethanol yield, which was unlikely to be achieved by other optimization techniques.

Screening and characterization of a β-xylosidase from Bifidobacterium breve K-110 and its application in the biotransformation of the total flavonoids of epimedium to icariin with α-l-rhamnosidase

Among the flavonoids of epimedium, epimedin B, epimedin C, and icariin are considered to be representative components and their structures are quite similar. Besides sharing the same backbone, the main difference is the sugar groups attached at the positions of C-3 and C-7. Despite their structural similarities, their potencies differ significantly, and only icariin is currently included in the Chinese Pharmacopoeia as a quality marker (Q-marker) for epimedium flavonoids. Furthermore, icariin has the functions of anti-aging, anti-inflammation, antioxidation, anti-osteoporosis, and ameliorating fibrosis. We used bioinformatics to look for the GH43 family β-xylosidase genes BbXyl from Bifidobacterium breve K-110, which has a length of 1347 bp and codes for 448 amino acids. This will allow us to convert epimedin B and epimedin C into icariin in a specific way. The expression level of recombinant BbXyl in TB medium containing 1 % inulin as carbon source, with an inducer concentration of 0.05 mmol/L and a temperature of 28 °C, was 86.4 U/mL. Previous studies found that the α-l-rhamnosidase BtRha could convert epoetin C to produce icariin, so we combined BbXyl and BtRha to catalyze the conversion of epimedium total flavonoids in vitro and in vivo to obtain the product icariin. Under optimal conditions, in vitro hydrolysis of 5 g/L of total flavonoids of epimedium eventually yielded a concentration of icariin of 678.1 μmol/L. To explore the conversion of total flavonoids of epimedium in vivo. Under the optimal conditions, the yield of icariin reached 97.27 μmol/L when the total flavonoid concentration of epimedium was 1 g/L. This study is the first to screen xylosidases for the targeted conversion of epimedin B to produce icariin, and the first to report that epimedin B and epimedin C in the raw epimedium flavonoids can convert efficiently to icariin by a collaborative of β-xylosidase and α-l-rhamnosidase.

Efficient bioconversion of lignocellulosic waste by a novel computationally screened hyperthermostable enzyme from a specialized microbiota

A large amount of lignocellulosic waste is generated every day in the world, and their accumulation in the agroecosystems, integration in soil compositions, or incineration for energy production has severe environmental pollution effects. Using enzymes as biocatalysts for the biodegradation of lignocellulosic materials, especially in harsh processing conditions, is a practical step towards green energy and environmental biosafety. Hence, the current study focuses on enzyme computationally screened from camel rumen metagenomics data as specialized microbiota that have the capacity to degrade lignocellulosic-rich and recalcitrant materials. The novel hyperthermostable xylanase named PersiXyn10 with the performance at extreme conditions was proper activity within a broad temperature (30-100 ℃) and pH range (4.0-11.0) but showed the maximum xylanolytic activity in severe alkaline and temperature conditions, pH 8.0 and temperature 90 ℃. Also, the enzyme had highly resistant to metals, surfactants, and organic solvents in optimal conditions. The introduced xylanase had unique properties in terms of thermal stability by maintaining over 82% of its activity after 15 days of incubation at 90 ℃. Considering the crucial role of hyperthermostable xylanases in the paper industry, the PersiXyn10 was subjected to biodegradation of paper pulp. The proper performance of hyperthermostable PersiXyn10 on the paper pulp was confirmed by structural analysis (SEM and FTIR) and produced 31.64 g/L of reducing sugar after 144 h hydrolysis. These results proved the applicability of the hyperthermostable xylanase in biobleaching and saccharification of lignocellulosic biomass for declining the environmental hazards.

The Preparation and Potential Bioactivities of Modified Pectins: A Review

Pectins are complex polysaccharides that are widely found in plant cells and have a variety of bioactivities. However, the high molecular weights (M_w) and complex structures of natural pectins mean that they are difficult for organisms to absorb and utilize, limiting their beneficial effects. The modification of pectins is considered to be an effective method for improving the structural characteristics and promoting the bioactivities of pectins, and even adding new bioactivities to natural pectins. This article reviews the modification methods, including chemical, physical, and enzymatic methods, for natural pectins from the perspective of their basic information, influencing factors, and product identification. Furthermore, the changes caused by modifications to the bioactivities of pectins are elucidated, including their anti-coagulant, anti-oxidant, anti-tumor, immunomodulatory, anti-inflammatory, hypoglycemic, and anti-bacterial activities and the ability to regulate the intestinal environment. Finally, suggestions and perspectives regarding the development of pectin modification are provided.

An environment-benign approach of bamboo pulp bleaching using extracellular xylanase of strain Bacillus stratosphericus EB-11 isolated from elephant dung

The use of microbial enzymes is highly encouraged in paper and pulp industries to reduce the excessive use of hazardous chemicals. During the study, xylanase of Bacillus stratosphericus EB-11 was characterized for pulp bleaching applications. The extracellular xylanase was produced under submerged fermentation using bamboo waste as a natural carbon source. There was fast cell division and enzyme production under optimized fermentation conditions in the bioreactor. The highest activity was 91,200U after 30 h of growth with Km and Vmax of 3.52 mg/mL and 391.5 μmol/min per mg respectively. The purified enzyme with molecular mass ~ 60 kDa had conferred positive activity on native PAGE. The strong inhibition by ethylenediaminetetraacetate and SDS showed the metallo-xylanase nature of the purified enzyme. The bacterial xylanase reduces the use of hydrogen peroxide by 0.4%. Similarly, biological oxygen demand and chemical oxygen demand were reduced by 42.6 and 35.2%. The xylanase-hydrogen peroxide combined treatment and conventional chlorine dioxide-alkaline (CDE₁D₁D₂) bleaching showed almost similar improvement in physicochemical properties of bamboo pulp. Xylanase-peroxide bleaching reduces the lignin content to 4.95% from 13.32% unbleached pulp. This content after CDE₁D₁D₂ treatment was 4.21%. The kappa number decreased from 15.2 to 9.46 with increasing the burst factor (15.51), crystallinity index (60.25%), viscosity (20.1 cp), and brightness (65.4%). The overall finding will encourage the development of new cleaner methods of bleaching in the paper and pulp industry.

Engineering of xylanases for the development of biotechnologically important characteristics

Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.

Differential scanning calorimetry (DSC) as a tool for studying thermal properties of a crude cellulase cocktail

Abstract

Differential scanning calorimetry (DSC) was used as an efficient and rapid tool in studying the conformational transitions between the folded and unfolded structures of cellulolytic enzymes. The thermal properties of two crude hydrolytic enzyme cocktails containing extracellular cellulases from Trichoderma longibrachiatum DIBAF-10 were analyzed and compared with three commercial cellulase preparations. Differences in the thermal behavior of fungal cellulases in the liquid phase, freeze-dried state, liquid formulations in sodium citrate buffer (pH 4.8), and contact with cellulose, carboxymethyl cellulose, and cellobiose were evaluated. DSC profiles of cellulases from the DIBAF-10 strain provided important thermodynamic information about the thermal stability of the included proteins. Crude enzyme cocktails underwent a reproducible and irreversible exothermic aggregation phenomenon at 52.45 ± 0.90 °C like commercial β-glucosidase. Freeze-dried and resuspended in a sodium citrate buffer, cellulases from T. longibrachiatum showed an endothermic peak dependent on buffer and enzyme concentration. In the enzyme-substrates systems, a shift of the same peak was recorded for all substrates tested. The thermal analysis of freeze-dried cellulase samples in the range of 20–150 °C gave information on the denaturation process. In conclusion, we demonstrated that DSC is a cost-effective tool for obtaining "conformational fingerprinting" of crude fungal cellulase preparations.

Graphical abstract

Characterization of thermo/halo stable cellulase produced from halophilic Virgibacillus salarius BM-02 using non-pretreated biomass

The production of extremozymes from halophilic bacteria has increased significantly due to their stability and efficiency in catalyzing a reaction, as well as their capacity to display optimum activity at various salt concentrations. In the current study, the halophilic bacterium Virgibacillus salarius strain BM-02 could utilize many non-pretreated substrates including cellulose, corn stover, sugarcane bagasse and wheat bran as a sole carbon source. However, wheat bran was the best substrate for achieving optimum saccharification yield (90.1%). The partially purified cellulase was active and stable at a wide range of pH (5-8) with residual activities > 58%. Moreover, it was stable at 5-12% of NaCl. Metal ions have a variable impact on the activity of partially purified cellulase however, Fe⁺³ exhibited the highest increase in the cellulase activity. The enzyme exhibited a thermal stability at 40, 50 and 60 °C with half-lives of 1049.50, 168.14 and 163.5 min, respectively. The value of V_max was 22.27 U/mL while Km was 2.1 mM. The activation energy of denaturation E_d 69.81 kJ/mol, the enthalpy values (ΔH_d) were positive, and the entropy values (ΔS) were negative. Therefore, V. Salarius is recommended as a novel promising halophilic extremozyme producer and agricultural waste remover in the bio-industrial applications.

The Thermostability of Nucleoside Phosphorylases from Prokaryotes. I. The Role of the Primary Structure of the N-terminal fragment of the Protein in the Thermostability of Uridine Phosphorylases

Mutant uridine phosphorylase genes from Shewanella oneidensis MR-1 (S. oneidensis) were constructed by site-directed mutagenesis and strains-producers of the corresponding recombinant (F5I and F5G) proteins were obtained on the basis of Escherichia coli cells. The mutant proteins were purified and their physicochemical and enzymatic properties were studied. It was shown that the N-terminal fragment of uridine phosphorylase plays an important role in the thermal stabilization of the enzyme as a whole. The role of the aminoacid (a.a.) residue phenylalanine (F5) in the formation of thermotolerance of uridine phosphorylases from gamma-proteobacteria was revealed.

The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates

Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates—oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates—Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.

Nanocellulose for Paper and Textile Coating: The Importance of Surface Chemistry

Nanocellulose has received enormous scientific interest for its abundance, easy manufacturing, biodegradability, and low cost. Cellulose nanocrystals (CNCs) and cellulose nanofibers (CNFs) are ideal candidates to replace plastic coating in the textile and paper industry. Thanks to their capacity to form an interconnected network kept together by hydrogen bonds, nanocelluloses perform an unprecedented strengthening action towards cellulose- and other fiber-based materials. Furthermore, nanocellulose use implies greener application procedures, such as deposition from water. The surface chemistry of nanocellulose plays a pivotal role in influencing the performance of the coating: tailored surface functionalization can introduce several properties, such as gas or grease barrier, hydrophobicity, antibacterial and anti-UV behavior. This review summarizes recent achievements in the use of nanocellulose for paper and textile coating, evidencing critical aspects of coating performances related to deposition technique, nanocellulose morphology, and surface functionalization. Furthermore, beyond focusing on the aspects strictly related to large-scale coating applications for paper and textile industries, this review includes recent achievements in the use of nanocellulose coating for the safeguarding of Cultural Heritage, an extremely noble and interesting emerging application of nanocellulose, focusing on consolidation of historical paper and archaeological textile. Finally, nanocellulose use in electronic devices as an electrode modifier is highlighted.

Engineering of enzymes using non-natural amino acids

In enzyme engineering, the main targets for enhancing properties are enzyme activity, stereoselective specificity, stability, substrate range, and the development of unique functions. With the advent of genetic code extension technology, non-natural amino acids (nnAAs) are able to be incorporated into proteins in a site-specific or residue-specific manner, which breaks the limit of 20 natural amino acids for protein engineering. Benefitting from this approach, numerous enzymes have been engineered with nnAAs for improved properties or extended functionality. In this review, we focus on applications and strategies for using nnAAs in enzyme engineering. Notably, approaches to computational modelling of enzymes with nnAAs are also addressed. Finally, we discuss the bottlenecks that currently need to be addressed in order to realise the broader prospects of this genetic code extension technique.

Biochemical, Sensory, and Molecular Evaluation of Flavour and Consumer Acceptability in Australian Papaya (Carica papaya L.) Varieties

Inconsistency in flavour is one of the major challenges to the Australian papaya industry. However, objectively measurable standards of the compound profiles that provide preferable taste and aroma, together with consumer acceptability, have not been set. In this study, three red-flesh papayas (i.e., ‘RB1’, ‘RB4’, and ‘Skybury’) and two yellow-flesh papayas (i.e., ‘1B’ and ‘H13’) were presented to a trained sensory panel and a consumer panel to assess sensory profiles and liking. The papaya samples were also examined for sugar components, total soluble solids, and 14 selected volatile compounds. Additionally, the expression patterns of 10 genes related to sweetness and volatile metabolism were assessed. In general, red papaya varieties had higher sugar content and tasted sweeter than yellow varieties, while yellow varieties had higher concentrations of citrus floral aroma volatiles and higher aroma intensity. Higher concentrations of glucose, linalool oxide, and terpinolene were significantly associated with decreased consumer liking. Significant differences were observed in the expression profiles of all the genes assessed among the selected papaya varieties. Of these, cpGPT2 and cpBGLU31 were positively correlated to glucose production and were expressed significantly higher in ‘1B’ than in ‘RB1’ or ‘Skybury’. These findings will assist in the strategic selective breeding for papaya to better match consumer and, hence, market demand.

Structure-based interface engineering methodology in designing a thermostable amylose-forming transglucosylase

Many drugs and prebiotics derive their activities from sugar substituents. Due to the prevalence and complexity of these biologically active compounds, enzymatic glycodiversification that facilitates easier access to these compounds can make profound contributions to the pharmaceutical, food, and feed industries. Amylosucrases (ASases) are attractive tools for glycodiversification because of their broad acceptor substrate specificity, but the lack of structural information and their poor thermostability limit their industrial applications. Herein, we reported the crystal structure of ASase from Calidithermus timidus, which displays a homotetrameric quaternary organization not previously observed for other ASases. We employed a workflow composed of five common strategies, including interface engineering, folding energy calculations, consensus sequence, hydrophobic effects enhancement, and B-factor analysis, to enhance the thermostability of C. timidus ASase. As a result, we obtained a quadruple-point mutant M31 ASase with a half-life at 65 °C increased from 22.91 h to 52.93 h, which could facilitate biosynthesis of glucans with a degree of polymerization of more than 20 using sucrose as a substrate at 50 °C. In conclusion, this study provides a structural basis for understanding the multifunctional biocatalyst ASase and presents a powerful methodology to effectively and systematically enhance protein thermostability.

Metagenomic mining and structure-function studies of a hyper-thermostable cellobiohydrolase from hot spring sediment

Enzymatic breakdown is an attractive cellulose utilisation method with a low environmental load. Its high temperature operation could promote saccharification and lower contamination risk. Here we report a hyper-thermostable cellobiohydrolase (CBH), named HmCel6A and its variant HmCel6A-3SNP that were isolated metagenomically from hot spring sediments and expressed in Escherichia coli. They are classified into glycoside hydrolases family 6 (GH6). HmCel6A-3SNP had three amino acid replacements to HmCel6A (P88S/L230F/F414S) and the optimum temperature at 95 °C, while HmCel6A did it at 75 °C. Crystal structure showed conserved features among GH6, a (β/α)₈-barrel core and catalytic residues, and resembles TfCel6B, a bacterial CBH II of Thermobifida fusca, that had optimum temperature at 60 °C. From structure-function studies, we discuss unique structural features that allow the enzyme to reach its high thermostability level, such as abundance of hydrophobic and charge-charge interactions, characteristic metal bindings and disulphide bonds. Moreover, structure and surface plasmon resonance analysis with oligosaccharides suggested that the contribution of an additional tryptophan located at the tunnel entrance could aid in substrate recognition and thermostability. These results may help to design efficient enzymes and saccharification methods for cellulose working at high temperatures.

Bacteria from hot springs are known for highly thermostable enzymes, which may have industrial potential. Here, a unique thermostable cellobiohydrolase is reported that can breakdown cellulose at temperature up to 95 degrees Celsius.

Biochemical Characterization of Thermostable Carboxymethyl Cellulase and β-Glucosidase from Aspergillus fumigatus JCM 10253

Second-generation biofuel production has emerged as a prominent sustainable and alternative energy. The biochemical properties of cellulolytic enzymes are imperative for cellulosic biomass conversion into fermentable sugars. In the present study, thermostable CMCase and β-glucosidase were purified and characterized from Aspergillus fumigatus JCM 10253. The enzymes were purified through 80% ammonium sulfate precipitation, followed by dialysis and DEAE-cellulose ion-exchange chromatography. The molecular masses of the purified CMCase and β-glucosidase were estimated to be 125 kDa and 90 kDa, respectively. The CMCase and β-glucosidase demonstrated optimum activities at pH 6.0 and 5.0, respectively. Their respective maximum temperatures were 50 and 60 °C. The cellulase activities were stimulated by 10 mM concentration of Ca²⁺, Ni²⁺, Fe²⁺, Mg²⁺, Cu²⁺, Mn²⁺, Zn²⁺, and Pb²⁺ ions. The CMCase activity was enhanced by surfactant Triton X-100 but marginally influenced by most inhibitors. The β-glucosidase retained its activity in the presence of organic solvents (30%) isoamyl alcohol, heptane, toluene, and ethyl acetate, while CMCase was retained with acetone during a prolonged incubation of 168 h. The K_m and V_max values of the two cellulases were studied. The properties of high thermostability and good tolerance against organic solvents could signify its potential use in biofuel production and other value-added products.

Recent advancements in prebiotic oligomers synthesis via enzymatic hydrolysis of lignocellulosic biomass

Interest in functional food, such as non-digestible prebiotic oligosaccharides is increasing day by day and their production is shifting toward sustainable manufacturing. Due to the presence of high carbohydrate content, lignocellulosic biomass (LCB) is the most-potential, cost-effective and sustainable substrate for production of many useful products, including lignocellulose-derived prebiotic oligosaccharides (LDOs). These have the same worthwhile properties as other common oligosaccharides, such as short chain carbohydrates digestible to the gut flora but not to humans mainly due to their resistance to the low pH and high temperature and their demand is constantly increasing mainly due to increased awareness about their potential health benefits. Despite several advantages over the thermo-chemical route of synthesis, comprehensive and updated information on the conversion of lignocellulosic biomass to prebiotic oligomers via controlled enzymatic saccharification is not available in the literature. Thus, the main objective of this review is to highlight recent advancements in enzymatic synthesis of LDOs, current challenges, and future prospects of sustainably producing prebiotic oligomers via enzymatic hydrolysis of LCB substrates. Enzyme reaction engineering practices, custom-made enzyme preparations, controlled enzymatic hydrolysis, and protein engineering approaches have been discussed with regard to their applications in sustainable synthesis of lignocellulose-derived oligosaccharide prebiotics. An overview of scale-up aspects and market potential of LDOs has also been provided.

Thermostable Cellulases / Xylanases From Thermophilic and Hyperthermophilic Microorganisms: Current Perspective

The bioconversion of lignocellulose into monosaccharides is critical for ensuring the continual manufacturing of biofuels and value-added bioproducts. Enzymatic degradation, which has a high yield, low energy consumption, and enhanced selectivity, could be the most efficient and environmentally friendly technique for converting complex lignocellulose polymers to fermentable monosaccharides, and it is expected to make cellulases and xylanases the most demanded industrial enzymes. The widespread nature of thermophilic microorganisms allows them to proliferate on a variety of substrates and release substantial quantities of cellulases and xylanases, which makes them a great source of thermostable enzymes. The most significant breakthrough of lignocellulolytic enzymes lies in lignocellulose-deconstruction by enzymatic depolymerization of holocellulose into simple monosaccharides. However, commercially valuable thermostable cellulases and xylanases are challenging to produce in high enough quantities. Thus, the present review aims at giving an overview of the most recent thermostable cellulases and xylanases isolated from thermophilic and hyperthermophilic microbes. The emphasis is on recent advancements in manufacturing these enzymes in other mesophilic host and enhancement of catalytic activity as well as thermostability of thermophilic cellulases and xylanases, using genetic engineering as a promising and efficient technology for its economic production. Additionally, the biotechnological applications of thermostable cellulases and xylanases of thermophiles were also discussed.

Fungal cellulases: protein engineering and post-translational modifications

Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.

Biological pretreatment of corn stover for enhancing enzymatic hydrolysis using Bacillus sp. P3

The biological pretreatment for the enzymatic hydrolysis of lignocellulosic biomasses depends exclusively on the effective pretreatment process. Herein, we report a significant enhancement of enzymatic saccharification obtained with corn stover using a bacterial strain Bacillus sp. P3. The hemicellulose removal from corn stover by the strain Bacillus sp. P3 was evaluated for enhancing subsequent enzymatic hydrolysis. Therefore, our study revealed that an alkaline-resistant xylanase as well as other enzymes produced by Bacillus sp. P3 in fermentation broth led to a substantially enhanced hemicellulose removal rate from corn stover within pH 9.36–9.68. However, after a 20-day pretreatment of corn stover by the strain P3, the glucan content was increased by 51% and the xylan content was decreased by 35%. After 72 h of saccharification using 20 U/g of commercial cellulase, the yield of reducing sugar released from 20-day pretreated corn stover was increased by 56% in comparison to the untreated corn stover. Therefore, the use of the strain P3 could be a promising approach to pretreat corn stover for enhancing the enzymatic hydrolysis process of industrial bioenergy productions.

Novel Enzymes From the Red Sea Brine Pools: Current State and Potential

The Red Sea is a marine environment with unique chemical characteristics and physical topographies. Among the various habitats offered by the Red Sea, the deep-sea brine pools are the most extreme in terms of salinity, temperature and metal contents. Nonetheless, the brine pools host rich polyextremophilic bacterial and archaeal communities. These microbial communities are promising sources for various classes of enzymes adapted to harsh environments - extremozymes. Extremozymes are emerging as novel biocatalysts for biotechnological applications due to their ability to perform catalytic reactions under harsh biophysical conditions, such as those used in many industrial processes. In this review, we provide an overview of the extremozymes from different Red Sea brine pools and discuss the overall biotechnological potential of the Red Sea proteome.

Thermostable cellulose saccharifying microbial enzymes: Characteristics, recent advances and biotechnological applications

Cellulases play a promising role in the bioconversion of renewable lignocellulosic biomass into fermentable sugars which are subsequently fermented to biofuels and other value-added chemicals. Besides biofuel industries, they are also in huge demand in textile, detergent, and paper and pulp industries. Low titres of cellulase production and processing are the main issues that contribute to high enzyme cost. The success of ethanol-based biorefinery depends on high production titres and the catalytic efficiency of cellulases functional at elevated temperatures with acid/alkali tolerance and the low cost. In view of their wider application in various industrial processes, stable cellulases that are active at elevated temperatures in the acidic-alkaline pH ranges, and organic solvents and salt tolerance would be useful. This review provides a recent update on the advances made in thermostable cellulases. Developments in their sources, characteristics and mechanisms are updated. Various methods such as rational design, directed evolution, synthetic & system biology and immobilization techniques adopted in evolving cellulases with ameliorated thermostability and characteristics are also discussed. The wide range of applications of thermostable cellulases in various industrial sectors is described.

De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars 'Bluecrop' and 'Legacy' at harvest and following post-harvest storage

Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, 'Bluecrop' and 'Legacy', at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for 'Bluecrop' and 'Legacy' respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in 'Legacy' only, 685 were up-regulated in 'Bluecrop', 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

Characterization of Two α-l-Arabinofuranosidases from Acetivibrio mesophilus and Their Synergistic Effect in Degradation of Arabinose-Containing Substrates

Arabinofuranosidases are important accessory enzymes involved in the degradation of arabinose-containing poly- and oligosaccharides. Two arabinofuranosidases from the recently described novel anaerobic cellulolytic bacterium Acetivibrio mesophilus, designated AmAraf51 and AmAraf43, were heterologously expressed in Escherichia coli and biochemically characterized. AmAraf51 not only removed arabinose moieties at O-3, O-2 and terminal O-5 positions of arabinose-containing oligosaccharides, but also exhibited exo-β-xylosidase side activity. In comparison, AmAraf43 preferably cleaved 1,3-linkages from arabinosyl disubstitutions. AmAraf51 and AmAraf43 demonstrated maximum activity at 70 °C and 57 °C, respectively. Judging from the genetic context and substrate specificity, AmAraf51 may decompose internalized arabino/xylo-oligosaccharides. The embedding of the AmAraf43 gene between genes for several putative xylanolytic enzymes, along with its enzymatic properties suggests that AmAraf43 cleaves arabinose decorations from heteroxylans extracellularly. The enzymes revealed completely converse activity profiles towards arabinan/arabinoxylan: AmAraf51 displayed strong activity on arabinan, while AmAraf43 prefers arabinoxylan. AmAraf51 dramatically stimulated the saccharification level of wheat arabinoxylan (WAX-RS) and sugar beet arabinan when administered along with xylanase M_Xyn10 or arabinanase PpAbn43, respectively. For WAX-RS degradation, the yield of arabinose and xylose was boosted 13.77-fold and 4.96-fold, respectively. The bifunctional activity, thermostability and high catalytic efficiency make AmAraf51 an interesting candidate for industrial applications.

Optimizing the catalytic activities of methanol and thermotolerant Kocuria flava lipases for biodiesel production from cooking oil wastes

In this study, two highly thermotolerant and methanol-tolerant lipase-producing bacteria were isolated from cooking oil and they exhibited a high number of catalytic lipase activities recording 18.65 ± 0.68 U/mL and 13.14 ± 0.03 U/mL, respectively. Bacterial isolates were identified according to phenotypic and genotypic 16S rRNA characterization as Kocuria flava ASU5 (MT919305) and Bacillus circulans ASU11 (MT919306). Lipases produced from Kocuria flava ASU5 showed the highest methanol tolerance, recording 98.4% relative activity as well as exhibited high thermostability and alkaline stability. Under the optimum conditions obtained from 3D plots of response surface methodology design, the Kocuria flava ASU5 biocatalyst exhibited an 83.08% yield of biodiesel at optimized reaction variables of, 60 ○C, pH value 8 and 1:2 oil/alcohol molar ratios in the reaction mixture. As well as, the obtained results showed the interactions of temperature/methanol were significant effects, whereas this was not noted in the case of temperature/pH and pH/methanol interactions. The obtained amount of biodiesel from cooking oil was 83.08%, which was analyzed by a GC/Ms profile. The produced biodiesel was confirmed by Fourier-transform infrared spectroscopy (FTIR) approaches showing an absorption band at 1743 cm-1, which is recognized for its absorption in the carbonyl group (C=O) which is characteristic of ester absorption. The energy content generated from biodiesel synthesized was estimated as 12,628.5 kJ/mol. Consequently, Kocuria flava MT919305 may provide promising thermostable, methanol-tolerant lipases, which may improve the economic feasibility and biotechnology of enzyme biocatalysis in the synthesis of value-added green chemicals.

From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi

In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation.

A Comprehensive Review on Valorization of Agro-Food Industrial Residues by Solid-State Fermentation

Agro-food industrial residues (AFIRs) are generated in large quantities all over the world. The vast majority of these wastes are lignocellulosic wastes that are a source of value-added products. Technologies such as solid-state fermentation (SSF) for bioconversion of lignocellulosic waste, based on the production of a wide range of bioproducts, offer both economic and environmental benefits. The versatility of application and interest in applying the principles of the circular bioeconomy make SSF one of the valorization strategies for AFIRs that can have a significant impact on the environment of the wider community. Important criteria for SSF are the selection of the appropriate and compatible substrate and microorganism, as well as the selection of the optimal process parameters for the growth of the microorganism and the production of the desired metabolites. This review provides an overview of the management of AFIRs by SSF: the current application, classification, and chemical composition of AFIRs; the catalytic function and potential application of enzymes produced by various microorganisms during SSF cultivation on AFIRs; the production of phenolic compounds by SSF; and a brief insight into the role of SSF treatment of AFIRs for feed improvement and biofuel production.

High-level expression of a novel multifunctional GH3 family β-xylosidase/α-arabinosidase/β-glucosidase from Dictyoglomus turgidum in Escherichia coli

A novel β-xylosidase Dt-2286 from Dictyoglomus turgidum was cloned and overexpressed in Escherichia coli BL21 (DE3). Dt-2286 belonging to glycoside hydrolase (GH) family 3 encodes a polypeptide with 762 amino acid residues with a molecular weight of 85.1 kDa. By optimization of the growth and induction conditions, the activity of β-xylosidase reached 273 U/mL, which is the highest yield reported to date from E. coli in a shake-flask. The optimal activities of the purified Dt-2286 were found at pH 5.0 and 98 °C. It also shows excellent thermostable/haloduric/organic solvent-tolerance. Dt-2286 was revealed to be a multifunctional enzyme with β-xylosidase, α-arabinofuranoside, α-arabinopyranoside and β-glucosidase activities, and K_cat/K_m was 5245.316 mM^-1 s^-1, 2077.353 mM^-1 s^-1, 1626.454 mM^-1 s^-1, and 470.432 mM^-1 s^-1 respectively. Dt-2286 showed significant synergistic effects on the degradation of xylans, releasing more reduced sugars (up to 15.08 fold) by simultaneous addition with endoxylanase. Moreover, this enzyme has good activity in the hydrolysis of epimedium B, demonstrating its versatility in practical applications.

Optimization of extracellular ethanol-tolerant β-glucosidase production from a newly isolated Aspergillus sp. DHE7 via solid state fermentation using jojoba meal as substrate: purification and biochemical characterization for biofuel preparation

BACKGROUND

The increasing demand and the continuous depletion in fossil fuels have persuaded researchers to investigate new sources of renewable energy. Bioethanol produced from cellulose could be a cost-effective and a viable alternative to petroleum. It is worth note that β-glucosidase plays a key role in the hydrolysis of cellulose and therefore in the production of bioethanol. This study aims to investigate a simple and standardized method for maximization of extracellular β-glucosidase production from a novel fungal isolate under solid-state fermentation using agro-industrial residues as the sole source of carbon and nitrogen. Furthermore, purification and characterization of β-glucosidase were performed to determine the conditions under which the enzyme displayed the highest performance.

RESULTS

A fungus identified genetically as a new Aspergillus sp. DHE7 was found to exhibit the highest extracellular β-glucosidase production among the sixty fungal isolates tested. Optimization of culture conditions improved the enzyme biosynthesis by 2.1-fold (174.6 ± 5.8 U/g of dry substrate) when the fungus grown for 72 h at 35 °C on jojoba meal with 60% of initial substrate moisture, pH 6.0, and an inoculum size of 2.54 × 107 spores/mL. The enzyme was purified to homogeneity through a multi-step purification process. The purified β-glucosidase is monomeric with a molecular mass of 135 kDa as revealed by the SDS-PAGE analysis. Optimum activity was observed at 60 °C and pH of 6.0, with a remarkable pH and thermal stability. The enzyme retained about 79% and 53% of its activity, after 1 h at 70 °C and 80 °C, respectively. The purified β-glucosidase hydrolysed a wide range of substrates but displaying its greater activity on p-nitrophenyl-β-D-glucopyranoside and cellobiose. The values of Km and Vmax on p-nitrophenyl β-D-glucopyranoside were 0.4 mM and 232.6 U/mL, respectively. Purified β-glucosidase displayed high catalytic activity (improved by 25%) in solutions contained ethanol up to 15%.

CONCLUSION

β-glucosidase characteristics associated with its ability to hydrolyse cellobiose, underscore its utilization in improving the quality of food and beverages. In addition, taking into consideration that the final concentration of ethanol produced by the conventional methods is about 10%, suggests its use in ethanol-containing industrial processes and in the saccharification processes for bioethanol production.

A review of NMR analysis in polysaccharide structure and conformation: Progress, challenge and perspective

Nuclear magnetic resonance (NMR) has been widely used as an analytical chemistry technique to investigate the molecular structure and conformation of polysaccharides. Combined with 1D spectra, chemical shifts and coupling constants in both homo- and heteronuclear 2D NMR spectra are able to infer the linkage and sequence of sugar residues. Besides, NMR has also been applied in conformation, quantitative analysis, cell wall in situ, degradation, polysaccharide mixture interaction analysis, as well as carbohydrates impurities profiling. This review summarizes the principle and development of NMR in polysaccharides analysis, and provides NMR spectra data collections of some common polysaccharides. It will help to promote the application of NMR in complex polysaccharides of biochemical interest, and provide valuable information on commercial polysaccharide products.

Microbial biotechnological approaches: renewable bioprocessing for the future energy systems

The accelerating energy demands of the increasing global population and industrialization has become a matter of great concern all over the globe. In the present scenario, the world is witnessing a considerably huge energy crisis owing to the limited availability of conventional energy resources and rapid depletion of non-renewable fossil fuels. Therefore, there is a dire need to explore the alternative renewable fuels that can fulfil the energy requirements of the growing population and overcome the intimidating environmental issues like greenhouse gas emissions, global warming, air pollution etc. The use of microorganisms such as bacteria has captured significant interest in the recent era for the conversion of the chemical energy reserved in organic compounds into electrical energy. The versatility of the microorganisms to generate renewable energy fuels from multifarious biological and biomass substrates can abate these ominous concerns to a great extent. For instance, most of the microorganisms can easily transform the carbohydrates into alcohol. Establishing the microbial fuel technology as an alternative source for the generation of renewable energy sources can be a state of art technology owing to its reliability, high efficiency, cleanliness and production of minimally toxic or inclusively non-toxic byproducts. This review paper aims to highlight the key points and techniques used for the employment of bacteria to generate, biofuels and bioenergy, and their foremost benefits.

Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common "-omics"-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.

Application 2D Descriptors and Artificial Neural Networks for Beta-Glucosidase Inhibitors Screening

Beta-glucosidase inhibitors play important medical and biological roles. In this study, simple two-variable artificial neural network (ANN) classification models were developed for beta-glucosidase inhibitors screening. All bioassay data were obtained from the ChEMBL database. The classifiers were generated using 2D molecular descriptors and the data miner tool available in the STATISTICA package (STATISTICA Automated Neural Networks, SANN). In order to evaluate the models' accuracy and select the best classifiers among automatically generated SANNs, the Matthews correlation coefficient (MCC) was used. The application of the combination of maxHBint3 and SpMax8_Bhs descriptors leads to the highest predicting abilities of SANNs, as evidenced by the averaged test set prediction results (MCC = 0.748) calculated for ten different dataset splits. Additionally, the models were analyzed employing receiver operating characteristics (ROC) and cumulative gain charts. The thirteen final classifiers obtained as a result of the model development procedure were applied for a natural compounds collection available in the BIOFACQUIM database. As a result of this beta-glucosidase inhibitors screening, eight compounds were univocally classified as active by all SANNs.

Applications of Microbial β-Mannanases

Mannans are main components of hemicellulosic fraction of softwoods and they are present widely in plant tissues. β-mannanases are the major mannan-degrading enzymes and are produced by different plants, animals, actinomycetes, fungi, and bacteria. These enzymes can function under conditions of wide range of pH and temperature. Applications of β-mannanases have therefore, been found in different industries such as animal feed, food, biorefinery, textile, detergent, and paper and pulp. This review summarizes the most recent studies reported on potential applications of β-mannanases and bioengineering of β-mannanases to modify and optimize their key catalytic properties to cater to growing demands of commercial sectors.

Draft genome sequence data of the anaerobic, thermophilic, chitinolytic bacterium strain UUS1-1 belonging to genus Hydrogenispora of the uncultured taxonomic OPB54 cluster

Strain UUS1-1 (=JCM33882 =DSM111537) is a novel chitinolytic, thermophilic, anaerobic bacterium belonging to the genus Hydrogenispora of the uncultured taxonomic OPB54 cluster within the phylum Firmicutes. Strain UUS1-1 has a unique, long, hair-like rod morphology and a strong ability to degrade crystalline chitin. The whole genome of strain UUS1-1 was sequenced on an Ion GeneStudio S5 system, which yielded 86 contigs comprising 2,482,547 bp, 2235 protein-coding sequences, and a G+C content of 52.1 mol%. Strain UUS1-1 is the second cultivable isolate, besides H. ethanolica, within the OPB54 cluster and may be classified as a novel species. The genomic data have been deposited at the National Center for Biotechnology Information (NCBI) under accession number JAAKDE00000000.

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.