Mining of camel rumen metagenome to identify novel alkali-thermostable xylanase capable of enhancing the recalcitrant lignocellulosic biomass conversion

Precision enzyme discovery through targeted mining of metagenomic data

Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.

Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach

BACKGROUND

Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities.

RESULTS

Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity.

CONCLUSIONS

In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.

Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows

Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.

Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses

Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.

Cloning, expression, and characterization of two pectate lyases isolated from the sheep rumen microbiome

Pectate lyases (Pels) have a vital function in degradation of the primary plant cell wall and the middle lamella and have been widely used in the industry. In this study, two pectate lyase genes, IDSPel16 and IDSPel17, were cloned from a sheep rumen microbiome. The recombinant enzymes were expressed in Escherichia coli and functionally characterized. Both IDSPel16 and IDSPel17 proteins had an optimal temperature of 60 ℃, and an optimal pH of 10.0. IDSPel16 was relatively stable below 60 °C, maintaining 77.51% residual activity after preincubation at 60 °C for 1 h, whereas IDSPel17 denatured rapidly at 60 °C. IDSPel16 was relatively stable between pH 6.0 and 12.0, after pretreatment for 1 h, retaining over 60% residual activity. IDSPel16 had high activity towards polygalacturonic acid, with a V_max of 942.90 ± 68.11, whereas IDSPel17 had a V_max of only 28.19 ± 2.23 μmol/min/mg. Reaction product analyses revealed that IDSPel17 liberated unsaturated digalacturonate (uG₂) and unsaturated trigalacturonate (uG₃) from the substrate, indicating a typical endo-acting pectate lyase (EC 4.2.2.2). In contrast, IDSPel16 initially generated unsaturated oligogalacturonic acids, then converted these intermediates into uG₂ and unsaturated galacturonic acid (uG₁) as end products, a unique depolymerization profile among Pels. To the best of our knowledge, the IDSPel16 discovered with both endo-Pel (EC 4.2.2.2) and exo-Pel (EC 4.2.2.9) activities. These two pectate lyases, particularly the relatively thermo- and pH-stable IDSPel16, will be of interest for potential application in the textile, food, and feed industries. KEY POINTS: • Two novel pectate lyase genes, IDSPel16 and IDSPel17, were isolated and characterized from the sheep rumen microbiome. • Both IDSPel16 and IDSPel17 are alkaline pectate lyases, releasing unsaturated digalacturonate and unsaturated trigalacturonate from polygalacturonic acid. • IDSPel16, a bifunctional pectate lyase with endo-Pel (EC 4.2.2.2) and exo-Pel (EC 4.2.2.9) activities, could be a potential candidate for industrial application.

Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass

Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.

A sustainable approach of turning potato waste towards bioethanol production using indigenous microbes of Himachal Pradesh, India

Potato peel waste is one of the zero-value wastes with the potential of bioethanol production through the Waste to Energy (WtE) approach. The newly isolated, phenotypically characterized, and molecular identified high-altitude strain, B. amyloliquefaciens, shown promising starch hydrolysis (12.06 g/L reducing sugars) over acid hydrolysis and is capable of working at 30-50 °C and pH 6.0-8.0. The ethanol production by Acinetobacter sp. (a newly isolated, phenotypically characterized, molecular identified) has been modelled and optimized through the central composite design of response surface methodology by taking the fermentation variables as input variables and ethanol yield as the output variable. The ethanol production by Acinetobacter sp. showcased a non-linear relationship of fermentation variables with the ethanol yield (5.83 g/L) with a 99.11% desirability function (R²) and 97.50 adj. R² values. Optimal fermentation variables of 38.8% substrate concentration, 7% inoculum, pH 5.45 have been utilized for bioethanol production in 55.27 h at 27 °C. Overall, the present study evaluated the efficiency of newly isolated, indigenous extremophilic microbes of The Himalayan region in sustainable bioethanol production from zero-value waste "Potato peel waste" through the WtE approach. Moreover, the present study introduces the promising, unexplored extremophilic microbial strains with the starch-hydrolyzing and fermentation capabilities to bioethanol biorefinery.

Characterization of a New Xylanase Found in the Rumen Metagenome and Its Effects on the Hydrolysis of Wheat

Wheat is the main ingredient of poultry diet, but its xylan has an adverse impact on poultry production. A novel xylanase from beef cattle rumen metagenome (RuXyn) and its effect on the wheat hydrolysis were investigated in the present study. The RuXyn coded for 377 amino acids and exhibited low identity (<40%) to previously reported proteins. The RuXyn was heterologously expressed in Escherichia coli and showed maximum activity at pH 6.0 and 40 °C. The activity of RuXyn could be increased by 79.8 and 36.0% in the presence of Ca²⁺ and Tween 20, respectively. The soluble xylan and insoluble xylan in wheat could be effectively degraded by RuXyn and xylooligosaccharides produced accounting for more than 80% of the products. This study demonstrates that RuXyn has substantial potential to improve the application of wheat in poultry production by degrading wheat xylan and the accompanying xylooligosaccharides produced.

Invitro bioprocessing of corn as poultry feed additive by the influence of carbohydrate hydrolyzing metagenome derived enzyme cocktail

The carbohydrate-hydrolyzing enzymes play a crucial role in increasing the phenolic content and nutritional properties of polysaccharides substrate, essential for cost-effective industrial applications. Also, improving the feed efficiency of poultry is essential to achieve significant economic benefits. The current study introduced a novel thermostable metagenome-derived xylanase named PersiXyn8 and investigated its synergistic effect with previously reported α-amylase (PersiAmy3) to enhance poultry feed utilization. The potential of the enzyme cocktail in the degradation of poultry feed was analyzed and showed 346.73 mg/g poultry feed reducing sugar after 72 h of hydrolysis. Next, the impact of solid-state fermentation on corn quality was investigated in the presence and absence of enzymes. The phenolic content increased from 36.60 mg/g GAE in control sample to 68.23 mg/g in the presence of enzymes. In addition, the enzyme-treated sample showed the highest reducing power OD 700 of 0.217 and the most potent radical scavenging activity against ABTS (40.36%) and DPPH (45.21%) radicals. Moreover, the protein and ash contents of the fermented corn increased by 4.88% and 6.46%, respectively. These results confirmed the potential of the carbohydrate-hydrolyzing enzymes cocktail as a low-cost treatment for improving the phenolic content, antioxidant activity, and nutritional values of corn for supplementation of corn-based poultry feed.

Application of free and immobilized novel bifunctional biocatalyst in biotransformation of recalcitrant lignocellulosic biomass

Herein, an innovative, green, and practical biocatalyst was developed using conjugation of a novel bifunctional mannanase/xylanase biocatalyst (PersiManXyn1) to the modified cellulose nanocrystals (CNCs). Firstly, PersiManXyn1 was multi-stage in-silico screened from rumen macrobiota, and then cloned, expressed, and purified. Next, CNCs were synthesized from sugar beet pulp using enzymatic and acid hydrolysis processes, and then Fe₃O₄ NPs were anchored on their surface to produce magnetic CNCs (MCNCs). This hybrid was modified by dopamine providing DA/MCNCs nano-carrier. The bifunctional PersiManXyn1 demonstrated the superior hydrolysis activity on corn cob compared with the monofunctional xylanase enzyme (PersiXyn2). Moreover, the immobilization of PersiManXyn1 on the nano-carrier resulted in an improvement of the thermal stability, kinetic parameters (K_cat), and storage stability of the enzyme. Incorporation of the Fe₃O₄ NPs on the CNCs made magnetic nano-carrier with high magnetization value (25.8 emu/g) which exhibited rapid response toward the external magnetic fields. Hence, the immobilized biocatalyst could be easily separated from the products by a magnet, and reused up to 8 cycles with maintaining more than 50% of its original activity. The immobilized PersiManXyn1 generated 22.2%, 38.7%, and 35.1% more reducing sugars after 168 h hydrolysis of the sugar beet pulp, coffee waste, and rice straw, respectively, compared to the free enzyme. Based on the results, immobilization of the bifunctional PersiManXyn1 exhibited the superb performance of the enzyme to improve the conversion of the lignocellulosic wastes into high value products and develop the cost-competition biomass operations.

Identification and characterization of a thermostable GH11 xylanase from Paenibacillus campinasensis NTU-11 and the distinct roles of its carbohydrate-binding domain and linker sequence

An extracellular thermostable xylanase (XynNTU) from Paenibacillus campinasensis NTU-11, consisted of a glycoside hydrolase (GH) family 11 catalytic domain, a Gly/Pro-rich linker sequence (LS) and a family 6 carbohydrate-binding module (CBM6), was identified and expressed in E. coli BL21. The purified XynNTU had a specific activity of 2750 U/mg and an optimal activity at 60 °C and pH 7.0, and retained a residual activity of 58.4% after incubation (60 °C, 48 h). Two truncated mutants, CBM6-truncated form XynNTU-CDLS, CBM6 and linker-truncated form XynNTU-CD, possessed similar values of optimum pH and temperature as the native XynNTU. XynNTU-CD displayed a lower thermostability than XynNTU, whereas for XynNTU-CDLS, more than 90% of residual activity was remained (60 °C, 48 h), indicating that this enzyme presented a higher thermostability than that of the majority of reported GH11 xylanases. Furthermore, XynNTU and two mutants maintained more than 70% of residual activity at pH values of 5-9. Kinetic measurements suggested that CBM6 had a crucial function in the ability of the enzyme to bind and hydrolyze xylan substrates, while LS had a relatively mild influence. Collectively, a noticeable thermostability and a high specific activity of XynNTU and its truncated form XynNTU-CDLS highlights their potentials for diverse industrial applications.

BdPUL12 depolymerizes β-mannan-like glycans into mannooligosaccharides and mannose, which serve as carbon sources for Bacteroides dorei and gut probiotics

Symbiotic bacteria, including members of the Bacteroides genus, are known to digest dietary fibers in the gastrointestinal tract. The metabolism of complex carbohydrates is restricted to a specified subset of species and is likely orchestrated by polysaccharide utilization loci (PULs) in these microorganisms. β-Mannans are plant cell wall polysaccharides that are commonly found in human nutrients. Here, we report the structural basis of a PUL cluster, BdPUL12, which controls β-mannan-like glycan catabolism in Bacteroides dorei. Detailed biochemical characterization and targeted gene disruption studies demonstrated that a key glycoside hydrolase, BdP12GH26, performs the initial attack on galactomannan or glucomannan likely via an endo-acting mode, generating mannooligosaccharides and mannose. Importantly, coculture assays showed that the B. dorei promoted the proliferation of Lactobacillus helveticus and Bifidobacterium adolescentis, likely by sharing mannooligosaccharides and mannose with these gut probiotics. Our findings provide new insights into carbohydrate metabolism in gut-inhabiting bacteria and lay a foundation for novel probiotic development.

In-silico discovery of bifunctional enzymes with enhanced lignocellulose hydrolysis from microbiota big data

Due to the importance of using lignocellulosic biomass, it is always important to find an effective novel enzyme or enzyme cocktail or fusion enzymes. Identification of bifunctional enzymes through a metagenomic approach is an efficient method for converting agricultural residues and a beneficial way to reduce the cost of enzyme cocktail and fusion enzyme production. In this study, a novel stable bifunctional cellulase/xylanase, PersiCelXyn1 was identified from the rumen microbiota by the multi-stage in-silico screening pipeline and computationally assisted methodology. The enzyme exhibited the optimal activity at pH 5 and 50°C. Analyzing the enzyme activity at extreme temperature, pH, long-term storage, and presence of inhibitors and metal ions, confirmed the stability of the bifunctional enzyme under harsh conditions. Hydrolysis of the rice straw by PersiCelXyn1 showed its capability to degrade both cellulose and hemicellulose polymers. Also, the enzyme improved the degradation of various biomass substrates after 168 h of hydrolysis. Our results demonstrated the power of the multi-stage in-silico screening to identify bifunctional enzymes from metagenomic big data for effective bioconversion of lignocellulosic biomass.

A novel bifunctional glucanase exhibiting high production of glucose and cellobiose from rumen bacterium

Herbivores gastrointestinal microbiota is of tremendous interest for mining novel lignocellulosic enzymes for bioprocessing. We previously reported a set of potential carbohydrate-active enzymes from the metatranscriptome of the Hu sheep rumen microbiome. In this study, we isolated and heterologously expressed two novel glucanase genes, Cel5A-h38 and Cel5A-h49, finding that both recombinant enzymes showed the optimum temperatures of 50 °C. Substrate-specificity determination revealed that Cel5A-h38 was exclusively active in the presence of mixed-linked glucans, such as barley β-glucan and Icelandic moss lichenan, whereas Cel5A-h49 (EC 3.2.1.4) exhibited a wider substrate spectrum. Surprisingly, Cel5A-h38 initially released only cellotriose from lichenan and further converted it into an equivalent amount of glucose and cellobiose, suggesting a dual-function as both endo-β-1,3-1,4-glucanase (EC 3.2.1.73) and exo-cellobiohydrolase (EC 3.2.1.91). Additionally, we performed enzymatic hydrolysis of sheepgrass (Leymus chinensis) and rice (Orysa sativa) straw using Cel5A-h38, revealing liberation of 1.91 ± 0.30 mmol/mL and 2.03 ± 0.09 mmol/mL reducing sugars, respectively, including high concentrations of glucose and cellobiose. These results provided new insights into glucanase activity and lay a foundation for bioconversion of lignocellulosic biomass.

Characterization of efficient xylanases from industrial-scale pulp and paper wastewater treatment microbiota

Xylanases are widely used enzymes in the food, textile, and paper industries. Most efficient xylanases have been identified from lignocellulose-degrading microbiota, such as the microbiota of the cow rumen and the termite hindgut. Xylanase genes from efficient pulp and paper wastewater treatment (PPWT) microbiota have been previously recovered by metagenomics, assigning most of the xylanase genes to the GH10 family. In this study, a total of 40 GH10 family xylanase genes derived from a certain PPWT microbiota were cloned and expressed in Escherichia coli BL21 (DE3). Among these xylanase genes, 14 showed xylanase activity on beechwood substrate. Two of these, PW-xyl9 and PW-xyl37, showed high activities, and were purified to evaluate their xylanase properties. Values of optimal pH and temperature for PW-xyl9 were pH 7 and 60 ℃, respectively, while those for PW-xyl37 were pH 7 and 55 ℃, respectively; their specific xylanase activities under optimal conditions were 470.1 U/mg protein and 113.7 U/mg protein, respectively. Furthermore, the Km values of PW-xyl9 and PW-xyl37 were determined as 8.02 and 18.8 g/L, respectively. The characterization of these two xylanases paves the way for potential application in future pulp and paper production and other industries, indicating that PPWT microbiota has been an undiscovered reservoir of efficient lignocellulase genes. This study demonstrates that a metagenomic approach has the potential to screen efficient xylanases of uncultured microorganisms from lignocellulose-degrading microbiota. In a similar way, other efficient lignocellulase genes might be identified from PPWT treatment microbiota in the future.

Application of the immobilized enzyme on magnetic graphene oxide nano-carrier as a versatile bi-functional tool for efficient removal of dye from water

Herein, we report bi-functional applications of a novel immobilized enzyme on the modified magnetic graphene oxide (GO) for effective removal of dyes from water. The amine functionalized GO nano-carrier was covalently attached to a model enzyme (PersiManXyn1). The enzyme assays showed that the specific activities of the free and immobilized enzyme were 856.05 and 1141.1 µmolmin^-1mg^-1, respectively. While the free enzyme showed only 5% of its maximum activity, the immobilized PersiManXyn1 preserved more than 35% of its activity, at 90 °C. After four weeks storage, the free enzyme has been deactivated, but the immobilized enzyme retained 54% of its initial activity. The immobilized PersiManXyn1 was proficiently applied for dye removal from water using two strategies. While only pristine nano-carrier and free enzyme showed no considerable catalytic ability, the immobilized PersiManXyn1 could catalytically reduce the concentrated dye solutions within 150 s with superior reusability (94% dye removal after 15^th cycle). Proficient treatment of a real textile effluent by the immobilized PersiManXyn1 approved its practical applications in the water remediation.

Immobilization of enzyme cocktails on dopamine functionalized magnetic cellulose nanocrystals to enhance sugar bioconversion: A biomass reusing loop

A combined enzymatic treatment/acid hydrolysis technique was utilized to synthesize cellulose nanocrystals (CNCs) from sugar beet pulp. CNCs were functionalized with magnetite nanoparticles and dopamine making a versatile nano-carrier (DA/Fe₃O₄NPs@CNCs) for covalent enzyme immobilization. Oxygene/amine functionalities, high magnetization value, and specific surface area of DA/Fe₃O₄NPs@CNCs made it a reusable and green candidate for conjugation to hydrolytic enzyme cocktails (three cellulases, two hemicellulases, and their combinations) to prepare an innovative and practical nano-biocatalyst for biomass conversion. The conjugated enzymes showed an enhanced optimum temperature (∼ 10 °C), improved thermal stability, and shifted optimum pH toward alkaline pHs. Covalent attachment could successfully suppress the enzyme leaching and provide easy recovery/reuse of the nano-biocatalyst up to 10 cycles, with > 50% of initial activity. Application of the nano-biocatalyst in hydrolysis of rice straw and sugar beet pulp showed an increase (20-76%) in the yield of fermentable sugars compared to the free enzyme cocktails.

A generalized machine-learning aided method for targeted identification of industrial enzymes from metagenome: A xylanase temperature dependence case study

Growing industrial utilization of enzymes and the increasing availability of metagenomic data highlight the demand for effective methods of targeted identification and verification of novel enzymes from various environmental microbiota. Xylanases are a class of enzymes with numerous industrial applications and are involved in the degradation of xylose, a component of lignocellulose. The optimum temperature of enzymes is an essential factor to be considered when choosing appropriate biocatalysts for a particular purpose. Therefore, in silico prediction of this attribute is a significant cost and time-effective step in the effort to characterize novel enzymes. The objective of this study was to develop a computational method to predict the thermal dependence of xylanases. This tool was then implemented for targeted screening of putative xylanases with specific thermal dependencies from metagenomic data and resulted in the identification of three novel xylanases from sheep and cow rumen microbiota. Here we present thermal activity prediction for xylanase, a new sequence-based machine learning method that has been trained using a selected combination of various protein features. This random forest classifier discriminates non-thermophilic, thermophilic, and hyper-thermophilic xylanases. The model's performance was evaluated through multiple iterations of sixfold cross-validations as well as holdout tests, and it is freely accessible as a web-service at arimees.com.

MCIC: Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence

As the availability of high-throughput metagenomic data is increasing, agile and accurate tools are required to analyze and exploit this valuable and plentiful resource. Cellulose-degrading enzymes have various applications, and finding appropriate cellulases for different purposes is becoming increasingly challenging. An in silico screening method for high-throughput data can be of great assistance when combined with the characterization of thermal and pH dependence. By this means, various metagenomic sources with high cellulolytic potentials can be explored. Using a sequence similarity-based annotation and an ensemble of supervised learning algorithms, this study aims to identify and characterize cellulolytic enzymes from a given high-throughput metagenomic data based on optimum temperature and pH. The prediction performance of MCIC (metagenome cellulase identification and characterization) was evaluated through multiple iterations of sixfold cross-validation tests. This tool was also implemented for a comparative analysis of four metagenomic sources to estimate their cellulolytic profile and capabilities. For experimental validation of MCIC’s screening and prediction abilities, two identified enzymes from cattle rumen were subjected to cloning, expression, and characterization. To the best of our knowledge, this is the first time that a sequence-similarity based method is used alongside an ensemble machine learning model to identify and characterize cellulase enzymes from extensive metagenomic data. This study highlights the strength of machine learning techniques to predict enzymatic properties solely based on their sequence. MCIC is freely available as a python package and standalone toolkit for Windows and Linux-based operating systems with several functions to facilitate the screening and thermal and pH dependence prediction of cellulases.

A novel high performance in-silico screened metagenome-derived alkali-thermostable endo-β-1,4-glucanase for lignocellulosic biomass hydrolysis in the harsh conditions

Background

Lignocellulosic biomass, is a great resource for the production of bio-energy and bio-based material since it is largely abundant, inexpensive and renewable. The requirement of new energy sources has led to a wide search for novel effective enzymes to improve the exploitation of lignocellulose, among which the importance of thermostable and halotolerant cellulase enzymes with high pH performance is significant.

Results

The primary aim of this study was to discover a novel alkali-thermostable endo-β-1,4-glucanase from the sheep rumen metagenome. At first, the multi-step in-silico screening approach was utilized to find primary candidate enzymes with superior properties. Among the computationally selected candidates, PersiCel4 was found and subjected to cloning, expression, and purification followed by functional and structural characterization. The enzymes’ kinetic parameters, including V_max, K_m, and specific activity, were calculated. The PersiCel4 demonstrated its optimum activity at pH 8.5 and a temperature of 85 °C and was able to retain more than 70% of its activity after 150 h of storage at 85 °C. Furthermore, this enzyme was able to maintain its catalytic activity in the presence of different concentrations of NaCl and several metal ions contains Mg²⁺, Mn²⁺, Cu²⁺, Fe²⁺ and Ca²⁺. Our results showed that treatment with MnCl₂ could enhance the enzyme’s activity by 78%. PersiCel4 was ultimately used for enzymatic hydrolysis of autoclave pretreated rice straw, the most abundant agricultural waste with rich cellulose content. In autoclave treated rice straw, enzymatic hydrolysis with the PersiCel4 increased the release of reducing sugar up to 260% after 72 h in the harsh condition (T = 85 °C, pH = 8.5).

Conclusion

Considering the urgent demand for stable cellulases that are operational on extreme temperature and pH conditions and due to several proposed distinctive characteristics of PersiCel4, it can be used in the harsh condition for bioconversion of lignocellulosic biomass.

Engineering of a thermo-alkali-stable lipase from Rhizopus chinensis by rational design of a buried disulfide bond and combinatorial mutagenesis

To improve the thermostability of the lipase (r27RCL) from Rhizopus chinensis through rational design, a newly introduced buried disulfide bond F223C/G247C was proved to be beneficial to thermostability. Interestingly, F223C/G247C was also found to improve the alkali tolerance of the lipase. Subsequently, six other thermostabilizing mutations from our previous work were integrated into the mutant F223C/G247C, leading to a thermo-alkali-stable mutant m32. Compared to the wild-type lipase, the associative effect of the beneficial mutations showed significant improvements on the thermostability of m32, with a 74.7-fold increase in half-life at 60 °C, a 21.2 °C higher [Formula: see text] value and a 10 °C elevation in optimum temperature. The mutated m32 was also found stable at pH 9.0-10.0. Furthermore, the molecular dynamics simulations of m32 indicated that its rigidity was enhanced due to the decreased solvent-accessible surface area, a newly formed salt bridge, and the increased ΔΔG values.

A Novel High Glucose-Tolerant β-Glucosidase: Targeted Computational Approach for Metagenomic Screening

The rate-limiting component of cellulase for efficient degradation of lignocellulosic biomass through the enzymatic route depends on glucosidase’s sensitivity to the end product (glucose). Therefore, there is still a keen interest in finding glucose-tolerant β-glucosidase (BGL) that is active at high glucose concentrations. The main objective of this study was to identify, isolate, and characterize novel highly glucose-tolerant and halotolerant β-glucosidase gene (PersiBGL1) from the mixed genome DNA of sheep rumen metagenome as a suitable environment for efficient cellulase by computationally guided experiments instead of costly functional screening. At first, an in silico screening approach was utilized to find primary candidate enzymes with superior properties. The structure-dependent mechanism of glucose tolerance was investigated for candidate enzymes. Among the computationally selected candidates, PersiBGL1 was cloned, isolated, and structurally characterized, which achieved very high activity in relatively high temperatures and alkaline pH and was successfully used for the hydrolysis of cellobiose. This enzyme exhibits a very high glucose tolerance, with the highest inhibition constant K_i (8.8 M) among BGLs reported so far and retained 75% of its initial activity in the presence of 10 M glucose. Furthermore, a group of multivalent metal, including Mg²⁺, Mn²⁺, and Ca²⁺, as a cofactor, could improve the catalytic efficiency of PersiBGL1. Our results demonstrated the power of computational selected candidates to discover novel glucose tolerance BGL, effective for the bioconversion of lignocellulosic biomass.

Stable cellulase immobilized on graphene oxide@CMC-g-poly(AMPS-co-AAm) hydrogel for enhanced enzymatic hydrolysis of lignocellulosic biomass

This study indicated tailoring efficient polymer-enzyme bioconjugates with superb stability and activity for practical utilization of cellulase enzyme in hydrolyzing lignocellulosic biomass. To this goal, a dual crosslinking (DC) strategy was presented to synthesize novel 3D networks of carboxymethyl cellulose grafted copolymers of 2-acrylamido-2methyl propane sulfonate and acrylamide (CMC-g-poly(AMPS-co-AAm)) hydrogels. Graphene oxide (GO) nano-sheets were utilized as nano-filler and physical cross-linker making H-bondings between polymeric chains to prepare GO@CMC-g-poly(AMPS-co-AAm) networks. The GO content effects on the performance of as-synthesized architectures in conjugation to a model enzyme (PersiCel1) were examined. PersiCel1 immobilization on the GO reinforced hydrogels resulted in noticeable retaining near 60 % of its maximum activity at 90 °C, along with the remarkable enhancement of its specific activity and storage stability. Compared with the free PersiCel1, the immobilized enzyme on the GO containing hydrogels showed 154.8 % increase in conversion of alkalin-treated sugar beet pulp, while the PersiCel1/neat-Hydrogel indicated an increment of 66.7 %, under the same conditions.