A novel trifunctional, family GH10 enzyme from Acidothermus cellulolyticus 11B, exhibiting endo-xylanase, arabinofuranosidase and acetyl xylan esterase activities

Structural and functional insights of starch processing α-amylase from hyperthermophilic archaeon Pyrococcusabyssi

The genomic screening of hyper-thermophilic Pyrococcus abyssi showed uncharacterized novel α-amylase sequences. Homology modelling analysis revealed that the α-amylase from P. abyssi consists of an N-terminal GH57 catalytic domain, α-amylase central, and C-terminal domain. Current studies emphasize in-silico structural and functional analysis, recombinant expression, characterization, structural studies through CD spectroscopy, and ligand binding studies of the novel α-amylase from P. abyssi. The soluble expression of PaAFG was observed in the E. coli Rosetta™ (DE3) pLysS strain upon incubation overnight at 18 °C in an orbital shaker. The optimum temperature and pH of the PaAFG were observed at 90 °C in 50 mM phosphate buffer pH 6. The Km value for PaAFG against wheat starch was determined as 0.20 ± 0.053 mg while the corresponding Vmax value was 25.00 ± 0.67 μmol min-1 mg-1 in the presence of 2 mM CaCl2 and 12.5 % glycerol. The temperature ramping experiments through CD spectroscopy reveal no significant change in the secondary structures and positive and negative ellipticities of the CD spectra showing the proper folding and optimal temperature of PaAFG protein. The RMSD and RMSF of the PaAFG enzyme determined through molecular dynamic simulation show the significant protein's stability and mobility. The soluble production, thermostability and broad substrate specificity make this enzyme a promising choice for various industrial applications.

Investigating the effect of SUMO fusion on solubility and stability of amylase-catalytic domain from Pyrococcus abyssi

Alpha amylase belonging to starch hydrolyzing enzymes has significant contributions to different industrial processes. The enzyme production through recombinant DNA technology faces certain challenges related to their expression, solubility and purification, which can be overcome through fusion tags. This study explored the influence of SUMO, a protein tag reported to enhance the solubility and stability of target proteins when fused to the N-terminal of the catalytic domain of amylase from Pyrococcus abyssi (PaAD). The insoluble expression of PaAD in E. coli was overcome when the enzyme was expressed in a fusion state (S-PaAD) and culture was cultivated at 18 °C. Moreover, the activity of S-PaAD increased by 1.5-fold as compared to that of PaAD. The ligand binding and enzyme activity assays against different substrates demonstrated that it was more active against 1 % glycogen and amylopectin. The analysis of the hydrolysates through HPLC demonstrated that the enzyme activity is mainly amylolytic, producing longer oligosaccharides as the major end product. The secondary structure analyses by temperature ramping in CD spectroscopy and MD simulation demonstrated the enzymes in the free, as well as fusion state, were stable at 90 °C. The soluble production, thermostability and broad substrate specificity make this enzyme a promising choice for various foods, feed, textiles, detergents, pharmaceuticals, and many industrial applications.

Structural engineering and truncation of α-amylase from the hyperthermophilic archaeon Methanocaldococcus jannaschii

Alpha amylases catalyse the hydrolysis of α-1, 4-glycosidic bonds in starch, yielding glucose, maltose, dextrin, and short oligosaccharides, vital to various industrial processes. Structural and functional insights on α-amylase from Methanocaldococcus jannaschii were computationally explored to evaluate a catalytic domain and its fusion with a small ubiquitin-like modifier (SUMO). The recombinant proteins' production, characterization, ligand binding studies, and structural analysis of the cloned amylase native full gene (MjAFG), catalytic domain (MjAD) and fusion enzymes (S-MjAD) were thoroughly analysed in this comparative study. The MjAD and S-MjAD showed 2-fold and 2.5-fold higher specific activities (μmol min-1 mg -1) than MjAFG at 95 °C at pH 6.0. Molecular modelling and MD simulation results showed that the removal of the extra loop (178 residues) at the C-terminal of the catalytic domain exposed the binding and catalytic residues near its active site, which was buried in the MjAFG enzyme. The temperature ramping and secondary structure analysis of MjAFG, MjAD and S-MjAD through CD spectrometry showed no notable alterations in the secondary structures but verified the correct folding of MjA variants. The chimeric fusion of amylases with thermostable α-glucosidases makes it a potential candidate for the starch degrading processes.

Orientation of Cel5A and Xyn10B in a fusion construct is important in facilitating synergistic degradation of plant biomass polysaccharides

One approach to achieve efficient and economical saccharification of plant biomass would be using thermostable and multifunctional enzymes from hyperthermophiles such as Thermotoga maritima. Thus, the bifunctional constructs, Cel5A-Xyn10B and Xyn10B-Cel5A, were produced by fusing cellulase Cel5A at the N- and C-terminals of xylanase Xyn10B, respectively. The Cel5A-Xyn10B fusion construct showed cellulase activity of 1483 U μmol^-1 against carboxymethyl cellulose, which was nearly the same as that of Cel5A in the free form. However, xylanase activity of this construct increased by 2-fold against beechwood xylan as compared to that of Xyn10B in free form. The synergistic effect between Cel5A and Xyn10B in the form of Cel5A-Xyn10B fusion resulted an overall increase in the release of reducing sugars. However, Xyn10B-Cel5A showed about 60% decrease in activities of both the component enzymes as compared to their activities in the free form. Both the fusion constructs were active in a wide range of pH from 4.0 to 9.0 and temperatures from 50 to 90 °C. Nearly 80% of cellulase and xylanase activities were retained in Cel5A-Xyn10B fusion after incubation at 60 °C for 1 h. Secondary structures of the component enzymes were retained in the Cel5A-Xyn10B fusion as observed by circular dichroism spectroscopy. Docking and simulation studies suggested that the enhanced xylanase activity in Cel5A-Xyn10B was due to the high binding energy, favorable orientation of the active sites, as well as relative positioning of the active site residues of Cel5A and Xyn10B in closer vicinity, which facilitated the substrate channeling.

Improved catalytic efficiency of chimeric xylanase 10B from Thermotoga petrophila RKU1 and its synergy with cellulases

TpXyl10B is a glycoside hydrolase family 10 xylanase of hyperthermophile Thermotoga petrophila RKU-1. This enzyme is of considerable importance due to its thermostability. However, in its native state, this enzyme does not possess any carbohydrate-binding module (CBM) for efficient binding to plant biomass. In this study CBM6 from Clostridium thermocellum was attached to the N- and C-termini of TpXyl10B, thereby producing the variants TpXyl10B-B6C and TpXyl10B-CB6, respectively. TpXyl10B-B6C showed 5-7 folds increased activity on Beechwood xylan and the different types of plant biomass as compared to that from the catalytic domain only. However, the activity of TpXyl10B-CB6 decreased 0.6-0.8 folds on Beechwood xylan and plant biomass compared to the catalytic domain. We explained these results through molecular modeling, which showed that binding residues of CBM6's cleft B, which were previously reported to show no contribution towards binding due to steric hindrance from a loop region, were exposed in a favorable position in TpXyl10B-B6C such that they efficiently bound the substrate. In contrast, these binding residues of CBM6 in TpXyl10B-CB6 were exposed opposite to the catalytic residues; thus, binding to the substrate resulted in decreased exposure of catalytic residues to the substrate. CD spectroscopy and thermostability assays showed that TpXyl10B-B6C was highly thermostable, having a melting point > 90 °C, which is relatively higher than that of the other variant, TpXyl10B-CB6. In addition, this xylanase variant showed synergism with cellulases for the hydrolysis of plant biomass. Therefore, TpXyl10B-B6C, an engineered xylanase in this study, can be a valuable candidate for industrial applications.

The preparation technology and application of xylo-oligosaccharide as prebiotics in different fields: A review

Xylo-oligosaccharide (XOS) is a class of functional oligosaccharides that have been demonstrated with prebiotic activity over several decades. XOS has several advantages relative to other oligosaccharide molecules, such as promoting root development as a plant regulator, a sugar supplement for people, and prebiotics to promote intestinal motility utilization health. Now, the preparation and extraction process of XOS is gradually mature, which can maximize the extraction and avoid waste. To fully understand the recent preparation and application of XOS in different areas, we summarized the various technologies for obtaining XOS (including acid hydrolysis, enzymatic hydrolysis, hydrothermal pretreatment, and alkaline extraction) and current applications of XOS, including in animal feed, human food additives, and medicine. It is hoped that this review will serve as an entry point for those looking into the prebiotic field of research, and perhaps begin to dedicate their work toward this exciting classification of bio-based molecules.

Cloning, expression and characterization of a glycoside hydrolase family 51 α-l-arabinofuranosidase from Thermoanaerobacterium thermosaccharolyticum DSM 571

The present study focused on the characterization of a glycoside hydrolase 51 family α-l-arabinofuranosidase named TtAbf51 from thermophile Thermoanaerobacterium thermosaccharolyticum DSM 571. The recombinant TtAbf51 with 497 amino acids was successfully expressed in Escherichia coli BL21(DE3) and purified via nickel affinity chromatography, and native protein was a dimer verified by size exclusion chromatography. The TtAbf51 showed an optimum pH and temperature of 5.5 and 55 °C, and was relatively stable at pH 5.0-8.0 and up to 60 °C for 2 h of incubation. In addition, TtAbf51 was significantly inhibited by Cu²⁺, Zn²⁺ and 1 mM or 10 mM SDS. In the presence of 800 mM arabinose, the residual activity remained over 40% of the initial activity. In addition, the recombinant enzyme possessed a good catalytic effect for both synthesized and natural substrates, and the specific enzyme activity toward CM-linear arabinan reached 426.5 μmol min^-1 mg^-1. In summary, this study provides an α-l-arabinofuranosidase with potential in the synergistic hydrolysis of hemicellulose to fermentable sugars in applications such as liquid biofuels, food and beverages, and related industries.

Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass

The field of enzymatic degradation of lignocellulose is actively growing and the recent updates of the last few years indicate that there is still much to learn. The growing number of protein sequences with unknown function in microbial genomes indicates that there is still much to learn on the mechanisms of lignocellulose degradation. In this review, a summary of the progress in the field is presented, including recent discoveries on the nature of the structural polysaccharides, new technologies for the discovery and functional annotation of gene sequences including omics technologies, and the novel lignocellulose-acting enzymes described. Novel enzymatic activities and enzyme families as well as accessory enzymes and their synergistic relationships regarding biomass breakdown are described. Moreover, it is shown that all the valuable knowledge of the enzymatic decomposition of plant biomass polymers can be employed towards the decomposition and upgrading of synthetic polymers, such as plastics.

Autodisplay of an endo-1,4-β-xylanase from Clostridium cellulovorans in Escherichia coli for xylans degradation

The goal of this work was the autodisplay of the endo β-1,4-xylanase (XynA) from Clostridium cellulovorans in Escherichia coli using the AIDA system to carry out whole-cell biocatalysis and hydrolysate xylans. For this, pAIDA-xynA vector containing a synthetic xynA gene was fused to the signal peptide of the toxin subunit B Vibro cholere (ctxB) and the auto-transporter of the synthetic aida gene, which encodes for the connector peptide and β-barrel of the auto-transporter (AT-AIDA). E. coli TOP10 cells were transformed and the biocatalyst was characterized using beechwood xylans as substrate. Optimal operational conditions were temperature of 55 °C and pH 6.5, and the Michaelis-Menten catalytic constants V_max and K_m were 149 U/g_DCW and 6.01 mg/mL, respectively. Xylanase activity was inhibited by Cu²⁺, Zn²⁺ and Hg²⁺ as well as EDTA, detergents, and organic acids, and improved by Ca²⁺, Co²⁺ and Mn²⁺ ions. Ca²⁺ ion strongly enhanced the xylanolytic activity up to 2.4-fold when 5 mM CaCl₂ were added. Also, Ca²⁺ improved enzyme stability at 60 and 70 °C. Results suggest that pAIDA-xynA vector has the ability to express functional xylanase to perform whole-cell biocatalysis in order to hydrolysate xylans from hemicellulose feedstock.

Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering

Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.

Sugarcane/peanut intercropping system improves the soil quality and increases the abundance of beneficial microbes

Sugarcane/peanut intercropping is a highly efficient planting pattern in South China. However, the effects of sugarcane/peanut intercropping on soil quality need to be clarified. This study characterized the soil microbial community and the soil quality in sugarcane/peanut intercropping systems by the Illumina MiSeq platform. The results showed that the intercropping sugarcane (IS) system significantly increased the total N (TN), available N (AN), available P (AP), pH value, and acid phosphatase activity (ACP), but it had little effect on the total P (TP), total K (TK), available K (AK), organic matter (OM), urease activity, protease activity, catalase activity, and sucrase activity, compared with those in monocropping sugarcane (MS) and monocropping peanut (MP) systems. Both intercropping peanut (IP) and IS soils contained more bacteria and fungi than soils in the MP and MS fields, and the microbes identified were mainly Chloroflexi and Acidobacteria, respectively. Intercropping significantly increased the number of unique microbes in IS soils (68 genera), compared with the numbers in the IP (14), MS (17), and MP (16) systems. The redundancy analysis revealed that the abundances of culturable Acidobacteriaceae subgroup 1, nonculturable DA111, and culturable Acidobacteria were positively correlated with the measured soil quality in the intercropping system. Furthermore, the sugarcane/peanut intercropping significantly increased the economic benefit by 87.84% and 36.38%, as compared with that of the MP and MS, respectively. These results suggest that peanut and sugarcane intercropping increases the available N and P content by increasing the abundance of rhizospheric microbes, especially Acidobacteriaceae subgroup 1, DA111, and Acidobacteria.

Arabinofuranosidases: Characteristics, microbial production, and potential in waste valorization and industrial applications

Alpha-L-arabinofuranoside arabinofuranohydrolase (ARA), more commonly known as alpha-L-arabinofuranosidase (E.C. number 3.2.1.55), is a hydrolytic enzyme, catalyzing the cleavage of alpha-L-arabinose by acting on the non-reducing ends of alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linked arabinoxylans and arabinogalactans. ARA functions as debranching enzyme removing arabinose substituents from arabinoxylan and arabinoxylooligomers, thereby, boosting the hydrolysis of arabinoxylan fraction of hemicellulose and improving bioconversion of lignocellulosic biomass. Previously, comprehensive information on this enzyme has not been reviewed thoroughly. Therefore, the main aim of this review is to highlight the important properties of this interesting enzyme, microorganisms used for its production, and enhanced production using genetic engineering approach. An account on synergism with other biomass hydrolyzing enzymes and various industrial applications of this enzyme has also been provided along with an outlook on further research and development.

Xylan in the Middle: Understanding Xylan Biosynthesis and Its Metabolic Dependencies Toward Improving Wood Fiber for Industrial Processing

Lignocellulosic biomass, encompassing cellulose, lignin and hemicellulose in plant secondary cell walls (SCWs), is the most abundant source of renewable materials on earth. Currently, fast-growing woody dicots such as Eucalyptus and Populus trees are major lignocellulosic (wood fiber) feedstocks for bioproducts such as pulp, paper, cellulose, textiles, bioplastics and other biomaterials. Processing wood for these products entails separating the biomass into its three main components as efficiently as possible without compromising yield. Glucuronoxylan (xylan), the main hemicellulose present in the SCWs of hardwood trees carries chemical modifications that are associated with SCW composition and ultrastructure, and affect the recalcitrance of woody biomass to industrial processing. In this review we highlight the importance of xylan properties for industrial wood fiber processing and how gaining a greater understanding of xylan biosynthesis, specifically xylan modification, could yield novel biotechnology approaches to reduce recalcitrance or introduce novel processing traits. Altering xylan modification patterns has recently become a focus of plant SCW studies due to early findings that altered modification patterns can yield beneficial biomass processing traits. Additionally, it has been noted that plants with altered xylan composition display metabolic differences linked to changes in precursor usage. We explore the possibility of using systems biology and systems genetics approaches to gain insight into the coordination of SCW formation with other interdependent biological processes. Acetyl-CoA, s-adenosylmethionine and nucleotide sugars are precursors needed for xylan modification, however, the pathways which produce metabolic pools during different stages of fiber cell wall formation still have to be identified and their co-regulation during SCW formation elucidated. The crucial dependence on precursor metabolism provides an opportunity to alter xylan modification patterns through metabolic engineering of one or more of these interdependent pathways. The complexity of xylan biosynthesis and modification is currently a stumbling point, but it may provide new avenues for woody biomass engineering that are not possible for other biopolymers.