Characterization of a novel psychrophilic and halophilic β-1, 3-xylanase from deep-sea bacterium, Flammeovirga pacifica strain WPAGA1

Production and biological activity of β-1,3-xylo-oligosaccharides using xylanase from Caulerpa lentillifera

In this study, β-1,3-xylanase (Xyl3088) was designed and prepared by constructing the expression vector plasmid and expressing and purifying the fusion protein. β-1,3-xylo-oligosaccharides were obtained through the specific enzymatic degradation of β-1, 3-xylan from Caulerpa lentillifera. The enzymolysis conditions were established and optimized as follows: Tris-HCl solution 0.05 mol/L, temperature of 37 °C, enzyme amount of 250 μL, and enzymolysis time of 24 h. The oligosaccharides' compositions and structural characterization were identified by thin-layer chromatography (TLC), ion chromatography (IC) and liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS). The IC50 values for scavenging 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2-azino-bis-3-ethyl-benzothiazoline-p-sulfonic acid (ABTS+), and superoxide anion radical (•O2-) were 13.108, 1.258, and 65.926 mg/mL for β-1,3-xylo-oligosaccharides, respectively, and 27.588, 373.048, and 269.12 mg/mL for β-1,4-xylo-oligosaccharides, respectively. Compared with β-1,4-xylo-oligosaccharides, β-1,3-xylo-oligosaccharides had substantial antioxidant activity and their antioxidant effects were concentration dependent. β-1,3-xylo-oligosaccharides also possessed a stronger anti-inflammatory effect on RAW 264.7 cells stimulated by lipopolysaccharide (LPS) than β-1,4-xylo-oligosaccharides. At a working concentration of 100 μg/mL, β-1,3-xylo-oligosaccharides inhibited the release of NO and affected the expression of IL-1β, TNF-α, and other proteins secreted by cells, effectively promoting the release of pro-inflammatory mediators by immune cells in response to external stimuli and achieving anti-inflammatory effects. Therefore, β-1,3-xylo-oligosaccharides are valuable products in food and pharmaceutical industries.

Critical Roles of Acidic Residues in Loop Regions of the Structural Surface for the Salt Tolerance of a GH39 β-d-Xylosidase

Xylan is the main component of hemicellulose. Complete hydrolysis of xylan requires synergistically acting xylanases, such as β-d-xylosidases. Salt-tolerant β-d-xylosidases have significant application benefits, but few reports have explored the critical amino acids affecting the salt tolerance of xylosidases. Herein, the site-directed mutation was used to demonstrate that negative electrostatic potentials generated by 19 acidic residues in the loop regions of the structural surface positively correlated with the improved salt tolerance of GH39 β-d-xylosidase JB13GH39P28. These mutants showed reduced negative potentials on structural surfaces as well as a 13-43% decrease in stability in 3.0-30.0% (w/v) NaCl. Six key residue sites, D201, D259, D297, D377, D395, and D474, were confirmed to influence both the stability and activity of GH39 β-d-xylosidase. The activity of the GH39 β-d-xylosidase was found promoting by SO42- and inhibiting by NO3-. Values of Km and Kcat/Km decreased aggravatedly in 30.0% (w/v) NaCl when mutation operated on residues E179 and D182 in the loop regions of the catalytic domain. Taken together, mutation on acidic residues in loop regions from catalytic and noncatalytic domains may cause the deformation of catalytic pocket and aggregation of protein particles then decrease the stability, binding affinity, and catalytic efficiency of the β-d-xylosidase.

A novel protein purification scheme based on salt inducible self-assembling peptides

BACKGROUND

Protein purification remains a critical need for biosciences and biotechnology. It frequently requires multiple rounds of chromatographic steps that are expensive and time-consuming. Our lab previously reported a cleavable self-aggregating tag (cSAT) scheme for streamlined protein expression and purification. The tag consists of a self-assembling peptide (SAP) and a controllable self-cleaving intein. The SAP drives the target protein into an active aggregate, then by intein-mediated cleavage, the target protein is released. Here we report a novel cSAT scheme in which the self-assembling peptide is replaced with a salt inducible self-assembling peptide. This allows a target protein to be expressed first in the soluble form, and the addition of salt then drives the target protein into the aggregated form, followed by cleavage and release.

RESULTS

In this study, we used MpA (MKQLEDKIEELLSKAAMKQLEDKIEELLSK) as a second class of self-assembling peptide in the cSAT scheme. This scheme utilizes low salt concentration to keep the fusion protein soluble, while eliminating insoluble cellular matters by centrifugation. Salt then triggers MpA-mediated self-aggregation of the fusion, removing soluble background host cell proteins. Finally, intein-mediated cleavage releases the target protein into solution. As a proof-of-concept, we successfully purified four proteins and peptides (human growth hormone, 22.1 kDa; LCB3, 7.7 kDa; SpyCatcherΔN-ELP-SpyCatcherΔN, 26.2 kDa; and xylanase, 45.3 kDa) with yields ranging from 12 to 87 mg/L. This was comparable to the classical His-tag method both in yield and purity (72-97%), but without the His-tag. By using a further two-step column purification process that included ion-exchange chromatography and size-exclusion chromatography, the purity was increased to over 99%.

CONCLUSION

Our results demonstrate that a salt-inducible self-assembling peptide can serve as a controllable aggregating tag, which might be advantageous in applications where soluble expression of the target protein is preferred. This work also demonstrates the potential and advantages of utilizing salt inducible self-assembling peptides for protein separation.

Cold-adapted enzymes: mechanisms, engineering and biotechnological application

Most cold-adapted enzymes display high catalytic activity at low temperatures (20-25 °C) and can still maintain more than 40-50% of their maximum activity at lower temperatures (0-10 °C) but are inactivated after a moderate increase in temperature. The activity of some cold-adapted enzymes increases significantly in the presence of high salt concentrations and metal ions. Interestingly, we also observed that some cold-adapted enzymes have a wide range of optimum temperatures, exhibiting not only maximum activity under low-temperature conditions but also the ability to maintain high enzyme activity under high-temperature conditions, which is a novel feature of cold-adapted enzymes. This unique property of cold-adapted enzymes is generally attractive for biotechnological and industrial applications because these enzymes can reduce energy consumption and the chance of microbial contamination, thereby lowering the production costs and maintaining the flavor, taste and quality of foods. How high catalytic activity is maintained at low temperatures remains unknown. The relationship between the structure of cold-adapted enzymes and their activity, flexibility and stability is complex, and thus far, a unified explanation has not been provided. Herein, we systematically review the sources, catalytic characteristics and cold adaptation of enzymes from four enzymes categories systematically and discuss how these properties may be exploited in biotechnology. A thorough understanding of the properties, catalytic mechanisms, and engineering of cold-adapted enzymes is critical for future biotechnological applications in the detergent industry and food and beverage industries.

A novel class of xylanases specifically degrade marine red algal β1,3/1,4-mixed-linkage xylan

Xylans are polysaccharides composed of xylose and include β1,4-xylan, β1,3-xylan, and β1,3/1,4-mixed-linkage xylan (MLX). MLX is widely present in marine red algae and constitutes a significant organic carbon in the ocean. Xylanases are hydrolase enzymes that play an important role in xylan degradation. While a variety of β1,4-xylanases and β1,3-xylanases involved in the degradation of β1,4-xylan and β1,3-xylan have been reported, no specific enzyme has yet been identified that degrades MLX. Herein, we report the characterization of a new MLX-specific xylanase from the marine bacterium Polaribacter sp. Q13 which utilizes MLX for growth. The bacterium secretes xylanases to degrade MLX, among which is Xyn26A, an MLX-specific xylanase that shows low sequence similarities (<27%) to β1,3-xylanases in the glycoside hydrolase family 26 (GH26). We show that Xyn26A attacks MLX precisely at β1,4-linkages, following a β1,3-linkage toward the reducing end. We confirm that Xyn26A and its homologs have the same specificity and mode of action on MLX, and thus represent a new xylanase group which we term as MLXases. We further solved the structure of a representative MLXase, AlXyn26A. Structural and biochemical analyses revealed that the specificity of MLXases depends critically on a precisely positioned β1,3-linkage at the -2/-1 subsite. Compared to the GH26 β1,3-xylanases, we found MLXases have evolved a tunnel-shaped cavity that is fine-tuned to specifically recognize and hydrolyze MLX. Overall, this study offers a foremost insight into MLXases, shedding light on the biochemical mechanism of bacterial degradation of MLX.

A Review on Psychrophilic β-D-Galactosidases and Their Potential Applications

The majority of the Earth's ecosystem is frigid and frozen, which permits a vast range of microbial life forms to thrive by triggering physiological responses that allow them to survive in cold and frozen settings. The apparent biotechnology value of these cold-adapted enzymes has been targeted. Enzymes' market size was around USD 6.3 billion in 2017 and will witness growth at around 6.8% CAGR up to 2024 owing to shifting consumer preferences towards packaged and processed foods due to the rising awareness pertaining to food safety and security reported by Global Market Insights (Report ID-GMI 743). Various firms are looking for innovative psychrophilic enzymes in order to construct more effective biochemical pathways with shorter reaction times, use less energy, and are ecologically acceptable. D-Galactosidase catalyzes the hydrolysis of the glycosidic oxygen link between the terminal non-reducing D-galactoside unit and the glycoside molecule. At refrigerated temperature, the stable structure of psychrophile enzymes adjusts for the reduced kinetic energy. It may be beneficial in a wide variety of activities such as pasteurization of food, conversion of biomass, biological role of biomolecules, ambient biosensors, and phytoremediation. Recently, psychrophile enzymes are also used in claning the contact lens. β-D-Galactosidases have been identified and extracted from yeasts, fungi, bacteria, and plants. Conventional (hydrolyzing activity) and nonconventional (non-hydrolytic activity) applications are available for these enzymes due to its transgalactosylation activity which produce high value-added oligosaccharides. This review content will offer new perspectives on cold-active β-galactosidases, their source, structure, stability, and application.

Gilvimarinus xylanilyticus sp. nov., a novel 1,3-xylanase-secreting bacterium isolated from a marine green alga

1,3-xylan, an important organic carbon in the ocean, is peculiar to marine algae. 1,3-xylanase-secreting bacteria and their extracellular 1,3-xylanases play pivotal roles in the degradation and biomass conversion of 1,3-xylan. However, only a few 1,3-xylanase-secreting bacteria and 1,3-xylanases have been reported. Here, we identified a novel marine bacterium capable of secreting 1,3-xylanases, designated as strain HB14^T. Phylogenetic analysis revealed that strain HB14^T clustered tightly with known species of the genus Gilvimarinus, showing the highest 16S rRNA gene sequence similarity (97.7%) with the type strain of Gilvimarinus chinensis. Based on phylogenetic, genomic, chemotaxonomic and phenotypic studies, strain HB14^T was classified as a representative of a novel species in the genus Gilvimarinus, for which the name Gilvimarinus xylanilyticus sp. nov. was proposed. The type strain is HB14^T (=CCTCC AB 2022109^T = KCTC 92379^T). Four 1,3-xylanases secreted by strain HB14^T were identified based on genome and secretome analyses, and the two (Xyn65 and Xyn80) with relatively higher abundance in secretome were successfully expressed in Escherichia coli and biochemically characterized. They showed the highest activity at pH 6.0–7.0 and 40°C and released mainly 1,3-xylobiose and 1,3-xylotriose from 1,3-xylan. These data suggest that strain HB14^T acts as a player in marine 1,3-xylan degradation and recycling and that its extracellular 1,3-xylanases may have a good potential in 1,3-xylooligosaccharides preparation.

Cold-Active Enzymes and Their Potential Industrial Applications-A Review

More than 70% of our planet is covered by extremely cold environments, nourishing a broad diversity of microbial life. Temperature is the most significant parameter that plays a key role in the distribution of microorganisms on our planet. Psychrophilic microorganisms are the most prominent inhabitants of the cold ecosystems, and they possess potential cold-active enzymes with diverse uses in the research and commercial sectors. Psychrophiles are modified to nurture, replicate, and retain their active metabolic activities in low temperatures. Their enzymes possess characteristics of maximal activity at low to adequate temperatures; this feature makes them more appealing and attractive in biotechnology. The high enzymatic activity of psychrozymes at low temperatures implies an important feature for energy saving. These enzymes have proven more advantageous than their mesophilic and thermophilic counterparts. Therefore, it is very important to explore the efficiency and utility of different psychrozymes in food processing, pharmaceuticals, brewing, bioremediation, and molecular biology. In this review, we focused on the properties of cold-active enzymes and their diverse uses in different industries and research areas. This review will provide insight into the areas and characteristics to be improved in cold-active enzymes so that potential and desired enzymes can be made available for commercial purposes.

Engineering and screening of novel β-1,3-xylanases with desired hydrolysate type by optimized ancestor sequence reconstruction and data mining

•

A novel integrative strategy for engineering β-1,3-xylanases with desired products.

•

AncXyl10 is the first successful example of ASR to shift the hydrolysate types.

•

The hydrolysates of AncXyl10 was only β-1,3-xylobiose and β-1,3-xylotriose.

•

The underlying mechanism laid a new groundwork towards hydrolase engineering.

Engineering of hydrolases to shift their hydrolysate types has not been attempted so far, though computer-assisted enzyme design has been successful. A novel integrative strategy for engineering and screening the β-1,3-xylanase with desired hydrolysate types was proposed, with the purpose to solve problems that the separation and preparation of β-1,3-xylo-oligosaccharides was in high cost yet in low yield as monosaccharides existed in the hydrolysates. By classifying the hydrolysate types and coding them into numerical values, two robust mathematical models with five selected attributes from molecular docking were established based on LogitBoost and partial least squares regression with overall accuracy of 83.3% and 100%, respectively. Then, they were adopted for efficient screening the potential mutagenesis library of β-1,3-xylanases that only product oligosaccharides. The virtually designed AncXyl10 was selected and experimentally verified to produce only β-1,3-xylobiose (60.38%) and β-1,3-xylotriose (39.62%), which facilitated the preparation of oligosaccharides with high purity. The underlying mechanism of AncXyl10 may associated with the gap processing and ancestral amino acid substitution in the process of ancestral sequence reconstruction. Since many carbohydrate-active enzymes have highly conserved active sites, the strategy and their biomolecular basis will shield a new light for engineering carbohydrates hydrolase to produce specific oligosaccharides.

Biotechnological potentials of halophilic microorganisms and their impact on mankind

Background

Halophiles are extremophilic organisms represented by archaea, bacteria and eukaryotes that thrive in hypersaline environment. They apply different osmoadaptation strategies to survive in hostile conditions. Habitat diversity of halophilic microorganisms in hypersaline system provides information pertaining the evolution of life on Earth.

Main body

The microbiome-gut-brain axis interaction contributes greatly to the neurodegenerative diseases. Gut resident halophilic bacteria are used as alternative medication for chronic brain diseases. Halophiles can be used in pharmaceuticals, drug delivery, agriculture, saline waste water treatment, biodegradable plastic production, metal recovery, biofuel energy generation, concrete crack repair and other sectors. Furthermore, versatile biomolecules, mainly enzymes characterized by broad range of pH and thermostability, are suitable candidate for industrial purposes. Reflectance pattern of halophilic archaeal pigment rhodopsin is considered as potential biosignature for Earth-like planets.

Short conclusions

This review represents important osmoadaptation strategies acquired by halophilic archaea and bacteria and their potential biotechnological applications to resolve present day challenges.

Graphical Abstract

Characterization of Some Salt-Tolerant Bacterial Hydrolases with Potential Utility in Cultural Heritage Bio-Cleaning

Salt-tolerant enzymes produced by halophilic and halotolerant microorganisms have been proposed to be used in various applications that involve high saline conditions. Considering their biotechnological significance and the current need for more efficient producers of such catalysts, the present study aimed to evaluate the extracellular proteolytic, esterolytic, cellulolytic and xylanolytic activities of some halotolerant strains, and to characterize their functional parameters. A total of 21 bacterial and fungal strains belonging to the genera Bacillus, Virgibacillus, Salinivibrio, Salinicoccus, Psychrobacter, Nocardiopsis, Penicillium, Aspergillus, and Emericellopsis were assayed by quantitative methods. Among them, the members of the Bacillus genus exhibited the highest catalytic activities. The exoenzymes produced by three selected Bacillus strains were active over wide ranges of salinity, temperature and pH. Proteases were active at 20–80 °C, pH 6–10, and 0–1 M NaCl, while esterases showed good catalytic activities at 20–80 °C, pH 7.5–10, and 0–4 M NaCl. Cellulases and xylanases were active at 20–80 °C, pH 5–10, and 0–5 M NaCl. Due to such properties, these hydrolases could be used in a newly proposed application, namely to clean aged consolidants and organic deposits accumulated over time from the surfaces of salt-loaded wall paintings.

Systematic investigation of the link between enzyme catalysis and cold adaptation

Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a dominant adaptive trait of enzymes to reduced temperature, and this expectation has informed physical models for enzyme catalysis and influenced bioprospecting strategies. To systematically test rate enhancement as an adaptive trait to cold, we paired kinetic constants of 2223 enzyme reactions with their organism's optimal growth temperature (T_Growth) and analyzed trends of rate constants as a function of T_Growth. These data do not support a general increase in rate enhancement in cold adaptation. In the model enzyme ketosteroid isomerase (KSI), there is prior evidence for temperature adaptation from a change in an active site residue that results in a tradeoff between activity and stability. Nevertheless, we found that little of the rate constant variation for 20 KSI variants was accounted for by T_Growth. In contrast, and consistent with prior expectations, we observed a correlation between stability and T_Growth across 433 proteins. These results suggest that temperature exerts a weaker selection pressure on enzyme rate constants than stability and that evolutionary forces other than temperature are responsible for the majority of enzymatic rate constant variation.

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.

Highly thermostable and promiscuous β-1,3-xylanasen designed by optimized ancestral sequence reconstruction

The ancestor of β-1,3-xylanases (AncXyl09) were reconstructed by the optimized ancestral sequences reconstruction strategy to solve the poor catalytic performances of existing β-1,3-xylanases. The results showed that the half-life at 50 °C was 65.08 h, indicating good thermostability. The large number of hydrogen bonds and the disulfide bonds were the major attributes related with the thermal stability of Anxyl09. Interestingly, AncXyl09 could hydrolyze lichen besides the original substrate of β-1, 3-xylan, which is the first reported β-1,3-xylanase with substrate promiscuity. Moreover, the hydrolytic products are mainly disaccharides, the content of β-1,3-xylobiose and lichoridiose more than 70% as determined by high performance liquid chromatography (HPLC), which could significantly facilitate the separation and purification of oligosaccharides. The successful design of AncXyl09 was the representative of the semi-rationally engineered β-1, 3-xylanase, which will shield a new light on the β-1,3-xylanase engineering, active oligosaccharide preparation and marine algae resource utilization.

Diversity of Marine 1,3-Xylan-Utilizing Bacteria and Characters of Their Extracellular 1,3-Xylanases

1,3-xylan is present in the cell walls of some red and green algae and is an important organic carbon in the ocean. However, information on its bacterial degradation is quite limited. Here, after enrichment with 1,3-xylan, the diversity of bacteria recovered from marine algae collected in Hainan, China, was analyzed with both the 16S rRNA gene amplicon sequencing and the culture-dependent method. Bacteria recovered were affiliated with more than 19 families mainly in phyla Proteobacteria and Bacteroidetes, suggesting a high bacterial diversity. Moreover, 12 strains with high 1,3-xylanase-secreting ability from genera Vibrio, Neiella, Alteromonas, and Gilvimarinus were isolated from the enrichment culture. The extracellular 1,3-xylanases secreted by Vibrio sp. EA2, Neiella sp. GA3, Alteromonas sp. CA13-2, and Gilvimarinus sp. HA3-2, which were taken as representatives due to their efficient utilization of 1,3-xylan for growth, were further characterized. The extracellular 1,3-xylanases secreted by these strains showed the highest activity at pH 6.0–7.0 and 30–40°C in 0–0.5M NaCl, exhibiting thermo-unstable and alkali-resistant characters. Their degradation products on 1,3-xylan were mainly 1,3-xylobiose and 1,3-xylotriose. This study reveals the diversity of marine bacteria involved in the degradation and utilization of 1,3-xylan, helpful in our understanding of the recycling of 1,3-xylan driven by bacteria in the ocean and the discovery of novel 1,3-xylanases.

Endo-xylanases from Cohnella sp. AR92 aimed at xylan and arabinoxylan conversion into value-added products

The genus Cohnella belongs to a group of Gram-positive endospore-forming bacteria within the Paenibacillaceae family. Although most species were described as xylanolytic bacteria, the literature still lacks some key information regarding their repertoire of xylan-degrading enzymes. The whole genome sequence of an isolated xylan-degrading bacterium Cohnella sp. strain AR92 was found to contain five genes encoding putative endo-1,4-β-xylanases, of which four were cloned, expressed, and characterized to better understand the contribution of the individual endo-xylanases to the overall xylanolytic properties of strain AR92. Three of the enzymes, CoXyn10A, CoXyn10C, and CoXyn11A, were shown to be effective at hydrolyzing xylans-derived from agro-industrial, producing oligosaccharides with substrate conversion values of 32.5%, 24.7%, and 10.6%, respectively, using sugarcane bagasse glucuronoarabinoxylan and of 29.9%, 19.1%, and 8.0%, respectively, using wheat bran-derived arabinoxylan. The main reaction products from GH10 enzymes were xylobiose and xylotriose, whereas CoXyn11A produced mostly xylooligosaccharides (XOS) with 2 to 5 units of xylose, often substituted, resulting in potentially prebiotic arabinoxylooligosaccharides (AXOS). The endo-xylanases assay displayed operational features (temperature optima from 49.9 to 50.4 °C and pH optima from 6.01 to 6.31) fitting simultaneous xylan utilization. Homology modeling confirmed the typical folds of the GH10 and GH11 enzymes, substrate docking studies allowed the prediction of subsites (- 2 to + 1 in GH10 and - 3 to + 1 in GH11) and identification of residues involved in ligand interactions, supporting the experimental data. Overall, the Cohnella sp. AR92 endo-xylanases presented significant potential for enzymatic conversion of agro-industrial by-products into high-value products.Key points• Cohnella sp. AR92 genome encoded five potential endo-xylanases.• Cohnella sp. AR92 enzymes produced xylooligosaccharides from xylan, with high yields.• GH10 enzymes from Cohnella sp. AR92 are responsible for the production of X2 and X3 oligosaccharides.• GH11 from Cohnella sp. AR92 contributes to the overall xylan degradation by producing substituted oligosaccharides.

Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment

Gram-stain-negative, strictly aerobic, non-spore-forming, non-motile, and rod-shaped bacterial strains, designated NC18^T and NC20, were isolated from the sediment near-vertical borehole effluent originating 714 m below the subsurface located in the Soudan Iron Mine in Minnesota, USA. The 16S rRNA gene sequence showed that strains NC18^T and NC20 grouped with members of the genus Martelella, including M. mediterranea DSM 17316^T and M. limonii YC7034^T. The genome sizes and G + C content of both NC18^T and NC20 were 6.1 Mb and 61.8 mol%, respectively. Average nucleotide identity (ANI), the average amino acid identity (AAI), and digital DNA–DNA hybridization (dDDH) values were below the species delineation threshold. Pan-genomic analysis showed that NC18^T, NC20, M. mediterranea DSM 17316^T, M. endophytica YC6887^T, and M. lutilitoris GH2-6^T had 8470 pan-genome orthologous groups (POGs) in total. Five Martelella strains shared 2258 POG core, which were mainly associated with amino acid transport and metabolism, general function prediction only, carbohydrate transport and metabolism, translation, ribosomal structure and biogenesis, and transcription. The two novel strains had major fatty acids (>5%) including summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C19:0 cyclo ω8c, C16:0, C18:1 ω7c 11-methyl, C18:0, and summed feature 2 (C12:0 aldehyde and/or iso-C16:1 I and/or C14:0 3-OH). The sole respiratory quinone was uniquinone-10 (Q-10). On the basis of polyphasic taxonomic analyses, strains NC18^T and NC20 represent novel species of the genus Martelella, for which the name Martelella soudanensis sp. nov. is proposed. The type strain is NC18^T (=KTCT 82174^T = NBRC 114661^T).

Biotechnological Aspects of Salt-Tolerant Xylanases: A Review

β-1,4-Xylan is the main component of hemicelluloses in land plant cell walls, whereas β-1,3-xylan is widely found in seaweed cell walls. Complete hydrolysis of xylan requires a series of synergistically acting xylanases. High-saline environments, such as saline-alkali lands and oceans, frequently occur in nature and are also involved in a broad range of various industrial processes. Thus, salt-tolerant xylanases may contribute to high-salt and marine food processing, aquatic feed production, industrial wastewater treatment, saline-alkali soil improvement, and global carbon cycle, with great commercial and environmental benefits. This review mainly introduces the definition, sources, classification, biochemical and molecular characteristics, adaptation mechanisms, and biotechnological applications of salt-tolerant xylanases. The scope of development for salt-tolerant xylanases is also discussed. It is anticipated that this review would serve as a reference for further development and utilization of salt-tolerant xylanases and other salt-tolerant enzymes.

A novel all-in-one strategy for purification and immobilization of β-1,3-xylanase directly from cell lysate as active and recyclable nanobiocatalyst

BACKGROUND

Exploring a simple and versatile technique for direct immobilization of target enzymes from cell lysate without prior purification is urgently needed. Thus, a novel all-in-one strategy for purification and immobilization of β-1,3-xylanase was proposed, the target enzymes were covalently immobilized on silica nanoparticles via elastin-like polypeptides (ELPs)-based biomimetic silicification and SpyTag/SpyCatcher spontaneous reaction. Thus, the functional carriers that did not require the time-consuming surface modification step were quickly and efficiently prepared. These carriers could specifically immobilize the SpyTag-fused target enzymes from the cell lysate without pre-purification.

RESULTS

The ELPs-SpyCatcher hardly leaked from the carriers (0.5%), and the immobilization yield of enzyme was up to 96%. Immobilized enzyme retained 85.6% of the initial activity and showed 88.6% of the activity recovery. Compared with free ones, the immobilized β-1,3-xylanase showed improved thermal stability, elevated storage stability and good pH tolerance. It also retained more than 70.6% of initial activity after 12 reaction cycles, demonstrating its excellent reusability.

CONCLUSIONS

The results clearly highlighted the effectiveness of the novel enzyme immobilization method proposed here due to the improvement of overall performance of immobilized enzyme in respect to free form for the hydrolysis of macromolecular substrates. Thus, it may have great potential in the conversion of algae biomass as well as other related fields.

Bioprospecting for Novel Halophilic and Halotolerant Sources of Hydrolytic Enzymes in Brackish, Saline and Hypersaline Lakes of Romania

Halophilic and halotolerant microorganisms represent promising sources of salt-tolerant enzymes that could be used in various biotechnological processes where high salt concentrations would otherwise inhibit enzymatic transformations. Considering the current need for more efficient biocatalysts, the present study aimed to explore the microbial diversity of five under- or uninvestigated salty lakes in Romania for novel sources of hydrolytic enzymes. Bacteria, archaea and fungi were obtained by culture-based approaches and screened for the production of six hydrolases (protease, lipase, amylase, cellulase, xylanase and pectinase) using agar plate-based assays. Moreover, the phylogeny of bacterial and archaeal isolates was studied through molecular methods. From a total of 244 microbial isolates, 182 (74.6%) were represented by bacteria, 22 (9%) by archaea, and 40 (16.4%) by fungi. While most bacteria synthesized protease and lipase, the most frequent hydrolase produced by fungi was pectinase. The archaeal isolates had limited hydrolytic activity, being able to produce only amylase and cellulase. Among the taxonomically identified isolates, the best hydrolytic activities were observed in halotolerant bacteria belonging to the genus Bacillus and in extremely halophilic archaea of the genera Haloterrigena and Halostagnicola. Therefore, the present study highlights that the investigated lakes harbor various promising species of microorganisms able to produce industrially valuable enzymes.

Cloning, expression and characterization of C. crescentus xynA2 gene and application of Xylanase II in the deconstruction of plant biomass

Biotechnology offers innovative alternatives for industrial bioprocesses mainly because it uses enzymes that biodegrade the hemicellulose releasing fermentable sugars. Caulobacter crescentus (C. crescentus) has seven genes responsible for xylanolytic cleavage, 5 to β-xylosidases (EC 3.2.1.37) and 2 for endoxylanases, like xynA2 (CCNA_03137) that encodes Xylanase II (EC 3.2.1.8) of the glycohydrolases-GH10 group. The xynA2 gene was amplified by PCR, cloned into the pTrcHisA vector e efficiently overexpressed in E. coli providing a His-tag fusion protein. Recombinant xylanase (XynA2) was purified by affinity chromatography using a nickel sepharose column and exhibited a single 43 kDa band on SDS-PAGE gel. XynA2 showed an optimum alkaline pH (8) and stability at alkaline pH for 24 h. Although C. crescentus is mesophilic, XynA2 has optimum temperature of 60 °C and is thermo-resistance at 65 °C. XynA maintains 66% of the enzymatic activity at high temperatures (90 °C) without being denatured.The enzyme displayed a xylanolitic activity free of cellulase to xylan from beechwood and it was not inhibited in the presence of 50 μmol mL^-1 of xylose. In addition, dithiothreitol (DTT) induced XynA2 activity, as it improved its kinetic parameters by lowering the K_M (5.78 μmol mL^-1) and increasing the K_Cat/K_M ratio (1.63 U s^-1). Finally, C. crescentus XynA2 efficiently hydrolyzed corn straw with high release of reducing sugars that can be applied in different branches of the industry.

Enzymatic degradation of algal 1,3-xylan: from synergism of lytic polysaccharide monooxygenases with β-1,3-xylanases to their intelligent immobilization on biomimetic silica nanoparticles

Lytic polysaccharide monooxygenases (LPMOs) with synergistic effect on polysaccharide hydrolase represent a revolution in biotechnology, which may accelerate the conversion of biomass to the second-generation biofuels. Discovering more hydrolases that have synergism with LPMOs will considerably expand the knowledge and application of biomass degradation. The LPMOs named CgAA9 were verified to exhibit 1.52-fold synergism when incubated with β-1,3-xylanase at a molar ratio of 3:1. The ion chromatography results proved that CgAA9 did not alter the endogenous hydrolysis mode of β-1,3-xylanase. Meanwhile, to decrease the operational cost of enzymes, a novel strategy for immobilizing LPMOs and β-1,3-xylanases based on the biomimetic silica nanoparticles was developed. It enabled preparation of immobilized enzymes directly from the cell lysate. The immobilization efficiency and activity recovery reached 84.6 and 81.4%. They showed excellent reusability for 12 cycles by retaining 68% of initial activity. The optimum temperature for both free and immobilized biocatalyst were 40 and 37 °C, indicating they were ideal candidates for typical simultaneous saccharification and fermentation (SSF) in ethanol production from algea biomass. This was the first report on the synergy between LPMOs and β-1,3-xylanase, and the strategy for enzyme self-immobilization was simple, timesaving, and efficient, which might have great potentials in algae biomass hydrolysis. KEY POINTS: • The lytic polysaccharide monooxygenases (LPMOs) from Chaetomium globosum were firstly verified to boost the hydrolysis of β-1,3-xylanases for β-1,3-xylan. • A novel strategy for simple preparation of SpyCather-modifed silica nanopartilcles and intelligent immobilization of target enzymes from the cell lysate was proposed. • The immobilized LPMOs and β-1,3-xylanases could be reasonable alternatives for typical simultaneous saccharification and fermentation (SSF) in manipulation of algae biomass.

Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review

The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.

Halophiles and Their Vast Potential in Biofuel Production

Global warming and the limitations of using fossil fuels are a main concern of all societies, and thus, the development of alternative fuel sources is crucial to improving the current global energy situation. Biofuels are known as the best alternatives of unrenewable fuels and justify increasing extensive research to develop new and less expensive methods for their production. The most frequent biofuels are bioethanol, biobutanol, biodiesel, and biogas. The production of these biofuels is the result of microbial activity on organic substrates like sugars, starch, oil crops, non-food biomasses, and agricultural and animal wastes. Several industrial production processes are carried out in the presence of high concentrations of NaCl and therefore, researchers have focused on halophiles for biofuel production. In this review, we focus on the role of halophilic microorganisms and their current utilization in the production of all types of biofuels. Also, the outstanding potential of them and their hydrolytic enzymes in the hydrolysis of different kind of biomasses and the production of biofuels are discussed.

Discovery of a novel ortho-haloacetophenones-specific carbonyl reductase from Bacillus aryabhattai and insight into the molecular basis for its catalytic performance

To exploit robust biocatalysts for chiral 1-(2-halophenyl)ethanols synthesis, an ortho-haloacetophenones-specific carbonyl reductase (BaSDR1) gene from Bacillus aryabhattai was cloned and expressed in Escherichia coli. The impressive properties regarding BaSDR1 application include preference for NADH as coenzyme, noticeable tolerance against high cosubstrate concentration, and remarkable catalytic performance over a broad pH range from 5.0 to 10.0. The optimal temperature was 35 °C, with a half-life of 3.1 h at 35 °C and 0.75 h at 45 °C, respectively. Notably, BaSDR1 displayed excellent catalytic performance toward various ortho-haloacetophenones, providing chiral 1-(2-halophenyl)ethanols with 99% ee for all the substrates tested. Most importantly, the docking results indicated that the enzyme-substrate interactions and the steric hindrance of halogen atoms act in a push-pull manner in regulating enzyme catalytic ability. These results provide valuable clues for the structure-function relationships of BaSDR1 and the role of halogen groups in catalytic performance, and offer important reference for protein engineering and mining of functional compounds.

Characterizing a Halo-Tolerant GH10 Xylanase from Roseithermus sacchariphilus Strain RA and Its CBM-Truncated Variant

A halo-thermophilic bacterium, Roseithermus sacchariphilus strain RA (previously known as Rhodothermaceae bacterium RA), was isolated from a hot spring in Langkawi, Malaysia. A complete genome analysis showed that the bacterium harbors 57 glycoside hydrolases (GHs), including a multi-domain xylanase (XynRA2). The full-length XynRA2 of 813 amino acids comprises a family 4_9 carbohydrate-binding module (CBM4_9), a family 10 glycoside hydrolase catalytic domain (GH10), and a C-terminal domain (CTD) for type IX secretion system (T9SS). This study aims to describe the biochemical properties of XynRA2 and the effects of CBM truncation on this xylanase. XynRA2 and its CBM-truncated variant (XynRA2ΔCBM) was expressed, purified, and characterized. The purified XynRA2 and XynRA2ΔCBM had an identical optimum temperature at 70 °C, but different optimum pHs of 8.5 and 6.0 respectively. Furthermore, XynRA2 retained 94% and 71% of activity at 4.0 M and 5.0 M NaCl respectively, whereas XynRA2ΔCBM showed a lower activity (79% and 54%). XynRA2 exhibited a turnover rate (k_cat) of 24.8 s⁻¹, but this was reduced by 40% for XynRA2ΔCBM. Both the xylanases hydrolyzed beechwood xylan predominantly into xylobiose, and oat-spelt xylan into a mixture of xylo-oligosaccharides (XOs). Collectively, this work suggested CBM4_9 of XynRA2 has a role in enzyme performance.