A high-molecular-weight, alkaline, and thermostable β-1,4-xylanase of a subseafloor Microcella alkaliphila

High-Molecular-Weight Xylanase from B. pumilus US570 Strain: Purification, Characterization and Application in Banana and Orange Peels Hydrolysis and Breadmaking

New xylanase (XylUS570) was purified from the Bacillus pumilus US570 strain. It has a molecular mass of about 232 kDa. This is the first report on the highest molecular weight monomeric xylanase produced by bacteria. The optimum pH and temperature recorded for enzyme activity were 7 and 55 °C, respectively with a half-life time of 10 min at 60 °C. At 37 °C, the enzyme retains more than 50% of its activity at a pH ranging from 6 to 9.5 for 24 h. The XylUS570 exhibited a high activity on xylan, but no activity was detected for cellulosic substrates. The Vmax and Km values exhibited by the purified enzyme on beechwood xylan were 37.05 U mL-1 and 4.189 mg mL-1, respectively. The XylUS570 was used in banana and orange peels hydrolysis and showed potential efficiency to liberate reducing sugars. It could be a good candidate for bio-ethanol production from fruit waste. The purified enzyme was used also as an additive in breadmaking. A decrease in water absorption, an increase in dough rising and improvements in volume and specific volume of the bread were recorded.

Glycoside hydrolases in the biodegradation of lignocellulosic biomass

Lignocellulose is a plentiful and intricate biomass substance made up of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are polysaccharides characterized by different compositions and degrees of polymerization. As renewable resources, their applications are eco-friendly and can help reduce reliance on petrochemical resources. This review aims to illustrate cellulose, hemicellulose, and their structures and hydrolytic enzymes. To obtain desirable enzyme sources for the high hydrolysis of lignocellulose, highly stable, efficient and thermophilic enzyme sources, and new technologies, such as rational design and machine learning, have been introduced in detail. Generally, the efficient biodegradation of abundant natural biomass into fermentable sugars or other intermediates has great potential in practical applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03819-1.

Enzymatic characterization of a novel thermostable and alkaline tolerant GH10 xylanase and activity improvement by multiple rational mutagenesis strategies

Thermo-alkaline xylanases are widely applied in paper pulping industry. In this study, a novel thermostable and alkaline tolerant GH10 xylanase (Xyn30Y5) gene from alkaliphilic Bacillus sp. 30Y5 was cloned and the surface-layer homology (SLH) domains truncated enzyme (Xyn30Y5-SLH) was expressed in Escherichia coli. The purified Xyn30Y5-SLH was most active at 70 °C and pH 7.0 and showed the highest specific activity of 349.4 U mg^-1. It retained more than 90% activity between pH 6.0 to 9.5 and was stable at pH 6.0-10.0. To improve the activity, 47 mutants were designed based on eight rational strategies and 21 mutants showed higher activity. By combinatorial mutagenesis, the best mutant 3B demonstrated specific activity of 1016.8 U mg^-1 with a doubled catalytic efficiency (k_cat/K_m) and RA60_1/2h value, accompanied by optimal pH shift to 8.0. The molecular dynamics simulation analysis indicated that the increase of flexibility of α5 helix and loop7 located near to the catalytic residues is likely responsible for its activity improvement. And the decrease of flexibility of the most unstable regions is vital for the thermostablity improvement. This work provided not only a novel thermostable and alkaline tolerant xylanase with industrial application potential but also an effective mutagenesis strategy for xylanase activity improvement.

Xylanolytic Extremozymes Retrieved From Environmental Metagenomes: Characteristics, Genetic Engineering, and Applications

Xylanolytic enzymes have extensive applications in paper, food, and feed, pharmaceutical, and biofuel industries. These industries demand xylanases that are functional under extreme conditions, such as high temperature, acidic/alkaline pH, and others, which are prevailing in bioprocessing industries. Despite the availability of several xylan-hydrolyzing enzymes from cultured microbes, there is a huge gap between what is available and what industries require. DNA manipulations as well as protein-engineering techniques are also not quite satisfactory in generating xylan-hydrolyzing extremozymes. With a compound annual growth rate of 6.6% of xylan-hydrolyzing enzymes in the global market, there is a need for xylanolytic extremozymes. Therefore, metagenomic approaches have been employed to uncover hidden xylanolytic genes that were earlier inaccessible in culture-dependent approaches. Appreciable success has been achieved in retrieving several unusual xylanolytic enzymes with novel and desirable characteristics from different extreme environments using functional and sequence-based metagenomic approaches. Moreover, the Carbohydrate Active Enzymes database includes approximately 400 GH-10 and GH-11 unclassified xylanases. This review discusses sources, characteristics, and applications of xylanolytic enzymes obtained through metagenomic approaches and their amelioration by genetic engineering techniques.

Alkaline Active Hemicellulases

Xylan and mannan are the two most abundant hemicelluloses, and enzymes that modify these polysaccharides are prominent hemicellulases with immense biotechnological importance. Among these enzymes, xylanases and mannanases which play the vital role in the hydrolysis of xylan and mannan, respectively, attracted a great deal of interest. These hemicellulases have got applications in food, feed, bioethanol, pulp and paper, chemical, and beverage producing industries as well as in biorefineries and environmental biotechnology. The great majority of the enzymes used in these applications are optimally active in mildly acidic to neutral range. However, in recent years, alkaline active enzymes have also become increasingly important. This is mainly due to some benefits of utilizing alkaline active hemicellulases over that of neutral or acid active enzymes. One of the advantages is that the alkaline active enzymes are most suitable to applications that require high pH such as Kraft pulp delignification, detergent formulation, and cotton bioscouring. The other benefit is related to the better solubility of hemicelluloses at high pH. Since the efficiency of enzymatic hydrolysis is often positively correlated to substrate solubility, the hydrolysis of hemicelluloses can be more efficient if performed at high pH. High pH hydrolysis requires the use of alkaline active enzymes. Moreover, alkaline extraction is the most common hemicellulose extraction method, and direct hydrolysis of the alkali-extracted hemicellulose could be of great interest in the valorization of hemicellulose. Direct hydrolysis avoids the time-consuming extensive washing, and neutralization processes required if non-alkaline active enzymes are opted to be used. Furthermore, most alkaline active enzymes are relatively active in a wide range of pH, and at least some of them are significantly or even optimally active in slightly acidic to neutral pH range. Such enzymes can be eligible for non-alkaline applications such as in feed, food, and beverage industries.This chapter largely focuses on the most important alkaline active hemicellulases, endo-β-1,4-xylanases and β-mannanases. It summarizes the relevant catalytic properties, structural features, as well as the real and potential applications of these remarkable hemicellulases in textile, paper and pulp, detergent, feed, food, and prebiotic producing industries. In addition, the chapter depicts the role of these extremozymes in valorization of hemicelluloses to platform chemicals and alike in biorefineries. It also reviews hemicelluloses and discusses their biotechnological importance.

A New Group of Modular Xylanases in Glycoside Hydrolase Family 8 from Marine Bacteria

Xylanases play a crucial role in the degradation of xylan in both terrestrial and marine environments. The endoxylanase XynB from the marine bacterium Glaciecola mesophila KMM 241 is a modular enzyme comprising a long N-terminal domain (NTD) (E44 to T562) with xylan-binding ability and a catalytic domain (CD) (T563 to E912) of glycoside hydrolase family 8 (GH8). In this study, the long NTD is confirmed to contain three different functional regions, which are NTD1 (E44 to D136), NTD2 (Y137 to A193), and NTD3 (L194 to T562). NTD1, mainly composed of eight β-strands, functions as a new type of carbohydrate-binding module (CBM), which has xylan-binding ability but no sequence similarity to any known CBM. NTD2, mainly forming two α-helices, contains one of the α-helices of the catalytic domain's (α/α)₆ barrel and therefore is essential for the activity of XynB, although it is far away from the catalytic domain in sequence. NTD3, next to the catalytic domain in sequence, is shown to be helpful in maintaining the thermostability of XynB. Thus, XynB represents a kind of xylanase with a new domain architecture. There are four other predicted glycoside hydrolase sequences with the same domain architecture and high sequence identity (≥80%) with XynB, all of which are from marine bacteria. Phylogenetic analysis shows that XynB and these homologs form a new group in GH8, representing a new class of marine bacterial xylanases. Our results shed light on xylanases, especially marine xylanases.IMPORTANCE Xylanases play a crucial role in natural xylan degradation and have been extensively used in industries such as food processing, animal feed, and kraft pulp biobleaching. Some marine bacteria have been found to secrete xylanases. Characterization of novel xylanases from marine bacteria has significance for both the clarification of xylan degradation mechanisms in the sea and the development of new enzymes for industrial application. With G. mesophila XynB as a representative, this study reveals a new group of the GH8 xylanases from marine bacteria, which have a distinct domain architecture and contain a novel carbohydrate-binding module. Thus, this study offers new knowledge on marine xylanases.

Xylanase production from marine derived Trichoderma pleuroticola 08ÇK001 strain isolated from Mediterranean coastal sediments

Xylanases constitutes one the most important enzymes with diverse applications in different industries such as bioethanol production, animal feedstock production, production of xylo-oligosaccharides, baking industry, paper and pulp industry, xylitol production, fruit juice, and beer finishing, degumming, and agriculture. Currently, industrial xylanases are mainly produced by Aspergillus and Trichoderma members. Since the marine environments are less studied compared to terrestrial environments and harbors great microbial diversity we aimed to investigate the xylanase production of 88 marine-derived filamentous fungal strains. These strains are semi-quantitatively screened for their extracellular xylanase production and Trichoderma pleuroticola 08ÇK001 xylanase activity was further characterized. Optimum pH and temperature was determined as 5.0 and 50 °C, respectively. The enzyme preparation retained 53% of its activity at pH 5.0 after 1 h and have found resistant against several ions and compounds such as K⁺ , Ba²⁺ , Na⁺ , β-mercaptoethanol, Triton X-100 and toluene. This study demonstrates that marine-derived fungal strains are prolific sources for xylanase production and presents the first report about the production and characterization of xylanase from a marine derived T. pleuroticola strain. The characteristics of T. pleuroticola 08ÇK001 xylanase activity indicate possible employment in some industrial processes such as animal feed, juice and wine industries or paper pulping applications.

A Novel Multi-domain High Molecular, Salt-Stable Alkaline Xylanase from Alkalibacterium sp. SL3

A novel multi-domain high molecular xylanase coding gene (xynSL3) was cloned from Alkalibacterium sp. SL3, an alkaliphilic bacterial strain isolated from the sediment of soda lake Dabusu. The deduced XynSL3 is composed of a putative signal peptide, three tandem domains of carbohydrate binding module (CBM) family 22, a catalytic domain of glycosyl hydrolase (GH) family 10 and a domain of CBM9. XynSL3 shares the highest identity of 66% to a hypothetical protein from Alkalibacterium sp. AK22 and has low identities (33-45%) with other functionally characterized xylanases. The gene xynSL3 was expressed heterologously in Escherichia coli and the recombinant enzyme demonstrated some particular characteristics. Purified recombinant XynSL3 (rXynSL3) was highly active and stable over the neutral and alkaline pH ranges from 7.0 to 12.0, with maximum activity at pH 9.0 and around 45% activity at pH 12.0. It had an apparent temperature optimum of 55°C and was stable at 50°C. The rXynSL3 was highly halotolerant, retaining more than 60% activity with 3 M NaCl and was stable at up to a 4 M concentration of NaCl. The hydrolysis products of rXynSL3 from corncob xylan were mainly xylobiose and xylotetraose. The activity of rXynSL3 was enhanced by Ca²⁺ and it has strong resistance to sodium dodecyl sulfate (SDS). This multi-domain, alkaline and salt-tolerant enzyme has great potential for basic research and industrial applications such as the biobleaching of paper pulp and production of xylo-oligosaccharides (XOS).