Overproduction and characterization of a lytic polysaccharide monooxygenase in Bacillus subtilis using an assay based on ascorbate consumption

Chitin Biodegradation by Lytic Polysaccharide Monooxygenases from Streptomyces coelicolor In Vitro and In Vivo

Lytic polysaccharide monooxygenases (LPMOs) have the potential to improve recalcitrant polysaccharide hydrolysis by the oxidizing cleavage of glycosidic bond. Streptomyces species are major chitin decomposers in soil ecological environments and encode multiple lpmo genes. In this study, we demonstrated that transcription of the lpmo gene, Sclpmo10G, in the Streptomyces coelicolor A3(2) (ScA3(2)) strain is strongly induced by chitin. The ScLPMO10G protein was further expressed in Escherichia coli and characterized in vitro. The ScLPMO10G protein showed oxidation activity towards chitin. Chitinase synergy experiments demonstrated that the addition of ScLPMO10G resulted in a substantial in vitro increase in the reducing sugar levels. Moreover, in vivo the LPMO-overexpressing strain ScΔLPMO10G(+) showed stronger chitin-degrading ability than the wild-type, leading to a 2.97-fold increase in reducing sugar level following chitin degradation. The total chitinase activity of ScΔLPMO10G(+) was 1.5-fold higher than that of ScA3(2). In summary, ScLPMO10G may play a role in chitin biodegradation in S. coelicolor, which could have potential applications in biorefineries.

Lytic polysaccharide monooxygenase - A new driving force for lignocellulosic biomass degradation

Lytic polysaccharide monooxygenases (LPMOs) can catalyze polysaccharides by oxidative cleavage of glycosidic bonds and have catalytic activity for cellulose, hemicellulose, chitin, starch and pectin, thus playing an important role in the biomass conversion of lignocellulose. The catalytic substrates of LPMOs are different and the specific catalytic mechanism has not been fully elucidated. Although there have been many studies related to LPMOs, few have actually been put into industrial biomass conversion, which poses a challenge for their expression, regulation and application. In this review, the origin, substrate specificity, structural features, and the relationship between structure and function of LPMOs are described. Additionally, the catalytic mechanism and electron donor of LPMOs and their heterologous expression and regulation are discussed. Finally, the synergistic degradation of biomass by LPMOs with other polysaccharide hydrolases is reviewed, and their current problems and future research directions are pointed out.

Lytic polysaccharide monooxygenase (LPMO)-derived saccharification of lignocellulosic biomass

Given that traditional biorefineries have been based on microbial fermentation to produce useful fuels, materials, and chemicals as metabolites, saccharification is an important step to obtain fermentable sugars from biomass. It is well-known that glycosidic hydrolases (GHs) are responsible for the saccharification of recalcitrant polysaccharides through hydrolysis, but the discovery of lytic polysaccharide monooxygenase (LPMO), which is a kind of oxidative enzyme involved in cleaving polysaccharides and boosting GH performance, has profoundly changed the understanding of enzyme-based saccharification. This review briefly introduces the classification, structural information, and catalytic mechanism of LPMOs. In addition to recombinant expression strategies, synergistic effects with GH are comprehensively discussed. Challenges and perspectives for LPMO-based saccharification on a large scale are also briefly mentioned. Ultimately, this review can provide insights for constructing an economically viable lignocellulose-based biorefinery system and a closed-carbon loop to cope with climate change.

Isolation of Chitinolytic Bacteria from European Sea Bass Gut Microbiota Fed Diets with Distinct Insect Meals

Simple Summary

The ever-growing human population is increasingly demanding more fish. As a response, aquaculture has become the fastest growing industry in its sector. Alternatives to fish meal, an unsustainable commodity used as the main protein source for carnivorous species, are urgently needed in aquafeeds. Recently, in Europe, seven insect species have been approved as potential ingredients for animal feeds, including fish feed. However, chitin, one of the components of an insect’s exoskeleton, is indigestible for several economically valuable fish species, decreasing fish performance upon inclusion. This work aimed to isolate, from the European sea bass gastrointestinal tract, probiotic bacteria capable of producing chitinases to improve the use of diets containing high levels of insect meal. Based on the enhanced adaptability of gut microbial communities and the selective pressure of chitin-enriched diets on fish gut microbiota, bacteria were first isolated from the gastrointestinal tract of European sea bass fed chitin-enriched diets. Isolates were then comprehensively screened in vitro for important traits such as their ability to utilize chitin, gut-survival aptitude, and biosafety-related issues required to be considered eligible as probiotics by the European Food Safety Authority (EFSA).

Abstract

Insect meal (IM), recently authorized for use in aquafeeds, positions itself as a promising commodity for aquafeed inclusion. However, insects are also rich in chitin, a structural polysaccharide present in the exoskeleton, which is not digested by fish, resulting in lower fish performance. Through the application of a dietary pressure, this study aimed to modulate European sea bass gut microbiota towards the enrichment of chitinolytic bacteria to allow the isolation of novel probiotics capable of improving the use of IM-containing diets, overcoming chitin drawbacks. Five isoproteic (44%) and isolipidic (18%) diets were used: a fish meal (FM)-based diet (diet CTR), a chitin-supplemented diet (diet CHIT5), and three diets with either 25% of Hermetia illucens and Tenebrio molitor larvae meals (HM25 and TM25, respectively) or H. illucens exuviae meal (diet HEM25) as partial FM substitutes. After an 8-week feeding trial, the results showed a clear modulatory effect towards spore-forming bacteria by HM25 and HEM25 diets, with the latter being responsible for the majority of the chitinolytic fish isolates (FIs) obtained. Sequential evaluation of the FI hemolytic activity, antibiotic resistance, total chitinolytic activity, sporulation, and survival in gastrointestinal-like conditions identified FI645 and FI658 as the most promising chitinolytic probiotics for in vivo application.

Heterologous expression and characterization of a novel lytic polysaccharide monooxygenase from Natrialbaceae archaeon and its application for chitin biodegradation

Lytic polysaccharide monooxygenases could enhance the enzymatic conversion of recalcitrant polysaccharides by glycoside hydrolases. This study reports the expression and identification of a novel AA10 LPMO from Natrialbaceae archaeon, named NaLPMO10A, as a C1 oxidizer of chitin. The optimal temperature and pH for NaLPMO10A activity were 40 °C and 9.0, respectively, and NaLPMO10A exhibited high thermostability and pH stability under alkaline conditions. NaLPMO10A was also highly tolerant and stable when treated with high concentration of metal ions (1 M). Moreover, metal ions (Na⁺, K⁺, Ca²⁺ and Mg²⁺) significantly promoted NaLPMO10A activity and improved the saccharification efficiency of chitin by 22.6%, 45.9%, 36.7% and 53.9%, respectively, compared to commercial chitinase alone. Together, the findings of this study fill a gap in archaeal LPMO research, and for the first time demonstrate that archaeal NaLPMO10A could be a promising enzyme for improving saccharification under extreme condition, with potential applications in biorefineries.

The ProUSER2.0 Toolbox: Genetic Parts and Highly Customizable Plasmids for Synthetic Biology in Bacillus subtilis

Versatile DNA assembly standards and compatible, well-characterized part libraries are essential tools for creating effective designs in synthetic biology. However, to date, vector standards for Gram-positive hosts have limited flexibility. As a result, users often revert to PCR-based methods for building the desired genetic constructs. These methods are inherently prone to introducing mutations, which is problematic considering vector backbone parts are often left unsequenced in cloning workflows. To circumvent this, we present the ProUSER2.0 toolbox: a standardized vector platform for building both integrative and replicative shuttle vectors forBacillus subtilis. The ProUSER2.0 vectors consist of a ProUSER cassette for easy and efficient insertion of cargo sequences and six exchangeable modules. Furthermore, the standard is semicompatible with several previously developed standards, allowing the user to utilize the parts developed for these. To provide parts for the toolbox, seven novel integration sites and six promoters were thoroughly characterized in B. subtilis. Finally, the capacity of the ProUSER2.0 system was demonstrated through the construction of signal peptide libraries for two industrially relevant proteins. Altogether, the ProUSER2.0 toolbox is a powerful and flexible framework for use in B. subtilis.

LyGo: A Platform for Rapid Screening of Lytic Polysaccharide Monooxygenase Production

Environmentally friendly sources of energy and chemicals are essential constituents of a sustainable society. An important step toward this goal is the utilization of biomass to supply building blocks for future biorefineries. Lytic polysaccharide monooxygenases (LPMOs) are enzymes that play a critical role in breaking the chemical bonds in the most abundant polymers found in recalcitrant biomass, such as cellulose and chitin. To use them in industrial processes they need to be produced in high titers in cell factories. Predicting optimal strategies for producing LPMOs is often nontrivial, and methods allowing for screening several strategies simultaneously are therefore needed. Here, we present a standardized platform for cloning LPMOs. The platform allows users to combine gene fragments with 14 different expression vectors in a simple 15 min reaction, thus enabling rapid exploration of several gene contexts, hosts, and expression strategies in parallel. The open-source LyGo platform is accompanied by easy-to-follow online protocols for both cloning and expression. As a demonstration of its utility, we explore different strategies for expressing several different LPMOs in Escherichia coli, Bacillus subtilis, and Komagataella phaffii.

Identification and characterization of a novel AA9-type lytic polysaccharide monooxygenase from a bagasse metagenome

Lytic polysaccharide monooxygenases (LPMOs) are auxiliary enzymes catalyzing oxidative cleavages of cellulose chains in crystalline regions, resulting in their increasing accessibility to the hydrolytic enzyme counterparts and hence higher released sugars from biomass saccharification. In this study, a novel auxiliary protein family 9 LPMO (BgAA9) was identified from a metagenomic library derived from a thermophilic microbial community in bagasse collection site where diverse AA9 and AA10 putative sequences were annotated. The enzyme showed highest similarity to a glycoside hydrolase family 61 from Chaetomium thermophilum. Recombinant BgAA9 expressed in Pichia pastoris cleaved cellohexaose (DP6) into shorter cellooligosaccharides (DP2, DP3, and DP4). Supplementation BgAA9 to a commercial cellulase, Accellerase® 1500 showed strong synergistic effect on saccharification of Avicel® PH101, decrystallized cellulose, filter paper, and alkaline-pretreated sugarcane bagasse, resulting in 63-93% increase in the total reducing sugar yield after incubation at 50 °C for 72 h. Strong synergism was shown between BgAA9 and the cellulase with the highest total fermentable sugar yield obtained from 75:25% of Accellerase®1500:BgAA9 which released 39 mg glucose/FPU (filter paper unit) equivalent to 38.7% higher than Accellerase®1500 alone at the same total protein dosage of 5 mg/g substrate according to the mixture design study. The enzyme represented the first characterized LPMO from environmental metagenome and a potent auxiliary component for biomass saccharification. KEY POINTS: • BgAA9 represents the first characterized LPMO from metagenome. • 12 AA families were annotated in thermophilic bagasse fosmid library by NGS. • BgAA9 showed homology to Cel61 in Chaetomium thermophilum. • BgAA9 oxidized cellohexaose and PASC to DP2, DP4, and DP6. • BgAA9 showed strong synergism to Accellerase on bagasse hydrolysis.

High-Efficiency Secretion and Directed Evolution of Chitinase BcChiA1 in Bacillus subtilis for the Conversion of Chitinaceous Wastes Into Chitooligosaccharides

Limitations of enzyme production and activity pose a challenge for efficient degradation of chitinaceous wastes. To solve this problem, we engineered a system for high-yielding extracellular secretion of chitinase A1 from Bacillus circulans (BcChiA1) in B. subtilis. Furthermore, an innovative chitinase high-throughput screening method based on colloidal chitin stained with Remazol Brilliant Blue R (CC-RBB) was established and used to identify three mutants with improved chitinase activity: Y10A/R301A/E327A (Mu1), Y10A/D81A/E327A (Mu2), and F38A/K88A/R301A (Mu3). Their highest specific activity reached 1004.83 ± 0.87 U/mg, representing a 16.89-fold increase in activity compared to native BcChiA1. Additionally, we found that there is a synergistic effect between BcChiA1 and a lytic polysaccharide monooxygenase from Bacillus atrophaeus (BatLPMO10), which increased the chitin processing efficiency by 50% after combining the two enzymes. The yield of chitooligosaccharide (COS) production using the mutant Mu1 and BatLPMO10 reached 2885.25 ± 2.22 mg/L. Taken together, the results indicated that the CC-RBB high-throughput screening method is a useful tool for chitinase screening, and evolution of BcChiA1 in collaboration with BatLPMO10 has tremendous application potential in the biological treatment of chitinaceous wastes for COS production.

A Random-Sequential Kinetic Mechanism for Polysaccharide Monooxygenases

Polysaccharide monooxygenases (PMOs) are mononuclear copper enzymes that catalyze the hydroxylation of polysaccharides leading to the scission of the glycosidic bond. The mechanism, in which PMOs utilize molecular oxygen to oxidize the polysaccharide substrate, still remains largely unknown. Here, steady-state kinetics assays were used to probe the mechanism of oxygen-dependent cellohexaose oxidation catalyzed by MtPMO9E. Kinetic analysis indicated that both k_cat/ K_M(O2) and k_cat/ K_M(Glc6) were dependent on the concentration of the second substrate. Inhibition studies using carbon monoxide were also carried out. In addition, K_D values for Glc6 were determined for the Cu(I) and Cu(II) forms of the enzyme. Taken together, PMOs follow a random-sequential kinetic mechanism to form a ternary ES-O₂ complex. The optimal pH for MtPMO9E turnover was determined to be between pH 6.00 and pH 7.00. Furthermore, the kinetic parameters k_cat, k_cat/ K_M(O2), and k_cat/ K_M(Glc6) demonstrate a decrease in PMO activity at a low pH and provide equivalent kinetic p K_a's of 5.10. This points to the protonation of a general base required for turnover. These results provide a basis for the initial chemical steps in the mechanism of PMOs.

Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars

Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.

Monitoring of reactions catalyzed by lytic polysaccharide monooxygenases using highly-sensitive fluorimetric assay of the oxygen consumption rate

Lytic polysaccharide monooxygenases (LPMOs) are recently discovered enzymes that catalyze the oxidative deconstruction of polysaccharides. However fast and reliable methods of determination of LPMO activity still need to be developed, especially those based on the initial reaction rates. A method based on the oxygen consumption rate (OCR) measurements, using a Seahorse XFp Analyzer with highly-sensitive fluorimetric sensors, was applied for monitoring the oxidation of amorphous cellulose by three fungal LPMOs: recombinant enzymes from Thielavia terrestris (GH61E), Trichoderma reesei (Cel61A), and a native LPMO9A from Myceliophthora thermophila. The turnover numbers for 4 μM enzymes acting on 4 mg mL^-1 cellulose at 37 °C were 0.88, 1.26 and 0.93 min^-1, respectively. A possibility of feeding the dissolved reagents into the reaction system during measurements with obtaining a simultaneous response in the OCR allowed in situ monitoring the LPMO inhibition and activation by EDTA and Cu²⁺ ions as well as studying other effects on the enzymatic reaction.