Structural and functional characterization of the catalytic domain of a cell-wall anchored bacterial lytic polysaccharide monooxygenase from Streptomyces coelicolor

Functional characterization of a lytic polysaccharide monooxygenase EbLPMO10A that contributes to β-chitin degradation by chitinase

The conversion of β-chitin, an abundant polysaccharide in cephalopod seafood byproducts, into high-value N-acetyl chitooligosaccharides (NCOSs) is crucial for the functional food and pharmaceutical industries. Lytic polysaccharide monooxygenases (LPMOs) oxidatively degrade insoluble polysaccharides and promote biomass degradation by hydrolases. However, the existence of LPMOs that specifically act on β-chitin remains unclear. In the study, we recombinantly expressed a novel AA10 LPMO, EbLPMO10A, from Enterobacteriaceae bacterium BIT-l23, which specifically oxidized β-chitin and was inactive against α-chitin. The oxidative depolymerization of β-chitin by EbLPMO10A exhibited a unique explosive granulation and enhanced regional activity of hydrolases. Combining 5.0 μM EbLPMO10A with 1.0 μM ChiB (chitinase from Serratia marcescens) achieved 76.74 % conversion of β-chitin to (GlcNAc)2, a 4.46-fold increase over ChiB alone. These promising results suggest that EbLPMO10A may benefit the targeted conversion of β-chitin in the food and chemical industries.

Insilico molecular characterization of a cyanobacterial lytic polysaccharide monooxygenase

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the oxidative cleavage of β(1-4) glycosidic bonds and have attracted considerable attention because of their potential for enhancing efficiency in degrading recalcitrant polymeric substrates, in synergism with hydrolytic enzymes. Fungal-derived LPMOs are the most prevalent type, while other taxonomic groups have been described as potential alternative sources of these enzymes. In the present study, we aimed to identify and characterize in silico a LPMO of cyanobacterial origin with putative functions in chitin depolymerization. A similarity search of sequences and conservation of domains with characterized LPMOs identified a 289 amino acid protein from the cyanobacterium Mastigocoleus testarum (Order Nostocales), likely belonging to the CAZy-AA10 class. This protein is referred to as MtLPMO10. Phylogenetic analysis revealed that MtLPMO10 is homologous to the protein Tma12 from the fern Tectaria macrodonta, with 52.11 % sequence identity, which was the first LPMO characterized as originating from the plant kingdom. The protein tertiary structure predicted by the AlphaFold server indicates structural features common to LPMOs, such as a histidine brace formed by His31 and His132 and an immunoglobulin-like domain composed of antiparallel beta strands. Molecular dynamics (MD) simulation allowed the assessment of the enzyme-substrate affinity, using an initial pose based on literature data. The MtLPMO10-chitin complex remained stable during 100ns of MD, while the MtLPMO10-cellulose complex dissociated within 30ns of MD. Additionally, there was a shorter Cu(I)-H4 distance in the protein-substrate complex compared to the Cu(I)-H1 distance (averages of 6.0 ± 0.7 Å and 7.9 ± 0.7 Å, respectively), suggesting a C4 regioselectivity. This study highlights the existence of lytic polysaccharide monooxygenases in cyanobacteria and paves the way for further investigations related to this enigmatic class of enzymes and their potential use in biotechnological applications.

Functional characterization of two AA10 lytic polysaccharide monooxygenases from Cellulomonas gelida

Lytic polysaccharide monooxygenases (LPMOs) are redox enzymes targeting the crystalline region of recalcitrant polysaccharides such as cellulose and chitin. Functional characterization of two LPMOs from the cellulose-degrading soil bacterium Cellulomonas gelida, CgLPMO10A and CgLPMO10B, showed expected activities on cellulose but also revealed novel features of AA10 LPMOs. While clustering together with strictly C1-oxidizing and strictly cellulose-active AA10 LPMOs, CgLPMO10A exhibits activity on both cellulose and chitin, oxidizing the C1 carbon of both substrates. This combination of substrate and oxidative specificity has not been previously observed for family 10 LPMOs and may be due to a conspicuous divergence in two hydrophobic residues on the substrate-binding surface. CgLPMO10B oxidizes cellulose at both the C1 and C4 positions and is also active on chitin, in line with predictions based on phylogeny. Interestingly, while coming from the same organism and both acting on cellulose, the two enzymes have markedly different redox properties with CgLPMO10B displaying the lowest redox potential and the highest oxidase activity observed for an AA10 LPMO so far. These results provide insight into the LPMO machinery of C. gelida and expand the known catalytic repertoire of bacterial LPMOs.

The upsurge of lytic polysaccharide monooxygenases in biomass deconstruction: characteristic functions and sustainable applications

Lytic polysaccharide monooxygenases (LPMOs) are one of the emerging classes of copper metalloenzymes that have received considerable attention due to their ability to boost the enzymatic conversion of intractable polysaccharides such as plant cell walls and chitin polymers. LPMOs catalyze the oxidative cleavage of β-1,4-glycosidic bonds using molecular O2 or H2O2 in the presence of an external electron donor. LPMOs have been classified as an auxiliary active (AA) class of enzymes and, further based on substrate specificity, divided into eight families. Until now, multiple LPMOs from AA9 and AA10 families, mostly from microbial sources, have been investigated; the exact mechanism and structure-function are elusive to date, and recently discovered AA families of LPMOs are just scratched. This review highlights the origin and discovery of the enzyme, nomenclature, three-dimensional protein structure, substrate specificity, copper-dependent reaction mechanism, and different techniques used to determine the product formation through analytical and biochemical methods. Moreover, the diverse functions of proteins in various biological activities such as plant-pathogen/pest interactions, cell wall remodeling, antibiotic sensitivity of biofilms, and production of nanocellulose along with certain obstacles in deconstructing the complex polysaccharides have also been summarized, while highlighting the innovative and creative ways to overcome the limitations of LPMOs in hydrolyzing the biomass.

Heterologous Expression and Biochemical Characterization of a Novel Lytic Polysaccharide Monooxygenase from Chitinilyticum aquatile CSC-1

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the oxidative cleavage of recalcitrant polysaccharides. There are limited reports on LPMOs capable of concurrently catalyzing the oxidative cleavage of both cellulose and chitin. In this study, we identified and cloned a novel LPMO from the newly isolated bacterium Chitinilyticum aquatile CSC-1, designated as CaLPMO10. When using 2, 6-dimethylphenol (2, 6-DMP) as the substrate, CaLPMO10 exhibited optimal activity at 50 °C and pH 8, demonstrating good temperature stability at 30 °C. Even after a 6 h incubation at pH 8 and 30 °C, CaLPMO10 retained approximately 83.03 ± 1.25% residual enzyme activity. Most metal ions were found to enhance the enzyme activity of CaLPMO10, with ascorbic acid identified as the optimal reducing agent. Mass spectrometry analysis indicated that CaLPMO10 displayed oxidative activity towards both chitin and cellulose, identifying it as a C1/C4-oxidized LPMO. CaLPMO10 shows promise as a key enzyme for the efficient utilization of biomass resources in future applications.

Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam

Background

White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study.

Method

In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay.

Result

Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.

Impact of the Copper Second Coordination Sphere on Catalytic Performance and Substrate Specificity of a Bacterial Lytic Polysaccharide Monooxygenase

Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides, such as cellulose and chitin, using a single copper cofactor bound in a conserved histidine brace with a more variable second coordination sphere. Cellulose-active LPMOs in the fungal AA9 family and in a subset of bacterial AA10 enzymes contain a His-Gln-Tyr second sphere motif, whereas other cellulose-active AA10s have an Arg-Glu-Phe motif. To shine a light on the impact of this variation, we generated single, double, and triple mutations changing the His216-Gln219-Tyr221 motif in cellulose- and chitin-oxidizing MaAA10B toward Arg-Glu-Phe. These mutations generally reduced enzyme performance due to rapid inactivation under turnover conditions, showing that catalytic fine-tuning of the histidine brace is complex and that the roles of these second sphere residues are strongly interconnected. Studies of copper reactivity showed remarkable effects, such as an increase in oxidase activity following the Q219E mutation and a strong dependence of this effect on the presence of Tyr at position 221. In reductant-driven reactions, differences in oxidase activity, which lead to different levels of in situ generated H2O2, correlated with differences in polysaccharide-degrading ability. The single Q219E mutant displayed a marked increase in activity on chitin in both reductant-driven reactions and reactions fueled by exogenously added H2O2. Thus, it seems that the evolution of substrate specificity in LPMOs involves both the extended substrate-binding surface and the second coordination sphere.

The Ustilago maydis AA10 LPMO is active on fungal cell wall chitin

Lytic polysaccharide monooxygenases (LPMOs) can perform oxidative cleavage of glycosidic bonds in carbohydrate polymers (e.g., cellulose, chitin), making them more accessible to hydrolytic enzymes. While most studies have so far mainly explored the role of LPMOs in a (plant) biomass conversion context, alternative roles and paradigms begin to emerge. The AA10 LPMOs are active on chitin and/or cellulose and mostly found in bacteria and in some viruses and archaea. Interestingly, AA10-encoding genes are also encountered in some pathogenic fungi of the Ustilaginomycetes class, such as Ustilago maydis, responsible for corn smut disease. Transcriptomic studies have shown the overexpression of the AA10 gene during the infectious cycle of U. maydis. In fact, U. maydis has a unique AA10 gene that codes for a catalytic domain appended with a C-terminal disordered region. To date, there is no public report on fungal AA10 LPMOs. In this study, we successfully produced the catalytic domain of this LPMO (UmAA10_cd) in Pichia pastoris and carried out its biochemical characterization. Our results show that UmAA10_cd oxidatively cleaves α- and β-chitin with C1 regioselectivity and boosts chitin hydrolysis by a GH18 chitinase from U. maydis (UmGH18A). Using a biologically relevant substrate, we show that UmAA10_cd exhibits enzymatic activity on U. maydis fungal cell wall chitin and promotes its hydrolysis by UmGH18A. These results represent an important step toward the understanding of the role of LPMOs in the fungal cell wall remodeling process during the fungal life cycle.IMPORTANCELytic polysaccharide monooxygenases (LPMOs) have been mainly studied in a biotechnological context for the efficient degradation of recalcitrant polysaccharides. Only recently, alternative roles and paradigms begin to emerge. In this study, we provide evidence that the AA10 LPMO from the phytopathogen Ustilago maydis is active against fungal cell wall chitin. Given that chitin-active LPMOs are commonly found in microbes, it is important to consider fungal cell wall as a potential target for this enigmatic class of enzymes.