Lytic polysaccharide monooxygenase synergized with lignin-degrading enzymes for efficient lignin degradation

Sun, Su; Li, Fei; Li, Muzi; Zhang, Wenqian; Jiang, Zhenxiong; Zhao, Honglu; Pu, Yunqiao; Ragauskas, Arthur J.; Dai, Susie Y.; Zhang, Xiaoyu; Yu, Hongbo; Yuan, Joshua S.; Xie, Shangxian

doi:10.1016/j.isci.2023.107870

Cited by 8 publications

(2 citation statements)

References 45 publications

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“…The greatest importance of the AA9 family is likely due to the role of oxidative cellulose degradation mechanisms in wood decay. It has also recently been suggested that LPMOs may also be involved in lignin degradation ( 32 , 33 ), and more detailed elucidation of the function of this family is needed.…”

Section: Resultsmentioning

confidence: 99%

Random forest machine-learning algorithm classifies white- and brown-rot fungi according to the number of the genes encoding Carbohydrate-Active enZyme families

Hasegawa,

Sugiyama,

Igarashi

2024

Appl Environ Microbiol

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Wood-rotting fungi play an important role in the global carbon cycle because they are the only known organisms that digest wood, the largest carbon stock in nature. In the present study, we used linear discriminant analysis and random forest (RF) machine learning algorithms to predict white- or brown-rot decay modes from the numbers of genes encoding Carbohydrate-Active enZymes with over 98% accuracy. Unlike other algorithms, RF identified specific genes involved in cellulose and lignin degradation, including auxiliary activities (AAs) family 9 lytic polysaccharide monooxygenases, glycoside hydrolase family 7 cellobiohydrolases, and AA family 2 peroxidases, as critical factors. This study sheds light on the complex interplay between genetic information and decay modes and underscores the potential of RF for comparative genomics studies of wood-rotting fungi. IMPORTANCE Wood-rotting fungi are categorized as either white- or brown-rot modes based on the coloration of decomposed wood. The process of classification can be influenced by human biases. The random forest machine learning algorithm effectively distinguishes between white- and brown-rot fungi based on the presence of Carbohydrate-Active enZyme genes. These findings not only aid in the classification of wood-rotting fungi but also facilitate the identification of the enzymes responsible for degrading woody biomass.

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Section: Resultsmentioning

confidence: 99%

Random forest machine-learning algorithm classifies white- and brown-rot fungi according to the number of the genes encoding Carbohydrate-Active enZyme families

Hasegawa,

Sugiyama,

Igarashi

2024

Appl Environ Microbiol

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“…Additionally, as shown by the reaction of syringol with SyoB, CYP255 enzymes may have evolved peroxygenase activity to avoid uncoupling via redox cycling by quinones. Hydroquinones including 2methoxyhydroquinone (MBQH2) and 2,6-dimethoxyhydroxyquinone (DBQH2) can be derived from products of lignin degradation (44,45). Thus, the CYP255 family may have evolved hybrid monooxygenase/peroxygenase enzyme activity as a mechanism to minimize uncoupling in the presence of quinones, using the hydrogen peroxide generated to drive catalysis.…”

Section: Discussionmentioning

confidence: 99%

The S-ligninO-demethylase SyoA: Structural insights into a new class of heme peroxygenase enzymes

Harlington,

Das,

Shearwin

et al. 2024

Preprint

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TheO-demethylation of lignin aromatics is a rate-limiting step in their bioconversion to high-value compounds. A recently discovered cytochrome P450 enzyme SyoA was found to demethylate the sinapyl alcohol-derived (S-lignin) aromatic syringol. In this work, we solved high-resolution X-ray crystal structures of SyoA in the substrate-free and substrate-bound states and evaluate the demethylation ofpara-substituted S-lignin aromatics via the monooxygenase pathway and peroxide shunt pathway. We found that SyoA demethylates S-lignin aromatics with the following activity: 4-methylsyringol > syringaldehyde > syringol exclusively using the peroxide shunt pathway. The atomic-resolution structure of SyoA reveals the position of the non-canonical residues in the I-helix (Gln252 and Glu253). Site-directed mutagenesis of this amide-acid pair of a homologous CYP255 enzyme GcoA, which can catalyze the O-demethylation of guaiacol using both monooxygenase and peroxygenase activity, showed the amide-acid pair is critical for both pathways. This work expands the enzymatic toolkit for improving the capacity to funnel lignin towards high-value compounds, and defines the new chemistry within the active site of the enzyme that enables efficient peroxygenase activity. These insights provide a framework for engineered peroxygenase activity in other cytochrome P450 enzymes, with the potential for more facile catalysis, relative to traditional P450 monooxygenases which require difficult to handle redox partners and expensive nicotinamide cofactors.

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Fungal endophytes and leaf litter fungi as sources of novel inhibitor-resistant cellulase for biofuel production: a basic study

Suryanarayanan,

Rajamani,

Aro

et al. 2024

3 Biotech

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Lytic polysaccharide monooxygenase synergized with lignin-degrading enzymes for efficient lignin degradation

Cited by 8 publications

References 45 publications

Random forest machine-learning algorithm classifies white- and brown-rot fungi according to the number of the genes encoding Carbohydrate-Active enZyme families

Random forest machine-learning algorithm classifies white- and brown-rot fungi according to the number of the genes encoding Carbohydrate-Active enZyme families

The S-ligninO-demethylase SyoA: Structural insights into a new class of heme peroxygenase enzymes

Fungal endophytes and leaf litter fungi as sources of novel inhibitor-resistant cellulase for biofuel production: a basic study

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