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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

Summary

This research examined special enzymes called LPMOs found in bacteria living around decomposing wood in a Vietnamese forest. These enzymes help break down tough plant materials and may play important roles in how bacteria and fungi interact in forest ecosystems. The study provides new insights into natural biomass degradation processes. Impacts on everyday life: – Helps understand how nature recycles plant materials in forests – Could lead to better industrial enzymes for biofuel production – Provides insights for developing more sustainable waste treatment processes – May help develop new antimicrobial strategies – Advances our understanding of complex ecological relationships in nature

Background

White-rot fungi and bacteria communities form unique ecosystems with different types of symbiotic interactions during wood decomposition, including cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is not fully understood.

Objective

To analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from bacterial metagenomic DNA of humus samples collected around white-rot fungi in Cuc Phuong primary forest, Vietnam. Additionally, to express, purify and test the enzymatic activity of two LPMOs and investigate their potential role in fungi-bacterial relationships.

Results

Thirty-one full-length proteins were confirmed as putative LPMOs through amino acid sequence comparison. Despite sequence diversity, they shared nine conserved amino acids, including two histidines and one phenylalanine that characterize bacterial LPMO active sites. Structural analysis revealed they are multidomain proteins with different functions. 3D structure prediction showed similar spatial structures despite sequence differences. Testing of proteins GL0247266 and GL0183513 confirmed they are chitin-active LPMOs. Thirteen proteins contained GbpA_2 and GbpA_3-like domains similar to Vibrio cholerae GbpA protein.

Conclusion

The 31 putative LPMOs showed characteristic amino acid sequences and spatial structures of cellulose- and chitin-active LPMOs. A group of multimodular LPMOs with functional domains similar to V. cholerae GbpA was identified. The structural characteristics suggest these chitin-active GbpA-like LPMOs may play important roles in fungal-bacterial community relationships in decomposing trees within primary forests.
  • Published in:PeerJ,
  • Study Type:Molecular Biology Research,
  • Source: 10.7717/peerj.17553
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