ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microbial Physiology and Metabolism
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1624253
Unraveling the Molecular Mechanisms of Inonotus hispidus Fruiting Body Formation through Multi-Omics Integration
Provisionally accepted
- Liaoning Academy of Agricultural Sciences, Shenyang, China
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Background: Inonotus hispidus fruiting body formation involves complex molecular transitions that remain poorly understood, limiting our ability to optimize bioactive compound production in this medicinally important fungus. Methods: We employed a multi-omics integration strategy combining enzyme activity analysis, transcriptomics, metabolomics, and molecular docking to systematically compare mycelium and fruiting body stages. Differential gene expression was analyzed using RNA-seq, metabolite profiles were characterized by liquid chromatography-mass spectrometry, and key enzyme activities were measured spectrophotometrically. Machine learning algorithms identified predictive biomarkers, while molecular docking predicted enzyme-metabolite interactions. Results: Fruiting bodies exhibited significantly higher superoxide dismutase, cellulase, and laccase activities compared to mycelium (P < 0.01), with enhanced accumulation of flavonoids and phenolic compounds. Transcriptomic analysis revealed 2,611 differentially expressed genes enriched in carbohydrate metabolism and oxidative phosphorylation pathways. Metabolomic profiling identified 908 differential metabolites involved in pyruvate and alpha-linolenic acid metabolism. Thirteen metabolic biomarkers achieved perfect classification accuracy (area under curve = 1.0), including prostaglandin F2α and phytosphingosine 1-phosphate. Citreoisocoumarin demonstrated high-affinity binding to laccase, cellulase and superoxide dismutase. Discussion: This study establishes the first comprehensive enzyme-gene-metabolite regulatory network governing I. hispidus development, revealing Citreoisocoumarin as a multi-target regulator balancing oxidative defense and substrate utilization. These findings provide molecular targets for optimizing bioactive compound production and advance our understanding of fungal developmental biology.
Keywords: enzyme activity, Fruiting body formation, Inonotus hispidus, Metabolomics, molecular docking, Transcriptomics
Received: 07 May 2025; Accepted: 04 Aug 2025.
Copyright: © 2025 MA, Xiao, Gong, Zhao, Chen and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Xiaoying MA, Liaoning Academy of Agricultural Sciences, Shenyang, China
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