Comparison of lignocellulosic enzymes and CAZymes between ascomycetes (Trichoderma) and basidiomycetes (Ganoderma) species: a proteomic approach

Akshay Shankar; Kavish Kumar Jain; Ramesh Chander Kuhad; Krishna Kant Sharma

doi:10.1515/znc-2023-0125

Abstract

Wood decomposing ascomycetes and basidiomycetes group of fungi are the most valuable microbes on the earth’s ecosystem that recycles the source of carbon; therefore, they are essential for the biorefinery industries. To understand the robustness of the enzymes and their metabolic pathways in the fungal system, label-free quantification of the total proteins was performed. The fungi showed a comparable quantity of protein abundance [Trichoderma citrinoviride (285), Thermoascus aurantiacus (206), Ganoderma lucidum MDU-7 (102), G. lucidum (242)]. Differentially regulated proteins of ascomycetes and basidiomycetes were analyzed, and their heatmap shows upregulated and downregulated proteins [25 differentially expressed proteins in T. citrinoviride (8.62 % up-regulated and 91.37 % down-regulated) and G. lucidum (5.74 % up-regulated and 94.25 % down-regulated)] by using the normalized peptide-spectrum match (PSMs) and log2fold change. These proteins were similarly matched to the carbohydrate active enzymes family (CAZymes) like glycoside hydrolase (GH family), carbohydrate-binding module (CBM family) with auxiliary activities, and also involved in the hydrolysis of carbohydrate, lignin, xylan, polysaccharides, peptides, and oxido-reductase activity that helps in antioxidant defense mechanism. The lignocellulolytic enzymes from two different divisions of fungi and proteomics studies gave a better understanding of carbon recycling and multi-product lignocellulosic biorefinery processes.

Keywords: CAZymes; glycoside hydrolase; oxido-reductase; ascomycetes; proteomics; basidiomycetes

Corresponding author: Krishna Kant Sharma, Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India, E-mail: kksharma.microbiology@mdurohtak.ac.in

Funding source: Department of Science and Technology, India

Award Identifier / Grant number: 1196SR/FST/LS-I/2017/4

Acknowledgments

The authors acknowledge the infrastructural support from the DST-FIST grant (Grant No. 1196SR/FST/LS-I/2017/4). Sincere thanks to Mr. Sonu and Mr. Pratik Shinde for their support and their valuable suggestions throughout the work. Also, thanks to Mr. Shubham, CIF, UDSC, New Delhi, for his help in proteomic analysis.

Research ethics: Not applicable.
Author contributions: Akshay Shankar: Data curation; Formal analysis; Investigation; Methodology; Software; Validation; Visualization; Writing – original draft. Kavish Kumar Jain: Data curation, Investigation, Investigation, Analysis. Ramesh Chander Kuhad: Conceptualization; Formal analysis; Funding acquisition; Investigation; Project administration; Resources; Supervision; Validation; Visualization Krishna Kant Sharma: Conceptualization; Formal analysis; Funding acquisition; Investigation; Project administration; Resources; Supervision; Validation; Visualization; Writing – review & editing.
Competing interests: The authors state no competing interests.
Research funding: Authors are also thankful to DST for FIST grant sanctioned to the Department of Microbiology, M. D. University, Rohtak. We wish to acknowledge SERB, DST, India (File no. PDF/2016/001068) for a contingency grant.
Data availability: Protein data were deposited to the ProteomeXchange Consortium (www.proteomexchange.org/submission/index.html) through the PRoteomics IDEntification Database (PRIDE; https://www.ebi.ac.uk/pride/) repository with the dataset identifier PXD033434.

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Supplementary Material

This article contains supplementary material (https://doi.org/10.1515/znc-2023-0125).

Received: 2023-09-17

Accepted: 2023-12-03

Published Online: 2023-12-14

Published in Print: 2025-01-29

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