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Transcriptome Analysis of Podoscypha petalodes Strain GGF6 Reveals the Diversity of Proteins Involved in Lignocellulose Degradation and Ligninolytic Function

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Abstract

The present study reports transcriptomic profiling of a Basidiomycota fungus, Podoscypha petalodes strain GGF6 belonging to the family Podoscyphaceae, isolated from the North-Western Himalayan ranges in Himachal Pradesh, India. Podoscypha petalodes strain GGF6 possesses significant biotechnological potential as it has been reported for endocellulase, laccase, and other lignocellulolytic enzymes under submerged fermentation conditions. The present study attempts to enhance our knowledge of its lignocellulolytic potential as no previous omics-based analysis is available for this white-rot fungus. The transcriptomic analysis of P. petalodes GGF6 reveals the presence of 280 CAZy proteins. Furthermore, bioprospecting transcriptome signatures in the fungi revealed a diverse array of proteins associated with cellulose, hemicellulose, pectin, and lignin degradation. Interestingly, two copper-dependent lytic polysaccharide monooxygenases (AA14) and one pyrroloquinolinequinone-dependent oxidoreductase (AA12) were also identified, which are known to help in the lignocellulosic plant biomass degradation. Overall, this transcriptome profiling-based study provides deeper molecular-level insights into this Basidiomycota fungi, P. petalodes, for its potential application in diverse biotechnological applications, not only in the biofuel industry but also in the environmental biodegradation of recalcitrant molecules.

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Data availability

Raw reads can be accessed using this link https://drive.google.com/drive/folders/1wnhbJvjAW3mYyJAFCpHYHAufwOY7PEvb?usp=sharing. The raw data can also be provided upon request.

Abbreviations

NCBI:

National centre for biotechnology information

BLAST:

Basic local alignment search tool

CAZyme:

Carbohydrate active enzymes

GH:

Glycoside hydrolases

GT:

Glycosyl transferases

CE:

Carbohydrate esterases

CBM:

Carbohydrate binding-module

PL:

Polysaccharide lyases

AA:

Auxiliary activity

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Acknowledgements

The authors thank their respective Universities/ Institutes for providing essential facilities and environment for research. Furthermore, the authors sincerely acknowledge the help provided by Dr. R.S. Chauhan and Dr. B.M. Sharma regarding providing the fungal culture.

Funding

The research was funded by the Department of Science and Technology, Government of India for the Indo-Russian collaborative project “Elucidating the linkage between key limiting processes and microorganisms during anaerobic degradation of lignocellulosic waste” INT/RUS/RFBR/P-175 to GG. GS is supported by the DST-INSPIRE Faculty Award from DST, Government of India. In addition, this work was partially supported by the Department of Electronics, IT, BT, and S&T of the Government of Karnataka, India.

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Author notes

  1. Rishi Mahajan, B. Shenu Hudson, Deepak Sharma: Equal first authors.

Authors and Affiliations

  1. Department of Microbiology, College of Basic Sciences, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur, 176062, India

    Rishi Mahajan

  2. Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, India

    Rishi Mahajan, Deepak Sharma & Gunjan Goel

  3. Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India

    B. Shenu Hudson, Vaishnavi Kolte & Gaurav Sharma

  4. Department of Microbiology, School of Interdisciplinary and Applied Sciences (SIAS), Central University of Haryana, Mahendergarh, Haryana, India

    Gunjan Goel

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Contributions

GG generated the idea. RM and DS cultured the fungi and isolated the RNA for transcriptome sequencing. SBH, VK, and GS performed the computational analysis. GS, RM, and GG wrote the manuscript. All authors edited and finalized the manuscript.

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Correspondence to Gaurav Sharma or Gunjan Goel.

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12088_2022_1037_MOESM1_ESM.xlsx

Supplementary Table 1: Heatmap of %identity scores amongst the close relatives identified from its phylogenetic clade.Supplementary Table 2: Distribution of P. petalodes strain GGF6 unigenes among all Pfam families and their respective functions.Supplementary Table 3: Distribution of P. petalodes strain GGF6 unigenes among all TIGR families and their respective functions. (XLSX 130 KB)

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Mahajan, R., Hudson, B.S., Sharma, D. et al. Transcriptome Analysis of Podoscypha petalodes Strain GGF6 Reveals the Diversity of Proteins Involved in Lignocellulose Degradation and Ligninolytic Function. Indian J Microbiol 62, 569–582 (2022). https://doi.org/10.1007/s12088-022-01037-6

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