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Article

A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum

by
Michelle A. de Assis
1,†,
Jovanderson J. B. da Silva
2,†,
Lucas M. de Carvalho
2,
Lucas S. Parreiras
2,
João Paulo L. F. Cairo
1,3,
Marina P. Marone
2,
Thiago A. Gonçalves
1,
Desireé S. Silva
4,
Miriam Dantzger
2,
Fernanda L. de Figueiredo
1,
Marcelo F. Carazzolle
2,
Gonçalo A. G. Pereira
2 and
André Damasio
1,*
1
Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil
2
Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil
3
York Structural Biology Laboratory (YSBL), Department of Chemistry, University of York, York YO10 5DD, UK
4
SENAI Institute for Biomass Innovation, Três Lagoas 79640-250, Brazil
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
J. Fungi 2024, 10(6), 407; https://doi.org/10.3390/jof10060407
Submission received: 8 April 2024 / Revised: 24 May 2024 / Accepted: 28 May 2024 / Published: 5 June 2024
(This article belongs to the Section Fungal Cell Biology, Metabolism and Physiology)
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Abstract

Trichoderma erinaceum is a filamentous fungus that was isolated from decaying sugarcane straw at a Brazilian ethanol biorefinery. This fungus shows potential as a source of plant cell wall-degrading enzymes (PCWDEs). In this study, we conducted a comprehensive multiomics investigation of T. erinaceum to gain insights into its enzymatic capabilities and genetic makeup. Firstly, we performed genome sequencing and assembly, which resulted in the identification of 10,942 genes in the T. erinaceum genome. We then conducted transcriptomics and secretome analyses to map the gene expression patterns and identify the enzymes produced by T. erinaceum in the presence of different substrates such as glucose, microcrystalline cellulose, pretreated sugarcane straw, and pretreated energy cane bagasse. Our analyses revealed that T. erinaceum highly expresses genes directly related to lignocellulose degradation when grown on pretreated energy cane and sugarcane substrates. Furthermore, our secretome analysis identified 35 carbohydrate-active enzymes, primarily PCWDEs. To further explore the enzymatic capabilities of T. erinaceum, we selected a β-glucosidase from the secretome data for recombinant production in a fungal strain. The recombinant enzyme demonstrated superior performance in degrading cellobiose and laminaribiose compared to a well-known enzyme derived from Trichoderma reesei. Overall, this comprehensive study provides valuable insights into both the genetic patterns of T. erinaceum and its potential for lignocellulose degradation and enzyme production. The obtained genomic data can serve as an important resource for future genetic engineering efforts aimed at optimizing enzyme production from this fungus.
Keywords: Trichoderma; hydrolysis; lignocellulose; multiomics; beta-glucosidase Trichoderma; hydrolysis; lignocellulose; multiomics; beta-glucosidase

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MDPI and ACS Style

de Assis, M.A.; da Silva, J.J.B.; de Carvalho, L.M.; Parreiras, L.S.; Cairo, J.P.L.F.; Marone, M.P.; Gonçalves, T.A.; Silva, D.S.; Dantzger, M.; de Figueiredo, F.L.; et al. A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum. J. Fungi 2024, 10, 407. https://doi.org/10.3390/jof10060407

AMA Style

de Assis MA, da Silva JJB, de Carvalho LM, Parreiras LS, Cairo JPLF, Marone MP, Gonçalves TA, Silva DS, Dantzger M, de Figueiredo FL, et al. A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum. Journal of Fungi. 2024; 10(6):407. https://doi.org/10.3390/jof10060407

Chicago/Turabian Style

de Assis, Michelle A., Jovanderson J. B. da Silva, Lucas M. de Carvalho, Lucas S. Parreiras, João Paulo L. F. Cairo, Marina P. Marone, Thiago A. Gonçalves, Desireé S. Silva, Miriam Dantzger, Fernanda L. de Figueiredo, and et al. 2024. "A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum" Journal of Fungi 10, no. 6: 407. https://doi.org/10.3390/jof10060407

APA Style

de Assis, M. A., da Silva, J. J. B., de Carvalho, L. M., Parreiras, L. S., Cairo, J. P. L. F., Marone, M. P., Gonçalves, T. A., Silva, D. S., Dantzger, M., de Figueiredo, F. L., Carazzolle, M. F., Pereira, G. A. G., & Damasio, A. (2024). A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum. Journal of Fungi, 10(6), 407. https://doi.org/10.3390/jof10060407

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