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

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de Assis, Michelle A. ; da Silva, Jovanderson J. B. ; de Carvalho, Lucas M. ; Parreiras, Lucas S. ; Cairo, Joao Paulo L. F. ; Marone, Marina P. ; Goncalves, Thiago A. ; Silva, Desiree S. ; Dantzger, Miriam ; de Figueiredo, Fernanda L. ; Carazzolle, Marcelo F. ; Pereira, Goncalo A. G. ; Damasio, Andre

• Document type: Journal article
• Source: JOURNAL OF FUNGI; v. 10, n. 6, p. 25-pg., 2024-06-01.

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 beta-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. (AU)

• FAPESP's process: 19/12914-3 - Integrated multi-omics analysis and metabolic network simulations applied to Saccharomyces cerevisiae for second generation ethanol production
• Grantee: Lucas Miguel de Carvalho
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 15/50612-8 - An integrated approach to explore a novel paradigm for biofuel production from lignocellulosic feedstocks
• Grantee: Telma Teixeira Franco
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 22/05731-2 - BEYOND: establishing a fungal cell factory for recombinant protein production
• Grantee: André Ricardo de Lima Damasio
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 16/02792-0 - Identification of enzymes with potential for biotechnological applications in a Trichoderma sp fungus
• Grantee: Michelle Alexandrino de Assis
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 16/09950-0 - Functional, structural characterizations and biotechnological application of lytic polysaccharide monooxygenases from the lower termite Coptotermes gestroi
• Grantee: João Paulo Lourenço Franco Cairo
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 21/02493-0 - Diurnal variation of transcripts and metabolites of sugarcane and energy-cane: an integrated analysis of transcriptomics and metabolomics
• Grantee: Jovanderson Jackson Barbosa da Silva
• Support Opportunities: Scholarships in Brazil - Doctorate