The enzyme interactome concept in filamentous fungi linked to biomass valorization

Monclaro, Antonielle Vieira; Silva, Caio de Oliveira Gorgulho; Gomes, Helder Andrey Rocha; Moreira, Leonora Rios de Souza; Filho, Edivaldo Ximenes Ferreira

doi:10.1016/j.biortech.2021.126200

Cited by 23 publications

(5 citation statements)

References 107 publications

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“…Laccases and class II peroxidases transform lignin into reactive quinones and phenoxy radicals in vitro , which leads to the formation of quinone and (re)polymerized lignin. To efficiently depolymerize lignin, partner enzymes in the white-rot fungi secretome are required to deactivate laccase- and peroxidase-generated quinones and phenol radicals ( Monclaro et al, 2022 ). These enzymes include dehydrogenases from the AA3 CAZymes family and quinone reductases from the AA6 CAZymes family.…”

Section: Resultsmentioning

confidence: 99%

Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroom Lyophyllum decastes reveals insights on evolution and lignocellulose degradation potential

Yang²,

Qiu

et al. 2023

Front. Microbiol.

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Lyophyllum decastes, also known as Luronggu in China, is a culinary edible and medicinal mushroom that was widely cultivated in China in recent years. In the present study, the complete high-quality genome of two mating compatible L. decastes strain was sequenced. The L. decastes LRG-d1-1 genome consists of 47.7 Mb in 15 contigs with a contig N90 of 2.08 Mb and 14,499 predicted gene models. Phylogenetic analysis revealed that L. decastes exhibits a close evolutionary relationship to the Termitomyces and Hypsizygus genus and was diverged from H. marmoreus ~ 45.53 Mya ago. Mating A loci of L. decastes compose of five and four HD genes in two monokaryotic strains, respectively. Mating B loci compose of five STE genes in both two monokaryotic strains. To accelerate the cross-breeding process, we designed four pairs of specific primers and successfully detected both mating types in L. decastes. As a wood-rotting mushroom, a total of 541 genes accounting for 577 CAZymes were identified in the genome of L. decastes. Proteomic analysis revealed that 1,071 proteins including 182 CAZymes and 258 secreted enzymes were identified from four groups (PDB, PDB + bran, PDB + cotton hull, and PDB + sawdust). Two laccases and a quinone reductase were strongly overproduced in lignin-rich cultures, and the laccases were among the top-3 secreted proteins, suggesting an important role in the synergistic decomposition of lignin. These results revealed the robustness of the lignocellulose degradation capacity of L. decastes. This is the first study to provide insights into the evolution and lignocellulose degradation of L. decastes.

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Section: Resultsmentioning

confidence: 99%

Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroom Lyophyllum decastes reveals insights on evolution and lignocellulose degradation potential

Yang²,

Qiu

et al. 2023

Front. Microbiol.

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“…This issue can be solved by co-cultivation strategies if T. reesei is cultivated together with Aspergiilus species [5,37,67] or by engineering filamentous fungi to produce multiple hydrolytic enzymes of desired top efficiencies in a single host, e.g., by introducing or up-regulating the demanded enzymes. The production of enzymes can be carried out on-site using cheap complex polymeric substrates e.g., containing agricultural sidestreams consisting of plant cell wall material for growth and enzyme production [38,68]. Co-cultivation with various fungi for enzyme production, especially using solid state fermentation (SSF) with different solid agricultural sidestreams, where the fungi do not necessarily have direct contact but can thrive in micro-niches in the substrate, has been shown in several cases to enable production of efficient enzyme cocktails [37,69], reviewed in [66].…”

Section: Production Of Enzymes For Plant Biomass Utilizationmentioning

confidence: 99%

Fungal Cell Factories for Efficient and Sustainable Production of Proteins and Peptides

Lübeck

2022

Microorganisms

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Filamentous fungi are a large and diverse taxonomically group of microorganisms found in all habitats worldwide. They grow as a network of cells called hyphae. Since filamentous fungi live in very diverse habitats, they produce different enzymes to degrade material for their living, for example hydrolytic enzymes to degrade various kinds of biomasses. Moreover, they produce defense proteins (antimicrobial peptides) and proteins for attaching surfaces (hydrophobins). Many of them are easy to cultivate in different known setups (submerged fermentation and solid-state fermentation) and their secretion of proteins and enzymes are often much larger than what is seen from yeast and bacteria. Therefore, filamentous fungi are in many industries the preferred production hosts of different proteins and enzymes. Edible fungi have traditionally been used as food, such as mushrooms or in fermented foods. New trends are to use edible fungi to produce myco-protein enriched foods. This review gives an overview of the different kinds of proteins, enzymes, and peptides produced by the most well-known fungi used as cell factories for different purposes and applications. Moreover, we describe some of the challenges that are important to consider when filamentous fungi are optimized as efficient cell factories.

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“…Despite the immense potential of fungi in biomass degradation, our current understanding of the molecular mechanisms involved remains limited. In order to optimize bioprocesses and develop innovative biotechnological applications, it is crucial to gain a better understanding of the complex interactions between fungal enzymes and lignocellulosic substrates (Monclaro et al., 2022). Additionally, exploring the diversity of fungal species and their unique capabilities in breaking down different types of biomass can provide valuable insights into the development of efficient and sustainable biorefinery processes (de Vries & Mäkelä, 2020).…”

Section: Introductionmentioning

confidence: 99%

Fungal systems for lignocellulose deconstruction: From enzymatic mechanisms to hydrolysis optimization

Ren,

Wu,

et al. 2024

GCB Bioenergy

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Lignocellulosic biomass is an abundant renewable feedstock, but its complex structure of lignocellulose poses barriers to its enzymatic hydrolysis and fermentation. Fungi possess diverse lignocellulolytic enzyme systems that synergistically deconstruct lignocellulose into soluble sugars for fermentation. This review elucidates recent advances in understanding the molecular mechanisms underpinning fungal degradation of lignocellulose. We analyze major enzyme classes tailored by fungi to depolymerize cellulose, hemicellulose, and lignin. Highlighted are the concerted actions and intimate partnerships between these biomass‐degrading enzymes. Current challenges impeding large‐scale implementation of enzymatic hydrolysis are discussed, along with emerging biotechnological opportunities. Advanced pretreatments, high‐throughput enzyme engineering platforms, and machine learning or artificial intelligence‐guided lignocellulolytic enzyme cocktail optimization represent promising ways to improve hydrolytic efficiencies. Elucidating the coordinated interplay and regulation of fungal lignocellulolytic machinery can facilitate optimization of fungal biotechnology platforms. Harnessing the efficiency of fungal biomass deconstruction promises to enhance the development of biorefinery processes for sustainable bioenergy.

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The enzyme interactome concept in filamentous fungi linked to biomass valorization

Cited by 23 publications

References 107 publications

Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroom Lyophyllum decastes reveals insights on evolution and lignocellulose degradation potential

Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroom Lyophyllum decastes reveals insights on evolution and lignocellulose degradation potential

Fungal Cell Factories for Efficient and Sustainable Production of Proteins and Peptides

Fungal systems for lignocellulose deconstruction: From enzymatic mechanisms to hydrolysis optimization

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