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(Functional) Genomics and Bioinformatics in Fungal Plant Biomass Conversion
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(Functional) Genomics and Bioinformatics in Fungal Plant Biomass Conversion

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 6810

Special Issue Editor

Dr. Mao Peng

E-Mail Website
Guest Editor
Westerdijk Fungal Biodiversity Institute, KNAW, Utrecht, The Netherlands
Interests: bioinformatics; machine learning; omics analysis; plant biomass conversion; fungal biodiversity

Special Issue Information

Dear Colleagues,

In nature, fungi are the major degraders of plant biomass, and play a key role in the global carbon cycle. The crucial enzymes or genes involved in fungal plant biomass conversion (FPC) have been widely applied or shown tremendous potential in many industrials, such as biofuel, papers, textile and food. In recent decades, genomics, functional genomics and bioinformatics have became indispensable methods for facilitating the discovery of crucial genes/pathways involved in FPC, including novel degrading enzymes, sugar transporters, sugar metabolic genes, signalling pathways, transcriptional regulatory networks and fungal biodiversity. In this Special Issue, we would like to bring together the cutting-edge research employing (functional-) genomics approaches or developing novel bioinformatics methods to improve our understanding of fungal plant biomass conversion.

Dr. Mao Peng
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fungal plant biomass conversion
  • bioinformatics
  • genomics
  • transcriptome
  • proteome
  • metabolome
  • signalling
  • regulatory network

Published Papers (3 papers)

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Research

21 pages, 4315 KiB  
Article
Overexpression of the Transcription Factor Azf1 Reveals Novel Regulatory Functions and Impacts β-Glucosidase Production in Trichoderma reesei
by David Batista Maués, Jhonatan Christian Maraschin, Diego Ângelo Duarte, Amanda Cristina Campos Antoniêto and Roberto N. Silva
J. Fungi 2023, 9(12), 1173; https://doi.org/10.3390/jof9121173 - 07 Dec 2023
Viewed by 1259
Abstract
The fungus Trichoderma reesei is an essential producer of enzymes that degrade lignocellulosic biomass to produce value-added bioproducts. The cellulolytic system of T. reesei is controlled by several transcription factors (TFs) that efficiently regulate the production of these enzymes. Recently, a new TF [...] Read more.
The fungus Trichoderma reesei is an essential producer of enzymes that degrade lignocellulosic biomass to produce value-added bioproducts. The cellulolytic system of T. reesei is controlled by several transcription factors (TFs) that efficiently regulate the production of these enzymes. Recently, a new TF named Azf1 was identified as a positive regulator of cellulase expression. Here, we investigated novel regulatory functions of Azf1 by its overexpression. In the mutant strain OEazf1, overexpression of azf1 was achieved under both repression and induction conditions. Although azf1 was more abundant in transcript and protein, overexpression of this TF did not activate transcription of the cellulase gene in the presence of the repressor glucose, suggesting that Azf1 may be subject to posttranslational regulation. In cellulose, the expression of swo, encoding the accessory protein swollenin, and the β-glucosidases cel1a, cel1b, cel3b, and cel3g increases in the early stages of cultivation. The increased production of these β-glucosidases increases the hydrolysis rate of cellobiose and sophorose, which activates carbon catabolite repression (CCR) and causes repression of cellulase genes and the regulator Xyr1 in the later stages of cultivation. Moreover, overexpression of azf1 led to increased cellulase activity in T. reesei during long-term cultivation in cellulose and sugarcane bagasse. Our results provide new insights into the mechanisms regulating Azf1 and novel genes that are important targets of this TF. This work contributes to a better understanding of the complex mechanisms regulating cellulase expression in T. reesei. It will contribute to the development of strains with higher production of these essential enzymes. Full article
(This article belongs to the Special Issue (Functional) Genomics and Bioinformatics in Fungal Plant Biomass Conversion)
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12 pages, 2633 KiB  
Article
Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa
by Byoungnam Min, Steven Ahrendt, Anna Lipzen, Cristina E. Toapanta, Robert A. Blanchette, Dan Cullen, David S. Hibbett and Igor V. Grigoriev
J. Fungi 2023, 9(10), 1029; https://doi.org/10.3390/jof9101029 - 19 Oct 2023
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Abstract
Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures [...] Read more.
Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures containing Wiley milled wood (5 days) and solid wood wafers (30 days), using aspen, pine, and spruce as a substrate. The comparative analysis revealed that wood species had a limited effect on the transcriptome: <3% of genes were differentially expressed between different wood species substrates. The comparison between gene expression during growth on milled wood and wood wafer conditions, however, indicated that the genes encoding plant cell wall-degrading enzymes, such as glycoside hydrolases and peptidases, were activated during growth on wood wafers, confirming previous reports. On the other hand, it was shown for the first time that the genes encoding Fenton chemistry enzymes, such as hydroquinone biosynthesis enzymes and oxidoreductases, were activated during submerged growth on ground wood. This illustrates the diversity of wood-decay reactions encoded in fungi and activated at different stages of this process. Full article
(This article belongs to the Special Issue (Functional) Genomics and Bioinformatics in Fungal Plant Biomass Conversion)
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23 pages, 5892 KiB  
Article
The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum
by Jiajia Li, Tania Chroumpi, Sandra Garrigues, Roland S. Kun, Jiali Meng, Sonia Salazar-Cerezo, Maria Victoria Aguilar-Pontes, Yu Zhang, Sravanthi Tejomurthula, Anna Lipzen, Vivian Ng, Chaevien S. Clendinen, Nikola Tolić, Igor V. Grigoriev, Adrian Tsang, Miia R. Mäkelä, Berend Snel, Mao Peng and Ronald P. de Vries
J. Fungi 2022, 8(12), 1315; https://doi.org/10.3390/jof8121315 - 17 Dec 2022
Cited by 6 | Viewed by 3764
Abstract
Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. We mapped the well-established sugar metabolic network of Aspergillus niger to five taxonomically distant species (Aspergillus nidulans [...] Read more.
Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. We mapped the well-established sugar metabolic network of Aspergillus niger to five taxonomically distant species (Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium and Dichomitus squalens) using an orthology-based approach. The diversity of sugar metabolism correlates well with the taxonomic distance of the fungi. The pathways are highly conserved between the three studied Eurotiomycetes (A. niger, A. nidulans, P. subrubescens). A higher level of diversity was observed between the T. reesei and A. niger, and even more so for the two Basidiomycetes. These results were confirmed by integrative analysis of transcriptome, proteome and metabolome, as well as growth profiles of the fungi growing on the corresponding sugars. In conclusion, the establishment of sugar pathway models in different fungi revealed the diversity of fungal sugar conversion and provided a valuable resource for the community, which would facilitate rational metabolic engineering of these fungi as microbial cell factories. Full article
(This article belongs to the Special Issue (Functional) Genomics and Bioinformatics in Fungal Plant Biomass Conversion)
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