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Biomolecules
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Regulation and Mechanisms of Plant Biomass Degrading Enzymes from Fungi
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Regulation and Mechanisms of Plant Biomass Degrading Enzymes from Fungi

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Enzymology".

Deadline for manuscript submissions: closed (1 June 2023) | Viewed by 15391

Special Issue Editors

Dr. Monika Schmoll

E-Mail Website
Guest Editor
Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria
Interests: Trichoderma reesei; signal transduction; light response; sexual development; plant cell wall degradation;
Dr. Daniel Kracher

E-Mail Website
Guest Editor
Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
Interests: biomass degradation; second-generation biofuels; cellulases; redox enzymes; biocatalysis
Special Issues, Collections and Topics in MDPI journals
Dr. Paul Daly

E-Mail Website
Guest Editor
Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
Interests: CAZymes; genomics; gene regulation; microbe-–microbe and plant-–microbe interactions

Special Issue Information

Dear Colleagues,

With their high potential to degrade recalcitrant plant biomass in nature, fungi contribute significantly to the global carbon cycle. To succeed in their habitat, fungi evolved sophisticated mechanisms for tight regulation of plant cell wall degrading enzymes, as well as efficient enzymes combined for optimal resource efficiency of energy input for enzyme biosynthesis and output of nutrient acquisition.

Understanding the natural heritage of fungi, in terms of the regulation of plant cell wall degradation and the required efficient enzyme combinations, serves to enhance biotechnology to achieve a more sustainable industry. Enzymes perform challenging chemical conversions in a stereo-selective and often more efficient way than conventional chemical strategies. From biofuels to food additives to washing agents—enzymes have become crucial components of numerous everyday products.

In several decades of research, enzyme production has improved considerably and knowledge on enzyme modification for enhanced efficiency has increased. Nevertheless, in many cases, the application of enzymes is still hampered by limited stability under the required conditions, as well as prohibitive production costs for large-scale applications. However, besides the industrial value of enzymes, the high ecological relevance of fungi in nature as major degraders of plant biomass, as well as their role in the complex microbiome, is of high importance to ensure biodiversity, fertile soils, and a healthy nutrient cycle.

For this Special Issue, we welcome original research manuscripts as well as reviews covering the breadth of the topic from regulatory impacts of environmental signals and nutrients on signaling pathways, also during fungus–plant interaction (the natural basis for plant biomass degradation), to transcriptional and posttranscriptional regulation, secretion to enzyme activity, optimization as well as enzyme-substrate interactions. Studies on model organisms, little studied fungi, and oomycetes with ecological, agricultural, or biotechnological relevance will be considered, as well as novel tools and methods to investigate regulation mechanisms or enzyme function in fungi.

Dr. Monika Schmoll
Dr. Daniel Kracher
Dr. Paul Daly
Guest Editors

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. Biomolecules 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 2700 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

  • fungi
  • gene regulation
  • plant biomass
  • CAZyme production
  • molecular tools

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Published Papers (5 papers)

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Research

20 pages, 2461 KiB  
Article
Growth, Enzymatic, and Transcriptomic Analysis of xyr1 Deletion Reveals a Major Regulator of Plant Biomass-Degrading Enzymes in Trichoderma harzianum
by Lunji Wang, Yishen Zhao, Siqiao Chen, Xian Wen, Wilfred Mabeche Anjago, Tianchi Tian, Yajuan Chen, Jinfeng Zhang, Sheng Deng, Min Jiu, Pengxiao Fu, Dongmei Zhou, Irina S. Druzhinina, Lihui Wei and Paul Daly
Biomolecules 2024, 14(2), 148; https://doi.org/10.3390/biom14020148 - 24 Jan 2024
Viewed by 1637
Abstract
The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in [...] Read more.
The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed through growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had ~90% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. The expression of a subset of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes. Full article
(This article belongs to the Special Issue Regulation and Mechanisms of Plant Biomass Degrading Enzymes from Fungi)
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14 pages, 2761 KiB  
Article
Intracellular Sugar Transporters Facilitate Cellulase Synthesis in Trichoderma reesei Using Lactose
by Haiyan Wang, Ai-Ping Pang, Bingzhi Li, Liujie Huo, Fu-Gen Wu and Fengming Lin
Biomolecules 2023, 13(2), 295; https://doi.org/10.3390/biom13020295 - 4 Feb 2023
Cited by 2 | Viewed by 2222
Abstract
Sugar transporters play an important role in the cellulase production of lignocellulose-degrading fungi. Nevertheless, the role and function of these transporters are still unclear. Here we first report intracellular sugar transporters assisting cellulase production in Trichoderma reesei (T. reesei) using lactose. The mRNA [...] Read more.
Sugar transporters play an important role in the cellulase production of lignocellulose-degrading fungi. Nevertheless, the role and function of these transporters are still unclear. Here we first report intracellular sugar transporters assisting cellulase production in Trichoderma reesei (T. reesei) using lactose. The mRNA levels of sugar transporter genes mfs, gst, and lac1 were substantially upregulated in T. reesei cultivated on lactose, with the most abundant mRNA levels at 24 h as compared to glucose. Moreover, the individual deletion of these sugar transporters significantly inhibited cellulase production, solid cell growth, and sporulation of T. reesei, suggesting they play a supporting role in cellulase production when grown in lactose. Surprisingly, MFS, GST, and LAC1 were mainly localized in the cytoplasm, with MFS and LAC1 in the endoplasmic reticulum (ER), representing the first discovery of intracellular sugar transporters involved in cellulase biosynthesis in lactose culture. The absence of the gene lac1 noticeably inhibited most of the crucial genes related to cellulase production, including cellulase-encoding genes, transcription factors, and sugar transporters, at 24 h, which was fully relieved at 48 h or 72 h, indicating that lac1 affects cellulase production more at the early step. This research advances the understanding of the function of intracellular sugar transporters in fungi, particularly for fungal cellulase production. Full article
(This article belongs to the Special Issue Regulation and Mechanisms of Plant Biomass Degrading Enzymes from Fungi)
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11 pages, 2239 KiB  
Article
Identification of an l-Arabitol Transporter from Aspergillus niger
by Jiali Meng, Miia R. Mäkelä and Ronald P. de Vries
Biomolecules 2023, 13(2), 188; https://doi.org/10.3390/biom13020188 - 17 Jan 2023
Cited by 1 | Viewed by 2268
Abstract
l-arabitol is an intermediate of the pentose catabolic pathway in fungi but can also be used as a carbon source by many fungi, suggesting the presence of transporters for this polyol. In this study, an l-arabitol transporter, LatA, was identified in [...] Read more.
l-arabitol is an intermediate of the pentose catabolic pathway in fungi but can also be used as a carbon source by many fungi, suggesting the presence of transporters for this polyol. In this study, an l-arabitol transporter, LatA, was identified in Aspergillus niger. Growth and expression profiles as well as sugar consumption analysis indicated that LatA only imports l-arabitol and is regulated by the arabinanolytic transcriptional activator AraR. Moreover, l-arabitol production from wheat bran was increased in a metabolically engineered A. niger mutant by the deletion of latA, indicating its potential for improving l-arabitol-producing cell factories. Phylogenetic analysis showed that homologs of LatA are widely conserved in fungi. Full article
(This article belongs to the Special Issue Regulation and Mechanisms of Plant Biomass Degrading Enzymes from Fungi)
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14 pages, 2652 KiB  
Article
Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora
by Mila Marinovíc, Marcos Di Falco, Maria Victoria Aguilar Pontes, András Gorzsás, Adrian Tsang, Ronald P. de Vries, Miia R. Mäkelä and Kristiina Hildén
Biomolecules 2022, 12(8), 1017; https://doi.org/10.3390/biom12081017 - 22 Jul 2022
Cited by 7 | Viewed by 2501
Abstract
The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them indispensable organisms in the global carbon cycle. In this study, we analyzed the proteomes of two closely related white rot fungi, Obba rivulosa and Gelatoporia [...] Read more.
The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them indispensable organisms in the global carbon cycle. In this study, we analyzed the proteomes of two closely related white rot fungi, Obba rivulosa and Gelatoporia subvermispora, during eight-week cultivation on solid spruce wood. Plant cell wall degrading carbohydrate-active enzymes (CAZymes) represented approximately 5% of the total proteins in both species. A core set of orthologous plant cell wall degrading CAZymes was shared between these species on spruce suggesting a conserved plant biomass degradation approach in this clade of basidiomycete fungi. However, differences in time-dependent production of plant cell wall degrading enzymes may be due to differences among initial growth rates of these species on solid spruce wood. The obtained results provide insight into specific enzymes and enzyme sets that are produced during the degradation of solid spruce wood in these fungi. These findings expand the knowledge on enzyme production in nature-mimicking conditions and may contribute to the exploitation of white rot fungi and their enzymes for biotechnological applications. Full article
(This article belongs to the Special Issue Regulation and Mechanisms of Plant Biomass Degrading Enzymes from Fungi)
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15 pages, 3436 KiB  
Article
Application of CRISPR/Cas9 Tools for Genome Editing in the White-Rot Fungus Dichomitus squalens
by Joanna E. Kowalczyk, Shreya Saha and Miia R. Mäkelä
Biomolecules 2021, 11(10), 1526; https://doi.org/10.3390/biom11101526 - 15 Oct 2021
Cited by 9 | Viewed by 4889
Abstract
Dichomitus squalens is an emerging reference species that can be used to investigate white-rot fungal plant biomass degradation, as it has flexible physiology to utilize different types of biomass as sources of carbon and energy. Recent comparative (post-) genomic studies on D. squalens [...] Read more.
Dichomitus squalens is an emerging reference species that can be used to investigate white-rot fungal plant biomass degradation, as it has flexible physiology to utilize different types of biomass as sources of carbon and energy. Recent comparative (post-) genomic studies on D. squalens resulted in an increasingly detailed knowledge of the genes and enzymes involved in the lignocellulose breakdown in this fungus and showed a complex transcriptional response in the presence of lignocellulose-derived compounds. To fully utilize this increasing amount of data, efficient and reliable genetic manipulation tools are needed, e.g., to characterize the function of certain proteins in vivo and facilitate the construction of strains with enhanced lignocellulolytic capabilities. However, precise genome alterations are often very difficult in wild-type basidiomycetes partially due to extremely low frequencies of homology directed recombination (HDR) and limited availability of selectable markers. To overcome these obstacles, we assessed various Cas9-single guide RNA (sgRNA) ribonucleoprotein (RNP) -based strategies for selectable homology and non-homologous end joining (NHEJ) -based gene editing in D. squalens. We also showed an induction of HDR-based genetic modifications by using single-stranded oligodeoxynucleotides (ssODNs) in a basidiomycete fungus for the first time. This paper provides directions for the application of targeted CRISPR/Cas9-based genome editing in D. squalens and other wild-type (basidiomycete) fungi. Full article
(This article belongs to the Special Issue Regulation and Mechanisms of Plant Biomass Degrading Enzymes from Fungi)
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