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New Perspectives on Fungal Molecular Biology Research
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New Perspectives on Fungal Molecular Biology Research

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 December 2023) | Viewed by 21007

Special Issue Editor

Dr. Paloma Sánchez-Torres

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Guest Editor
Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain
Interests: fungal biotechnology, synthetic biology; fungal control; fungicide resistance; fungal virulence; signal transduction pathways; host–pathogen interaction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fungi have been studied for their importance from the biotechnological point of view due to their ability to produce different compounds (enzymes, primary and secondary metabolites, etc.) and at the same time for their pathogenicity. Recent developments in fungal genome engineering have opened a new frontier by implementing the CRISPR-Cas9 technology and synthetic biology tools contributing to the development of new perspectives on fungal molecular biology research.

This Special Issue will focus on any type of study addressing the different molecular approaches developed for fungal biotechnology and on potential new target strategies to control fungal infections based on virulence factors and signal transduction pathways underlying the control of infection mechanisms.

We believe that this Special Issue will provide an up-to-date overview and new insights into the potential of molecular studies in fungi.

Dr. Paloma Sánchez-Torres
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.

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Published Papers (7 papers)

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Research

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17 pages, 3288 KiB  
Article
Discovery and Transcriptional Profiling of Penicillium digitatum Genes That Could Promote Fungal Virulence during Citrus Fruit Infection
by Paloma Sánchez-Torres, Luis González-Candelas and Ana Rosa Ballester
J. Fungi 2024, 10(4), 235; https://doi.org/10.3390/jof10040235 - 22 Mar 2024
Cited by 1 | Viewed by 1428
Abstract
Green mold caused by Penicillium digitatum (Pers.:Fr.) Sacc is the most prevalent postharvest rot concerning citrus fruits. Using the subtractive suppression hybridization (SSH) technique, different P. digitatum genes have been identified that could be involved in virulence during citrus infection in the early [...] Read more.
Green mold caused by Penicillium digitatum (Pers.:Fr.) Sacc is the most prevalent postharvest rot concerning citrus fruits. Using the subtractive suppression hybridization (SSH) technique, different P. digitatum genes have been identified that could be involved in virulence during citrus infection in the early stages, a crucial moment that determines whether the infection progresses or not. To this end, a comparison of two P. digitatum strains with high and low virulence has been carried out. We conducted a study on the gene expression profile of the most relevant genes. The results indicate the importance of transcription and regulation processes as well as enzymes involved in the degradation of the plant cell wall. The most represented expressed sequence tag (EST) was identified as PDIP_11000, associated with the FluG domain, which is putatively involved in the activation of conidiation. It is also worth noting that PDIP_02280 encodes a pectin methyl esterase, a cell wall remodeling protein with a high expression level in the most virulent fungal strains, which is notably induced during citrus infection. Furthermore, within the group with the greatest representation and showing significant induction in the early stages of infection, regulatory proteins (PDIP_68700, PDIP_76160) and a chaperone (PDIP_38040) stand out. To a lesser extent, but not less relevant, it is worth distinguishing different regulatory proteins and transcription factors, such as PDIP_00580, PDIP_49640 and PDIP_78930. Full article
(This article belongs to the Special Issue New Perspectives on Fungal Molecular Biology Research)
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11 pages, 13867 KiB  
Communication
Effects of MAT1-2 Spore Ratios on Fruiting Body Formation and Degeneration in the Heterothallic Fungus Cordyceps militaris
by Tao Xuan Vu, Hanh-Dung Thai, Bich-Hang Thi Dinh, Huong Thi Nguyen, Huyen Thi Phuong Tran, Khanh-Linh Thi Bui, Tram Bao Tran, Hien Thanh Pham, Linh Thi Dam Mai, Diep Hong Le, Huy Quang Nguyen and Van-Tuan Tran
J. Fungi 2023, 9(10), 971; https://doi.org/10.3390/jof9100971 - 27 Sep 2023
Cited by 5 | Viewed by 2631
Abstract
The medicinal mushroom Cordyceps militaris is widely exploited in traditional medicine and nutraceuticals in Asian countries. However, fruiting body production in C. militaris is facing degeneration through cultivation batches, and the molecular mechanism of this phenomenon remains unclear. This study showed that fruiting [...] Read more.
The medicinal mushroom Cordyceps militaris is widely exploited in traditional medicine and nutraceuticals in Asian countries. However, fruiting body production in C. militaris is facing degeneration through cultivation batches, and the molecular mechanism of this phenomenon remains unclear. This study showed that fruiting body formation in three different C. militaris strains, namely G12, B12, and HQ1, severely declined after three successive culturing generations using the spore isolation method. PCR analyses revealed that these strains exist as heterokaryons and possess both the mating-type loci, MAT1-1 and MAT1-2. Further, monokaryotic isolates carrying MAT1-1 or MAT1-2 were successfully separated from the fruiting bodies of all three heterokaryotic strains. A spore combination of the MAT1-1 monokaryotic isolate and the MAT1-2 monokaryotic isolate promoted fruiting body formation, while the single monokaryotic isolates could not do that themselves. Notably, we found that changes in ratios of the MAT1-2 spores strongly influenced fruiting body formation in these strains. When the ratios of the MAT1-2 spores increased to more than 15 times compared to the MAT1-1 spores, the fruiting body formation decreased sharply. In contrast, when MAT1-1 spores were increased proportionally, fruiting body formation was only slightly reduced. Our study also proposes a new solution to mitigate the degeneration in the heterokaryotic C. militaris strains caused by successive culturing generations. Full article
(This article belongs to the Special Issue New Perspectives on Fungal Molecular Biology Research)
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28 pages, 6924 KiB  
Article
Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors
by Karla Gisel Carreón-Anguiano, Rufino Gómez-Tah, Efren Pech-Balan, Gemaly Elisama Ek-Hernández, César De los Santos-Briones, Ignacio Islas-Flores and Blondy Canto-Canché
J. Fungi 2023, 9(10), 970; https://doi.org/10.3390/jof9100970 - 27 Sep 2023
Cited by 2 | Viewed by 1756
Abstract
Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the [...] Read more.
Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen–Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors. Full article
(This article belongs to the Special Issue New Perspectives on Fungal Molecular Biology Research)
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12 pages, 4690 KiB  
Article
A Putative TRAPα Protein of Microsporidia Nosema bombycis Exhibits Non-Canonical Alternative Polyadenylation in Transcripts
by Yujiao Wu, Ying Yu, Quan Sun, Yixiang Yu, Jie Chen, Tian Li, Xianzhi Meng, Guoqing Pan and Zeyang Zhou
J. Fungi 2023, 9(4), 407; https://doi.org/10.3390/jof9040407 - 25 Mar 2023
Cited by 1 | Viewed by 1715
Abstract
Microsporidia are obligate intracellular eukaryotic parasites that have significantly reduced genomes and that have lost most of their introns. In the current study, we characterized a gene in microsporidia Nosema bombycis, annotated as TRAPα (HNbTRAPα). The homologous of TRAPα are [...] Read more.
Microsporidia are obligate intracellular eukaryotic parasites that have significantly reduced genomes and that have lost most of their introns. In the current study, we characterized a gene in microsporidia Nosema bombycis, annotated as TRAPα (HNbTRAPα). The homologous of TRAPα are a functional component of ER translocon and facilitates the initiation of protein translocation in a substrate-specific manner, which is conserved in animals but absent from most fungi. The coding sequence of HNbTRAPα consists of 2226 nucleotides, longer than the majority of homologs in microsporidia. A 3′ RACE analysis indicated that there were two mRNA isoforms resulting from non-canonical alternative polyadenylation (APA), and the polyadenylate tail was synthesized after the C951 or C1167 nucleotide, respectively. Indirect immunofluorescence analysis showed two different localization characteristics of HNbTRAPα, which are mainly located around the nuclear throughout the proliferation stage and co-localized with the nuclear in mature spores. This study demonstrated that the post-transcriptional regulation mechanism exists in Microsporidia and expands the mRNA isoform repertoire. Full article
(This article belongs to the Special Issue New Perspectives on Fungal Molecular Biology Research)
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24 pages, 4343 KiB  
Article
In Vitro Fermentation of Pleurotus eryngii Mushrooms by Human Fecal Microbiota: Metataxonomic Analysis and Metabolomic Profiling of Fermentation Products
by Paris Christodoulou, Marigoula Vlassopoulou, Maria Zervou, Evangelos Xanthakos, Panagiotis Moulos, Georgios Koutrotsios, Georgios I. Zervakis, Evangelia N. Kerezoudi, Evdokia K. Mitsou, Georgia Saxami, Adamantini Kyriacou, Vasiliki Pletsa and Panagiotis Georgiadis
J. Fungi 2023, 9(1), 128; https://doi.org/10.3390/jof9010128 - 16 Jan 2023
Cited by 3 | Viewed by 3954
Abstract
Edible mushrooms contain biologically active compounds with antioxidant, antimicrobial, immunomodulatory and anticancer properties. The link between their anticancer and immunomodulatory properties with their possible prebiotic activity on gut micro-organisms has been the subject of intense research over the last decade. Lyophilized Pleurotus eryngii [...] Read more.
Edible mushrooms contain biologically active compounds with antioxidant, antimicrobial, immunomodulatory and anticancer properties. The link between their anticancer and immunomodulatory properties with their possible prebiotic activity on gut micro-organisms has been the subject of intense research over the last decade. Lyophilized Pleurotus eryngii (PE) mushrooms, selected due to their strong lactogenic effect and anti-genotoxic, immunomodulatory properties, underwent in vitro static batch fermentation for 24 h by fecal microbiota from eight elderly apparently healthy volunteers (>65 years old). The fermentation-induced changes in fecal microbiota communities were examined using Next Generation Sequencing of the hypervariable regions of the 16S rRNA gene. Primary processing and analysis were conducted using the Ion Reporter Suite. Changes in the global metabolic profile were assessed by 1H NMR spectroscopy, and metabolites were assigned by 2D NMR spectroscopy and the MetaboMiner platform. PLS-DA analysis of both metataxonomic and metabolomic data showed a significant cluster separation of PE fermented samples relative to controls. DEseq2 analysis showed that the abundance of families such as Lactobacillaceae and Bifidobacteriaceae were increased in PE samples. Accordingly, in metabolomics, more than twenty metabolites including SCFAs, essential amino acids, and neurotransmitters discriminate PE samples from the respective controls, further validating the metataxonomic findings. Full article
(This article belongs to the Special Issue New Perspectives on Fungal Molecular Biology Research)
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23 pages, 2545 KiB  
Article
Unraveling the Secrets of a Double-Life Fungus by Genomics: Ophiocordyceps australis CCMB661 Displays Molecular Machinery for Both Parasitic and Endophytic Lifestyles
by Thaís Almeida de Menezes, Flávia Figueira Aburjaile, Gabriel Quintanilha-Peixoto, Luiz Marcelo Ribeiro Tomé, Paula Luize Camargos Fonseca, Thairine Mendes-Pereira, Daniel Silva Araújo, Tarcisio Silva Melo, Rodrigo Bentes Kato, Jacques Hubert Charles Delabie, Sérvio Pontes Ribeiro, Bertram Brenig, Vasco Azevedo, Elisandro Ricardo Drechsler-Santos, Bruno Silva Andrade and Aristóteles Góes-Neto
J. Fungi 2023, 9(1), 110; https://doi.org/10.3390/jof9010110 - 13 Jan 2023
Cited by 4 | Viewed by 3890
Abstract
Ophiocordyceps australis (Ascomycota, Hypocreales, Ophiocordycipitaceae) is a classic entomopathogenic fungus that parasitizes ants (Hymenoptera, Ponerinae, Ponerini). Nonetheless, according to our results, this fungal species also exhibits a complete set of genes coding for plant cell wall degrading Carbohydrate-Active enZymes (CAZymes), enabling a full [...] Read more.
Ophiocordyceps australis (Ascomycota, Hypocreales, Ophiocordycipitaceae) is a classic entomopathogenic fungus that parasitizes ants (Hymenoptera, Ponerinae, Ponerini). Nonetheless, according to our results, this fungal species also exhibits a complete set of genes coding for plant cell wall degrading Carbohydrate-Active enZymes (CAZymes), enabling a full endophytic stage and, consequently, its dual ability to both parasitize insects and live inside plant tissue. The main objective of our study was the sequencing and full characterization of the genome of the fungal strain of O. australis (CCMB661) and its predicted secretome. The assembled genome had a total length of 30.31 Mb, N50 of 92.624 bp, GC content of 46.36%, and 8,043 protein-coding genes, 175 of which encoded CAZymes. In addition, the primary genes encoding proteins and critical enzymes during the infection process and those responsible for the host–pathogen interaction have been identified, including proteases (Pr1, Pr4), aminopeptidases, chitinases (Cht2), adhesins, lectins, lipases, and behavioral manipulators, such as enterotoxins, Protein Tyrosine Phosphatases (PTPs), and Glycoside Hydrolases (GHs). Our findings indicate that the presence of genes coding for Mad2 and GHs in O. australis may facilitate the infection process in plants, suggesting interkingdom colonization. Furthermore, our study elucidated the pathogenicity mechanisms for this Ophiocordyceps species, which still is scarcely studied. Full article
(This article belongs to the Special Issue New Perspectives on Fungal Molecular Biology Research)
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Review

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19 pages, 4330 KiB  
Review
Exploring the Mycovirus Universe: Identification, Diversity, and Biotechnological Applications
by Diana Carolina Villan Larios, Brayan Maudiel Diaz Reyes, Carlos Priminho Pirovani, Leandro Lopes Loguercio, Vinícius Castro Santos, Aristóteles Góes-Neto, Paula Luize Camargos Fonseca and Eric Roberto Guimarães Rocha Aguiar
J. Fungi 2023, 9(3), 361; https://doi.org/10.3390/jof9030361 - 15 Mar 2023
Cited by 13 | Viewed by 4731
Abstract
Viruses that infect fungi are known as mycoviruses and are characterized by the lack of an extracellular phase. In recent years, the advances on nucleic acids sequencing technologies have led to a considerable increase in the number of fungi-infecting viral species described in [...] Read more.
Viruses that infect fungi are known as mycoviruses and are characterized by the lack of an extracellular phase. In recent years, the advances on nucleic acids sequencing technologies have led to a considerable increase in the number of fungi-infecting viral species described in the literature, with a special interest in assessing potential applications as fungal biocontrol agents. In the present study, we performed a comprehensive review using Scopus, Web of Science, and PubMed databases to mine mycoviruses data to explore their molecular features and their use in biotechnology. Our results showed the existence of 267 mycovirus species, of which 189 are recognized by the International Committee on Taxonomy of Viruses (ICTV). The majority of the mycoviruses identified have a dsRNA genome (38.6%), whereas the Botourmiaviridae (ssRNA+) alone represents 14% of all mycoviruses diversity. Regarding fungal hosts, members from the Sclerotinicaeae appeared as the most common species described to be infected by mycoviruses, with 16 different viral families identified so far. It is noteworthy that such results are directly associated with the high number of studies and strategies used to investigate the presence of viruses in members of the Sclerotinicaeae family. The knowledge about replication strategy and possible impact on fungi biology is available for only a small fraction of the mycoviruses studied, which is the main limitation for considering these elements potential targets for biotechnological applications. Altogether, our investigation allowed us to summarize the general characteristics of mycoviruses and their hosts, the consequences, and the implications of this knowledge on mycovirus–fungi interactions, providing an important source of information for future studies. Full article
(This article belongs to the Special Issue New Perspectives on Fungal Molecular Biology Research)
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