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Biology Open Dec 2020Basidiomycota are a large and diverse phylum of fungi. They can make bioactive metabolites that are used or have inspired the synthesis of antibiotics and agrochemicals.... (Review)
Review
Basidiomycota are a large and diverse phylum of fungi. They can make bioactive metabolites that are used or have inspired the synthesis of antibiotics and agrochemicals. Terpenoids are the most abundant class of natural products encountered in this taxon. Other natural product classes have been described, including polyketides, peptides, and indole alkaloids. The discovery and study of natural products made by basidiomycete fungi has so far been hampered by several factors, which include their slow growth and complex genome architecture. Recent developments of tools for genome and metabolome studies are allowing researchers to more easily tackle the secondary metabolome of basidiomycete fungi. Inexpensive long-read whole-genome sequencing enables the assembly of high-quality genomes, improving the scaffold upon which natural product gene clusters can be predicted. CRISPR/Cas9-based engineering of basidiomycete fungi has been described and will have an important role in linking natural products to their genetic determinants. Platforms for the heterologous expression of basidiomycete genes and gene clusters have been developed, enabling natural product biosynthesis studies. Molecular network analyses and publicly available natural product databases facilitate data dereplication and natural product characterisation. These technological advances combined are prompting a revived interest in natural product discovery from basidiomycete fungi.This article has an associated Future Leader to Watch interview with the first author of the paper.
Topics: Basidiomycota; Biological Products; CRISPR-Cas Systems; Gene Expression Regulation, Fungal; Genetic Engineering; Genomics; Metabolomics; Research; Secondary Metabolism; Structure-Activity Relationship
PubMed: 33268478
DOI: 10.1242/bio.056010 -
Current Opinion in Microbiology Dec 2008The mating-type locus (MAT) orchestrates sexual reproduction in fungi. Sexual reproduction is related not only to fitness of an organism, but also correlated with... (Review)
Review
The mating-type locus (MAT) orchestrates sexual reproduction in fungi. Sexual reproduction is related not only to fitness of an organism, but also correlated with virulence in certain pathogens. In the dandruff-associated fungus Malassesia globosa, although the sexual cycle remains to be discovered, whole genome analysis has led to the hypothesis that mating may occur on host skin. Furthermore, the MAT locus of M. globosa and U. hordei provides evidence that transitions between tetrapolar and bipolar systems have independently occurred. These results, together with studies recapitulating the ancestral tetrapolar mating system in Cryptococcus and the structure of MAT in related smut fungi, have furthered understanding on transitions between different mating systems and the evolution of MAT in the Basidiomycota.
Topics: Adaptation, Biological; Animals; Basidiomycota; Genes, Mating Type, Fungal; Humans; Recombination, Genetic; Virulence
PubMed: 18935978
DOI: 10.1016/j.mib.2008.09.014 -
Applied Microbiology and Biotechnology Aug 2022The nonconventional yeast Xanthophyllomyces dendrorhous is an established platform for genetic pathway modification. A genetic tool box is available and can be used... (Review)
Review
The nonconventional yeast Xanthophyllomyces dendrorhous is an established platform for genetic pathway modification. A genetic tool box is available and can be used extensively to select from for different engineering strategies. Due to the diploid nature of X. dendrorhous, genetic transformation typically results in heterozygous lines. They are genetically unstable and lose their phenotypes caused by mitotic recombination. In addition, targeted integration for inactivation of genes of the carotenoid pathway resulted in an intermediary phenotype of incomplete pathway disruption. This issue is the main scope of this review. It is illustrated by using genetic modification of the carotenoid pathway of X. dendrorhous as a model system with a focus on the demonstration of how to solve these problems by generation of homozygous lines. They can be selected from heterozygous transformants after spontaneous mitotic recombination and selection or after induced meiotic recombination. Corresponding methods of how to proceed including the initiation of a sexual cycle are described. The selected segregated lines are stable in fermenter cultures without the need of selection pressure. This is an essential requirement for any industrial application. KEY POINTS: • Genetic interventions of diploid yeasts result in heterozygous transformants that are unstable without selection pressure. • This is due to mitotic recombination leading to the elimination of inserted DNA. • Stable homozygous lines can be obtained and selected after either meiotic or mitotic recombination.
Topics: Basidiomycota; Carotenoids; Diploidy; Yeasts
PubMed: 35831455
DOI: 10.1007/s00253-022-12054-2 -
BMC Genomics Mar 2021Hericium erinaceus, a rare edible and medicine fungus, is widely used in the food and medical field. Polysaccharides from H. erinaceus are the main bioactive compound...
BACKGROUND
Hericium erinaceus, a rare edible and medicine fungus, is widely used in the food and medical field. Polysaccharides from H. erinaceus are the main bioactive compound that exert high bioactive value in the medical and healthcare industries.
RESULTS
The genome of H. erinaceus original strain HEA was reported 38.16 Mb, encoding 9780 predicted genes by single-molecule, real-time sequencing technology. The phylogenomic analysis showed that H. erinaceus had the closest evolutionary affinity with Dentipellis sp. The polysaccharide content in the fermented mycelia of mutated strains HEB and HEC, which obtained by ARTP mutagenesis in our previous study, was improved by 23.25 and 47.45%, and a new β-glucan fraction with molecular weight 1.056 × 10 Da was produced in HEC. Integrative analysis of transcriptome and proteomics showed the upregulation of the carbohydrate metabolism pathway modules in HEB and HEC might lead to the increased production of glucose-6P and promote the repeating units synthesis of polysaccharides. qPCR and PRM analysis confirmed that most of the co-enriched and differentially co-expressed genes involved in carbohydrate metabolism shared a similar expression trend with the transcriptome and proteome data in HEB and HEC. Heatmap analysis showed a noticeably decreased protein expression profile of the RAS-cAMP-PKA pathway in HEC with a highly increased 47.45% of polysaccharide content. The S phase progression blocking experiment further verified that the RAS-cAMP-PKA pathway's dysfunction might promote high polysaccharide and β-glucan production in the mutant strain HEC.
CONCLUSIONS
The study revealed the primary mechanism of the increased polysaccharide synthesis induced by ARTP mutagenesis and explored the essential genes and pathways of polysaccharide synthesis.
Topics: Basidiomycota; Hericium; Molecular Weight; Mycelium; Polysaccharides
PubMed: 33676419
DOI: 10.1186/s12864-021-07480-x -
Microbial Cell Factories Oct 2021The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with...
BACKGROUND
The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available.
RESULTS
In this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide.
CONCLUSIONS
Relative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus.
Topics: Basidiomycota; Carbohydrate Metabolism; Fungal Proteins; Hydrolases; Industrial Microbiology; Lipid Metabolism; Proteome; Systems Biology
PubMed: 34711240
DOI: 10.1186/s12934-021-01692-2 -
The New Phytologist Apr 2018The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world,... (Review)
Review
The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability. As one of the most species-diverse ectomycorrhizal lineages, the Russulaceae has recently been the focus of a dense sampling and genome sequencing initiative with the Joint Genome Institute aimed at untangling their functional roles and testing whether functional niche specialization exists for independent lineages of ectomycorrhizal fungi. Here we present a review of important studies on this group to contextualize what we know about its members' evolutionary history and ecosystem functions, as well as to generate hypotheses establishing the Russulaceae as a valuable experimental system.
Topics: Basidiomycota; Biological Evolution; Ecosystem; Genome, Fungal; Mycorrhizae; Trees
PubMed: 29381218
DOI: 10.1111/nph.15001 -
Journal of Microbiology (Seoul, Korea) Sep 2015A number of pathogenic species of basidiomycete fungi are either life-threatening pathogens of humans or major economic pests for crop production. Sensing the host is a... (Review)
Review
A number of pathogenic species of basidiomycete fungi are either life-threatening pathogens of humans or major economic pests for crop production. Sensing the host is a key aspect of pathogen proliferation during disease, and signal transduction pathways are critically important for detecting environmental conditions and facilitating adaptation. This review focuses on the contributions of the cAMP/protein kinase A (PKA) signaling pathway in Cryptococcus neoformans, a species that causes meningitis in humans, and Ustilago maydis, a model phytopathogen that causes a smut disease on maize. Environmental sensing by the cAMP/PKA pathway regulates the production of key virulence traits in C. neoformans including the polysaccharide capsule and melanin. For U. maydis, the pathway controls the dimorphic transition from budding growth to the filamentous cell type required for proliferation in plant tissue. We discuss recent advances in identifying new components of the cAMP/PKA pathway in these pathogens and highlight an emerging theme that pathway signaling influences iron acquisition.
Topics: Basidiomycota; Cryptococcus neoformans; Cyclic AMP; Cyclic AMP-Dependent Protein Kinases; Genes, Fungal; Homeostasis; Hydrogen-Ion Concentration; Iron; Signal Transduction; Ustilago
PubMed: 26231374
DOI: 10.1007/s12275-015-5247-5 -
Biomolecules May 2023f. sp. () is the causative agent of wheat stripe rust, which can lead to a significant loss in annual wheat yields. Therefore, there is an urgent need for a deeper... (Review)
Review
f. sp. () is the causative agent of wheat stripe rust, which can lead to a significant loss in annual wheat yields. Therefore, there is an urgent need for a deeper comprehension of the basic mechanisms underlying infection. Effectors are known as the agents that plant pathogens deliver into host tissues to promote infection, typically by interfering with plant physiology and biochemistry. Insights into effector activity can significantly aid the development of future strategies to generate disease-resistant crops. However, the functional analysis of effectors is still in its infancy, which hinders our understanding of the molecular mechanisms of the interaction between and wheat. In this review, we summarize the potential roles of validated and proposed effectors during wheat infection, including proteinaceous effectors, non-coding RNAs (sRNA effectors), and secondary metabolites (SMs effectors). Further, we suggest specific countermeasures against pathogenesis and future research directions, which may promote our understanding of effector functions during wheat immunity attempts.
Topics: Triticum; Puccinia; Basidiomycota
PubMed: 37371469
DOI: 10.3390/biom13060889 -
PLoS Pathogens Jul 2017
Review
Topics: Basidiomycota; Disease Resistance; Host-Parasite Interactions; Plant Diseases
PubMed: 28704545
DOI: 10.1371/journal.ppat.1006380 -
FEMS Microbiology Reviews Dec 2000Ectomycorrhizas, the dominating mycorrhizal symbiosis in boreal, temperate and some tropical forests, are formed by 5000-6000 species of the asco- and basidiomycetes.... (Review)
Review
Ectomycorrhizas, the dominating mycorrhizal symbiosis in boreal, temperate and some tropical forests, are formed by 5000-6000 species of the asco- and basidiomycetes. This high diversity of fungal partners allows optimal foraging and mobilisation of various nitrogen and phosphorus forms from organic soil layers. In this review, two approaches to study the functioning of this multitude of symbiotic associations are presented. On selected culture models, physiological and molecular investigations have shown that the supply of hexoses has a key function in controlling the plant-fungus interaction via partner-specific regulation of gene expression. Environmental factors which affect fungal carbon supply, such as increased nitrogen availability, also affect mycorrhiza formation. Based on such laboratory results, the adaptative capability of ectomycorrhizas to changing field conditions is discussed. The second approach consists of analysing the distribution of mycorrhizas in ecosystem compartments and to relate distribution patterns to variations of ecological factors. Recent advances in identification of fungal partners in ectomycorrhizas by analysing the internal transcribed spacer of ribosomal DNA are presented, which can help to resolve sampling problems in field studies. The limits of the laboratory and the field approaches are discussed. Despite some problems, this combined approach is the most promising. Direct investigation of gene expression, which has been introduced for soil bacteria, will be difficult in the case of mycorrhizal fungi which constitute organisms with functionally varying structures.
Topics: Ascomycota; Basidiomycota; Ecosystem; Plant Roots; Symbiosis; Trees
PubMed: 11077153
DOI: 10.1111/j.1574-6976.2000.tb00561.x