Molecular Mechanisms of Interactions of Trichoderma with other Fungal Species

A tomato mutant with reduced mycorrhizal colonisation, rmc, confers resistance to almost all arbuscular mycorrhizal (AM) fungal species tested, although there is variation in colonisation of different root cell layers by different fungi and one species of AM fungus can colonise this mutant relatively normally. These variations indicate a high degree of specificity in relation to AM colonisation. We explored the possibility of specificity or otherwise in interactions between rmc and three non-AM root-infecting fungi, Rhizoctonia solani anastomosis groups (AG) 4 and AG8, and binucleate Rhizoctonia (BNR). There were no differences between the wild type tomato 76R and rmc in the speed or extent to which these fungi infected roots or caused disease. Infection by R. solani induced high levels of defence-related gene expression in both tomato genotypes relative to non-infected plants. In contrast, with BNR the expression of these genes was not induced or induced to a much lower extent than with R. solani. The expression of defence-related genes with these two non-AM fungi was very similar in the two plant genotypes. It was different from effects observed during colonisation by AM fungi, which enhanced expression of defence-related genes in rmc compared with the wild type tomato. The specificity and molecular mechanisms of rmc in control of AM colonisation are discussed.

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Forward genetic screens identified mutants with defects in trap morphogenesis in the nematode-trapping fungus Arthrobotrys oligospora

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa022 ◽

2020 ◽

Vol 11 (2) ◽

Author(s):

Tsung-Yu Huang ◽

Yi-Yun Lee ◽

Guillermo Vidal-Diez de Ulzurrun ◽

Yen-Ping Hsueh

Keyword(s):

Genome Sequencing ◽

Genetic Screening ◽

Molecular Mechanisms ◽

Fungal Species ◽

Screening Methods ◽

Whole Genome ◽

Genetic Screens ◽

Arthrobotrys Oligospora ◽

Forward Genetic Screens ◽

Functional Analyses

Abstract Nematode-trapping fungi (NTF) are carnivorous fungi that prey on nematodes under nutrient-poor conditions via specialized hyphae that function as traps. The molecular mechanisms involved in the interactions between NTF and their nematode prey are largely unknown. In this study, we conducted forward genetic screens to identify potential genes and pathways that are involved in trap morphogenesis and predation in the NTF Arthrobotrys oligospora. Using Ethyl methanesulfonate and UV as the mutagens, we generated 5552 randomly mutagenized A. oligospora strains and identified 15 mutants with strong defects in trap morphogenesis. Whole-genome sequencing and bioinformatic analyses revealed mutations in genes with roles in signaling, transcription or membrane transport that may contribute to the defects of trap morphogenesis in these mutants. We further conducted functional analyses on a candidate gene, YBP-1, and demonstrate that mutation of that gene was causative of the phenotypes observed in one of the mutants. The methods established in this study might provide helpful insights for establishing forward genetic screening methods for other non-model fungal species.

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Antifungal Resistance: Specific Focus on Multidrug Resistance in Candida auris and Secondary Azole Resistance in Aspergillus fumigatus

Journal of Fungi ◽

10.3390/jof4040129 ◽

2018 ◽

Vol 4 (4) ◽

pp. 129 ◽

Cited By ~ 16

Author(s):

Sevtap Arikan-Akdagli ◽

Mahmoud Ghannoum ◽

Jacques Meis

Keyword(s):

Aspergillus Fumigatus ◽

Molecular Mechanisms ◽

Multidrug Resistant ◽

Fungal Species ◽

Antifungal Resistance ◽

Current Status ◽

Clinical Implications ◽

Azole Resistance ◽

Candida Auris

Antifungal resistance is a topic of concern, particularly for specific fungal species and drugs. Among these are the multidrug-resistant Candida auris and azole-resistant Aspergillus fumigatus. While the knowledge on molecular mechanisms of resistance is now accumulating, further data are also available for the clinical implications and the extent of correlation of in vitro resistance to clinical outcomes. This review article summarizes the epidemiology of C. auris infections, animal models focusing on the activity of novel antifungal compounds in C. auris infections, virulence factors, and the mechanisms of antifungal resistance for this multi-resistant Candida species. Regarding A. fumigatus, the significance of azoles in the treatment of A. fumigatus infections, reference methods available for the detection of resistance in vitro, molecular mechanisms of secondary azole resistance, routes of acquisition, and clinical implications of in vitro resistance are covered to provide guidance for the current status of azole resistance in A. fumigatus.

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Autophagy and LAP in the Fight against Fungal Infections: Regulation and Therapeutics

Mediators of Inflammation ◽

10.1155/2018/6195958 ◽

2018 ◽

Vol 2018 ◽

pp. 1-7 ◽

Cited By ~ 6

Author(s):

Vasileios Oikonomou ◽

Giorgia Renga ◽

Antonella De Luca ◽

Monica Borghi ◽

Marilena Pariano ◽

...

Keyword(s):

Molecular Mechanisms ◽

Fungal Infections ◽

Cell Types ◽

Fungal Species ◽

Host Immune Responses ◽

Host Protection ◽

Pathogen Clearance ◽

The Relationship ◽

Broad Role

Phagocytes fight fungi using canonical and noncanonical, also called LC3-associated phagocytosis (LAP), autophagy pathways. However, the outcomes of autophagy/LAP in shaping host immune responses appear to greatly vary depending on fungal species and cell types. By allowing efficient pathogen clearance and/or degradation of inflammatory mediators, autophagy proteins play a broad role in cellular and immune homeostasis during fungal infections. Indeed, defects in autophagic machinery have been linked with aberrant host defense and inflammatory states. Thus, understanding the molecular mechanisms underlying the relationship between the different forms of autophagy may offer a way to identify drugable molecular signatures discriminating between selective recognition of cargo and host protection. In this regard, IFN-γ and anakinra are teaching examples of successful antifungal agents that target the autophagy machinery. This article provides an overview of the role of autophagy/LAP in response to fungi and in their infections, regulation, and therapeutic exploitation.

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A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress

Scientific Reports ◽

10.1038/s41598-021-82136-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Nivedita ◽

Abdul Rawoof ◽

Nirala Ramchiary ◽

Malik Z. Abdin

Keyword(s):

Salt Stress ◽

Molecular Mechanisms ◽

Transcriptional Response ◽

Fungal Species ◽

Piriformospora Indica ◽

Rna Seq ◽

Oxidoreductase Activity ◽

High Salt Stress ◽

Comparative Functional Genomics ◽

And Oxidative Stress

AbstractPiriformospora indica, a root endophytic fungus, augments plant nutrition and productivity as well as protects plants against pathogens and abiotic stresses. High salinity is a major problem faced by plants as well as by microbes. Until now, the precise mechanism of salt stress tolerance in P. indica has remained elusive. In this study, the transcriptomes of control and salt-treated (0.5 M NaCl) P. indica were sequenced via the RNA-seq approach. A total of 30,567 transcripts and 15,410 unigenes for P. indica were obtained from 7.3 Gb clean reads. Overall 661 differentially expressed genes (DEGs) between control and treated samples were retrieved. Gene ontology (GO) and EuKaryotic Orthologous Groups (KOG) enrichments revealed that DEGs were specifically involved in metabolic and molecular processes, such as “response to salt stress”, “oxidoreductase activity”, “ADP binding”, “translation, ribosomal structure and biogenesis”, “cytoskeleton”, and others. The unigenes involved in “cell wall integrity”, “sterol biosynthesis”, and “oxidative stress” such as Rho-type GTPase, hydroxymethylglutaryl-CoA synthase, and thioredoxin peroxidase were up-regulated in P. indica subjected to salt stress. The salt-responsive DEGs have shown that they might have a potential role in salt stress regulation. Our study on the salt-responsive DEGs established a foundation for the elucidation of molecular mechanisms related to P. indica stress adaptation and a future reference for comparative functional genomics studies of biotechnologically important fungal species.

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Forward genetic screens identified mutants with defects in trap morphogenesis in the nematode-trapping fungus Arthrobotrys oligospora

10.1101/2020.09.15.298422 ◽

2020 ◽

Author(s):

Tsung-Yu Huang ◽

Yi-Yun Lee ◽

Guillermo Vidal-Diez de Ulzurrun ◽

Yen-Ping Hsueh

Keyword(s):

Genome Sequencing ◽

Genetic Screening ◽

Molecular Mechanisms ◽

Fungal Species ◽

Screening Methods ◽

Whole Genome ◽

Genetic Screens ◽

Arthrobotrys Oligospora ◽

Forward Genetic Screens ◽

Functional Analyses

AbstractNematode-trapping fungi (NTF) are carnivorous fungi that prey on nematodes under nutrient-poor conditions via specialized hyphae that function as traps. The molecular mechanisms involved in the interactions between nematode-trapping fungi and their nematode prey are largely unknown. In this study, we conducted forward genetic screens to identify potential genes and pathways that are involved in trap morphogenesis and predation in the NTF Arthrobotrys oligospora. Using Ethyl methanesulfonate and UV as the mutagens, we generated 5552 randomly-mutagenized A. oligospora strains and identified 15 mutants with strong defects in trap morphogenesis. Whole genome sequencing and bioinformatic analyses revealed mutations in genes with roles in signaling, transcription or membrane transport that may contribute to the defects of trap morphogenesis in these mutants. We further conducted functional analyses on a candidate gene, YBP-1, and demonstrate that mutation of that gene was causative of the phenotypes observed in one of the mutants. The methods established in this study might provide helpful insights for establishing forward genetic screening methods for other non-model fungal species.

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Fungal chromatin mapping identifies BasR, as the regulatory node of bacteria-induced fungal secondary metabolism

10.1101/211979 ◽

2017 ◽

Cited By ~ 1

Author(s):

Juliane Fischer ◽

Sebastian Y. Müller ◽

Tina Netzker ◽

Nils Jäger ◽

Agnieszka Gacek-Matthews ◽

...

Keyword(s):

Secondary Metabolism ◽

Gene Cluster ◽

Molecular Mechanisms ◽

Effective Interaction ◽

Chromatin Modification ◽

Gene Clusters ◽

Fungal Species ◽

Transcriptional Initiation ◽

Genome Wide ◽

Eukaryotic Microorganisms

AbstractThe eukaryotic epigenetic machinery is targeted by bacteria to reprogram the response of eukaryotes during their interaction with microorganisms. In line, we discovered that the bacterium Streptomyces rapamycinicus triggered increased chromatin acetylation and thus activation of the silent secondary metabolism ors gene cluster leading to the production of orsellinic acid in the fungus Aspergillus nidulans. Using this model we aim at understanding molecular mechanisms of communication between bacteria and eukaryotic microorganisms based on bacteria-triggered chromatin modification. By genome-wide ChIP-seq analysis of acetylated histone H3 (H3K9ac, H3K14ac) we uncovered the unique chromatin landscape in A. nidulans upon co-cultivation with S. rapamycinicus. Genome-wide acetylation of H3K9 correlated with increased gene expression, whereas H3K14 appears to function in transcriptional initiation by providing a docking side for regulatory proteins. In total, histones belonging to six secondary metabolism gene clusters showed higher acetylation during co-cultivation including the ors, aspercryptin, cichorine, sterigmatocystin, anthrone and 2,4-dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde gene cluster with the emericellamide cluster being the only one with reduced acetylation and expression. Differentially acetylated histones were also detected in genes involved in amino acid and nitrogen metabolism, signaling, and genes encoding transcription factors. In conjunction with LC-MS/MS and MALDI-MS imaging, molecular analyses revealed the cross-pathway control and Myb-like transcription factor BasR as regulatory nodes for transduction of the bacterial signal in the fungus. The presence of basR in other fungal species allowed forecasting the inducibility of ors-like gene clusters by S. rapamycinicus in these fungi, and thus their effective interaction with activation of otherwise silent gene clusters.

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The Quiet and Underappreciated Rise of Drug-Resistant Invasive Fungal Pathogens

Journal of Fungi ◽

10.3390/jof6030138 ◽

2020 ◽

Vol 6 (3) ◽

pp. 138 ◽

Cited By ~ 6

Author(s):

Amir Arastehfar ◽

Cornelia Lass-Flörl ◽

Rocio Garcia-Rubio ◽

Farnaz Daneshnia ◽

Macit Ilkit ◽

...

Keyword(s):

Fungal Pathogens ◽

Molecular Mechanisms ◽

Fungal Infections ◽

Multidrug Resistant ◽

Resistance Mechanisms ◽

Fungal Species ◽

Antifungal Resistance ◽

Candida Auris ◽

Recent Emergence ◽

Invasive Infections

Human fungal pathogens are attributable to a significant economic burden and mortality worldwide. Antifungal treatments, although limited in number, play a pivotal role in decreasing mortality and morbidities posed by invasive fungal infections (IFIs). However, the recent emergence of multidrug-resistant Candida auris and Candida glabrata and acquiring invasive infections due to azole-resistant C. parapsilosis, C. tropicalis, and Aspergillus spp. in azole-naïve patients pose a serious health threat considering the limited number of systemic antifungals available to treat IFIs. Although advancing for major fungal pathogens, the understanding of fungal attributes contributing to antifungal resistance is just emerging for several clinically important MDR fungal pathogens. Further complicating the matter are the distinct differences in antifungal resistance mechanisms among various fungal species in which one or more mechanisms may contribute to the resistance phenotype. In this review, we attempt to summarize the burden of antifungal resistance for selected non-albicansCandida and clinically important Aspergillus species together with their phylogenetic placement on the tree of life. Moreover, we highlight the different molecular mechanisms between antifungal tolerance and resistance, and comprehensively discuss the molecular mechanisms of antifungal resistance in a species level.

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Investigating Common Pathogenic Mechanisms between Homo sapiens and Different Strains of Candida albicans for Drug Design: Systems Biology Approach via Two-Sided NGS Data Identification

Toxins ◽

10.3390/toxins11020119 ◽

2019 ◽

Vol 11 (2) ◽

pp. 119

Author(s):

Shan-Ju Yeh ◽

Chun-Chieh Yeh ◽

Chung-Yu Lan ◽

Bor-Sen Chen

Keyword(s):

Candida Albicans ◽

Cross Talk ◽

Drug Targets ◽

Molecular Mechanisms ◽

Homo Sapiens ◽

Fungal Species ◽

Pathogenic Mechanisms ◽

Host Pathogen ◽

Different Strains ◽

Ngs Data

Candida albicans (C. albicans) is the most prevalent fungal species. Although it is a healthy microbiota, genetic and epigenetic alterations in host and pathogen, and microenvironment changes would lead to thrush, vaginal yeast infection, and even hematogenously disseminated infection. Despite the fact that cytotoxicity is well-characterized, few studies discuss the genome-wide genetic and epigenetic molecular mechanisms between host and C. albicans. The aim of this study is to identify drug targets and design a multiple-molecule drug to prevent the infection from C. albicans. To investigate the common and specific pathogenic mechanisms in human oral epithelial OKF6/TERT-2 cells during the C. albicans infection in different strains, systems modeling and big databases mining were used to construct candidate host–pathogen genetic and epigenetic interspecies network (GEIN). System identification and system order detection are applied on two-sided next generation sequencing (NGS) data to build real host–pathogen cross-talk GEINs. Core host–pathogen cross-talk networks (HPCNs) are extracted by principal network projection (PNP) method. By comparing with core HPCNs in different strains of C. albicans, common pathogenic mechanisms were investigated and several drug targets were suggested as follows: orf19.5034 (YBP1) with the ability of anti-ROS; orf19.939 (NAM7), orf19.2087 (SAS2), orf19.1093 (FLO8) and orf19.1854 (HHF22) with high correlation to the hyphae growth and pathogen protein interaction; orf19.5585 (SAP5), orf19.5542 (SAP6) and orf19.4519 (SUV3) with the cause of biofilm formation. Eventually, five corresponding compounds—Tunicamycin, Terbinafine, Cerulenin, Tetracycline and Tetrandrine—with three known drugs could be considered as a potential multiple-molecule drug for therapeutic treatment of C. albicans.

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Transcription factor/DNA interactions visualized by electron spectroscopic imaging

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100122654 ◽

1992 ◽

Vol 50 (1) ◽

pp. 450-451

Author(s):

David P. Bazett-Jones ◽

Mark L. Brown

Keyword(s):

Transcription Factor ◽

Dna Sequences ◽

Transcription Initiation ◽

Molecular Mechanisms ◽

Phosphorus Content ◽

Spectroscopic Imaging ◽

Electron Spectroscopic Imaging ◽

Dna Backbone ◽

Two Parameters ◽

High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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