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Sass G, Martinez M, Kotta-Loizou I, Stevens D. AfuPmV-1-Infected Aspergillus fumigatus Is More Susceptible to Stress Than Virus-Free Fungus. J Fungi (Basel) 2023; 9:750. [PMID: 37504738 PMCID: PMC10381315 DOI: 10.3390/jof9070750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Infection with Aspergillus fumigatus polymycovirus 1 (AfuPmV-1) affects Aspergillus fumigatus Af293's growth in vitro, iron metabolism, resistance in intermicrobial competition with Pseudomonas aeruginosa, resistance to osmotic stress, and resistance to the chitin synthase inhibitor nikkomycin Z. Here, we show that response to high temperature, Congo Red-induced stress, and hydrogen peroxide are also dependent on the viral infection status of A. fumigatus. AfuPmV-1- infected Af293 was more susceptible than virus-free Af293 to growth inhibition by high temperature, hydrogen peroxide, Congo Red exposure, and nutrient restriction. Increased resistance of virus-free fungus was observed when cultures were started from conidia but, in the case of high temperature and hydrogen peroxide, not when cultures were started from hyphae. This indicates that the virus impairs the stress response during the growth phase of germination of conidia and development into hyphae. In conclusion, our work indicates that AfuPmV-1 infection in A. fumigatus impairs host responses to stress, as shown by exposure to high temperature, oxidative stress such as hydrogen peroxide, and some cell wall stresses, as shown by exposure to Congo Red (in agreement with our previous observations using nikkomycin Z) and nutrient restriction.
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Affiliation(s)
- Gabriele Sass
- California Institute for Medical Research, San Jose, CA 95128, USA
| | - Marife Martinez
- California Institute for Medical Research, San Jose, CA 95128, USA
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW72AZ, UK
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL109AB, UK
| | - David Stevens
- California Institute for Medical Research, San Jose, CA 95128, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Hough B, Steenkamp E, Wingfield B, Read D. Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses. Viruses 2023; 15:1202. [PMID: 37243288 PMCID: PMC10224137 DOI: 10.3390/v15051202] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.
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Affiliation(s)
| | | | - Brenda Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria 0002, South Africa; (B.H.); (E.S.); (D.R.)
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Sass G, Kotta-Loizou I, Martinez M, Larwood DJ, Stevens DA. Polymycovirus Infection Sensitizes Aspergillus fumigatus for Antifungal Effects of Nikkomycin Z. Viruses 2023; 15:197. [PMID: 36680240 PMCID: PMC9864188 DOI: 10.3390/v15010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Infection with Aspergillus fumigatus polymycovirus 1 (AfuPmV-1) weakens resistance of Aspergillus fumigatus common reference strain Af293 biofilms in intermicrobial competition with Pseudomonas aeruginosa. We compared the sensitivity of two infected and one virus-free Af293 strains to antifungal drugs. All three were comparably sensitive to drugs affecting fungal membranes (voriconazole, amphotericin) or cell wall glucan synthesis (micafungin, caspofungin). In contrast, forming biofilms of virus-free Af293 were much more resistant than AfuPmV-1-infected Af293 to nikkomycin Z (NikZ), a drug inhibiting chitin synthase. The IC50 for NikZ on biofilms was between 3.8 and 7.5 µg/mL for virus-free Af293 and 0.94-1.88 µg/mL for infected strains. The IC50 for the virus-free A. fumigatus strain 10AF was ~2 µg/mL in most experiments. NikZ also modestly affected the planktonic growth of infected Af293 more than the virus-free strain (MIC 50%, 2 and 4 µg/mL, respectively). Virus-free Af293 biofilm showed increased metabolism, and fungus growing as biofilm or planktonically showed increased growth compared to infected; these differences do not explain the resistance of the virus-free fungus to NikZ. In summary, AfuPmV-1 infection sensitized A. fumigatus to NikZ, but did not affect response to drugs commonly used against A. fumigatus infection. Virus infection had a greater effect on NikZ inhibition of biofilm than planktonic growth.
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Affiliation(s)
- Gabriele Sass
- California Institute for Medical Research, San Jose, CA 95128, USA
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, UK
| | - Marife Martinez
- California Institute for Medical Research, San Jose, CA 95128, USA
| | | | - David A. Stevens
- California Institute for Medical Research, San Jose, CA 95128, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Nazik H, Kotta-Loizou I, Sass G, Coutts RHA, Stevens DA. Virus Infection of Aspergillus fumigatus Compromises the Fungus in Intermicrobial Competition. Viruses 2021; 13:v13040686. [PMID: 33923408 PMCID: PMC8073786 DOI: 10.3390/v13040686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Aspergillus and Pseudomonas compete in nature, and are the commonest bacterial and fungal pathogens in some clinical settings, such as the cystic fibrosis lung. Virus infections of fungi occur naturally. Effects on fungal physiology need delineation. A common reference Aspergillus fumigatus strain, long studied in two (of many) laboratories, was found infected with the AfuPmV-1 virus. One isolate was cured of virus, producing a virus-free strain. Virus from the infected strain was purified and used to re-infect three subcultures of the virus-free fungus, producing six fungal strains, otherwise isogenic. They were studied in intermicrobial competition with Pseudomonasaeruginosa. Pseudomonas culture filtrates inhibited forming or preformed Aspergillus biofilm from infected strains to a greater extent, also seen when Pseudomonas volatiles were assayed on Aspergillus. Purified iron-chelating Pseudomonas molecules, known inhibitors of Aspergillus biofilm, reproduced these differences. Iron, a stimulus of Aspergillus, enhanced the virus-free fungus, compared to infected. All infected fungal strains behaved similarly in assays. We show an important consequence of virus infection, a weakening in intermicrobial competition. Viral infection may affect the outcome of bacterial–fungal competition in nature and patients. We suggest that this occurs via alteration in fungal stress responses, the mechanism best delineated here is a result of virus-induced altered Aspergillus iron metabolism.
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Affiliation(s)
- Hasan Nazik
- California Institute for Medical Research, 2260 Clove Dr., San Jose, CA 95128, USA; (H.N.); (G.S.)
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK;
| | - Gabriele Sass
- California Institute for Medical Research, 2260 Clove Dr., San Jose, CA 95128, USA; (H.N.); (G.S.)
| | - Robert H. A. Coutts
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK;
| | - David A. Stevens
- California Institute for Medical Research, 2260 Clove Dr., San Jose, CA 95128, USA; (H.N.); (G.S.)
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 95128, USA
- Correspondence: ; Tel.: +1-408-998-4554
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Chiba Y, Oiki S, Yaguchi T, Urayama SI, Hagiwara D. Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses. Virus Evol 2020; 7:veaa101. [PMID: 33505709 PMCID: PMC7816673 DOI: 10.1093/ve/veaa101] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
By identifying variations in viral RNA genomes, cutting-edge metagenome
technology has potential to reshape current concepts about the evolution of RNA
viruses. This technology, however, cannot process low-homology genomic regions
properly, leaving the true diversity of RNA viruses unappreciated. To overcome
this technological limitation, we applied an advanced method, Fragmented and
Primer-Ligated Double-stranded (ds) RNA Sequencing (FLDS), to screen RNA viruses
from 155 fungal isolates, which allowed us to obtain complete viral genomes in a
homology-independent manner. We created a high-quality catalog of 19 RNA viruses
(12 viral species) that infect Aspergillus isolates. Among
them, nine viruses were not detectable by the conventional methodology involving
agarose gel electrophoresis of dsRNA, a hallmark of RNA virus infections.
Segmented genome structures were determined in 42 per cent of the viruses. Some
RNA viruses had novel genome architectures; one contained a dual
methyltransferase domain and another had a separated RNA-dependent RNA
polymerase (RdRp) gene. A virus from a different fungal taxon
(Pyricularia) had an RdRp sequence that was separated on
different segments, suggesting that a divided RdRp is widely present among
fungal viruses, despite the belief that all RNA viruses encode RdRp as a single
gene. These findings illustrate the previously hidden diversity and evolution of
RNA viruses, and prompt reconsideration of the structural plasticity of
RdRp.
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Affiliation(s)
- Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Sayoko Oiki
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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van de Sande WWJ, Vonk AG. Mycovirus therapy for invasive pulmonary aspergillosis? Med Mycol 2019; 57:S179-S188. [PMID: 30816971 DOI: 10.1093/mmy/myy073] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/21/2018] [Indexed: 12/13/2022] Open
Abstract
With the current revived interest in the use of bacteriophages for the treatment of bacterial infections, the study of mycoviruses as novel therapeutic solutions for invasive aspergillosis is the logical next step. Although ssRNA, dsRNA, and ssDNA mycoviruses have been identified, the majority of characterised mycoviruses have dsRNA genomes. Prevalence of dsRNA mycoviruses in Aspergillus spp. varies, and mycoviruses can have different effects on their fungal hosts: hypovirulence, hypervirulence, or a killer phenotype. Therapeutically, extracellular transmission of the mycovirus is essential. DsRNA mycoviruses lack an extracellular phase; however, a single ssDNA mycovirus with homologues in Aspergillus genomes has been described with an extracellular mode of transmission. Mycoviruses can induce hypovirulence or a killer phenotype, and both can be exploited therapeutically. Mycoviruses inducing hypovirulence have been used to control chestnut blight, however for aspergillosis no such mycovirus has been identified yet. Mycovirus encoded killer toxins or anti-idiotypic antibodies and killer peptides derived from these have been demonstrated to control fungal infections including aspergillosis in animals. This indicates that mycoviruses inducing both phenotypes could be exploited therapeutically as long as the right mycovirus has been identified.
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Affiliation(s)
- Wendy W J van de Sande
- ErasmusMC, Department of Medical Microbiology and Infectious Diseases, Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
| | - Alieke G Vonk
- ErasmusMC, Department of Medical Microbiology and Infectious Diseases, Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
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Ejmal MA, Holland DJ, MacDiarmid RM, Pearson MN. A novel chrysovirus from a clinical isolate of Aspergillus thermomutatus affects sporulation. PLoS One 2018; 13:e0209443. [PMID: 30571748 PMCID: PMC6301774 DOI: 10.1371/journal.pone.0209443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
A clinical isolate of Aspergillus thermomutatus (Teleomorph: Neosartorya pseudofischeri) was found to contain ~35 nm isometric virus-like particles associated with four double-stranded (ds) RNA segments, each of which coded for a single open reading frame. The longest dsRNA element (3589 nt) encodes a putative RNA-dependent RNA polymerase (1114 aa), the second longest dsRNA element (2772 nt) encodes a coat protein (825 aa), and the other two dsRNAs (2676 nt, 2514 nt) encode hypothetical proteins of 768 aa and 711 aa, respectively. Phylogenetic analysis of the amino acid sequences showed 41-60% similarity to the proteins coded by the dsRNAs of the most closely related virus, Penicillium janczewskii chrysovirus 2, indicating that it is a new species based on the International Committee on Taxonomy of Viruses criteria for the genus Chrysovirus. This is the first virus reported from A. thermomutatus and was tentatively named Aspergillus thermomutatus chrysovirus 1. A virus free line of the fungal isolate, cured by cycloheximide treatment, produced large numbers of conidia but no ascospores at both 20°C and 37°C, whereas the virus infected line produced ten-fold fewer conidia at 20°C and a large number of ascospores at both temperatures. The effects of the virus on fungal sporulation have interesting implications for the spread of the fungus and possible use of the virus as a biological control agent.
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Affiliation(s)
- Mahjoub A. Ejmal
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
| | - David J. Holland
- Infectious Diseases Unit, Division of Medicine, Staff Centre, Middlemore Hospital, Auckland, New Zealand
| | - Robin M. MacDiarmid
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Michael N. Pearson
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
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8
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Ejmal MA, Holland DJ, MacDiarmid RM, Pearson MN. The Effect of Aspergillus Thermomutatus Chrysovirus 1 on the Biology of Three Aspergillus Species. Viruses 2018; 10:E539. [PMID: 30279352 PMCID: PMC6213286 DOI: 10.3390/v10100539] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/25/2018] [Accepted: 09/29/2018] [Indexed: 12/16/2022] Open
Abstract
This study determined the effects of Aspergillus thermomutatus chrysovirus 1 (AthCV1), isolated from Aspergillus thermomutatus, on A. fumigatus, A. nidulans and A. niger. Protoplasts of virus-free isolates of A. fumigatus, A. nidulans and A. niger were transfected with purified AthCV1 particles and the phenotype, growth and sporulation of the isogenic AthCV1-free and AthCV1-infected lines assessed at 20 °C and 37 °C and gene expression data collected at 37 °C. AthCV1-free and AthCV1-infected A. fumigatus produced only conidia at both temperatures but more than ten-fold reduced compared to the AthCV1-infected line. Conidiation was also significantly reduced in infected lines of A. nidulans and A. niger at 37 °C. AthCV1-infected lines of A. thermomutatus and A. nidulans produced large numbers of ascospores at both temperatures, whereas the AthCV1-free line of the former did not produce ascospores. AthCV1-infected lines of all species developed sectoring phenotypes with sclerotia produced in aconidial sectors of A. niger at 37 °C. AthCV1 was detected in 18% of sclerotia produced by AthCV1-infected A. niger and 31% of ascospores from AthCV1-infected A. nidulans. Transcriptome analysis of the naturally AthCV1-infected A. thermomutatus and the three AthCV1-transfected Aspergillus species showed altered gene expression as a result of AthCV1-infection. The results demonstrate that AthCV1 can infect a range of Aspergillus species resulting in reduced sporulation, a potentially useful attribute for a biological control agent.
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Affiliation(s)
- Mahjoub A Ejmal
- School of Biological Sciences, the University of Auckland, Auckland 1142 New Zealand.
| | - David J Holland
- Infectious Diseases Unit, Division of Medicine, Middlemore Hospital, Auckland 1640, New Zealand.
| | - Robin M MacDiarmid
- School of Biological Sciences, the University of Auckland, Auckland 1142 New Zealand.
- Plant and Food Research, Auckland 1142, New Zealand.
| | - Michael N Pearson
- School of Biological Sciences, the University of Auckland, Auckland 1142 New Zealand.
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Zoll J, Verweij PE, Melchers WJG. Discovery and characterization of novel Aspergillus fumigatus mycoviruses. PLoS One 2018; 13:e0200511. [PMID: 30044844 PMCID: PMC6059430 DOI: 10.1371/journal.pone.0200511] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/27/2018] [Indexed: 11/20/2022] Open
Abstract
In the last few years, increasing numbers of viruses infecting fungi have been identified. In this study, we used an in silico approach for the analysis of deep RNA sequencing data in order to discover and characterize putative genomic ssRNA or dsRNA mycovirus sequences in Aspergillus fumigatus. RNA sequencing reads of A. fumigatus strains were mapped against the A. fumigatus Af293 reference genome. Unmapped reads were collected for de novo assembly. Contigs were analyzed by Blastx comparison with a mycovirus protein database. Assembled viral genomes were used as template for remapping of RNA sequencing reads. In total, deep RNA sequencing results from 11 A. fumigatus strains were analyzed for the presence of mycoviral genomic RNAs. In 9 out of 11 strains, putative mycoviral RNA genomes were identified. Three strains were infected with two different mycovirus species. Two strains were infected with Aspergillus fumigatus polymycovirus type-1 (AfuPmV-1). Four strains contained fully recovered genomic RNA of unknown narna-like viruses designated as Aspergillus fumigatus narnavirus-1 and Aspergillus fumigatus narnavirus-2 (AfuNV-1 and AfuNV-2). Both viruses showed 38% amino acid sequence identity to Beihai narna-like virus-21. Three strains contained partially recovered genomic RNA of an unknown narna-like virus. Two strains contained fully recovered genomic RNAs of an unknown partitivirus designated as Aspergillus fumigatus partitivirus-2 (AfuPV-2) which showed 50% amino acid sequence identity to Alternaria alternata partitivirus-1. Finally, one strain contained fully recovered genomic RNA of an unknown mitovirus designated as Aspergillus fumigatus mitovirus-1 (AfuMV-1) which showed 34% amino acid sequence identity to Sclerotina sclerotiorum mitovirus. In silico analysis of deep RNA sequencing results showed that a majority of the A. fumigatus strains used here were infected with mycoviruses. Four novel A. fumigatus RNA mycoviruses could be identified: two different Aspergillus fumigatus narna-like viruses, one Aspergillus fumigatus partitivirus, and one Aspergillus fumigatus mitovirus.
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Affiliation(s)
- Jan Zoll
- Department of Medical Microbiology, Radboud University Medical Center, and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
- * E-mail:
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud University Medical Center, and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
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10
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Özkan-Kotiloğlu S, Coutts RHA. Multiplex Detection of Aspergillus fumigatus Mycoviruses. Viruses 2018; 10:E247. [PMID: 29738445 PMCID: PMC5977240 DOI: 10.3390/v10050247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/05/2018] [Accepted: 05/06/2018] [Indexed: 01/16/2023] Open
Abstract
Mycoviruses are viruses that naturally infect and replicate in fungi. They are widespread in all major fungal groups including plant and animal pathogenic fungi. Several dsRNA mycoviruses have been reported in Aspergillus fumigatus. Multiplex polymerase chain reaction (PCR) amplification is a version of PCR that enables amplification of different targets simultaneously. This technique has been widely used for detection and differentiation of viruses especially plant viruses such as those which infect tobacco, potato and garlic. For rapid detection, multiplex RT-PCR was developed to screen new isolates for the presence of A. fumigatus mycoviruses. Aspergillus fumigatus chrysovirus (AfuCV), Aspergillus fumigatus partitivirus (AfuPV-1), and Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1) dsRNAs were amplified in separate reactions using a mixture of multiplex primer pairs. It was demonstrated that in the presence of a single infection, primer pair mixtures only amplify the corresponding single virus infection. Mixed infections using dual or triple combinations of dsRNA viruses were also amplified simultaneously using multiplex RT-PCR. Up until now, methods for the rapid detection of Aspergillus mycoviruses have been restricted to small scale dsRNA extraction approaches which are laborious and for large numbers of samples not as sensitive as RT-PCR. The multiplex RT-PCR assay developed here will be useful for studies on determining the incidence of A. fumigatus mycoviruses. This is the first report on multiplex detection of A. fumigatus mycoviruses.
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Affiliation(s)
- Selin Özkan-Kotiloğlu
- Department of Molecular Biology and Genetics, Ahi Evran University, Kırşehir 40100, Turkey.
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Robert H A Coutts
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
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11
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Kotta-Loizou I, Coutts RHA. Mycoviruses in Aspergilli: A Comprehensive Review. Front Microbiol 2017; 8:1699. [PMID: 28932216 PMCID: PMC5592211 DOI: 10.3389/fmicb.2017.01699] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/23/2017] [Indexed: 12/31/2022] Open
Abstract
Fungi, similar to all species, are susceptible to viral infection. Aspergillus is arguably the most well studied fungal genus because of its medical, ecological and economical significance. Mycoviruses were initially detected in Aspergillus species almost 50 years ago and the field continues to be active today with ground-breaking discoveries. The aim of the present review is to cover the scientific progress in all aspects of mycovirology as exemplified by Aspergillus-focused research. Initially an overview of the population studies illustrating the presence of mycoviruses in numerous important Aspergillus species, such as A. niger, A. flavus, and A. fumigatus with be presented. Moreover the intricacies of mycovirus transmission, both inter- and intra-species, will be discussed together with the methodologies used to investigate viral dispersion in a laboratory setting. Subsequently, the genomic features of all molecularly characterized mycoviruses to date will be analyzed in depth. These include members of established viral families, such as Partitiviridae, Chrysoviridae and Totiviridae, but also more recent, novel discoveries that led to the proposal of new viral families, such as Polymycoviridae, Alternaviridae and, in the context of the present review, Exartaviridae. Finally, the major issue of phenotypic effects of mycoviral infection on the host is addressed, including aflatoxin production in A. flavus, together with growth and virulence in A. fumigatus. Although the molecular mechanisms behind these phenomena are yet to be elucidated, recent studies suggest that by implication, RNA silencing may be involved.
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Affiliation(s)
- Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College LondonLondon, United Kingdom
| | - Robert H A Coutts
- Department of Biological and Environmental Sciences, University of HertfordshireHatfield, United Kingdom
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12
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Özkan S, Mohorianu I, Xu P, Dalmay T, Coutts RHA. Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses. BMC Genomics 2017; 18:416. [PMID: 28558690 PMCID: PMC5450132 DOI: 10.1186/s12864-017-3773-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/08/2017] [Indexed: 12/18/2022] Open
Abstract
Background Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencing. The A. fumigatus genome encodes essential components of the RNA silencing machinery, including Dicer, Argonaute and RNA-dependent RNA polymerase (RdRP) homologues. Active silencing of double-stranded (ds)RNA and the generation of small RNAs (sRNAs) has been shown for several mycoviruses and it is anticipated that a similar mechanism will be activated in A. fumigatus isolates infected with mycoviruses. Results To investigate the existence and nature of A. fumigatus sRNAs, sRNA-seq libraries of virus-free and virus-infected isolates were created using Scriptminer adapters and compared. Three dsRNA viruses were investigated: Aspergillus fumigatus partitivirus-1 (AfuPV-1, PV), Aspergillus fumigatus chrysovirus (AfuCV, CV) and Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1, NK) which were selected because they induce phenotypic changes such as coloration and sectoring. The dsRNAs of all three viruses, which included two conventionally encapsidated ones PV and CV and one unencapsidated example NK, were silenced and yielded characteristic vsiRNAs together with co-incidental silencing of host fungal genes which shared sequence homology with the viral genomes. Conclusions Virus-derived sRNAs were detected and characterised in the presence of virus infection. Differentially expressed A. fumigatus microRNA-like (miRNA-like) sRNAs and small interfering RNAs (siRNAs) were detected and validated. Host sRNA loci which were differentially expressed as a result of virus infection were also identified. To our knowledge, this is the first study reporting the sRNA profiles of A. fumigatus isolates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3773-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Selin Özkan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK. .,Current Address: Vocational School of Health Services, Ahi Evran University, Kırşehir, Turkey.
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Computing Sciences, University of East Anglia, Norwich, UK
| | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Robert H A Coutts
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.,Current Address: Geography, Environment and Agriculture Division, Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK
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Mycoviruses in the Plant Pathogen Ustilaginoidea virens Are Not Correlated with the Genetic Backgrounds of Its Hosts. Int J Mol Sci 2017; 18:ijms18050963. [PMID: 28467379 PMCID: PMC5454876 DOI: 10.3390/ijms18050963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/21/2017] [Accepted: 04/26/2017] [Indexed: 11/27/2022] Open
Abstract
Ustilaginoidea virens, the causal agent of rice false smut, is one of the most devastating grain diseases that causes loss of yield in most rice-growing areas worldwide. In this study, we performed a dsRNA screen to isolate mycoviruses from 35 U. virens strains. The results revealed that 34 of the tested isolates were infected by various dsRNA elements, displaying highly viral diversity and mixed infections. We characterized a 5.3 kbp dsRNA from a typical isolate containing dsRNA segments with sizes ranging from 0.5 to 5.3 kbp. Sequence analysis of its genomic properties indicated that it is a novel victorivirus, named Ustilaginoidea virens RNA virus 5 (UvRV5), that belongs to the family Totiviridae. RT-PCR detection was performed and indicated that not all the dsRNA bands that were 5.3 kbp in size contained UvRV5. Moreover, the genetic relatedness of all the U. virens strains was estimated according to phylogenetic analysis of the partial intergenic spacer region (IGS) sequences. However, concordance was not found between the dsRNA profiles and the IGS-based genetic relatedness of their host fungi.
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Paulussen C, Hallsworth JE, Álvarez‐Pérez S, Nierman WC, Hamill PG, Blain D, Rediers H, Lievens B. Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species. Microb Biotechnol 2017; 10:296-322. [PMID: 27273822 PMCID: PMC5328810 DOI: 10.1111/1751-7915.12367] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/08/2016] [Accepted: 04/18/2016] [Indexed: 01/26/2023] Open
Abstract
Fungi of the genus Aspergillus are widespread in the environment. Some Aspergillus species, most commonly Aspergillus fumigatus, may lead to a variety of allergic reactions and life-threatening systemic infections in humans. Invasive aspergillosis occurs primarily in patients with severe immunodeficiency, and has dramatically increased in recent years. There are several factors at play that contribute to aspergillosis, including both fungus and host-related factors such as strain virulence and host pulmonary structure/immune status, respectively. The environmental tenacity of Aspergilllus, its dominance in diverse microbial communities/habitats, and its ability to navigate the ecophysiological and biophysical challenges of host infection are attributable, in large part, to a robust stress-tolerance biology and exceptional capacity to generate cell-available energy. Aspects of its stress metabolism, ecology, interactions with diverse animal hosts, clinical presentations and treatment regimens have been well-studied over the past years. Here, we synthesize these findings in relation to the way in which some Aspergillus species have become successful opportunistic pathogens of human- and other animal hosts. We focus on the biophysical capabilities of Aspergillus pathogens, key aspects of their ecophysiology and the flexibility to undergo a sexual cycle or form cryptic species. Additionally, recent advances in diagnosis of the disease are discussed as well as implications in relation to questions that have yet to be resolved.
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Affiliation(s)
- Caroline Paulussen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - John E. Hallsworth
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Sergio Álvarez‐Pérez
- Faculty of Veterinary MedicineDepartment of Animal HealthUniversidad Complutense de MadridMadridE‐28040Spain
| | | | - Philip G. Hamill
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - David Blain
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Hans Rediers
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
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Fungal DNA virus infects a mycophagous insect and utilizes it as a transmission vector. Proc Natl Acad Sci U S A 2016; 113:12803-12808. [PMID: 27791095 DOI: 10.1073/pnas.1608013113] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycoviruses are usually transmitted horizontally via hyphal anastomosis and vertically via sexual/asexual spores. Previously, we reported that a gemycircularvirus, Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), could infect its fungal host extracellularly. Here, we discovered that SsHADV-1 could infect a mycophagous insect, Lycoriella ingenua, and use it as a transmission vector. Virus acquired by larvae feeding on colonies of a virus-infected strain of S. sclerotiorum was replicated and retained in larvae, pupae, adults, and eggs. Virus could be transmitted to insect offspring when larvae were injected with virus particles and allowed to feed on a nonhost fungus. Virus replication in insect cells was further confirmed by inoculating Spodoptera frugiperda cells with virus particles and analyzing with RT-PCR, Northern blot, immunofluorescence, and flow cytometry assays. Larvae could transmit virus once they acquired virus by feeding on virus-infected fungal colony. Offspring larvae hatched from viruliferous eggs were virus carriers and could also successfully transmit virus. Virus transmission between insect and fungus also occurred on rapeseed plants. Virus-infected isolates produced less repellent volatile substances to attract adults of L. ingenua Furthermore, L. ingenua was easily observed on Sclerotinia lesions in rapeseed fields, and viruliferous adults were captured from fields either sprayed with a virus-infected fungal strain or nonsprayed. Our findings may facilitate the exploration of mycoviruses for control of fungal diseases and enhance our understanding of the ecology of SsHADV-1 and other newly emerging SsHADV-1-like viruses, which were recently found to be widespread in various niches including human HIV-infected blood, human and animal feces, insects, plants, and even sewage.
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Parker MT. An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:339-351. [PMID: 27698618 PMCID: PMC5045143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recent advances in sequencing technologies have opened the door for the classification of the human virome. While taxonomic classification can be applied to the viruses identified in such studies, this gives no information as to the type of interaction the virus has with the host. As follow-up studies are performed to address these questions, the description of these virus-host interactions would be greatly enriched by applying a standard set of definitions that typify them. This paper describes a framework with which all members of the human virome can be classified based on principles of ecology. The scaffold not only enables categorization of the human virome, but can also inform research aimed at identifying novel virus-host interactions.
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Affiliation(s)
- Michael T Parker
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens. J Virol 2016; 90:6846-6863. [PMID: 27194764 DOI: 10.1128/jvi.00357-16] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/11/2016] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts. IMPORTANCE Plant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution.
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Özkan S, Coutts RHA. Aspergillus fumigatus mycovirus causes mild hypervirulent effect on pathogenicity when tested on Galleria mellonella. Fungal Genet Biol 2015; 76:20-6. [PMID: 25626171 DOI: 10.1016/j.fgb.2015.01.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 01/12/2015] [Accepted: 01/14/2015] [Indexed: 11/28/2022]
Abstract
Mycoviruses are a specific group of viruses that naturally infect and replicate in fungi. The importance of mycoviruses was revealed after their effects were identified not only in economically important fungi but also in the human pathogenic fungus Aspergillus fumigatus. The latter was shown recently to harbor at least three different types of mycoviruses including a chrysovirus, a partitivirus and an as yet uncharacterized virus. Assessment of virulence in the presence and absence of mycoviruses in A. fumigatus is pivotal to understanding its pathogenicity. Here, we have investigated, for the first time, the effects of mycoviruses on the pathogenicity of A. fumigatus as assessed using larvae of the greater wax moth Galleria mellonella. In order to observe the effects of mycoviruses on pathogenicity, G. mellonella were injected with virus-free and virus-infected isolates of A. fumigatus and post-infection survival times were analyzed along with the fungal burden. Neither chrysovirus nor partitivirus infection affected fungal pathogenicity when survival rates were assessed which, for the chrysovirus, agreed with a previous study on murine pathogenicity. However statistically significant differences were observed in survival rates and fungal burden in the presence of the uncharacterized A78 virus. Here we show, for the first time, the effects of a partitivirus and an uncharacterized A78 virus on the pathogenicity of A. fumigatus.
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Affiliation(s)
- Selin Özkan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK.
| | - Robert H A Coutts
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK; Geography, Environment and Agriculture, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, UK
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