Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses

Abstract

BackgroundMycoviruses 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.ResultsTo 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.ConclusionsVirus-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 materialThe online version of this article (doi:10.1186/s12864-017-3773-8) contains supplementary material, which is available to authorized users.

Analysis of an Intrinsic Mycovirus Associated With Reduced Virulence of the Human Pathogenic Fungus Aspergillus fumigatus

“…The study of mycoviruses has the potential to yield clinically useful information, as many mycoviruses are known to induce hypovirulence in their fungal hosts. Although several mycoviruses are associated with latent infection of human pathogenic fungi (Jamal et al, 2010;Özkan et al, 2017), to our knowledge there have been no reports of mycovirusmediated reduction or elimination of fungal pathogenicity in vertebrate infection models. The present study newly identified that AfuCV41362, a dsRNA mycovirus carried by A. fumigatus strain IFM 41362, causes hypovirulence of this human pathogenic fungus in a mouse infection model.…”

“…RNA silencing is an internal defense mechanism that protects the genome from invasion by mobile genetic elements such as viruses (Agrawal et al, 2003). The presence of mycovirus-derived siRNAs impairs the antiviral defense system in fungi (Hammond et al, 2008b;Zhang et al, 2008;Himeno et al, 2010;Özkan et al, 2017). If AfuCV41362 also suppresses host RNA silencing, it is predicted that this function would be relevant to hypovirulence.…”

Mycoviruses in Aspergilli: A Comprehensive Review

“…Additionally, the papain-like protease encoded by Cryphonectria hypovirus 1 was identified as a RNA silencing suppressor both in fungi and plants (Segers et al, 2006 ). More recently, Özkan et al ( 2017 ) demonstrated using high throughput small (s) RNA sequencing that non-conventionally encapsidated viruses, such as AfuPmV-1, and to a lesser extent encapsidated viruses, such as AfuPV-1 and AfuCV, are silenced in A. fumigatus . More specifically, 50% of total sRNAs where derived from AfuPmV-1, while the percentage was approximately half, 25 and 22% for AfuPV-1 and AfuCV, respectively.…”

“…More specifically, 50% of total sRNAs where derived from AfuPmV-1, while the percentage was approximately half, 25 and 22% for AfuPV-1 and AfuCV, respectively. Additionally, sRNAs differentially expressed in virus-free and virus-infected samples were identified, suggesting a putative pathway for mediating observed mycovirus effects on fungal hosts (Özkan et al, 2017 ).…”

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

“…siRNAs are excised from a double-stranded RNA and can act at transcription and post-transcription [ 3 ]. sRNAs play an important role in plants [ 4 ], animals [ 5 ] and fungi [ 6 ] in gene regulation or defence against pathogens.…”