Fungal viruses

Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment?

Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.

Three-dimensional structure of victorivirus HvV190S suggests coat proteins in most totiviruses share a conserved core

Double-stranded (ds)RNA fungal viruses are currently assigned to six different families. Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids, 300–450 Å in diameter. Helminthosporium victoriae virus 190S (HvV190S), prototype of recently recognized genus Victorivirus, infects the filamentous fungus Helminthosporium victoriae (telomorph: Cochliobolus victoriae), which is the causal agent of Victoria blight of oats. The HvV190S genome is 5179 bp long and encompasses two large, slightly overlapping open reading frames that encode the coat protein (CP, 772 aa) and the RNA-dependent RNA polymerase (RdRp, 835 aa). To our present knowledge, victoriviruses uniquely express their RdRps via a coupled termination–reinitiation mechanism that differs from the well-characterized Saccharomyces cerevisiae virus L-A (ScV-L-A, prototype of genus Totivirus), in which the RdRp is expressed as a CP/RdRp fusion protein due to ribosomal frameshifting. Here, we used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structures of HvV190S virions and two types of virus-like particles (capsids lacking dsRNA and capsids lacking both dsRNA and RdRp) at estimated resolutions of 7.1, 7.5, and 7.6 Å, respectively. The HvV190S capsid is thin and smooth, and contains 120 copies of CP arranged in a “T = 2” icosahedral lattice characteristic of ScV-L-A and other dsRNA viruses. For aid in our interpretations, we developed and used an iterative segmentation procedure to define the boundaries of the two, chemically identical CP subunits in each asymmetric unit. Both subunits have a similar fold, but one that differs from ScV-L-A in many details except for a core α-helical region that is further predicted to be conserved among many other totiviruses. In particular, we predict the structures of other victoriviruses to be highly similar to HvV190S and the structures of most if not all totiviruses including, Leishmania RNA virus 1, to be similar as well.

Of the known dsRNA fungal viruses, the best characterized is Saccharomyces cerevisiae virus L-A (ScV-L-A), prototype of the genus Totivirus, family Totiviridae. Until the current study, there have been no subnanometer structures of dsRNA fungal viruses from the genus Victorivirus, which is the largest in family Totiviridae. The 3D cryo-reconstruction presented here of prototype victorivirus Helminthosporium victoriae virus 190S (HvV190S) approaches 7-Å resolution and shows the asymmetric unit of the capsid is a dimer comprising two, chemically identical coat-protein subunits organized in a so called “T = 2” lattice. These HvV190S subunits have a similar fold, but one that differs from ScV-L-A in many details except for a core α-helical region that is further predicted to be conserved among many other totiviruses. In particular, we predict the structures of other victoriviruses to be highly similar to HvV190S and the structures of most if not all totiviruses, including Leishmania RNA virus 1, to be similar as well.

Antifungal activity of a virally encoded gene in transgenic wheat

The cDNA encoding the antifungal protein KP4 from Ustilago maydis-infecting virus was inserted behind the ubiquitin promoter of maize and genetically transferred to wheat varieties particularly susceptible to stinking smut (Tilletia tritici) disease. The transgene was integrated and inherited over several generations. Of seven transgenic lines, three showed antifungal activity against U. maydis. The antifungal activity correlated with the presence of the KP4 transgene. KP4-transgenic, soil-grown wheat plants exhibit increased endogenous resistance against stinking smut.

Double-stranded RNA virus in the human pathogenic fungus Blastomyces dermatitidis

Double-stranded RNA viruses were detected in a strain of Blastomyces dermatitidis isolated from a patient in Uganda. The viral particles are spherical (mostly 44 to 50 nm in diameter) and consist of about 25% double-stranded RNA (5 kb) and 75% protein (90 kDa). The virus contains transcriptional RNA polymerase activity; it synthesized single-stranded RNA in vitro in a conservative manner. The newly synthesized single-stranded RNA was a full-length strand, and the rate of chain elongation was approximately 170 nucleotides per min. The virus-containing strain shows no morphological difference from virus-free strains in the mycelial phase. Although the association with the presence of the virus is unclear, the virus-infected strain converts to the yeast form at 37 degrees C, but the yeast cells fail to multiply at that temperature.

Virus-like particles in Basidiobolus species

Transmission electron microscopy of ultrathin sections of hyphal cells of Basidiobolus haptosporus and B. ranarum revealed the presence of particulate inclusions consistent in morphology with that described in certain other fungi as virus-like particles. Two types of particles were observed which differed in substructure and distribution within the host cytoplasm. Relative numbers of these particles were never great, and their presence in the host was not associated with any demonstrable cytopathological changes detectable at the ultrastructural level. We believe this report to be the first description of an association of virus-like particles with fungi of the Entomophthoraceae.

Conservative replication and transcription of Saccharomyces cerevisiae viral double-stranded RNA in vitro

All double-stranded RNA viruses have capsid-associated RNA polymerase activities. In the reoviruses, the transcriptase synthesizes the viral plus strand in a conservative mode and the replicase synthesizes the viral minus strand, again conservatively. In bacteriophage phi 6 and in some fungal viruses, the transcriptase activity is semiconservative, acting by displacement synthesis. In this work we demonstrate Saccharomyces cerevisiae viral RNA replication in vitro for the first time and, using more sensitive techniques than those previously used, show that both the transcriptase and the replicase appear to act conservatively, like those of reovirus. There is therefore clearly no universal life cycle for the double-stranded RNA viruses.

The genetic basis for the meiotic disorder of Coprinus congregatus

A "pale-mushroom" phenotype in the fungus Coprinus congregatus has previously been reported to be caused by a cytoplasmic, infectious agent that inhibits the formation of synaptonemal complexes. After a period of 5 years of successful extraction of infectious material from carrier homokaryons, infectivity has now been lost and even cytoplasmic contact through somatic fusions no longer transmits the pale phenotype. In attempts to obtain new carrier homokaryons, a genetic analysis has been done. This study demonstrates that the pale phenotype in this species is primarily determined by a nuclear gene, symbolized pal (-). The pale phenotype appears predictably when the dikaryon is homoallelic for the pal (-) allele. Homoallelic wild type (pal (+)) and heteroallelic dikaryons display the dark phenotype. The former infectious nature of the pale phenotype and the current anomalous behavior of one homokaryon is discussed in the context that the pale phenotype may involve both a nuclear gene and a cytoplasmic element under some conditions.

Encapsidation of yeast killer double-stranded ribonucleic acids: dependence of M on L

Virus-like particles containing either L or M double-stranded ribonucleic acid (dsRNA) were isolated from a killer toxin-producing strains of Saccharomyces cerevisiae (K+ R+). At least 95% of M- and 87% of L-dsRNA were recovered in virus-like particle-containing fractions. The major capsid polypeptides (ScV-P1) of both L and M virus-like particles were shown to be identical, and 95% of the cellular ScV-P1 was found in the virus-like particle-containing fractions. Since L-dsRNA encodes ScV-P1, provision of this protein for encapsidation of M-dsRNA defines at least one functional relationship between these dsRNA genomes and associates the L-dsRNA with the killer character. If encapsidation of M-dsRNA is essential for its replication or expression, then L-dsRNA plays an essential role in maintenance or expression of the killer phenotype. The relationship between the L- and M-dsRNA genomes would be analogous to that between a helper and a defective virus. The presence of only minor quantities or uncomplexed dsRNA and ScV-P1 suggests that their production is stringently coupled.

Antiviral activity of virus-like particles from Lentinus edodes (Shiitake). Brief report

Interferon (IF) induction and antiviral activity by purified spherical (S) or filamentous (F) virus-like particles and S-derived RNA was studied. A single administration of S particles prior to virus challenge reduced significantly the mortality of mice infected with western equine encephalitis (WEE) virus.

No homology between double-stranded RNA and nuclear DNA of yeast

We investigated the possibility of sequence of homology between yeast DNA and one of the double-stranded RNAs present in many strains of Saccharomyces cerevisiae. These double-stranded RNAs are encapsidated in virus-like particles, which appear to be similar to the viruses of higher fungi. Contrary to a recent report (M. Vodkin, J. Virol. 21:516--521, 1976), we find no such homology.

Relatedness of the double-stranded RNAs present in yeast virus-like particles

The relatedness of several double-stranded RNAs (dsRNA's) present in the virus-like particles of yeast was examined by T1 fingerprint analysis. The dsRNA's examined were L, the dsRNA encoding the capsid polypeptide of yeast virus-like particles; M, which appears to code for a toxic polypeptide and for resistance to the effects of the toxin; and two S dsRNA's present in particles analogous to the defective interfering particles of animal viruses. S3, a dsRNA of 0.46 X 10(6) daltons, was derived entirely from M, a dsRNA of 1.2 X 10(6) daltons. S1, a dsRNA of 0.92 X 10(6) daltons, was a duplication of S3. This conclusion has also been reached independently by heteroduplex mapping techniques (H. M. Fried and G. R. Fink, personal communication). S1 and S3, at least in one yeast strain, were unstable in sequence, apparently due to the accumulation of sequence variants of the same molecular weight. L was a species of 3 X 10(6) daltons, unrelated in sequence to M, S1, or S3. S1, S3, and M had a 3' T1 dodecanucleotide in common.

Ribonucleoprotein particle appearing during sporulation in yeast

During sporulation of Saccharomyces cerevisiae, most strains accumulate an unmethylated 20S RNA. Contrary to previous reports, this sporulation 20S RNA is distinct from the short-lived methylated 20S RNA precursor of 18S rRNA. This RNA species was found in a cytoplasmic 32S ribonucleoprotein particle consisting of one single-stranded 20S RNA molecule and 18 to 20 identical protein subunits of molecular weight 23,000. The ribonucleoprotein particle was resistant to ribonuclease digestion, although purified 20S RNA was ribonuclease sensitive. Both the RNA and the protein of the 32S ribonucleoprotein particle were only synthesized under conditions that induce sporulation. The accumulation of 20S RNA depended on continued protein synthesis but was actinomycin D insensitive, despite a high guanine-plus-cytosine content. Synthesis of 20S RNA stopped when cells were removed from sporulation conditions and placed in growth medium.

Complex of Virus-Like Particles Containing Double-Stranded RNA from Thielaviopsis basicola

Six randomly selected isolates of Thielaviopsis basicola were found to contain spherical virus-like particles (VLPs) approximately 40 nm in diameter. One isolate, ATCC 34114, selected for further analysis contained a complex of VLPs that sedimented as eight or more bands in sucrose density gradients and contained five size classes of double-stranded RNA. Five discrete precipitation lines were obtained in immunoelectrophoresis, which indicated that this isolate of T. basicola contains five distinct species of VLPs.

Evidence for the parasexual cycle in a strain of Aspergillus flavus containing virus-like particles

Eight isolates of A. flavus and A. parasiticus were screened for the presence of virus-like-particles (VLP). Only A. flavus strain NRRL 5565 contained detectable VLP. Spore color and auxotrophic mutants were induced in this strain and evidence for the parasexual cycle was obtained. Attempts to form heterokaryons between 3 auxotrophs of the VLP-containing strain and 9 auxotrophs from two different aflatoxigenic strains were unsuccessful.

Homology between double-stranded RNA and nuclear DNA of yeast

The relationship between mycoviral double-stranded (ds) RNA and host cell DNA was investigated. Radiolabeled ds RNA was denatured and reannealed in the presence and absence of denatured DNA. RNA from killer strains of the yeast Saccharomyces cerevisiae and from nonkiller derivatives was utilized. The above-mentioned strains, as well as one that lacks all ds RNA, were sources for extracted DNA. Net hybridization of ds RNA to DNA occurred regardless of the strains from which the respective nucleic acids were prepared.

The 5' ends of yeast killer factor RNAs are pppGp

The 5' nucleotides of the double-stranded RNAs of yeast killer factor have been isolated by digestion with pancreatic, T1 and T2 RNase followed by two-dimensional electrophoresis. They were identified by bacterial alkaline phosphatase and snake venom phosphodiesterase digestions. Both the larger double-stranded RNA (L, of 2.5 x 10(6) daltons) and the smaller double-stranded RNA (M, of 1.4 x 10(6) daltons) have the 5' end groups pppGp. These 5' ends are dissimilar to those of the double-stranded RNAs of animal viruses but may be characteristic of the 5' ends of the double-stranded RNAs of fungal viruses.

Killer of Saccharomyces cerevisiae: a double-stranded ribonucleic acid plasmid

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Double-stranded ribonucleic acid in Agaricus bisporus

Double-stranded ribonucleic acid present in virus-infected mushrooms of Agaricus bisporus has been resolved through polyacrylamide gel electrophoresis into six molecular-weight forms. Identification of these six double-stranded ribonucleic acids in mushrooms by this procedure has proven to be a useful and diagnostic method for viral infection in the cultivated mushroom.

Inheritance of killer phenotypes and double-stranded RNA in Ustilago maydis

Three different killer specificities in U. maydis are inherited cytoplasmically and transmitted by cell fusion. Each killer generates low frequencies of specifically immune forms in crosses with sensitive strains. The properties of immunity to each killer are also inherited cytoplasmically and transmitted by cell fusion. Killer strains carry virus-like particles about 41 nm in diameter. Each killer possesses distinct double-stranded RNA components that range in molecular weight from 0.46 X 10(6) to 2.9 X 10(6). Two components are shared by all three killers. Immune strains possess new forms. Crosses and heterokaryons between different killers revealed unilateral or mutual restrictions that prevent inclusion of two killer specificities in the same cell.

Specificity of Ustilago maydis killer proteins

Bacteria and fungi were tested for sensitivity to Ustilago maydis killer strains carrying virus-like particles. Various species taxonomically related to U. maydis were sensitive.

Presence of two virus-like particles in Penicillium citrinum

Two icosahedral virus-like particles (28 and 19 nm in diameter, respectively) have been detected in sporogenic and asporogenic segregants of a strain of Penicillium citrinum. The distribution of the two particles differed among the two segregants.

Ionic strength effects on the stability and conformation of Penicillium chrysogenum mycophage double stranded RNA

The effect of [Na+] on the stability and conformation of penicillium chrysogenum mycophage dsRNA (PCMdsRNA) was investigated using CD and UV optical techniques. Thermal melting profiles reveal prominent fine structure attributed to at least four regions of structural dissimilarity. A constant increased thermal stability of the dsRNA compared to DNA of the same base composition was observed over a concentration range of 1.5 times 10- minus 4 M to 4.5 times 10- minus 2 M Na+. At low ionic strengths ([Na+] less than 10- minus 3 M) Tm becomes independent of further decrease in [Na+] unless the dsRNA is exposed to high concentrations of EDTA, suggesting the involvement to tightly bound divalent cation. At relatively high ionic strengths ([Na+] greater than 0.1 M) a postulated A leads to A' ... conformation change occurs.