Occurrence of diverse dsRNA in a Korean population of the chestnut blight fungus, Cryphonectria parasitica

A Transfectable Fusagravirus from a Japanese Strain of Cryphonectria carpinicola with Spherical Particles

A novel dsRNA virus (Cryphonectria carpinicola fusagravirus 1, CcFGV1), isolated from a Japanese strain (JS13) of Cryphonectria carpinicola, was thoroughly characterized. The biological comparison of a set of isogenic CcFGV1-infected and -free (JS13VF) strains indicated asymptomatic infection by CcFGV1. The sequence analysis showed that the virus has a two open reading frame (ORF) genome of 9.6 kbp with the RNA-directed RNA polymerase domain encoded by ORF2. The N-terminal sequencing and peptide mass fingerprinting showed an N-terminally processed or degraded product (150 kDa) of the 5′-proximal ORF1-encoded protein (1462 amino acids) to make up the CcFGV1 spherical particles of ~40 nm in diameter. Interestingly, a portion of CcFGV1 dsRNA co-fractionated with a host protein of 70 kDa. The purified CcFGV1 particles were used to transfect protoplasts of JS13VF as well as the standard strain of an experimental model filamentous fungal host Cryphonectria parasitica. CcFGV1 was confirmed to be associated with asymptomatic infection of both fungi. RNA silencing was shown to target the virus in C. parasitica, resulting in reduced CcFGV1 accumulation by comparing the CcFGV1 content between RNA silencing-competent and -deficient strains. These results indicate the transfectability of spherical particles of a fusagravirus associated with asymptomatic infection.

Distinct Roles of Two DNA Methyltransferases from Cryphonectria parasitica in Fungal Virulence, Responses to Hypovirus Infection, and Viral Clearance

Two DNA methyltransferase (DNMTase) genes from Cryphonectria parasitica have been previously identified as CpDmt1 and CpDmt2, which are orthologous to rid and dim-2 of Neurospora crassa, respectively. While global changes in DNA methylation have been associated with fungal sectorization and CpDmt1 but not CpDmt2 has been implicated in the sporadic sectorization, the present study continues to investigate the biological functions of both DNMTase genes. Transcription of both DNMTases is regulated in response to infection with the Cryphonectria hypovirus 1 (CHV1-EP713). CpDmt1 is upregulated and CpDmt2 is downregulated by CHV1 infection. Conidium production and response to heat stress are affected only by mutation of CpDmt1, not by CpDmt2 mutation. Significant changes in virulence are observed in opposite directions; i.e., the CpDmt1-null mutant is hypervirulent, while the CpDmt2-null mutant is hypovirulent. Compared to the CHV1-infected wild type, CHV1-transferred single and double mutants show severe growth retardation: the colony size is less than 10% that of the parental virus-free null mutants, and their titers of transferred CHV1 are higher than that of the wild type, implying that no defect in viral replication occurs. However, as cultivation proceeds, spontaneous viral clearance is observed in hypovirus-infected colonies of the null mutants, which has never been reported in this fungus-virus interaction. This study demonstrates that both DNMTases are significant factors in fungal development and virulence. Each fungal DNMTase affects fungal biology in both common and separate ways. In addition, both genes are essential to the antiviral responses, including viral clearance which depends on their mutations.

Cryphonectria nitschkei chrysovirus 1 with unique molecular features and a very narrow host range

Cryphonectria nitschkei chrysovirus 1 (CnCV1), was described earlier from an ascomycetous fungus, Cryphonectria nitschkei strain OB5/11, collected in Japan; its partial sequence was reported a decade ago. Complete sequencing of the four genomic dsRNA segments revealed molecular features similar to but distinct from previously reported members of the family Chrysoviridae. Unique features include the presence of a mini-cistron preceding the major large open reading frame in each genomic segment. Common features include the presence of CAA repeats in the 5'-untranslated regions and conserved terminal sequences. CnCV1-OB5/11 could be laterally transferred to C. nitschkei and its relatives C. radicalis and C. naterciae via coculturing, virion transfection and protoplast fusion, but not to fungal species other than the three species mentioned above, even within the genus Cryphonectria, suggesting a very narrow host range. Phenotypic comparison of a few sets of CnCV1-infected and -free isogenic strains showed symptomless infection in new hosts.

Co-infection of a novel fusagravirus and a partitivirus in a Korean isolate of Rosellinia necatrix KACC40168

We report here the presence of dsRNA mycoviruses in a Korean isolate of Rosellinia necatrix. A multiple band pattern of double-stranded RNA (dsRNA) from R. necatrix suggested mixed mycovirus infection. Next-generation sequencing analysis of purified dsRNAs indicated the presence of two dsRNA mycoviruses related to the members of families "Fusagraviridae" (proposed) and Partitiviridae. The first dsRNA virus revealed that the complete genome sequence was 8868 bp in size and contained two large open reading frames (ORFs 1 and 2), overlapped by 22 bp containing a canonical (- 1) slippery heptanucelotide sequence of UUUAAAC. The deduced amino acid sequence of ORF1 and ORF2 showed highest similarity to the hypothetical protein and RNA-dependent RNA polymerase (RdRp) of Rosellinia necatrix fusagravirus 3 (RnFGV3). Phylogenetic analysis showed that this dsRNA virus clustered with RnFGV3 and other fusagraviruses. Gene organization, sequence similarity, and phylogenetic analysis indicate that this virus seems to belong to a novel species of "Fusagraviridae", which we have named Rosellinia necatrix fusagravirus 4. The second virus has two dsRNA segments with sizes of 1907 bp and 1918 bp, each of which encoded a single ORF showing highest similarity to the RdRp and capsid protein of known members of Partitiviridae. Evaluation of genome structure, sequence similarity, and phylogeny indicate this to be a new member of the genus Alphapartitivirus in the family Partitiviridae, hereafter designated as Rosellinia necatrix partitivirus 26. This is the first report of the presence of a fusagravirus in an Asian R. necatrix isolate and of its mixed infection with a partitivirus.

Characterization of a novel dsRNA mycovirus of Trichoderma atroviride NFCF377 reveals a member of "Fusagraviridae" with changes in antifungal activity of the host fungus

Trichoderma atroviride is a common fungus found in various ecosystems that shows mycoparasitic ability on other fungi. A novel dsRNA virus was isolated from T. atroviride NFCF377 strain and its molecular features were analyzed. The viral genome consists of a single segmented double-stranded RNA and is 9,584 bp in length, with two discontinuous open reading frames (ORF1 and ORF2). A mycoviral structural protein and an RNA-dependent RNA polymerase (RdRp) are encoded by ORF1 and ORF2, respectively, between which is found a canonical shifty heptameric signal motif (AAAAAAC) followed by an RNA pseudoknot. Analysis of sequence similarity and phylogeny showed that it is closely related to members of the proposed family "Fusagraviridae", with a highest similarity to the Trichoderma atroviride mycovirus 1 (TaMV1). Although the sequence similarity of deduced amino acid to TaMV1 was evident, sequence deviations were distinctive at untranslated regions (UTRs) due to the extended size. Thus, we inferred this dsRNA to be a different strain of Trichoderma atroviride mycovirus 1 (TaMV1-NFCF377). Electron microscopy image exhibited an icosahedral viral particle of 40 nm diameter. Virus-cured isogenic isolates were generated and no differences in growth rate, colony morphology, or conidia production were observed between virus-infected and virus-cured strains. However, culture filtrates of TaMV1-NFCF377-infected strain showed enhanced antifungal activity against the plant pathogen Rhizoctonia solani but not to edible mushroom Pleurotus ostreatus. These results suggested that TaMV1-NFCF377 affected the metabolism of the fungal host to potentiate antifungal compounds against a plant pahogen, but this enhanced antifungal activity appeared to be species-specific.

Identification of a Novel Partitivirus of Trichoderma harzianum NFCF319 and Evidence for the Related Antifungal Activity

We have reported 15 agarose gel band patterns of double-stranded RNA (dsRNA) from Trichoderma spp. We describe herein that band pattern IX in Trichoderma harzianum NFCF319, which appeared to be a single band but consisted of two dsRNAs of similar size, was identified as a novel mycovirus, designated Trichoderma harzianum partitivirus 1 (ThPV1). The larger segment (dsRNA1) of the ThPV1 genome comprised 2,289 bp and contained a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). The smaller segment (dsRNA2) consisted of 2,245 bp with a single ORF encoding a capsid protein (CP). Evaluation of the deduced amino acid sequence and phylogenetic analysis indicated that ThPV1 is a new member of the genus Betapartitivirus in the family Partitiviridae. Curing of virus infection by single-sporing generated 31 virus-free single-spore clones. No significant differences in growth rate, conidia production, or pigmentation were observed between ThPV1-infected and -cured isogenic strains. In addition, comparison of the newly ThPV1-transmitted isolates with their ThPV1-cured parental strain showed no significant difference in colony morphology or pigmentation. However, inhibition of growth in co-cultured Pleurotus ostreatus and Rhizoctonia solani by T. harzianum was increased in ThPV1-containing strains compared with ThPV1-cured isogenic strains. Moreover, β-1,3-glucanase activity was significantly increased in the ThPV1-containing strains. However, no difference in chitinase activity was observed, suggesting that ThPV1 regulates the activity of a specific fungal enzyme.

Identification and Molecular Characterization of a Novel Partitivirus from Trichoderma atroviride NFCF394

An increasing number of novel mycoviruses have been described in fungi. Here, we report the molecular characteristics of a novel bisegmented double-stranded RNA (dsRNA) virus from the fungus Trichoderma atroviride NFCF394. We designated this mycovirus as Trichoderma atroviride partitivirus 1 (TaPV1). Electron micrographs of negatively stained, purified viral particles showed an isometric structure approximately of 30 nm in diameter. The larger segment (dsRNA1) of the TaPV1 genome comprised 2023 bp and contained a single open reading frame (ORF) encoding 614 amino acid (AA) residues of RNA-dependent RNA polymerase (RdRp). The smaller segment (dsRNA2) consisted of 2012 bp with a single ORF encoding 577 AA residues of capsid protein (CP). The phylogenetic analysis, based on deduced amino acid sequences of RdRp and CP, indicated that TaPV1 is a new member of the genus Alphapartitivirus in the family Partitiviridae. Virus-cured isogenic strains did not show significant changes in colony morphology. In addition, no changes in the enzymatic activities of β-1,3-glucanase and chitinase were observed in virus-cured strains. To the best of our knowledge, this is the first report of an Alphapartitivirus in T. atroviride.

Full-length sequence and genome analysis of CHV1-CN280, a North China isolate of cryphonectria hypovirus 1

CHV1-CN280 is a North China isolate of cryphonectria hypovirus 1 (CHV1), which has high horizontal transmission ability. The complete genomic sequence of CHV1-CN280 was determined and analyzed. Compared with other reported CHV1s, the genome of CHV1-CN280 shows some significantly different characteristics. The junction of the two open reading frames (ORFs) of CHV1-CN280 is AUGUAUAA, while in other reported CHV1s, it is UAAUG. The genomic sequence of CHV1-CN280 shows a high level of similarity to other reported CHV1s in the 3' portion, but in some sections of the 5' portion (the region around the start codon of ORFA, the region around the predicted cleavage site of p29 and p40, and the 5'-portion of p48 coding region), the nucleotide sequence identity is lower than 50%. The p29 of CHV1-CN280 shares only about 60% identity with other sequenced CHV1 isolates at the amino acid level. Full-length genomic recombination analysis suggests that several recombination events have occurred in the ORFB coding region between CHV1-CN280 and two subtype I CHV1 isolates (CHV1-Euro7 or CHV1-EP721). RT-PCR primers were designed according to the genomic sequence of CHV1-CN280 to study the genetic diversity of CHV1 in East Asia. Phylogenetic analysis showed that the East Asian CHV1s were quite different from the five assigned subtypes in Europe, and seven new CHV1 subtypes were identified in this study.

Viral Effects of a dsRNA Mycovirus (PoV-ASI2792) on the Vegetative Growth of the Edible Mushroom Pleurotus ostreatus

A double-stranded RNA (dsRNA) mycovirus was detected in malformed fruiting bodies of Pleurotus ostreatus strain ASI2792, one of bottle cultivated commercial strains of the edible oyster mushroom. The partial RNA-dependent RNA polymerase (RdRp) gene of the P. ostreatus ASI2792 mycovirus (PoV-ASI2792) was cloned, and a cDNA sequences alignment revealed that the sequence was identical to the RdRp gene of a known PoSV found in the P. ostreatus strain. To investigate the symptoms of PoV-ASI2792 infection by comparing the isogenic virus-free P. ostreatus strains with a virus-infected strain, isogenic virus-cured P. ostreatus strains were obtained by the mycelial fragmentation method for virus curing. The absence of virus was verified with gel electrophoresis after dsRNA-specific virus purification and Northern blot analysis using a partial RdRp cDNA of PoV-ASI2792. The growth rate and mycelial dry weight of virus-infected P. ostreatus strain with PoV-ASI2792 mycovirus were compared to those of three virus-free isogenic strains on 10 different media. The virus-cured strains showed distinctly higher mycelial growth rates and dry weights on all kinds of experimental culture media, with at least a 2.2-fold higher mycelial growth rate on mushroom complete media (MCM) and Hamada media, and a 2.7-fold higher mycelial dry weight on MCM and yeastmalt-glucose agar media than those of the virus-infected strain. These results suggest that the infection of PoV mycovirus has a deleterious effect on the vegetative growth of P. ostreatus.

Incidence of diverse dsRNA mycoviruses in Trichoderma spp. causing green mold disease of shiitake Lentinula edodes

A total of 315 fungal isolates causing green mold disease were collected from contaminated artificial logs and sawdust bags used for cultivating shiitake Lentinula edodes in Korea and were analyzed for the presence of double-stranded RNA (dsRNA). dsRNA, which was purified using dsRNA-specific chromatography and verified by dsRNA-specific RNaseIII digestion, was detected in 32 isolates. The molecular taxonomy of dsRNA-infected isolates indicated that all isolates belonged to the Trichoderma spp.. The number and size of dsRNAs varied among isolates and the band patterns could be categorized into 15 groups. Although there were seven dsRNA groups observed in multiple isolates, eight groups were found to occur in single isolates. The most common dsRNA group, group VI, which contained a band of 10 kb, occurred in 10 isolates encompassing three species of Trichoderma. Partial sequence analysis of two selected dsRNA groups revealed a high degree of similarity to sequences of a RNA-dependent RNA polymerase, hypothetical protein and polyprotein genes of other hypoviruses such as Macrophomina phaseolina hypovirus 1, Trichoderma hypovirus, and Fusarium graminearum hypovirus 2, respectively, indicating the occurrence of mycoviruses in Trichoderma spp.. Northern blot analysis suggested that many different mycoviruses, which have not been identified yet, exist in Trichoderma.

Changes in the mycovirus (LeV) titer and viral effect on the vegetative growth of the edible mushroom Lentinula edodes

This study attempted to cure the edible mushroom Lentinula edodes strain FMRI0339 of the L. edodes mycovirus (LeV) in order to obtain an isogenic virus-free fungal strain as well as a virus-infected strain for comparison. Mycelial fragmentation, followed by being spread on a plate with serial dilutions resulted in a virus-free colony. Viral absence was confirmed with gel electrophoresis after dsRNA-specific virus purification, Northern blot analysis, and PCR using reverse transcriptase (RT-PCR). Once cured, all of fungal cultures remained virus-free over the next two years. Interestingly, the viral titer of LeV varied depending on the culture condition. The titer from the plate culture showed at least a 20-fold higher concentration than that grown in the liquid culture. However, the reduced virus titer in the liquid culture was recovered by transferring the mycelia to a plate containing the same medium. In addition, oxygen-depleted culture conditions resulted in a significant decrease of viral concentration, but not to the extent seen in the submerged liquid culture. Although no discernable phenotypic changes in colony morphology were observed, virus-cured strains showed significantly higher growth rates and mycelial mass than virus-infected strains. These results indicate that LeV infection has a deleterious effect on mycelial growth.

Biological function of a novel chrysovirus, CnV1-BS122, in the Korean Cryphonectria nitschkei BS122 strain

Curing Cryphonectria nitschkei BS122 of a novel chrysovirus CnV1-BS122 infection was achieved by plating small hyphal fragments from an old plate and protoplasting followed by regeneration. Uneven distribution of mycoviruses within colonies was suggested. Comparing the CnV1-BS122-cured and -infected isogenic strains revealed that CnV1-BS122 infection resulted in reduced mycelial growth.

Occurrence of two different species of mitoviruses in the European race of Gremmeniella abietina var. abietina, both hosted by the genetically unique Spanish population

The genetic structure of the genus Mitovirus community hosted by the European pathogenic conifer fungus Gremmeniella abietina var. abietina was investigated. Gremmeniella abietina is a species complex with a divergent mycovirus community, composed mainly of Totivirus, Partitivirus, and Mitovirus species. In this work, the total doubled-stranded (ds)RNA from 353 isolates from Canada, Finland, Spain, Switzerland, Turkey, and USA was extracted to look for the presence of a ca. 2.5 kb band typical of mitoviruses' genomes. Based on the banding data, 60 partial RNA-dependent RNA polymerase (RdRp) DNA sequences (ca. 500 bp) were amplified with reverse transcription-polymerase chain reaction (RT-PCR) and sequenced. Two distantly related mitovirus groups (species) were observed in the clustering analysis, one of them related to GMV1-1 and the other one related to a new putative species described in this study, GMV2-1. Viruses in these two clusters seemed to be subjected to purifying selection. The cluster with GMV1-1 included viruses observed in the Finnish biotype A and Spanish strains, whereas the cluster including GMV2-1 was composed of viruses of the Finnish biotype B and one from the Spanish population. Thereby, the Spanish population of G. abietina harboured mitovirus strains occurring in both biotype A and B strains, and it is the first one hosting distantly related mycoviruses of a single genus in one population of G. abietina. This may suggest that horizontal transmission of viruses could have occurred between biotype B and the Spanish population.

A DnaJ-like homolog from Cryphonectria parasitica is not responsive to hypoviral infection but is important for fungal growth in both wild-type and hypovirulent strains

A DnaJ-like gene, Cpdj1, a molecular chaperone and regulator of Hsp70 in Cryphonectria parasitica, was characterized. The protein product of Cpdj1 gene consists of 379 amino acids with a predicted molecular mass of 40.6 kDa and a pI of 7.79. The deduced protein sequence revealed preservation of the conserved hall-mark J-region and exhibited high homolo y to all known DnaJ-like proteins. Disruption of the Cpdj1 gene resulted in slow growth and produced colonies characterized by retarded growth and deep orange color. Accordingly, reduced virulence of the Cpdj1-null mutant was observed. This reduced growth rate was magnified when the Cpdj1-null mutant was cultured under heat-stress conditions. Reduced conidiation was also observed in the Cpdj1-null mutant, indicating that Cpdj1 gene, although not essential for cell viability, is required for appropriate cellular processes including growth and sporulation. Northern analysis showed that Cpdj1 was constitutively expressed, and when the culture was subject to high temperature, a strong induction of the transcript was observed. No significant difference in the expression and induction pattern of Cpdj1 was observed between virus-free EP155/2 and virus-infected hypovirulent UEP1 strains. However, further severe defects in mycelia growth and conidiation were observed in the hypovirus-infected Cpdj1-null mutant suggesting that the presence of Cpdj1 is required for mycelia growth and sporulation of the hypovirus-infected strain.

Nucleotide sequences of four segments of chrysovirus in Korean Cryphonectria nitschkei BS122 strain

The near full-length genome consisting of four segments of dsRNA from a chrysovirus infecting Korean Cryphonectria nitschkei BS122 strain (CnV1-BS122) was sequenced. The open reading frames of segments 1, 2, 3, and 4 were 2,889, 2,721, 2,475, and 2,232 nucleotides (nt) in length, respectively. Sequence analysis and homology searches of the amino acid sequences deduced from the ORFs of each segment revealed that segments 1, 2, 3, and 4 encoded RNA-dependent RNA polymerase, capsid protein, a putative cysteine protease, and replication-associated protein, respectively. The entire 5' ends of segments 1, 2, and 4 were 82, 242, and 698 nt in length, respectively; the sequence of the 5' end of segment 3 was not determined because of difficulty in amplification. The entire 3' end of segment 3 was 77 nt in length. Partial amplification of the 3' ends of segments 1, 2, and 4 yielded amplimers of 7, 17, and 30 nt, respectively.

Molecular diversity of chrysoviruses in Korean isolates of a new fungal species, Cryphonectria nitschkei

Genetic diversity of the chrysovirus within the four fungal strains was analyzed by comparing the full-length sequences of cloned chrysoviral genes encoding the RNA-dependent RNA polymerase (RdRp) and capsid protein (CP). Because the morphological characteristics of four chrysovirus-infected Cryphonectria spp. strains were different, strain identification was conducted via sequence comparison of the internal transcribed spacers (ITSs) of the fungal rRNA gene. Phylogenic analysis of the ITS regions revealed that the four strains were closely clustered with the reference strain of Cryphonectria nitschkei, while they were more distantly related to other common Cryphonectria species, indicating that they were likely C. nitschkei. Sequence comparison among chrysoviruses from Korean C. nitschkei strains revealed that similarities of the RdRp and CP genes ranged from 98% to 100% and from 95% to 100%, respectively, at the protein level. Their corresponding nucleotide sequences showed 97% to 100% and 84% to 100% identities, respectively. Compared to RdRp, the CP gene had more divergence, suggesting the presence of genes possessing different evolutionary rates within the chrysovirus genome. Sequence comparisons with other known chrysoviruses showed that the four Korean chrysoviruses were clustered together at the next lineage level. Discovering why two strains (bsl31 and bsl32) containing identical ITS sequences and chrysoviruses display different phenotypes should prove interesting.

Viruses of plant pathogenic fungi

Mycoviruses are widespread in all major groups of plant pathogenic fungi. They are transmitted intracellularly during cell division, sporogenesis, and cell fusion, but apparently lack an extracellular route for infection. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups. Recent advances, however, allowed the establishment of experimental host ranges for a few mycoviruses. Although the majority of known mycoviruses have dsRNA genomes that are packaged in isometric particles, an increasing number of usually unencapsidated mycoviruses with positive-strand RNA genomes have been reported. We discuss selected mycoviruses that cause debilitating diseases and/or reduce the virulence of their phytopathogenic fungal hosts. Such fungal-virus systems are valuable for the development of novel biocontol strategies and for gaining an insight into the molecular basis of fungal virulence. The availability of viral and host genome sequences and of transformation and transfection protocols for some plant pathogenic fungi will contribute to progress in fungal virology.