Structural properties of double-stranded RNAs associated with biological control of chestnut blight fungus

New Insights on the Integrated Management of Plant Diseases by RNA Strategies: Mycoviruses and RNA Interference

RNA-based strategies for plant disease management offer an attractive alternative to agrochemicals that negatively impact human and ecosystem health and lead to pathogen resistance. There has been recent interest in using mycoviruses for fungal disease control after it was discovered that some cause hypovirulence in fungal pathogens, which refers to a decline in the ability of a pathogen to cause disease. Cryphonectria parasitica, the causal agent of chestnut blight, has set an ideal model of management through the release of hypovirulent strains. However, mycovirus-based management of plant diseases is still restricted by limited approaches to search for viruses causing hypovirulence and the lack of protocols allowing effective and systemic virus infection in pathogens. RNA interference (RNAi), the eukaryotic cell system that recognizes RNA sequences and specifically degrades them, represents a promising. RNA-based disease management method. The natural occurrence of cross-kingdom RNAi provides a basis for host-induced gene silencing, while the ability of most pathogens to uptake exogenous small RNAs enables the use of spray-induced gene silencing techniques. This review describes the mechanisms behind and the potential of two RNA-based strategies, mycoviruses and RNAi, for plant disease management. Successful applications are discussed, as well as the research gaps and limitations that remain to be addressed.

Hypovirus molecular biology: from Koch's postulates to host self-recognition genes that restrict virus transmission

The idea that viruses can be used to control fungal diseases has been a driving force in mycovirus research since the earliest days. Viruses in the family Hypoviridae associated with reduced virulence (hypovirulence) of the chestnut blight fungus, Cryphonectria parasitica, have held a prominent place in this research. This has been due in part to the severity of the chestnut blight epidemics in North America and Europe and early reports of hypovirulence-mediated mitigation of disease in European forests and successful application for control of chestnut blight in chestnut orchards. A more recent contributing factor has been the development of a hypovirus/C. parasitica experimental system that has overcome many of the challenges associated with mycovirus research, stemming primarily from the exclusive intracellular lifestyle shared by all mycoviruses. This chapter will focus on hypovirus molecular biology with an emphasis on the development of the hypovirus/C. parasitica experimental system and its contributions to fundamental and practical advances in mycovirology and the broader understanding of virus-host interactions and fungal pathogenesis.

Mycoviruses, RNA silencing, and viral RNA recombination

In contrast to viruses of plants and animals, viruses of fungi, mycoviruses, uniformly lack an extracellular phase to their replication cycle. The persistent, intracellular nature of the mycovirus life cycle presents technical challenges to experimental design. However, these properties, coupled with the relative simplicity and evolutionary position of the fungal host, also provide opportunities for examining fundamental aspects of virus-host interactions from a perspective that is quite different from that pertaining for most plant and animal virus infections. This chapter presents support for this view by describing recent advances in the understanding of antiviral defense responses against one group of mycoviruses for which many of the technical experimental challenges have been overcome, the hypoviruses responsible for hypovirulence of the chestnut blight fungus Cryphonectria parasitica. The findings reveal new insights into the induction and suppression of RNA silencing as an antiviral defense response and an unexpected role for RNA silencing in viral RNA recombination.

A novel mycovirus associated with four double-stranded RNAs affects host fungal growth in Alternaria alternata

Four double-stranded RNAs (dsRNAs), referred to as dsRNA 1 (3617 bp), dsRNA 2 (2794 bp), dsRNA 3 (2576 bp) and dsRNA 4 (1420 bp), were detected in the EGS 35-193 strain of Alternaria alternata at high concentration ( approximately 3 microg/g dried mycelium). This strain had an impaired growth phenotype. By exposing the strain to cycloheximide during hyphal tip isolation, we isolated strains which had normal mycelial growth and pigmentation, in which decreased levels of the dsRNAs were observed ( approximately 0.3 microg/g dried mycelium). These results indicate that this dsRNA mycovirus might be involved in modulating traits of its fungal host, A. alternata. The buoyant density of isometric virus particles (about 33 nm in diameter) containing these dsRNAs in CsCl was 1.35-1.40 g/cm(3) depending on the size of the packaged dsRNAs. The dsRNA 1 encodes a single open reading frame (3447 nt) containing the conserved motifs of viral RNA-dependent RNA polymerase (RdRp), which is related to the ORF encoded by dsRNA 1 of Aspergillus mycovirus 341. It is noteworthy that all of the coding strands of the four dsRNA genomes have 3'-poly (A) tails ranging from 33 to 50 nt in length. We named this novel dsRNA mycovirus in the EGS 35-193 strain A. alternata virus-1 (AaV-1).

Diversity, complexity and transmission of double-stranded RNA elements in Chalara elegans (synanam. Thielaviopsis basicola)

Double-stranded (ds) RNA banding patterns were determined in 21 wild-type strains of the soilborne plant pathogen Chalara elegans originating from different geographic regions worldwide. Five strains, each with a unique dsRNA pattern, were selected for cDNA cloning, northern blot analysis and dsRNA transmission experiments. Four strains contained multiple (up to 6) dsRNA elements (2.0kbp to 12kbp in size) and one strain contained a single 2.8kbp fragment. These five strains were distinguished from one another by their unique RAPD-PCR patterns. Seven partial cDNA clones were derived from the predominant 2.8, 5.3, and 12kbp dsRNA elements. Nucleotide sequence analysis and northern blot hybridizations revealed a high degree of genetic dissimilarity among the different molecular-size dsRNA elements, even those found within a single strain. Four clones from the 5.3kbp dsRNA fragment showed a 23-43 % amino acid identity to either the coat protein or RNA-dependent RNA polymerase regions of viruses in the Totiviridae. One clone from the 2.8kbp dsRNA fragment had a 55-57 % amino acid identity to the RdRp region of viruses in the Narnaviridae. Two clones from the 12kbp dsRNA fragment showed no significant homology to any known virus group. Colonies derived from 100 single-conidia isolates of C. elegans strains with the 2.8, 5.3 and 12kbp elements all contained the corresponding dsRNA element, indicating that dsRNA transmission through conidia was highly efficient, regardless of molecular size. However, transmission of dsRNA between the mycelium of strains of C. elegans could not be achieved in this study. Genetically unique strains carrying diverse dsRNA elements appear to have evolved within populations of C. elegans. Based on our findings, there are at least 3 groups of viruses present in C. elegans.

Dynamics of double-stranded RNA segments in a Helicobasidium mompa clone from a tulip tree plantation

Eighty-three isolates of the violet root rot fungus, Helicobasidium mompa, were collected in a tulip tree plantation and analyzed for the dynamics of double-stranded (ds) RNA for five years. They were divided into eight mycelial compatibility groups (MCGs). Prevalent MCGs 60 and 68 included 61 and 11 isolates, respectively. Electrophoretic profiles of dsRNA in the first year collection of MCG 60 contained no or a single large dsRNA (more than 10 kb) with or without small dsRNAs (ca. 2.0-2.5 kb). Additional dsRNA fragments, i.e., a middle dsRNA (ca. 8.0 kb) or another type of small dsRNAs, became evident within MCG 60 isolates with time. Northern hybridization revealed the relatedness of all large and middle dsRNA fragments within MCG 60 but small fragments of dsRNA were variable. Large dsRNA fragment differed from that in other MCGs even in the same field. Correlation between specific dsRNA fragments and hypovirulence was not observed. Possible explanations for the accumulation of dsRNA fragments during the growth of disease patch by MCG 60 are discussed in terms of their internal changes such as evolution of novel dsRNA fragments from pre-existing viruses or fungal genomic DNA and horizontal transmissions.

Diversity and vertical transmission of double-stranded RNA elements in root rot pathogens of trees, Helicobasidium mompa and Rosellinia necatrix

The diversity and vertical transmission of double-stranded (ds) RNA in Helicobasidium mompa and Rosellinia necatrix was examined by electrophoresis and Northern hybridization. These two fungi share the similar niche as root rot pathogens of trees in forests and orchards, and had diverse dsRNAs. The detection frequency of dsRNA in both fungi was different; in H. mompa, 68.4% (132 out of 193 MCGs; mycelial compatibility groups) had dsRNA, whereas 20.9% (53 out of 254 MCGs) in R. necatrix. dsRNA banding patterns and Northern blot analyses revealed the presence of various dsRNA elements in both fungi. Hyphal tip isolation was mostly unsuccessful to remove dsRNA with some exceptions. Sexual reproduction functioned to remove dsRNA in both fungi since dsRNA was not detected from single sexual spore cultures. Possible explanations for the difference in the detection frequency of dsRNA are discussed in terms of the differences in their sexual reproduction and other factors.

Double-stranded RNA elements associated with the MVX disease of Agaricus bisporus

Double-stranded RNA (dsRNA) has been isolated from Agaricus bisporus fruit bodies exhibiting a wide range of disease symptoms. The symptoms which occurred singularly or in combination included; bare cropping areas on commercial beds (primordia disruption), crop delay, premature veil opening, off- or brown-coloured mushrooms, sporophore malformations and loss of crop yield. All symptoms were associated with loss of yield and/or product quality. Collectively, these symptoms are described as mushroom virus X (MVX) disease. The dsRNA titre was much lower than that previously encountered with the La France viral disease of mushrooms and a modified cellulose CF11 protocol was used for their detection. A broad survey of cultivated mushrooms from the British industry identified dsRNA elements ranging between 640 bp and 20.2 kbp; the majority have not previously been described in A. bisporus. 26 dsRNA elements were identified with a maximum of 17, apparently non-encapsidated dsRNA elements, in any one sample. Three dsRNAs (16.2, 9.4 and 2.4 kbp) were routinely found in mushrooms asymptomatic for MVX. Previously, La France disease was effectively contained and controlled by minimising the on-farm production and spread of basidiospores. Our on-farm observations suggest that MVX could be spread by infected spores and/or mycelial fragments.

Hypoviruses and chestnut blight: exploiting viruses to understand and modulate fungal pathogenesis

Fungal viruses are considered unconventional because they lack an extracellular route of infection and persistently infect their hosts, often in the absence of apparent symptoms. Because mycoviruses are limited to intracellular modes of transmission, they can be considered as intrinsic fungal genetic elements. Such long-term genetic interactions, even involving apparently asymptomatic mycoviruses, are likely to have an impact on fungal ecology and evolution. One of the clearest examples supporting this view is the phenomenon of hypovirulence (virulence attenuation) observed for strains of the chestnut blight fungus, Cryphonectria parasitica, harboring members of the virus family Hypoviridae. The goal of this chapter is to document recent advances in hypovirus molecular genetics and to provide examples of how that progress is leading to the identification of virus-encoded determinants responsible for altering fungal host phenotype, insights into essential and dispensable elements of hypovirus replication, revelations concerning the role of G-protein signaling in fungal pathogenesis, and new avenues for enhancing biological control potential.

Presence of double-stranded RNA and virus-like particles in Rhizopus isolates

Fungal isolates belonging to four Rhizopus species were screened for the presence of double-stranded RNA (dsRNA) molecules. Five (two R. stolonifer, two R. microsporus, and one R. oryzae) of the 27 isolates examined harboured such genetic elements. Electrophoresis of the nucleic acids revealed five RNA patterns, with 1-5 discrete dsRNA bands. The molecular sizes corresponding to these bands were 2.2-14.8 kb. Gel electrophoresis of purified virus-like particles (VLPs) indicated only one capsid of similar size in all virus-harbouring strains; when investigated by electron microscopy, they were found to be polyhedral VLPs 40 nm in diameter. In one of the R. microsporus isolates an uncapsidated large dsRNA segment (14.8 kb) was observed. No phenotypic differences were observed between uninfected and virus-harbouring Rhizopus isolates.

In vitro translational analysis of genomic, defective, and satellite RNAs of Cryphonectria hypovirus 3-GH2

Cryphonectria hypovirus 3-GH2 (CHV3-GH2) is a member of the fungal virus family Hypoviridae that differs from previously characterized members in having a single large open reading frame with the potential to encode a protein of 326 kDa from its 9.8-kb genome. The N-terminal portion of the ORF contains sequence motifs that are somewhat similar to papain-like proteinases identified in other hypoviruses. Translation of the ORF is predicted to release autocatalytically a 32.5-kDa protein. A defective RNA, predicted to encode a 91.6-kDa protein representing most of the N-terminal proteinase fused to the entire putative helicase domain, and two satellite RNAs, predicted to encode very small proteins, also are associated with CHV3-GH2 infected fungal cultures. We performed in vitro translation experiments to examine expression of these RNAs. Translation of three RT-PCR clones representing different lengths of the amino-terminal portion of the ORF of the genomic RNA resulted in autocatalytic release of the predicted 32.5-kDa protein. Site-directed mutagenesis was used to map the processing site between Gly(297) and Thr(298). In vitro translation of multiple independent cDNA clones of CHV3-GH2-defective RNA 2 resulted in protein products of approximately 92 kDa, predicted to be the full-length translation product, 32 kDa, predicted to represent the N-terminal proteinase, and 60 kDa, predicted to represent the C-terminal two-thirds of the full-length product. In vitro translation of cDNA clones representing satellite RNA 4 resulted in products of slightly less than 10 kDa, consistent with the predicted 9.4 kDa product.

Satellite and defective RNAs of Cryphonectria hypovirus 3-grand haven 2, a virus species in the family Hypoviridae with a single open reading frame

Cryphonectria parasitica hypovirus 3-Grand Haven 2 (CHV3-GH2) is the most recently characterized member of the Hypoviridae family of viruses associated with hypovirulence of the chestnut blight fungus. Isolates of CHV3-GH2 contain either three or four double-stranded (ds) RNAs that are visible on ethidium bromide-stained agarose or polyacrylamide gels. Only the largest dsRNA appears to be required for virus infectivity, and was characterized previously (C. D. Smart et al., 1999, Virology 265, 66-73). In this study, we report the cloning, sequencing, and analysis of the other three dsRNAs. Sizes of the accessory dsRNAs are 3.6 kb (dsRNA 2), 1.9 kb (dsRNA 3), and 0.9 kb (dsRNA 4), compared to 9.8 kb for the genomic dsRNA segment (dsRNA 1). All three accessory dsRNA species are polyadenylated on the 3'-end of one strand, as is genomic dsRNA. DsRNA 2 represents a defective form of dsRNA 1, with the 5'-terminal 1.4 kb derived from the 5'-end of dsRNA 1 and the 3'-terminal 2.2 kb from the 3'-end of dsRNA 1. A single major open reading frame (ORF) is evident from deduced translations of dsRNA 2. The deduced translation product is a 91-kDa protein that represents a fusion consisting of the entire N-terminal protease and the entire putative helicase domain. DsRNAs 3 and 4 represent satellite RNAs that share very little sequence with dsRNA 1 and 2. DsRNA 4 is 937 nucleotides, excluding the poly(A)(+). The first AUG of the polyadenylated strand of dsRNA 4 occurs eight residues in from the 5'-terminus and would initiate the largest ORF on dsRNA 4, with the coding capacity for a 9.4-kDa protein. Within the deduced ORF and approximately 100 nucleotides from the 5'-end of dsRNA 4 is a 22-base sequence that is identical to sequences found in the nontranslated leaders of dsRNAs 1 and 2. DsRNA 3 accumulation in infected cultures varied, but it was less abundant than dsRNA 4. DsRNA 3 was found to represent a head-to-tail dimer of dsRNA 4 linked by a poly(A)/(U) stretch of 40-70 residues.

Cryphonectria hypovirus 3, a virus species in the family hypoviridae with a single open reading frame

Isolate Grand Haven (GH) 2 is a naturally occurring isolate of the chestnut blight fungus, Cryphonectria parasitica, that is greatly reduced in virulence due to the presence of a double-stranded RNA virus. Unlike many other virus-infected, hypovirulent isolates, GH2 is not substantially reduced in pigmentation, conidiation, or laccase expression compared to its virus-free counterpart. The dsRNA genome of the GH2 virus was cloned, sequenced, and compared to hypovirulence-associated viruses of the family Hypoviridae. GH2 dsRNA is considerably smaller than previously characterized members of the family, 9.8 kb compared to 12.5-12.7 kb for other members. The genome organization of GH2 dsRNA reflected the substantial difference in genome size. Like other members of the family, one strand contained a poly(A)(+) tail at the 3' end and a long sequence with several minicistrons at the 5' end of the same strand. Only a single open reading frame (ORF) of 8622 nucleotides was predicted from deduced translations of the poly(A)(+)-containing strand, however. This contrasts with the two-ORF structures of previously characterized members. Analysis of the deduced ORF of GH2 dsRNA revealed putative proteinase, RNA polymerase, and helicase domains similar to those previously identified in confirmed members of the virus family Hypoviridae. GH2 dsRNA was more distantly related to Cryphonectria hypovirus (CHV) 1-EP713 and CHV2-NB58 than the latter two were to each other but has features in common with each of those viruses. We propose that the GH2 virus be included in this taxon as a member of the genus Hypovirus, representing a strain of a new species, CHV3.

Infectious cDNA clone of hypovirus CHV1-Euro7: a comparative virology approach to investigate virus-mediated hypovirulence of the chestnut blight fungus Cryphonectria parasitica

We report the construction of a full-length infectious cDNA clone for hypovirus CHV1-Euro7, which is associated with reduced virulence (hypovirulence) of the chestnut blight fungus Cryphonectria parasitica. Field strains infected with CHV1-Euro7 are more virulent and exhibit less severe phenotypic changes (hypovirulence-associated traits) than strains infected with the prototypic hypovirus CHV1-EP713, for which the first infectious cDNA clone was developed. These differences exist even though the two hypoviruses show extensive sequence identities: 87 to 93% and 90 to 98% at the nucleotide and amino acid levels, respectively. The relative contributions of viral and host genomes to phenotypic traits associated with hypovirus infection were examined by transfecting synthetic transcripts of the two hypovirus cDNAs independently into two different virus-free C. parasitica strains, EP155 and Euro7(-v). Although the contribution of the viral genome was clearly predominant, the final magnitude and constellation of phenotypic changes were a function of contributions by both genomes. The high level of sequence identity between the two hypoviruses also allowed construction of viable chimeras and mapping of the difference in symptom expression observed for the two viruses to the open reading frame B coding domain. Implications of these results for engineering enhanced biological control and elucidating the basis for hypovirus-mediated attenuation of fungal virulence are discussed.

Origin, adaptation and evolutionary pathways of fungal viruses

Fungal viruses or mycoviruses are widespread in fungi and are believed to be of ancient origin. They have evolved in concert with their hosts and are usually associated with symptomless infections. Mycoviruses are transmitted intracellularly during cell division, sporogenesis and cell fusion, and they lack an extracellular phase to their life cycles. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups. Typically, fungal viruses are isometric particles 25-50 nm in diameter, and possess dsRNA genomes. The best characterized of these belong to the family Totiviridae whose members have simple undivided dsRNA genomes comprised of a coat protein (CP) gene and an RNA dependent RNA polymerase (RDRP) gene. A recently characterized totivirus infecting a filamentous fungus was found to be more closely related to protozoan totiviruses than to yeast totiviruses suggesting these viruses existed prior to the divergence of fungi and protozoa. Although the dsRNA viruses at large are polyphyletic, based on RDRP sequence comparisons, the totiviruses are monophyletic. The theory of a cellular self-replicating mRNA as the origin of totiviruses is attractive because of their apparent ancient origin, the close relationships among their RDRPs, genome simplicity and the ability to use host proteins efficiently. Mycoviruses with bipartite genomes (partitiviruses), like the totiviruses, have simple genomes, but the CP and RDRP genes are on separate dsRNA segments. Because of RDRP sequence similarity, the partitiviruses are probably derived from a totivirus ancestor. The mycoviruses with unencapsidated dsRNA-like genomes (hypoviruses) and those with bacilliform (+) strand RNA genomes (barnaviruses) have more complex genomes and appear to have common ancestry with plant (+) strand RNA viruses in supergroup 1 with potyvirus and sobemovirus lineages, respectively. The La France isometric virus (LIV), an unclassified virus with multipartite dsRNA genome, is associated with a severe die-back disease of the cultivated mushroom. LIV appears to be of recent origin since it differs from its host in codon usage.

Diversity of Hypoviruses and Other Double-Stranded RNAs in Cryphonectria parasitica in North America

ABSTRACT Double-stranded (ds) RNAs in Cryphonectria parasitica were randomly sampled from nine subpopulations in North America using an antibody-based detection system for dsRNA. dsRNA was detected in 166 (28%) of a total of 595 C. parasitica isolates sampled by immunoblotting. Incidence of dsRNA infection within subpopulations ranged from 0% in samples from New Hampshire and Ontario to 100% in County Line, MI. Most of the dsRNAs sampled were approximately 9 to 13 kb in size. dsRNAs from 72 isolates analyzed by probing Northern blots with (32)P-labeled dsRNAs were in one of three hybridization groups. One hybridization group was widespread throughout eastern North America, being found in New York, New Jersey, Maryland, West Virginia, Kentucky, and Michigan. These dsRNAs hybridized to dsRNA from the previously described C. parasitica isolate SR2 from Maryland and are referred to as SR2-type dsRNAs. The second hybridization group was found almost exclusively in Michigan. The Michigan dsRNAs cross-hybridized to Cryphonectria hypovirus 3-GH2 (CHV3-GH2) and are referred to as CHV3-type dsRNAs.One dsRNA sampled from Kentucky hybridized to CHV3-type dsRNAs from Michigan. This dsRNA was probably derived from a fungal isolate that had been intentionally released for biological control at this same site 10 years previously and had become established in Kentucky. The third hybridization group was found only in New Jersey. These dsRNAs were much smaller than all other dsRNAs (3 and 5 kb) and were found in all 11 isolates that were probed; two of these isolates also had SR2-type dsRNA in mixed infections. None of the North American dsRNAs hybridized to CHV1 from Europe, even though CHV1 has been released in numerous locations in eastern North America for biological control of chestnut blight. Similarly, no dsRNAs hybridized to CHV2-NB58, a hypovirus found previously in New Jersey. Mixed infections of SR2-type and CHV3-type dsRNAs were found in 13 of 15 isolates from Frankfort, MI, while another nearby subpopulation (County Line) was infected with only CHV3-type dsRNAs. The distribution of dsRNA hybridization groups in C. parasitica thus presents a mixed picture, since one hybridization group is widespread, whereas two others are primarily restricted to smaller geographic areas.

Control of plant pathogens with viruses and related agents

Cytoplasmically transmissible agents causing diseases of plant pathogenic fungi characterized by reductions in pathogenicity, ability to form sexual and asexual spores, spore viability and growth rate, are often associated with the presence of one or more specific segments of virus-like double-stranded RNA (dsRNA). In Italy, hypovirulent dsRNA-containing strains of the chestnut blight fungus,Endothia(Cryphonectria)parasitica, have become predominant in many areas where blight is no longer a serious problem. dsRNA-containing strains of other pathogens, with various degrees of debilitation, survive in natural populations but have not become predominant or resulted in any great reduction in disease. Examples include the Dutch elm disease fungus,Ophiostoma(Ceratocystis)ulmi, and the wheat take-all fungus,Gaeumannomyces graminisvar.tritici. Successful biological control of such pathogens could probably be achieved, however, if methods could be developed to suppress the loss of dsRNA that occurs during the sexual and other stages of their life cycles, and to suppress the vegetative incompatibility reactions that reduce the cytoplasmic transmission of dsRNA. Systemic infection with attenuated strains of plant viruses can protect plants from later infection by virulent strains of the same or closely related viruses. Despite some notable successes, e.g. control of citrus tristeza and tomato mosaic viruses, such ‘cross-protection’ has not been widely applied because of the cost and difficulty of application, and caution about the widespread distribution of infectious agents in the environment. These problems could be overcome if cross-protection could be achieved by the expression of a single viral gene rather than infection with intact virus, and consideration of possible mechanisms of cross protection suggests novel ways of producing virus-resistant plants.

Vesicle-associated double-stranded ribonucleic acid genetic elements in Agaricus bisporus

Double-stranded ribonucleic acids (dsRNAs) were isolated from fruit bodies of commercial strains of the cultivated mushroom (Agaricus bisporus) by polyethylene glycol-NaCl precipitation, differential centrifugation, rate-zonal centrifugation in sucrose, and equilibrium centrifugation in cesium sulphate. In all seven of the mushroom isolates examined, three dsRNAs were identified: two major dsRNA segments of > 13.1-kb (L-RNA) and 2.4-kb (S-RNA) and a minor segment of 5.2-kb (M-RNA). L-, M-, and S-RNAs co-purified with spherical fungal vesicles measuring approximately 75 nm in diameter. The three dsRNAs were intimately associated with the vesicles as suggested by their lower buoyant density in cesium sulphate (1.27 g/cc) compared to that of phenol-extracted dsRNAs (1.42 g/cc) and by their resistance to hydrolysis by ribonuclease at low ionic strength. Using a variety of conditions during purification, no virus-like particles were found to be associated with the dsRNAs. In Northern analysis, L-, M-, and S-RNAs failed to cross-hybridize with the genomic dsRNAs of La France isometric virus. We report here the first description of non-encapsidated, vesicle-associated, dsRNA genetic elements in the common cultivated mushroom.

New developments in fungal virology

Although viruses are widely distributed in fungi, their biological significance to their hosts is still poorly understood. A large number of fungal viruses are associated with latent infections of their hosts. With the exception of the killer-immune character in the yeasts, smuts, and hypovirulence in the chestnut blight fungus, fungal properties that can specifically be related to virus infection are not well defined. Mycoviruses are not known to have natural vectors; they are transmitted in nature intracellularly by hyphal anastomosis and heterokaryosis, and are disseminated via spores. Because fungi have a potential for plasmogamy and cytoplasmic exchange during extended periods of their life cycles and because they produce many types of propagules (sexual and asexual spores), often in great profusion, mycoviruses have them accessible to highly efficient means for transmission and spread. It is no surprise, therefore, that fungal viruses are not known to have an extracellular phase to their life cycles. Although extracellular transmission of a few fungal viruses have been demonstrated, using fungal protoplasts, the lack of conventional methods for experimental transmission of these viruses have been, and remains, an obstacle to understanding their biology. The recent application of molecular biological approaches to the study of mycoviral dsRNAs and the improvements in DNA-mediated fungal transformation systems, have allowed a clearer understanding of the molecular biology of mycoviruses to emerge. Considerable progress has been made in elucidating the genome organization and expression strategies of the yeast L-A virus and the unencapsidated RNA virus associated with hypovirulence in the chestnut blight fungus. These recent advances in the biochemical and molecular characterization of the genomes of fungal viruses and associated satellite dsRNAs, as they relate to the biological properties of these viruses and to their interactions with their hosts are the focus of this chapter.

Biological control of chestnut blight: an example of virus-mediated attenuation of fungal pathogenesis

Environmental concerns have focused attention on natural forms of disease control as potentially safe and effective alternatives to chemical pesticides. This has led to increased efforts to develop control strategies that rely on natural predators and parasites or that involve genetically engineered microbial pest control agents. This review deals with a natural form of biological control in which the virulence of a fungal pathogen is attenuated by an endogenous viral RNA genetic element: the phenomenon of transmissible hypovirulence in the chestnut blight fungus, Cryphonectria parasitica. Recent progress in the molecular characterization of a hypovirulence-associated viral RNA has provided an emerging view of the genetic organization and basic expression strategy of this class of genetic elements. Several lines of evidence now suggest that specific hypovirulence-associated virus-encoded gene products selectively modulate the expression of subsets of fungal genes and the activity of specific regulatory pathways. The construction of an infectious cDNA clone of a hypovirulence-associated viral RNA represents a major advancement that provides exciting new opportunities for examining the molecular basis of transmissible hypovirulence and for engineering hypovirulent strains for improved biocontrol. These developments have significantly improved the prospects of using this system to identify molecular determinants of virulence and elucidate signal transduction pathways involved in pathogenic responses. In addition, novel approaches are now available for extending the application of transmissible hypovirulence for management of chestnut blight and possibly other fungal diseases.

Cutinase in Cryphonectria parasitica, the chestnut blight fungus: suppression of cutinase gene expression in isogenic hypovirulent strains containing double-stranded RNAs

Plant-pathogenic fungi produce cutinase, an enzyme required to degrade plant cuticles and facilitate penetration into the host. The absence of cutinase or a decrease in its production has been associated with a decrease in pathogenicity of the fungus. A set of isogenic strains of Cryphonectria parasitica, the chestnut blight fungus, was tested for the presence and amounts of cutinase activity. The virulent strain of C. parasitica produced and secreted significantly higher amounts of cutinase than the hypovirulent strains. Use of both nucleic acid and polyclonal antibody probes for cutinase from Fusarium solani f. sp. pisi showed that cutinase in C. parasitica is 25 kDa in size and is coded by a 1.1-kb mRNA. Both mRNA and protein were inducible by cutin hydrolysate, while hypovirulence agents suppressed the level of mRNA and the enzyme. Since all the strains had the cutinase gene, the suppression of expression was due to the hypovirulence agents. The data presented are the first report indicating that hypovirulence agents in C. parasitica regulate a gene associated with pathogenicity in other plant-pathogenic fungi.

Cutinase in Cryphonectria parasitica, the chestnut blight fungus: suppression of cutinase gene expression in isogenic hypovirulent strains containing double-stranded RNAs

Plant-pathogenic fungi produce cutinase, an enzyme required to degrade plant cuticles and facilitate penetration into the host. The absence of cutinase or a decrease in its production has been associated with a decrease in pathogenicity of the fungus. A set of isogenic strains of Cryphonectria parasitica, the chestnut blight fungus, was tested for the presence and amounts of cutinase activity. The virulent strain of C. parasitica produced and secreted significantly higher amounts of cutinase than the hypovirulent strains. Use of both nucleic acid and polyclonal antibody probes for cutinase from Fusarium solani f. sp. pisi showed that cutinase in C. parasitica is 25 kDa in size and is coded by a 1.1-kb mRNA. Both mRNA and protein were inducible by cutin hydrolysate, while hypovirulence agents suppressed the level of mRNA and the enzyme. Since all the strains had the cutinase gene, the suppression of expression was due to the hypovirulence agents. The data presented are the first report indicating that hypovirulence agents in C. parasitica regulate a gene associated with pathogenicity in other plant-pathogenic fungi.

Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses

Computer-assisted analysis of the putative polypeptide products encoded by the two open reading frames present in a large virus-like double-stranded RNA, L-dsRNA, associated with hypovirulence of the chestnut blight fungus, Cryphonectria parasitica, revealed five distinct domains with significant sequence similarity to previously described conserved domains within plant potyvirus-encoded polyproteins. These included the putative RNA-dependent RNA polymerase, RNA helicase, two papain-like cysteine proteases related to the potyvirus helper-component protease, and a cysteine-rich domain of unknown function similar to the N-terminal portion of the potyvirus helper-component protein. Phylogenetic trees derived from the alignment of the polymerase domains of L-dsRNA, a subset of positive-stranded RNA viruses, and double-stranded RNA viruses, using three independent algorithms, suggested that the hypovirulence-associated dsRNA and potyvirus genomes share a common ancestry. However, comparison of the organization of the conserved domains within the encoded polyproteins of the respective viruses indicated that the proposed subsequent evolution involved extensive genome rearrangement.

Sequences of three dsRNAs associated with La France disease of the cultivated mushroom (Agaricus bisporus)

La France disease of the cultivated mushroom, Agaricus bisporus, is known to be associated with the presence of a number of dsRNA segments. The nucleotide sequences of the dsRNAs M2 (1.3 kb), M1 (1.55 kb) and L3 (2.8 kb), invariably associated with the disease, were determined. Putative coding sequences for proteins with molecular weights of 38, 40 and 87 kDa were found for M2, M1 and L3 dsRNAs, respectively. The average G + C content of these dsRNAs was 43%, close to that of A. bisporus nuclear DNA. The nucleotide sequences, as well as the amino acid sequences, appear to be unique, as no matching sequences could be found among databases. S3 dsRNA (0.39 kb), which is occasionally found in large amounts in diseased mushrooms, is an internally deleted variant of M2 dsRNA and is largely composed of the non-coding ends of that dsRNA.

From interferon induction to fungal viruses

Viruses of fungi (mycoviruses) were first discovered in diseased mushrooms. However the finding that the antiviral and interferon-inducing activities of extracts of apparently healthy isolates of a number of Penicillium species were due to the presence of double-stranded (ds) RNA arising from mycovirus infections sparked off an explosion of interest in what has now become a distinct area of virology. Two families of dsRNA mycoviruses are now established: the Totiviridae and the Partitiviridae which comprise isometric viruses with genomes of one or two dsRNA segments respectively. Virus isolates in both families often contain additional satellite dsRNAs, which may in some fungi (e.g. Saccharomyces cerevisiae, Ustilago maydis) code for "killer" proteins which are toxic to other sensitive strains of the same or closely related species. In Endothia parasitica, which causes chestnut blight disease, dsRNA is associated with hypovirulence and is enclosed in lipid-rich vesicles. In Ophiostoma (Ceratocystis) ulmi, which causes Dutch elm disease, dsRNA is associated with the mitochondria and, in some diseased isolates of the fungus, specific dsRNA segments are associated with reduction of cytochrome oxidase and respiratory deficiency, resulting in slow growth and abnormal morphology.

Double stranded RNA in natural isolates of Neurospora

Thirty-six wild type isolates of Neurospora were surveyed for the presence of dsRNA. The survey identified seven strains which contain dsRNA molecules. These seven strains are all from different geographic locations. The sizes of the dsRNAs range from 500 bp to 18 kb and a total of seven distinct dsRNA species was identified. Cross homologies of some of the dsRNAs were apparent. There was homology between the 9.0 kb dsRNA and genomic DNA prepared from all strains in the survey, indicating a possible cellular rather than viral origin for this dsRNA species. None of the other dsRNAs hybridized with genomic DNA suggesting a viral origin for these dsRNAs.