Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus

Identification and characterization of Phaseolus vulgaris endornavirus 1, 2 and 3 in common bean cultivars of East Africa

Persistent viruses include members of the family Endornavirus that cause no apparent disease and are transmitted exclusively via seed or pollen. It is speculated that these RNA viruses may be mutualists that enhance plant resilience to biotic and abiotic stresses. Using reverse transcription coupled polymerase chain reactions, we investigated if common bean (Phaseolus vulgaris L.) varieties popular in east Africa were hosts for Phaseolus vulgaris endornavirus (PvEV) 1, 2 or 3. Out of 26 bean varieties examined, four were infected with PvEV1, three were infected with both PvEV1 and PvEV2 and three had infections of all three (PvEV) 1, 2 and 3. Notably, this was the first identification of PvEV3 in common bean from Africa. Using high-throughput sequencing of two east African bean varieties (KK022 and KK072), we confirmed the presence of these viruses and generated their genomes. Intra- and inter-species sequence comparisons of these genomes with comparator sequences from GenBank revealed clear species demarcation. In addition, phylogenetic analyses based on sequences generated from the helicase domains showed that geographical distribution does not correlate to genetic relatedness or the occurrence of endornaviruses. These findings are an important first step towards future investigations to determine if these viruses engender positive effects in common bean, a vital crop in east Africa.

Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

Endornaviruses are capsidless linear (+) ssRNA viruses in the family Endornaviridae. In this study, Scelrotinia sclerotiorum endornavirus 11 (SsEV11), a novel endornavirus infecting hypovirulent Sclerotinia sclerotiorum strain XY79, was identified and cloned using virome sequencing analysis and rapid amplification of cDNA ends (RACE) techniques. The full-length genome of SsEV11 is 11906 nt in length with a large ORF, which encodes a large polyprotein of 3928 amino acid residues, containing a viral methyltransferase domain, a cysteine-rich region, a putative DEADc, a viral helicase domain, and an RNA-dependent RNA polymerase (RdRp) 2 domain. The 5’ and 3’ untranslated regions (UTR) are 31 nt and 90 nt, respectively. According to the BLAST result of the nucleotide sequence, SsEV11 shows the highest identity (45%) with Sclerotinia minor endornavirus 1 (SmEV1). Phylogenetic analysis based on amino acid sequence of RdRp demonstrated that SsEV11 clusters to endornavirus and has a close relationship with Betaendornavirus. Phylogenetic analysis based on the sequence of endornaviral RdRp domain indicated that there were three large clusters in the phylogenetic tree. Combining the results of alignment analysis, Cluster I at least has five subclusters including typical members of Alphaendornavirus and many unclassified endornaviruses that isolated from fungi, oomycetes, algae, and insects; Cluster II also has five subclusters including typical members of Betaendornavirus, SsEV11, and other unclassified viruses that infected fungi; Cluster III includes many endorna-like viruses that infect nematodes, mites, and insects. Viruses in Cluster I and Cluster II are close to each other and relatively distant to those in Cluster III. Our study characterized a novel betaendornavirus, SsEV11, infected fungal pathogen S. sclerotiorum, and suggested that notable phylogenetic diverse exists in endornaviruses. In addition, at least, one novel genus, Gammaendornavirus, should be established to accommodate those endorna-like viruses in Cluster III.

Broad and systemic immune-modulating capacity of plant-derived dsRNA

Double-stranded RNA (dsRNA) is well characterized as an inducer of anti-viral interferon responses. We previously reported that dsRNA extracted from a specific edible plant possesses an immune-modulating capacity to confer, in mice, resistance against respiratory viruses, including the H1N1 strain of the influenza A virus (IAV). We report here that the systemic immune-activating capacity of the plant-derived dsRNA protected mice from infection by a highly virulent H5N1 strain of the IAV. In addition, subcutaneous inoculation of the dsRNA together with the inactivated virion of the H5N1 strain of the IAV suppressed the lethality of the viral infection as compared with individual inoculation of either dsRNA or HA protein, suggesting its potential usage as a vaccination adjuvant. Moreover, intra-peritoneal inoculation of the dsRNA limited the growth of B16-F10 melanoma cells through the activation of NK cells in murine models. Taken together, this study demonstrated the systemic immune-modulating capacity of a plant-derived dsRNA and its potential for nucleic acid-based clinical applications.

Effect of asymptomatic infection with southern tomato virus on tomato plants

Southern tomato virus (STV) is often found infecting healthy tomato plants (Solanum lycopersicum). In this study, we compared STV-free and STV-infected plants of cultivar M82 to determine the effect of STV infection on the host plant. STV-free plants exhibited a short and bushy phenotype, whereas STV-infected plants were taller. STV-infected plants produced more fruit than STV-free plants, and the germination rate of seeds from STV-infected plants was higher than that of seeds from STV-free plants. This phenotypic difference was also observed in progeny plants (siblings) derived from a single STV-infected plant in which the transmission rate of STV to progeny plants via the seeds was approximately 86%. These results suggest that the interaction between STV and host plants is mutualistic. Transcriptome analysis revealed that STV infection affects gene expression in the host plant and results in downregulation of genes involved in ethylene biosynthesis and signaling. STV-infected tomato plants might thus be artificially selected due to their superior traits as a crop.

ICTV Virus Taxonomy Profile: Endornaviridae

The family Endornaviridae includes viruses with linear, single-stranded, positive-sense RNA genomes that range from 9.7 to 17.6 kb and have been reported infecting plants, fungi and oomycetes. The family consists of two genera, Alphaendornavirus and Betaendornavirus, into which viruses are classified based on their genome size, host and presence of unique domains. Alphaendornavirus includes species whose members infect plants, fungi and oomycetes, while the genus Betaendornavirus includes species whose members infect ascomycete fungi. This is a summary of the ICTV Report on the family Endornaviridae, which is available at www.ictv.global/report/endornaviridae.

Complete genomic sequence of barley (Hordeum vulgare) endornavirus (HvEV) determined by next-generation sequencing

Endornaviruses are unusual plant-, fungus- and oomycete-infecting viruses with a large, ca 14- to 17-kb linear double-stranded RNA (dsRNA) genome and a persistent lifestyle. The complete genome sequence of an endornavirus from the barley (Hordeum vulgare) Nerz variety was determined from paired Illumina MySeq reads derived from purified dsRNAs. The genome is 14,243 nt long, with 5' and 3' non-coding regions of 207 and 47 nt, respectively. It encodes a single large protein of 4663 amino acids that carries conserved motifs for a methyltransferase, a helicase and an RNA-dependent RNA polymerase. The sequence of Hordeum vulgare endornavirus (HvEV) carries all the hallmarks of a typical member of the genus Endornavirus, with the exception of an UDP-glycosyltransferase motif observed in many, but not all, endornaviral genomes.

Widespread mitovirus sequences in plant genomes

The exploration of the evolution of RNA viruses has been aided recently by the discovery of copies of fragments or complete genomes of non-retroviral RNA viruses (Non-retroviral Endogenous RNA Viral Elements, or NERVEs) in many eukaryotic nuclear genomes. Among the most prominent NERVEs are partial copies of the RNA dependent RNA polymerase (RdRP) of the mitoviruses in plant mitochondrial genomes. Mitoviruses are in the family Narnaviridae, which are the simplest viruses, encoding only a single protein (the RdRP) in their unencapsidated viral plus strand. Narnaviruses are known only in fungi, and the origin of plant mitochondrial mitovirus NERVEs appears to be horizontal transfer from plant pathogenic fungi. At least one mitochondrial mitovirus NERVE, but not its nuclear copy, is expressed.

Virus world as an evolutionary network of viruses and capsidless selfish elements

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.

Unique symbiotic viruses in plants: Endornaviruses

Linear double-stranded RNAs (dsRNAs) of about 15 kbp in length are often found from healthy plants, such as bell pepper and rice plants. Nucleotide sequencing and phylogenetic analyses reveal that these dsRNAs are not transcribed from host genomic DNAs, encode a single long open reading frame (ORF) with a viral RNA-dependent RNA polymerase domain, and contain a site-specific nick in the 5' region of their coding strands. Consequently the International Committee on Taxonomy of Viruses has approved that these dsRNAs are viruses forming a distinct taxon, the family Endornaviridae the genus Endornavirus. Endornaviruses have common properties that differ from those of conventional viruses: they have no obvious effect on the phenotype of their host plants, and they are efficiently transmitted to the next generation via both pollen and ova, but their horizontal transfer to other plants has never been proven. Conventional single-stranded RNA viruses, such as cucumber mosaic virus, propagate hugely and systemically in host plants to sometime kill their hosts eventually and transmit horizontally (infect to other plants). In contrast, copy numbers of endornaviruses are low and constant (about 100 copies/cell), and they symbiotically propagate with host plants and transmit vertically. Therefore, endornaviruses are unique plant viruses with symbiotic properties.

Molecular characterisation of an endornavirus from Rhizoctonia solani AG-3PT infecting potato

Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) is a soil-borne plant pathogenic fungus that has a broad host range, including potato. In this study, the double-stranded RNA (dsRNA) profiles were defined for 39 Rhizoctonia solani isolates representative of two different anastomosis groups (AGs) associated with black scurf of potato in New Zealand. A large dsRNA of c. 12 kb-18 kb was detected in each of the isolates, regardless of AG or virulence on potato. Characterisation of the large dsRNA from R. solani AG-3PT isolate RS002, using random amplification of total dsRNA and analyses of overlapping cDNA sequences, resulted in the assembly of a consensus sequence of 14 694 nt. A single, large open reading frame was identified on the positive strand of the assembled sequence encoding a putative polypeptide of at least 4893 amino acids, with a predicted molecular mass of 555.6 kDa. Conserved domains within this polypeptide included those for a viral methyltransferase, a viral RNA helicase 1 and an RNA-dependent RNA polymerase. The domains and their sequential organisation revealed the polyprotein was very similar to those encoded by dsRNA viruses of the genus Endornavirus, in the family Endornaviridae. This is the first report of an endornavirus in R. solani, and thus the putative virus is herein named Rhizoctonia solani endornavirus - RS002 (RsEV-RS002). Partial characterisation of the large dsRNAs in five additional AG-3PT isolates of R. solani also identified them as probable endornaviruses, suggesting this family of viruses is widespread in R. solani infecting potato. The ubiquitous nature of endornaviruses in this plant pathogen implies they may have an important, but yet uncharacterised, role in R. solani.

Molecular characterisation of an endornavirus infecting the phytopathogen Sclerotinia sclerotiorum

The complete sequence and genome organisation of an endornavirus from the phytopathogenic fungus Sclerotinia sclerotiorum isolate 11691 was described and the name Sclerotinia sclerotiorum endornavirus 1 (SsEV1/11691) proposed. The genome is 10,513 nucleotides (nts) long with a single open reading frame (ORF) that codes for a single polyprotein of 3459 amino acid (aa) residues. The polyprotein contains cysteine-rich region (CRR), viral methyltransferase (MTR), putative DEXDc, viral helicase (Hel), phytoreo_S7 (S7) and RNA-dependent RNA polymerase (RdRp) domains. The polyprotein and the conserved domains are phylogenetically related to endornaviruses. However, the coding strand of SsEV1/11691 does not contain a site-specific nick characteristic of most previously described endornaviruses. The elimination of SsEV1/11691 did not result in any significant changes in the host phenotype and virulence.

Complete nucleotide sequence and genome organization of an endornavirus from bottle gourd (Lagenaria siceraria) in California, U.S.A

The full-length nucleotide sequence and genome organization of an Endornavirus isolated from ornamental hard shell bottle gourd plants (Lagenaria siceraria (Molina) Standl.) in California (CA), USA tentatively named L. siceraria endornavirus-California (LsEV-CA) was determined. The LsEV-CA genome was 15088 bp in length, with a G + C content of 36.55 %. The lengths of the 5' and 3' untranslated regions were 111 and 52 bp, respectively. The genome of LsEV-CA contained one large ORF encoding a 576 kDa polyprotein. The predicted protein contains two glycosyltransferase motifs, as well as RNA-dependent RNA polymerase and helicase domains. LsEV-CA was detected in healthy-looking field-grown gourd plants, as well as plants expressing yellows symptoms. It was also detected in non-symptomatic greenhouse-grown gourd seedlings grown from seed obtained from the same field sites. These preliminary data indicate that LsEV-CA is likely not associated with the gourd-yellows syndrome observed in the field.

Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods

Background

Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition.

Results

We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed “advanced” phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses.

Conclusions

We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of probability of the tree topologies) of the evolutionary affinities between double-stranded RNA and positive strand RNA viruses. In particular, we were able to show that there exists a good statistical support for the claims that dsRNA viruses are not monophyletic and that viruses with permuted RdRps belong to a common evolution lineage as previously proposed by other groups. We also propose a tree topology with a good statistical support describing the evolutionary relationships between the Picornaviridae, Caliciviridae, Flaviviridae families and a group including the Alphatetraviridae, Nodaviridae, Permutotretraviridae, Birnaviridae, and Cystoviridae families.

Evolution of and horizontal gene transfer in the Endornavirus genus

The transfer of genetic information between unrelated species is referred to as horizontal gene transfer. Previous studies have demonstrated that both retroviral and non-retroviral sequences have been integrated into eukaryotic genomes. Recently, we identified many non-retroviral sequences in plant genomes. In this study, we investigated the evolutionary origin and gene transfer of domains present in endornaviruses which are double-stranded RNA viruses. Using the available sequences for endornaviruses, we found that Bell pepper endornavirus-like sequences homologous to the glycosyltransferase 28 domain are present in plants, fungi, and bacteria. The phylogenetic analysis revealed the glycosyltransferase 28 domain of Bell pepper endornavirus may have originated from bacteria. In addition, two domains of Oryza sativa endornavirus, a glycosyltransferase sugar-binding domain and a capsular polysaccharide synthesis protein, also exhibited high similarity to those of bacteria. We found evidence that at least four independent horizontal gene transfer events for the glycosyltransferase 28 domain have occurred among plants, fungi, and bacteria. The glycosyltransferase sugar-binding domains of two proteobacteria may have been horizontally transferred to the genome of Thalassiosira pseudonana. Our study is the first to show that three glycome-related viral genes in the genus Endornavirus have been acquired from marine bacteria by horizontal gene transfer.

Molecular characterization of two evolutionarily distinct endornaviruses co-infecting common bean (Phaseolus vulgaris)

Two high-molecular-mass dsRNAs of approximately 14 and 15 kbp were isolated from the common bean (Phaseolus vulgaris) cultivar Black Turtle Soup. These dsRNAs did not appear to cause obvious disease symptoms, and were transmitted through seeds at nearly 100 % efficiency. Sequence information indicates that they are the genomes of distinct endornavirus species, for which the names Phaseolus vulgaris endornavirus 1 (PvEV-1) and Phaseolus vulgaris endornavirus 2 (PvEV-2) are proposed. The PvEV-1 genome consists of 13 908 bp and potentially encodes a single polyprotein of 4496 aa, while that of PvEV-2 consists of 14 820 bp and potentially encodes a single ORF of 4851 aa. PvEV-1 is more similar to Oryza sativa endornavirus, while PvEV-2 is more similar to bell pepper endornavirus. Both viruses have a site-specific nick near the 5′ region of the coding strand, which is a common property of the endornaviruses. Their polyproteins contain domains of RNA helicase, UDP-glycosyltransferase and RNA-dependent RNA polymerase, which are conserved in other endornaviruses. However, a viral methyltransferase domain was found in the N-terminal region of PvEV-2, but was absent in PvEV-1. Results of cell-fractionation studies suggested that their subcellular localizations were different. Most endornavirus-infected bean cultivars tested were co-infected with both viruses.

Bell pepper endornavirus: molecular and biological properties, and occurrence in the genus Capsicum

Bell peppers (Capsicum annuum) harbour a large dsRNA virus. The linear genome (14.7 kbp) of two isolates from Japanese and USA bell pepper cultivars were completely sequenced and compared. They shared extensive sequence identity and contained a single, long ORF encoding a 4815 aa protein. This polyprotein contained conserved motifs of putative viral methyltransferase (MTR), helicase 1 (Hel-1), UDP-glycosyltransferase and RNA-dependent RNA polymerase. This unique arrangement of conserved domains has not been reported in any of the known endornaviruses. Hence this virus, for which the name Bell pepper endornavirus (BPEV) is proposed, is a distinct species in the genus Endornavirus (family Endornaviridae). The BPEV-encoded polyprotein contains a cysteine-rich region between the MTR and Hel-1 domains, with conserved CXCC motifs shared among several endornaviruses, suggesting an additional functional domain. In agreement with general endornavirus features, BPEV contains a nick in the positive-strand RNA molecule. The virus was detected in all bell pepper cultivars tested and transmitted through seed but not by graft inoculations. Analysis of dsRNA patterns and RT-PCR using degenerate primers revealed putative variants of BPEV, or closely related species, infecting other C. annuum genotypes and three other Capsicum species (C. baccatum, C. chinense and C. frutescens).

The hallmarks of "green" viruses: do plant viruses evolve differently from the others?

All viruses are obligatory parasites that must develop tight interactions with their hosts to complete their infectious cycle. Viruses infecting plants share many structural and functional similarities with those infecting other organisms, particularly animals and fungi. Quantitative data regarding their evolutionary mechanisms--generation of variability by mutation and recombination, changes in populations by selection and genetic drift have been obtained only recently, and appear rather similar to those measured for animal viruses.This review presents an update of our knowledge of the phylogenetic and evolutionary characteristics of plant viruses and their relation to their plant hosts, in comparison with viruses infecting other organisms.

Lifestyles of plant viruses

The vast majority of well-characterized eukaryotic viruses are those that cause acute or chronic infections in humans and domestic plants and animals. However, asymptomatic persistent viruses have been described in animals, and are thought to be sources for emerging acute viruses. Although not previously described in these terms, there are also many viruses of plants that maintain a persistent lifestyle. They have been largely ignored because they do not generally cause disease. The persistent viruses in plants belong to the family Partitiviridae or the genus Endornavirus. These groups also have members that infect fungi. Phylogenetic analysis of the partitivirus RNA-dependent RNA polymerase genes suggests that these viruses have been transmitted between plants and fungi. Additional families of viruses traditionally thought to be fungal viruses are also found frequently in plants, and may represent a similar scenario of persistent lifestyles, and some acute or chronic viruses of crop plants may maintain a persistent lifestyle in wild plants. Persistent, chronic and acute lifestyles of plant viruses are contrasted from both a functional and evolutionary perspective, and the potential role of these lifestyles in host evolution is discussed.

A novel putative virus of Gremmeniella abietina type B (Ascomycota: Helotiaceae) has a composite genome with endornavirus affinities

Ascospore and mycelial isolates of Gremmeniella abietina type B were found to contain three different dsRNA molecules with approximate lengths of 11, 5 and 3 kb. The 11 kb dsRNA encoded the genome of a putative virus and is named Gremmeniella abietina type B RNA virus XL (GaBRV-XL). GaBRV-XL probably exists in an unencapsulated state. We identified two distinct dsRNAs (10 374 and 10 375 bp) of GaBRV-XL, both of which coded for the same putative polyprotein (3249 amino acids) and contained four regions similar to putative viral methyltransferases, DExH box helicases, viral RNA helicase 1 and RNA-dependent RNA polymerases. While a cysteine-rich region with several CxCC motifs in GaBRV-XL was similar to that of putative endornaviruses, cluster analyses of conserved regions revealed GaBRV-XL to be distinct from a broad range of viral taxa but most closely related to Discula destructiva virus 3. Collectively, these findings suggest that GaBRV-XL represents a novel virus group related to endornaviruses.

The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups

The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA viruses. The phylogenetic analyses of RNA polymerases and helicases presented in this Analysis article reveal close evolutionary relationships between RNA viruses infecting hosts from the Chromalveolate and Excavate supergroups and distinct families of picorna-like viruses of plants and animals. Thus, diversification of picorna-like viruses probably occurred in a 'Big Bang' concomitant with key events of eukaryogenesis. The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.

Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: a genomic resource for studying agricultural pests

Background

The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background.

Results

More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site.

Conclusion

The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest.

Molecular characterization and detection of Vicia cryptic virus in different Vicia faba cultivars

After extraction of double-stranded (ds) RNAs from Vicia faba, dsRNA1 and dsRNA2 of Vicia cryptic virus (VCV), a member of the genus Alphacryptovirus (family Partitiviridae), were detected in six out of seven different cultivars by agarose gel electrophoresis. In attempts to sequence the complete VCV genome, the dsRNA1 and dsRNA2 sequences from a total of five different V. faba cultivars were determined. Analysis of these sequences indicated that V. faba cultivars contain almost indistinguishable VCV sequences. The larger dsRNA1 was 2012 bp in length and contained a major open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 was 1779 bp in length and comprised a single ORF on its plus-strand encoding the coat protein (CP). The sequences of the dsRNA1 and dsRNA2 ORFs shared highest amino acid sequence identities (84 and 56%, respectively) with the corresponding gene products of the alphacryptovirus white clover cryptic virus 1 (WCCV-1). The 5'-terminal untranslated regions of dsRNA1 and dsRNA2 of VCV were highly conserved and were strikingly similar to the corresponding regions of WCCV-1. RdRp amino acid sequence alignments revealed conserved motifs, which correlate with the phylogenetic clustering of the family Partitiviridae.

An endornavirus from a hypovirulent strain of the violet root rot fungus, Helicobasidium mompa

We determined the complete nucleotide (nt) sequence (16,614 nt) of a large double-stranded (ds) RNA (referred to as L1 dsRNA), previously identified as the hypovirulence factor from strain V670 of the violet root rot fungus, Helicobasidium mompa. The positive-strand of L1 dsRNA contained a long open reading frame (ORF) potentially encoding a protein of 5,373 amino acids (molecular mass 603,080 Da) with conserved motifs characteristic of RNA-dependent RNA polymerase (RdRp) and helicase. The ORF is the longest so far reported in the fungal kingdom. The putative RdRp and helicase were shown to be related to putative RdRps and helicases of members of the genus Endornavirus. As is the case with endornaviruses, the coding (sense) strand of L1 dsRNA contained a discontinuity (nick) at nt position 2,552. A region between the RdRp and helicase domains of the polyprotein also had an amino acid sequence, resembling UDP glycosyltransferases (UGTs) in Oryza sativa endornavirus and Phytophthora endornavirus 1. Regions in the L1 dsRNA-encoded protein presumed to contain putative helicase, UGT and RdRp motifs were present at comparable positions to those in other endornaviruses. L1 dsRNA of H. mompa strain V670 was assigned to the genus Endornavirus, and here, we designate it as H. mompa endornavirus 1-670 (HmEV1-670). This represents the first report of a fungal endornavirus whose complete nucleotide sequence has been determined.

The wide distribution of endornaviruses, large double-stranded RNA replicons with plasmid-like properties

The International Committee on Taxonomy of Viruses (ICTV) recently accepted Endornavirus as a new genus of plant dsRNA virus. We have determined the partial nucleotide sequences of the RNA-dependent RNA polymerase regions from the large dsRNAs (about 14 kbp) isolated from barley (Hordeum vulgare), kidney bean (Phaseolus vulgaris), melon (Cucumis melo), bottle gourd (Lagenaria siceraria), Malabar spinach (Basella alba), seagrass (Zostera marina), and the fungus Helicobasidium mompa. Phylogenetic analyses of these seven dsRNAs indicate that these dsRNAs are new members of the genus Endornavirus that are widely distributed over the plant and fungal kingdoms.

Three unrelated viruses occur in a single isolate of Gremmeniella abietina var. abietina type A

Five enclosed double-stranded RNA (dsRNA) bands in electrophoresis, probably of viral origin, were found from a single isolate (SurS4) of Gremmeniella abietina var. abietina type A. Analysis of the dsRNAs revealed that they represented three different viruses, named as Gremmeniella abietina mitochondrial RNA virus S2 (GaMRV-S2), Gremmeniella abietina RNA virus MS2 (GaRV-MS2) and Gremmeniella abietina RNA virus L2 (GaRV-L2). The genome of GaMRV-S2 was 2587 base pairs (bp) long and had a very low GC content (31%). Sequence variations occurred at both ends. The genome coded for a putative RNA-dependent RNA polymerase (RdRp) under a mitochondrial translation code. The GaRV-MS2 genome was composed of three dsRNA molecules (1781 bp, 1586 bp and 1186 bp). They coded for a putative RdRp, a coat protein (CP) and a protein with an unknown function, respectively. The GaRV-L2 genome was 5129 bp long and contained two ORFs. The 5'-proximal ORF coded for a putative CP, whereas the 3'-proximal ORF encoded for a putative RdRp. The buoyant density of GaRV-MS2 and GaRV-L2 were 1.37 and 1.42 g/ml, respectively. GaMRV-S2, GaRV-MS2 and GaRV-L2 were closely related to the previously described viruses GaMRV-S1, GaRV-MS1 and GaRV-L1, respectively, and are putative members of the genera Mitovirus, Partitivirus and Totivirus, respectively. This is the first report on the occurrence of viruses of all these different genera in a single fungal isolate.

A double-stranded RNA from a Phytophthora species is related to the plant endornaviruses and contains a putative UDP glycosyltransferase gene

A new dsRNA was isolated from a Phytophthora isolate from Douglas fir. Sequence analysis showed the dsRNA to consist of 13 883 bp and to contain a single open reading frame with the potential to encode a polyprotein of 4548 aa. This polyprotein contained amino acid sequence motifs characteristic of virus RNA-dependent RNA polymerases (RdRps) in its C-terminal region and motifs characteristic of RNA helicases in its N-terminal region. These sequence motifs were related to corresponding motifs in plant viruses in the genus Endornavirus. In phylogenetic trees constructed from the RdRp and helicase motifs of a range of ssRNA and dsRNA viruses, the Phytophthora RdRp and helicase sequences clustered with those of the plant endornaviruses with good bootstrap support. The properties of the Phytophthora dsRNA are consistent with its being classified as the first non-plant member of the genus Endornavirus, for which we propose the name phytophthora endornavirus 1 (PEV1). A region between the RdRp and helicase domains of the PEV1 protein had significant amino acid sequence similarity to UDP glycosyltransferases (UGTs). Two sequence motifs were identified, one characteristic of all UGTs and the other characteristic of sterol UGTs. The PEV1 UGT would be the first for an RNA virus, although ecdysteroid UGT genes have been found in many baculoviruses. The PEV1 UGT was only distantly related to baculovirus ecdysteroid UGTs, which belong to a family distinct from the sterol UGTs.

The Microbial Rosetta Stone Database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents

BACKGROUND

Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks.

RESULTS

We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents.

CONCLUSION

The Microbial Rosetta Stone is available at http://www.microbialrosettastone.com/. The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases.

Putative Replication Intermediates in Endornavirus, a Novel Genus of Plant dsRNA Viruses

Oryza sativa endornavirus (OSV) belongs to a new genus (Endornavirus) and family (Endoviridae) with members containing large double-stranded RNA (dsRNA) replicons with plasmid-like properties. Analysis of products obtained from in vitro reaction of the OSV RNA-dependent RNA polymerase revealed a rapid increase of a population of the non-coding strand RNA molecules with a head-to-tail composition. Northern hybridization of total RNA from OSV-carrier cells with riboprobes specific for the coding strand RNA, revealed two types of RNA molecules (i) with a site specific nick and (ii) full-length unnicked molecules. Quantitative analyses of these RNAs showed about 50-fold higher amounts of full-length unnicked molecules in cultured cells in which the OSV copy number increases compared with those found in the seedling cells. Both the head-to-tail linked non-coding strand and the full-length coding strand molecules were also found in wild rice and broad beans infected with other endornaviruses indicating that the presence of these unique types of RNA molecules should be considered as a characteristic feature of Endoviridae .

RNA-dependent RNA polymerases of dsRNA bacteriophages

Genome replication and transcription of riboviruses are catalyzed by an RNA-dependent RNA polymerase (RdRP). RdRPs are normally associated with other virus- or/and host-encoded proteins that modulate RNA polymerization activity and template specificity. The polymerase complex of double-stranded dsRNA viruses is a large icosahedral particle (inner core) containing RdRP as a minor constituent. In phi6 and other dsRNA bacteriophages from the Cystoviridae family, the inner core is composed of four virus-specific proteins. Of these, protein P2, or Pol subunit, has been tentatively identified as RdRP by sequence comparisons, but the role of this protein in viral RNA synthesis has not been studied until recently. Here, we overview the work on the Pol subunits of phi6 and related viruses from the standpoints of function, structure and evolution.

Coevolution of viruses with hosts and vectors and possible paleontology

The coevolution of viruses with their hosts and vectors depends on the evolution of the hosts and vectors coupled with factors involved in virus evolution. The long-term perspective involves the origin of life forms, the evolution of host and vector (especially arthropods) kingdoms and families, and changes in biological diversity induced mainly by the last five great extinctions. In the medium term, the diversification of hosts and vectors is important, and in the short term, recent events, especially humans, have had a great impact on virus coevolution. As there are few, if any, examples of conventional fossils of viruses, evidence for their evolution related to host and vector evolution is being found from other sources, especially virus-induced cellular structures and recent developments in molecular biology. Recognizing these other sources is becoming important for paleontologists gaining an understanding of the influence that viruses have had on the development of higher organisms.

Presence of potential allergy-related linear epitopes in novel proteins from conventional crops and the implication for the safety assessment of these crops with respect to the current testing of genetically modified crops

Mitochondria of cytoplasmic male sterile crop plants contain novel, chimeric open reading frames. In addition, a number of crops carry endogenous double-stranded ribonucleic acid (dsRNA). In this study, the novel proteins encoded by these genetic components were screened for the presence of potential binding sites (epitopes) of allergy-associated IgE antibodies, as was previously done with transgenic proteins from genetically modified crops. The procedure entails the identification of stretches of at least six contiguous amino acids that are shared by novel proteins and known allergenic proteins. These stretches are further checked for potential linear IgE-binding epitopes. Of the 16 novel protein sequences screened in this study, nine contained stretches of six or seven amino acids that were also present in allergenic proteins. Four cases of similarity are of special interest, given the predicted antigenicity of the identical stretch within the allergenic and novel protein, the IgE-binding by a peptide containing an identical stretch reported in literature, or the multiple incidence of identical stretches of the same allergen within a novel protein. These selected stretches are present in novel proteins derived from oilseed rape and radish (ORF138), rice (dsRNA), and fava bean (dsRNA), and warrant further clinical testing. The frequency of positive outcomes and the sizes of the identical stretches were comparable to those previously found for transgenic proteins in genetically modified crops. It is discussed whether novel proteins from conventional crops should be subject to an assessment of potential allergenicity, a procedure which is currently mandatory for transgenic proteins from genetically modified crops.

Inheritance of Oryza sativa endornavirus in F1 and F2 hybrids between japonica and indica rice

We have found a 14 kbp double-stranded RNA (dsRNA) in many cultivars of japonica rice (Oryza sativa L.) but not in any cultivars of indica rice. This dsRNA is an RNA replicon with plasmid-like properties and is proposed to be a novel dsRNA virus, Oryza sativa endornavirus (OSV). Reciprocal crosses between the OSV-carrier japonica variety (Nipponbare) and the OSV-free indica variety (IR 26 or Kasalath) were performed to investigate whether OSV can be transmitted to F1 hybrids. When IR 26 and Nipponbare were used, efficient transmission of OSV from ova (93%) and pollen (89%) was observed. When Kasalath and Nipponbare were used, the OSV transmission efficiency to F1 progeny was 68% from ova and 20% from pollen. The transmission of OSV to F2 progeny plants was also complicated, showing non-Mendelian inheritance. These results suggest that the dsRNA replicon (OSV) is unstable in indica rice plants.

A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases

A systematic bioinformatic approach to identifying the evolutionarily conserved regions of proteins has verified the universality of a newly described conserved motif in RNA-dependent RNA polymerases (motif F). In combination with structural comparisons, this approach has defined two regions that may be involved in unwinding double-stranded RNA (dsRNA) for transcription. One of these is the N-terminal portion of motif F and the second is a large insertion in motif F present in the RNA-dependent RNA polymerases of some dsRNA viruses.

RNA-dependent RNA polymerase activity associated with endogenous double-stranded RNA in rice

RNA-dependent RNA polymerase (RdRp) activity was detected in the crude microsomal fraction of rice cultured cells that contain a 14 kbp double-stranded RNA (dsRNA). RdRp activity is maximal in the presence of all four nucleotide triphosphates and Mg2+ ion and is resistant to inhibitors of DNA-dependent RNA polymerases (actinomycin D and alpha-amanitin). RdRp activity increases approximately 2.5-fold in the presence of 0.5% deoxycholate. Treatment of purified microsomal fraction with proteinase K plus deoxycholate suggests that the RdRp enzyme complex with its own 14 kb RNA template is located in vesicles. The RdRp enzyme complex was solubilized with Nonidet P-40 and purified by glycerol gradient centrifugation, then exogenous RNA templates were added. Results indicate that exogenous dsRNA reduces RNA synthesis from the endogenous 14 kb RNA template.