Nucleotide sequence analysis of six satellite RNAs of cucumber mosaic virus: Primary sequence and secondary structure alterations do not correlate with differences in pathogenicity

Small non-coding satellite RNAs - the 'game changers' at the virus-host plant interaction?

Satellite RNAs (satRNAs) are RNA molecules associated with many plant viruses and fully dependent on them for replication, encapsidation, and movement within the plant or transmission from plant to plant. Their classification is based on their length, functional protein-coding capacity, and RNA structure (whether linear or circular). They have been of interest for a long time as some of them, in particular systems, cause significant changes in the pathogenesis and epidemiology of plant viruses. The outcomes of how satRNAs affect pathogenesis depend on the components of the pathosystem: host plant species or variety, virus species or even strain, and the sequence of satRNA. These can be additionally affected by biotic and abiotic factors, for example, environmental conditions such as the presence of their vectors or ambient temperature. satRNAs may interfere with primary metabolism, signalling, plant defence [including post-transcriptional gene silencing (PTGS)], as well as the efficiency of virus transmission from plant to plant. In recent years, due to wider access to high-throughput technologies and the extension of studies on satRNAs to include the involvement of external factors in plant-virus-satRNA systems, we are gaining a broader view of the consequences of the presence of these small molecules in viral infections. This review presents the state of the art of satRNA interactions with the helper virus and host plant as well as the influence of satRNAs on the insect vector's behaviour. Moreover, areas requiring further research are identified and knowledge gaps indicated.

The Virome of ‘Lamon Bean’: Application of MinION Sequencing to Investigate the Virus Population Associated with Symptomatic Beans in the Lamon Area, Italy

‘Lamon bean’ is a protected geographical indication (PGI) for a product of four varieties of bean (Phaseolus vulgaris L.) grown in a specific area of production, which is located in the Belluno district, Veneto region (N.E. of Italy). In the last decade, the ‘Lamon bean’ has been threatened by severe virus epidemics that have compromised its profitability. In this work, the full virome of seven bean samples showing different foliar symptoms was obtained by MinION sequencing. Evidence that emerged from sequencing was validated through RT-PCR and ELISA in a large number of plants, including different ecotypes of Lamon bean and wild herbaceous hosts that may represent a virus reservoir in the field. Results revealed the presence of bean common mosaic virus (BCMV), cucumber mosaic virus (CMV), peanut stunt virus (PSV), and bean yellow mosaic virus (BYMV), which often occurred as mixed infections. Moreover, both CMV and PSV were reported in association with strain-specific satellite RNAs (satRNAs). In conclusion, this work sheds light on the cause of the severe diseases affecting the ‘Lamon bean’ by exploitation of MinION sequencing.

A conserved RNA structure is essential for a satellite RNA-mediated inhibition of helper virus accumulation

As a class of parasitic, non-coding RNAs, satellite RNAs (satRNAs) have to compete with their helper virus for limited amounts of viral and/or host resources for efficient replication, by which they usually reduce viral accumulation and symptom expression. Here, we report a cucumber mosaic virus (CMV)-associated satRNA (sat-T1) that ameliorated CMV-induced symptoms, accompanied with a significant reduction in the accumulation of viral genomic RNAs 1 and 2, which encode components of the viral replicase. Intrans replication assays suggest that the reduced accumulation is the outcome of replication competition. The structural basis of sat-T1 responsible for the inhibition of viral RNA accumulation was determined to be a three-way branched secondary structure that contains two biologically important hairpins. One is indispensable for the helper virus inhibition, and the other engages in formation of a tertiary pseudoknot structure that is essential for sat-T1 survival. The secondary structure containing the pseudoknot is the first RNA element with a biological phenotype experimentally identified in CMV satRNAs, and it is structurally conserved in most CMV satRNAs. Thus, this may be a generic method for CMV satRNAs to inhibit the accumulation of the helper virus via the newly-identified RNA structure.

Repair of the 3' proximal and internal deletions of a satellite RNA associated with Cucumber mosaic virus is directed toward restoring structural integrity

The phenomenon of rapid turnover of 3' proximal nucleotides (nt) lost by the action of nuclease in RNA viruses is integral to replication. Here, a set of six deletions encompassing the 3' 23 nt region of a satellite RNA (satRNA) of Cucumber mosaic virus (CMV) strain Q (Q-sat), were engineered. Repair of the 3' end was not observed in the absence of CMV. However, co-expression with CMV in planta revealed that Q-sat mutants lacking the 3' 18 nt but not the 3' 23 nt are repaired and the progeny accumulation was inversely proportional to the extent of the deletion. Progeny of the 3'Δ3 mutant were repaired to wild type (wt) while those from the remaining four mutants were heterogeneous, exhibiting a wt secondary structure. Analysis of additional 3' internal deletions mutants revealed that progeny with a repaired sequence reminiscent of wt secondary structure were competent for replication and systemic spread.

A new satellite RNA is associated with natural infections of cucumber mosaic virus in succulent snap bean

Cucumber mosaic virus (CMV) was consistently recovered from symptomatic snap bean plants during surveys conducted in 2007 and 2008 in central Wisconsin. A large proportion of these CMV-infected plants contained a single-stranded linear RNA molecule consisting of 339 nucleotides and sharing 90–94% sequence identity with other satellite (sat) RNAs of CMV. Comparison of this satRNA sequence with currently available CMV satRNA sequences suggests this to be a novel satRNA.

Characterisation of a satellite RNA of Cucumber mosaic virus that induces chlorosis in Capsicum annuum

The presence of Cucumber mosaic virus (CMV) satellite RNA dramatically changes symptoms on some hosts. A satellite RNA present in a strain of CMV (PepY-CMV) that induced chlorosis in pepper (Capsicum annuum) was shown to induce chlorosis in pepper in combination with another strain (Fny-CMV) that by itself induced a green mosaic symptom. The location of sequences within the PepY satellite RNA (PepY-satRNA) of CMV that conferred the ability to induce chlorosis on pepper plants were analyzed by exchanging sequence domains between cDNA clones of PepY-satRNA and an attenuated mosaic satellite RNA (Paf-satRNA), as well as site-directed mutagenesis of various clusters of the 22-nt sequence differences between the two satellite RNAs in the delimited central domain. The symptoms induced by site-directed mutants of PepY-satRNA and Paf-satRNA in the presence of Fny-CMV demonstrated an insertion within PepY-satRNA of 11 nt at positions 86-96 relative to Paf-satRNA determined the chlorosis-inducing phenotype. Within the chlorosis-inducing domain, deletion of nucleotides did not affect the satRNA replication but abolished the ability of PepY-satRNA to elicit chlorosis symptom. Conversely, a mutant satellite RNA derived from Paf-satRNA in which eleven nucleotides were inserted indicated that sequences of 11 nucleotides were found to be sufficient for chlorosis induction in pepper.

Biological activity of T7 transcripts of a prototype clone and a sequence variant clone of a satellite RNA of cucumber mosaic virus

Molecular cloning of the (D)CARNA 5 (previously known as n-CARNA 5) necrosis-inducing satellite RNA of cucumber mosaic virus produced a prototype clone (pDsat4) and a sequence variant clone (pDsat1). pDsat1 contained 10 nucleotide changes between positions 70 and 160 which rendered that region identical to the corresponding region of a satellite RNA which does not induce necrosis. T7 RNA polymerase transcripts of each clone replicated in both tobacco and tomato, and the progeny satellite RNAs did not retain the 57-nucleotide non-satellite sequence at the 5' ends of the T7 transcripts. RNase T1 fingerprint analysis of both T7 transcripts and progeny satellite RNAs proved that the satellite sequence portion of each transcript was faithfully replicated in tobacco, and the variations in pDsat1 relative to pDsat4 were maintained. Replication of transcripts of either pDsat4 or pDsat1 in tomato resulted in lethal necrosis, suggesting that the determinant of necrosis induction lies outside the region between nucleotides 70 and 160.

Molecular mapping of the viral determinants of systemic wilting induced by a Lettuce mosaic virus (LMV) isolate in some lettuce cultivars

The isolate AF199 of Lettuce mosaic virus (LMV, genus Potyvirus) causes local lesions followed by systemic wilting and plant death in the lettuce cultivars Ithaca and Vanguard 75. Analysis of the phenotype of virus chimeras revealed that a region within the P1 protein coding region (nucleotides 112-386 in the viral genome) and/or another one within the CI protein coding region (nucleotides 5496-5855) are sufficient together to cause the lethal wilting in Ithaca, but not in Vanguard 75. This indicates that the determinants of this particular symptom are different in these two lettuce cultivars. The wilting phenotype was not directly correlated with differences in the deduced amino acid sequence of these two regions. Furthermore, transient expression of the LMV-AF199 proteins, separately or in combination, did not induce local necrosis or any other visible reaction in the plants. Together, these results suggest that the systemic wilting reaction might be due to RNA rather than protein sequences.

Cucumoviruses

Research on the molecular biology of cucumoviruses and their plant-virus interactions has been very extensive in the last decade. Cucumovirus genome structures have been analyzed, giving new insights into their genetic variability, evolution, and taxonomy. A new viral gene has been discovered, and its role in promoting virus infection has been delineated. The localization and various functions of each viral-encoded gene product have been established. The particle structures of Cucumber mosaic virus (CMV) and Tomato aspermy virus have been determined. Pathogenicity domains have been mapped, and barriers to virus infection have been localized. The movement pathways of the viruses in some hosts have been discerned, and viral mutants affecting the movement processes have been identified. Host responses to viral infection have been characterized, both temporally and spatially. Progress has been made in determining the mechanisms of replication, gene expression, and transmission of CMV. The pathogenicity determinants of various satellite RNAs have been characterized, and the importance of secondary structure in satellite RNA-mediated interactions has been recognized. Novel plant genes specifying resistance to infection by CMV have been identified. In some cases, these genes have been mapped, and one resistance gene to CMV has been isolated and characterized. Pathogen-derived resistance has been demonstrated against CMV using various segments of the CMV genome, and the mechanisms of some of these forms of resistances have been analyzed. Finally, the nature of synergistic interactions between CMV and other viruses has been characterized. This review highlights these various achievements in the context of the previous work on the biology of cucumoviruses and their interactions with plants.

Plant virus satellite and defective interfering RNAs: new paradigms for a new century

Although many subviral RNAs reduce or intensify disease symptoms caused by the helper virus, only recently have clues concerning the mechanism of disease modulation been revealed. New models for DI RNA-mediated reduction in helper virus levels and symptom attenuation include DI RNA enhancement of posttranscriptional gene silencing (PTGS), which is an antiviral defense mechanism in plants. Symptom enhancement by the satRNA of Cucumber mosaic virus is caused by minus-strand induction of the programmed cell death pathway. In contrast, symptom enhancement by satC of Turnip crinkle virus is due to satC interference with virion formation, leading to increased levels of free coat protein, which is the viral suppressor of PTGS. Mutualism between satRNA and helper virus can be seen for the satRNA of Groundnut rosette virus, which contributes to the virus by allowing virion assembly. These novel findings are leading to re-evaluation of the relationships between subviral RNAs, helper viruses, and hosts.

Lessons learned from the core RNA promoters of Brome mosaic virus and Cucumber mosaic virus

summary RNA core promoters are nucleotide sequences needed to direct proper initiation of viral RNA synthesis by the viral replicase. Minimal length core promoter-templates that can direct accurate initiation of the genomic plus-, genomic minus-, and subgenomic RNAs of Brome mosaic virus and Cucumber mosaic virus were characterized in previous works. Several common themes and differences were observed in how each of the core promoters directed the initiation of viral RNA synthesis in vitro. These observations are summarized and compared in this short review.

Naturally occurring variants of satellite tobacco mosaic virus

ABSTRACT Four natural variants of satellite tobacco mosaic virus (STMV) were compared with each other and with the type strain. Differences were detected in double-stranded RNA, single-stranded RNA, and virion electrophoretic mobility patterns, while the size and antigenicity of the coat protein were similar for all. RNase protection assays detected differences in the genomes of each of the four new variants, which differed not only from each other, but also from that of type STMV. Infectious RNA transcripts were made from complementary DNA clones of one variant (STMV 10) with a genome apparently smaller than that of type STMV. A 71-base deletion in the region that contains the 6.8-kDa protein in type STMV was detected by sequence analysis of the STMV 10 clones, a result that is confirmed by the lack of a 6.8-kDa in vitro translation product for STMV 10. Only minor sequence differences exist elsewhere in the genome compared with that of type STMV. Type STMV and STMV 10 each successfully cross-protected against the other when tobacco plants were inoculated 10 days apart.

Template-independent repair of the 3' end of cucumber mosaic virus satellite RNA controlled by RNAs 1 and 2 of helper virus

RNA viruses which do not have a poly(A) tail or a tRNA-like structure for the protection of their vulnerable 3' termini may have developed a different strategy to maintain their genome integrity. We provide evidence that deletions of up to 7 nucleotides from the 3' terminus of cucumber mosaic cucumovirus (CMV) satellite RNA (satRNA) were repaired in planta in the presence of the helper virus (HV) CMV. Sequence comparison of 3'-end-repaired satRNA progenies, and of satRNA and HV RNA, suggested that the repair was not dependent on a viral template. The 3' end of CMV satRNA lacking the last three cytosines was not repaired in planta in the presence of tomato aspermy cucumovirus (TAV), although TAV is an efficient helper for the replication of CMV satRNA. With use of pseudorecombinants constructed by the interchange of RNAs 1 and 2 of TAV and CMV, evidence was provided that the 3'-end repair was controlled by RNAs 1 and 2 of CMV, which encode subunits of the viral RNA replicase. These results, and the observation of short repeated sequences close to the 3' terminus of repaired molecules, suggest that the HV replicase maintains the integrity of the satRNA genome, playing a role analogous to that of cellular telomerases.

Structural analysis of a necrogenic strain of cucumber mosaic cucumovirus satellite RNA in planta

Structural studies of plant viral RNA molecules have been based on in vitro chemical and enzymatic modification. That approach, along with mutational analysis, has proven valuable in predicting structural models for some plant viruses such as tobacco mosaic tobamovirus and brome mosaic bromovirus. However, in planta conditions may be dramatically different from those found in vitro. In this study we analyzed the structure of cucumber mosaic cucumovirus satellite RNA (sat RNA) strain D4 in vivo and compared it to the structures found in vitro and in purified virions. Following a methodology developed to determine the structure of 18S rRNA within intact plant tissues, different patterns of adenosine and cytosine modification were found for D4-sat RNA molecules in vivo, in vitro, and in virions. This chemical probing procedure identifies adenosine and cytosine residues located in unpaired regions of the RNA molecules. Methylation data, a genetic algorithm in the STAR RNA folding program, and sequence alignment comparisons of 78 satellite CMV RNA sequences were used to identify several helical regions located at the 5' and 3' ends of the RNA molecule. Data from previous mutational and sequence comparison studies between satellite RNA strains inducing necrosis in tomato plants and those strains not inducing necrosis allowed us to identify one helix and two tetraloop regions correlating with the necrogenicity syndrome.

Contribution of mutation and RNA recombination to the evolution of a plant pathogenic RNA

The nucleotide sequence of 17 variants of the satellite RNA of cucumber mosaic virus (CMV-satRNA) isolated from field-infected tomato plants in the springs of 1989, 1990, and 1991 was determined. The sequence of each of the 17 satRNAs was unique and was between 334 and 340 nucleotides in length; 57 positions were polymorphic. There was much genetic divergence, ranging from 0.006 to 0.141 nucleotide substitutions per site for pairwise comparisons, and averaging 0.074 for any pair. When the polymorphic positions were analyzed relative to a secondary structure model proposed for CMV-satRNAs, it was found that there were significantly different numbers of changes in base-paired and non-base-paired positions, and that mutations that did not disrupt base pairing were preferred at the putatively paired sites. This supports the concept that the need to maintain a functional structure may limit genetic divergence of CMV-satRNA. Phylogenetic analyses showed that the 17 CMV-satRNA variants clustered into two subgroups, I and II, and evolutionary lines proceeding by the sequential accumulation of mutations were apparent. Three satRNA variants were outliers for these two phylogenetic groups. They were shown to be recombinants of subgroup I and II satRNAs by calculating phylogenies for different molecular regions and by using Sawyer's test for gene conversion. At least two recombination events were required to produce these three recombinant satRNAs. Thus, recombinants were found to be frequent ( approximately 17%) in natural populations of CMV-satRNA, and recombination may make an important contribution to the generation of new variants. To our knowledge this is the first report of data allowing the frequency of recombinant isolates in natural populations of an RNA replicon to be estimated.

Mechanisms of plant virus evolution

Plant viruses utilize several mechanisms to generate the large amount of genetic diversity found both within and between species. Plant RNA viruses and pararetroviruses probably have highly error prone replication mechanisms, that result in numerous mutations and a quasispecies nature. The plant DNA viruses also exhibit diversity, but the source of this is less clear. Plant viruses frequently use recombination and reassortment as driving forces in evolution, and, occasionally, other mechanisms such as gene duplication and overprinting. The amount of variation found in different species of plant viruses is remarkably different, even though there is no evidence that the mutation rate varies. The origin of plant viruses is uncertain, but several possible theories are proposed. The relationships between some plant and animal viruses suggests a common origin, possibly an insect virus. The propensity for rapid adaptation makes tracing the evolutionary history of viruses difficult, and long term control of virus disease nearly impossible, but it provides an excellent model system for studying general mechanisms of molecular evolution.

The complete nucleotide sequence of odontoglossum ringspot virus (Cy-1 strain) genomic RNA

The complete nucleotide sequence of the genomic RNA of odontoglossum ringspot virus Cy-1 strain (ORSV Cy-1) was determined using cloned cDNA. This sequence is 6611 nucleotides long containing four open reading frames, which correspond to 126 K, 183 K, 31 K, and 18 K proteins. Its genomic organization is similar to other tobamoviruses, TMV-V(vulgare), TMV-L (tomato strain), tobacco mild green mosaic virus (TMGMV) and cucumber green mottle mosaic virus (CGMMV). The 5' non-coding regions of ORSV Cy-1 is 62 nucleotides. The ORFs encoded a 126 K polypeptide and a 183 K read-through product in which helicase-sequence and polymerase-sequence motifs are found. The ORFs encoding the 126 K and 183 K proteins have 61% and 63% identities with those of TMV-V. The third ORF encoded a 31 K protein homologous to TMV cell-to-cell movement protein. It has 63% identities with that of TMV-V. The fourth ORF encoded an 18 K coat protein. The 5' non-coding region, which extends from base 1 to 62 has 2 G residues and a ribosome binding site (AUU). The 3' non-coding region, 414 nucleotides in length, is entirely different from that of other tobamoviruses.

Experimental evaluation of the ribonuclease protection assay method for the assessment of genetic heterogeneity in populations of RNA viruses

The ribonuclease (RNase) protection assay (RPA) was evaluated as a method to estimate genetic distances among sequence variants of RNA viruses. The patterns of fragments generated, under different RPA conditions, by three sets of RNA sequence variants of known nucleotide sequence, were analyzed. Both the effectiveness of cleavage (i.e. the probability of cleavage in a certain heteroduplex) and its degree (i.e. in all the molecules in the assay or in a part of them) varied largely according to the nature of the mismatch. Probability and degree of cleavage were also dependent on distant sequence context effects. No correlation could be established between context and cleavage, so that the pattern of fragments in RPA cannot be unequivocally predicted from sequence information. Accordingly, nucleotide sequence differences between two sequence variants cannot be directly derived from RPA data. For all three sequence sets linear relationships were found between the number of non-shared fragments in the RPAs of two variants and their nucleotide sequence differences. Nevertheless, both linearity and the linear regression parameters varied largely according to the sequence set and according to RPA conditions, in a non-predictable way. Thus, under experimental conditions, RPA may not be as appropriate a method to estimate genetic distances between RNA sequences as simulation under an ideal model suggested. Possible ways to diminish the gap between the ideal model and the experimental procedure are proposed.

Variation in the hypervariable region of cucumber mosaic virus satellite RNAs is affected by the helper virus and the initial sequence context

The D satellite RNA (sat RNA) of cucumber mosaic virus (CMV) was previously shown to contain a region of hypervariability around nucleotide 230, in wild-type populations and in cDNA clones and progeny of one such clone (pDsat4) after passage with the subgroup I strain Fny-CMV. This hypervariable region (HVR) consists of a series of consecutive A and/or U residues. We found that variability is also generated in the HVR of transcript derived from pDsat4 after passage with the subgroup II strain LS-CMV and with tomato aspermy virus (TAV). However, the progeny differ with respect to the sequence of the HVR after passage with both LS-CMV and TAV. Another D-sat RNA cDNA clone that contains a C residue in the HVR, pDsat1, was previously shown not to develop variability in the HVR upon passage with Fny-CMV. However, when the C (position 231) was changed to an A residue, variability developed by the third passage with Fny-CMV. An additional cDNA clone derived from the B1-sat RNA, pBsat5, also contains a C residue in the region analogous to the D-sat RNA HVR and did not develop variability upon passage with either Fny- or LS-CMV. Changing this C to a U residue did not result in the development of hypervariability in the progeny of transcript from this mutant. Models to explain the generation of hypervariability are discussed.

Genetic analysis of helper virus-specific selective amplification of cucumber mosaic virus satellite RNAs

Satellite RNAs (sat-RNAs) are small molecular parasites associated with a number of plant RNA viruses. The cucumber mosaic virus (CMV) sat-RNAs are ca. 335 nucleotides and have evolved to produce a large number of closely related sat-RNAs. Different cucumoviruses can act as helper viruses in the amplification of CMV sat-RNAs. We have found that different helper viruses show a preference for a particular sat-RNA in a mixed infection. In this study the specificity of WL47 sat-RNA amplification by LS-CMV and of D4 sat-RNA amplification by tomato aspermy virus in mixed infections was examined. Recombinant cDNA clones of D4 sat-RNA and WL47 sat-RNA were used to map the sat-RNA sequences responsible for the helper virus selection of a specific sat-RNA for amplification.

The replication of a necrogenic cucumber mosaic virus satellite is temperature-sensitive in tomato

Lethal necrosis development in tomato plants infected with cucumber mosaic virus (CMV) strain D containing the necrogenic satellite D-CARNA 5 and held at 32 degrees C is shown to be impaired. CARNA 5 accumulation in tomato at 32 degrees C is reduced about 100-fold compared to accumulation in plants held at 24 degrees C, while viral RNA accumulation is reduced about 5-fold. CMV-infected tomato held for 3 days at 24 degrees C prior to shift to 32 degrees C do not develop lethal necrosis. Longer incubations at 24 degrees C prior to shift to 32 degrees C allow necrosis to develop. CMV-infected plants held for up to 4 weeks at 32 degrees C required an additional 8-10 days at 24 degrees C to develop necrosis. Necrogenic CMV-infected plants held at 24 degrees C and analyzed 3 days p.i. contained detectable amounts of ss- and ds-CARNA 5; upon shift to 32 degrees C, such CARNA 5 declined to undetectable levels and lethal necrosis did not occur. There appear to be temperature-sensitive factors that are required for efficient satellite replication which are not required for efficient viral RNA replication. Whether these factor(s) are of host or satellite origin is uncertain.

Cucumber mosaic virus-associated RNA 5. XIII.--Opposite necrogenicities in tomato of variants with large 5' half insertion/deletion regions

Two satellite RNA of cucumber mosaic virus (CMV) designated J876-CARNA-5 (for cucumber mosaic virus-associated RNA-5) and D27-CARNA-5 have been molecularly and biologically characterized. J876-CARNA-5 (387 nucleotides (nt)) and D27-CARNA-5 (391 nt) have nearly identical 5' half insertion/deletion regions where 120 nt replace approximately 70 nt of D-CARNA-5 (335 nt), the first variant described and sequenced. J876-CARNA-5 possesses the 15-nt conserved sequence element in its 3' half which is present in all tomato necrogenic variants and induces the same level of necrosis in tomatoes as the prototype necrogenic D-CARNA-5. D27-CARNA-5 lacks the 3' half necrosis-determining element and attenuates the CMV symptoms in tomato. Transcripts of cloned cDNA of J876-CARNA-5 were stably propagated in tomato in the presence of CMV-1. Purified J876-CARNA-5 progeny, inoculated with CMV-1 in a quantitative bioassay, induced tomato necrosis at the same dilution level as the natural satellite. Several computer-generated secondary structures of CMV satellites were examined and the possible correlation of a defined secondary structural element with necrosis induction is discussed.

Peanut stunt virus satellite RNA: analysis of sequences that affect symptom attenuation in tobacco

The V-satellite RNA (V-satRNA) of peanut stunt virus (PSV) has no effect on symptoms produced in tobacco by PSV. In contast, the G-satRNA induced complete or nearly complete suppression of systemic symptom development. Because G-satRNA differs from V-satRNA in only five nucleotide positions, these two satRNAs provide excellent material for investigating the molecular basis of satRNA-mediated symptom attenuation. For this purpose, we constructed transcription vectors containing full-length cDNA clones from which infectious RNA transcripts can be synthesized in vitro, and produced chimeric and mutant satRNA molecules. Although an A----C substitution at position 362 of the V-satRNA molecule delayed systemic symptom development and reduced symptom severity, changes at both nucleotide positions 226 (C----U) and 362 (A----C) of V-satRNA were required for suppression of systemic symptom development. Our results are consistent with the idea that PSV satRNAs are noncoding molecules that exert their biological activities by directly interacting with host/viral components.

Differential interactions among strains of tomato aspermy virus and satellite RNAs of cucumber mosaic virus

Tomato and tobacco plants were inoculated with either of two strains of tomato aspermy virus, 1-TAV or V-TAV, and each of six isolates of cucumber mosaic virus satellite RNA (CMV-satRNA), B1, B2, B3, Ix, or WL2. Ribonuclease protection assays, used to detect total satRNA and encapsidated satRNA, revealed that G-satRNA generated new satellite RNA not of the inoculated sequence. The other CMV-satRNAs were compared for their ability (1) to replicate, (2) to modulate symptoms, (3) to reduce TAV accumulation, and (4) to alter the extent of encapsidation of TAV genomic RNAs. The fraction of B2- and B3-satRNAs encapsidated was greater for 1-TAV than for V-TAV, although spread and accumulation of the satRNA were similar for both helper viruses. These results suggest that CMV-satRNA may spread in a nonencapsidated form. Accumulation of CMV-satRNA in systemically infected leaves was detected for all inoculum combinations except V-TAV and Ix-satRNA, for which the satellite RNA increased only in protoplasts and inoculated leaves of tobacco or tomato. In such inoculated leaves, Ix-satRNA was not detected in capsids. Thus the effectiveness of the TAV helpers of CMV-satRNAs may be controlled in at least some instances by the extent of satRNA spread or encapsidation rather than by the efficiency of satRNA replication. In contrast to infections initiated by inoculation of CMV and CMV-satRNA, inoculation of 1-TAV or V-TAV and CMV-satRNA did not alter the relative amounts of viral genomic RNAs encapsidated or result in accumulation of large amounts of double-stranded satRNA.

Secondary structure as a constraint on the evolution of a plant viral satellite RNA

The genetic variability and evolution of the satellite RNA (satRNA) of cucumber mosaic virus (CMV) was analyzed. Twenty-five CMV-satRNAs compared clustered into three main groups, and no correlation was found between genetic proximity and other characteristics (pathogenicity, geographical origin) of the satRNAs. Values for the number of nucleotide substitutions per site between any two satRNAs suggest that divergence is checked by functional constraints. The analysis of mutations relative to an ancestral sequence, and the number of substitutions per site at first, second and third positions of codons in putative open reading frames, show that the variation of CMV-satRNAs does not follow a pattern typical of coding sequences, and indicates that preservation of the sequence of encoded products is not a constraint to evolution. On the other hand, when the observed variation was analyzed relative to a secondary structure model proposed for CMV-satRNAs, several lines of evidence indicated that the maintenance of the secondary structure is a constraint to evolution: the number of substitutions per site, the number of point insertions and deletions and the number of base substitutions that would disrupt base-pairing were significantly higher for unpaired than for base-paired positions. Also, compensatory mutations at base-paired positions occurred more frequently than expected from random. The results suggest that CMV-satRNAs are non-coding, functional RNAs whose biology would be determined by their direct interaction with components of the host and/or the helper virus.

Host-associated selection of sequence variants from a satellite RNA of cucumber mosaic virus

The sequence of lx-satRNA, a CMV-satRNA necrogenic for tomato that shows the unusual property of accumulating in cucumber and in squash to levels similar to those in tomato and in tobacco, was determined. When compared with the sequences of other necrogenic CMV-satRNAs that do not show this property, or with a sequence variant of lx-satRNA that retains it, the high accumulation of lx-satRNA in squash was correlated with the presence of two U/C transitions. The sequences of progeny lx-satRNA from passage experiments in tomato and in squash show that a sequence variant having a U at position 102 was selected in tomato and that the parent sequence with a C at 102 was consistently restored in squash when this U-variant was used as inoculum. The results from these passage experiments may be explained by the heterogeneous nature of RNA populations, built from a number of variants of a master sequence, and illustrate the validity of this concept for CMV-satRNAs. The data also show that a minor sequence change, such as the transition C/U at 102, may have a major effect on the fitness of sequence variants of CMV-satRNAs in different hosts, and this may be relevant to the evolution in nature of these small RNAs.

Nonmutant forms of the avirulent satellite D of turnip crinkle virus are produced following inoculation of plants with mutant forms synthesized in vitro

The avirulent satellite RNA D (sat D) of turnip crinkle virus (TCV) has been cloned as a copy DNA. RNA transcripts synthesized in vitro from the cloned cDNA are infectious when coinoculated with RNA transcripts of the cloned TCV genome. Sat D is the smallest and most likely the progenitor of the other TCV satellites and, in contrast to the virulent satellite RNA C (sat C), does not intensify viral symptoms. Mutant forms of sat D including internal deletions up to 50 bases yielded sat D in infected plants. However, sat D mutants were not recovered in mutant form, but reverted to normal size and sequence in infected turnip plants. Mutations at a site with homology to the catalytic strand of self-cleaving sequences in certain viroids and satellites appeared to confer virulence on sat D in that test plants showed severe crinkling and stunting normally associated with sat C. However, sat C appeared along with a restored form of sat D in the progeny RNAs of these severely infected plants. Sat C was presumably generated by recombination between sat D and the TCV genome. In contrast, when plants were inoculated with transcripts containing the equivalent mutations in sat C, sat C was recovered from infected plants in mutant form. These findings demonstrate the tendency for mutant forms of the avirulent satellite, sat D, to revert, but raise questions about the source of information used in the reversion process.

Differential replication in zucchini squash of a cucumber mosaic virus satellite RNA maps to RNA 1 of the helper virus

Cucumber mosaic virus (CMV) supports the replication and encapsidation of its satellite RNA, both in solanaceous and cucurbit host plants; however, different strains of CMV support the replication of satellite RNAs with different efficiency. In addition, replication of satellite RNA is very efficient in solanaceous host plants and generally poor in cucurbit host plants. The WL1-satellite (WL1-sat) RNA is an exception, and replicates to high levels in both solanaceous and curcubit host plants with most CMV strains as the helper virus. Two strains of CMV were used in this study: Fny-CMV, which replicates the WL1-sat RNA efficiently in all hosts tested; and Sny-CMV, which does not replicate the WL1-sat RNA to detectable levels in zucchini squash (Cucurbita pepo), but does replicate WL1-sat RNA efficiently in other hosts. Using pseudorecombinants constructed between Fny-CMV and Sny-CMV we have mapped to RNA 1 the ability to support the efficient replication of WL1-sat RNA in zucchini squash.

The complete nucleotide sequence of the genomic RNA of the tobamovirus tobacco mild green mosaic virus

The complete nucleotide sequence of the genomic RNA of the tobamovirus tobacco mild green mosaic virus (TM-GMV) was determined. It shows 64.4% sequence homology with the genomic RNA of tobacco mosaic virus (TMV) and 66.0% with that of tomato mosaic virus (ToMV). Its genomic organization is similar to that of TMV and ToMV. The 5' proximal open reading frame (ORF) encodes a 126K polypeptide and a 183K readthrough product in which nucleotide-binding and polymerase-sequence motifs are found. The third ORF encodes a 28.5K protein homologous to TMV and ToMV movement proteins. A conserved core is found with four other tobamoviruses and two tobraviruses suggesting a common mechanism of cell-to-cell movement for tobamo- and tobraviruses. The fourth ORF encodes the 17.5K coat protein. Homology between the RNAs of TMGMV and its satellite virus STMV is limited to their 3' termini, and structural comparisons suggest that this region may determine the nature of the satellite/helper virus interaction.

In-vitro translation of cucumoviral satellites. III. Translational efficiencies of cucumber mosaic virus-associated RNA 5 sequence variants can be related to the predicted secondary structures of their first 55 nucleotides

The cucumber mosaic virus (CMV) satellites D- and S-CARNA 5 (CARNA 5 = Cucumber mosaic virus-Associated RNA 5), their full-length cDNA clone transcripts, and DNA clone transcripts of their open reading frames (ORFs) were used as mRNAs in the wheat-germ in-vitro translation system. Natural D-CARNA 5 yielded an anomalously large polypeptide, while transcripts made from cDNA clones of D-CARNA 5 or its first ORF had no mRNA activity. Transcripts made from the second major ORF in D-CARNA 5 yielded a smaller product, consistent with its size. Natural S-CARNA 5 and its cDNA clone transcripts both yielded the two polypeptides previously reported, while transcripts of its only major ORF yielded exclusively the smaller of the two products. The potential for an alternate initiation codon, 36 nucleotides upstream, being the source of the larger of the two polypeptides was tested. The differences in the translational properties of D- and S-CARNA 5 were related to the predicted secondary structures of the first 55 nucleotides in these CARNA 5 sequence variants. The calculated free energies of the predicted hairpins correlated inversely with their in-vitro translational activities.

Induction of tobacco chlorosis by certain cucumber mosaic virus satellite RNAs is specific to subgroup II helper strains

Two satellite (sat) RNAs of cucumber mosaic virus (CMV), B2- and WL3-sat RNAs, which induce systemic chlorosis on tobacco, were inoculated onto tobacco with a number of CMV strains. Systemic chlorosis was observed only when these satellite RNAs were associated with subgroup II CMV strains. Infection of tobacco with various pseudorecombinants of subgroup I and II CMV strains, together with WL3- or B2-sat RNA, suggests that chlorosis is associated with RNA 2 of subgroup II CMV strains. Chlorosis was not induced when B2- or WL3-sat RNAs were inoculated onto tobacco with tomato aspermy virus. In contrast, the induction of chlorosis on tomato by B1-sat RNA did not show any clear dependence on the subgroup of its CMV helper strain although chlorosis did tend to be more severe in association with subgroup II CMV strains.

RNA sequence heterogeneity in natural populations of three satellite RNAs of cucumber mosaic virus

Sequence heterogeneity within populations of three satellite RNAs of cucumber mosaic virus (CMV) was assessed using two different approaches. Comparison of the nucleotide sequences of several cDNA clones of each satellite RNA revealed microsequence heterogeneity, which is often seen in populations of RNA genomes. RNase protection assays using minus-sense satellite RNA probes were used to detect major sites of heterogeneity within natural populations of each satellite RNA. In RNase protection assays of WL1-sat RNA populations, no major sites of heterogeneity were detected within seven different populations, including preparations from four different host plant species. In contrast, RNase protection assays of nine populations of B1-sat RNA showed three different patterns, which were most likely due to the existence of the B1-sat RNA populations as mixtures in which different sequence variants predominated in different preparations. Assays of five independent populations of D-sat RNA revealed a single major site of heterogeneity which was common to each population and was localized at approximately nucleotide 225 of the 335-nucleotide satellite sequence. This common site of heterogeneity is a feature of the D-sat RNA population structure which may represent an equilibrium between alternative nucleotides at a selectively neutral position, or may be actively selected for and maintained.

A simple method for detection of viral satellite RNAs in small plant tissue samples

A procedure is described that allows extraction and can estimate the total amount of single-stranded and double-stranded viral satellite RNAs and viral RNA present in a minimal amount of infected plant tissue, and is capable of distinguishing different cucumber mosaic viral and nepoviral satellites by polyacrylamide gel electrophoresis under semi-denaturing or fully-denaturing conditions.

Nucleotide sequence analysis of cDNA encoding the coat protein of cucumber mosaic virus: genome organization and molecular features of the protein

The cDNA sequence coding for the coat protein of cucumber mosaic virus (Japanese Y strain) was cloned, and its nucleotide sequence was determined. The sequence contains an open reading frame that encodes the coat protein composed of 218 amino acids. The nucleotide and deduced amino acid sequences of the coat protein of this strain were compared with those of the Q strain; the homologies of the sequences were 78% and 81%, respectively. Further study of the sequences gave an insight into the genome organization and the molecular features of the coat protein. The coding region can be divided into three characteristic regions. The N-terminal region has conserved features in the positively charged structure, the hydropathy pattern and the predicted secondary structure, although the amino acid sequence is varied mainly due to frameshift mutations. It is noteworthy that the positions of arginine residues in this region are highly conserved. Both the nucleotide and amino acid sequences of the central region are well conserved. The amino acid sequence of the C-terminal region is not conserved, because of frameshift mutations, however, the total number of amino acids is conserved. The nucleotide sequence of the 3'-noncoding region is divergent, but it could form a tRNA-like structure similar to those reported for other viruses. Detailed investigation suggests that the Y and Q strains are evolutionarily distant.

Complete nucleotide sequence of two new satellite RNAs associated with cucumber mosaic virus

Complete nucleotide sequences of two new satellite RNAs (satRNA) of cucumber mosaic virus (CMV), E-satRNA and OY2-satRNA, have been determined and compared with known satellite RNA sequences. E-satRNA contained 339 nucleotide residues and OY2-satRNA had 386 nucleotide residues. Comparison of the sequences among satRNAs including these new satRNAs revealed extensive homologous regions in the 5'-terminus and the 3'-half. The former region contains about 95 nucleotide residues (80-100% homology) and the latter has about 175 nucleotide residues (81-99% homology), but there was less homology in the middle of the RNA. A possible secondary structure for E-satRNA, OY2-satRNA, and Y-satRNA [S. Hidaka et al. (1984) FEBS Lett. 174, 38-42] was constructed and compared with that of a satellite RNA from CMV-Q (Q-satRNA) [K. H. J. Gordon and R. H. Symons (1983), Nucl. Acids Res. 11, 947-960]. Two similar hairpin-loop structures in the 5'-terminal region were common features of the RNAs; one of them was found in E-satRNA, the other in OY2-satRNA, and both in Y-satRNA and Q-satRNA. Analyses of in vitro messenger properties of the satRNAs suggested that the first open reading frame of E-sat and Y-satRNAs was a possible coding region for protein synthesis.

Cucumber mosaic virus-associated RNA 5. XI. Comparison of 14 CARNA 5 variants relates ability to induce tomato necrosis to a conserved nucleotide sequence

Seven CARNA 5 (Cucumber mosaic virus-Associated RNA 5) variants were obtained from an Indonesian cucumber mosaic virus isolate (designated CMV-In) by serial passage of this virus in squash, Chenopodium quinoa, tobacco, and tomato. Bioassays of the isolated CARNA 5 variants for their capability to induce lethal necrosis in tomato allowed categorization of the CARNA 5 variants as either necrogenic or nonnecrogenic. Comparison of the CARNA 5 sequences with sequences previously published shows that in general CMV satellites display a high degree of nucleotide sequence conservation. Except for two sharply defined domains of variability, the sequences of the necrogenic CARNA 5s are essentially conserved, whereas those of the nonnecrogenic CARNA 5s possess at least nine additional hypervariable domains. In eight positions of the CARNA 5 sequences all necrogenic variants differ uniquely from those that are nonnecrogenic. All CMV satellites compared in this work possess open reading frames (ORFs), with equivalent initiation codons, capable of encoding polypeptides of significant lengths. Two equivalent or identical ORFs were found only in the necrogenic CARNA 5s, whereas a variable-length ORF was found in the sequences of all the CARNA 5 variants compared. These findings constitute a basis for experiments aimed at determining the biological significance, if any, of these ORFs.

Site-directed mutagenesis of potential protein-coding regions in expressible cloned cDNAs of cucumber mosaic viral satellites

Site-directed mutagenesis was used to alter potential protein-coding regions (open reading frames or ORFs) within the cloned, expressible cDNAs of two satellites of cucumber mosaic virus (CMV), S-CARNA 5 and D-CARNA 5. RNA transcripts synthesized in vitro from the mutant and wild-type satellite cDNAs were tested for biological activity on tomato plants by coinfection with CMV RNAs 1, 2, and 3, and progeny CARNA 5s generated from such transcripts were isolated and sequenced. Two mutants of S-CARNA 5 were constructed in attempts to test whether the ORF (ORF IIB, beginning at nucleotide 135) responsible for synthesis in vitro of two small proteins (M. J. Avila-Rincon, C. W. Collmer, and J. M. Kaper (1986). Virology 152, 455-458) could be eliminated without loss of the satellite's biological activity. Biological tests with mutant transcripts that either lacked the AUG initiation codon or contained a premature translation termination codon were foiled by instability and/or reversion in the progeny. With progeny CARNA 5 of the former mutant, one of two altered nucleotides reverted, thus restoring the AUG but not the nucleotide immediately preceding it. In contrast, a mutation in the necrogenic D-CARNA 5 which altered the initiation codon of ORF I (nucleotides 11-94), whose predicted amino acid sequence is conserved in all necrogenic CMV satellites sequenced to date, was stable in biological testing and did not destroy necrogenicity. This was shown by nucleotide sequencing of the progeny CARNA 5 from necrotic test plants and by its direct comparison with wild-type D-CARNA 5 progeny in a tomato necrosis dilution assay. This experiment provides convincing evidence that a possible protein product of ORF I is not involved in the induction of tomato necrosis by D-CARNA 5.

The cDNA of cucumber mosaic virus-associated satellite RNA has in vivo biological properties

Two isolates of cucumber mosaic virus (CMV)-associated satellite RNA, differing in their biological properties, have been reverse transcribed. One was able to induce the tomato necrotic syndrome whereas the other one attenuated fernleaf symptoms on tomato plants after co-inoculation with the helper virus. cDNAs representing partial or full-length copies have been cloned in the plasmid pAT 153 and sequenced. The two RNAs showed a very limited number of variations (2 to 5 substitutions depending on the clones and a one base deletion). Full-length cDNA copies possessed the same biological properties that characterized the parent satellite RNA. Efficiency of the cDNA depended upon its form in the inoculum (circular or linear plasmid or excised cDNA) and upon the form of the helper virus (viral RNAs or virions) with which it seemed to compete for installation and/or expression.