Comparative sequence and structure of viroid-like RNAs of two plant viruses

A Novel Self-Cleaving Viroid-Like RNA Identified in RNA Preparations from a Citrus Tree Is Not Directly Associated with the Plant

Viroid and viroid-like satellite RNAs are infectious, circular, non-protein coding RNAs reported in plants only so far. Some viroids (family Avsunviroidae) and viroid-like satellite RNAs share self-cleaving activity mediated by hammerhead ribozymes (HHRzs) endowed in both RNA polarity strands. Using a homology-independent method based on the search for conserved structural motifs of HHRzs in reads and contigs from high-throughput sequenced RNAseq libraries, we identified a novel small (550 nt) viroid-like RNA in a library from a Citrus reticulata tree. Such a viroid-like RNA contains a HHRz in both polarity strands. Northern blot hybridization assays showed that circular forms of both polarity strands of this RNA (tentatively named citrus transiently-associated hammerhead viroid-like RNA1 (CtaHVd-LR1)) exist, supporting its replication through a symmetric pathway of the rolling circle mechanism. CtaHVd-LR1 adopts a rod-like conformation and has the typical features of quasispecies. Its HHRzs were shown to be active during transcription and in the absence of any protein. CtaHVd-LR1 was not graft-transmissible, and after its first identification, it was not found again in the original citrus source when repeatedly searched in the following years, suggesting that it was actually not directly associated with the plant. Therefore, the possibility that this novel self-cleaving viroid-like RNA is actually associated with another organism (e.g., a fungus), in turn, transiently associated with citrus plants, is proposed.

Yellow Dwarf Viruses of Cereals: Taxonomy and Molecular Mechanisms

Yellow dwarf viruses are the most economically important and widespread viruses of cereal crops. Although they share common biological properties such as phloem limitation and obligate aphid transmission, the replication machinery and associated cis-acting signals of these viruses fall into two unrelated taxa represented by Barley yellow dwarf virus and Cereal yellow dwarf virus. Here, we explain the reclassification of these viruses based on their very different genomes. We also provide an overview of viral protein functions and their interactions with the host and vector, replication mechanisms of viral and satellite RNAs, and the complex gene expression strategies. Throughout, we point out key unanswered questions in virus evolution, structural biology, and genome function and replication that, when answered, may ultimately provide new tools for virus management.

A life of research on circular RNAs and ribozymes: towards the origin of viroids, deltaviruses and life

The first examples of circular RNAs (circRNAs) were reported in the '70s as a family of minimal infectious agents of flowering plants; the viroids and viral satellites of circRNA. In some cases, these small circular genomes encode self-cleaving RNA motifs or ribozymes, including an exceptional circRNA infecting not plants but humans: the Hepatitis Delta Virus. Autocatalytic ribozymes not only allowed to propose a common rolling-circle replication mechanism for all these subviral agents, but also a tentative link with the origin of life as molecular fossils of the so-called RNA world. Despite the weak biologic connection between angiosperm plants and the human liver, diverse scientists, and most notably Ricardo Flores, firmly supported an evolutionary relationship between plant viroids and human deltavirus agents. The tireless and inspiring work done by Ricardo's lab in the field of infectious circRNAs fuelled multiple hypotheses for the origin of these entities, allowing advances in other fields, from eukaryotic circRNAs to small ribozymes in genomes from all life kingdoms. The recent discovery of a plethora of viral-like circRNAs with ribozymes in disparate biological samples may finally allow us to connect plant and animal subviral agents, confirming again that Ricardo's eye for science was always a keen eye.

Molecular variability of apple hammerhead viroid from Italian apple varieties supports the relevance in vivo of its branched conformation stabilized by a kissing loop interaction

In the absence of protein-coding ability, viroid RNAs rely on direct interactions with host factors for their infectivity. RNA structural elements are likely involved in these interactions. Therefore, preservation of a structural element, despite the sequence variability existing between the variants of a viroid population, is considered a solid evidence of its relevant role in vivo. In this study, apple hammerhead viroid (AHVd) was first identified in the two apple cultivars 'Mela Rosa Guadagno' (MRG) and 'Agostinella' (AG), which are cultivated since long in Southern Italy, thus providing the first solid evidence of its presence in this country. Then, the natural variability of AHVd viroid populations infecting MRG and AG was studied. The sequence variants from the two Italian isolates shared only 82.1-87.7% sequence identity with those reported previously from other geographic areas, thus providing the possibility of exploring the impact of this sequence divergence on the proposed secondary structure. Interestingly, all the AHVd sequence variants considered in this study preserved a branched secondary structure stabilized by a kissing-loop interaction, resembling the conformation proposed previously for variants from other isolates. Indeed, most mutations did not modify the proposed conformation because they were co-variations, conversions of canonical into wobble base-pairs, or vice versa, as well as changes mapping at loops. Importantly, a cruciform structural element formed by four hairpins, one of which is implicated in the proposed kissing-loop interaction, was also preserved because several nucleotide changes actually resulted into two, three and up to five consecutive co-variations associated with other changes that did not affect the secondary structure. These data provide very strong evidence for the relevance in vivo of this cruciform structure which, together with kissing-loop interaction, likely contribute to further stabilizing the branched AHVd secondary structure.

Viroids, infectious long non-coding RNAs with autonomous replication

Transcriptome deep-sequencing studies performed during the last years confirmed that the vast majority of the RNAs transcribed in higher organisms correspond to several types of non-coding RNAs including long non-coding RNAs (lncRNAs). The study of lncRNAs and the identification of their functions, is still an emerging field in plants but the characterization of some of them indicate that they play an important role in crucial regulatory processes like flowering regulation, and responses to abiotic stress and plant hormones. A second group of lncRNAs present in plants is formed by viroids, exogenous infectious subviral plant pathogens well known since many years. Viroids are composed of circular RNA genomes without protein-coding capacity and subvert enzymatic activities of their hosts to complete its own biological cycle. Different aspects of viroid biology and viroid-host interactions have been elucidated in the last years and some of them are the main topic of this review together with the analysis of the state-of-the-art about the growing field of endogenous lncRNAs in plants.

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae

The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.

Nucleotide sequence diversity in Velvet tobacco mottle virus: a virus with a unique Australian pathosystem

Velvet tobacco mottle virus (VTMoV) is a naturally occurring mirid-transmitted sobemovirus of native velvet tobacco (Nicotiana velutina) plants in the Australian arid zone. We have sequenced the coding region of a typical field isolate of VTMoV (isolate I-17-04, satellite-plus) and show that it differed by nine polymorphisms from the previously sequenced atypical ‘satellite-minus’ variant VTMoV-K1 (represented here as L-K1-04), while retaining the same genomic and amino acid sequence motifs. We also report that although L-K1-04 was confirmed to be free of detectable satellite RNA by gel electrophoretic assay, the satellite sequence was detected in it by RT-PCR assay. Nucleotide sequence variation among the RNA-dependent RNA polymerase open reading frames of 15 field and laboratory isolates identified four phylogenetic groups, but these did not show a pattern related to site or time of sampling. This result would be consistent with nucleotide sequence variants of VTMoV being dispersed widely by migrating adult mirid vectors.

Structural and sequence integrity are essential for the replication of the viroid-like satellite RNA of lucerne transient streak virus

Lucerne transient streak virus (LTSV, genus Sobemovirus) supports the replication and encapsidation of a 322 nt untranslated small-circular RNA (scLTSV). Since scLTSV does not code for any proteins or share sequence similarity with its helper virus (LTSV), it is presumed that it uses structural and sequence motifs to signal the helper virus (and host) machinery for its replication and encapsidation. Insertion and deletion mutations were introduced at various locations within the scLTSV molecule. Our results showed that most mutants were not infectious, with only two exceptions, a (-1) nucleotide deletion and a 9 nt, palindromic insertion mutant which preserved the overall rod-like structure of the scLTSV. Sequence analysis of cDNA clones revealed that the palindromic sequence was replicated for up to 12 days of infection, before the sequence reverted back to its wild-type form. Our results indicate that scLTSV has an optimal sequence and secondary structure for replication, movement and/or packaging within the LTSV helper virus.

Isolation of velvet tobacco mottle virus capable of replication with and without a viroid-like RNA

Field isolates of velvet tobacco mottle virus (VTMoV) induce severe symptoms in Nicotiana clevelandii and encapsidate viroid-like RNA reported to be essential for virus infection. An isolate of the virus producing only mild symptoms on N. clevelandii and devoid of viroid-like RNA has now been isolated from a plant inoculated by a single viruliferous Cyrtopeltis nicotianae, the mirid vector. However, after adding viroid-like RNA isolated from normal VTMoV to the inoculum, the new isolate was shown to support the synthesis of, and encapsidated the viroid-like RNA, thereby reverting to virulence characteristic of the normal isolate. This indicates that the viroid-like RNA can behave as a satellite RNA of VTMoV. The data are discussed in relation to previously published conclusions that viroid-like RNA is essential for the infectivity of VTMoV.

Nucleotide sequence of satellite tobacco ringspot virus RNA and its relationship to multimeric forms

Tobacco ringspot virus, a member of the nepovirus group, supports the increase and encapsidation of coinoculated satellite tobacco ringspot virus RNA (STobRV RNA). The nucleotide sequence of the unit length STobRV RNA, found here to be 359 nucleotide residues for the budblight strain, occurs also in multimeric, repetitive sequence forms. These are able to undergo an autolytic processing reaction to generate biologically active, unit length STobRV RNA (G. A. Prody, J. T. Bakos, J. M. Buzayan, I. R. Schneider, and G. Bruening,1984, In "Abstracts of the 3rd Cold Spring Harbor RNA Processing Meeting, May 16-20,1 984," p. 8). We determined the nucleotide sequence of the monomeric STobRV RNA by combining results from partial enzymatic digestions of the RNA, partial chemical cleavage of cDNA transcribed from the RNA, and analyses of cDNA clones. Other analyses gave the terminal residues of monomeric STobRV RNA: a cytosine-2':3'-cyclic phosphodiester and a 5' terminal adenosine. The terminal residues of monomeric RNA and their adjacent nucleotide sequences are consistent with the sequence in the junction region of dimeric RNA, derived from transcripts and cDNA clones, and with the formation of two monomeric STobRV RNAs upon autolysis of dimer, without the gain or loss of a nucleotide residue.

Cucumber mosaic virus-associated RNA 5: X. The complete nucleotide sequence of a CARNA 5 incapable of inducing tomato necrosis

The complete nucleotide sequence of a cucumber mosaic virus-associated RNA 5 (CARNA 5) that does not induce the tomato necrosis disease (J. M. Kaper, M. E. Tousignant, and S. M. Thompson, Virology 114, 526-533, 1981) has been determined and compared with the known sequence of a necrosis-inducing CARNA 5 (K. E. Richards, G. Jonard, M. Jacquemond, and H. Lot, Virology 89, 395-408, 1978). The nonnecrotic satellite RNA, (1)CARNA 5, is one nucleotide smaller yet 93% homologous with (n)CARNA 5, the necrosis-inducing satellite RNA. (1)CARNA 5 differs from (n)CARNA 5 by 21 substitutions, 3 deletions, and 2 insertions, with more changes in the 3' half than in the 5' half of the molecule. (1)CARNA 5, like (n)CARNA 5, is capped at its 5' terminus; the nucleotide sequences predict that putative translational products of the two RNAs could be significantly different.

Structural characterization of the 69 nucleotide potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis

The 69 nucleotide left-terminal domain (T(L)) of the potato spindle tuber RNA viroid (PSTVd) constitutes one of its five structural elements. Due to a twofold complementary sequence repeat, two possible conformations are proposed for the T(L) secondary structure; an elongated-rod and a bifurcated form. In the present study, two T(L) mutants were designed that remove the symmetry of the sequence repeats and ensure that either the bifurcated or the elongated-rod conformation is thermodynamically favored. Imino 1H and 15N resonances were assigned for both mutants and the native T(L) domain based on 1H-1H NOESY and heteronuclear 1H-15N HSQC high-resolution NMR spectra. The NMR secondary structure analysis of all constructs establishes unambiguously the elongated-rod form as the secondary structure of the native T(L) domain. Temperature-gradient gel electrophoresis and UV melting experiments corroborate these results. A combined secondary structure and sequence analysis of T(L) domains of other Pospiviroidae family members indicates that the elongated-rod form is thermodynamically favored for the vast majority of these viroids.

Satellite cereal yellow dwarf virus-RPV (satRPV) RNA requires a douXble hammerhead for self-cleavage and an alternative structure for replication

The 110 nt hammerhead ribozyme in the satellite RNA of cereal yellow dwarf virus-RPV (satRPV RNA) folds into an alternative conformation that inhibits self-cleavage. This alternative structure comprises a pseudoknot with base-pairing between loop (L1) and a single-stranded bulge (L2a), which are located in hammerhead stems I and II, respectively. Mutations that disrupt this base-pairing, or otherwise cause the ribozyme to more closely resemble a canonical hammerhead, greatly increase self-cleavage. In a more natural multimeric sequence context containing the full-length satRPV RNA and two copies of the hammerhead, wild-type RNA cleaves much more efficiently than in the 110 nt context. Mutations in the upstream hammerhead, including a knock-out in the catalytic core, affect cleavage at the downstream cleavage site, indicating that multimers of satRPV RNA cleave via a double hammerhead. The double hammerhead includes base-pairing between two copies of the L1 sequence which extends stem I. Disruption of L1-L1 base-pairing slows cleavage of the multimer. L1-L2a base-pairing is required for efficient replication of satRPV RNA in oat protoplasts. Mutations that affect self-cleavage of the multimer do not correlate with replication efficiency, indicating that the ability to self-cleave is not a primary determinant of replication. We present a replication model in which multimeric satRPV RNA folds into alternative conformations that cannot form in the monomer. One potential metastable intermediate conformation involves L1-L2a base-pairing that may facilitate formation of the double hammerhead. However, we conclude that L1-L2a also performs some other essential function in the satRPV RNA replication cycle, because the L1-L2a base-pairing is more important than efficient self-cleavage for replication.

Compilation and analysis of viroid and viroid-like RNA sequences

We have created a catalogue comprising all viroid and viroid-like RNA sequences which to our knowledge have been either published or were available from on-line sequence libraries as of October 1, 1995. In the development of this catalogue nomenclature ambiguities were removed, the likely ancestral sequence of most species was determined and the most stable secondary structures of these sequences were predicted using the MulFold package. Only viroids of PSTVd-type possessed a rod-like secondary structure, while most other viroids adopted branched secondary structures. Several viroids have predicted secondary structures that include either a Y or cruciform structure reminiscent of the tRNA-like end of virus genomes at an extremity. However, it remains unknown whether or not these predicted structures are adopted in solution, and if they serve a particular function in vivo. Additional information such as the position of the self-catalytic domains are included in the catalogue. An analysis of the data compilated in the catalogue is included. The catalogue will be available on the world wide web (http://www.callistro.si.usherb.ca/jpperra), on computer disk and in printed form. It should provide an excellent reference point for further studies.

Prominent polypurine and polypyrimidine tracts in plant viroids and in RNA of the human hepatitis delta agent

To seek patterns of nucleotide usage in the three types of circular subviral RNA pathogens, trimer frequencies and nearest-neighbor biases were studied in 12 plant viroid sequences; five sequences of circular plant viral satellite RNAs; and the sequence of RNA from the human hepatitis delta agent. The viroids and RNA of the delta agent contain tracts of polypurines and polypyrimidines which make up substantial portions of their genomes. Such tracts are not common in the virusoids or in the satellite RNA of tobacco ringspot virus. Viroids, the delta hepatitis agent, and the circular satellite RNAs of certain plant viruses have several features in common: all have circular genomic RNA and replicate through an RNA to RNA rolling circle replication cycle. However, virusoids and related satellite RNAs are directly or indirectly dependent on their helper viruses for replication, while the delta agent and viroids are not. The difference in the pattern of nucleotide usage between the plant viral satellite RNAs on the one hand, and viroids and delta RNA on the other, may relate to this difference in replication strategy.

Satellite RNAs of plant viruses: structures and biological effects

Plant viruses often contain parasites of their own, referred to as satellites. Satellite RNAs are dependent on their associated (helper) virus for both replication and encapsidation. Satellite RNAs vary from 194 to approximately 1,500 nucleotides (nt). The larger satellites (900 to 1,500 nt) contain open reading frames and express proteins in vitro and in vivo, whereas the smaller satellites (194 to 700 nt) do not appear to produce functional proteins. The smaller satellites contain a high degree of secondary structure involving 49 to 73% of their sequences, with the circular satellites containing more base pairing than the linear satellites. Many of the smaller satellites produce multimeric forms during replication. There are various models to account for their formation and role in satellite replication. Some of these smaller satellites encode ribozymes and are able to undergo autocatalytic cleavage. The enzymology of satellite replication is poorly understood, as is the replication of their helper viruses. In many cases the coreplication of satellites suppresses the replication of the helper virus genome. This is usually paralleled by a reduction in the disease induced by the helper virus; however, there are notable exceptions in which the satellite exacerbates the pathogenicity of the helper virus, albeit on only a limited number of hosts. The ameliorative satellites are being assessed as biocontrol agents of virus-induced disease. In greenhouse studies, satellites have been known to "spontaneously" appear in virus cultures. The possible origin of satellites will be briefly considered.

Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA

We report a phylogenetic study of viroids, some plant satellite RNAs, and the viroidlike domain of human hepatitis delta virus RNA. Our results support a monophyletic origin of these RNAs and are consistent with the hypothesis that they may be "living fossils" of a precellular RNA world. Moreover, the viroidlike domain of human hepatitis delta virus RNA appears closely related to the viroidlike satellite RNAs of plants, with which it shares some structural and functional properties. On the basis of our phylogenetic analysis, we propose a taxonomic classification of these RNAs.

Circular single-stranded RNA replicon in Saccharomyces cerevisiae

Circular RNA replicons have been reported in plants and, in one case, in animal cells. We describe such an element in yeast. In certain yeast strains, a 20S RNA species appears on transfer of cells to acetate medium. This phenotype shows cytoplasmic (non-Mendelian) inheritance and the 20S RNA is associated with 23-kDa protein subunits as a 32S particle. We demonstrate that yeast 20S RNA is an independent replicon with no homology to host genomic, mitochondrial, or 2-microns plasmid DNA or to the L-A, L-BC, or M1 double-stranded RNA viruses of yeast. The circularity of the 20S RNA is shown by the apparent absence of 3' and 5' ends, by two-dimensional gel electrophoresis, and by electron microscopy. Replication of yeast 20S RNA proceeds through an RNA-RNA pathway, and a 10,000-fold amplification occurs on shift to acetate medium. The copy number of 20S RNA is also reduced severalfold by the SKI gene products, a host antiviral system that also lowers the copy numbers of yeast double-stranded RNA viruses. Yeast 20S RNA and the hepatitis delta virus show some similarities.

Structure, self-cleavage, and replication of two viroid-like satellite RNAs (virusoids) of subterranean clover mottle virus

Both the genomic and viroid-like satellite RNAs (virusoids) from four subterranean clover mottle virus isolates described by Francki et al. were analyzed in detail. Restriction endonuclease mapping of cDNAs prepared from the genomic RNAs from all isolates showed that these RNAs are closely related if not identical. The two virusoids, which can occur together in the same isolate or individually, were sequenced and shown to be able to form highly base-paired viroid-like secondary structures. The left-hand portions of these structures are almost entirely homologous but the right-hand portions show little similarity. The plus, but not the minus, virusoid RNAs contain sequences that can form the hammerhead self-cleavage structure of certain other self-cleaving viroid, virusoid, and satellite RNAs. Plus, but not minus, RNA transcripts from cDNA clones self-cleaved essentially to completion at the predicted site during transcription in vitro. Northern blot analysis of infected leaf tissue extracts revealed the presence of an oligomeric series of plus RNAs (of monomer size and greater) but minus RNAs were present only as high molecular weight species of heterogeneous size. These findings are in agreement with the lack of minus RNA self-cleavage in vitro. Hence, these virusoid RNAs appear to replicate by a rolling-circle mechanism in which only the plus RNAs self-cleave to form monomeric RNAs.

Kinetics of velvet tobacco mottle virus satellite RNA synthesis and encapsidation

Synthesis of circular (RNA 2) and linear (RNA 3) molecules of velvet tobacco mottle virus (VTMoV) satellite RNA (sat RNA) has been studied by incubating strips of tissues excised from systemically infected Nicotiana clevelandii in solutions of [14C]uridine. After a short lag, RNA and virus synthesis proceeded at a constant rate for at least 24 hr, during which time most of the synthesis was directed to the production of RNAs 2 and 3. The kinetics of [14C]uridine incorporation into the sat RNA molecules after increasing times of incubation and during pulses of [14C]uridine followed by chase incubation with excess [12C]uridine suggest that RNA 3 is a percursor of RNA 2. However, not all the RNA 3 synthesized was shown to end up as RNA 2, even after 72 hr of incubation. Several lines of evidence are presented supporting the conclusion that VTMoV-infected cells contain large pools of unencapsidated sat RNA. It is suggested that the sat RNA may have a greater affinity for the VTMoV replicase than the helper viral RNA which results in copious production of the sat RNA.

Simple RNA enzymes with new and highly specific endoribonuclease activities

In vitro mutagenesis of sequences required for the self-catalysed cleavage of a plant virus satellite RNA has allowed definition of an RNA segment with endoribonuclease activity. General rules have been deduced for the design of new RNA enzymes capable of highly specific RNA cleavage, and have been successfully tested against a new target sequence.

Nucleotide sequence and secondary structure of apple scar skin viroid

The complete nucleotide sequence of apple scar skin viroid(ASSV) has been established, and a probable secondary structure is proposed. A single-stranded circular ASSV RNA consists of 330 nucleotides and can assume the rodlike conformation with extensive base-pairing characteristic of all the known viroids. ASSV shows low sequence homologies with other viroids and lacks the central conserved region. These indicate that ASSV should be allocated to a separate viroid group. However, homologous sequences with potato spindle tuber viroid(PSTV) in ASSV occur in limited and scattered regions of both viroids. These homologous regions fall within the particular domains in the viroid domain model which has been previously proposed by Keese and Symons(Proc. Natl. Acad. Sci. USA. 82, 4582-4586, 1985).

Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites

Virusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation. Virusoid replication appears to involve longer-than-unit-length plus and minus RNAs, indicating that unit-length plus RNA is generated by specific cleavage reactions. Here, we synthesize plus and minus partial-length RNAs of the 324-nucleotide virusoid from lucerne transient streak virus in vitro. Both RNAs self-cleave at a unique site in the presence of magnesium ions to give 5' hydroxyl and 2',3' cyclic phosphodiester termini. Conformations other than the native structures are necessary for cleavage. Similar secondary structures with considerable sequence homology are proposed for the active sites of these and other plant pathogenic RNAs. Our results are consistent with certain rolling-circle replication models.

Structure, sequence and expression of the hepatitis delta (delta) viral genome

Biochemical and electron microscopic data indicate that the human hepatitis delta viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants. The sequence of the viral genome (1,678 nucleotides) has been determined and an open reading frame within the complementary strand has been shown to encode an antigen that binds specifically to antisera from patients with chronic hepatitis delta viral infections.

Viroids and virusoids are related to group I introns

Group I introns are found in nuclear rRNA genes, mitochondrial mRNA and rRNA genes, and chloroplast tRNA genes. The hallmarks of this intron class are a 16-nucleotide consensus sequence and three sets of complementary sequences. The viroids (circular pathogenic plant RNAs) and the virusoids (plant satellite RNAs) also contain the consensus sequence and the three sets of complementary bases. Pairing of the complementary bases would generate a viroid structure resembling a group I intron, which might be stabilized in vivo through interactions with proteins. The Tetrahymena self-splicing rRNA intron further has sequences homologous with regions of potato spindle tuber viroid associated with the severity of viroid symptoms.

Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid

Self-cleavage of both plus and minus RNA transcripts of the 247-residue avocado sunblotch viroid (ASBV), prepared from tandem dimeric cDNA clones, occurs specifically at two sites in each transcript to give monomeric plus and minus species. The cleavage reaction occurs both during transcription and on incubation of purified transcripts at pH 8 and 37 degrees C in the presence of magnesium ions to give a 3'-terminal 2',3'-cyclic phosphate and a 5'-terminal hydroxyl group. Although the self-cleavage occurs at different sites in the ASBV molecule for the plus and minus species, very similar secondary structures with high sequence homology can be drawn at each site. The results are considered to provide further evidence that ASBV is replicated in vivo by a rolling circle mechanism involving non-enzymic cleavage of high molecular weight RNA precursors of ASBV.

Relationship of viroids and certain other plant pathogenic nucleic acids to group I and II introns

The nucleotide sequences of viroids contain features believed to be essential for the splicing of group I introns. Common sequence elements include a 16-nucleotide consensus sequence and three pairs of short sequences arranged in the same sequential order in both types of RNAs. The calculated probability of finding sequences resembling the 16-nucleotide consensus sequence in random nucleotide chains showed that at low fidelity (up to 5 mismatched nucleotides), the number of such sequences in viroids, plant viral satellite RNAs, plant viral RNAs and one plant viral DNA, group I introns and flanking exons does not significantly differ from the number expected at random. As the degree of fidelity is increased, the number in both introns and viroids, but not in exons or the other plant pathogens examined, greatly exceeds that expected in random chains. These findings suggest that viroids may have evolved from group I introns and/or that processing of viroid oligomers to monomers may have structural requirements similar to those of group I introns. The nucleotide sequences of viroids do not show close homology with two conserved regions of group II introns, the 14-base pair consensus region and the 5' terminal segment. However, close homology does exist between the conserved sequence of the 3' terminal segment of group II introns and viroids thus suggesting a possible evolutionary or functional relationship.

Comparison of multimeric plus and minus forms of viroids and virusoids

In order to investigate the mechanism of replication of viroids and virusoids, we have compared the replication intermediates of three members of each group in nucleic acid extracts of infected plants. Viroids were avocado sunblotch viroid (ASBV), citrus exocortis viroid (CEV) and coconut cadang cadang viroid (CCCV). Virusoids were from velvet tobacco mottle virus (VTMoV), solanum nodiflorum mottle virus (SNMV) and lucerne transient streak virus (LTSV). Analysis of intermediates was by the Northern hybridization technique with single-strand DNA and RNA probes prepared from recombinant DNA clones. The results obtained are discussed in terms of current models of viroid and virusoid replication.The plus RNA species consisted of an oligomeric series up to decamers based on the unit of full-length viroid or virusoid, which was always the major component, except for CEV where only monomer and dimer species were found. In the case of ASBV and the virusoids of VTMoV and SNMV, a minor, multimeric series of components (X-bands) was superimposed on the main oligomeric series.The complementary minus species proved more difficult to detect and characterise, with each viroid and virusoid exhibiting a unique pattern on Northern hybridization. However, they all had greater than unit-length minus species. In addition, minus species analogous to the plus X-bands were found in ASBV and CEV. The experimental difficulties encountered in this work are discussed in terms of the problem of detecting minus species by Northern analysis in the presence of excess complementary plus species.

Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution

On the basis of sequence homology a model is proposed for five structural and functional domains in viroids. These domains include (i) a conserved central region capable of forming two alternative structures that may regulate two phases of the viroid replication cycle, (ii) a region associated with pathogenicity, (iii) a domain with high sequence variability, (iv and v) two terminal domains that are interchangeable between viroids. That the evolution of viroids has involved RNA rearrangements of domains is supported by the partial duplication of coconut cadang cadang viroid, which arises de novo during each infection. Similar RNA rearrangements have been established for animal viral defective interfering RNAs, which arise by some form of discontinuous transcription. This mechanism could account for the origin of viroids and also RNA viruses, whereby modules of genetic information may have undergone repeated exchange between RNA pathogens and the RNA of their hosts.

Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity

Full-length double-stranded cDNA was prepared from purified circular RNA of two new Australian field isolates of citrus exocortis viroid (CEV) using two synthetic oligodeoxynucleotide primers. The cDNA was then cloned into the phage vector M13mp9 for sequence analysis. Sequencing of nine cDNA clones of isolate CEV-DE30 and eleven cDNA clones of isolate CEV-J indicated that both isolates consisted of a mixture of viroid species and led to the discovery of eleven new sequence variants of CEV. These new variants, together with the six reported previously, form two classes of sequence which differ by a minimum of 26 nucleotides in a total of 370 to 375 residues. These two classes correlate with two biologically distinct groups when propagated on tomato plants where one produces severe symptoms and the other gives rise to mild symptoms. Two regions of the native structure of CEV, comprising 18% of the total residues, differ between the sequence variants of mild and severe isolates. Whether or not both of these regions are essential for the variation in pathogenicity has yet to be determined.

2' phosphomonoester, 3'-5' phosphodiester bond at a unique site in a circular viral RNA

Solanum nodiflorum mottle virus (SNMV) RNA2 is a single-stranded, covalently closed circular molecule. RNase T2 or nuclease P1 digests of this RNA contain a minor nucleotide of unusual chromatographic and electrophoretic mobility. This nucleotide is resistant to further digestion by T2 or P1 ribonucleases, or by alkali, but is sensitive to venom phosphodiesterase digestion. Alkaline phosphatase digestion yields a product which is RNase T2 and P1 sensitive. The products of these various digests show that the minor nucleotide is a ribonuclease-resistant dinucleotide carrying a 2' phosphomonoester group with the core structure C2'p3'p5'A. This dinucleotide is found in a unique RNase T1 product of SNMV RNA2, thus establishing a unique location in the sequence for the 2' phosphomonoester group at residue 49. Identical results have been obtained with a second related virus. The phosphomonoester group probably results from the RNA ligation event by which the molecules were circularised.

Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data

Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but replicate only as genomic part of a plant virus. Their structure and structural transitions have been investigated by thermo-dynamic, kinetic and hydrodynamic methods. The special features of the sequences of these RNAs, which are the basis for their secondary structures and structural flexibility, are investigated with theoretical methods. A set of thermodynamic parameters for helix growth and loop formation is selected from the literature to calculate secondary structures and structural transitions of single-stranded RNAs. Appropriate modifications of the chosen parameter set are discussed. For calculations we used either Tinoco-plots and the model of "cooperative helices" or the Zuker-program based on the exact algorithm of Nussinov et al, or both. Calculations were done for viroids and virusoids. As both are single-stranded, circular RNAs we had to modify the Zuker-program as described in the appendix. Calculations are done for different viroids, i.e. potato spindle tuber, citrus exocortis, chrysanthemum stunt, coconut cadang-cadang, and avocado sunblotch, and for two virusoids, i.e. the circular RNAs of Solanum nodiflorum mottle virus, and velvet tobacco mottle virus. For viroids the calculations confirm our earlier theoretical and experimental results about the extended native structure and the highly cooperative transition into a branched structure. Virusoids show less base pairing, branching in the native secondary structure, and only low cooperativity during denaturation. They resemble more closely the properties of random sequences with length, G:C content, and circularity as in viroids but statistical sequences. The comparison of viroids, virusoids, and circular RNA or random sequences confirms the uniqueness of viroid structure.

Viroid replication: equilibrium association constant and comparative activity measurements for the viroid-polymerase interaction

The binding and replication of purified potato spindle tuber viroid (PSTV) by DNA-dependent RNA polymerase II from wheat germ was studied in analytical ultracentrifugation experiments and in vitro transcription assays. The equilibrium association constant for the viroid-polymerase interaction is 1.9 X 10(7) M-1. Both ultraviolet and fluorescent monitoring during the sedimentation experiments showed two distinguishable viroid-polymerase complexes. These are interpreted as resulting from a 1:1 and 2:1 enzyme-to-viroid binding stoichiometry. A265/A280 ratios across the sedimenting boundaries, the sedimentation velocity of the complexes, as well as electron microscopic data support this interpretation. The role of viroid secondary structure in enzyme binding and polymerization is discussed in the light of these results and compared with binding and polymerization data for virusoid RNA, single- and double-stranded RNA, and double-stranded DNA.

Translational strategy of Solanum nodiflorum mottle virus RNA: synthesis of a coat protein precursor in vitro and in vivo

Solanum nodiflorum mottle virus RNA (Mr = 1.5 X 10(6)) was translated in vitro in a wheat embryo extract. Four major products were synthesized: 2 related proteins of molecular weight 100K (P100) and 67K (P67), a protein of molecular weight 38K (P38), and a methionine-lacking protein of molecular weight 28K (P28). P38 was synthesized by a minor RNA component (Mr approximately 0.4 X 10(6)) and comigrated with the only viral product detected in SNMV-infected N. clevelandii protoplasts. Antiserum raised against purified SNMV virions precipitated both in vitro- and in vivo-synthesized P38, suggesting that it is either a precursor to or an intact form of SNMV coat protein whose apparent molecular weight in purified virus preparations is 30K.

Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy

The complete cDNA of hop stunt viroid (HSV) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170. (1982] and the complete nucleotide sequence has been established. The covalently closed circular single-stranded HSV RNA consists of 297 nucleotides. The secondary structure predicted for HSV contains 67% of its residues base-paired. The native HSV can possess an extended rod-like structure characteristic of viroids previously established. The central region of the native HSV has a similar structure to the conserved region found in all viroids sequenced so far except for avocado sunblotch viroid. The sequence homologous to the 5'-end of U1a RNA is also found in the sequence of HSV but not in the central conserved region.

RNA 3'-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract

HeLa cell extract contains RNA ligase activity that converts linear polyribonucleotides to covalently closed circles. RNA substrates containing 2',3'-cyclic phosphate and 5'-hydroxyl termini are circularized by formation of a normal 3',5' phosphodiester bond. This activity differs from a previously described wheat germ RNA ligase which circularizes molecules with 2',3'-cyclic and 5' phosphate ends by a 2'-phosphomonester, 3',5'-phosphodiester linkage (Konarska et al., Nature 293, 112-116, 1981; Proc. Natl. Acad. Sci. USA 79, 1474-1478, 1982). The HeLa cell ligase can also utilize molecules with 3'-phosphate ends. However, in this case ligation is preceded by an ATP-dependent conversion of the 3'-terminal phosphate to the 2',3' cyclic form by a novel activity, RNA 3'-terminal phosphate cyclase. Both RNA ligase and RNA 3'-terminal phosphate cyclase activities are also present in extract of Xenopus oocyte nuclei, consistent with a role in RNA processing.

Satellite RNA of cucumber mosaic virus forms a secondary structure with partial 3'-terminal homology to genomal RNAs

Sat-RNA is one of several replicating satellite RNAs which have been isolated from RNA encapsidated in cucumber mosaic virus (CMV) and which are totally dependent on CMV for replication. The 336 residue sequence of Sat-RNA obtained using the dideoxynucleotide chain termination and partial enzymic digestion procedures shows only a few short stretches (up to 11 residues) of sequence homology with one of the three CMV genomal RNAs so far sequenced. Sat-RNA has 88% sequence homology with another, previously sequenced, satellite RNA of CMV, CARNA 5. Analysis of partial digests of 5'- or 3' -32P-Sat-RNA with nuclease S1 or RNase T1 under non-denaturing conditions showed that only about 10% of the residues in Sat-RNA were cleaved. Further data on base-paired segments of Sat-RNA were obtained using digestion with RNase T1 followed by electrophoretic fractionation of the resulting fragments under both non-denaturing and denaturing conditions. On the basis of this data, a complete secondary structure model is proposed for Sat-RNA with 52% of its residues involved in base pairs. A prominent hairpin at the 3'-terminus of Sat-RNA shows considerable sequence and structural homology with parts of the 3'-terminal tRNA-like structure of the CMV genomal RNAs.

Structural transitions in viroid-like RNAs associated with cadang-cadang disease, velvet tobacco mottle virus, and Solanum nodiflorum mottle virus

The conformational transitions of viroid-like RNAs associated with cadang-cadang disease, velvet tobacco mottle virus, and solanum nodiflorum mottle virus were studied by melting analysis and fast temperature jump technique in 1 mM sodium-cacodylate, 10 mM NaCl, 0.1 mM EDTA, pH 6.8. The 4 circular RNAs of cadang-cadang show a highly cooperative transition between 45 and 49 degrees C, respectively, and a second transition of less hypochromicity at about 10 degrees C higher temperatures. The data are interpreted quantitatively on the basis of the sequences and secondary structure models. A very similar scheme for the structure and structural transitions as derived earlier for other viroids applies to the cadang-cadang RNAs. In the main transition the total native secondary structure is disrupted and a stable hairpin consisting of 9 base pairs is newly formed which dissociates in the second transition. The thermal denaturation of the circular RNAs from the viruses mentioned above is clearly distinct from viroid RNA in respect to stability and cooperativity. The results on cadang-cadang RNA are discussed in the light of recent hypotheses about the interference of viroids with the splicing process of the host cell.