Nucleotide sequence and proposed secondary structure of<i>Columnea</i>latent viroid: a natural mosaic of viroid sequences

Hammond, R. W.; Smith, D. B.; Diener, T.O.

doi:10.1093/nar/17.23.10083

Cited by 97 publications

(66 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…CLVd, for example, is mostly a mosaic of viroid sequences known from other viroids. Its left and right terminal domains are essentially identical with those of Pospiviroids, whereas its CCR is identical with that of HSVd (22). Thus, placement of CLVd with one of these groups depends on what one considers as the most important criteria for classification.…”

Section: Phylogenetic Methodsmentioning

confidence: 99%

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

Elena

Dopazo

Flores

et al. 1991

Proc. Natl. Acad. Sci. U.S.A.

111

View full text Add to dashboard Cite

We report a phylogenetic study of viroids, some plant satellite RNAs, and the viroidlike domain of human hepatitis 8 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 8 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.assumed an intracellular mode of existence sometime after the evolution of cellular organisms.Implicit in this proposal is the possibility that all viroids and viroidlike RNAs may have been derived from a common ancestor. To obtain evidence for or against this proposition, we have conducted a phylogenetic analysis of these small pathogenic RNAs and report here that our results are consistent with a monophyletic origin of viroids and viroidlike satellite RNAs, as well as possibly of the viroidlike domain of HDV RNA.Viroids, subviral pathogens of higher plants, are small (246-375 nucleotide residues), unencapsidated, single-stranded, circular RNAs characterized by highly base-paired, rodlike secondary structures (1). Viroids do not code for any proteins, yet they replicate autonomously (without the assistance of helper viruses) in susceptible cells. Viroidlike satellite RNAs resemble viroids, but they are found within the capsids of specific helper viruses required for their replication (2). Human hepatitis 8 virus (HDV) RNA is a circular RNA requiring hepatitis B virus as a helper virus for packaging and transmission (3). HDV RNA contains a region, termed the viroidlike domain, with significant similarities with viroid and viroidlike satellite RNAs (4). Viroids, viroidlike satellite RNAs, and HDV RNA appear to replicate via oligomeric RNA intermediates by some type of rolling-circle mechanism (2-6).Several hypotheses have been advanced to explain the evolution of viroids. It has been suggested, for example, that viroids may have originated from retroviruses or transposable elements by deletion of interior sequences (7), that they may represent escaped introns (8, 9), or that they have evolved comparatively recently from hypothetical "antenna" or "signal" RNAs, which eukaryotic cells are assumed to interchange (10).With the demonstration that certain RNAs have catalytic properties (11,12), the idea that RNA preceded DNA as a carrier of genetic information has gained support. Most recent models for self-replicating precellular RNAs assume the existence of primitive RNA enzymes with properties that are derived from extant self-splicing introns (13,14). Because one viroid, all known viroidlike satellite RNAs, and the viroidlike domain of HDV RNA are self-cleaving (3, 15, 16), it is equally plausible to consider these RNAs as relics of the RNA world, thus leading to an alternative hypothesis for the evolution of viroids and viroidlike satellite R...

show abstract

Section: Phylogenetic Methodsmentioning

confidence: 99%

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

Elena

Dopazo

Flores

et al. 1991

Proc. Natl. Acad. Sci. U.S.A.

111

View full text Add to dashboard Cite

show abstract

“…Furthermore, one of the critical loops for PSTVd trafficking has also been mapped to this domain (Zhong et al, 2008). Unlike the T L and T R domains, the P domain has not been associated with the contribution of the origin of new viroids (divergence) by molecular recombinant or rearrangement processes (Haseloff et al, 1982;Diener, 1983;Keese & Symons, 1985;Hammond et al, 1989;Szychowski et al, 2005;Darò s et al, 2006). Therefore, the functional role of…”

Section: Discussionmentioning

confidence: 99%

Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of citrus exocortis viroid

Bernad

Duran-Vila

Elena

2009

Journal of General Virology

View full text Add to dashboard Cite

Citrus exocortis viroid (CEVd) populations are composed of closely related haplotypes whose frequencies in the population result from the equilibrium between mutation, selection and genetic drift. The genetic diversity of CEVd populations infecting different citrus hosts was studied by comparing populations recovered from infected trifoliate orange and sour orange seedling trees after 10 years of evolution, with the ancestral population maintained for the same period in the original host, Etrog citron. Furthermore, populations isolated from these trifoliate orange and sour orange trees were transmitted back to Etrog citron plants and the evolution of their mutant spectra was studied. The results indicate that (i) the amount and composition of the within-plant genetic diversity generated varies between these two hosts and is markedly different from that which is characteristic of the original Etrog citron host and (ii) the genetic diversity found after transmitting back to Etrog citron is indistinguishable from that which is characteristic of the ancestral Etrog citron population, regardless of the citrus plant from which the evolved populations were isolated. The relationship between the CEVd populations from Etrog citron and trifoliate orange, both sensitive hosts, and those from sour orange, which is a tolerant host, is discussed. INTRODUCTIONViroids are small plant pathogens consisting of a naked single-stranded circular RNA molecule of 246-475 nt, that do not encode any proteins but are endowed with autonomous replication in their host plants. It is very likely that viroids have been co-evolving with their hosts since their origin, although many of them show a wide host range. The identification of viroids in wild and cultivated plants, as symptomless carriers, suggests that certain hosts may act as natural viroid reservoirs (Diener, 1995).Viroids are taxonomically classified into two families, Pospiviroidae and Avsunviroidae (Elena et al., 1991). These families mainly differ in three characteristics. First, all pospiviroidae present a central conserved region (CCR) in their rod-like secondary structure, whereas the avsunviroidae lack such a region. Second, the pospiviroidae rely on cellular factors to process their multimeric replication intermediates into unit-length molecules, while the avsunviroidae present hammerhead ribozyme structures that are able to self-cleave the multimeric forms. Third, the pospiviroidae replicate in the nucleus whereas the avsunviroidae replicate in the chloroplast (reviewed by Flores et al., 2005).Like most RNA and some DNA viruses, viroids replicate within their hosts as polymorphic populations composed of closely related sequence variants generally distributed around a predominant one. This polymorphic population structure arises as a result of (i) the high mutation rates inherent to the cellular DNA-dependent RNA polymerases involved in viroid replication subverted to replicate an RNA template and (ii) the diverse and fluctuating selective pressures imposed by the different ...

show abstract

“…The adjective ''polythetic'' means that the viruses (or viroids) do not need to exhibit a common core set of biological, genetic or structural properties, but rather that their properties overlap to varying degrees. As discussed below, this definition provides a useful framework in which to consider the classification of columnea latent viroid (CLVd, [31] and dahlia latent viroid, DLVd, [63]), two viroids whose CCRs most closely resemble that of HSVd but also, like PSTVd, contain a TCR (see below).…”

Section: Criteria For Viroid Species Demarcationmentioning

confidence: 99%

“…Pairwise sequence comparisons strongly suggested that the terminal domains of certain pospiviroids such as tomato apical stunt viroid (TASVd) and TPMVd have undergone recombination in vivo, most likely as the result of discontinuous transcription by the RNA polymerase II involved in viroid replication. On the other hand, the genesis of several viroids, including CLVd [31] and Australian grapevine viroid (AGVd, [52]), was proposed to result from recombination events between viroids belonging to species of different genera co-infecting the same host. Internal recombination events within the same viroid, generating terminal repeats, have also been reported for some nuclear-replicating viroids, such as coconut cadang-cadang viroid (CCCVd) and CEVd [14,32,57].…”

Section: Recombinant Viroidsmentioning

confidence: 99%

See 1 more Smart Citation

Current status of viroid taxonomy

Serio

Flores

Verhoeven³

et al. 2014

Arch Virol

161

View full text Add to dashboard Cite

Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of nextgeneration sequencing and bioinformatics for known and previously unrecognized viroids.

show abstract

Nucleotide sequence and proposed secondary structure ofColumnealatent viroid: a natural mosaic of viroid sequences

Cited by 97 publications

References 28 publications

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

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

Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of citrus exocortis viroid

Current status of viroid taxonomy

Contact Info

Product

Resources

About