Viroids: The Noncoding Genomes

doi:10.1006/smvy.1997.0107

Seminars in Virology

Volume 8, Issue 1, February 1997, Pages 65-73

https://doi.org/10.1006/smvy.1997.0107 Get rights and content

Abstract

Viroids are independently replicating small circular RNAs which apparently do not code for proteins. They code, in a broad sense, for a conformation which is recognized and replicated by the host cell; two viroids also express ribozyme activities which probably mediate self-cleavage of the oligomeric replicative intermediates generated by a rolling circle mechanism. Viroids are classified into subgroups according to their sequence and to the presence and type of some conserved motifs. Viroid infections which induce symptoms, do so as a result of the direct interaction of the viroid itself, or a product of its replication, with a cellular target(s) of unknown nature.

References (62)

J.M. Sogo et al.
Potato spindle tuber viroid. X. Visualization and size determination by electron microscopy
Virology
(1973)
F.U. Gast et al.
Secondary structure probing of potato spindle tuber viroid (PSTVd) and sequence comparison with other small pathogenic RNA replicons provides evidence for central non-canonical base-pairs, large A-rich loops, and a terminal branch
J. Mol. Biol.
(1996)
I.M. Schindler et al.
Involvement of nuclear DNA-dependent RNA polymerases in potato spindle tuber viroid replication: A reevaluation
Plant Sci.
(1992)
J.F. Marcos et al.
Characterization of RNAs specific to avocado sunblotch viroid synthesizedin vitro
Virology
(1992)
M. Tabler et al.
Processing of linear longer-than-unit-length potato spindle tuber viroid RNAs into infectious monomeric circular molecules by a G-specific endoribonuclease
Virology
(1992)
R.W. Hammond et al.
Infectivity of chimeric viroid transcripts reveals the presence of alternative processing sites in potato spindle tuber viroid
Virology
(1989)
T. Candresse et al.
The role of the viroid central conserved region in cDNA infectivity
Virology
(1990)
A.G. Rakowski et al.
Infectivity of linear monomeric transcripts of citrus exocortis viroid: Terminal sequence requirements for processing
Virology
(1994)
D. Lafontaine et al.
Intra- and intermolecular nonenzymatic ligations occur within transcripts derived from the peach latent mosaic viroid
Virology
(1995)
T.O. Diener
The viroid: Big punch in a small package
Trends Microbiol.
(1993)

R.A. Owens et al.

RNA structural features responsible for potato spindle tuber viroid pathogenicity

Virology

(1996)

C.L. Niblett et al.

Cross-protection among four viroids

Virology

(1978)

A.D. Branch et al.

Interference between coinoculated viroids

Virology

(1988)

R. Gruner et al.

Interdependence of pathogenicity and replicability with potato spindle tuber viroid

Virology

(1995)

T.O. Diener

The Viroids

(1987)

J.S. Semancik

Viroids and Viroid-like Pathogens

(1987)

R.H. Symons

Viroids and related pathogenic agents

Semin. Virol.

(1990)

R.H. Symons

The intriguing viroids and virusoids: What is their information content and how did they evolve?

Mol. Plant-Microbe Interact.

(1991)

D. Riesner

Viroids: From thermodynamics to cellular structure and function

Mol. Plant-Microbe Interact.

(1991)

T.O. Diener

Origin and evolution of viroids and viroid-like satellite RNAs

Virus Genes

(1996)

H.L. Sänger et al.

Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures

Proc. Natl. Acad. Sci. USA

(1976)

A.M. Koltunow et al.

A scheme for viroid classification

Intervirology

(1989)

S.F. Elena et al.

Phylogeny of viroids, viroid-like satellite RNAs, and the viroidlike domain of hepatitis δ virus RNA

Proc. Natl. Acad. Sci. USA

(1991)

A.M. Koltunow et al.

Grapevine yellow speckle viroid: Structural features of a new viroid group

Nucleic Acids Res.

(1988)

R.L. Spieker et al.

Primary and secondary structure of a new viroid ‘species’ (CbVd 1) present in theColeus blumei

Nucleic Acids Res.

(1990)

R.L. Spieker

In vitroColeus blumeiin vivo

J. Gen. Virol.

(1996)

H. Puchta et al.

The molecular structure of hop latent viroid (HLV), a new viroid occurring worldwide in hops

Nucleic Acids Res.

(1988)

C.J. Hutchins et al.

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

Nucleic Acids Res.

(1986)

C. Hernández et al.

Plus and minus RNAs of peach latent mosaic viroid self cleavein vitro

Proc. Natl. Acad. Sci. USA

(1992)

J. Haseloff et al.

Viroid RNAs of the cadang-cadang disease of coconuts

Nature

(1982)

Cited by (93)

Viroid taxonomy
2023, Fundamentals of Viroid Biology
Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life
2021, Journal of Theoretical Biology
Citation Excerpt :
Furthermore, the circular templates required for rolling-circle replication need not be exceedingly long. Viroids and satellite RNAs have typical sizes of ~ 220–400 bases (Flores et al., 1997, 2012; Collins et al., 1998). Whereas rolling-circle synthesis of ssDNA has been shown for much shorter templates containing 13–74 bases (Fire and Xu, 1995; Liu et al., 1996; Frieden et al., 1999).
It is likely that RNA replication began non-enzymatically, and that polymerases were later selected to speed up the process. We consider replication mechanisms in modern viruses and ask which of these is possible non-enzymatically, using mathematical models and experimental data found in the literature to estimate rates of RNA synthesis and replication. Replication via alternating plus and minus strands is found in some single-stranded RNA viruses. However, if this occurred non-enzymatically it would lead to double-stranded RNA that would not separate. With some form of environmental cycling, such as temperature, salinity, or pH cycling, double-stranded RNA can be melted to form single-stranded RNA, although re-annealing of existing strands would then occur much faster than synthesis of new strands. We show that re-annealing blocks this form of replication at a very low concentration of strands. Other kinds of viruses synthesize linear double strands from single strands and then make new single strands from double strands via strand-displacement. This does not require environmental cycling and is not blocked by re-annealing. However, under non-enzymatic conditions, if strand-displacement occurs from a linear template, we expect the incomplete new strand to be almost always displaced by the tail end of the old strand through toehold-mediated displacement. A third kind of replication in viruses and viroids is rolling-circle replication which occurs via strand-displacement on a circular template. Rolling-circle replication does not require environmental cycling and is not prevented by toehold-mediated displacement. Rolling-circle replication is therefore expected to occur non-enzymatically and is a likely starting point for the evolution of polymerase-catalysed replication.
Dendrobium viroid, a new monocot-infecting apscaviroid
2020, Virus Research
Citation Excerpt :
They also share a central conserved region (CCR) that contains two sets of conserved nucleotides flanked by inverted repeats that can assume an alternative hairpin conformation (hairpin I) which plays a major role in replication (McInnes and Symons, 1991; Gas et al., 2007). These viroids also possess either a terminal conserved region (TCR) or terminal conserved hairpin (TCH) (Keese and Symons, 1985; Flores et al., 1997). To be considered as a novel species, a viroid-like circular RNA molecule must i) contain certain conserved sequence or structural regions/motifs, ii) be capable of autonomous replication, and iii) exhibit less than 90% sequence similarity to known viroids and differ in at least one biological property (Owens et al., 2011; Verhoeven et al., 2013; Di Serio et al., 2014).
Viroids are small circular RNA molecules which have been found to infect many dicot species. Only coconut cadang-cadang viroid and coconut tinangaja viroid have been reported so far to infect a monocot (coconut). Data mining in silico has proven an efficient approach to identify new viruses/viroids, and a systematic screen of public transcriptomic data revealed a 648 nucleotides (nt) sequence potentially representing a novel viroid-like RNA in a transcriptome shotgun assembly from Dendrobium officinale. This sequence contained two central conserved regions (CCRs) characteristic of members of the genus Apscaviroid, indicating that the viroid-like RNA is 324 nt in length. The infectivity of dimeric RNA transcripts generated by in vitro transcription of a synthetic cDNA, was demonstrated by directly injecting into the stems of young Dendrobium officinale plants. The presence of this novel viroid, tentatively designated as Dendrobium viroid (DVd), in the inoculated plants was confirmed by 2D-PAGE together with northern hybridization. DVd is predicted to have a rod-like secondary structure containing a CCR and a terminal conserved region (TCR), and phylogenetic analysis shows that it groups with the known members of the genus Apscaviroid. It is most closely related to citrus viroid V (56% nt identity). A field survey revealed a low DVd incidence (0.96%) in Dendrobium species in China. To our best knowledge, DVd is the only viroid known to infect orchids and the third one from monocotyledonous plants.
Identification of a viroid-like RNA in a lychee Transcriptome Shotgun Assembly
2017, Virus Research
Citation Excerpt :
Note also that the sequence of the TCR is identical to those found in CVd VI and PVd 2, except two nucleotide mutations (Fig. 2B). All viroids in the family Pospiviroidae can form an alternative, metastable structural element known as “hairpin I” (HPI), which includes the upper strand of the CCR together with flanking inverted repeats (Flores et al., 1997; Keese and Symons, 1985). Formation of the HPI can promote the cleavage that generates the oligomeric (+) RNA intermediates during replication.
In the course of a systematic screen of plant transcriptomic data, the sequence of a novel viroid-like RNA was identified in four contigs in a recent Transcriptome Shotgun Assembly (TSA) from lychee in China. Portions of this sequence are closely related to the central conserved region (CCR) and terminal conserved region (TCR) present in members of the genus Apscaviroid, sequences that are important criteria for viroid classification. RT-PCR with two divergent adjacent primers amplified the full 304 nucleotide sequence of this viroid-like RNA which can be folded into the rod-like secondary structure that is a typical feature of viroids in the family Pospiviroidae. Northern-blot hybridization following denaturing PAGE and sequential polyacrylamide gel electrophoresis (sPAGE) revealed the presence of both circular and linear forms of the viroid-like RNA in lychee leaf tissue. Phylogenetic analysis indicates that this RNA groups with known members of the genus Apscaviroid with a maximum pairwise sequence identity of <62%. Field surveys revealed the presence of this viroid-like RNA in most lychee samples collected in China; however, it was not found in the accessions in a germplasm collection of lychees that originated from a wide range of other countries. None of the four herbaceous hosts and one woody host tested were susceptible to infection with the lychee viroid-like RNA via agroinoculation and RNA inoculation. The provisional name lychee viroid-like RNA (LVd-like RNA) is proposed for this tentative new species in the genus Apscaviroid.
Viroid Taxonomy
2017, Viroids and Satellites
The International Committee on Virus Taxonomy (ICTV) is the organization responsible for establishing the rules to classify viroids into species, genera, and families, and ultimately to endorse viroid taxonomy. The ICTV recently called for more stringent rules to create new virus and viroid species, which must be based on at least two independent criteria. This chapter discusses the resulting implications and presents an updated viroid classification scheme that takes into account the identification of new viroids by next-generation sequencing and bioinformatics tools, which ICTV may finally accept as new species.
Apscaviroids Infecting Grapevine
2017, Viroids and Satellites
Four apscaviroids (family Pospiviroidae), grapevine yellow speckle viroids 1 and 2 (GYSVd-1 and -2), Australian grapevine viroid (AGVd), and grapevine latent viroid (GLVd) infect grapevines. Apscaviroids are phylogenetically classified into two major subclades, one comprising GYSVd-1 and -2, the other comprising apple scar skin viroid and GLVd. GYSVd-1 and -2 may induce symptoms in the field in Australia, but are rarely symptomatic elsewhere. GYSVd-1 and -2 are symptomatic in cv. “Chardonnay” during hotter years, but asymptomatic in milder years. Unlike GYSVd-1 and -2, AGVd is asymptomatic in grapevine but symptomatic in tomato, cucumber, and other herbaceous experimental hosts and is apparently very stable both structurally and phylogenetically. For example, full-length sequences of GYSVd-1 and AGVd have been recovered from a 10-year old bottled Cabernet Sauvignon wine. GLVd has been discovered in China and there is no report on its occurrence in other vine growing areas of the world.

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^☆: R. S. Fraser, Ed.

¹: To whom correspondence and reprint requests should be addressed.

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Regular ArticleViroids: The Noncoding Genomes☆

Abstract

Virology

J. Mol. Biol.

Plant Sci.

Virology

Virology

Virology

Virology

Virology

Virology

Trends Microbiol.

Virology

Virology

Virology

Virology

The Viroids

Viroids and Viroid-like Pathogens

Viroids and related pathogenic agents

Semin. Virol.

The intriguing viroids and virusoids: What is their information content and how did they evolve?

Mol. Plant-Microbe Interact.

Viroids: From thermodynamics to cellular structure and function

Mol. Plant-Microbe Interact.

Origin and evolution of viroids and viroid-like satellite RNAs

Virus Genes

Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures

Proc. Natl. Acad. Sci. USA

A scheme for viroid classification

Intervirology

Phylogeny of viroids, viroid-like satellite RNAs, and the viroidlike domain of hepatitis δ virus RNA

Proc. Natl. Acad. Sci. USA

Grapevine yellow speckle viroid: Structural features of a new viroid group

Nucleic Acids Res.

Primary and secondary structure of a new viroid ‘species’ (CbVd 1) present in theColeus blumei

Nucleic Acids Res.

In vitroColeus blumeiin vivo

J. Gen. Virol.

The molecular structure of hop latent viroid (HLV), a new viroid occurring worldwide in hops

Nucleic Acids Res.

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

Nucleic Acids Res.

Plus and minus RNAs of peach latent mosaic viroid self cleavein vitro

Proc. Natl. Acad. Sci. USA

Viroid RNAs of the cadang-cadang disease of coconuts

Nature

Regular Article
Viroids: The Noncoding Genomes☆