SEARCH · PubMed Health

Results for “Viroids”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed1988

Coconut tinangaja viroid: sequence homology with coconut cadang-cadang viroid and other potato spindle tuber viroid related RNAs.

The nucleotide sequence of two variants of coconut tinangaja viroid (CTiV) were obtained. Both sequence variants are 254 nucleotide residues in size but differ in sequence at two positions. In comparisons with other viroids, the sequences and proposed secondary structure of CTiV show most homology with the 246 nucleotide residue variant of coconut cadang-cadang viroid (CCCV (246]. Several regions throughout the rod-like molecules of CTiV show significant structural and sequence homology with other RNAs related to potato spindle tuber viroid. These homologies include a centrally positioned uridine bulged G:C helix and a 17 nucleotide residue sequence found in common with hop stunt viroid in the left-hand end loop of both viroids.

Base Sequence↗

PubMed1989

Grapevine viroid 1B, a new member of the apple scar skin viroid group contains the left terminal region of tomato planta macho viroid.

GV1B is one of five viroids that have recently been purified from grapevines. GV1B has now been sequenced and its 363 nucleotide residues can potentially form the typical rod-like structure of viroids with 67% of nucleotides base-paired. GV1B has highest sequence similarity with grapevine yellow speckle viroid (GYSV; 73%) and has a central sequence which is conserved in GYSV and apple scar skin viroid (ASSV) which have been reported to constitute the ASSV group. Therefore, we have placed GV1B into the ASSV group. GV1B contains a direct repeat sequence at the terminal portions of its T1 and T2 regions. GV1B also contains a sequence of 69 nucleotides in the terminal portion of its T1 region which is almost identical to the corresponding region in tomato planta macho viroid (TPMV). This provides further evidence of the importance of RNA recombination in viroid evolution.

Base Sequence↗

PubMed2001

Characterization of a new citrus viroid species tentatively termed Citrus viroid OS.

A new viroid was obtained from a viroid sample, named 'OS', collected from a citrus plant. The viroid consists of 330-331 nucleotides, contains the central conserved region (CCR) characteristic of the genus Apscaviroid, and has the highest sequence similarity (only 68%) with Citrus III viroid (CVd-III) among known viroids. This viroid, by itself, caused only mild petiole necrosis and characteristically very mild leaf bending in Arizona 861-S1 Etrog citrons (Citrus medica L.), the degree of which differed from that induced by other citrus viroids. This viroid could be a new citrus viroid species belonging to the genus Apscaviroid; for convenience, it was tentatively named Citrus viroid OS (CVd-OS) after the original sample. CVd-OS has chimeric features related to other viroids. In particular, CVd-OS has high sequence similarity with CVd-III and Apple dimple fruit viroid in the putative central and terminal left domains, including a duplicative sequence from the lower CCR of the genus Pospiviroid in the left terminus. Further, CVd-OS shares high sequence similarity with Citrus exocortis viroid (CEVd) in the lower strand of the putative variable and terminal right domains, including the sequence identical to that of the right termini of CEVd and of Citrus IV viroid.

Base Sequence↗

PubMed1992

A viroid from Nematanthus wettsteinii plants closely related to the Columnea latent viroid.

A viroid was isolated from symptomless Nematanthus wettsteinii plants using the return-PAGE method for analysis of low M(r) nucleic acids. The RNA was transmitted to tomato, three cultivars of potato, and Scopolia sinensis plants by mechanical inoculation or by grafting. Infected solanaceous plants developed symptoms similar to those caused by potato spindle tuber viroid (PSTVd). The Nematanthus viroid consists of 372 nucleotides, 214 G+C, 158 A+U, with a G+C/A+U ratio of 1.35. One of seven cDNA clones showed a sequence heterogeneity (G to A) at position 73. The most stable secondary structure of this viroid has 78 G:C, 37 A:U and 11 G:U base pairs with a minimum free energy of -456.9 kJ. The viroid is closely related to the 370 nucleotide Columnea latent viroid. The Nematanthus viroid possesses regions of 100% sequence identity with six viroids belonging to the PSTVd and apple scar skin viroid groups. The viroid also replicated in tomato plants when mixed with PSTVd. Tomato plants were cross-protected against PSTVd when preinfected with the viroid from N. wettsteinii.

Base Sequence↗

PubMed1996

A viroid from Brunfelsia undulata closely related to the Columnea latent viroid.

A viroid was isolated from symptomless Brunfelsia undulata plants using the bidirectional PAGE method for analysis of small circular RNA molecules. The viroid was transmitted to tomato by mechanical inoculation. Infected tomato plants developed symptoms similar to those caused by intermediate strains of potato spindle tuber viroid (PSTVd). Cloning and sequencing revealed that the viroid from Brunfelsia undulata is closely related to the Columnea latent viroid (CLVd). Therefore, the new viroid sequence variant has been named CLVd-B. The Brunfelsia viroid CLVd-B consists of 373 nucleotides, 215 G + C, 158 A + U with a GC content of 57.6%. The most stable rod-like secondary structure of this viroid has 80 G:C, 39 A:U and 11 G:U base pairs with a minimum free energy of -157.2 kcal/mol (-657.1 kJ/mol). The sequence similarity of the right terminal domain of CLVd-B and of tomato apical stunt viroid (TASVd) is higher than the sequence similarity of these domains comparing CLVd and TASVd.

Base Sequence↗

PubMed1996

A viroid from Solanum pseudocapsicum closely related to the tomato apical stunt viroid.

A viroid was isolated from symptomless Solanum pseudocapsicum cultivar (cv) 'New Patterson' plants using the bidirectional PAGE method for analysis of small circular RNA molecules. The viroid was transmitted to tomato by mechanical inoculation. Infected tomato plants developed symptoms similar to those caused by potato spindle tuber viroid (PSTVd). Cloning and sequencing revealed that the viroid from Solanum pseudocapsicum is closely related to the tomato apical stunt viroid (TASVd). Therefore, the new viroid sequence variant has been named TASVd-S. The circular RNA of TASVd-S consists of 360 nucleotides which can potentially form a rod-like structure with a high degree of base-pairing like all the other known viroids. The nucleotide composition is 99 G, 72 A, 101 C and 88 U, corresponding to 200 G + C, 160 A + U with a GC content of 55.6%. In total 71% of the residues are base-paired and the basepaired residues consist of 73 G:C (57%), 43 A:U (34%) and 11 G:U (9%) base pairs. The most stable rod-like secondary structure of this viroid has 80 G:C, 39 A:U and 11 G:U base pairs with a minimum free energy of -147.5 kcal/mol (-616.6 kJ/mol). The sequence similarity of the left terminal (T1) domain of TASVd-S and the T1 domain of tomato planta macho viroid (TPMVd) is higher than the sequence similarity of these domains of TASVd-S and TASV-d.

Base Sequence↗

PubMed1988

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

A new viroid which does not seem to produce any symptoms of disease, and is therefore tentatively named hop latent viroid (HLV) was found to occur worldwide in hops. HLV proved to be infectious when mechanically inoculated onto viroid- and virus-free hops. The viroid nature of HLV was also substantiated by sequence analysis which revealed that HLV is a circular RNA consisting of 256 nucleotides, that can be arranged into the viroid-specific, rod-like secondary structure. HLV also contains the central conserved region typical for most of the presently known viroids. However HLV does not contain the viroid-specific oligo(A) stretch in the upper left part of its rod-like molecule. Because of this feature and a sequence similarity with the prototypes of the other viroid groups below 55%, HLV can be regarded as the first member of a new viroid group.

Base Sequence↗

PubMed1995

Origin and evolution of viroids and viroid-like satellite RNAs.

Viroids, the smallest and simplest agents of infectious disease, cause a number of economically important diseases of crop plants. Present evidence indicates that most of these diseases originated recently (in the 20th century) by chance transfer of viroids from endemically infected wild plants or by use of viroid-infected germplasm during plant breeding. Modern agricultural practices, such as widespread monoculture of genetically identical plants, and worldwide distribution of planting material, has made it possible for the pathogens to maintain themselves in the crop plants and to conquer new territories. Phylogenetic analysis of their nucleotide sequences indicates that viroids and satellite RNAs represent a monophyletic group, with all but the two self-cleaving viroids forming one cluster and the satellite RNAs another. The two self-cleaving viroids are phylogenetically distant from either cluster; they may represent ancestral forms. Results from site-directed mutagenesis experiments indicate that, upon exposure to selective pressures, viroids can evolve extremely rapidly, with another, fitter, component of the quasi-species often becoming dominant within days or weeks. This extreme plasticity of their nucleotide sequences establishes viroids as the most rapidly evolving biological system known.

Base Sequence↗

PubMed1996

Mexican papita viroid: putative ancestor of crop viroids.

The potato spindle tuber disease was first observed early in the 20th century in the northeastern United States and shown, in 1971, to be incited by a viroid, potato spindle tuber viroid (PSTVd). No wild-plant PSTVd reservoirs have been identified; thus, the initial source of PSTVd infecting potatoes has remained a mystery. Several variants of a novel viroid, designated Mexican papita viroid (MPVd), have now been isolated from Solanum cardiophyllum Lindl. (papita güera, cimantli) plants growing wild in the Mexican state of Aguascalientes. MPVd's nucleotide sequence is most closely related to those of the tomato planta macho viroid (TPMVd) and PSTVd. From TPMVd, MPVd may be distinguished on the basis of biological properties, such as replication and symptom formation in certain differential hosts. Phylogenetic and ecological data indicate that MPVd and certain viroids now affecting crop plants, such as TPMVd, PSTVd, and possibly others, have a common ancestor. We hypothesize that commercial potatoes grown in the United States have become viroid-infected by chance transfer of MPVd or a similar viroid from endemically infected wild solanaceous plants imported from Mexico as germplasm, conceivably from plants known to have been introduced from Mexico to the United States late in the 19th century in efforts to identify genetic resistance to the potato late blight fungus, Phytophthora infestans.

Base Sequence↗

PubMed1999

Viroids and the nature of viroid diseases.

In its methodology, the unexpected discovery of the viroid in 1971 resembles that of the virus by Beijerinck some 70 years earlier. In either case, a novel type of plant pathogen was recognized by its ability to penetrate through a medium with pores small enough to exclude even the smallest previously known pathogen: bacteria as compared with the tobacco mosaic agent; viruses as compared with the potato spindle tuber agent. Interestingly, one of the two methods used by Beijerinck, diffusion of the tobacco mosaic agent into agar gels, is conceptually similar to one method used to establish the size of the potato spindle tuber agent, namely polyacrylamide gel electrophoresis. Further work demonstrated that neither agent is an unusually small conventional pathogen (a microbe in the case of the tobacco mosaic agent; a virus in the case of the potato spindle tuber agent), but that either agent represents the prototype of a fundamentally distinct class of pathogen, the viruses and the viroids, respectively. With the viroids, this distinction became evident once their unique molecular structure, lack of mRNA activity, and autonomous replication had become elucidated. Functionally, viroids rely to a far greater extent than viruses on their host's biosynthetic systems: Whereas translation of viral genetic information is essential for virus replication, viroids are totally dependent on their hosts' transcriptional system and, in contrast to viruses, no viroid-coded proteins are involved. Because of the viroids' simplicity and extremely small size they approach more closely even than viruses Beijerinck's concept of a contagium vivum fluidum.

History, 20th Century↗

PubMed1988

Grapevine yellow speckle viroid: structural features of a new viroid group.

A single stranded circular RNA was isolated from grapevines infected with yellow speckle disease. The RNA which we have called grapevine yellow speckle viroid (GYSV), contains 367 nucleotide residues and has the potential to form the rod-like secondary structure characteristic of viroids. GYSV has 37% sequence homology with the recently described apple scar skin viroid (ASSV; 330 residues) and has some sequence homology with the viroids in the potato spindle tuber viroid (PSTV) group. The sequence of GYSV has characteristics which fit the structural domains described for the PSTV group. However, GYSV lacks the PSTV central conserved sequence. Instead, there is a conserved sequence in the central region of GYSV and ASSV which has the potential to form a stem loop configuration and a stable palindromic structure as does the central conserved region of the PSTV group. These structural features suggest there is a different central conserved region for GYSV and ASSV. The results support the viroid nature of GYSV and its inclusion into a separate viroid group which we suggest should be represented by ASSV.

Base Sequence↗

PubMed1989

Nucleotide sequence and proposed secondary structure of Columnea latent viroid: a natural mosaic of viroid sequences.

The Columnea latent viroid (CLV) occurs latently in certain Columnea erythrophae plants grown commercially. In potato and tomato, CLV causes potato spindle tuber viroid (PSTV)-like symptoms. Its nucleotide sequence and proposed secondary structure reveal that CLV consists of a single-stranded circular RNA of 370 nucleotides which can assume a rod-like structure with extensive base-pairing characteristic of all known viroids. The electrophoretic mobility of circular CLV under nondenaturing conditions suggests a potential tertiary structure. CLV contains extensive sequence homologies to the PSTV group of viroids but contains a central conserved region identical to that of hop stunt viroid (HSV). CLV also shares some biological properties with each of the two types of viroids. Most probably, CLV is the result of intracellular RNA recombination between an HSV-type and one or more PSTV-type viroids replicating in the same plant.

Base Composition↗

PubMed1990

Australian grapevine viroid--evidence for extensive recombination between viroids.

Australian grapevine viroid (AGV, 369 residues) is a novel viroid with less than 50% sequence similarity with any known viroid. Nevertheless its entire sequence can be divided into regions, each with a high sequence similarity with segments from one of citrus exocortis, potato spindle tuber, apple scar skin, and grapevine yellow speckle viroids. AGV contains the entire central conserved region of the apple scar skin viroid group and is proposed as a member of this group. AGV appears to have originated from extensive RNA recombination involving other viroids. The vegetatively propagated grapevines which have been exposed to multiple viroid infections during their long history of cultivation may have allowed such recombination.

Base Sequence↗

PubMed1996

The molecular structure of Iresine viroid, a new viroid species from Iresine herbstii ('beefsteak plant').

A viroid was isolated from Iresine herbstii plants using the bidirectional PAGE method for analysis of small circular RNA molecules. The viroid was transmitted to viroid-free Iresine herbstii plants of the cultivar 'Aureoreticulata' by mechanical inoculation. Infected plants did not develop any symptoms. The new viroid species has been named Iresine viroid (IrVd). It is a member of the potato spindle tuber viroid group and consists of 370 nucleotides, 227 G+C, 143 A+U (GC content, 61.4%). The most stable rod-like secondary structure of this viroid has 86 G:C, 34 A:U and 12 G:U base pairs with a minimum free energy of -153.4 kcal/mol (-641.2 kJ/mol). The sequence and the position of the terminal conserved region (TCR) within the rod-like secondary structure of IrVd differ from the other known TCRs. The structure of the left terminal domain of IrVd may reflect the result of an intramolecular RNA recombination event.

Base Sequence↗

PubMed2005

Viroids and viroid-host interactions.

Although they induce symptoms in plants similar to those accompanying virus infections, viroids have unique structural, functional, and evolutionary characteristics. They are composed of a small, nonprotein-coding, single-stranded, circular RNA, with autonomous replication. Viroid species are clustered into the families Pospiviroidae and Avsunviroidae, whose members replicate (and accumulate) in the nucleus and chloroplast, respectively. Viroids replicate in three steps through an RNA-based rolling-circle mechanism: synthesis of longer-than-unit strands catalyzed by host RNA polymerases; processing to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes; and circularization. Within the initially infected cells, viroid RNA must move to its replication organelle, with the resulting progeny then invading adjacent cells through plasmodesmata and reaching distal parts via the vasculature. To carry out these movements, viroids must interact with host factors. The mature viroid RNA could be the primary pathogenic effector or, alternatively, viroids could exert their pathogenic effects via RNA silencing.

Host-Parasite Interactions↗

PubMed1988

Synthetic oligonucleotide hybridization probes to diagnose hop stunt viroid strains and citrus exocortis viroid.

Four species of synthetic oligonucleotide probes for the diagnosis of hop stunt viroid (HSV) and citrus exocortis viroid (CEV) were devised. Probe HSV-1 detected all the members of HSV group, such as HSV-hop, HSV-grapevine, HSV-cucumber, HSV-citrus and a viroid-like RNA isolated from plum trees affected by plum dapple fruit disease. Probe HSV-2 discriminated HSV-grapevine from the other members of HSV group. HSV-hop and HSV-grapevine consist of the same numbers of nucleotides, with only one nucleotide exchange. It was also shown that the two viroids were indistinguishable by their biological and physicochemical properties. However, by using probe HSV-2, HSV-hop and HSV-grapevine were apparently differentiated. Probe CEV-1 detected all the members of potato spindle tuber viroid (PSTV) group, such as PSTV, CEV and chrysanthemum stunt viroid (CSV). Probe CEV-2 discriminated CEV from the other members of PSTV group. It is thus emphasized that synthetic oligonucleotide probes are useful for the diagnosis of viroids and their related strains. It was discussed that the method can be used for the diagnosis of viruses and their related strains.

Base Sequence↗

PubMed1985

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.

Base Sequence↗

PubMed1997

Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes.

The causal agent of chrysanthemum chlorotic mottle (CChM) disease has been identified, cloned, and sequenced. It is a viroid RNA (CChMVd) of 398-399 nucleotides. In vitro transcripts with the complete CChMVd sequence were infectious and induced the typical symptoms of the CChM disease. CChMVd can form hammerhead structures in both polarity strands. Plus and minus monomeric CChMVd RNAs self-cleaved during in vitro transcription and after purification as predicted by these structures, which are stable and most probably act as single hammerhead structures as in peach latent mosaic viroid (PLMVd), but not in avocado sunblotch viroid (ASBVd). Moreover, the plus CChMVd hammerhead structure also appears to be active in vivo, because the 5' terminus of the linear plus CChMVd RNA isolated from infected tissue is that predicted by the corresponding hammerhead ribozyme. Both hammerhead structures of CChMVd display some peculiarities: the plus self-cleaving domain has an unpaired A after the conserved A9 residue, and the minus one has an unusually long helix II. The most stable secondary structure predicted for CChMVd is a branched conformation that does not fulfill the rod-like or quasi-rod-like model proposed for the in vitro structure of most viroids with the exception of PLMVd, whose proposed secondary structure of lowest free energy also is branched. The unusual conformation of CChMVd and PLMVd is supported by their insolubility in 2 M LiCl, in contrast to ASBVd and a series of representative non-self-cleaving viroids that are soluble under the same high salt conditions. These results support the classification of self-cleaving viroids into two subgroups, one formed by ASBVd and the other one by PLMVd and CChMVd.

Asteraceae↗