Mexican papita viroid: putative ancestor of crop viroids

Viroid and viroid-like elements in plants and plant-associated microbiota: a new layer of biodiversity for plant holobionts

The functional relevance of plant-associated microorganisms is theoretically framed within the holobiont concept. The role of viruses in plant holobionts is being recognized both for their direct effects when hosted in plants (cryptic plant viruses) and for their indirect effects when infecting microorganisms associated with plants in tripartite interactions (e.g. mycoviruses and bacteriophages). We argue that viroids, the smallest infectious agents typically infecting only plant hosts, must also be included in plant holobiont studies. The same applies to the recently discovered large number of viroid-like elements infecting hosts of other life kingdoms that are closely associated with plants. Here we also describe in depth the diversity of such viroid-like elements and their initial functional characterization in plant-associated fungi.

High-Throughput Sequencing Reveals New Viroid Species in Opuntia in Mexico

In the main cactus pear (Opuntia ficus-indica)-producing region in the State of Mexico, fruit production occupies the largest cultivated area with 15,800 ha, while 900 ha are cultivated for edible young Opuntia pads ("nopalitos") which are consumed as vegetables. Two composite samples consisting of cladodes of plants for fruit production (n = 6) and another of "nopalitos" (n = 6) showing virus-like symptoms were collected. Both sample sets were subjected to high-throughput sequencing (HTS) to identify the viruses and viroids. The HTS results were verified using RT-PCR and Sanger sequencing. Subsequently, 86 samples including cladodes from "nopalitos", plants for fruit production, xoconostles, and some wild Opuntia were analyzed via RT-PCR with specific primers for the viruses and viroids previously detected via HTS. Three viruses were discovered [Opuntia virus 2 (OV2), cactus carlavirus 1 (CCV-1), and Opuntia potexvirus A (OPV-A)], along with a previously reported viroid [Opuntia viroid 1 (OVd-1)]. Additionally, two new viroids were identified, provisionally named the Mexican opuntia viroid (MOVd, genus Pospiviroid) and Opuntia viroid 2 (OVd-2, genus Apscaviroid). A phylogenetic analysis, pairwise identity comparison, and conserved structural elements analysis confirmed the classification of these two viroids as new species within the Pospiviroidae family. This is the first report of a pospiviroid and two apscaviroids infecting cactus pears in the world. Overall, this study enhances our understanding of the virome associated with cactus pears in Mexico.

A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield

Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.

Mexico: A Landscape of Viroid Origin and Epidemiological Relevance of Endemic Species

Viroids are single-stranded, circular RNA molecules (234-406 nt) that infect a wide range of crop species and cause economic losses in agriculture worldwide. They are characterized by the existence of a population of sequence variants, attributed to the low fidelity of RNA polymerases involved in their transcription, resulting in high mutation rates. Therefore, these biological entities exist as quasispecies. This feature allows them to replicate within a wide range of host plants, both monocots and dicots. Viroid hosts include economically important crops such as tomato, citrus, and fruit trees such as peach and avocado. Given the high risk of introducing viroids to viroid disease-free countries, these pathogens have been quarantined globally. As discussed herein, Mexico represents a geographical landscape of viroids linked to their origin and comprises considerable biodiversity. The biological features of viroid species endemic to Mexico are highlighted in this communication. In addition, we report the phylogenetic relationships among viroid and viroid strains, their economic impact, geographical distribution, and epidemiological features, including a broad host range and possible long-distance, seed, or insect-mediated transmission. In summary, this review could be helpful for a better understanding of the biology of viroid diseases and future programs on control of movement and spread to avoid economic losses in agricultural industries.

Pospiviroid Infection of Tomato Regulates the Expression of Genes Involved in Flower and Fruit Development

Viroids are unencapsidated, single-stranded, covalently-closed circular, highly structured, noncoding RNAs of 239–401 nucleotides that cause disease in several economically important crop plants. In tomato (Solanum lycopersicum cv. Rutgers), symptoms of pospiviroid infection include stunting, reduced vigor, flower abortion, and reduced size and number of fruits, resulting in significant crop losses. Dramatic alterations in plant development triggered by viroid infection are the result of differential gene expression; in our study, we focused on the effect of tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) infection on gene networks associated with the regulation of flower and fruit development. The expression of several of the genes were previously reported to be affected by viroid infection, but two genes not previously studied were included. Changes in gene expression of SlBIGPETAL1 (bHLH transcription factor) and SlOVA6 (proline-like tRNA synthetase) are involved in petal morphology and fertility, respectively. Expression of SlOVA6 was down-regulated in flowers of TPMVd- and MPVd-infected plants, while expression of SlBIGPETAL1 was up-regulated in flowers. Up-regulation of SlBIGPETAL1 and down-regulation of SlOVA6 were positively correlated with symptoms such as reduced petal size and flower abortion. Expression analysis of additional tomato genes and a prediction of a global network association of genes involved in flower and fruit development and impacted by viroid infection may further elucidate the pathways underlying viroid pathogenicity.

Classification of the Pospiviroidae based on their structural hallmarks

The simplest known plant pathogens are the viroids. Because of their non-coding single-stranded circular RNA genome, they depend on both their sequence and their structure for both a successful infection and their replication. In the recent years, important progress in the elucidation of their structures was achieved using an adaptation of the selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) protocol in order to probe viroid structures in solution. Previously, SHAPE has been adapted to elucidate the structures of all of the members of the family Avsunviroidae, as well as those of a few members of the family Pospiviroidae. In this study, with the goal of providing an entire compendium of the secondary structures of the various viroid species, a total of thirteen new Pospiviroidae members were probed in solution using the SHAPE protocol. More specifically, the secondary structures of eleven species for which the genus was previously known were initially elucidated. At this point, considering all of the SHAPE elucidated secondary structures, a classification system for viroids in their respective genera was proposed. On the basis of the structural classification reported here, the probings of both the Grapevine latent viroid and the Dahlia latent viroid provide sound arguments for the determination of their respective genera, which appear to be Apscaviroid and Hostuviroid, respectively. More importantly, this study provides the complete repertoire of the secondary structures, mapped in solution, of all of the accepted viroid species reported thus far. In addition, a classification scheme based on structural hallmarks, an important tool for many biological studies, is proposed.

A single base pair in the right terminal domain of tomato planta macho viroid is a virulence determinant factor on tomato

Tomato planta macho viroid (TPMVd), including isolates previously designated as Mexican papita viroid (MPVd), causes serious disease on tomatoes in North America. Two predominant variants, sharing 93.8% sequence identity, incited distinct severe (MPVd-S) or mild (MPVd-M) symptoms on tomato. To identify virulence determinant factor, a series of chimeric infectious clones were generated using synthetic DNA approach to progressively replace each structural domain between the two variants. In bioassays on tomato 'Rutgers', three chimeras containing Terminal Left and Pathogenicity (MPVd-H1), Central (MPVd-H2), or Variable (MPVd-H3) of MPVd-S, incited mild to intermediate symptoms. However, a chimera containing Terminal Right (T_R) of MPVd-S (MPVd-H4) incited severe symptoms. Only one base-pair mutation in the T_R domain between MPVd-M (₁₇₆U:A₁₈₅) and MPVd-S (₁₇₄G:C₁₈₃) was identified. A reciprocal mutant (MPVd-H5) rendered the chimeric viroid mild on tomato. This single base-pair in the T_R domain was determined as the virulence determinant factor for TPMVd.

Current status of viroid taxonomy

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 next-generation sequencing and bioinformatics for known and previously unrecognized viroids.

Mexican papita viroid and tomato planta macho viroid belong to a single species in the genus Pospiviroid

Tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) are two closely related (>90% sequence identity) members of the genus Pospiviroid. Their current status as members of separate species is based upon the reported ability of TPMVd to replicate in Gomphrena globosa and the inability of this viroid to evoke flower break in N. glutinosa. Characterization of a viroid recently isolated from diseased tomato plants grown in Mexico (identical to GenBank accession GQ131573) casts doubt on this earlier report and indicates that these viroids should be classified as members of a single species. Giving priority to the older name, we propose including both of these viroids in the current species Tomato planta macho viroid.

High stability of original predominant pospiviroid genotypes upon mechanical inoculation from ornamentals to potato and tomato

Eleven pospiviroid isolates from ornamental plants and one from pepper were successfully transmitted to potato and tomato by mechanical inoculation. All isolates with characteristic predominant genotypes were inoculated to a series of potato and tomato plants and propagated for up to four passages. In total, 385 nucleotide sequences were determined, in which 17 new predominant genotypes were identified with minimal differences to the original predominant genotype. In addition, in the original ornamental hosts, only one of eleven predominant pospiviroid genotypes had changed during the experiments over a period of 2 years. These results confirm the high stability of predominant pospiviroid genotypes.

Potato spindle tuber viroid: the simplicity paradox resolved?

TAXONOMY

Potato spindle tuber viroid (PSTVd) is the type species of the genus Posipiviroid, family Pospiviroidae. An absence of hammerhead ribozymes and the presence of a 'central conserved region' distinguish PSTVd and related viroids from members of a second viroid family, the Avsunviroidae.

PHYSICAL PROPERTIES

Viroids are small, unencapsidated, circular, single-stranded RNA molecules which replicate autonomously when inoculated into host plants. Because viroids are non-protein-coding RNAs, designation of the more abundant, highly infectious polarity strand as the positive strand is arbitrary. PSTVd assumes a rod-like, highly structured conformation that is resistant to nuclease degradation in vitro. Naturally occurring sequence variants of PSTVd range in size from 356 to 361 nt. HOSTS AND SYMPTOMS: The natural host range of PSTVd-cultivated potato, certain other Solanum spp., and avocado-appears to be quite limited. Foliar symptoms in potato are often obscure, and the severity of tuber symptoms (elongation with the appearance of prominent bud scales/eyebrows and growth cracks) depends on both temperature and length of infection. PSTVd has a broad experimental host range, especially among solanaceous species, and strains are classified as mild, intermediate or severe based upon the symptoms observed in sensitive tomato cultivars. These symptoms include shortening of internodes, petioles and mid-ribs, severe epinasty and wrinkling of the leaves, and necrosis of mid-ribs, petioles and stems.

Eggplant latent viroid, the candidate type species for a new genus within the family Avsunviroidae (hammerhead viroids)

Viroids, small circular RNAs that replicate independently and in most cases incite diseases in plants, are classified into the families Pospiviroidae, composed of species with a central conserved region (CCR) and without hammerhead ribozymes, and Avsunviroidae, composed of three members lacking CCR but able to self-cleave in both polarity strands through hammerhead ribozymes. Here we report the biological and molecular properties of Eggplant latent viroid (ELVd). Purified circular ELVd induces symptomless infections when inoculated into eggplant seedlings. ELVd can be transmitted horizontally and through seed. Sequencing 10 complete cDNA clones showed that ELVd is a circular RNA of 332 to 335 nucleotides with high variability. This RNA can adopt a quasi-rod-like secondary structure of minimal free energy and alternative foldings that permit formation of stable hammerhead structures in plus and minus strands. The ribozymes are active in vitro and, most likely, in vivo. Considering the ELVd properties to be intermediate between those of the two genera of family Avsunviroidae, we propose ELVd as the type species of a third genus with the name ELAVIROID:

A new structural motif in the left terminal domain of large viroids identified by covariation analysis

Sequence alignment of non-hammerhead viroids (Pospiviroidae) reveals that they can be divided into large and small viroids. Covariation analysis of these groups provides evidence for a rod-like secondary structure, but also for two proposed suboptimal structures, namely hairpin I and a bifurcation in the left terminus of large viroids. The strongest covariation within the branched T1 domain of all large Pospiviroidae indicates a new tertiary interaction, resulting in a double-pseudoknot within the (+) strand or an additional hairpin in the (-) strand. The structural element is expected to play a role in the viroid's life cycle.

Tomato chlorotic dwarf viroid: an evolutionary link in the origin of pospiviroids

Over 40 isolates of potato spindle tuber viroid (PSTVd) have been reported from potato, other Solanum species and greenhouse tomato. These isolates have sequence similarities in the range 95-99%. A viroid which caused chlorotic leaves and severe dwarfing of plants in greenhouse tomato crops was detected. The viroid was found to hybridize readily with PSTVd probes. It migrated faster than PSTVd in return-polyacrylamide gel electrophoresis and was not amplified in RT-PCR by a primer pair based on the lower strand of the central conserved region of PSTVd. Nucleotide sequencing of the viroid indicated that it is a circular RNA of 360 nt, with less than 90% sequence similarities with PSTVd isolates. The Variable domain (V) has less than 60% and the Terminal Right domain less than 90% sequence similarity, while the remainder of the molecule has greater than 97% similarity with PSTVd. Because of its less-than 90% sequence similarities, unique V domain, lack of seed-transmission and lack of cross-protection by PSTVd, the viroid from tomato is proposed to be a distinct viroid species (tomato chlorotic dwarf viroid; TCDVd) which also differs from two viroids infecting tomato in nature. TCDVd may be an evolutionary link in the development of crop viroids, with Mexican papita viroid as the ancestral viroid.

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.

Specific RNA self-cleavage in coconut cadang cadang viroid: potential for a role in rolling circle replication

The rolling circle replication of the small, single-stranded viroid RNAs requires a specific processing reaction to produce monomeric RNAs that are ligated into the final circular form. For avocado sunblotch viroid, peach latent mosaic viroid, and chrysanthemum chlorotic mottle viroid, the hammerhead self-cleavage reaction is considered to provide this processing reaction. We have searched for a similar type of reaction in the 246-nt coconut cadang cadang viroid, the smallest viroid of the 24-member potato spindle tuber viroid (PSTV) group. RNA transcripts prepared from the cloned central or C domain of this viroid self-cleaved specifically after denaturation with methylmercuric hydroxide followed by incubation in the presence of spermidine but in the absence of added magnesium ions. The unique cleavage site was located in the bottom strand of the C domain within a potential hairpin structure that is conserved within members of all three subgroups of the PSTV group of viroids.

Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm

The folding pathways of viroid RNAs were studied using computer simulations by the genetic algorithm for RNA folding. The folding simulations were performed for PSTVd RNAs of both polarities, using the wild-type sequence and some previously known mutants with suggested changes in the stable or metastable structures. It is shown that metastable multihairpin foldings in the minus strand replicative intermediates are established due to the specific folding pathway that ensures the absence of the most stable rod-like structure. Simulations of the PSTVd minus strand folding during transcription reveal a metastable hairpin, formed in the left terminal domain region of the PSTVd. Despite high sequence variability, this hairpin is conserved in all known large viroids of both subgroups of PSTVd type, and is presumably necessary to guide the folding of the HPII hairpin which is functional in the minus strand. The folding simulations are able to demonstrate the changes in the balance between metastable and stable structures in mutant PSTVd RNAs. The stable rod-like structure of the circular viroid (+) RNA is also folded via a dynamic folding pathway. Furthermore, the simulations show that intermediate steps in the forced evolution of a shortened PSTVd replicon may be reconstructed by a mechanistic model of different folding pathway requirements in plus- and minus-strand RNAs. Thus the formation of viroid RNA structure strongly depends on dynamics of competition between alternative RNA structures. This also suggests that the replication efficiency of viroid sequences may be estimated by a simulation of the folding process.