Existence in vivo of the loop E motif in potato spindle tuber viroid RNA

Conserved Motifs and Domains in Members of Pospiviroidae

In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family Pospiviroidae: their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of Pospiviroidae which were unknown in 1985. Indeed, individual members of Pospiviroidae consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders.

Progress in 50 years of viroid research-Molecular structure, pathogenicity, and host adaptation

Viroids are non-encapsidated, single-stranded, circular RNAs consisting of 246-434 nucleotides. Despite their non-protein-encoding RNA nature, viroids replicate autonomously in host cells. To date, more than 25 diseases in more than 15 crops, including vegetables, fruit trees, and flowers, have been reported. Some are pathogenic but others replicate without eliciting disease. Viroids were shown to have one of the fundamental attributes of life to adapt to environments according to Darwinian selection, and they are likely to be living fossils that have survived from the pre-cellular RNA world. In 50 years of research since their discovery, it was revealed that viroids invade host cells, replicate in nuclei or chloroplasts, and undergo nucleotide mutation in the process of adapting to new host environments. It was also demonstrated that structural motifs in viroid RNAs exert different levels of pathogenicity by interacting with various host factors. Despite their small size, the molecular mechanism of viroid pathogenicity turned out to be more complex than first thought.

Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA

While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system. This study identifies critical roles for G/U pairs in the survival of an infectious RNA, and increases understanding of structure-based regulation of replication and trafficking of pathogen and cellular RNAs.

In silico survey of the central conserved regions in viroids of the Pospiviroidae family for conserved asymmetric loop structures

Viroids are the smallest replicative pathogens, consisting of RNA circles (∼300 nucleotides) that require host machinery to replicate. Structural RNA elements recruit these host factors. Currently, many of these structural elements and the nature of their interactions are unknown. All Pospiviroidae have homology in the central conserved region (CCR). The CCR of potato spindle tuber viroid (PSTVd) contains a sarcin/ricin domain (SRD), the only viroid structural element with an unequivocal replication role. We assumed that every member of this family uses this region to recruit host factors, and that each CCR has an SRD-like asymmetric loop within it. Potential SRD or SRD-like motifs were sought in the CCR of each Pospiviroidae member as follows. Motif location in each CCR was predicted with MUSCLE alignment and Vienna RNAfold. Viroid-specific models of SRD-like motifs were built by superimposing noncanonical base pairs and nucleotides on a model of an SRD. The RNA geometry search engine FR3D was then used to find nucleotide groups close to the geometry suggested by this superimposition. Atomic resolution structures were assembled using the molecular visualization program Chimera, and the stability of each motif was assessed with molecular dynamics (MD). Some models required a protonated cytosine. To be stable within a cell, the pK_a of that cytosine must be shifted up. Constant pH-replica exchange MD analysis showed such a shift in the proposed structures. These data show that every Pospiviroidae member could form a motif that resembles an SRD in its CCR, and imply there could be undiscovered mimics of other RNA domains.

Dissecting the secondary structure of the circular RNA of a nuclear viroid in vivo: A "naked" rod-like conformation similar but not identical to that observed in vitro

With a minimal (250-400 nt), non-protein-coding, circular RNA genome, viroids rely on sequence/structural motifs for replication and colonization of their host plants. These motifs are embedded in a compact secondary structure whose elucidation is crucial to understand how they function. Viroid RNA structure has been tackled in silico with algorithms searching for the conformation of minimal free energy, and in vitro by probing in solution with RNases, dimethyl sulphate and bisulphite, and with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), which interrogates the RNA backbone at single-nucleotide resolution. However, in vivo approaches at that resolution have not been assayed. Here, after confirming by 3 termodynamics-based predictions and by in vitro SHAPE that the secondary structure adopted by the infectious monomeric circular (+) RNA of potato spindle tuber viroid (PSTVd) is a rod-like conformation with double-stranded segments flanked by loops, we have probed it in vivo with a SHAPE modification. We provide direct evidence that a similar, but not identical, rod-like conformation exists in PSTVd-infected leaves of Nicotiana benthamiana, verifying the long-standing view that this RNA accumulates in planta as a "naked" form rather than tightly associated with protecting host proteins. However, certain nucleotides of the central conserved region, including some of the loop E involved in key functions such as replication, are more SHAPE-reactive in vitro than in vivo. This difference is most likely due to interactions with proteins mediating some of these functions, or to structural changes promoted by other factors of the in vivo habitat.

Modelling the three-dimensional structure of the right-terminal domain of pospiviroids

Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding protein 1 (Virp1) is indispensable for replication of pospiviroids, the largest genus of viroids, in a host plant as well as in protoplasts. Virp1 is known to bind at two sites in the terminal right (TR) domain of pospiviroids; each site consists of a purine- (R-) and a pyrimidine- (Y-)rich motif that are partially base-paired to each other. Here we model the important structural features of the domain and show that it contains an internal loop of two Y · Y cis Watson-Crick/Watson-Crick (cWW) pairs, an asymmetric internal loop including a cWW and a trans Watson/Hoogsteen pair, and a thermodynamically quite stable hairpin loop with several stacking interactions. These features are discussed in connection to the known biological functions of the TR domain.

Structure and Associated Biological Functions of Viroids

Mature viroids consist of a noncoding, covalently closed circular RNA that is able to autonomously infect respective host plants. Thus, they must utilize proteins of the host for most biological functions such as replication, processing, transport, and pathogenesis. Therefore, viroids can be regarded as minimal parasites of the host machinery. They have to present to the host machinery the appropriate signals based on either their sequence or their structure. Here, we summarize such sequence and structural features critical for the biological functions of viroids.

Apple scar skin viroid naked RNA is actively transmitted by the whitefly Trialeurodes vaporariorum

Nucleic acid transfer between plants is a phenomenon which is likely to occur in many ways in nature. We report here the active transmission of Apple scar skin viroid (ASSVd) naked ssRNA species by the whitefly Trialeurodes vaporariorum (Tv). Not only the viroid RNA, its DNA form was also identified from the insect. The viroid transfer efficiency was enhanced with the help of Cucumis sativus Phloem protein 2 (CsPP2), a plant protein known to translocate viroid RNAs. This PP2/ASSVd complex is stably present in the viroid infected cucumber plants, as was identified with the help of immunological reaction. As viroid-like secondary structures are found in some plant RNAs, and PP2 is known to bind and translocate several RNAs, the results have huge implications in transfer of these RNA species between plants visited by the whitefly.

Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs

As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson–Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures – either global or local – determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs

Viroids are small, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic from cell to cell and from organ to organ to establish systemic infection. Viroids achieve nearly all of the biological functions by directly interacting with host cellular factors. Viroid replication, together with replication of human hepatitis delta virus, demonstrates the biological novelty and significance of RNA-dependent RNA polymerase activities of DNA-dependent RNA polymerases. Viroid systemic infection uncovers a new biological principle--the role of three-dimensional RNA structural motifs mediating RNA trafficking between specific cells. Viroid diseases are virtually the consequences of host gene regulation by noncoding RNAs. A viroid RNA has the highest in vivo mutation rate among all known nucleic acid replicons. The host range of many viroids is expanding, essentially as a result of continuing and fast evolution of noncoding sequences/structures to gain new biological functions. Here, I discuss recent progress in these areas, emphasizing the broad significance of viroid research to the discovery of fundamental biological principles.

Ribosomal protein L5 and transcription factor IIIA from Arabidopsis thaliana bind in vitro specifically Potato spindle tuber viroid RNA

Potato spindle tuber viroid (PSTVd) contains an element of tertiary structure -loop E- also present in eukaryotic 5S rRNA. The ribosomal protein L5 and transcription factor IIIA (TFIIIA) from Arabidopsis thaliana bind 5S rRNA in vitro and in vivo, mediating different functions that include nucleocytoplasmic transport and transcription activation, respectively. We show that A. thaliana L5 and TFIIIA also bind PSTVd (+) RNA in vitro with the same affinity as they bind 5S rRNA, whereas the affinity for a chloroplastic viroid is significantly lower. These two proteins might participate in the synthesis and delivery of PSTVd RNA in vivo.

VIROIDES, PEQUENOS RNAS PATOGÊNICOS CAPAZES DE REPLICAÇÃO AUTÔNOMA: MODELOS MOLECULARES PARA O ESTUDO DE INTERAÇÕES PATÓGENO-HOSPEDEIRO E EVOLUÇÃO

RESUMO Os viroides, apesar de serem constituídos por um pequeno RNA de fita simples, fortemente estruturado, circular, que não codifica proteínas, são capazes de se replicar de maneira autônoma em plantas superiores e causar doença interagindo diretamente com fatores do hospedeiro. Nesta revisão, serão apresentados e discutidos alguns dos mais recentes trabalhos envolvendo a interação de viroides com fatores do hospedeiro, incluindo aspectos relacionados à replicação, movimento e patogênese, além de suas características evolutivas. Nos últimos anos, alguns grupos de pesquisa têm se aventurado na busca por fatores do hospedeiro e mecanismos moleculares relacionados ao ciclo infeccioso dos viroides, tentando desvendar como esses pequenos RNAs interagem com o hospedeiro induzindo sintomas. Os viroides não codificam proteínas supressoras de silenciamento e, portanto, devem garantir sua existência utilizando estratégias baseadas em sua estrutura secundária, na compartimentalização em organelas, associação com fatores do hospedeiro e eficiência na replicação. A complexidade do ciclo infeccioso desses minúsculos RNAs indica que muitas interações desses patógenos com fatores do hospedeiro ainda devem ser identificadas.

Viroid replication: rolling-circles, enzymes and ribozymes

Viroids, due to their small size and lack of protein-coding capacity, must rely essentially on their hosts for replication. Intriguingly, viroids have evolved the ability to replicate in two cellular organella, the nucleus (family Pospiviroidae) and the chloroplast (family Avsunviroidae). Viroid replication proceeds through an RNA-based rolling-circle mechanism with three steps that, with some variations, operate in both polarity strands: i) synthesis of longer-than-unit strands catalyzed by either the nuclear RNA polymerase II or a nuclear-encoded chloroplastic RNA polymerase, in both instances redirected to transcribe RNA templates, ii) cleavage to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes embedded in both polarity strands, while in the family Pospiviroidae the oligomeric RNAs provide the proper conformation but not the catalytic activity, and iii) circularization. The host RNA polymerases, most likely assisted by additional host proteins, start transcription from specific sites, thus implying the existence of viroid promoters. Cleavage and ligation in the family Pospiviroidae is probably catalyzed by an RNase III-like enzyme and an RNA ligase able to circularize the resulting 5′ and 3′ termini. Whether a chloroplastic RNA ligase mediates circularization in the family Avsunviroidae, or this reaction is autocatalytic, remains an open issue.

The biology of viroid-host interactions

Viroids are single-stranded, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic cell-to-cell through plasmodesmata and long distance through the phloem to establish systemic infection. They also cause diseases in certain hosts. All functions are mediated directly by the viroid RNA genome or genome-derived RNAs. I summarize recent advances in the understanding of viroid structures and cellular factors enabling these functions, emphasizing conceptual developments, major knowledge gaps, and future directions. Newly emerging experimental systems and research tools are discussed that are expected to enable significant progress in a number of key areas. I highlight examples of groundbreaking contributions of viroid research to the development of new biological principles and offer perspectives on using viroid models to continue advancing some frontiers of life science.

Processing of nuclear viroids in vivo: an interplay between RNA conformations

Replication of viroids, small non-protein-coding plant pathogenic RNAs, entails reiterative transcription of their incoming single-stranded circular genomes, to which the (+) polarity is arbitrarily assigned, cleavage of the oligomeric strands of one or both polarities to unit-length, and ligation to circular RNAs. While cleavage in chloroplastic viroids (family Avsunviroidae) is mediated by hammerhead ribozymes, where and how cleavage of oligomeric (+) RNAs of nuclear viroids (family Pospiviroidae) occurs in vivo remains controversial. Previous in vitro data indicated that a hairpin capped by a GAAA tetraloop is the RNA motif directing cleavage and a loop E motif ligation. Here we have re-examined this question in vivo, taking advantage of earlier findings showing that dimeric viroid (+) RNAs of the family Pospiviroidae transgenically expressed in Arabidopsis thaliana are processed correctly. Using this methodology, we have mapped the processing site of three members of this family at equivalent positions of the hairpin I/double-stranded structure that the upper strand and flanking nucleotides of the central conserved region (CCR) can form. More specifically, from the effects of 16 mutations on Citrus exocortis viroid expressed transgenically in A. thaliana, we conclude that the substrate for in vivo cleavage is the conserved double-stranded structure, with hairpin I potentially facilitating the adoption of this structure, whereas ligation is determined by loop E and flanking nucleotides of the two CCR strands. These results have deep implications on the underlying mechanism of both processing reactions, which are most likely catalyzed by enzymes different from those generally assumed: cleavage by a member of the RNase III family, and ligation by an RNA ligase distinct from the only one characterized so far in plants, thus predicting the existence of at least a second plant RNA ligase.

A genomic map of viroid RNA motifs critical for replication and systemic trafficking

RNA replication and systemic trafficking play significant roles in developmental regulation and host-pathogen interactions. Viroids are the simplest noncoding eukaryotic RNA pathogens and genetic units that are capable of autonomous replication and systemic trafficking and offer excellent models to investigate the role of RNA structures in these processes. Like other RNAs, the predicted secondary structure of a viroid RNA contains many loops and bulges flanked by double-stranded helices, the biological functions of which are mostly unknown. Using Potato spindle tuber viroid infection of Nicotiana benthamiana as the experimental system, we tested the hypothesis that these loops/bulges are functional motifs that regulate replication in single cells or trafficking in a plant. Through a genome-wide mutational analysis, we identified multiple loops/bulges essential or important for each of these biological processes. Our results led to a genomic map of viroid RNA motifs that mediate single-cell replication and systemic trafficking, respectively. This map provides a framework to enable high-throughput studies on the tertiary structures and functional mechanisms of RNA motifs that regulate viroid replication and trafficking. Our model and approach should also be valuable for comprehensive investigations of the replication and trafficking motifs in other RNAs.

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.

Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking

Vascular entry is a decisive step for the initiation of long-distance movement of infectious and endogenous RNAs, silencing signals and developmental/defense signals in plants. However, the mechanisms remain poorly understood. We used Potato spindle tuber viroid (PSTVd) as a model to investigate the direct role of the RNA itself in vascular entry. We report here the identification of an RNA motif that is required for PSTVd to traffic from nonvascular into the vascular tissue phloem to initiate systemic infection. This motif consists of nucleotides U/C that form a water-inserted cis Watson-Crick/Watson-Crick base pair flanked by short helices that comprise canonical Watson-Crick/Watson-Crick base pairs. This tertiary structural model was inferred by comparison with X-ray crystal structures of similar motifs in rRNAs and is supported by combined mutagenesis and covariation analyses. Hydration pattern analysis suggests that water insertion induces a widened minor groove conducive to protein and/or RNA interactions. Our model and approaches have broad implications to investigate the RNA structural motifs in other RNAs for vascular entry and to study the basic principles of RNA structure-function relationships.