Exocortis viroid: alteration in the proteins of Gynura aurantiaca accompanying viroid infection

Understanding Citrus Viroid Interactions: Experience and Prospects

Citrus is the natural host of at least eight viroid species, providing a natural platform for studying interactions among viroids. The latter manifests as antagonistic or synergistic phenomena. The antagonistic effect among citrus viroids intuitively leads to reduced symptoms caused by citrus viroids, while the synergistic effect leads to an increase in symptom severity. The interaction phenomenon is complex and interesting, and a deep understanding of the underlying mechanisms induced during this viroid interaction is of great significance for the prevention and control of viroid diseases. This paper summarizes the research progress of citrus viroids in recent years, focusing on the interaction phenomenon and analyzing their interaction mechanisms. It points out the core role of the host RNA silencing mechanism and viroid-derived siRNA (vd-siRNA), and provides suggestions for future research directions.

SlS5H silencing reveals specific pathogen-triggered salicylic acid metabolism in tomato

BACKGROUND

Salicylic acid (SA) is a major plant hormone that mediates the defence pathway against pathogens. SA accumulates in highly variable amounts depending on the plant-pathogen system, and several enzyme activities participate in the restoration of its levels. Gentisic acid (GA) is the product of the 5-hydroxylation of SA, which is catalysed by S5H, an enzyme activity regarded as a major player in SA homeostasis. GA accumulates at high levels in tomato plants infected by Citrus Exocortis Viroid (CEVd), and to a lesser extend upon Pseudomonas syringae DC3000 pv. tomato (Pst) infection.

RESULTS

We have studied the induction of tomato SlS5H gene by different pathogens, and its expression correlates with the accumulation of GA. Transient over-expression of SlS5H in Nicotiana benthamiana confirmed that SA is processed by SlS5H in vivo. SlS5H-silenced tomato plants were generated, displaying a smaller size and early senescence, together with hypersusceptibility to the necrotrophic fungus Botrytis cinerea. In contrast, these transgenic lines exhibited an increased defence response and resistance to both CEVd and Pst infections. Alternative SA processing appears to occur for each specific pathogenic interaction to cope with SA levels. In SlS5H-silenced plants infected with CEVd, glycosylated SA was the most discriminant metabolite found. Instead, in Pst-infected transgenic plants, SA appeared to be rerouted to other phenolics such as feruloyldopamine, feruloylquinic acid, feruloylgalactarate and 2-hydroxyglutarate.

CONCLUSION

Using SlS5H-silenced plants as a tool to unbalance SA levels, we have studied the re-routing of SA upon CEVd and Pst infections and found that, despite the common origin and role for SA in plant pathogenesis, there appear to be different pathogen-specific, alternate homeostasis pathways.

Revisiting the Non-Coding Nature of Pospiviroids

Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study.

Pathogenesis by subviral agents: viroids and hepatitis delta virus

The viroids of plants are the simplest known infectious genetic elements. They have RNA genomes of up to 400 nucleotides in length and no protein encoding capacity. Hepatitis delta virus (HDV), an infectious agent found only in humans co-infected with hepatitis B virus (HBV), is just slightly more complex, with an RNA genome of about 1700 nucleotides, and the ability to express just one small protein. Viroid and HDV RNAs share several features that include circular structure, compact folding, and replication via a rolling-circle mechanism. Both agents were detected because of their obvious pathogenic effects. Their simplicity demands a greater need than conventional RNA or DNA viruses to redirect host components for facilitating their infectious cycle, a need that directly and indirectly incites pathogenic effects. The mechanisms by which these pathogenic effects are produced are the topic of this review. In this context, RNA silencing mediates certain aspects of viroid pathogenesis.

Salicylic acid and gentisic acid induce RNA silencing-related genes and plant resistance to RNA pathogens

We have observed that treatments with salicylic acid (SA) or gentisic acid (GA) induced resistance to RNA pathogens such as ToMV and CEVd in tomato and Gynura auriantiaca, respectively. Accumulation of SA and GA has been found to occur in plants infected by these pathogens, thus pointing out a possible defence role of both molecules. To study the molecular basis of the observed induced resistance to RNA pathogens the induction of silencing-related genes by SA and GA was considered. For that purpose, we searched for tomato genes which were orthologous to those described in Arabidopsis thaliana, such as AtDCL1, AtDCL2, AtDCL4, AtRDR1, AtRDR2 and AtRDR6, and we tracked their induction in tomato along virus and viroid infections. We observed that CEVd significantly induced all these genes in tomato, with the exception of ToRDR6, being the induction of ToDCL4 the most outstanding. Regarding the ToMV asymptomatic infection, with the exception of ToRDR2, we observed a significant induction of all the indicated silencing-related genes, being ToDCL2 the most induced gene. Subsequently, we analyzed their transcriptional activation by SA and at the time when ToMV was inoculated on plants. ToDCL2, ToRDR1 and ToRDR2 were significantly induced by both SA and GA, whereas ToDCL1 was only induced by SA. Such an induction resulted more effective by SA treatment, which is in agreement with the stronger SA-induced resistance observed. Our results suggest that the observed delay in the RNA pathogen accumulation could be due to the pre-induction of RNA silencing-related genes by SA or GA.

Metabolic fingerprinting of Tomato Mosaic Virus infected Solanum lycopersicum

(1)H nuclear magnetic resonance (NMR)-based metabolomics has been applied to study the compatible interaction between tomato plants and Tomato Mosaic Virus (ToMV). A detailed time course of metabolic fingerprinting of ToMV-inoculated and non-inoculated systemically infected tomato leaves has provided a fundamental understanding of the metabolic state of the plant not only in response to ToMV infection, but also under various physiological conditions. By this analytical platform a total of 32 metabolites including amino/organic acids, sugars, phenylpropanoids, flavonoids and other miscellaneous compounds were detected. Using multivariate data analysis, we have identified a subset of metabolites induced during the plant defence response and metabolites whose accumulation was dependent on the developmental stage, the position of the leaf on the stem, and the harvesting time. Specifically, a general time-dependent decrease in organic acids, amino acids (excluding asparagine), phenylpropanoids and rutin was observed in individual leaves. In addition, metabolite alterations were also found to correlate with the developmental stage of the leaf: high levels of organic acids, some amino acids, phenylpropanoids, and flavonoids were found in lower leaves while elevated amounts of sugars were present in the upper ones. Moreover, a marked variation in the content of some metabolites was also observed to be associated to the asymptomatic ToMV infection both in inoculated and systemically infected leaves. While flavonoids accumulated in virus-inoculated leaves, increased levels of phenylpropanoids were observed in non-inoculated leaves where ToMV actively replicates. Finally, diurnal changes in the metabolite content were also observed: an increase of amino acids and organic acids (except glutamic acid) were observed in the samples collected in the morning, whereas sugars and secondary metabolite levels increased in the tomato leaves harvested in the evening.

Biological function of pathogenesis-related proteins: Four tobacco pathogenesis-related proteins are chitinases

Four endochitinases (poly[1,4-(N-acetyl-beta-D-glucosaminide)] glycanohydrolase, EC 3.2.1.14) have been purified from leaves of Nicotiana tabacum cv. Samsun NN reacting hypersensitively to tobacco mosaic virus. Two of them are acidic proteins of molecular weights 27,500 and 28,500 and have been identified as 2 of the 10 pathogenesis-related proteins that are known to accumulate in tobacco in response to stress or pathogen attack. These two pathogenesis-related proteins, named "P" and "Q" when their biological function was unknown, account for one-third of tobacco mosaic virus-induced chitinase activity of tobacco leaves. They are serologically closely related to the two other chitinases, which can be considered as new basic pathogenesis-related proteins. These two basic chitinases exhibit higher molecular weights (32,000 and 34,000) and higher specific enzyme activity than the two acidic isoforms.

RNA sequences complementary to citrus exocortis viroid in nucleic acid preparations from infected Gynura aurantiaca

Molecular hybridization with (125)I-labeled citrus exocortis viroid RNA has been used to survey nucleic acid preparations from Gynura aurantiaca for viroid complementary molecules. A differential hybridization effect was detected between nucleic acid extracts from healthy and infected tissue in which significant RNase-resistant (125)I-labeled citrus exocortis viroid resulted in hybridization studies with the infected tissue extracts. Subsequent characterization indicated that RNA from infected tissue was involved in the formation of a duplex molecule with citrus exocortis viroid RNA and had properties of an RNA.RNA hybrid. Subcellular fractionation of infected tissue indicates that the complementary RNA is present in nuclear and soluble RNA fractions. This RNA may represent an intermediate molecule in the replication of the viroid or a pathogenic expression and may have a regulatory role in the host cell.

Avsunviroidae family: viroids containing hammerhead ribozymes

This chapter focuses on the second viroid family, whose members are also referred to as hammerhead viroids, taking into account their most outstanding feature. If the word “small” is the first to come to mind when considering viroids, perhaps the second word is “hammerhead,” because this class of ribozymes, which because of its structural simplicity has an enormous biotechnological potential, is described in avocado sunblotch viroid (ASBVd) as well as in a viroid-like satellite RNA. The most outstanding feature of the Avsunviroidae members is their potential to adopt hammerhead structures in both polarity strands and to self-cleave in vitro accordingly. Viroids differ from viruses not only in their genome size but also in other fundamental aspects, prominent among which is the lack of messenger activity of both viroid RNAs and their complementary strands.

Subviral pathogens of plants: the viroids

Research during the last 15 years has conclusively shown that viroids are not only fundamentally different from viruses at the molecular level, but that they are most likely not directly related to viruses in an evolutionary sense. Today, viroids are among the most thoroughly studied biological macromolecules. Their molecular structures have been elucidated to a large extent, but much needs to be learned regarding the correlation between molecular structure and biological function. The availability of the tools of recombinant DNA technology in viroid research promises rapid progress in these areas of inquiry.

Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity

Full-length double-stranded cDNA was prepared from purified circular RNA of two new Australian field isolates of citrus exocortis viroid (CEV) using two synthetic oligodeoxynucleotide primers. The cDNA was then cloned into the phage vector M13mp9 for sequence analysis. Sequencing of nine cDNA clones of isolate CEV-DE30 and eleven cDNA clones of isolate CEV-J indicated that both isolates consisted of a mixture of viroid species and led to the discovery of eleven new sequence variants of CEV. These new variants, together with the six reported previously, form two classes of sequence which differ by a minimum of 26 nucleotides in a total of 370 to 375 residues. These two classes correlate with two biologically distinct groups when propagated on tomato plants where one produces severe symptoms and the other gives rise to mild symptoms. Two regions of the native structure of CEV, comprising 18% of the total residues, differ between the sequence variants of mild and severe isolates. Whether or not both of these regions are essential for the variation in pathogenicity has yet to be determined.

Purification and partial characterization of the major "pathogenesis-related" tomato leaf protein P14 from potato spindle tuber viroid (PSTV)-infected tomato leaves

The acid-extractable leaf proteins of potato spindle tuber viroid (PSTV) infected tomato plants were analysed electrophoretically on polyacrylamide gels. The most prominent alteration found during disease development was the appearance of a "pathogenesis-related" protein with an apparent molecular weight of 14,000 (called P14) which is drastically increased in concentration. Its induction, however, is not viroid-specific because it is also accumulating after viral and fungal infections. The degree of P14 accumulation could be directly correlated with the severity of the disease symptoms and its concentration was found to be highest in leaves of the tomato cultivar "Rutgers" four weeks after infection. P14 was isolated from such leaf material by acid-extraction of the leaf proteins, which were concentrated from the clarified homogenates by ultrafiltration through hollow fiber systems or by precipitation at 60 per cent ammonium sulphate saturation. P14 was finally purified by ion exchange chromatography on sulfopropyl (SP-C25) Sephadex and on DEAE cellulose. A protein with properties similar to those of P14 could also be isolated from healthy tomato leaves, where its concentration is about forty to fifty times lower than PSTV-infected tissue. P14 can be stained with Coomassie Brilliant Blue, silver and ethidium bromide, it is sensitive to digestion with pronase and not altered when treated with RNase and DNase. P14 is a basic protein with an estimated isoelectric point of 10.7 and its unusual behaviour during ultrafiltration indicates that it represents an elongated rather than a globular molecule in solution. P14 seems to be different from any of the so-called "pathogenesis-related" proteins described so far in Gynura aurantiaca, "Etrog" citron, potato and tomato after viroid-infection and in tobacco, cucumber and bean leaves after virus- or fungus-induced hypersensitive reactions.

Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy

The complete cDNA of hop stunt viroid (HSV) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170. (1982] and the complete nucleotide sequence has been established. The covalently closed circular single-stranded HSV RNA consists of 297 nucleotides. The secondary structure predicted for HSV contains 67% of its residues base-paired. The native HSV can possess an extended rod-like structure characteristic of viroids previously established. The central region of the native HSV has a similar structure to the conserved region found in all viroids sequenced so far except for avocado sunblotch viroid. The sequence homologous to the 5'-end of U1a RNA is also found in the sequence of HSV but not in the central conserved region.

Comparative sequence and structure of viroid-like RNAs of two plant viruses

A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, velvet tobacco mottle virus and solanum nodiflorum mottle virus, have been determined. RNA 2 of solanum nodiflorum mottle virus consists of 377 residues whereas that of velvet tobacco mottle virus consists of two approximately equimolar species, one of 366 residues and the other, with a single nucleotide deletion, of 365 residues. There is 92-95% sequence homology between the RNA 2 species of the two viruses. The predicted secondary structures possess extensive intramolecular base pairing to give rod-like structures similar to those of viroids. The structural similarities between the RNAs 2 of velvet tobacco mottle virus and solanum nodiflorum mottle virus and viroids may reflect functional similarities.

Gelelectrophoretic analysis of phenol-extractable leaf proteins from different viroid/host combinations

The phenol-soluble proteins from leaves of healthy and viroid-infected plants were compared after separation on SDS-polyacrylamide gels. After staining with Coomassie blue, alterations in the protein patterns of infected plants were found which resulted from an increase or decrease of certain protein bands. After infection with the same viroid, different hosts show characteristic changes in the protein pattern which suggest that these alterations are host-specific rather than pathogenspecific. After infection of tomato plants with different viroid "species" a protein with the apparent MW of 14,000 (p14 tom) was found to accumulate dramatically. This protein also accumulates in tomato plants after viral and fungus infections and the rate of its accumulation is directly related to the severity of symptoms developed by the diseased plants. It is assumed, therefore, that it is a response of tomato plants to infection in general.

Analysis of acid-extractable tomato leaf proteins after infection with a viroid, two viruses and a fungus and partial purification of the "pathogenesis-related" protein p 14

Gel electrophoretic analysis revealed marked alterations in the pattern of acid-extractable proteins from tomato leaves after infection with a viroid (PSTV), two viruses [tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV)], and a fungus (Cladosporium fulvum) when compared to the pattern from healthy leaves. A pathogen-specific appearance of new protein bands was only found after infection with TMV (MW 17,400 and 65,000), CMV (MW 9000 and 8000) and Cladosporium fulvum (MW 28,000). With the exception of the TMV coat protein (MW 17,400) it could not be established whether the other four proteins are coded for by the corresponding pathogen or by the host. Nine proteins with the apparent NW of 10,000, 11,000, 12,000, 13,000, 14,000, 25,000, 31,000, 33,000 and 38,000 showed an increase in their relative concentration which is most dramatic in the case of the protein with the MW of 14,000 called p14. A decrease was observed in four proteins with molecular weights of 14,500, 23,000, 30,000 and 105,000. Since all these alterations could be correlated with the severity of the disease symptoms but not with the nature of the pathogen they must be considered as a general pathophysiological response of the tomato plant to infection and symptom development. A partial purification of the most prominent "pathogenesis-related" protein p14 from tomato plants is described.

Chrysanthemum stunt viroid: primary sequence and secondary structure

The sequence of the 356 nucleotide residues of chrysanthemum stunt viroid (CSV) has been determined. Overlapping linear viroid fragments were obtained by partial ribonuclease digestion, radiolabelled in vitro at their 5'-ends, and sequenced using partial enzymic cleavage methods. Of the CSV sequence, 69% is contained in the published sequence of potato spindle tuber viroid (PSTV). Differences in the primary sequence of CSV and PSTV suggest that neither the positive nor putative negative strands of these two viroids code for functional polypeptide products. However, the two viroids can form similar secondary structures, implicating a role for viroid structure in replication.

Viroids: structure and function

Viroids are nucleic acid species of relatively low molecular weight and unique structure that cause several important diseases of cultivated plants. Similar nucleic acid species may be responsible for certain diseases of animals and humans. Viroids are the smallest known agents of infectious disease. Unlike viral nucleic acids, viroids are not encapsidated. Despite their small size, viroids replicate autonomously in cells of susceptible plant species. Known viroids are single-stranded, covalently closed circular, as well as linear, RNA molecules with extensive regions of intramolecular complementarity; they exist in their native state as highly base-paired rods.