Identification and Molecular Mechanisms of Key Nucleotides Causing Attenuation in Pathogenicity of Dahlia Isolate of Potato Spindle Tuber Viroid

Abstract

While the potato spindle tuber viroid (PSTVd) variant, PSTVd-Dahlia (PSTVd-D or PSTVd-Dwt) induces very mild symptoms in tomato cultivar ‘Rutgers’, PSTVd-Intermediate (PSTVd-I or PSTVd-Iwt) induces severe symptoms. These two variants differ by nine nucleotides, of which six mutations are located in the terminal left (TL) to the pathogenicity (P) domains. To evaluate the importance of mutations located in the TL to the P domains, ten types of point mutants were created by swapping the nucleotides between the two viroid variants. Bioassay in tomato plants demonstrated that two mutants created on PSTVd-Iwt at positions 42 and 64 resulted in symptom attenuation. Phenotypic and RT-qPCR analysis revealed that mutation at position 42 of PSTVd-Iwt significantly reduced disease severity and accumulation of the viroid, whereas mutation at position 64 showed a significant reduction in stunting when compared to the PSTVd-Iwt infected plant. RT-qPCR analysis on pathogenesis-related protein 1b1 and chalcone synthase genes showed a direct correlation with symptom severity whereas the expansin genes were down-regulated irrespective of the symptom severity. These results indicate that the nucleotides at positions 42 and 64 are in concert with the ones at positions 43, 310, and 311/312, which determines the slower and stable accumulation of PSTVd-D without eliciting excessive host defense responses thus contributing in the attenuation of disease symptom.

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

“…2). 63)- 66) In particular, a C42U mutation significantly impaired PSTVd replication and did not elicit excessive host defense responses, thus contributing to the attenuation of disease symptoms. Although mutations at sites 310-312 in the VM region did not play a significant role in pathogenicity, these nucleotides, in cooperation with nucleotides 42, 43, and 64 in the paired strand, contributed to replication of the dahlia isolate by maintaining the local structure of the TL-P domains (Fig.…”

“…2). 66) Bending of the molecule within the pathogenicity domain. Mutational analysis also indicated that in certain cases, downregulation of pathogenicity was correlated with suppression of the rate of PSTVd replication/accumulation.…”

Potato spindle tuber viroid

“…64 affects stunting. In general, enrichment of mutations in genomic RNAs revealed positions with importance to symptom severity and viroid replication intensity (Kitabayashi et al, 2020). The viroid genome encodes no proteins and its replication depends on the host cellular machinery.…”

“…The most frequent PSTVd genomic variants were analyzed at different time points after inoculation of tomato plants. It was found that at seven DAI only 25 % of the sequenced PSTVd genomes were identical to the master copy, but its frequency grew up to 70 % at 14 DAI and remained the same at 28 DAI (Adkar-Purushothama et al, 2020). It is likely that viroid replication produces a large variety of structural variants with different effects on host defense and the severity of disease symptoms.…”

sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling

“…Viroids are both the simplest and the smallest known plant pathogens. They consist of a circular, single-stranded, non-coding RNA genome of 246–434 nucleotides (nt) in length [ 1 ]. Since viroids do not encode for any known peptides, they rely entirely on their sequence, structure and host factors in order to replicate and induce disease symptoms in their host plants.…”