scholarly journals Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid

2021 ◽  
Vol 22 (7) ◽  
pp. 3725
Author(s):  
Beatriz Navarro ◽  
Andreas Gisel ◽  
Pedro Serra ◽  
Michela Chiumenti ◽  
Francesco Di Serio ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Rna Silencing ◽  
High Throughput Sequencing ◽  
Potato Spindle Tuber Viroid ◽  
Degradome Analysis ◽  
Tomato Plants ◽  
Leaf Curling ◽  
Mrna Targets ◽  
Infected Tomato ◽  
Bona Fide

Viroids are infectious non-coding RNAs that infect plants. During infection, viroid RNAs are targeted by Dicer-like proteins, generating viroid-derived small RNAs (vd-sRNAs) that can guide the sequence specific cleavage of cognate host mRNAs via an RNA silencing mechanism. To assess the involvement of these pathways in pathogenesis associated with nuclear-replicating viroids, high-throughput sequencing of sRNAs and degradome analysis were carried out on tomato and Nicotiana benthamiana plants infected by potato spindle tuber viroid (PSTVd). Both hosts develop similar stunting and leaf curling symptoms when infected by PSTVd, thus allowing comparative analyses. About one hundred tomato mRNAs potentially targeted for degradation by vd-sRNAs were initially identified. However, data from biological replicates and comparisons between mock and infected samples reduced the number of bona fide targets—i.e., those identified with high confidence in two infected biological replicates but not in the mock controls—to only eight mRNAs that encode proteins involved in development, transcription or defense. Somewhat surprisingly, results of RT-qPCR assays revealed that the accumulation of only four of these mRNAs was inhibited in the PSTVd-infected tomato. When these analyses were extended to mock inoculated and PSTVd-infected N. benthamiana plants, a completely different set of potential mRNA targets was identified. The failure to identify homologous mRNA(s) targeted by PSTVd-sRNA suggests that different pathways could be involved in the elicitation of similar symptoms in these two species. Moreover, no significant modifications in the accumulation of miRNAs and in the cleavage of their targeted mRNAs were detected in the infected tomato plants with respect to the mock controls. Taken together, these data suggest that stunting and leaf curling symptoms induced by PSTVd are elicited by a complex plant response involving multiple mechanisms, with RNA silencing being only one of the possible components.

scholarly journals Potato spindle tuber viroid as Inducer of RNA Silencing in Infected Tomato

2001 ◽  
Vol 14 (11) ◽  
pp. 1332-1334 ◽  
Author(s):  
Asuka Itaya ◽  
Alexey Folimonov ◽  
Yoshie Matsuda ◽  
Richard S. Nelson ◽  
Biao Ding
Keyword(s):  
Plant Pathogen ◽  
Small Rnas ◽  
Rna Silencing ◽  
Potato Spindle Tuber Viroid ◽  
Sequence Specificity ◽  
Tomato Plants ◽  
Biological Features ◽  
Severe Strain ◽  
Infected Tomato ◽  
Systemic Symptoms

Potato spindle tuber viroid (PSTVd), an RNA plant pathogen encoding no known proteins, induces systemic symptoms on tomato plants. We report detection of small RNAs of approximately 25 nucleotides with sequence specificity to PSTVd in infected plants: an indication of the presence of RNA silencing. RNA silencing, however, did not appear to be responsible for the differing symptoms induced by a mild and a severe strain of PSTVd. The unique structural and biological features of viroids make them attractive experimental tools to investigate mechanisms of RNA silencing and pathogen counterdefense.

Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato

2010 ◽  
Vol 391 (12) ◽  
Author(s):  
Natalie Diermann ◽  
Jaroslav Matoušek ◽  
Markus Junge ◽  
Detlev Riesner ◽  
Gerhard Steger
Keyword(s):  
Transcription Factors ◽  
Small Rnas ◽  
Rna Silencing ◽  
Potato Spindle Tuber Viroid ◽  
Regulation Of Transcription ◽  
Tomato Plants ◽  
Sequence Variations ◽  
Infected Tomato ◽  
Minor Sequence

Abstract To defend against invading pathogens, plants possess RNA silencing mechanisms involving small RNAs (miRNAs, siRNAs). Also viroids – plant infectious, non-coding, unencapsidated RNA – cause the production of viroid-specific small RNAs (vsRNA), but viroids do escape the cytoplasmic silencing mechanism. Viroids with minor sequence variations can produce different symptoms in infected plants, suggesting an involvement of vsRNAs in symptom production. We analyzed by deep sequencing the spectrum of vsRNAs induced by the PSTVd strain AS1, which causes strong symptoms such as dwarfing and necrosis upon infection of tomato plants cv Rutgers. Indeed, vsRNAs found with highest frequency mapped to the pathogenicity-modulating domain of PSTVd, supporting an involvement of vsRNAs in symptom production. Furthermore, in PSTVd AS1-infected plants the accumulation of some endogenous miRNAs, which are involved in leaf development via regulation of transcription factors, is suppressed. The latter finding supports the hypothesis that a miRNA-dependent (mis)regula-tion of transcription factors causes the viroid symptoms.

scholarly journals Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Ivett Baksa ◽  
Tibor Nagy ◽  
Endre Barta ◽  
Zoltán Havelda ◽  
Éva Várallyay ◽  
...  
Keyword(s):  
High Throughput ◽  
Nicotiana Benthamiana ◽  
High Throughput Sequencing ◽  
Degradome Analysis

scholarly journals Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants

Plant Disease ◽  
2015 ◽  
Vol 99 (6) ◽  
pp. 770-775 ◽  
Author(s):  
A. E. Mackie ◽  
B. A. Coutts ◽  
M. J. Barbetti ◽  
B. C. Rodoni ◽  
S. J. McKirdy ◽  
...  
Keyword(s):  
Human Skin ◽  
Skim Milk ◽  
Potato Spindle Tuber Viroid ◽  
Control Measures ◽  
Effective Management ◽  
Tomato Plants ◽  
Hygiene Practices ◽  
Infected Tomato ◽  
Polymerase Chain ◽  
The Stability

The length of time Potato spindle tuber viroid (PSTVd) remained infective in extracted tomato leaf sap on common surfaces and the effectiveness of disinfectants against it were investigated. When sap from PSTVd-infected tomato leaves was applied to eight common surfaces (cotton, wood, rubber tire, leather, metal, plastic, human skin, and string) and left for various periods of time (5 min to 24 h) before rehydrating the surface and rubbing onto healthy tomato plants, PSTVd remained infective for 24 h on all surfaces except human skin. It survived best on leather, plastic, and string. It survived less well after 6 h on wood, cotton, and rubber and after 60 min on metal. On human skin, PSTVd remained infective for only 30 min. In general, rubbing surfaces contaminated with dried infective sap directly onto leaves caused less infection than when the sap was rehydrated with distilled water but overall results were similar. The effectiveness of five disinfectant agents at inactivating PSTVd in sap extracts was investigated by adding them to sap from PSTVd-infected leaves before rubbing the treated sap onto leaves of healthy tomato plants. Of the disinfectants tested, 20% nonfat dried skim milk and a 1:4 dilution of household bleach (active ingredient sodium hypochlorite) were the most effective at inactivating PSTVd infectivity in infective sap. When reverse-transcription polymerase chain reaction was used to test the activity of the five disinfectants against PSTVd in infective sap, it detected PSTVd in all instances except in sap treated with 20% nonfat dried skim milk. This study highlights the stability of PSTVd in infective sap and the critical importance of utilizing hygiene practices such as decontamination of clothing, tools, and machinery, along with other control measures, to ensure effective management of PSTVd and, wherever possible, its elimination in solanaceous crops.

scholarly journals Successive accumulation of two size classes of viroid-specific small RNA in potato spindle tuber viroid-infected tomato plants

2007 ◽  
Vol 88 (12) ◽  
pp. 3452-3457 ◽  
Author(s):  
Satoru Machida ◽  
Naoki Yamahata ◽  
Hiromi Watanuki ◽  
Robert A. Owens ◽  
Teruo Sano
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Rna Silencing ◽  
Time Course ◽  
Leaf Tissue ◽  
Potato Spindle Tuber Viroid ◽  
Size Classes ◽  
Infected Tomato ◽  
Symptomatic Leaf ◽  
Rna Accumulation

Like many plant RNA viruses, infection by potato spindle tuber viroid (PSTVd) is known to lead to RNA silencing and a marked reduction in visible disease. To examine the relationship between RNA silencing and this recovery phenomenon in greater detail, we have carried out time-course analyses of viroid-specific small RNA accumulation using several viroid–host combinations. These analyses revealed the presence of two size classes of viroid-specific small RNAs in infected plants, and sequence analysis subsequently demonstrated the presence of a previously undescribed cluster of small RNAs derived primarily from negative-strand PSTVd RNA. Although the clustering patterns were similar, the size distribution of PSTVd small RNAs isolated from symptomatic leaf tissue became more heterogeneous with time. The process by which viroid-specific small RNAs are generated appears to be more complicated than previously believed, possibly involving multiple DICER-LIKE activities, viroid RNA substrates and subcellular compartments.

scholarly journals A Multifunctional Protein Encoded by Turkey Herpesvirus Suppresses RNA Silencing in Nicotiana benthamiana

2011 ◽  
Vol 85 (23) ◽  
pp. 12792-12803 ◽  
Author(s):  
X.-l. Jing ◽  
M.-n. Fan ◽  
G. Jia ◽  
L.-w. Liu ◽  
L. Ma ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Rna Silencing ◽  
Multifunctional Protein
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