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 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 Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Miyuki Nakamura ◽  
Claudia Köhler ◽  
Lars Hennig
Keyword(s):  
Norway Spruce ◽  
Small Rnas ◽  
Male Gametophyte ◽  
Leaf Tissue ◽  
Tissue Specific ◽  
Size Classes ◽  
Vegetative Tissues ◽  
Male Cones ◽  
Transposon Activity ◽  
Angiosperm Pollen

Abstract Background Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms. Results Here, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture. Conclusion Our data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.

scholarly journals Rice Dwarf Virus Small RNA Profiles in Rice and Leafhopper Reveal Distinct Patterns in Cross-Kingdom Hosts

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 847
Author(s):  
Yu Wang ◽  
Rui Qiao ◽  
Chunhong Wei ◽  
Yi Li
Keyword(s):  
Oryza Sativa ◽  
Virus Infection ◽  
High Throughput ◽  
Small Rna ◽  
Small Rnas ◽  
Rna Silencing ◽  
Small Rna Sequencing ◽  
Rice Dwarf Virus ◽  
Rna Dependent Rna Polymerase ◽  
Eukaryotic Organisms

RNA silencing has evolved as a widespread antiviral strategy in many eukaryotic organisms. Antiviral RNA silencing is mediated by virus-derived small RNAs (vsiRNAs), created by the cleavage of double-stranded viral RNA substrates by Dicer (Dcr) in animals or Dicer-like (DCL) proteins in plants. However, little is known about how the RNA silencing mechanisms of different hosts respond to the same virus infection. We performed high-throughput small RNA sequencing in Nephotettix cincticeps and Oryza sativa infected with Rice dwarf phytoreovirus and analyzed the distinct accumulation of vsiRNAs in these two hosts. The results suggested a potential branch in the evolution of antiviral RNA silencing of insect and plant hosts. The rice vsiRNAs were predominantly 21 and 22 nucleotides (nt) long, suggesting that OsDCL4 and OsDCL2 are involved in their production, whereas 21-nt vsiRNAs dominated in leafhopper, suggesting the involvement of a Dcr-2 homolog. Furthermore, we identified ~50-fold more vsiRNAs in rice than in leafhoppers, which might be partially attributable to the activity of RNA-dependent RNA polymerase 6 (RDR6) in rice and the lack of RDR genes in leafhoppers. Our data established a basis for further comparative studies on the evolution of RNA silencing-based interactions between a virus and its hosts, across kingdoms.

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 Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species

2020 ◽  
Vol 165 (12) ◽  
pp. 2953-2959
Author(s):  
Ramesh R. Vetukuri ◽  
Pruthvi B. Kalyandurg ◽  
Ganapathi Varma Saripella ◽  
Diya Sen ◽  
Jose Fernando Gil ◽  
...  
Keyword(s):  
Size Distribution ◽  
Small Rna ◽  
Small Rnas ◽  
Rna Silencing ◽  
Transcriptional Activator ◽  
Lower Abundance ◽  
Silencing Suppression ◽  
The Impact ◽  
Small Rna Species ◽  
Suppressor Of Rna Silencing

Abstract Chrysanthemum virus B encodes a multifunctional p12 protein that acts as a transcriptional activator in the nucleus and as a suppressor of RNA silencing in the cytoplasm. Here, we investigated the impact of p12 on accumulation of major classes of small RNAs (sRNAs). The results show dramatic changes in the sRNA profiles characterised by an overall reduction in sRNA accumulation, changes in the pattern of size distribution of canonical siRNAs and in the ratio between sense and antisense strands, lower abundance of siRNAs with a U residue at the 5′-terminus, and changes in the expression of certain miRNAs, most of which were downregulated.

scholarly journals A Structured Viroid RNA Serves as a Substrate for Dicer-Like Cleavage To Produce Biologically Active Small RNAs but Is Resistant to RNA-Induced Silencing Complex-Mediated Degradation

2007 ◽  
Vol 81 (6) ◽  
pp. 2980-2994 ◽  
Author(s):  
Asuka Itaya ◽  
Xuehua Zhong ◽  
Ralf Bundschuh ◽  
Yijun Qi ◽  
Ying Wang ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Small Rnas ◽  
Rna Silencing ◽  
Effective Means ◽  
Critical Role ◽  
Potato Spindle Tuber Viroid ◽  
Biologically Active ◽  
Antiviral Defense ◽  
Silencing Suppressor ◽  
Rna Structures

ABSTRACT RNA silencing is a potent means of antiviral defense in plants and animals. A hallmark of this defense response is the production of 21- to 24-nucleotide viral small RNAs via mechanisms that remain to be fully understood. Many viruses encode suppressors of RNA silencing, and some viral RNAs function directly as silencing suppressors as counterdefense. The occurrence of viroid-specific small RNAs in infected plants suggests that viroids can trigger RNA silencing in a host, raising the question of how these noncoding and unencapsidated RNAs survive cellular RNA-silencing systems. We address this question by characterizing the production of small RNAs of Potato spindle tuber viroid (srPSTVds) and investigating how PSTVd responds to RNA silencing. Our molecular and biochemical studies provide evidence that srPSTVds were derived mostly from the secondary structure of viroid RNAs. Replication of PSTVd was resistant to RNA silencing, although the srPSTVds were biologically active in guiding RNA-induced silencing complex (RISC)-mediated cleavage, as shown with a sensor system. Further analyses showed that without possessing or triggering silencing suppressor activities, the PSTVd secondary structure played a critical role in resistance to RISC-mediated cleavage. These findings support the hypothesis that some infectious RNAs may have evolved specific secondary structures as an effective means to evade RNA silencing in addition to encoding silencing suppressor activities. Our results should have important implications in further studies on RNA-based mechanisms of host-pathogen interactions and the biological constraints that shape the evolution of infectious RNA structures.

scholarly journals Mechanism of Stochastic Resonance in a Quorum Sensing Network Regulated by Small RNAs

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Ya-nan Zhu ◽  
Jianwei Shen ◽  
Yong Xu
Keyword(s):  
Quorum Sensing ◽  
Stochastic Resonance ◽  
Small Rna ◽  
Small Rnas ◽  
Cell Communication ◽  
The Other ◽  
Important Process ◽  
Positive Role ◽  
Bacterial Quorum Sensing ◽  
Bacterial Quorum

Bacterial quorum sensing (QS) is an important process of cell communication and more and more attention is paid to it. Moreover, the noises are ubiquitous in nature and often play positive role. In this paper, we investigate how the noise enhances the QS though the stochastic resonance (SR) and explain the mechanism of SR in this quorum sensing network. In addition, we also discuss the interaction between the small RNA and the other genes in this network and discover the biological importance.

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