scholarly journals Suppression of RNA-Dependent RNA Polymerase 6 Favors the Accumulation of Potato Spindle Tuber Viroid in Nicotiana Benthamiana

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 345 ◽  
Author(s):  
Charith Raj Adkar-Purushothama ◽  
Jean-Pierre Perreault
Keyword(s):  
Nicotiana Benthamiana ◽  
Small Rnas ◽  
Rna Viruses ◽  
Fold Increase ◽  
Potato Spindle Tuber Viroid ◽  
Rna Dependent Rna Polymerase ◽  
Viroid Infection ◽  
Genes Encoding ◽  
Plant Genes

To date, two plant genes encoding RNA-dependent RNA polymerases (RdRs) that play major roles in the defense against RNA viruses have been identified: (i) RdR1, which is responsible for the viral small RNAs (vsRNAs) found in virus-infected plants, and, (ii) RdR6, which acts as a surrogate in the absence of RdR1. In this study, the role of RdR6 in the defense against viroid infection was examined by knock-down of RdR6 followed by potato spindle tuber viroid (PSTVd) infection. The suppression of RdR6 expression increased the plant’s growth, as was illustrated by the plant’s increased height. PSTVd infection of RdR6 compromised plants resulted in an approximately three-fold increase in the accumulation of viroid RNA as compared to that seen in control plants. Additionally, RNA gel blot assay revealed an increase in the number of viroids derived small RNAs in RdR6 suppressed plants as compared to control plants. These data provide a direct correlation between RdR6 and viroid accumulation and indicate the role of RDR6 in the plant’s susceptibility to viroid infection.

scholarly journals Root-Specific Role for Nicotiana benthamiana RDR6 in the Inhibition of Chinese wheat mosaic virus Accumulation at Higher Temperatures

2013 ◽  
Vol 26 (10) ◽  
pp. 1165-1175 ◽  
Author(s):  
Ida Bagus Andika ◽  
Liying Sun ◽  
Rong Xiang ◽  
Junmin Li ◽  
Jianping Chen
Keyword(s):  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Small Rnas ◽  
Potato Virus Y ◽  
Temperature Shift ◽  
Specific Role ◽  
Wild Type ◽  
Rna Dependent Rna Polymerase ◽  
Chinese Wheat

Some viruses only infect plants at cool temperatures but the molecular mechanism underlying this low-temperature dependence remains unclear. Chinese wheat mosaic virus (CWMV, genus Furovirus) was able to infect wheat and Nicotiana benthamiana plants at 16 but not at 24°C. When CWMV-infected plants were transferred to 24°C for 2 weeks, the newly emerged leaves and roots became virus free. Co-infection with Potato virus Y rescued CWMV accumulation in N. benthamiana plants after a temperature shift to 24°C. In transgenic N. benthamiana plants silenced for the N. benthamiana RNA-dependent RNA polymerase 6 (NbRDR6), CWMV was able to accumulate in roots but not in leaves after a temperature shift to 24°C. Deep sequencing of small RNAs showed that, at 16°C, abundant CWMV small interfering (si)RNAs accumulated in infected N. benthamiana plants. Silencing of NbRDR6 increased the abundance of CWMV siRNAs and the generation of siRNAs from hotspots in the CWMV genome. In contrast, when shifted to 24°C for 1 week, CWMV siRNAs were markedly fewer in roots of NbRDR6-silenced than in roots of wild-type plants but were similar in the leaves of those plants. Our results demonstrate the root-specific role of NbRDR6 in the inhibition of CWMV accumulation and biogenesis of CWMV siRNAs at higher temperatures.

scholarly journals Genes Encoding Cucumber Full-Size ABCG Proteins Show Different Responses to Plant Growth Regulators and Sclareolide

2015 ◽  
Vol 34 (4) ◽  
pp. 720-736 ◽  
Author(s):  
Adam Rajsz ◽  
Anna Warzybok ◽  
Magdalena Migocka
Keyword(s):  
Plant Growth ◽  
Plant Growth Regulators ◽  
Growth Regulators ◽  
Expression Profiles ◽  
Plant Responses ◽  
Full Size ◽  
Genes Encoding ◽  
Plant Genes ◽  
Cucumber Roots

AbstractFull-size members of the ABCG (ATP-binding cassette, subfamily G) subfamily of ABC transporters have been found only in plants and fungi. The plant genes encoding full-size ABCGs identified so far appeared to be differentially regulated under various environmental constraints, plant growth regulators, and microbial elicitors, indicating a broad functional role of these proteins in plant responses to abiotic and biotic stress. Nevertheless, the structure and physiological function of full-size ABCGs in many plant species are still unknown. We have recently identified 16 genes encoding full-size ABCG proteins in cucumber and found that the transcripts of two of them, CsABCG36 (CsPDR8) and CsABCG40 (CsPDR12), are most abundant in roots and are significantly affected by phytohormones and auxin herbicide. In this study, we analyzed the structure and phylogeny of all the full-size cucumber ABCG transporters and studied the organ expression profiles of the remaining 14 CsABCG genes. In addition, we investigated the effect of different plant growth regulators and the diterpene sclareolide on CsABCG expression in cucumber roots. Until now, the full-size plant ABCG transporters have been grouped into five different clusters. The new phylogenetic analysis of full-size ABCGs from model plants and cucumber clustered these proteins into six different subgroups. Interestingly, the expression profiles of cucumber ABCG genes assigned to the same clusters were not correlated, suggesting functional diversification or different regulatory mechanisms of the full-size cucumber ABCG proteins.

scholarly journals Intronic regions of plant genes potentially encode RDR (RNA-dependent RNA polymerase)-dependent small RNAs

2015 ◽  
Vol 66 (7) ◽  
pp. 1763-1768 ◽  
Author(s):  
Jingping Qin ◽  
Xiaoxia Ma ◽  
Zili Yi ◽  
Yijun Meng ◽  
Zhonghai Tang
Keyword(s):  
Rna Polymerase ◽  
Small Rnas ◽  
Rna Dependent Rna Polymerase ◽  
Double Stranded Rna ◽  
Plant Genes ◽  
Dependent Pathway

The opinion is put forward here that certain intronic regions of plant genes could be converted to double-stranded RNA precursors for sRNA production through an RDR-dependent pathway.

scholarly journals RNAi-Mediated Down-Regulation of Dicer-Like 2 and 4 Changes the Response of ‘Moneymaker’ Tomato to Potato Spindle Tuber Viroid Infection from Tolerance to Lethal Systemic Necrosis, Accompanied by Up-Regulation of miR398, 398a-3p and Production of Excessive Amount of Reactive Oxygen Species

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 344 ◽  
Author(s):  
Takahiro Suzuki ◽  
Sho Ikeda ◽  
Atsushi Kasai ◽  
Akito Taneda ◽  
Misato Fujibayashi ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Reactive Oxygen ◽  
Potato Spindle Tuber Viroid ◽  
Ros Production ◽  
Oxygen Species ◽  
Superoxide Dismutase 1 ◽  
Systemic Necrosis ◽  
Viroid Infection ◽  
Infected Line

To examine the role of RNA silencing in plant defenses against viroids, a Dicer-like 2 and 4 (DCL2&4)–double knockdown transgenic tomato plant line, 72E, was created. The expression of endogenous SlDCL2s and SlDCL4 in line 72E decreased to about a half that of the empty cassette line, EC. When challenged with potato spindle tuber viroid (PSTVd), line 72E showed significantly higher levels of PSTVd accumulation early in the course of the infection and lethal systemic necrosis late in the infection. The size distribution of PSTVd-derived small RNAs was significantly different with the number of RNAs of 21 and 22 nucleotides (nt) in line 72E, at approximately 66.7% and 5% of those in line EC, respectively. Conversely, the numbers of 24 nt species increased by 1100%. Furthermore, expression of the stress-responsive microRNA species miR398 and miR398a-3p increased 770% and 868% in the PSTVd-infected line 72E compared with the PSTVd-infected EC. At the same time, the expression of cytosolic and chloroplast-localized Cu/Zn-superoxide dismutase 1 and 2 (SOD1 and SOD2) and the copper chaperon for SOD (CCS1) mRNAs, potential targets of miR398 or 398a-3p, decreased significantly in the PSTVd-infected line 72E leaves, showing necrosis. In concert with miR398 and 398a-3p, SODs control the detoxification of reactive oxygen species (ROS) generated in cells. Since high levels of ROS production were observed in PSTVd-infected line 72E plants, it is likely that the lack of full dicer-likes (DCL) activity in these plants made them unable to control excessive ROS production after PSTVd infection, as disruption in the ability of miR398 and miR398a-3p to regulate SODs resulted in the development of lethal systemic necrosis.

scholarly journals Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasiteLeishmania

2017 ◽  
Vol 115 (3) ◽  
pp. E506-E515 ◽  
Author(s):  
Danyil Grybchuk ◽  
Natalia S. Akopyants ◽  
Alexei Y. Kostygov ◽  
Aleksandras Konovalovas ◽  
Lon-Fye Lye ◽  
...  
Keyword(s):  
Visceral Leishmaniasis ◽  
Rna Polymerase ◽  
Human Disease ◽  
Rna Viruses ◽  
Biological Role ◽  
Viral Diversity ◽  
Rna Dependent Rna Polymerase ◽  
Human Parasite ◽  
Viral Lineage

Knowledge of viral diversity is expanding greatly, but many lineages remain underexplored. We surveyed RNA viruses in 52 cultured monoxenous relatives of the human parasiteLeishmania(CrithidiaandLeptomonas), as well as plant-infectingPhytomonas.Leptomonas pyrrhocoriswas a hotbed for viral discovery, carrying a virus (Leptomonas pyrrhocoris ostravirus 1) with a highly divergent RNA-dependent RNA polymerase missed by conventional BLAST searches, an emergent clade of tombus-like viruses, and an example of viral endogenization. A deep-branching clade of trypanosomatid narnaviruses was found, notable asLeptomonas seymouribearing Narna-like virus 1 (LepseyNLV1) have been reported in cultures recovered from patients with visceral leishmaniasis. A deep-branching trypanosomatid viral lineage showing strong affinities to bunyaviruses was termed “Leishbunyavirus” (LBV) and judged sufficiently distinct to warrant assignment within a proposed family termed “Leishbunyaviridae.” Numerous relatives of trypanosomatid viruses were found in insect metatranscriptomic surveys, which likely arise from trypanosomatid microbiota. Despite extensive sampling we found no relatives of the totivirusLeishmaniavirus(LRV1/2), implying that it was acquired at about the same time theLeishmaniabecame able to parasitize vertebrates. As viruses were found in over a quarter of isolates tested, many more are likely to be found in the >600 unsurveyed trypanosomatid species. Viral loss was occasionally observed in culture, providing potentially isogenic virus-free lines enabling studies probing the biological role of trypanosomatid viruses. These data shed important insights on the emergence of viruses within an important trypanosomatid clade relevant to human disease.

scholarly journals Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Florian Dunker ◽  
Adriana Trutzenberg ◽  
Jan S Rothenpieler ◽  
Sarah Kuhn ◽  
Reinhard Pröls ◽  
...  
Keyword(s):  
Small Rnas ◽  
Plant Pathogens ◽  
Gene Knockout ◽  
Gus Reporter ◽  
Knockout Mutants ◽  
Plant Genes ◽  
Hyaloperonospora Arabidopsidis ◽  
Short Tandem

The exchange of small RNAs (sRNAs) between hosts and pathogens can lead to gene silencing in the recipient organism, a mechanism termed cross-kingdom RNAi (ck-RNAi). While fungal sRNAs promoting virulence are established, the significance of ck-RNAi in distinct plant pathogens is not clear. Here, we describe that sRNAs of the pathogen Hyaloperonospora arabidopsidis, which represents the kingdom of oomycetes and is phylogenetically distant from fungi, employ the host plant’s Argonaute (AGO)/RNA-induced silencing complex for virulence. To demonstrate H. arabidopsidis sRNA (HpasRNA) functionality in ck-RNAi, we designed a novel CRISPR endoribonuclease Csy4/GUS reporter that enabled in situ visualization of HpasRNA-induced target suppression in Arabidopsis. The significant role of HpasRNAs together with AtAGO1 in virulence was revealed in plant atago1 mutants and by transgenic Arabidopsis expressing a short-tandem-target-mimic to block HpasRNAs, that both exhibited enhanced resistance. HpasRNA-targeted plant genes contributed to host immunity, as Arabidopsis gene knockout mutants displayed quantitatively enhanced susceptibility.

scholarly journals The Critical Role of Small RNAs in Regulating Plant Innate Immunity

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 184
Author(s):  
Saquib Waheed ◽  
Muhammad Anwar ◽  
Muhammad Asif Saleem ◽  
Jinsong Wu ◽  
Muhammad Tayyab ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Small Rnas ◽  
Plant Immunity ◽  
Critical Role ◽  
Innate Immune ◽  
Genes Encoding ◽  
Effector Triggered Immunity ◽  
Available Information ◽  
Regulatory Functions

Plants, due to their sessile nature, have an innate immune system that helps them to defend against different pathogen infections. The defense response of plants is composed of a highly regulated and complex molecular network, involving the extensive reprogramming of gene expression during the presence of pathogenic molecular signatures. Plants attain proper defense against pathogens through the transcriptional regulation of genes encoding defense regulatory proteins and hormone signaling pathways. Small RNAs are emerging as versatile regulators of plant development and act in different tiers of plant immunity, including pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). The versatile regulatory functions of small RNAs in plant growth and development and response to biotic and abiotic stresses have been widely studied in recent years. However, available information regarding the contribution of small RNAs in plant immunity against pathogens is more limited. This review article will focus on the role of small RNAs in innate immunity in plants.

scholarly journals Three Ribosomal Operons of Escherichia coli Contain Genes Encoding Small RNAs That Interact With Hfq and CsrA in vitro

2021 ◽  
Vol 12 ◽  
Author(s):  
Thomas Søndergaard Stenum ◽  
Mette Kongstad ◽  
Erik Holmqvist ◽  
Birgitte Kallipolitis ◽  
Sine Lo Svenningsen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Rna ◽  
Small Rnas ◽  
Genes Encoding ◽  
Ribosomal Operons ◽  
Dependent Processes ◽  
Fine Tune

Three out of the seven ribosomal RNA operons in Escherichia coli end in dual terminator structures. Between the two terminators of each operon is a short sequence that we report here to be an sRNA gene, transcribed as part of the ribosomal RNA primary transcript by read-through of the first terminator. The sRNA genes (rrA, rrB and rrF) from the three operons (rrnA, rrnB and rrnD) are more than 98% identical, and pull-down experiments show that their transcripts interact with Hfq and CsrA. Deletion of rrA, B, F, as well as overexpression of rrB, only modestly affect known CsrA-regulated phenotypes like biofilm formation, pgaA translation and glgC translation, and the role of the sRNAs in vivo may not yet be fully understood. Since RrA, B, F are short-lived and transcribed along with the ribosomal RNA components, their concentration reflect growth-rate regulation at the ribosomal RNA promoters and they could function to fine-tune other growth-phase-dependent processes in the cell. The primary and secondary structure of these small RNAs are conserved among species belonging to different genera of Enterobacteriales.

scholarly journals Virp1 Is a Host Protein with a Major Role in Potato Spindle Tuber Viroid Infection in Nicotiana Plants

2007 ◽  
Vol 81 (23) ◽  
pp. 12872-12880 ◽  
Author(s):  
K. Kalantidis ◽  
M. A. Denti ◽  
S. Tzortzakaki ◽  
E. Marinou ◽  
M. Tabler ◽  
...  
Keyword(s):  
Rna Binding ◽  
Potato Spindle Tuber Viroid ◽  
Plant Diseases ◽  
Host Protein ◽  
Rna Molecules ◽  
Viroid Infection ◽  
Transgenic Lines ◽  
Localization Signal ◽  
Positive Strand Rna

ABSTRACT Viroids are small, circular, single-stranded RNA molecules that, while not coding for any protein, cause several plant diseases. Viroids rely for their infectious cycle on host proteins, most of which are likely to be involved in endogenous RNA-mediated phenomena. Therefore, characterization of host factors interacting with the viroid may contribute to the elucidation of RNA-related pathways of the hosts. Potato spindle tuber viroid (PSTVd) infects several members of the Solanaceae family. In an RNA ligand screening we have previously isolated the tomato protein Virp1 by its ability to specifically interact with PSTVd positive-strand RNA. Virp1 is a bromodomain-containing protein with an atypical RNA binding domain and a nuclear localization signal. Here we investigate the role of Virp1 in the viroid infection cycle by the use of transgenic lines of Nicotiana tabacum and Nicotiana benthamiana that either overexpress the tomato Virp1 RNA or suppress the orthologous Nicotiana genes through RNA silencing. Plants of the Virp1-suppressed lines were not infected by PSTVd or Citrus exocortis viroid through mechanical inoculation, indicating a major role of Virp1 in viroid infection. On the other hand, overexpression of tomato Virp1 in N. tabacum and N. benthamiana plants did not affect PSTVd KF 440-2 infectivity or symptomatology in these species. Transfection experiments with isolated protoplasts revealed that Virp1-suppressed cells were unable to sustain viroid replication, suggesting that resistance to viroid infection in Virp1-suppressed plants is likely the result of cell-autonomous events.

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