The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

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.

Download Full-text

Mycoviruses as Triggers and Targets of RNA Silencing in White Mold Fungus Sclerotinia sclerotiorum

10.20944/preprints201803.0244.v1 ◽

2018 ◽

Author(s):

Pauline Mochama ◽

Prajakta Jadhav ◽

Achal Neupane ◽

Shin-Yi Lee Marzano

Keyword(s):

Virus Infection ◽

Viral Infection ◽

Small Rna ◽

Rna Silencing ◽

Type Strain ◽

Plant Pathogens ◽

Wild Type Strain ◽

Wild Type ◽

Fungal Plant Pathogens ◽

Mold Fungus

This study aimed to demonstrate the existence of antiviral RNA silencing mechanisms in Sclerotinia sclerotiorum by probing wild-type and RNA-silencing-deficient strains of the fungus with an RNA virus and a circular DNA virus. Key silencing-related genes, specifically dicers, were disrupted in order to dissect the RNA silencing pathway and provide useful information on fungal control. Dicers Dcl-1, Dcl-2, and both Dcl-1/Dcl-2- genes were displaced by selective marker(s). Disruption mutants were then compared for changes in phenotype, virulence, susceptibility to viral infection, and small RNA accumulation compared to the wild-type strain. Disruption of Dcl-1 or Dcl-2 resulted in no changes in phenotype compared to wild-type S. sclerotiorum; however, the double dicer mutant strain exhibited slower growth. To examine the effect of viral infection on strains containing null-mutations of Dcl-1, Dcl-2 or both genes, mutants were transfected with full-length RNA transcripts of a hypovirus SsHV2L and copies of a single-stranded DNA mycovirus- SsHADV-1 as a synthetic virus. Results indicate that the ΔDcl-1/Dcl-2 double mutant which was slow growing without virus infection exhibited much more severe debilitation following virus infection. Altered colony morphology including: reduced pigmentation, significantly slower growth, and delayed sclerotial formation. Additionally, there is an absence of virus-derived small RNAs in the virus-infected ∆Dcl-1/Dcl-2 mutant compared to the virus-infected wild-type strain which displays a high percentage of virus-derived small RNA. The findings of these studies suggest that if both dicers are silenced, invasive nucleic acids which include mycoviruses ubiquitous in nature- can greatly debilitate the virulence of fungal plant pathogens.

Download Full-text

Faculty Opinions recommendation of Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1157170.617284 ◽

2009 ◽

Author(s):

Elizabeth Dennis

Keyword(s):

Transposable Elements ◽

Small Rna ◽

Rna Silencing ◽

Epigenetic Reprogramming

Download Full-text

Key Importance of Small RNA Binding for the Activity of a Glycine-Tryptophan (GW) Motif-containing Viral Suppressor of RNA Silencing

Journal of Biological Chemistry ◽

10.1074/jbc.m114.593707 ◽

2014 ◽

Vol 290 (5) ◽

pp. 3106-3120 ◽

Cited By ~ 28

Author(s):

Miryam Pérez-Cañamás ◽

Carmen Hernández

Keyword(s):

Small Rna ◽

Rna Silencing ◽

Rna Binding ◽

Viral Suppressor ◽

Suppressor Of Rna Silencing

Download Full-text

Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1421475112 ◽

2015 ◽

Vol 112 (18) ◽

pp. 5850-5855 ◽

Cited By ~ 82

Author(s):

Yongli Qiao ◽

Jinxia Shi ◽

Yi Zhai ◽

Yingnan Hou ◽

Wenbo Ma

Keyword(s):

Small Rna ◽

Rna Silencing ◽

Effector Proteins ◽

Helicase Domain ◽

Small Interfering Rnas ◽

Developmental Defects ◽

Interacting Protein ◽

Homologous Genes ◽

Unidentified Component ◽

Virulence Target

A broad range of parasites rely on the functions of effector proteins to subvert host immune response and facilitate disease development. The notorious Phytophthora pathogens evolved effectors with RNA silencing suppression activity to promote infection in plant hosts. Here we report that the Phytophthora Suppressor of RNA Silencing 1 (PSR1) can bind to an evolutionarily conserved nuclear protein containing the aspartate–glutamate–alanine–histidine-box RNA helicase domain in plants. This protein, designated PSR1-Interacting Protein 1 (PINP1), regulates the accumulation of both microRNAs and endogenous small interfering RNAs in Arabidopsis. A null mutation of PINP1 causes embryonic lethality, and silencing of PINP1 leads to developmental defects and hypersusceptibility to Phytophthora infection. These phenotypes are reminiscent of transgenic plants expressing PSR1, supporting PINP1 as a direct virulence target of PSR1. We further demonstrate that the localization of the Dicer-like 1 protein complex is impaired in the nucleus of PINP1-silenced or PSR1-expressing cells, indicating that PINP1 may facilitate small RNA processing by affecting the assembly of dicing complexes. A similar function of PINP1 homologous genes in development and immunity was also observed in Nicotiana benthamiana. These findings highlight PINP1 as a previously unidentified component of RNA silencing that regulates distinct classes of small RNAs in plants. Importantly, Phytophthora has evolved effectors to target PINP1 in order to promote infection.

Download Full-text

The IDR-containing protein PID-2 affects Z granules and is required for piRNA-induced silencing in the embryo

10.1101/2020.04.14.040584 ◽

2020 ◽

Author(s):

Maria Placentino ◽

António Miguel de Jesus Domingues ◽

Jan Schreier ◽

Sabrina Dietz ◽

Svenja Hellmann ◽

...

Keyword(s):

Gene Regulation ◽

Caenorhabditis Elegans ◽

Rna Polymerase ◽

Small Rna ◽

Rna Silencing ◽

Rna Dependent Rna Polymerase ◽

Prolyl Aminopeptidase ◽

C Elegans

AbstractIn Caenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG-1-bound 21U RNAs trigger silencing mechanisms mediated by RNA-dependent RNA polymerase (RdRP)-synthetized 22G RNAs. This silencing can become PRG-1-independent, and heritable over many generations. This state is named RNAe. It is unknown how and when RNAe is established, and how it is maintained. We show that maternally provided 21U RNAs can be sufficient to trigger RNAe in embryos. Additionally, we identify the IDR-containing protein PID-2, as a factor required to establish and maintain RNAe. PID-2 interacts with two novel, partially redundant, eTudor domain proteins, PID-4 and PID-5. Additionally, PID-5 has a domain related to the X-prolyl aminopeptidase protein APP-1, and binds APP-1, implicating N-terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci, affect Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in the C. elegans small RNA silencing network.

Download Full-text

FOXO regulates RNA interference in Drosophila and protects from RNA virus infection

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1517124112 ◽

2015 ◽

Vol 112 (47) ◽

pp. 14587-14592 ◽

Cited By ~ 33

Author(s):

Michael J. Spellberg ◽

Michael T. Marr

Keyword(s):

Rna Interference ◽

Virus Infection ◽

Gene Silencing ◽

Small Rna ◽

Stress Responses ◽

Posttranscriptional Regulation ◽

Rna Virus ◽

Regulation Of Gene Expression ◽

Cellular Physiology ◽

Metabolic Conditions

Small RNA pathways are important players in posttranscriptional regulation of gene expression. These pathways play important roles in all aspects of cellular physiology from development to fertility to innate immunity. However, almost nothing is known about the regulation of the central genes in these pathways. The forkhead box O (FOXO) family of transcription factors is a conserved family of DNA-binding proteins that responds to a diverse set of cellular signals. FOXOs are crucial regulators of cellular homeostasis that have a conserved role in modulating organismal aging and fitness. Here, we show that Drosophila FOXO (dFOXO) regulates the expression of core small RNA pathway genes. In addition, we find increased dFOXO activity results in an increase in RNA interference (RNAi) efficacy, establishing a direct link between cellular physiology and RNAi. Consistent with these findings, dFOXO activity is stimulated by viral infection and is required for effective innate immune response to RNA virus infection. Our study reveals an unanticipated connection among dFOXO, stress responses, and the efficacy of small RNA-mediated gene silencing and suggests that organisms can tune their gene silencing in response to environmental and metabolic conditions.

Download Full-text

tRNA 2′-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila

Nucleic Acids Research ◽

10.1093/nar/gkaa002 ◽

2020 ◽

Vol 48 (4) ◽

pp. 2050-2072 ◽

Cited By ~ 4

Author(s):

Margarita T Angelova ◽

Dilyana G Dimitrova ◽

Bruno Da Silva ◽

Virginie Marchand ◽

Caroline Jacquier ◽

...

Keyword(s):

Small Rna ◽

Rna Structure ◽

Rna Silencing ◽

Defense Mechanisms ◽

Rna Virus ◽

Virus Infections ◽

Self Recognition ◽

Silencing Pathways ◽

Rna Pathways ◽

And Function

Abstract 2′-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

Download Full-text