Small RNAs in viral infection and host defense

Mlotshwa, Sizolwenkosi; Pruss, Gail J.; Vance, Vicki

doi:10.1016/j.tplants.2008.04.009

Cited by 143 publications

(106 citation statements)

References 87 publications

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“…RNAi is involved in a wide range of biological processes and plays a major role in maintaining the balance between investment in growth and development and defence against biotic and abiotic stress (Carrington and Ambros 2003; Lai 2003; Matzke and Birchler 2005; Zhao et al 2016b). Many studies disclose that one important example is its role as an inducible plant defence pathway that targets or inactivates invading nucleic acids from viruses (Mlotshwa et al 2008; Zhao et al 2016b). Apart from viral defence, evidence accumulates for RNAi involving in interactions with other pathogen types (Pumplin and Voinnet 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide profiling of sRNAs in the Verticillium dahliae-infected Arabidopsis roots

et al. 2018

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Small RNAs (sRNAs, including small interfering RNAs [siRNAs] and micro RNAs [miRNAs]) are key mediators of RNA silencing (or RNA interference), which play important roles in plant development and response to biotic and abiotic stimulation. Verticillium wilt is a plant vascular disease caused by the soil-borne fungal pathogens, such as Verticillium dahliae. We previously reported that V. dahliae infection increased two plant endogenous miRNAs that were exported to fungal cell to silence virulence genes. To investigate plant sRNAs in genome-wide response to V. dahliae infection, in this study, we constructed two sRNA libraries from Arabidopsis roots with and without V. dahliae infection, respectively. In total, 31 conserved miRNAs were found to be differentially expressed during the early stage of infection with V. dahliae using sRNA sequencing. Among these, the expression levels of miR160, miR164, miR166, miR167, miR390 and miR156h were confirmed by northern blot. Reverse transcription quantitative real time polymerase chain reaction results showed that the induction of miRNAs (miR160, miR164, miR166 and miR167) upon V. dahliae infection downregulated the expression of their targeted genes (ARF10, NAC1, PHV and ARF6), respectively. In addition, we identified specific phased siRNAs generated from distinct regions of two libraries. Profiling of these miRNAs and sRNAs lay the foundation for further understanding and utilising the host-induced gene silencing strategy to control plant vascular pathogens.

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Section: Introductionmentioning

confidence: 99%

Genome-wide profiling of sRNAs in the Verticillium dahliae-infected Arabidopsis roots

et al. 2018

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“…arboviruses | piRNAs | siRNAs | viral immunity | massively parallel sequencing T he Dicer family of host immune receptors mediates antiviral immunity in fungi, plants, and invertebrate animals by RNA interference (RNAi) or RNA silencing (1)(2)(3). In this immunity, a viral dsRNA is recognized by Dicer and diced into siRNAs.…”

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confidence: 99%

“…The Dicer proteins involved in the production of siRNAs targeting both +RNA viruses and DNA viruses have been identified in Arabidopsis thaliana (2,3), and plants encode AGOs in the AGO subfamily but none from the PIWI subfamily (15). Cloning and sequencing of plant viral siRNAs suggest that they may be processed either from vRI-dsRNAs or hairpin regions of single-stranded RNA precursors (16)(17)(18)(19)(20).…”

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confidence: 99%

Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

Luo

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

429

411

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In response to infection, invertebrates process replicating viral RNA genomes into siRNAs of discrete sizes to guide virus clearance by RNA interference. Here, we show that viral siRNAs sequenced from fruit fly, mosquito, and nematode cells were all overlapping in sequence, suggesting a possibility of using siRNAs for viral genome assembly and virus discovery. To test this idea, we examined contigs assembled from published small RNA libraries and discovered five previously undescribed viruses from cultured Drosophila cells and adult mosquitoes, including three with a positive-strand RNA genome and two with a dsRNA genome. Notably, four of the identified viruses exhibited only low sequence similarities to known viruses, such that none could be assigned into an existing virus genus. We also report detection of virus-derived PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster that have not been previously described in any other host species and demonstrate viral genome assembly from viral piRNAs in the absence of viral siRNAs. Thus, this study provides a powerful culture-independent approach for virus discovery in invertebrates by assembling viral genomes directly from host immune response products without prior virus enrichment or amplification. We propose that invertebrate viruses discovered by this approach may include previously undescribed human and vertebrate viral pathogens that are transmitted by arthropod vectors.arboviruses | piRNAs | siRNAs | viral immunity | massively parallel sequencing T he Dicer family of host immune receptors mediates antiviral immunity in fungi, plants, and invertebrate animals by RNA interference (RNAi) or RNA silencing (1-3). In this immunity, a viral dsRNA is recognized by Dicer and diced into siRNAs. These virus-derived siRNAs are then loaded into an RNA silencing complex to act as specificity determinants and to guide slicing of the target viral RNAs by an Argonaute protein (AGO) present in the complex. Dicer proteins typically contain an RNA helicase domain, a PAZ domain shared with AGOs, and two tandem type III endoribonuclease (RNase III) domains. Dicer cleaves dsRNA with a simple preference toward a terminus of dsRNA, producing duplex small RNA fragments of discrete sizes progressively from the terminus (4).In addition to siRNAs, micro-RNAs (miRNAs) and PIWIinteracting RNAs (piRNAs) guide RNA silencing in similar complexes but with distinct AGOs (4-6). In Drosophila melanogaster, miRNAs and siRNAs are predominantly 22 and 21 nucleotides in length, dependent on Dicer-1 (DCR1) and DCR2 for their biogenesis, and act in silencing complexes containing AGO1 and AGO2 in the AGO subfamily, respectively (4-6). In contrast, ∼24-30-nt piRNAs are Dicer-independent and require AGO3, Aubergine (AUB), and PIWI in the PIWI subfamily for their biogenesis (4-6). Genetic analyses (7-10) have clearly demonstrated a role for D. melanogaster DCR2 in the immunity and biogenesis of viral siRNAs targeting diverse positive-strand (+) RNA viruses, including Flock house virus (FHV), cricket par...

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“…RNA silencing controls antiviral immunity in fungi, plants, and invertebrates by producing virus-derived siRNAs to be loaded in an Argonaute protein for antiviral silencing (10)(11)(12). In A. thaliana, DCL4 and DCL2 produce viral siRNAs against distinct positive (+)-strand RNA viruses in a hierarchical and redundant manner (13)(14)(15)(16).…”

mentioning

confidence: 99%

RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana

Wang

Ito

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

397

413

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In diverse eukaryotic organisms, Dicer-processed, virus-derived small interfering RNAs direct antiviral immunity by RNA silencing or RNA interference. Here we show that in addition to core dicing and slicing components of RNAi, the RNAi-mediated viral immunity in Arabidopsis thaliana requires host RNA-directed RNA polymerase (RDR) 1 or RDR6 to produce viral secondary siRNAs following viral RNA replication-triggered biogenesis of primary siRNAs. We found that the two antiviral RDRs exhibited specificity in targeting the tripartite positive-strand RNA genome of cucumber mosaic virus (CMV). RDR1 preferentially amplified the 5′-terminal siRNAs of each of the three viral genomic RNAs, whereas an increased production of siRNAs targeting the 3′ half of RNA3 detected in rdr1 mutant plants appeared to be RDR6-dependent. However, siRNAs derived from a single-stranded 336-nucleotide satellite RNA of CMV were not amplified by either antiviral RDR, suggesting avoidance of the potent RDR-dependent silencing as a strategy for the molecular parasite of CMV to achieve preferential replication. Our work thus identifies a distinct mechanism for the amplification of immunity effectors, which together with the requirement for the biogenesis of endogenous siRNAs, may play a role in the emergence and expansion of eukaryotic RDRs.antiviral immunity | cucumber mosaic virus | RNA silencing | RNAdependent RNA polymerase | secondary small interfering RNA R NA silencing or RNA interference in fungi, nematodes and plants requires amplification of small interfering RNAs by eukaryotic RNA-directed RNA polymerases (RDRs) (1-3). Plant and fungal RDRs convert transcripts of target genes into dsRNA that is subsequently processed into secondary siRNAs by a Dicer or Dicer-like (DCL) nuclease. In contrast, Caenorhabditis elegans RDRs, such as RRF-1, may directly manufacture secondary siRNAs without dicing a dsRNA precursor (1-3). The genome of Arabidopsis thaliana encodes six RDRs that are grouped into four clusters (1, 2, 4), among which little is known about cluster III, consisting of RDRs 3a, 3b, and 3c. RDR2 and RDR6 are both required for the short-distance spread of transgene silencing and for the perception, but not the production, of the long-distance mobile silencing signal (1, 5-9). RDR2 is also essential for the biogenesis of the DCL3-dependent 24-nucleotide (nt) repeat-associated siRNAs (rasiRNAs) derived from transposons, retroelements, and other elements, which are the most abundant endogenous small RNAs in A. thaliana (3). Similarly, RDR6 coupled with DCL4 or DCL1 is responsible for the biogenesis of transacting siRNAs (tasiRNAs) and natural antisense siRNAs (nat-siRNAs), which silence expression of their target genes like microRNAs (miRNAs) (1-3).RNA silencing controls antiviral immunity in fungi, plants, and invertebrates by producing virus-derived siRNAs to be loaded in an Argonaute protein for antiviral silencing (10-12). In A. thaliana, DCL4 and DCL2 produce viral siRNAs against distinct positive (+)-strand RNA viruses in a hierarc...

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Small RNAs in viral infection and host defense

Cited by 143 publications

References 87 publications

Genome-wide profiling of sRNAs in the Verticillium dahliae-infected Arabidopsis roots

Genome-wide profiling of sRNAs in the Verticillium dahliae-infected Arabidopsis roots

Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana

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