The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs in <i>Arabidopsis</i>

Bologna, Nicolas Gerardo; Voinnet, Olivier

doi:10.1146/annurev-arplant-050213-035728

Cited by 541 publications

(544 citation statements)

References 151 publications

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“…RNAi is an evolutionary conserved and sequence-specific mechanism that induces mRNA degradation or inhibits translation at either the post-transcriptional level or the transcriptional level (Duan et al 2012; Bologna and Voinnet 2014; Zhao et al 2016b). sRNAs are the key mediators of RNAi and are produced from double-stranded RNA (dsRNA) by an RNase III-type enzyme(Bologna and Voinnet 2014).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…sRNAs are the key mediators of RNAi and are produced from double-stranded RNA (dsRNA) by an RNase III-type enzyme(Bologna and Voinnet 2014). Based on their origin and formation, these sRNAs are mainly classified into two major types: the small interfering RNAs (siRNAs) and the miRNAs (Bologna and Voinnet 2014). 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).…”

Section: Introductionmentioning

confidence: 99%

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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%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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“…The cellular machinery for RNAi is present in animals, plants and fungi (Meister & Tuschl 2004;Chang et al, 2012). During RNA silencing, RNase III endoribonucleases called Dicers (or Dicer-like in plants) detect and cleave double-stranded RNA (dsRNA) templates into small interfering RNAs (siRNAs), which are typically 21, 22 or 24 nt long in plants (Bologna & Voinnet, 2014). The siRNAs then associate with an RNA-induced silencing complex in which a protein of the Argonaute family catalyses the sequence-guided degradation of target mRNA.…”

Section: Introductionmentioning

confidence: 99%

Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs

Vainio¹,

Jurvansuu²,

Streng

et al. 2015

Journal of General Virology

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Analysis of virus-derived small RNAs with high-throughput sequencing has been successful for detecting novel viruses in plants and invertebrates. However, the applicability of this method has not been demonstrated in fungi, although fungi were among the first organisms reported to utilize RNA silencing. Here, we used virus-infected isolates of the fungal species complex Heterobasidion annosum sensu lato as a model system to test whether mycovirus genome segments can be detected with small RNA deep sequencing. Species of the genus Heterobasidion are some of the most devastating forest pathogens in boreal forests. These fungi cause wood decay and are commonly infected with species of the family Partitiviridae and the unassigned virus species Heterobasidion RNA virus 6. Small RNA deep sequencing allowed the simultaneous detection of all eight double-stranded RNA virus strains known to be present in the tested samples and one putative mitovirus species (family Narnaviridae) with a single-stranded RNA genome, designated here as Heterobasidion mitovirus 1. Prior to this study, no members of the family Narnaviridae had been described as infecting species of Heterobasidion. Quantification of viral double-and single-stranded RNA with quantitative PCR indicated that co-infecting viral species and viruses with segmented genomes can be detected with small RNA deep sequencing despite vast differences in the amount of RNA. This is the first study demonstrating the usefulness of this method for detecting fungal viruses. Moreover, the results suggest that viral genomes are processed into small RNAs by different species of Heterobasidion.

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“…These enzymes synthesize dsRNA by using ssRNA as template. Then, the new dsRNAs are cleaved by different DCLs, producing secondary siRNAs that are able to move systemically and amplify the silencing signal (for reviews, see Voinnet, 2008;Bologna and Voinnet, 2014). In Arabidopsis thaliana, six different RDRs have already been identified (RDR1-RDR6) (reviewed in Willmann et al, 2011).…”

Section: Rna Interference-mediated Resistancementioning

confidence: 99%

Modulation of host plant immunity by Tobamovirus proteins

Conti

Rodríguez

Venturuzzi

et al. 2016

Ann Bot

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Background To establish successful infection, plant viruses produce profound alterations of host physiology, disturbing unrelated endogenous processes and contributing to the development of disease. In tobamoviruses, emerging evidence suggests that viral-encoded proteins display a great variety of functions beyond the canonical roles required for virus structure and replication. Among these, their modulation of host immunity appears to be relevant in infection progression.Scope In this review, some recently described effects on host plant physiology of Tobacco mosaic virus (TMV)-encoded proteins, namely replicase, movement protein (MP) and coat protein (CP), are summarized. The discussion is focused on the effects of each viral component on the modulation of host defense responses, through mechanisms involving hormonal imbalance, innate immunity modulation and antiviral RNA silencing. These effects are described taking into consideration the differential spatial distribution and temporality of viral proteins during the dynamic process of replication and spread of the virus.Conclusion In discussion of these mechanisms, it is shown that both individual and combined effects of viralencoded proteins contribute to the development of the pathogenesis process, with the host plant's ability to control infection to some extent potentially advantageous to the invading virus.

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The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs in Arabidopsis

Cited by 541 publications

References 151 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

Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs

Modulation of host plant immunity by Tobamovirus proteins

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