Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV

Wang, Tian; Deng, Zhiqi; Zhang, Xi; Wang, Hongzheng; Wang, Yu; Liu, Xiuying; Liu, Songyu; Xu, Feng; Li, Tao; Fu, Daqi; Zhu, Beiwei; Luo, Yunbo; Zhu, Hongliang

doi:10.1038/s41438-018-0073-7

Cited by 59 publications

(44 citation statements)

References 49 publications

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“…Further research of non-model plants is needed to characterize components of the RNAi machinery and their roles in biogenesis and function of viral siRNAs. This research will certainly be facilitated by CRISPR-based gene editing technology, as for example recently implemented in tomato to reveal the role of one of the four paralogs of DCL2 in 22-nt siRNA biogenesis and antiviral defense ( Wang T. et al, 2018 ). As mentioned above, combination of small RNA sequencing with direct sequencing of long RNA and DNA molecules using PacBio and Nanopore technologies should enable reconstruction of complete viral genomes and discovery of their mutant and recombinant variants in mixed virome quasispecies.…”

Section: Concluding Remarks and Outlookmentioning

confidence: 99%

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

Pooggin

2018

Front. Microbiol.

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RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.

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Section: Concluding Remarks and Outlookmentioning

confidence: 99%

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

Pooggin

2018

Front. Microbiol.

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“…Recently, the DCL2b-dependent miRNA pathway in tomato was shown to affect susceptibility to PVX and TMV [43]. DCL2b is also required for the biosynthesis of 22-nt small RNAs to defend against ToMV [44].…”

Section: Discussionmentioning

confidence: 99%

“…The values with the double asterisk (**p < 0.01) and single asterisk (*p < 0.05) were statistically significant at the 1% and 5% levels, respectively, compared with those of healthy empty vector-transformed plants biogenesis. We recently showed a defect in the biogenesis of siRNAs, especially 22 nt siRNAs, derived from viroid RNA in hpDCL2.4 plants infected with the potato spindle tuber viroid [44]. Studies have reported the increased accumulation of CMV genomic RNAs [12] and increased susceptibility to PVX and the TuMV helper componentprotease mutant in Arabidopsis DCL double (DCL2 and 4) and triple mutants (DCL2, 3, and 4) [56].…”

Section: Discussionmentioning

confidence: 99%

“…Thus, symptom exacerbations may be attributed to differences in the expression of endogenous genes via the knockdown of DCL2, DCL4, AGO2 and AGO3. We recently showed that symptom exacerbations in hpDCL2.4 plants infected with potato spindle tuber viroid could be attributed to the increased expression of miR398a-3p, which increased the production of reactive oxygen species [44].…”

Section: Discussionmentioning

confidence: 99%

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RNA silencing-related genes contribute to tolerance of infection with potato virus X and Y in a susceptible tomato plant

Kwon

Kasai

Maoka

et al. 2020

Virol J

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Background In plants, the RNA silencing system functions as an antiviral defense mechanism following its induction with virus-derived double-stranded RNAs. This occurs through the action of RNA silencing components, including Dicer-like (DCL) nucleases, Argonaute (AGO) proteins, and RNA-dependent RNA polymerases (RDR). Plants encode multiple AGOs, DCLs, and RDRs. The functions of these components have been mainly examined in Arabidopsis thaliana and Nicotiana benthamiana. In this study, we investigated the roles of DCL2, DCL4, AGO2, AGO3 and RDR6 in tomato responses to viral infection. For this purpose, we used transgenic tomato plants (Solanum lycopersicum cv. Moneymaker), in which the expression of these genes were suppressed by double-stranded RNA-mediated RNA silencing. Methods We previously created multiple DCL (i.e., DCL2 and DCL4) (hpDCL2.4) and RDR6 (hpRDR6) knockdown transgenic tomato plants and here additionally did multiple AGO (i.e., AGO2 and AGO3) knockdown plants (hpAGO2.3), in which double-stranded RNAs cognate to these genes were expressed to induce RNA silencing to them. Potato virus X (PVX) and Y (PVY) were inoculated onto these transgenic tomato plants, and the reactions of these plants to the viruses were investigated. In addition to observation of symptoms, viral coat protein and genomic RNA were detected by western and northern blotting and reverse transcription-polymerase chain reaction (RT-PCR). Host mRNA levels were investigated by quantitative RT-PCR. Results Following inoculation with PVX, hpDCL2.4 plants developed a more severe systemic mosaic with leaf curling compared with the other inoculated plants. Systemic necrosis was also observed in hpAGO2.3 plants. Despite the difference in the severity of symptoms, the accumulation of PVX coat protein (CP) and genomic RNA in the uninoculated upper leaves was not obviously different among hpDCL2.4, hpRDR6, and hpAGO2.3 plants and the empty vector-transformed plants. Moneymaker tomato plants were asymptomatic after infection with PVY. However, hpDCL2.4 plants inoculated with PVY developed symptoms, including leaf curling. Consistently, PVY CP was detected in the uninoculated symptomatic upper leaves of hpDCL2.4 plants through western blotting. Of note, PVY CP was rarely detected in other asymptomatic transgenic or wild-type plants. However, PVY was detected in the uninoculated upper leaves of all the inoculated plants using reverse transcription-polymerase chain reactions. These findings indicated that PVY systemically infected asymptomatic Moneymaker tomato plants at a low level (i.e., no detection of CP via western blotting). Conclusion Our results indicate that the tomato cultivar Moneymaker is susceptible to PVX and shows mild mosaic symptoms, whereas it is tolerant and asymptomatic to systemic PVY infection with a low virus titer. In contrast, in hpDCL2.4 plants, PVX-induced symptoms became more severe and PVY infection caused symptoms. These results indicate that DCL2, DCL4, or both contribute to tolerance to infection with PVX and PVY. PVY CP and genomic RNA accumulated to a greater extent in DCL2.4-knockdown plants. Hence, the contribution of these DCLs to tolerance to infection with PVY is at least partly attributed to their roles in anti-viral RNA silencing, which controls the multiplication of PVY in tomato plants. The necrotic symptoms observed in the PVX-infected hpAGO2.3 plants suggest that AGO2, AGO3 or both are also distinctly involved in tolerance to infection with PVX.

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“…CRISPR-Cas9 technology has also been used to knock out crucial genes involved in resistance pathways, aiming to test whether these genes can confer immunity against viruses. Tomato Dicer-like 2 ( DCL2 ) genes were targeted, and the dcl2 mutants displayed viral symptoms when infected by potato virus X, tobacco mosaic virus, and tomato mosaic virus, suggesting that DCL2 is involved in the defense mechanism against RNA viruses 84,85 .…”

Section: Applications Of Crispr-cas9 In Fruit Cropsmentioning

confidence: 99%

CRISPR technology is revolutionizing the improvement of tomato and other fruit crops

2019

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Fruits are major sources of essential nutrients and serve as staple foods in some areas of the world. The increasing human population and changes in climate experienced worldwide make it urgent to the production of fruit crops with high yield and enhanced adaptation to the environment, for which conventional breeding is unlikely to meet the demand. Fortunately, clustered regularly interspaced short palindromic repeat (CRISPR) technology paves the way toward a new horizon for fruit crop improvement and consequently revolutionizes plant breeding. In this review, the mechanism and optimization of the CRISPR system and its application to fruit crops, including resistance to biotic and abiotic stresses, fruit quality improvement, and domestication are highlighted. Controversies and future perspectives are discussed as well.

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Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV

Cited by 59 publications

References 49 publications

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

RNA silencing-related genes contribute to tolerance of infection with potato virus X and Y in a susceptible tomato plant

CRISPR technology is revolutionizing the improvement of tomato and other fruit crops

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