A Short Indel-Lacking-Resistance Gene Triggers Silencing of the Photosynthetic Machinery Components Through TYLCSV-Associated Endogenous siRNAs in Tomato.

Michela Chiumenti,Vitantonio Pantaleo,Mario Ventura,Laura Miozzi,Walter Pirovano,Claudia Rita Catacchio

doi:10.3389/fpls.2018.01470

Abstract

Plant viruses modify gene expression in infected tissues by altering the micro (mi)RNA-mediated regulation of genes. Among conserved miRNA targets there are transcripts coding for transcription factors, RNA silencing core, and disease-resistance proteins. Paralogs in these gene families are widely present in plant genomes and are known to respond differently to miRNA-mediated regulation during plant virus infections. Using genome-wide approaches applied to Solanum lycopersicum infected by a nuclear-replicating virus, we highlighted miRNA-mediated cleavage events that could not be revealed in virus-free systems. Among them we confirmed miR6024 targeting and cleavage of RX-coiled-coil (RX-CC), nucleotide binding site (NBS), leucine-rich (LRR) mRNA. Cleavage of paralogs was associated with short indels close to the target sites, indicating a general functional significance of indels in fine-tuning gene expression in plant–virus interaction. miR6024-mediated cleavage, uniquely in virus-infected tissues, triggers the production of several 21–22 nt secondary siRNAs. These secondary siRNAs, rather than being involved in the cascade regulation of other NBS–LRR paralogs, explained cleavages of several mRNAs annotated as defence-related proteins and components of the photosynthetic machinery. Outputs of these data explain part of the phenotype plasticity in plants, including the appearance of yellowing symptoms in the viral pathosystem.

Highlights

RNA silencing refers to conserved pathways affecting gene expression through negative regulation mediated by non-coding RNAs, such as short interferingRNAs
Our study revealed that one mRNA transcript coding for a CC–nucleotide binding site (NBS)–LRR protein holds both the miR482 and miR6024 target sites, which overlap to some extent
Given that AGO1 mRNA is known in Arabidopsis and tomato to have secondary siRNAs initiated by miR168 (Mallory and Vaucheret, 2009; Shivaprasad et al, 2012), we focused on sly-AGO1a and sly-AGO1b

Summary

Introduction

RNA silencing refers to conserved pathways affecting gene expression through negative regulation mediated by non-coding RNAs, such as short interfering (si)RNAs. MiRNAs function as a guide by base-pairing with their target RNAs, whereas AGO1 [mainly, but not exclusively (Adenot et al, 2006)] plays a role as effector, recruiting factors that induce mRNA translational repression and/or mRNA cleavage (Bartel, 2004; Voinnet, 2009; Iwakawa and Tomari, 2013). The 5 -uncapped fragments detected by 5 RACE correspond to cleavage between the 10th and 11th nucleotides of miRNA/target site pairs. A genome-wide 5 -RACE analysis using next-generation sequencing, commonly known as parallel analysis of RNA ends (PARE), has been developed and used in plants for miRNA discovery and target validation (Addo-Quaye et al, 2008; German et al, 2008)

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Conclusion