Potato Virus Y Infection Alters Small RNA Metabolism and Immune Response in Tomato.

Maria I Prigigallo,Fabrizio Cillo,Domenico De Paola,Mariella M Finetti-Sialer,Kristina Gruden,Maja Križnik,Domenico Catalano

doi:10.3390/v11121100

Abstract

Potato virus Y (PVY) isolate PVYC-to induces growth reduction and foliar symptoms in tomato, but new vegetation displays symptom recovery at a later stage. In order to investigate the role of micro(mi)RNA and secondary small(s)RNA-regulated mechanisms in tomato defenses against PVY, we performed sRNA sequencing from healthy and PVYC-to infected tomato plants at 21 and 30 days post-inoculation (dpi). A total of 792 miRNA sequences were obtained, among which were 123 canonical miRNA sequences, many isomiR variants, and 30 novel miRNAs. MiRNAs were mostly overexpressed in infected vs. healthy plants, whereas only a few miRNAs were underexpressed. Increased accumulation of isomiRs was correlated with viral infection. Among miRNA targets, enriched functional categories included resistance (R) gene families, transcription and hormone factors, and RNA silencing genes. Several 22-nt miRNAs were shown to target R genes and trigger the production of 21-nt phased sRNAs (phasiRNAs). Next, 500 phasiRNA-generating loci were identified, and were shown to be mostly active in PVY-infected tissues and at 21 dpi. These data demonstrate that sRNA-regulated host responses, encompassing miRNA alteration, diversification within miRNA families, and phasiRNA accumulation, regulate R and disease-responsive genes. The dynamic regulation of miRNAs and secondary sRNAs over time suggests a functional role of sRNA-mediated defenses in the recovery phenotype.

Highlights

In the last two decades, thanks to the recognition of noncoding small RNAs as leading regulatory factors, studies on long-established mechanisms that intervene in the evolution, development, and control of many biological processes have seen an impressive degree of progress
A phylogenetic analysis was performed for the 19 disease-related NLRs and receptor-like proteins (RLPs)/receptor-like kinases (RLKs) genes, selected by generating phasiRNAs and representing targets of 22-nt miRNAs
When we focused on processes involved in plant response to biotic stress [61] (Figure 4), we discovered that several differentially expressed miRNAs (DEMs) were targeting mRNAs coding for different immune receptors (NLRs, RLKs), RNA silencing (RS) proteins such as AGOs and DCLs, proteins maintaining redox homeostasis, proteins involved in biosynthesis and signaling of different phytohormones, calcium signaling, as well as transcription factors belonging to AP2/ERF, MYB, ARF, and bZIP family proteins were upregulated at 21 dpi and 30 dpi (Figure 4, Table S6)

Summary

Introduction

In the last two decades, thanks to the recognition of noncoding small RNAs (sRNAs) as leading regulatory factors, studies on long-established mechanisms that intervene in the evolution, development, and control of many biological processes have seen an impressive degree of progress. Different classes of sRNAs have been identified to date as important regulators of gene expression and adaptive responses to adverse conditions [1,2]. The mechanism that produces sRNAs entails the cleavage of double-stranded RNA (dsRNA), or of single-stranded RNAs forming stable secondary structures of endogenous or exogenous origins, yielding miRNAs or siRNAs of predominantly 21 to 24 nucleotides (nt) in length. Precursors of sRNAs are processed by Dicer-like (DCL) enzymes and loaded into Argonaute (AGO) proteins to form the RNA-silencing complexes (RISC). The expression profiles of many of these genes were shown to be altered by viral infections [10]

Results

Discussion

Conclusion