Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato -Phytophthora infestans interaction

Abstract

Our previous studies indicated that tomato miR482b could negatively regulate the resistance of tomato to Phytophthora infestans and the expression of miR482b was decreased after inoculation with P. infestans. However, the mechanism by which the accumulation of miR482b is suppressed remains unclear. In this study, we wrote a program to identify 89 long noncoding RNA (lncRNA)-originated endogenous target mimics (eTMs) for 46 miRNAs from our RNA-Seq data. Three tomato lncRNAs, lncRNA23468, lncRNA01308 and lncRNA13262, contained conserved eTM sites for miR482b. When lncRNA23468 was overexpressed in tomato, miR482b expression was significantly decreased, and the expression of the target genes, NBS-LRRs, was significantly increased, resulting in enhanced resistance to P. infestans. Silencing lncRNA23468 in tomato led to the increased accumulation of miR482b and decreased accumulation of NBS-LRRs, as well as reduced resistance to P. infestans. In addition, the accumulation of both miR482b and NBS-LRRs was not significantly changed in tomato plants that overexpressed lncRNA23468 with a mutated eTM site. Based on the VIGS system, a target gene of miR482b, Solyc02g036270.2, was silenced. The disease symptoms of the VIGS- Solyc02g036270.2 tomato plants were in accordance with those of tomato plants in which lncRNA23468 was silenced after inoculation with P. infestans. More severe disease symptoms were found in the modified plants than in the control plants. Our results demonstrate that lncRNAs functioning as eTMs may modulate the effects of miRNAs in tomato and provide insight into how the lncRNA23468-miR482b-NBS-LRR module regulates tomato resistance to P. infestans.

A barrier against blight

The interplay between various non-protein-coding RNA molecules plays a critical role in managing tomato plants’ defenses against infection. Long non-coding RNA (lncRNA) molecules can modulate gene function by binding to other, complementary RNA molecules. Researchers led by Jun Meng and Yushi Luan at the Dalian University of Technology recently set out to identify lncRNAs that contribute to tomato resistance to the pathogen that causes late blight. Their team specifically sought lncRNAs targeting another RNA molecule known as miR482b, which they had previously found to weaken plant resistance to infection. They found that one such molecule, lncRNA23468, can counter the effects of miR482b and protect tomatoes against late blight by boosting the activity of genes involved in the immune response. These results thus offer important insights into the mechanisms underlying disease resistance in this important crop.