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Elf18-induced long noncoding RNA associates with Mediator to enhance expression of innate immune response genes in Arabidopsis

ABSTRACT: Plant immune response is a complex process involving both transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis long-noncoding (lnc) RNA, designated elf18-induced long noncoding RNA 1 (ELENA1), as a factor enhancing resistance against Pseudomonas syringe pv. tomato DC3000. ELENA1 knock-down plants show a decreased expression of PR1 and the plants are susceptible to pathogens. By contrast, plants over-expressing ELENA1 show elevated Pathogenesis-Related gene 1 (PR1) expression after elf18 treatment and display pathogen resistance phenotype. RNA-seq analysis of ELENA1 overexpressing plants after elf18 treatment confirms increased expression of defense-related genes compared to WT. ELENA1 directly interacts with Mediator subunit 19a (MED19a) and affects enrichment of MED19a on PR1 promoter. These results show that ELENA1 is a novel lncRNA that regulates PR1 expression through MED19a. Our findings uncover an additional layer of complexity implicating lncRNA in the transcriptional regulation of plant innate immunity.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE93560 | GEO | 2017/05/19

SECONDARY ACCESSION(S): PRJNA361118

REPOSITORIES: GEO

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Project description:Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to cluster 19A mutants and individual sub-deletions for the cluster 19A genes tin1, tin3, tin4 and tin5. We found plant responses to the mutants were significantly different although the macroscopic phenotypes of the individual mutants were very similar. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200∆19A, SG200∆tin1, SG200∆tin3, SG200∆tin4 and SG200∆tin5, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023). These data served as controls for this experiment.

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Elf18-induced long noncoding RNA associates with Mediator to enhance expression of innate immune response genes in Arabidopsis

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