Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

Flávia Thiebaut,Berenice De Lima,Laurent Farinelli,Barbara Peixoto,Adriana Hemerly,Lucas Vieira,Clícia Grativol,Helkin Ballesteros,Maria Walter,Paulo Ferreira,Júlio Entenza,Elvismary De Armas,Mariana Motta,Sergio Lifschitz,Cristian Rojas,Edmundo Calixto

doi:10.3390/ncrna3040025

Abstract

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

Highlights

Sugarcane is an economically important crop for sugar and ethanol production [1]
Many small interfering RNAs (siRNAs) aligned to a transcript encoding a coppertransporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae
To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR

Summary

Introduction

Sugarcane is an economically important crop for sugar and ethanol production [1]. Crop productivity is negatively affected by environmental stress conditions, such as biotic stress induced by pathogenic bacteria [4]. Avenae affects crops practically worldwide [5]. Among important pathogens of sugarcane, Acidovorax avenae subsp. This bacterium was previously classified as Pseudomonas, and recently reclassified to the Acidovorax genus [6]. A. avenae causes the Red Stripe Disease, which damages leaves and leaf sheaths [7]. Despite of the harm caused by the disease, little is known about the molecular mechanisms triggered in sugarcane in response to the infection

Results

Discussion

Conclusion