MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress. Increasing evidence also supports that plant miRNAs contribute to immune responses to pathogens. Here, we used deep sequencing of small RNA libraries for global identification of rice miRNAs that are regulated by fungal elicitors. We also describe 9 previously uncharacterized miRNAs in rice. Combined small RNA and degradome analyses revealed regulatory networks enriched in elicitor-regulated miRNAs supported by the identification of their corresponding target genes. Specifically, we identified an important number of miRNA/target gene pairs involved in small RNA pathways, including miRNA, heterochromatic and trans-acting siRNA pathways. We present evidence for miRNA/target gene pairs implicated in hormone signaling and cross-talk among hormone pathways having great potential in regulating rice immunity. Furthermore, we describe miRNA-mediated regulation of Conserved-Peptide upstream Open Reading Frame (CPuORF)-containing genes in rice, which suggests the existence of a novel regulatory network that integrates miRNA and CPuORF functions in plants. The knowledge gained in this study will help in understanding the underlying regulatory mechanisms of miRNAs in rice immunity and develop appropriate strategies for rice protection.

Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms

“…In Arabidopsis, miR408 and miR160a aid in the induction of physical cell wall reinforcement by positively regulating callose deposition and lignification (Feng et al, 2013). In rice and Medicago, a number of miRNAs target ET, JA and SA biogenesis during the early stages of pathogenesis (Wong et al, 2014;Baldrich et al, 2015). A number of miRNAs also repress the cellular detoxification processes during challenge by pathogens.…”

Phosphate excess increases susceptibility to pathogen infection in rice

“…MicroRNAs (miRNAs) are small noncoding RNAs that mediate post‐transcriptional gene silencing through degradation or translational repression of target transcripts (Llave et al , ; Brodersen et al , ). They are essential regulators of gene expression in plant developmental processes and adaptation to biotic and abiotic stress (Navarro et al , ; Chen, ; Li et al , ; ; Shivaprasad et al , ; Campo et al , ; Jeong and Green, ; Baldrich et al , ; Baldrich and San Segundo, ; Song et al , ). Evidence also supports a regulation of nutrient homeostasis by certain miRNAs in plants (Liang et al , ; Paul et al , ; Chien et al , ).…”

Osa-miR169 Negatively Regulates Rice Immunity against the Blast Fungus Magnaporthe oryzae

“…For example, silencing OsDCL1 , the key gene for miRNA biogenesis, results in enhancement of resistance to virulent rice blast strains due to the constitutive expression of 13 pathogenesis-related ( PR ) genes and two PTI-related genes OsKS4 and OsNAC4 (Zhang et al, 2015). Recently, nine new miRNAs were identified by deep sequencing of small RNA libraries derived from leaves treated with M. oryzae elicitors (Baldrich et al, 2015). In addition, the M. oryzae elicitor-responsive miRNA, Osa-miR7695, was identified as a positive regulator for rice resistance against M. oryzae by down-regulating the expression of OsNramp6 ( Natural resistance-associated macrophage protein 6 ) (Campo et al, 2013).…”

“…In rice, different miR169 isoforms are differentially accumulated in the resistant and susceptible accessions upon M . oryzae infection (Li et al, 2014, 2016), and are differentially responsive to elicitor treatment (Campo et al, 2013; Baldrich et al, 2015), indicating the involvement of miR169/NF-YA modules in rice responses to M . oryzae .…”