Rice microRNAs: identification of novel genes controlling development and adaptation to biotic stresses in a model cereal – OsMir

SITUATION DE LA THEMATIQUE MicroRNAs represent a large family of small non-coding RNAs that have recently been identified as regulators of diverse biological functions in eukaryotes. Until recently only very few of them were known, such as the two founding members of the family Lin4 and Let7 in C. elegans. However, the recent availability of complete genome sequences from different species, associated with the development of techniques to clone cDNAs derived from small RNAs has led to the discovery of hundreds of miRNAs that control development and other biological functions. MicroRNAs are single-stranded RNAs of 18 to 26 nucleotides derived from a precursor (pre-miRNA) encoded by an endogenous gene transcribed by RNA pol II (Kurihara and Watanabe, 2004). In Arabidopsis, genetic characterisation of mutants identified DCL1, a gene encoding a Dicer-like activity required for processing of the pre-miRNA, HEN1, encoding an miRNA methylase (Yu et al, 2005) and HYL1, which binds double-stranded (ds)RNA (Han et al, 2004). All miRNAs target a specific mRNA via an miRNA/mRNA interaction to direct its cleavage or inhibit its translation. In either case this is accomplished by the large RNA Inducing Silencing Complex (RISC) associated with the miRNA and containing AGO-like proteins. Genetic studies in Arabidopsis suggest that AGO1 could be a component of the RISC associated with miRNAs (Vaucheret et al, 2004). In plants, hundreds of miRNA genes have been predicted in the Arabidopsis genome using both experimental and in silico approaches (Dugas and Bartel, 2004). At present, ~30 miRNAs displaying tissue-specific expression have been characterised and shown to control different stages of development. Most direct the cleavage of the mRNA target in vivo (Llave et al, 2002; Palatnik et al, 2003; Xie et al, 2003) or in vitro (Tang et al, 2003). One of them, targeting an AP2 transcription factor controlling flower development, was shown to inhibit translation of its target (Aukerman and Sakai, 2003). In Arabidopsis, mRNA targets could be predicted on the basis of near-perfect complementarity to the miRNAs (Rhoades et al, 2002). Remarkably, many of these targets encode transcription factors and signalling proteins controlling different stages of development, as well as proteins that control other biological processes like RNA processing and stress responses (Dugas and Bartel, 2004; Rhoades-Jones et al, 2004; Sunkar and Zhu, 2004). MicroRNAs are also closely-related to Short Interfering RNAs (siRNAs), another class of small non-coding RNAs mediating Post-Transcriptional Gene Silencing (PTGS) and the silencing of retroelements (Baulcombe, 2004). PTGS is a natural defence mechanism induced in response to viral infection. In Arabidopsis, siRNAs are induced by viral infection and accumulate as dsRNAs of 21-26 nucleotides that derive from viral dsRNA replication intermediates processed by DCL2 (Xie et al, 2004). They are then incorporated into a RISC to direct viral RNA degradation. Importantly, miRNA and siRNA mediated pathways share common components (Baulcombe, 2004). Consequently, it has been shown in Arabidopsis and tobacco that some viral protein acting as suppressor of PTGS also interfere with miRNA accumulation and function. The mechanism of viral suppressors of PTGS is poorly known and has never been studied in cereals. The discovery of miRNAs opens a completely new field in the study of plant development and plant response to the environment which needs to be explored extensively because of its potential in improving plant breeding and crop yield. It can also provide explanations for certain agronomic traits. Until recently, studies on miRNAs in plants had been restricted to Arabidopsis thaliana. Progress on rice genomics now allows the extension of these studies to cereals. Rice is a diploid species with a very small genome of 440 Mb, compared to cryptic tetraploid maize (3,500Mb), diploid barley (5000Mb) and hexaploid wheat (16,000M.