Grapevine (Vitis vinifera L.) microRNA expression profiling with miRNA bioarrays: indications for an involvement of miRNA in apoptosis and pathogenesis

摘要

MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are small, noncoding RNAs that can play crucial regulatory roles in eukaryotes- by targeting mRNAs for silencing. They have recently emerged as important regulators of mRNA degradation, translational repression, and chromatin modification. In Arabidopsis thaliana, 43 miRNAs comprising 15 families have been reported thus far. In an attempt to identify novel and apoptosis/pathogen regulated miRNAs and siRNAs, we performed a robust microarray screening of small RNAs population from Vitis vinifera L., cv. Limberger cell suspension exposed to apoptosis inducers (e.g. methyl jasmonate) or elicitors (botrycin and cinerein) derived from necrotrophic fungus Botrytis cinerea Pers et. Fries. Using a microarray expression profiling approach we identified 22 miRNAs. We have also found that a majority of these miRNAs were predicted to target stress/defense-related genes of plants. Of the 22 V. vinifera miRNA, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental and/or stress/defense-related expression patterns. Ten of the miRNAs are highly conserved in other plant species, suggesting that even conserved miRNAs may have different regulatory roles in different species.rnOur results show that grapevine miRNAs can be induced by apoptosis inducers and may function in one of the most critical defense systems for structural and mechanical fitness. Subsequent analysis revealed that some of the miRNAs are preferentially expressed in specific tissues, and several are either upregulated or downregulated by biotic/abiotic stresses. Fifty-one potential targets with diverse function were predicted for the newly identified miRNAs based on sequence complementarity. In addition to miRNAs, we identified 102 other novel endogenous small RNAs in Vitis. These findings suggest that a large number of miRNAs and other small regulatory RNAs are encoded by the Vitis vinifera genome and that some of them may play important roles in plant responses to environmental stresses as well as in development and genome maintenance.