Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2011
Publication Date: 1/18/2012
Citation: Li, F., Pignatta, D., Bendix, C., Brunkard, J., Cohn, M., Tung, J., Sun, H., Kumar, P., Baker, B.J. 2012. miRNA regulation of plant innate receptors. Proceedings of the National Academy of Sciences. 5:1790-1795. Interpretive Summary: The manuscript describes the discovery of structurally and functionally unique microRNAs that silence and regulate plant innate immune receptor genes in three Solanaceae species –tobacco, tomato, and potato. These novel miRNAs target receptor gene transcripts for cleavage and trigger production of a second group of silencing small RNAs from “sliced” transcripts. This two part small RNA regulatory system has broader implications. miRNAs are regulators of several fundamental processes in higher eukaryotes, and this work demonstrates that regulation of agronomically significant innate immune receptor genes (resistance (R)-genes) and their encoded cell-death response is another miRNA-regulated process. The wide distribution of plant miRNAs targeting innate immune receptor genes described in this work suggests that this two-part silencing system is a conserved mechanism.
Technical Abstract: Plant genomes contain large numbers of cell surface leucine-rich repeat (LRR) and intracellular nucleotide binding (NB)-LRR immune receptors encoded by resistance (R) genes that recognize specific pathogen effectors and trigger resistance responses. The unregulated expression of NB-LRR genes can trigger autoimmunity in the absence of pathogen infection and inhibit plant growth. Despite the potential serious consequence on agricultural production, the mechanisms regulating R-gene expression are not well understood. We identified microRNA (miRNA) progenitor genes precursor transcripts, and two miRNAs [nta-miR6019 (22-nt) and nta-miR6020 (21-nt)] that guide cleavage of transcripts of the Toll and Interleukin-1 receptor-NB-LRR immune receptor N from tobacco that confers resistance to tobacco mosaic virus (TMV). We further showed that cleavage by nta-miR6019 triggers RNA-dependent RNA polymerase 6- and ribonuclease Dicer-like 4-dependent biogenesis of 21-nt secondary siRNAs "in phase" with the 22-nt miR6019 cleavage site. Furthermore, we found that processing of the 22-nt nta-miR6019 depended on an asymmetric bulge caused by mismatch in the nta-miR6019 precursor. Interestingly, coexpression of N with nta-miR6019 and nta-miR6020 resulted in attenuation of N-mediated resistance to TMV, indicating that these miRNAs have functional roles in NB-LRR regulation. Using a bioinformatics approach, we identified six additional 22-nt miRNA and two 21-nt miRNA families from three Solanaceae species-tobacco, tomato, and potato. We show that members of these miRNA families cleave transcripts of predicted functional R genes and trigger production of phased secondary 21-nt siRNAs. Our results demonstrate a conserved role for miRNAs and secondary siRNAs in NB-LRR/LRR immune receptor gene regulation and pathogen resistance in Solanaceae.