, Volume 75, Issue 1-2, pp 93-105,
Open Access This content is freely available online to anyone, anywhere at any time.
Date: 12 Dec 2010

Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks


MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses in most eukaryotes. We globally profiled plant miRNAs in response to infection of bacterial pathogen Pseudomonas syringae pv. tomato (Pst). We sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 and 14 h post infection of non-pathogenic, virulent and avirulent strains of Pst. We identified 15, 27 and 20 miRNA families being differentially expressed upon Pst DC3000 hrcC, Pst DC3000 EV and Pst DC3000 avrRpt2 infections, respectively. In particular, a group of bacteria-regulated miRNAs targets protein-coding genes that are involved in plant hormone biosynthesis and signaling pathways, including those in auxin, abscisic acid, and jasmonic acid pathways. Our results suggest important roles of miRNAs in plant defense signaling by regulating and fine-tuning multiple plant hormone pathways. In addition, we compared the results from sequencing-based profiling of a small set of miRNAs with the results from small RNA Northern blot and that from miRNA quantitative RT-PCR. Our results showed that although the deep-sequencing profiling results are highly reproducible across technical and biological replicates, the results from deep sequencing may not always be consistent with the results from Northern blot or miRNA quantitative RT-PCR. We discussed the procedural differences between these techniques that may cause the inconsistency.

Weixiong Zhang, Shang Gao, Xiang Zhou, and Padmanabhan Chellappan contributed equally to this work.
Accession numbers: The raw and processed deep-sequencing data from the thirteen libraries used in the current study have been deposited into NCBI/GEO database and are available under accession number GSE19694. Arabidopsis microarray gene expression data used in our study were from the AtGenExpress project, available at TAIR with accession number ME00331.
An erratum to this article can be found at http://dx.doi.org/10.1007/s11103-011-9760-6.