title: Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks.
abstract: 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.
authors.affiliation: Department of Computer Science and Engineering, Washington University in Saint Louis, Campus Box 1045, Saint Louis, MO 63130, USA. weixiong.zhang@wustl.edu
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
authors.forename: Shang
authors.initials: S
authors.lastname: Gao
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhou
authors.forename: Padmanabhan
authors.initials: P
authors.lastname: Chellappan
authors.forename: Zheng
authors.initials: Z
authors.lastname: Chen
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Zhou
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Zhang
authors.forename: Nyssa
authors.initials: N
authors.lastname: Fromuth
authors.forename: Gabriela
authors.initials: G
authors.lastname: Coutino
authors.forename: Michael
authors.initials: M
authors.lastname: Coffey
authors.forename: Hailing
authors.initials: H
authors.lastname: Jin
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000382:microbiology; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D015152:Blotting, Northern; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D007113:Immunity, Innate / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D010937:Plant Growth Regulators / Q000096:biosynthesis*; D044224:Pseudomonas syringae / Q000276:immunology / Q000472:pathogenicity / Q000502:physiology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction; D014774:Virulence
chemical_list: D029681:Arabidopsis Proteins; D035683:MicroRNAs; D010937:Plant Growth Regulators