title: A non-canonical plant microRNA target site.
abstract: Plant microRNAs (miRNAs) typically form near-perfect duplexes with their targets and mediate mRNA cleavage. Here, we describe an unconventional miRNA target of miR398 in Arabidopsis, an mRNA encoding the blue copper-binding protein (BCBP). BCBP mRNA carries an miR398 complementary site in its 5'-untranslated region (UTR) with a bulge of six nucleotides opposite to the 5' region of the miRNA. Despite the disruption of a target site region thought to be especially critical for function, BCBP mRNAs are cleaved by ARGONAUTE1 between nucleotides 10th and 11th, opposite to the miRNA, like conventional plant target sites. Levels of BCBP mRNAs are inversely correlated to levels of miR398 in mutants lacking the miRNA, or transgenic plants overexpressing it. Introducing two mutations that disrupt the miRNA complementarity around the cleavage site renders the target cleavage-resistant. The BCBP site functions outside of the context of the BCBP mRNA and does not depend on 5'-UTR location. Reducing the bulge does not interfere with miR398-mediated regulation and completely removing it increases the efficiency of the slicing. Analysis of degradome data and target predictions revealed that the miR398-BCBP interaction seems to be rather unique. Nevertheless, our results imply that functional target sites with non-perfect pairings in the 5' region of an ancient conserved miRNA exist in plants.
authors.affiliation: INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France, AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France and Department of Biology and Plant Biology Ph.D. Program, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Cécile
authors.initials: C
authors.lastname: Brousse
authors.forename: Qikun
authors.initials: Q
authors.lastname: Liu
authors.forename: Linda
authors.initials: L
authors.lastname: Beauclair
authors.forename: Aurélie
authors.initials: A
authors.lastname: Deremetz
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bouché
mesh_terms: D020121:5' Untranslated Regions; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D020029:Base Pairing; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D020121:5' Untranslated Regions; D029681:Arabidopsis Proteins; C085507:BCB protein, Arabidopsis; D002352:Carrier Proteins; C543882:MIRN398 microRNA, Arabidopsis; D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant