Biology and Function of miR159 in Plants

Abstract

MicroR159 (miR159) is ancient, being present in the majority of land plants where it targets a class of regulatory genes called GAMYB or GAMYB-like via highly conserved miR159-binding sites. These GAMYB genes encode R2R3 MYB domain transcription factors that transduce the gibberellin (GA) signal in the seed aleurone and the anther tapetum. Here, GAMYB plays a conserved role in promoting the programmed cell death of these tissues, where miR159 function appears weak. By contrast, GAMYB is not involved in GA-signaling in vegetative tissues, but rather its expression is deleterious, leading to the inhibition of growth and development. Here, the major function of miR159 is to mediate strong silencing of GAMYB to enable normal growth. Highlighting this requirement of strong silencing are conserved RNA secondary structures associated with the miR159-binding site in GAMYB mRNA that promotes miR159-mediated repression. Although the miR159-GAMYB pathway in vegetative tissues has been implicated in a number of different functions, presently no conserved role for this pathway has emerged. We will review the current knowledge of the different proposed functions of miR159, and how this ancient pathway has been used as a model to help form our understanding of miRNA biology in plants.

Keywords: GAMYB; aleurone; flowering; miR159; programmed cell death; tapetum; vegetative growth.

Figure 1

The microR159 (miR159)-GAMYB regulatory pathway appears highly conserved in land plants. Similar/identical miR159 isomiRs (shown in red) are found in most plant linages, including Lycopods (Selaginella uncinata; [3]) ferns (Salvinia cucullata; [3]), pine (Pinus densata; [36]), Amborella [37], dicots, and monocots (miRbase; [11]). Highly similar and complementary miR159 binding sites (shown in blue) are found in GAMYB homologues from lycopods (Selaginella moellendorffii; [20]), ferns (Salvinia cucullata; [11]), pine (Larix kaempferi; [38]), Amborella and many different monocots and dicots. Variant nucleotide positions are shown in black. However, throughout the plant kingdom, variation is not limited to these positions; for example, see [39].

Figure 2

The miR159-GAMYB-like pathway in Arabidopsis. miR159a is the predominant family member, being expressed in seed and throughout plant development at a constantly high level, but it is absent in anthers [8,14,46]. miR159b is expressed at a lower level than miR159a [8,15,46], but its expression pattern appears highly similar to miR159a [14]. miR159c, is weakly expressed and appears mainly confined to anthers [15]. In seeds, miR159 efficacy appears attenuated [48], enabling GAMYB-like gene expression which promotes PCD of the aleurone [41]. In contrast, throughout vegetative development, miR159 efficacy is strong, and MYB33/65 expression is strongly silenced. Only via inhibition of miR159, or mutation of the miR159 binding site within MYB33 or MYB65, will expression occur, which leads to strong deleterious outcomes, such as stunted growth and curled leaves [14,41]. Although the function of the pathway has been suggested to be involved in flowering-time and phase change, the purpose of this pathway in vegetative development is still unclear. In anthers, miR159 activity is low. Here, MYB33 and MYB65 are expressed to promote PCD in the tapetum [43]. MYB97/101/120 expression is required for pollen function [49,50]. Finally, miR159 is required for fertilization [51].

Figure 3

(A) Multiple alignment of MYB33 homologues from different plants species. The binding site is boxed in red, and the conserved flanking sequences in yellow, pink, and green throughout the Figure. (B) phyloP score of the multiple sequence alignment of MYB33 sequences. A positive score denotes evolutionary conservation, whereas, a negative score denotes acceleration [54]. A likelihood ratio test (LRT) was used as the method to detect non-neutral substitution rates. Scores were generated using rPHAST [55]. (C) Sequence logo of the binding site and conserved flanking sequences generated using WebLogo [56]. (D) RNA secondary structure prediction of the consensus sequence from the multiple alignment in A. generated using RNAalifold [57] at 22 °C and default parameters. Colours represent the number of base pairs types (i.e., AU, UA, CG, GC, UG, GU), and hue the number of non-conserved nucleotides at that position.