Phenotypic Plasticity of Adventitious Rooting in Arabidopsis Is Controlled by Complex Regulation of AUXIN RESPONSE FACTOR Transcripts and MicroRNA Abundance

Abstract

The development of shoot-borne roots, or adventitious roots, is indispensable for mass propagation of elite genotypes. It is a complex genetic trait with a high phenotypic plasticity due to multiple endogenous and environmental regulatory factors. We demonstrate here that a subtle balance of activator and repressor AUXIN RESPONSE FACTOR (ARF) transcripts controls adventitious root initiation. Moreover, microRNA activity appears to be required for fine-tuning of this process. Thus, ARF17, a target of miR160, is a negative regulator, and ARF6 and ARF8, targets of miR167, are positive regulators of adventitious rooting. The three ARFs display overlapping expression domains, interact genetically, and regulate each other's expression at both transcriptional and posttranscriptional levels by modulating miR160 and miR167 availability. This complex regulatory network includes an unexpected feedback regulation of microRNA homeostasis by direct and nondirect target transcription factors. These results provide evidence of microRNA control of phenotypic variability and are a significant step forward in understanding the molecular mechanisms regulating adventitious rooting.

The role of decapping proteins in the miRNA accumulation inArabidopsis thaliana

“…The reason is probably because of the differences between the expression patterns of miR167 and that of its targets. 24 Unlike pri-miR167s, ARF6 and ARF8 mRNAs are expressed only in limited regions in the hypocotyls. 24 Alternatively, it is possible that miR167-mediated gene silencing represses the translation and results in no degradation or less accumulation of the mRNAs.…”

“…24 Unlike pri-miR167s, ARF6 and ARF8 mRNAs are expressed only in limited regions in the hypocotyls. 24 Alternatively, it is possible that miR167-mediated gene silencing represses the translation and results in no degradation or less accumulation of the mRNAs. The fact that ARF6 and ARF8 mRNAs in se-1 increased by only 2-fold compared with the level in 15 d Col-0, despite that the levels of NAC1, CUC1 and CUC2 mRNAs in se-1 increased by 8-fold compared with 15 d Col-0 (Fig.…”

“…[18][19][20][21] dcl1-and ago1-null mutants show lethal phenotypes, indicating that miRNAs participate in plant development. [22][23][24][25] siRNAs originate from endogenous and exogenous doublestranded RNAs (dsRNAs). The dsRNAs are processed by DCL2, Decapping 1 (Dcp1), Decapping 2 (Dcp2) and VARIcOse (Vcs) are components of the decapping complex that removes the 7-methyl-guanosine 5'-diphosphate from the 5' end of mRNAs.…”

Branching Out in Roots: Uncovering Form, Function, and Regulation

“…The major players mediating auxin signaling during adventitious rooting are the activating ARF6 and ARF8 and the repressing ARF17 ( Fig. 3; Gutierrez et al, 2009). The expression of ARF6 and ARF8 is controlled by MIR167, while ARF17 expression is regulated by MIR160.…”

Ancient microRNA families that regulate transcription factors are preferentially preserved during plant radiation

“…For example, in Arabidopsis, miR160/miR167 and ARFs form this feedback loop to regulate different developmental processes including adventitious root formation. 9 Similarly, miR156-SPLs, miR172-AP2 also form as 2 negative feedback loops in regulation of developmental timing in Arabidopsis. 10 Moreover, the miRNA-regulated TFs usually have multiple duplicates in the plant genome and preserve the same miRNA-binding sites.…”