miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves    

Abstract

The phytohormone auxin is a key regulator of plant growth and development that exerts its functions through F-box receptors. Arabidopsis (Arabidopsis thaliana) has four partially redundant of these receptors that comprise the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX1 auxin receptor (TAAR) clade. Recent studies have shown that the microRNA miR393 regulates the expression of different sets of TAAR genes following pathogen infection or nitrate treatment. Here we report that miR393 helps regulate auxin-related development of leaves. We found that AtMIR393B is the predominant source for miR393 in all aerial organs and that miR393 down-regulates all four TAAR genes by guiding the cleavage of their mRNAs. A mutant unable to produce miR393 shows developmental abnormalities of leaves and cotyledons reminiscent of enhanced auxin perception by TAARs. Interestingly, miR393 initiates the biogenesis of secondary siRNAs from the transcripts of at least two of the four TAAR genes. Our results indicate that these siRNAs, which we call siTAARs, help regulate the expression of TAAR genes as well as several unrelated genes by guiding the cleavage of their mRNAs. Thus, miR393 and possibly siTAARs regulate auxin perception and certain auxin-related aspects of leaf development.

miR393: Integrator of environmental cues in auxin signaling?

“…mild morphological changes (e.g., leaf and cotyledon epinasty) when grown in short-day conditions (10 h light 20°C/14 h dark 18°C). 5 As we hypothesized, other conditional phenotypes were also revealed by different growth conditions: when grown under continuous light at 20°C, mir393b-1 plants had dentated rather than lobed leaf margins, had roundish rather than elongated leaf blades and developed significantly more and longer axillary stems than wild type plants ( Fig. 2A, B and Table 1).…”

“…In leaves this led to accumulation of higher levels of TAAR transcripts than in wild-type plants. 5 We have performed additional real-time qPCR experiments on leaf samples and found that mir393b-1 also accumulates higher mRNA levels of primary auxin-responsive genes such as IAA12 (1.2-fold), DFL2 (3.0-fold), IAA1 (4.1-fold) or IAA19 (1.7-fold) than Col-0 plants ( Fig. 1).…”

“…9 Error bars are SD for three measurements of cDNAs obtained for pools of at least 20 plants. 5 The primers used are communicated upon request. …”

“…[2][3][4][5] So far, three types of regulations were identified: (1) cleavage of TIR1, AFB2 and AFB3 mRNAs and transcriptional regulation of AFB1 in bacteria-infected leaves guided by miR393 originating primarily from AtMIR393A, one of the two miR393-encoding genes, 2 (2) miR393-guided cleavage of only AFB3 mRNAs in the response of roots to nitrate, 3 and (3) cleavage of all four TAAR mRNAs in developing leaves guided by miR393 originating from AtMIR393B. 5 We showed in this latter case that miR393 also eventually triggers the biogenesis of secondary siRNAs, termed siTAARs, that function to regulate the expression of TAAR genes, as well as that of unrelated genes, and help maintaining proper leaf development. …”

Proteomic Identification of Putative MicroRNA394 Target Genes in Arabidopsis thaliana Identifies Major Latex Protein Family Members Critical for Normal Development

“…The post-transcriptional regulation of the TIR1 F-box by miR393 is well established (12,65). TIR1 post-translationally targets several Aux/IAA family members for ubiquitin-mediated degradation (12,65).…”