Hypocotyl Transcriptome Reveals Auxin Regulation of Growth-Promoting Genes through GA-Dependent and -Independent Pathways

Abstract

Many processes critical to plant growth and development are regulated by the hormone auxin. Auxin responses are initiated through activation of a transcriptional response mediated by the TIR1/AFB family of F-box protein auxin receptors as well as the AUX/IAA and ARF families of transcriptional regulators. However, there is little information on how auxin regulates a specific cellular response. To begin to address this question, we have focused on auxin regulation of cell expansion in the Arabidopsis hypocotyl. We show that auxin-mediated hypocotyl elongation is dependent upon the TIR1/AFB family of auxin receptors and degradation of AUX/IAA repressors. We also use microarray studies of elongating hypocotyls to show that a number of growth-associated processes are activated by auxin including gibberellin biosynthesis, cell wall reorganization and biogenesis, and others. Our studies indicate that GA biosynthesis is required for normal response to auxin in the hypocotyl but that the overall transcriptional auxin output consists of PIF-dependent and -independent genes. We propose that auxin acts independently from and interdependently with PIF and GA pathways to regulate expression of growth-associated genes in cell expansion.

Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth

“…This suggests that following shade treatment, it might be possible to observe a temporal delay in the regulation of auxin-responsive genes between cotyledons and hypocotyls. To verify this prediction, we analyzed shade regulation of genes that rapidly (within 30 minutes) respond to picloram (a synthetic auxin) application in hypocotyls (Chapman et al, 2012). We detected expression of 46 (70%) picloram-regulated genes in our data set, among which 43 were regulated by shade.…”

“…However, while in the hypocotyl, the expression levels of many of these genes continued to rise until 90 min; in the cotyledons, the peak of expression was typically at 45 min ( Figure 4A). As this initial analysis did not provide evidence for an obvious temporal delay of auxin-regulated genes between hypocotyls and cotyledons, we tested this further by analyzing the expression of genes in response to a 2-h picloram application (Chapman et al, 2012). These genes displayed a more organ-specific shade response but did not provide evidence for an earlier auxin response in cotyledons than hypocotyls (Supplemental Figure 4A).…”

“…These genes displayed a more organ-specific shade response but did not provide evidence for an earlier auxin response in cotyledons than hypocotyls (Supplemental Figure 4A). In addition, we analyzed shade regulation of all the genes identified as being auxin regulated in two studies (Nemhauser et al, 2006;Chapman et al, 2012). The 539 auxin-regulated genes that are regulated by shade in both hypocotyls and cotyledons were categorized as follows: regulated simultaneously by shade in both organs, regulated first in the hypocotyl, and regulated first in the cotyledons.…”

PIFs: Systems Integrators in Plant Development

“…In response to shade and high temperatures, and possibly under diurnal conditions or in response to Suc (Lilley et al, 2012), PIFs induce auxin synthesis and responses (see below), placing PIFs upstream of auxin signaling. However, transcriptome analysis to identify auxin-regulated genes expressed in elongating hypocotyls (Chapman et al, 2012) suggested a model whereby auxin might promote growth partly through PIF-dependent pathways, potentially placing auxin upstream of PIFs, although this possibility needs further testing. Importantly, pif4 pif5 double mutants displayed altered responsiveness to exogenous auxin, suggesting that PIFs modulate auxin signaling (Nozue et al, 2011;Hornitschek et al, 2012).…”

A Triple Helix-Loop-Helix/Basic Helix-Loop-Helix Cascade Controls Cell Elongation Downstream of Multiple Hormonal and Environmental Signaling Pathways inArabidopsis

“…PRE1 was initially identified as a positive regulator of GA responses , but other studies have elucidated roles of PRE1 and its homologs in growth regulation by a wide range of signals, including BR, auxin, and light (Zhang et al, 2009;Bai et al, 2012;Oh et al, 2012;Chapman et al, 2012). Overexpression of PRE1 and its rice (Oryza sativa) homolog INCREASED LAMINA INCLINATION1 (ILI1) increased BR-induced cell elongation in both Arabidopsis and rice (Zhang et al, 2009), and overexpression of PRE3/ATBS1/TMO7 suppressed the bri1 mutant ).…”