Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression

Regulation of Arabidopsis SHY2/IAA3 protein turnover

Auxin/indole acetic acid (Aux/IAA) proteins regulate transcriptional responses to the plant hormone auxin. Gain-of-function mutations in the Arabidopsis SHORT HYPOCOTYL 2 (SHY2/IAA3) gene encoding an Aux/IAA protein increase steady-state levels of SHY2/IAA3 protein and decrease auxin responses, indicating that SHY2/IAA3 negatively regulates auxin signaling. These shy2 mutations also cause ectopic light responses, suggesting that SHY2/IAA3 may promote light signaling. Auxin regulates turnover of the related Auxin-resistant (AXR)2/IAA7 and AXR3/IAA17 proteins by increasing their interaction with the Skp1-Cdc53/cullin-F-box (SCFTIR1) E3 ubiquitin ligase complex. To investigate whether SHY2/IAA3 is regulated similarly, we have used a turnover assay to reveal that axr1 and transport inhibitor resistant (tir)1 mutations affecting SCFTIR1 decrease SHY2/IAA3 turnover. In pull-down assays, SHY2/IAA3 protein interacted with TIR1, the F-box component of SCFTIR1 and with the photoreceptor phytochrome B. Auxin stimulated SHY2/IAA3 interaction with TIR1, whereas the shy2-2 gain-of-function mutation decreased this interaction. Light did not affect the interaction, suggesting that light regulates some other aspect of Aux/IAA gene or protein function. The chemical juglone (5-hydroxy-1,4-naphthoquinone) inhibited the interaction, suggesting that peptidyl-prolyl isomerization may mediate auxin-induced SHY2/IAA3 protein turnover.

AXR3 and SHY2 interact to regulate root hair development

Signal transduction of the plant hormone auxin centres on the regulation of the abundance of members of the Aux/IAA family of transcriptional regulators, of which there are 29 in Arabidopsis. Auxin can influence Aux/IAA abundance by promoting the transcription of Aux/IAA genes and by reducing the half-life of Aux/IAA proteins. Stabilising mutations, which render Aux/IAA proteins resistant to auxin-mediated degradation, confer a wide range of phenotypes consistent with disruptions in auxin response. Interestingly, similar mutations in different family members can confer opposite phenotypic effects. To understand the molecular basis for this functional specificity in the Aux/IAA family, we have studied a pair of Aux/IAAs, which have contrasting roles in root hair development. We have found that stabilising mutations in AXR3/IAA17 blocks root hair initiation and elongation, whereas similar mutations in SHY2/IAA3 result in early initiation of root hair development and prolonged hair elongation, giving longer root hairs. The phenotypes resulting from double mutant combinations, the transient induction of expression of the proteins, and the pattern of transcription of the cognate genes suggest that root hair initiation is controlled by the relative abundance of SHY2 and AXR3 in a cell. These results suggest a general model for auxin signalling in which the modulation of the relative abundance of different Aux/IAA proteins can determine which down-stream responses are induced.

Ethylene and auxin control the Arabidopsis response to decreased light intensity

Morphological responses of plants to shading have long been studied as a function of light quality, in particular the ratio of red to far red light that affects phytochrome activity. However, changes in light quantity are also expected to be important for the shading response because plants have to adapt to the reduction in overall energy input. Here, we present data on the involvement of auxin and ethylene in the response to low light intensities. Decreased light intensities coincided with increased ethylene production in Arabidopsis rosettes. This response was rapid because the plants reacted within minutes. In addition, ethylene- and auxin-insensitive mutants are impaired in their reaction to shading, which is reflected by a defect in leaf elevation and an aberrant leaf biomass allocation. On the molecular level, several auxin-inducible genes are up-regulated in wild-type Arabidopsis in response to a reduction in light intensity, including the primary auxin response gene IAA3 and a protein with similarity to AUX22 and the 1-aminocyclopropane-1-carboxylic acid synthase genes ACS6, ACS8, and ACS9 that are involved in ethylene biosynthesis. Taken together, the data show that ethylene and auxin signaling are required for the response to low light intensities.

DFL2, a new member of the Arabidopsis GH3 gene family, is involved in red light-specific hypocotyl elongation

A new GH3-related gene, designated DFL2, causes a short hypocotyl phenotype when overexpressed under red and blue light and a long hypocotyl when antisensed under red light conditions. Higher expression of this gene was observed in continuous white, blue and far-red light but the expression level was low in red light and darkness. DFL2 gene expression was induced transiently with red light pulse treatment. DFL2 transgenic plants exhibited a normal root phenotype including primary root elongation and lateral root formation, although primary root elongation was inhibited in antisense transgenic plants only under red light. The adult phenotypes of sense and antisense transgenic plants were not different from that of wild type. DFL2 promoter activity was observed in the hypocotyl. Our results suggest that DFL2 is located downstream of red light signal transduction and determines the degree of hypocotyl elongation.

Yokonolide B, a novel inhibitor of auxin action, blocks degradation of AUX/IAA factors

Yokonolide B (YkB; also known as A82548A), a spiroketal-macrolide, was isolated from Streptomyces diastatochromogenes B59 in a screen for inhibitors of beta-glucoronidase expression under the control of an auxin-responsive promoter in Arabidopsis. YkB inhibits the expression of auxin-inducible genes as shown using native and synthetic auxin promoters as well as using expression profiling of 8300 Arabidopsis gene probes but does not affect expression of an abscisic acid- and a gibberellin A3-inducible gene. The mechanism of action of YkB is to block AUX/IAA protein degradation; however, YkB is not a general proteasome inhibitor. YkB blocks auxin-dependent cell division and auxin-regulated epinastic growth mediated by auxin-binding protein 1. Gain of function mutants such as shy2-2, slr1, and axr2-1 encoding AUX/IAA transcriptional repressors and loss of function mutants encoding components of the ubiquitin-proteolytic pathway such as axr1-3 and tir1-1, which display increased AUX/IAAs protein stability, are less sensitive to YkB, although axr1 and tir1 mutants were sensitive to MG132, a general proteasome inhibitor, consistent with a site of action downstream of AXR1 and TIR. YkB-treated seedlings displayed similar phenotypes as dominant AUX/IAA mutants. Taken together, these results indicate that YkB acts to block AUX/IAA protein degradation upstream of AXR and TIR, links a shared element upstream of AUX/IAA protein stability to auxin-induced cell division/elongation and to auxin-binding protein 1, and provides a new tool to dissect auxin signal transduction.

Phytochrome-hormonal signalling networks

Through time, plants have evolved an extraordinary ability to interpret environmental cues. One of the most reliable of these cues is light, and plants are particularly adept at sensing and translating environmental light signals. The phytochrome family of photoreceptors monitor cues such as daylength or vegetative shade and adjust development to reflect change in these parameters. Indeed, it is their ability to coordinate these complex developmental changes that underpins the remarkable success of plants. Evidence is mounting that hormones control many of these light-mediated changes. Therefore, if we are to understand how light manipulates development we need to explore the interplay between light and hormonal signalling. Toward this goal, this review highlights the known convergence points of the phytochrome and the hormonal networks and explores their interactions. Contents Summary 449 I. Introduction 449 II. The phytochrome protein 450 III. Bacteriophytochromes 450 IV. IBacteriophytochrome signalling 450 V. Plant phytochrome signalling 451 VI. Ethylene perception and signalling 451 VII. Cytokinin perception and signalling 452 VIII. Brassinosteroid perception and signalling 453 IX. Gibberellin signalling 455 X. Auxin signalling 456 XI. Proteolysis in light and hormonal signalling 458 XII. Conclusion 459 Acknowledgements 459 References 459.

Simple hormones but complex signalling

It has not been easy to make sense of the pleiotropic effects of plant hormones, especially of auxins; but now, it has become possible to study these effects within the framework of what we know about signal transduction in general. Changes in local auxin concentrations, perhaps even actively maintained auxin gradients, signal to networks of transcription factors, which in turn signal to downstream effectors. Transcription factors can also signal back to hormone biosynthetic pathways.

Expression profiling of plant development

Microarrays have been used to study the response of plants to many signals, including light, hormones and transcription factors. The results in each case can give an overall view of the global response to the signal or identify direct targets of the signal, and can reveal new links between different signaling pathways.

The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affects auxin response in Arabidopsis

The plant hormone, auxin, regulates many aspects of growth and development. Despite its importance, the molecular mechanisms underlying the action of auxin are largely unknown. To gain a more comprehensive understanding of the primary responses to auxin, we analyzed the expression of genes in Arabidopsis seedlings treated with indole-3-acetic acid (IAA) for 15 min. We identified a single gene that is downregulated early, and 29 genes that are upregulated early. Several types of typical transcription factors are identified as early upregulated genes, suggesting that auxin signals are mediated by a master set of diverse transcriptional regulators. Of the genes that responded to auxin, the expression of the homeobox gene, HAT2, was induced rapidly. Furthermore, we show that the expression of HAT2 is induced by auxin, but not by other phytohormones. To analyze the function of HAT2 in the plant's response to auxin, we generated 35S::HAT2 transgenic plants. These produced long hypocotyls, epinastic cotyledons, long petioles, and small leaves, which are characteristic of the phenotypes of the auxin-overproducing mutants, superroot1 (sur1) and superroot2 (sur2). On the other hand, 35S::HAT2 plants showed reduced lateral root elongation, and reduced auxin sensitivity compared to wild-type plants. Together with the results of RNA blotting and biochemical analyses, these findings suggest that HAT2 plays opposite roles in the shoot and root tissues in regulating auxin-mediated morphogenesis.

Down-regulation of DR12, an auxin-response-factor homolog, in the tomato results in a pleiotropic phenotype including dark green and blotchy ripening fruit

Following differential screening of gene expression during tomato fruit development, we isolated developmentally regulated (DR) clones, including several putative transcription factors. Based on sequence homology, DR1, DR3, DR4 and DR8 are members of the Aux/IAA family, and DR12 belongs to the auxin response factor (ARF) family of transcription factors. Importantly, mRNA accumulation for the Aux/IAA-like genes was regulated by ethylene in tomato fruit but not in the leaves, indicating that these putative auxin response components also participate to the ethylene-dependent regulation of gene expression in a tissue-specific manner. The functional significance of DR12, the ARF-like gene, was investigated by cellular biology and reverse genetics approaches. Heterologous protein targeting studies, carried out using a DR12-GFP gene fusion construct, revealed specific nuclear localization of the DR12-encoded protein, in accordance with its putative function as a transcriptional regulator. Transgenic plants over- and under-expressing DR12 were generated in order to explore the physiological role of the gene. Both antisense and sense co-suppressed DR12-inhibited lines displayed a pleiotropic phenotype that included dark-green immature fruit, unusual cell division in the fruit pericarp, blotchy ripening, enhanced fruit firmness, upward curling leaves and increased hypocotyl and cotyledon growth. While a perturbation of the response to auxin may explain some of the phenotypes, surprisingly, the expression of members of four classes of early auxin-regulated genes was unaffected in the DR12-inhibited plants. The involvement of this ARF-like encoded protein in mediating the auxin response is discussed along with the possibility that it might affect responsiveness to other phytohormones in the tomato.

The Arabidopsis BODENLOS gene encodes an auxin response protein inhibiting MONOPTEROS-mediated embryo patterning

Developmental responses to the plant hormone auxin are thought to be mediated by interacting pairs from two protein families: short-lived inhibitory IAA proteins and ARF transcription factors binding to auxin-response elements. monopteros mutants lacking activating ARF5 and the auxin-insensitive mutant bodenlos fail to initiate the root meristem during early embryogenesis. Here we show that the bodenlos phenotype results from an amino-acid exchange in the conserved degradation domain of IAA12. BODENLOS and MONOPTEROS interact in the yeast two-hybrid assay and the two genes are coexpressed in early embryogenesis, suggesting that BODENLOS inhibits MONOPTEROS action in root meristem initiation.