Jordi Bou-Torrent

Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins.

Plants sense the presence of potentially competing nearby individuals as a reduction in the red to far‐red ratio of the incoming light. In anticipation of eventual shading, a set of plant responses known as the shade avoidance syndrome (SAS) is initiated soon after detection of this signal by the phytochrome photoreceptors. Here we analyze the function of PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and PAR2, two Arabidopsis thaliana genes rapidly upregulated after simulated shade perception. These genes encode two closely related atypical basic helix–loop–helix proteins with no previously assigned function in plant development. Using reverse genetic approaches, we show that PAR1 and PAR2 act in the nucleus to broadly control plant development, acting as negative regulators of a variety of SAS responses, including seedling elongation and photosynthetic pigment accumulation. Molecularly, PAR1 and PAR2 act as direct transcriptional repressors of two auxin‐responsive genes, SMALL AUXIN UPREGULATED15 (SAUR15) and SAUR68. Additional results support that PAR1 and PAR2 function in integrating shade and hormone transcriptional networks, rapidly connecting phytochrome‐sensed light changes with auxin responsiveness.

The HY5-PIF Regulatory Module Coordinates Light and Temperature Control of Photosynthetic Gene Transcription

The ability to interpret daily and seasonal alterations in light and temperature signals is essential for plant survival. This is particularly important during seedling establishment when the phytochrome photoreceptors activate photosynthetic pigment production for photoautotrophic growth. Phytochromes accomplish this partly through the suppression of PHYTOCHROME INTERACTING FACTORS (PIFs), negative regulators of chlorophyll and carotenoid biosynthesis. While the bZIP transcription factor LONG HYPOCOTYL 5 (HY5), a potent PIF antagonist, promotes photosynthetic pigment accumulation in response to light. Here we demonstrate that by directly targeting a common promoter cis-element (G-box), HY5 and PIFs form a dynamic activation-suppression transcriptional module responsive to light and temperature cues. This antagonistic regulatory module provides a simple, direct mechanism through which environmental change can redirect transcriptional control of genes required for photosynthesis and photoprotection. In the regulation of photopigment biosynthesis genes, HY5 and PIFs do not operate alone, but with the circadian clock. However, sudden changes in light or temperature conditions can trigger changes in HY5 and PIFs abundance that adjust the expression of common target genes to optimise photosynthetic performance and growth.

ATHB4, a regulator of shade avoidance, modulates hormone response in Arabidopsis seedlings.

Plants sense the presence of competing neighboring vegetation as a change in light quality: i.e. they sense the reduced ratio of red light to far-red light. The responses to shade are generally referred to as the shade avoidance syndrome (SAS), and involve various developmental changes intended to outgrow or outcompete the neighboring plants. Here, we analyze the function of ATHB4, a gene encoding a homeodomain-leucine zipper (HD-Zip) class-II transcription factor from Arabidopsis thaliana, the expression of which is rapidly and directly upregulated after proximity perception by the phytochrome photoreceptors. ATHB4 acts redundantly with other members of the HD-Zip class-II transcription factors. The expression of these genes is regulated by other members of the same class, forming a small transcriptional network of factors in which homeostasis is mutually controlled. Our results suggest that some members of this small gene subfamily can modulate SAS responses by controlling auxin, brassinosteroid and gibberellin molecular and/or physiological responsiveness. In particular, we propose ATHB4 as a new shade signaling component that participates in integrating shade perception and hormone-mediated growth.

Genome‐wide binding‐site analysis of REVOLUTA reveals a link between leaf patterning and light‐mediated growth responses

Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.

A DELLA in Disguise: SPATULA Restrains the Growth of the Developing Arabidopsis Seedling

This study examines the role of the PHYTOCHROME INTERACTING FACTOR3 homolog SPATULA (SPT) in the control of the developing seedling and shows that SPT is a potent regulator of cotyledon size, acting in parallel to DELLAs. As DELLAs negatively regulate SPT abundance, the light regulation of DELLAs drives the DELLA-SPT counterbalance, enforcing growth restraint across a range of ambient light conditions that are prevalent in nature. The period following seedling emergence is a particularly vulnerable stage in the plant life cycle. In Arabidopsis thaliana, the phytochrome-interacting factor (PIF) subgroup of basic-helix-loop-helix transcription factors has a pivotal role in regulating growth during this early phase, integrating environmental and hormonal signals. We previously showed that SPATULA (SPT), a PIF homolog, regulates seed dormancy. In this article, we establish that unlike PIFs, which mainly promote hypocotyl elongation, SPT is a potent regulator of cotyledon expansion. Here, SPT acts in an analogous manner to the gibberellin-dependent DELLAs, REPRESSOR OF GA1-3 and GIBBERELLIC ACID INSENSITIVE, which restrain cotyledon expansion alongside SPT. However, although DELLAs are not required for SPT action, we demonstrate that SPT is subject to negative regulation by DELLAs. Cross-regulation of SPT by DELLAs ensures that SPT protein levels are limited when DELLAs are abundant but rise following DELLA depletion. This regulation provides a means to prevent excessive growth suppression that would result from the dual activity of SPT and DELLAs, yet maintain growth restraint under DELLA-depleted conditions. We present evidence that SPT and DELLAs regulate common gene targets and illustrate that the balance of SPT and DELLA action depends on light quality signals in the natural environment.

The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix–loop–helix proteins as transcriptional cofactors

The shade avoidance syndrome (SAS) refers to a set of plant responses aimed at anticipating eventual shading by potential competitors. The SAS is initiated after perception of nearby vegetation as a reduction in the red to far-red ratio (R:FR) of the incoming light. Low R:FR light is perceived by the phytochromes, triggering dramatic changes in gene expression that, in seedlings, eventually result in an increased hypocotyl elongation to overgrow competitors. This response is inhibited by genes such as PHYTOCHROME RAPIDLY REGULATED 1 (PAR1), PAR2 and LONG HYPOCOTYL IN FR 1 (HFR1), which are transcriptionally induced by low R:FR. Although PAR1/PAR2 and HFR1 proteins belong to different groups of basic helix-loop-helix (bHLH) transcriptional regulators, they all lack a typical basic domain required for binding to E-box and G-box motifs in the promoter of target genes. By overexpressing derivatives of PAR1 and HFR1 we show that these proteins are actually transcriptional cofactors that do not need to bind DNA to directly regulate transcription. We conclude that protein-protein interactions involving the HLH domain of PAR1 and HFR1 are a fundamental aspect of the mechanism by which these proteins regulate gene expression, most likely through interaction with true transcription factors that do bind to the target genes and eventually unleash the observed SAS responses.

Regulatory Components of Shade Avoidance Syndrome

Abstract Competition for light has an important impact on plant development. Plants sense the presence of nearby competitor vegetation as a change in the light quality, i.e. a reduced red to far-red ratio. The responses to shade are generally referred to as the shade avoidance syndrome (SAS), and involve various developmental changes aimed to outgrow the neighbouring plants, and are characterized by enhanced elongation, reduced leaf expansion, decreased branching and ultimately early flowering. These responses can be detrimental in agriculture, because they induce reallocation of resources into elongation growth at the expense of harvestable organs, hence lowering the crop yield. Genetic analyses performed on the SAS response of seedlings have shown the involvement of several transcription factors in the regulation of this response. At least in a few cases, it has been shown that phytochrome rapidly regulates the expression levels of several modulators of hormone responsiveness, rapidly linking shade perception, massive changes in gene expression and modification of hormone sensitivity of the responsive tissues. Here we develop our view on how shade-modulated changes in the transcriptional profiles result in complex SAS responses.

Light signaling: back to space

Recent work has increased our understanding of the molecular and cellular mechanisms of the phytochrome family of photoreceptors in controlling plant photomorphogenesis. However, the importance of long-distance communication in controlling light responses has received relatively little attention and is poorly understood. In this article, by taking a closer look at old and new experiments that extend the analysis of light signaling beyond the limits of the plant cell, we offer to look at the field in a new light. Furthermore, we discuss how intercellular and inter-organ communication might integrate with the transcriptional networks controlling light-regulated responses in plants, a novel view that might help to re-assess the parameters by which we screen for photomorphogenic mutants in the future.

ATHB4 and HAT3, two class II HD-ZIP transcription factors, control leaf development in Arabidopsis.

In response to plant proximity or canopy shade, plants can react by altering elongation growth and development. Several members of the class II homeodomain-leucine zipper (HD-ZIPII) transcription factor family have been shown to play an instrumental role in the responses to shade. HD-ZIP members of the class III (HD-ZIPIII), by contrast, are involved in basic patterning processes. We recently showed that REVOLUTA (REV), a member of the HD-ZIPIII family, directly and positively regulates the expression of several genes involved in shade-induced growth, such as those encoding HD-ZIPII factors HAT2, HAT3, ATHB2/HAT4 and ATHB4, and of the components of the auxin biosynthesis pathway YUCCA5 and TAA1. Furthermore, we could demonstrate a novel role for HD-ZIPIII in shade-induced promotion of growth. Here we show that besides responding to shade, ATHB4 and HAT3 have a critical role in establishing the dorso-ventral axis in cotyledons and developing leaves. Loss-of-function mutations in these two HD-ZIPII genes (athb4 hat3) results in severely abaxialized, entirely radialized leaves. Conversely, overexpression of HAT3 results in adaxialized leaf development. Taken together, our findings unravel a so far unappreciated role for an HD-ZIPII/HD-ZIPIII module required for dorso-ventral patterning of leaves. The finding that HD-ZIPII/HD-ZIPIII also function in shade avoidance suggests that this module is at the nexus of patterning and growth promotion.

Plant proximity perception dynamically modulates hormone levels and sensitivity in Arabidopsis

Summary Shade perception involves altered hormone synthesis and sensitivity. Here, we showed that several shade regulators act as positive and negative modulators of the hypocotyl auxin and/or brassinosteroid-induced elongation.