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Title: A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth}
Article:
Abstract:
Most organisms use daily light/dark cycles as timing cues to control many essential physiological processes. In plants, growth rates of the embryonic stem( hypocotyl) are maximal at different times of day, depending on external photoperiod and the internal circadian clock. However, the interactions between light signaling, the circadian clock, and growth-promoting hormone pathways in growth control remain poorly understood. At the molecular level, such growth rhythms could be attributed to several different layers of time-specific control such as phasing of transcription, signaling, or protein abundance. To determine the transcriptional component associated with the rhythmic control of growth, we applied temporal analysis of the Arabidopsis thaliana seedling transcriptome under multiple growth conditions and mutant backgrounds using DNA microarrays. We show that a group of plant hormone-associated genes are coexpressed at the time of day when hypocotyl growth rate is maximal. This expression correlates with overrepresentation of a cis-acting element( CACATG) in phytohormone gene promoters, which is sufficient to confer the predicted diurnal and circadian expression patterns in vivo. Using circadian clock and light signaling mutants, we show that both internal coincidence of phytohormone signaling capacity and external coincidence with darkness are required to coordinate wild-type growth. From these data, we argue that the circadian clock indirectly controls growth by permissive gating of light-mediated phytohormone transcript levels to the proper time of day. This temporal integration of hormone pathways allows plants to fine tune phytohormone responses for seasonal and shade-appropriate growth regulation.
Introduction:
Plant growth involves the coordination of cell division and expansion, which is the result of developmental programs initiated by both intrinsic and extrinsic factors. Of the various environmental parameters that regulate plant development, light quality, quantity, and duration play important roles. In dark-grown dicotyledonous seedlings such as Arabidopsis thaliana, the embryonic stem or hypocotyl grows rapidly by longitudinal cell expansion in a process referred to as hypocotyl elongation. At the same time, the embryonic leaves, or cotyledons, remain small and unexpanded. In contrast, the rate of hypocotyl elongation is inhibited and cotyledon expansion is promoted by light[1]. In mature plants, a similar differential growth process occurs when light is limiting or in response to shade, whereby stems and petioles elongate at the expense of leaf expansion[2]. However, it remains unclear how the plant regulates these distinct growth states. Differential growth responses are executed by small-molecule hormones, also called phytohormones, that are synthesized and transported throughout the plant[3]. At least six classes of phytohormones nonredundantly control growth[1]. Gibberellins( GA), auxin( IAA), and brassinosteroids( BR) promote cell expansion along longitudinal axes, and abscisic acid( ABA) antagonizes both GA- and BR-regulated growth; whereas cytokinin( CK) and ethylene( referred to here as ACC) promote cell expansion along transverse axes[4]. One apparent paradox regarding how phytohormones orchestrate growth programs revolves around their simultaneous redundancy and specificity. As an example, mutations in biosynthetic enzymes of either GA or BR result in severe dwarf phenotypes, consistent with these pathways acting nonredundantly[3]. This is also consistent with recent analysis of global gene expression profiles from seedlings treated with specific phytohormones, which suggests that hormonal pathways do not converge on a core early transcriptional growth-regulatory module, but instead regulate distinct target genes[4]. In contrast, BR and IAA treatments result in the up-regulation of many common target genes, suggesting that there can be significant integration and crosstalk between these hormone pathways[5]. Finally, one model suggests that a family of nuclear-localized proteins, identified from GA response pathway mutations, acts as a central transcriptional integrator of growth controlling pathways[6]. How these pathways are coordinated to achieve an optimal body plan for a particular environment is currently a key question in plant development. It is known that phytohormone levels vary over the course of the day. Bioactive phytohormone levels of BR, IAA, ACC, GA, and ABA accumulate from dawn to midday under light/dark cycles[7–12]. In addition, either light/dark cycles or the circadian clock have been shown to regulate certain phytohormone-associated transcripts[7, 9, 13, 14], suggesting that there is an intimate connection between phytohormone activity and time-of-day specificity. The circadian clock and light/dark cycles interact to control daily hypocotyl growth through the activity of the transcription factors phytochrome interacting factor 4( PIF4) and PIF5[15–18]. In addition, the circadian clock gates both IAA pathways and IAA-mediated growth[14]. However, the mechanisms defining the relationship between the circadian clock, light signaling, and phytohormone-controlled growth remain unclear. Organisms have evolved circadian clocks with internal periods of about 24 h/ that allow synchrony with their external environment[19, 20]. Plants with circadian period lengths that match that of their environment display enhanced fitness because they are able to correctly phase key metabolic and physiological events relative to the daily changes in the environment, such as the light/dark cycle[21]. Underlying the ability to properly anticipate and respond to daily changes in the environment is an extensive transcriptional network governed by the circadian clock, light, and temperature cycles, which ensures that almost 90% of transcripts in Arabidopsis accumulate at specific times over the day[19, 22]. Since growth is time-of-day specific, we reasoned that a temporal integration of a transcriptional component of the phytohormone pathways could be part of the specificity and redundancy. Here, we find that the circadian clock and light signaling pathways interact to coordinate the expression of biosynthetic, catabolic, receptor, and signaling genes from multiple phytohormone pathways. The coordination of phytohormone transcript abundance correlated well with the time of maximum growth, consistent with phytohormone pathways directly controlling growth. We identified and characterized a cis-regulatory element that is overrepresented in phytohormone gene promoters and showed that it confers both diurnal and circadian cycling to the luciferase( LUC) reporter in vivo. On the basis of our observations, we propose a model in which the circadian clock indirectly controls growth by maintaining light signaling during the early part of the evening, which ensures that peak phytohormone transcript abundance coincides with the end of the dark period. Our findings provide a framework for understanding how seedlings transition from dark-dependent to light-dependent growth after germination and respond appropriately to both acute and long-term changes in the light environment.
Discussion:
We have described a transcriptional module that is closely associated with increase in growth rate. It appears to be regulated by coordination of the internal coincidence of multiple phytohormone pathways with the external coincidence of a key environmental signal, the dark-to-light transition at dawn( Figure 9). Our analysis suggests that the circadian clock acts upstream of light signaling to gate phytohormone gene expression during the early evening. This program constitutes a key mechanism to ensure effective growth during the long periods of darkness early in Arabidopsis development( short days of fall or early spring) or low-light conditions experienced during shading. We demonstrate that PHYB( or light signaling) directly controls phytohormone transcript abundance and that this correlates with increased hypocotyl growth rate in Arabidopsis. We propose a gated convergence model, to provide a framework to understand the intimate connection between the circadian clock, light signaling, and phytohormone control of growth that has eluded the field to date( Figure 9). In this model, the circadian clock mitigates the effect of darkness on growth by gating the expression of the growth-associated HUD-containing phytohormone genes. Although the molecular mechanism by which the circadian clock gates light signaling is yet to be identified, PHYB is downstream and directly controls the expression of phytohormone genes. At least two cis-acting elements, HUD and an unknown element, constitute the downstream targets of light signaling( and PHYB activation). As the night proceeds, circadian-mediated maintenance of light signaling diminishes and phytohormone transcript abundance increases, leading to maximal rate of growth at dawn. This model predicts that environment-tuned growth is governed by both the internal coincidence of phytohormone transcript abundance and external coincidence with the dark period of the diurnal cycle. Consistent with this model, when we misexpressed BRI1 to the early evening using the ML1 promoter, we observed longer hypocotyls. The model predicts that an increase of the phytohormone genes during the dark phase of the day would lead to an increase in growth. This is what we observe in the circadian mutants, a phyB mutant and an AtML1::BRI1 line grown under short-day photocycles. The gated convergence model can be used to explain the transition from etiolated( dark) to de-etiolated( light) growth. In its typical geographic range, Arabidopsis germinates under natural conditions in late fall or early spring, both of which are short-day conditions. While the seedling is under the soil, it elongates rapidly and most likely continuously[15] until it breaks the soil and experiences its first light, which marks the beginning of the developmental shift to photomorphogenesis. Over the next 7 d, daily hypocotyl elongation will decrease and cotyledons will start to green and grow. However, the plant is still experiencing large segments( >12 h) of darkness, and must mitigate the effect of darkness on promoting growth. According to the gated convergence model, the circadian clock reads out day length and modulates the waveforms of cyclic phytohormone transcript abundance during the early night to slow hypocotyl growth. This model would also predict that the circadian clock provides some level of memory of developmental state, such as it does for flowering time[38]. Recently, it has been shown in multiple organisms, including Arabidopsis, that the circadian clock mediates changes in chromatin modifications[39–41], suggesting that these developmental states may be reflected in chromatin modifications that change transcriptional activities. The gated convergence model provides a time-of-day framework for understanding the relationship between the circadian clock, light signaling, and phytohormone-regulated growth. One possible mechanism by which the circadian clock could mitigate increased growth and gene expression in the dark is by maintaining light signaling during the early evening through retention of the active form of PHYB in the nucleus. PHYB:GFP is imported into the nucleus in a light-dependent diurnal pattern[42]. Therefore, it is interesting to speculate that the circadian clock may also play a role in this process to maintain active light signaling in the early part of the night. Active forms of PHYB destabilize members of the PIF bHLH transcription factor family[43], which bind Gbox binding sites, like the HUD, to promote hypocotyl elongation[15]. In addition, the DELLA GA-signaling repressors bind PIF3 and PIF4 in the absence of GA, whereas they are degraded in the presence of GA, leading to the regulation of growth-promoting gene expression[43–45]. Therefore, the temporal coordination and balance of GA and light at dawn directly controls downstream growth-promoting pathways. Although some of these activities are at the level of protein activity, underlying transcriptional regulation of the PIFs[15] and other phytohormone signaling components provides a temporal window for this regulation. For instance, the circadian transcriptional regulation of the IAA-signaling pathway plays a pivotal role in how IAA-mediated growth proceeds[14]. In a previous study, we developed a time-of-day expression atlas and showed that photocycles, thermocycles, and the circadian clock control the transcript abundance of 90% of Arabidopsis genes[19]. The implication of this finding is that many pathways are coordinated and have maximum abundance at specific times over the day. Our results support that transcriptional coordination of phytohormone genes is indeed important for establishing temporal interactions of growth pathways. It is becoming increasingly clear that a unifying principle for circadian function in both plants and animals is the gating of convergent, stochastic signals such that physiological processes with complex inputs are provided a temporal organization. The temporal coordination of flux through systemic signaling pathways thus appears to be a universal feature of clock regulation from growth control in plants to blood pressure regulation in humans[46, 47].
In plants , stems elongate faster at dawn . This time-of-day–specific growth is controlled by integration of environmental cues and the circadian clock . The specific effectors of growth in plants are the phytohormones: auxin , ethylene , gibberellins , abscisic acid , brassinosteroids , and cytokinins . Each phytohormone plays an independent as well as an overlapping role in growth , and understanding the interactions of the phytohormones has dominated plant research over the past century . The authors present a model in which the circadian clock coordinates growth by synchronizing phytohormone gene expression at dawn , allowing a plant to control growth in a condition-specific manner . Furthermore , the results presented provide a new framework for future experiments aimed at understanding the integration and crosstalk of the phytohormones .