Phytochrome functions in Arabidopsis development
TL;DR: In this review, current knowledge of phytochrome functions in the light-regulated development of Arabidopsis is summarized and novel regulatory roles for this important photoreceptor family are revealed.
Abstract: Light signals are fundamental to the growth and development of plants. Red and far-red light are sensed using the phytochrome family of plant photoreceptors. Individual phytochromes display both unique and overlapping roles throughout the life cycle of plants, regulating a range of developmental processes from seed germination to the timing of reproductive development. The evolution of multiple phytochrome photoreceptors has enhanced plant sensitivity to fluctuating light environments, diversifying phytochrome function, and facilitating conditional cross-talk with other signalling systems. The isolation of null mutants, deficient in all individual phytochromes, has greatly advanced understanding of phytochrome functions in the model species, Arabidopsis thaliana. The creation of mutants null for multiple phytochrome combinations has enabled the dissection of redundant interactions between family members, revealing novel regulatory roles for this important photoreceptor family. In this review, current knowledge of phytochrome functions in the light-regulated development of Arabidopsis is summarised.
Citations
More filters
TL;DR: Genetic and photobiological studies performed in Arabidopsis have shown that these light sensors mediate numerous adaptive responses and developmental transitions and some physiological responses are specifically triggered by a single photoreceptor but in many cases multiple light sensors ensure a coordinated response.
Abstract: Plants are sessile and photo-autotrophic; their entire life cycle is thus strongly influenced by the ever-changing light environment. In order to sense and respond to those fluctuating conditions higher plants possess several families of photoreceptors that can monitor light from UV-B to the near infrared (far-red). The molecular nature of UV-B sensors remains unknown, red (R) and far-red (FR) light is sensed by the phytochromes (phyA-phyE in Arabidopsis) while three classes of UV-A/blue photoreceptors have been identified: cryptochromes, phototropins, and members of the Zeitlupe family (cry1, cry2, phot1, phot2, ZTL, FKF1, and LKP2 in Arabidopsis). Functional specialization within photoreceptor families gave rise to members optimized for a wide range of light intensities. Genetic and photobiological studies performed in Arabidopsis have shown that these light sensors mediate numerous adaptive responses (e.g., phototropism and shade avoidance) and developmental transitions (e.g., germination and flowering). Some physiological responses are specifically triggered by a single photoreceptor but in many cases multiple light sensors ensure a coordinated response. Recent studies also provide examples of crosstalk between the responses of Arabidopsis to different external factors, in particular among light, temperature, and pathogens. Although the different photoreceptors are unrelated in structure, in many cases they trigger similar signaling mechanisms including light-regulated protein-protein interactions or light-regulated stability of several transcription factors. The breath and complexity of this topic forced us to concentrate on specific aspects of photomorphogenesis and we point the readers to recent reviews for some aspects of light-mediated signaling (e.g., transition to flowering).
651 citations
Cites background from "Phytochrome functions in Arabidopsi..."
...Among all photoreceptors the phytochromes play the most predominant role to promote germination under favorable light conditions and to prevent it when the light conditions are suboptimal as, for example, under a canopy (Franklin and Quail, 2010)....
[...]
...The shade avoidance response (SAR) is a good illustration of this concept (Franklin, 2008; Franklin and Quail, 2010; Vandenbussche et al., 2005)....
[...]
...2.1B; Franklin and Quail, 2010; Rockwell et al., 2006)....
[...]
...The light-stable phytochromes (phyB–phyE) with phyB playing a prevalent function repress the SAR in direct sunlight (Franklin, 2008; Franklin and Quail, 2010)....
[...]
...The early flowering in short days of mutants such as phyB presumably reflects the constitutive shade avoidance phenotype of these plants (Franklin, 2008; Franklin and Quail, 2010)....
[...]
State University of New York System1, Centre de coopération internationale en recherche agronomique pour le développement2, ENEA3, University of Ottawa4, French Alternative Energies and Atomic Energy Commission5, Bioversity International6, Nestlé7, Bielefeld University8, Institut national de la recherche agronomique9, Chongqing University of Science and Technology10, University of Illinois at Urbana–Champaign11, University of Barcelona12, University of Maryland, College Park13, University of Trieste14, Empresa Brasileira de Pesquisa Agropecuária15, Analytica16, University of Queensland17, Coffee production in India18, University of Arizona19, University of Évry Val d'Essonne20, Centre national de la recherche scientifique21
TL;DR: The Coffea canephora (coffee) genome was sequenced and identified a conserved gene order, and comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
Abstract: Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
513 citations
TL;DR: The identification of genome-wide PIF5-binding sites during shade avoidance revealed that this bHLH transcription factor regulates the expression of a subset of previously identified SAS genes, and this study suggests that PIF4 and Pif5 regulate elongation growth by controlling directly the expression for auxin biosynthesis and auxin signaling components.
Abstract: Plant growth is strongly influenced by the presence of neighbors that compete for light resources. In response to vegetational shading shade-intolerant plants such as Arabidopsis display a suite of developmental responses known as the shade-avoidance syndrome (SAS). The phytochrome B (phyB) photoreceptor is the major light sensor to mediate this adaptive response. Control of the SAS occurs in part with phyB, which controls protein abundance of phytochrome-interacting factors 4 and 5 (PIF4 and PIF5) directly. The shade-avoidance response also requires rapid biosynthesis of auxin and its transport to promote elongation growth. The identification of genome-wide PIF5-binding sites during shade avoidance revealed that this bHLH transcription factor regulates the expression of a subset of previously identified SAS genes. Moreover our study suggests that PIF4 and PIF5 regulate elongation growth by controlling directly the expression of genes that code for auxin biosynthesis and auxin signaling components.
505 citations
Cites background from "Phytochrome functions in Arabidopsi..."
...These responses include elongation of hypocotyls, stems and petioles, elevated leaf angles (hyponasty), reduced leaf blade development and early flowering (Ballare 2009, Franklin 2008, Franklin and Quail 2010, Morelli and Ruberti 2000, Vandenbussche et al. 2005)....
[...]
...(Ballare 2009, Franklin and Quail 2010, Kami et al. 2010)....
[...]
...Upon light absorption it converts to the active Pfr form (far-red absorption maximum) that accumulates in the nucleus where it leads to rapid changes in gene expression (Nagatani 2004, Fankhauser and Chen 2008, Franklin and Quail 2010, Kami et al. 2010)....
[...]
...In Arabidopsis phyB is the major sensor of low R/FR although phyD and phyE contribute to the response (Franklin and Quail 2010)....
[...]
...although phyD and phyE contribute to the response (Franklin and Quail 2010)....
[...]
TL;DR: In this paper, photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation.
Abstract: Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.
419 citations
Cites background from "Phytochrome functions in Arabidopsi..."
...Phytochrome functions in Arabidopsis development were recently reviewed by Franklin and Quail (2010), and this chapter will mainly discuss the roles of phytochromes in seed germination, seedling de-etiolation, and shade avoidance....
[...]
TL;DR: Recent advances in knowledge of the mechanisms linking phytochrome photoactivation in the cytoplasm and transcriptional regulation in the nucleus are discussed.
355 citations
References
More filters
TL;DR: This work focuses on recent progress in transcriptional, post-transcriptional and post- translational regulation of gene expression that is critical for cold acclimation in temperate plants.
1,569 citations
TL;DR: It is shown that a substantial photosynthetic advantage is conferred by correct matching of the circadian clock period with that of the external light-dark cycle, which explains why plants gain advantage from circadian control.
Abstract: Circadian clocks are believed to confer an advantage to plants, but the nature of that advantage has been unknown. We show that a substantial photosynthetic advantage is conferred by correct matching of the circadian clock period with that of the external light-dark cycle. In wild type and in long- and short-circadian period mutants of Arabidopsis thaliana, plants with a clock period matched to the environment contain more chlorophyll, fix more carbon, grow faster, and survive better than plants with circadian periods differing from their environment. This explains why plants gain advantage from circadian control.
1,276 citations
Book•
06 Nov 1880
TL;DR: This chapter discusses the circumnutating movements of seedling plants, modified circumnutation, and localised sensitiveness to gravitation and its transmitted effects.
Abstract: Charles Robert Darwin (1809-1882) has been widely recognized since his own time as one of the most influential writers in the history of Western thought. His books were widely read by specialists and the general public, and his influence had been extended by almost continuous public debate over the past 150 years. New York University Press's new paperback edition makes it possible to review Darwin's public literary output as a whole, plus his scientific journal articles, his private notebooks, and his correspondence. This is complete edition contains all of Darwin's published books, featuring definitive texts recording original pagination with Darwin's indexes retained. The set also features a general introduction and index, and introductions to each volume.
982 citations
TL;DR: It is reported here that previously described hy3 mutants have mutations in the gene coding for phytochrome B (PhyB), the first mutations shown to lie in a plant photoreceptor gene.
Abstract: Phytochromes are a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions. In Arabidopsis, there are genes for at least five phytochrome proteins. These photoreceptors control such responses as germination, stem elongation, flowering, gene expression, and chloroplast and leaf development. However, it is not known which red light responses are controlled by which phytochrome species, or whether the different phytochromes have overlapping functions. We report here that previously described hy3 mutants have mutations in the gene coding for phytochrome B (PhyB). These are the first mutations shown to lie in a plant photoreceptor gene. A number of tissues are abnormally elongated in the hy3(phyB) mutants, including hypocotyls, stems, petioles, and root hairs. In addition, the mutants flower earlier than the wild type, and they accumulate less chlorophyll. PhyB thus controls Arabidopsis development at numerous stages and in multiple tissues.
935 citations
"Phytochrome functions in Arabidopsi..." refers background or methods in this paper
...…Poppe et al., 1996; Robson et al., 1996 Regulation of root gravitropic curvature phyB Correll and Kiss, 2005 Suppression of root hair growth phyB Reed et al., 1993 Regulation of leaf architecture phyA, phyB, phyC, phyD, phyE Nagatani et al., 1991; Reed et al., 1994; Devlin et al., 1998, 1999;…...
[...]
...Interestingly, phyD does not appear to perform these roles in La-er, revealing natural genetic variation in phytochrome function (Aukerman et al., 1997)....
[...]
...Mutants, deficient in phyB display significantly elongated petioles, reduced leaf area, and increased apical dominance (Fig. 2; Nagatani et al., 1991; Reed et al., 1993)....
[...]
...This was later confirmed by the Chory laboratory through DNA sequence analysis and genetic complementation (Reed et al., 1993)....
[...]
...These shoot architectural adaptations are accompanied by increased root hair growth (Reed et al., 1993)....
[...]
TL;DR: Progress in defining the molecular mechanisms that activate this module in response to changing day length and the increasing evidence that FT protein is a major component of florigen are described.
Abstract: The transition from vegetative to reproductive growth is controlled by day length in many plant species. Day length is perceived in leaves and induces a systemic signal, called florigen, that moves through the phloem to the shoot apex. At the shoot apical meristem (SAM), florigen causes changes in gene expression that reprogram the SAM to form flowers instead of leaves. Analysis of flowering of Arabidopsis thaliana placed the CONSTANS/FLOWERING LOCUS T (CO/FT) module at the core of a pathway that promotes flowering in response to changes in day length. We describe progress in defining the molecular mechanisms that activate this module in response to changing day length and the increasing evidence that FT protein is a major component of florigen. Finally, we discuss conservation of FT function in other species and how variation in its regulation could generate different flowering behaviors.
908 citations
"Phytochrome functions in Arabidopsi..." refers background in this paper
...Transcriptional regulators act on floral integrators which, in turn, alter expression of meristem identity genes to promote flowering (reviewed in Turck et al., 2008)....
[...]