light signalling review Light-regulated transcriptional networks in higher plants

Light is one of the most important environmental factors for plants, as it provides the source of energy for plant life. It is therefore not surprising that plants have adopted the ability to sense multiple parameters of ambient light signals, including light quantity (fluence), quality (wavelength), direction and duration. Light signals are perceived through at least four distinct families of photoreceptors, which include phytochromes, crypto- chromes, phototropins and unidentified ultraviolet B (UVB) photoreceptor(s) (BOX 1). Plant responses to light occur in the context of multiple developmental processes, including seed germination, seedling photo- morphogenesis, phototropism, gravitropism, chloroplast movement, shade avoidance, circadian rhythms and flower induction (BOX 2). Transcriptional regulatory networks have a key role in mediating light signalling through the coordinated activation and repression of specific downstream genes. Therefore, there is considerable interest in elucidating the hierarchy of networks that are formed by tran- scription factors, and in identifying the key regulatory elements in different light-responsive developmental processes. For each developmental response, more than one photoreceptor can contribute to the perception of light signals, indicating that signal integration points for different light signals must exist in transcriptional hier- archies. Added to this complexity are organ-specific and developmental stage-specific responses to light, which represent a multitude of variations among light-responsive transcriptional networks. Furthermore, light and other environmental stimuli often work together to trigger specific developmental responses, indicating the existence of integration points between these different signalling networks. Extensive progress has been made in recent years towards characterizing the organization of light-regulated transcriptional networks in the model plant Arabidopsis thaliana; in particular, in characterizing the networks that regulate seedling photomorphogenesis. Classical genetic and molecular approaches have identified various regulators downstream of photoreceptors1. Many of these encode transcription factors, as well as kinases, phos- phatases and degradation-pathway proteins. Although some of these regulators are specific for light quality, others regulate signal transduction networks in response to various light signals, representing potential signal inte- gration points. Furthermore, recent genomic analysis has started to address how light influences transcription at the genomic scale. Light induces massive reprogramming of the plant transcriptome. For example, we now know that a significant portion of the genome, at least 20% in both A. thaliana and rice, shows differential expression between seedlings that are under photomorphogenesis and those that are under skotomorphogenesis2–4. Light effects are so profound that most of the major biochemi- cal pathways that are located within the main subcellular organelles are coordinately regulated by light3,4. Here we review the current understanding of light- regulated transcriptional networks, derived mainly from research in A. thaliana. We first provide a brief overview Department of Molecular, Cellular and Developmental Biology, 165 Prospect Street, Yale University, New Haven, Connecticut 06520-8104, USA. Correspondence to X.W.D. e-mail: xingwang.deng@yale.edu doi:10.1038/nrg2049 Phototropism Directional plant growth that is determined by the direction of the light source. Gravitropism A growth movement in response to gravity. Light-regulated transcriptional networks in higher plants Yuling Jiao, On Sun Lau and Xing Wang Deng Abstract | Plants have evolved complex and sophisticated transcriptional networks that mediate developmental changes in response to light. These light-regulated processes include seedling photomorphogenesis, seed germination and the shade-avoidance and photoperiod responses. Understanding the components and hierarchical structure of the transcriptional networks that are activated during these processes has long been of great interest to plant scientists. Traditional genetic and molecular approaches have proved powerful in identifying key regulatory factors and their positions within these networks. Recent genomic studies have further revealed that light induces massive reprogramming of the plant transcriptome, and that the early light-responsive genes are enriched in transcription factors. These combined approaches provide new insights into light-regulated transcriptional networks. R E V I E W S NATURE REVIEWS | GENETICS VOLUME 8 | MARCH 2007 | 217 © 2007 Nature Publishing Group Cryptochrome Phytochrome Pterin FAD CNT/PHR CCT/DAS PHY PAS PAS HKRD FMNFMN PΦB Phototropin UVA 300 400 Blue 500 600 Red Far red 700 800 LOV LOV Serine/threonine kinase Chromophore The part of a molecule that absorbs specific wavelengths of light and is responsible for its colour. of the basic principles of light-responsive signal trans- duction. We then focus our discussion on four important light-regulated developmental processes — seedling photomorphogenesis, seed germination, shade avoid- ance and the photoperiod response — and highlight emerging insights regarding the integration of infor- mation that is provided by different light qualities, the generation of organ-specific responses and the interac- tion of light-responsive transcriptional networks with inputs from other environmental stimuli. Photoreceptor regulation and activity As photosensory switches, photoreceptors are tightly controlled by light in multiple ways. Photoreceptor genes are largely ubiquitously expressed, and the regulation of their functions is mainly at the post-translational level. Light can modulate photoreceptor activity by inducing changes that alter their cellular localization. Phytochromes are synthesized in the inactive Pr form, and are activated on light absorption by conversion to the biologically active Pfr form5. The photoconversion of phytochromes results in their translocation from the cytoplasm into the nucleus, which is crucial for allowing them to interact with transducers in initiat- ing downstream transcriptional cascades5. In terms of the cryptochromes, A. thaliana CRY2 is constitutively nuclear-localized whereas CRY1 is nuclear in the dark but largely cytoplasmic under light6. Nuclear-localized cryptochromes closely interact with the chromatin6. On the other hand, CRY3 has a dual targeting signal that mediates its transport to chloroplasts and mito- chondria, suggesting a potential role in regulating transcription in organelles7. Both of the A. thaliana phototropins, PHOT1 and PHOT2, are largely associ- ated with the plasma membrane, although following activation by light, a fraction of PHOT1 is released to the cytoplasm1. The contribution of phototropins on transcriptional regulation, however, is relatively small, and only a limited number of genes are under their control. Photoreceptors are also subject to phosphorylation control. For example, the phosphorylation of PHYA modulates photoresponses in several ways: through controlling the subcellular localization of PHYA, its stability and its affinity towards downstream signal transducers8,9. In several cases, signal transduction in response to light is thought to involve kinase activity of the photoreceptors themselves — for example, in the case of the phytochromes10. It has been proposed that phyto- chromes have intrinsic kinase activity, with the Pfr form being more active11. Controversially, however, in vivo studies have indicated that the proposed C-terminal Box 1 | Light signals and photoreceptors To monitor the light environment, plants have evolved a series of photoreceptors. Cryptochromes and phototropins perceive blue and ultraviolet A (UVA) wavelengths. Phytochromes predominately absorb the far-red and red wavelengths, and an unidentified photoreceptor, or photoreceptors, absorbs UVB. In higher plants, phytochromes form a small family, which further evolved independently in dicots138. There are five phytochromes (PHYA to PHYE) in Arabidopsis thaliana. PHYA is a type I phytochrome, which is most abundant in the dark and degrades rapidly after light exposure. All other phytochromes are relatively stable in the light and are classified as type II (REF. 139). The phytochromes are dimeric chromoproteins. Each polypeptide consists of an N-terminal photosensory domain that covalently binds a single bilin chromophore (PΦB), followed by a C-terminal domain that contains several motifs and functions in dimerization, light-dependent nuclear localization and, possibly, regulation of signalling140. There are two well-characterized cryptochromes in A. thaliana5, CRY1 and CRY2, and a more divergent CRY3 (REFS 7,141). CRY1 and CRY2 have an N-terminal photolysase-related (PHR) domain (CNT) and a less-conserved, intrinsically unstructured C-terminal DAS domain (CCT), which is not present in CRY3 (REFS 141,142). The PHR domain non-covalently binds to two chromophores, a flavin adenine dinucleotide (FAD), and a pterin. CCT mediates a constitutive light response through direct interaction with CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) (REFS 143–145). Phototropins are plant-specific blue light receptors, which have a photosensory N-terminal half and a C-terminal half with serine/threonine kinase function146. The N terminus contains two flavin mononucleotide (FMN) chromophore-binding LOV domains (LOV1 and LOV2). R E V I E W S 218 | MARCH 2007 | VOLUME 8 www.nature.com/reviews/genetics © 2007 Nature Publishing Group Photoperiod and flowering Photomorphogenesis Germination • Phototropism • Chloroplast movement • Stomal opening Plant growth and response to environment Shade avoidance PhototropinsPhytochromes Cryptochromes Proplastid Precursors of plastids, which are plant organelles that include chloroplasts. Etioplast An immature chloroplast that has not been exposed to light. kinase-related domain of PHYB is dispensable for signal- ling12. In A. thaliana, the autophosphorylation of CRY1 and CRY2 is also important for their functions6. It has been suggested that light activation of the N terminus of CRY1 (CNT) induces a conformational change in its C terminus (CCT) (BOX 1), allowing its autophosphorylation and dimerization, and possible interactions with downstream partner proteins13. Phototropins also have well-established kinase activity. The blue-light-triggered autophosphor- ylation of these receptors initiates the transduction of the light signal14,15, involving several downstream signalling pathways1. Box 2 | Light-regulated plant development Light controls growth and development throughout the plant life cycle. In unfavourable environmental conditions, an intact and healthy seed remains dormant in a dry state147. In Aradopsis thaliana, seed dormancy is terminated by environmental signals such as light, temperature, nutrient availability and duration of storage in the dried state147. Low-fluence red light induces germination, which can be inhibited by subsequent far-red light treatment5. The phytochrome PHYB is the photoreceptor largely responsible for red:far-red reversible control of seed germination with the help of the phytochromes PHYA and PHYE. After germination, seedlings follow one of two developmental patterns. Skotomorphogenesis (or etiolation) in the dark is characterized by long hypocotyls, closed cotyledons protected by apical hooks in A. thaliana, and the development of proplastids into etioplasts. By contrast, growth in the light results in photomorphogenesis (or de-etiolation) characterized by short hypocotyls, expanded open cotyledons and the development of mature green chloroplasts that can photosynthesize. A wide spectrum of light, in particular far-red, red, blue and ultraviolet (UV) light conditions, induces photomorphogenesis. PHYA is the primary photoreceptor under far-red light in A. thaliana, whereas PHYB has a major role under white or red light with the aid of PHYA, PHYC and PHYD. Rice PHYA and PHYB equally contribute to seedling photomorphogenesis under red light and both rice PHYA and PHYC are involved in far-red light responses148. Both CRY1 and CRY2 cryptochromes are responsible for photomorphogenesis under blue and UVA light. When plants grow in close proximity there is competition for light. Higher plants have evolved an impressive capacity to avoid shade. A plant canopy is associated with a reduction in the ratio of red:far-red light. Changes in the red:far-red ratio are detected as a change in the relative proportions of Pr and Pfr forms of phytochromes and PHYB has the most significant role5. The perception of photoperiod (or day length) is crucial for plants to adjust their development to fit into annual seasonal changes. The interaction of light signals with intrinsic circadian rhythms measures changes in day length. In A. thaliana, both phytochromes and cryptochromes contribute to synchronizing the circadian clock. The perception of day length is an important signal in the control of flowering. Several other transient developmental processes, including phototropism, chloroplast movement and stomatal opening, are under light control mainly through phototropins146. These rapid light-responsive processes are not under extensive transcriptional regulation, and are therefore beyond the scope of this Review. R E V I E W S NATURE REVIEWS | GENETICS VOLUME 8 | MARCH 2007 | 219 © 2007 Nature Publishing Group Ubiquitin E3 ligase Enzymes that covalently attach ubiquitin to a lysine residue on a target protein. 26S proteasome A large, ATP-dependent, multicatalytic protease, which degrades ubiquitylated proteins to short peptides. The activation of photoreceptors, mainly phyto- chromes and cryptochromes, can significantly affect transcription through signal transduction pathways and, in a few cases, by direct effects on transcription factors. Regulation of transcription factors by light Light-responsive transcription factors have been iden- tified through screens for light-responsive cis-element (LRE)-binding proteins and through genetic analyses of mutants that are deficient in their response to specific types of light. Some of these transcription factors are regulated by just one type of light, whereas many more respond to a wide spectrum of light. Transcriptional regulation, post-translational modification and degra- dation of these transcription factors are all important in the light-regulated control of development. Both positive and negative transcriptional regulation of transcription factors by light has been documented. For example, the transcription of COMMON PLANT REGULATORY FACTORS 1 (CPRF1) from parsley is rapidly induced by light16 (FIG. 1a). CPRF1 has the ability to bind to G-box, a well-defined LRE16. However, CPRF1 levels increase only transiently after light treatment, and transcription might be blocked by the binding of CPRF1 to its own promoter17. Such a ‘gas-and-brake’ mechanism is widely seen in light-regulated networks, as discussed later. It is worth noting that downstream targets of CPRF1 and other CPRFs are still unknown owing to the arduous nature of carrying out genetic studies in parsley. Several basic post-translational mechanisms are involved in regulating transcription factor activities in response to light. The phosphorylation of transcription factors is a common modification that can influence their ability to bind to promoters (FIG. 1b). For example, the level of G-BOX BINDING FACTOR 1 (GBF1) is constant but its affinity for the G-box is modulated by its phosphorylation status: its phosphorylation by nuclear CASEIN KINASE II (CKII) enables G-box binding18,19. Light might also regulate the subcellular localization of transcription factors through phosphorylation20 (FIG. 1c). For example, CPRF2 from parsley is localized in the cytosol in the dark and treatment with light causes an import in the nucleus21; light-dependent in vivo phos- phorylation of CPRF2 is probably the key event that triggers its nuclear import22. Finally, recent advances have demonstrated the importance of ubiquitin-mediated proteolysis in light signalling23. Suppression of photomorphogen- esis in dark-grown seedlings requires the repressor CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a RING-finger type ubiquitin E3 ligase24. In the dark, some transcription factors that positively regulate gene expres- sion in response to light, such as LONG AFTER FAR- RED LIGHT 1 (LAF1), are ubiquitylated by COP1 under far-red light for subsequent degradation by the 26S proteasome, with the help of the PHYTOCHROME A SUPRESSOR 1 (SPA1) protein25 (FIG. 1d). Light inhibits its E3 ligase activity in part by excluding COP1 from the nucleus26. In many cases, light affects multiple steps in the regulation of a transcription factor, thereby achieving extensive flexibility and precision. For example, the multi-facet regulation of two transcription factors, ELONGATED HYPOCOTYL 5 (HY5), a positive regulator, and PHYTOCHROME INTERACTING FACTOR 3 (PIF3), a negative regulator for seedling pho- tomorphogenesis, has been well defined and is illustrated in FIG. 1e,f. Adding a further level of complexity to the regu- lation of transcription in response to light, certain light-regulated transcription factor families tend to form dimers, such as bHLH (basic helix–loop–helix) and bZIP (basic leucine zipper) families27–29. Various degrees of homodimerization and heterodimerization suggest that these transcription factor families have the potential to participate in multiple sets of combinato- rial interactions, endowing them with the capacity to function in the regulation of several transcriptional programmes30,31. It is reasonable to suspect that such interactions are involved in integrating signals from dif- ferent light signalling branches and from light and other factors, such as temperature. In addition, interactions between different families further extend the complexity of regulation32,33. LREs in transcriptional regulation LREs, which commonly occur in light-regulated pro- moters, are essential for light-controlled transcriptional activity34,35. A combination of various methods has been used to identify these LREs. Traditional deletion and mutagenesis analysis of promoters of known light- responsive genes has been used to pinpoint LREs, and footprinting and gel-retardation assays have been used to screen for binding motifs of known light-responsive transcription factors34. Recently developed computa- tional approaches use genome-scale expression data from microarray studies to look at enriched sequence ele- ments among promoters of co-expressed or differentially expressed genes36. A range of LREs have been documented in different promoters, many of which positively or negatively medi- ate gene expression in response to light. Although many LREs and their binding proteins have been identified, no single element is found in all light-regulated promoters, suggesting a complex light-regulation network and a lack of a universal switch. It has been suggested that combi- nations of LREs, rather than individual elements, could confer proper light-responsiveness to a light-insensitive basal promoter. Most information relating to LREs has been derived from studies on photomorphogenesis, which are discussed in detail in the next section. Seedling photomorphogenesis networks The process of seedling photomorphogenesis, during which plants undergo profound developmental changes, is one of the most extensively studied light-regulated responses (BOX