EMBO reports Phytochrome-mediated photoperception and signal transduction in higher plants Eberhard Schäfer & Chris Bowler1,+ Universitat Freiburg, Institut fur Biologie II/Botanik, Schanzlestrasse 1, D-79104 Freiburg, Germany and 1Molecular Plant Biology Laboratory, Stazione Zoologica ‘Anton Dohrn’, Villa Comunale, I-80121 Naples, Italy Received July 1, 2002; revised September 30, 2002; accepted October 1, 2002 Light provides a major source of information from the environ- Phytochromes are typically encoded by small multigene ment during plant growth and development. Light perception families, e.g. PHYA-PHYE in Arabidopsis (Møller et al., 2002; is mediated through the action of several photoreceptors, Nagy and Schäfer, 2002; Quail, 2002a,b). Each forms a including the phytochromes. Recent results demonstrate that homodimer of ∼240 kDa and light sensitivity is conferred by the light responses involve the regulation of several thousand presence of a tetrapyrrole chromophore covalently bound to the genes. Some of the key events controlling this gene expression N-terminal half of each monomer (Montgomery and Lagarias, are the translocation of the phytochrome photoreceptors into 2002). Dimerization domains are located within the C-terminal the nucleus followed by their binding to transcription factors. half of the proteins, as are other domains involved in the activa- Coupled with these events, the degradation of positively tion of signal transduction (Quail et al., 1995; Quail, 2002a). acting intermediates appears to be an important process Each phytochrome can exist in two photointerconvertible whereby photomorphogenesis is repressed in darkness. This conformations, denoted Pr (a red light-absorbing form) and Pfr review summarizes our current knowledge of these processes. (a far red light-absorbing form) (Figure 1A). Because sunlight is enriched in red light (compared with far red light), phytochrome Introduction is predominantly in the Pfr form in the light, and this can convert back to the Pr form during periods of darkness by a process Plants utilize light as a source of energy and as a source of inform- known as dark reversion. Photoconversion back to Pr can also ation about their environment. Dark-grown (etiolated) seed- be mediated by pulses of far red light. lings display an apical hook, closed and unexpanded cotyledons In dark-grown seedlings, phyA is the most abundant phyto- and elongated hypocotyls. This developmental programme chrome, although it is rapidly degraded upon exposure to light (known as skotomorphogenesis) is necessary for newly germin- (Møller et al., 2002; Nagy and Schäfer, 2002). Expression of the ating seedlings to grow through soil or fallen leaves to reach the PHYA gene is also repressed in the light. The other PHY genes light. Upon light exposure, seedlings undergo de-etiolation: are expressed at much lower levels and their expression is not cotyledons open, expand and begin to photosynthesize, hypocotyl elongation is inhibited and cell differentiation is strongly influenced by light. phyB is more abundant than phyC–E, initiated in vegetative meristems. These events are known as but its mRNA levels are typically only ~1% of those of phyA photomorphogenesis and result largely from light-mediated mRNA in the dark (Quail et al., 1995). In sunlight, however, alterations in gene expression (Ma et al., 2001; Tepperman et al., phyB is the most abundant phytochrome due to phyA degradation. 2001; Schroeder et al., 2002). The physiological functions of phyA and phyB are the best characterized (see below), and only recently has some inform- ation been obtained about the roles of phyC–E (Møller et al., The phytochromes 2002). In plants, light-dependent responses are controlled by a series of Classically, phytochrome responses have been defined by photoreceptors that can be classified into three known groups—the their wavelength and fluence or fluence-rate (i.e. intensity) phytochromes, cryptochromes and phototropins (Quail, 2002a). requirements into three groups—very low fluence responses +Corresponding author. Tel: +39 081 583 3241; Fax +39 081 764 1355; E-mail: [email protected] 1042 EMBO reports vol. 3 | no. 11 | pp 1042–1048 | 2002 © 2002 European Molecular Biology Organization review Phytochrome-mediated photoperception to the nucleus in R-HIR conditions whereas phyA nuclear localization is most effective in FR-HIR conditions. Phytochrome localization to the nucleus is a highly significant finding given that many phytochrome responses are dependent upon changes in gene expression. However, it should be noted that phytochrome translocation is rather slow, except for phyA, and that the majority of the intracellular Pfr pool is not trans- located to the nucleus (Nagy and Schäfer, 2002). These and other observations (see below) suggest that phytochromes may activate signalling pathways in both the cytoplasm and the nucleus. Dissection of phytochrome signal transduction pathways Photomorphogenic mutants. Many putative light signal trans- duction intermediates have been identified from mutant screens aimed principally at isolating mutants insensitive to light or mutants displaying constitutive photomorphogenesis in darkness (Møller et al., 2002). The most severe white light-insensitive mutants include photoreceptor mutants, as well as one mutated in a gene encoding a bZIP transcription factor known as HY5 (Oyama et al., 1997). The severity of this mutant demonstrates that HY5 plays a key role in the control of photomorphogenesis (see below). While hy5 mutants are affected in both phyA and phyB signalling, other mutants are affected in one or the other, the majority being specific for phyA (Møller et al., 2002; Nagy Fig. 1. Phytochrome response modes. (A) The phytochrome photocycle. Pr and Schäfer, 2002; Quail, 2002a). and Pfr denote the red and far red light-absorbing conformations of Most phyA signalling mutants are defective in genes encoding phytochrome, respectively, which are reversible depending on light conditions. Pfr can also be converted to Pr in a light-independent process nuclear-localized proteins, e.g. FHY1, FHY3, SPA1, FAR1, LAF1 known as dark reversion (Nagy and Schäfer, 2002). (B) The different and EID1 (see Møller et al., 2002; Nagy and Schäfer, 2002; phytochrome response modes. The influence of red and far red light on each Quail, 2002a,b; Wang and Deng, 2002). However, some have response mode is shown, together with the phytochrome principally involved mutations in genes encoding the cytoplasmic proteins PAT1, in initiating the response. FIN219 and SUB1. Genetic analyses suggest that, apart from SPA1, EID1 and SUB1, all of these proteins act as positive elements in the pathway, i.e. the mutants display reduced sensi- (VLFR), low fluence responses (LFR) and high irradiance tivity to far red light (Nagy and Schäfer, 2002). Interestingly, responses (HIR) (Figure 1B). HIRs are now further subdivided SPA1 and EID1 play distinct roles in phyA signalling, SPA1 being into red (R)- and far red (FR)-HIRs (Nagy and Schäfer, 2002). primarily involved in VLFR and EIDI in FR-HIR signalling (Zhou Studies with phytochrome-deficient mutants grown in defined et al., 2002). Constitutively photomorphogenic mutants are defective in VLFR, LFR and HIR light environments have revealed that genes encoding the COP/DET/FUS family of proteins. Eleven specific phytochromes can be ascribed to individual responses loci have been assigned to this group (det1, cop1, cop8, cop9, (Figure 1B), although significant redundancy exists (Møller et al., cop10, cop11, cop16, fus5, fus8, fus11 and fus12) (Hardtke and 2002; Nagy and Schäfer, 2002). FR-HIR responses are, however, Deng, 2000). The phenotypes of these mutants indicate that specifically mediated by phyA due to the unusual spectral prop- these genes encode negative regulators of light signalling, all of erties of this phytochrome. It has been proposed that a novel which are localized predominantly within the nucleus (see + form of PrA (denoted Pr A), which has photocycled through Pfr, below). is responsible (Shinomura et al., 2000). Phytochrome-interacting proteins. Attempts to identify phyto- chrome-interacting partners have been most successful using the Phytochrome localization yeast two-hybrid approach. Due to the difficulties of generating a chromophore-reconstituted phytochrome in yeast cells, most In the dark, de novo synthesized phytochrome is in the Pr form yeast two-hybrid experiments have used the C-terminal region. and is localized within the cytoplasm. Upon conversion to Pfr This is far from ideal because the C-termini of phyA and phyB each of the Arabidopsis phytochromes have been found to have been shown to be functionally interchangeable (Quail translocate to the nucleus and to form discrete speckles et al., 1995; Quail, 2002a,b), and because the absence of the (Kircher et al., 2002; Nagy and Schäfer, 2002). The physio- N-terminal chromophore-binding domain presumably creates a logical significance of these observations can be inferred, at least rather artificial bait. Nevertheless, a number of proteins have for phyA and phyB, from the correlations that have been found been identified (Table I). In some cases, these proteins interact between nuclear translocation and response, e.g. phyB localizes with different domains within the phytochrome, but whether EMBO reports vol. 3 | no. 11 | 2002 1043 review E. Schäfer and C. Bowler Table I. Phytochrome-interacting proteins Interacting partner Method Phy A Pfr or Cellular localization Proposed role in phy signalling Reference or B? Pr? ARR4 Y2H B Both N, C Positive regulator of B Sweere et al. (2001) Pull-down Co-IP Aux/IAA Pull-down A Both N Cross-talk with auxin Colón-Carmona et al. (2000) Cry1 Y2H A ? N Photoreceptor co-action Ahmad et al. (1998) Pull-down Cry2 Co-IP B ? N Photoreceptor co-action Màs et al. (2000) FRET ELF3 Y2H B Both N Positive regulator of B in Liu et al. (2001) Pull-down circadian clock NDPK2 Y2H A Pfr>Pr C, N Positive regulator of A and B Choi et al. (1999) Pull-down PIF3 Y2H B(A) Pfr N Positive regulator of B (and A) Ni et al. (1999) Pull-down PIF4 Pull-down B Pfr N Negative regulator of B Huq and Quail (2002) PKS1 Y2H A, B Both C Negative regulator of B Fankhauser et al.