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Dissecting the phytochrome A-dependent signaling network in higher plants

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Dissecting the phytochrome A-dependent signaling network in higher plantsMolecular properties and functional roles of phyAPhyA control of gene expressionLight-induced nuclear import of phyAPhyA as a light-regulated kinaseGenetically identified phyA-specific signaling intermediatesPhyA can directly target light signals to light-responsive promotersRegulated proteolysis in phyA signalingHow are the COP proteins inactivated?Conclusions and prospectsAcknowledgementsReferencesDissecting the phytochromeA-dependent signaling network inhigher plantsHaiyang Wang1and Xing Wang Deng21Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA2Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USAPlants monitor their ambient light environment using anetwork of photoreceptors. In Arabidopsis, phyto-chrome A (phyA) is the primary photoreceptor respon-sible for perceiving and mediating various responses tofar-red light. Several breakthroughs in understandingthe signaling network mediating phyA-activatedresponses have been made in recent years. Here, wehighlight several key advances: the demonstration thatlight regulates nuclear translocation of phyA and itsassociated kinase activity; the revelation of a tran-scriptional cascade controlling phyA-regulated geneexpression; the detection of a direct interactionbetween phyA and a transcription factor; and the identi-fication and characterization of many phyA-specificsignaling intermediates, some of them suggesting theinvolvement of the ubiquitin–proteasome pathway.Sessile plants have adopted a high degree of develop-mental plasticity to optimize their growth and reproduc-tion in response to their ambient environments. Light isone of the major environmental signals that influenceplant growth and development. Not only is light theprimary energy source for plants but also it provides themwith positional information to modulate their develop-mental processes, including seed germination, seedlingde-etiolation, gravitropism, phototropism, chloroplastmovement, shade avoidance, circadian rhythms andflowering time. Plants can detect almost all facets oflight, including its direction, duration, quantity andwavelength, using three major classes of photoreceptors.Phytochromes predominantly absorb the red and far-redwavelengths (600–750 nm), whereas cryptochromes andphototropins perceive blue and ultraviolet A (UV-A)wavelengths (320 – 500 nm), and unidentified UV-B photo-receptors absorb UV-B (282–320 nm) [1,2]. These photo-receptors perceive and interpret ambient light signals andtransduce them to modulate plant growth and develop-ment. The light control of seedling development has beenconveniently used as a model for dissecting the signalingmechanisms of these photoreceptors [3–7]. In this article,we focus on recent advances in our understanding of thesignaling network of phytochrome A (phyA). We attempt tooutline the recent conceptual breakthroughs, the standingissues and possible future directions in phyA-signaling-mechanism research.Molecular properties and functional roles of phyAHistorically, phyA was the first phytochrome discovered inhigher plants [1] and all higher plants have a distinct phyAamong phytochrome families of variable sizes. All knownphyAs from higher plants are abundant in dark-grownplants and are rapidly degraded upon light exposure. Theyare therefore classified as a light-labile phytochrome. Thepurified phyA molecule is a soluble, dimeric chromoproteinthat consists of two , 125-kDa polypeptides with a singlecovalently attached tetrapyrrole chromophore, phytochro-mobilin. The photosensory activity of the molecule resultsfrom its capacity to undergo a light-induced, reversibleswitch between two conformers: the red-light-absorbing Prform and the far-red-light-absorbing Pfr form. Phyto-chrome is synthesized in the Pr form in dark-grownseedlings. Upon exposure to red light, the Pr form isconverted to the Pfr form, and exposure to far-red lightreverts the Pfr form to the Pr form [8].There are five distinct phytochromes in Arabidopsis,designated phyA to phyE. These photoreceptors haveunique, sometimes partially redundant or antagonistic,roles in different photomorphogenic responses [9] (Box 1).PhyB to phyE predominantly regulate light responsesunder continuous red and white light. Most of theirknown responses can be grouped into the classicalred–far-red photoreversible phytochrome responses,the so-called low-fluence responses (LFRs, fluencerequirement 1 –1000 mmol m2). The classical exampleof a phytochrome-mediated LFR is red-light-inducedgermination of lettuce seeds. This induction can beinhibited by subsequent far-red light treatment. Theseeds can be repeatedly treated by sequential red orfar-red light, and the ultimate germination responsedepends only on the last light treatment. Thus,photoreversibility is one characteristic feature of LFRresponses. Another distinguishing feature of LFR isthat it conforms to the law of reciprocity – a responsedepends onthetotal number ofphotonsreceivedirrespectiveof the duration of exposure [7,8].PhyA is unique among all phytochromes because it issolely responsible for the very-low-fluence response (VLFR)and for the far-red-light-dependent high-irradianceCorresponding author: Xing Wang Deng ([email protected]).Review TRENDS in Plant Science Vol.8 No.4 April 2003172http://plants.trends.com 1360-1385/03/$ - see front matter q 2003 Elsevier Science Ltd. All rights reserved. doi:10.1016/S1360-1385(03)00049-9response (HIR). The VLFR includes light effects on theexpression of some genes, seed germination and thegravitropic control of hypocotyl growth, and it can beinduced with extremely low photon fluences of0.001–1.000 mmol m2of either red or far-red light pulses.Although the VLFR is not photoreversible, it does obeythe law of reciprocity (i.e. the VLFR senses photonfluences). The HIR requires relatively high photonfluence rates and a long duration of irradiation, and itis fluence rate and not total fluence that defines thistype of responses. Typical HIRs include inhibition ofhypocotyl elongation, opening of the apical hook,expansion of the cotyledons, accumulation of anthocya-nin and a far-red light preconditioned block of greeningduring seedling development [7,8] (Fig. 1). The centraldogma for phytochrome action (that Pfr is thebiologically active form) applies to the LFRs mediatedby phyB–phyE and the


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