701
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Müller R, Fernández AP, Hiltbrunner A, Schäfer E, Kretsch T. The histidine kinase-related domain of Arabidopsis phytochrome a controls the spectral sensitivity and the subcellular distribution of the photoreceptor. PLANT PHYSIOLOGY 2009; 150:1297-309. [PMID: 19403732 PMCID: PMC2705050 DOI: 10.1104/pp.109.135988] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 04/26/2009] [Indexed: 05/19/2023]
Abstract
Phytochrome A (phyA) is the primary photoreceptor for sensing extremely low amounts of light and for mediating various far-red light-induced responses in higher plants. Translocation from the cytosol to the nucleus is an essential step in phyA signal transduction. EID1 (for EMPFINDLICHER IM DUNKELROTEN LICHT1) is an F-box protein that functions as a negative regulator in far-red light signaling downstream of the phyA in Arabidopsis (Arabidopsis thaliana). To identify factors involved in EID1-dependent light signal transduction, pools of ethylmethylsulfonate-treated eid1-3 seeds were screened for seedlings that suppress the hypersensitive phenotype of the mutant. The phenotype of the suppressor mutant presented here is caused by a missense mutation in the PHYA gene that leads to an amino acid transition in its histidine kinase-related domain. The novel phyA-402 allele alters the spectral sensitivity and the persistence of far-red light-induced high-irradiance responses. The strong eid1-3 suppressor phenotype of phyA-402 contrasts with the moderate phenotype observed when phyA-402 is introgressed into the wild-type background, which indicates that the mutation mainly alters functions in an EID1-dependent signaling cascade. The mutation specifically inhibits nuclear accumulation of the photoreceptor molecule upon red light irradiation, even though it still interacts with FHY1 (for far-red long hypocotyl 1) and FHL (for FHY1-like protein), two factors that are essential for nuclear accumulation of phyA. Degradation of the mutated phyA is unaltered even under light conditions that inhibit its nuclear accumulation, indicating that phyA degradation may occur mostly in the cytoplasm.
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Affiliation(s)
- Rebecca Müller
- Albert-Ludwigs-Universität Freiburg, Institut für Biologie 2/Botanik, 79104 Freiburg, Germany
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702
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OsHAL3 mediates a new pathway in the light-regulated growth of rice. Nat Cell Biol 2009; 11:845-51. [PMID: 19543273 DOI: 10.1038/ncb1892] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 04/13/2009] [Indexed: 11/08/2022]
Abstract
Plants show distinct morphologies in different light conditions through a process called photomorphogenesis. A predominant feature of photomorphogenesis is the reduced growth of seedlings under light conditions compared with darkness. For this adaptive event, the most well-known molecular mechanism involves photoreceptor-mediated inhibition of cell elongation. However, it is not known whether additional pathways exist. Here, we describe a newly discovered pathway of light-modulated plant growth mediated by the halotolerance protein HAL3, a flavin mononucleotide (FMN)-binding protein involved in cell division. We found that light, especially blue light, suppresses growth of rice seedlings by reducing the activity of Oryza sativa (Os) HAL3. Both in vitro and in vivo studies showed that OsHAL3 is structurally inactivated by light through photo-oxidation and by direct interaction with photons. In addition, the transcriptional expression of OsHAL3 is synergistically regulated by different light conditions. Further investigation suggested that OsHAL3 promotes cell division by recruiting a ubiquitin system, rather than by its 4'-phosphopantothenoylcysteine (PPC) decarboxylase activity. Our results uncover a new mechanism for light-regulated plant growth, namely, light not only inhibits cell elongation but also suppresses cell division through HAL3 and E3 ubiquitin ligase. This study thus brings new insights into our understanding of plant photomorphogenesis.
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703
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Transduction mechanisms of photoreceptor signals in plant cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2009. [DOI: 10.1016/j.jphotochemrev.2009.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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704
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Mittmann F, Dienstbach S, Weisert A, Forreiter C. Analysis of the phytochrome gene family in Ceratodon purpureus by gene targeting reveals the primary phytochrome responsible for photo- and polarotropism. PLANTA 2009; 230:27-37. [PMID: 19330350 DOI: 10.1007/s00425-009-0922-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/06/2009] [Indexed: 05/13/2023]
Abstract
Using gene targeting by homologous recombination in Ceratodon purpureus, we were able to knock out four phytochrome photoreceptor genes independently and to analyze their function with respect to red light dependent phototropism, polarotropism, and chlorophyll content. The strongest phenotype was found in knock-out lines of a newly described phytochrome gene termed CpPHY4 lacking photo- and polarotropic responses at moderate fluence rates. Eliminating the atypical phytochrome gene CpPHY1, which is the only known phytochrome-like gene containing a putative C-terminal tyrosine kinase-like domain, affects red light-induced chlorophyll accumulation. This result was surprising, since no light dependent function was ever allocated to this unusual gene.
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Affiliation(s)
- Franz Mittmann
- Department of Plant Physiology, Justus Liebig University, Senckenbergstrasse 3, 35390 Giessen, Germany
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705
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Shu X, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA, Tsien RY. Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science 2009; 324:804-7. [PMID: 19423828 PMCID: PMC2763207 DOI: 10.1126/science.1168683] [Citation(s) in RCA: 533] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Visibly fluorescent proteins (FPs) from jellyfish and corals have revolutionized many areas of molecular and cell biology, but the use of FPs in intact animals, such as mice, has been handicapped by poor penetration of excitation light. We now show that a bacteriophytochrome from Deinococcus radiodurans, incorporating biliverdin as the chromophore, can be engineered into monomeric, infrared-fluorescent proteins (IFPs), with excitation and emission maxima of 684 and 708 nm, respectively; extinction coefficient >90,000 M(-1) cm(-1); and quantum yield of 0.07. IFPs express well in mammalian cells and mice and spontaneously incorporate biliverdin, which is ubiquitous as the initial intermediate in heme catabolism but has negligible fluorescence by itself. Because their wavelengths penetrate tissue well, IFPs are suitable for whole-body imaging. The IFPs developed here provide a scaffold for further engineering.
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Affiliation(s)
- Xiaokun Shu
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
| | - Antoine Royant
- Institut de Biologie Structurale UMR 5075 CNRS-CEA-UJF, 41, rue Jules Horowitz, 38027 Grenoble CEDEX 1, France
| | - Michael Z. Lin
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
| | - Todd A. Aguilera
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
| | - Varda Lev-Ram
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
| | - Paul A. Steinbach
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
| | - Roger Y. Tsien
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0647, USA
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706
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Mouget JL, Gastineau R, Davidovich O, Gaudin P, Davidovich NA. Light is a key factor in triggering sexual reproduction in the pennate diatom Haslea ostrearia. FEMS Microbiol Ecol 2009; 69:194-201. [PMID: 19486155 DOI: 10.1111/j.1574-6941.2009.00700.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Sexual reproduction is an obligatory phase in the life cycle of most diatoms, as cell size decreases with successive vegetative divisions and the maximal cell size is only restored by a specialized cell, the auxospore, which follows zygote formation as a result of sexual reproduction. While in pennate diatoms the induction of sexual reproduction depends primarily on cell-cell interactions, the importance of different external factors for the induction of sexual reproduction is less well known. Here, we investigated the effects of light on sexualization in the marine benthic pennate diatom Haslea ostrearia (Gaillon) R. Simonsen. Compatible clones were crossed and exposed to different combinations of light levels, qualities, and photoperiods. Light was found to be a key factor for sexualization, and to a certain extent, to control auxosporulation in H. ostrearia. The light conditions most favorable for sexual reproduction were low irradiances (<50 micromolphotons m(-2) s(-1)) and short photoperiods (6-10 h), conditions that prevail during winter, and to a lesser extent, the higher irradiances and longer photoperiods that correspond to the spring and fall, when blooms of this organism form in the natural environment. Auxospore formation was very rare in continuous light, and maximum in presence of red radiation, while it was never observed in darkness or in radiation other than red.
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Affiliation(s)
- Jean-Luc Mouget
- Laboratoire de Physiologie, Université du Maine, Le Mans, France.
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707
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Li X, Yang Y, Li Y, Wang J, Xiao X, Guo X, Tang D, Liu X. Protein identification and mRNA analysis of phytochrome-regulated genes in Arabidopsis under red light. ACTA ACUST UNITED AC 2009; 52:371-80. [PMID: 19381463 DOI: 10.1007/s11427-009-0045-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 10/06/2008] [Indexed: 10/20/2022]
Abstract
Phytochromes are a family of plant photoreceptors that mediate physiological and developmental responses to red and far-red light. According to the affymetrix ATH1 microarray, phytochrome A (phyA) and phytochrome B (phyB) together play a key role in transducing the Rc signals to light-responsive genes. In order to select those red light-responsive genes associated with phyA or phyB, a proteomic approach based on two-dimensional gel electrophoresis (2-DE) was used to compare the protein expression patterns of the phyAphyB double mutant and the wild type of Arabidopsis thaliana (col-4) which grew under constant red light conditions for 7 d. Thirty-two protein spots which exhibited differences in protein abundance were identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry. The expression of ten genes corresponding to ten protein spots was analyzed by a semiquantitative reverse transcription-polymerase chain reaction. Two of the ten genes were confirmed by quantitative PCR (Q-PCR). The results showed that phytochromes may exert their function by regulating mRNA or protein expressions. Proteomic analysis may provide a novel pathway for identifying phytochrome-dependent genes.
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Affiliation(s)
- Xu Li
- Bioenergy and Biomaterial Research Center, College of Life Science and Biotechnology, Hunan University, Changsha 410082, China
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708
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Abstract
The phytochrome-interacting factor PIF3 has been proposed to act as a positive regulator of chloroplast development. Here, we show that the pif3 mutant has a phenotype that is similar to the pif1 mutant, lacking the repressor of chloroplast development PIF1, and that a pif1pif3 double mutant has an additive phenotype in all respects. The pif mutants showed elevated protochlorophyllide levels in the dark, and etioplasts of pif mutants contained smaller prolamellar bodies and more prothylakoid membranes than corresponding wild-type seedlings, similar to previous reports of constitutive photomorphogenic mutants. Consistent with this observation, pif1, pif3, and pif1pif3 showed reduced hypocotyl elongation and increased cotyledon opening in the dark. Transfer of 4-d-old dark-grown seedlings to white light resulted in more chlorophyll synthesis in pif mutants over the first 2 h, and analysis of gene expression in dark-grown pif mutants indicated that key tetrapyrrole regulatory genes such as HEMA1 encoding the rate-limiting step in tetrapyrrole synthesis were already elevated 2 d after germination. Circadian regulation of HEMA1 in the dark also showed reduced amplitude and a shorter, variable period in the pif mutants, whereas expression of the core clock components TOC1, CCA1, and LHY was largely unaffected. Expression of both PIF1 and PIF3 was circadian regulated in dark-grown seedlings. PIF1 and PIF3 are proposed to be negative regulators that function to integrate light and circadian control in the regulation of chloroplast development.
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709
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Riemann M, Bouyer D, Hisada A, Müller A, Yatou O, Weiler EW, Takano M, Furuya M, Nick P. Phytochrome A requires jasmonate for photodestruction. PLANTA 2009; 229:1035-45. [PMID: 19184094 DOI: 10.1007/s00425-009-0891-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 01/07/2009] [Indexed: 05/23/2023]
Abstract
The plant photoreceptor phytochrome is organised in a small gene family with phytochrome A (phyA) being unique, because it is specifically degraded upon activation by light. This so called photodestruction is thought to be important for dynamic aspects of sensing such as measuring day length or shading by competitors. Signal-triggered proteolytic degradation has emerged as central element of signal crosstalk in plants during recent years, but many of the molecular players are still unknown. We therefore analyzed a jasmonate (JA)-deficient rice mutant, hebiba, that in several aspects resembles a mutant affected in photomorphogenesis. In this mutant, the photodestruction of phyA is delayed as shown by in vivo spectroscopy and Western blot analysis. Application of methyl-JA (MeJA) can rescue the delayed phyA photodestruction in the mutant in a time- and dose-dependent manner. Light regulation of phyA transcripts thought to be under control of stable phytochrome B (phyB) is still functional. The delayed photodestruction is accompanied by an elevated sensitivity of phytochrome-dependent growth responses to red and far-red light.
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Affiliation(s)
- Michael Riemann
- Institute of Botany 1, Universität Karlsruhe, Kaiserstrasse 2, 76128 Karlsruhe, Germany.
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710
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Distinct classes of red/far-red photochemistry within the phytochrome superfamily. Proc Natl Acad Sci U S A 2009; 106:6123-7. [PMID: 19339496 DOI: 10.1073/pnas.0902370106] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Phytochromes are a widespread family of photosensory proteins first discovered in plants, which measure the ratio of red to far-red light to control many aspects of growth and development. Phytochromes interconvert between red-absorbing P(r) and far-red-absorbing P(fr) states via photoisomerization of a covalently-bound linear tetrapyrrole (bilin) chromophore located in a conserved photosensory core. From recent crystal structures of this core region, it has been inferred that the chromophore structures of P(r) and P(fr) are conserved in most phytochromes. Using circular dichroism spectroscopy and ab initio calculations, we establish that the P(fr) states of the biliverdin-containing bacteriophytochromes DrBphP and PaBphP are structurally dissimilar from those of the phytobilin-containing cyanobacterial phytochrome Cph1. This conclusion is further supported by chromophore substitution experiments using semisynthetic bilin monoamides, which indicate that the propionate side chains perform different functional roles in the 2 classes of phytochromes. We propose that different directions of bilin D-ring rotation account for these distinct classes of red/far-red photochemistry.
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711
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Kaminski S, Daminelli G, Mroginski MA. Molecular dynamics simulations of the chromophore binding site of Deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore. J Phys Chem B 2009; 113:945-58. [PMID: 19123828 DOI: 10.1021/jp8047532] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational flexibility of the tetrapyrrolic phytochromobilin (PPhiB) chromophore of the bacteriophytochrome Deinococcus radiodurans (DrCBD) in the Pr state has been investigated by molecular dynamics simulations. Because these simulations require accurate force field parameters for the prosthetic group, in the present work we developed new empirical force field parameters for the PPhiB molecule that are compatible with the CHARMM22 force field for proteins. For this reason, the new force field parameters for the nonbonded (partial atomic charges) and bonded (bonds, angles, dihedrals, improper) energy terms were derived by reproducing ab initio target data following the methodology used in the development of the CHARMM22 force field. This new set of parameters was employed to analyze structural and dynamical features of PPhiB inside DrCBD. The 45 ns all-atom molecular dynamics (MD) simulation reveals the existence of two stable conformational states of the chromophore characterized by distinct torsional angles around the C-C bond at the methine bridge connecting rings A and B of the tetrapyrrole. This result supports experimental observations derived from NMR and resonance Raman spectroscopy. Furthermore, statistical analysis of H-bonding events allowed us to identify (a) important H-bonds between the propionic side chains of the chromophore and the apoprotein which may be relevant for the signal transduction step during the photoinduced cycle and (b) a network of eight water molecules which remain in the vicinity of the chromophore during the entire 45 ns production run.
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Affiliation(s)
- Steve Kaminski
- Technische Universitat Berlin, Institut fur Chemie, Max-Volmer-Laboratorium, D-10623 Berlin, Germany
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712
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Tightening the knot in phytochrome by single-molecule atomic force microscopy. Biophys J 2009; 96:1508-14. [PMID: 19217867 DOI: 10.1016/j.bpj.2008.11.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 11/05/2008] [Indexed: 11/23/2022] Open
Abstract
A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We used protein engineering and atomic force microscopy to explore the single-molecule mechanics of the figure-eight knot in the chromophore-binding domain of the red/far-red photoreceptor, phytochrome. Under load, apo phytochrome unfolds at forces of approximately 47 pN, whereas phytochrome carrying its covalently bound tetrapyrrole chromophore unfolds at approximately 73 pN. These forces are not unusual in mechanical protein unfolding, and thus the presence of the knot does not automatically indicate a superstable protein. Our experiments reveal a stable intermediate along the mechanical unfolding pathway, reflecting the sequential unfolding of two distinct subdomains in phytochrome, potentially the GAF and PAS domains. For the first time (to the best of our knowledge), our experiments allow a direct determination of knot size under load. In the unfolded chain, the tightened knot is reduced to 17 amino acids, resulting in apparent shortening of the polypeptide chain by 6.2 nm. Steered molecular-dynamics simulations corroborate this number. Finally, we find that covalent phytochrome dimers created for these experiments retain characteristic photoreversibility, unexpectedly arguing against a dramatic rearrangement of the native GAF dimer interface upon photoconversion.
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713
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Nieder JB, Brecht M, Bittl R. Dynamic intracomplex heterogeneity of phytochrome. J Am Chem Soc 2009; 131:69-71. [PMID: 19128172 DOI: 10.1021/ja8058292] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Low temperature single-molecule fluorescence emission spectroscopy on individual phytochromes from Agrobacterium tumefaciens corroborates findings from ensemble spectroscopy concerning intercomplex heterogeneity. Furthermore, time-dependent intracomplex heterogeneity has been observed.
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Affiliation(s)
- Jana B Nieder
- Fachbereich Physik, Freie Universitat Berlin, Arnimallee 14, 14195 Berlin, Germany
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714
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Blue light induces degradation of the negative regulator phytochrome interacting factor 1 to promote photomorphogenic development of Arabidopsis seedlings. Genetics 2009; 182:161-71. [PMID: 19255368 DOI: 10.1534/genetics.108.099887] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytochrome interacting factors (PIFs) are nuclear basic helix-loop-helix (bHLH) transcription factors that negatively regulate photomorphogenesis both in the dark and in the light in Arabidopsis. The phytochrome (phy) family of photoreceptors induces the rapid phosphorylation and degradation of PIFs in response to both red and far-red light conditions to promote photomorphogenesis. Although phys have been shown to function under blue light conditions, the roles of PIFs under blue light have not been investigated in detail. Here we show that PIF1 negatively regulates photomorphogenesis at the seedling stage under blue light conditions. pif1 seedlings displayed more open cotyledons and slightly reduced hypocotyl length compared to wild type under diurnal (12 hr light/12 hr dark) blue light conditions. Double-mutant analyses demonstrated that pif1phyA, pif1phyB, pif1cry1, and pif1cry2 have enhanced cotyledon opening compared to the single photoreceptor mutants under diurnal blue light conditions. Blue light induced the rapid phosphorylation, polyubiquitination, and degradation of PIF1 through the ubi/26S proteasomal pathway. PIF1 interacted with phyA and phyB in a blue light-dependent manner, and the interactions with phys are necessary for the blue light-induced degradation of PIF1. phyA played a dominant role under pulses of blue light, while phyA, phyB, and phyD induced the degradation of PIF1 in an additive manner under prolonged continuous blue light conditions. Interestingly, the absence of cry1 and cry2 enhanced the degradation of PIF1 under blue light conditions. Taken together, these data suggest that PIF1 functions as a negative regulator of photomorphogenesis under blue light conditions and that blue light-activated phys induce the degradation of PIF1 through the ubi/26S proteasomal pathway to promote photomorphogenesis.
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715
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Clack T, Shokry A, Moffet M, Liu P, Faul M, Sharrock RA. Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor. THE PLANT CELL 2009; 21:786-99. [PMID: 19286967 PMCID: PMC2671712 DOI: 10.1105/tpc.108.065227] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 02/17/2009] [Accepted: 03/02/2009] [Indexed: 05/18/2023]
Abstract
Phytochromes are dimeric chromoproteins that regulate plant responses to red (R) and far-red (FR) light. The Arabidopsis thaliana genome encodes five phytochrome apoproteins: type I phyA mediates responses to FR, and type II phyB-phyE mediate shade avoidance and classical R/FR-reversible responses. In this study, we describe the complete in vivo complement of homodimeric and heterodimeric type II phytochromes. Unexpectedly, phyC and phyE do not homodimerize and are present in seedlings only as heterodimers with phyB and phyD. Roles in light regulation of hypocotyl length, leaf area, and flowering time are demonstrated for heterodimeric phytochromes containing phyC or phyE. Heterodimers of phyC and chromophoreless phyB are inactive, indicating that phyC subunits require spectrally intact dimer partners to be active themselves. Consistent with the obligate heterodimerization of phyC and phyE, phyC is made unstable by removal of its phyB binding partner, and overexpression of phyE results in accumulation of phyE monomers. Following a pulse of red light, phyA, phyB, phyC, and phyD interact in vivo with the PHYTOCHROME INTERACTING FACTOR3 basic helix-loop-helix transcription factor, and this interaction is FR reversible. Therefore, most or all of the type I and type II phytochromes, including heterodimeric forms, appear to function through PIF-mediated pathways. These findings link an unanticipated diversity of plant R/FR photoreceptor structures to established phytochrome signaling mechanisms.
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Affiliation(s)
- Ted Clack
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, USA
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716
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Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness. Curr Biol 2009; 18:1815-23. [PMID: 19062289 DOI: 10.1016/j.cub.2008.10.058] [Citation(s) in RCA: 444] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 10/22/2008] [Accepted: 10/23/2008] [Indexed: 12/18/2022]
Abstract
BACKGROUND An important contributing factor to the success of terrestrial flowering plants in colonizing the land was the evolution of a developmental strategy, termed skotomorphogenesis, whereby postgerminative seedlings emerging from buried seed grow vigorously upward in the subterranean darkness toward the soil surface. RESULTS Here we provide genetic evidence that a central component of the mechanism underlying this strategy is the collective repression of premature photomorphogenic development in dark-grown seedlings by several members of the phytochrome (phy)-interacting factor (PIF) subfamily of bHLH transcription factors (PIF1, PIF3, PIF4, and PIF5). Conversely, evidence presented here and elsewhere collectively indicates that a significant component of the mechanism by which light initiates photomorphogenesis upon first exposure of dark-grown seedlings to irradiation involves reversal of this repression by rapid reduction in the abundance of these PIF proteins, through degradation induced by direct interaction of the photoactivated phy molecule with the transcription factors. CONCLUSIONS We conclude that bHLH transcription factors PIF1, PIF3, PIF4, and PIF5 act as constitutive repressors of photomorphogenesis in the dark, action that is rapidly abrogated upon light exposure by phy-induced proteolytic degradation of these PIFs, allowing the initiation of photomorphogenesis to occur.
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717
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Abstract
Despite recent elucidation of the three-dimensional structure of major photosynthetic complexes, our understanding of light energy conversion in plant chloroplasts and microalgae under physiological conditions requires exploring the dynamics of photosynthesis. The photosynthetic apparatus is a flexible molecular machine that can acclimate to metabolic and light fluctuations in a matter of seconds and minutes. On a longer time scale, changes in environmental cues trigger acclimation responses that elicit intracellular signaling between the nucleo-cytosol and chloroplast resulting in modification of the biogenesis of the photosynthetic machinery. Here we attempt to integrate well-established knowledge on the functional flexibility of light-harvesting and electron transfer processes, which has greatly benefited from genetic approaches, with data derived from the wealth of recent transcriptomic and proteomic studies of acclimation responses in photosynthetic eukaroytes.
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Affiliation(s)
- Stephan Eberhard
- Université Pierre et Marie Curie, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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718
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Narikawa R, Muraki N, Shiba T, Ikeuchi M, Kurisu G. Crystallization and preliminary X-ray studies of the chromophore-binding domain of cyanobacteriochrome AnPixJ from Anabaena sp. PCC 7120. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:159-62. [PMID: 19194010 PMCID: PMC2635879 DOI: 10.1107/s1744309108044151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 12/29/2008] [Indexed: 05/27/2023]
Abstract
Cyanobacteriochromes form a recently defined superfamily of tetrapyrrole-based photoreceptors that are distantly related to conventional red/far-red photoreceptor phytochromes. Among these molecules, AnPixJ from Anabaena sp. PCC 7120 is a novel photoreceptor that shows reversible photoconversion between green-absorbing and red-absorbing forms, which is in contrast to the properties of conventional phytochromes. In order to better understand the structural basis of this unique photoconversion mechanism, the chromophore-binding domain of AnPixJ (AnPixJ-GAF2) was heterologously overproduced and purified, and crystallization of both forms was attempted. Blue crystals of the red-absorbing form of AnPixJ-GAF2 were successfully obtained; they belonged to space group P4(3)2(1)2 and contained one monomer per asymmetric unit. Diffraction data were collected to a resolution of 1.8 A using synchrotron-radiation beamline BL-5A at the Photon Factory.
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Affiliation(s)
- Rei Narikawa
- Department of Life Sciences, Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan.
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719
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Dietzek B, Tarnovsky AN, Yartsev A. Visualizing overdamped wavepacket motion: Excited-state isomerization of pseudocyanine in viscous solvents. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.10.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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720
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Oh E, Kang H, Yamaguchi S, Park J, Lee D, Kamiya Y, Choi G. Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. THE PLANT CELL 2009; 21:403-19. [PMID: 19244139 PMCID: PMC2660632 DOI: 10.1105/tpc.108.064691] [Citation(s) in RCA: 273] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 02/02/2009] [Accepted: 02/09/2009] [Indexed: 05/18/2023]
Abstract
PHYTOCHROME INTERACTING FACTOR 3-LIKE5 (PIL5) is a basic helix-loop-helix transcription factor that inhibits seed germination by regulating the expression of gibberellin (GA)- and abscisic acid (ABA)-related genes either directly or indirectly. It is not yet known, however, whether PIL5 regulates seed germination solely through GA and ABA. Here, we used Chromatin immunoprecipitation-chip (ChIP-chip) analysis to identify 748 novel PIL5 binding sites in the Arabidopsis thaliana genome. Consistent with the molecular function of PIL5 as a transcription regulator, most of the identified binding sites are located in gene promoter regions. Binding site analysis shows that PIL5 binds to its target sites mainly through the G-box motif in vivo. Microarray analysis reveals that phytochromes regulate a large number of genes mainly through PIL5 during seed germination. Comparison between the ChIP-chip and microarray data indicates that PIL5 regulates 166 genes by directly binding to their promoters. Many of the identified genes encode transcription regulators involved in hormone signaling, while some encode enzymes involved in cell wall modification. Interestingly, PIL5 directly regulates many transcription regulators of hormone signaling and indirectly regulates many genes involved in hormone metabolism. Taken together, our data indicate that PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds.
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Affiliation(s)
- Eunkyoo Oh
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
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721
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Inomata K, Khawn H, Chen LY, Kinoshita H, Zienicke B, Molina I, Lamparter T. Assembly of Agrobacterium Phytochromes Agp1 and Agp2 with Doubly Locked Bilin Chromophores. Biochemistry 2009; 48:2817-27. [DOI: 10.1021/bi802334u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Katsuhiko Inomata
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Htoi Khawn
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Li-Yi Chen
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Hideki Kinoshita
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Benjamin Zienicke
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Isabel Molina
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Tilman Lamparter
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan, and Universität Karlsruhe, Botanik I, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
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722
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Ultrafast excited-state isomerization in phytochrome revealed by femtosecond stimulated Raman spectroscopy. Proc Natl Acad Sci U S A 2009; 106:1784-9. [PMID: 19179399 DOI: 10.1073/pnas.0812056106] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Photochemical interconversion between the red-absorbing (P(r)) and the far-red-absorbing (P(fr)) forms of the photosensory protein phytochrome initiates signal transduction in bacteria and higher plants. The P(r)-to-P(fr) transition commences with a rapid Z-to-E photoisomerization at the C(15)=C(16) methine bridge of the bilin prosthetic group. Here, we use femtosecond stimulated Raman spectroscopy to probe the structural changes of the phycocyanobilin chromophore within phytochrome Cph1 on the ultrafast time scale. The enhanced intensity of the C(15)-H hydrogen out-of-plane (HOOP) mode, together with the appearance of red-shifted C=C stretch and N-H in-plane rocking modes within 500 fs, reveal that initial distortion of the C(15)=C(16) bond occurs in the electronically excited I* intermediate. From I*, 85% of the excited population relaxes back to P(r) in 3 ps, whereas the rest goes on to the Lumi-R photoproduct consistent with the 15% photochemical quantum yield. The C(15)-H HOOP and skeletal modes evolve to a Lumi-R-like pattern after 3 ps, thereby indicating that the C(15)=C(16) Z-to-E isomerization occurs on the excited-state surface.
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723
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Kikis EA, Oka Y, Hudson ME, Nagatani A, Quail PH. Residues clustered in the light-sensing knot of phytochrome B are necessary for conformer-specific binding to signaling partner PIF3. PLoS Genet 2009; 5:e1000352. [PMID: 19165330 PMCID: PMC2621353 DOI: 10.1371/journal.pgen.1000352] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 12/22/2008] [Indexed: 11/18/2022] Open
Abstract
The bHLH transcription factor, PHYTOCHROME INTERACTING FACTOR 3 (PIF3), interacts specifically with the photoactivated, Pfr, form of Arabidopsis phytochrome B (phyB). This interaction induces PIF3 phosphorylation and degradation in vivo and modulates phyB-mediated seedling deetiolation in response to red light. To identify missense mutations in the phyB N-terminal domain that disrupt this interaction, we developed a yeast reverse-hybrid screen. Fifteen individual mutations identified in this screen, or in previous genetic screens for Arabidopsis mutants showing reduced sensitivity to red light, were shown to also disrupt light-induced binding of phyB to PIF3 in in vitro co-immunoprecipitation assays. These phyB missense mutants fall into two general classes: Class I (eleven mutants) containing those defective in light signal perception, due to aberrant chromophore attachment or photoconversion, and Class II (four mutants) containing those normal in signal perception, but defective in the capacity to transduce this signal to PIF3. By generating a homology model for the three-dimensional structure of the Arabidopsis phyB chromophore-binding region, based on the crystal structure of Deinococcus radiodurans phytochrome, we predict that three of the four Class II mutated phyB residues are solvent exposed in a cleft between the presumptive PAS and GAF domains. This deduction suggests that these residues could be directly required for the physical interaction of phyB with PIF3. Because these three residues are also necessary for phyB-imposed inhibition of hypocotyl elongation in response to red light, they are functionally necessary for signal transfer from photoactivated phyB, not only to PIF3 and other related bHLH transcription factors tested here, but also to other downstream signaling components involved in regulating seedling deetiolation. Plants monitor their environment for informational light signals that are used to direct adaptive morphogenic responses. The phytochrome (phy) family of photoreceptors are central to this process. Upon photoperception, phy molecules rapidly translocate to the nucleus where they interact with basic helix-loop-helix transcription factors, termed PIFs (phy-Interacting Factors), and induce gene-expression changes that control morphogenic responses. The molecular determinants in the phy protein responsible for direct intermolecular signal transfer from the activated photoreceptor to transduction partners are undefined. Using random mutagenesis of Arabidopsis phyB, coupled with a reverse-hybrid protein-interaction screen, we identified missense mutations in the N-terminal domain that abrogate the binding of the photoreceptor molecule to PIF3. A subset of these mutated phyB molecules retain the capacity for light-signal perception but are defective in the capacity to transduce that signal to PIF3 and other related PIFs. The mutated residues in these molecules are predicted to cluster at the surface of the protein in a structure termed the “light-sensing knot.” These residues are necessary for phyB-regulated growth in the living plant, establishing that the protein region identified appears to function as a component of the molecular interface responsible for direct signal transfer to transduction partners in the cell.
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Affiliation(s)
- Elise A. Kikis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- USDA/ARS – Plant Gene Expression Center, Albany, California, United States of America
| | - Yoshito Oka
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- USDA/ARS – Plant Gene Expression Center, Albany, California, United States of America
| | - Matthew E. Hudson
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Akira Nagatani
- Department of Biology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- USDA/ARS – Plant Gene Expression Center, Albany, California, United States of America
- * E-mail:
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724
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Durbeej B. On the primary event of phytochrome: quantum chemical comparison of photoreactions at C4, C10 and C15. Phys Chem Chem Phys 2009; 11:1354-61. [PMID: 19224036 DOI: 10.1039/b811813b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phytochromes are widespread photoreceptors responsive to red and far-red light that exist in two photochromic forms Pr (inactive) and Pfr (active). The Pr --> Pfr conversion proceeds through a series of events initiated by Z-->E photoisomerization of the tetrapyrrole chromophore, believed to occur at C15 of the methine bridge between rings C and D. Recent crystal structures show that ring D in Pr is less tightly packed by the protein than rings A, B and C, which should favor the C15 reaction over reactions at C4 (AB methine bridge) and C10 (BC). In the present work, quantum chemical methods are used to establish the intrinsic reactivity of the chromophore towards all three possible Z-->E isomerization events in the absence of steric effects and specific interactions with the protein. Using a level of theory that reproduces spectroscopic data with an accuracy of approximately 0.2 eV, it is demonstrated that isolated conditions allow the C10 photoreaction to substantially dominate. This finding suggests that the different degrees of ring-packing observed in the protein are crucial not only to facilitate a reaction at C15, but also to prevent an intrinsically more favorable reaction at C10 from taking place.
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Affiliation(s)
- Bo Durbeej
- Department of Chemistry, University of Siena, Via Aldo Moro 2, I-53100, Siena, Italy.
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725
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A novel protein phosphatase indirectly regulates phytochrome-interacting factor 3 via phytochrome. Biochem J 2009; 415:247-55. [PMID: 18564962 DOI: 10.1042/bj20071555] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Light signal transduction in plants involves an intricate series of pathways which is finely regulated by interactions between specific signalling proteins, as well as by protein modifications such as phosphorylation and ubiquitination. The identification of novel phytochrome-interacting proteins and the precise signalling mechanisms that they mediate is still ongoing. In our present study, we show that the newly identified putative phytochrome-associated protein, PAPP2C (phytochrome-associated protein phosphatase type 2C), interacts in the nucleus with phyA (phytochrome A) and phyB, both in vitro and in vivo. Moreover, the phosphatase activity of PAPP2C and its association with phytochromes were found to be enhanced by red light, indicating that it plays a role in mediating phytochrome signalling. In particular, PAPP2C specifically binds to the N-terminal PHY domain of the phytochromes. We thus speculate that this interaction reflects a unique regulatory function of this phosphatase toward established phytochrome-associated proteins. We also show that PAPP2C effectively dephosphorylates phytochromes in vitro. Interestingly, PAPP2C indirectly mediates the dephosphorylation of PIF3 (phytochrome-interacting factor 3) in vitro. Taken together, we suggest that PAPP2C functions as a regulator of PIF3 by dephosphorylating phytochromes in the nucleus.
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726
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Hu W, Su YS, Lagarias JC. A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks. MOLECULAR PLANT 2009; 2:166-82. [PMID: 19529817 PMCID: PMC2639728 DOI: 10.1093/mp/ssn086] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 11/08/2008] [Indexed: 05/20/2023]
Abstract
Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su and Lagarias, 2007). In the present study, comparative transcription profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole-genome transcription profiles of dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to but quantitatively greater than those of wild-type seedlings grown under 15 or 50 micromol m(-2) m(-1) continuous red light (Rc). Among the 2977 genes statistically significant two-fold (SSTF) regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways, and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-regulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway(s) strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.
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Affiliation(s)
- Wei Hu
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Yi-Shin Su
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
- Present address: Carnegie Institution of Washington, Department of Plant Biology, Stanford, CA 94305, USA
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
- To whom correspondence should be addressed. E-mail , fax +1-530-752-3085
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727
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Bacteriophytochromes Control Photosynthesis in Rhodopseudomonas palustris. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4020-8815-5_40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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728
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Walter A, Silk WK, Schurr U. Environmental effects on spatial and temporal patterns of leaf and root growth. ANNUAL REVIEW OF PLANT BIOLOGY 2009; 60:279-304. [PMID: 19575584 DOI: 10.1146/annurev.arplant.59.032607.092819] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Leaves and roots live in dramatically different habitats, but are parts of the same organism. Automated image processing of time-lapse records of these organs has led to understanding of spatial and temporal patterns of growth on time scales from minutes to weeks. Growth zones in roots and leaves show distinct patterns during a diel cycle (24 h period). In dicot leaves under nonstressful conditions these patterns are characterized by endogenous rhythms, sometimes superimposed upon morphogenesis driven by environmental variation. In roots and monocot leaves the growth patterns depend more strongly on environmental fluctuations. Because the impact of spatial variations and temporal fluctuations of above- and belowground environmental parameters must be processed by the plant body as an entire system whose individual modules interact on different levels, growth reactions of individual modules are often highly nonlinear. A mechanistic understanding of plant resource use efficiency and performance in a dynamically fluctuating environment therefore requires an accurate analysis of leaf and root growth patterns in conjunction with knowledge of major intraplant communication systems and metabolic pathways.
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Affiliation(s)
- Achim Walter
- Institute of Chemistry and Dynamics of Geosphere ICG-3: Phytosphere Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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729
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730
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731
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Yamada S, Shiro Y. Structural Basis of the Signal Transduction in the Two-Component System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:22-39. [DOI: 10.1007/978-0-387-78885-2_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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732
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Matute RA, Contreras R, Pérez-Hernández G, González L. The Chromophore Structure of the Cyanobacterial Phytochrome Cph1 As Predicted by Time-Dependent Density Functional Theory. J Phys Chem B 2008; 112:16253-6. [DOI: 10.1021/jp807471e] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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733
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Kozma-Bognár L, Káldi K. Synchronization of the Fungal and the Plant Circadian Clock by Light. Chembiochem 2008; 9:2565-73. [DOI: 10.1002/cbic.200800385] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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734
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Girault T, Bergougnoux V, Combes D, Viemont JD, Leduc N. Light controls shoot meristem organogenic activity and leaf primordia growth during bud burst in Rosa sp. PLANT, CELL & ENVIRONMENT 2008; 31:1534-44. [PMID: 18643902 DOI: 10.1111/j.1365-3040.2008.01856.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Light controls bud burst in many plants, which subsequently affects their architecture. Nevertheless, very little is known about this photomorphogenic process. This study ascertains the effects of light on bud burst and on two of its components, i.e. growth of preformed leaves and meristem organogenesis in six cultivars from three Rosa species (R. hybrida L., R. chinensis L., R. wichurana L.). Defoliated plants were severed above the third basal bud and exposed, either to darkness or to different intensities of white light, to blue, red or to FR, at constant temperature. Bud bursting was inhibited in darkness in the six cultivars of Rosa, but not in Arabidopsis, tomato and poplar plants under the same condition. In all Rosa cultivars, bud burst, growth of preformed leaves and meristem organogenesis were triggered by blue and red lights, and extended by increasing light intensities. FR was inhibitory of bud burst. Partial shading experiments demonstrated that bud and not stem was the active site for light perception in bud burst.
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Affiliation(s)
- Tiffanie Girault
- Université d'Angers, UFR Sciences, UMR-462 SAGAH (Université d'Angers, INH, INRA), Angers cedex, France
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735
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Mathews S, McBreen K. Phylogenetic relationships of B-related phytochromes in the Brassicaceae: Redundancy and the persistence of phytochrome D. Mol Phylogenet Evol 2008; 49:411-23. [DOI: 10.1016/j.ympev.2008.07.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Revised: 07/18/2008] [Accepted: 07/26/2008] [Indexed: 11/27/2022]
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736
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Wollenberg AC, Strasser B, Cerdán PD, Amasino RM. Acceleration of flowering during shade avoidance in Arabidopsis alters the balance between FLOWERING LOCUS C-mediated repression and photoperiodic induction of flowering. PLANT PHYSIOLOGY 2008; 148:1681-94. [PMID: 18790998 PMCID: PMC2577263 DOI: 10.1104/pp.108.125468] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 09/02/2008] [Indexed: 05/18/2023]
Abstract
The timing of the floral transition in Arabidopsis (Arabidopsis thaliana) is influenced by a number of environmental signals. Here, we have focused on acceleration of flowering in response to vegetative shade, a condition that is perceived as a decrease in the ratio of red to far-red radiation. We have investigated the contributions of several known flowering-time pathways to this acceleration. The vernalization pathway promotes flowering in response to extended cold via transcriptional repression of the floral inhibitor FLOWERING LOCUS C (FLC); we found that a low red to far-red ratio, unlike cold treatment, lessened the effects of FLC despite continued FLC expression. A low red to far-red ratio required the photoperiod-pathway genes GIGANTEA (GI) and CONSTANS (CO) to fully accelerate flowering in long days and did not promote flowering in short days. Together, these results suggest a model in which far-red enrichment can bypass FLC-mediated late flowering by shifting the balance between FLC-mediated repression and photoperiodic induction of flowering to favor the latter. The extent of this shift was dependent upon environmental parameters, such as the length of far-red exposure. At the molecular level, we found that far-red enrichment generated a phase delay in GI expression and enhanced CO expression and activity at both dawn and dusk. Finally, our analysis of the contribution of PHYTOCHROME AND FLOWERING TIME1 (PFT1) to shade-mediated rapid flowering has led us to suggest a new model for the involvement of PFT1 in light signaling.
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Affiliation(s)
- Amanda C Wollenberg
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706, USA
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737
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Fankhauser C, Chen M. Transposing phytochrome into the nucleus. TRENDS IN PLANT SCIENCE 2008; 13:596-601. [PMID: 18824397 DOI: 10.1016/j.tplants.2008.08.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 08/05/2008] [Accepted: 08/06/2008] [Indexed: 05/19/2023]
Abstract
To control many physiological responses, phytochromes directly modulate gene expression. A key regulatory event in this signal transduction pathway is the light-controlled translocation of the photoreceptor from the cytoplasm into the nucleus. Recent publications are beginning to shed light on the molecular mechanisms underlying this central control point. Interestingly, there is a specific mechanism for phytochrome A (phyA) nuclear accumulation. The dedicated phyA nuclear import pathway might be important for the distinct photosensory specificity of this atypical phytochrome. Recent studies in the field also provide a starting point for investigating how the different subcellular pools of phytochrome can control distinct responses to light.
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Affiliation(s)
- Christian Fankhauser
- Centre for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, Switzerland.
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738
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Light-induced chromophore activity and signal transduction in phytochromes observed by 13C and 15N magic-angle spinning NMR. Proc Natl Acad Sci U S A 2008; 105:15229-34. [PMID: 18832155 DOI: 10.1073/pnas.0805696105] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Both thermally stable states of phytochrome, Pr and Pfr, have been studied by (13)C and (15)N cross-polarization (CP) magic-angle spinning (MAS) NMR using cyanobacterial (Cph1) and plant (phyA) phytochrome sensory modules containing uniformly (13)C- and (15)N-labeled bilin chromophores. Two-dimensional homo- and heteronuclear experiments allowed most of the (13)C chemical shifts to be assigned in both states. Chemical shift differences reflect changes of the electronic structure of the cofactor at the atomic level as well as its interactions with the chromophore-binding pocket. The chromophore in cyanobacterial and plant phytochromes shows very similar features in the respective Pr and Pfr states. The data are interpreted in terms of a strengthened hydrogen bond at the ring D carbonyl. The red shift in the Pfr state is explained by the increasing length of the conjugation network beyond ring C including the entire ring D. Enhanced conjugation within the pi-system stabilizes the more tensed chromophore in the Pfr state. Concomitant changes at the ring C propionate carboxylate and the ring D carbonyl are explained by a loss of hydrogen bonding to Cph1-His-290 and transmittance of conformational changes to the ring C propionate via a water network. These and other conformational changes may lead to modified surface interactions, e.g., along the tongue region contacting the bilin chromophore.
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739
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Krieger A, Molina I, Oberpichler I, Michael N, Lamparter T. Spectral properties of phytochrome Agp2 from Agrobacterium tumefaciens are specifically modified by a compound of the cell extract. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2008; 93:16-22. [DOI: 10.1016/j.jphotobiol.2008.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 05/24/2008] [Accepted: 07/04/2008] [Indexed: 11/29/2022]
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740
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Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction. Proc Natl Acad Sci U S A 2008; 105:14715-20. [PMID: 18799746 DOI: 10.1073/pnas.0806718105] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 A resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an "arm" structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.
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741
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The structure of a complete phytochrome sensory module in the Pr ground state. Proc Natl Acad Sci U S A 2008; 105:14709-14. [PMID: 18799745 DOI: 10.1073/pnas.0806477105] [Citation(s) in RCA: 333] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Phytochromes are red/far-red photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is still unclear. Here, we report the ground state structure of the complete sensory module of Cph1 phytochrome from the cyanobacterium Synechocystis 6803. Although the phycocyanobilin (PCB) chromophore is attached to Cys-259 as expected, paralleling the situation in plant phytochromes but contrasting to that in bacteriophytochromes, the ZZZssa conformation does not correspond to that expected from Raman spectroscopy. We show that the PHY domain, previously considered unique to phytochromes, is structurally a member of the GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) family. Indeed, the tandem-GAF dumbbell revealed for phytochrome sensory modules is remarkably similar to the regulatory domains of cyclic nucleotide (cNMP) phosphodiesterases and adenylyl cyclases. A unique feature of the phytochrome structure is a long, tongue-like protrusion from the PHY domain that seals the chromophore pocket and stabilizes the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. The structure that we present provides a framework for light-driven signal transmission in phytochromes.
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742
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Abstract
In higher plants, light is crucial for regulation of nitrate uptake, translocation and assimilation into organic compounds. Part of this metabolism is tightly coupled to photosynthesis because the enzymes involved, nitrite reductase and glutamate synthase, are localized to the chloroplasts and receive reducing power from photosynthetic electron transport. However, important enzymes in nitrate acquisition and reduction are localized to cellular compartments other than chloroplasts and are also up-regulated by light, i.e. transporters in cell and organellar membranes and nitrate reductase in the cytosol. This review describes the different light-dependent signalling cascades regulating nitrate metabolism at the transcriptional as well as post-transcriptional level, and how reactions in different compartments of the cell are co-ordinated. Essential players in this network are phytochrome and HY5 (long hypocotyls 5)/HYH (HY5 homologue)-dependent signalling pathways, the energy-related AMPK (AMP-activated protein kinase) protein kinase homologue SNRK1 (sucrose non-fermenting kinase 1-related kinase), chloroplastic thioredoxins and the prokaryotically originated PII protein. A complex light-dependent network of regulation emerges, which appears to be necessary for optimal nitrogen assimilation and for avoiding the accumulation of toxic intermediates and side products, such as nitrite and reactive oxygen compounds.
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743
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Zhu D, Maier A, Lee JH, Laubinger S, Saijo Y, Wang H, Qu LJ, Hoecker U, Deng XW. Biochemical characterization of Arabidopsis complexes containing CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA proteins in light control of plant development. THE PLANT CELL 2008; 20:2307-23. [PMID: 18812498 PMCID: PMC2570740 DOI: 10.1105/tpc.107.056580] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 07/20/2008] [Accepted: 09/10/2008] [Indexed: 05/18/2023]
Abstract
COP1 (for CONSTITUTIVELY PHOTOMORPHOGENIC1) and the four partially redundant SPA (for SUPPRESSOR OF PHYA) proteins work in concert to repress photomorphogenesis in Arabidopsis thaliana by targeting key transcription factors and phytochrome A for degradation via the 26S proteasome. Here, we report a detailed biochemical characterization of the SPA-COP1 complexes. The four endogenous SPA proteins can form stable complexes with COP1 in vivo regardless of light conditions but exhibit distinct expression profiles in different tissues and light conditions. The SPA proteins can self-associate or interact with each other, forming a heterogeneous group of SPA-COP1 complexes in which the exact SPA protein compositions vary depending on the abundance of individual SPA proteins. The four SPA proteins could be divided into two functional groups depending on their interaction affinities, their regulation of ELONGATED HYPOCOTYL5 degradation, and their opposite effects on COP1 protein accumulation. Loss-of-function mutations in a predominant SPA protein may cause a significant reduction in the overall SPA-COP1 E3 ligase activity, resulting in a partial constitutive photomorphogenic phenotype. This study thus provides an in-depth biochemical view of the SPA-COP1 E3 ligase complexes and offers new insights into the molecular basis for their distinct roles in the light control of plant development.
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Affiliation(s)
- Danmeng Zhu
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
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744
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Abstract
The phytochrome protein superfamily reveals a diversity of mechanisms of action. Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensing domains from bacteria have been determined.
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745
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Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway. Proc Natl Acad Sci U S A 2008; 105:12797-802. [PMID: 18728185 DOI: 10.1073/pnas.0801232105] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
General methods to engineer genetically encoded, reversible, light-mediated control over protein function would be useful in many areas of biomedical research and technology. We describe a system that yields such photo-control over actin assembly. We fused the Rho family GTPase Cdc42 in its GDP-bound form to the photosensory domain of phytochrome B (PhyB) and fused the Cdc42 effector, the Wiskott-Aldrich Syndrome Protein (WASP), to the light-dependent PhyB-binding domain of phytochrome interacting factor 3 (Pif3). Upon red light illumination, the fusion proteins bind each other, activating WASP, and consequently stimulating actin assembly by the WASP target, the Arp2/3 complex. Binding and WASP activation are reversed by far-red illumination. Our approach, in which the biochemical specificity of the nucleotide switch in Cdc42 is overridden by the light-dependent PhyB-Pif3 interaction, should be generally applicable to other GTPase-effector pairs.
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746
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Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD. Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. J Mol Biol 2008; 383:403-13. [PMID: 18762196 DOI: 10.1016/j.jmb.2008.08.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 08/11/2008] [Accepted: 08/14/2008] [Indexed: 01/31/2023]
Abstract
The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B' cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80 degrees relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B' GAF domain can, by itself, complete the Pr --> Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework.
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Affiliation(s)
- Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, WI 53706, USA
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747
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Ikeuchi M, Ishizuka T. Cyanobacteriochromes: a new superfamily of tetrapyrrole-binding photoreceptors in cyanobacteria. Photochem Photobiol Sci 2008; 7:1159-67. [PMID: 18846279 DOI: 10.1039/b802660m] [Citation(s) in RCA: 232] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new group of photoreceptors has been experimentally revealed in cyanobacteria. They are phototaxis regulator SyPixJ1, TePixJ and AnPixJ, chromatic acclimation regulator SyCcaS, circadian input kinase homolog SyCikA and many other candidates, which have been found only in cyanobacteria to date. These new photoreceptors are now proposed to be "cyanobacteriochromes". They are characterized by the presence of a chromophore-binding GAF domain that is homologous to the tetrapyrrole-binding GAF domain of the phytochrome. Here, we summarized unique features of those representatives: (1) only the GAF domain is sufficient for full photoconversion, (2) the GAF domain is homologous to but distinct from the phytochrome GAF, (3) the GAF domain binds a linear tetrapyrrole pigment such as phycoviolobilin or phycocyanobilin, (4) spectral properties are very diverse from near ultra-violet to red region. We also discussed the functionality of the other candidate GAFs, structure and evolution.
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Affiliation(s)
- Masahiko Ikeuchi
- Department of Life Sciences, Biology, The University of Tokyo, Komaba, Meguro, Tokyo, 153-8902, Japan.
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748
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Mutant screen distinguishes between residues necessary for light-signal perception and signal transfer by phytochrome B. PLoS Genet 2008; 4:e1000158. [PMID: 18704165 PMCID: PMC2494609 DOI: 10.1371/journal.pgen.1000158] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 07/10/2008] [Indexed: 01/21/2023] Open
Abstract
The phytochromes (phyA to phyE) are a major plant photoreceptor family that regulate a diversity of developmental processes in response to light. The N-terminal 651–amino acid domain of phyB (N651), which binds an open tetrapyrrole chromophore, acts to perceive and transduce regulatory light signals in the cell nucleus. The N651 domain comprises several subdomains: the N-terminal extension, the Per/Arnt/Sim (PAS)-like subdomain (PLD), the cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) subdomain, and the phytochrome (PHY) subdomain. To define functional roles for these subdomains, we mutagenized an Arabidopsis thaliana line expressing N651 fused in tandem to green fluorescent protein, β-glucuronidase, and a nuclear localization signal. A large-scale screen for long hypocotyl mutants identified 14 novel intragenic missense mutations in the N651 moiety. These new mutations, along with eight previously identified mutations, were distributed throughout N651, indicating that each subdomain has an important function. In vitro analysis of the spectral properties of these mutants enabled them to be classified into two principal classes: light-signal perception mutants (those with defective spectral activity), and signaling mutants (those normal in light perception but defective in intracellular signal transfer). Most spectral mutants were found in the GAF and PHY subdomains. On the other hand, the signaling mutants tend to be located in the N-terminal extension and PLD. These observations indicate that the N-terminal extension and PLD are mainly involved in signal transfer, but that the C-terminal GAF and PHY subdomains are responsible for light perception. Among the signaling mutants, R110Q, G111D, G112D, and R325K were particularly interesting. Alignment with the recently described three-dimensional structure of the PAS-GAF domain of a bacterial phytochrome suggests that these four mutations reside in the vicinity of the phytochrome light-sensing knot. Adapting to the light environment, plants have evolved several photoreceptors, of which the phytochromes are specialized in perceiving the red and far-red light region of the spectrum. Although phytochrome was first discovered in plants, the phytochrome species are present in several organisms, including bacteria. The mechanisms by which phytochromes transduce light signals to downstream components are most well studied in plants. Upon light activation, phytochromes translocate from the cytoplasm into nucleus and regulate the gene expression network through interaction with nuclear transcription factors. The phytochrome molecule can be divided into two major domains: the N-terminal moiety, which is responsible for the light perception, and the C-terminal moiety. Although the C-terminal moiety was though to be involved in signal transduction, it has recently been shown that the N-terminal moiety has a role not only in the light perception, but also in light signal transfer to the downstream network. However, no signaling motifs have been found in the N-terminal moiety. In this study, we analyzed intragenic mutations derived from a genetic screen and found a cluster of residues necessary for signal transduction in a small region neighboring the light-sensing chromophore moiety on the three-dimensional structure. This is an important step towards understanding how a major plant photoreceptor, phytochrome, intramolecularly processes the light signal to trigger diverse physiological responses.
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749
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von Stetten D, Günther M, Scheerer P, Murgida DH, Mroginski MA, Krauss N, Lamparter T, Zhang J, Anstrom DM, Vierstra RD, Forest KT, Hildebrandt P. Chromophore heterogeneity and photoconversion in phytochrome crystals and solution studied by resonance Raman spectroscopy. Angew Chem Int Ed Engl 2008; 47:4753-5. [PMID: 18484576 DOI: 10.1002/anie.200705716] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- David von Stetten
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
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750
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Guo L, Zhou J, Elling AA, Charron JBF, Deng XW. Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions. PLANT PHYSIOLOGY 2008; 147:2070-83. [PMID: 18550682 PMCID: PMC2492627 DOI: 10.1104/pp.108.122929] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 06/03/2008] [Indexed: 05/19/2023]
Abstract
Here, we analyzed the effects of light regulation on four selected histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) and the relationship of these histone modifications with the expression of representative light-regulated genes. We observed that the histone modifications examined and gene transcription were cooperatively regulated in response to changing light environments. Using H3K9ac as an example, our analysis indicated that histone modification patterns are set up very early and are relatively stable during Arabidopsis (Arabidopsis thaliana) seedling development. Distinct photoreceptor systems are responsible for mediating the effects of different light qualities on histone modifications. Moreover, we found that light regulation of gene-specific histone modifications involved the known photomorphogenesis-related proteolytic system defined by the pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETOLIATED proteins and histone modification enzymes (such as HD1). Furthermore, our data suggest that light-regulated changes in histone modifications might be an intricate part of light-controlled gene transcription. Thus, it is possible that variations in histone modifications are an important physiological component of plant responses to changing light environments.
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Affiliation(s)
- Lan Guo
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
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