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First published online September 17, 2004; 10.1105/tpc.104.023879 © 2004 American Society of Plant Biologists
Phytochrome Phosphorylation Modulates Light Signaling by Influencing the ProteinProtein Interaction
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| ABSTRACT |
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| INTRODUCTION |
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Posttranslational modification is important for the modulation of many signal transductions (e.g., rhodopsin is desensitized by phosphorylation by rhodopsin kinase) (Sokal et al., 2002
). Phytochrome has been known as a phosphoprotein because it could be readily labeled with 32P isotope in vivo (Quail et al., 1978
). Several observations and indirect lines of evidence for the possible role of protein phosphorylation downstream of the phytochrome-mediated light signal transduction pathway have been discussed (Singh and Song, 1990
; Elich and Chory, 1997a
; Fankhauser and Chory, 1999
; Watson, 2000
; Sharma, 2001
). For example, mutation of N-terminal Ser to Ala results in an increased biological activity of phytochrome A (phyA), suggesting that phytochrome responses might be desensitized by this photoreceptor phosphorylation (Stockhaus et al., 1992
; Jordan et al., 1997
). However, the in vivo functional role of phytochrome phosphorylation is still unknown.
The sites of phytochrome phosphorylation in vivo and in vitro have been identified with oat (Avena sativa) phyA (McMichael and Lagarias, 1990
; Lapko et al., 1996
, 1997
, 1999
). There are two Ser sites, Serine-7 (Ser7) and Serine-598 (Ser598), that are phosphorylated in vivo. Phosphorylation at Ser7 in the N-terminal extension region (NTE) is similar in both Pr and Pfr forms, whereas Ser598 in the hinge region is phosphorylated in a Pfr preferential manner (Lapko et al., 1997
, 1999
). The in vitro phosphorylation sites of oat phyA have also been identified using protein kinase A (PKA). Two Ser, Serine-17 (Ser17) and Ser598, are detected as the in vitro phosphorylation sites by PKA. Ser17 is phosphorylated primarily in a Pr preferential manner, whereas Ser598 phosphorylation is preferred in the Pfr form (McMichael and Lagarias, 1990
; Lapko et al., 1996
). Because this Ser598 residue is phosphorylated only in the Pfr form that is considered the active form of phytochrome, it was suggested that the phosphorylation and dephosphorylation of Ser598 serves as a switch in phytochrome signaling (Park et al., 2000
; Kim et al., 2002b
).
Here, we demonstrate that phytochrome phosphorylation at Ser598 in the hinge region controls the interaction of phytochrome with its putative signal transducers, providing the functional role of a phytochrome phosphorylation site. The phosphorylation at Ser598 of oat phyA inhibits the interaction between phytochrome and its putative signal transducers, NDPK2 and PIF3. The transgenic plants with Ser598Ala mutant phyA are hypersensitive to light compared with the transgenic plants with wild-type oat phyA, suggesting that phytochrome phosphorylation at Ser598 plays an inhibitory role. Our findings suggest that the phosphorylation and dephosphorylation of phytochrome be a key regulatory mechanism in its light-signaling pathway.
| RESULTS |
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Role of Phytochrome Phosphorylation in Light Signaling
Because the protein expression levels of wild-type and S598A mutant phyA were similar in transgenic seedlings and mature plants, we tested several hypotheses on the phosphorylation of phytochromes and its functional role (Fankhauser, 2000
) to understand the hypersensitivity of the S598A mutant transgenic plants to light (Figure 2A): (1) the photochemical and conformational changes by phosphorylation, (2) effects on phytochrome degradation, (3) dependence of nuclear localization of phyA on phosphorylation, (4) the autophosphorylation and kinase site of phyA, whether or not Ser598 is involved in phytochrome autophosphorylation and its kinase activity, and (5) effects of phytochrome phosphorylation on the proteinprotein interaction between phyA and the phytochrome-interacting signal transducer proteins.
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Phytochrome phosphorylation at Ser598 might inhibit the translocalization of phyA, and the phyA interaction with its positive signaling molecules in the nucleus could then be prevented (Smith, 2000
). We tested the translocalization of oat phyA and S598A mutant phyA into the nucleus in a time-dependent manner (Figure 2D). To study the subcellular localization of oat phyA-green fluorescent protein (GFP) and S598A-GFP, transgenic seedlings expressing these phyA-GFP fusion proteins were kept in darkness or treated with FRc. In darkness, oat phyA-GFP and S598A-GFP showed no nuclear localization. In FRc, both phyA GFP fusion proteins showed nuclear localization and formed the intranuclear speckles. No qualitative or quantitative differences were detectable, in darkness or in FRc (Figure 2D), indicating that the S598A mutation did not affect the light-induced nuclear import and speckle formation of phyA.
We next compared the phosphorylation of oat phyA versus S598A mutant because phytochromes are known as autophosphorylating Ser/Thr protein kinases (Yeh and Lagarias, 1998
). For this purpose, recombinant phytochromes were expressed in the Pichia expression system and purified using streptavidin affinity chromatography (see Supplemental Figure 1 online). Because it is known that phytochrome phosphorylation is stimulated in the presence of histone H1 (Wong et al., 1986
, 1989
; Yeh and Lagarias, 1998
), we also included it to check the stimulated phosphorylation of phyA by histone H1. The results showed that S598A mutant phyA still retained autophosphorylation and its phosphorylation was also stimulated by histone H1 (Figure 3), ruling out the possible involvement of Ser598 in the phytochrome autophosphorylation and phosphorylation activity on histone H1. These results also indicate that S598 is not the residue for phytochrome autophosphorylation and kinase activities.
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65, 66 to 1129 amino acids) and
65/S598A combination mutant phyA, were used for further study. These mutants interacted with NDPK2 normally unless they were phosphorylated (data not shown). Because Ser7 and Ser17 were removed in
65 mutants, only Ser598 could be phosphorylated by PKA. Results showed that PKA phosphorylated only the Pfr form of
65 mutant but not the Pr form (Figure 5A). Both Pr and Pfr forms of
65/S598A were not phosphorylated under the conditions employed. In NDPK2 activation assays,
65 phyA as well as full-length phyA (wild type) could activate the NDPK2 activity. However, only the phosphorylated Pfr of
65 mutant (
65 PfrP) showed a reduction in the level of NDPK2 activation (Figure 5B), indicating that Ser598 phosphorylation suppressed NDPK2 activation as expected. The inhibition was not complete because the percentage of phosphorylation on Ser598 was not stoichiometrically complete. These results indicate that Ser598 phosphorylation in fact inhibits the interaction of phytochrome with its signal transducer(s), such as NDPK2.
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Phytochrome Phosphorylation Also Influences Its Interaction with PIF3
Although Ser598 phosphorylation inhibits the interaction between phyA and NDPK2, the phenotypes of S598A transgenic plants could not be explained in terms of NDPK2 knockout or overexpression. There could be other mechanism(s) involving Ser598 phosphorylation, (i.e., multiple regulation of signaling by Ser598 phosphorylation). Thus, we also tested the phytochrome interaction with another phytochrome-interacting protein, PIF3, that is also known as a putative signal transducer of phytochrome and interacts with the Pfr form of phyA and phyB (Ni et al., 1998
). Using unphosphorylated (wild-type) and PKA-phosphorylated Pfr-phyA, we assessed the interaction with PIF3 by pull-down assay (Figure 6). The PKA-phosphorylated Pfr-phyA was purified using a Bio-gel P-6 column before this pull-down assay. Each Pfr form of native and phosphorylated phyA was incubated with glutathione S-transferase (GST)-PIF3, and protein gel blot analysis was performed with supernatant and precipitate fractions of the reactions. The results showed that phytochrome phosphorylation also prevented its interaction with PIF3 (Figure 6A). The unphosphorylated Pfr-phyA interacted with GST-PIF3 as reported (Ni et al., 1998
), whereas phosphorylated Pfr-phyA did not interact with PIF3. We also demonstrated the interaction of PIF3 with PKA-phosphorylated S598A mutant phyA (Figure 6B). To rule out the possible nonspecific effects of PKA or ATP/Mg2+, the phyA:PIF3 interactions were also examined in the presence of ATP/Mg2+ or PKA as controls. These results show that neither PKA nor ATP/Mg2+ affected the interaction between phyA and PIF3. The PKA phosphorylation of Pfr-S598A did not show any difference in the phyA:PIF3 interaction, but that of the wild-type Pfr form prevented its interaction with PIF3. This is consistent with the Ser598 to be the signal-modulating site. Thus, we suggest that phytochrome phosphorylation in the hinge region controls interactions of the photoactivated phyA with its putative signal transducers.
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| DISCUSSION |
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Ser598 phosphorylation occurs only in the Pfr form of phyA in red lighttreated oat seedlings (McMichael and Lagarias, 1990
; Lapko et al., 1999
), whereas phosphorylation of other sites (Ser7 and Ser17) was found either Pr/Pfr indifferent or Pr specific (Lapko et al., 1996
, 1997
). In fact, the Ser598 phosphorylation was thought to play an active role in the phyA-mediated light-signal transduction (Lapko et al., 1999
; Park et al., 2000
; Kim et al., 2002b
). Here, we showed that the transgenic plants of the S598A mutant were hypersensitive to light. In the case of oat wild-type phyA transgenics, their seedlings under FRc displayed shorter hypocotyls than wild-type Arabidopsis (Ler), suggesting that they are hypersensitive to light. However, when they were grown under white light, their phenotype is similar to Ler plants. These results are consistent with the previous report (Boylan and Quail, 1991
). In the case of S598A transgenics, they exhibited reduced inflorescence lengths under white light. The heights of S598A transgenics under white light were also much shorter (three to four times) than those of Ler and oat phyA transgenic plants. Their hypocotyls under FRc were also much shorter than wild-type Arabidopsis and oat phyA transgenics. Comparing these S598A transgenic phenotypes with wild-type Arabidopsis and oat phyA transgenic plants, we conclude that the Ser598 mutation confers hypersensitivity to light in the transgenic plants, suggesting that S598A phyA is hyperactive in plants.
We tested the possible hypotheses to explain the hypersensitive phenotype of S598A in terms of protein integrity, stability (degradation), nuclear localization, phosphorylation (kinase site), and proteinprotein interaction. Our results are consistent with the last hypothesis (i.e., the interaction between the phytochrome and its positive signal transducers is favored by the phosphorylation-deficient mutant phyA). Our data clearly showed that the phosphorylation of phyA influences the proteinprotein interaction between phyA and its putative signal transducers, NDPK2 and PIF3, whose binding sites are near to the hinge region and to PER-ARNT-SIMrelated domains implicated in mediating proteinprotein interaction in other systems (Lindebro et al., 1995
; Choi et al., 1999
; Zhu et al., 2000
). Another phytochrome-interacting protein, PKS1, which is known to bind the His kinase-related domain at the C-terminal end region (Fankhauser et al., 1999
), normally bound with phosphorylated phyA (data not shown). Thus, the Ser598 phosphorylation might influence the phyA interaction with its signal transducers whose binding regions are near to the hinge region. However, how this inhibition of proteinprotein interaction can be related to the hypersensitivity to light remains to be answered. NDPK2 is known as a positive signaling component of phytochrome signaling, so the removal of the inhibitory site of phytochrome interaction with this positive component can make phytochrome hyperactive. On the contrary, PIF3 was recently reported to play dual roles depending on the type of light response and the light conditions: negative roles in phyB- but not phyA-mediated inhibition of hypocotyl elongation and in both phyA- and phyB-induced cotyledon expansion and a positive role in phyA- and phyB-induced anthocyanin accumulation (Kim et al., 2003
). Thus, phytochrome phosphorylation at the hinge region may positively or negatively influence on the PIF3-mediated signaling, which remained to be elucidated.
Recently, we found that an Arabidopsis Ser/Thr-specific protein phosphatase 2A (FyPP) interacts with phyA (Kim et al., 2002a
). The FyPP-overexpressing transgenic plants stimulated phytochrome activity in flowering and hypocotyl shortening, whereas the antisense repression of FyPP transgenic plants displayed reduced phytochrome activity. These results are consistent with the negative regulation of phytochrome signaling in plants through protein phosphorylation. Specifically, phytochrome phosphorylation at Ser598 attenuates the signaling, whereas dephosphorylation by phytochrome phosphatase, such as FyPP, can amplify the signaling. It is reminiscent of rhodopsin signaling, also modulated by phosphorylation and dephosphorylation. On stimulation, rhodopsin is phosphorylated at several sites on its C terminus as the first step in deactivation (Lee et al., 2002
). The phytochrome signal transduction is thus modulated by protein phosphorylation and dephosphorylation; the phosphorylation blocks the interaction with its signal transducers, whereas the dephosphorylation enforces the interaction. S598A mutation might assure maintaining a higher level of the active pool of the unphosphorylated phytochrome molecules in displaying the hypersensitive phenotype to light. Ser598 can also be considered a switching site for modulating the interaction of phytochrome with its signal transducers, NDPK2 and PIF3.
Because Ser598 is not autophosphorylated to a significant extent, a protein kinase(s) is likely to play a regulatory role by catalyzing the phosphorylation of S598 residue. A phytochrome-associated kinase in oat seedlings that specifically and substantially phosphorylated Ser598 was detected during the preparation of native oat phyA (V.N. Lapko and P.-S. Song, unpublished data). Therefore, there may be several protein kinases and phosphatases for the phytochrome phosphorylation and dephosphorylation, but we still do not know what specific kinases and phosphatases are involved in phosphorylation/dephosphorylation at specific sites and their importance in the signaling.
We wondered whether the corresponding site to Ser598 of oat phyA exists in other phyA. So far, the phosphorylation sites of oat phyA have only been determined, so there is no available information for the phosphorylation site(s) of other phytochromes. Actually, the amino acid sequences are poorly conserved in the hinge region of phyA (Leu585 to Gly604 region in oat phyA). When we analyzed the amino acid sequences for possible phosphorylation sites using the NetPhos 2.0 server (http://www.cbs.dtu.dk/services/NetPhos), only Ser598 showed a high score (>0.9) for a phosphorylation site in the 20amino acid hinge region of oat phyA. Although the amino acid sequences in the hinge region are not conserved among the phytochromes, we found that phyA usually has a possibly reactive phosphorylation site in the hinge region, for example, Ser600 in rice (Oryza sativa) phyA and Thr592 in Arabidopsis phyA that shows scores of >0.9 in the NetPhos search results. There are two Ser residues at 589 and 601 in the hinge region of Arabidopsis phyA, however. Further studies will be necessary to confirm whether the same mechanism based on phosphorylation/dephosphorylation at the hinge is applicable to other phytochromes, including phyB.
For the phytochrome Pr
Pfr phototransformation, we proposed that the primary step of phytochrome signaling involves phototransformation-dependent conformational changes (Park et al., 2000
; Kim et al., 2002b
). On Pr
Pfr phototransformation, the NTE region undergoes a conformational change from random coil to amphiphilic
-helix, which then interacts with the chromophore in the Pfr form (Parker et al., 1992
; Deforce et al., 1994
). Also, two Trp residues near the core regulatory region of oat phyA become preferentially exposed in the Pfr form (Wells et al., 1994
). Based on these results, it was proposed that part of the NTE chain interacts with the regulatory C-terminal core motif in the Pr form (switch off conformation) (Park et al., 2000
; Kim et al., 2002b
). After the Pr
Pfr phototransformation (switch on conformation), the NTE chain is withdrawn by its interaction with the chromophore, exposing and thus activating the regulatory core motif (or Quail box) for the interaction with PIPs to initiate the signal transduction cascade. In this model, the phosphorylation in the hinge region can block the access of phytochrome signal transducers to the regulatory domain. We propose that the phosphorylated Pfr phytochrome represents a switch off conformation, and the phosphorylation/dephosphorylation of phytochrome provides a way to modulate the phytochrome-mediated light signaling (signal attenuation and amplification, respectively); light absorption by the photoreceptor generates an active Pfr signal, and the Ser598 phosphorylation by a kinase provides a signal-attenuating mode in the phytochrome signaling.
| METHODS |
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To assess the expression of oat phyA and S598A mutant proteins in adult plants, protein gel blot analysis was performed as described (Jordan et al., 1995
): four leaves were removed before bolting, the leaves were incubated between soaked Whatman papers for at least 12 h in the dark condition, leaf tissues were ground with sea sand, and 50 µg of protein samples were loaded onto 10% SDS-PAGE gels for electrophoresis (Laemmli, 1970
). The protein bands on the SDS-PAGE gel were transferred to a polyvinylidene difluoride membrane (Hybond-P; Amersham Pharmacia Biotech), and the membrane was incubated with oat phyA-specific monoclonal antibody, oat22 or oat25 (Cordonnier et al., 1983
), for 2 h and developed using an ECL protein gel blotting analysis system (Amersham Pharmacia Biotech). To assess the expression of oat phyA and S598A mutant proteins in 4-d-old dark-grown seedlings, crude extracts were purified by the EZ method as described (Martínez-García et al., 1999
). Five micrograms of crude extracts were loaded onto 10% SDS-PAGE gels. The membrane was incubated with oat phyA-specific oat22 or ß-tubulinspecific monoclonal antibody (Sigma, St. Louis, MO) and developed using an ECL advanced protein gel blotting analysis system (Amersham Pharmacia Biotech).
Hypocotyl lengths were measured as described (Boylan and Quail, 1991
). The seeds were sown onto MS media (Sigma) and cold treated for 2 d. The seeds were exposed to white light for 12 h to promote germination and then grown under far-red light (7 µmol/m2/s) or in darkness for 4 d. The hypocotyl lengths were photographed with a digital camera (Nikon, Tokyo) and then analyzed with the image analysis software (NIH Image; Bethesda, MD). Five-week-old mature plants were used for the height measurements.
Phytochrome in Vivo Degradation Assay
The transgenic plant seeds were obtained, germinated, and grown for 3.5 d in the dark. Seedlings were then illuminated with red light (10 µmol/m2/s) and harvested at time intervals (0, 6, 12, and 24 h) for 24 h. The harvested seedlings were stored in liquid nitrogen, and the protein samples were prepared as described (Jordan et al., 1995
). Five micrograms of crude extracts were loaded onto SDS-PAGE gels, and protein gel blot analysis was performed to detect phytochromes. For the detection of Arabidopsis phyA, regulatory domainspecific P25 antibody (Cordonnier, 1989
) was used.
Nuclear Localization
The subcellular localization of oat wild-type phyA-GFP and S598A phyA-GFP were examined as described (Kim et al., 2000
). Dark-grown seedlings were either kept in the dark or exposed to 1, 3, 9, or 24 h of FRc (3.5 W/m2). All subsequent manipulations were performed under dim green light. The seedlings were transferred to glass slides and analyzed with an Axioskop microscope (Zeiss, Oberkochem, Germany). Excitation and detection of GFP was performed with a standard GFP filter set (AHF Analysentechnik, Tübingen, Germany). Representative nuclei were photographed with an Axiocam camera and Axiovision software (Zeiss). Only epidermal cells of the hypocotyls were analyzed. To minimize nuclear import of phyA GFP fusion proteins induced by microscopic light, photographs of the GFP fluorescence were taken during the first minute of microscopic analysis.
Phytochrome Protein Preparations
Native 124-kD phytochrome was purified from 3.5-d-old etiolated oat seedlings (A. sativa) in the Pfr form as described (Lapko and Song, 1995
). The specific absorbance ratio of native phytochrome preparations was >1.00.
To express recombinant phytochrome proteins, phytochrome constructs were subcloned into a Pichia expression vector, pPIC3.5K (Invitrogen, Carlsbad, CA). Tenamino acid streptavidin affinity-tag from pASK75 vector (Biometra, Goettingen, Germany) was attached to the 3' end of the oat phyA gene. The primers 5'-CGGGATCCACCATGGCTTCCTCAAGGCCTGCTTCC-3' (forward, BamHI) and 5'-TCGCGTCGACTTGTCCCATTGCTGTTGGAGC-3' (reverse, SalI), were used for the subcloning of phyA genes into pPIC3.5K. For the first 65 amino acids, deleted phyA (
65, 1 to 65amino acid deletion) and a combination mutant of S598A and
65 (S598A/
65), the forward primer was 5'-CGGGATCCACCATGGTCATAGCCTACTTACAGCAC-3'.
The pPIC3.5K constructs with phytochrome genes were transformed into Pichia cells using a Micropulser electroporation apparatus (Bio-Rad, Hercules, CA). Recombinant phytochrome proteins were expressed in the Pichia expression system, according to the manufacturer's recommendations (Invitrogen), and purified using streptavidin affinity chromatography (Sigma-Genosys, Haverhill, UK). Phytochromobilin and phycoerythrobilin were extracted from the red alga Porphyridium cruentum by methanolysis and subsequently purified by chromatography as previously described (Beale and Cornejo, 1991
). Phycocyanobilin was purified using spirulina extracts (Sigma) by methanolysis. Holophytochromes were prepared by adding chromophores in DMSO to apoproteins at a final concentration of 20 µM, and the mixture was incubated on ice for 1 h. From the harvested Pichia cells, crude extract were prepared by breaking cells in liquid nitrogen using a homogenizer (Nihonseiki Kaisha, Tokyo, Japan). The phytochrome samples were precipitated by adding 0.23 g/L of ammonium sulfate, resuspended in a buffer (100 mM Tris, pH 7.8, and 1 mM EDTA), and then chromophores were added to the samples for in vitro reconstitution. The direct addition of chromophores to ammonium sulfate fraction makes better reconstitution and removal of free chromophores, compared with the addition to purified apoproteins. After dialysis to remove free chromophores, the samples were loaded to streptavidin affinity chromatography and purified holophytochromes without free chromophores.
Preparations for PIPs
Two known putative phytochrome signal transducers (PIF3 and NDPK2) were subcloned into pGEX 4T (Amersham Pharmacia Biotech) for the protein expression in Escherichia coli. Because the first 57 amino acids of NDPK2 are postulated to be a signal peptide for protein localization, they were removed for recombinant protein expression. The primers used were 5'-CTCGGATCCATGGAGGACGTTGAGGAGACTTAC-3' (BamHI) and 5'-CGGAATTCTCACTCCCTTAGCCATGTAGC-3' (EcoRI) for NDPK2 (80 to 231 amino acids) and 5'-CTCGGATCCATGCCTCTGTTTGAGCTTTTCAG-3' (BamHI) and 5'-CGGAATTCTCACGACGATCCACAAAACTG-3' (EcoRI) for full-length PIF3 (1 to 450 amino acids). The constructs were transformed into E. coli strain BL21 (Invitrogen) and used for the protein induction. Protein purification was performed using glutathione affinity chromatography (Amersham Pharmacia Biotech).
Phytochrome Autophosphorylation and Kinase Assay
Phytochrome autophosphorylation experiments were performed as described (Yeh et al., 1997
; Yeh and Lagarias, 1998
) with minor modifications. The reaction mixtures (total volume of 30 µL) contained kinase buffer (25 mM Tris-HCl, pH 7.5, 0.2 mM EDTA, 4 mM DTT, and 5 mM MgCl2) and 1 µg of purified recombinant phytochromes in either Pr or Pfr. Phytochrome samples were irradiated with red or far-red light for 2 min before the start of reaction. A fiber optic illuminator system (Cole-Parmer, Vernon Hills, IL) equipped with 656- and 730-nm interference filters (Oriel, Franklin, MA) was used as a light source. The light intensity was 8 W/m2 for red light and 6 W/m2 for far-red light. Histone H1 is known to stimulate phytochrome kinase activity and is also a phosphate acceptor from phytochromes. Depending on the experiments, histone H1 was included in the phosphorylation reaction (1 µg histone H1 per 1 µg phytochrome) to see the stimulation of phytochrome phosphorylation activity.
The PKA-phosphorylated phytochromes were obtained by incubating PKA (Pierce, Rockford, IL; 80 units/µL) and phytochromes, as either Pr or Pfr, at 30°C for 30 min in a kinase buffer (25 mM Tris-HCl, pH 7.5, 0.2 mM EDTA, 4 mM DTT, and 5 mM MgCl2) with 100 µM ATP. The reaction was initiated by adding 1 µL of PKA (10 times diluted in 0.1% BSA) to 1 µg of phytochrome samples and then quenched by adding 25 mM EDTA in 20 mM Tris buffer, pH 7.5. The phosphorylated phytochromes were purified using a Bio-gel P-6 column (Bio-Rad) for native phyA or streptavidin affinity column for recombinant phytochromes and dialyzed against 20 mM Tris, pH 7.8. After exposure on x-ray films, the bands were quantified using ImageMaster VDS (Pharmacia Biotech, Piscataway, NJ).
Immunoprecipitation and Pull-Down Analysis
Ten micrograms of purified phytochrome and 20 µg of NDPK2 were incubated in TBS (50 mM Tris-HCl, pH 7.5, and 150 mM NaCl) containing 1 mM dCDP and protease inhibitors at 4°C for 30 min. Oat phyA specific antibody (oat22) was then added to the reaction mixtures. The antibody/phytochrome complexes were recovered by incubating with one-tenth volumes of Protein A/G beads (Oncogene, San Diego, CA) for an additional 30 min with occasional mixing and then collected by centrifugation. The beads were washed five times in TBS containing 0.1% (v/v) Nonidet P-40. The attached proteins were solubilized by boiling for 3 min in 1x SDS sample buffer. The proteins of the pellet were resolved on 10% (w/v) SDS-polyacrylamide gels, and protein gel blot analysis was performed. For the interaction assay between phyA and PIF3, a pull-down analysis was performed with phyA and GST-PIF3 using glutathione beads. Two micrograms of phyA and 0.5 µg of PIF3 were incubated for 30 min at 4°C and then the glutathione resin was added and incubated for 20 min (50 µL reaction mixture in PBS and 1% [v/v] Triton X-100). The supernatant and precipitate were separated by centrifugation, and the same amount (50 µL) of 1x SDS sample buffer was added to precipitates. Both supernatants and precipitates were analyzed with phyA-specific antibody (oat22) or GST-specific monoclonal antibody (Oncogene).
NDPK2 Activation Assay by PhyA
The NDPK2 enzymatic activity can be activated by the Pfr form of phytochrome (Choi et al., 1999
). The
-phosphate-exchanging activity of NDPK was measured as described with minor modifications (Choi et al., 1999
). The reaction buffer contained 100 mM Tris-HCl, pH 7.5, 100 mM KCl, 25 mM MgCl2, 3 mM phosphoenolpyruvate, 2 mM ATP, 0.3 mM NADH, 2.5 units of pyruvate kinase, 2.5 units of lactate dehydrogenase, and 1 mM dCDP. The reaction was started by adding purified NDPK2 to a final concentration of 3 nM. The NDPK activity was measured by monitoring the absorbance decrease at 340 nm for 10 min in the lactate dehydrogenase-pyruvate kinase-coupled reaction using a UV-VIS spectrophotometer. The
-phosphate-exchange activity of NDPK2 was analyzed in the presence of dephosphorylated or phosphorylated wild-type phyA with a concentration of
268 nM. For the NDPK2 activation using mutant phytochromes, either phosphorylated or unphosphorylated, 67-nM phytochromes and 27-nM NDPK2 were used.
| Acknowledgments |
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| Footnotes |
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The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Pill-Soon Song (pssong{at}kkpc.com).
Online version contains Web-only data. ![]()
Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.104.023879.
Received May 5, 2004; accepted July 6, 2004.
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