Small-angle X-ray scattering studies on the macromolecular structure of the red-light-absorbing form of 121 kDa pea phytochrome and its 114 kDa chromopeptide

Time-resolved detection of conformational changes in oat phytochrome A: time-dependent diffusion

Conformational changes in oat phytochrome A (phy) in solution after photoexcitation of the red-absorbing form (Pr) were studied in time-domain by the pulsed laser-induced transient grating technique. It was found that the diffusion coefficient (D) of far-red-absorbing form (Pfr) of large phy (1.3 x 10(-11) m(2) s(-1)) is markedly reduced compared with that of Pr (5.8 x 10(-11) m(2) s(-1)). This large reduction indicates that the conformation of Pfr is significantly changed from that of Pr, so that the intermolecular interaction with water molecules increases. This change completes within 1 ms after the photoexcitation. On the other hand, D of Pr of intact phy (4.1 x 10(-11) m(2) s(-1)) first decreases upon photoexcitation to 0.89 x 10(-11) m(2) s(-1) within 1 ms and then gradually increases with a time constant of 100 ms to the value of Pfr, 1.7 x 10(-11) m(2) s(-1). This slower phase suggests that the conformation of the N-terminal region changes with 100 ms to decrease the intermolecular interaction with water after a global change in the large phy region. The increase of D was interpreted in terms of alpha-helix formation in the Pfr form from the random coil structure in the Pr form.

Light-induced global structural changes in phytochrome A regulating photomorphogenesis in plants

Phytochromes are photoreceptor proteins that monitor the light environment and regulate a variety of photomorphogenic responses to optimize the growth and development of plants. Phytochromes comprise N-terminal photosensory and C-terminal regulatory domains. They are mutually photoconvertible between a red-light-absorbing (Pr) and a far-red-light-absorbing (Pfr) form. Their interconversion by light stimuli initiates downstream signaling cascades. Here we report the molecular structures of pea phytochrome A lacking the N-terminal 52 amino-acid residues in the Pr and Pfr forms studied by small-angle X-ray scattering. A new purification protocol yielded monodispersive sample solutions. The molecular mass and the maximum dimension of Pr determined from scattering data indicated its dimeric association. The molecular structure of Pr predicted by applying the ab initio simulation method to the scattering profile was approximated as a stack of two flat bodies, comprising two lobes assignable to the functional regions. Scattering profiles recorded under red-light irradiation showed small but definite changes from those of Pr. The molecular dimensions and predicted molecular structure of Pfr suggest global structural changes such as movement of the C-terminal domains in the Pr-to-Pfr phototransformation. Red-light-induced structural changes in Pfr were reversible, mostly due to thermal relaxation processes.

Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling

Desensitization of activated receptors is an important mechanism for terminating signal transduction. Here we show that phytochrome (phy) A, a predominant photoreceptor for seedling deetiolation, colocalizes in nuclear bodies with CONSTITUTIVELY PHOTOMORPHOGENIC (COP) 1, a RING motif-containing E3 ligase. The phyA PAS domain interacts with the COP1 WD40 domain. Both the Pr and the Pfr forms of phyA, as well as the PHYA apoprotein, are ubiquitinated by COP1 in vitro. The phyA destruction rate is decreased in cop1 mutants and by expression of a COP1 RING motif mutant. Our results indicate that COP1 acts as an E3 ligase to regulate phyA signaling by targeting elimination of the phyA photoreceptor itself.

Resonance Raman spectra of the intermediates in phototransformation of large phytochrome: deprotonation of the chromophore in the bleached intermediate

Resonance Raman (RR) scattering from type A large phytochrome of pea was measured at cryogenic as well as ambient temperatures to determine an intermediate in which deprotonation of the chromophore takes place. The RR bands of the red-absorbing (Pr) and far-red-absorbing forms (Pfr) of large pea phytochromes at ambient temperatures are almost the same in their frequencies as those of the intact form reported previously (Mizutani et al., 1991). The RR spectrum of large phytochrome excited at 364 nm at -120 degrees C, where Pr and a photointermediate, I700 (= lumi-R), are trapped, showed a strong band at 1625 cm-1 with a shoulder at 1648 cm-1 in the C C=C stretching region. The shoulder disappeared, and a new band appeared at 1597 cm-1 upon raising the temperature to -80 degrees C, where transformation from I700 to meta-Ra proceeds. The RR spectra remained unchanged until -10 degrees C, indicating that the RR spectra of meta-Rb and meta-Rc are close to that of meta-Ra, and we call them comprehensively the bleached intermediate, Ibl. At ambient temperatures where photo-steady-states among a few species are attained, strong RR bands were observed at 1625 and 1599 cm-1 upon excitation at 364 nm under simultaneous far-red illumination, and the 1599-cm-1 band was appreciably intensified under simultaneous red- instead of far-red illumination. By comparison of these spectra with those at low temperatures, the 1625- and 1599-cm-1 bands were reasonably assigned to Pr and Ibl, respectively. A chemically prepared model of the bleached form, Pbl, also gave a prominent band at 1599 cm-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Resonance Raman study on intact pea phytochrome and its model compounds: evidence for proton migration during the phototransformation

Resonance Raman (RR) scattering from intact pea phytochrome was observed in resonance with the blue band at ambient temperature. The relative populations of the red-light-absorbing form (Pr) and far-red-light-absorbing form (Pfr) under laser illumination were estimated from the absorption spectra. The most prominent RR band of Pr obtained by 364-nm excitation under 740-nm pumping exhibited a frequency shift between H2O and D2O solutions, but that of Pfr obtained by 407-nm excitation under 633-nm pumping did not, indicating a distinct difference in a protonation state of their chromophores. Since the protonation level of a whole molecule of intact phytochrome remains unchanged between Pr and Pfr, this observation indicates migration of a proton from the chromophore of Pr to the protein moiety of Pfr. As model compounds, octaethylbiliverdin (OEBV-h3), its deuterated and 15N derivatives, and their protonated forms were also studied with both RR and 1H and 15N NMR spectroscopies. The RR spectrum of the protonated form, for which the protonation site was determined to be C-ring pyrrole nitrogen by NMR, displayed a deuteration shift corresponding to that of Pr, suggesting a similar protonated structure for the pyrrolic rings of Pr. The RR spectral difference between OEBV-h3 and OEBV-d3 and that between H2O and D2O solutions of Pfr suggested that the N-H protons of the A-, B-, and D-rings of intact phytochrome are replaced with deuterons in D2O. A role of the 7-kDa segment of phytochrome is discussed on the basis of RR spectral differences between the intact and large phytochromes.

Formation of aggregates of tryptic fragments derived from the carboxyl-terminal half of pea phytochrome and localization of the site of contact between the fragments by amino-terminal amino acid sequence analysis

Limited trypsinization of large pea (Pisum sativum cv. Alaska) phytochrome and subsequent size-exclusion chromatography (SEC) in 0.1 M Na phosphate, pH 7.8, yielded a high-molecular-mass aggregate of tryptic fragments of phytochrome. Further SEC in 0.1 M Tris-HCl, pH 7.5, plus various concentrations of NaSCN, indicated that the tryptic-fragment complex contained an aggregate of 7 fragments of molecular mass from 38 to 55 kDa. The amino-terminal sequence of each fragment was determined from the samples electroblotted from sodium dodecylsulfate polyacrylamide gels onto polyvinylidene difluoride membranes, in order to localize the various fragments on the phytochrome polypeptide chain. All of the 7 fragments in the aggregate were found to be derived from the carboxyl-terminal half of phytochrome. A portion of the polypeptide chain (from Ala-752 to Arg-1000) common to all the tryptic fragments has been assigned as the site(s) of contact of the fragments. The tryptic-fragment complex, as well as large phytochrome itself, has been shown by SEC to dissociate to monomers in 2 M NaSCN. The result indicates that the main force involved in maintaining the complex and in contacts between monomers of phytochrome is non-ionic in nature. Relationship between the contact site(s) of the tryptic-fragment complex and large phytochrome monomer is discussed.