Tissue localization of phytochrome in dark-grown barley leaves

Phytochrome was spectrophotometrically determined to be differentially concentrated among separated tissues of dark-grown, norflurazon-treated barley l     

Influence of cytokinins and phytochrome on nitrate reductase activity in etiolated leaves of maize

Of the different hormones tested, cytokinins stimulated nitrate-induced nitrate reductase (NR) activity in the dark. The optimal stimulation was obtained at 16 hr and this was sensitive to tungstate, 6-methylpurine and cycloheximide. The cytokinin stimulation of NR activity was further enhanced by brief irradiation with red light, but this effect was not noticed when leaves were exposed to far-red light. Both kinetin and red light, when given together, or given with a darkness interruption, stimulated the NR activity more than with either of them alone.     

Spectral properties and chromophore rotation of phytochrome bound to substituted Sepharose

Brushite purified phytochrome from Avena sativa L. cv. Sol II was bound to phenyl Sepharose, octyl Sepharose, CNBr-activated Sepharose and to anti-phytochrome immunoglobulins immobilized on Sepharose. The spectral properties of phytochrome bound to anti-phytochrome immunoglobulins and to phenyl Sepharose were similar to phytochrome in solution. Phytochrome bound to CNBr-activated Sepharose or to octyl Sepharose showed reduced P_fr formation after red irradiation. The reversal to P_r with far-red light was only partial but a further increase at 667 nm took place slowly in the dark. A peak at 657 nm was seen in the difference spectrum between CNBr-activated Sepharose-bound phytochrome kept in darkness and the identical sample immediately after a far-red irradiation.
The change in linear dichroism at 660 nm and 730 nm, induced by plane polarized red or far-red light, was measured. It was computed that the long-wavelength transition moment of phytochrome had an average rotation angle of 31.5° or 180°–31.5°. The substrate used for immobilization had a limited effect on the rotation angle. Phytochrome immobilized on CNBr-activated Sepharose gave an angle of 27.8° and phytochrome immobilized on phenyl Sepharose gave an angle of 32.6°.     

Circular dichroism of phytochrome intermediates

Phototransformation P_t to P_fr was investigated with 124-kDa phytochrome from etiolated oat seedlings ( Avena sativa L. cv. Pirol) using circular dichroism spectroscopy at -110°C to +30°C. Using absorption spectra of the intermediates formed at the respective temperatures, circular dichroism spectra (300–800 nm) of pure intermediates were calculated.
The sign of the circular dichroic absorption bands changed upon formation of lumi-R, the primary photoproduct of P_r. This would be compatible with a Z→E isomerization taking place at this reaction step. The subsequent intermediates (meta-R_a and meta-R_c) as well as P_fr showed only small circular dichroism. Their absorption spectra were drastically shifted, but had similar spectral shapes. The results are discussed in terms of conformational changes of the phytochrome chromophore presumably taking place at the early steps of phototransformation P_r to P_fr.     

Photoreversible association of phytochrome with membranes. I. Distinguishing between two light-induced binding responses

Abstract Two types of association between phytochrome and crude membrane fractions from oat (Avena sativa L.) are distinguished and compared, and that which comprises only a small fraction of the total phytochrome in extracts prepared in the absence of added divalent cations (Watson & Smith. 1982b) has been studied in detail. Extraction in the presence of phenylmethylsulphonyl fluoride shows that proteolysis of P_r (the red-light absorbing form) probably does not account for the lower levels of membrane-associated phytochrome measured after far-red light than after red light. Difference spectra of soluble and membrane-associated phytochrome indicate that the latter is much less susceptible to spectral degradation in vitro than is the soluble pool. The stoichiometry of association with the membranes is such that for each phytochrome molecule associated after far-red light there are three associated after red light and it is argued that this stoichiometry is maintained independent of the extraction pH. The characteristics of this photo-reversible association of phytochrome with membranes are compared to the characteristics of the widely studied light-induced enhancement of phytochrome pelletabilily that is dependent on electrostatic interaction of phytochrome and membranes.     

Aphototropic mutants of the moss Ceratodon purpureus with spectrally normal and with spectrally dysfunctional phytochrome

Following UV mutagenesis of protonemal tissue of the moss Ceratodon purpureus we have isolated different aphototropic mutant lines that can be divided into two distinct classes. One class, represented by the line ptr1, shows characteristic features of phytochrome chromophore deficiency. ptrl shows negligible photoreversibility (<5% of wild type), whereas immunoblots show normal apoprotein levels. The aphototropic phenotype could be partially restored with biliverdin, a precursor of the phytochrome chromophore. It was found that, whereas in wild type formation of Pfr leads to suppression of gravitropism, there is no such suppression ptrl. In addition, ptr1 shows lower chlorophyll levels than the wild type. These findings indicate that, as expected for a chromophore-deficient mutant, multiple phytochrome effects are lost. The other class of mutants, represented by the line ptr103, shows more specific effects. In this mutant, only phototropism is affected. Suppression of gravitropism, the content of chlorophyll and photoreversibility of phytochrome were similar to those of the wild type.     

Rapid,reverse reciprocity failure for phytochrome control of its own accumulation*

Abstract. Fluence–response curves have been obtained for end-of-day far-red stimulation and red reversal of phytochrome accumulation in leaves of light-grown corn during darkness following a white-light period. The response to end-of-day far-red, but not to R, shows rapid, reverse reciprocity failure which cannot be explained by escape from photoreversibility. Because the Pfr/Ptot established by long, low fluence rate and short, high fluence rate exposures of the same total fluence is the same and can lead to vastly different responses, explanations for this phenomenon based simply on Pfr levels or Pfr/Ptot are inadequate. Reciprocity failure for end-of-day far-red is not necessarily coupled to reciprocity failure for red reversal of the far-red effect. The two phenomena must stem from different causes.     

Integral association of phytochrome with a membranous fraction from etiolatedAvena shoots: red/far-red photoreversibility and in vitro characterization

The results reported in this paper provide strong evidence to support the belief that the small percentage of phytochrome recovered in low-speed centrifugation pellets, when prepared in the absence of divalent cations after various in vivo irradiations, is not simply a manifestation of non-specific co-precipitation of soluble phytochrome.The far-red reversibility of the observed near-doubling of phytochrome pelletability after in vivo red irradiation indicates that phytochrome pelletability in the absence of divalent cations is a phytochrome-controlled response. The characteristics of the pelleted phytochrome indicate a strong, hydrophobic interaction with membranes. A tentative proposal to explain the observed characteristics of the association of phytochrome with membranous material in the absence of divalent cations after different in vivo irradiations has been put forward.Abbreviations Pfr phytochrome in the far-red light absorbing form - Pr phytochrome in the fat-red light absorbing form - Ptot total phytochrome - R red light irradiation - FR far-red light irradiation     

Photoreversible association of phytochrome with membranes. II. Reciprocity tests and a model for the binding reaction

Abstract A series of fluence-response curves for the binding of phytochrome to membranes in the absence of divalent cations, as described by Watson & Smith (1982), were constructed to demonstrate that the response obeys the law of reciprocity. Analysis of the binding of P_fr (the far-red-absorbing form of phytochrome) showed that two P_fr molecules bind to the membrane for each P_r (the form with an absorption maximum in the red) photoconverted to P_fr in the intrinsic membrane-bound phytochrome pool. Using this stoichiometry we have been able to model the binding curve of Pr and match the binding data. P_r binding can be simulated if P_r binds only as a consequence of the binding of P_fr, i.e. when P_fr is part of a P_r: P_fr dimer. The enrichment of the membranes with P_fr as a result of the binding of P_fr was also accurately simulated. There is no binding cooperativity. Phytochrome binding is a low-fluence response and the possibility that it has physiological significance as a mediator of phytochrome action is discussed.     

Dual effect of phytochrome A on hypocotyl growth under continuous red light

The role of phytochrome A in the control of hypocotyl growth under continuous red light (Rc) was investigated using phyA and phyB mutants of Arabidopsis thaliana, which lack phytochrome A (phyA) or phytochrome B (phyB), respectively, and transgenic seedlings of Nicotiana tabacum overexpressing Avena phyA, compared to the corresponding wild type (WT). In WT seedlings of A. thaliana, hypocotyl growth inhibition showed a biphasic response to the fluence rate of Rc, with a brake at 10^?2μmol m^?2 s^?1. At equal total fluence rate, hourly pulses of red light caused slightly more inhibition than Rc. The response to very low fluences of continuous or pulsed red light was absent in the phyA and phyA phyB mutants and present in the phyB mutant. The second part of the response was steeper in the phyA mutant than in the WT but was absent in the phyB mutant. In WT tobacco the response to Rc was biphasic. Overexpression of Avena phyA enhanced the response only at very low fluence rates of Rc (< 10^?2μmol m^?2 s^?1). In both species, the effect of hourly pulses of far-red light was similar to the maximum inhibition observed in the first phase of the response to Rc. Using reciprocity failure (i.e. higher inhibition under continuous than pulsed light) as the operational criterion, a ‘true’ high-irradiance reaction occurred under continuous far-red light but not under Rc or red plus far-red light mixtures. Native and overexpressed phyA are proposed to mediate very low fluence responses under Rc. In WT A. thaliana, this effect is counteracted by a negative action of phyA on phyB-mediated low-fluence responses.     

Thoughts on the possible role of phytochrome destruction in phytochrome controlled responses

Abstract. Fluence-response curves for low-energy phytochrome responses show two steps at red light exposures c . two orders of magnitude apart. This Feature of the fluence-response relationship can be interpreted as the consequence of the following processes:

• 1. 

  Induction of a photoresponse by a very low level of Pfr.
• 2. 

  Activation of a Pfr-destroying enzyme above a threshold level of [Pfr].
• 3. 

  Dependency of the rate of Pfr destruction on [Pfr] once the threshold level is reached.

In this way, adaptation of the phytochrome control system to a broad range of light doses could be realized.     

Haem oxygenase: A functionally diverse enzyme of photosynthetic organisms and its role in phytochrome chromophore biosynthesis,cellular signalling and defence mechanisms

Haem oxygenase (HO) is a universal enzyme that catalyses stereospecific cleavage of haem to BV IX α and liberates Fe⁺² ion and CO as by‐product. Beside haem degradation, it has important functions in plants that include cellular defence, stomatal regulation, iron mobilization, phytochrome chromophore synthesis, and lateral root formation. Phytochromes are an extended family of photoreceptors with a molecular mass of 250 kDa and occur as a dimer made up of 2 equivalent subunits of 125 kDa each. Each subunit is made of two components: the chromophore, a light‐capturing pigment molecule and the apoprotein. Biosynthesis of phytochrome (phy) chromophore includes the oxidative splitting of haem to biliverdin IX by an enzyme HO, which is the decisive step in the biosynthesis. In photosynthetic organisms, BVα is reduced to 3Z PΦB by a ferredoxin‐dependent PΦB synthase that finally isomerised to PΦB. The synthesized PΦB assembles with the phytochrome apoprotein in the cytoplasm to generate holophytochrome. Thus, necessary for photomorphogenesis in plants, which has confirmed from the genetic studies, conducted on Arabidopsis thaliana and pea. Besides the phytochrome chromophore synthesis, the review also emphasises on the current advances conducted in plant HO implying its developmental and defensive role.     

Native phytochrome: immunoblot analysis of relative molecular mass and in-vitro proteolytic degradation for several plant species

The relative molecular mass (M_r) of the native phytochrome monomer from etiolated Cucurbita pepo L., Pisum sativum L., Secale cereale L. and Zea mays L. seedlings has been determined using immunoblotting to visualize the chromoprotein in crude extracts subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A single phytochrome band is observed for each plant species when the molecule is extracted under conditions previously demonstrated to inhibit the proteolysis of native Avena sativa L. phytochrome. A comparison among plant species indicates that the M_r of native phytochrome is variable: Zea mays=127000; Secale=Avena=124000; Pisum=121000; Cucurbita=120000. The in-vitro phototransformation difference spectrum for native phytochrome from each species is similar to that observed in vivo in each case and is indistinguishable from that described for native Avena phytochrome. The difference minima between the red- and far-red-absorbing forms of the pigment (Pr-Pfr) are all at 730 nm and the spectral change ratios (A_r/A_fr) are near unity. When incubated in crude extracts, phytochrome from all four species is susceptible to Pr-specific limited proteolysis in a manner qualitatively similar to that observed for Avena phytochrome, albeit with slower rates and with the production of different M_r degradation products. Further examination of the in-vitro proteolysis of Avena phytochrome by endogeneous proteases has identified several additional phytochrome degradation products and permitted construction of a peptide map of the molecule. The results indicate that both the 6000- and 4000-M_r polypeptide segments cleaved by Pr-specific proteolysis are located at the NH₂-terminus of the chromoprotein and are adjacent to a 64000-M_r polypeptide that contains the chromophore.Abbreviations and symbols A_minimum phototransformation difference spectrum (Pr-Pfr) minimum - Ig immunoglobulin - Mops 3-(N-morpholino)propanesulfonic acid - M_r relative molecular mass - PAGE polyacrylamide gel electrophoresis - PMSF phenylmethylsulfonyl fluoride - SDS sodium dodecyl sulfate     

Proteolysis alters the spectral properties of 124 kdalton phytochrome from Avena

Native phytochrome from Avena sativa L. is homogeneous with a monomeric molecular weight of 124 kdalton; 6–10 kdalton larger than the heterogeneous 120 kdalton preparations previously considered to be undegraded (Vierstra and Quail, 1982, Proc. Natl. Acad. Sci. USA, 79: 5272–5276). The phototransformation difference spectrum (Pr-Pfr) of 124 kdalton phytochrome measured in crude extracts has a minimum in the farred region at 730 nm, the same as that observed in vivo. These spectral properties contrast with those of 120 kdalton phytochrome purified by column immunoaffinity chromatography where the difference minimum is at 724 nm. When 124 kdalton phytochrome is incubated as Pr in crude extracts, the difference minimum shifts progressively to shorter wavelengths (from 730 to 722 nm) concomitant with the proteolytic degradation of the chromoprotein to the mixture of 118 and 114 kdalton species that comprise 120 kdalton phytochrome preparations. These two effects are inhibited in concert by the serine protease inhibitor, phenylmethylsulfonylfluoride, and or maintenance of the phytochrome in the Pfr form. These results provide further evidence that 124 kdalton phytochrome is the native molecule in Avena and indicate that the peptide segments removed by proteolysis of the Pr form are important to the pigment's spectral integrity. The present data thus resolve the previously unsettled question of why the Pfr form of 120 kdalton phytochrome isolated by various procedures from Avena has been found to absorb at shorter wavelengths than that observed in vivo. Previous spectral studies with 120 kdalton phytochrome preparations are open to reexamination.Abbreviations, symbols PMSF phenylmethylsulfonylfluoride - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis - Ig immunoglobulin - A_minimum, A_maximum phototransformation difference spectrum (Pr-Pfr) minimum and maximum - A_r/A_fr ratio spectral change ratio     

Molecular modeling of the structures of human and rat pancreatic cholesterol esterases.

Structural models have been generated for rat and human cholesterol esterases by molecular modeling. For rat cholesterol esterase, three separate models were generated according to the following procedure: (1) the cholesterol esterase sequence was aligned with those of three template enzymes: Torpedo californica acetylcholinesterase, Geotrichum candidum lipase and Candida rugosa lipase; (2) the X-ray structure coordinates of the three template enzymes were used to construct cholesterol esterase models by amino acid replacements of matched sequence positions and by making sequence insertions and deletions as required; (3) bad contracts in each of the cholesterol esterase models were relaxed by molecular dynamics and mechanics; (4) the three cholesterol esterase models were merged into one by arithmetic averaging of atomic coordinates; (5) Ramachandran analysis indicated that the model generated from the AChE template possessed the best set of phi/psi angles. Therefore, this model was subjected to molecular dynamics, with harmonic constraints imposed on the C(alpha) coordinates to drive them toward the coordinates of the averaged model. (6) Subsequent relaxation by molecular mechanics produced the final rat cholesterol esterase model. A model for human cholesterol esterase was produced by repeating steps 1-3 above, albeit with the rat cholesterol esterase model as the template. Hydrophobic and electrostatic analyses of the rat and human cholesterol esterase models suggest the structural origins of molecular recognition of hydrophobic substrates and interfaces, of charged interfaces, and of bile salt activators.     

The effects of SAN 9789 and light on phytochrome and the germination of lettuce seeds

Photoblastic seeds (akenes) of lettuce (Lactuca sativa (L.) cv. Grand Rapids) were treated with SAN 9789 [4-chloro-5-(methylamine)-2-a, a, a,-trifluoro-m-tolyl-3-(2H)-pyridasinone]. The seeds weere placed in Petri dishes on filter paper soaked with water or SAN solution. The treatment increased the germination in darkness from 17% for water to 78% for SAN treated seeds. An irradiation with 5 min red light gave a germination of 98% both in water and in SAN. In water the effect of red irradiation could be reversed with a short irradiation (8 min) of far red light (17% germination), while in SAN solution the far red reversibility was poor (92% germination). If the far red light was given repeatedly (5 min per h) it had a slightly larger effect. If given continuously for 24 hours, the germination in water was decreased to 0.3% and in SAN solution to 9%. Possible mechanisms for the SAN effect are discussed.     

PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics

A key regulator of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor traffic, PICK1 is known to interact with over 40 other proteins, including receptors, transporters and ionic channels, and to be active mostly as a homodimer. The current lack of a complete PICK1 structure determined at atomic resolution hinders the elucidation of its functional mechanisms. Here, we identify interactions between the component PDZ and BAR domains of PICK1 by calculating possible binding sites for the PDZ domain of PICK1 (PICK1-PDZ) to the homology-modeled, crescent-shaped dimer of the PICK1-BAR domain using multiplexed replica-exchange molecular dynamics (MREMD) and canonical molecular dynamics simulations with the coarse-grained UNRES force field. The MREMD results show that the preferred binding site for the single PDZ domain is the concave cavity of the BAR dimer. A second possible binding site is near the N-terminus of the BAR domain that is linked directly to the PDZ domain. Subsequent short canonical molecular dynamics simulations used to determine how the PICK1-PDZ domain moves to the preferred binding site on the BAR domain of PICK1 revealed that initial hydrophobic interactions drive the progress of the simulated binding. Thus, the concave face of the BAR dimer accommodates the PDZ domain first by weak hydrophobic interactions and then the PDZ domain slides to the center of the concave face, where more favorable hydrophobic interactions take over.     

Comparison of the effects of hydrophobicity,amphiphilicity, and α-helicity on the activities of antimicrobial peptides

Multiple linear regression was used to quantify the dependence of the antimicrobial activity of 13 peptides upon three calculated or experimentally determined parameters: mean hydrophobicity, mean hydrophobic moment, and α-helix content. Mean hydrophobic moment is a measure of the amphiphilicity of peptides in an α-helical conformation. Antimicrobial activity was quantified as the reciprocal of the measured minimal inhibitory concentration (MIC) against Escherichia coli. One of the peptides was magainin 2, and the remainder were novel peptides designed for this study. The multiple linear regression results revealed that the amphiphilicity of the peptides was the most important factor governing anti-microbial activity compared to mean hydrophobicity orα-helix content. A better regression cf the data was obtained using In(1/MIC + constant) as the dependent variable than with either 1/MIC or In(1/MIC). These results should be useful in designing peptides with higher antimicrobial activity. © 1995 Wiley-Liss, Inc.