PURIFICATION OF PHYTOCHROME FROM OAT SEEDLINGS

Light signaling in plants-a selective history

In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.

A Spectroscopy-based Methodology for Rapid Screening and Characterization of Phytochrome Photochemistry in Search of Pfr-favored Variants

Phytochromes are photosensitive proteins with a covalently bound open-chain chromophore that can switch between two principal states: red light absorbing Pr and far-red light absorbing Pfr. Our group has previously shown that the bacteriophytochrome from Xanthomonas campestris pv. campestris (XccBphP) is a bathy-like phytochrome that uses biliverdin IXα as a co-factor and is involved in bacterial virulence. To date, the XccBphP crystal structure could only be solved in the Pr state, while the structure of its Pfr state remains elusive. The aims of this work were to develop an efficient screening methodology for the rapid characterization and to identify XccBphP variants that favor the Pfr form. The screening approach developed here consists in analyzing the UV-Vis absorption behavior of clarified crude extracts containing recombinant phytochromes. This strategy has allowed us to quickly explore over a hundred XccBphP variants, characterize multiple variants and identify Pfr-favored candidates. The high-quality data obtained enabled not only a qualitative, but also a quantitative characterization of their photochemistry. This method could be easily adapted to other phytochromes or other photoreceptor families.

KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1

The completion of seed germination is an irrevocable event for plants, determining, for most plants, the site of the remainder of their life cycle. One environmental cue important to the completion of seed germination is light, which, in Arabidopsis thaliana, can influence a host of transcription factors, including PHYTOCHROME-INTERACTING FACTOR1 (PIF1), a negative regulator of the completion of germination and seedling de-etiolation. The KELCH F-BOX protein COLD TEMPERATURE GERMINATING10 (CTG10) can recognize and bind to PIF1, negatively influencing PIF1 stability, stimulating the completion of germination, and promoting a de-etiolated seedling morphology. PIF1, in turn, can downregulate CTG10 expression, revealing a complex coregulation orchestrated by light presence and quality that dictates whether the seed completes germination.

Seeds employ sensory systems that assess various environmental cues over time to maximize the successful transition from embryo to seedling. Here we show that the Arabidopsis F-BOX protein COLD TEMPERATURE-GERMINATING (CTG)-10, identified by activation tagging, is a positive regulator of this process. When overexpressed (OE), CTG10 hastens aspects of seed germination. CTG10 is expressed predominantly in the hypocotyl, and the protein is localized to the nucleus. CTG10 interacts with PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) and helps regulate its abundance in planta. CTG10-OE accelerates the loss of PIF1 in light, increasing germination efficiency, while PIF1-OE lines fail to complete germination in darkness, which is reversed by concurrent CTG10-OE. Double-mutant (pif1 ctg10) lines demonstrated that PIF1 is epistatic to CTG10. Both CTG10 and PIF1 amounts decline during seed germination in the light but reaccumulate in the dark. PIF1 in turn down-regulates CTG10 transcription, suggesting a feedback loop of CTG10/PIF1 control. The genetic, physiological, and biochemical evidence, when taken together, leads us to propose that PIF1 and CTG10 coexist, and even accumulate, in the nucleus in darkness, but that, following illumination, CTG10 assists in reducing PIF1 amounts, thus promoting the completion of seed germination and subsequent seedling development.

Streptophyte phytochromes exhibit an N-terminus of cyanobacterial origin and a C-terminus of proteobacterial origin

Background

Phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. Prototypical phytochromes exhibit an N-terminal tridomain (PGP) consisting of PAS, GAF and PHY domains and a C-terminal histidine kinase (HK).

Results

The mode of evolution of streptophyte, fungal and diatom phytochromes from bacteria is analyzed using two programs for sequence alignment and six programs for tree construction. Our results suggest that Bacteroidetes present the most ancient types of phytochromes. We found many examples of lateral gene transfer and rearrangements of PGP and HK sequences. The PGP and HK of streptophyte phytochromes seem to have different origins. In the most likely scenario, PGP was inherited from cyanobacteria, whereas the C-terminal portion originated from a proteobacterial protein with multiple PAS domains and a C-terminal HK. The plant PhyA and PhyB lineages go back to an early gene duplication event before the diversification of streptophytes. Fungal and diatom PGPs could have a common prokaryotic origin within proteobacteria. Early gene duplication is also obvious in fungal phytochromes.

Conclusions

The dominant question of the origin of plant phytochromes is difficult to tackle because the patterns differ among phylogenetic trees. We could partially overcome this problem by combining several alignment and tree construction algorithms and comparing many trees. A rearrangement of PGP and HK can directly explain the insertion of the two PAS domains by which streptophyte phytochromes are distinguished from all other phytochromes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-015-1082-3) contains supplementary material, which is available to authorized users.

Photoconversion mechanism of the second GAF domain of cyanobacteriochrome AnPixJ and the cofactor structure of its green-absorbing state

Cyanobacteriochromes are members of the phytochrome superfamily. In contrast to classical phytochromes, these small photosensors display a considerable variability of electronic absorption maxima. We have studied the light-induced conversions of the second GAF domain of AnPixJ, AnPixJg2, a phycocyanobilin-binding protein from the cyanobacterium Anabaena PCC 7120, using low-temperature resonance Raman spectroscopy combined with molecular dynamics simulations. AnPixJg2 is formed biosynthetically as a red-absorbing form (Pr) and can be photoconverted into a green-absorbing form (Pg). Forward and backward phototransformations involve the same reaction sequences and intermediates of similar cofactor structures as the corresponding processes in canonical phytochromes, including a transient cofactor deprotonation. Whereas the cofactor of the Pr state shows far-reaching similarities to the Pr states of classical phytochromes, the Pg form displays significant upshifts of the methine bridge stretching frequencies concomitant to the hypsochromically shifted absorption maximum. However, the cofactor in Pg is protonated and adopts a conformation very similar to the Pfr state of classical phytochromes. The spectral differences are probably related to an increased solvent accessibility of the chromophore which may reduce the π-electron delocalization in the phycocyanobilin and thus raise the energies of the first electronic transition and the methine bridge stretching modes. Molecular dynamics simulations suggest that the Z → E photoisomerization of the chromophore at the C-D methine bridge alters the interactions with the nearby Trp90 which in turn may act as a gate, allowing the influx of water molecules into the chromophore pocket. Such a mechanism of color tuning AnPixJg2 is unique among the cyanobacteriochromes studied so far.

Bacterial phytochromes: more than meets the light

Phytochromes are environmental sensors, historically thought of as red/far-red photoreceptors in plants. Their photoperception occurs through a covalently linked tetrapyrrole chromophore, which undergoes a light-dependent conformational change propagated through the protein to a variable output domain. The phytochrome composition is modular, typically consisting of a PAS-GAF-PHY architecture for the N-terminal photosensory core. A collection of three-dimensional structures has uncovered key features, including an unusual figure-of-eight knot, an extension reaching from the PHY domain to the chromophore-binding GAF domain, and a centrally located, long α-helix hypothesized to be crucial for intramolecular signaling. Continuing identification of phytochromes in microbial systems has expanded the assigned sensory abilities of this family out of the red and into the yellow, green, blue, and violet portions of the spectrum. Furthermore, phytochromes acting not as photoreceptors but as redox sensors have been recognized. In addition, architectures other than PAS-GAF-PHY are known, thus revealing phytochromes to be a varied group of sensory receptors evolved to utilize their modular design to perceive a signal and respond accordingly. This review focuses on the structures of bacterial phytochromes and implications for signal transmission. We also discuss the small but growing set of bacterial phytochromes for which a physiological function has been ascertained.

Bathy phytochromes in rhizobial soil bacteria

Phytochromes are biliprotein photoreceptors that are found in plants, bacteria, and fungi. Prototypical phytochromes have a Pr ground state that absorbs in the red spectral range and is converted by light into the Pfr form, which absorbs longer-wavelength, far-red light. Recently, some bacterial phytochromes have been described that undergo dark conversion of Pr to Pfr and thus have a Pfr ground state. We show here that such so-called bathy phytochromes are widely distributed among bacteria that belong to the order Rhizobiales. We measured in vivo spectral properties and the direction of dark conversion for species which have either one or two phytochrome genes. Agrobacterium tumefaciens C58 contains one bathy phytochrome and a second phytochrome which undergoes dark conversion of Pfr to Pr in vivo. The related species Agrobacterium vitis S4 contains also one bathy phytochrome and another phytochrome with novel spectral properties. Rhizobium leguminosarum 3841, Rhizobium etli CIAT652, and Azorhizobium caulinodans ORS571 contain a single phytochrome of the bathy type, whereas Xanthobacter autotrophicus Py2 contains a single phytochrome with dark conversion of Pfr to Pr. We propose that bathy phytochromes are adaptations to the light regime in the soil. Most bacterial phytochromes are light-regulated histidine kinases, some of which have a C-terminal response regulator subunit on the same protein. According to our phylogenetic studies, the group of phytochromes with this domain arrangement has evolved from a bathy phytochrome progenitor.

Phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803. Purification, assembly, and quaternary structure

The phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803 forms holoprotein adducts with close spectral similarity to plant phytochromes when autoassembled in vitro with bilin chromophores. Cph1 is a 85-kDa protein that acts as a light-regulated histidine kinase seemingly involved in 'two-component' signalling. This paper describes the improvement of Cph1 purification, estimation of the extinction coefficient of holo-Cph1, spectral analyses of the assembly procedure and studies on quaternary structure. During assembly with the natural chromophore phycocyanobilin (PCB), a red-shifted intermediate is observed. A similar result was obtained when phycoerythrobilin was used as chromophore. As shown by SDS/PAGE and Zn2+ fluorescence, the covalent attachment of PCB is blocked by 1 mM iodoacetamide, a cysteine-derivatizing agent. When PCB was incubated with blocked apo-Cph1, again a shoulder at longer wavelengths appeared. It is therefore proposed that the long-wavelength-absorbing form represents the protonated, noncovalently bound bilin. Biliverdin, which is neither protonated nor covalently attached, undergoes spectral changes in its blue-absorbing band upon incubation with apo-Cph1. On the basis of these data we therefore propose a three-step model for phytochrome autoassembly. Size-exclusion chromatography revealed different mobilities for the apoprotein, red-absorbing Cph1-PCB and far-red-absorbing Cph1-PCB. The major peaks of both holoprotein adducts had apparent molecular masses approximately 200 kDa, a result in agreement with the notion that autophosphorylation in sensory histidine kinases requires dimerization. When Cph1-PCB was further purified by preparative native electrophoresis, the mobility on size-exclusion chromatography was approximately 100 kDa, and it was found to have lost its kinase activity, results implying that the material had lost its capacity to dimerize.

Phycobiliprotein synthesis in protoplasts of the unicellular cyanophyte, Anacystis nidulans

Stable and metabolically active protoplasts were prepared from the unicellular cyanophyte, Anacystis nidulans, by enzymatic digestion of the cell wall with 0.1% lysozyme. The yield of protoplasts from intact algal cells was approx. 50%. Incorporation of L-[U-14C]leucine into cold trichloroacetic acid-insoluble material from protoplasts preparations was linear for 1.5 h and continued for an additional 2.5 h. Incorporation of radiolabeled leucine into hot trichloroacetic acid-insoluble material from protoplast preparations demonstrated protein synthesis in protoplasts in vitro. Phycocyanin is the principal phycobiliprotein and allophycocyanin is a minor phycobiliprotein in A. nidulans cells. The light-absorbing chromophore of both of these phycobiliproteins is the linear tetrapyrrole (bile pigment), phycocyanobilin. Radiolabeled phycocyanin and allophycocyanin were isolated from protoplast preparations which had been incubated with L-[U-14]leucine or delta-amino[4-14C] levulinic acid (a precursor of phycocyanobilin). The radio-labeled phycobiliproteins were purified by ammonium sulfate fractionation and ion-exchange chromatography on brushite columns. The specific radioactivity of phycocyanin and allophycocyanin in brushite column eluates (protoplasts incubated with radiolabeled leucine) was 106 000 and 82 000 dpm/mg, respectively. The specific radioactivity of phycocyanin and allophycocyanin in brushite column eluates (protoplasts incubated with radiolabeled delta-aminolevulinic acid) was 33 000 and 38 000 dpm/mg, respectively. Phycobiliproteins from protoplasts incubated with radiolabeled leucine were examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. 25% of the incorporated radioactivity in protoplast lysates and approx. 60% of the incorporated radioactivity in protoplast lysates and approx. 60% of the incorporated ratioactivity in phycocyanin and allophycocyanin (in brushite column eluates) comigrated with the subunits of these phycobiliproteins on sodium dodecyl sulfate-polyacrylamide gels. Chromic acid degradation of phycobiliproteins from protoplast preparations incubated with delta-amino[4-14C] levulinic acid yielded radiolabeled imides which were derived from the phycocyanobilin chromophore. Imides from radiolabeled phycobiliproteins isolated from protoplast preparations incubated with L-[U-14C]leucine did not contain radioactivity. These results show that both the apoprotein and tetrapyrrolic moieties of phycocyanin and allophycocyanin were synthesized in A. nidulans protoplasts in vitro.

Properties and N-terminal sequence of allophycocyanin from the unicellular rhodophyte Cyanidium caldarium

Allophycocyanin from the unicellular rhodophyte Cyanidium caldarium was purified by (NH4)2SO4 fractionation and ion-exchange chromatography on brushite (calcium phosphate) columns and on DEAE-Sephadex A-25 columns. The specific absorption coefficient (A0.1%1cm) at 650nm of purified allophycocyanin was 6.35 in 0.05M-potassium phosphate buffer, pH7.0. Absorption maxima of allophycocyanin occurred at 650, 618 (shoulder), 350 and 275 nm. Circular-dichroic spectra displayed positive-ellipticity bands at 658 and 630 nm and a major negative-ellipticity band at 340nm. Computer analysis of the circular-dichroic spectrum of allophycocyanin from 207 to 243 nm indicated 42% alpha-helix and 58% beta-form. The estimated molecular weight of purified allophycocyanin on calibrated Sephadex G-200 columns at pH7.0. was 196000. Electrophoretic examination of allophycocyanin on sodium dodecyl sulphate/polyacrylamide gels revealed a single band with apparent mol.wt. 16000. The presence of two polypeptide subunits, with nearly the same molecular weight, was revealed on polyacrylamide gels by using a modified electrophoresis buffer. Spectral analysis of the allophycocyanin subunits resolved by ion-exchange chromatography on Bio-Rex 70 columns indicated that a single phycocyanobilin chromophore was present on each polypeptide chain. Treatment of allophycocyanin with 8M-urea (pH3.0) and subsequent removal of urea by dialysis against water yielded a derivative phycobiliprotein with spectroscopic characteristics similar to those of phycocyanin. The original allophycocyanin spectrum was regenerated after incubation in phosphate buffer, pH7.0. Automated sequences analysis of the N-terminus of allophycocyanin showed that (a) the sequences of the two subunits were different from one another and were different from the subunits of phycocyanin from the same alga, (b) the subunits occurred in a molar ratio of 1:1 and (c) the sequences homology at the N-terminus among alpha- and beta-subunits of allophycocyanin from blue-green and red algae approached 90%.

Allophycocyanin from the filamentous cyanophyte, Phormidium luridum

Allophycocyanin from the filamentous cyanophyte, Phormidium luridum, was purified by ammonium sulfate fractionation and ion exchange chromatography on brushite columns. The specific absorption coefficient (E 0.1% 1cm) of purified allophycocyanin was 6.1 in distilled water and 7.3 in 0.05 M potassium phosphate buffer (pH 7). Absorption maxima of allophycocyanin occurred at 650, 618 (shoulder), 350, and 275 nm. Circular dichroic spectra displayed positive ellipticity bands at 655 and 625 nm, and a major negative ellipticity band at 340 nm. Computer analysis of the circular dichroic spectrum of allophycocyanin from 207 to 243 nm indicated that the secondary structure contained 60% alpha helix and 40% beta form. The estimated molecular weight of allophycocyanin on Sephadex G-200 columns at pH 7.0 was 155,000. Electrophoretic examination of allophycocyanin on sodium dodecyl sulfate polyacrylamide gels revealed two subunits, alpha and beta, with apparent molecular weights of 17,300 and 19,000, respectively. Densitometric analysis of unstained gels at 600 nm indicated that one phycocyanobilin chromophore was associated with each subunit. Treatment of allophycocyanin with 12% formic acid or 8 M urea and subsequent removal of the denaturant yielded a derivative with spectroscopic characteristics similar to phycocyanin. Subsequent incubation in phosphate buffer (pH 7), but not in acetate buffer (pH 5) or in water, was accompanied by a progressive reappearance of absorption maxima at 650 and 618 nm (shoulder), and positive ellipticity bands at 655 and 617 nm. Automated sequence analysis of allophycocyanin (a) showed that the sequence of amino acids at the amino terminus of the alpha and beta subunits is different, (b) showed that the subunits occur in a ratio of 1:1, and (c) demonstrated sequence homology at the amino terminus of allophycocyanin, phycocyanin, and phycoerythrin.

Particle-bound phytochrome: Spectral properties of bound and unbound fractions

In-vitro irradiation of extracts of maize (Zea mays L.) coleoptiles with red light enhances phytochrome pelletability as was previously reported for Cucurbita pepo L. In neither case is this the result of an irradiation-induced increase in the level of total pelletable protein. The transformation difference spectra of bound and unbound phytochrome fractions obtained after both in-vivo and in-vitro irradiations are not significantly different. The data, therefore, do not indicate that irradiation-enhanced pelletability either in vivo or in vitro results from phytochrome denaturation. Other non-photoreversible changes in the molecule external to the chromophore environment might however still account for the observed pelletability.

Studies on phytochrome. Two photoreversible chromoproteins from etiolated oat seedlings

1. The photoreversible chromoprotein phytochrome was extracted from etiolated oat seedlings. The final purification step revealed that there were two photoreversible coloured components. 2. The amino acid composition, spectra and Svedberg coefficients of each component are reported.

Studies on phytochrome. Some properties of electrophoretically pure phytochrome

1. Phytochrome was purified from etiolated oat (Avena sativa) seedlings either by gel-filtration chromatography and ion-exchange chromatography or by gel-filtration chromatography and calcium phosphate chromatography. Differences were observed in the spectral properties of phytochrome isolated by the two methods. 2. Electrophoresis of pure phytochrome at pH values between 9.0 and 6.0 showed the tendency of phytochrome to form different molecular species. Studies in the ultracentrifuge did not show a corresponding change in the sedimentation coefficient with the change in pH. 3. Tryptic digestion of electrophoretically pure phytochrome gave 17 peptides and a photoactive core. The amino acid composition of the core is reported and compared with the analysis of whole phytochrome. 4. Some properties of phytochrome isolated from Pisum sativum are compared with those of phytochrome from A. sativa. 5. The properties of phytochrome purified by other workers are compared with our findings.

Actinomycin-D inhibition of phytochrome-mediated responses

Actinomycin-D inhibits phytochrome-mediated responses of etiolated plants. In the unrolling response of a barley first leaf the inhibition by act. D is greater when the antibiotic is applied 80 minutes after irradiation; earlier or later applications are less inhibitory. Inhibition is relieved by deoxyguanosine applied before or after act. D. Similar effects are found with the plumular hooks of peas and beans. These results suggest that phytochrome-mediated responses involve RNA production on a DNA template. The location of phytochrome in the cell is discussed in relation to its possible association with DNA, especially that of the plastids and mitochondria. Phytochrome may thus act as a repressor of gene sequences involved (for instance) in the removal of etiolation symptoms, red light (660 nm) causing its dissociation from DNA. Far-red radiation may reverse the effects by causing re-association of phytochrome.

RHYTHMIC FLOWERING RESPONSES AND PHYTOCHROME CHANGES IN A SELECTION OF CHENOPODIUM RUBRUM

Flowering of Chenopodium rubrum L., selection 374, was examined with respect to an endogenous circadian rhythm, the state of phytochrome, and the result of changing the form of phytochrome during a single dark period of 2 to 96 hours interrupting continuous light. Darkness was imposed either 4 or 5 days after seeds were placed on moist filter paper in Petri dishes.The following working hypothesis, which is partly retrospective, is projected to explain the main features of the experimental results. Flowering is controlled by a product of the enzymatic action of the far-red absorbing form of phytochrome (Pfr) on a single but unknown substrate. In acting, Pfr finally reverts to the inactive red-absorbing form of phytochrome (Pr) or is changed from the Pfr form in some other way. The available substrate, if not utilized by Pfr action, is soon depleted by other reactions. The substrate for Pfr action is low during the skotophile but high during the photophile phases. The significant time for phasing is the beginning of darkness. The initial substrate supply appears to be derived from the preceding light period but some time in the region of the 9th to 12th hour of darkness a significant rhythmic change of substrate starts up. The dependence of flowering on the time that darkness is interrupted by light is directly related to a rhythmic change in the optimum Pfr level required for the processes leading to flowering.The role of the endogenous rhythm in flowering under natural conditions is questioned. Similarities that are shown in the control of flowering, whether the display is governed by an endogenous rhythm or by a daily photoperiodic cycle, indicate that phytochrome acts as a "pacemaker". It is suggested that the distinct ecotypic populations of C. rubrum that differ in flowering response have dissimilar levels and rates of supply of substrate for phytochrome action. In C. rubrum-374, complete reversion or loss of Pfr does not occur during a long dark period of 72 hours at 20 °C, but Pfr does decrease to low levels.A hydrodynamic system is discussed as an analogy to rhythmic flowering response.