Light-induced linear dichroism in photoreversibly photochromic sensor pigments. – III. Chromophore rotation estimated by polarized light reversal of dichroism

Phytochrome from oats ( Avena sativa L. cv. Sol II), partially purified on brushite, was immobilized on Sepharose beads to which antiphytochrome immunoglobulin had been covalently linked. The immobilized phytochrome was first brought to the Pr form with unpolarized far-red light. The change in linear dichroism at 660 nm induced by plane polarized red light, and its reversal by plane polarized far-red light were then studied using a dual-wavelength spectrophotometer equipped with polarizing filters. The far-red light was most effective in reversing red-induced dichroism when the angle between the planes of polarization of red and far-red light was approximately 23°. From this it was computed that the long-wavelength transition moment of phytochrome rotates about 29° (or 180°–29°) with respect to the protein during conversion from Pr to Pfr. The reverse experiment, using unpolarized red light followed first by polarized far-red light and then polarized red light, with dichroism monitored at 730 nm, also gives most effective reversal for an angle of about 23° between polarization planes, but this corresponds to a transition moment rotation of about 36° (or 180°–36°). The present method is more straightforward but less accurate and confirms our earlier conclusion that the rotation angle is close to 32° (or 180°–32°) in contrast to the "in vivo" value of 90° found by several workers.     

Light-induced linear dichroism in photoreversibly photochromic sensor pigments. – V. Reinterpretation of the experiments on in vivo action dichroism of phytochrome

Experiments by several authors on the effects of polarized light on phytochromemediated responses in fern gametophytes and in the green alga Mougeotia have earlier been interpreted as showing that the transition moment of phytochrome in the P_r form is parallel to the plasmalemma, but perpendicular to the plasmalemma for the P_fr form of phytochrome. It is now shown that the experimental results can be interpreted differently, and that they are also consistent with a chromophore rotation of about 30° (instead of 90°), as found for immobilized phytochrome molecules in vitro. Thus there is no evidence for a rotation of the whole phytochrome protein. For the gametophyte of Adiantum it is calculated that the P_r transition moment is inclined 17° to the plasmalemma, and the P_fr transition moment ca 50°, corresponding to an in vivo chromophore rotation of ca 33°; however, these values are very approximate.     

Growth and leaf senescence in spring wheat (Triticum aestivum) grown at different ozone concentrations in open-top field chambers

The light harvesting biliprotein phycoerythrocyanin isolated from the cyanobacterium Mastigocladus laminosus Cohn was separated into its subunits by isoelectric focusing in a granulated gel in the presence of urea with subsequent renaturation. Smaller amounts of the subunits were obtained from Tolypothrix distorta Kützing var. symplocoides Hansgirg, strain IUCC 424 (now UTEX 424), by chromatography of phycoerythrocyanin on hydroxylapatite. In both cases the isolated α-subunits showed the photoreversible photochemistry characterizing phycochrome b , a photoreversibly photochromic pigment so far found only in extracts of phycoerythrocyanin-containing organisms. Light-induced absorbance changes in the β-subunit and in phycoerythrocyanin were also studied.     

Phycochromes b and d: their occurrence in some phycoerythrocyanin-containing blue-green algae (cyanobacteria)

Abstract
Phycochromes b and d, two types of photoreversibly photochromic pigments previously extracted from the blue-green alga Tolypothrix distorta , which contains phycoerythrocyanin, have now been found in three Anabaena strains also containing phycoerythrocyanin. Tests for the presence of phycochromes b and d in a number of blue-green algae lacking phycoerythrocyanin have been negative. The possibility that phycochrome b-type absorbance changes are due to changes in the α-subunit of phycoerythrocyanin is discussed.     

Phycochrome d, a New Photochromic Pigment from the Blue-Green Alga, Tolypothrix distorta

A new reversibly photochromic pigment, phycochrome d, has been found in extracts of the blue-green alga Tolypothrix distorta. This phycochrome exhibits an absorbance increase in the red region (maximum at about 650 nm) when irradiated with 650 nm light, and a corresponding absorbance decrease when irradiated with 610 nm light. The absorbance difference spectrum and action spectra for in vitro conversions were determined.     

Phototransformation of oat phytochrome with millisecond and submillisecond flashes: The level of the photostationary Pfr/Ptot ratio is modified by photoreversible intermediates

Photoconversion of the red-absorbing form of phytochrome (P_r) to the far-red-absorbing form of phytochrome (P_fr) and vice versa has been measured spectrophotometrically at 10°C in immobilized and soluble phytochrome (118 kdalton), prepared from 5-day-old etiolated oat seedlings ( Avena saliva L. cv. Sol II). The photostationary equilibrium φ= P_frP_tot (with P_tot= total amount of phytochrome P_r+ P_fr) for red light depends on whether it is established by repetitive pulses (≥ 5 s) or by repetitive flashes (≥ 4 ms). In the wavelength region around 660 nm, a lower φ is reached with flashes as compared to that with pulses. This difference becomes negligible if the wavelength is shortened to the 600 nm region, and it also disappears if the fluence of each individual flash is reduced. In contrast, in long-wavelength red light and short-wavelength far-red light, a higher φ is reached with flashes than with pulses.
We relate the differences in φ for flash and pulse irradiation to photochromic systems between P_r and photoreversible intermediates in the phototransformation pathway P_r→ P_fr. Thus, light absorption by phytochrome intermediates can be limiting for the quantitative relationship between light signal and P_fr formed.     

Photochromic Pigments from Blue-Green Algae: Phycochromes a, b, and c

Aqueous extracts of blue-green algae were fractionated by electrofocusing. In all algae investigated, fractions with iso-electric points at or near 4.6 showed photochromic behaviour analogous to that of phytochrome, although they were sensitive to light of shorter wavelength. Three main types of photochromic pigments were found: Phycochrome a (in Tolypothrix distorta, Phormidium luridum, Nostoc muscorum 1453/12, and Anacystis nidulans) has one form absorbing maximally at about 590 nm (formed under red light) and one absorbing maximally at about 630 nm (formed under green light). Phycochrome b (in Tolypothrix distorta) has one form absorbing maximally near 510 nm and one form absorbing maximally at 570 nm (formed in yellow-green and blue-green light, respectively). Phycochrome c (in Nostoc muscorum A and probably in Tolypothrix tenuis) has one form absorbing maximally at 650 nm (formed under green light) and one absorbing very weakly in the green region (formed under red light). The conversion of Phormidium phycochrome a from its red-absorbing form to its green-absorbing form causes the same spectral change as if an f-chromophore of phycocyanin were transformed into an s-chromophore. The quantum yield for this conversion is estimated to be 0.1, while the quantum yield for the reversion is estimated to be 0.4 on the assumption that the absorption coefficients are those of f- and s-chromophores. Phycochrome c is less light-sensitive than phycochromes a and b.     

Action Spectra for in vivo and in vitro Conversions of Phycochrome b, a Reversibly Photochromic Pigment in a Blue-Green Alga, and Its Separation from Other Pigments

Phycochrome b, one of the reversibly photochromic pigments found in Tolypothrix distorta seems to exist in only two forms: P^b₅₀₀ and P^b₅₇₀. The pigment has been spectroscopically demonstrated in vivo. It has also been separated from other pigments. Two different methods for separation have been used: isoelectric focusing and gel filtration. Preparations of purified phycobilisomes contain phycochrome b. The in vivo and in vitro absorption difference spectra were determined as well as action spectra for the conversions in vitro and in vivo of P^b₅₀₀ to P^b₅₇₀ and vice versa. Transformation kinetics of phycochrome b show that the conversions in both directions are initially first-order reactions.     

Angle of the retinal of bacteriorhodopsin in blue membrane

The electric dichroism of purple and cation-depleted (blue) membrane was measured in a.c. electric fields at saturation. A decrease of 5.5° in the direction of the chromophore transition moment with respect to the membrane normal was found upon removal of cations from purple membrane.     

Chromophore structure in phytochrome intermediates and bleached forms of phytochrome

Phytochrome (120 kdalton or 60 kdalton) was isolated from etiolated seedlings of Avena sativa L. cv. Pirol (Baywa München). Irradiation with red light of the P_r form at −23°C in aqueous medium or at −40°C in 66% glycerol leads to the intermediate meta-Rb. Acidification of the glycerol solution at −40°C leads to the absorption of the 15(E) phytochrome chromophore (= P_fr chromophore). Subsequent irradiation transforms this into the 15(Z) chromophore (= P_r chromophore). The presence of the 15(E) chromophore was demonstrated by the same methods also in phytochrome bleached either as P_fr in the dark by 4 M urea, methanol, acetone, ethylene glycol, 8-anilinonaphthalene-1-sulfonate, or as P_r by irradiation with red light in the presence of the same agents. Phytochrome bleached by sodium dodecylsulfate or by dehydration was also investigated. It was concluded that bleached phytochrome contains the P_fr chromophore without specific interaction with the protein.     

Crystallization and preliminary X-ray crystallographic analysis of the N-terminal photosensory module of phytochrome Agp1, a biliverdin-binding photoreceptor from Agrobacterium tumefaciens

Phytochromes are photochromic photoreceptors with a bilin chromophore that have been found in plants and bacteria. Typical bacterial phytochromes are composed of an N-terminal photosensory chromophore module and a C-terminal protein kinase. The former contains the chromophore, which allows phytochromes to adopt the two interconvertible spectral forms, Pr and Pfr. The N-terminal photosensory module of Agrobacterium phytochrome Agp1, Agp1-M15, was used for crystallization studies. The protein was either assembled with the natural chromophore biliverdin or a sterically locked synthetic biliverdin-derivative, termed 15Za. The last-named adduct does not undergo photoisomerization due to an additional carbon chain between the rings C and D of the chromophore. Both adducts could be crystallized, but the resolution was largely improved by the use of 15Za. Crystals of biliverdin-Agp1-M15 diffract to 6A resolution and belong to the tetragonal space group I422 with unit cell dimensions a = b = 171 Angstroms, c = 81 Angstroms, crystals of 15Za-Agp1-M15 belong to the same space group with similar unit cell dimensions a = b = 174 Angstroms, c = 80 Angstroms, but diffract to 3.4 Angstroms resolution. Assuming the asymmetric unit to be occupied by one monomer of 55kDa, the unit cell contains 54-55% solvent with a crystal volume per protein mass, V(m), of 2.7 Angstroms(3) Da(-1).     

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°.     

Protein conformational changes of Agrobacterium phytochrome Agp1 during chromophore assembly and photoconversion

Phytochromes are widely distributed photochromic biliprotein photoreceptors. Typical bacterial phytochromes such as Agrobacterium Agp1 have a C-terminal histidine kinase module; the N-terminal chromophore module induces conformational changes in the protein that lead to modulation of kinase activity. We show by protein cross-linking that the C-terminal histidine kinase module of Agp1 mediates stable dimerization. The fragment Agp1-M15, which comprises the chromophore module but lacks the histidine kinase module, can also form dimers. In this fragment, dimer formation was stronger for the far-red-absorbing form Pfr than for the red-absorbing form Pr. The same or similar behavior was found for Agp1-M15Delta9N and Agp1-M15Delta18N, which lack 9 and 18 amino acids of the N-terminus, respectively. The fragment Agp1-M20, which is derived from Agp1-M15 by truncation of the C-terminal "PHY domain" (191 amino acids), can also form dimers, but dimerization is independent of irradiation conditions. The cross-linking data also showed that the PHY domain is in tight contact with Lys 16 of the protein and that the nine N-terminal amino acids mediate oligomer formation. Limited proteolysis shows that the hinge region between the chromophore module and the histidine kinase and a part of the PHY domain become exposed upon Pr to Pfr photoconversion.     

Protochlorophyllide transformations and chlorophyll accumulation in epicotyls of pea (Pisum sativum)

Low-temperature fluorescence emission spectra of epicotyls of 6.5-day-old dark-grown seedlings of pea ( Pisum sativum L.) showed the dominance of short-wavelength protoch lorophyllide forms with emission maxima at 629 and 636 nm, respectively. The presence of long-wavelength protochlorophyllide with emission maxima around 650 nm was just detectable. Accordingly, irradiation with millisecond flashes gave a minute formation of chlorophyllide. The chlorophyll(ide) formation varied along the epicotyl. Irradiation with continuous light for 1.5 h resulted in an evident accumulation of chlorophyll(ide) in the upper part of the epicotyl. Only small amounts accumulated in the middle section. The conversion of protochlorophyllide to chlorophyllide was temperature dependent and almost arrested at 0°C. The chlorophyll(ide) formed had one dominating fluorescence peak at 681 nm. Irradiation for 24 h gave almost 100 times more chlorophyll in the upper part of the epicotyl than in the lower part. Electron micrographs from the upper part of the epicotyl irradiated for 6 h showed plastids with several developing thylakoids, while the plastids in the lower part of the epicotyl had only a few thylakoids. The dominance of short-wavelength protochlorophyllide forms indicated the presence of protochlorophyllide not bound to the active site of NADPH-protochlorophyllide oxidoreductase (EC 1.3.1.33). The inability of the short-wavelength form to transform into chlorophyllide with flash light denotes a dislocation from the active site. The time and temperature dependence of the chlorophyll(ide) formation in continuous light indicates that a relocation is required of the short-wavelength protochlorophyllide before chlorophyllide formation can occur.     

Orientation of the protonated retinal Schiff base group in bacteriorhodopsin from absorption linear dichroism.

Linear dichroism experiments are performed on light-adapted bacteriorhodopsin (BR568) films containing native retinal (A1) and its 3,4-dehydroretinal (A2) analogue to measure the angle between the chromophore transition dipole moment and the membrane normal. QCFF/pi calculations show that the angle between the transition moment and the long axis of the polyene is changed by 3.4 degrees when the C3-C4 bond is unsaturated. The difference vector between the two transition moments points in the same direction as the Schiff base (N----H) bond for the all-trans BR568 chromophore. Because the plane of the chromophore is perpendicular to the membrane plane, a comparison of the transition moment orientations in the A1- and A2-pigments enables us to determine the orientation of the N----H bond with respect to the absolute chromophore (N----C5 vector) orientation. The angles of the transition moments are 70.3 degrees +/- 0.4 degrees and 67.8 degrees +/- 0.4 degrees for the A1- and A2-pigments, respectively. The fact that the change in the transition moment angle (2.5 degrees) is close to the predicted 3.4 degrees supports the idea that the chromophore plane is nearly perpendicular to the membrane plane. The decreased transition moment angle in the A2-analogue requires that the N----H bond and the N----C5 vector point toward the same membrane surface. Available results indicate that the N----C5 vector points toward the exterior in BR568. With this assignment, we conclude that the N----H bond points toward the exterior surface and its most likely counterion Asp-212. This information makes possible the construction of a computer graphics model for the active site in BR568.     

A structural basis for reversible photoswitching of absorbance spectra in red fluorescent protein rsTagRFP

rsTagRFP is the first monomeric red fluorescent protein (FP) with reversibly photoswitchable absorbance spectra. The switching is realized by irradiation of rsTagRFP with blue (440 nm) and yellow (567 nm) light, turning the protein fluorescence ON and OFF, respectively. It is perhaps the most useful probe in this color class that has yet been reported. Because of the photoswitchable absorbance, rsTagRFP can be used as an acceptor in photochromic Förster resonance energy transfer. Yellow FPs, YPet and mVenus, are demonstrated to be excellent photochromic Förster resonance energy transfer donors for the rsTagRFP acceptor in its fusion constructs. Analysis of X-ray structures has shown that photoswitching of rsTagRFP is accompanied by cis–trans isomerization and protonation/deprotonation of the chromophore, with the deprotonated cis- and protonated trans-isomers corresponding to its ON and OFF states, respectively. Unlike in other photoswitchable FPs, both conformers of rsTagRFP chromophore are essentially coplanar. Two other peculiarities of the rsTagRFP chromophore are an essentially hydrophobic environment of its p-hydroxyphenyl site and the absence of direct hydrogen bonding between this moiety and the protein scaffold. The influence of the immediate environment on rsTagRFP chromophore was probed by site-directed mutagenesis. Residues Glu145 and His197 were found to participate in protonation/deprotonation of the chromophore accompanying the photoswitching of rsTagRFP fluorescence, whereas residues Met160 and Leu174 were shown to spatially restrict chromophore isomerization, favoring its radiative decay.     

Photochromic pigments in akinetes and pigment characteristics of akinetes in comparison with vegetative cells of Anabaena variabilis

Since akinete germination is triggered by light and the action spectrum for this process has features in common with the spectra of the two photochromic pigments, phycochromes b and d, a search was made for the presence of these phycochromes in akinetes of the blue-green alga. Anabaena variabilis Kützing. Allophycocyanin-B was also looked for, since the action spectrum for akinete germination points to a possible participation of this pigment too. Isoelectric focusing was used for purification of the pigments. The different fractions were investigated for phycochromes b and d by measuring the absorbance difference spectra: for phycochrome b. 500 nm irradiated minus 570 nm irradiated, and for phycochrome d, 650 nm irradiated minus 610 nm irradiated. For determination of allophycocyanin-B. fourth derivative analysis of absorption spectra was made for some of the fractions from the isoelectric focusing column. Phycochrome b was also assayed for by measuring in vivo absorption difference spectra. The assays were positive for all three pigments. The complete photosynthetic pigment systems were also studied by in vivo fluorescence measurements on both akinetes and vegetative cells of Anabaena variabilis. Fluorescence emission and excitation spectra at selected emission wavelengths were measured at room temperature and liquid nitrogen temperature. The energy transfer from phycoerythrocyanin to phycocyanin is very efficient under all conditions, as is the energy transfer from phycocyanin to allophycocyanin at room temperature. At low temperature, however, phycocyanin is partly decoupled from allophycocyanin, particularly in the akinetes; the energy transfer from allophycocyanin to chlorophyll a is less efficient at low temperature in both types of cells, but especially in akinetes. Delayed light emission was measured for both types of cells and found to be very weak in akinetes compared to vegetative cells. From this study it would seem that akinetes lack an active photosystem II, although the 691 nm peak in the 570 nm excited low temperature fluorescence emission spectrum proves the presence of photosystem II chlorophyll, and also its energetic connection to the phycobilisomes.     

Chromophore: apoprotein interactions in phytochrome A*

Phytochromes are molecular light switches by virtue of their photochromic red/far-red reversibility. The His-324 residue next to the chromophore-linked Cys-323 plays a critical role in conferring photochromism to the tetrapyrrole chromophore in native phytochrome A. The chromophore appears to be enclosed between the amphiphilic α-helical chains in a hydrophobic pocket. The absorbance maxima of both the Pr and the Pfr forms of pea phytochrome A are blue-shifted by 10 and 20 nm, respectively, upon C-terminal truncation. We speculate that the quaternary structure of the phytochrome A molecule involves some interactions of the C-terminal half with the chromophore domain. The Pfr conformation of phytochrome includes an amphiphilic α-helix of the amino terminal chain, which occurs in 113 ms after picosecond photoisomerization of the Pr form. Compared to α-helical folding, unfolding of the α-helix occurs faster in about 310 μs upon phototransformation of the Pfr form of phytochrome A. The photochromic transformation of phytochrome A modulates protein kinase-catalysed phosphorylation sites in vivo and in vitro, but only a subtle local change in conformation is detectable in the phosphorylated phytochromes. This suggests that the post-translational modification serves as a surface label, rather than a transducer-activating trigger, for the recognition of a putative phytochrome receptor.     

Biochemical and spectroscopic characterization of the bacterial phytochrome of Pseudomonas aeruginosa

Phytochromes are photochromic biliproteins found in plants as well as in some cyanotrophic, photoautotrophic and heterotrophic bacteria. In many bacteria, their function is largely unknown. Here we describe the biochemical and spectroscopic characterization of recombinant bacterial phytochrome from the opportunistic pathogen Pseudomonas aeruginosa (PaBphP). The recombinant protein displays all the characteristic features of a bonafide phytochrome. In contrast with cyanobacteria and plants, the chromophore of this bacterial phytochrome is biliverdin IXalpha, which is produced by the heme oxygenase BphO in P. aeruginosa. This chromophore was shown to be covalently attached via its A-ring endo-vinyl group to a cysteine residue outside the defined bilin lyase domain of plant and cyanobacterial phytochromes. Site-directed mutagenesis identified Cys12 and His247 as being important for chromophore binding and photoreversibility, respectively. PaBphP is synthesized in the dark in the red-light-absorbing Pr form and immediately converted into a far-red-light-absorbing Pfr-enriched form. It shows the characteristic red/far-red-light-induced photoreversibility of phytochromes. A chromophore analog that lacks the C15/16 double bond was used to show that this photoreversibility is due to a 15Z/15E isomerization of the biliverdin chromophore. Autophosphorylation of PaBphP was demonstrated, confirming its role as a sensor kinase of a bacterial two-component signaling system.     

Light-induced linear dichroism in photoreversibly photochromic sensor pigments. – VI. Relation between the two pigments of the mycochrome system in Alternaria cichorii

Conidiation in Alternaria cichorii Nattras is reversibly stimulated by near ultraviolet radiation (NUV, ca 313 nm) and inhibited by blue light (ca 450 nm) and seems to be a mycochrome-mediated process. After induction with plane-polarized NUV, blue light polarized perpendicularly to the NUV was more effective in counteracting the induction than was blue light polarized parallel to the NUV. From this the conclusions are drawn that (a) both the blue-absorbing component (presumably a flavo-protein) and the P_NUV of the mycochrome system are membrane-bound and that (b) the transition moment associated with blue light absorption in the presumed flavoprotein forms an angle of at least 53° with the transition moment associated with NUV absorption in P_NUV.