Recombinant Phytochrome A in Yeast Differs by its Spectroscopic and Photochemical Properties from the Major phyA′ and is Close to the Minor phyA″: Evidence for Posttranslational Modification of the Pigment in Plants¶

Applications of fluorescence spectroscopy in the investigation of plant phytochrome invivo

Fluorometry is an effective research tool in biology and medicine; it is widely used in the study of the photosynthetic pigment apparatus in vivo. This method can be applied to the key plant photoreceptor phytochrome (phy). The fluorescence of phytochrome in plants was recorded for the first time in the group of the author, and a spectrofluorometric technique for its in vivo study was developed. The photophysical and photochemical properties of the pigment were described, and the photoreceptor was shown to be present in plants as two phenomenological types-active (at cryogenic temperatures) and water-soluble (Pr') and inactive and amphiphilic (Pr″). The scheme of the photoreaction explaining their photochemical distinctions was proposed. Phytochrome A was shown to comprise both types (phyA' and phyA″), whereas phytochrome B was only the second type. For phyA', distinct conformers have been detected. phyA' and phyA″ differ by the N-terminus of the molecule, possibly by serine phosphorylation. They mediate, respectively, the very low fluence and high irradiance photoresponses. Light, internal factors (kinase/phosphatase balance, pH), and hormones (jasmonate) were shown to affect the content and functions of the two phyA pools. All this points to the effectiveness of the developed method for invivo investigations of the phytochrome system. The data obtained can be applied in practical terms in agrobiology and light culture, as well as in the use of phytochrome as a new nanotool and a fluorescent probe.

Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning

Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red-far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions-the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant's survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants' successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types-major, light-labile and soluble phyA' and minor, relatively light-stable and amphiphilic phyA″-is presented as what may account for the diverse modes of phyA action.

Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning

Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red—far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant’s survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants′ successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types—major, light-labile and soluble phyA′ and minor, relatively light-stable and amphiphilic phyA″—is presented as what may account for the diverse modes of phyA action.

Two molecular species of phytochrome A with distinct modes of action

Adaptation of plants to environmental light conditions is achieved via operation of a highly complex photoreceptor apparatus. It includes the phytochrome system comprising phytochromes A and B (phyA and phyB) as the major components. phyA differs from phyB by several properties, including its ability to mediate all three photoresponse modes – the very low and low fluence responses (VLFR and LFR respectively) and the high irradiance responses (HIR), whereas phyB is responsible for LFR. This review discusses the uniqueness of phyA in terms of its structural and functional heterogeneity. The photoreceptor is presented in monocots and dicots by two native molecular species, phyAʹ and phyAʹʹ, differing by spectroscopic, photochemical and phenomenological properties. phyA differentiation into substates includes post-translational phosphorylation of a serine residue(s) at the N-terminal extension of the molecule with phyAʹ being the phosphorylated species and phyAʹʹ, dephosphorylated. They differ also by their mode of action, which depends on the cellular context. The current working hypothesis is that phyAʹ mediates VLFR and phyAʹʹ, HIR and LFR. The content and functional activity of the two pools are regulated by light and by phosphatase/kinase equilibrium and pH in darkness, what contributes to the fine-tuning of the phytochrome system. Detection of the native pools of the cryptogamic plant fern Adiantum capillus-veneris phy1 (phy1ʹ and phy1ʹʹ) similar to those of phyA suggests that the structural and functional heterogeneity of phyA is not a unique phenomenon and may have arisen earlier in the molecular evolution of the phytochrome system than the appearance of the angiosperm phytochromes.

Two molecular species of phytochrome A with distinct modes of action

Adaptation of plants to environmental light conditions is achieved via operation of a highly complex photoreceptor apparatus. It includes the phytochrome system comprising phytochromes A and B (phyA and phyB) as the major components. phyA differs from phyB by several properties, including its ability to mediate all three photoresponse modes - the very low and low fluence responses (VLFR and LFR respectively) and the high irradiance responses (HIR), whereas phyB is responsible for LFR. This review discusses the uniqueness of phyA in terms of its structural and functional heterogeneity. The photoreceptor is presented in monocots and dicots by two native molecular species, phyA' and phyA'', differing by spectroscopic, photochemical and phenomenological properties. phyA differentiation into substates includes post-translational phosphorylation of a serine residue(s) at the N-terminal extension of the molecule with phyA' being the phosphorylated species and phyA'', dephosphorylated. They differ also by their mode of action, which depends on the cellular context. The current working hypothesis is that phyA' mediates VLFR and phyA'', HIR and LFR. The content and functional activity of the two pools are regulated by light and by phosphatase/kinase equilibrium and pH in darkness, what contributes to the fine-tuning of the phytochrome system. Detection of the native pools of the cryptogamic plant fern Adiantum capillus-veneris phy1 (phy1' and phy1'') similar to those of phyA suggests that the structural and functional heterogeneity of phyA is not a unique phenomenon and may have arisen earlier in the molecular evolution of the phytochrome system than the appearance of the angiosperm phytochromes.

The dephosphorylated S8A and S18A mutants of (oat) phytochrome A comprise its two species, phyA′ and phyA′′, suggesting that autophosphorylation at these sites is not involved in the phyA differentiation

Modification of phytochrome A at the N-terminus yields its two types, phyA′ and phyA′′. This work excludes the known (oat) phyA autophosphorylation at serine 8 and serine 18 as its possible mechanism.

phyA-GFP is spectroscopically and photochemically similar to phyA and comprises both its native types, phyA' and phyA''

Low-temperature fluorescence investigations of phyA-GFP used in experiments on its nuclear-cytoplasmic partitioning were carried out. In etiolated hypocotyls of phyA-deficient Arabidopsis thaliana expressing phyA-GFP, it was found that it is similar to phyA in spectroscopic parameters with both its native types, phyA' and phyA'', present and their ratio shifted towards phyA'. In transgenic tobacco hypocotyls, native phyA and rice phyA-GFP were also identical to phyA in the wild type whereas phyA-GFP belonged primarily to the phyA' type. Finally, truncated oat Δ6-12 phyA-GFP expressed in phyA-deficient Arabidopsis was represented by the phyA' type in contrast to full-length oat phyA-GFP with an approximately equal proportion of the two phyA types. This correlates with a previous observation that Δ6-12 phyA-GFP can form only numerous tiny subnuclear speckles while its wild-type counterpart can also localize into bigger and fewer subnuclear protein complexes. Thus, phyA-GFP is spectroscopically and photochemically similar or identical to the native phyA, suggesting that the GFP tag does not affect the chromophore. phyA-GFP comprises phyA'-GFP and phyA''-GFP, suggesting that both of them are potential participants in nuclear-cytoplasmic partitioning, which may contribute to its complexity.

Fern Adiantum capillus-veneris phytochrome 1 comprises two native photochemical types similar to seed plant phytochrome A

Phytochrome (phy) in etiolated seedlings of wild-type (WT) Arabidopsis (Ler) and its transgenic lines (TL) L15 and L20 transformed with Adiantum capillus-veneris PHY1 cDNA (Okamoto et al., 1997) was investigated using low-temperature (85K) fluorescence spectroscopy and photochemistry. It was found that while WT seed germination requires stimulation by light, the TL germinated equally well with or without pre-illumination. Phytochrome content [Ptot] was 2-fold higher in TL whereas the level of Pr→lumi-R phototransformation at 85K (γ1) was similar between WT (0.25) and TL (0.27). When seeds germinated with pre-illumination, the proportion of the photochemical types Pr' active and Pr″ inactive at 85K was 50/50 in WT and 54/46 in TL, respectively. Dark-germinated TL had a γ1 value of 0.16 and the proportion of Pr' and Pr″ was 32/68, respectively, without changes in [Ptot]. Evaluations based on these data revealed that phy1 has Pr' and Pr″, designated phy1' and phy1″, akin to phyA, which comprises both Pr photochemical types (phyA' and phyA″), and in contrast to phyB that possesses only Pr″. The proportion of phy1' and phy1″ depends on pre-illumination for induction of germination. The pigment most likely accumulated in the seeds and was active in promoting Arabidopsis seed germination.

Protein Phosphatase Activity and Acidic/Alkaline Balance as Factors Regulating the State of Phytochrome A and its Two Native Pools in the Plant Cell

Phytochrome A (phyA), the most versatile plant phytochrome, exists in the two isoforms, phyA′ and phyA′′, differing by the character of its posttranslational modification, possibly, by phosphorylation at the N‐terminal extension [Sineshchekov, V. (2010) J. Botany 2010, Article ID 358372]. This heterogeneity may explain the diverse modes of phyA action. We investigated possible roles of protein phosphatases activity and pH in regulation of the phyA pools' content in etiolated seedlings of maize and their extracts using fluorescence spectroscopy and photochemistry of the pigment. The phyA′/phyA′′ ratio varied depending on the state of development of seedlings and the plant tissue/organ used. This ratio qualitatively correlated with the pH in maize root tips. In extracts, it reached a maximum at pH ≈ 7.5 characteristic for the cell cytoplasm. Inhibition of phosphatases of the PP1 and PP2A types with okadaic and cantharidic acids brought about phyA′ decline and/or concomitant increase of phyA′′ in coleoptiles and mesocotyls, but had no effect in roots, revealing a tissue/organ specificity. Thus, pH and phosphorylation status regulate the phyA′/phyA′′ equilibrium and content in the etiolated (maize) cells and this regulation is connected with alteration of the processes of phyA′ destruction and/or its transformation into the more stable phyA′′.

Protein phosphatase activity and acidic/alkaline balance as factors regulating the state of phytochrome A and its two native pools in the plant cell

Phytochrome A (phyA), the most versatile plant phytochrome, exists in the two isoforms, phyA' and phyA'', differing by the character of its posttranslational modification, possibly, by phosphorylation at the N-terminal extension [Sineshchekov, V. (2010) J. Botany 2010, Article ID 358372]. This heterogeneity may explain the diverse modes of phyA action. We investigated possible roles of protein phosphatases activity and pH in regulation of the phyA pools' content in etiolated seedlings of maize and their extracts using fluorescence spectroscopy and photochemistry of the pigment. The phyA'/phyA'' ratio varied depending on the state of development of seedlings and the plant tissue/organ used. This ratio qualitatively correlated with the pH in maize root tips. In extracts, it reached a maximum at pH ≈ 7.5 characteristic for the cell cytoplasm. Inhibition of phosphatases of the PP1 and PP2A types with okadaic and cantharidic acids brought about phyA' decline and/or concomitant increase of phyA'' in coleoptiles and mesocotyls, but had no effect in roots, revealing a tissue/organ specificity. Thus, pH and phosphorylation status regulate the phyA'/phyA'' equilibrium and content in the etiolated (maize) cells and this regulation is connected with alteration of the processes of phyA' destruction and/or its transformation into the more stable phyA''.

A switchable light-input, light-output system modelled and constructed in yeast

Background

Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies on solid media.

Results

The reversible activation of the phytochrome by red light, and its inactivation by far-red light, is retained. We use this quantitative readout to construct a mathematical model that matches the system's behaviour and predicts the molecular targets for future manipulation.

Conclusion

Our model, methods and materials together constitute a novel system for a eukaryotic host with the potential to convert a dynamic pattern of light input into a predictable gene expression response. This system could be applied for the regulation of genetic networks - both known and synthetic.

Two Native Pools of Phytochrome A in Monocots: Evidence from Fluorescence Investigations of Phytochrome Mutants of Rice

Fluorescence investigations of phytochrome (phy) in rice (Oryza sativa L. cv. Nipponbare) mutants deficient in phyA, phyB and phyA plus phyB were performed. Total content of the pigment (Ptot) and its spectroscopic and photochemical characteristics were determined in different parts of the dark‐grown and far‐red light (FR)‐grown coleoptiles. Spectroscopically, phyA in the phyB mutant was identical to phyA in the wild‐type (WT) and the extent of the conversion from Pr to lumi‐R at 85 K was the same for phyA in both lines and varied similarly, depending on the part of the coleoptile used. The latter finding proved that phyA in rice is heterogeneous and comprises two phyA populations, phyA′ and phyA″. Functional properties of phyA were also determined. In the dark the phyB mutant had a higher content of phyA, inactive protochlorophyllide (Pchlide633) and active protochlorophyllide (Pchlide655) than WT and its coleoptile was longer, indicating that phyB may affect the development of WT seedlings in the dark. Constant FR drastically reduced the content of phyA, Pchlide633 and Pchlide655 and brought about coleoptile shortening and appearance of the first leaf, whereas pulsed FR of equal fluence was less effective. This suggested that the reactions were primarily of the high irradiance responses type, which are likely to be mediated by phyA′. The effects on protochlorophyllide biosynthesis and growth responses type were more pronounced in the phyB mutant than in the WT seedlings, which can be connected with the higher phyA′ content in the phyB mutant and/or phyB interference with its action in WT seedlings. In the phyA mutant induction of Pchlide633 and Pchlide655 biosynthesis was observed under constant FR, indicating that phyC may be responsible for this effect.

Two modes of the light-induced phytochrome A decline--with and without changes in the proportion of its isoforms (phyA' and phyA''): evidence from fluorescence investigations of mutant phyA-3D pea

Different modes of the phytochrome function are connected with its polymorphism, the major isoforms being phytochromes A and B (phyA and phyB). In its turn, phyA comprises two native species, phyA' and phyA'', whose precise nature and functions remain obscure. With the use of in situ fluorescence spectroscopy, we investigated their properties in a mutant of pea, phyA-3D, characterized by exaggerated photoresponses and impaired photodestruction of phyA. The mutation is a substitution of alanine by valine at the position 194 in phyA. The phyA-3DphyB and phyB mutants were also investigated. In dark-grown plants, all the lines had the content and properties of the two phyA species very similar to the wild type. However, a considerably more intense reduction in [phyA] without changes in the phyA'/phyA'' equilibrium was found in far-red grown mutant plants suggesting a hypersensitivity of phyA-3D with regard to its autoregulation. On the contrary, under red illumination, a higher stability of phyA-3D was observed confirming our earlier findings. This allows a conclusion that the A194V substitution in phyA-3D not only impairs its destruction but also enhances its signaling ability, suggesting a role of this locus in modulation of its activity.

The jasmonate-free rice mutant hebiba is affected in the response of phyA′/phyA″ pools and protochlorophyllide biosynthesis to far-red light

Phytochrome (phy) A in its two native isoforms (phyA' and phyA") and the active (Pchlide(655)) and inactive (Pchlide(633)) protochlorophyllides were investigated by low-temperature fluorescence spectroscopy in the tips of rice (Oryza sativa L. Japonica cv Nihonmasari) coleoptiles from wild type (WT) and the jasmonate-deficient mutant hebiba. The seedlings were either grown in the dark or under pulsed (FRp) or continuous (FRc) far-red light (lambda(a) >/= 720 nm) of equal fluences. In the dark, the mutant had a long mesocotyl and a short coleoptile, whereas the situation was reversed under FR: short mesocotyl and long coleoptile, suggesting that the effect is mediated by phyA. Under these conditions the WT displayed a short coleoptile and emergence of the first leaf. In the dark, the spectroscopic and photochemical properties of phyA, its content and the proportion of its two pools, phyA' and phyA", were virtually identical between WT and hebiba. However, the total content of protochlorophyllides was higher in the mutant. Upon illumination with FRc, [phyA] declined in the WT and the ratio between phyA' and phyA" shifted towards phyA". In hebiba, the light-induced decline of [phyA] was less pronounced and the ratio between phyA' and phyA" did not shift. Moreover, in the WT, FRp stimulated the biosynthesis of Pchlide(655), whereas FRc was inhibiting. In contrast, in the mutant, both FRp and FRc stimulated the synthesis of Pchlide(655). This means that FRc caused the opposite effect in hebiba. This difference correlates with a slower photodestruction of primarily the light-labile phyA' pool in hebiba.

Heterologous expression and characterization of recombinant phytochrome from the green alga Mougeotia scalaris

The full-length apoprotein (124 kDa) and the chromophore-binding N-terminal half (66 kDa) of the phytochrome of the unicellular green alga Mougeotia scalaris have been heterologously expressed in the methylotrophic yeast Pichia pastoris. Assembly with the tetrapyrrole phycocyanobilin (PCB) yielded absorption maxima (for the full-length protein) at 646 and 720 nm for red- and far-red absorbing forms of phytochrome (Pr and Pfr), respectively, whereas the maxima of the N-terminal 66 kDa domain are slightly blueshifted (639 and 714 nm, Pr and Pfr, respectively). Comparison with an action spectrum reported earlier gives evidence that in Mougeotia, as formerly reported for the green alga Mesotaenium caldariorum, PCB constitutes the genuine chromophore. The full-length protein, when converted into its Pfr form and kept in the dark, reverted rapidly into the Pr form (lifetimes of 1 and 24 min, ambient temperature), whereas the truncated chromopeptide (66 kDa construct) was more stable and converted into Pr with time constants of 18 and 250 min. Also, time-resolved analysis of the light-induced Pfr formation revealed clear differences between both recombinant chromoproteins in the various steps involved. The full-length phytochrome showed slower kinetics in the long milliseconds-to-seconds time domain (with dominant Pfr formation processes of ca 130 and 800 ms), whereas for the truncated phytochrome the major component of Pfr formation had a lifetime of 32 ms.

Fluorescence investigation of the recombinant cyanobacterial phytochrome (Cph1) and its C-terminally truncated monomeric species (Cph1Delta2): implication for holoprotein assembly, chromophore-apoprotein interaction and photochemistry

Recombinant dimeric full-length Cph1 holophytochrome and its C-terminally-truncated monomeric species [Cph1Delta2, comprising the chromophore-bearing N-terminal sensory module (residues 1 to 514)] from the cyanobacterium Synechocystis expressed in E. coli and reconstituted in vitro with phycocyanobilin (PCB) were investigated with the use of fluorescence spectroscopy and photochemistry in the temperature range from 85 to 293 K. Holoprotein assembly in Cph1 apparently proceeds via intermediate states with the emission maximum at 680-690 nm (I685) and 700 nm (I700) and a half-life time, at room temperature, of < or =5 s. Conversion of the putative I685 into mature Cph1 involves relaxation of the chromophore into a more flexible conformation. Cph1 and Cph1Delta2 were closely similar in their spectroscopic and photochemical characteristics (position of the emission band and its width, character of the temperature dependence of the fluorescence and activation energy of the fluorescence decay, kinetics and extent of the Pr conversion at low and ambient temperatures), suggesting that there is no immediate effect of the C-terminus on the photochemical properties of the chromophore in Cph1 and that chromophore-chromophore interactions in the dimer are not significant. The latter is also supported by the lack of energy transfer from the phycoerythrobilin (PEB) to PCB in the mixed PEB/PCB adduct of Cph1. At the same time, certain variations in the fluorescence and photochemical parameters of Cph1 with temperature of the sample and intensity of the excitation light and dependence of the emission spectra on excitation wavelength were observed. These variations are interpreted as a manifestation of the Cph1 heterogeneity which may be due to the existence of different conformers of the chromophore and photoproduct formation under excitation light.

Fluorescence and photochemical properties of phytochromes in wild‐type wheat and a transgenic line overexpressing an oat phytochrome A (PHYA) gene: functional implications

Etiolated seedlings of wild‐type wheat and a transgenic line overexpressing an oat PHYA gene were investigated by the use of in situ low‐temperature fluorescence spectroscopy. The red‐absorbing phytochrome form, Pr, was characterized by (1) fluorescence emission spectrum; (2) total phytochrome content, and (3) by the extent of the Pr → lumi‐R photoconversion at low temperature (γ1), and of the Pr → Pfr photoconversion at ambient temperature (γ2) as derived from emission data. All the characteristics were shown to be variable and to depend on (1) organ and tissue used; (2) seedling age; (3) transgenic wheat modification, and (4) continuous far‐red irradiation of seedlings during their growth. These variations were interpreted in terms of the existence in wheat seedlings of the two phenomenological Pr types: (a), Pr′– major longer wavelength (687/673 nm, emission/absorption maxima) variable and light‐labile with γ1 ≈ 0·5; and (b), Pr′′– minor, shorter wavelength (682/668 nm), relatively constant with its concentration not changing significantly with the increase of total phytochrome content in tissues and light‐stable with γ1 ≤ 0·05–0·1. Overexpression of oat phyA increases primarily the content of Pr′ suggesting that it is comprised of phyA (phyA′) whereas Pr′′ is believed to consist of the minor phyA fraction (phyA′′) and phyB. The transgenic wheat line has been demonstrated to have a modified phenotype – the appearance of the far‐red high irradiance reaction (FR‐HIR) (Shlumukov et al. Plant, Cell and Environment 24, 703–712). The increased content of phyA′ in the transgenic line, whereas the total [phyA′′ + phyB] remains the same as in the wild type, indicates that the phyA′ pool is primarily responsible for the observed modification of the phenotype and suggests that even in wild‐type plants the phyA′ component of the phyA pool may mediate the FR‐HIR.