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1.
Biochemistry ; 59(22): 2047-2054, 2020 06 09.
Article in English | MEDLINE | ID: mdl-32420731

ABSTRACT

Phytochromes regulate central responses of plants and microorganisms such as shade avoidance and photosystem synthesis. Canonical phytochromes comprise a photosensory module of three domains. The C-terminal phytochrome-specific (PHY) domain interacts via a tongue element with the bilin chromophore in the central GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA) domain. The bilin isomerizes upon illumination with red light, transforming the receptor from the Pr state to the Pfr state. The "knotless" phytochrome All2699 from the cyanobacterium Nostoc sp. PCC7120 comprises three GAF domains as a sensory module and a histidine kinase as an effector. GAF1 and GAF3 both bind a bilin, and GAF2 contains a tongue-like element. We studied the response of All2699, GAF1-GAF2, and GAF1 to red light by Fourier transform infrared difference spectroscopy, including a 13C-labeled protein moiety for assignment. In GAF1-GAF2, a refolding of the tongue from ß-sheet to α-helix and an upshift of the ring D carbonyl stretch from 1700 to 1712 cm-1 were observed. Therefore, GAF1-GAF2 is regarded as the smallest model system available to study the tongue response and interaction with the chromophore. Replacement of an arginine in the tongue with proline (R387P) did not affect the unfolding of the ß-sheet to Pfr but strongly impaired α-helix formation. In contrast, the Y55H mutation close to bilin ring D did not interfere with conversion to Pfr. Strikingly, the presence of GAF3 in the full-length All2699 diminished the response of the tongue and generated the signal pattern found for GAF1 alone. These results point to a regulatory or integrative role of GAF3 in All2699 that is absent in canonical phytochromes.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Nostoc/chemistry , Phytochrome/chemistry , Phytochrome/metabolism , Protein Refolding , Bacterial Proteins/isolation & purification , Models, Molecular , Nostoc/metabolism , Phytochrome/isolation & purification
2.
ACS Appl Mater Interfaces ; 12(18): 20922-20932, 2020 May 06.
Article in English | MEDLINE | ID: mdl-32297732

ABSTRACT

Nontargeted analysis of food safety requires selective removal of interference matrices and highly efficient recovery of chemical hazards. Porous materials such as covalent organic frameworks (COFs) show great promise in selective adsorption of matrix molecules via size selectivity. Considering the complexity of interference matrices, we prepared crystalline heteropore COFs whose two kinds of pores have comparable sizes to those of several common phytochromes, main interference matrices in vegetable sample analysis. By controlling the growth of COFs on the surface of Fe3O4 nanoparticles or by utilizing a facile co-electrospinning method, heteropore COF-based magnetic nanospheres or electrospun nanofiber films were prepared, respectively. Both the nanospheres and the films maintain the dual-pore structures of COFs and show good stability and excellent reusability. Via simple magnetic separation or immersion operation, respectively, they were successfully used for the complete removal of phytochromes and highly efficient recovery of 15 pesticides from the extracts of four vegetable samples, and the recoveries are in the range of 83.10-114.00 and 60.52-107.35%, respectively. Film-based immersion operation gives better sample pretreatment performance than the film-based filtration one. This work highlights the great application potentials of heteropore COFs in sample pretreatment for nontargeted analysis, thus opening up a new way to achieve high-performance sample preparation in many fields such as food safety analysis, environment monitoring, and so on.


Subject(s)
Magnetite Nanoparticles/chemistry , Metal-Organic Frameworks/chemistry , Nanospheres/chemistry , Pesticide Residues/isolation & purification , Phytochrome/isolation & purification , Adsorption , Brassica napus/chemistry , Capsicum/chemistry , Food Contamination/analysis , Kelp/chemistry , Magnetic Phenomena , Nanofibers/chemistry , Pesticide Residues/chemistry , Phytochrome/chemistry , Solid Phase Extraction/methods , Spinacia oleracea/chemistry , Vegetables/chemistry
3.
Methods Mol Biol ; 2026: 95-111, 2019.
Article in English | MEDLINE | ID: mdl-31317405

ABSTRACT

Expression and purification of recombinant proteins are important for the structure-function study of phytochromes. However, it is difficult to purify phytochrome proteins from natural sources or using a bacterial expression system, due to the presence of multiple phytochrome species and low expression and solubility, respectively. Here we describe the expression of recombinant full-length plant phytochromes in the yeast Pichia pastoris, and the spectral analysis of chromophore-assembled phytochromes before and after the purification by streptavidin affinity chromatography.


Subject(s)
Phytochrome/chemistry , Phytochrome/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Chromatography, Affinity , Phytochrome/isolation & purification , Pichia/metabolism , Recombinant Proteins/isolation & purification , Saccharomyces cerevisiae/metabolism
4.
Photochem Photobiol ; 93(3): 642-655, 2017 05.
Article in English | MEDLINE | ID: mdl-28500698

ABSTRACT

Agrobacterium fabrum is a widely used model bacterium for gene transfer from pro- to eukaryote, for genetics and metabolism. The phytochrome system of Agrobacterium, encompassing the two phytochromes Agp1 and Agp2, has provided deep insight into phytochrome action in a bacterial organism. This review summarizes recent results on phytochrome evolution, phytochrome regulation of conjugation and plant infection and biochemical studies including the crystal structure of Agp1-PCM, the photosensory core module of Agp1.


Subject(s)
Agrobacterium/metabolism , Bacterial Proteins/metabolism , Phytochrome/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Biological Evolution , Crystallography, X-Ray , Light , Phytochrome/chemistry , Phytochrome/genetics , Phytochrome/isolation & purification , Protein Conformation
5.
Photochem Photobiol Sci ; 11(6): 1026-31, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22415794

ABSTRACT

The plant pathogen Pseudomonas syringae pv. tomato carries two genes encoding bacterial phytochromes. Sequence motifs identify both proteins (PstBphP1 and PstBphP2, respectively) as biliverdin IXα (BV)-binding phytochromes. PstbphP1 is arranged in an operon with a heme oxygenase (PstBphO)-encoding gene (PstbphO), whereas PstbphP2 is flanked downstream by a gene encoding a CheY-type response regulator. Expression of the heme oxygenase PstBphO yielded a green protein (λ(max) = 650 nm), indicative for bound BV. Heterologous expression of PstbphP1 and PstbphP2 and in vitro assembly with BV IXα yielded the apoproteins for both phytochromes, but only in the case of PstBphP1 a light-inducible chromoprotein. Attempts to express the endogenous heme oxygenase BphO and either of the two phytochromes from two plasmids yielded only holo-PstBphP1. Relatively small amounts of soluble holo-PstBphP2 were just obtained upon co-expression with BphO from P. aeruginosa. Expression of the operon containing PstbphO:PstbphP1 led to an improved yield and better photoreactivity for PstBphP1, whereas an identical construct, exchanging PstbphP1 for PstbphP2 (PstbphO:PstbphP2), again yielded only minute amounts of chromophore-loaded BphP2-holoprotein. The improved yield for PstBphP1 from the PstbphO:PstbphP1 operon expression is apparently caused by complex formation between both proteins during biosynthesis as affinity chromatography of either protein using two different tags always co-purified the reaction partner. These results support the importance of protein-protein interactions during tetrapyrrole metabolism and phytochrome assembly.


Subject(s)
Bacterial Proteins/biosynthesis , Heme Oxygenase (Decyclizing)/biosynthesis , Phytochrome/biosynthesis , Pseudomonas syringae/enzymology , Solanum lycopersicum/microbiology , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Chromatography, Affinity , Heme Oxygenase (Decyclizing)/genetics , Heme Oxygenase (Decyclizing)/isolation & purification , Light , Phytochrome/genetics , Phytochrome/isolation & purification , Protein Interaction Domains and Motifs , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Tetrapyrroles/chemistry , Tetrapyrroles/metabolism
6.
J Mol Biol ; 413(1): 115-27, 2011 Oct 14.
Article in English | MEDLINE | ID: mdl-21888915

ABSTRACT

Phytochromes are biliprotein photoreceptors that can be photoswitched between red-light-absorbing state (Pr) and far-red-light-absorbing state (Pfr). Although three-dimensional structures of both states have been reported, the photoconversion and intramolecular signaling mechanisms are still unclear. Here, we report UV-Vis absorbance, fluorescence and CD spectroscopy along with various photochemical parameters of the wild type and Y263F, Y263H and Y263S mutants of the Cph1 photosensory module, as well as a 2.0-Å-resolution crystal structure of the Y263F mutant in its Pr ground state. Although Y263 is conserved, we show that the aromatic character but not the hydroxyl group of Y263 is important for Pfr formation. The crystal structure of the Y263F mutant (Protein Data Bank ID: 3ZQ5) reaffirms the ZZZssa chromophore configuration and provides a detailed picture of its binding pocket, particularly conformational heterogeneity around the chromophore. Comparison with other phytochrome structures reveals differences in the relative position of the PHY (phytochrome specific) domain and the interaction of the tongue with the extreme N-terminus. Our data support the notion that native phytochromes in their Pr state are structurally heterogeneous.


Subject(s)
Amino Acid Substitution/genetics , Bacterial Proteins/chemistry , Phytochrome/chemistry , Protein Kinases/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Binding Sites , Crystallography, X-Ray , Cyanobacteria/chemistry , Models, Molecular , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/isolation & purification , Photoreceptors, Microbial , Phytochrome/genetics , Phytochrome/isolation & purification , Protein Conformation , Protein Kinases/genetics , Protein Kinases/isolation & purification , Spectrum Analysis
7.
Protein J ; 30(2): 124-31, 2011 Feb.
Article in English | MEDLINE | ID: mdl-21318274

ABSTRACT

Phytochrome-like proteins have been recently identified in prokaryotes but their features and functions are not clear. We cloned a gene encoding the phytochrome-like protein (XoBphP) in a pathogenic bacteria, Xanthomonas oryzae pv. oryzae (Xoo) and investigated characteristics of the protein using a recombinant XoBphP. The N-terminal region of XoBphP containing the PAS/GAF/PHY domains is highly similar to most bacteriophytochromes, but Cys4, corresponding to Cys24 of DrBphP, isn't involved in chromophore attachment. Recombinant XoBphP could bind a bilin molecule and a differential spectrum from Pr/Pfr shows that XoBphP has similar characteristics of known bacteriophytochromes with shifted absorption maxima of 683 and 757 nm for the Pr and Pfr forms. Unlike other bacteriophytochromes, XoBphP has no histidine kinase domain at C-terminus. The domain was predicted from amino-acid 279 to 342 with less significance than the required threshold. This result suggests that XoBphP probably has different signal transduction mechanisms for its intracellular function.


Subject(s)
Phytochrome/chemistry , Recombinant Proteins/chemistry , Xanthomonas/metabolism , Amino Acid Sequence , Cloning, Molecular , Histidine Kinase , Molecular Sequence Data , Photoreceptors, Plant/chemistry , Phylogeny , Phytochrome/genetics , Phytochrome/isolation & purification , Protein Binding , Protein Kinases/chemistry , Protein Structure, Tertiary , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Xanthomonas/genetics
8.
J Mol Biol ; 380(5): 844-55, 2008 Jul 25.
Article in English | MEDLINE | ID: mdl-18571200

ABSTRACT

We report the discovery of a novel cyanobacteriochrome, the green/red photoreceptor AnPixJ (All1069), isolated from the heterocyst-forming cyanobacterium Anabaena (Nostoc) sp. PCC 7120. Cyanobacteriochromes are a recently emerging tetrapyrrole-based photoreceptor superfamily that are distantly related to the conventional red/far-red photoreceptor phytochromes (Phys). The chromophore-binding domains of AnPixJ produced in cyanobacterial and Escherichia coli cells both showed a reversible and full photoconversion between a green-absorbing form (lambda(max)=543 nm) and a red-absorbing form (lambda(max)=648 nm). Denaturation analysis revealed that the green-absorbing form and the red-absorbing form covalently ligated phycocyanobilin with E-configuration and Z-configuration at the C15C16 double bond, respectively. Time-resolved spectral analysis showed the formation of the first intermediate state peaking at 680 nm from the dark-stable red-absorbing form. This step resembles the first photoconversion step from the red-absorbing form to the red-shifted lumi-R intermediate state of the Phys. These results suggest that the Pr of AnPixJ is almost equivalent to that of the Phys and starts a primary photoreaction with Z-to-E isomerization in a mechanism similar to that in the Phys, but is finally photoconverted to the unique green-absorbing form.


Subject(s)
Anabaena/chemistry , Photoreceptor Cells/metabolism , Photosynthetic Reaction Center Complex Proteins/metabolism , Phytochrome/chemistry , Phytochrome/metabolism , Alanine/metabolism , Amino Acid Sequence , Amino Acid Substitution , Escherichia coli/genetics , Histidine/metabolism , Hydrogen-Ion Concentration , Light , Molecular Sequence Data , Molecular Structure , Photoreceptor Cells/chemistry , Photoreceptor Cells/radiation effects , Photosynthetic Reaction Center Complex Proteins/genetics , Photosynthetic Reaction Center Complex Proteins/radiation effects , Phycobilins/metabolism , Phycocyanin/metabolism , Phytochrome/genetics , Phytochrome/isolation & purification , Protein Denaturation , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Spectrophotometry, Ultraviolet , Urea/pharmacology
9.
EMBO J ; 26(14): 3322-31, 2007 Jul 25.
Article in English | MEDLINE | ID: mdl-17581629

ABSTRACT

Bacteriophytochromes are red/far-red photoreceptors that bacteria use to mediate sensory responses to their light environment. Here, we show that the photosynthetic bacterium Rhodopseudomonas palustris has two distinct types of bacteriophytochrome-related protein (RpBphP4) depending upon the strain considered. The first type binds the chromophore biliverdin and acts as a light-sensitive kinase, thus behaving as a bona fide bacteriophytochrome. However, in most strains, RpBphP4 does not to bind this chromophore. This loss of light sensing is replaced by a redox-sensing ability coupled to kinase activity. Phylogenetic analysis is consistent with an evolutionary scenario, where a bacteriophytochrome ancestor has adapted from light to redox sensing. Both types of RpBphP4 regulate the synthesis of light harvesting (LH2) complexes according to the light or redox conditions, respectively. They modulate the affinity of a transcription factor binding to the promoter regions of LH2 complex genes by controlling its phosphorylation status. This is the first complete description of a bacteriophytochrome signal transduction pathway involving a two-component system.


Subject(s)
Bacterial Proteins/metabolism , Evolution, Molecular , Light , Rhodopseudomonas/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Light-Harvesting Protein Complexes/biosynthesis , Light-Harvesting Protein Complexes/drug effects , Light-Harvesting Protein Complexes/radiation effects , Models, Biological , Molecular Sequence Data , Oxidation-Reduction/radiation effects , Oxygen/pharmacology , Photosynthesis/drug effects , Photosynthesis/radiation effects , Phylogeny , Phytochrome/chemistry , Phytochrome/genetics , Phytochrome/isolation & purification , Phytochrome/metabolism , Promoter Regions, Genetic/genetics , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Rhodopseudomonas/drug effects , Rhodopseudomonas/genetics , Rhodopseudomonas/radiation effects , Signal Transduction/drug effects , Transcription Factors/metabolism
10.
Int J Biol Macromol ; 39(1-3): 100-3, 2006 Aug 15.
Article in English | MEDLINE | ID: mdl-16616774

ABSTRACT

The plant photoreceptor phytochrome senses light quality and quantity in the red region of the spectrum, directing adaptation and development. The functional holo-protein is a dimeric chromoprotein which is formed by an autoassembly reaction between the translation product and the open chain tetrapyrroles phytochromobilin (PPhiB) or phycocyanobilin (PCB). We are interested in structure/function relationships within the phytochrome molecule, in particular chromophore/protein interaction during the assembly and photoactivation, using IR and NMR spectroscopy. For this we use an automated F/HPLC system running in a darkroom to purify large amounts of protein and chromophore separately. To obtain highly pure PCB chromophore we developed improved extraction and purification methods in which the final step is RPC-18 HPLC. As there are many spectrally only slightly different tetrapyrroles in the extract, the triple-wavelength monitoring offered by the F/HPLC detector was inadequate for distinguishing between PCB and impurities. Furthermore, lambda(max) for the phytochrome Pfr signalling state lies between 705 and 730 nm, beyond the range of the detector. Also, as both holo-protein and chromophore are photoactive, we wished to minimize light exposure of the eluate. We therefore implemented a miniature CCD-based flow UV-vis spectrophotometer using a xenon flash and quartz fiber optics enabling us monitor the entire 250-800 nm spectrum of the eluate to an accuracy of +/-3 x 10(-3)A in real time. The instrumentation described can be added to any chromatographic system, thereby allowing the purification of any molecule to be monitored easily and efficiently.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Phytochrome/chemistry , Phytochrome/isolation & purification , Protein Kinases/chemistry , Protein Kinases/isolation & purification , Bacterial Proteins/genetics , Chromatography, High Pressure Liquid/instrumentation , Chromatography, High Pressure Liquid/methods , Cyanobacteria/chemistry , Cyanobacteria/genetics , Escherichia coli/chemistry , Escherichia coli/genetics , Photoreceptors, Microbial , Phytochrome/genetics , Protein Kinases/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Spectrometry, Fluorescence/instrumentation , Spectrometry, Fluorescence/methods
11.
Eukaryot Cell ; 4(12): 2140-52, 2005 Dec.
Article in English | MEDLINE | ID: mdl-16339731

ABSTRACT

Phytochromes (Phys) comprise a superfamily of red-/far-red-light-sensing proteins. Whereas higher-plant Phys that control numerous growth and developmental processes have been well described, the biochemical characteristics and functions of the microbial forms are largely unknown. Here, we describe analyses of the expression, regulation, and activities of two Phys in the filamentous fungus Neurospora crassa. In addition to containing the signature N-terminal domain predicted to covalently associate with a bilin chromophore, PHY-1 and PHY-2 contain C-terminal histidine kinase and response regulator motifs, implying that they function as hybrid two-component sensor kinases activated by light. A bacterially expressed N-terminal fragment of PHY-2 covalently bound either biliverdin or phycocyanobilin in vitro, with the resulting holoprotein displaying red-/far-red-light photochromic absorption spectra and a photocycle in vitro. cDNA analysis of phy-1 and phy-2 revealed two splice isoforms for each gene. The levels of the phy transcripts are not regulated by light, but the abundance of the phy-1 mRNAs is under the control of the circadian clock. Phosphorylated and unphosphorylated forms of PHY-1 were detected; both species were found exclusively in the cytoplasm, with their relative abundances unaffected by light. Strains containing deletions of phy-1 and phy-2, either singly or in tandem, were not compromised in any known photoresponses in Neurospora, leaving their function(s) unclear.


Subject(s)
Neurospora crassa/chemistry , Neurospora crassa/metabolism , Phytochrome/chemistry , Phytochrome/genetics , Phytochrome/metabolism , Alternative Splicing , Amino Acid Motifs , Amino Acid Sequence , Base Sequence , Chromosome Mapping , Chromosomes, Fungal , Circadian Rhythm , Cytoplasm/metabolism , DNA, Complementary/analysis , DNA, Complementary/genetics , DNA, Fungal , Escherichia coli/genetics , Exons , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/isolation & purification , Fungal Proteins/metabolism , Gene Deletion , Gene Expression Regulation, Fungal , Genes, Fungal , Genetic Linkage , Genome, Fungal , Histidine Kinase , Introns , Kinetics , Light , Molecular Sequence Data , Neurospora crassa/genetics , Neurospora crassa/growth & development , Neurospora crassa/radiation effects , Open Reading Frames , Phosphorylation , Phytochrome/isolation & purification , Pigments, Biological/chemistry , Pigments, Biological/genetics , Pigments, Biological/isolation & purification , Pigments, Biological/metabolism , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protein Kinases/chemistry , Protein Kinases/genetics , Protein Kinases/isolation & purification , Protein Kinases/metabolism , Protein Structure, Tertiary , RNA, Messenger/metabolism , Sequence Homology, Amino Acid
12.
Biochemistry ; 44(23): 8461-9, 2005 Jun 14.
Article in English | MEDLINE | ID: mdl-15938635

ABSTRACT

Photoconversion of phytochrome from the red-absorbing form Pr to the far-red-absorbing form Pfr is initiated by a Z to E isomerization around the ring C-ring D connecting double bond; the chromophore undergoes a ZZZ to ZZE isomerization. In vivo, phytochrome chromophores are covalently bound to the protein, but several examples of noncovalent in vitro adducts have been reported which also undergo Pr to Pfr photoconversion. We show that free biliverdin or phycocyanobilin, highly enriched in the ZZE isomer, can easily be obtained from chromophores bound in a noncovalent manner to Agrobacterium phytochrome Agp1, and used for spectral assays. Photoconversion of free biliverdin in a methanol/HCl solution from ZZE to ZZZ proceeded with a quantum yield of 1.8%, but was negligible in neutral methanol solution, indicating that this process is proton-dependent. The ZZE form of biliverdin and phycocyanobilin were tested for their ability to assemble with Agp1 and cyanobacterial phytochrome Cph1, respectively. In both cases, a Pfr-like adduct was formed but the chromophore was bound in a noncovalent manner to the protein. Agp1 Pfr undergoes dark reversion to Pr; the same feature was found for the noncovalent ZZE adduct. After dark reversion, the chromophore became covalently bound to the protein. In analogy, the PCB chromophore became covalently bound to Cph1 upon irradiation with strong far-red light which initiated ZZE to ZZZ isomerization. Agrobacterium Agp2 belongs to a yet small group of phytochromes which also assemble in the Pr form but convert from Pr to Pfr in darkness. When the Agp2 apoprotein was assembled with the ZZE form of biliverdin, the formation of the final adduct was accelerated compared to the formation of the ZZZ control, indicating that the ZZE chromophore fits directly into the chromophore pocket of Agp2.


Subject(s)
Agrobacterium tumefaciens/enzymology , Bile Pigments/biosynthesis , Phytochrome/chemistry , Phytochrome/metabolism , Agrobacterium tumefaciens/genetics , Alanine/genetics , Amino Acid Substitution/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Biliverdine/chemistry , Biliverdine/isolation & purification , Biliverdine/metabolism , Chromatography, High Pressure Liquid , Cysteine/genetics , Isomerism , Light , Methanol/chemistry , Photochemistry , Photoreceptors, Microbial , Phycobilins , Phycocyanin/chemistry , Phycocyanin/metabolism , Phytochrome/genetics , Phytochrome/isolation & purification , Protein Kinases/chemistry , Protein Kinases/metabolism , Protein Processing, Post-Translational , Pyrroles/chemistry , Pyrroles/metabolism , Spectrophotometry, Ultraviolet , Tetrapyrroles
14.
Plant Cell Physiol ; 45(12): 1729-37, 2004 Dec.
Article in English | MEDLINE | ID: mdl-15653792

ABSTRACT

The gene, pixJ1 (formerly pisJ1), is predicted to encode a phytochrome-like photoreceptor that is essential for positive phototaxis in the unicellular cyanobacterium Synechocystis sp. PCC 6803 [Yoshihara et al. (2000) Plant Cell Physiol. 41: 1299]. The PixJ1 protein was overexpressed as a fusion with a poly-histidine tag (His-PixJ1) and isolated from Synechocystis cells. A zinc-fluorescence assay suggested that a linear tetrapyrrole was covalently attached to the His-PixJ1 protein as a chromophore. His-PixJ1 showed novel photoreversible conversion between a blue light-absorbing form (Pb, lambdaAmax=425-435 nm) and a green light-absorbing form (Pg, lambdaAmax=535 nm). Dark incubation led Pg to revert to Pb, indicative of stability of the Pb form in darkness. Red or far-red light irradiation, which is effective for photochemical conversion of the known phytochromes, produced no change in the spectra of Pb and Pg forms. Site-directed mutagenesis revealed that a Cys-His motif in the second GAF domain of PixJ1 is responsible for binding of the chromophore. Possible chromophore species are discussed with regard to the novel photoconversion spectrum.


Subject(s)
Bacterial Proteins/metabolism , Photoreceptors, Microbial/metabolism , Photosynthetic Reaction Center Complex Proteins/metabolism , Phytochrome/metabolism , Synechocystis/metabolism , Amino Acid Motifs/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Binding Sites/genetics , Darkness , Genome, Bacterial , Light , Photoreceptors, Microbial/chemistry , Photoreceptors, Microbial/radiation effects , Photosynthetic Reaction Center Complex Proteins/genetics , Photosynthetic Reaction Center Complex Proteins/radiation effects , Phytochrome/chemistry , Phytochrome/isolation & purification , Protein Structure, Tertiary/genetics , Signal Transduction/physiology , Signal Transduction/radiation effects , Synechocystis/genetics , Tetrapyrroles/chemistry
15.
Eur J Biochem ; 268(17): 4720-30, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11532008

ABSTRACT

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.


Subject(s)
Bacterial Proteins , Cyanobacteria/enzymology , Phytochrome/chemistry , Protein Kinases/chemistry , Chromatography, Gel , Cyanobacteria/metabolism , Electrophoresis, Polyacrylamide Gel , Molecular Sequence Data , Molecular Weight , Phosphorylation , Photoreceptors, Microbial , Phytochrome/isolation & purification , Phytochrome/metabolism , Protein Kinases/isolation & purification , Protein Kinases/metabolism , Protein Structure, Quaternary
16.
Eur J Biochem ; 268(7): 2055-63, 2001 Apr.
Article in English | MEDLINE | ID: mdl-11277928

ABSTRACT

The cph1 gene from the unicellular cyanobacterium Synechoycstis sp. PCC 6803 encodes a protein with the characteristics of plant phytochromes and histidine kinases of two-component phospho-relay systems. Spectral and biochemical properties of Cph1 have been intensely studied in vitro using protein from recombinant systems, but virtually nothing is known about the situation in the natural host. In the present study, His6-tagged Cph1 was isolated from Synechocystis cells. The cph1-his gene was expressed either under the control of the natural cph1 promoter or over-expressed using the strong promoter of the psbA2 gene. Upon purification with nickel affinity chromatography, the presence of Cph1 in extracts was confirmed by immunoblotting and Zn2+-induced fluorescence. The Cph1 extracts exhibited a red/far-red photoactivity characteristic of phytochromes. Difference spectra were identical with those of the phycocyanobilin adduct of recombinant Cph1, implying that phycocyanobilin is the chromophore of Cph1 in Synechocystis.


Subject(s)
Bacterial Proteins , Cyanobacteria/enzymology , Phytochrome/isolation & purification , Protein Kinases/isolation & purification , Blotting, Northern , Chromatography, Affinity , Cyanobacteria/genetics , Electrophoresis, Polyacrylamide Gel , Fluorescence , Histidine/genetics , Histidine/metabolism , Nickel , Photoreceptors, Microbial , Phycobilins , Phycocyanin/chemistry , Phytochrome/chemistry , Phytochrome/genetics , Promoter Regions, Genetic , Protein Kinases/chemistry , Protein Kinases/genetics , Pyrroles/chemistry , Recombinant Proteins/chemistry , Spectrophotometry, Atomic , Tetrapyrroles , Transcription, Genetic , Zinc/metabolism
17.
Plant Cell ; 13(3): 521-34, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11251094

ABSTRACT

To elucidate phytochrome A (phyA) function in rice, we screened a large population of retrotransposon (Tos17) insertional mutants by polymerase chain reaction and isolated three independent phyA mutant lines. Sequencing of the Tos17 insertion sites confirmed that the Tos17s interrupted exons of PHYA genes in these mutant lines. Moreover, the phyA polypeptides were not immunochemically detectable in these phyA mutants. The seedlings of phyA mutants grown in continuous far-red light showed essentially the same phenotype as dark-grown seedlings, indicating the insensitivity of phyA mutants to far-red light. The etiolated seedlings of phyA mutants also were insensitive to a pulse of far-red light or very low fluence red light. In contrast, phyA mutants were morphologically indistinguishable from wild type under continuous red light. Therefore, rice phyA controls photomorphogenesis in two distinct modes of photoperception--far-red light-dependent high irradiance response and very low fluence response--and such function seems to be unique and restricted to the deetiolation process. Interestingly, continuous far-red light induced the expression of CAB and RBCS genes in rice phyA seedlings, suggesting the existence of a photoreceptor(s) other than phyA that can perceive continuous far-red light in the etiolated seedlings.


Subject(s)
Genes, Plant , Oryza/growth & development , Oryza/genetics , Phytochrome/physiology , Blotting, Southern , Carrier Proteins , Darkness , Gene Expression/radiation effects , Gene Expression Regulation, Plant , Genes, Reporter , Gravitropism/genetics , Gravitropism/physiology , Light , Mutation , Oryza/radiation effects , Peptide Termination Factors , Phenotype , Photosynthetic Reaction Center Complex Proteins/biosynthesis , Phytochrome/genetics , Phytochrome/isolation & purification , Phytochrome/radiation effects , Phytochrome A , Plant Roots/growth & development , Retroelements , Signal Transduction
18.
Biochemistry ; 39(35): 10840-7, 2000 Sep 05.
Article in English | MEDLINE | ID: mdl-10978170

ABSTRACT

It now appears that photosynthetic prokaryotes and lower eukaryotes possess higher plant phytochrome-like proteins. In this work, a second phytochrome-like gene was isolated, in addition to the recently identified Cph1 phytochrome, from the Synechocystis sp. PCC 6803, and its gene product was characterized photochemically. The open reading frame sll0821 (designated cph2 in this work) has structural characteristics similar to those of the plant phytochromes and the Synechocystis Cph1 with high amino acid sequence homology in the N-terminal chromophore binding domain. The predicted Cph2 protein consists of 1276 amino acids with a calculated molecular mass of 145 kDa. Interestingly, the Cph2 protein has two putative chromophore binding domains, one around Cys-129 and the other around Cys-1022. The Cph2 was overexpressed in E. coli as an Intein/CBD (chitin binding domain) fusion and in vitro reconstituted with phycocyanobilin (PCB) or phytochromobilin (PPhiB). Both the Cph2-PCB and Cph2-PPhiB adducts showed the typical photochromic reversibility with the difference spectral maxima at 643/690 and 655/701 nm, respectively. The Cys-129 was confirmed to be the chromophore binding residue by in vitro mutagenesis and Zn(2+) fluorescence. The microenvironment of the chromophore in Cph2 seems to be similar to that in plant phytochromes. The cph2 gene expression was dark-induced and down-regulated to a basal level by light, like the cph1 gene. These observations suggest that Synechocystis species have multiple photosensory proteins, probably with distinct roles, as in higher plants.


Subject(s)
Bacterial Proteins/chemistry , Cyanobacteria/chemistry , Down-Regulation/radiation effects , Light , Phytochrome/chemistry , Amino Acid Sequence , Bacterial Chromatophores/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Bacterial Proteins/radiation effects , Cyanobacteria/genetics , Cyanobacteria/radiation effects , Escherichia coli/genetics , Gene Expression Regulation, Bacterial/radiation effects , Histidine Kinase , Molecular Sequence Data , Photochemistry , Phytochrome/genetics , Phytochrome/isolation & purification , Phytochrome/radiation effects , Protein Binding , Protein Kinases/chemistry , Spectrometry, Fluorescence
19.
Biochemistry ; 39(21): 6349-56, 2000 May 30.
Article in English | MEDLINE | ID: mdl-10828948

ABSTRACT

The secondary, tertiary, and quaternary structures of the Synechocystis Cph1 phytochrome were investigated by absorption and circular dichroism spectroscopy, size exclusion chromatography, and limited proteolysis. The Cph1 protein was coexpressed with a bacterial thioredoxin in Escherichia coli, reconstituted in vitro with tetrapyrrole chromophores, and purified by chitin affinity chromatography. The resultant Cph1 holoproteins were essentially pure and had the specific absorbance ratio (SAR) of 0.8-0.9. Circular dichroism spectroscopy and limited proteolysis showed that the chromophore binding induced marked conformational changes in the Cph1 protein. The alpha-helical content increased to 42-44% in the holoproteins from 37% in the apoprotein. However, no significant difference in the secondary structure was detected between the Pr and Pfr forms. The tertiary structure of the Cph1 apoprotein appeared to be relatively flexible but became more compact and resistant to tryptic digestion upon chromophore binding. Interestingly, a small chromopeptide of about 30 kDa was still predominant even after longer tryptic digestion. The N-terminal location of this chromopeptide was confirmed by expression in E. coli and in vitro reconstitution with chromophores of the 32.5 kDa N-terminal fragment of the Cph1 protein. This chromopeptide was fully photoreversible with the spectral characteristic similar to that of the full-size Cph1 protein. The Cph1 protein forms dimers through the C-terminal region. These results suggest that the prokaryotic Cph1 phytochrome shares the structural and conformational characteristics of plant phytochromes, such as the two-domain structure consisting of the relatively compact N-terminal and the relatively flexible C-terminal regions, in addition to the chromophore-induced conformational changes.


Subject(s)
Cyanobacteria/metabolism , Phytochrome/chemistry , Protein Conformation , Apoproteins/chemistry , Apoproteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Biliverdine/analogs & derivatives , Biliverdine/metabolism , Chromatography, Affinity , Circular Dichroism , Dimerization , Escherichia coli/metabolism , Molecular Weight , Phycobilins , Phycoerythrin/metabolism , Phytochrome/isolation & purification , Phytochrome/metabolism , Protein Structure, Quaternary , Protein Structure, Tertiary , Pyrroles/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism , Spectrophotometry , Tetrapyrroles , Thioredoxins/chemistry , Thioredoxins/metabolism
20.
Plant J ; 18(5): 499-507, 1999 Jun.
Article in English | MEDLINE | ID: mdl-10417700

ABSTRACT

Phytochrome A (phyA) and phytochrome B (phyB) share the control of many processes but little is known about mutual signaling regulation. Here, we report on the interactions between phyA and phyB in the control of the activity of an Lhcb1*2 gene fused to a reporter, hypocotyl growth and cotyledon unfolding in etiolated Arabidopsis thaliana. The very-low fluence responses (VLFR) induced by pulsed far-red light and the high-irradiance responses (HIR) observed under continuous far-red light were absent in the phyA and phyA phyB mutants, normal in the phyB mutant, and reduced in the fhy1 mutant that is defective in phyA signaling. VLFR were also impaired in Columbia compared to Landsberg erecta. The low-fluence responses (LFR) induced by red-light pulses and reversed by subsequent far-red light pulses were small in the wild type, absent in phyB and phyA phyB mutants but strong in the phyA and fhy1 mutants. This indicates a negative effect of phyA and FHY1 on phyB-mediated responses. However, a pre-treatment with continuous far-red light enhanced the LFR induced by a subsequent red-light pulse. This enhancement was absent in phyA, phyB, or phyA phyB and partial in fhy1. The levels of phyB were not affected by the phyA or fhy1 mutations or by far-red light pre-treatments. We conclude that phyA acting in the VLFR mode (i.e. under light pulses) is antagonistic to phyB signaling whereas phyA acting in the HIR mode (i.e. under continuous far-red light) operates synergistically with phyB signaling, and that both types of interaction require FHY1.


Subject(s)
Arabidopsis/physiology , Light-Harvesting Protein Complexes , Photoreceptor Cells , Photosystem II Protein Complex , Phytochrome/metabolism , Transcription Factors , Arabidopsis/radiation effects , Arabidopsis Proteins , Dose-Response Relationship, Radiation , Genes, Reporter , Light , Mutation , Photosynthetic Reaction Center Complex Proteins/biosynthesis , Phytochrome/isolation & purification , Phytochrome A , Phytochrome B , Plants, Genetically Modified , Signal Transduction , Species Specificity
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