Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF).

Blue-light sensing proteins that use FAD (BLUF) are members of a blue-light receptor family that is widely distributed among microorganisms. The Escherichia coli YcgF protein is a BLUF protein consisting of the N-terminal FAD-binding hold (BLUF domain) and the C-terminal EAL domain. The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.

Inelastic photoemission due to scattering by surface adsorbate vibrations.

By measuring the very low energy photoemission spectra of the CO/Cu(001) surface with a high resolution, we have found the energy loss components due to inelastic scattering of electrons near the Fermi level by the CO vibrational modes. The main energy loss structure appears as a step at 254 meV below the Fermi edge for 12C16O. An isotope shift of the step to 240 meV was observed when 13C18O was adsorbed.

FTIR detection of structural changes in a histidine ligand during S-state cycling of photosynthetic oxygen-evolving complex.

Changes in structural coupling between the Mn cluster and a putative histidine ligand during the S-state cycling of the oxygen-evolving complex (OEC) have been detected directly by Fourier transform infrared (FTIR) spectroscopy in photosystem (PS) II core particles from the cyanobacterium Synechocystis sp. PCC6803, in which histidine residues were selectively labeled with l-[(15)N(3)]histidine. The bands sensitive to the histidine-specific isotope labeling appeared at 1120-1090 cm(-)(1) in the spectra induced upon the first-, second-, and fourth-flash illumination, for the S(2)/S(1), S(3)/S(2), and S(1)/S(0) differences, at similar frequencies with different sign and/or intensity depending on the respective S-state transitions.

Changes in structural and functional properties of oxygen-evolving complex induced by replacement of D1-glutamate 189 with glutamine in photosystem II: ligation of glutamate 189 carboxylate to the manganese cluster.

A carboxylate group of D1-Glu-189 in photosystem II has been proposed to serve as a direct ligand for the manganese cluster. Here we constructed a mutant that eliminates the carboxylate by replacing D1-Glu-189 with Gln in the cyanobacterium Synechocystis sp. PCC 6803, and we examined the resulting effects on the structural and functional properties of the oxygen-evolving complex (OEC) in photosystem II.

Studies on photosynthetic oxygen-evolving complex by means of Fourier transform infrared spectroscopy: calcium and chloride cofactors.

Structural roles of functional Ca2+ and Cl- ions in photosynthetic oxygen-evolving complexes (OEC) were studied using low- (640-350 cm-1) and mid- (1800-1200 cm-1) frequency S2/S1 Fourier transform infrared (FTIR) difference spectroscopy. Studies using highly active Photosystem (PS) II core particles from spinach enabled the detection of subtle spectral changes. Ca2+-depleted and Ca2+-reconstituted particles produced very similar mid- and low-frequency spectra.

Adenylyl cyclase activity of Cya1 from the cyanobacterium Synechocystis sp. strain PCC 6803 is inhibited by bicarbonate.

Bicarbonate stimulates the activities of several class III adenylyl cyclases studied to date. However, we show here that bicarbonate decreased V(max) and substrate affinity in Cya1, a major adenylyl cyclase in the cyanobacterium Synechocystis sp. strain PCC 6803.

Density functional theory calculations on the dielectric constant dependence of the oxidation potential of chlorophyll: implication for the high potential of P680 in photosystem II.

The primary donor chlorophyll (Chl) of photosystem II (PSII), P680, has an extremely high oxidation redox potential (E(ox)) of approximately 1.2 V, which is essential for photosynthetic water oxidation. The mechanism for achieving a high potential such as that of P680 has been one of the central questions in photosynthesis research.

Water-sensitive low-frequency vibrations of reaction intermediates during S-state cycling in photosynthetic water oxidation.

In photosynthetic water oxidation, two water molecules are converted to an oxygen molecule through five reaction intermediates, designated S(n) (n = 0-4), at the catalytic Mn cluster of photosystem II. To understand the mechanism of water oxidation, changes in the chemical nature of the substrate water as well as the Mn cluster need to be defined during S-state cycling. Here, we report for the first time a complete set of Fourier transform infrared difference spectra during S-state cycling in the low-frequency (670-350 cm(-1)) region, in which interactions between the Mn cluster and its ligands can be detected directly, in PS II core particles from Thermosynechococcus elongatus.

Light-induced structural changes of apoprotein and chromophore in the sensor of blue light using FAD (BLUF) domain of AppA for a signaling state.

AppA is a new class blue-light receptor controlling photosynthesis gene expression in the purple bacterium Rhodobacter sphaeroides and retains a characteristic flavin adenine dinucleotide (FAD)-binding domain named the "sensor of blue light using FAD" (BLUF). AppA functions as an antirepressor controlling transcription of photosynthesis genes through the direct association with a transcriptional repressor PpsR in a blue-light-dependent manner [Masuda and Bauer (2002) Cell 110, 613-623]. Illumination of AppA induces a red shift in the UV-visible absorption of FAD, which results in a signaling state of AppA.

Spectroscopic analysis of the dark relaxation process of a photocycle in a sensor of blue light using FAD (BLUF) protein Slr1694 of the cyanobacterium Synechocystis sp. PCC6803.

Slr1694 is a BLUF (sensor of blue light using flavin adenine dinucleotide) protein and a putative photoreceptor in the cyanobacterium Synechocystis sp. PCC6803. Illumination of Slr1694 induced a signaling light state concurrent with a red shift in the UV-visible absorption of flavin, and formation of the bands from flavin and apo-protein in the light-minus-dark Fourier transform infrared (FTIR) difference spectrum.

Structural intermediate in the photocycle of a BLUF (sensor of blue light using FAD) protein Slr1694 in a Cyanobacterium Synechocystis sp. PCC6803.

Slr1694 in Synechocystis sp. PCC6803 is a family of blue-light photoreceptors based on flavin adenine dinucleotide (FAD) called BLUF (sensor of blue light using FAD) proteins, which include AppA from Rhodobacter sphaeroides and PAC from Euglena gracilis. Illumination of dark-state Slr1694 at 15 degrees C reversibly induced a signaling light state characterized by the red shift in the UV-visible spectrum and by the light-induced Fourier transform infrared (FTIR) difference spectrum for structural changes of a bound flavin and apo protein.

Changes in the functional and structural properties of the Mn cluster induced by replacing the side group of the C-terminus of the D1 protein of photosystem II.

A free alpha-COO(-) in the C-terminal alanine-344 (Ala344) in the D1 protein of photosystem II is thought to be responsible for ligating the Mn cluster. The effects of the side group of the C-terminus of the D1 protein on the functional and structural properties of the oxygen-evolving complex (OEC) were comprehensively studied by replacing Ala344 with glycine (Gly), valine (Val), aspartate (Asp), or asparagine (Asn). All the mutants grew photoautotrophically under low-light conditions with lower O(2) evolution activity depending on the mutants when compared with the activity of the control wild type.

Structural changes of D1 C-terminal alpha-carboxylate during S-state cycling in photosynthetic oxygen evolution.

Changes in the chemical structure of alpha-carboxylate of the D1 C-terminal Ala-344 during S-state cycling of photosynthetic oxygen-evolving complex were selectively measured using light-induced Fourier transform infrared (FTIR) difference spectroscopy in combination with specific [(13)C]alanine labeling and site-directed mutagenesis in photosystem II core particles from Synechocystis sp. PCC 6803. Several bands for carboxylate symmetric stretching modes in an S(2)/S(1) FTIR difference spectrum were affected by selective (13)C labeling of the alpha-carboxylate of Ala with l-[1-(13)C]alanine, whereas most of the isotopic effects failed to be induced in a site-directed mutant in which Ala-344 was replaced with Gly.

Biochemical characterization of the major adenylyl cyclase, Cya1, in the cyanobacterium Synechocystis sp. PCC 6803.

We report herein the biochemical properties of an adenylyl cyclase, Cya1, from the cyanobacterium Synechocystis sp. PCC 6803. Heterologously expressed Cya1 catalyzed cyclic AMP formation with a Km for ATP of approximately 2.

Energy loss of photoelectrons by interaction with image charge.

By measuring the photoelectron spectra of the Cu(001) and Cu(110) surfaces excited by tunable-laser photons of very low energy (4.50-4.95 eV), we have found that the photoelectron can lose energy through interaction with its image charge.

Impact of replacement of D1 C-terminal alanine with glycine on structure and function of photosynthetic oxygen-evolving complex.

The C-terminal alanine 344 (Ala-344) in the D1 protein of photosystem II is conserved in all of the organisms performing oxygenic photosynthesis. A free alpha-COO(-) of Ala-344 has been proposed to be responsible for ligating the Mn cluster. Here, we constructed a mutant having D1 in which D1-Ala-344 was replaced with glycine (Gly) in cyanobacterium Synechocystis sp.

Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of synechocystis sp. PCC6803.

The sensor of blue-light using FAD (BLUF) domain is the flavin-binding fold categorized to a new class of blue-light sensing domain found in AppA from Rhodobacter sphaeroides and PAC from Euglena gracilis, but little is known concerning the mechanism of blue-light perception. An open reading frame slr1694 in a cyanobacterium Synechocystis sp. PCC6803 encodes a protein possessing the BLUF domain.

Oxidation of the Mn cluster induces structural changes of NO3- functionally bound to the Cl- site in the oxygen-evolving complex of photosystem II.

Cl(-) is an indispensable cofactor for photosynthetic O(2) evolution and is functionally replaced by NO(3)(-). Structural changes of an isotopically labeled NO(3)(-) ion, induced by the oxidation of the Mn cluster (S(1)-to-S(2)), were detected by FTIR spectroscopy. NO(3)(-)-substituted photosystem II core particles showed (14)N(16)O(3)(-)/(15)N(16)O(3)(-) and (14)N(16)O(3)(-)/(14)N(18)O(3)(-) isotopic bands in the S(2)/S(1) spectra with markedly high signal/noise ratio.

Null mutation of HvrA compensates for loss of an essential relA/spoT-like gene in Rhodobacter capsulatus.

We report that a single relA/spoT-like gene exists on the Rhodobacter capsulatus chromosome, and its mutational loss is lethal. This gene could be mutated only under a mutational background of a null mutation in the nucleoid protein HvrA. This result suggests that there may be a direct link between HvrA-regulated promoters and the ppGpp-related stringent response.

Changes of low-frequency vibrational modes induced by universal 15N- and 13C-isotope labeling in S2/S1 FTIR difference spectrum of oxygen-evolving complex.

The effects of universal (15)N- and (13)C-isotope labeling on the low- (650-350 cm(-1)) and mid-frequency (1800-1200 cm(-1)) S(2)/S(1) Fourier transform infrared (FTIR) difference spectrum of the photosynthetic oxygen-evolving complex (OEC) were investigated in histidine-tagged photosystem (PS) II core particles from Synechocystis sp. PCC 6803. In the mid-frequency region, the amide II modes were predominantly affected by (15)N-labeling, whereas, in addition to the amide II, the amide I and carboxylate modes were markedly affected by (13)C-labeling.

Functional and structural study on chelator-induced suppression of S2/S1 FTIR spectrum in photosynthetic oxygen-evolving complex.

Chelating agents have been shown to induce characteristic changes in the light-minus-dark Fourier transform infrared (FTIR) difference spectrum for the S(2)/S(1) difference in the oxygen-evolving complex (OEC). Addition of various ethylenediamine-N,N,N',N'-tetraacetic acid (EDTA)-type chelators, such as EDTA, O,O'-bis(2-aminoethyl)ethyleneglycol-N,N,N',N'-tetraacetic acid (EGTA), trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid (CyDTA), or N-(2-hydroxyethyl)ethylenediamine-N,N',N'-triacetic acid (HEDTA), to Ca(2+)-depleted PS II membranes resulted in the suppression of typical S(2)/S(1) vibrational features, including the symmetric (1365(+)/1404(-) cm(-1)) and the asymmetric (1587(+)/1566(-) cm(-1)) carboxylate stretching vibrations, as well as the amide I and II modes of the backbone polypeptides. In contrast, the addition of ethylenediamine-N,N'-diacetic acid (EDDA) showed less inhibitory effects.

Nonlineal relationship between g=2 doublet and multiline signals in Ca(2+)-depleted Photosystem II.

Illuminating of the Ca(2+)-depleted PS II in the S(2) state for a short period induced the doublet signal at g=2 with concomitant diminution of the multiline signal, both in the presence and absence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). In the absence of DCMU, the doublet signal decayed (t(1/2) approximately 7 min) during subsequent dark incubation at 273 K and the multiline signal was regenerated to the original amplitude with the same kinetics of the doublet decay. In the presence of DCMU, the doublet signal decayed much faster (t(1/2) approximately 1 min) by charge recombination with Q(A)(-), while the time course of the multiline recovery was inherently identical with that observed in the absence of DCMU.

Chloride cofactor in the photosynthetic oxygen-evolving complex studied by fourier transform infrared spectroscopy.

Fourier transform infrared (FTIR) spectroscopy, using midfrequency S2/S1 FTIR difference spectra, has been applied to studies of chloride cofactor in the photosynthetic oxygen-evolving complex (OEC) to determine the effects of Cl(-) depletion and monovalent anion substitution. Cl(-) depletion resulted in the disappearance of a large part of the amide I and II vibrational modes, and induced characteristic modification in the features of the stretching modes of the carboxylate ligands of the Mn cluster. The normal spectral features were largely restored by replenishment of Cl(-) except for some changes in amide bands.

Characteristic changes of the S2/S1 difference FTIR spectrum induced by Ca2+ depletion and metal cation substitution in the photosynthetic oxygen-evolving complex.

Effects of Ca2+ depletion and substitution with other metal cations on the structure of the protein matrices of the oxygen-evolving complex (OEC) and their corresponding changes upon the S1 to S2 transition were examined using Fourier transform infrared (FTIR) spectroscopy. Ca2+ depletion and further supplementation with Li+, Na+, Mg2+, Ca2+, or Sr2+ did not significantly affect the typical vibrational features in the double difference S2/S1 spectrum, including the symmetric [1365(+)/1404(-) cm(-1)] and the asymmetric [1587(+)/1566(-) cm(-1)] stretching modes of the carboxylate ligand and the amide I and II modes of the backbone polypeptides. On the other hand, supplementation with K+, Rb+, Cs+, or Ba2+ significantly modified the S2/S1 spectrum, in which the carboxylate modes disappeared and the amide I and II modes were modified.

Chelator-induced disappearance of carboxylate stretching vibrational modes in S2/S1 FTIR spectrum in oxygen-evolving complex of photosystem II.

Fourier transform infrared (FTIR) spectroscopy has been applied toward studies of photosynthetic oxygen evolution, especially on the effects of Ca(2+) depletion and chelating agents using S(2)/S(1) FTIR difference spectrum in the mid-IR region. Ca(2+) depletion showed little influences on the symmetric (1365/1404 cm(-1)) and the asymmetric (1587/1562 cm(-1)) stretching bands of a carboxylate, which are typical of the S(2)/S(1) vibrational features induced by the oxidation of the Mn-cluster; however, minor changes were observed in the amide regions. Addition of a chelating agent (EDTA or EGTA) to the Ca(2+)-depleted membranes resulted in the disappearance of the carboxylate bands concurrent with large modifications of the amide bands with an apparent K(d) value of approximately 0.