On the signaling mechanism and the absence of photoreversibility in the AppA BLUF domain

The flavoprotein AppA from Rhodobacter sphaeroides contains an N-terminal, FAD-binding BLUF photoreceptor domain. Upon illumination, the AppA BLUF domain forms a signaling state that is characterized by red-shifted absorbance by 10 nm, a state known as AppA_RED. We have applied ultrafast spectroscopy on the photoaccumulated AppA_RED state to investigate the photoreversible properties of the AppA BLUF domain. On light absorption by AppA_RED, the FAD singlet excited state decays monoexponentially in 7 ps to form the neutral semiquinone radical FADH^•, which subsequently decays to the original AppA_RED molecular ground state in 60 ps. Thus, is deactivated rapidly via electron and proton transfer, probably from the conserved tyrosine Tyr-21 to FAD, followed by radical-pair recombination. We conclude that, in contrast to many other photoreceptors, the AppA BLUF domain is not photoreversible and does not enter alternative reaction pathways upon absorption of a second photon. To explain these properties, we propose that a molecular configuration is formed upon excitation of AppA_RED that corresponds to a forward reaction intermediate previously identified for the dark-state BLUF photoreaction. Upon excitation of AppA_RED, the BLUF domain therefore enters its forward reaction coordinate, readily re-forming the AppA_RED ground state and suppressing reverse or side reactions. The monoexponential decay of FAD* indicates that the FAD-binding pocket in AppA_RED is significantly more rigid than in dark-state AppA. Steady-state fluorescence experiments on wild-type, W104F, and W64F mutant BLUF domains show tryptophan fluorescence maxima that correspond with a buried conformation of Trp-104 in dark and light states. We conclude that Trp-104 does not become exposed to solvent during the BLUF photocycle.     

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. Light-induced structural changes for the signaling state formation were studied using the light-induced Fourier transform infrared (FTIR) difference spectroscopy of both the full-length YcgF protein (YcgF-Full) and its BLUF domain (YcgF-BLUF). YcgF-Full and YcgF-BLUF showed identical UV-visible absorption spectra of flavin in the dark state and a light-induced absorption red shift for the signaling state, which relaxed to the dark state showing identical kinetics. The light-induced FTIR difference spectrum of YcgF-Full, however, was markedly different from that of YcgF-BLUF. The spectrum of YcgF-BLUF lacked most of the IR bands that were induced in the YcgF-Full spectrum. These bands were assigned to the light-induced structural changes of the protein. However, the bands for the C4=O stretching of a FAD isoalloxazine ring were induced at the same frequency with the same band intensity in the spectra for YcgF-Full and YcgF-BLUF. Furthermore, the YcgF-Full spectrum resembled that of the YcgF-BLUF when illuminated at medium-low temperatures because of the selective suppression of protein bands. The possibility that full-length-specific protein bands are predominantly ascribed to structural changes of the C-terminal EAL domain in the signaling state as a consequence of light excitation of the N-terminal BLUF domain is discussed.     

Photocycle features of heterologously expressed and assembled eukaryotic flavin-binding BLUF domains of photoactivated adenylyl cyclase (PAC), a blue-light receptor in Euglena gracilis.

Photoactivated adenylyl cyclase (PAC) is a recently discovered blue-light photoreceptor that mediates photomovement in Euglena gracilis(Iseki et al., Nature, 2002, 415, 1047--1051). PAC appears to be a heterotetramer composed of two FAD-binding subunits (PACalpha and PACbeta). Both subunits have a pair of homologous regions (F1 and F2) which show homology with prokaryotic "sensors of blue-light using FAD"(BLUF) domains. The F1 and F2 domains of PAC are the only eukaryotic BLUF domains found thus far. We obtained soluble recombinant F1 and F2 proteins in PACalpha by heterologous expression with fused glutathione-S-transferase (GST) in E. coli. The expressed F1 samples did not bind flavins, but the F2 samples contained both FAD and FMN with trace amounts of riboflavin. We also assembled the histidine-tagged recombinant F2 (6His-F2) from inclusion bodies in E. coli with exogenous FAD or FMN. Blue-light-induced changes in absorption spectra of these assembled samples were highly similar to those reported for prokaryotic BLUF domains. The FAD- or FMN-assembled 6His-F2 photocycled with nearly the same rate constants of light-reaction and dark-relaxation, which were slightly lower than those of GST-cleaved F2. The estimated quantum efficiency for the phototransformation was 0.28--0.32, and the half-life was 34--44 s at 25 degrees C for the recombinant PACalpha F2, whereas that reported for prokaryotic BLUF domains varied from ca. 3.5 s (Tll0078) to ca. 900 s (AppA). The mutated recombinant Y472F and Q514G of PACalpha F2 and the F2 domain of the PACalpha homologue from Eutreptiella gymnastica, which lacks the Gln residue conserved in other BLUF domains, showed no photoinduced transformation.     

Adenosine diphosphate moiety does not participate in structural changes for the signaling state in the sensor of blue-light using FAD domain of AppA

A sensor of blue light using FAD (BLUF) protein is a flavin adenine dinucleotide (FAD) based new class blue-light sensory flavoprotein. The BLUF domain of AppA was reconstituted in vitro from apoprotein and flavin adenine dinucleotide, flavin adenine mononucleotide or riboflavin. The light-induced FTIR spectra of the domain reconstituted from various flavins and the 13C-labeled apoprotein showed that identical light-induced structural changes occur in both the flavin chromophore and protein for the signaling state in all of the reconstituted holoproteins. The results showed that an adenosine 5'-dinucleotide moiety is not required for signaling-state formation in a BLUF domain.     

Structure of a cyanobacterial BLUF protein, Tll0078, containing a novel FAD-binding blue light sensor domain

The sensor proteins for blue light using the FAD (BLUF) domain belong to the third family of the photoreceptor proteins using a flavin chromophore, where the other two families are phototropins and cryptochromes. As the first structure of this BLUF domain, we have determined the crystal structure of the Tll0078 protein from Thermosynechococcus elongatus BP-1, which contains a BLUF domain bound to FAD, at 2A resolution. Five Tll0078 monomers are located around the non-crystallographic 5-fold axis to form a pentamer, and two pentamers related by 2-fold non-crystallographic symmetry form a decameric assembly. The monomer consists of two domains, the BLUF domain at the N-terminal region and the C-terminal domain. The overall structure of the BLUF domain consists of a five-stranded mixed beta-sheet with two alpha-helices running parallel with it. The isoalloxazine ring of FAD is accommodated in a pocket formed by several highly conserved amino acid residues in the BLUF domain. Of these, the three apparent key residues (Asn31, Asn32 and Gln50) were substituted with Ala. Mutant proteins of N31A and N32A showed a nearly normal 10nm spectral shift of the flavin upon illumination, while the Q50A mutant did not exhibit such a shift at all. On the basis of the crystal structure, we discussed a possible role of Gln50, which is structurally and functionally linked with the critical Tyr8 (FAD-Gln50-Tyr8 network), with regard to the light-induced spectral shift of the BLUF proteins.     

On the role of aromatic side chains in the photoactivation of BLUF domains

BLUF (blue-light sensing using FAD) domain proteins are a novel group of blue-light sensing receptors found in many microorganisms. The role of the aromatic side chains Y21 and W104, which are in close vicinity to the FAD cofactor in the AppA BLUF domain from Rhodobacter sphaeroides, is investigated through the introduction of several amino acid substitutions at these positions. NMR spectroscopy indicated that in the W104F mutant, the local structure of the FAD binding pocket was not significantly perturbed as compared to that of the wild type. Time-resolved fluorescence and absorption spectroscopy was applied to explore the role of Y21 and W104 in AppA BLUF photochemistry. In the Y21 mutants, FADH*-W* radical pairs are transiently formed on a ps time scale and recombine to the ground state on a ns time scale. The W104F mutant shows a spectral evolution similar to that of wild type AppA but with an increased yield of signaling state formation. In the Y21F/W104F double mutant, all light-driven electron-transfer processes are abolished, and the FAD singlet excited-state evolves by intersystem crossing to the triplet state. Our results indicate that two competing light-driven electron-transfer pathways are available in BLUF domains: one productive pathway that involves electron transfer from the tyrosine, which leads to signaling state formation, and one nonproductive electron-transfer pathway from the tryptophan, which leads to deactivation and the effective lowering of the quantum yield of the signaling state formation. Our results are consistent with a photoactivation mechanism for BLUF domains where signaling state formation proceeds via light-driven electron and proton transfer from the conserved tyrosine to FAD, followed by a hydrogen-bond rearrangement and radical-pair recombination.     

Structural Refinement of a Key Tryptophan Residue in the BLUF Photoreceptor AppA by Ultraviolet Resonance Raman Spectroscopy

The flavin-adenine-dinucleotide-binding BLUF domain constitutes a new class of blue-light receptors, and the N-terminal domain of AppA is a representative of this family. The BLUF domain is of special interest because it uses a rigid flavin rather than an isomerizable chromophore, such as a rhodopsin or phytochrome, for its light-activation process. Crystal and solution structures of several BLUF domains were recently obtained, and their overall structures are consistent. However, there is a key ambiguity regarding the position of a conserved tryptophan (Trp-104 in AppA), in that this residue was found either close to flavin (Trp_in conformation) or exposed to the solvent (Trp_out conformation). The location of Trp-104 is a crucial factor in understanding the photocycle mechanism of BLUF domains, because this residue has been shown to play an essential role in the activation of AppA. In this study, we demonstrated a Trp_in conformation for the BLUF domain of AppA through direct observation of the vibrational spectrum of Trp-104 by ultraviolet resonance Raman spectroscopy, and also observed light-induced conformational and environmental changes in Trp-104. This study provides a structural basis for future investigations of the photocycle mechanism of BLUF proteins.     

Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1

The first biochemical and structural characterization of the full-length active photoreceptor BlrP1 from Klebsiella pneumoniae was recently reported by Barends et al. [Nature 459:1015–1018, (2009)]. The light-regulated catalytic function of its C-terminal c-di-guanosine monophosphate phosphodiesterase, the EAL (Glu-Ala-Leu) domain, is activated by the N-terminal sensor of blue light using the flavin adenine dinucleotide (BLUF) domain. We performed molecular dynamics simulations on the dimeric BlrP1 protein in order to examine the coupling regions that are presumably involved in transmitting light-induced structural changes which occur in the BLUF domain to the EAL domain. According to the results of simulations and an analysis of the hydrogen bonding between the respective polypeptide chains, the region containing the site on the α3α4 loop of BLUF is responsible for communication between the photosensing and catalytic domains in the dimeric BlrP1 protein.     

Biochemical and functional characterization of BLUF-type flavin-binding proteins of two species of cyanobacteria

BLUF (a sensor of Blue-Light Using FAD) is a novel putative photoreceptor domain that is found in many bacteria and some eukaryotic algae. As found on genome analysis, certain cyanobacteria have BLUF proteins with a short C-terminal extension. As typical examples, Tll0078 from thermophilic Thermosynechococcus elongatus BP-1 and Slr1694 from mesophilic Synechocystis sp. PCC 6803 were comparatively studied. FAD of both proteins was hardly reduced by exogenous reductants or mediators except methylviologen but showed a typical spectral shift to a longer wavelength upon excitation with blue light. In particular, freshly prepared Tll0078 protein showed slow but reversible aggregation, indicative of light-induced conformational changes in the protein structure. Tll0078 is far more stable as to heat treatment than Slr1694, as judged from flavin fluorescence. The slr1694-disruptant showed phototactic motility away from the light source (negative phototaxis), while the wild type Synechocystis showed positive phototaxis toward the source. Yeast two-hybrid screening with slr1694 showed self-interaction of Slr1694 (PixD) with itself and interaction with a novel PatA-like response regulator, Slr1693 (PixE). These results were discussed in relation to the signaling mechanism of the "short" BLUF proteins in the regulation of cyanobacterial phototaxis.     

Biochemical and physiological characterization of a BLUF protein-EAL protein complex involved in blue light-dependent degradation of cyclic diguanylate in the purple bacterium Rhodopseudomonas palustris

Organisms adapt their physiologies in response to the quality and quantity of environmental light. Members of a recently identified photoreceptor protein family, BLUF domain proteins, use a flavin chromophore to sense blue light. Herein, we report that PapB, which contains a BLUF domain, controls the biofilm formation of the purple photosynthetic bacterium Rhodopseudomonas palustris. Purified PapB undergoes a typical BLUF-type photocycle, and light-excited PapB enhances the phosphodiesterase activity of the EAL domain protein, PapA, which degrades the second messenger, cyclic dimeric GMP (c-di-GMP). PapB directly interacts with PapA in vitro in a light-independent manner and induces a conformational change in the preformed PapA-PapB complex. A PapA-PapB docking simulation, as well as a site-directed mutagenesis study, identified amino acids partially responsible for the interaction between the PapA EAL domain and the two C-terminal α-helices of the PapB BLUF domain. Thus, the conformational change, which involves the C-terminal α-helices, transfers the flavin-sensed blue light signal to PapA. Deletion of papB in R. palustris enhances biofilm formation under high-intensity blue light conditions, indicating that PapB functions as a blue light sensor, which negatively regulates biofilm formation. These results demonstrate that R. palustris can control biofilm formation via a blue light-dependent modulation of its c-di-GMP level by the BLUF domain protein, PapB.     

Structure of l-aspartate oxidase from the hyperthermophilic archaeon Sulfolobus tokodaii

The crystal structure of the highly thermostable l-aspartate oxidase (LAO) from the hyperthermophilic archaeon Sulfolobus tokodaii was determined at a 2.09 A resolution. The factors contributing to the thermostability of the enzyme were analyzed by comparing its structure to that of Escherichia coli LAO. Like E. coli LAO, the S. tokodaii enzyme consists of three domains: an FAD-binding domain, an alpha+beta capping domain, and a C-terminal three-helix bundle. However, the situation of the linker between the FAD-binding domain and C-terminal three-helix bundle in S. tokodaii LAO is completely different from that in E. coli LAO, where the linker is situated near the FAD-binding domain and has virtually no interaction with the rest of the protein. In S. tokodaii LAO, this linker is situated near the C-terminal three-helix bundle and contains a beta-strand that runs parallel to the C-terminal strand. This results in the formation of an additional beta-sheet, which appears to reduce the flexibility of the C-terminal region. Furthermore, the displacement of the linker enables formation of a 5-residue ion-pair network between the FAD-binding and C-terminal domains, which strengthens the interdomain interactions. These features might be the main factors contributing to the high thermostability of S. tokodaii LAO.     

A PixD--PapB Chimeric Protein Reveals the Function of the BLUF Domain C-Terminal α-Helices for Light Signal Transduction

Blue light-using flavin (BLUF) proteins form a subfamily of blue light photoreceptors, are found in many bacteria and algae, and are further classified according to their structures. For one type of BLUF-containing protein, e.g. PixD, the central axes of its two C-terminal α-helices are perpendicular to the β-sheet of its N-terminal BLUF domain. For another type, e.g. PapB, the central axes of its two C-terminal α-helices are parallel to its BLUF domain β-sheet. However, the functional significance of the different orientations with respect to phototransduction is not clear. For the study reported herein, we constructed a chimeric protein, Pix0522, containing the core of the PixD BLUF domain and the C-terminal region of PapB, including the two α-helices, and characterized its biochemical and spectroscopic properties. Fourier transform infrared spectroscopy detected similar light-induced conformational changes in the C-terminal α-helices of Pix0522 and PapB. Pix0522 interacts with and activates the PapB-interacting enzyme, PapA, demonstrating the functionality of Pix0522. These results provide direct evidence that the BLUF C-terminal α-helices function as an intermediary that accepts the flavin-sensed blue light signal and transmits it downstream during phototransduction.     

Crucial role in light signal transduction for the conserved Met93 of the BLUF protein PixD/Slr1694

PixD/Slr1694 from the cyanobacterium Synechocystis sp. PCC6803 is a member of a new class of flavin-containing blue-light sensory proteins containing a BLUF (blue light using flavin) domain. The photocycle reaction mechanism of BLUF is unique because only small structural changes of a bound chromophore are accompanied by a few hydrogen bond rearrangements in the chromophore-binding site. Here, we show that in PixD, Met93, the residue conserved in all BLUF domains, is crucial for light-dependent signal transduction. Specifically, the light-insensitive M93A mutant of PixD revealed biochemical and physiological activities compatible with those of the light-adapted wild-type PixD. However, the W91A mutant of PixD retained light sensitivity and biological function, although the corresponding mutant of another BLUF protein, AppA, has been reported to be locked in the light signaling state. These observations suggest that the pathway through which the light signal is transformed into apoprotein structural changes has been modified in BLUF proteins for their respective functions.     

Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family.

BACKGROUND: Given the vital role of NAD+ in cell metabolism, the enzymes involved in bacterial de novo NAD+ biosynthesis are possible targets for drug design against pathogenic bacteria. The first reaction in the pathway is catalysed by L-aspartate oxidase (LASPO), a flavoenzyme that converts aspartate to iminoaspartate using either molecular oxygen or fumarate as electron acceptors. LASPO has considerable sequence homology with the flavoprotein subunits of succinate dehydrogenase (SDH) and fumarate reductase (FRD). RESULTS: The crystal structure of the apoform of LASPO from Escherichia coli has been determined to 2.2 A resolution. The enzyme shows a novel fold for an FAD-dependent protein, comprising a three-domain structure: an FAD-binding domain with the dinucleotide-binding fold, a C-terminal three-helical bundle domain, and an alpha + beta capping domain, which is topologically similar to the small subunit of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. The interface between the FAD-binding and capping domains defines a cleft in which the active site is located. CONCLUSIONS: A number of strictly conserved residues present in all three domains indicate that LASPO, SDH and FRD share the same overall folding topology. Many of these conserved residues are in the FAD-binding site and active centre, suggesting a similar catalytic mechanism. Thus, LASPO, SDH and FRD form a class of functionally and structurally related oxidoreductases that are all able to reduce fumarate and to oxidise a dicarboxylate substrate.     

The critical role of a hydrogen bond between Gln63 and Trp104 in the blue-light sensing BLUF domain that controls AppA activity

AppA is a novel blue-light receptor that controls photosynthetic gene expression in the purple bacterium Rhodobacter sphaeroides. The photocycle reaction of the light-sensing domain, BLUF, is unique in the sense that a few hydrogen bond rearrangements are accompanied by only slight structural changes of the bound chromophore. However, the exact features of the hydrogen bond network around the active site are still the subject of some controversy. Here we present biochemical and genetic evidence showing that either Gln63 or Trp104 in the active site of the BLUF domain is crucial for light sensing, which in turn controls the antirepressor activity of AppA. Specifically, the Q63L and W104A mutants of AppA are insensitive to blue light in vivo and in vitro, and their activity is similar to that of the light-adapted wild-type AppA. Based on spectroscopic and structural information described previously, we conclude that light-dependent formation and breakage of the hydrogen bond between Gln63 and Trp104 are critical for the light-sensing mechanism of AppA.