Vibrational assignment of the flavin-cysteinyl adduct in a signaling state of the LOV domain in FKF1

Red Shift in the Absorption Spectrum of Phototropin LOV1 upon the Formation of a Semiquinone Radical: Reconstructing the Orbital Architecture

Flavin mononucleotide (FMN) is a ubiquitous blue-light pigment due to its ability to drive one- and two-electron transfer reactions. In both light-oxygen-voltage (LOV) domains of phototropin from the green algae Chlamydomonas reinhardtii, FMN is noncovalently bound. In the LOV1 cysteine-to-serine mutant (C57S), light-induced electron transfer from a nearby tryptophan occurs, and a transient spin-correlated radical pair (SCRP) is formed. Within this photocycle, nuclear hyperpolarization is created by the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect. In a side reaction, a stable protonated semiquinone radical (FMNH·) forms undergoing a significant bathochromic shift of the first electronic transition from 445 to 591 nm. The incorporation of phototropin LOV1-C57S into an amorphous trehalose matrix, stabilizing the radical, allows for application of various magnetic resonance experiments at ambient temperatures, which are combined with quantum-chemical calculations. As a result, the bathochromic shift of the first absorption band is explained by lifting the degeneracy of the molecular orbital energy levels for electrons with alpha and beta spins in FMNH· due to the additional electron.

Quantitative insights in tissue growth and morphogenesis with optogenetics

Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.

QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors

Photosensory receptors containing the flavin-binding light-oxygen-voltage (LOV) domain are modular proteins that fulfil a variety of biological functions ranging from gene expression to phototropism. The LOV photocycle is initiated by blue-light and involves a cascade of intermediate species, including an electronically excited triplet state, that leads to covalent bond formation between the flavin mononucleotide (FMN) chromophore and a nearby cysteine residue. Subsequent conformational changes in the polypeptide chain arise due to the remodelling of the hydrogen bond network in the cofactor binding pocket, whereby a conserved glutamine residue plays a key role in coupling FMN photochemistry with LOV photobiology. Although the dark-to-light transition of LOV photosensors has been previously addressed by spectroscopy and computational approaches, the mechanistic basis of the underlying reactions is still not well understood. Here we present a detailed computational study of three distinct LOV domains: EL222 from Erythrobacter litoralis, AsLOV2 from the second LOV domain of Avena sativa phototropin 1, and RsLOV from Rhodobacter sphaeroides LOV protein. Extended protein-chromophore models containing all known crucial residues involved in the initial steps (femtosecond-to-microsecond) of the photocycle were employed. Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path. In turn, for each evolving species, infrared difference spectra were constructed and compared to experimental EL222 and AsLOV2 transient infrared spectra, the former from original work presented here and the latter from the literature. The good agreement between theory and experiment permitted the assignment of the majority of observed bands, notably the ∼1635 cm-1 transient of the adduct state to the carbonyl of the glutamine side chain after rotation. Moreover, both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration. Additionally, the computed infrared shifts of the glutamine and interacting residues could guide experimental research addressing early events of signal transduction in LOV proteins.

Temporal induction of Lhx8 by optogenetic control system for efficient bone regeneration

BACKGROUND

The spatiotemporal regulation of essential genes is crucial for controlling the growth and differentiation of cells in a precise manner during regeneration. Recently, optogenetics was considered as a potent technology for sophisticated regulation of target genes, which might be a promising tool for regenerative medicine. In this study, we used an optogenetic control system to precisely regulate the expression of Lhx8 to promote efficient bone regeneration.

METHODS

Quantitative real-time PCR and western blotting were used to detect the expression of Lhx8 and osteogenic marker genes. Alkaline phosphatase staining and alizarin red staining were used to detect alkaline phosphatase activity and calcium nodules. A customized optogenetic expression system was constructed to regulate Lhx8, of which the expression was activated in blue light but not in dark. We also used a critical calvarial defect model for the analysis of bone regeneration in vivo. Moreover, micro-computed tomography (micro-CT), three-dimensional reconstruction, quantitative bone measurement, and histological and immunohistochemistry analysis were performed to investigate the formation of new bone in vivo.

RESULTS

During the osteogenic differentiation of BMSCs, the expression levels of Lhx8 increased initially but then decreased thereafter. Lhx8 promoted the early proliferation of BMSCs but inhibited subsequent osteogenic differentiation. The optogenetic activation of Lhx8 in BMSCs in the early stages of differentiation by blue light stimulation led to a significant increase in cell proliferation, thus allowing a sufficient number of differentiating BMSCs to enter the later osteogenic differentiation stage. Analysis of the critical calvarial defect model revealed that the pulsed optogenetic activation of Lhx8 in transplanted BMSCs over a 5-day period led to a significant increase in the generation of bone in vivo.

CONCLUSIONS

Lhx8 plays a critical role in balancing proliferation and osteogenic differentiation in BMSCs. The optogenetic activation of Lhx8 expression at early stage of BMSCs differentiation led to better osteogenesis, which would be a promising strategy for precise bone regeneration.

Optogenetic control of mesenchymal cell fate towards precise bone regeneration

Rationale: Spatial-temporal control of cell fate in vivo is of great importance for regenerative medicine. Currently, there remain no practical strategies to tune cell-fate spatial-temporally. Optogenetics is a biological technique that widely used to control cell activity in genetically defined neurons in a spatiotemporal-specific manner by light. In this study, optogenetics was repurposed for precise bone tissue regeneration.

Methods: Lhx8 and BMP2 genes, which are considered as the master genes for mesenchymal stem cell proliferation and differentiation respectively, were recombined into a customized optogenetic control system. In the system, Lhx8 was constitutively expressed, while BMP2 together with shLhx8 expression was driven by blue light.

Results: As expected, blue light induced BMP2 expression and inactivated Lhx8 expression in cells infected with the optogenetic control system. Optogenetic control of BMP2 and Lhx8 expression inversely regulates MSC fate in vitro. By animal study, we found that blue light could fine-tune the regeneration in vivo. Blue light illumination significantly promotes bone regeneration when the scaffold was loaded with MSCs infected with adeno-Lhx8, GI-Gal4DBD, LOV-VP16, and BMP2-shLhx8.

Conclusions: Together, our study revealed that optogenetic control of the master genes for mesenchymal stem cell proliferation and differentiation would be such a candidate strategy for precise regenerative medicine.

Characterization of the Blue-Light-Activated Adenylyl Cyclase mPAC by Flash Photolysis and FTIR Spectroscopy

The recently discovered photo-activated adenylyl cyclase (mPAC from Microcoleus chthonoplastes) is the first PAC that owes a light-, oxygen- and voltage-sensitive (LOV) domain for blue-light sensing. The photoreaction of the mPAC receptor was studied by time-resolved UV/vis and light-induced Fourier transform infrared (FTIR) absorption difference spectroscopy. The photocycle comprises of the typical triplet state LOV₇₁₅ and the thio-adduct state LOV₃₉₀ . While the adduct state decays with a time constant of 8 s, the lifetime of the triplet state is with 656 ns significantly shorter than in all other reported LOV domains. The light-induced FTIR difference spectrum shows the typical bands of the LOV₃₉₀ and LOV₄₅₀ intermediates. The negative S-H stretching vibration at 2573 cm^-1 is asymmetric suggesting two rotamer configurations of the protonated side chain of C194. A positive band at 3632 cm^-1 is observed, which is assigned to an internal water molecule. In contrast to other LOV domains, mPAC exhibits a second positive feature at 3674 cm^-1 which is due to the O-H stretch of a second intrinsic water molecule and the side chain of Y476. We conclude that the latter might be involved in the dimerization of the cyclase domain which is crucial for ATP binding.

Modulation of the flavin-protein interactions in NADH peroxidase and mercuric ion reductase: a resonance Raman study

NADH peroxidase (Npx) and mercuric ion reductase (MerA) are flavoproteins belonging to the pyridine nucleotide:disulfide oxidoreductases (PNDO) and catalyzing the reduction of toxic substrates, i.e., hydrogen peroxide and mercuric ion, respectively. To determine the role of the flavin adenine dinucleotide (FAD) in the detoxification mechanism, the resonance Raman (RR) spectra of these enzymes under various redox and ligation states have been investigated using blue and/or near-UV excitation(s). These data were compared to those previously obtained for glutathione reductase (GR), another enzyme of the PNDO family, but catalyzing the reduction of oxidized glutathione. Spectral differences have been detected for the marker bands of the isoalloxazine ring of Npx, MerA, and GR. They provide evidence for different catalytic mechanisms in these flavoproteins. The RR modes of the oxidized and two-electron reduced (EH₂) forms of Npx are related to very tight flavin-protein interactions maintaining a nearly planar conformation of the isoalloxazine tricycle, a low level of H-bonding at the N₁/N₅ and O₂/O₄ sites, and a strong H-bond at N₃H. They also indicate minimal changes in FAD structure and environment upon either NAD(H) binding or reduction of the sulfinic redox center. All these spectroscopic data support an enzyme functioning centered on the Cys-SO^-/Cys-S^- redox moiety and a neighbouring His residue. On the contrary, the RR data on various functional forms of MerA are indicative of a modulation of both ring II distortion and H-bonding states of the N₅ site and ring III. The Cd(II) binding to the EH₂-NADP(H) complexes, biomimetic intermediates in the reaction of Hg(II) reduction, provokes important spectral changes. They are interpreted in terms of flattening of the isoalloxazine ring and large decreases in H-bonding at the N₅ site and ring III. The large flexibility of the FAD structure and environment in MerA is in agreement with proposed mechanisms involving C_4a(flavin) adducts.

Hydrogen Bonding Environment of the N3-H Group of Flavin Mononucleotide in the Light Oxygen Voltage Domains of Phototropins

The light oxygen voltage (LOV) domain is a flavin-binding blue-light receptor domain, originally found in a plant photoreceptor phototropin (phot). Recently, LOV domains have been used in optogenetics as the photosensory domain of fusion proteins. Therefore, it is important to understand how LOV domains exhibit light-induced structural changes for the kinase domain regulation, which enables the design of LOV-containing optogenetics tools with higher photoactivation efficiency. In this study, the hydrogen bonding environment of the N3-H group of flavin mononucleotide (FMN) of the LOV2 domain from Adiantum neochrome (neo) 1 was investigated by low-temperature Fourier transform infrared spectroscopy. Using specifically ¹⁵N-labeled FMN, [1,3-¹⁵N₂]FMN, the N3-H stretch was identified at 2831 cm^-1 for the unphotolyzed state at 150 K, indicating that the N3-H group forms a fairly strong hydrogen bond. The N3-H stretch showed temperature dependence, with a shift to lower frequencies at ≤200 K and to higher frequencies at ≥250 K from the unphotolyzed to the intermediate states. Similar trends were observed in the LOV2 domains from Arabidopsis phot1 and phot2. By contrast, the N3-H stretch of the Q1029L mutant of neo1-LOV2 and neo1-LOV1 was not temperature dependent in the intermediate state. These results seemed correlated with our previous finding that the LOV2 domains show the structural changes in the β-sheet region and/or the adjacent Jα helix of LOV2 domain, but that such structural changes do not take place in the Q1029L mutant or neo1-LOV1 domain. The environment around the N3-H group was also investigated.

The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy

The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.

A search for radical intermediates in the photocycle of LOV domains

LOV domains are the light sensitive parts of phototropins and many other light-activated enzymes that regulate the response to blue light in plants and algae as well as some fungi and bacteria. Unlike all other biological photoreceptors known so far, the photocycle of LOV domains involves the excited triplet state of the chromophore. This chromophore is flavin mononucleotide (FMN) which forms a covalent adduct with a cysteine residue in the signaling state. Since the formation of this adduct from the triplet state involves breaking and forming of two bonds as well as a change from the triplet to the singlet spin state, various intermediates have been proposed, e.g. a protonated triplet state (3)FMNH(+), the radical anion (2)FMN˙(-), or the neutral semiquinone radical (2)FMNH˙. We performed an extensive search for these intermediates by two-dimensional transient absorption (2D-TA) with a streak camera. However, no transient with a rate constant between the decay of fluorescence and the decay of the triplet state could be detected. Analysis of the decay associated difference spectra results in quantum yields for the formation of the adduct from the triplet of ΦA(LOV1) ≈ 0.75 and ΦA(LOV2) ≈ 0.80. This is lower than the values ΦA(LOV1) ≈ 0.95 and ΦA(LOV2) ≈ 0.99 calculated from the rate constants, giving indirect evidence of an intermediate that reacts either to form the adduct or to decay back to the ground state. Since there is no measurable delay between the decay of the triplet and the formation of the adduct, we conclude that this intermediate reacts much faster than it is formed. The LOV1-C57S mutant shows a weak and slowly decaying (τ > 100 μs) transient whose decay associated spectrum has bands at 375 and 500 nm, with a shoulder at 400 nm. This transient is insensitive to the pH change in the range 6.5-10.0 but increases on addition of β-mercaptoethanol as the reducing agent. We assign this intermediate to the radical anion which is protected from protonation by the protein. We propose that the adduct is formed via the same intermediate by combination of the radical ion pair.

Resonance Raman spectroscopy

Flavin is a general name given to molecules having the heteroaromatic ring system of 7,8-dimethylisoalloxazine but practically means riboflavin (Rfl), flavin adenine dinucleotide (FAD), and flavin mononucleotide (FMN) in biological systems, whose structures are illustrated in Fig. 1, together with the atomic numbering scheme and ring numbering of the isoalloxazine moiety. As the isoalloxazine skeleton cannot be synthesized in human cells, it is obtained from diet as Rfl (vitamin B2). FAD and FMN can act as cofactors in flavoenzymes but Rfl does not. Most flavoenzymes catalyze redox reactions of substrates (Miura, Chem Rec 1:183-194, 2001). When O2 serves as the oxidant in the oxidation half cycle of an enzymic reaction, the enzyme is called "flavo-oxidase" but when others do, the enzyme is called "flavo-dehydrogenase." The difference between the two types of oxidative catalysis arises from delicate differences in the π-electron distributions in the isoalloxazine ring, which can be revealed by Raman spectroscopy (Miura, Chem Rec 1:183-194, 2001). Since a flavin is an extremely versatile molecule, the scientific field including chemistry, biochemistry, and enzymology is collectively called "flavonology." It was found recently, however, that the flavin also acts as a chromophore to initiate light-induced DNA repair and signal transductions (Sancar, Chem Rev 103:2203-2237, 2003).

N-terminal truncation does not affect the location of a conserved tryptophan in the BLUF domain of AppA from Rhodobacter sphaeroides

The flavin-binding BLUF domains are a class of blue-light receptors, and AppA is a representative of this family. Although the crystal and solution structures of several BLUF domains have already been obtained, there is a key uncertainty regarding the position of a functionally important tryptophan (Trp104 in AppA). In the first crystal structure of an N-terminally truncated BLUF domain of AppA133 (residues 17-133), Trp104 was found in close proximity to flavin (Trp(in)), whereas in a subsequent structure with an intact N-terminus AppA126 (residues 1-126), Trp104 was exposed to the solvent (Trp(out)). A recent study compared spectroscopic properties of AppA126 and AppA133 and claimed that the Trp(in) conformation is an artifact of N-terminal truncation in AppA133. In this study, we compared the flavin vibrational spectra of AppA126 and AppA133 by using near-infrared excited Raman spectroscopy. In addition, the conformations as well as the environments of Trp104 were directly monitored by ultraviolet resonance Raman spectroscopy. These studies demonstrate that the N-terminal truncation does not induce the conformational switch between Trp(in) and Trp(out).

LOV domain-containing F-box proteins: light-dependent protein degradation modules in Arabidopsis

Plants constantly survey the surrounding environment using several sets of photoreceptors. They can sense changes in the quantity (=intensity) and quality (=wavelength) of light and use this information to adjust their physiological responses, growth, and developmental patterns. In addition to the classical photoreceptors, such as phytochromes, cryptochromes, and phototropins, ZEITLUPE (ZTL), FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), and LOV KELCH PROTEIN 2 (LKP2) proteins have been recently identified as blue-light photoreceptors that are important for regulation of the circadian clock and photoperiodic flowering. The ZTL/FKF1/LKP2 protein family possesses a unique combination of domains: a blue-light-absorbing LOV (Light, Oxygen, or Voltage) domain along with domains involved in protein degradation. Here, we summarize recent advances in our understanding of the function of the Arabidopsis ZTL/FKF1/LKP2 proteins. We summarize the distinct photochemical properties of their LOV domains and discuss the molecular mechanisms by which the ZTL/FKF1/LKP2 proteins regulate the circadian clock and photoperiodic flowering by controlling blue-light-dependent protein degradation.

Modulation of the photocycle of a LOV domain photoreceptor by the hydrogen-bonding network

An extended hydrogen-bonding (HB) network stabilizes the isoalloxazine ring of the flavin mononucleotide (FMN) chromophore within the photosensing LOV domain of blue-light protein receptors, via interactions between the C(2)═O, N(3)H, C(4)═O, and N(5) groups and conserved glutamine and asparagine residues. In this work we studied the influence of the HB network on the efficiency, kinetics, and energetics of a LOV protein photocycle, involving the reversible formation of a FMN-cysteine covalent adduct. The following results were found for mutations of the conserved amino acids N94, N104, and Q123 in the Bacillus subtilis LOV protein YtvA: (i) Increased (N104D, N94D) or strongly reduced (N94A) rate of adduct formation; this latter mutation extends the lifetime of the flavin triplet state, i.e., adduct formation, more than 60-fold, from 2 μs for the wild-type (WT) protein to 129 μs. (ii) Acceleration of the overall photocycle for N94S, N94A, and Q123N, with recovery lifetimes 20, 45, and 85 times faster than for YtvA-WT, respectively. (iii) Slight modifications of FMN spectral features, correlated with the polarization of low-energy transitions. (iv) Strongly reduced (N94S) or suppressed (Q123N) structural volume changes accompanying adduct formation, as determined by optoacoustic spectroscopy. (v) Minor effects on the quantum yield, with the exception of a considerable reduction for Q123N, i.e., 0.22 vs 0.49 for YtvA-WT. The data stress the importance of the HB network in modulating the photocycle of LOV domains, while at the same time establishing a link with functional responses.

(TD-)DFT calculation of vibrational and vibronic spectra of riboflavin in solution

The photophysics and photochemistry of flavin molecules are of great interest due to their role for the biological function of flavoproteins. An important analysis tool toward the understanding of the initial photoexcitation step of flavins is electronic and vibrational spectroscopy, both in frequency and time domains. Here we present quantum chemical [(time-dependent) density functional theory ((TD-)DFT)] calculations for vibrational spectra of riboflavin, the parent molecule of biological blue-light receptor chromophores, in its electronic ground (S(0)) and lowest singlet excited states (S(1)). Further, vibronic absorption spectra for the S(0) --> S(1) transition and vibronic emission spectra for the reverse process are calculated, both including mode mixing. Solvent effects are partially accounted for by using a polarizable continuum model (PCM) or a conductor-like screening model (COSMO). Calculated vibrational and electronic spectra are in good agreement with measured ones and help to assign the experimental signals arising from photoexcitation of flavins. In particular, upon photoexcitation a loss of double bond character in the polar region of the ring system is observed which leads to vibronic fine structure in the electronic spectra. Besides vibronic effects, solvent effects are important for understanding the photophysics of flavins in solution quantitatively.