Reaction dynamics of the UV-B photosensor UVR8

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length. This article is protected by copyright. All rights reserved.

A seed-specific transcription factor, HSFA9, anticipates UV-B light responses by mimicking the activation of the UV-B receptor in tobacco

Sunflower heat shock factor A9 (HSFA9, hereafter A9) is a transcription factor involved in seed desiccation tolerance and longevity. A9 also links the regulation of seed maturation with that of seedling photomorphogenesis through visible light receptors. Analyses in transgenic Nicotiana tabacum (tobacco) indicated that A9 also affects responses mediated by NtUVR8, the receptor of ultraviolet light B (UV-B). We compared the effects of A9 and UV-B illumination on the nuclear localization of GFP-NtUVR8 in Nicotiana benthamiana leaves. We also used co-immunoprecipitation and limited proteolysis for analyzing the interaction between A9 and NtUVR8. We found that A9, by binding to NtUVR8, induced structural changes that resulted in enhancing the nuclear localization of NtUVR8 by hindering its nuclear export. The localization of UVR8 is crucial for receptor activation and function in Arabidopsis, where UV-B-activated nuclear UVR8 binds the E3 ubiquitin ligase COP1, leading to enhanced UV-B responses and photoprotection. A9 similarly activated NtUVR8 by enhancing COP1 binding without UV-B light. Seedlings and dark-germinated seeds that overexpress A9 showed primed UV-B light stress protection. Our results unveil a UV-B-independent activation mechanism and a role for UVR8 in plant seeds that might contribute to early stress protection, facilitating seedling establishment.

Cysteines have a role in conformation of the UVR8 photoreceptor

The UV RESISTANCE LOCUS 8 (UVR8) photoreceptor mediates plant responses to Ultraviolet-B (UV-B) wavelengths. The UVR8 dimer dissociates into monomers following UV-B photoreception, a process accompanied by conformational changes that facilitate interaction of UVR8 with proteins that initiate responses. However, the importance of particular amino acids in maintaining UVR8 conformation and modulating protein interactions is poorly understood. Here we examine the roles of cysteine amino acids C231 and C335 in UVR8 structure and function. UVR8^C231S,C335S mutant protein forms dimers and monomerizes similarly to wild-type UVR8. UVR8^C231S,C335S interacts with CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) in plants to initiate photomorphogenic responses to UV-B, although the interaction is weaker when examined in yeast two-hybrid assays. Similarly, the interaction of UVR8^C231S,C335S with REPRESSOR OF UV-B PHOTOMORPHOGENESIS (RUP) proteins is weaker in both plants and yeast compared with wild-type UVR8. Re-dimerization of UVR8 in plants, which is mediated by RUP proteins, occurs with reduced efficiency in UVR8^C231S,C335S . Fluorescence resonance energy transfer analysis indicates that UVR8^C231S,C335S has an altered conformation in plants, in that the N- and C-termini appear closer together, which may explain the altered protein interactions.

Dynamics and mechanism of dimer dissociation of photoreceptor UVR8

Photoreceptors are a class of light-sensing proteins with critical biological functions. UVR8 is the only identified UV photoreceptor in plants and its dimer dissociation upon UV sensing activates UV-protective processes. However, the dissociation mechanism is still poorly understood. Here, by integrating extensive mutations, ultrafast spectroscopy, and computational calculations, we find that the funneled excitation energy in the interfacial tryptophan (Trp) pyramid center drives a directional Trp-Trp charge separation in 80 ps and produces a critical transient Trp anion, enabling its ultrafast charge neutralization with a nearby positive arginine residue in 17 ps to destroy a key salt bridge. A domino effect is then triggered to unzip the strong interfacial interactions, which is facilitated through flooding the interface by channel and interfacial water molecules. These detailed dynamics reveal a unique molecular mechanism of UV-induced dimer monomerization.

A unique photochromic UV-A sensor protein, Rc-PYP, interacting with the PYP-binding protein

Photoactive yellow protein (PYP) is one of the typical light sensor proteins. Although its photoreaction has been extensively studied, no downstream partner protein has been identified to date. In this study, the intermolecular interaction dynamics observed between PYP from Rhodobacter capsulatus (Rc-PYP) and a possible downstream protein, PYP-binding protein (PBP), were investigated. It was found that UV light induced a long-lived product (pUV*), which interacts with PBP to form a stable hetero-hexamer (Complex-2). The reaction scheme for this interaction was revealed using transient absorption and transient grating methods. Time-resolved diffusion detection showed that a hetero-trimer (Complex-1) is formed transiently, which produced Complex-2 via a second-order reaction. Any other intermediates, including those from pBL, do not interact with PBP. The reaction scheme and kinetics are determined. Interestingly, long-lived Complex-2 dissociates upon excitation with blue light. These results demonstrate that Rc-PYP is a photochromic and new type of UV sensor to sense the relative intensities of UV-A and blue light.

Perception and Signaling of Ultraviolet-B Radiation in Plants

Ultraviolet-B (UV-B) radiation is an intrinsic fraction of sunlight that plants perceive through the UVR8 photoreceptor. UVR8 is a homodimer in its ground state that monomerizes upon UV-B photon absorption via distinct tryptophan residues. Monomeric UVR8 competitively binds to the substrate binding site of COP1, thus inhibiting its E3 ubiquitin ligase activity against target proteins, which include transcriptional regulators such as HY5. The UVR8-COP1 interaction also leads to the destabilization of PIF bHLH factor family members. Additionally, UVR8 directly interacts with and inhibits the DNA binding of a different set of transcription factors. Each of these UVR8 signaling mechanisms initiates nuclear gene expression changes leading to UV-B-induced photomorphogenesis and acclimation. The two WD40-repeat proteins RUP1 and RUP2 provide negative feedback regulation and inactivate UVR8 by facilitating redimerization. Here, we review the molecular mechanisms of the UVR8 pathway from UV-B perception and signal transduction to gene expression changes and physiological UV-B responses.

Blue and UV-B light synergistically induce anthocyanin accumulation by co-activating nitrate reductase gene expression in Anthocyanin fruit (Aft) tomato

The tomato accession LA1996, which carries a dominant allele of anthocyanin fruit (Aft) locus, accumulates anthocyanins in the epidermis of fruits when exposed to sunlight. The involvement of blue, UV-A, UV-B and a combination of these wavelengths on anthocyanin accumulation and the molecular mechanism of their regulation was investigated in LA1996. The most effective treatment for inducing anthocyanin biosynthesis in Aft fruits was co-irradiation with blue and UV-B (blue + UV-B) light. Finding the correlated genes is an important approach towards understanding their molecular mechanisms. In the present study, the nitrate reductase (NR) gene SlNIA was isolated using RNA-seq profiling of Aft fruits given different light treatments. The functions of NR-mediated anthocyanin induction by blue + UV-B were confirmed using a series of chemical treatments, followed by assessment of NR activity and nitric oxide (NO) detection. The expression of NR was highly induced by blue + UV-B, and this specificity was also confirmed with the enzyme activity of NR and the NO concentration. The NR inhibitors, which reduce NO generation, the expression levels of anthocyanin related genes and decreased anthocyanin accumulation in LA1996. Our results suggest that NR plays a key role in blue + UV-B-mediated anthocyanin accumulation in LA1996 fruits.

Photoreaction Dynamics of a Full-Length Protein YtvA and Intermolecular Interaction with RsbRA

YtvA from Bacillus subtilis is a sensor protein that responds to blue light stress and regulates the activity of transcription factor σ^B. It is composed of the N-terminal LOV (light-oxygen-voltage) domain, the C-terminal STAS (sulfate transporter and anti-sigma factor antagonist) domain, and a linker region connecting them. In this study, the photoreaction and kinetics of full-length YtvA and the intermolecular interaction with a downstream protein, RsbRA, were revealed by the transient grating method. Although N-YLOV-linker, which is composed of the LOV domain of YtvA with helices A'α and Jα, exhibits a diffusion change due to the rotational motion of the helices, the YtvA dimer does not show the diffusion change. This result suggests that the STAS domain inhibits the rotational movement of helices A'α and Jα. We found that the YtvA dimer formed a heterotetramer with the RsbRA dimer probably via the interaction between the STAS domains, and we showed the diffusion change upon blue light illumination with a time constant faster than 70 μs. This result suggests a conformational change of the STAS domains; i.e., the interface between the STAS domains of the proteins changes to enhance the friction with water by the rotation structural change of helices A'α and Jα of YtvA.

Dynamics and mechanism of light harvesting in UV photoreceptor UVR8

Photosynthetic pigments form light-harvesting networks to enable nearly perfect quantum efficiency in photosynthesis via excitation energy transfer. However, similar light-harvesting mechanisms have not been reported in light sensing processes in other classes of photoreceptors during light-mediated signaling. Here, based on our earlier report, we mapped out a striking energy-transfer network composed of 26 structural tryptophan residues in the plant UV-B photoreceptor UVR8. The spectra of the tryptophan chromophores are tuned by the protein environments, funneling all excitation energy to a cluster of four tryptophan residues, a pyramid center, where the excitation-induced monomerization is initiated for cell signaling. With extensive site-directed mutagenesis, various time-resolved fluorescence techniques, and combined QM/MM simulations, we determined the energy-transfer rates for all donor–acceptor pairs, revealing the time scales from tens of picoseconds to nanoseconds. The overall light harvesting quantum efficiency by the pyramid center is significantly increased to 73%, compared to a direct excitation probability of 35%. UVR8 is the only photoreceptor discovered so far using a natural amino-acid tryptophan without utilizing extrinsic chromophores to form a network to carry out both light harvesting and light perception for biological functions.

The light-harvesting network from distal and peripheral to central tryptophans with transfer efficiencies determined from measured energy-transfer rates.

A dynamic model of UVR8 photoreceptor signalling in UV-B-acclimated Arabidopsis

The photoreceptor UVR8 mediates numerous photomorphogenic responses of plants to UV-B wavelengths by regulating transcription. Studies with purified UVR8 and seedlings not previously exposed to UV-B have generated a model for UVR8 action in which dimeric UVR8 rapidly monomerises in response to UV-B exposure to initiate signalling. However, the mechanism of UVR8 action in UV-B-acclimated plants growing under photoperiodic conditions, where UVR8 exists in a dimer/monomer photo-equilibrium, is poorly understood. We examined UVR8 dimer/monomer status, gene expression responses, amounts of key UVR8 signalling proteins and their interactions with UVR8 in UV-B-acclimated Arabidopsis. We show that in UV-B-acclimated plants UVR8 can mediate a response to a 15-fold increase in UV-B without any increase in abundance of UVR8 monomer. Following transfer to elevated UV-B, monomers show increased interaction with both COP1, to initiate signalling and RUP2, to maintain the photo-equilibrium when the dimer/monomer cycling rate increases. Native RUP1 is present in low abundance compared with RUP2. We present a model for UVR8 action in UV-B-acclimated plants growing in photoperiodic conditions that incorporates dimer and monomer photoreception, dimer/monomer cycling, abundance of native COP1 and RUP proteins, and interactions of the monomer population with COP1, RUP2 and potentially other proteins.

UVR8-dependent reporters reveal spatial characteristics of signal spreading in plant tissues

The UV Resistance Locus 8 (UVR8) photoreceptor controls UV-B mediated photomorphogenesis in Arabidopsis. The aim of this work is to collect and characterize different molecular reporters of photomorphogenic UV-B responses. Browsing available transcriptome databases, we identified sets of genes responding specifically to this radiation and are controlled by pathways initiated from the UVR8 photoreceptor. We tested the transcriptional changes of several reporters and found that they are regulated differently in different parts of the plant. Our experimental system led us to conclude that the examined genes are not controlled by light piping of UV-B from the shoot to the root or signalling molecules which may travel between different parts of the plant body but by local UVR8 signalling. The initiation of these universal signalling steps can be the induction of Elongated Hypocotyl 5 (HY5) and its homologue, HYH transcription factors. We found that their transcript and protein accumulation strictly depends on UVR8 and happens in a tissue autonomous manner. Whereas HY5 accumulation correlates well with the UVR8 signal across cell layers, the induction of flavonoids depends on both UVR8 signal and a yet to be identified tissue-dependent or developmental determinant.

A FRET method for investigating dimer/monomer status and conformation of the UVR8 photoreceptor

The photoreceptor UVR8 has a pivotal role in mediating plant responses to UV-B wavelengths. Dimeric UVR8 dissociates into monomers following UV-B photoreception, and there is evidence that this process is accompanied by conformational changes that may facilitate interaction of UVR8 with other proteins to initiate signaling. Hence monitoring UVR8 dimer/monomer status and conformation is key to understanding UVR8 action. Here we have used Fluorescence Resonance Energy Transfer (FRET) to study these processes in both wild-type and mutant UVR8 proteins in vivo. UVR8 was fused to GFP and mCherry at the C- and N-termini, respectively and both the FRET efficiency and loss of GFP fluorescence after photobleaching were measured. In addition, measurements were made for UVR8 fused to either GFP or mCherry to eliminate intra-molecular FRET signals. The results indicate that dissociation of UVR8 dimer to monomer principally accounts for the loss of FRET signal for wild-type UVR8 and there is little evidence of a contribution from conformational change in vivo. Examination of plants expressing UVR8W285F and UVR8D96N,D107N are consistent with these mutant proteins being constitutively dimeric and monomeric, respectively. The methods employed here will be valuable for monitoring UVR8 dimer/monomer status in vivo in relation to signaling, and will facilitate characterization of dimer/monomer status and conformation of further UVR8 mutants.

A theoretical study of 5,6,7,8-tetrahydro-6-hydroxymethylpterin: insight into intrinsic photoreceptor properties of 6-substituted tetrahydropterins

Tetrahydropterins are essential biological cofactors, which play a crucial role in DNA and RNA syntheses, NO synthesis, hydroxylation of aromatic amino acids, etc. In the last few years, it has been shown that 6-substituted "unconjugated" tetrahydropterins can also play a photoreceptor chromophoric role in plants and cyanobacteria. However, the nature of the initial light signal transduction act in which H4pterins participate is unknown. Our quantum chemical calculations have shown the possibility of the fast internal conversion of excited states of H4pterins. The potential energy surface scan along the 1ππ* state shows no energy barrier leading to 1ππ*/S0 conical intersection, this explains the absence of fluorescence for H4pterins. Other trajectories of the internal conversion relate to the stretching vibrations of the N-H bonds of the pyrimidine ring for the Rydberg state. The presence of several trajectories of nonradiative quenching of the photoexcited singlet states provides the photostability of the molecule. It was demonstrated for the first time that the nature of the excited states of H4pterins is similar to the nature of the excited states of guanine.

Difference in the action spectra for UVR8 monomerisation and HY5 transcript accumulation in Arabidopsis

The action spectrum for monomerisation of the plant UV-B photoreceptor UVR8 peaks at a shorter wavelength than that for HY5 transcript accumulation, mediated by UVR8, in the same tissue.

Photomorphogenic responses to ultraviolet-B light

Exposure to ultraviolet B (UV-B) light regulates numerous aspects of plant metabolism, morphology and physiology through the differential expression of hundreds of genes. Photomorphogenic responses to UV-B are mediated by the photoreceptor UV RESISTANCE LOCUS8 (UVR8). Considerable progress has been made in understanding UVR8 action: the structural basis of photoreceptor function, how interaction with CONSTITUTIVELY PHOTOMORPHOGENIC 1 initiates signaling and how REPRESSOR OF UV-B PHOTOMORPHOGENESIS proteins negatively regulate UVR8 action. In addition, recent research shows that UVR8 mediates several responses through interaction with other signaling pathways, in particular auxin signaling. Nevertheless, many aspects of UVR8 action remain poorly understood. Most research to date has been undertaken with Arabidopsis, and it is important to explore the functions and regulation of UVR8 in diverse plant species. Furthermore, it is essential to understand how UVR8, and UV-B signaling in general, regulates processes under natural growth conditions. Ultraviolet B regulates the expression of many genes through UVR8-independent pathways, but the activity and importance of these pathways in plants growing in sunlight are poorly understood.

How plants cope with UV-B: from perception to response

Ultraviolet-B radiation (UV-B) is an intrinsic part of the solar radiation that reaches the Earth's surface and affects the biosphere. Plants have evolved a specific UV-B signaling pathway mediated by the UVR8 photoreceptor that regulates growth, development, and acclimation. Major recent advances have contributed to our understanding of the UVR8 photocycle, UV-B-responsive protein-protein interactions, regulation of UVR8 subcellular localization, and UVR8-regulated physiological responses. Here, we review the latest progress in our understanding of UVR8 signaling and UV-B responses, which includes studies in the unicellular alga Chlamydomonas reinhardtii and the flowering plant Arabidopsis.