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Scientific Reports Sep 2021Flavocoenzymes are nearly ubiquitous cofactors that are involved in the catalysis and regulation of a wide range of biological processes including some light-induced...
Flavocoenzymes are nearly ubiquitous cofactors that are involved in the catalysis and regulation of a wide range of biological processes including some light-induced ones, such as the photolyase-mediated DNA repair, magnetoreception of migratory birds, and the blue-light driven phototropism in plants. One of the factors that enable versatile flavin-coenzyme biochemistry and biophysics is the fine-tuning of the cofactor's frontier orbital by interactions with the protein environment. Probing the singly-occupied molecular orbital (SOMO) of the intermediate radical state of flavins is therefore a prerequisite for a thorough understanding of the diverse functions of the flavoprotein family. This may be ultimately achieved by unravelling the hyperfine structure of a flavin by electron paramagnetic resonance. In this contribution we present a rigorous approach to obtaining a hyperfine map of the flavin's chromophoric 7,8-dimethyl isoalloxazine unit at an as yet unprecedented level of resolution and accuracy. We combine powerful high-microwave-frequency/high-magnetic-field electron-nuclear double resonance (ENDOR) with C isotopologue editing as well as spectral simulations and density functional theory calculations to measure and analyse C hyperfine couplings of the flavin cofactor in DNA photolyase. Our data will provide the basis for electronic structure considerations for a number of flavin radical intermediates occurring in blue-light photoreceptor proteins.
PubMed: 34521887
DOI: 10.1038/s41598-021-97588-7 -
Physical Chemistry Chemical Physics :... Jun 2021Photosensory receptors containing the flavin-binding light-oxygen-voltage (LOV) domain are modular proteins that fulfil a variety of biological functions ranging from...
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.
Topics: Amino Acid Sequence; Avena; Cysteine; Flavin Mononucleotide; Glutamine; Hydrogen Bonding; Isomerism; Models, Molecular; Normal Distribution; Photochemical Processes; Phototropins; Protein Binding; Protein Conformation; Spectrophotometry, Infrared; Sphingomonadaceae; Structure-Activity Relationship; Thermodynamics
PubMed: 34142688
DOI: 10.1039/d1cp00447f -
The New Phytologist Sep 2021Characterising the processes that control auxin dynamics is essential to understanding how auxin regulates plant development. Over recent years, several studies have... (Review)
Review
Characterising the processes that control auxin dynamics is essential to understanding how auxin regulates plant development. Over recent years, several studies have investigated auxin diffusion through plasmodesmata, characterising this cell-to-cell diffusion and demonstrating that it affects auxin distributions. Furthermore, studies have shown that plasmodesmatal auxin diffusion affects developmental processes, including phototropism, lateral root emergence and leaf hyponasty. This short Tansley Insight review describes how these studies have contributed to our understanding of auxin dynamics and discusses potential future directions in this area.
Topics: Gene Expression Regulation, Plant; Indoleacetic Acids; Phototropism; Plant Development; Plant Roots; Plasmodesmata
PubMed: 34053083
DOI: 10.1111/nph.17517 -
The New Phytologist Sep 2021Shade and warmth promote the growth of the stem, but the degree of mechanistic convergence and functional association between these responses is not clear. We analysed...
Shade and warmth promote the growth of the stem, but the degree of mechanistic convergence and functional association between these responses is not clear. We analysed the quantitative impact of mutations and natural genetic variation on the hypocotyl growth responses of Arabidopsis thaliana to shade and warmth, the relationship between the abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and growth stimulation by shade or warmth, the effects of both cues on the transcriptome and the consequences of warm temperature on carbon balance. Growth responses to shade and warmth showed strong genetic linkage and similar dependence on PIF4 levels. Temperature increased growth and phototropism even within a range where damage by extreme high temperatures is unlikely to occur in nature. Both cues enhanced the expression of growth-related genes and reduced the expression of photosynthetic genes. However, only warmth enhanced the expression of genes involved in responses to heat. Warm temperatures substantially increased the amount of light required to compensate for the daily carbon dioxide balance. We propose that the main ecological function of hypocotyl growth responses to warmth is to increase the access of shaded photosynthetic organs to light, which implies functional convergence with shade avoidance.
Topics: Arabidopsis; Arabidopsis Proteins; Gene Expression Regulation, Plant; Hypocotyl; Phototropism
PubMed: 33909310
DOI: 10.1111/nph.17430 -
Plant Biotechnology (Tokyo, Japan) Dec 2020Environmental stimuli such as gravity and light modify the plant development to optimize overall architecture. Many physiological and molecular biological studies of...
Environmental stimuli such as gravity and light modify the plant development to optimize overall architecture. Many physiological and molecular biological studies of gravitropism and phototropism have been carried out. However, sufficient analysis has not been performed from a mechanical point of view. If the biological and mechanical characteristics of gravitropism and phototropism can be accurately grasped, then controlling the environmental conditions would be helpful to control the growth of plants into a specific shape. In this study, to clarify the mechanical characteristics of gravitropism, we examined the transverse bending moment occurring in cantilevered pea () sprouts in response to gravistimulation. The force of the pea sprouts lifting themselves during gravitropism was measured using an electronic balance. The gravitropic bending force of the pea sprouts was in the order of 10 Nmm in the conditions set for this study, although there were wide variations due to individual differences.
PubMed: 33850437
DOI: 10.5511/plantbiotechnology.20.1201b -
Journal of Plant Research Jul 2021Organisms have a variety of three-dimensional (3D) structures that change over time. These changes include twisting, which is 3D deformation that cannot happen in two...
Organisms have a variety of three-dimensional (3D) structures that change over time. These changes include twisting, which is 3D deformation that cannot happen in two dimensions. Twisting is linked to important adaptive functions of organs, such as adjusting the orientation of leaves and flowers in plants to align with environmental stimuli (e.g. light, gravity). Despite its importance, the underlying mechanism for twisting remains to be determined, partly because there is no rigorous method for quantifying the twisting of plant organs. Conventional studies have relied on approximate measurements of the twisting angle in 2D, with arbitrary choices of observation angle. Here, we present the first rigorous quantification of the 3D twisting angles of Arabidopsis petioles based on light sheet microscopy. Mathematical separation of bending and twisting with strict definition of petiole cross-sections were implemented; differences in the spatial distribution of bending and twisting were detected via the quantification of angles along the petiole. Based on the measured values, we discuss that minute degrees of differential growth can result in pronounced twisting in petioles.
Topics: Arabidopsis; Arabidopsis Proteins; Flowers; Plant Leaves
PubMed: 33839995
DOI: 10.1007/s10265-021-01291-7 -
International Journal of Molecular... Mar 2021Plants are exposed to numerous biotic and abiotic stresses, and light is one of the most important factors that influences the plant morphology. This study was carried...
Plants are exposed to numerous biotic and abiotic stresses, and light is one of the most important factors that influences the plant morphology. This study was carried out to examine how the lighting direction affected the plant morphology by investigating the growth parameters, epidermal cell elongation, stomatal properties, and physiological changes. Seedlings of two head lettuce ( L.) cultivars, Caesar Green and Polla, were subjected to a 12 h photoperiod with a 300 μmol·m·s photosynthetic photon flux density (PPFD) provided by light emitting diodes (LEDs) from three directions: the top, side, and bottom, relative to the plants. Compared with the top and side lighting, the bottom lighting increased the leaf angle and canopy by stimulating the epidermal cell elongation in leaf midrib, reduced the leaf number and root biomass, and induced large stomata with a low density, which is associated with reduced stomatal conductance and carbohydrate contents. However, the proline content and quantum yield exhibited no significant differences with the different lighting directions in both cultivars, which implies that the plants were under normal physiological conditions. In a conclusion, the lighting direction had a profound effect on the morphological characteristics of lettuce, where the plants adapted to the changing lighting environments.
Topics: Carbohydrate Metabolism; Chlorophyll; Gene Expression Regulation, Plant; Lactuca; Lighting; Photosynthesis; Plant Development; Plant Epidermis; Plant Leaves; Plant Physiological Phenomena; Plant Stomata; Quantitative Trait, Heritable
PubMed: 33808879
DOI: 10.3390/ijms22063157 -
Molecules (Basel, Switzerland) Mar 2021Light is a key factor that affects phytochemical synthesis and accumulation in plants. Due to limitations of the environment or cultivated land, there is an urgent need... (Review)
Review
Light is a key factor that affects phytochemical synthesis and accumulation in plants. Due to limitations of the environment or cultivated land, there is an urgent need to develop indoor cultivation systems to obtain higher yields with increased phytochemical concentrations using convenient light sources. Light-emitting diodes (LEDs) have several advantages, including consumption of lesser power, longer half-life, higher efficacy, and wider variation in the spectral wavelength than traditional light sources; therefore, these devices are preferred for in vitro culture and indoor plant growth. Moreover, LED irradiation of seedlings enhances plant biomass, nutrient and secondary metabolite levels, and antioxidant properties. Specifically, red and blue LED irradiation exerts strong effects on photosynthesis, stomatal functioning, phototropism, photomorphogenesis, and photosynthetic pigment levels. Additionally, ex vitro plantlet development and acclimatization can be enhanced by regulating the spectral properties of LEDs. Applying an appropriate LED spectral wavelength significantly increases antioxidant enzyme activity in plants, thereby enhancing the cell defense system and providing protection from oxidative damage. Since different plant species respond differently to lighting in the cultivation environment, it is necessary to evaluate specific wavebands before large-scale LED application for controlled in vitro plant growth. This review focuses on the most recent advances and applications of LEDs for in vitro culture organogenesis. The mechanisms underlying the production of different phytochemicals, including phenolics, flavonoids, carotenoids, anthocyanins, and antioxidant enzymes, have also been discussed.
Topics: Agriculture; Anthocyanins; Antioxidants; Biomass; Carotenoids; Crops, Agricultural; Flavonoids; Luminescence; Nutritive Value; Phenols; Photosynthesis; Phytochemicals; Plant Development; Plants, Medicinal
PubMed: 33803168
DOI: 10.3390/molecules26051477 -
Plant Physiology Apr 2021Plants perceive dynamic light conditions and optimize their growth and development accordingly by regulating gene expression at multiple levels. Alternative splicing...
Plants perceive dynamic light conditions and optimize their growth and development accordingly by regulating gene expression at multiple levels. Alternative splicing (AS), a widespread mechanism in eukaryotes that post-transcriptionally generates two or more messenger RNAs (mRNAs) from the same pre-mRNA, is rapidly controlled by light. However, a detailed mechanism of light-regulated AS is still not clear. In this study, we demonstrate that histone 3 lysine 36 trimethylation (H3K36me3) rapidly and differentially responds to light at specific gene loci with light-regulated intron retention (IR) of their transcripts in the moss Physcomitrella patens. However, the level of H3K36me3 following exposure to light is inversely related to that of IR events. Physcomitrella patens MORF-related gene 1 (PpMRG1), a chromatin adaptor, bound with higher affinity to H3K36me3 in light conditions than in darkness and was differentially targeted to gene loci showing light-responsive IR. Transcriptome analysis indicated that PpMRG1 functions in the regulation of light-mediated AS. Furthermore, PpMRG1 was also involved in red light-mediated phototropic responses. Our results suggest that light regulates histone methylation, which leads to alterations of AS patterns. The chromatin adaptor PpMRG1 potentially participates in light-mediated AS, revealing that chromatin-coupled regulation of pre-mRNA splicing is an important aspect of the plant's response to environmental changes.
Topics: Alternative Splicing; Bryopsida; Chromatin; Gene Expression Regulation, Plant; Introns; RNA Splicing
PubMed: 33793927
DOI: 10.1093/plphys/kiaa103 -
Nature Communications Mar 2021Natural systems display sophisticated control of light-matter interactions at multiple length scales for light harvesting, manipulation, and management, through...
Natural systems display sophisticated control of light-matter interactions at multiple length scales for light harvesting, manipulation, and management, through elaborate photonic architectures and responsive material formats. Here, we combine programmable photonic function with elastomeric material composites to generate optomechanical actuators that display controllable and tunable actuation as well as complex deformation in response to simple light illumination. The ability to topographically control photonic bandgaps allows programmable actuation of the elastomeric substrate in response to illumination. Complex three-dimensional configurations, programmable motion patterns, and phototropic movement where the material moves in response to the motion of a light source are presented. A "photonic sunflower" demonstrator device consisting of a light-tracking solar cell is also illustrated to demonstrate the utility of the material composite. The strategy presented here provides new opportunities for the future development of intelligent optomechanical systems that move with light on demand.
PubMed: 33712607
DOI: 10.1038/s41467-021-21764-6