Magnetic sensitivity mediated by the Arabidopsis blue-light receptor cryptochrome occurs during flavin reoxidation in the dark

Avian cryptochrome 4 binds superoxide

Flavin-binding cryptochromes are blue-light sensitive photoreceptors that have been implicated with magnetoreception in some species. The photocycle involves an intra-protein photo-reduction of the flavin cofactor, generating a magnetosensitive radical pair, and its subsequent re-oxidation. Superoxide (O2 • - ) is generated in the re-oxidation with molecular oxygen. The resulting O2 • - -containing radical pairs have also been hypothesised to underpin various magnetosensitive traits, but due to fast spin relaxation when tumbling in solution would require immobilisation. We here describe our insights in the binding of superoxide to cryptochrome 4 from C. livia based on extensive all-atom molecular dynamics studies and density-functional theory calculations. The positively charged "crypt" region that leads to the flavin binding pocket transiently binds O2 • - at 5 flexible binding sites centred on arginine residues. Typical binding times amounted to tens of nanoseconds, but exceptional binding events extended to several hundreds of nanoseconds and slowed the rotational diffusion, thereby realising rotational correlation times as large as 1 ns. The binding sites are particularly efficient in scavenging superoxide escaping from a putative generation site close to the flavin-cofactor, possibly implying a functional relevance. We discuss our findings in view of a potential magnetosensitivity of biological flavin semiquinone/superoxide radical pairs.

Comparative transcriptomic analysis revealed important processes underlying the static magnetic field effects on Arabidopsis

Static magnetic field (SMF) plays important roles in various biological processes of many organisms including plants, though the molecular mechanism remains largely unclear. Here in this study, we evaluated different magnetic setups to test their effects on growth and development on Arabidopsis (Arabidopsis thaliana), and discovered that plant growth was significantly enhanced by inhomogeneous SMF generated by a regular triangular prism magnet perpendicular to the direction of gravity. Comparative transcriptomic analysis revealed that auxin synthesis and signal transduction genes were upregulated by SMF exposure. SMF also facilitated plants to maintain the iron homeostasis. The expression of iron metabolism-related genes was downregulated by SMF, however, the iron content in plant tissues remains relatively unchanged. Furthermore, SMF exposure also helped the plants to reduce ROS level and synergistically maintain the oxidant balance by enhanced activity of antioxidant enzymes and accumulation of nicotinamide. Taken together, our data suggested that SMF is involved in regulating the growth and development of Arabidopsis thaliana through maintaining iron homeostasis and balancing oxidative stress, which could be beneficial for plant survival and growth. The work presented here would extend our understanding of the mechanism and the regulatory network of how magnetic field affects the plant growth, which would provide insights into the development of novel plant synthetic biology technologies to engineer stress-resistant and high-yielding crops.

Structural Rearrangements of Pigeon Cryptochrome 4 Undergoing a Complete Redox Cycle

Cryptochrome is currently the major contender of a protein to underpin magnetoreception, the ability to sense the Earth's magnetic field. Among various types of cryptochromes, cryptochrome 4 has been identified as the likely magnetoreceptor in migratory birds. All-atom molecular dynamics (MD) studies have offered first insights into the structural dynamics of cryptochrome but are limited to a short time scale due to large computational demands. Here, we employ coarse-grained MD simulations to investigate the emergence of long-lived states and conformational changes in pigeon cryptochrome 4. Our coarse-grained simulations complete the picture by permitting observation on a significantly longer time scale. We observe conformational transitions in the phosphate-binding loop of pigeon cryptochrome 4 upon activation and identify prominent motions in residues 440-460, suggesting a possible role as a signaling state of the protein or as a gated interaction site for forming protein complexes that might facilitate downstream processes. The findings highlight the importance of considering longer time scales in studying cryptochrome dynamics and magnetoreception. Coarse-grained MD simulations offer a valuable tool to unravel the complex behavior of cryptochrome proteins and shed new light on the mechanisms underlying their role in magnetoreception. Further exploration of these conformational changes and their functional implications may contribute to a deeper understanding of the molecular mechanisms of magnetoreception in birds.

'Seeing' the electromagnetic spectrum: spotlight on the cryptochrome photocycle

Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or 'lit' state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or 'resting' state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of 'magneto-genetics' for future applications in synthetic biology and medicine.

Hypomagnetic Conditions and Their Biological Action (Review)

The geomagnetic field plays an important role in the existence of life on Earth. The study of the biological effects of (hypomagnetic conditions) HMC is an important task in magnetobiology. The fundamental importance is expanding and clarifying knowledge about the mechanisms of magnetic field interaction with living systems. The applied significance is improving the training of astronauts for long-term space expeditions. This review describes the effects of HMC on animals and plants, manifested at the cellular and organismal levels. General information is given about the probable mechanisms of HMC and geomagnetic field action on living systems. The main experimental approaches are described. We attempted to systematize quantitative data from various studies and identify general dependencies of the magnetobiology effects' value on HMC characteristics (induction, exposure duration) and the biological parameter under study. The most pronounced effects were found at the cellular level compared to the organismal level. Gene expression and protein activity appeared to be the most sensitive to HMC among the molecular cellular processes. The nervous system was found to be the most sensitive in the case of the organism level. The review may be of interest to biologists, physicians, physicists, and specialists in interdisciplinary fields.

Magnetic Stimulation as a Therapeutic Approach for Brain Modulation and Repair: Underlying Molecular and Cellular Mechanisms

Neurological and psychiatric diseases generally have no cure, so innovative non-pharmacological treatments, including non-invasive brain stimulation, are interesting therapeutic tools as they aim to trigger intrinsic neural repair mechanisms. A common brain stimulation technique involves the application of pulsed magnetic fields to affected brain regions. However, investigations of magnetic brain stimulation are complicated by the use of many different stimulation parameters. Magnetic brain stimulation is usually divided into two poorly connected approaches: (1) clinically used high-intensity stimulation (0.5-2 Tesla, T) and (2) experimental or epidemiologically studied low-intensity stimulation (μT-mT). Human tests of both approaches are reported to have beneficial outcomes, but the underlying biology is unclear, and thus optimal stimulation parameters remain ill defined. Here, we aim to bring together what is known about the biology of magnetic brain stimulation from human, animal, and in vitro studies. We identify the common effects of different stimulation protocols; show how different types of pulsed magnetic fields interact with nervous tissue; and describe cellular mechanisms underlying their effects-from intracellular signalling cascades, through synaptic plasticity and the modulation of network activity, to long-term structural changes in neural circuits. Recent advances in magneto-biology show clear mechanisms that may explain low-intensity stimulation effects in the brain. With its large breadth of stimulation parameters, not available to high-intensity stimulation, low-intensity focal magnetic stimulation becomes a potentially powerful treatment tool for human application.

Cryptochrome and quantum biology: unraveling the mysteries of plant magnetoreception

Magnetoreception, the remarkable ability of organisms to perceive and respond to Earth's magnetic field, has captivated scientists for decades, particularly within the field of quantum biology. In the plant science, the exploration of the complicated interplay between quantum phenomena and classical biology in the context of plant magnetoreception has emerged as an attractive area of research. This comprehensive review investigates into three prominent theoretical models: the Radical Pair Mechanism (RPM), the Level Crossing Mechanism (LCM), and the Magnetite-based MagR theory in plants. While examining the advantages, limitations, and challenges associated with each model, this review places a particular weight on the RPM, highlighting its well-established role of cryptochromes and in-vivo experiments on light-independent plant magnetoreception. However, alternative mechanisms such as the LCM and the MagR theory are objectively presented as convincing perspectives that permit further investigation. To shed light on these theoretical frameworks, this review proposes experimental approaches including cutting-edge experimental techniques. By integrating these approaches, a comprehensive understanding of the complex mechanisms driving plant magnetoreception can be achieved, lending support to the fundamental principle in the RPM. In conclusion, this review provides a panoramic overview of plant magnetoreception, highlighting the exciting potential of quantum biology in unraveling the mysteries of magnetoreception. As researchers embark on this captivating scientific journey, the doors to deciphering the diverse mechanisms of magnetoreception in plants stand wide open, offering a profound exploration of nature's adaptations to environmental cues.

A Review of the Current State of Magnetic Force Microscopy to Unravel the Magnetic Properties of Nanomaterials Applied in Biological Systems and Future Directions for Quantum Technologies

Magnetism plays a pivotal role in many biological systems. However, the intensity of the magnetic forces exerted between magnetic bodies is usually low, which demands the development of ultra-sensitivity tools for proper sensing. In this framework, magnetic force microscopy (MFM) offers excellent lateral resolution and the possibility of conducting single-molecule studies like other single-probe microscopy (SPM) techniques. This comprehensive review attempts to describe the paramount importance of magnetic forces for biological applications by highlighting MFM's main advantages but also intrinsic limitations. While the working principles are described in depth, the article also focuses on novel micro- and nanofabrication procedures for MFM tips, which enhance the magnetic response signal of tested biomaterials compared to commercial nanoprobes. This work also depicts some relevant examples where MFM can quantitatively assess the magnetic performance of nanomaterials involved in biological systems, including magnetotactic bacteria, cryptochrome flavoproteins, and magnetic nanoparticles that can interact with animal tissues. Additionally, the most promising perspectives in this field are highlighted to make the reader aware of upcoming challenges when aiming toward quantum technologies.

Cryptochromes in mammals: a magnetoreception misconception?

Cryptochromes are flavoproteins related to photolyases that are widespread throughout the plant and animal kingdom. They govern blue light-dependent growth in plants, control circadian rhythms in a light-dependent manner in invertebrates, and play a central part in the circadian clock in vertebrates. In addition, cryptochromes might function as receptors that allow animals to sense the Earth's magnetic field. As cryptochromes are also present in mammals including humans, the possibility of a magnetosensitive protein is exciting. Here we attempt to provide a concise overview of cryptochromes in mammals. We briefly review their canonical role in the circadian rhythm from the molecular level to physiology, behaviour and diseases. We then discuss their disputed light sensitivity and proposed role in the magnetic sense in mammals, providing three mechanistic hypotheses. Specifically, mammalian cryptochromes could form light-induced radical pairs in particular cellular milieus, act as magnetoreceptors in darkness, or as secondary players in a magnetoreception signalling cascade. Future research can test these hypotheses to investigate if the role of mammalian cryptochromes extends beyond the circadian clock.

14-3-3 Proteins and the Plasma Membrane H+-ATPase Are Involved in Maize (Zea mays) Magnetic Induction

The geomagnetic field (GMF) is a natural component of the biosphere, and, during evolution, all organisms experienced its presence while some evolved the ability to perceive magnetic fields (MF). We studied the response of 14-3-3 proteins and the plasma membrane (PM) proton pump H+-ATPase to reduced GMF values by lowering the GMF intensity to a near-null magnetic field (NNMF). Seedling morphology, H+-ATPase activity and content, 14-3-3 protein content, binding to PM and phosphorylation, gene expression, and ROS quantification were assessed in maize (Zea mays) dark-grown seedlings. Phytohormone and melatonin quantification were also assessed by LG-MS/MS. Our results suggest that the GMF regulates the PM H+-ATPase, and that NNMF conditions alter the proton pump activity by reducing the binding of 14-3-3 proteins. This effect was associated with both a reduction in H2O2 and downregulation of genes coding for enzymes involved in ROS production and scavenging, as well as calcium homeostasis. These early events were followed by the downregulation of IAA synthesis and gene expression and the increase in both cytokinin and ABA, which were associated with a reduction in root growth. The expression of the homolog of the MagR gene, ZmISCA2, paralleled that of CRY1, suggesting a possible role of ISCA in maize magnetic induction. Interestingly, melatonin, a widespread molecule present in many kingdoms, was increased by the GMF reduction, suggesting a still unknown role of this molecule in magnetoreception.

Molecular Biological Effects of Weak Low-Frequency Magnetic Fields: Frequency-Amplitude Efficiency Windows and Possible Mechanisms

This review covers the phenomenon of resonance-like responses of biological systems to low-frequency magnetic fields (LFMF). The historical development of this branch of magnetobiology, including the most notable biophysical models that explain the resonance-like responses of biological systems to LFMF with a specific frequency and amplitude, is given. Two groups can be distinguished among these models: one considers ion-cofactors of proteins as the primary targets for the LFMF influence, and the other regards the magnetic moments of particles in biomolecules. Attention is paid to the dependence of resonance-like LFMF effects on the cell type. A radical-pair mechanism of the magnetic field's influence on biochemical processes is described with the example of cryptochrome. Conditions for this mechanism's applicability to explain the biological effects of LFMF are given. A model of the influence of LFMF on radical pairs in biochemical oscillators, which can explain the frequency-amplitude efficiency windows of LFMF, is proposed.

Molecular Bases of Signaling Processes Regulated by Cryptochrome Sensory Photoreceptors in Plants

The blue-light sensors, cryptochromes, compose the extensive class of flavoprotein photoreceptors, regulating signaling processes in plants underlying their development, growth, and metabolism. In several algae, cryptochromes may act not only as sensory photoreceptors but also as photolyases, catalyzing repair of the UV-induced DNA lesions. Cryptochromes bind FAD as the chromophore at the photolyase homologous region (PHR) domain and contain the cryptochrome C-terminal extension (CCE), which is absent in photolyases. Photosensory process in cryptochrome is initiated by photochemical chromophore conversions, including formation of the FAD redox forms. In the state with the chromophore reduced to neutral radical (FADH×), the photoreceptor protein undergoes phosphorylation, conformational changes, and disengagement from the PHR domain and CCE with subsequent formation of oligomers of cryptochrome molecules. Photooligomerization is a structural basis of the functional activities of cryptochromes, since it ensures formation of their complexes with a variety of signaling proteins, including transcriptional factors and regulators of transcription. Interactions in such complexes change the protein signaling activities, leading to regulation of gene expression and plant photomorphogenesis. In recent years, multiple papers, reporting novel, more detailed information about the molecular mechanisms of above-mentioned processes were published. The present review mainly focuses on analysis of the data contained in these publications, particularly regarding structural aspects of the cryptochrome transitions into photoactivated states and regulatory signaling processes mediated by the cryptochrome photoreceptors in plants.

Effects of weak static magnetic fields on the development of seedlings of Arabidopsis thaliana

To study magnetoreception of Arabidopsis thaliana, we analysed several developmental responses including cryptochrome-independent seed germination and the phytochrome- and cryptochrome-dependent hypocotyl elongation and photo-accumulation of anthocyanins and chlorophylls in weak static magnetic fields ranging from near null to 122 μT. A field of 50 μT accelerated seed germination by about 20 h relative to samples maintained in a near-null field. The double mutant, cry1cry2, lacking cryptochromes 1 and 2 displayed the same magnetic field-induced germination acceleration under blue light as the wild-type strain. Magnetic field-induced germination acceleration was masked in the presence of exogenous sucrose. Stimulus-response curves for hypocotyl elongation in a range between near-null to 122 μT indicated maxima near 9 and 60 μT for the wild-type strain as well as mutant cry1cry2. The photo-accumulation of anthocyanins and chlorophylls could be effectively modulated by magnetic fields in the presence of low-irradiance red and blue light, respectively. The findings indicate that Arabidopsis thaliana possesses light-independent mechanisms of magnetic field reception, which remain presently unidentified. Our results are in better agreement with predictions of the level crossing mechanism (LCM) of magnetoreception rather than those of the cryptochrome-associated radical-pair mechanism (RPM).

Essential elements of radical pair magnetosensitivity in Drosophila

Many animals use Earth's magnetic field (also known as the geomagnetic field) for navigation1. The favoured mechanism for magnetosensitivity involves a blue-light-activated electron-transfer reaction between flavin adenine dinucleotide (FAD) and a chain of tryptophan residues within the photoreceptor protein CRYPTOCHROME (CRY). The spin-state of the resultant radical pair, and therefore the concentration of CRY in its active state, is influenced by the geomagnetic field2. However, the canonical CRY-centric radical-pair mechanism does not explain many physiological and behavioural observations2-8. Here, using electrophysiology and behavioural analyses, we assay magnetic-field responses at the single-neuron and organismal levels. We show that the 52 C-terminal amino acid residues of Drosophila melanogaster CRY, lacking the canonical FAD-binding domain and tryptophan chain, are sufficient to facilitate magnetoreception. We also show that increasing intracellular FAD potentiates both blue-light-induced and magnetic-field-dependent effects on the activity mediated by the C terminus. High levels of FAD alone are sufficient to cause blue-light neuronal sensitivity and, notably, the potentiation of this response in the co-presence of a magnetic field. These results reveal the essential components of a primary magnetoreceptor in flies, providing strong evidence that non-canonical (that is, non-CRY-dependent) radical pairs can elicit magnetic-field responses in cells.

The Geomagnetic Field (GMF) Is Necessary for Black Garden Ant (Lasius niger L.) Foraging and Modulates Orientation Potentially through Aminergic Regulation and MagR Expression

The geomagnetic field (GMF) can affect a wide range of animal behaviors in various habitats, primarily providing orientation cues for homing or migratory events. Foraging patterns, such as those implemented by Lasius niger, are excellent models to delve into the effects of GMF on orientation abilities. In this work, we assessed the role of GMF by comparing the L. niger foraging and orientation performance, brain biogenic amine (BA) contents, and the expression of genes related to the magnetosensory complex and reactive oxygen species (ROS) of workers exposed to near-null magnetic fields (NNMF, ~40 nT) and GMF (~42 µT). NNMF affected workers' orientation by increasing the time needed to find the food source and return to the nest. Moreover, under NNMF conditions, a general drop in BAs, but not melatonin, suggested that the lower foraging performance might be correlated to a decrease in locomotory and chemical perception abilities, potentially driven by dopaminergic and serotoninergic regulations, respectively. The variation in the regulation of genes related to the magnetosensory complex in NNMF shed light on the mechanism of ant GMF perception. Overall, our work provides evidence that the GMF, along with chemical and visual cues, is necessary for the L. niger orientation process.

Quantum-mechanical insights into the anisotropic response of the cryptochrome radical pair to a weak magnetic field

Cryptochrome photoreceptors contain a photochemically generated radical pair, which is thought to mediate sensing of the geomagnetic field direction in many living organisms. To gain insight into the response of the cryptochrome to a weak magnetic field, we have studied the quantum-mechanical hyperfine spin states of the radical pair. We identify quantum states responsible for the precise detection of the magnetic field direction, taking into account the strongly axial hyperfine interactions of each radical in the radical pair. The contribution of these states to the formation of the cryptochrome signaling state sharply increases when the magnetic field becomes orthogonal to the hyperfine axis of either radical. Due to such a response, the radical pair may be able to detect the particular field direction normal to the plane containing the hyperfine axes of the radicals.

Isotope Substitution Effects on the Magnetic Compass Properties of Cryptochrome-Based Radical Pairs: A Computational Study

The biophysical mechanism of the magnetic compass sense of migratory songbirds is thought to rely on the photochemical reactions of flavin-containing radical pairs in cryptochrome proteins located in the birds' eyes. A consequence of this hypothesis is that the effect of the Earth's magnetic field on the quantum yields of reaction products should be sensitive to isotopic substitutions that modify the hyperfine interactions in the radicals. In this report, we use spin dynamics simulations to explore the effects of ¹H → ²H, ¹²C → ¹³C, and ¹⁴N → ¹⁵N isotopic substitutions on the functioning of cryptochrome 4a as a magnetic direction sensor. Two main conclusions emerge. (1) Uniform deuteration of the flavin chromophore appears to be the best way to boost the anisotropy of the magnetic field effect and to change its symmetry. (2) ¹³C substitution of three of the 12 flavin carbons, in particular C4, C4a, and C8α, seems to be the best recipe for attenuating the anisotropy. These predictions should give insight into the factors that control the magnetic sensitivity once spectroscopic techniques are available for measuring magnetic field effects on oriented protein samples.

Growth, physiological, biochemical and molecular changes in plants induced by magnetic fields: A review

The Earth's geomagnetic field (GMF) is an inescapable environmental factor for plants that affects all growth and yield parameters. Both strong and weak magnetic fields (MF), as compared to the GMF, have specific roles in plant growth and development. MF technology is an eco-friendly technique that does not emit waste or generate harmful radiation, nor require any external power supply, so it can be used in sustainable modern agriculture. Thus, exposure of plants to MF is a potential affordable, reusable and safe practice for enhancing crop productivity by changing physiological and biochemical processes. However, the effect of MF on plant physiological and biochemical processes is not yet well understood. This review describes the effects of altering MF conditions (higher or lower values than the GMF) on physiological and biochemical processes of plants. The current contradictory and inconsistent outcomes from studies on varying effects of MF on plants could be related to species and/or MF exposure time and intensity. The reviewed literature suggests MF have a role in changing physiological processes, such as respiration, photosynthesis, nutrient uptake, water relations and biochemical attributes, including genes involved in ROS, antioxidants, enzymes, proteins and secondary metabolites. MF application might efficiently increase growth and yield of many crops, and as such, should be the focus for future research.

Biological Effects of Electric, Magnetic, and Electromagnetic Fields from 0 to 100 MHz on Fauna and Flora: Workshop Report

This report summarizes effects of anthropogenic electric, magnetic, and electromagnetic fields in the frequency range from 0 to 100 MHz on flora and fauna, as presented at an international workshop held on 5-7 November in 2019 in Munich, Germany. Such fields may originate from overhead powerlines, earth or sea cables, and from wireless charging systems. Animals and plants react differentially to anthropogenic fields; the mechanisms underlying these responses are still researched actively. Radical pairs and magnetite are discussed mechanisms of magnetoreception in insects, birds, and mammals. Moreover, several insects as well as marine species possess specialized electroreceptors, and behavioral reactions to anthropogenic fields have been reported. Plants react to experimental modifications of their magnetic environment by growth changes. Strong adverse effects of anthropogenic fields have not been described, but knowledge gaps were identified; further studies, aiming at the identification of the interaction mechanisms and the ecological consequences, are recommended.

Transcriptomics and Metabolomics of Reactive Oxygen Species Modulation in Near-Null Magnetic Field-Induced Arabidopsis thaliana

The geomagnetic field (GMF) is a natural component of Earth's biosphere. GMF reduction to near-null values (NNMF) induces gene expression modulation that generates biomolecular, morphological, and developmental changes. Here, we evaluate the effect of NNMF on gene expression and reactive oxygen species (ROS) production in time-course experiments on Arabidopsis thaliana. Plants exposed to NNMF in a triaxial Helmholtz coils system were sampled from 10 min to 96 h to evaluate differentially expressed genes (DEGs) of oxidative stress responses by gene microarray. In 24-96 h developing stages, H₂O₂ and polyphenols were also analyzed from roots and shoots. A total of 194 DEGs involved in oxidative reactions were selected, many of which showed a fold change ≥±2 in at least one timing point. Heatmap clustering showed DEGs both between roots/shoots and among the different time points. NNMF induced a lower H₂O₂ than GMF, in agreement with the expression of ROS-related genes. Forty-four polyphenols were identified, the content of which progressively decreased during NNMF exposition time. The comparison between polyphenols content and DEGs showed overlapping patterns. These results indicate that GMF reduction induces metabolomic and transcriptomic modulation of ROS-scavenging enzymes and H₂O₂ production in A. thaliana, which is paralleled by the regulation of antioxidant polyphenols.

Iron-sulfur complex assembly: Potential players of magnetic induction in plants

Iron-sulfur (Fe-S) clusters are involved in fundamental biological reactions and represent a highly regulated process involving a complex sequence of mitochondrial, cytosolic and nuclear-catalyzed protein-protein interactions. Iron-sulfur complex assembly (ISCA) scaffold proteins are involved in Fe-S cluster biosynthesis, nitrogen and sulfur metabolism. ISCA proteins are involved in abiotic stress responses and in the pigeon they act as a magnetic sensor by forming a magnetosensor (MagS) complex with cryptochrome (Cry). MagR gene exists in the genomes of humans, plants, and microorganisms and the interaction between Cry and MagR is highly conserved. Owing to the extensive presence of ISCA proteins in plants and the occurrence of homology between animal and human MagR with at least four Arabidopsis ISCAs and several ISCAs from different plant species, we believe that a mechanism similar to pigeon magnetoperception might be present in plants. We suggest that plant ISCA proteins, homologous of the animal MagR, are good candidates and could contribute to a better understanding of plant magnetic induction. We thus urge more studies in this regard to fully uncover the plant molecular mechanisms underlying MagR/Cry mediated magnetic induction and the possible coupling between light and magnetic induction.

Radical triads, not pairs, may explain effects of hypomagnetic fields on neurogenesis

Adult hippocampal neurogenesis and hippocampus-dependent cognition in mice have been found to be adversely affected by hypomagnetic field exposure. The effect concurred with a reduction of reactive oxygen species in the absence of the geomagnetic field. A recent theoretical study suggests a mechanistic interpretation of this phenomenon in the framework of the Radical Pair Mechanism. According to this model, a flavin-superoxide radical pair, born in the singlet spin configuration, undergoes magnetic field-dependent spin dynamics such that the pair’s recombination is enhanced as the applied magnetic field is reduced. This model has two ostensible weaknesses: a) the assumption of a singlet initial state is irreconcilable with known reaction pathways generating such radical pairs, and b) the model neglects the swift spin relaxation of free superoxide, which abolishes any magnetic sensitivity in geomagnetic/hypomagnetic fields. We here suggest that a model based on a radical triad and the assumption of a secondary radical scavenging reaction can, in principle, explain the phenomenon without unnatural assumptions, thus providing a coherent explanation of hypomagnetic field effects in biology.

The hippocampal region of the brain plays a major role in learning and memory functionality. In male mice, shielding of the Earth’s magnetic field was found to decrease hippocampal neurogenesis, i.e. the formation of new neurons, following from a decrease in levels of reactive oxygen species. In this study, we suggest an explanation in terms of spin dynamics of a three radical system composed of flavin-semiquinone, superoxide and ascorbyl radical. This model agrees with the experimental data whilst retaining realistic parameters for a biological system, unlike the Radical Pair Mechanism.

The Static Magnetic Field Regulates the Structure, Biochemical Activity, and Gene Expression of Plants

The purpose of this paper is to review the scientific results and summarise the emerging topic of the effects of statistic magnetic field on the structure, biochemical activity, and gene expression of plants. The literature on the subject reports a wide range of possibilities regarding the use of the magnetic field to modify the properties of plant cells. MFs have a significant impact on the photosynthesis efficiency of the biomass and vigour accumulation indexes. Treating plants with SMFs accelerates the formation and accumulation of reactive oxygen species. At the same time, the influence of MFs causes the high activity of antioxidant enzymes, which reduces oxidative stress. SMFs have a strong influence on the shape of the cell and the structure of the cell membrane, thus increasing their permeability and influencing the various activities of the metabolic pathways. The use of magnetic treatments on plants causes a higher content of proteins, carbohydrates, soluble and reducing sugars, and in some cases, lipids and fatty acid composition and influences the uptake of macro- and microelements and different levels of gene expression. In this study, the effect of MFs was considered as a combination of MF intensity and time exposure, for different varieties and plant species. The following article shows the wide-ranging possibilities of applying magnetic fields to the dynamics of changes in the life processes and structures of plants. Thus far, the magnetic field is not widely used in agricultural practice. The current knowledge about the influence of MFs on plant cells is still insufficient. It is, therefore, necessary to carry out detailed research for a more in-depth understanding of the possibilities of modifying the properties of plant cells and achieving the desired effects by means of a magnetic field.

Genetic analysis of cryptochrome in insect magnetosensitivity

The earth’s magnetic field plays an important role in the spectacular migrations and navigational abilities of many higher animals, particularly birds. However, these organisms are not amenable to genetic analysis, unlike the model fruitfly, Drosophila melanogaster, which can respond to magnetic fields under laboratory conditions. We therefore review the field of insect magnetosensitivity focusing on the role of the Cryptochromes (CRYs) that were first identified in Arabidopsis and Drosophila as key molecular components of circadian photo-entrainment pathways. Physico-chemical studies suggest that photo-activation of flavin adenine dinucleotide (FAD) bound to CRY generates a FAD^o− Trp^o+ radical pair as electrons skip along a chain of specific Trp residues and that the quantum spin chemistry of these radicals is sensitive to magnetic fields. The manipulation of CRY in several insect species has been performed using gene editing, replacement/rescue and knockdown methods. The effects of these various mutations on magnetosensitivity have revealed a number of surprises that are discussed in the light of recent developments from both in vivo and in vitro studies.

Magnetic field effects in biology from the perspective of the radical pair mechanism

Hundreds of studies have found that weak magnetic fields can significantly influence various biological systems. However, the underlying mechanisms behind these phenomena remain elusive. Remarkably, the magnetic energies implicated in these effects are much smaller than thermal energies. Here, we review these observations, and we suggest an explanation based on the radical pair mechanism, which involves the quantum dynamics of the electron and nuclear spins of transient radical molecules. While the radical pair mechanism has been studied in detail in the context of avian magnetoreception, the studies reviewed here show that magnetosensitivity is widespread throughout biology. We review magnetic field effects on various physiological functions, discussing static, hypomagnetic and oscillating magnetic fields, as well as isotope effects. We then review the radical pair mechanism as a potential unifying model for the described magnetic field effects, and we discuss plausible candidate molecules for the radical pairs. We review recent studies proposing that the radical pair mechanism provides explanations for isotope effects in xenon anaesthesia and lithium treatment of hyperactivity, magnetic field effects on the circadian clock, and hypomagnetic field effects on neurogenesis and microtubule assembly. We conclude by discussing future lines of investigation in this exciting new area of quantum biology.

Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome

The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.

Anisotropic magnetic field effects in the re-oxidation of cryptochrome in the presence of scavenger radicals

The avian compass and many other of nature's magnetoreceptive traits are widely ascribed to the protein cryptochrome. There, magnetosensitivity is thought to emerge as the spin dynamics of radicals in the applied magnetic field enters in competition with their recombination. The first and dominant model makes use of a radical pair. However, recent studies have suggested that magnetosensitivity could be markedly enhanced for a radical triad, the primary radical pair of which undergoes a spin-selective recombination reaction with a third radical. Here, we test the practicality of this supposition for the reoxidation reaction of the reduced FAD cofactor in cryptochrome, which has been implicated with light-independent magnetoreception but appears irreconcilable with the classical radical pair mechanism (RPM). Based on the available realistic cryptochrome structures, we predict the magnetosensitivity of radical triad systems comprising the flavin semiquinone, the superoxide, and a tyrosine or ascorbyl scavenger radical. We consider many hyperfine-coupled nuclear spins, the relative orientation and placement of the radicals, their coupling by the electron-electron dipolar interaction, and spin relaxation in the superoxide radical in the limit of instantaneous decoherence, which have not been comprehensively considered before. We demonstrate that these systems can provide superior magnetosensitivity under realistic conditions, with implications for dark-state cryptochrome magnetoreception and other biological magneto- and isotope-sensitive radical recombination reactions.

Broadband 75-85 MHz radiofrequency fields disrupt magnetic compass orientation in night-migratory songbirds consistent with a flavin-based radical pair magnetoreceptor

The light-dependent magnetic compass sense of night-migratory songbirds can be disrupted by weak radiofrequency fields. This finding supports a quantum mechanical, radical-pair-based mechanism of magnetoreception as observed for isolated cryptochrome 4, a protein found in birds’ retinas. The exact identity of the magnetically sensitive radicals in cryptochrome is uncertain in vivo, but their formation seems to require a bound flavin adenine dinucleotide chromophore and a chain of four tryptophan residues within the protein. Resulting from the hyperfine interactions of nuclear spins with the unpaired electrons, the sensitivity of the radicals to radiofrequency magnetic fields depends strongly on the number of magnetic nuclei (hydrogen and nitrogen atoms) they contain. Quantum-chemical calculations suggested that electromagnetic noise in the frequency range 75–85 MHz could give information about the identity of the radicals involved. Here, we show that broadband 75–85 MHz radiofrequency fields prevent a night-migratory songbird from using its magnetic compass in behavioural experiments. These results indicate that at least one of the components of the radical pair involved in the sensory process of avian magnetoreception must contain a substantial number of strong hyperfine interactions as would be the case if a flavin–tryptophan radical pair were the magnetic sensor.

Seed priming with non-ionizing physical agents: plant responses and underlying physiological mechanisms

Seed priming has long been explored as an effective value-added potential technique that results in improved germination, reduced seedling emergence time, shortened crop duration, increased stress tolerance and eventually increased higher grain production. However, the wider applicability of water or chemical-based conventional methods of seed priming is often restricted considering its deleterious effects on post-treatment storability or agricultural pollution due to the persistence of chemicals in plant systems or in the environment. In this context, the utilization of physical methods of seed priming for enhancing plant productivity has created a new horizon in the domain of seed technology. Being eco-friendly and cost-effective approaches, priming with extra-terrestrial or physical agents such as ionizing radiation such as X-rays and gamma rays and non-ionizing radiation such as ultrasonic wave, magnetic field, microwaves, and infrared light offers many advantages along with ensuring enhanced production over conventional methods. Ultraviolet radiations, bridging between ionizing and non-ionizing radiation, are important electromagnetic waves that would also be an effective priming agent. Non-ionizing radiation has certain biological advantages over ionizing radiation since it does not generate charged ions while passing through a subject, but has enough energy to cause biological effects. Extensive research works to study the effects of various non-ionizing physical priming methods are required before their wider exploitation in agriculture. With this background, this review aims to highlight the current understanding of non-ionizing physical methods of seed priming and its applicability to combat present-day challenges to achieve agro-ecological resilience.

Radical Scavenging Could Answer the Challenge Posed by Electron-Electron Dipolar Interactions in the Cryptochrome Compass Model

Many birds are endowed with a visual magnetic sense that may exploit magnetosensitive radical recombination processes in the protein cryptochrome. In this widely accepted but unproven model, geomagnetic sensitivity is suggested to arise from variations in the recombination rate of a pair of radicals, whose unpaired electron spins undergo coherent singlet-triplet interconversion in the geomagnetic field by coupling to nuclear spins via hyperfine interactions. However, simulations of this conventional radical pair mechanism (RPM) predicted only tiny magnetosensitivities for realistic conditions because the RPM's directional sensitivity is strongly suppressed by the intrinsic electron-electron dipolar (EED) interactions, casting doubt on its viability as a magnetic sensor. We show how this RPM-suppression problem is overcome in a three-radical system in which a third "scavenger" radical reacts with one member of the primary pair. We use this finding to predict substantial magnetic field effects that exceed those of the RPM in the presence of EED interactions in animal cryptochromes.

Cryptochrome magnetoreception: four tryptophans could be better than three

The biophysical mechanism of the magnetic compass sensor in migratory songbirds is thought to involve photo-induced radical pairs formed in cryptochrome (Cry) flavoproteins located in photoreceptor cells in the eyes. In Cry4a-the most likely of the six known avian Crys to have a magnetic sensing function-four radical pair states are formed sequentially by the stepwise transfer of an electron along a chain of four tryptophan residues to the photo-excited flavin. In purified Cry4a from the migratory European robin, the third of these flavin-tryptophan radical pairs is more magnetically sensitive than the fourth, consistent with the smaller separation of the radicals in the former. Here, we explore the idea that these two radical pair states of Cry4a could exist in rapid dynamic equilibrium such that the key magnetic and kinetic properties are weighted averages. Spin dynamics simulations suggest that the third radical pair is largely responsible for magnetic sensing while the fourth may be better placed to initiate magnetic signalling particularly if the terminal tryptophan radical can be reduced by a nearby tyrosine. Such an arrangement could have allowed independent optimization of the essential sensing and signalling functions of the protein. It might also rationalize why avian Cry4a has four tryptophans while Crys from plants have only three.

Cryptochrome-dependent magnetoreception in a heteropteran insect continues even after 24 h in darkness

Sensitivity to magnetic fields is dependent on the intensity and color of light in several animal species. The light-dependent magnetoreception working model points to cryptochrome (Cry) as a protein cooperating with its co-factor flavin, which possibly becomes magnetically susceptible upon excitation by light. The type of Cry involved and what pair of magnetosensitive radicals are responsible is still elusive. Therefore, we developed a conditioning assay for the firebug Pyrrhocoris apterus, an insect species that possesses only the mammalian cryptochrome (Cry II). Here, using the engineered Cry II null mutant, we show that: (i) vertebrate-like Cry II is an essential component of the magnetoreception response, and (ii) magnetic conditioning continues even after 25 h in darkness. The light-dependent and dark-persisting magnetoreception based on Cry II may inspire new perspectives in magnetoreception and cryptochrome research.

The diversity of photosensitivity and its implications for light pollution

Artificial light at night (ALAN) is a pervasive anthropogenic pollutant, emanating from urban and suburban developments and reaching nearly all ecosystems from dense forests to coastlines. One proposed strategy for attenuating the consequences of ALAN is to modify its spectral composition to forms that are less disruptive for photosensory systems. However, ALAN is a complicated pollutant to manage due to the extensive variation in photosensory mechanisms and the diverse ways these mechanisms manifest in biological and ecological contexts. Here, we highlight the diversity in photosensitivity across taxa and the implications of this diversity in predicting biological responses to different forms of night lighting. We curated this paper to be broadly accessible and inform current decisions about the spectrum of electric lights used outdoors. We advocate that efforts to mitigate light pollution should consider the unique ways species perceive ALAN, as well as how diverse responses to ALAN scale up to produce diverse ecological outcomes.

Effect of temperature on the Arabidopsis cryptochrome photocycle

Cryptochromes are blue light-absorbing photoreceptors found in plants and animals with many important signalling functions. These include control of plant growth, development, and the entrainment of the circadian clock. Plant cryptochromes have recently been implicated in adaptations to temperature variation, including temperature compensation of the circadian clock. However, the effect of temperature directly on the photochemical properties of the cryptochrome photoreceptor remains unknown. Here we show that the response to light of purified Arabidopsis Cry1 and Cry2 proteins was significantly altered by temperature. Spectral analysis at 15°C showed a pronounced decrease in flavin reoxidation rates from the biologically active, light-induced (FADH°) signalling state of cryptochrome to the inactive (FADox) resting redox state as compared to ambient (25°C) temperature. This result indicates that at low temperatures, the concentration of the biologically active FADH° redox form of Cry is increased, leading to the counterintuitive prediction that there should be an increased biological activity of Cry at lower temperatures. This was confirmed using Cry1 cryptochrome C-terminal phosphorylation as a direct biological assay for Cry activation in vivo. We conclude that enhanced cryptochrome function in vivo at low temperature is consistent with modulation by temperature of the cryptochrome photocycle.

Magnetic sensitivity of cryptochrome 4 from a migratory songbird

Night-migratory songbirds are remarkably proficient navigators¹. Flying alone and often over great distances, they use various directional cues including, crucially, a light-dependent magnetic compass^2,3. The mechanism of this compass has been suggested to rely on the quantum spin dynamics of photoinduced radical pairs in cryptochrome flavoproteins located in the retinas of the birds^4-7. Here we show that the photochemistry of cryptochrome 4 (CRY4) from the night-migratory European robin (Erithacus rubecula) is magnetically sensitive in vitro, and more so than CRY4 from two non-migratory bird species, chicken (Gallus gallus) and pigeon (Columba livia). Site-specific mutations of ErCRY4 reveal the roles of four successive flavin-tryptophan radical pairs in generating magnetic field effects and in stabilizing potential signalling states in a way that could enable sensing and signalling functions to be independently optimized in night-migratory birds.

The Magnetic Compass of Birds: The Role of Cryptochrome

The geomagnetic field provides directional information for birds. The avian magnetic compass is an inclination compass that uses not the polarity of the magnetic field but the axial course of the field lines and their inclination in space. It works in a flexible functional window, and it requires short-wavelength light. These characteristics result from the underlying sensory mechanism based on radical pair processes in the eyes, with cryptochrome suggested as the receptor molecule. The chromophore of cryptochrome, flavin adenine dinucleotide (FAD), undergoes a photocycle, where radical pairs are formed during photo-reduction as well as during re-oxidation; behavioral data indicate that the latter is crucial for detecting magnetic directions. Five types of cryptochromes are found in the retina of birds: cryptochrome 1a (Cry1a), cryptochrome 1b, cryptochrome 2, cryptochrome 4a, and cryptochrome 4b. Because of its location in the outer segments of the ultraviolet cones with their clear oil droplets, Cry1a appears to be the most likely receptor molecule for magnetic compass information.

Cryptochromes: Photochemical and structural insight into magnetoreception

Cryptochromes (CRYs) function as blue light photoreceptors in diverse physiological processes in nearly all kingdoms of life. Over the past several decades, they have emerged as the most likely candidates for light-dependent magnetoreception in animals, however, a long history of conflicts between in vitro photochemistry and in vivo behavioral data complicate validation of CRYs as a magnetosensor. In this review, we highlight the origins of conflicts regarding CRY photochemistry and signal transduction, and identify recent data that provides clarity on potential mechanisms of signal transduction in magnetoreception. The review primarily focuses on examining differences in photochemistry and signal transduction in plant and animal CRYs, and identifies potential modes of convergent evolution within these independent lineages that may identify conserved signaling pathways.

Cryptochromes and the Circadian Clock: The Story of a Very Complex Relationship in a Spinning World

Cryptochromes are flavin-containing blue light photoreceptors, present in most kingdoms, including archaea, bacteria, plants, animals and fungi. They are structurally similar to photolyases, a class of flavoproteins involved in light-dependent repair of UV-damaged DNA. Cryptochromes were first discovered in Arabidopsis thaliana in which they control many light-regulated physiological processes like seed germination, de-etiolation, photoperiodic control of the flowering time, cotyledon opening and expansion, anthocyanin accumulation, chloroplast development and root growth. They also regulate the entrainment of plant circadian clock to the phase of light-dark daily cycles. Here, we review the molecular mechanisms by which plant cryptochromes control the synchronisation of the clock with the environmental light. Furthermore, we summarise the circadian clock-mediated changes in cell cycle regulation and chromatin organisation and, finally, we discuss a putative role for plant cryptochromes in the epigenetic regulation of genes.

Differential root and shoot magnetoresponses in Arabidopsis thaliana

The geomagnetic field (GMF) is one of the environmental stimuli that plants experience continuously on Earth; however, the actions of the GMF on plants are poorly understood. Here, we carried out a time-course microarray experiment to identify genes that are differentially regulated by the GMF in shoot and roots. We also used qPCR to validate the activity of some genes selected from the microarray analysis in a dose-dependent magnetic field experiment. We found that the GMF regulated genes in both shoot and roots, suggesting that both organs can sense the GMF. However, 49% of the genes were regulated in a reverse direction in these organs, meaning that the resident signaling networks define the up- or downregulation of specific genes. The set of GMF-regulated genes strongly overlapped with various stress-responsive genes, implicating the involvement of one or more common signals, such as reactive oxygen species, in these responses. The biphasic dose response of GMF-responsive genes indicates a hormetic response of plants to the GMF. At present, no evidence exists to indicate any evolutionary advantage of plant adaptation to the GMF; however, plants can sense and respond to the GMF using the signaling networks involved in stress responses.

The Geomagnetic Field (GMF) Modulates Nutrient Status and Lipid Metabolism during Arabidopsis thaliana Plant Development

The Geomagnetic field (GMF) is a typical component of our planet. Plant perception of the GMF implies that any magnetic field (MF) variation would induce possible metabolic changes. In this work was we assessed the role of the GMF on Arabidopsis thaliana Col0 mineral nutrition and lipid metabolism during plant development. We reduced the local GMF (about 40 μT) to Near Null Magnetic Field (NNMF, about 30 nT) to evaluate the effects of GMF on Arabidopsis in a time-course (from rosette to seed-set) experiment by studying the lipid content (fatty acids, FA; and surface alkanes, SA) and mineral nutrients. The expression of selected genes involved in lipid metabolism was assessed by Real-Time PCR (qPCR). A progressive increase of SA with carbon numbers between 21 and 28 was found in plants exposed to NNMF from bolting to flowering developmental stages, whereas the content of some FA significantly (p < 0.05) increased in rosette, bolting and seed-set developmental stages. Variations in SA composition were correlated to the differential expression of several Arabidopsis 3-ketoacyl-CoAsynthase (KCS) genes, including KCS1, KCS5, KCS6, KCS8, and KCS12, a lipid transfer protein (LTPG1) and a lipase (LIP1). Ionomic analysis showed a significant variation in some micronutrients (Fe, Co, Mn and Ni) and macronutrients (Mg, K and Ca) during plant development of plants exposed to NNMF. The results of this work show that A. thaliana responds to variations of the GMF which are perceived as is typical of abiotic stress responses.

HEK293 cell response to static magnetic fields via the radical pair mechanism may explain therapeutic effects of pulsed electromagnetic fields

PEMF (Pulsed Electromagnetic Field) stimulation has been used for therapeutic purposes for over 50 years including in the treatment of memory loss, depression, alleviation of pain, bone and wound healing, and treatment of certain cancers. However, the underlying cellular mechanisms mediating these effects have remained poorly understood. In particular, because magnetic field pulses will induce electric currents in the stimulated tissue, it is unclear whether the observed effects are due to the magnetic or electric component of the stimulation. Recently, it has been shown that PEMFs stimulate the formation of ROS (reactive oxygen species) in human cell cultures by a mechanism that requires cryptochrome, a putative magnetosensor. Here we show by qPCR analysis of ROS-regulated gene expression that simply removing cell cultures from the Earth’s geomagnetic field by placing them in a Low-Level Field condition induces similar effects on ROS signaling as does exposure of cells to PEMF. This effect can be explained by the so-called Radical Pair mechanism, which provides a quantum physical means by which the rates and product yields (e.g. ROS) of biochemical redox reactions may be modulated by magnetic fields. Since transient cancelling of the Earth’s magnetic field can in principle be achieved by PEMF exposure, we propose that the therapeutic effects of PEMFs may be explained by the ensuing modulation of ROS synthesis. Our results could lead to significant improvements in the design and therapeutic applications of PEMF devices.

Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

Background

Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. The critical genetic architecture of non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells in a highly regenerable cotton genotype is unknown.

Results

In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages during somatic embryogenesis, non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells. The rate of EC formation in Jin668 is 96%. Differential gene expression analysis revealed a total of 5333 differentially expressed genes (DEG) with 2534 genes upregulated and 2799 genes downregulated in EC. A total of 144 genes were unique to NEC cells and 174 genes were unique to EC. Clustering and enrichment analysis identified genes upregulated in EC that function as transcription factors/DNA binding, phytohormone response, oxidative reduction, and regulators of transcription; while genes categorized in methylation pathways were downregulated. Four key transcription factors were identified based on their sharp upregulation in EC tissue; LEAFY COTYLEDON 1 (LEC1), BABY BOOM (BBM), FUSCA (FUS3) and AGAMOUS-LIKE15 with distinguishable subgenome expression bias.

Conclusions

This comparative analysis of NEC and EC transcriptomes gives new insights into the genes involved in somatic embryogenesis in cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12861-020-00230-4.

Arabidopsis cryptochrome is responsive to Radiofrequency (RF) electromagnetic fields

How living systems respond to weak electromagnetic fields represents one of the major unsolved challenges in sensory biology. Recent evidence has implicated cryptochrome, an evolutionarily conserved flavoprotein receptor, in magnetic field responses of organisms ranging from plants to migratory birds. However, whether cryptochromes fulfill the criteria to function as biological magnetosensors remains to be established. Currently, theoretical predictions on the underlying mechanism of chemical magnetoreception have been supported by experimental observations that exposure to radiofrequency (RF) in the MHz range disrupt bird orientation and mammalian cellular respiration. Here we show that, in keeping with certain quantum physical hypotheses, a weak 7 MHz radiofrequency magnetic field significantly reduces the biological responsivity to blue light of the cryptochrome receptor cry1 in Arabidopsis seedlings. Using an in vivo phosphorylation assay that specifically detects activated cryptochrome, we demonstrate that RF exposure reduces conformational changes associated with biological activity. RF exposure furthermore alters cryptochrome-dependent plant growth responses and gene expression to a degree consistent with theoretical predictions. To our knowledge this represents the first demonstration of a biological receptor responding to RF exposure, providing important new implications for magnetosensing as well as possible future applications in biotechnology and medicine.

Mechanisms of Cryptochrome-Mediated Photoresponses in Plants

Cryptochromes are blue-light receptors that mediate photoresponses in plants. The genomes of most land plants encode two clades of cryptochromes, CRY1 and CRY2, which mediate distinct and overlapping photoresponses within the same species and between different plant species. Photoresponsive protein-protein interaction is the primary mode of signal transduction of cryptochromes. Cryptochromes exist as physiologically inactive monomers in the dark; the absorption of photons leads to conformational change and cryptochrome homooligomerization, which alters the affinity of cryptochromes interacting with cryptochrome-interacting proteins to form various cryptochrome complexes. These cryptochrome complexes, collectively referred to as the cryptochrome complexome, regulate transcription or stability of photoresponsive proteins to modulate plant growth and development. The activity of cryptochromes is regulated by photooligomerization; dark monomerization; cryptochrome regulatory proteins; and cryptochrome phosphorylation, ubiquitination, and degradation. Most of the more than 30 presently known cryptochrome-interacting proteins are either regulated by other photoreceptors or physically interactingwith the protein complexes of other photoreceptors. Some cryptochrome-interacting proteins are also hormonal signaling or regulatory proteins. These two mechanisms enable cryptochromes to integrate blue-light signals with other internal and external signals to optimize plant growth and development.

Electron-Electron Dipolar Interaction Poses a Challenge to the Radical Pair Mechanism of Magnetoreception

A visual magnetic sense in migratory birds has been hypothesized to rely on a radical pair reaction in the protein cryptochrome. In this model, magnetic sensitivity originates from coherent spin dynamics, as the radicals couple to magnetic nuclei via hyperfine interactions. Prior studies have often neglected the electron-electron dipolar (EED) coupling from this hypothesis. We show that EED interactions suppress the anisotropic response to the geomagnetic field by the radical pair mechanism in cryptochrome and that this attenuation is unlikely to be mitigated by mutual cancellation of the EED and electronic exchange coupling, as previously suggested. We then demonstrate that this limitation may be overcome by extending the conventional model to include a third, nonreacting radical. We predict that hyperfine effects could work in concert with three-radical dipolar interactions to tailor a superior magnetic response, thereby providing a new principle for magnetosensitivity with applications for sensing, navigation, and the assessment of biological magnetic field effects.

Viability of superoxide-containing radical pairs as magnetoreceptors

The ability of night-migratory songbirds to sense the direction of the Earth's magnetic field is increasingly attributed to a photochemical mechanism in which the magnetic field acts on transient radical pairs in cryptochrome flavoproteins located in the birds' eyes. The magnetically sensitive species is commonly assumed to be [FAD^•- TrpH^•+], formed by sequential light-induced intraprotein electron transfers from a chain of tryptophan residues to the flavin adenine dinucleotide chromophore. However, some evidence points to superoxide, O₂ ^•-, as an alternative partner for the flavin radical. The absence of hyperfine interactions in O₂ ^•- could lead to a more sensitive magnetic compass, but only if the electron spin relaxation of the O₂ ^•- radical is much slower than normally expected for a small mobile radical with an orbitally degenerate electronic ground state. In this study we use spin dynamics simulations to model the sensitivity of a flavin-superoxide radical pair to the direction of a 50 μT magnetic field. By varying parameters that characterize the local environment and molecular dynamics of the radicals, we identify the highly restrictive conditions under which a O₂ ^•--containing radical pair could form the basis of a geomagnetic compass sensor. We conclude that the involvement of superoxide in compass magnetoreception must remain highly speculative until further experimental evidence is forthcoming.

Cryptochrome mediated magnetic sensitivity in Arabidopsis occurs independently of light-induced electron transfer to the flavin

Arabidopsis cryptochrome-dependent magnetosensitivity occurs via a reaction that does not require light. This excludes radical pairs formed during light-triggered electron transfer to the flavin.

Static magnetic field regulates Arabidopsis root growth via auxin signaling

Static magnetic field (SMF) plays important roles in biological processes of many living organisms. In plants, however, biological significance of SMF and molecular mechanisms underlying SMF action remain largely unknown. To address these questions, we treated Arabidopsis young seedlings with different SMF intensities and directions. Magnetic direction from the north to south pole was adjusted in parallel (N0) with, opposite (N180) and perpendicular to the gravity vector. We discovered that root growth is significantly inhanced by 600 mT treatments except for N180, but not by any 300 mT treatments. N0 treatments lead to more active cell division of the meristem, and higher auxin content that is regulated by coordinated expression of PIN3 and AUX1 in root tips. Consistently, N0-promoted root growth disappears in pin3 and aux1 mutants. Transcriptomic and gene ontology analyses revealed that in roots 85% of the total genes significantly down-regulated by N0 compared to untreatment are enriched in plastid biological processes, such as metabolism and chloroplast development. Lastly, no difference in root length is observed between N0-treated and untreated roots of the double cryptochrome mutant cry1 cry2. Taken together, our data suggest that SMF-regulated root growth is mediated by CRY and auxin signaling pathways in Arabidopsis.