The dual-action mechanism of Arabidopsis cryptochromes

Cryptochromes (CRYs) in pepper: Genome-wide identification, evolution and functional analysis of the negative role of CaCRY1 under Phytophthora capsici infection

Cryptochromes (CRYs) are ultraviolet-A (UV-A) and blue light photoreceptors that perceive UV-A and blue light to mediate a range of physiological processes including disease response in plants. However, there has been no report about the roles of CRY genes in pepper, which often suffers from Phytophthora blight caused by Phytophthora capsici. In this work, three pepper CRY genes were identified and their characteristics were examined by bioinformatics analysis. CaCRY1 is an ortholog of AtCRY1 located in the cytoplasm and nucleus, and expression analysis by RT-qPCR showed that its transcription was differentially regulated by jasmonic acid (JA) and salicylic acid (SA), as well as by P. capsici infection (PCI). Overexpression of CaCRY1 in pepper and Nicotiana benthamiana promoted the susceptibility of plants to PCI. Further virus-induced gene silencing (VIGS) analysis showed that silencing of CaCRY1 promoted the resistance of pepper plants to PCI with decreased disease index and transcripts of genes associated with SA biosynthesis. RNA-seq analysis showed that CaCRY1 silencing affected many genes in stress-related metabolic pathways. In summary, our findings show that CaCRY1 plays a negative role in the defense response of pepper to PCI, laying a foundation for studying the roles of CRYs in the future.

The CRY1-COP1-HY5 axis mediates blue-light regulation of Arabidopsis thermotolerance

High-temperature stress, also referred to as heat stress, often has detrimental effects on plant growth and development. Phytochromes have been implicated in the regulation of plant heat-stress responses, but the role of blue-light receptors, such as cryptochromes, in plant blue-light-dependent heat-stress responses remains unclear. We found that cryptochrome 1 (CRY1) negatively regulates heat-stress tolerance (thermotolerance) in Arabidopsis. Heat stress represses CRY1 phosphorylation. Unphosphorylated CRY1 exhibits decreased activity in suppressing the interaction of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) with ELONGATED HYPOCOTYL 5 (HY5), leading to excessive degradation of HY5 under heat stress in blue light. This reduction in HY5 protein levels subsequently relieves its repression of the transcription of HY5 target genes, especially the heat-shock transcription factors. Our study thus reveals a novel mechanism by which CRY1-mediated blue-light signaling suppresses plant thermotolerance and highlights the dual function of the CRY1-COP1-HY5 module in both light- and heat-stress signaling, providing insights into how plants integrate heat stress and light signals to optimize their survival under heat stress.

Dissecting sequence-structure-function-diversity in plant cryptochromes

Ubiquitous to every stratum of life, cryptochromes regulate numerous light dependent functions in terrestrial plants. These include light-dependent transcription, circadian rhythm, inhibition of hypocotyl elongation, programmed cell death, promotion of floral initiation, mediation of gravitropic response, responding to biotic and abiotic stress etc. There have been quite a few seminal reviews including on plant cryptochromes, focusing mostly on the detailed functional aspects. This review primarily focuses on understanding the link connecting sequence-structure hierarchy behind the functional diversity in plant cryptochromes. With available sequence information and 3D structure data, we hereby explore the molecular origin of functional diversity in both the subtypes i.e., CRY1 and CRY2. First, we discuss the structural details and functional distinctiveness of all subtypes of plant cryptochromes. Next we draw a comparison not just between two cryptochromes but also other Cryptochrome/Photolyase Family (CPF) members e.g. CRY-DASH/CRY3 and CPD/6-4 photolyases of plant origin. Further, by constructing a phylogenetic profile from multiple sequence alignment we investigate how a crucial activity like DNA repair is restricted to some members of CPF and not all. It is a well-known fact that the function of a protein is heavily if not solely guided by the structure-sequence relationship. Therefore, the resultant hypothesis as drawn from this comparative and collective study could predict functions of many under-studied plant cryptochromes when compared with their well-studied counterparts like Arabidopsis cryptochromes. An extensive sequence-structure-function analysis complemented with evolutionary studies and bibliographic survey is useful towards understanding the immensely diverse CPF.

Light and high temperatures control epigenomic and epitranscriptomic events in Arabidopsis

Light and temperature are two key environmental factors that control plant growth and adaptation by influencing biomolecular events. This review highlights the latest milestones on the role of light and high temperatures in modulating the epigenetic and epitranscriptomic landscape of Arabidopsis to trigger developmental and adaptive responses to a changing environment. Recent discoveries on how light and high temperature signals are integrated in the nucleus to modulate gene expression are discussed, as well as highlighting research gaps and future perspectives in further understanding how to promote plant resilience in times of climate change.

The two action mechanisms of plant cryptochromes

Plant cryptochromes (CRYs) are photolyase-like blue-light receptors that contain a flavin adenine dinucleotide (FAD) chromophore. In plants grown in darkness, CRYs are present as monomers. Photoexcited CRYs oligomerize to form homo-tetramers. CRYs physically interact with non-constitutive or constitutive CRY-interacting proteins to form the non-constitutive or constitutive CRY complexes, respectively. The non-constitutive CRY complexes exhibit a different affinity for CRYs in response to light, and act by a light-induced fit (lock-and-key) mechanism. The constitutive CRY complexes have a similar affinity for CRYs regardless of light, and act via a light-induced liquid-liquid phase separation (LLPS) mechanism. These CRY complexes mediate blue-light regulation of transcription, mRNA methylation, mRNA splicing, protein modification, and proteolysis to modulate plant growth and development.

Plant physiology: Rethinking CRY photoreceptors

The CRY2 photoreceptor is known to form homotetramers that bind to transcription regulators to affect gene expression in response to light. A new study provides evidence that the CRY2 monomer binds different transcription regulators to affect gene expression in darkness, suggesting that photoreceptors change activity in response to light.

The Arabidopsis blue-light photoreceptor CRY2 is active in darkness to inhibit root growth

Cryptochromes (CRYs) are blue-light receptors that regulate diverse aspects of plant growth. However, whether and how non-photoexcited CRYs function in darkness or non-blue-light conditions is unknown. Here, we show that CRY2 affects the Arabidopsis transcriptome even in darkness, revealing a non-canonical function. CRY2 suppresses cell division in the root apical meristem to downregulate root elongation in darkness. Blue-light oligomerizes CRY2 to de-repress root elongation. CRY2 physically interacts with FORKED-LIKE 1 (FL1) and FL3, and these interactions are inhibited by blue light, with only monomeric but not dimeric CRY2 able to interact. FL1 and FL3 associate with the chromatin of cell division genes to facilitate their transcription. This pro-growth activity is inhibited by CRY2's physical interaction with FLs in darkness. Plants have evolved to perceive both blue-light and dark cues to coordinate activation and repression of competing developmental processes in above- and below-ground organs through economical and dichotomous use of ancient light receptors.

Origin and evolution of the blue light receptor cryptochromes (CRY1/2) in aquatic angiosperms

Cryptochromes (CRYs), which are responsible for sensing blue light in plants, play a critical role in regulating blue light signals and circadian rhythms. However, their functions extend beyond light detection, as they also aid plants in adapting to stress and potentially other regulatory mechanisms. Aquatic angiosperms, which independently evolved from various angiosperm lineages, have developed specific adaptations to unique light qualities and environmental stressors found in aquatic habitats compared to terrestrial ones. It was hypothesized that the sequences and regulatory networks of angiosperm CRY1/2 underwent adaptive evolution in different aquatic angiosperm lineages. To test this hypothesis, we compiled comprehensive datasets consisting of 55 green plant genomes (including 37 angiosperm genomes), 80 angiosperm transcriptomes, and 4 angiosperm expression networks. Through comparative analysis, we found that CRY1 originated from a common ancestor of seed plants, whereas CRY2 originated from a common ancestor of land plants. In angiosperms, the CRY1/2 sequences of aquatic lineages exhibited positive selection, and the conserved valine-proline motif of CRY2 showed a convergent loss in 2 aquatic species. Coexpressed genes associated with blue light receptors (CRY) showed adaptations to aquatic environments, specifically in relation to flooding and osmotic stress. These discoveries shed light on the adaptive evolution of CRY1/2, encompassing their origins, sequences, and regulatory networks. Furthermore, these results provide valuable insights for investigating the uncharacterized functions and regulatory pathways of CRY and offer potential targets for enhancing growth and adaptation in agricultural plants.

Light-induced cryptochrome 2 liquid-liquid phase separation and mRNA methylation

Light is essential not only for photosynthesis but also for the regulation of various physiological and developmental processes in plants. While the mechanisms by which light regulates transcription and protein stability are well established, the effects of light on RNA methylation and their subsequent impact on plant growth and development are less understood. Upon exposure to blue light, the photoreceptor cryptochromes form nuclear speckles or nuclear bodies, termed CRY photobodies. The CRY2 photobodies undergo light-induced homo-oligomerization and liquid-liquid phase separation (LLPS), which are crucial for their physiological activity. Recent studies have proposed that blue light-induced CRY2 LLPS increases the local concentration or directly enhances the biochemical activities of RNA N6-methyladenosine (m6A) methyltransferases, thus, to regulate circadian clock and maintain Chl homeostasis through processes of RNA decay or translation. This review aimed to elucidate the functions of CRY2 and LLPS in RNA methylation, focusing on the light-controlled reversible phase transitions regulon and the outstanding questions that remain in RNA methylation.

Regulation of cryptochrome-mediated blue light signaling by the ABI4-PIF4 module

ABSCISIC ACID-INSENSITIVE 4 (ABI4) is a pivotal transcription factor which coordinates multiple aspects of plant growth and development as well as plant responses to environmental stresses. ABI4 has been shown to be involved in regulating seedling photomorphogenesis; however, the underlying mechanism remains elusive. Here, we show that the role of ABI4 in regulating photomorphogenesis is generally regulated by sucrose, but ABI4 promotes hypocotyl elongation of Arabidopsis seedlings under blue (B) light under all tested sucrose concentrations. We further show that ABI4 physically interacts with PHYTOCHROME INTERACTING FACTOR 4 (PIF4), a well-characterized growth-promoting transcription factor, and post-translationally promotes PIF4 protein accumulation under B light. Further analyses indicate that ABI4 directly interacts with the B light photoreceptors cryptochromes (CRYs) and inhibits the interactions between CRYs and PIF4, thus relieving CRY-mediated repression of PIF4 protein accumulation. In addition, while ABI4 could directly activate its own expression, CRYs enhance, whereas PIF4 inhibits, ABI4-mediated activation of the ABI4 promoter. Together, our study demonstrates that the ABI4-PIF4 module plays an important role in mediating CRY-induced B light signaling in Arabidopsis.

A structural decryption of cryptochromes

Cryptochromes (CRYs), which are signaling proteins related to DNA photolyases, play pivotal roles in sensory responses throughout biology, including growth and development, metabolic regulation, circadian rhythm entrainment and geomagnetic field sensing. This review explores the evolutionary relationships and functional diversity of cryptochromes from the perspective of their molecular structures. In general, CRY biological activities derive from their core structural architecture, which is based on a Photolyase Homology Region (PHR) and a more variable and functionally specific Cryptochrome C-terminal Extension (CCE). The α/β and α-helical domains within the PHR bind FAD, modulate redox reactive residues, accommodate antenna cofactors, recognize small molecules and provide conformationally responsive interaction surfaces for a range of partners. CCEs add structural complexity and divergence, and in doing so, influence photoreceptor reactivity and tailor function. Primary and secondary pockets within the PHR bind myriad moieties and collaborate with the CCEs to tune recognition properties and propagate chemical changes to downstream partners. For some CRYs, changes in homo and hetero-oligomerization couple to light-induced conformational changes, for others, changes in posttranslational modifications couple to cascades of protein interactions with partners and effectors. The structural exploration of cryptochromes underscores how a broad family of signaling proteins with close relationship to light-dependent enzymes achieves a wide range of activities through conservation of key structural and chemical properties upon which function-specific features are elaborated.

How plants sense and respond to osmotic stress

Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.