Regulation of flowering time by Arabidopsis photoreceptors

Constitutively active Arabidopsis cryptochrome 2 alleles identified using yeast selection and deep mutational scanning

The Arabidopsis blue light photoreceptor cryptochrome 2 (CRY2) responds to blue light to initiate a variety of plant light-based behaviors and has been widely used for optogenetic engineering. Despite these important biological functions, the precise photoactivation mechanism of CRY2 remains incompletely understood. In light, CRY2 undergoes tetramerization and binds to partner proteins, including the transcription factor CIB1. Here we used yeast-two hybrid screening and deep mutational scanning to identify CRY2 amino acid changes that result in constitutive interaction with CIB1 in dark. The majority of CRY2 variants showing constitutive CIB1 interaction mapped to two regions, one near the FAD chromophore, and a second region located near the ATP binding site. Further testing of CRY2 variants from each region revealed three mapping near to the FAD binding pocket (D393S, D393A, and M378R) that also form constitutive CRY2-CRY2 homomers in dark, suggesting they adopt global conformational changes that mimic the photoactive state. Characterization of D393S in the homolog pCRY from Chlamydomonas reinhardtii using time-resolved UV-vis spectroscopy revealed that the FAD chromophore fails to form the neutral radical as signaling state upon illumination. Size exclusion chromatography of D393S shows the presence of homomers instead of a monomer in the dark, providing support for a hyperactive variant decoupled from the FAD. Our work provides new insight into photoactivation mechanisms of plant cryptochromes relevant for physiology and optogenetic application by revealing and localizing distinct activation pathways for light-driven CRY2-CIB1 and CRY2-CRY2 interactions.

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.

Circadian rhythm gene cryptochrome 2 (Cry2) interacts with lipid metabolism to promote vascular aging

BACKGROUND

Vascular aging is the basis of many chronic diseases of the aged, such as hypertension, coronary heart disease and stroke.

OBJECTIVE

This study aims to deepen our understanding of the pathological mechanisms of vascular aging by combining multiple big data research methods, and reveal potential therapeutic targets and biomarkers.

METHODS

WGCNA method was used to integrate the aortic transcriptome data of multiple age stages, and extract the key module and key pathway. The gene of aortic rhythm was integrated by JTK algorithm. Correlation calculation was performed for core gene and associated pathways. Finally, the expression of the core gene and their interaction with the associated pathways were verified in cell senescence.

RESULTS

WGCNA showed that circadian rhythm is the key pathway of vascular aging, and circadian rhythm and metabolism interact to promote the occurrence of vascular aging. Cry2 has been identified as the most critical core rhythm gene. Lipid metabolism is the most Cry2-related subpathway, among which phospholipid metabolism and Serac1 have the strongest and most significant correlation with Cry2. Cry2 is mainly distributed in endothelial cells in both young and senescent blood vessels, and affects five lipid-related metabolic processes including lipid transport during endothelial senescence.

CONCLUSION

This study suggests that circadian rhythm and Cry2 may be potential targets of vascular aging, and further studies on their interaction with lipid metabolism will provide effective strategies for the prevention and treatment of age-related vascular diseases.

Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

Function diversification of CONSTANS-like genes in Pyrus and regulatory mechanisms in response to different light quality

Pear (Pyrus L.) is a significant commercial fruit globally, with diverse species exhibiting variations in their flowering periods due to environmental factors. CONSTANS-like (COL) genes, known from previous studies in Arabidopsis, are key regulators of flowering time by sensing photoperiod. However, the evolutionary history and functions of COL genes in different pear species remain unclear. In this study, we identified a total of 79 COL genes in different pear species, including 12 COL genes in Pyrus bretschneideri 'DangshanSuli', 9 in Pyrus ussuriensis × hybrid 'Zhongai 1', 11 in Pyrus communis 'Bartlett', 13 in Pyrus betulifolia, 18 in Pyrus pyrifolia 'Cuiguan', 16 in Pyrus pyrifolia 'Nijisseiki'. Analysis of gene structure, phylogenetic tree, and multiple sequences provided valuable insights into the fundamental understanding of COL genes in pear. The impact of selection pressure on the PbrCOLs in Chinese white pear was assessed using Ka/Ks, revealing that the evolution rate of PbrCOLs was influenced by purification selection factors. The study also revealed different tissue-specific expression patterns of PbrCOLs under varying light quality. Real-time quantitative PCR revealed that under natural light conditions, the expression patterns of PbrCOL2, PbrCOL3, and PbrCOL4 are similar to previous studies on CONSTANS gene in Arabidopsis, with increased expression levels during the day and decreased levels at night. However, PbrCOL1, PbrCOL6, and PbrCOL9 exhibit different expression patterns, with decreased expression levels both during the day and at night. After red light treatment, high expression of PbrCOL3 and PbrCOL4 was observed at night, while the expression patterns of the other four genes did not show significant changes. Following blue light treatment, the expression peaks of PbrCOL1 and PbrCOL6 occurred during the night, showing opposite expression patterns compared to the study in Arabidopsis. The overexpression of PbrCOL3 significantly increase the chlorophyll content in pear seedlings, and its expression significantly affected the expression of other key flowering-related genes. Also, overexpression of PbrCOL3 resulted in a late-flowering phenotype in Arabidopsis. These findings indicate diverse responsive mechanisms and functions of PbrCOL genes on flowering time in pear. In conclusion, this study established a foundation for a deeper understanding of the specific roles of PbrCOLs in regulating the reproductive development of pear, particularly in the context of the photoperiodic flowering process.

Plastid- and photoreceptor-dependent signaling is required for the response to photoperiod stress

Prolongation of the light period causes photoperiod stress in plants. The response to photoperiod stress includes the induction of a distinct set of stress marker genes, of reactive oxygen species (ROS), and of stress hormones. In this study, the impact of light intensity and light quality on the photoperiod stress response was investigated. A threshold light intensity of circa 50 μmol m-2 s-1 is necessary for inducing photoperiod stress, indicating the involvement of chloroplasts. Lower photoperiod stress symptoms in retrograde signaling mutants (gun4, gun5) and mutants with constrained plastid function (glk1 glk2) corroborated the role of chloroplasts. Genetic analysis revealed that the photoreceptors phyB and particularly CRY2 are important to perceive photoperiod stress. Overall, these results showed that both plastid-dependent and photoreceptor-dependent signaling pathways are involved in sensing the light conditions causing photoperiod stress and governing the response to it.

Combined transcriptional and metabolomic analysis of flavonoids in the regulation of female flower bud differentiation in Juglans sigillata Dode

Juglans sigillata Dode is rich in flavonoids, but the low ratio of female to male flower buds limits the development of the J. sigillata industry. While the abundance of flavonoids in J. sigillata is known, whether flavonoids influence female flower bud differentiation has not been reported. In this study, we explored the regulatory mechanisms of gene expression and metabolite accumulation during female flower bud differentiation through integrated transcriptomic and metabolomic analyses. Our findings revealed that flavonoid biosynthesis is a key pathway influencing female flower bud differentiation, with metabolites primarily shifting towards the isoflavonoid, flavone, and flavonol branches. Structural genes such as chalcone synthase, dihydroflavonol 4-reductase, flavonol synthase, and flavonoid 3',5'-hydroxylase were identified as playing crucial regulatory roles. The expression of these genes promoted the accumulation of flavonoids, which in turn influenced female flower bud differentiation by modulating key regulatory genes including Suppressor of Overexpression of Constans1, Constans, Flowering Locus T, and APETALA1. Furthermore, transcription factors (TFs) highly expressed during the physiological differentiation of female flower buds, particularly M-type MADS, WRKY, and MYB, were positively correlated with flavonoid biosynthesis genes, indicating their significant role in the regulation of flavonoid production. These results offer valuable insights into the mechanisms of female flower bud differentiation in J. sigillata and highlight the regulatory role of flavonoids in plant bud differentiation.

Interplay of light and abscisic acid signaling to modulate plant development

Exogenous light cues and the phytohormone abscisic acid (ABA) regulate several aspects of plant growth and development. In recent years, the role of crosstalk between the light and ABA signaling pathways in regulating different physiological processes has become increasingly evident. This includes regulation of germination and early seedling development, control of stomatal development and conductance, growth, and development of roots, buds, and branches, and regulation of flowering. Light and ABA signaling cascades have various convergence points at both DNA and protein levels. The molecular crosstalk involves several light signaling factors such as HY5, COP1, PIFs, and BBXs that integrate with ABA signaling components such as the PYL receptors and ABI5. In particular, ABI5 and PIF4 promoters are key 'hotspots' for integrating these two pathways. Plants acquired both light and ABA signaling pathways before they colonized land almost 500 million years ago. In this review, we discuss recent advances in the interplay of light and ABA signaling regulating plant development and provide an overview of the evolution of these two pathways.

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.

Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species

Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. We found that oak species exhibited a higher degree of genomic conservation and stability, as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events. In addition, we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense (e.g., cuticle biosynthesis and oxidosqualene cyclase genes), which may represent the foundation for the ecological adaptation of oak species. Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks. This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic, genome evolutionary, and functional genomic analyses.

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.

Cryptochrome magnetoreception: Time course of photoactivation from non-equilibrium coarse-grained molecular dynamics

Magnetoreception, the ability to sense magnetic fields, is widespread in animals but remains poorly understood. The leading model links this ability in migratory birds to the photo-activation of the protein cryptochrome. Magnetic information is thought to induce structural changes in cryptochrome via a transient radical pair intermediate. This signal transduction pathway has been the subject of previous all-atom molecular dynamics (MD) simulations, but insights were limited to short timescales and equilibrium structures. To address this, we developed a non-equilibrium coarse-grained MD simulation approach, exploring cryptochrome's photo-reduction over 20 replicates of 20 µs each. Our results revealed significant structural changes across the protein, with an overall time constant of 3 µs. The C-terminal (CT) region responded on a timescale of 4.7 µs, followed by the EEE-motif, while the phosphate binding loop (PBL) showed slower dynamics (9 µs). Network analysis highlighted direct pathways connecting the tryptophan tetrad to the CT, and distant pathways involving the EEE and PBL regions. The CT-dynamics are significantly impacted by a rearrangement of tryptophan residues in the central electron transfer chain. Our findings underscore the importance of considering longer timescales when studying cryptochrome magnetoreception and highlight the potential of non-equilibrium coarse-grained MD simulations as a powerful tool to unravel protein photoactivation reactions.

Optogenetic Control of Condensates: Principles and Applications

Biomolecular condensates appear throughout cell physiology and pathology, but the specific role of condensation or its dynamics is often difficult to determine. Optogenetics offers an expanding toolset to address these challenges, providing tools to directly control condensation of arbitrary proteins with precision over their formation, dissolution, and patterning in space and time. In this review, we describe the current state of the field for optogenetic control of condensation. We survey the proteins and their derivatives that form the foundation of this toolset, and we discuss the factors that distinguish them to enable appropriate selection for a given application. We also describe recent examples of the ways in which optogenetic condensation has been used in both basic and applied studies. Finally, we discuss important design considerations when engineering new proteins for optogenetic condensation, and we preview future innovations that will further empower this toolset in the coming years.

Over-expression of SiADCL1 in Arabidopsis modulates folate and amino acid metabolism to impact on flowering time

Foxtail millet is a C4 crop rich in folate (FA). This study explores the roles of the 4-amino-4-deoxychorismate lyase (ADCL) - a member of the transaminase IV group of enzymes - in FA metabolism and conferred phenotypes. Phylogenetic comparisons identified diversity in the transaminase IV/ADCL gene family in the foxtail millet genome which was associated with genomic duplications. Molecular docking studies suggested that SiADCL1 bound most strongly to aminodeoxychorismate (ADC) and most likely had the highest catalytic activities. SiADCL1 which was highly expressed in roots, peduncles and flag leaves. Over-expression of SiADCL1 in Arabidopsis significantly increased total FA content (1.14-1.84 fold) and this was linked to a delayed flowering time. Metabolomic and transcriptomic characterization of the derived over-expression lines, found that FA promotes the change of methylation-related genes, ethylene synthesis, amino acid metabolism and flowering-related genes. This study revealed a potential gene coexpression network linked with FA and targeted key genes that could be exploited in foxtail millet breeding programs.

Genome-wide exploration of the CONSTANS-like (COL) gene family and its potential role in regulating plant flowering time in foxtail millet (Setaria italica)

In photoperiod-sensitive plants, the CO-like gene (CONSTANS-like, COL) has a crucial function in regulating the timing of flowering. The blooming period in foxtail millet is greatly influenced by the duration of daylight; however, there is a scarcity of data regarding the molecular properties of the COL genes in the foxtail millet. In this study, we conducted a comprehensive analysis of the COL gene family in foxtail millet at the genome-wide level. We identified 11 SiCOL genes and performed gene structure analysis, which showed pronounced variation in gene length and intron number among the genes. The examination of COL proteins in foxtail millet and other plant species using phylogenetic analysis revealed that they could be clustered into three distinct groups. Cis-element analysis identified elements related to light-responsiveness, hormones, and abiotic stress in the promoter region of the SiCOL gene. Furthermore, tissue-specific expression analysis showed widespread expression of all 11 SiCOL genes in various foxtail millet tissues and organs, particularly in leaves and panicles. Collinearity analysis identified 14 syntenic gene pairs in both foxtail millet and rice. The results also revealed diurnal oscillations in the transcription levels of SiCOL genes under different light conditions. Moreover, among the 11 genes, SiCO, SiCOL1, and SiCOL6 expression levels were negatively correlated with flowering time variation in two foxtail cultivars. Additionally, upon constructing a network of predicted molecular interactions, FLOWER LOCUS-like (FTL) and Phytochromea A (PHY A) were suggested to potentially interact with SiCO, SiCOL1, and SiCOL6. SiCO, SiCOL1, and SiCOL6 have the potential for flowering and heading in foxtail millet. This research enhances our comprehension of the role and control of the SiCOL gene family constituents in foxtail millet, establishing a basis for future investigations.

Genome-Wide Identification and Role of the bHLH Gene Family in Dendrocalamus latiflorus Flowering Regulation

The basic helix-loop-helix (bHLH) gene family is a crucial regulator in plants, orchestrating various developmental processes, particularly flower formation, and mediating responses to hormonal signals. The molecular mechanism of bamboo flowering regulation remains unresolved, limiting bamboo breeding efforts. In this study, we identified 309 bHLH genes and divided them into 23 subfamilies. Structural analysis revealed that proteins in specific DlbHLH subfamilies are highly conserved. Collinearity analysis indicates that the amplification of the DlbHLH gene family primarily occurs through segmental duplications. The structural diversity of these duplicated genes may account for their functional variability. Many DlbHLHs are expressed during flower development, indicating the bHLH gene's significant role in this process. In the promoter region of DlbHLHs, different homeopathic elements involved in light response and hormone response co-exist, indicating that DlbHLHs are related to the regulation of the flower development of D. latiflorus.

TRANSPARENT TESTA GLABRA1 regulates high-intensity blue light-induced phototropism by reducing CRYPTOCHROME1 levels

The asymmetrical distribution of auxin supports high intensity blue light (HBL)-mediated phototropism. Flavonoids, secondary metabolites induced by blue light and TRANSPARENT TESTA GLABRA1 (TTG1), alter auxin transport. However, the role of TTG1 in HBL-induced phototropism in Arabidopsis (Arabidopsis thaliana) remains unclear. We found that TTG1 regulates HBL-mediated phototropism. HBL-induced degradation of CRYPTOCHROME 1 (CRY1) was repressed in ttg1-1, and depletion of CRY1 rescued the phototropic defects of the ttg1-1 mutant. Moreover, overexpression of CRY1 in a cry1 mutant background led to phototropic defects in response to HBL. These results indicated that CRY1 is involved in the regulation of TTG1-mediated phototropism in response to HBL. Further investigation showed that TTG1 physically interacts with CRY1 via its N-terminus and that the added TTG1 promotes the dimerization of CRY1. The interaction between TTG1 and CRY1 may promote HBL-mediated degradation of CRY1. TTG1 also physically interacted with blue light inhibitor of cryptochrome 1 (BIC1) and Light-Response Bric-a-Brack/Tramtrack/Broad 2 (LRB2), and these interactions either inhibited or promoted their interaction with CRY1. Exogenous gibberellins (GA) and auxins, two key plant hormones that crosstalk with CRY1, may confer the recovery of phototropic defects in the ttg1-1 mutant and CRY1-overexpressing plants. Our results revealed that TTG1 participates in the regulation of HBL-induced phototropism by modulating CRY1 levels, which are coordinated with GA or IAA signaling.

Arabidopsis cryptochromes interact with SOG1 to promote the repair of DNA double-strand breaks

Cryptochromes (CRYs) are blue light (BL) photoreceptors to regulate a variety of physiological processes including DNA double-strand break (DSB) repair. SUPPRESSOR OF GAMMA RADIATION 1 (SOG1) acts as the central transcription factor of DNA damage response (DDR) to induce the transcription of downstream genes, including DSB repair-related genes BRCA1 and RAD51. Whether CRYs regulate DSB repair by directly modulating SOG1 is unknown. Here, we demonstrate that CRYs physically interact with SOG1. Disruption of CRYs and SOG1 leads to increased sensitivity to DSBs and reduced DSB repair-related genes' expression under BL. Moreover, we found that CRY1 enhances SOG1's transcription activation of DSB repair-related gene BRCA1. These results suggest that the mechanism by which CRYs promote DSB repair involves positive regulation of SOG1's transcription of its target genes, which is likely mediated by CRYs-SOG1 interaction.

Photoexcited Cryptochrome 1 Interacts With SPCHLESS to Regulate Stomatal Development in Arabidopsis

Stomata are epidermal openings that facilitate plant-atmosphere gas and water exchange during photosynthesis, respiration and water evaporation. SPEECHLESS (SPCH) is a master basic helix-loop-helix (bHLH) transcription factor that determines the initiation of stomatal development. It is known that blue light promotes stomatal development through the blue light photoreceptor cryptochromes (CRYs, CRY1 and CRY2). Whether CRYs regulate stomatal development through directly modulating SPCH is unknown. Here, we demonstrate by biochemical studies that CRY1 physically interacts with SPCH in a blue light-dependent manner. Genetic studies show that SPCH acts downstream of CRY1 to promote stomatal development in blue light. Furthermore, we show that CRY1 enhances the DNA-binding activity of SPCH and promotes the expression of its target genes in blue light. These results suggest that the mechanism by which CRY1 promotes stomatal development involves positive regulation of the DNA-binding activity of SPCH, which is likely mediated by blue light-induced CRY1-SPCH interaction. The precise regulation of SPCH DNA-binding activity by CRY1 may allow plants to optimize stomatal density and pattern according to ambient light conditions.

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.

ADA2b acts to positively regulate blue light-mediated photomorphogenesis in Arabidopsis

Cryptochromes (CRYs) act as blue light photoreceptors to regulate various plant physiological processes including photomorphogenesis and repair of DNA double strand breaks (DSBs). ADA2b is a conserved transcription co-activator that is involved in multiple plant developmental processes. It is known that ADA2b interacts with CRYs to mediate blue light-promoted DSBs repair. Whether ADA2b may participate in CRYs-mediated photomorphogenesis is unknown. Here we show that ADA2b acts to inhibit hypocotyl elongation and hypocotyl cell elongation in blue light. We found that the SWIRM domain-containing C-terminus mediates the blue light-dependent interaction of ADA2b with CRYs in blue light. Moreover, ADA2b and CRYs act to co-regulate the expression of hypocotyl elongation-related genes in blue light. Based on previous studies and these results, we propose that ADA2b plays dual functions in blue light-mediated DNA damage repair and photomorphogenesis.

Photoregulatory protein kinases fine-tune plant photomorphogenesis by directing a bifunctional phospho-code on HY5 in Arabidopsis

Photomorphogenesis is a light-dependent plant growth and development program. As the core regulator of photomorphogenesis, ELONGATED HYPOCOTYL 5 (HY5) is affected by dynamic changes in its transcriptional activity and protein stability; however, little is known about the mediators of these processes. Here, we identified PHOTOREGULATORY PROTEIN KINASE 1 (PPK1), which interacts with and phosphorylates HY5 in Arabidopsis, as one such mediator. The phosphorylation of HY5 by PPK1 is essential to establish high-affinity binding with B-BOX PROTEIN 24 (BBX24) and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), which inhibit the transcriptional activity and promote the degradation of HY5, respectively. As such, PPKs regulate not only the binding of HY5 to its target genes under light conditions but also HY5 degradation when plants are transferred from light to dark. Our data identify a PPK-mediated phospho-code on HY5 that integrates the molecular mechanisms underlying the regulation of HY5 to precisely control plant photomorphogenesis.

Twilight length alters growth and flowering time in Arabidopsis via LHY/CCA1

Decades of research have uncovered how plants respond to two environmental variables that change across latitudes and over seasons: photoperiod and temperature. However, a third such variable, twilight length, has so far gone unstudied. Here, using controlled growth setups, we show that the duration of twilight affects growth and flowering time via the LHY/CCA1 clock genes in the model plant Arabidopsis. Using a series of progressively truncated no-twilight photoperiods, we also found that plants are more sensitive to twilight length compared to equivalent changes in solely photoperiods. Transcriptome and proteome analyses showed that twilight length affects reactive oxygen species metabolism, photosynthesis, and carbon metabolism. Genetic analyses suggested a twilight sensing pathway from the photoreceptors PHY E, PHY B, PHY D, and CRY2 through LHY/CCA1 to flowering modulation through the GI-FT pathway. Overall, our findings call for more nuanced models of day-length perception in plants and posit that twilight is an important determinant of plant growth and development.

Blue light photoreceptor cryptochrome 1 promotes wood formation and anthocyanin biosynthesis in Populus

Blue light photoreceptor cryptochrome 1 (CRY1) in herbaceous plants plays crucial roles in various developmental processes, including cotyledon expansion, hypocotyl elongation and anthocyanin biosynthesis. However, the function of CRY1 in perennial trees is unclear. In this study, we identified two ortholog genes of CRY1 (PagCRY1a and PagCRY1b) from Populus, which displayed high sequence similarity to Arabidopsis CRY1. Overexpression of PagCRY1 substantially inhibited plant growth and promoted secondary xylem development in Populus, while CRISPR/Cas9-mediated knockout of PagCRY1 enhanced plant growth and delayed secondary xylem development. Moreover, overexpression of PagCRY1 dramatically increased anthocyanin accumulation. The further analysis supported that PagCRY1 functions specifically in response to blue light. Taken together, our results demonstrated that modulating the expression of blue light photoreceptor CRY1 ortholog gene in Populus could significantly influence plant biomass production and the process of wood formation, laying a foundation for further investigating the light-regulated tree growth.

The dual-action mechanism of Arabidopsis cryptochromes

Photoreceptor cryptochromes (CRYs) mediate blue-light regulation of plant growth and development. It has been reported that Arabidopsis CRY1and CRY2 function by physically interacting with at least 84 proteins, including transcription factors or co-factors, chromatin regulators, splicing factors, messenger RNA methyltransferases, DNA repair proteins, E3 ubiquitin ligases, protein kinases and so on. Of these 84 proteins, 47 have been reported to exhibit altered binding affinity to CRYs in response to blue light, and 41 have been shown to exhibit condensation to CRY photobodies. The blue light-regulated composition or condensation of CRY complexes results in changes of gene expression and developmental programs. In this mini-review, we analyzed recent studies of the photoregulatory mechanisms of Arabidopsis CRY complexes and proposed the dual mechanisms of action, including the "Lock-and-Key" and the "Liquid-Liquid Phase Separation (LLPS)" mechanisms. The dual CRY action mechanisms explain, at least partially, the structural diversity of CRY-interacting proteins and the functional diversity of the CRY photoreceptors.

Light signaling in plants-a selective history

In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.

Photoperiodic and lighting treatments for flowering control and its genetic regulation in sugarcane breeding

Improvement of sugarcane is hampered due to its narrow genetic base, and the difficulty in synchronizing flowering further hinders the exploitation of the genetic potential of available germplasm resources. Therefore, the continuous evaluation and optimization of flowering control and induction techniques are vital for sugarcane improvement. In view of this, the review was conducted to investigate the current understanding of photoperiodic and lighting treatment effects on sugarcane flowering and its genetic regulation. Photoperiod facilities have made a significant contribution to flowering control in sugarcane; however, inductive photoperiods are still unknown for some genotypes, and some intended crosses are still impossible to produce because of unresponsive varieties. The effectiveness of lower red/far-red ratios in promoting sugarcane flowering has been widely understood. Furthermore, there is vast potential for utilizing blue, red, and far-red light wavelengths in the flowering control of sugarcane. In this context, light-emitting diodes (LEDs) remain efficient sources of light. Therefore, the combined use of photoperiod regimes with different light wavelengths and optimization of such treatment combinations might help to control and induce flowering in sugarcane parental clones. In sugarcane, FLOWERING LOCUS T (ScFT) orthologues from ScFT1 to ScFT13 have been identified, and interestingly, ScFT3 has evidently been identified as a floral inducer in sugarcane. However, independent assessments of different FT-like gene family members are recommended to comprehensively understand their role in the regulation of flowering. Similarly, we believe this review provides substantial information that is vital for the manipulation of flowering and exploitation of germplasm resources in sugarcane breeding.

Light quality-dependent roles of REVEILLE proteins in the circadian system

Several closely related Myb-like activator proteins are known to have partially redundant functions within the plant circadian clock, but their specific roles are not well understood. To clarify the function of the REVEILLE 4, REVEILLE 6, and REVEILLE 8 transcriptional activators, we characterized the growth and clock phenotypes of CRISPR-Cas9-generated single, double, and triple rve mutants. We found that these genes act synergistically to regulate flowering time, redundantly to regulate leaf growth, and antagonistically to regulate hypocotyl elongation. We previously reported that increasing intensities of monochromatic blue and red light have opposite effects on the period of triple rve468 mutants. Here, we further examined light quality-specific phenotypes of rve mutants and report that rve468 mutants lack the blue light-specific increase in expression of some circadian clock genes observed in wild type. To investigate the basis of these blue light-specific circadian phenotypes, we examined RVE protein abundances and degradation rates in blue and red light and found no significant differences between these conditions. We next examined genetic interactions between RVE genes and ZEITLUPE and ELONGATED HYPOCOTYL5, two factors with blue light-specific functions in the clock. We found that the RVEs interact additively with both ZEITLUPE and ELONGATED HYPOCOTYL5 to regulate circadian period, which suggests that neither of these factors are required for the blue light-specific differences that we observed. Overall, our results suggest that the RVEs have separable functions in plant growth and circadian regulation and that they are involved in blue light-specific circadian signaling via a novel mechanism.

Cryptochrome 1b represses gibberellin signaling to enhance lodging resistance in maize

Maize (Zea mays L.) is one of the most important crops worldwide. Photoperiod, light quality, and light intensity in the environment can affect the growth, development, yield, and quality of maize. In Arabidopsis (Arabidopsis thaliana), cryptochromes are blue-light receptors that mediate the photocontrol of stem elongation, leaf expansion, shade tolerance, and photoperiodic flowering. However, the function of maize cryptochrome ZmCRY in maize architecture and photomorphogenic development remains largely elusive. The ZmCRY1b transgene product can activate the light signaling pathway in Arabidopsis and complement the etiolation phenotype of the cry1-304 mutant. Our findings show that the loss-of-function mutant of ZmCRY1b in maize exhibits more etiolation phenotypes under low blue light and appears slender in the field compared with wild-type plants. Under blue and white light, overexpression of ZmCRY1b in maize substantially inhibits seedling etiolation and shade response by enhancing protein accumulation of the bZIP transcription factors ELONGATED HYPOCOTYL 5 (ZmHY5) and ELONGATED HYPOCOTYL 5-LIKE (ZmHY5L), which directly upregulate the expression of genes encoding gibberellin (GA) 2-oxidase to deactivate GA and repress plant height. More interestingly, ZmCRY1b enhances lodging resistance by reducing plant and ear heights and promoting root growth in both inbred lines and hybrids. In conclusion, ZmCRY1b contributes blue-light signaling upon seedling de-etiolation and integrates light signals with the GA metabolic pathway in maize, resulting in lodging resistance and providing information for improving maize varieties.

The mechanism of low blue light-induced leaf senescence mediated by GmCRY1s in soybean

Leaf senescence is a crucial trait that has a significant impact on crop quality and yield. Previous studies have demonstrated that light is a key factor in modulating the senescence process. However, the precise mechanism by which plants sense light and control senescence remains largely unknown, particularly in crop species. In this study, we reveal that the reduction in blue light under shading conditions can efficiently induce leaf senescence in soybean. The blue light receptors GmCRY1s rather than GmCRY2s, primarily regulate leaf senescence in response to blue light signals. Our results show that GmCRY1s interact with DELLA proteins under light-activated conditions, stabilizing them and consequently suppressing the transcription of GmWRKY100 to delay senescence. Conversely, LBL reduces the interaction between GmCRY1s and the DELLA proteins, leading to their degradation and premature senescence of leaves. Our findings suggest a GmCRY1s-GmDELLAs-GmWRKY100 regulatory cascade that is involved in mediating LBL-induced leaf senescence in soybean, providing insight into the mechanism of how light signals regulate leaf senescence. Additionally, we generate GmWRKY100 knockout soybeans that show delayed leaf senescence and improved yield under natural field conditions, indicating potential applications in enhancing soybean production by manipulating the leaf senescence trait.

Synthetic Biology Approaches to Posttranslational Regulation in Plants

To date synthetic biology approaches involving creation of functional genetic modules are used in a wide range of organisms. In plants, such approaches are used both for research in the field of functional genomics and to increase the yield of agricultural crops. Of particular interest are methods that allow controlling genetic apparatus of the plants at post-translational level, which allow reducing non-targeted effects from interference with the plant genome. This review discusses recent advances in the plant synthetic biology for regulation of the plant metabolism at posttranslational level and highlights their future directions.

Asparagine-rich protein (NRP) mediates stress response by regulating biosynthesis of plant secondary metabolites in Arabidopsis

The plant-specific stress response protein NRP (asparagine-rich protein) is characterized by an asparagine-rich domain at its N-terminus and a conserved development and cell death (DCD) domain at its C-terminus. Previous transcriptional studies and phenotypic analyses have demonstrated the involvement of NRP in response to severe stress conditions, such as high salt and ER Endoplasmic reticulum-stress. We have recently identified distinct roles for NRP in biotic- and abiotic-stress signaling pathways, in which NRP interacts with different signaling proteins to change their subcellular localizations and stability. Here, to further explore the function of NRP, a transcriptome analysis was carried out on nrp1nrp2 knock-out lines at different life stages or under different growing conditions. The most significant changes in the transcriptome at both stages and conditions turned out to be the induction of the synthesis of secondary metabolites (SMs). Such an observation implicates that NRP is a general stress-responsive protein involved in various challenges faced by plants during their life cycle, which might involve a broad alteration in the distribution of SMs.

Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis

Light regulates chlorophyll homeostasis and photosynthesis via various molecular mechanisms in plants. The light regulation of transcription and protein stability of nuclear-encoded chloroplast proteins have been extensively studied, but how light regulation of mRNA metabolism affects abundance of nuclear-encoded chloroplast proteins and chlorophyll homeostasis remains poorly understood. Here we show that the blue light receptor cryptochrome 2 (CRY2) and the METTL16-type m6A writer FIONA1 (FIO1) regulate chlorophyll homeostasis in response to blue light. In contrast to the CRY2-mediated photo-condensation of the mRNA adenosine methylase (MTA), photoexcited CRY2 co-condenses FIO1 only in the presence of the CRY2-signalling protein SUPPRESSOR of PHYTOCHROME A (SPA1). CRY2 and SPA1 synergistically or additively activate the RNA methyltransferase activity of FIO1 in vitro, whereas CRY2 and FIO1, but not MTA, are required for the light-induced methylation and translation of the mRNAs encoding multiple chlorophyll homeostasis regulators in vivo. Our study demonstrates that the light-induced liquid-liquid phase separation of the photoreceptor/writer complexes is commonly involved in the regulation of photoresponsive changes of mRNA methylation, whereas the different photo-condensation mechanisms of the CRY/FIO1 and CRY/MTA complexes explain, at least partially, the writer-specific functions in plant photomorphogenesis.

Long-Time Oxygen and Superoxide Localization in Arabidopsis thaliana Cryptochrome

Cryptochromes are proteins that are highly conserved across species and in many instances bind the flavin adenine dinucleotide (FAD) cofactor within their photolyase-homology region (PHR) domain. The FAD cofactor has multiple redox states that help catalyze reactions, and absorbs photons at about 450 nm, a feature linked to the light-related functions of cryptochrome proteins. Reactive oxygen species (ROS) are produced from redox reactions involving molecular oxygen and are involved in a myriad of biological processes. Superoxide O2•- is an exemplary ROS that may be formed through electron transfer from FAD to O2, generating an electron radical pair. Although the formation of a superoxide-FAD radical pair has been speculated, it is still unclear if the required process steps could be realized in cryptochrome. Here, we present results from molecular dynamics (MD) simulations of oxygen interacting with the PHR domain of Arabidopsis thaliana cryptochrome 1 (AtCRY1). Using MD simulation trajectories, oxygen binding locations are characterized through both the O2-FAD intermolecular distance and the local protein environment. Oxygen unbinding times are characterized through replica simulations of the bound oxygen. Simulations reveal that oxygen molecules can localize at certain sites within the cryptochrome protein for tens of nanoseconds, and superoxide molecules can localize for significantly longer. This relatively long-duration molecule binding suggests the possibility of an electron-transfer reaction leading to superoxide formation. Estimates of electron-transfer rates using the Marcus theory are performed for the identified potential binding sites. Molecular oxygen binding results are compared with recent results demonstrating long-time oxygen binding within the electron-transfer flavoprotein (ETF), another FAD binding protein.

Transcription factor CsTT8 promotes fruit coloration by positively regulating the methylerythritol 4-phosphate pathway and carotenoid biosynthesis pathway in citrus (Citrus spp.)

Carotenoids directly influence citrus fruit color and nutritional value, which is critical to consumer acceptance. Elucidating the potential molecular mechanism underlying carotenoid metabolism is of great importance for improving fruit quality. Despite the well-established carotenoid biosynthetic pathways, the molecular regulatory mechanism underlying carotenoid metabolism remains poorly understood. Our previous studies have reported that the Myc-type basic helix-loop-helix (bHLH) transcription factor (TF) regulates citrus proanthocyanidin biosynthesis. Transgenic analyses further showed that overexpression of CsTT8 could significantly promote carotenoid accumulation in transgenic citrus calli, but its regulatory mechanism is still unclear. In the present study, we found that overexpression of CsTT8 enhances carotenoid content in citrus fruit and calli by increasing the expression of CsDXR, CsHDS, CsHDR, CsPDS, CsLCYE, CsZEP, and CsNCED2, which was accompanied by changes in the contents of abscisic acid and gibberellin. The in vitro and in vivo assays indicated that CsTT8 directly bound to the promoters of CsDXR, CsHDS, and CsHDR, the key metabolic enzymes of the methylerythritol 4-phosphate (MEP) pathway, thus providing precursors for carotenoid biosynthesis and transcriptionally activating the expression of these three genes. In addition, CsTT8 activated the promoters of four key carotenoid biosynthesis pathway genes, CsPDS, CsLCYE, CsZEP, and CsNCED2, directly promoting carotenoid biosynthesis. This study reveals a novel network of carotenoid metabolism regulated by CsTT8. Our findings will contribute to manipulating carotenoid metabolic engineering to improve the quality of citrus fruit and other crops.

An interplay between bZIP16, bZIP68, and GBF1 regulates nuclear photosynthetic genes during photomorphogenesis in Arabidopsis

The development of a seedling into a photosynthetically active plant is a crucial process. Despite its importance, we do not fully understand the regulatory mechanisms behind the establishment of functional chloroplasts. We herein provide new insight into the early light response by identifying the function of three basic region/leucine zipper (bZIP) transcription factors: bZIP16, bZIP68, and GBF1. These proteins are involved in the regulation of key components required for the establishment of photosynthetically active chloroplasts. The activity of these bZIPs is dependent on the redox status of a conserved cysteine residue, which provides a mechanism to finetune light-responsive gene expression. The blue light cryptochrome (CRY) photoreceptors provide one of the major light-signaling pathways, and bZIP target genes overlap with one-third of CRY-regulated genes with an enrichment for photosynthesis/chloroplast-associated genes. bZIP16, bZIP68, and GBF1 were demonstrated as novel interaction partners of CRY1. The interaction between CRY1 and bZIP16 was stimulated by blue light. Furthermore, we demonstrate a genetic link between the bZIP proteins and cryptochromes as the cry1cry2 mutant is epistatic to the cry1cry2bzip16bzip68gbf1 mutant. bZIP16, bZIP68, and GBF1 regulate a subset of photosynthesis associated genes in response to blue light critical for a proper greening process in Arabidopsis.

A deazariboflavin chromophore kinetically stabilizes reduced FAD state in a bifunctional cryptochrome

An animal-like cryptochrome derived from Chlamydomonas reinhardtii (CraCRY) is a bifunctional flavoenzyme harboring flavin adenine dinucleotide (FAD) as a photoreceptive/catalytic center and functions both in the regulation of gene transcription and the repair of UV-induced DNA lesions in a light-dependent manner, using different FAD redox states. To address how CraCRY stabilizes the physiologically relevant redox state of FAD, we investigated the thermodynamic and kinetic stability of the two-electron reduced anionic FAD state (FADH-) in CraCRY and related (6-4) photolyases. The thermodynamic stability of FADH- remained almost the same compared to that of all tested proteins. However, the kinetic stability of FADH- varied remarkably depending on the local structure of the secondary pocket, where an auxiliary chromophore, 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF), can be accommodated. The observed effect of 8-HDF uptake on the enhancement of the kinetic stability of FADH- suggests an essential role of 8-HDF in the bifunctionality of CraCRY.

Blue light receptor CRY1 regulates HSFA1d nuclear localization to promote plant thermotolerance

Temperature increases as light intensity rises, but whether light signals can be directly linked to high temperature response in plants is unclear. Here, we find that light pre-treatment enables plants to survive better under high temperature, designated as light-induced thermotolerance (LIT). With short-term light treatment, plants induce light-signaling pathway genes and heat shock genes. Blue light photoreceptor cryptochrome 1 (CRY1) is required for LIT. We also find that CRY1 physically interacts with the heat shock transcription factor A1d (HsfA1d) and that HsfA1d is involved in thermotolerance under light treatment. Furthermore, CRY1 promotes HsfA1d nuclear localization through importin alpha 1 (IMPα1). Consistent with this, CRY1 shares more than half of the chromatin binding sites with HsfA1d. Mutation of CRY1 (cry1-304) diminishes a large number of HsfA1d binding sites that are shared with CRY1. We present a model where, by coupling light sensing to high-temperature stress, CRY1 confers thermotolerance in plants via HsfA1d.

Light response of gametophyte in Adiantum flabellulatum: transcriptome analysis and identification of key genes and pathways

Light serves not only as a signaling cue perceived by plant photoreceptors but also as an essential energy source captured by chloroplasts. However, excessive light can impose stress on plants. Fern gametophytes possess the unique ability to survive independently and play a critical role in the alternation of generations. Due to their predominantly shaded distribution under canopies, light availability becomes a limiting factor for gametophyte survival, making it imperative to investigate their response to light. Previous research on fern gametophytes' light response has been limited to the physiological level. In this study, we examined the light response of Adiantum flabellulatum gametophytes under different photosynthetic photon flux density (PPFD) levels and identified their high sensitivity to low light. We thereby determined optimal and stress-inducing light conditions. By employing transcriptome sequencing, weighted gene co-expression network analysis, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified 10,995 differentially expressed genes (DEGs). Notably, 3 PHYBs and 5 Type 1 CRYs (CRY1s) were significantly down-regulated at low PPFD (0.1 μmol m-2 s-1). Furthermore, we annotated 927 DEGs to pathways related to photosynthesis and 210 to the flavonoid biosynthesis pathway involved in photoprotection. Additionally, we predicted 34 transcription factor families and identified a close correlation between mTERFs and photosynthesis, as well as a strong co-expression relationship between MYBs and bHLHs and genes encoding flavonoid synthesis enzymes. This comprehensive analysis enhances our understanding of the light response of fern gametophytes and provides novel insights into the mechanisms governing their responses to light.

XAANTAL1 Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis

Light and photoperiod are environmental signals that regulate flowering transition. In plants like Arabidopsis thaliana, this regulation relies on CONSTANS, a transcription factor that is negatively posttranslational regulated by phytochrome B during the morning, while it is stabilized by PHYA and cryptochromes 1/2 at the end of daylight hours. CO induces the expression of FT, whose protein travels from the leaves to the apical meristem, where it binds to FD to regulate some flowering genes. Although PHYB delays flowering, we show that light and PHYB positively regulate XAANTAL1 and other flowering genes in the shoot apices. Also, the genetic data indicate that XAL1 and FD participate in the same signaling pathway in flowering promotion when plants are grown under a long-day photoperiod at 22 °C. By contrast, XAL1 functions independently of FD or PIF4 to induce flowering at higher temperatures (27 °C), even under long days. Furthermore, XAL1 directly binds to FD, SOC1, LFY, and AP1 promoters. Our findings lead us to propose that light and temperature influence the floral network at the meristem level in a partially independent way of the signaling generated from the leaves.

Co-condensation with photoexcited cryptochromes facilitates MAC3A to positively control hypocotyl growth in Arabidopsis

Cryptochromes (CRYs) are blue light receptors that mediate plant photoresponses through regulating gene expressions. We recently reported that Arabidopsis CRY2 could form light-elicited liquid condensates to control RNA methylation. However, whether CRY2 condensation is involved in other gene expression-regulatory processes remains unclear. Here, we show that MOS4-associated complex subunits 3A and 3B (MAC3A/3B) are CRY-interacting proteins and assembled into nuclear CRY condensates. mac3a3b double mutants exhibit hypersensitive photoinhibition of hypocotyl elongation, suggesting that MAC3A/3B positively control hypocotyl growth. We demonstrate the noncanonical activity of MAC3A as a DNA binding protein that modulates transcription. Genome-wide mapping of MAC3A-binding sites reveals that blue light enhances the association of MAC3A with its DNA targets, which requires CRYs. Further evidence indicates that MAC3A and ELONGATED HYPOCOTYL 5 (HY5) occupy overlapping genomic regions and compete for the same targets. These results argue that photocondensation of CRYs fine-tunes light-responsive hypocotyl growth by balancing the opposed effects of HY5 and MAC3A.

Arabidopsis NF-YC7 Interacts with CRY2 and PIF4/5 to Repress Blue Light-Inhibited Hypocotyl Elongation

Light is an important environmental factor. Plants adapt to their light environment by developing the optimal phenotypes. Light-mediated hypocotyl growth is an ideal phenotype for studying how plants respond to light. Thus far, many signaling components in light-mediated hypocotyl growth have been reported. Here, we focused on identifying the transcription factors (TFs) involved in blue light-mediated hypocotyl growth. We analyzed the blue-light-mediated hypocotyl lengths of Arabidopsis TF-overexpressing lines and identified three NF-YC proteins, NF-YC7, NF-YC5, and NF-YC8 (NF-YCs being the short name), as the negative regulators in blue light-inhibited hypocotyl elongation. NF-YC-overexpressing lines developed longer hypocotyls than those of the wild type under blue light, while the deficient mutants nf-yc5nf-yc7 and nf-yc7nf-yc8 failed to exhibit hypocotyl elongation under blue light. NF-YCs physically interacted with CRY2 (cryptochrome 2) and PIF4/5 (phytochrome interacting factor 4 or 5), while the NF-YCs-PIF4/5 interactions were repressed by CRY2. Moreover, the overexpression of CRY2 or deficiency of PIF4/5 repressed NF-YC7-induced hypocotyl elongation under blue light. Further investigation revealed that NF-YC7 may increase CRY2 degradation and regulate PIF4/5 activities under blue light. Taken together, this study will provide new insight into the mechanism of how blue light inhibits hypocotyl elongation.

Photoexcited cryptochromes interact with ADA2b and SMC5 to promote the repair of DNA double-strand breaks in Arabidopsis

Cryptochromes (CRYs) act as blue-light photoreceptors that regulate development and circadian rhythms in plants and animals and as navigating magnetoreceptors in migratory birds. DNA double-strand breaks (DSBs) are the most serious type of DNA damage and threaten genome stability in all organisms. Although CRYs have been shown to respond to DNA damage, whether and how they participate in DSB repair is not well understood. Here we report that Arabidopsis CRYs promote the repair of DSBs through direct interactions with ADA2b and SMC5 in a blue-light-dependent manner to enhance their interaction. Mutations in CRYs and in ADA2b lead to similar enhanced DNA damage accumulation. In response to DNA damage, CRYs are localized at DSBs, and the recruitment of SMC5 to DSBs is dependent on CRYs. These results suggest that CRY-enhanced ADA2b-SMC5 interaction promotes ADA2b-mediated recruitment of SMC5 to DSBs, leading to DSB repair.

Two types of GLR channels cooperate differently in light and dark growth of Arabidopsis seedlings

BACKGROUND

GLutamate Receptor-like (GLR) channels are multimeric, ionotropic, ligand-gated plant transmembrane receptors. They are homologous to mammalian glutamate receptors, iGLuRs, which are critical to neuronal function. GLRs have been reported several times to play a role in photomorphogenesis. However, to date, no study has looked at the mechanism of their involvement in this process. Here we focused on examining the impact of GLRs on the regulation of early seedling growth in blue light, red light, and in the dark.

RESULTS

Wild type and six photoreceptor mutant seedlings were grown on media supplemented with known iGLuR/GLR channel antagonists: MK-801, which non-competitively blocks NMDA channels in mammalian cells, and CNQX, known for competitive blocking of AMPA channels in mammalian cells. The lengths of hypocotyls and roots were measured in seedlings of phyA, phyB, phot1, phot2, cry1, and cry2 mutants after 7 days of in vitro culture. Changes in growth parameters, both in light and in darkness upon application of chemical antagonists, show that both types of GLR channels, NMDA-like and AMPA-like, are involved in the regulation of seedling growth irrespective of light conditions. Analysis of seedling growth of photoreceptor mutants indicates that the channels are influenced by signaling from phot1, phot2, and cry1. To extend our analysis, we also evaluated the elicitation of a calcium wave, which is likely to be partially driven by GLRs, in Arabidopsis seedlings. The changes in cellobiose-induced calcium waves observed after applying GLR inhibitors suggest that both types of channels likely cooperate in shaping Arabidopsis seedling growth and development.

CONCLUSIONS

Our work provides the first experimental evidence that two types of GLR channels function in plants: NMDA-like and AMPA-like. We also demonstrate that the channels are involved in seedling growth and development, at least partially through modulation of calcium signaling, but they are unlikely to play a major role in photomorphogenesis.

Machine learning classification of plant genotypes grown under different light conditions through the integration of multi-scale time-series data

In order to mitigate the effects of a changing climate, agriculture requires more effective evaluation, selection, and production of crop cultivars in order to accelerate genotype-to-phenotype connections and the selection of beneficial traits. Critically, plant growth and development are highly dependent on sunlight, with light energy providing plants with the energy required to photosynthesize as well as a means to directly intersect with the environment in order to develop. In plant analyses, machine learning and deep learning techniques have a proven ability to learn plant growth patterns, including detection of disease, plant stress, and growth using a variety of image data. To date, however, studies have not assessed machine learning and deep learning algorithms for their ability to differentiate a large cohort of genotypes grown under several growth conditions using time-series data automatically acquired across multiple scales (daily and developmentally). Here, we extensively evaluate a wide range of machine learning and deep learning algorithms for their ability to differentiate 17 well-characterized photoreceptor deficient genotypes differing in their light detection capabilities grown under several different light conditions. Using algorithm performance measurements of precision, recall, F1-Score, and accuracy, we find that Suport Vector Machine (SVM) maintains the greatest classification accuracy, while a combined ConvLSTM2D deep learning model produces the best genotype classification results across the different growth conditions. Our successful integration of time-series growth data across multiple scales, genotypes and growth conditions sets a new foundational baseline from which more complex plant science traits can be assessed for genotype-to-phenotype connections.

Shift in the Light Quality of Night Interruption Affects Flowering and Morphogenesis of Petunia hybrida

Petunia hybrida Hort. "Easy Wave Pink", a qualitative long-day plant (LDP), was investigated to study the effects of the night interruption light (NIL) provided by light-emitting diodes (LEDs) quality shifting on the morphogenesis, blooming, and transcription of photoreceptor genes. Plants were grown in a closed-type plant factory employing white (W) LEDs at an intensity of 180 μmol·m-2·s-1 PPFD provided for short day (SD, 10 h light, 14 h dark), long day (LD, 16 h light, 8 h dark), or SD with 4 h night interruption (NI) with LEDs at an intensity of 10 μmol·m-2·s-1 PPFD. The NIL quality was shifted from one light spectrum to another after the first 2 h of NI. Light treatments consisting of all possible pairings of W, far-red (Fr), red (R), and blue (B) light were tested. The SD and LD were referenced as the control, while 12 NI treatments involved altering LED NIL qualities, as follows: from R to B (NI-RB), from B to R (NI-BR), from Fr to R (NI-FrR), from R to Fr (NI-RFr), from Fr to B (NI-FrB), from B to Fr (NI-BFr), from B to W (NI-BW), from W to B (NI-WB), from W to Fr (NI-WFr), from Fr to W (NI-FrW), from W to R (NI-WR), and from R to W (NI-RW). The NI-RFr resulted in the longest shoots, while the NI-WR and NI-RW resulted in the shortest shoots. NI-WR, NI-RW, NI-BW, NI-WB, NI-RFr, NI-RB, NI-BR, and LD all exhibited flowering. High-level expressions of photoreceptor genes were confirmed in the NI-RFr, NI-FrR, NI-BFr, NI-RW, and NI-WR treatments. Morphogenesis and blooming were both impacted by the photoperiod. The first NIL had no effects on the flowering or the morphogenesis, but the second NIL had a profound impact on both.

Photoperiodic flowering in Arabidopsis: Multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T

The timing of flowering affects the success of sexual reproduction. This developmental event also determines crop yield, biomass, and longevity. Therefore, this mechanism has been targeted for improvement along with crop domestication. The underlying mechanisms of flowering are highly conserved in angiosperms. Central to these mechanisms is how environmental and endogenous conditions control transcriptional regulation of the FLOWERING LOCUS T (FT) gene, which initiates floral development under long-day conditions in Arabidopsis. Since the identification of FT as florigen, efforts have been made to understand the regulatory mechanisms of FT expression. Although many transcriptional regulators have been shown to directly influence FT, the question of how they coordinately control the spatiotemporal expression patterns of FT still requires further investigation. Among FT regulators, CONSTANS (CO) is the primary one whose protein stability is tightly controlled by phosphorylation and ubiquitination/proteasome-mediated mechanisms. In addition, various CO interaction partners, some of them previously identified as FT transcriptional regulators, positively or negatively modulate CO protein activity. The FT promoter possesses several transcriptional regulatory "blocks," highly conserved regions among Brassicaceae plants. Different transcription factors bind to specific blocks and affect FT expression, often causing topological changes in FT chromatin structure, such as the formation of DNA loops. We discuss the current understanding of the regulation of FT expression mainly in Arabidopsis and propose future directions related to this topic.

OsCRY2 and OsFBO10 co-regulate photomorphogenesis and photoperiodic flowering in indica rice

Cryptochromes (CRYs) are a class of photoreceptors that perceive blue/ultraviolet-A light of the visible spectrum to mediate a vast number of physiological responses in bacteria, fungi, animals and plants. In the present study, we have characterized OsCRY2 in a photoperiod sensitive indica variety, Basmati 370, by generating and analyzing overexpression (OE) and knock-down (KD) transgenic lines. The OsCRY2^OE lines displayed dwarfism as shown in their reduced plant height and leaf length, attributed largely by an overall reduction in their cell size. The OsCRY2^OE lines flowered significantly earlier and showed shorter and broader seeds with an overall reduced seed weight. The OsCRY2^KD lines showed contrasting phenotypes, such as increased plant height and delayed flowering, however, decreased seed size and weight were also observed in the KD lines, along with reduced spikelet fertility and high seed shattering rate in mature panicles. Novel interactions were confirmed between OsCRY2 and members of ZEITLUPE family of blue/ultraviolet-A light photoreceptors, encoded by OsFBO8, OsFBO9 and OsFBO10 which are orthologous to ZEITLUPE (ZTL), LOV KELCH PROTEIN2 (LKP2) and FLAVIN BINDING, KELCH REPEAT F-BOX1 (FKF1), respectively, of Arabidopsis thaliana. Since FKF1 is known to play a role in regulating photoperiodic flowering, OsFBO10 was chosen for further studies. OsCRY2 and OsFBO10 interacted in the nucleus and cytoplasm of the cell and cross-regulated the expression of each other. They were also found to regulate the expression of several genes involved in photoperiodic flowering in rice. Both OsCRY2 and OsFBO10 played a positive role in photomorphogenic responses in different light conditions. The physical interaction of OsCRY2 with OsFBO10, their involvement in common physiological and developmental pathways and their cross-regulation of each other suggest that the two photoreceptors may regulate common developmental pathways in plants, either jointly or redundantly.

Green means go: Green light promotes hypocotyl elongation via brassinosteroid signaling

Although many studies have elucidated the mechanisms by which different wavelengths of light (blue, red, far-red, or ultraviolet-B [UV-B]) regulate plant development, whether and how green light regulates plant development remains largely unknown. Previous studies reported that green light participates in regulating growth and development in land plants, but these studies have reported conflicting results, likely due to technical problems. For example, commercial green light-emitting diode light sources emit a little blue or red light. Here, using a pure green light source, we determined that unlike blue, red, far-red, or UV-B light, which inhibits hypocotyl elongation, green light promotes hypocotyl elongation in Arabidopsis thaliana and several other plants during the first 2-3 d after planting. Phytochromes, cryptochromes, and other known photoreceptors do not mediate green-light-promoted hypocotyl elongation, but the brassinosteroid (BR) signaling pathway is involved in this process. Green light promotes the DNA binding activity of BRI1-EMS-SUPPRESSOR 1 (BES1), a master transcription factor of the BR pathway, thus regulating gene transcription to promote hypocotyl elongation. Our results indicate that pure green light promotes elongation via BR signaling and acts as a shade signal to enable plants to adapt their development to a green-light-dominant environment under a canopy.

Cryptochromes suppress leaf senescence in response to blue light in Arabidopsis

The induction and progression of leaf senescence are effectively changed according to the light environment. The leaf senescence response is enhanced when plants are grown under a dense shade cast by neighboring vegetation. Although the fluence rate of the red and blue regions in the light spectrum is strongly attenuated under shade, photosensory mechanisms that underpin the blue light response are still unclear. In this study, we analyzed leaf senescence in response to blue light in Arabidopsis (Arabidopsis thaliana). We found that leaf senescence was promoted by the elimination of active phytochrome Pfr by pulsed far-red (FR) light, whereas irradiation with blue light suppressed leaf senescence in the wild type but not in the cryptochrome (CRY)-deficient mutant, cry1 cry2. Hence, two light-sensing modes contributed to the suppression of leaf senescence that was dependent on light spectrum features. First was the leaf senescence response to blue light, which was mediated exclusively by cryptochromes. Second was the phytochrome-mediated leaf senescence response to red/FR light. Physiological analysis of transgenic plants expressing green fluorescent protein (GFP)-tagged CRY2 revealed that photo-activation of cryptochromes was required to suppress leaf senescence in response to blue light. Transcriptomic analysis further uncovered the molecular and cellular processes involved in the regulation of leaf senescence downstream of cryptochromes. Furthermore, analysis of cryptochrome-downstream components indicated that ELONGATED HYPOCOTYL 5 (HY5) and PHYTOCHROME INTERACTING FACTOR (PIF) 4 and PIF5 were required for suppression and promotion of leaf senescence, respectively.