Antagonistic actions of Arabidopsis cryptochromes and phytochrome B in the regulation of floral induction

The phytochrome B signaling regulates salt-mediated seedling growth in the dark

Light is an essential environmental factor that facilitates the robust upward growth of post-germinative seedlings emerging from buried seeds that is partly mediated by the photoreceptors. Salinity stress hampers plant growth and development and reduces yield. However, the involvement and regulatory role of photoreceptors and light signaling factors to salt stress are largely unknown. Here, we report that mutants of the phytochrome B (phyB) photoreceptor showed reduced sensitivity to salt-inhibited hypocotyl elongation in darkness, and that PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) acts downstream of phyB in regulating this process in Arabidopsis thaliana. We also show that SALT OVERLY SENSITIVE 2 (SOS2) regulates phyB protein accumulation under salt stress in darkness. Surprisingly, salt treatment induces phyB nuclear body formation in darkness. Moreover, we found that the phosphorylation at residue Ser-86 of phyB is essential for its function, and the scaffold protein 14-3-3κ is involved in the regulation of phyB under salt stress in darkness. Taken together, our study reveals a regulatory role of the phyB-PIF3 module in mediating post-germination growth in darkness in response to salt stress.

Complex Signaling Networks Underlying Blue-Light-Mediated Floral Transition in Plants

Blue light (BL) is important in regulating floral transition. In a controlled environment production system, BL can be manipulated easily and precisely in aspects like peak wavelength, intensity, duration, and co-action with other wavelengths. However, the results of previous studies about BL-mediated floral transition are inconsistent, which implies that an in-depth critical examination of the relevant physiological mechanisms is necessary. This review consolidates the recent findings on the role of BL in mediating floral transition not only in model plants, such as Arabidopsis thaliana, but also in crops, especially horticultural crops. The photoreceptors, floral integrator proteins, signal pathways, and key network components involved in BL-mediated floral transition are critically reviewed. This review provides possible explanations for the contrasting results of previous studies on BL-mediated flowering; it provides valuable information to explain and develop BL manipulation strategies for mediating flowering, especially in horticultural plants. The review also identifies the knowledge gaps and outlines future directions for research in related fields.

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.

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.

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.

Paradise by the far-red light: Far-red and red:blue ratios independently affect yield, pigments, and carbohydrate production in lettuce, Lactuca sativa

In controlled environment agriculture, customized light treatments using light-emitting diodes are crucial to improving crop yield and quality. Red (R; 600-700 nm) and blue light (B; 400-500 nm) are two major parts of photosynthetically active radiation (PAR), often preferred in crop production. Far-red radiation (FR; 700-800 nm), although not part of PAR, can also affect photosynthesis and can have profound effects on a range of morphological and physiological processes. However, interactions between different red and blue light ratios (R:B) and FR on promoting yield and nutritionally relevant compounds in crops remain unknown. Here, lettuce was grown at 200 µmol m-2 s-1 PAR under three different R:B ratios: R:B87.5:12.5 (12.5% blue), R:B75:25 (25% blue), and R:B60:40 (40% blue) without FR. Each treatment was also performed with supplementary FR (50 µmol m-2 s-1; R:B87.5:12.5+FR, R:B75:25+FR, and R:B60:40+FR). White light with and without FR (W and W+FR) were used as control treatments comprising of 72.5% red, 19% green, and 8.5% blue light. Increasing the R:B ratio from R:B87.5:12.5 to R:B60:40, there was a decrease in fresh weight (20%) and carbohydrate concentration (48% reduction in both sugars and starch), whereas pigment concentrations (anthocyanins, chlorophyll, and carotenoids), phenolic compounds, and various minerals all increased. These results contrasted the effects of FR supplementation in the growth spectra; when supplementing FR to different R:B backgrounds, we found a significant increase in plant fresh weight, dry weight, total soluble sugars, and starch. Additionally, FR decreased concentrations of anthocyanins, phenolic compounds, and various minerals. Although blue light and FR effects appear to directly contrast, blue and FR light did not have interactive effects together when considering plant growth, morphology, and nutritional content. Therefore, the individual benefits of increased blue light fraction and supplementary FR radiation can be combined and used cooperatively to produce crops of desired quality: adding FR increases growth and carbohydrate concentration while increasing the blue fraction increases nutritional value.

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.

Functional divergence of Arabidopsis REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 and 2 in repression of flowering

Photoperiodic plants coordinate the timing of flowering with seasonal light cues, thereby optimizing their sexual reproductive success. The WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2 (RUP2) functions as a potent repressor of UV RESISTANCE LOCUS 8 (UVR8) photoreceptor-mediated UV-B induction of flowering under noninductive, short-day conditions in Arabidopsis (Arabidopsis thaliana); however, in contrast, the closely related RUP1 seems to play no major role. Here, analysis of chimeric ProRUP1:RUP2 and ProRUP2:RUP1 expression lines suggested that the distinct functions of RUP1 and RUP2 in repressing flowering are due to differences in both their coding and regulatory DNA sequences. Artificial altered expression using tissue-specific promoters indicated that RUP2 functions in repressing flowering when expressed in mesophyll and phloem companion cells, whereas RUP1 functions only when expressed in phloem companion cells. Endogenous RUP1 expression in vascular tissue was quantified as lower than that of RUP2, likely underlying the functional difference between RUP1 and RUP2 in repressing flowering. Taken together, our findings highlight the importance of phloem vasculature expression of RUP2 in repressing flowering under short days and identify a basis for the functional divergence of Arabidopsis RUP1 and RUP2 in regulating flowering time.

Genomic insight into variations associated with flowering-time and early-maturity in pigeonpea mutant TAT-10 and its wild type parent T21

Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important grain legume crop with a broad range of 90 to 300 days for maturity. To identify the genomic variations associated with the early maturity, we conducted whole-genome resequencing of an early-maturing pigeonpea mutant TAT-10 and its wild type parent T21. A total of 135.67 and 146.34 million sequencing reads were generated for T21 and TAT-10, respectively. From this resequencing data, 1,397,178 and 1,419,904 SNPs, 276,741 and 292,347 InDels, and 87,583 and 92,903 SVs were identified in T21 and TAT-10, respectively. We identified 203 genes in the pigeonpea genome that are homologs of flowering-related genes in Arabidopsis and found 791 genomic variations unique to TAT-10 linked to 94 flowering-related genes. We identified three candidate genes for early maturity in TAT-10; Suppressor of FRI 4 (SUF4), Early Flowering In Short Days (EFS), and Probable Lysine-Specific Demethylase ELF6. The variations in ELF6 were predicted to be possibly damaging and the expression profiles of EFS and ELF6 also supported their probable role during early flowering in TAT-10. The present study has generated information on genomic variations associated with candidate genes for early maturity, which can be further studied and exploited for developing the early-maturing pigeonpea cultivars.

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.

UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 for Plant Survival in Sunlight under Field Conditions

As sessile, photoautotrophic organisms, plants are subjected to fluctuating sunlight that includes potentially detrimental ultraviolet-B (UV-B) radiation. Experiments under controlled conditions have shown that the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) controls acclimation and tolerance to UV-B in Arabidopsis thaliana; however, its long-term impact on plant fitness under naturally fluctuating environments remain poorly understood. Here, we quantified the survival and reproduction of different Arabidopsis mutant genotypes under diverse field and laboratory conditions. We found that uvr8 mutants produced more fruits than wild type when grown in growth chambers under artificial low-UV-B conditions but not under natural field conditions, indicating a fitness cost in the absence of UV-B stress. Importantly, independent double mutants of UVR8 and the blue light photoreceptor gene CRYPTOCHROME 1 (CRY1) in two genetic backgrounds showed a drastic reduction in fitness in the field. Experiments with UV-B attenuation in the field and with supplemental UV-B in growth chambers demonstrated that UV-B caused the cry1 uvr8 conditional lethal phenotype. Using RNA-seq data of field-grown single and double mutants, we explicitly identified genes showing significant statistical interaction of UVR8 and CRY1 mutations in the presence of UV-B in the field. They were enriched in Gene Ontology categories related to oxidative stress, photoprotection and DNA damage repair in addition to UV-B response. Our study demonstrates the functional importance of the UVR8-mediated response across life stages in natura, which is partially redundant with that of cry1. Moreover, these data provide an integral picture of gene expression associated with plant responses under field conditions.

IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle

BACKGROUND

Plants adjust their growth orientations primarily in response to light and gravity signals. Considering that the gravity vector is fixed and the angle of light incidence is constantly changing, plants must somehow integrate these signals to establish organ orientation, commonly referred to as gravitropic set-point angle (GSA). The IGT gene family contains known regulators of GSA, including the gene clades LAZY, DEEPER ROOTING (DRO), and TILLER ANGLE CONTROL (TAC).

RESULTS

Here, we investigated the influence of light on different aspects of GSA phenotypes in LAZY and DRO mutants, as well as the influence of known light signaling pathways on IGT gene expression. Phenotypic analysis revealed that LAZY and DRO genes are collectively required for changes in the angle of shoot branch tip and root growth in response to light. Single lazy1 mutant branch tips turn upward in the absence of light and in low light, similar to wild-type, and mimic triple and quadruple IGT mutants in constant light and high-light conditions, while triple and quadruple IGT/LAZY mutants show little to no response to changing light regimes. Further, the expression of IGT/LAZY genes is differentially influenced by daylength, circadian clock, and light signaling.

CONCLUSIONS

Collectively, the data show that differential expression of LAZY and DRO genes are required to enable plants to alter organ angles in response to light-mediated signals.

Cooperative transcriptional regulation by ATAF1 and HY5 promotes light-induced cotyledon opening in Arabidopsis thaliana

The opening of the embryonic leaves (cotyledons) as seedlings emerge from the dark soil into the light is crucial to ensure the survival of the plant. Seedlings that sprout in the dark elongate rapidly to reach light but keep their cotyledons closed. During de-etiolation, the transition from dark to light growth, elongation slows and the cotyledons open. Here, we report that the transcription factor ACTIVATING FACTOR1 (ATAF1) participates in de-etiolation and facilitates light-induced cotyledon opening. The transition from dark to light rapidly induced ATAF1 expression and ATAF1 accumulation in cotyledons. Seedlings lacking or overexpressing ATAF1 exhibited reduced or enhanced cotyledon opening, respectively, and transcriptomic analysis indicated that ATAF1 repressed the expression of genes associated with growth and cotyledon closure. The activation of the photoreceptor phytochrome A (phyA) by far-red light induced its association with the ATAF1 promoter and stimulation of ATAF1 expression. The transcription factor ELONGATED HYPOCOTYL5 (HY5), which is also activated in response far-red light, cooperated with phyA to induce ATAF1 expression. ATAF1 and HY5 interacted with one another and cooperatively repressed the expression of growth-promoting and cotyledon closure genes. Together, our study reveals a mechanism through which far-red light promotes cotyledon opening.

Genome-wide association study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation

Varying light conditions elicit metabolic responses as part of acclimation with changes in ascorbate levels being an important component. Here, we adopted a genome-wide association-based approach to characterize the response in ascorbate levels on high light (HL) acclimation in a panel of 315 Arabidopsis (Arabidopsis thaliana) accessions. These studies revealed statistically significant SNPs for total and reduced ascorbate under HL conditions at a locus in chromosome 2. Ascorbate levels under HL and the region upstream and within PAS/LOV PROTEIN (PLP) were strongly associated. Intriguingly, subcellular localization analyses revealed that the PLPA and PLPB splice variants co-localized with VITAMIN C DEFECTIVE2 (VTC2) and VTC5 in both the cytosol and nucleus. Yeast 2-hybrid and bimolecular fluorescence complementation analyses revealed that PLPA and PLPB interact with VTC2 and that blue light diminishes this interaction. Furthermore, PLPB knockout mutants were characterized by 1.5- to 1.7-fold elevations in their ascorbate levels, whereas knockout mutants of the cry2 cryptochromes displayed 1.2- to 1.3-fold elevations compared to WT. Our results collectively indicate that PLP plays a critical role in the elevation of ascorbate levels, which is a signature response of HL acclimation. The results strongly suggest that this is achieved via the release of the inhibitory effect of PLP on VTC2 upon blue light illumination, as the VTC2-PLPB interaction is stronger under darkness. The conditional importance of the cryptochrome receptors under different environmental conditions suggests a complex hierarchy underpinning the environmental control of ascorbate levels. However, the data we present here clearly demonstrate that PLP dominates during HL acclimation.

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.

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.

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.

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.

A 5.5-kb LTR-retrotransposon insertion inside phytochrome B gene (CsPHYB) results in long hypocotyl and early flowering in cucumber (Cucumis sativus L.)

The novel spontaneous long hypocotyl and early flowering (lhef) mutation in cucumber is due to a 5551-bp LTR-retrotransposon insertion in CsPHYB gene encoding PHYTOCHROME B, which plays a major role in regulating photomorphogenic hypocotyl growth and flowering. Hypocotyl length and flowering time are important for establishing high-quality seedlings in modern cucumber production, but little is known for the underlying molecular mechanisms of these two traits. In this study, a spontaneous cucumber long hypocotyl and early flowering mutant was identified and characterized. Based on multiple lines of evidence, we show that cucumber phytochrome B (CsPHYB) is the candidate gene for this mutation, and a 5551-bp LTR-retrotransposon insertion in the first exon of CsPHYB was responsible for the mutant phenotypes. Uniqueness of the mutant allele at CsPHYB was verified in 114 natural cucumber lines. Ectopic expression of the CsPHYB in Arabidopsis phyB mutant rescued the long hypocotyl and early flowering phenotype of phyB-9 mutant. The wild-type CsPHYB protein was localized on the membrane and cytoplasm under white light condition, whereas in the nucleus under red light, it is consistent with its roles as a red-light photoreceptor in Arabidopsis. However, the mutant csphyb protein was localized on the membrane and cytoplasm under both white and red-light conditions. Expression dynamics of CsPHYB and several cell elongation-related genes were positively correlated with hypocotyl elongation; the transcription levels of key positive and negative regulators for flowering time were also consistent with the anthesis dates in the mutant and wild-type plants. Yeast two hybrid and bimolecular fluorescence complementation assays identified physical interactions between CsPHYB and phytochrome interacting factor 3/4 (CsPIF3/4). These findings will provide new insights into the roles of the CsPHYB in cucumber hypocotyl growth and flowering time.

The blue light receptor CRY1 interacts with FIP37 to promote N6 -methyladenosine RNA modification and photomorphogenesis in Arabidopsis

Light is a particularly important environmental cue that regulates a variety of diverse plant developmental processes, such as photomorphogenesis. Blue light promotes photomorphogenesis mainly through the activation of the photoreceptor cryptochrome 1 (CRY1). However, the mechanism underlying the CRY1-mediated regulation of growth is not fully understood. Here, we found that blue light induced N⁶ -methyladenosine (m⁶ A) RNA modification during photomorphogenesis partially via CRY1. Cryptochrome 1 mediates blue light-induced expression of FKBP12-interacting protein 37 (FIP37), which is a component of m⁶ A writer. Moreover, we showed that CRY1 physically interacted with FIP37 in vitro and in vivo, and mediated blue light activation of FIP37 binding to RNA. Furthermore, CRY1 and FIP37 modulated m⁶ A on photomorphogenesis-related genes PIF3, PIF4, and PIF5, thereby accelerating the decay of their transcripts. Genetically, FIP37 repressed hypocotyl elongation under blue light, and fip37 mutation could partially rescue the short-hypocotyl phenotype of CRY1-overexpressing plants. Together, our results provide a new insight into CRY1 signal in modulating m⁶ A methylation and stability of PIFs, and establish an essential molecular link between m⁶ A modification and determination of photomorphogenesis in plants.

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Cryptochromes (CRYs) are evolutionarily conserved blue-light receptors that evolved from bacterial photolyases that repair damaged DNA. Today, CRYs have lost their ability to repair damaged DNA; however, prior reports suggest that human CRYs can respond to DNA damage. Currently, the role of CRYs in the DNA damage response (DDR) is lacking, especially in plants. Therefore, we evaluated the role of plant CRYs in DDR along with UBP12/13 deubiquitinases, which interact with and regulate the CRY2 protein. We found that cry1cry2 was hypersensitive, while ubp12ubp13 was hyposensitive to UVC-induced DNA damage. Elevated UV-induced cyclobutane pyrimidine dimers (CPDs) and the lack of DNA repair protein RAD51 accumulation in cry1cry2 plants indicate that CRYs are required for DNA repair. On the contrary, CPD levels diminished and RAD51 protein levels elevated in plants lacking UBP12 and UBP13, indicating their role in DDR repression. Temporal transcriptomic analysis revealed that DDR-induced transcriptional responses were subdued in cry1cry2, but elevated in ubp12ubp13 compared to WT. Through transcriptional modeling of the time-course transcriptome, we found that genes quickly induced by UVC (15 min) are targets of CAMTA 1-3 transcription factors, which we found are required for DDR. This transcriptional regulation seems, however, diminished in the cry1cry2 mutant, indicating that CAMTAs are required for CRY2-mediated DDR. Furthermore, we observed enhanced CRY2-UBP13 interaction and formation of CRY2 nuclear speckles under UVC, suggesting that UVC activates CRY2 similarly to blue light. Together, our data reveal the temporal dynamics of the transcriptional events underlying UVC-induced genotoxicity and expand our knowledge of the role of CRY and UBP12/13 in DDR.

CRY2 gene of rice (Oryza sativa subsp. indica) encodes a blue light sensory receptor involved in regulating flowering, plant height and partial photomorphogenesis in dark

OsiCRY2 is involved in light-regulated plant development and plays a role in regulating photomorphogenesis, plant height, flowering and most strikingly partial photomorphogenesis in dark. Cryptochrome 2 (CRY2), the blue/UV-A light photoreceptor in plants, has been reported to regulate photoperiod-dependent flowering and seedling photomorphogenesis (under low-intensity light). Among monocots, CRY2 has been reported from japonica rice, wheat, sorghum and barley. The two sub-species of rice, indica and japonica, exhibit a high degree of genetic variation and morphological and physiological differences. This article describes the characterization of CRY2 of indica rice (OsiCRY2). While the transcript levels of OsiCRY2 did not change significantly under blue light, its protein levels were found to decline with increased time duration under blue light. For phenotypic characterization, OsiCRY2 over-expression (OX) transgenics were generated in Oryza sativa Pusa Sugandh 2 (PS2) cultivar, a highly scented Basmati cultivar. The OsiCRY2^OX transgenics displayed shorter coleoptiles and dwarfism than wild-type under blue light, white, and far-red light. Interestingly, even the dark-grown transgenics were shorter, concomitant with higher OsiCRY2 protein levels in transgenics than wild-type. Histological analysis revealed that the decrease in the length of the seedlings was due to a decrease in the length of the epidermal cells. The fully mature rice transgenics were shorter than the untransformed plants but flowered at the same time as wild-type. However, the OsiCRY2 Arabidopsis over-expressors exhibited early flowering by 10-15 days, indicating the potential and conservation of function of OsiCRY2. The whole-genome transcriptome profiling of rice transgenics revealed the differential up-regulation of several light-regulated genes in dark-grown coleoptiles. These data provide evidence that OsiCRY2 regulates photomorphogenesis, plant height, and flowering in indica rice.

Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes

Light initiates chloroplast biogenesis in Arabidopsis by eliminating PHYTOCHROME-INTERACTING transcription FACTORs (PIFs), which in turn de-represses nuclear photosynthesis genes, and synchronously, generates a nucleus-to-plastid (anterograde) signal that activates the plastid-encoded bacterial-type RNA polymerase (PEP) to transcribe plastid photosynthesis genes. However, the identity of the anterograde signal remains frustratingly elusive. The main challenge has been the difficulty to distinguish regulators from the plethora of necessary components for plastid transcription and other essential chloroplast functions, such as photosynthesis. Here, we show that the genome-wide induction of nuclear photosynthesis genes is insufficient to activate the PEP. PEP inhibition is imposed redundantly by multiple PIFs and requires PIF3's activator activity. Among the nuclear-encoded components of the PEP holoenzyme, we identify four light-inducible, PIF-repressed sigma factors as anterograde signals. Together, our results elucidate that light-dependent inhibition of PIFs activates plastid photosynthesis genes via sigma factors as anterograde signals in parallel with the induction of nuclear photosynthesis genes.

Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean

Global climate change has threatened world crop production and food security. Decoding the adaptive genetic basis of wild relatives provides an invaluable genomic resource for climate-smart crop breedinG. Here, we performed whole-genome sequencing of 185 diverse wild soybean (Glycine soja) accessions collected from three major agro-ecological zones in China to parse the genomic basis of local adaptation in wild soybean. The population genomic diversity pattern exhibited clear agro-ecological zone-based population structure, and multiple environmental factors were observed to contribute to the genetic divergence. Demographic analysis shows that wild soybeans from the three ecological zones diverged about 1 × 105 years ago, and then the effective population sizes have undergone different degrees of expansions. Genome-environment association identified multiple genes involved in the local adaptation, such as flowering time and temperature-related genes. A locus containing two adjacent MADS-box transcription factors on chromosome 19 was identified for multiple environmental factors, and it experienced positive selection that enables the adaptation to high-latitude environment. This study provides insights into the genetic mechanism of ecological adaptation in wild soybean that may facilitate climate-resilient soybean breeding.

The flowering of SDP chrysanthemum in response to intensity of supplemental or night-interruptional blue light is modulated by both photosynthetic carbon assimilation and photoreceptor-mediated regulation

The photoreceptor-mediated photoperiodic sensitivity determines the obligate short-day flowering in chrysanthemum (Chrysanthemum morifolium Ramat.) when the night length is longer than a critical minimum, otherwise, flowering is effectively inhibited. The reversal of this inhibition by subsequent exposure to a short period of supplemental (S) or night-interruptional (NI) blue (B) light (S-B; NI-B) indicates the involvement of B light-received photoreceptors in the flowering response. Flowering is mainly powered by sugars produced through photosynthetic carbon assimilation. Thus, the light intensity can be involved in flowering regulation by affecting photosynthesis. Here, it is elucidated that the intensity of S-B or NI-B in photoperiodic flowering regulation of chrysanthemums by applying 4-h of S-B or NI-B with either 0, 10, 20, 30, or 40 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) in a 10-h short-day (SD10) [SD10 + 4B or + NI-4B (0, 10, 20, 30, or 40)] or 13-h long-day (LD13) condition [LD13 + 4B or + NI-4B (0, 10, 20, 30, or 40)] provided by 300 ± 5 μmol·m-2·s-1 PPFD white (W) LEDs. After 60 days of photoperiodic light treatments other than the LD13 and LD13 + NI-4B (40), flowering with varying degrees was observed, although the SD10 gave the earliest flowering. And the LD13 + 4B (30) produced the greatest number of flowers. The flowering pattern in response to the intensity of S-B or NI-B was consistent as it was gradually promoted from 10 to 30 μmol m-2 s-1 PPFD and inhibited by 40B regardless of the photoperiod. In SD conditions, the same intensity of S-B and NI-B did not significantly affect flowering, while differential flowering inhibition was observed with any intensity of NI-B in LDs. Furthermore, the 30 μmol·m-2·s-1 PPFD of S-B or NI-B up-regulated the expression of floral meristem identity or florigen genes, as well as the chlorophyll content, photosynthetic efficiency, and carbohydrate accumulation. The 40B also promoted these physiological traits but led to the unbalanced expression of florigen or anti-florigen genes. Overall, the photoperiodic flowering in response to the intensity of S-B or NI-B of the SDP chrysanthemum suggests the co-regulation of photosynthetic carbon assimilation and differential photoreceptor-mediated control.

Characterization of Cry2 genes (CRY2a and CRY2b) of B. napus and comparative analysis of BnCRY1 and BnCRY2a in regulating seedling photomorphogenesis

Cryptochrome 2 (CRY2) perceives blue/UV-A light and regulates photomorphogenesis in plants. However, besides Arabidopsis, CRY2 has been functionally characterized only in native species of japonica rice and tomato. In the present study, the BnCRY2a, generating a relatively longer cDNA and harboring an intron in its 5'UTR, has been characterized in detail. Western blot analysis revealed that BnCRY2a is light labile and degraded rapidly by 26S proteasome when seedlings are irradiated with blue light. For functional analysis, BnCRY2a was over-expressed in Brassica juncea, a related species more amenable to transformation. The BnCRY2a over-expression (BnCRY2a^OE) transgenics developed short hypocotyl and expanded cotyledons, accumulated more anthocyanin in light-grown seedlings, and displayed early flowering on maturity. Early flowering in BnCRY2a^OE transgenics was coupled with the up-regulation of many flowering-related genes such as FT. The present study also highlights the differential light sensitivity of cry1 and cry2 in controlling hypocotyl elongation growth in Brassica. BnCRY2a^OE seedlings developed much shorter hypocotyl under the low-intensity of blue light, while BnCRY1^OE seedling hypocotyls were shorter under the high-intensity blue light, compared to untransformed seedlings.

PIF7 is a master regulator of thermomorphogenesis in shade

The size of plant organs is highly responsive to environmental conditions. The plant’s embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The hypocotyl of shade avoiding species elongates to outcompete neighboring plants and secure access to sunlight. Similar elongation occurs in high temperature. However, it is poorly understood how environmental light and temperature cues interact to effect plant growth. We found that shade combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and auxin. This unique but agriculturally relevant scenario was almost totally independent on PIF4 activity. We show that warm temperature is sufficient to promote PIF7 DNA binding but not transcriptional activation and we demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. Our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density.

Plant hypocotyl elongation response to light and temperature. Here the authors show that shade combined with warm temperature synergistically enhances the hypocotyl growth response via the PIF7 transcription factor, auxin, and as yet unknown factor.

UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue light receptor to regulate Arabidopsis growth

Light is a crucial exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. However, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. Furthermore, CRY2 protein levels and activity are tightly regulated in light to fine-tune hypocotyl growth; however, details of the mechanisms that explain precise control of CRY2 levels are not fully understood. We show that in Arabidopsis, UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulates CRY2 by promoting its ubiquitination and turnover to modulate hypocotyl growth. Growth and development were explicitly affected in blue light when UBP12/13 were disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted with and stabilized COP1, which is partially required for CRY2 turnover. Our combined genetic and molecular data support a mechanistic model in which UBP12/13 interact with CRY2 and COP1, leading to the stabilization of COP1. Stabilized COP1 then promotes the ubiquitination and degradation of CRY2 under blue light. Despite decades of studies on deubiquitinases, the knowledge of how their activity is regulated is limited. Our study provides insight into how exogenous signals and ligands, along with their receptors, regulate deubiquitinase activity by protein-protein interaction. Collectively, our results provide a framework of cryptochromes and deubiquitinases to detect and interpret light signals to control plant growth at the most appropriate time.

Arabidopsis SPA2 represses seedling de-etiolation under multiple light conditions

In Arabidopsis, phytochrome (phy) A, phyB, and cryptochrome 1 (cry1) are representative far-red, red, and blue light photoreceptors, respectively. Members of the SUPPRESSOR OF PHYA-105 (SPA) protein family (SPA1-SPA4) form E3 ubiquitin ligase complexes with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), which mediates the degradation of photomorphogenesis-promoting factors to desensitize light signaling. SPA2 has been reported to promote seedling etiolation in the dark. However, the unique roles of SPA2 and its three functional domains in suppressing photomorphogenesis under different light conditions are largely unknown. Here, we demonstrate that overexpression of the full-length or the central coiled-coil and C-terminal WD-repeat domains of SPA2 cause hyper-etiolation phenotypes under several light conditions. The SPA2 central coiled-coil and C-terminal WD-repeat domains are necessary and sufficient for repressing seedling de-etiolation, cotyledon unfolding, and promoting hypocotyl negative gravitropism under several light conditions. Furthermore, phyA, phyB, cry1, and COP1 repress protein accumulation or nuclear translocation of SPA2 through direct interactions with its kinase-like and coiled-coil domains located in the N-terminus in response to far-red, red, and blue light treatments, respectively. Taken together, our results demonstrate that SPA2 functions under multiple light conditions; moreover, light-activated photoreceptors rapidly suppress SPA2 activity via direct interactions in response to different light treatments.

Differential photoregulation of the nuclear and cytoplasmic CRY1 in Arabidopsis

Arabidopsis cryptochrome 1 (CRY1) is a blue light receptor distributed in the nucleus and cytoplasm. The nuclear CRY1, but not cytoplasmic CRY1, mediates blue light inhibition of hypocotyl elongation. However, the photobiochemical mechanisms distinguishing the CRY1 protein in the two subcellular compartments remains unclear. Here we show that the nuclear CRY1, but not the cytoplasmic CRY1, is regulated by phosphorylation, polyubiquitination and 26S proteasome-dependent proteolysis in response to blue light. The blue light-dependent CRY1 degradation is observed only under high fluences of blue light. The nuclear specificity and high fluence dependency of CRY1 explain why this photochemical regulatory mechanism of CRY1 was not observed previously and it further supports the hypothesis that CRY1 is a high light receptor regulating photomorphogenesis. We further show that the nuclear CRY1, but not cytoplasmic CRY1, undergoes blue light-dependent phosphorylation by photoregulatory protein kinase 1 (PPK1) followed by polyubiquitination by the E3 ubiquitin ligase Cul4^COP1/SPAs , resulting in the blue light-dependent proteolysis. Both phosphorylation and ubiquitination of nuclear CRY1 are inhibited by blue-light inhibitor of cryptochromes 1 (BIC1), demonstrating the involvement of photo-oligomerization of the nuclear CRY1. These finding reveals a photochemical mechanism that differentially regulates the physiological activity of the CRY1 photoreceptor in distinct subcellular compartments.

Low-Intensity Blue Light Supplemented during Photoperiod in Controlled Environment Induces Flowering and Antioxidant Production in Kalanchoe

Kalanchoe (Kalanchoe blossfeldiana) is a qualitative short-day plant with a high aesthetic value. When the night length is less than a specified cultivar-dependent critical value, however, it does not develop flowers. This study investigated the effects of low-intensity supplementary or night interrupting (NI) blue (B) light on the plant performance and flower induction in kalanchoe 'Rudak'. During the photoperiod in a closed-type plant factory with day/night temperatures of 23 °C/18 °C, white (W) LEDs were utilized to produce a photosynthetic photon flux density (PPFD) of 300 μmol m-2 s-1, and B LEDs were used to give supplementary/NI light at a PPFD of 10 μmol m-2 s-1. The control plants were exposed to a 10-h short day (SD, positive control) or a 13-h long day (LD, negative control) treatment without any B light. The B light was used for 4 h either (1) to supplement the W LEDs at the end of the SD (SD + 4B) and LD (LD + 4B), or (2) to provide night interruption (NI) in the SD (SD + NI-4B) and LD (LD + NI-4B). The LD + 4B and LD + NI-4B significantly enhanced plant growth and development, followed by the SD + 4B and SD + NI-4B treatments. In addition, the photosynthesis, physiological parameters, and activity of antioxidant systems were improved in those treatments. Except in the LD and LD + NI-4B, all plants flowered. It is noteworthy that kalanchoe 'Rudak' flowered in the LD + 4B treatment and induced the greatest number of flowers, followed by SD + NI-4B and SD + 4B. Plants grown in the LD + 4B treatment had the highest expression levels of certain monitored genes related to flowering. The results indicate that a 4-h supplementation of B light during the photoperiod in both the SD and LD treatments increased flower bud formation, promoted flowering, and enhanced plant performance. Kalanchoe 'Rudak' flowered especially well in the LD + 4B, presenting a possibility of practically inducing flowering in long-day seasons with B light application.

Upregulation of GLRs expression by light in Arabidopsis leaves

BACKGROUND

Glutamate receptor-like (GLR) channels are plant homologs of iGluRs, animal ionotropic glutamate receptors which participate in neurotransmission. GLRs mediate plant adaptive processes and photomorphogenesis. Despite their contribution to light-dependent processes, signaling mechanisms that modulate GLR response to light remain unknown. Here we show that leaf expression of 7 out of 20 Arabidopsis GLRs is significantly up-regulated by monochromatic irradiation.

RESULTS

Our data indicates that both red and blue light stimulate the expression of selected AtGLRs. Using a photosynthesis inhibitor and different irradiation regimes, we demonstrated that retrograde signaling from photosystem II is unlikely to be involved in light-dependent GLR up-regulation. Analysis of transcriptional patterns in mutants of key photoreceptors allowed us to observe that both phytochromes and cryptochromes are likely to be involved in the control of light-dependent up-regulation of AtGLR expression, with phytochromes playing a clearly dominating role in this process.

CONCLUSIONS

In mature Arabidopsis leaves, phytochromes, assisted by cryptochromes, mediate light-driven transcriptional up-regulation of several genes encoding GLR proteins. Since GLRs are known to be involved in a wide range of plant developmental processes our results provide mechanistic insight into how light may influence plant growth and development.

OsBIC1 Directly Interacts with OsCRYs to Regulate Leaf Sheath Length through Mediating GA-Responsive Pathway

Cryptochrome 1 and 2 (CRY1 and CRY2) are blue light receptors involved in the regulation of hypocotyl elongation, cotyledon expansion, and flowering time in Arabidopsisthaliana. Two cryptochrome-interacting proteins, Blue-light Inhibitor of Cryptochrome 1 and 2 (BIC1 and BIC2), have been found in Arabidopsis. BIC1 plays critical roles in suppressing the physiological activities of CRY2, which include the blue light-dependent dimerization, phosphorylation, photobody formation, and degradation process, but the functional characterization of BIC protein in other crops has not yet been performed. To investigate the function of BIC protein in rice (Oryza sativa), two homologous genes of Arabidopsis BIC1 and BIC2, namely OsBIC1 and OsBIC2 (OsBICs), were identified. The overexpression of OsBIC1 and OsBIC2 led to increased leaf sheath length, whereas mutations in OsBIC1 displayed shorter leaf sheath in a blue light intensity-dependent manner. OsBIC1 regulated blue light-induced leaf sheath elongation through direct interaction with OsCRY1a, OsCRY1b, and OsCRY2 (OsCRYs). Longitudinal sections of the second leaf sheath demonstrated that OsBIC1 and OsCRYs controlled leaf sheath length by influencing the ratio of epidermal cells with different lengths. RNA-sequencing (RNA-seq) and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) analysis further proved that OsBIC1 and OsCRYs regulated similar transcriptome changes in regulating Gibberellic Acids (GA)-responsive pathway. Taken together, these results suggested that OsBIC1 and OsCRYs worked together to regulate epidermal cell elongation and control blue light-induced leaf sheath elongation through the GA-responsive pathway.

Circadian Clock in Arabidopsis thaliana Determines Flower Opening Time Early in the Morning and Dominantly Closes Early in the Afternoon

Many plant species exhibit diurnal flower opening and closing, which is an adaptation influenced by the lifestyle of pollinators and herbivores. However, it remains unclear how these temporal floral movements are modulated. To clarify the role of the circadian clock in flower movement, we examined temporal floral movements in Arabidopsis thaliana. Wild-type (accessions; Col-0, Ler-0 and Ws-4) flowers opened between 0.7 and 1.4 h in a 16-h light period and closed between 7.5 and 8.3 h in a diurnal light period. In the arrhythmic mutants pcl1-1 and prr975, the former flowers closed slowly and imperfectly and the latter ones never closed. Under continuous light conditions, new flowers emerged and opened within a 23-26 h window in the wild-type, but the flowers in pcl1-1 and prr975 developed straight petals, whose curvatures were extremely small. Anti-phasic circadian gene expression of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYLE (LHY) and TIMING OF CAB EXPRESSION 1 (TOC1) occurred in wild-type flowers, but non-rhythmic expression was observed in pcl1-1 and prr975 mutants. Focusing on excised petals, bioluminescence monitoring revealed rhythmic promoter activities of genes expressed (CCA1, LHY and PHYTOCLOCK 1/LUX ARRHYTHMO, PCL1/LUX) in the morning and evening. These results suggest that the clock induces flower opening redundantly with unknown light-sensing pathways. By contrast, flower closing is completely dependent on clock control. These findings will lead to further exploration of the molecular mechanisms and evolutionary diversity of timing in flower opening and closing.

A photoregulatory mechanism of the circadian clock in Arabidopsis

Cryptochromes (CRYs) are photoreceptors that mediate light regulation of the circadian clock in plants and animals. Here we show that CRYs mediate blue-light regulation of N⁶-methyladenosine (m⁶A) modification of more than 10% of messenger RNAs in the Arabidopsis transcriptome, especially those regulated by the circadian clock. CRY2 interacts with three subunits of the METTL3/14-type N⁶-methyladenosine RNA methyltransferase (m⁶A writer): MTA, MTB and FIP37. Photo-excited CRY2 undergoes liquid-liquid phase separation (LLPS) to co-condense m⁶A writer proteins in vivo, without obviously altering the affinity between CRY2 and the writer proteins. mta and cry1cry2 mutants share common defects of a lengthened circadian period, reduced m⁶A RNA methylation and accelerated degradation of mRNA encoding the core component of the molecular oscillator circadian clock associated 1 (CCA1). These results argue for a photoregulatory mechanism by which light-induced phase separation of CRYs modulates m⁶A writer activity, mRNA methylation and abundance, and the circadian rhythms in plants.

The blue light receptor CRY1 interacts with GID1 and DELLA proteins to repress GA signaling during photomorphogenesis in Arabidopsis

Light is a critical environmental cue that regulates a variety of diverse plant developmental processes. Cryptochrome 1 (CRY1) is the major photoreceptor that mediates blue light-dependent photomorphogenic responses such as the inhibition of hypocotyl elongation. Gibberellin (GA) participates in the repression of photomorphogenesis and promotes hypocotyl elongation. However, the antagonistic interaction between blue light and GA is not well understood. Here, we report that blue light represses GA-induced degradation of the DELLA proteins (DELLAs), which are key negative regulators in the GA signaling pathway, via CRY1, thereby inhibiting the GA response during hypocotyl elongation. Both in vitro and in vivo biochemical analyses demonstrated that CRY1 physically interacts with GA receptors-GA-INSENSITIVE DWARF 1 proteins (GID1s)-and DELLAs in a blue light-dependent manner. Furthermore, we showed that CRY1 inhibits the association between GID1s and DELLAs. Genetically, CRY1 antagonizes the function of GID1s to repress the expression of cell elongation-related genes and thus hypocotyl elongation. Taken together, our findings demonstrate that CRY1 coordinates blue light and GA signaling for plant photomorphogenesis by stabilizing DELLAs through the binding and inactivation of GID1s, providing new insights into the mechanism by which blue light antagonizes the function of GA in photomorphogenesis.

A microbiota-root-shoot circuit favours Arabidopsis growth over defence under suboptimal light

Bidirectional root-shoot signalling is probably key in orchestrating stress responses and ensuring plant survival. Here, we show that Arabidopsis thaliana responses to microbial root commensals and light are interconnected along a microbiota-root-shoot axis. Microbiota and light manipulation experiments in a gnotobiotic plant system reveal that low photosynthetically active radiation perceived by leaves induces long-distance modulation of root bacterial communities but not fungal or oomycete communities. Reciprocally, microbial commensals alleviate plant growth deficiency under low photosynthetically active radiation. This growth rescue was associated with reduced microbiota-induced aboveground defence responses and altered resistance to foliar pathogens compared with the control light condition. Inspection of a set of A. thaliana mutants reveals that this microbiota- and light-dependent growth-defence trade-off is directly explained by belowground bacterial community composition and requires the host transcriptional regulator MYC2. Our work indicates that aboveground stress responses in plants can be modulated by signals from microbial root commensals.

Near-Null Magnetic Field Suppresses Fruit Growth in Arabidopsis

We previously found that a near-null magnetic field affected reproductive growth in Arabidopsis under white light. To test whether the effect of a near-null magnetic field on fruit growth of Arabidopsis is related to cryptochrome, we grew wild-type Arabidopsis and cryptochrome double mutant, cry1/cry2, in a near-null magnetic field under blue light. We found that fruit growth of wild-type Arabidopsis instead of the cry1/cry2 mutant was suppressed by the near-null magnetic field. Furthermore, gibberellin (GA) levels of GA₄ , GA₉ , GA₃₄ , and GA₅₁ in fruits of wild-type plants in the near-null magnetic fields were significantly lower than local geomagnetic field controls. However, in cry1/cry2 mutants, levels of the four detected GAs in fruits in the near-null magnetic fields did not differ significantly from controls. Expressions of GA20-oxidase (GA20ox) genes (GA20ox1 and GA20ox2) and GA3-oxidase (GA3ox) genes (GA3ox1 and GA3ox3) in fruits of wild-type plants rather than cry1/cry2 mutants were downregulated by the near-null magnetic field. In contrast, expressions of GA2-oxidase (GA2ox) genes and GA signaling genes were not affected by the near-null magnetic field. These results indicate that suppression of fruit growth by the near-null magnetic field is mediated by cryptochrome and that GAs are involved in the regulation of fruit growth by the near-null magnetic field. © 2021 Bioelectromagnetics Society.

Regulation of Arabidopsis photoreceptor CRY2 by two distinct E3 ubiquitin ligases

Cryptochromes (CRYs) are photoreceptors or components of the molecular clock in various evolutionary lineages, and they are commonly regulated by polyubiquitination and proteolysis. Multiple E3 ubiquitin ligases regulate CRYs in animal models, and previous genetics study also suggest existence of multiple E3 ubiquitin ligases for plant CRYs. However, only one E3 ligase, Cul4COP1/SPAs, has been reported for plant CRYs so far. Here we show that Cul3LRBs is the second E3 ligase of CRY2 in Arabidopsis. We demonstrate the blue light-specific and CRY-dependent activity of LRBs (Light-Response Bric-a-Brack/Tramtrack/Broad 1, 2 & 3) in blue-light regulation of hypocotyl elongation. LRBs physically interact with photoexcited and phosphorylated CRY2, at the CCE domain of CRY2, to facilitate polyubiquitination and degradation of CRY2 in response to blue light. We propose that Cul4COP1/SPAs and Cul3LRBs E3 ligases interact with CRY2 via different structure elements to regulate the abundance of CRY2 photoreceptor under different light conditions, facilitating optimal photoresponses of plants grown in nature.

The SNL-HDA19 histone deacetylase complex antagonizes HY5 activity to repress photomorphogenesis in Arabidopsis

Reprogramming of the transcriptome during photomorphogenesis requires dynamic changes in chromatin and distribution of histone modifications. However, the chromatin-based regulation of this process remains to be elucidated. Here, we identify the conserved SWI-INDEPENDENT3 LIKE (SNL)-HISTONE DEACETYLASE19 (HDA19) deacetylase complex, including HDA19 and SNL1-SNL6, as a negative regulator of the light signaling pathway. Light-repression of HDA19 and SNLs expression is mediated by photoreceptors. HDA19 and SNLs are required for histone deacetylation and chromatin inactivation of PHYA gene. We further examined the interaction between SNL-HDA19 complex and ELONGATED HYPOCOTYL5 (HY5), and their antagonistic regulation on the expressions of target genes. The HDA19 deacetylase complex is recruited by HY5 to the chromatin regions of two positive light signaling genes, HY5 and B-BOX CONTAINING PROTEIN 22 (BBX22), thereby reduces the accessibility and histone acetylation and represses their expression. HDA19, SNL1, and HY5 associate with the same regulatory regions of HY5 and BBX22, and HY5 binding to these loci is enhanced upon SNL-HDA19 dysfunction. Our study reveals a crucial role for the HDA19 deacetylase complex in light signaling and demonstrates that the functional interplay between chromatin regulators and transcription factors regulates photomorphogenetic responses to the changing light environments.

The Universally Conserved Residues Are Not Universally Required for Stable Protein Expression or Functions of Cryptochromes

Universally conserved residues (UCRs) are invariable amino acids evolutionarily conserved among members of a protein family across diverse kingdoms of life. UCRs are considered important for stability and/or function of protein families, but it has not been experimentally examined systematically. Cryptochromes are photoreceptors in plants or light-independent components of the circadian clocks in mammals. We experimentally analyzed 51 UCRs of Arabidopsis cryptochrome 2 (CRY2) that are universally conserved in eukaryotic cryptochromes from Arabidopsis to human. Surprisingly, we found that UCRs required for stable protein expression of CRY2 in plants are not similarly required for stable protein expression of human hCRY1 in human cells. Moreover, 74% of the stably expressed CRY2 proteins mutated in UCRs retained wild-type-like activities for at least one photoresponses analyzed. Our finding suggests that the evolutionary mechanisms underlying conservation of UCRs or that distinguish UCRs from non-UCRs determining the same functions of individual cryptochromes remain to be investigated.

A Positive Feedback Loop of BBX11-BBX21-HY5 Promotes Photomorphogenic Development in Arabidopsis

Light is the most important environmental factor affecting many aspects of plant development. In this study, we report that B-box protein 11 (BBX11) acts as a positive regulator of red light signaling. BBX11 loss-of-function mutant seedlings display significantly elongated hypocotyls under conditions of both red light and long day, whereas BBX11 overexpression causes markedly shortened hypocotyls under various light states. BBX11 binds to the HY5 promoter to activate its transcription, while both BBX21 and HY5 associate with the promoter of BBX11 to positively regulate its expression. Taken together, our results reveal positive feedback regulation of photomorphogenesis consisting of BBX11, BBX21, and HY5, thus substantiating a transcriptional regulatory mechanism in the response of plants to light during normal development.

CONSTITUTIVELY PHOTOMORPHOGENIC1 promotes ABA-mediated inhibition of post-germination seedling establishment

Under acute stress conditions, precocious seedling development may result in the premature death of young seedlings, before they switch to autotrophic growth. The phytohormone abscisic acid (ABA) inhibits seed germination and post-germination seedling establishment under unfavorable conditions. Various environmental signals interact with the ABA pathway to optimize these early developmental events under stress. Here, we show that light availability critically influences ABA sensitivity during early seedling development. In dark conditions, the ABA-mediated inhibition of post-germination seedling establishment is strongly enhanced. COP1, a central regulator of seedling development in the dark, is necessary for this enhanced post-germination ABA sensitivity in darkness. Despite their slower germination, cop1 seedlings establish faster than wild type in the presence of ABA in both light and dark. PHY and CRY photoreceptors that inhibit COP1 activity in light modulate ABA-mediated inhibition of seedling establishment in light. Genetically, COP1 acts downstream to ABI5, a key transcriptional regulator of ABA signaling, and does not influence the transcriptional and protein levels of ABI5 during the early post-germination stages. COP1 promotes post-germination growth arrest independent of the antagonistic interaction between ABA and cytokinin signaling pathways. COP1 facilitates the binding of ABI5 on its target promoters and the ABA-mediated upregulation of these target genes is reduced in cop1-4. Together, our results suggest that COP1 positively regulates ABA signaling to inhibit post-germination seedling establishment under stress.

PHYTOCHROME INTERACTING FACTOR 7 is important for early responses to elevated temperature in Arabidopsis seedlings

In response to elevated ambient temperature Arabidopsis thaliana seedlings display a thermomorphogenic response that includes elongation of hypocotyls and petioles. Phytochrome B and cryptochrome 1 are two photoreceptors also playing a role in thermomorphogenesis. Downstream of both environmental sensors PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is essential to trigger this response at least in part through the production of the growth promoting hormone auxin. Using a genetic approach, we identified PHYTOCHROME INTERACTING FACTOR 7 (PIF7) as a novel player for thermomorphogenesis and compared the phenotypes of pif7 and pif4 mutants. We investigated the role of PIF7 during temperature-regulated gene expression and the regulation of PIF7 transcript and protein by temperature. Furthermore, pif7 and pif4 loss-of-function mutants were similarly unresponsive to increased temperature. This included hypocotyl elongation and induction of genes encoding auxin biosynthetic or signalling proteins. PIF7 bound to the promoters of auxin biosynthesis and signalling genes. In response to temperature elevation PIF7 transcripts decreased while PIF7 protein levels increased rapidly. Our results reveal the importance of PIF7 for thermomorphogenesis and indicate that PIF7 and PIF4 likely depend on each other possibly by forming heterodimers. Elevated temperature rapidly enhances PIF7 protein accumulation, which may contribute to the thermomorphogenic response.

Cryptochromes integrate green light signals into the circadian system

Plants are acutely sensitive of their light environment, adapting their growth habit and prioritizing developmental decisions to maximize fecundity. In addition to providing an energy source and directional information, light quality also contributes to entrainment of the circadian system, an endogenous timing mechanism that integrates endogenous and environmental signalling cues to promote growth. Whereas plants' perception of red and blue portions of the spectrum are well defined, green light sensitivity remains enigmatic. In this study, we show that low fluence rates of green light are sufficient to entrain and maintain circadian rhythms in Arabidopsis and that cryptochromes contribute to this response. Importantly, green light responses are distinguishable from low blue light-induced phenotypes. These data suggest a distinct signalling mechanism enables entrainment of the circadian system in green light-enriched environments, such as those found in undergrowth and in densely planted monoculture.

Multiple steps of leaf thickening during sun-leaf formation in Arabidopsis

Plant morphological and physiological traits exhibit plasticity in response to light intensity. Leaf thickness is enhanced under high light (HL) conditions compared with low light (LL) conditions through increases in both cell number and size in the dorsoventral direction; however, the regulation of such phenotypic plasticity in leaf thickness (namely, sun- or shade-leaf formation) during the developmental process remains largely unclear. By modifying observation techniques for tiny leaf primordia in Arabidopsis thaliana, we analysed sun- and shade-leaf development in a time-course manner and found that the process of leaf thickening can be divided into early and late phases. In the early phase, anisotropic cell elongation and periclinal cell division on the adaxial side of mesophyll tissue occurred under the HL conditions used, which resulted in the dorsoventral growth of sun leaves. Anisotropic cell elongation in the palisade tissue is triggered by blue-light irradiation. We discovered that anisotropic cell elongation processes before or after periclinal cell division were differentially regulated independent of or dependent upon signalling through blue-light receptors. In contrast, during the late phase, isotropic cell expansion associated with the endocycle, which determined the final leaf thickness, occurred irrespective of the light conditions. Sucrose production was high under HL conditions, and we found that sucrose promoted isotropic cell expansion and the endocycle even under LL conditions. Our analyses based on this method of time-course observation addressed the developmental framework of sun- and shade-leaf formation.

Network trade-offs and homeostasis in Arabidopsis shoot architectures

Understanding the optimization objectives that shape shoot architectures remains a critical problem in plant biology. Here, we performed 3D scanning of 152 Arabidopsis shoot architectures, including wildtype and 10 mutant strains, and we uncovered a design principle that describes how architectures make trade-offs between competing objectives. First, we used graph-theoretic analysis to show that Arabidopsis shoot architectures strike a Pareto optimal that can be captured as maximizing performance in transporting nutrients and minimizing costs in building the architecture. Second, we identify small sets of genes that can be mutated to shift the weight prioritizing one objective over the other. Third, we show that this prioritization weight feature is significantly less variable across replicates of the same genotype compared to other common plant traits (e.g., number of rosette leaves, total volume occupied). This suggests that this feature is a robust descriptor of a genotype, and that local variability in structure may be compensated for globally in a homeostatic manner. Overall, our work provides a framework to understand optimization trade-offs made by shoot architectures and provides evidence that these trade-offs can be modified genetically, which may aid plant breeding and selection efforts.

In both engineered and biological systems, there is often no single structure that performs optimally on all tasks. For example, a transport system that can very quickly shuttle people to and from work will often not be very cheap to build, and vice-versa. Thus, trade-offs are born, and it is natural to ask how well evolution has resolved trade-offs between competing tasks. Here, we use 3D laser scanning and network analysis to show that Arabidopsis plant architectures make Pareto optimal trade-offs, which means that improving upon one task requires a sacrifice in the other task. In other words, an architecture that performs better on both tasks cannot be built. We also identify a small set of genes that can change how the architecture prioritizes one task versus the other, which may allow for better crop design in the future. Finally, we show that two replicate architectures that look visually diverse (e.g., variation in size, number of leaves, number of branches, etc.) often prioritize each task similarly. This suggests that despite local variability in the architecture, there may be a homeostatic drive to maintain globally balanced trade-offs.

Neighbour signals perceived by phytochrome B increase thermotolerance in Arabidopsis

Due to the preeminence of reductionist approaches, understanding of plant responses to combined stresses is limited. We speculated that light-quality signals of neighbouring vegetation might increase susceptibility to heat shocks because shade reduces tissue temperature and hence the likeness of heat shocks. In contrast, plants of Arabidopsis thaliana grown under low-red/far-red ratios typical of shade were less damaged by heat stress than plants grown under simulated sunlight. Neighbour signals reduce the activity of phytochrome B (phyB), increasing the abundance of PHYTOCHROME-INTERACTING FACTORS (PIFs). The phyB mutant showed high tolerance to heat stress even under simulated sunlight, and a pif multiple mutant showed low tolerance under simulated shade. phyB and red/far-red ratio had no effects on seedlings acclimated with nonstressful warm temperatures before the heat shock. The phyB mutant showed reduced expression of several fatty acid desaturase (FAD) genes and less proportion of fully unsaturated fatty acids and electrolyte leakage of membranes exposed to heat shocks. Red-light-activated phyB also reduced thermotolerance of dark-grown seedlings but not via changes in FADs expression and membrane stability. We propose that the reduced photosynthetic capacity linked to thermotolerant membranes would be less costly under shade, where the light input limits photosynthesis.

OsBBX14 promotes photomorphogenesis in rice by activating OsHY5L1 expression under blue light conditions

In rice, OsBBX14, a B-box (BBX) transcription factor, reportedly delays heading. Here, we revealed that OsBBX14 positively regulates rice photomorphogenesis. The OsBBX14-overexpressing (OsBBX14-OX) seedlings were hypersensitive to light, especially blue light, and exhibited dwarfism, while the OsBBX14 knock-out plants (osbbx14) were taller than wild-type plants under blue light. Histological analyses indicated that the observed dwarfism was mainly due to decreased cell length. Additionally, OsBBX14 abundance (mRNA and protein levels) was influenced by different light wavelengths in a time-dependent manner. The expression levels of HY5Ls (LONG HYPOCOTYL 5 LIKE) and ELIPs (EARLY LIGHT-INDUCIBLE PROTEIN) genes, whose Arabidopsis thaliana homologs function as positive regulators in the light signaling pathway, were significantly upregulated in OsBBX14-OX lines. In contrast, the expression of genes related to cell wall organization and dwarfism was downregulated in OsBBX14-OX lines. Chromatin immunoprecipitation (ChIP) assays confirmed that OsBBX14 binds to the T/G-box of HY5L1 (LONG HYPOCOTYL 5 LIKE 1) promoter. LUC complementation imaging (LCI) results suggested that OsBBX14 had physical interaction with OsCRY2 protein. Collectively, in response to blue light, OsBBX14 promotes photomorphogenesis, probably by directly or indirectly regulating the expression of HY5L1 or other genes related to cell wall organization and dwarfism.