Overexpression of Brassica napus COMT1 in Arabidopsis heightens UV-B-mediated resistance to Plutella xylostella herbivory

UV-B radiation regulates numerous morphogenic, biochemical and physiological responses in plants, and can stimulate some responses typically associated with other abiotic and biotic stimuli, including invertebrate herbivory. Removal of UV-B from the growing environment of various plant species has been found to increase their susceptibility to consumption by invertebrate pests, however, to date, little research has been conducted to investigate the effects of UV-B on crop susceptibility to field pests. Here, we report findings from a multi-omic and genetic-based study investigating the mechanisms of UV-B-stimulated resistance of the crop, Brassica napus (oilseed rape), to herbivory from an economically important lepidopteran specialist of the Brassicaceae, Plutella xylostella (diamondback moth). The UV-B photoreceptor, UV RESISTANCE LOCUS 8 (UVR8), was not found to mediate resistance to this pest. RNA-Seq and untargeted metabolomics identified components of the sinapate/lignin biosynthetic pathway that were similarly regulated by UV-B and herbivory. Arabidopsis mutants in genes encoding two enzymes in the sinapate/lignin biosynthetic pathway, CAFFEATE O-METHYLTRANSFERASE 1 (COMT1) and ELICITOR-ACTIVATED GENE 3-2 (ELI3-2), retained UV-B-mediated resistance to P. xylostella herbivory. However, the overexpression of B. napus COMT1 in Arabidopsis further reduced plant susceptibility to P. xylostella herbivory in a UV-B-dependent manner. These findings demonstrate that overexpression of a component of the sinapate/lignin biosynthetic pathway in a member of the Brassicaceae can enhance UV-B-stimulated resistance to herbivory from P. xylostella.

HHL1 and SOQ1 synergistically regulate nonphotochemical quenching in Arabidopsis

Nonphotochemical quenching (NPQ) is an important photoprotective mechanism that quickly dissipates excess light energy as heat. NPQ can be induced in a few seconds to several hours; most studies of this process have focused on the rapid induction of NPQ. Recently, a new, slowly induced form of NPQ, called qH, was found during the discovery of the quenching inhibitor suppressor of quenching 1 (SOQ1). However, the specific mechanism of qH remains unclear. Here, we found that hypersensitive to high light 1 (HHL1)-a damage repair factor of photosystem II-interacts with SOQ1. The enhanced NPQ phenotype of the hhl1 mutant is similar to that of the soq1 mutant, which is not related to energy-dependent quenching or other known NPQ components. Furthermore, the hhl1 soq1 double mutant showed higher NPQ than the single mutants, but its pigment content and composition were similar to those of the wildtype. Overexpressing HHL1 decreased NPQ in hhl1 to below wildtype levels, whereas NPQ in hhl1 plants overexpressing SOQ1 was lower than that in hhl1 but higher than that in the wildtype. Moreover, we found that HHL1 promotes the SOQ1-mediated inhibition of plastidial lipoprotein through its von Willebrand factor type A domain. We propose that HHL1 and SOQ1 synergistically regulate NPQ.

Highlight Induced Transcriptional Priming against a Subsequent Drought Stress in Arabidopsis thaliana

In plants, priming allows a more rapid and robust response to recurring stresses. However, while the nature of plant response to a single stress can affect the subsequent response to the same stress has been deeply studied, considerably less is known on how the priming effect due to one stress can help plants cope with subsequent different stresses, a situation that can be found in natural ecosystems. Here, we investigate the potential priming effects in Arabidopsis plants subjected to a high light (HL) stress followed by a drought (D) stress. The cross-stress tolerance was assessed at the physiological and molecular levels. Our data demonstrated that HL mediated transcriptional priming on the expression of specific stress response genes. Furthermore, this priming effect involves both ABA-dependent and ABA-independent responses, as also supported by reduced expression of these genes in the aba1-3 mutant compared to the wild type. We have also assessed several physiological parameters with the aim of seeing if gene expression coincides with any physiological changes. Overall, the results from the physiological measurements suggested that these physiological processes did not experience metabolic changes in response to the stresses. In addition, we show that the H3K4me3 epigenetic mark could be a good candidate as an epigenetic mark in priming response. Overall, our results help to elucidate how HL-mediated priming can limit D-stress and enhance plant responses to stress.

Role of guard cell- or mesophyll cell-localized phytochromes in stomatal responses to blue, red, and far-red light

Guard cell- or mesophyll cell-localized phytochromes do not have a predominant direct light sensory role in red- or blue-light-mediated stomatal opening or far-red-light-mediated stomatal closure of Arabidopsis. The role of phytochromes in blue- and red-light-mediated stomatal opening, and far-red-light- mediated decrease in opening, is still under debate. It is not clear whether reduced stomatal opening in a phytochrome B (phyB) mutant line, is due to phytochrome acting as a direct photosensor or an indirect growth effect. The exact tissue localization of the phytochrome photoreceptor important for stomatal opening is also not known. We studied differences in stomatal opening in an Arabidopsis phyB mutant, and lines showing mesophyll cell-specific or guard cell-specific inactivation of phytochromes. Stomatal conductance (g_s) of intact leaves was measured under red, blue, and blue + far-red light. Lines exhibiting guard cell-specific inactivation of phytochrome did not show a change in g_s under blue or red light compared to Col-0. phyB consistently exhibited a reduction in g_s under both blue and red light. Addition of far-red light did not have a significant impact on the blue- or red-light-mediated stomatal response. Treatment of leaves with DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea), a photosynthetic electron transport (PET) inhibitor, eliminated the response to red light in all lines, indicating that stomatal opening under red light is controlled by PET, and not directly by phytochrome. Similar to previous studies, leaves of the phyB mutant line had fewer stomata. Overall, phytochrome does not appear have a predominant direct sensory role in stomatal opening under red or blue light. However, phytochromes likely have an indirect effect on the degree of stomatal opening under light through effects on leaf growth and stomatal development.

Genotype-dependent contribution of CBF transcription factors to long-term acclimation to high light and cool temperature

When grown under cool temperature, winter annuals upregulate photosynthetic capacity as well as freezing tolerance. Here, the role of three cold-induced C-repeat-binding factor (CBF1-3) transcription factors in photosynthetic upregulation and freezing tolerance was examined in two Arabidopsis thaliana ecotypes originating from Italy (IT) or Sweden (SW), and their corresponding CBF1-3-deficient mutant lines it:cbf123 and sw:cbf123. Photosynthetic, morphological and freezing-tolerance phenotypes, as well as gene expression profiles, were characterized in plants grown from the seedling stage under different combinations of light level and temperature. Under high light and cool (HLC) growth temperature, a greater role of CBF1-3 in IT versus SW was evident from both phenotypic and transcriptomic data, especially with respect to photosynthetic upregulation and freezing tolerance of whole plants. Overall, features of SW were consistent with a different approach to HLC acclimation than seen in IT, and an ability of SW to reach the new homeostasis through the involvement of transcriptional controls other than CBF1-3. These results provide tools and direction for further mechanistic analysis of the transcriptional control of approaches to cold acclimation suitable for either persistence through brief cold spells or for maximisation of productivity in environments with continuous low temperatures.

HY5 regulates light-dependent expression and accumulation of miR858a-encoded peptide, miPEP858a

microRNA encoded peptide (miPEP) has been shown to have potential to regulate corresponding miRNA and associated function. miPEP858a regulate phenylpropanoid pathway and plant development. Several studies have suggested that various factors like light, temperature, heavy metals etc. can regulate gene and their associated functions. However, what are the regulators of miPEP are not reported till date. In this study we have reported that light directly regulates miPEP858a accumulation in Arabidopsis thaliana. Peptide assay in light and dark clearly showed the essential requirement of light. Along with this, we have reported that HY5 a shoot-to-root mobile, light-mediated transcription factor plays a crucial role in the function of miPEP858a. The transcript and endogenous protein accumulation of miPEP858a in hy5-215, OXHY5/hy5, and cop1-4 suggested that the HY5 positively regulates miPEP858a. In addition to that this study also include grafting assay between shoot of different mutant and transgenic lines with root of miPEP858a promoter:reporter lines and promoter deletion construct experiment clearly suggested that HY5 a transcription factor regulates light-dependent expression and accumulation of miPEP858a.

Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis

Radiation-induced mutations have been detected by whole-genome sequencing analyses of self-pollinated generations of mutagenized plants. However, large DNA alterations and mutations in non-germline cells were likely missed. In this study, in order to detect various types of mutations in mutagenized M1 plants, anthocyanin pigmentation was used as a visible marker of mutations. Arabidopsis seeds heterozygous for the anthocyanin biosynthetic genes were irradiated with gamma-rays. Anthocyanin-less vegetative sectors resulting from a loss of heterozygosity were isolated from the gamma-irradiated M1 plants. The whole-genome sequencing analysis of the sectors detected various mutations, including structural variations (SVs) and large deletions (≥100 bp), both of which have been less characterized in the previous researches using gamma-irradiated plant genomes of M2 or later generations. Various types of rejoined sites were found in SVs, including no-insertion/deletion (indel) sites, only-deletion sites, only-insertion sites, and indel sites, but the rejoined sites with 0–5 bp indels represented most of the SVs. Examinations of the junctions of rearrangements (SVs and large deletions), medium deletions (10–99 bp), and small deletions (2–9 bp) revealed unique features (i.e., frequency of insertions and microhomology) at the rejoined sites. These results suggest that they were formed preferentially via different processes. Additionally, mutations that occurred in putative single M1 cells were identified according to the distribution of their allele frequency. The estimated mutation frequencies and spectra of the M1 cells were similar to those of previously analyzed M2 cells, with the exception of the greater proportion of rearrangements in the M1 cells. These findings suggest there are no major differences in the small mutations (<100 bp) between vegetative and germline cells. Thus, this study generated valuable information that may help clarify the nature of gamma-irradiation-induced mutations and their occurrence in cells that develop into vegetative or reproductive tissues.

Mutations that occur in plant genome are not only related to plant evolution and speciation in nature, and also useful to identify novel gene functions and to develop new cultivars. Ionizing radiations induce various types of mutations throughout genomes in individual cells of an irradiated/mutagenized plant. However, current knowledge on radiation-induced genome-wide mutations in plants relied on the analyses of self-pollinated generations (M2 or later generations) of the mutagenized plants (M1 generation). Thus, mutations that are hardly transmitted to the next generation and those occurred in non-germline cells could not be investigated. Here, using anthocyanin pigmentation as a visible marker to reduce the genomic complexity in M1 plants, we achieved reliable detection of radiation-induced genome-wide mutations. We demonstrated that rearrangements, which were hardly detected in previous analyses using M2 genomes, occurred substantially often in gamma-irradiated M1 cells. We also revealed that mutation profile of the M1 cells was comparable with that of M2 genomes reported in previous analyses, except for the higher proportion of rearrangements in the M1 genome. Together with unique features at rejoined sites of rearrangements, medium deletions, and small deletions in the M1 genome, our findings are helpful to know the nature of genome-wide mutations induced by gamma-irradiation.

Redesigning the photosynthetic light reactions to enhance photosynthesis - the PhotoRedesign consortium

In this Perspective article, we describe the visions of the PhotoRedesign consortium funded by the European Research Council of how to enhance photosynthesis. The light reactions of photosynthesis in individual phototrophic species use only a fraction of the solar spectrum, and high light intensities can impair and even damage the process. In consequence, expanding the solar spectrum and enhancing the overall energy capacity of the process, while developing resilience to stresses imposed by high light intensities, could have a strong positive impact on food and energy production. So far, the complexity of the photosynthetic machinery has largely prevented improvements by conventional approaches. Therefore, there is an urgent need to develop concepts to redesign the light-harvesting and photochemical capacity of photosynthesis, as well as to establish new model systems and toolkits for the next generation of photosynthesis researchers. The overall objective of PhotoRedesign is to reconfigure the photosynthetic light reactions so they can harvest and safely convert energy from an expanded solar spectrum. To this end, a variety of synthetic biology approaches, including de novo design, will combine the attributes of photosystems from different photoautotrophic model organisms, namely the purple bacterium Rhodobacter sphaeroides, the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana. In parallel, adaptive laboratory evolution will be applied to improve the capacity of reimagined organisms to cope with enhanced input of solar energy, particularly in high and fluctuating light.

The Role of Topoisomerase II in DNA Repair and Recombination in Arabidopsis thaliana

DNA entanglements and supercoiling arise frequently during normal DNA metabolism. DNA topoisomerases are highly conserved enzymes that resolve the topological problems that these structures create. Topoisomerase II (TOPII) releases topological stress in DNA by removing DNA supercoils through breaking the two DNA strands, passing a DNA duplex through the break and religating the broken strands. TOPII performs key DNA metabolic roles essential for DNA replication, chromosome condensation, heterochromatin metabolism, telomere disentanglement, centromere decatenation, transmission of crossover (CO) interference, interlock resolution and chromosome segregation in several model organisms. In this study, we reveal the endogenous role of Arabidopsis thaliana TOPII in normal root growth and cell cycle, and mitotic DNA repair via homologous recombination. Additionally, we show that the protein is required for meiotic DSB repair progression, but not for CO formation. We propose that TOPII might promote mitotic HR DNA repair by relieving stress needed for HR strand invasion and D-loop formation.

Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops

The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes. This large number suggests the functional significance of amino acid transporters in plant growth and development. The current article summarizes the substrate specificity, cellular localization, tissue-specific expression, and expression of the amino acid transporter genes in response to environmental cues. However, till date functionality of a majority of amino acid transporter genes in plant development and stress tolerance is unexplored. Considering, that gene expression is mainly regulated by the regulatory motifs localized in their promoter regions at the transcriptional levels. The promoter regions ( ~ 1-kbp) of these amino acid transporter genes were analysed for the presence of cis-regulatory motifs responsive to developmental and external cues. This analysis can help predict the functionality of known and unexplored amino acid transporters in different tissues, organs, and various growth and development stages and responses to external stimuli. Furthermore, based on the promoter analysis and utilizing the microarray expression data we have attempted to identify plausible candidates (listed below) that might be targeted for agricultural benefits.

Low light intensity delays vegetative phase change

Plants that develop under low light (LL) intensity often display a phenotype known as the "shade tolerance syndrome (STS)". This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis (Arabidopsis thaliana). We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase in the expression of the master regulators of vegetative phase change, miR156 and miR157, and a decrease in the expression of their SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) targets. Exogenous sucrose partially corrected the effect of LL on seedling development and miR156 expression. Our results suggest that the response of Arabidopsis to LL is mediated by an increase in miR156/miR157 expression and by factors that repress SPL gene expression independently of miR156/miR157, and is caused in part by a decrease in carbohydrate production. The effect of LL on vegetative phase change does not require the photoreceptors and transcription factors responsible for the shade avoidance syndrome, implying that light intensity and light quality regulate rosette development through different pathways.

Phototropin-mediated perception of light direction in leaves regulates blade flattening

One conserved feature among angiosperms is the development of flat thin leaves. This developmental pattern optimizes light capture and gas exchange. The blue light (BL) receptors phototropins are required for leaf flattening, with the null phot1phot2 mutant showing curled leaves in Arabidopsis (Arabidopsis thaliana). However, key aspects of their function in leaf development remain unknown. Here, we performed a detailed spatiotemporal characterization of phototropin function in Arabidopsis leaves. We found that phototropins perceive light direction in the blade, and, similar to their role in hypocotyls, they control the spatial pattern of auxin signaling, possibly modulating auxin transport, to ultimately regulate cell expansion. Phototropin signaling components in the leaf partially differ from hypocotyls. Moreover, the light response on the upper and lower sides of the leaf blade suggests a partially distinct requirement of phototropin signaling components on each side. In particular, NON PHOTOTROPIC HYPOCOTYL 3 showed an adaxial-specific function. In addition, we show a prominent role of PHYTOCHROME KINASE SUBSTRATE 3 in leaf flattening. Among auxin transporters, PIN-FORMED 3,4,7 and AUXIN RESISTANT 1 (AUX1)/LIKE AUXIN RESISTANT 1 (LAX1) are required for the response while ABCB19 has a regulatory role. Overall, our results show that directional BL perception by phototropins is a key aspect of leaf development, integrating endogenous and exogenous signals.

How plants protect themselves from ultraviolet-B radiation stress

Ultraviolet-B (UV-B) radiation has a wavelength range of 280-315 nm. Plants perceive UV-B as an environmental signal and a potential abiotic stress factor that affects development and acclimation. UV-B regulates photomorphogenesis including hypocotyl elongation inhibition, cotyledon expansion, and flavonoid accumulation, but high intensity UV-B can also harm plants by damaging DNA, triggering accumulation of reactive oxygen species, and impairing photosynthesis. Plants have evolved "sunscreen" flavonoids that accumulate under UV-B stress to prevent or limit damage. The UV-B receptor UV RESISTANCE LOCUS 8 (UVR8) plays a critical role in promoting flavonoid biosynthesis to enhance UV-B stress tolerance. Recent studies have clarified several UVR8-mediated and UVR8-independent pathways that regulate UV-B stress tolerance. Here, we review these additions to our understanding of the molecular pathways involved in UV-B stress tolerance, highlighting the important roles of ELONGATED HYPOCOTYL 5, BRI1-EMS-SUPPRESSOR1, MYB DOMAIN PROTEIN 13, MAP KINASE PHOSPHATASE 1, and ATM- and RAD3-RELATED. We also summarize the known interactions with visible light receptors and the contribution of melatonin to UV-B stress responses. Finally, we update a working model of the UV-B stress tolerance pathway.

Gibberellin regulates UV-B-induced hypocotyl growth inhibition in Arabidopsis thaliana

Plant response to light is a complex and diverse phenomenon. Several studies have elucidated the mechanisms via which light and hormones regulate hypocotyl growth. However, the hormone-dependent ultraviolet-B (UV-B) response in plants remains obscure. Involvement of gibberellins (GAs) in UV-B-induced hypocotyl inhibition and its mechanisms in Arabidopsis thaliana were investigated in the present research. UV-B exposure remarkably decreased the endogenous GA₃ content through the UV RESISTANCE LOCUS 8 (UVR8) receptor pathway, and exogenous GA₃ partially restored the hypocotyl growth. UV-B irradiation affected the expression levels of GA metabolism-related genes (GA20ox1, GA2ox1 and GA3ox1) in the hy5-215 mutant, resulting in increased GA content.ELONGATED HYPOCOTYL 5 (HY5) promoted the accumulation of DELLA proteins under UV-B radiation; HY5 appeared to regulate the abundance of DELLAs at the transcriptional level under UV-B. As a result, the GA₃ content decreased, which eventually led to the shortening of the hypocotyl. To conclude, the present study provides new insight into the regulation of plant photomorphogenesis under UV-B.

Arabidopsis cryptochrome 1 promotes stomatal development through repression of AGB1 inhibition of SPEECHLESS DNA-binding activity

Cryptochromes are blue light photoreceptors that mediate various light responses in plants and mammals. The heterotrimeric G-protein is known to regulate various physiological processes in plants and mammals. In Arabidopsis, cryptochrome 1 (CRY1) and the G-protein β subunit AGB1 act antagonistically to regulate stomatal development. The molecular mechanism by which CRY1 and AGB1 regulate this process remains unknown. Here, we show that Arabidopsis CRY1 acts partially through AGB1, and AGB1 acts through SPEECHLESS (SPCH), a master transcription factor that drives stomatal initiation and proliferation, to regulate stomatal development. We demonstrate that AGB1 physically interacts with SPCH to block the bHLH DNA-binding domain of SPCH and inhibit its DNA-binding activity. Moreover, we demonstrate that photoexcited CRY1 represses the interaction of AGB1 with SPCH to release AGB1 inhibition of SPCH DNA-binding activity, leading to the expression of SPCH-target genes promoting stomatal development. Taken together, our results suggest that the mechanism by which CRY1 promotes stomatal development involves positive regulation of the DNA-binding activity of SPCH mediated by CRY1 inhibition of the AGB1-SPCH interaction. We propose that the antagonistic regulation of SPCH DNA-binding activity by CRY1 and AGB1 may allow plants to balance light and G-protein signaling and optimize stomatal density and pattern.

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.

Impact of high irradiance and UV-B on the photosynthetic activity, pro-/antioxidant balance and expression of light-activated genes in Arabidopsis thaliana hy4 mutants grown under blue light

The impacts of high-intensity light (HIL) (4 h) and UV-B radiation (1 h) on the photosynthetic activity, content of photosynthetic and UV-absorbing pigments (UAPs), activity of antioxidant enzymes (ascorbate peroxidase (APX) and guaiacol-dependent peroxidase (GPX)), content of thiobarbituric acid reactive substances (TBARs), expression of some light-regulated genes in 25-day-old wild type (WT) and the cryptochrome 1 (Cry1) hy4 mutant of A. thaliana Col-0 plants grown under blue light (BL) were studied. HIL and UV-B treatments led to decreases in the photosynthetic rate (P_n), photochemical activity of PSII (F_V/F_M) and PSII performance index (PI_ABS) of WT and mutant plants grown under high-intensity BL (HBL) and moderate intensity BL (MBL). However, in HBL plants, the decrease in the photosynthetic activity in hy4 plants was significantly greater than that in WT plants. In addition, hy4 HBL plants demonstrated lowered UAP and carotenoid contents as well as lower activity of APX and GPX enzymes. The difference in the decline in the photosynthetic activity of WT and hy4 plants grown at MBL in response to HIL was nonsignificant, while that in response to UV-B was small. We assume that the deficiency in cryptochrome 1 under HIL irradiation disrupts the interaction between HY5 and HFR1 transcription factors and photoreceptors, which affects the transcription of light-induced genes, such as CAB1, PSY and PAL1 linked to carotenoid and flavonoid biosynthesis. It was concluded that PA stress resistance in WT and hy4 plants depends on the light intensity and reduced stress resistance of hy4 at HBL, is likely linked to low UAP and carotenoid contents as well as lowered APX and GPX enzyme activities in hy4 mutants.

Jasmonic acid and salicylic acid play minor roles in stomatal regulation by CO2 , abscisic acid, darkness, vapor pressure deficit and ozone

Jasmonic acid (JA) and salicylic acid (SA) regulate stomatal closure, preventing pathogen invasion into plants. However, to what extent abscisic acid (ABA), SA and JA interact, and what the roles of SA and JA are in stomatal responses to environmental cues, remains unclear. Here, by using intact plant gas-exchange measurements in JA and SA single and double mutants, we show that stomatal responsiveness to CO₂ , light intensity, ABA, high vapor pressure deficit and ozone either did not or, for some stimuli only, very slightly depended upon JA and SA biosynthesis and signaling mutants, including dde2, sid2, coi1, jai1, myc2 and npr1 alleles. Although the stomata in the mutants studied clearly responded to ABA, CO₂ , light and ozone, ABA-triggered stomatal closure in npr1-1 was slightly accelerated compared with the wild type. Stomatal reopening after ozone pulses was quicker in the coi1-16 mutant than in the wild type. In intact Arabidopsis plants, spraying with methyl-JA led to only a modest reduction in stomatal conductance 80 min after treatment, whereas ABA and CO₂ induced pronounced stomatal closure within minutes. We could not document a reduction of stomatal conductance after spraying with SA. Coronatine-induced stomatal opening was initiated slowly after 1.5-2.0 h, and reached a maximum by 3 h after spraying intact plants. Our results suggest that ABA, CO₂ and light are major regulators of rapid guard cell signaling, whereas JA and SA could play only minor roles in the whole-plant stomatal response to environmental cues in Arabidopsis and Solanum lycopersicum (tomato).

Thioredoxins m are major players in the multifaceted light-adaptive response in Arabidopsis thaliana

Thioredoxins (TRXs) are well-known redox signalling players, which carry out post-translational modifications in target proteins. Chloroplast TRXs are divided into different types and have central roles in light energy uptake and the regulation of primary metabolism. The isoforms TRX m1, m2, and m4 from Arabidopsis thaliana are considered functionally related. Knowing their key position in the hub of plant metabolism, we hypothesized that the impairment of the TRX m signalling would not only have harmful consequences on chloroplast metabolism but also at different levels of plant development. To uncover the physiological and developmental processes that depend on TRX m signalling, we carried out a comprehensive study of Arabidopsis single, double, and triple mutants defective in the TRX m1, m2, and m4 proteins. As light and redox signalling are closely linked, we investigated the response to high light (HL) of the plants that are gradually compromised in TRX m signalling. We provide experimental evidence relating the lack of TRX m and the appearance of novel phenotypic features concerning mesophyll structure, stomata biogenesis, and stomatal conductance. We also report new data indicating that the isoforms of TRX m fine-tune the response to HL, including the accumulation of the protective pigment anthocyanin. These results reveal novel signalling functions for the TRX m and underline their importance for plant growth and fulfilment of the acclimation/response to HL conditions.

Functional comparison of the WD-repeat domains of SPA1 and COP1 in suppression of photomorphogenesis

The Arabidopsis COP1/SPA complex acts as a cullin4-based E3 ubiquitin ligase to suppress photomorphogenesis in darkness. It is a tetrameric complex of two COP1 and two SPA proteins. Both COP1 and SPA are essential for the activity of this complex, and they both contain a C-terminal WD-repeat domain responsible for substrate recruitment and binding of DDB1. Here, we used a WD domain swap-approach to address the cooperativity of COP1 and SPA proteins. We found that expression of a chimeric COP1 carrying the WD-repeat domain of SPA1 mostly complemented the cop1-4-mutant phenotype in darkness, indicating that the WD repeat of SPA1 can replace the WD repeat of COP1. In the light, SPA1-WD partially substituted for COP1-WD. In contrast, expression of a chimeric SPA1 protein carrying the WD repeat of COP1 did not rescue the spa-mutant phenotype. Together, our findings demonstrate that a SPA1-type WD repeat is essential for COP1/SPA activity, while a COP1-type WD is in part dispensible. Moreover, a complex with four SPA1-WDs is more active than a complex with only two SPA1-WDs. A homology model of SPA1-WD based on the crystal structure of COP1-WD uncovered two insertions and several amino acid substitutions at the predicted substrate-binding pocket of SPA1-WD.

Long-distance blue light signalling regulates phosphate deficiency-induced primary root growth inhibition

Although roots are mainly embedded in the soil, recent studies revealed that light regulates mineral nutrient uptake by roots. However, it remains unclear whether the change in root system architecture in response to different rhizosphere nutrient statuses involves light signaling. Here, we report that blue light regulates primary root growth inhibition under phosphate-deficient conditions through the cryptochromes and their downstream signaling factors. We showed that the inhibition of root elongation by low phosphate requires blue light signal perception at the shoot and transduction to the root. In this process, SPA1 and COP1 play a negative role while HY5 plays a positive role. Further experiments revealed that HY5 is able to migrate from the shoot to root and that the shoot-derived HY5 autoactivates root HY5 and regulates primary root growth by directly activating the expression of LPR1, a suppressor of root growth under phosphate starvation. Taken together, our study reveals a regulatory mechanism by which blue light signaling regulates phosphate deficiency-induced primary root growth inhibition, providing new insights into the crosstalk between light and nutrient signaling.

B-box protein BBX32 integrates light and brassinosteroid signals to inhibit cotyledon opening

Cotyledon opening is a key morphological change that occurs in seedlings during de-etiolation. Brassinosteroids (BRs) inhibit the opening of cotyledons in darkness while light promotes cotyledon opening. The molecular regulation of the interplay between light and BR to regulate cotyledon opening is not well understood. Here, we show the B-box protein BBX32 negatively regulates light signaling and promotes BR signaling to inhibit cotyledon opening in Arabidopsis (Arabidopsis thaliana). BBX32 is highly expressed in the cotyledons of seedlings during de-etiolation. bbx32 and 35S:BBX32 seedlings exhibit enhanced and reduced cotyledon opening, respectively, in response to both light and brassinazole treatment in dark, suggesting that BBX32 mediates cotyledon opening through both light and BR signaling pathways. BBX32 expression is induced by exogenous BR and is upregulated in bzr1-1D (BRASSINAZOLE RESISTANT1-1D). Our in vitro and in vivo interaction studies suggest that BBX32 physically interacts with BZR1. Further, we found that PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) interacts with BBX32 and promotes BR-mediated cotyledon closure. BBX32, BZR1, and PIF3 regulate the expression of common target genes that modulate the opening and closing of cotyledons. Our work suggests BBX32 integrates light and BR signals to regulate cotyledon opening during de-etiolation.

Light-induced degradation of SPA2 via its N-terminal kinase domain is required for photomorphogenesis

Arabidopsis (Arabidopsis thaliana) CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and members of the SUPPRESSOR OF PHYTOCHROMEA-105 (SPA) protein family form an E3 ubiquitin ligase that suppresses light signaling in darkness by polyubiquitinating positive regulators of the light response. COP1/SPA is inactivated by light to allow photomorphogenesis to proceed. Mechanisms of inactivation include light-induced degradation of SPA1 and, in particular, SPA2, corresponding to a particularly efficient inactivation of COP1/SPA2 by light. Here, we show that SPA3 and SPA4 proteins are stable in the light, indicating that light-induced destabilization is specific to SPA1 and SPA2, possibly related to the predominant function of SPA1 and SPA2 in dark-grown etiolating seedlings. SPA2 degradation involves cullin and the COP10-DEETIOLATED-DAMAGED-DNA BINDING PROTEIN (DDB1) CDD complex, besides COP1. Consistent with this finding, light-induced SPA2 degradation required the DDB1-interacting Trp-Asp (WD)-repeat domain of SPA2. Deletion of the N-terminus of SPA2 containing the kinase domain led to strong stabilization of SPA2 in darkness and fully abolished light-induced degradation of SPA2. This prevented seedling de-etiolation even in very strong far-red and blue light and reduced de-etiolation in red light, indicating destabilization of SPA2 through its N-terminal domain is essential for light response. SPA2 is exclusively destabilized by phytochrome A in far-red and blue light. However, deletion of the N-terminal domain of SPA2 did not abolish SPA2-phytochrome A interaction in yeast nor in vivo. Our domain mapping suggests there are two SPA2-phytochrome A interacting domains, the N-terminal domain and the WD-repeat domain. Conferring a light-induced SPA2-phyA interaction only via the WD-repeat domain may thus not lead to COP1/SPA2 inactivation.

HY5 and ABI5 transcription factors physically interact to fine tune light and ABA signaling in Arabidopsis

Cross-talk between light and ABA signaling is mediated by physical interaction between HY5 and ABI5 Arabidopsis. Plants undergo numerous transitions during their life-cycle and have developed a very complex network of signaling to integrate information from their surroundings to effectively survive in the ever-changing environment. Light signaling is one of the crucial factors that govern the plant growth and development from the very first step of that is from seedling germination to the flowering. Similarly, Abscisic acid (ABA) signaling transduces the signals from external unfavorable condition to the internal developmental pathways and is crucial for regulation of seed maturation, dormancy germination and early seedling development. These two fundamental factors coordinately regulate plant wellbeing, but the underlying molecular mechanisms that drive this regulation are poorly understood. Here, we identified that two bZIP transcription factors, ELONGATED HYPOCOTYLE 5 (HY5), a positive regulator of light signaling and ABA-INSENSITIVE 5 (ABI5), a positive regulator of ABA signaling interacts and integrates the two pathways together. Our phenotypic data suggest that ABI5 may act as a negative regulator during photomorphogenesis in contrast, HY5 acts as a positive regulator of ABA signaling in an ABA dependent manner. We further showed that over-expression of HY5 leads to ABA-hypersensitive phenotype and late flowering phenotype. Taken together, our data provides key insights regarding the mechanism of interaction between ABI5-HY5 that fine tunes the stress and developmental response in Arabidopsis.

Karrikins control seedling photomorphogenesis and anthocyanin biosynthesis through a HY5-BBX transcriptional module

The butenolide molecule, karrikin (KAR), emerging in smoke of burned plant material, enhances light responses such as germination, inhibition of hypocotyl elongation, and anthocyanin accumulation in Arabidopsis. The KAR signaling pathway consists of KARRIKIN INSENSITIVE 2 (KAI2) and MORE AXILLARY GROWTH 2 (MAX2), which, upon activation, act in an SCF E3 ubiquitin ligase complex to target the downstream signaling components SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 2 (SMXL2) for degradation. How degradation of SMAX1 and SMXL2 is translated into growth responses remains unknown. Although light clearly influences the activity of KAR, the molecular connection between the two pathways is still poorly understood. Here, we demonstrate that the KAR signaling pathway promotes the activity of a transcriptional module consisting of ELONGATED HYPOCOTYL 5 (HY5), B-BOX DOMAIN PROTEIN 20 (BBX20), and BBX21. The bbx20 bbx21 mutant is largely insensitive to treatment with KAR₂ , similar to a hy5 mutant, with regards to inhibition of hypocotyl elongation and anthocyanin accumulation. Detailed analysis of higher order mutants in combination with RNA-sequencing analysis revealed that anthocyanin accumulation downstream of SMAX1 and SMXL2 is fully dependent on the HY5-BBX module. However, the promotion of hypocotyl elongation by SMAX1 and SMXL2 is, in contrast to KAR₂ treatment, only partially dependent on BBX20, BBX21, and HY5. Taken together, these results suggest that light- and KAR-dependent signaling intersect at the HY5-BBX transcriptional module.

Time-series transcriptomics reveals a BBX32-directed control of acclimation to high light in mature Arabidopsis leaves

The photosynthetic capacity of mature leaves increases after several days' exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast-level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL-dependent changes in transcript abundance of 3844 genes in a 0-6 h time-series transcriptomics experiment. It was hypothesized that among such genes were those that contribute to the initiation of HL acclimation. By focusing on differentially expressed transcription (co-)factor genes and applying dynamic statistical modelling to the temporal transcriptomics data, a regulatory network of 47 predominantly photoreceptor-regulated transcription (co-)factor genes was inferred. The most connected gene in this network was B-BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants overexpressing BBX32 were strongly impaired in acclimation to HL and displayed perturbed expression of photosynthesis-associated genes under LL and after exposure to HL. These observations led to demonstrating that as well as regulation of chloroplast-level acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA-105 are important. In addition, the BBX32-centric gene regulatory network provides a view of the transcriptional control of acclimation in mature leaves distinct from other photoreceptor-regulated processes, such as seedling photomorphogenesis.

Long-term adaptation of Arabidopsis thaliana to far-red light

Vascular plants use carotenoids and chlorophylls a and b to harvest solar energy in the visible region (400-700 nm), but they make little use of the far-red (FR) light. Instead, some cyanobacteria have developed the ability to use FR light by redesigning their photosynthetic apparatus and synthesizing red-shifted chlorophylls. Implementing this strategy in plants is considered promising to increase crop yield. To prepare for this, a characterization of the FR light-induced changes in plants is necessary. Here, we explore the behaviour of Arabidopsis thaliana upon exposure to FR light by following the changes in morphology, physiology and composition of the photosynthetic complexes. We found that after FR-light treatment, the ratio between the photosystems and their antenna size drastically readjust in an attempt to rebalance the energy input to support electron transfer. Despite a large increase in PSBS accumulation, these adjustments result in strong photoinhibition when FR-adapted plants are exposed to light again. Crucially, FR light-induced changes in the photosynthetic membrane are not the result of senescence, but are a response to the excitation imbalance between the photosystems. This indicates that an increase in the FR absorption by the photosystems should be sufficient for boosting photosynthetic activity in FR light.

HY5 regulates light-responsive transcription of microRNA163 to promote primary root elongation in Arabidopsis seedlings

MicroRNAs (miRNAs) play key roles in the post-transcriptional regulation of gene expression in plants. Many miRNAs are responsive to environmental signals. Light is the first environmental signal perceived by plants after emergence from the soil. However, less is known about the roles and regulatory mechanism of miRNAs in response to light signal. Here, using small RNA sequencing, we determined that miR163 is significantly rapidly induced by light signaling in Arabidopsis thaliana seedlings. The light-inducible response of miR163 functions genetically downstream of LONG HYPOCOTYL 5 (HY5), a central positive regulator of photomorphogenesis. HY5 directly binds to the two G/C-hybrid elements in the miR163 promoter with unequal affinity; one of these elements, which is located next to the transcription start site, plays a major role in light-induced expression of miR163. Overexpression of miR163 rescued the defective primary root elongation of hy5 seedlings without affecting lateral root growth, whereas overexpressing of miR163 target PXMT1 inhibited primary root elongation. These findings provide insight into understanding the post-transcriptional regulation of root photomorphogenesis mediated by the HY5-miR163-PXMT1 network.

Arabidopsis CHLOROPHYLLASE 1 protects young leaves from long-term photodamage by facilitating FtsH-mediated D1 degradation in photosystem II repair

The proteolytic degradation of the photodamaged D1 core subunit during the photosystem II (PSII) repair cycle is well understood, but chlorophyll turnover during D1 degradation remains unclear. Here, we report that Arabidopsis thaliana CHLOROPHYLLASE 1 (CLH1) plays important roles in the PSII repair process. The abundance of CLH1 and CLH2 peaks in young leaves and is induced by high-light exposure. Seedlings of clh1 single and clh1-1/2-2 double mutants display increased photoinhibition after long-term high-light exposure, whereas seedlings overexpressing CLH1 have enhanced light tolerance compared with the wild type. CLH1 is localized in the developing chloroplasts of young leaves and associates with the PSII-dismantling complexes RCC1 and RC47, with a preference for the latter upon exposure to high light. Furthermore, degradation of damaged D1 protein is retarded in young clh1-1/2-2 leaves after 18-h high-light exposure but is rescued by the addition of recombinant CLH1 in vitro. Moreover, overexpression of CLH1 in a variegated mutant (var2-2) that lacks thylakoid protease FtsH2, with which CLH1 interacts, suppresses the variegation and restores D1 degradation. A var2-2 clh1-1/2-2 triple mutant shows more severe variegation and seedling death. Taken together, these results establish CLH1 as a long-sought chlorophyll dephytylation enzyme that is involved in PSII repair and functions in long-term adaptation of young leaves to high-light exposure by facilitating FtsH-mediated D1 degradation.

An illuminated respiratory activity monitoring system identifies priming-active compounds in plant seedlings

BACKGROUND

Growing large crop monocultures and heavily using pesticides enhances the evolution of pesticide-insensitive pests and pathogens. To reduce pesticide use in crop cultivation, the application of priming-active compounds (PrimACs) is a welcome alternative. PrimACs strengthen the plant immune system and could thus help to protect plants with lower amounts of pesticides. PrimACs can be identified, for example, by their capacity to enhance the respiratory activity of parsley cells in culture as determined by the oxygen transfer rate (OTR) using the respiration activity monitoring system (RAMOS) or its miniaturized version, µRAMOS. The latter was designed for with suspensions of bacteria and yeast cells in microtiter plates (MTPs). So far, RAMOS or µRAMOS have not been applied to adult plants or seedlings, which would overcome the limitation of (µ)RAMOS to plant suspension cell cultures.

RESULTS

In this work, we introduce a modified µRAMOS for analysis of plant seedlings. The novel device allows illuminating the seedlings and records the respiratory activity in each well of a 48-well MTP. To validate the suitability of the setup for identifying novel PrimAC in Arabidopsis thaliana, seedlings were grown in MTP for seven days and treated with the known PrimAC salicylic acid (SA; positive control) and the PrimAC candidate methyl 1-(3,4-dihydroxyphenyl)-2-oxocyclopentane-1-carboxylate (Tyr020). Twenty-eight h after treatment, the seedlings were elicited with flg22, a 22-amino acid peptide of bacterial flagellin. Upon elicitation, the respiratory activity was monitored. The evaluation of the OTR course reveals Tyr020 as a likely PrimAC. The priming-inducing activity of Tyr020 was confirmed using molecular biological analyses in A. thaliana seedlings.

CONCLUSION

We disclose the suitability of µRAMOS for identifying PrimACs in plant seedlings. The difference in OTR during a night period between primed and unprimed plants was distinguishable after elicitation with flg22. Thus, it has been shown that the µRAMOS device can be used for a reliable screening for PrimACs in plant seedlings.

Resolving diurnal dynamics of the chloroplastic glutathione redox state in Arabidopsis reveals its photosynthetically derived oxidation

Plants are subjected to fluctuations in light intensity, and this might cause unbalanced photosynthetic electron fluxes and overproduction of reactive oxygen species (ROS). Electrons needed for ROS detoxification are drawn, at least partially, from the cellular glutathione (GSH) pool via the ascorbate-glutathione cycle. Here, we explore the dynamics of the chloroplastic glutathione redox potential (chl-EGSH) using high-temporal-resolution monitoring of Arabidopsis (Arabidopsis thaliana) lines expressing the reduction-oxidation sensitive green fluorescent protein 2 (roGFP2) in chloroplasts. This was carried out over several days under dynamic environmental conditions and in correlation with PSII operating efficiency. Peaks in chl-EGSH oxidation during dark-to-light and light-to-dark transitions were observed. Increasing light intensities triggered a binary oxidation response, with a threshold around the light saturating point, suggesting two regulated oxidative states of the chl-EGSH. These patterns were not affected in npq1 plants, which are impaired in non-photochemical quenching. Oscillations between the two oxidation states were observed under fluctuating light in WT and npq1 plants, but not in pgr5 plants, suggesting a role for PSI photoinhibition in regulating the chl-EGSH dynamics. Remarkably, pgr5 plants showed an increase in chl-EGSH oxidation during the nights following light stresses, linking daytime photoinhibition and nighttime GSH metabolism. This work provides a systematic view of the dynamics of the in vivo chloroplastic glutathione redox state during varying light conditions.

A BLUS1 kinase signal and a decrease in intercellular CO2 concentration are necessary for stomatal opening in response to blue light

Light-induced stomatal opening stimulates CO2 uptake and transpiration in plants. Weak blue light under strong red light effectively induces stomatal opening. Blue light-dependent stomatal opening initiates light perception by phototropins, and the signal is transmitted to a plasma membrane H+-ATPase in guard cells via BLUE LIGHT SIGNALING 1 (BLUS1) kinase. However, it is unclear how BLUS1 transmits the signal to H+-ATPase. Here, we characterized BLUS1 signaling in Arabidopsis thaliana, and showed that the BLUS1 C-terminus acts as an auto-inhibitory domain and that phototropin-mediated Ser-348 phosphorylation within the domain removes auto-inhibition. C-Terminal truncation and phospho-mimic Ser-348 mutation caused H+-ATPase activation in the dark, but did not elicit stomatal opening. Unexpectedly, the plants exhibited stomatal opening under strong red light and stomatal closure under weak blue light. A decrease in intercellular CO2 concentration via red light-driven photosynthesis together with H+-ATPase activation caused stomatal opening. Furthermore, phototropins caused H+-ATPase dephosphorylation in guard cells expressing constitutive signaling variants of BLUS1 in response to blue light, possibly for fine-tuning stomatal opening. Overall, our findings provide mechanistic insights into the blue light regulation of stomatal opening.

Phytochrome regulates cellular response plasticity and the basic molecular machinery of leaf development

Plants are plastic organisms that optimize growth in response to a changing environment. This adaptive capability is regulated by external cues, including light, which provides vital information about the habitat. Phytochrome photoreceptors detect far-red light, indicative of nearby vegetation, and elicit the adaptive shade-avoidance syndrome (SAS), which is critical for plant survival. Plants exhibiting SAS are typically more elongated, with distinctive, small, narrow leaf blades. By applying SAS-inducing end-of-day far-red (EoD FR) treatments at different times during Arabidopsis (Arabidopsis thaliana) leaf 3 development, we have shown that SAS restricts leaf blade size through two distinct cellular strategies. Early SAS induction limits cell division, while later exposure limits cell expansion. This flexible strategy enables phytochromes to maintain control of leaf size through the proliferative and expansion phases of leaf growth. mRNAseq time course data, accessible through a community resource, coupled to a bioinformatics pipeline, identified pathways that underlie these dramatic changes in leaf growth. Phytochrome regulates a suite of major development pathways that control cell division, expansion, and cell fate. Further, phytochromes control cell proliferation through synchronous regulation of the cell cycle, DNA replication, DNA repair, and cytokinesis, and play an important role in sustaining ribosome biogenesis and translation throughout leaf development.

Inflorescence abscission protein SlIDL6 promotes low light intensity-induced tomato flower abscission

In many fruiting plant species, flower abscission is induced by low light stress. Here, we elucidated how signaling mediated by the peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) controls low light-induced flower drop in tomato (Solanum lycopersicum). We analyzed the expression patterns of an IDA-Like gene (SlIDL6) during low light-induced flower abscission, and used tandem mass spectrometry to identify and characterize the mature SlIDL6 peptide. Tomato knockout lines were created to investigate the in vivo function of SlIDL6. In addition, yeast one-hybrid assays were used to investigate the binding of the SlWRKY17 transcription factor to the SlIDL6 promoter, and silencing of SlWRKY17 expression delayed low light-induced flower abscission. SlIDL6 was specifically expressed in the abscission zone and at high levels during low light-induced abscission and ethylene treatment. SlIDL6 knockout lines showed delayed low light-induced flower drop, and the application of SlIDL6 peptide accelerated abscission. Overexpression of SlIDL6 rescued the ida mutant phenotype in Arabidopsis (Arabidopsis thaliana), suggesting functional conservation between species. SlIDL6-mediated abscission was via an ethylene-independent pathway. We report a SlWRKY17-SlIDL6 regulatory module that functions in low light promoted abscission by increasing the expression of enzymes involved in cell wall remodeling and disassembly.

Direct phosphorylation of HY5 by SPA kinases to regulate photomorphogenesis in Arabidopsis

Elongated hypocotyl5 (HY5) is a key transcription factor that promotes photomorphogenesis. Constitutive photomorphogenic1 (COP1)-Suppressor of phytochrome A-105 (SPA) E3 ubiquitin ligase complex promotes ubiquitination and degradation of HY5 to repress photomorphogenesis in darkness. HY5 is also regulated by phosphorylation at serine 36 residue. However, the kinase responsible for phosphorylation of HY5 remains unknown. Here, using extensive in vitro and in vivo biochemical, genetic, and photobiological techniques, we have identified a new kinase that phosphorylates HY5 and demonstrated the significance of phosphorylation of HY5 in Arabidopsis thaliana. We show that SPA proteins are the missing kinases necessary for HY5 phosphorylation. SPAs can directly phosphorylate HY5 in vitro, and the phosphorylated HY5 is absent in the spaQ background in vivo. We also demonstrate that the unphosphorylated HY5 interacts strongly with both COP1 and SPA1 and is the preferred substrate for degradation, whereas the phosphorylated HY5 is more stable in the dark. In addition, the unphosphorylated HY5 actively binds to the target promoters and is the physiologically more active form. Consistently, the transgenic plants expressing the unphosphorylated form of HY5 display enhanced photomorphogenesis. Collectively, our study revealed the missing kinase responsible for direct phosphorylation of HY5 that fine-tunes its stability and activity to regulate photomorphogenesis.

Direct phosphorylation of HY5 by SPA kinases to regulate photomorphogenesis in Arabidopsis

Elongated hypocotyl5 (HY5) is a key transcription factor that promotes photomorphogenesis. Constitutive photomorphogenic1 (COP1)-Suppressor of phytochrome A-105 (SPA) E3 ubiquitin ligase complex promotes ubiquitination and degradation of HY5 to repress photomorphogenesis in darkness. HY5 is also regulated by phosphorylation at serine 36 residue. However, the kinase responsible for phosphorylation of HY5 remains unknown. Here, using extensive in vitro and in vivo biochemical, genetic, and photobiological techniques, we have identified a new kinase that phosphorylates HY5 and demonstrated the significance of phosphorylation of HY5 in Arabidopsis thaliana. We show that SPA proteins are the missing kinases necessary for HY5 phosphorylation. SPAs can directly phosphorylate HY5 in vitro, and the phosphorylated HY5 is absent in the spaQ background in vivo. We also demonstrate that the unphosphorylated HY5 interacts strongly with both COP1 and SPA1 and is the preferred substrate for degradation, whereas the phosphorylated HY5 is more stable in the dark. In addition, the unphosphorylated HY5 actively binds to the target promoters and is the physiologically more active form. Consistently, the transgenic plants expressing the unphosphorylated form of HY5 display enhanced photomorphogenesis. Collectively, our study revealed the missing kinase responsible for direct phosphorylation of HY5 that fine-tunes its stability and activity to regulate photomorphogenesis.

Phytochrome B interacts with SWC6 and ARP6 to regulate H2A.Z deposition and photomorphogensis in Arabidopsis

Light serves as a crucial environmental cue which modulates plant growth and development, and which is controlled by multiple photoreceptors including the primary red light photoreceptor, phytochrome B (phyB). The signaling mechanism of phyB involves direct interactions with a group of basic helix-loop-helix (bHLH) transcription factors, PHYTOCHROME-INTERACTING FACTORS (PIFs), and the negative regulators of photomorphogenesis, COP1 and SPAs. H2A.Z is an evolutionarily conserved H2A variant which plays essential roles in transcriptional regulation. The replacement of H2A with H2A.Z is catalyzed by the SWR1 complex. Here, we show that the Pfr form of phyB physically interacts with the SWR1 complex subunits SWC6 and ARP6. phyB and ARP6 co-regulate numerous genes in the same direction, some of which are associated with auxin biosynthesis and response including YUC9, which encodes a rate-limiting enzyme in the tryptophan-dependent auxin biosynthesis pathway. Moreover, phyB and HY5/HYH act to inhibit hypocotyl elongation partially through repression of auxin biosynthesis. Based on our findings and previous studies, we propose that phyB promotes H2A.Z deposition at YUC9 to inhibit its expression through direct phyB-SWC6/ARP6 interactions, leading to repression of auxin biosynthesis, and thus inhibition of hypocotyl elongation in red light.

Sugar inhibits brassinosteroid signaling by enhancing BIN2 phosphorylation of BZR1

Sugar, light, and hormones are major signals regulating plant growth and development, however, the interactions among these signals are not fully understood at the molecular level. Recent studies showed that sugar promotes hypocotyl elongation by activating the brassinosteroid (BR) signaling pathway after shifting Arabidopsis seedlings from light to extended darkness. Here, we show that sugar inhibits BR signaling in Arabidopsis seedlings grown under light. BR induction of hypocotyl elongation in seedlings grown under light is inhibited by increasing concentration of sucrose. The sugar inhibition of BR response is correlated with decreased effect of BR on the dephosphorylation of BZR1, the master transcription factor of the BR signaling pathway. This sugar effect is independent of the sugar sensors Hexokinase 1 (HXK1) and Target of Rapamycin (TOR), but requires the GSK3-like kinase Brassinosteroid-Insensitive 2 (BIN2), which is stabilized by sugar. Our study uncovers an inhibitory effect of sugar on BR signaling in plants grown under light, in contrast to its promotive effect in the dark. Such light-dependent sugar-BR crosstalk apparently contributes to optimal growth responses to photosynthate availability according to light-dark conditions.

Tangent algorithm for photogravitropic balance in plants and Phycomyces blakesleeanus: Roles for EHB1 and NPH3 of Arabidopsis thaliana

Plant organs that are exposed to continuous unilateral light reach in the steady-state a photogravitropic bending angle that results from the mutual antagonism between the photo- and gravitropic responses. To characterize the interaction between the two tropisms and their quantitative relationship we irradiated seedlings of Arabidopsis thaliana that were inclined at various angles and determined the fluence rates of unilateral blue light required to compensate the gravitropism of the inclined hypocotyls. We found the compensating fluence rates to increase with the tangent of the inclination angles (0° < γ < 90° or max. 120°) and decrease with the cotangent (90°< γ < 180° or max. 120°of the inclination angles. The tangent dependence became also evident from analysis of previous data obtained with Avena sativa and the phycomycete fungus, Phycomyces blakesleeanus. By using loss-of function mutant lines of Arabidopsis, we identified EHB1 (enhanced bending 1) as an essential element for the generation of the tangent and cotangent relationships. Because EHB1 possesses a C2-domain with two putative calcium binding sites, we propose that the ubiquitous calcium dependence of gravi- and phototropism is in part mediated by Ca²⁺-bound EHB1. Based on a yeast-two-hybrid analysis we found evidence that EHB1 does physically interact with the ARF-GAP protein AGD12. Both proteins were reported to affect gravi- and phototropism antagonistically. We further showed that only AGD12, but not EHB1, interacts with its corresponding ARF-protein. Evidence is provided that AGD12 is able to form homodimers as well as heterodimers with EHB1. On the basis of these data we present a model for a mechanism of early tropism events, in which Ca²⁺-activated EHB1 emerges as the central processor-like element that links the gravi- and phototropic transduction chains and that generates in coordination with NPH3 and AGD12 the tangent / cotangent algorithm governing photogravitropic equilibrium.

UV-B signalling in rice: Response identification, gene expression profiling and mutant isolation

Responses of rice seedlings to UV-B radiation (UV-B) were investigated, aiming to establish rice as a model plant for UV-B signalling studies. The growth of japonica rice coleoptiles, grown under red light, was inhibited by brief irradiation with UV-B, but not with blue light. The effective UV-B fluences (10^-1 -10³ μmol m^-2 ) were much lower than those reported in Arabidopsis. The response was much less in indica rice cultivars and its extent varied among Oryza species. We next identified UV-B-specific anthocyanin accumulation in the first leaf of purple rice and used this visible phenotype to isolate mutants. Some isolated mutants were further characterized, and one was found to have a defect in the growth response. Using microarrays, we identified a number of genes that are regulated by low-fluence-rate UV-B in japonica coleoptiles. Some up-regulated genes were analysed by real-time PCR for UV-B specificity and the difference between japonica and indica. More than 70% of UV-B-regulated rice genes had no homologs in UV-B-regulated Arabidopsis genes. Many UV-B-regulated rice genes are related to plant hormones and especially to jasmonate biosynthetic and responsive genes in apparent agreement with the growth response. Possible involvement of two rice homologs of UVR8, a UV-B photoreceptor, is discussed.

Differential root and shoot magnetoresponses in Arabidopsis thaliana

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

Response of transgenic Arabidopsis expressing maize C4 photosynthetic enzyme genes to high light

This study assessed the responses of wild-type (WT) and transgenic Arabidopsis expressing seven combinations of maize (Zea mays) genes phosphoenolpyruvate carboxylase (pepc), pyruvate phosphate dikinase (ppdk), and NADP-malic enzyme (nadp-me) to high light. Our results showed that the net CO₂ assimilation rate (P_n) and shoot dry weight of four of the transgenic Arabidopsis genotypes were significantly different from those of WT under high-light treatment, being in the order of Zmpepc+Zmppdk+Zmnadp-me (PC-K-M) > Zmpepc+Zmppdk (PC-K) > Zmpepc (PC), Zmpepc+Zmnadp-me (PC-M) > WT. The other genotypes did not differ from WT. This indicated that Zmpepc was essential for maintaining high photosynthetic performance under high light, Zmppdk had a positive synergistic effect on Zmpepc, and the combination of all three genes had the greatest synergistic effect. These four genotypes also maintained higher photosystem II (PSII) activity (K-phase, J-phase, RC/CSm), electron transfer capacity (J-phase), and photochemical efficiency (TRo/ABS), and accumulated less reactive oxygen species (O₂·^-, H₂O₂) and suffered less damage to the membrane system (MDA) than WT under high light. Collectively, PC, PC-K, PC-M, and PC-K-M used most of the absorbed energy for CO₂ assimilation through a significantly higher P_n, which reduced the generation of excess electrons in the photosynthetic apparatus, thereby reducing damage to the membrane system and PSII. This ultimately resulted in improved high-light tolerance. P_n was the main reason for the significant difference in the high-light tolerance of the four genotypes. Joint expression of the three maize genes may be of great value in the genetic improvement of high-light tolerance in C₃ crops.

A novel UV-B priming system reveals an UVR8-depedent memory, which provides resistance against UV-B stress in Arabidopsis leaves

Single treatment of plants with pathogens like Pseudomonas syringae can trigger systemic acquired resistance (SAR) that lasts several days to several weeks in Arabidopsis thaliana. Similar primed resistances were described for abiotic stresses like drought and heat stress. Most studies about plant resistance to ultraviolet (UV)-radiation used low UV-B radiations over a long period. These experimental designs make it difficult to distinguish acclimation effects from real cellular memory which facilitate transcriptional and other responses to a second UV-radiation after a latent phase. Here we present a novel UV-B priming system. We demonstrate that a single UV-B treatment, which causes neither visible damage nor accumulation of pigments, can stimulate resistance against UV-B stress. After a second damaging UV-B treatment, UV-primed plants showed significantly reduced damage in comparison to non-primed plants. Furthermore, the acquirement of the induced UV-B resistance was impaired in uvr8-6 mutants suggesting that the UV-B receptor is essential for UV-B stress memory in Arabidopsis. We discuss advantages and limits of our UV-B priming system which will be a powerful tool to investigate UV-B memory in future studies.

Magnesium maintains the length of the circadian period in Arabidopsis

The circadian clock coordinates the physiological responses of a biological system to day and night rhythms through complex loops of transcriptional/translational regulation. It can respond to external stimuli and adjust generated circadian oscillations accordingly to maintain an endogenous period close to 24 h. However, the interaction between nutritional status and circadian rhythms in plants is poorly understood. Magnesium (Mg) is essential for numerous biological processes in plants, and its homeostasis is crucial to maintain optimal development and growth. Magnesium deficiency in young Arabidopsis thaliana seedlings increased the period of circadian oscillations of the CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) promoter (pCCA1:LUC) activity and dampened their amplitude under constant light in a dose-dependent manner. Although the circadian period increase caused by Mg deficiency was light dependent, it did not depend on active photosynthesis. Mathematical modeling of the Mg input into the circadian clock reproduced the experimental increase of the circadian period and suggested that Mg is likely to affect global transcription/translation levels rather than a single component of the circadian oscillator. Upon addition of a low dose of cycloheximide to perturb translation, the circadian period increased further under Mg deficiency, which was rescued when sufficient Mg was supplied, supporting the model's prediction. These findings suggest that sufficient Mg supply is required to support proper timekeeping in plants.

The gene expression profiles of mitochondrial respiratory components in Arabidopsis plants with differing amounts of ALTERNATIVE OXIDASE1a under high intensity light

We compared the expression of mitochondrial alternative oxidase (AOX) and other non-phosphorylating respiratory components (NPhPs) in wild type and AOX1a transgenic Arabidopsis thaliana following short-term transfer of plants to higher irradiance conditions to gain more insight into the mechanisms of AOX functioning under light. The AOX1a overexpressing line (XX-2) showed the highest amount of AOX1a transcripts and AOX1A synthesis during the entire experiment, and many NPhPs genes were down-regulated after 6-8 h under the higher light conditions. Antisense AS-12 plants displayed a compensatory effect, typically after 8 h of exposure to higher irradiance, by up-regulating their expression of the majority of genes encoding AOX and other respiratory components. In addition, AS-12 plants displayed 'overcompensation effects' prior to their transfer to high light conditions, i.e., they showed a higher expression level of certain genes. As a result, the ROS content in AS-12, as in XX-2, was consistently lower than in the wild type. All NPhPs genes share, in common with AOX1a, light- and stress-related cis-acting regulatory elements (CAREs) in their promoters. However, the expression of respiratory genes does not always depend on the level of AOX1a expression. This suggests the presence of multiple combinations of signaling pathways in gene induction. Based on our results, we outline possible directions for future research.

TGA class II transcription factors are essential to restrict oxidative stress in response to UV-B stress in Arabidopsis

Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription-PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure.

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region

mRNA secondary structure influences translation. Proteins that modulate the mRNA secondary structure around the translation initiation region may regulate translation in plastids. To test this hypothesis, we exposed Arabidopsis thaliana to high light, which induces translation of psbA mRNA encoding the D1 subunit of photosystem II. We assayed translation by ribosome profiling and applied two complementary methods to analyze in vivo RNA secondary structure: DMS-MaPseq and SHAPE-seq. We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation. Furthermore, we identified the footprint of a putative regulatory protein in the 5' UTR of psbA at a position where occlusion of the nucleotide sequence would cause the structure of the translation initiation region to open up, thereby facilitating ribosome access. Moreover, we show that other plastid genes with weak Shine-Dalgarno sequences (SD) are likely to exhibit psbA-like regulation, while those with strong SDs do not. This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes.

Recognition of CCA1 alternative protein isoforms during temperature acclimation

CCA1α and CCA1β protein variants respond to environmental light and temperature cues, and higher temperature promotes CCA1β protein production and causes its retention detectable in the cytoplasm. CIRCADIAN CLOCK ASSOCIATED1 (CCA1), as the core transcription factor of circadian clock, is involved in the regulation of endogenous circadian rhythm in Arabidopsis. Previous studies have shown that CCA1 consists of two abundant splice variants, fully spliced CCA1α and intron-retaining CCA1β. CCA1β is believed to form a nonfunctional heterodimer with CCA1α and its closed-related homolog LHY. Many studies have established that CCA1β is a transcription product, while how CCA1β protein is produced and how two CCA1 isoforms respond to environmental cues have not been elucidated. In this study, we identified CCA1α and CCA1β protein variants under different photoperiods with warm or cold temperature cycles, respectively. Our results showed that CCA1 protein production is regulated by prolonged light exposure and warm temperature. The protein levels of CCA1α and CCA1β peak in the morning, but the detection of CCA1β is dependent on immunoprecipitation enrichment at 22 °C. Higher temperature of 37 °C promotes CCA1β protein production and causes its retention to be detectable in the cytoplasm. Overall, our results indicate that two splice variants of the CCA1 protein respond to environmental light and temperature signals and may, therefore, maintain the circadian rhythms and give individuals the ability to adapt to environment.