Light Photoreceptor Research Articles

Protein Phosphatase PP2C19 Controls Hypocotyl Phototropism Through the Phosphorylation Modification of NPH3 in Arabidopsis.

Plants exhibit shoot growth in the direction of the light source to facilitate photosynthesis, known as positive phototropism. In Arabidopsis hypocotyl phototropism, it is thought that a gradient of the signal intensity of the blue light photoreceptor phototropin1 (phot1) between the light-irradiated and shaded sides leads to the differential growth of hypocotyls. The intensity of phot1 signal is regulated not only by the protein kinase activity of phot1 but also by the phosphorylation status of the NONPHOTOTROPIC HYPOCOTYL3 (NPH3) protein, which has a dark form and a blue light form of the phosphorylation modification. Previous studies have shown that phot1 drives the forward reaction from the dark form to the blue light form of NPH3. However, the molecular mechanism underlying the reverse reaction remains unknown. Here, we show that protein phosphatase PP2C19 controls the reverse reaction that converts the blue light form of NPH3 to the dark form of NPH3. The PP2C19 protein possesses the PP2C domain, two cNMP-binding domains, and the protein kinase domain. Similar to phot1 and NPH3, PP2C19 localizes to the plasma membrane, and its PP2C domain is necessary and sufficient for PP2C19 function in hypocotyl phototropism. The pp2c19 mutants show abnormalities in second positive hypocotyl phototropism with a delay in the reverse reaction of NPH3 phosphorylation modification. The present study suggests that continuous blue light irradiation induces an equilibrium state of the reversible reaction of NPH3 phosphorylation, which acts as a phot1 signaling gradient with phot1 kinase activity to induce the second positive phototropism.

GPATCH11 variants cause mis-splicing and early-onset retinal dystrophy with neurological impairment

Here we conduct a study involving 12 individuals with retinal dystrophy, neurological impairment, and skeletal abnormalities, with special focus on GPATCH11, a lesser-known G-patch domain-containing protein, regulator of RNA metabolism. To elucidate its role, we study fibroblasts from unaffected individuals and patients carrying the recurring c.328+1 G > T mutation, which specifically removes the main part of the G-patch domain while preserving the other domains. Additionally, we generate a mouse model replicating the patients’ phenotypic defects, including retinal dystrophy and behavioral abnormalities. Our results reveal a subcellular localization of GPATCH11 characterized by a diffuse presence in the nucleoplasm, as well as centrosomal localization, suggesting potential functions in RNA and cilia metabolism. Transcriptomic analysis performed on mouse retina detect dysregulation in both gene expression and splicing activity, impacting key processes such as photoreceptor light responses, RNA regulation, and primary cilia-associated metabolism. Proteomic analysis of mouse retina confirms the roles GPATCH11 plays in RNA processing, splicing, and transcription regulation, while also suggesting additional functions in synaptic plasticity and nuclear stress response. Our research provides insights into the diverse roles of GPATCH11 and identifies that the mutations affecting this protein are responsible for a recently characterized described syndrome.

Predictably manipulating photoreceptor light responses to reveal their role in downstream visual responses.

Computation in neural circuits relies on the judicious use of nonlinear circuit components. In many cases, multiple nonlinear components work collectively to control circuit outputs. Separating the contributions of these different components is difficult, and this limits our understanding of the mechanistic basis of many important computations. Here, we introduce a tool that permits the design of light stimuli that predictably alter rod and cone phototransduction currents - including stimuli that compensate for nonlinear properties such as light adaptation. This tool, based on well-established models for the rod and cone phototransduction cascade, permits the separation of nonlinearities in phototransduction from those in downstream circuits. This will allow, for example, direct tests of how adaptation in rod and cone phototransduction affects downstream visual signals and perception.

Predictably manipulating photoreceptor light responses to reveal their role in downstream visual responses

Computation in neural circuits relies on the judicious use of nonlinear circuit components. In many cases, multiple nonlinear components work collectively to control circuit outputs. Separating the contributions of these different components is difficult, and this limits our understanding of the mechanistic basis of many important computations. Here, we introduce a tool that permits the design of light stimuli that predictably alter rod and cone phototransduction currents – including stimuli that compensate for nonlinear properties such as light adaptation. This tool, based on well-established models for the rod and cone phototransduction cascade, permits the separation of nonlinearities in phototransduction from those in downstream circuits. This will allow, for example, direct tests of how adaptation in rod and cone phototransduction affects downstream visual signals and perception.

Potato NPH3/RPT2-like (NRL) member StNRL-9 interacts with Stphots and negatively regulates late blight resistance.

Blue light enhances the susceptibility of Nicotiana benthamiana to Phytophthora infestans, a causative agent of late blight disease. Investigating how blue light affects potato late blight resistance is an interesting aspect of exploring new ways to control late blight disease. Blue light photoreceptor phototropins (phot1, phot2) and their downstream interact protein StNRL1 have been shown to negatively regulate late blight resistance. In order to investigate whether other potato NPH3/RPT2-Like (NRL) family members are involved in regulating late blight resistance, this study focused on the potato NRL proteins containing RxSxS motif at the C-terminus. Another potato NRL protein StNRL-9, containing RxSxS motifs, was found to negatively regulate P. infestans resistance in potato and N. benthamiana. Overexpression of StNRL-9 in potato and N. benthamiana suppresses the accumulation of reactive oxygen species (ROS) and expression of the PTI marker genes NbWRKY7 and NbWRKY8. Similar to StNRL1, StNRL-9 interacts with the blue light receptors Stphot1 and Stphot2 on the cell membrane and could promote the degradation of a positive immune regulator StSWAP70. However StNRL-9 does not inhibit INF1-mediated cell death (ICD), whichis different from the StNRL1 that inhibits ICD, indicating that both StNRL1 and StNRL-9 inhibit plant immunity in diverse ways. This study provides valuable information for further exploration of how plant phototropins and NRL family proteins regulate plant immunity.

Chromosome-level genome assembly of the cosmopolitan diatom Skeletonema costatum provides insights into ecological adaptation

The cosmopolitan diatom species Skeletonema costatum is an ecologically important dominant phytoplankton frequently found in the coastal estuarine and marine waters, and often causes harmful algae blooms. Despite of its critical ecological importance, chromosome-level genome assemble is still unavailable, hindering in-depth understanding of their evolution and environmental adaption. Here, we report a chromosome-level genome assembly for the marine diatom species S. costatum. The assembled genome size was 136.49 Mb, with a contig N50 of 302 Kb and 95.30 % of the reads anchored into 23 pseudo-chromosomes with a scaffold N50 of 6.19 Mb. A total of 28,321 protein-coding genes were predicted, with 86.03 % being functional annotated. The BUSCO assessment of genome assembly and genome annotation were both above 90 %. Phylogenetic analysis showed the expected topology, with S. costatum and its closely related species S. marinoi diverged from their common ancestor around 22.6 million years ago. The genome size of S. costatum is comparatively larger than those of its closely related diatoms, due mostly to its higher transposable element contents and larger number of proteincoding genes. Collinearity analysis revealed strong collinearity between S. costatum and other Skeletonema with most chromosomes showing clear one-to-one correspondences. A larger family of nine copies of the cryptochrome genes that function as blue light photoreceptors were identified in S. costatum, which could contribute its ecological success. The availability of the high-quality chromosome-level genome assembly for S. costatum represents a valuable resource that may facilitate comparative genomics for revealing important ecological clues and gene families, and future genetics and environmental studies among Skeletonema species.

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

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

Predictably manipulating photoreceptor light responses to reveal their role in downstream visual responses.

Computation in neural circuits relies on the judicious use of nonlinear circuit components. In many cases, multiple nonlinear components work collectively to control circuit outputs. Separating the contributions of these different components is difficult, and this limits our understanding of the mechanistic basis of many important computations. Here, we introduce a tool that permits the design of light stimuli that predictably alter rod and cone phototransduction currents - including stimuli that compensate for nonlinear properties such as light adaptation. This tool, based on well-established models for the rod and cone phototransduction cascade, permits the separation of nonlinearities in phototransduction from those in downstream circuits. This will allow, for example, direct tests of how adaptation in rod and cone phototransduction affects downstream visual signals and perception.

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.

Optical Assessment of Photoreceptor Function Over the Macula.

The purpose of this study was to develop next-generation functional photoreceptor imaging using ultrahigh-speed swept-source optical coherence tomography (UHS-SS-OCT) and split-spectrum amplitude-decorrelation optoretinography (SSADOR) algorithm. The advancement enables rapid surveying of large retinal areas, promising non-contact, objective, and quantifiable measurements of macular visual function. We designed and built a UHS-SS-OCT prototype instrument using a wavelength tunable laser with 1 MHz A-scan rate. The functional scanning protocol records 5 repeated volumes in 3 seconds. A flash pattern selectively exposes the imaged retina area. SSADOR quantifies photoreceptor light response by extracting optical coherence tomography (OCT) signal changes within the photoreceptor outer segment before and after the flash. The study prospectively enrolled 16 eyes from 8 subjects, demonstrating the ability to measure photoreceptor light response over a record field of view (3 × 3mm2) with high topographical resolution (approximately 100 µm). The measured SSADOR signal corresponds to the flashed pattern, whose amplitude also correlates with flash strength, showing consistency and reproducibility across subjects. The integration of high-performance UHS-SS-OCT and SSADOR enables characterizing photoreceptor function over a clinically meaningful field of view, while maintaining a workflow that can be integrated into routine clinical tests and trials. The new approach allows detecting changes in photoreceptor light response with high sensitivity and can detect small focal impairments. This innovative advance can enable us to detect early photoreceptor abnormalities, as well as help to stage and monitor degenerative retinal diseases, potentially providing a surrogate visual function marker for retinal diseases and accelerating therapeutic development through a safe and efficient outcome endpoint.

BBX9 forms feedback loops with PIFs and BBX21 to promote photomorphogenic development.

Light is one of the most essential environmental factors that tightly and precisely control various physiological and developmental processes in plants. B-box CONTAINING PROTEINs (BBXs) play central roles in the regulation of light-dependent development. In this study, we report that BBX9 is a positive regulator of light signaling. BBX9 interacts with the red light photoreceptor PHYTOCHROME B (phyB) and transcription factors PHYTOCHROME-INTERACTING FACTORs (PIFs). phyB promotes the stabilization of BBX9 in light, while BBX9 inhibits the transcriptional activation activity of PIFs. In turn, PIFs directly bind to the promoter of BBX9 to repress its transcription. On the other hand, BBX9 associates with the positive regulator of light signaling, BBX21, and enhances its biochemical activity. BBX21 associates with the promoter regions of BBX9 and transcriptionally up-regulates its expression. Collectively, this study unveiled that BBX9 forms a negative feedback loop with PIFs and a positive one with BBX21 to ensure that plants adapt to fluctuating light conditions.

Rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE interacts with OsCRY2 and promotes flowering by upregulatingEarly heading date 1.

Flowering time is a crucial adaptive response to seasonal variation in plants and is regulated by environmental cues such as photoperiod and temperature. In this study, we demonstrated the regulatory function of rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE (OsCIBL1) in flowering time. Overexpression of OsCIB1L promoted flowering, whereas the oscib1l knockout mutation did not alter flowering time independent of photoperiodic conditions. Cryptochromes (CRYs) are blue light photoreceptors that enable plants to sense photoperiodic changes. OsCIBL1 interacted with OsCRY2, a member of the rice CRY family (OsCRY1a, OsCRY1b, and OsCRY2), and bound to theEarly heading date 1(Ehd1) promoter, activating the rice-specific Ehd1-Heading date 3a/RICE FLOWERING LOCUS T 1pathway for flowering induction. Dual-luciferase reporter assays showed that the OsCIBL1-OsCRY2 complex required blue light to induce Ehd1 transcription. Natural alleles resulting from nonsynonymous single nucleotide polymorphisms in OsCIB1L and OsCRY2 may contribute to the adaptive expansion of rice cultivation areas. These results expand our understanding of the molecular mechanisms controlling rice flowering and highlight the importance of blue light-responsive genes in the geographic distribution of rice.

A cytosol-tethered YHB variant of phytochrome B retains photomorphogenic signaling activity

The red and far-red light photoreceptor phytochrome B (phyB) transmits light signals following cytosol-to-nuclear translocation to regulate transcriptional networks therein. This necessitates changes in protein–protein interactions of phyB in the cytosol, about which little is presently known. Via introduction of a nucleus-excluding G767R mutation into the dominant, constitutively active phyBY276H (YHB) allele, we explore the functional consequences of expressing a cytosol-localized YHBG767R variant in transgenic Arabidopsis seedlings. We show that YHBG767R elicits selective constitutive photomorphogenic phenotypes in dark-grown phyABCDE null mutants, wild type and other phy-deficient genotypes. These responses include light-independent apical hook opening, cotyledon unfolding, seed germination and agravitropic hypocotyl growth with minimal suppression of hypocotyl elongation. Such phenotypes correlate with reduced PIF3 levels, which implicates cytosolic targeting of PIF3 turnover or PIF3 translational inhibition by YHBG767R. However, as expected for a cytoplasm-tethered phyB, YHBG767R elicits reduced light-mediated signaling activity compared with similarly expressed wild-type phyB in phyABCDE mutant backgrounds. YHBG767R also interferes with wild-type phyB light signaling, presumably by formation of cytosol-retained and/or otherwise inactivated heterodimers. Our results suggest that cytosolic interactions with PIFs play an important role in phyB signaling even under physiological conditions.

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

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

The development and nutritional quality of Lyophyllum decastes affected by monochromatic or mixed light provided by light-emitting diode.

Edible fungi has certain photo-sensitivity during the mushroom emergence stage, but there has been few relevant studies on the responses of Lyophyllum decastes to different light quality. L. decastes were planted in growth chambers with different light qualities that were, respectively, white light (CK), monochromatic red light (R), monochromatic blue light (B), mixed red and blue light (RB), and the mixture of far-red and blue light (FrB). The photo-sensitivity of L. decastes was investigated by analyzing the growth characteristics, nutritional quality, extracellular enzymes as well as the light photoreceptor genes in mushroom exposed to different light treatments. The results showed that R led to mycelium degeneration, fungal skin inactivation and failure of primordial formation in L. decastes. The stipe length, stipe diameter, pileus diameter and the weight of fruiting bodies exposed to RB significantly increased by 8.0, 28.7, 18.3, and 58.2% respectively, compared to the control (p < 0.05). B significantly decreased the stipe length and the weight of fruiting body, with a decrease of 8.5 and 20.2% respectively, compared to the control (p < 0.05). Increased color indicators and deepened simulated color were detected in L. decastes pileus treated with B and FrB in relative to the control. Meanwhile, the expression levels of blue photoreceptor genes such as WC-1, WC-2 and Cry-DASH were significantly up-regulated in mushroom exposed to B and FrB (p < 0.05). Additionally, the contents of crude protein and crude polysaccharide in pileus treated with RB were, respectively, increased by 26.5 and 9.4% compared to the control, while those in stipes increased by 5.3 and 58.8%, respectively. Meanwhile, the activities of extracellular enzyme such as cellulase, hemicellulase, laccase, manganese peroxidase, lignin peroxidase and amylase were significant up-regulated in mushroom subjected to RB (p < 0.05), which may promote the degradation of the culture materials. On the whole, the largest volume and weight as well as the highest contents of nutrients were all detected in L. decastes treated with RB. The study provided a theoretical basis for the regulation of light environment in the industrial production of high quality L. decastes.

Time-Resolved Ion Mobility Mass Spectrometry to Solve Conformational Changes in a Cryptochrome.

Many biological mechanisms rely on the precise control of conformational changes in proteins. Understanding such dynamic processes requires methods for determining structures and their temporal evolution. In this study, we introduce a novel approach to time-resolved ion mobility mass spectrometry. We validated the method on a simple photoreceptor model and applied it to a more complex system, the animal-like cryptochrome from Chlamydomonas reinhardtii (CraCRY), to determine the role of specific amino acids affecting the conformational dynamics as reaction to blue light activation. In our setup, using a high-power LED mounted in the source region of an ion mobility mass spectrometer, we allow a time-resolved evaluation of mass and ion mobility spectra. Cryptochromes like CraCRY are a widespread type of blue light photoreceptors and mediate various light-triggered biological functions upon excitation of their inbuilt flavin chromophore. Another hallmark of cryptochromes is their flexible carboxy-terminal extension (CTE), whose structure and function as well as the details of its interaction with the photolyase homology region are not yet fully understood and differ among different cryptochromes types. Here, we addressed the highly conserved C-terminal domain of CraCRY, to study the effects of single mutations on the structural transition of the C-terminal helix α22 and the attached CTE upon lit-state formation. We show that D321, the putative proton acceptor of the terminal proton-coupled electron transfer event from Y373, is essential for triggering the large-scale conformational changes of helix α22 and the CTE in the lit state, while D323 influences the timing.

Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor.

Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.

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

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

Research progress on insect visual electrophysiological techniques.

Insect visual electrophysiological techniques are important to study the electrical characteristics of photoreceptor cells and visual neurons in insects, including electroretinography (ERG) and microelectrode intracellular recording (MIR). ERG records the changes of voltage or electric current in the retina of insects in response to different light stimuli, which occurs outside the cell. MIR records the changes in individual photoreceptor cells or visual neurons of an insect exposed to different lights, which occurs inside the cell. Insect visual electrophysiological techniques can explore the mechanism of electrophysiological response of insects' vision to light and reveal their sensitive light spectra and photoreceptor types. This review introduced the basic structure and the principle of ERG and MIR, and summarized their applications in insect researches in the past 20 years, which would provide references for elucidating the mechanism of light perception in insects and the use of insect phototropism to control pests.

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

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