Reconstituting Arabidopsis CRY2 Signaling Pathway in Mammalian Cells Reveals Regulation of Transcription by Direct Binding of CRY2 to DNA

Phytochrome B photobody components

Phytochrome B (phyB) is a red and far-red photoreceptor that promotes light responses. Upon photoactivation, phyB enters the nucleus and forms a molecular condensate called a photobody through liquid-liquid phase separation. Phytochrome B photobody comprises phyB, the main scaffold molecule, and at least 37 client proteins. These clients belong to diverse functional categories enriched with transcription regulators, encompassing both positive and negative light signaling factors, with the functional bias toward the negative factors. The functionally diverse clients suggest that phyB photobody acts either as a trap to capture proteins, including negatively acting transcription regulators, for processes such as sequestration, modification, or degradation or as a hub where proteins are brought into close proximity for interaction in a light-dependent manner.

From epidermal cells to functional pores: Understanding stomatal development

Stomata, small hydromechanical valves in the leaf epidermis, are fundamental in regulating gas exchange and water loss between plants and the environment. Stomatal development involves a series of coordinated events ranging from the initial cell division that determines the meristemoid mother cells to forming specialized structures such as guard cells. These events are orchestrated by the transcription factors SPEECHLESS, FAMA, and MUTE through signaling networks. The role of plant hormones (e.g., abscisic acid, jasmonic acid, and brassinosteroids) in regulating stomatal development has been elucidated through these signaling cascades. In addition, environmental factors, such as light availability and CO2 concentration, also regulate the density and distribution of stomata in leaves, ultimately affecting overall water use efficiency. In this review, we highlight the mechanisms underlying stomatal development, connecting key signaling processes that activate or inhibit cell differentiation responsible for forming guard cells in the leaf epidermis. The factors responsible for integrating transcription factors, hormonal responses, and the influence of climatic factors on the signaling network that leads to stomatal development in plants are further discussed. Understanding the intricate connections between these factors, including the metabolic regulation of plant development, may enable us to maximize plant productivity under specific environmental conditions in changing climate scenarios.

SlSPX1-SlPHR complexes mediate the suppression of arbuscular mycorrhizal symbiosis by phosphate repletion in tomato

Forming mutualistic symbioses with arbuscular mycorrhizae (AMs) improves the acquisition of mineral nutrients for most terrestrial plants. However, the formation of AM symbiosis usually occurs under phosphate (Pi)-deficient conditions. Here, we identify SlSPX1 (SYG1 (suppressor of yeast GPA1)/Pho81(phosphate 81)/XPR1 (xenotropic and polytropic retrovirus receptor 1) as the major repressor of the AM symbiosis in tomato (Solanum lycopersicum) under phosphate-replete conditions. Loss of SlSPX1 function promotes direct Pi uptake and enhances AM colonization under phosphate-replete conditions. We determine that SlSPX1 integrates Pi signaling and AM symbiosis by directly interacting with a set of arbuscule-induced SlPHR proteins (SlPHR1, SlPHR4, SlPHR10, SlPHR11, and SlPHR12). The association with SlSPX1 represses the ability of SlPHR proteins to activate AM marker genes required for the arbuscular mycorrhizal symbiosis. SlPHR proteins exhibit functional redundancy, and no defective AM symbiosis was detected in the single mutant of SlPHR proteins. However, silencing SlPHR4 in the Slphr1 mutant background led to reduced AM colonization. Therefore, our results support the conclusion that SlSPX1-SlPHRs form a Pi-sensing module to coordinate the AM symbiosis under different Pi-availability conditions.

Arabidopsis cryptochrome 2 forms photobodies with TCP22 under blue light and regulates the circadian clock

Cryptochromes are blue light receptors that regulate plant growth and development. They also act as the core components of the central clock oscillator in animals. Although plant cryptochromes have been reported to regulate the circadian clock in blue light, how they do so is unclear. Here we show that Arabidopsis cryptochrome 2 (CRY2) forms photobodies with the TCP22 transcription factor in response to blue light in plant cells. We provide evidence that PPK kinases influence the characteristics of these photobodies and that together these components, along with LWD transcriptional regulators, can positively regulate the expression of CCA1 encoding a central component of the circadian oscillator.

Cryptochrome signaling has been reported to regulate circadian oscillations in plants. Here the authors show that CRY2 and the TCP22 transcription factors can form photobodies in a blue light dependent manner and induce expression of CCA1, a core component of the circadian oscillator.

Signaling Mechanisms by Arabidopsis Cryptochromes

Cryptochromes (CRYs) are blue light photoreceptors that regulate growth, development, and metabolism in plants. In Arabidopsis thaliana (Arabidopsis), CRY1 and CRY2 possess partially redundant and overlapping functions. Upon exposure to blue light, the monomeric inactive CRYs undergo phosphorylation and oligomerization, which are crucial to CRY function. Both the N- and C-terminal domains of CRYs participate in light-induced interaction with multiple signaling proteins. These include the COP1/SPA E3 ubiquitin ligase, several transcription factors, hormone signaling intermediates and proteins involved in chromatin-remodeling and RNA N6 adenosine methylation. In this review, we discuss the mechanisms of Arabidopsis CRY signaling in photomorphogenesis and the recent breakthroughs in Arabidopsis CRY research.

AGROBEST: A Highly Efficient Agrobacterium-Mediated Transient Expression System in Arabidopsis Seedlings

Agrobacterium-mediated transient transformation for gene expression is a simple and fast method to analyze transgene functions in plants. Agroinfiltration in leaves of Nicotiana benthamiana is a common method for transient expression. However, agroinfiltration in leaves of Arabidopsis thaliana is challenging due to the low and variable efficiency. Here, we describe procedures of a highly efficient and robust Agrobacterium-mediated transient expression system, named AGROBEST (Agrobacterium-mediated enhanced seedling transformation) for gene expression in A. thaliana seedlings. High efficiency of AGROBEST has been achieved by virulence (vir) gene pre-induction of a specific disarmed Agrobacterium tumefaciens strain C58C1(pTiB6S3ΔT)^H followed by co-cultivation with Arabidopsis seedlings in an optimized medium with AB salts and buffered acidic plant culture medium. The stable acidic medium largely increases Agrobacterium-mediated transient expression levels and reduces plant defense responses, suggesting that AGROBEST enables high transient expression efficiency by compromising plant immunity. In summary, AGROBEST is a simple, fast, reliable, and robust transient expression system offering a quick and convenient method to observe protein localization, protein-protein interactions, promoter activities, and gene functional studies in Arabidopsis seedlings.

GPR15-C10ORF99 functional pairing initiates colonic Treg homing in amniotes

Regulatory T lymphocyte (Treg) homing reactions mediated by G protein‐coupled receptor (GPCR)–ligand interactions play a central role in maintaining intestinal immune homeostasis by restraining inappropriate immune responses in the gastrointestinal tract. However, the origin of Treg homing to the colon remains mysterious. Here, we report that the C10ORF99 peptide (also known as CPR15L and AP57), a cognate ligand of GPR15 that controls Treg homing to the colon, originates from a duplication of the flanking CDHR1 gene and is functionally paired with GPR15 in amniotes. Evolutionary analysis and experimental data indicate that the GPR15–C10ORF99 pair is functionally conserved to mediate colonic Treg homing in amniotes and their expression patterns are positively correlated with herbivore diet in the colon. With the first herbivorous diet in early amniotes, a new biological process (herbivorous diet short‐chain fatty acid‐C10ORF99/GPR15‐induced Treg homing colon immune homeostasis) emerged, and we propose an evolutionary model whereby GPR15–C10ORF99 functional pairing has initiated the first colonic Treg homing reaction in amniotes. Our findings also highlight that GPCR–ligand pairing leads to physiological adaptation during vertebrate evolution.

Functions of COP1/SPA E3 Ubiquitin Ligase Mediated by MpCRY in the Liverwort Marchantia polymorpha under Blue Light

COP1/SPA1 complex in Arabidopsis inhibits photomorphogenesis through the ubiquitination of multiple photo-responsive transcription factors in darkness, but such inhibiting function of COP1/SPA1 complex would be suppressed by cryptochromes in blue light. Extensive studies have been conducted on these mechanisms in Arabidopsis whereas little attention has been focused on whether another branch of land plants bryophyte utilizes this blue-light regulatory pathway. To study this problem, we conducted a study in the liverwort Marchantia polymorpha and obtained a MpSPA knock-out mutant, in which Mpspa exhibits the phenotype of an increased percentage of individuals with asymmetrical thallus growth, similar to MpCRY knock-out mutant. We also verified interactions of MpSPA with MpCRY (in a blue light-independent way) and with MpCOP1. Concomitantly, both MpSPA and MpCOP1 could interact with MpHY5, and MpSPA can promote MpCOP1 to ubiquitinate MpHY5 but MpCRY does not regulate the ubiquitination of MpHY5 by MpCOP1/MpSPA complex. These data suggest that COP1/SPA ubiquitinating HY5 is conserved in Marchantia polymorpha, but dissimilar to CRY in Arabidopsis, MpCRY is not an inhibitor of this process under blue light.

Arabidopsis CIB3 regulates photoperiodic flowering in an FKF1-dependent way

Arabidopsis cryptochrome 2 (CRY2) and FLAVIN-BINDING, KELCH REPEAT, and F-BOX 1 (FKF1) are blue light receptors mediating light regulation of growth and development, such as photoperiodic flowering. CRY2 interacts with a basic helix-loop-helix transcription factor CIB1 in response to blue light to activate the transcription of the flowering integrator gene FLOWERING LOCUS T (FT). CIB1, CIB2, CIB4, and CIB5 function redundantly to promote flowering in a CRY2-dependent way and form various heterodimers to bind to the noncanonical E-box sequence in the FT promoter. However, the function of CIB3 has not been described. We discovered that CIB3 promotes photoperiodic flowering independently of CRY2. Moreover, CIB3 does not interact with CRY2 but interacts with CIB1 and functions synergistically with CIB1 to promote the transcription of the GI gene. FKF1 is required for CIB3 to promote flowering and enhances the CIB1-CIB3 interaction in response to blue light.

Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering

CONSTANS, CONSTANS-LIKE, and TIMING OF CAB EXPRESSION1 (CCT) domain-containing proteins are a large family unique to plants. They transcriptionally regulate photoperiodic flowering, circadian rhythms, vernalization, and other related processes. Through their CCT domains, CONSTANS and HEADING DATE1 (HD1) coordinate with the NUCLEAR FACTOR Y (NF-Y) B/C dimer to specifically target a conserved 'CCACA' motif within the promoters of their target genes. However, the mechanism underlying DNA recognition by the CCT domain remains unclear. Here we determined the crystal structures of the rice (Oryza sativa) NF-YB/YC dimer and the florigen gene Heading date 3a (Hd3a)-bound HD1CCT/NF-YB/YC trimer with resolutions of 2.0 Å and 2.55 Å, respectively. The CCT domain of HD1 displays an elongated structure containing two α-helices and two loops, tethering Hd3a to the NF-YB/YC dimer. Helix α2 and loop 2 are anchored into the minor groove of the 'CCACA' motif, which determines the specific base recognition. Our structures reveal the interaction mechanism among the CCT domain, NF-YB/YC dimer, and the target DNA. These results not only provide insight into the network between the CCT proteins and NF-Y subunits, but also offer potential approaches for improving productivity and global adaptability of crops by manipulating florigen expression.

Using phage-assisted continuous evolution (PACE) to evolve human PD1

PD1/PDL1 pathway plays a critical role in cancer immune responses. The immune checkpoint inhibitors of PD1/PDL1 have been well explored and developed for immunotherapies of solid tumors. Recently, various monoclonal antibodies targeting the PD1/PDL1 pathway have emerged and achieved remarkable success in clinical trials. However, challenges with these monoclonal antibodies have appeared during cancer therapies, including predictors of response, patient selection, and innate resistance. Thus, a competitive antagonist of native PD1/PDL1, with smaller size and lower side-effect, is required for future cancer therapies. In this study, we utilized a protein evolution system of phage-assisted continuous evolution (PACE) to evolve PD1 continuously. Our results indicated that the newly evolved PD1 bound to PDL1 with higher affinity. The interactome analysis further suggested that these evolved PD1s exhibited higher specificity with PDL1. Therefore, these evolved PD1s may be applied as a new tool for tumor immunotherapy.

Transcriptional regulatory network of the light signaling pathways

The developmental program by which plants respond is tightly controlled by a complex cascade in which photoreceptors perceive and transduce the light signals that drive signaling processes and direct the transcriptional reprogramming, yielding specific cellular responses. The molecular mechanisms involved in the transcriptional regulation include light-regulated nuclear localization (the phytochromes and UVR8) and nuclear accumulation (the cryptochrome, cry2) of photoreceptors. This regulatory cascade also includes master regulatory transcription factors (TFs) that bridge photoreceptor activation with chromatin remodeling and regulate the expression of numerous light-responsive genes. Light signaling-related TFs often function as signal convergence points in concert with TFs in other signaling pathways to integrate complex endogenous and environmental cues that help the plant adapt to the surrounding environment. Increasing evidence suggests that chromatin modifications play a critical role in regulating light-responsive gene expression and provide an additional layer of light signaling regulation. Here, we provide an overview of our current knowledge of the transcriptional regulatory network involved in the light response, particularly the roles of TFs and chromatin in regulating light-responsive gene expression.

Mechanisms of Cryptochrome-Mediated Photoresponses in Plants

Cryptochromes are blue-light receptors that mediate photoresponses in plants. The genomes of most land plants encode two clades of cryptochromes, CRY1 and CRY2, which mediate distinct and overlapping photoresponses within the same species and between different plant species. Photoresponsive protein-protein interaction is the primary mode of signal transduction of cryptochromes. Cryptochromes exist as physiologically inactive monomers in the dark; the absorption of photons leads to conformational change and cryptochrome homooligomerization, which alters the affinity of cryptochromes interacting with cryptochrome-interacting proteins to form various cryptochrome complexes. These cryptochrome complexes, collectively referred to as the cryptochrome complexome, regulate transcription or stability of photoresponsive proteins to modulate plant growth and development. The activity of cryptochromes is regulated by photooligomerization; dark monomerization; cryptochrome regulatory proteins; and cryptochrome phosphorylation, ubiquitination, and degradation. Most of the more than 30 presently known cryptochrome-interacting proteins are either regulated by other photoreceptors or physically interactingwith the protein complexes of other photoreceptors. Some cryptochrome-interacting proteins are also hormonal signaling or regulatory proteins. These two mechanisms enable cryptochromes to integrate blue-light signals with other internal and external signals to optimize plant growth and development.

Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs

Plants sense different parts of the sun's light spectrum using distinct photoreceptors, which signal through the E3 ubiquitin ligase COP1. Here, we analyze why many COP1‐interacting transcription factors and photoreceptors harbor sequence‐divergent Val‐Pro (VP) motifs that bind COP1 with different binding affinities. Crystal structures of the VP motifs of the UV‐B photoreceptor UVR8 and the transcription factor HY5 in complex with COP1, quantitative binding assays, and reverse genetic experiments together suggest that UVR8 and HY5 compete for COP1. Photoactivation of UVR8 leads to high‐affinity cooperative binding of its VP motif and its photosensing core to COP1, preventing COP1 binding to its substrate HY5. UVR8–VP motif chimeras suggest that UV‐B signaling specificity resides in the UVR8 photoreceptor core. Different COP1–VP peptide motif complexes highlight sequence fingerprints required for COP1 targeting. The blue‐light photoreceptors CRY1 and CRY2 also compete with transcription factors for COP1 binding using similar VP motifs. Thus, our work reveals that different photoreceptors and their signaling components compete for COP1 via a conserved mechanism to control different light signaling cascades.

Plant Chromatin Catches the Sun

Plants use solar radiation as energy source for photosynthesis. They also take advantage of the information provided by the varying properties of sunlight, such as wavelength, orientation, and periodicity, to trigger physiological and developmental adaptations to a changing environment. After more than a century of research efforts in plant photobiology, multiple light signaling pathways converging onto chromatin-based mechanisms have now been identified, which in some instances play critical roles in plant phenotypic plasticity. In addition to locus-specific changes linked to transcription regulation, light signals impact higher-order chromatin organization. Here, we summarize current knowledge on how light can affect the global composition and the spatial distribution of chromatin domains. We introduce emerging questions on the functional links between light signaling and the epigenome, and further discuss how different chromatin regulatory layers may interconnect during plant adaptive responses to light.

Sweet sorghum (Sorghum bicolor L.) SbSTOP1 activates the transcription of a β-1,3-glucanase gene to reduce callose deposition under Al toxicity: A novel pathway for Al tolerance in plants

Aluminum (Al) toxicity is a primary limiting factor for crop production in acid soils. Callose deposition, an early indicator and likely a contributor to Al toxicity, is induced rapidly in plant roots under Al stress. SbGlu1, encoding a β-1,3-glucanase for callose degradation, showed important roles in sorghum Al resistance, yet its regulatory mechanisms remain unclear. The STOP1 transcription factors mediate Al signal transduction in various plants. Here, we identified their homolog in sweet sorghum, SbSTOP1, transcriptionally activated the expression of SbGlu1. Moreover, the DNA sequence recognized by SbSTOP1 on the promoter of SbGlu1 lacked the reported cis-acting element. Complementation lines of Atstop1 with SbSTOP1 revealed enhanced transcription levels of SbGlu1 homologous gene and reduced callose accumulation in Arabidopsis. These results indicate, for the first time, that SbSTOP1 is involved in the modulation of callose deposition under Al stress via transcriptional regulation of a β-1,3-glucanase gene.