Integration of light and temperature sensing by liquid-liquid phase separation of phytochrome B.

Light and temperature in plants are perceived by a common receptor, phytochrome B (phyB). How phyB distinguishes these signals remains elusive. Here, we report that phyB spontaneously undergoes phase separation to assemble liquid-like droplets. This capacity is driven by its C terminus through self-association, whereas the intrinsically disordered N-terminal extension (NTE) functions as a biophysical modulator of phase separation. Light exposure triggers a conformational change to subsequently alter phyB condensate assembly, while temperature sensation is directly mediated by the NTE to modulate the phase behavior of phyB droplets. Multiple signaling components are selectively incorporated into phyB droplets to form concentrated microreactors, allowing switch-like control of phyB signaling activity through phase transitions. Therefore, light and temperature cues are separately read out by phyB via allosteric changes and spontaneous phase separation, respectively. We provide a conceptual framework showing how the distinct but highly correlated physical signals are interpreted and sorted by one receptor.

The MBD-ACD DNA methylation reader complex recruits MICRORCHIDIA6 to regulate ribosomal RNA gene expression in Arabidopsis.

DNA methylation is an important epigenetic mark implicated in selective rRNA gene expression, but the DNA methylation readers and effectors remain largely unknown. Here, we report a protein complex that reads DNA methylation to regulate variant-specific 45S ribosomal RNA (rRNA) gene expression in Arabidopsis (Arabidopsis thaliana). The complex, consisting of METHYL-CpG-BINDING DOMAIN PROTEIN5 (MBD5), MBD6, ALPHA-CRYSTALLIN DOMAIN PROTEIN15.5 (ACD15.5), and ACD21.4, directly binds to 45S rDNA. While MBD5 and MBD6 function redundantly, ACD15.5 and ACD21.4 are indispensable for variant-specific rRNA gene expression. These 4 proteins undergo phase separation in vitro and in vivo and are interdependent for their phase separation. The α-crystallin domain of ACD15.5 and ACD21.4, which is essential for their function, enables phase separation of the complex, likely by mediating multivalent protein interactions. The effector MICRORCHIDIA6 directly interacts with ACD15.5 and ACD21.4, but not with MBD5 and MBD6, and is recruited to 45S rDNA by the MBD-ACD complex to regulate variant-specific 45S rRNA expression. Our study reveals a pathway in Arabidopsis through which certain 45S rRNA gene variants are silenced, while others are activated.

A review on recent advances in plasma-activated water for food safety: current applications and future trends.

Plasma-activated water (PAW), the water or solutions treated with atmospheric cold plasma, is an eco-friendly technique with minimal changes in food products, making it a befitting alternative to traditional disinfection methods. Due to its potential microbicidal properties, PAW has been receiving increasing attention for applications in the food, agricultural, and biomedical fields. In this article, we aimed at presenting an overview of recent studies on the generation methods, physicochemical properties, and antimicrobial activity of PAW, as well as its application in the food industry. Specific areas were well discussed including microbial decontamination of food products, reduction of pesticide residues, meat curing, sprouts production, and disinfection of food contact materials. In addition, the factors influencing PAW efficiency were also well illustrated in detail, such as discharge parameters, types and amounts of microorganisms, characteristics of the liquid solution and food products, and treatment time. Moreover, the strategies to improve the efficacy of PAW were also presented in combination with other technologies. Furthermore, the salient drawbacks of this technology were discussed and the important areas for future research were also highlighted. Overall, the present review provides important insights for the application of PAW in the food industry.

Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis.

Nitrogen (N) availability is a major limiting factor for plant growth and agricultural productivity. Although the gene regulation network in response to N starvation has been extensively studied, it remains unknown whether N starvation has an impact on the activity of transposable elements (TEs). Here, we report that TEs can be transcriptionally activated in Arabidopsis under N starvation conditions. Through genetic screening of idm1-14 suppressors, we cloned GLU1, which encodes a glutamate synthase that catalyzes the synthesis of glutamate in the primary N assimilation pathway. We found that glutamate synthase 1 (GLU1) and its functional homologs GLU2 and glutamate transport 1 (GLT1) are redundantly required for TE silencing, suggesting that N metabolism can regulate TE activity. Transcriptome and methylome analyses revealed that N starvation results in genome-wide TE activation without inducing obvious alteration of DNA methylation. Genetic analysis indicated that N starvation-induced TE activation is also independent of other well-established epigenetic mechanisms, including histone methylation and heterochromatin decondensation. Our results provide new insights into the regulation of TE activity under stressful environments in planta.

Egg cell-secreted aspartic proteases ECS1/2 promote gamete attachment to prioritize the fertilization of egg cells over central cells in Arabidopsis.

Double fertilization is an innovative phenomenon in angiosperms, in which one sperm cell first fuses with the egg cell to produce the embryo, and then the other sperm fuses with the central cell to produce the endosperm. However, the molecular mechanism of the preferential fertilization of egg cells is poorly understood. In this study, we report that two egg cell-secreted aspartic proteases, ECS1 and ECS2, play an important role in promoting preferential fertilization of egg cells in Arabidopsis. We show that simultaneous loss of ECS1 and ECS2 function resulted in an approximately 20% reduction in fertility, which can be complemented by the full-length ECS1/2 but not by corresponding active site mutants or by secretion-defective versions of ECS1/2. Detailed phenotypic analysis revealed that the egg cell-sperm cell attachment was compromised in ecs1 ecs2 siliques. Limited pollination assays with cyclin-dependent kinase a1 (cdka;1) pollen showed that preferential egg cell fertilization was impaired in the ecs1 ecs2 mutant. Taken together, these results demonstrate that egg cells secret two aspartic proteases, ECS1 and ECS2, to facilitate the attachment of sperm cells to egg cells so that preferential fertilization of egg cells is achieved. This study reveals the molecular mechanism of preferential fertilization in Arabidopsis thaliana.

B-BOX DOMAIN PROTEIN28 Negatively Regulates Photomorphogenesis by Repressing the Activity of Transcription Factor HY5 and Undergoes COP1-Mediated Degradation.

Plants have evolved a delicate molecular system to fine-tune their growth and development in response to dynamically changing light environments. In this study, we found that BBX28, a B-box domain protein, negatively regulates photomorphogenic development in a dose-dependent manner in Arabidopsis thaliana BBX28 interferes with the binding of transcription factor HY5 to the promoters of its target genes through physical interactions, thereby repressing its activity and negatively affecting HY5-regulated gene expression. In darkness, BBX28 associates with CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and undergoes COP1-mediated degradation via the 26S proteasome system. Collectively, these results demonstrate that BBX28 acts as a key factor in the COP1-HY5 regulatory hub by maintaining proper HY5 activity to ensure normal photomorphogenic development in plants.

RSM1, an Arabidopsis MYB protein, interacts with HY5/HYH to modulate seed germination and seedling development in response to abscisic acid and salinity.

MYB transcription factors are involved in many biological processes, including metabolism, development and responses to biotic and abiotic stresses. RADIALIS-LIKE SANT/MYB 1 (RSM1) belongs to a MYB-related subfamily, and previous transcriptome analysis suggests that RSM1 may play roles in plant development, stress responses and plant hormone signaling. However, the molecular mechanisms of RSM1 action in response to abiotic stresses remain obscure. We show that down-regulation or up-regulation of RSM1 expression alters the sensitivity of seed germination and cotyledon greening to abscisic acid (ABA), NaCl and mannitol in Arabidopsis. The expression of RSM1 is dynamically regulated by ABA and NaCl. Transcription factors ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOG (HYH) regulate RSM1 expression via binding to the RSM1 promoter. Genetic analyses reveal that RSM1 mediates multiple functions of HY5 in responses of seed germination, post-germination development to ABA and abiotic stresses, and seedling tolerance to salinity. Pull-down and BiFC assays show that RSM1 interacts with HY5/HYH in vitro and in vivo. RSM1 and HY5/HYH may function as a regulatory module in responses to ABA and abiotic stresses. RSM1 binds to the promoter of ABA INSENSITIVE 5 (ABI5), thereby regulating its expression, while RSM1 interaction also stimulates HY5 binding to the ABI5 promoter. However, no evidence was found in the dual-luciferase transient expression assay to support that RSM enhances the activation of ABI5 expression by HY. In summary, HY5/HYH and RSM1 may converge on the ABI5 promoter and independently or somehow dependently regulate ABI5 expression and ABI5-downstream ABA and abiotic stress-responsive genes, thereby improving the adaption of plants to the environment.

Phosphorylation and negative regulation of CONSTITUTIVELY PHOTOMORPHOGENIC 1 by PINOID in Arabidopsis.

CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) plays crucial roles in various cellular processes via its E3 ubiquitin ligase activity in organisms, ranging from fungi to humans. As a key component in regulating various biological events, COP1 itself is precisely controlled at multiple layers. Here, we report a negative regulator of COP1, PINOID (PID), which positively mediates photomorphogenic development. Specifically, PID genetically and physically interacts with COP1 and directly phosphorylates COP1 at Ser20. As a result, this posttranslational modification serves to repress COP1 activity and promote photomorphogenesis. Our findings signify a key regulatory mechanism for precisely maintaining COP1 activity, thereby ensuring appropriate development in plants.

Effect of rosemary extract on lipid oxidation of cooked pork during simulated gastric digestion.

BACKGROUND: Oxidation of food lipids occurs in the gastrointestinal tract, resulting in potential adverse health effects. Rosemary extract (RE), as one of the most popular naturally sourced antioxidants, is widely used in the food industry. However, the effect of RE on lipid oxidation during gastrointestinal digestion has not been well investigated. Therefore, this study aimed to evaluate the effect of RE on lipid oxidation of cooked pork during simulated gastric digestion. RESULTS: Results showed that RE at 12.5, 25, 50, and 100 mg kg-1 pork effectively decreased the formation of malondialdehyde during simulated gastric digestion of cooked pork. RE also effectively mitigated the decline of fatty acids during the simulated gastric digestion of pork. The total phenolic content in RE was calculated to be 170.67 mg gallic acid equivalent (GAE) g-1 . RE dissolved in distilled water (pH 6.5) or potassium hydrogen phthalate-hydrochloric acid buffer solution (0.2 mol L-1 , pH 3.0) both exhibited strong 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) and 1,1-diphenyl-2-picrylhydrazyl radical-scavenging activities as well as ferric reducing capacity. The inhibitory effects of RE on lipid oxidation of cooked pork during simulated gastric digestion may be attributed to the phenolic compounds with antioxidant properties. CONCLUSION: The results lend support to the possible application of rosemary or RE as a rich source of natural antioxidants to inhibit the oxidation of food lipids during gastrointestinal digestion. © 2019 Society of Chemical Industry.

Natural variation of H3K27me3 modification in two Arabidopsis accessions and their hybrid.

Histone modifications affect gene expression, but the mechanism and biological consequence of natural variation in histone modifications remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid. A total of 1,828 genomic regions showing variation in H3K27me3 modification between Col and C24 were identified, most of which were associated with genic regions. Natural variation of H3K27me3 modification between parents could result in allelic bias of H3K27me3 in hybrids. Furthermore, we found that H3K27me3 variation between Col and C24 was negatively correlated with gene expression differences between two accessions, especially with those arising from the cis-effect. Importantly, mutation of CLF, an Arabidopsis methyltransferase for H3K27, altered gene expression patterns between the parents. Together, these data provide insights into natural variation of histone modifications and their association with gene expression differences between Arabidopsis ecotypes.

Coordinated regulation of Arabidopsis thaliana development by light and gibberellins.

Light and gibberellins (GAs) mediate many essential and partially overlapping plant developmental processes. DELLA proteins are GA-signalling repressors that block GA-induced development. GA induces degradation of DELLA proteins via the ubiquitin/proteasome pathway, but light promotes accumulation of DELLA proteins by reducing GA levels. It was proposed that DELLA proteins restrain plant growth largely through their effect on gene expression. However, the precise mechanism of their function in coordinating GA signalling and gene expression remains unknown. Here we characterize a nuclear protein interaction cascade mediating transduction of GA signals to the activity regulation of a light-responsive transcription factor. In the absence of GA, nuclear-localized DELLA proteins accumulate to higher levels, interact with phytochrome-interacting factor 3 (PIF3, a bHLH-type transcription factor) and prevent PIF3 from binding to its target gene promoters and regulating gene expression, and therefore abrogate PIF3-mediated light control of hypocotyl elongation. In the presence of GA, GID1 proteins (GA receptors) elevate their direct interaction with DELLA proteins in the nucleus, trigger DELLA protein's ubiquitination and proteasome-mediated degradation, and thus release PIF3 from the negative effect of DELLA proteins.

Radio frequency drying on functional diversity of tiger nut flour: Effects on physicochemical, structural, and rheological properties.

Tiger nut (TN) is a valuable nutrient and gluten-free tuber. To achieve high-quality TN flour as functional ingredients in food, it is essential to develop effective drying technologies for TN. Five drying methods including natural drying (Control), hot-air drying (HD), radio frequency single drying (RFSD), RF assisted hot-air drying (RFHD), and RF- vacuum drying (RFVD) were selected and compared to determine their effects on physiochemical, structural, and rheological properties of TN flour. Results showed that RF drying (RFD) significantly improved the hydration, oil-absorbing, and antioxidant activity capacity, especially for RFVD. RFHD exhibited greater color (BI = 13.80 ± 0.05 and C = 10.26 ± 0.05) and reducing sugar content (253.50 ± 2.27 mg d.b.) than RFSD and RFVD. The gelatinization temperature, enthalpy value, and particle size (57.30-269.33 µm) of TN flour were reduced. The structural property results indicated that RFD reduced the relative crystallinity and short-range ordering of the flour, altered protein secondary structure, and caused the damaged microstructure in comparison with Control and HD groups. All sample gels exhibited a weak strain overshoot behavior (type III) under large amplitude oscillations, and RFD resulted in a reduced viscoelastic behavior. RFD could be an effective method to produce functional TN flour.

Effect of radio frequency energy on buckwheat quality: An insight into structure and physicochemical properties of protein and starch.

Radio frequency (RF) heating as an emerging technology is widely used to improve cereal-based food quality. To further investigate effects of RF treatment on buckwheat quality, structures and physicochemical properties of protein and starch in buckwheat were evaluated under various temperatures (80, 90, and 100 °C) and holding times (0, 5, and 10 min). Results showed that protein-starch complexes were reaggregated with the increases of RF heating temperature and time, as well as the values of R1047/1022, crystallinity, random coil, and α-helix significantly decreased, and the values of ß-sheet obviously increased. Moreover, viscosities and rheological properties of buckwheat were reduced by the raised RF treatment intensity. Besides, the RF processing had a mostly positive effect on swelling power at low temperature of 30 °C, but contrary effect at high temperatures of 60 °C and 90 °C. However, changes of water solubility index, emulsifying capacity, and emulsion stability depended on the RF processing intensity. These results of the study suggested that buckwheat quality was affected by multiple RF treatment conditions, which can be tailored to develop a RF process having the potential to improve the function of buckwheat flour.

ALBA proteins confer thermotolerance through stabilizing HSF messenger RNAs in cytoplasmic granules.

High temperature is one of the major environmental stresses affecting plant growth and fitness. Heat stress transcription factors (HSFs) play critical roles in regulating the expression of heat-responsive genes. However, how HSFs are regulated remains obscure. Here, we show that ALBA4, ALBA5 and ALBA6, which phase separate into stress granules (SGs) and processing bodies (PBs) under heat stress, directly bind selected messenger RNAs, including HSF mRNAs, and recruit them into SGs and PBs to protect them from degradation under heat stress in Arabidopsis. The alba456 triple mutants, but not single and double mutants, display pleiotropic developmental defects and hypersensitivity to heat stress. Mutations in XRN4, a cytoplasmic 5' to 3' exoribonuclease, can rescue the observed developmental and heat-sensitive phenotypes of alba456 seedlings. Our study reveals a new layer of regulation for HSFs whereby HSF mRNAs are stabilized by redundant action of ALBA proteins in SGs and PBs for plant thermotolerance.

Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.).

Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica-Japonica subspecific differentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice genome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica-Japonica and Indica-Indica crosses.

Abscisic acid regulation of guard-cell K+ and anion channels in Gbeta- and RGS-deficient Arabidopsis lines.

In mammals, basal currents through G protein-coupled inwardly rectifying K(+) (GIRK) channels are repressed by Galpha(i/o)GDP, and the channels are activated by direct binding of free Gbetagamma subunits released upon stimulation of Galpha(i/o)-coupled receptors. However, essentially all information on G protein regulation of GIRK electrophysiology has been gained on the basis of coexpression studies in heterologous systems. A major advantage of the model organism, Arabidopsis thaliana, is the ease with which knockout mutants can be obtained. We evaluated plants harboring mutations in the sole Arabidopsis Galpha (AtGPA1), Gbeta (AGB1), and Regulator of G protein Signaling (AtRGS1) genes for impacts on ion channel regulation. In guard cells, where K(+) fluxes are integral to cellular regulation of stomatal apertures, inhibition of inward K(+) (K(in)) currents and stomatal opening by the phytohormone abscisic acid (ABA) was equally impaired in Atgpa1 and agb1 single mutants and the Atgpa1 agb1 double mutant. AGB1 overexpressing lines maintained a wild-type phenotype. The Atrgs1 mutation did not affect K(in) current magnitude or ABA sensitivity, but K(in) voltage-activation kinetics were altered. Thus, Arabidopsis cells differ from mammalian cells in that they uniquely use the Galpha subunit or regulation of the heterotrimer to mediate K(in) channel modulation after ligand perception. In contrast, outwardly rectifying (K(out)) currents were unaltered in the mutants, and ABA activation of slow anion currents was conditionally disrupted in conjunction with cytosolic pH clamp. Our studies highlight unique aspects of ion channel regulation by heterotrimeric G proteins and relate these aspects to stomatal aperture control, a key determinant of plant biomass acquisition and drought tolerance.

O-fucosylation of CPN20 by SPINDLY Derepresses Abscisic Acid Signaling During Seed Germination and Seedling Development.

SPINDLY is involved in some aspects of plant development. However, the nature of this protein as an O-fucosyltransferase was recently discovered. In this study, we show that SPINDLY (SPY) interacts with CPN20 in yeast two-hybrid and split-luc assays, and the interaction is promoted by ABA. CPN20 is a chloroplast-localized co-chaperonin that negatively regulates ABAR-mediated ABA signaling. By using Electron Transfer Dissociation-MS/MS analysis, two O-fucosylation sites, e.g., 116th and 119th threonines, were detected in ectopically expressed CPN20 in mammalian cells and in Arabidopsis. The O-fucosylation at both threonine residues was confirmed by in vitro peptide O-fucosylation assay. We further show that CPN20 accumulates in the chloroplast of spy mutants, suggesting that SPY negatively regulates CPN20 localization in the chloroplast. In vivo protein degradation assay along with CPN20 localization behavior suggest that import of CPN20 into the chloroplast is negatively regulated by SPY. Genetic analysis shows that ABA insensitive phenotypes of spy-3 in terms of seed germination and early seedling development are partially suppressed by the cpn20 mutation, suggesting that CPN20 acts downstream of SPY in this ABA signaling pathway and that there may exist other pathways in parallel with CPN20. Collectively, the above data support the notion that the O-fucosylation of CPN20 by SPY fine-tunes ABA signaling in Arabidopsis.

Rapid and reliable detection of 11 food-borne pathogens using thin-film biosensor chips.

Traditional methods for identifying food-borne pathogens are time-consuming and laborious, so it is necessary to develop innovative methods for the rapid identification of food-borne pathogens. Here, we report the development of silicon-based optical thin-film biosensor chips for sensitive detection of 11 food-borne pathogens. Briefly, aldehyde-labeled probes were arrayed and covalently attached to a hydrazine-derivatized chip surface, and then, biotinylated polymerase chain reaction (PCR) amplicons were hybridized with the probes. After washing and brief incubation with an antibiotin immunoglobulin G-horseradish peroxidase conjugate and a precipitable horseradish peroxidase substrate, biotinylated chains bound to the probes were visualized as a color change on the chip surface (gold to blue/purple). Highly sensitive and accurate examination of PCR fragment targets can be completed within 30 min. This assay is extremely robust, sensitive, specific, and economical and can be adapted to different throughputs. Thus, a rapid, sensitive, and reliable technique for detecting 11 food-borne pathogens was successfully developed.

Synergistic Inactivation Mechanism of Combined Plasma-Activated Water and Mild Heat against Saccharomyces cerevisiae.

ABSTRACT: This study aimed to elucidate the mechanism of synergistic inactivation of Saccharomyces cerevisiae by the combined use of plasma-activated water (PAW) and mild heat (40 to 50°C). A reduction of 4.40 log CFU/mL in S. cerevisiae was observed after the synergistic combination of PAW and mild heat at 50°C for 6 min, whereas the individual treatments of PAW at 25°C and mild heat at 50°C for 6 min resulted in a reduction of 0.27 and 1.92 log CFU/mL, respectively. The simultaneous application of PAW and mild heat caused significant increases in membrane permeability, resulting in the leakage of intracellular components (such as nucleic acids and proteins) and increased uptake of propidium iodide. The combined treatment of PAW and mild heat also resulted in significant increases in the intracellular levels of reactive oxygen species and disruption of mitochondrial membrane potential in S. cerevisiae cells. In summary, this study illustrates the potential of PAW treatment combined with mild heat to rapidly inactivate microorganisms in food products.

The Asymmetric Expression of SAUR Genes Mediated by ARF7/19 Promotes the Gravitropism and Phototropism of Plant Hypocotyls.

The asymmetric distribution of auxin leads to the bending growth of hypocotyls during gravitropic and phototropic responses, but the signaling events downstream of auxin remain unclear. Here, we identify many SAUR genes showing asymmetric expression in soybean hypocotyls during gravistimulation and then study their homologs in Arabidopsis. SAUR19 subfamily genes have asymmetric expression in Arabidopsis hypocotyls during gravitropic and phototropic responses, induced by the lateral redistribution of auxin. Both the mutation of SAUR19 subfamily genes and the ectopic expression of SAUR19 weaken these tropic responses, indicating the critical role of their asymmetric expression. The auxin-responsive transcription factor ARF7 may directly bind the SAUR19 promoter and activate SAUR19 expression asymmetrically in tropic responses. Taken together, our results reveal that a gravity- or light-triggered asymmetric auxin distribution induces the asymmetric expression of SAUR19 subfamily genes by ARF7 and ARF19 in the hypocotyls, which leads to bending growth during gravitropic and phototropic responses.