SEUSS and PIF4 Coordinately Regulate Light and Temperature Signaling Pathways to Control Plant Growth

NAC transcription factor ATAF1 negatively modulates the PIF-regulated hypocotyl elongation under a short-day photoperiod

Day length modulates hypocotyl elongation in seedlings to optimize their overall fitness. Variations in cell growth-associated genes are regulated by several transcription factors. However, the specific transcription factors through which the plant clock increases plant fitness are still being elucidated. In this study, we identified the no apical meristem, Arabidopsis thaliana-activating factor (ATAF-1/2), and cup-shaped cotyledon (NAC) family transcription factor ATAF1 as a novel repressor of hypocotyl elongation under a short-day (SD) photoperiod. Variations in day length profoundly affected the transcriptional and protein levels of ATAF1. ATAF1-deficient mutant exhibited increased hypocotyl length and cell growth-promoting gene expression under SD conditions. Moreover, ATAF1 directly targeted and repressed the expression of the cycling Dof factor 1/5 (CDF1/5), two key transcription factors involved in hypocotyl elongation under SD conditions. Additionally, ATAF1 interacted with and negatively modulated the effects of phytochrome-interacting factor (PIF), thus inhibiting PIF-promoted gene expression and hypocotyl elongation. Taken together, our results revealed ATAF1-PIF as a crucial pair modulating the expression of key transcription factors to facilitate plant growth during day/night cycles under fluctuating light conditions.

How plants sense and respond to osmotic stress

Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

Heat Stress Responsive Aux/IAA Protein, OsIAA29 Regulates Grain Filling Through OsARF17 Mediated Auxin Signaling Pathway

High temperature during grain filling considerably reduces yield and quality in rice, but its molecular mechanisms are not fully understood. We investigated the functions of a seed preferentially expressed Aux/IAA gene, OsIAA29, under high temperature-stress in grain filling using CRISPR/Cas9, RNAi, and overexpression. We observed that the osiaa29 had a higher percentage of shrunken and chalkiness seed, as well as lower 1000-grain weight than ZH11 under high temperature. Meanwhile, the expression of OsIAA29 was induced and the IAA content was remarkably reduced in the ZH11 seeds under high temperature. In addition, OsIAA29 may enhance the transcriptional activation activity of OsARF17 through competition with OsIAA21 binding to OsARF17. Finally, chromatin immunoprecipitation quantitative real-time PCR (ChIP-qPCR) results proved that OsARF17 regulated expression of several starch and protein synthesis related genes (like OsPDIL1-1, OsSS1, OsNAC20, OsSBE1, and OsC2H2). Therefore, OsIAA29 regulates seed development in high temperature through competition with OsIAA21 in the binding to OsARF17, mediating auxin signaling pathway in rice. This study provides a theoretical basis and gene resources for auxin signaling and effective molecular design breeding.

Epigenetic insight into floral transition and seed development in plants

Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.

PIFs interact with SWI2/SNF2-related 1 complex subunit 6 to regulate H2A.Z deposition and photomorphogenesis in Arabidopsis

Light is an essential environmental signal perceived by a broad range of photoreceptors in plants. Among them, the red/far-red light receptor phytochromes function to promote photomorphogenesis, which is critical to the survival of seedlings after seeds germination. The basic-helix-loop-helix transcription factors phytochrome-interacting factors (PIFs) are the pivotal direct downstream components of phytochromes. H2A.Z is a highly conserved histone variant regulating gene transcription, and its incorporation into nucleosomes is catalyzed by SWI2/SNF2-related 1 complex, in which SWI2/SNF2-related 1 complex subunit 6 (SWC6) and actin-related protein 6 (ARP6) serve as core subunits. Here, we show that PIFs physically interact with SWC6 in vitro and in vivo, leading to the disassociation of HY5 from SWC6. SWC6 and ARP6 regulate hypocotyl elongation partly through PIFs in red light. PIFs and SWC6 coregulate the expression of auxin-responsive genes such as IAA6, IAA19, IAA20, and IAA29 and repress H2A.Z deposition at IAA6 and IAA19 in red light. Based on previous studies and our findings, we propose that PIFs inhibit photomorphogenesis, at least in part, through repression of H2A.Z deposition at auxin-responsive genes mediated by the interactions of PIFs with SWC6 and promotion of their expression in red light.

Temperature regulation of auxin-related gene expression and its implications for plant growth

Twenty-five years ago, a seminal paper demonstrated that warm temperatures increase auxin levels to promote hypocotyl growth in Arabidopsis thaliana. Here we highlight recent advances in auxin-mediated thermomorphogenesis and identify unanswered questions. In the warmth, PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF7 bind the YUCCA8 gene promoter and, in concert with histone modifications, enhance its expression to increase auxin synthesis in the cotyledons. Once transported to the hypocotyl, auxin promotes cell elongation. The meta-analysis of expression of auxin-related genes in seedlings exposed to temperatures ranging from cold to hot shows complex patterns of response. Changes in auxin only partially account for these responses. The expression of many SMALL AUXIN UP RNA (SAUR) genes reaches a maximum in the warmth, decreasing towards both temperature extremes in correlation with the rate of hypocotyl growth. Warm temperatures enhance primary root growth, the response requires auxin, and the hormone levels increase in the root tip but the impacts on cell division and cell expansion are not clear. A deeper understanding of auxin-mediated temperature control of plant architecture is necessary to face the challenge of global warming.

Histone H3 lysine 27 trimethylation suppresses jasmonate biosynthesis and signaling to affect male fertility under high temperature in cotton

High-temperature (HT) stress causes male sterility in crops, thus decreasing yields. To explore the possible contribution of histone modifications to male fertility under HT conditions, we defined the histone methylation landscape for the marks histone H3 lysine 27 trimethylation (H3K27me3) and histone H3 lysine 4 trimethylation (H3K4me3) by chromatin immunoprecipitation sequencing (ChIP-seq) in two differing upland cotton (Gossypium hirsutum) varieties. We observed a global disruption in H3K4me3 and H3K27me3 modifications, especially H3K27me3, in cotton anthers subjected to HT. HT affected the bivalent H3K4me3-H3K27me3 modification more than either monovalent modification. We determined that removal of H3K27me3 at the promoters of jasmonate-related genes increased their expression, maintaining male fertility under HT in the HT-tolerant variety at the anther dehiscence stage. Modulating jasmonate homeostasis or signaling resulted in an anther indehiscence phenotype under HT. Chemical suppression of H3K27me3 deposition increased jasmonic acid contents and maintained male fertility under HT. In summary, our study provides new insights into the regulation of male fertility by histone modifications under HT and suggests a potential strategy for improving cotton HT tolerance.

Epigenetic and transcription factors synergistically promote the high temperature response in plants

Temperature is one of the main environmental cues affecting plant growth and development, and plants have evolved multiple mechanisms to sense and acclimate to high temperature. Emerging research has shown that transcription factors, epigenetic factors, and their coordination are essential for plant temperature responses and the resulting phenological adaptation. Here, we summarize recent advances in molecular and cellular mechanisms to understand how plants acclimate to high temperature and describe how plant meristems sense and integrate environmental signals. Furthermore, we lay out future directions for new technologies to reveal heterogeneous responses in different cell types thus improving plant environmental plasticity.

MYB112 connects light and circadian clock signals to promote hypocotyl elongation in Arabidopsis

Ambient light and the endogenous circadian clock play key roles in regulating Arabidopsis (Arabidopsis thaliana) seedling photomorphogenesis. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) acts downstream of both light and the circadian clock to promote hypocotyl elongation. Several members of the R2R3-MYB transcription factor (TF) family, the most common type of MYB TF family in Arabidopsis, have been shown to be involved in regulating photomorphogenesis. Nonetheless, whether R2R3-MYB TFs are involved in connecting the light and clock signaling pathways during seedling photomorphogenesis remains unknown. Here, we report that MYB112, a member of the R2R3-MYB family, acts as a negative regulator of seedling photomorphogenesis in Arabidopsis. The light signal promotes the transcription and protein accumulation of MYB112. myb112 mutants exhibit short hypocotyls in both constant light and diurnal cycles. MYB112 physically interacts with PIF4 to enhance the transcription of PIF4 target genes involved in the auxin pathway, including YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), and IAA29. Furthermore, MYB112 directly binds to the promoter of LUX ARRHYTHMO (LUX), the central component of clock oscillators, to repress its expression mainly in the afternoon and relieve LUX-inhibited expression of PIF4. Genetic evidence confirms that LUX acts downstream of MYB112 in regulating hypocotyl elongation. Thus, the enhanced transcript accumulation and transcriptional activation activity of PIF4 by MYB112 additively promotes the expression of auxin-related genes, thereby increasing auxin synthesis and signaling and fine-tuning hypocotyl growth under diurnal cycles.

The F-box protein SHORT PRIMARY ROOT modulates primary root meristem activity by targeting SEUSS-LIKE protein for degradation in rice

Root meristem activity is essential for root morphogenesis and adaptation, but the molecular mechanism regulating root meristem activity is not fully understood. Here, we identify an F-box family E3 ubiquitin ligase named SHORT PRIMARY ROOT (SHPR) that regulates primary root (PR) meristem activity and cell proliferation in rice. SHPR loss-of-function mutations impair PR elongation in rice. SHPR is involved in the formation of an SCF complex with the Oryza sativa SKP1-like protein OSK1/20. We show that SHPR interacts with Oryza sativa SEUSS-LIKE (OsSLK) in the nucleus and is required for OsSLK polyubiquitination and degradation by the ubiquitin 26S-proteasome system (UPS). Transgenic plants overexpressing OsSLK display a shorter PR phenotype, which is similar to the SHPR loss-of-function mutants. Genetic analysis suggests that SHPR promotes PR elongation in an OsSLK-dependent manner. Collectively, our study establishes SHPR as an E3 ubiquitin ligase that targets OsSLK for degradation, and uncovers a protein ubiquitination pathway as a mechanism for modulating root meristem activity in rice.

Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review

Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.

PHYTOCHROME INTERACTING FACTOR 4 regulates microtubule organization to mediate high temperature-induced hypocotyl elongation in Arabidopsis

Hypocotyl elongation is an important morphological response during plant thermomorphogenesis. Multiple studies indicate that the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) is a key regulator of high temperature-induced hypocotyl elongation. However, the underlying cellular mechanisms regarding PIF4-mediated hypocotyl elongation are largely unclear. In this study, we found that PIF4 regulates the PLANT U-BOX TYPE E3 UBIQUITIN LIGASE 31 (PUB31)-SPIRAL1 (SPR1) module and alters cortical microtubule reorganization to promote hypocotyl cell elongation during Arabidopsis thaliana (Arabidopsis) thermomorphogenesis. SPR1 loss-of-function mutants exhibit much shorter hypocotyls when grown at 28 °C, indicating a positive role for SPR1 in high ambient temperature-induced hypocotyl elongation. High ambient temperature induces SPR1 expression in a PIF4-dependent manner, and stabilizes SPR1 protein to mediate microtubule reorganization. Further investigation showed that PUB31 interacts with and ubiquitinates SPR1. In particular, the ubiquitinated effect on SPR1 was moderately decreased at high temperature, which was due to the direct binding of PIF4 to the PUB31 promoter and down-regulating its expression. Thus, this study reveals a mechanism in which PIF4 induces SPR1 expression and suppresses PUB31 expression, resulting in the accumulation and stabilization of SPR1 protein, and further promoting hypocotyl cell elongation by altering cortical microtubule organization during Arabidopsis thermomorphogenesis.

Precise Regulation of the TAA1/TAR-YUCCA Auxin Biosynthesis Pathway in Plants

The indole-3-pyruvic acid (IPA) pathway is the main auxin biosynthesis pathway in the plant kingdom. Local control of auxin biosynthesis through this pathway regulates plant growth and development and the responses to biotic and abiotic stresses. During the past decades, genetic, physiological, biochemical, and molecular studies have greatly advanced our understanding of tryptophan-dependent auxin biosynthesis. The IPA pathway includes two steps: Trp is converted to IPA by TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS/TRYPTOPHAN AMINOTRANSFERASE RELATED PROTEINs (TAA1/TARs), and then IPA is converted to IAA by the flavin monooxygenases (YUCCAs). The IPA pathway is regulated at multiple levels, including transcriptional and post-transcriptional regulation, protein modification, and feedback regulation, resulting in changes in gene transcription, enzyme activity and protein localization. Ongoing research indicates that tissue-specific DNA methylation and miRNA-directed regulation of transcription factors may also play key roles in the precise regulation of IPA-dependent auxin biosynthesis in plants. This review will mainly summarize the regulatory mechanisms of the IPA pathway and address the many unresolved questions regarding this auxin biosynthesis pathway in plants.

The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis

Thermomorphogenesis is, among other traits, characterized by enhanced hypocotyl elongation due to the induction of auxin biosynthesis genes like YUCCA8 by transcription factors, most notably PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Efficient binding of PIF4 to the YUCCA8 locus under warmth depends on HISTONE DEACETYLASE 9 (HDA9) activity, which mediates histone H2A.Z depletion at the YUCCA8 locus. However, HDA9 lacks intrinsic DNA-binding capacity, and how HDA9 is recruited to YUCCA8, and possibly other PIF4-target sites, is currently not well understood. The Mediator complex functions as a bridge between transcription factors bound to specific promoter sequences and the basal transcription machinery containing RNA polymerase II. Mutants of Mediator component Mediator25 (MED25) exhibit reduced hypocotyl elongation and reduced expression of YUCCA8 at 27°C. In line with a proposed role for MED25 in thermomorphogenesis in Arabidopsis (Arabidopsis thaliana), we demonstrated an enhanced association of MED25 to the YUCCA8 locus under warmth and interaction of MED25 with both PIF4 and HDA9. Genetic analysis confirmed that MED25 and HDA9 operate in the same pathway. Intriguingly, we also showed that MED25 destabilizes HDA9 protein. Based on our findings, we propose that MED25 recruits HDA9 to the YUCCA8 locus by binding to both PIF4 and HDA9.

Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis

Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants often associate with specific chromatin states; yet, how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive. In Arabidopsis thaliana, temperature elevation-induced transcriptional activation at thermo-responsive genes entails the chromatin eviction of a histone variant H2A.Z by INO80, which is recruited to these loci via interacting with a key thermomorphogenesis regulator PIF4. Here, we show that both INO80 and the deposition chaperones of another histone variant H3.3 associate with ELF7, a critical component of the transcription elongator PAF1 complex. H3.3 promotes thermomorphogenesis and the high temperature-enhanced RNA Pol II transcription at PIF4 targets, and it is broadly required for the H2A.Z removal-induced gene activation. Reciprocally, INO80 and ELF7 regulate H3.3 deposition, and are necessary for the high temperature-induced H3.3 enrichment at PIF4 targets. Our findings demonstrate close coordination between H2A.Z eviction and H3.3 deposition in gene activation induced by high temperature, and pinpoint the importance of histone variants dynamics in transcriptional regulation.

OsWRKY28 positively regulates salinity tolerance by directly activating OsDREB1B expression in rice

OsWRKY28 confers salinity tolerance by directly binding to OsDREB1B promoter and increasing its transcriptional activity, and negatively regulates abscisic acid mediated seedling establishment in rice. WRKY transcription factors have been reported to play a vital role in plants growth, development, abiotic and biotic stress responses. In this study, we explored the functions of a transcription factor OsWRKY28 in rice. The transcript level of OsWRKY28 was strikingly increased under drought, chilling, salt and abscisic acid treatments. The OsWRKY28 overexpression lines showed enhanced salinity stress tolerance, whereas the oswrky28 mutants displayed salt sensitivity compared to wild-type plants. Under salt stress treatment, the expression levels of OsbZIP05, OsHKT1;1 and OsDREB1B were significantly lower yet the level of OsHKT2;1 was significantly higher in oswrky28 mutants than those in wide type plants. Our data of yeast one-hybrid assay and dual-luciferase assay supported that OsWRKY28 could directly bind to the promoter of OsDREB1B to enhance salinity tolerance in rice. In addition, OsWRKY28 overexpression lines displayed hyposensitivity and the oswrky28 mutants showed hypersensitivity compared to wild-type plants under exogenous abscisic acid treatment. Based on the results of yeast two-hybrid assay and GAL4-dependent chimeric transactivation assay, OsWRKY28 physically interacts with OsMPK11 and its transcriptional activity could be regulated by OsMPK11. Together, OsWRKY28 confers salinity tolerance through directly targeting OsDREB1B promoter and further activating its transcription in rice.

OsWRKY76 positively regulates drought stress via OsbHLH148-mediated jasmonate signaling in rice

Drought stress is a major environmental threat that limits plant growth and crop productivity. Therefore, it is necessary to uncover the molecular mechanisms behind drought tolerance in crops. Here, OsWRKY76 positively regulated drought stress in rice. OsWRKY76 expression was induced by PEG treatment, dehydration stress, and exogenous MeJA rather than by no treatment. Notably, OsWRKY76 knockout weakened drought tolerance at the seedling stage and decreased MeJA sensitivity. OsJAZ12 was significantly induced by drought stress, and its expression was significantly higher in OsWRKY76-knockout mutants than in wild-type ZH11 under drought stress. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsWRKY76 interacted with OsJAZ12. OsWRKY76 weakened the interaction between OsbHLH148 and OsJAZ12 in yeast cells. The OsJAZ12 protein repressed the transactivation activity of OsbHLH148, and this repression was partly restored by OsWRKY76 in rice protoplasts. Moreover, OsDREB1E expression was lower in OsWRKY76-knockout mutants than in wild-type ZH11 under drought stress, but it was upregulated under normal growth conditions. Yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays showed that OsWRKY76 and OsbHLH148 bound directly to the OsDREB1E promoter and activated OsDREB1E expression in response to drought stress. These results suggest that OsWRKY76 confers drought tolerance through OsbHLH148-mediated jasmonate signaling in rice, offering a new clue to uncover the mechanisms behind drought tolerance.

High temperature restricts cell division and leaf size by coordination of PIF4 and TCP4 transcription factors

High ambient temperature suppresses Arabidopsis (Arabidopsis thaliana) rosette leaf area and elongates the stem and petiole. While the mechanism underlying the temperature-induced elongation response has been extensively studied, the genetic basis of temperature regulation of leaf size is largely unknown. Here, we show that warm temperature inhibits cell proliferation in Arabidopsis leaves, resulting in fewer cells compared to the control condition. Cellular phenotyping and genetic and biochemical analyses established the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and TEOSINTE BRANCHED1/CYCLOIDEA/PCF4 (TCP4) transcription factors in the suppression of Arabidopsis leaf area under high temperature by a reduction in cell number. We show that temperature-mediated suppression of cell proliferation requires PIF4, which interacts with TCP4 and regulates the expression of the cell cycle inhibitor KIP-RELATED PROTEIN1 (KRP1) to control leaf size under high temperature. Warm temperature induces binding of both PIF4 and TCP4 to the KRP1 promoter. PIF4 binding to KRP1 under high temperature is TCP4 dependent as TCP4 regulates PIF4 transcript levels under high temperature. We propose a model where a warm temperature-mediated accumulation of PIF4 in leaf cells promotes its binding to the KRP1 promoter in a TCP4-dependent way to regulate cell production and leaf size. Our finding of high temperature-mediated transcriptional upregulation of KRP1 integrates a developmental signal with an environmental signal that converges on a basal cell regulatory process.

The RNA helicase UAP56 and the E3 ubiquitin ligase COP1 coordinately regulate alternative splicing to repress photomorphogenesis in Arabidopsis

Light is a key environmental signal that regulates plant growth and development. While posttranscriptional regulatory mechanisms of gene expression include alternative splicing (AS) of pre-messenger RNA (mRNA) in both plants and animals, how light signaling affects AS in plants is largely unknown. Here, we identify DExD/H RNA helicase U2AF65-associated protein (UAP56) as a negative regulator of photomorphogenesis in Arabidopsis thaliana. UAP56 is encoded by the homologs UAP56a and UAP56b. Knockdown of UAP56 led to enhanced photomorphogenic responses and diverse developmental defects during vegetative and reproductive growth. UAP56 physically interacts with the central light signaling repressor constitutive photomorphogenic 1 (COP1) and U2AF65. Global transcriptome analysis revealed that UAP56 and COP1 co-regulate the transcription of a subset of genes. Furthermore, deep RNA-sequencing analysis showed that UAP56 and COP1 control pre-mRNA AS in both overlapping and distinct manners. Ribonucleic acid immunoprecipitation assays showed that UAP56 and COP1 bind to common small nuclear RNAs and mRNAs of downstream targets. Our study reveals that both UAP56 and COP1 function as splicing factors that coordinately regulate AS during light-regulated plant growth and development.

The OsWRKY63-OsWRKY76-OsDREB1B module regulates chilling tolerance in rice

Rice (Oryza sativa) is sensitive to low temperatures, which affects the yield and quality of rice. Therefore, uncovering the molecular mechanisms behind chilling tolerance is a critical task for improving cold tolerance in rice cultivars. Here, we report that OsWRKY63, a WRKY transcription factor with an unknown function, negatively regulates chilling tolerance in rice. OsWRKY63-overexpressing rice lines are more sensitive to cold stress. Conversely, OsWRKY63-knockout mutants generated using a CRISPR/Cas9 genome editing approach exhibited increased chilling tolerance. OsWRKY63 was expressed in all rice tissues, and OsWRKY63 expression was induced under cold stress, dehydration stress, high salinity stress, and ABA treatment. OsWRKY63 localized in the nucleus plays a role as a transcription repressor and downregulates many cold stress-related genes and reactive oxygen species scavenging-related genes. Molecular, biochemical, and genetic assays showed that OsWRKY76 is a direct target gene of OsWRKY63 and that its expression is suppressed by OsWRKY63. OsWRKY76-knockout lines had dramatically decreased cold tolerance, and the cold-induced expression of five OsDREB1 genes was repressed. OsWRKY76 interacted with OsbHLH148, transactivating the expression of OsDREB1B to enhance chilling tolerance in rice. Thus, our study suggests that OsWRKY63 negatively regulates chilling tolerance through the OsWRKY63-OsWRKY76-OsDREB1B transcriptional regulatory cascade in rice.

Effects of light spectrum on the morphophysiology and gene expression of lateral branching in Pepino (Solanum muricatum)

In the present study, we determined the morphological and physiological indicators of Pepino to elucidate its lateral branching responses to different light qualities using a full-spectrum lamp (F) as the control and eight different light ratios using blue light (B) and red light (R). In addition, correlation analysis revealed that the gene expression patterns correlated with lateral branching under various light treatments. Compared with the F treatment, the R treatment increased the plant height and inhibited the elongation of lateral branches, in contrast with the B treatment. The number of lateral branches did not change significantly under different light quality treatments. Moreover, correlation analysis showed that the ratio of blue light was significantly positively correlated with the length of lateral branches and significantly negatively correlated with plant height, aboveground dry weight, and other indicators. We conducted transcriptome sequencing of the sites of lateral branching at three periods under different light quality treatments. The gene related to photodynamic response, cryptochrome (CRY), was the most highly expressed under B treatment, negatively regulated lateral branch length, and positively correlated with plant height. Branched 1, a lateral branch regulation gene, was upregulated under R treatment and inhibited branching. Overall, the red light facilitated internode elongation, leaf area expansion, plant dry weight increase, and inhibition of lateral branching. Soluble sugar content increased, and the lateral branches elongated under blue light. Different light qualities regulated lateral branching by mediating different pathways involving strigolactones and CRY. Our findings laid a foundation for further clarifying the response mechanism of Pepino seedlings to light and provided a theoretical reference for elucidating the regulation of different light qualities on the lateral branching of Pepino.

MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis

Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9, which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.

PIF4 Promotes Expression of HSFA2 to Enhance Basal Thermotolerance in Arabidopsis

Heat stress (HS) seriously restricts the growth and development of plants. When plants are exposed to extreme high temperature, the heat stress response (HSR) is activated to enable plants to survive. Sessile plants have evolved multiple strategies to sense and cope with HS. Previous studies have established that PHYTOCHROME INTERACTING FACTOR 4 (PIF4) acts as a key component in thermomorphogenesis; however, whether PIF4 regulates plant thermotolerance and the molecular mechanism linking this light transcriptional factor and HSR remain unclear. Here, we show that the overexpression of PIF4 indeed provides plants with a stronger basal thermotolerance and greatly improves the survival ability of Arabidopsis under severe HS. Via phylogenetic analysis, we identified two sets (six) of PIF4 homologs in wheat, and the expression patterns of the PIF4 homologs were conservatively induced by heat treatment in both wheat and Arabidopsis. Furthermore, the PIF4 protein was accumulated under heat stress and had an identical expression level. Additionally, we found that the core regulator of HSR, HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2), was highly responsive to light and heat. Followed by promoter analysis and ChIP-qPCR, we further found that PIF4 can bind directly to the G-box motifs of the HSFA2 promoter. Via effector–reporter assays, we found that PIF4 binding could activate HSFA2 gene expression, thereby resulting in the activation of other HS-inducible genes, such as heat shock proteins. Finally, the overexpression of PIF4 led to a stronger basal thermotolerance under non-heat-treatment conditions, thereby resulting in an enhanced tolerance to severe heat stress. Taken together, our findings propose that PIF4 is linked to heat stress signaling by directly binding to the HSFA2 promoter and triggering the HSR at normal temperature conditions to promote the basal thermotolerance. These functions of PIF4 provide a candidate direction for breeding heat-resistant crop cultivars.

Epigenetic regulation of thermomorphogenesis and heat stress tolerance

Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.

How plants coordinate their development in response to light and temperature signals

Light and temperature change constantly under natural conditions and profoundly affect plant growth and development. Light and warmer temperatures promote flowering, higher light intensity inhibits hypocotyl and petiole elongation, and warmer temperatures promote hypocotyl and petiole elongation. Moreover, exogenous light and temperature signals must be integrated with endogenous signals to fine-tune phytohormone metabolism and plant morphology. Plants perceive and respond to light and ambient temperature using common sets of factors, such as photoreceptors and multiple light signal transduction components. These highly structured signaling networks are critical for plant survival and adaptation. This review discusses how plants respond to variable light and temperature conditions using common elements to coordinate their development. Future directions for research on light and temperature signaling pathways are also discussed.

Epigenetic regulation of thermomorphogenesis in Arabidopsis thaliana

Temperature is a key factor in determining plant growth and development, geographical distribution, and seasonal behavior. Plants accurately sense subtle changes in ambient temperature and alter their growth and development accordingly to improve their chances of survival and successful propagation. Thermomorphogenesis encompasses a variety of morphological changes that help plants acclimate to warm environmental temperatures. Revealing the molecular mechanism of thermomorphogenesis is important for breeding thermo-tolerant crops and ensuring food security under global climate change. Plant adaptation to elevated ambient temperature is regulated by multiple signaling pathways and epigenetic mechanisms such as histone modifications, histone variants, and non-coding RNAs. In this review, we summarize recent advances in the mechanism of epigenetic regulation during thermomorphogenesis with a focus on the model plant Arabidopsis thaliana and briefly discuss future prospects for this field.

Role of sugar and auxin crosstalk in plant growth and development

Under the natural environment, nutrient signals interact with phytohormones to coordinate and reprogram plant growth and survival. Sugars are important molecules that control almost all morphological and physiological processes in plants, ranging from seed germination to senescence. In addition to their functions as energy resources, osmoregulation, storage molecules, and structural components, sugars function as signaling molecules and interact with various plant signaling pathways, such as hormones, stress, and light to modulate growth and development according to fluctuating environmental conditions. Auxin, being an important phytohormone, is associated with almost all stages of the plant's life cycle and also plays a vital role in response to the dynamic environment for better growth and survival. In the previous years, substantial progress has been made that showed a range of common responses mediated by sugars and auxin signaling. This review discusses how sugar signaling affects auxin at various levels from its biosynthesis to perception and downstream gene activation. On the same note, the review also highlights the role of auxin signaling in fine-tuning sugar metabolism and carbon partitioning. Furthermore, we discussed the crosstalk between the two signaling machineries in the regulation of various biological processes, such as gene expression, cell cycle, development, root system architecture, and shoot growth. In conclusion, the review emphasized the role of sugar and auxin crosstalk in the regulation of several agriculturally important traits. Thus, engineering of sugar and auxin signaling pathways could potentially provide new avenues to manipulate for agricultural purposes.

PIF4: Integrator of light and temperature cues in plant growth

Plants are sessile and lack behavioural responses to avoid extreme environmental changes linked to annual seasons. For survival, they have evolved elaborate sensory systems coordinating their architecture and physiology with fluctuating diurnal and seasonal temperatures. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) was initially identified as a key component of the Arabidopsis thaliana phytochrome signalling pathway. It was then identified as playing a central role in promoting plant hypocotyl growth via the activation of auxin synthesis and signalling-related genes. Recent studies expanded its known regulatory functions to thermomorphogenesis and defined PIF4 as a central molecular hub for the integration of environmental light and temperature cues. The present review comprehensively summarizes recent progress in our understanding of PIF4 function in Arabidopsis thaliana, including PIF4-mediated photomorphogenesis and thermomorphogenesis, and the contribution of PIF4 to plant growth via the integration of environmental light and temperature cues. Remaining questions and possible directions for future research on PIF4 are also discussed.

The Epigenetic Mechanisms Underlying Thermomorphogenesis and Heat Stress Responses in Arabidopsis

Integration of temperature cues is crucial for plant survival and adaptation. Global warming is a prevalent issue, especially in modern agriculture, since the global rise in average temperature is expected to impact crop productivity worldwide. Hence, better understanding of the mechanisms by which plants respond to warmer temperatures is very important. This review focuses on the epigenetic mechanisms implicated in plant responses to high temperature and distinguishes the different epigenetic events that occur at warmer average temperatures, leading to thermomorphogenic responses, or subjected to extreme warm temperatures, leading to heat stress.

A genetic approach reveals different modes of action of prefoldins

The prefoldin complex (PFDc) was identified in humans as a co-chaperone of the cytosolic chaperonin T-COMPLEX PROTEIN RING COMPLEX (TRiC)/CHAPERONIN CONTAINING TCP-1 (CCT). PFDc is conserved in eukaryotes and is composed of subunits PFD1-6, and PFDc-TRiC/CCT folds actin and tubulins. PFDs also participate in a wide range of cellular processes, both in the cytoplasm and in the nucleus, and their malfunction causes developmental alterations and disease in animals and altered growth and environmental responses in yeast and plants. Genetic analyses in yeast indicate that not all of their functions require the canonical complex. The lack of systematic genetic analyses in plants and animals, however, makes it difficult to discern whether PFDs participate in a process as the canonical complex or in alternative configurations, which is necessary to understand their mode of action. To tackle this question, and on the premise that the canonical complex cannot be formed if one subunit is missing, we generated an Arabidopsis (Arabidopsis thaliana) mutant deficient in the six PFDs and compared various growth and environmental responses with those of the individual mutants. In this way, we demonstrate that the PFDc is required for seed germination, to delay flowering, or to respond to high salt stress or low temperature, whereas at least two PFDs redundantly attenuate the response to osmotic stress. A coexpression analysis of differentially expressed genes in the sextuple mutant identified several transcription factors, including ABA INSENSITIVE 5 (ABI5) and PHYTOCHROME-INTERACTING FACTOR 4, acting downstream of PFDs. Furthermore, the transcriptomic analysis allowed assigning additional roles for PFDs, for instance, in response to higher temperature.

SUMOylation of different targets fine-tunes phytochrome signaling

Plants monitor their surrounding ambient light environment by specialized photoreceptor proteins. Among them, phytochromes monitor red and far-red light. These molecules perceive photons, undergo a conformational change, and regulate diverse light signaling pathways, resulting in the mediation of key developmental and growth responses throughout the whole life of plants. Posttranslational modifications of the photoreceptors and their signaling partners may modify their function. For example, the regulatory role of phosphorylation has been investigated for decades by using different methodological approaches. In the past few years, a set of studies revealed that ubiquitin-like short protein molecules, called small ubiquitin-like modifiers (SUMOs) are attached reversibly to different members of phytochrome signaling pathways, including phytochrome B, the dominant receptor of red light signaling. Furthermore, SUMO attachment modifies the action of the target proteins, leading to altered light signaling and photomorphogenesis. This review summarizes recent results regarding SUMOylation of various target proteins, the regulation of their SUMOylation level, and the physiological consequences of SUMO attachment. Potential future research directions are also discussed.

Transcriptional memory and response to adverse temperatures in plants

Temperature is one of the major environmental signals controlling plant development, geographical distribution, and seasonal behavior. Plants perceive adverse temperatures, such as high, low, and freezing temperatures, as stressful signals that can cause physiological defects and even death. As sessile organisms, plants have evolved sophisticated mechanisms to adapt to recurring stressful environments through changing gene expression or transcriptional reprogramming. Transcriptional memory refers to the ability of primed plants to remember previously experienced stress and acquire enhanced tolerance to similar or different stresses. Epigenetic modifications mediate transcriptional memory and play a key role in adapting to adverse temperatures. Understanding the mechanisms of the formation, maintenance, and resetting of stress-induced transcriptional memory will not only enable us to understand why there is a trade-off between plant defense and growth, but also provide a theoretical basis for generating stress-tolerant crops optimized for future climate change. In this review, we summarize recent advances in dissecting the mechanisms of plant transcriptional memory in response to adverse temperatures, based mainly on studies of the model plant Arabidopsis thaliana. We also discuss remaining questions that are important for further understanding the mechanisms of transcriptional memory during the adverse temperature response.

PIF4 and PIF4-Interacting Proteins: At the Nexus of Plant Light, Temperature and Hormone Signal Integrations

Basic helix-loop-helix (bHLH) family transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is necessary for plant adaption to light or high ambient temperature. PIF4 directly associates with plenty of its target genes and modulates the global transcriptome to induce or reduce gene expression levels. However, PIF4 activity is tightly controlled by its interacting proteins. Until now, twenty-five individual proteins have been reported to physically interact with PIF4. These PIF4-interacting proteins act together with PIF4 and form a unique nexus for plant adaption to light or temperature change. In this review, we will discuss the different categories of PIF4-interacting proteins, including photoreceptors, circadian clock regulators, hormone signaling components, and transcription factors. These distinct PIF4-interacting proteins either integrate light and/or temperature cues with endogenous hormone signaling, or control PIF4 abundances and transcriptional activities. Taken together, PIF4 and PIF4-interacting proteins play major roles for exogenous and endogenous signal integrations, and therefore establish a robust network for plants to cope with their surrounding environmental alterations.

FHY3 interacts with phytochrome B and regulates seed dormancy and germination

Seed dormancy and germination are fundamental processes for plant propagation, both of which are tightly regulated by internal and external cues. Phytochrome B (phyB) is a major red/far-red-absorbing photoreceptor that senses light signals that modulate seed dormancy and germination. However, the components that directly transduce that signal downstream of phyB are mostly unknown. Here, we show that the transposase-derived transcription factor FAR-RED ELONGATED HYPOCOTYL3 (FHY3) inhibits seed dormancy and promotes phyB-mediated seed germination in Arabidopsis thaliana. FHY3 physically interacts with phyB in vitro and in vivo. RNA-sequencing and reverse transcription-quantitative polymerase chain reaction analyses showed that FHY3 regulates multiple downstream genes, including REVEILLE2 (RVE2), RVE7, and SPATULA (SPT). Yeast one-hybrid, electrophoresis mobility shift, and chromatin immunoprecipitation assays demonstrated that FHY3 directly binds these genes via a conserved FBS cis-element in their promoters. Furthermore, RVE2, RVE7, and GIBBERELLIN 3-OXIDASE 2 (GA3ox2) genetically act downstream of FHY3. Strikingly, light and phyB promote FHY3 protein accumulation. Our study reveals a transcriptional cascade consisting of phyB-FHY3-RVE2/RVE7/SPT-GA3ox2 that relays environmental light signals and thereby controls seed dormancy and germination.

SUMOylation: A critical transcription modulator in plant cells

Gene transcription is critical for various cellular processes and is precisely controlled at multiple levels, and posttranslational modification (PTM) is a fast and powerful way to regulate transcription factors (TFs). SUMOylation, which conjugates small ubiquitin-related modifier (SUMO) molecules to protein substrates, is a crucial PTM that modulates the activity, stability, subcellular localization, and partner interactions of TFs in plant cells. Here, we summarize the mechanisms of SUMOylation in the regulation of transcription in plant development and stress responses. We also discuss the crosstalk between SUMOylation and other PTMs, as well as the potential functions of SUMOylation in the regulation of transcription-associated complexes on plant chromatin. This summary and perspective will improve understanding of the molecular mechanism of PTMs in plant transcription regulation.

BBX11 promotes red light-mediated photomorphogenic development by modulating phyB-PIF4 signaling

phytochrome B (phyB) acts as the red light photoreceptor and negatively regulates the growth-promoting factor PHYTOCHROME INTERACTING 4 (PIF4) through a direct physical interaction, which in turn changes the expression of a large number of genes. phyB-PIF4 module regulates a variety of biological and developmental processes in plants. In this study, we demonstrate that B-BOX PROTEIN 11 (BBX11) physically interacts with both phyB and PIF4. BBX11 negatively regulates PIF4 accumulation as well as its biochemical activity, consequently leading to the repression of PIF4-controlled genes' expression and promotion of photomorphogenesis in the prolonged red light. This study reveals a regulatory mechanism that mediates red light signal transduction and sheds a light on phyB-PIF4 module in promoting red light-dependent photomorphognenesis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00037-2.

Histone methylation in epigenetic regulation and temperature responses

Methylation of histones on different lysine residues is dynamically added by distinct writer enzymes, interpreted by reader proteins, and removed by eraser enzymes. This epigenetic mark has widespread, dynamic roles in plant development and environmental responses. For example, histone methylation plays a key role in mediating plant responses to temperature, including alterations of flowering time. In this review, we summarize recent advances in understanding the mechanism by which histone methylation regulates these processes, and discuss the role of histone methylation in temperature responses, based on data from Arabidopsis thaliana.

Auxin-Environment Integration in Growth Responses to Forage for Resources

Plant fitness depends on the adequate morphological adjustment to the prevailing conditions of the environment. Therefore, plants sense environmental cues through their life cycle, including the presence of full darkness, light, or shade, the range of ambient temperatures, the direction of light and gravity vectors, and the presence of water and mineral nutrients (such as nitrate and phosphate) in the soil. The environmental information impinges on different aspects of the auxin system such as auxin synthesis, degradation, transport, perception, and downstream transcriptional regulation to modulate organ growth. Although a single environmental cue can affect several of these points, the relative impacts differ significantly among the various growth processes and cues. While stability in the generation of precise auxin gradients serves to guide the basic developmental pattern, dynamic changes in the auxin system fine-tune body shape to optimize the capture of environmental resources.

Genome-Wide Identification and Characterization of the CsFHY3/FAR1 Gene Family and Expression Analysis under Biotic and Abiotic Stresses in Tea Plants (Camellia sinensis)

The FHY3/FAR1 transcription factor family, derived from transposases, plays important roles in light signal transduction, and in the growth and development of plants. However, the homologous genes in tea plants have not been studied. In this study, 25 CsFHY3/FAR1 genes were identified in the tea plant genome through a genome-wide study, and were classified into five subgroups based on their phylogenic relationships. Their potential regulatory roles in light signal transduction and photomorphogenesis, plant growth and development, and hormone responses were verified by the existence of the corresponding cis-acting elements. The transcriptome data showed that these genes could respond to salt stress and shading treatment. An expression analysis revealed that, in different tissues, especially in leaves, CsFHY3/FAR1s were strongly expressed, and most of these genes were positively expressed under salt stress (NaCl), and negatively expressed under low temperature (4 °C) stress. In addition, a potential interaction network demonstrated that PHYA, PHYC, PHYE, LHY, FHL, HY5, and other FRSs were directly or indirectly associated with CsFHY3/FAR1 members. These results will provide the foundation for functional studies of the CsFHY3/FAR1 family, and will contribute to the breeding of tea varieties with high light efficiency and strong stress resistance.

Fight hard or die trying: when plants face pathogens under heat stress

In their natural environment, plants are exposed to biotic or abiotic stresses that occur sequentially or simultaneously. Plant responses to these stresses have been studied widely and have been well characterised in simplified systems involving single plant species facing individual stress. Temperature elevation is a major abiotic driver of climate change and scenarios have predicted an increase in the number and severity of epidemics. In this context, here we review the available data on the effect of heat stress on plant-pathogen interactions. Considering 45 studies performed on model or crop species, we discuss the possible implications of the optimum growth temperature of plant hosts and pathogens, mode of stress application and temperature variation on resistance modulations. Alarmingly, most identified resistances are altered under temperature elevation, regardless of the plant and pathogen species. Therefore, we have listed current knowledge on heat-dependent plant immune mechanisms and pathogen thermosensory processes, mainly studied in animals and human pathogens, that could help to understand the outcome of plant-pathogen interactions under elevated temperatures. Based on a general overview of the mechanisms involved in plant responses to pathogens, and integrating multiple interactions with the biotic environment, we provide recommendations to optimise plant disease resistance under heat stress and to identify thermotolerant resistance mechanisms.

Functional and transcriptomic analyses of the NF-Y family provide insights into the defense mechanisms of honeybees under adverse circumstances

As predominant pollinators, honeybees are important for crop production and terrestrial ecosystems. Recently, various environmental stresses have led to large declines in honeybee populations in many regions. The ability of honeybees to respond to these stresses is critical for their survival. However, the details of the stress defense mechanisms of honeybees have remained elusive. Here, we found that the Nuclear Factor Y (NF-Y) family (containing NF-YA, NF-YB, and NF-YC) is a novel stress mediator family that regulates honeybee environmental stress resistance. NF-YA localized in the nucleus, NF-YB accumulated in the cytoplasm, and NF-YC presented in both the nucleus and cytoplasm. NF-YC interacted with NF-YA and NF-YB in vitro and in vivo, and the nuclear import of NF-YB relied on its interaction with NF-YC. We further found that the expression of NF-Y was induced under multiple stress conditions. In addition, NF-Y regulated many stress responses and antioxidant genes at the transcriptome-wide level, and knockdown of NF-Y repressed the expression of stress-inducible genes, particularly LOC108003540 and LOC107994062, under adverse circumstances. Silencing NF-Y lowered honeybee stress resistance by reducing total antioxidant capacity and enhancing oxidative impairment. Collectively, these results indicate that NF-Y plays important roles in stress responses. Our study sheds light on the underlying defense mechanisms of honeybees under environmental stress.

Transcriptomic and metabolomic landscape of the molecular effects of glyphosate commercial formulation on Apis mellifera ligustica and Apis cerana cerana

Understanding the causes of the decline in bee population has attracted intensive attention worldwide. The indiscriminate use of agrochemicals is a persistent problem due to their physiological and behavioural damage to bees. Glyphosate and its commercial formulation stand out due to their wide use in agricultural areas and non-crop areas, such as parks, railroads, roadsides, industrial sites, and recreational and residential areas, but the mode of action of glyphosate on bees at the molecular level remains largely unelucidated. Here, we found that the numbers of differentially expressed genes and metabolites under glyphosate commercial formulation (GCF) stress were significantly higher in Apis cerana cerana than in Apis mellifera ligustica. Despite these differences, the number of differentially expressed transcripts increased following an increase in the GCF treatment time in both A. cerana cerana and A. mellifera ligustica. GCF exerted adverse impacts on the immune system, digestive system, nervous system, amino acid metabolism, carbohydrate metabolism, growth and development of both bee species by influencing their key genes and metabolites to some extent. The expression of many genes involved in immunity, agrochemical detoxification and resistance, such as antimicrobial peptides, cuticle proteins and cytochrome P450 families, was upregulated by GCF in both bee species. Collectively, our results indicate that both A. cerana cerana and A. mellifera ligustica strive to mitigate the pernicious effects caused by GCF by regulating detoxification and immune systems. Moreover, A. cerana cerana might be better able to withstand the toxic effects of GCF with lower fitness costs than A. mellifera ligustica. Our work will contribute to elucidating the deleterious physiological and behavioural impacts of GCF on bees.

Regional response of grassland productivity to changing environment conditions influenced by limiting factors

Regional differences and regulatory mechanisms of vegetation productivity response to changing environmental conditions constitute a core issue in macroecological researches. To verify the main limiting factors of different macrosystems [temperature-limited Tibetan Plateau (TP), precipitation-limited Mongolian Plateau (MP), and nutrient-limited Loess Plateau (LP)], we conducted a comparative survey of the east-west grassland transects on the three plateaus and explored the factors limiting regional productivity and their underlying mechanisms. The results showed that aboveground net primary productivity (ANPP) of LP (109.10 ± 16.76 g m-2 yr-1) was significantly higher than that of MP (66.71 ± 11.11 g m-2 yr-1) and TP (57.02 ± 10.59 g m-2 yr-1). The response rate of ANPP with environmental changes was different among different plateaus, being closely related to the main limiting factors. On MP, this was precipitation, on LP it was temperature and nutrients, and on TP, it was non-specific, reflecting restriction by the extremely low temperature. After autocorrelation screening of environmental factors, different regions exhibited different productivity response mechanisms. MP was mainly influenced by temperature and precipitation, LP was influenced by temperature and nutrient, and TP was influenced by nutrient, reflecting the modifying effect of the main limiting factors. The effect of each regional environment on ANPP was 72.56% on average and only 27.18% after simple regional integration. The regional model could optimize the simulation error of the integrated model, and the relative deviations in MP, LP, and TP were reduced by 31.76%, 17.22%, and 2.23%, respectively. These findings indicate that the grasslands on the three plateaus may have different or even the opposite mechanisms to control productivity.

SEUSS integrates transcriptional and epigenetic control of root stem cell organizer specification

Proper regulation of homeotic gene expression is critical for stem cell fate in both plants and animals. In Arabidopsis thaliana, the WUSCHEL (WUS)-RELATED HOMEOBOX 5 (WOX5) gene is specifically expressed in a group of root stem cell organizer cells called the quiescent center (QC) and plays a central role in QC specification. Here, we report that the SEUSS (SEU) protein, homologous to the animal LIM-domain binding (LDB) proteins, assembles a functional transcriptional complex that regulates WOX5 expression and QC specification. SEU is physically recruited to the WOX5 promoter by the master transcription factor SCARECROW. Subsequently, SEU physically recruits the SET domain methyltransferase SDG4 to the WOX5 promoter, thus activating WOX5 expression. Thus, analogous to its animal counterparts, SEU acts as a multi-adaptor protein that integrates the actions of genetic and epigenetic regulators into a concerted transcriptional program to control root stem cell organizer specification.

SIZ1-Mediated SUMO Modification of SEUSS Regulates Photomorphogenesis in Arabidopsis

Small ubiquitin-like modifier (SUMO) post-translational modification (SUMOylation) plays essential roles in regulating various biological processes; however, its function and regulation in the plant light signaling pathway are largely unknown. SEUSS (SEU) is a transcriptional co-regulator that integrates light and temperature signaling pathways, thereby regulating plant growth and development in Arabidopsis thaliana. Here, we show that SEU is a substrate of SUMO1, and that substitution of four conserved lysine residues disrupts the SUMOylation of SEU, impairs its function in photo- and thermomorphogenesis, and enhances its interaction with PHYTOCHROME-INTERACTING FACTOR 4 transcription factors. Furthermore, the SUMO E3 ligase SIZ1 interacts with SEU and regulates its SUMOylation. Moreover, SEU directly interacts with phytochrome B photoreceptors, and the SUMOylation and stability of SEU are activated by light. Our study reveals a novel post-translational modification mechanism of SEU in which light regulates plant growth and development through SUMOylation-mediated protein stability.

The impact of light and temperature on chromatin organization and plant adaptation

Light and temperature shape the developmental trajectory and morphology of plants. Changes in chromatin organization and nuclear architecture can modulate gene expression and lead to short- and long-term plant adaptation to the environment. Here, we review recent reports investigating how changes in chromatin composition, structure, and topology modulate gene expression in response to fluctuating light and temperature conditions resulting in developmental and physiological responses. Furthermore, the potential application of novel revolutionary techniques, such Hi-C, RNA fluorescence in situ hybridization (FISH) and padlock-FISH, to study the impact of environmental stimuli such as light and temperature on nuclear compartmentalization in plants is discussed.

Glycosyltransferase UGT76F1 is involved in the temperature-mediated petiole elongation and the BR-mediated hypocotyl growth in Arabidopsis

The signaling network formed by external environmental signals and endogenous hormone signals is an important basis for the adaptive growth of plants. We recently identified a UDP-glucosyltransferase gene, UGT76F1, which controls the glucosylation of auxin precursor IPyA and mediates light-temperature signaling to regulate auxin-dependent hypocotyl elongation in Arabidopsis. However, it is unclear whether UGT76F1 is involved in the adaptive growth of other tissues and whether it is related to the signaling of other hormones besides auxin. Here we investigated the petiole elongation of UGT76F1 overexpression lines and knockout mutant lines, and also studied the effects of UGT76F1 on BR signaling. Experimental results indicated that UGT76F1 is involved in the PIF4-mediated petiole growth under high temperature and that UGT76F1 is also related to the BR signaling in controlling hypocotyl growth. These results suggest that UGT76F1 may have a wider significance in the plant adaptations to surrounding environments.

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.

Regulation of PIF4-mediated thermosensory growth

Ambient temperature has profound impacts on almost every aspect of plant growth and development, including seed germination, stem and petiole elongation, leaf movement, stomata development, flowering, and pathogen defense. Although the signal transduction pathways underlying plant responses to extreme cold and heat temperatures have been well studied, our understanding, at the molecular level, of how plants adjust phenotypic plasticity in response to nonstressful ambient temperature is still rudimentary. This review summarizes studies related to PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), the cardinal regulator of thermoresponsive growth in the model dicotyledonous plant Arabidopsis thaliana, emphasizing recent progress in the light-quality- and photoperiod-dependent regulation of PIF4-mediated thermomorphogenesis.