The Arabidopsis B-BOX protein BBX25 interacts with HY5, negatively regulating BBX22 expression to suppress seedling photomorphogenesis

OsBBX14 promotes photomorphogenesis in rice by activating OsHY5L1 expression under blue light conditions

In rice, OsBBX14, a B-box (BBX) transcription factor, reportedly delays heading. Here, we revealed that OsBBX14 positively regulates rice photomorphogenesis. The OsBBX14-overexpressing (OsBBX14-OX) seedlings were hypersensitive to light, especially blue light, and exhibited dwarfism, while the OsBBX14 knock-out plants (osbbx14) were taller than wild-type plants under blue light. Histological analyses indicated that the observed dwarfism was mainly due to decreased cell length. Additionally, OsBBX14 abundance (mRNA and protein levels) was influenced by different light wavelengths in a time-dependent manner. The expression levels of HY5Ls (LONG HYPOCOTYL 5 LIKE) and ELIPs (EARLY LIGHT-INDUCIBLE PROTEIN) genes, whose Arabidopsis thaliana homologs function as positive regulators in the light signaling pathway, were significantly upregulated in OsBBX14-OX lines. In contrast, the expression of genes related to cell wall organization and dwarfism was downregulated in OsBBX14-OX lines. Chromatin immunoprecipitation (ChIP) assays confirmed that OsBBX14 binds to the T/G-box of HY5L1 (LONG HYPOCOTYL 5 LIKE 1) promoter. LUC complementation imaging (LCI) results suggested that OsBBX14 had physical interaction with OsCRY2 protein. Collectively, in response to blue light, OsBBX14 promotes photomorphogenesis, probably by directly or indirectly regulating the expression of HY5L1 or other genes related to cell wall organization and dwarfism.

The B-box zinc finger protein MdBBX20 integrates anthocyanin accumulation in response to ultraviolet radiation and low temperature

Ultraviolet-B (UV-B) radiation and low temperature promote the accumulation of anthocyanins, which give apple skins their red colour. Although many transcription regulators have been characterized in the UV-B and low-temperature pathways, their interregulation and synergistic effects are not well understood. Here, a B-box transcription factor gene, MdBBX20, was characterized in apple and identified to promote anthocyanin biosynthesis under UV-B conditions in field experiments and when overexpressed in transgenic apple calli. The transcript level of MdBBX20 was significantly induced by UV-B. Specific G-box elements in the promoters of target genes were identified as interaction sites for MdBBX20. Further experimental interrogation of the UV-B signalling pathways showed that MdBBX20 could interact with MdHY5 in vitro and in vivo and that this interaction was required to significantly enhance the promoter activity of MdMYB1. MdBBX20 also responded to low temperature (14°C) with the participation of MdbHLH3, which directly bound a low temperature-response cis elements in the MdBBX20 promoter. These findings demonstrate the molecular mechanism by which MdBBX20 integrates low-temperature- and UV-B-induced anthocyanin accumulation in apple skin.

B-Box Containing Proteins BBX30 and BBX31, Acting Downstream of HY5, Negatively Regulate Photomorphogenesis in Arabidopsis

Light-mediated seedling development is coordinately controlled by a variety of key regulators. Here, we identified two B-box (BBX)-containing proteins, BBX30 and BBX31, as repressors of photomorphogenesis. ELONGATED HYPOCOTYL5, a central regulator of light signaling, directly binds to the G-box cis-element present in the promoters of BBX30 and BBX31 and negatively controls their transcription levels in the light. Seedlings with mutations in BBX30 or BBX31 are hypersensitive to light, whereas the overexpression of BBX30 or BBX31 leads to hypo-photomorphogenic growth in the light. Furthermore, transgenic and phenotypic analysis revealed that the B-box domain of BBX30 or BBX31 is essential for their respective functioning in the regulation of photomorphogenic development in plants. In conclusion, BBX30 and BBX31 act as key negative regulators of light signaling, and their transcription is repressed by ELONGATED HYPOCOTYL5 through directly associating with their promoters.

The B-Box-Containing MicroProtein miP1a/BBX31 Regulates Photomorphogenesis and UV-B Protection

The bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) represents a major hub in the light-signaling cascade both under visible and UV-B light. The mode of transcriptional regulation of HY5, especially under UV-B light, is not well characterized. B-BOX (BBX) transcription factors regulate HY5 transcription and also posttranscriptionally modulate HY5 to control photomorphogenesis under white light. Here, we identify BBX31 as a key signaling intermediate in visible and UV-B light signal transduction in Arabidopsis (Arabidopsis thaliana). BBX31 expression is induced by UV-B radiation in a fluence-dependent manner. HY5 directly binds to the promoter of BBX31 and regulates its transcript levels. Loss- and gain-of-function mutants of BBX31 indicate that it acts as a negative regulator of photomorphogenesis under white light but is a positive regulator of UV-B signaling. Genetic interaction studies suggest that BBX31 regulates photomorphogenesis independent of HY5 We found no evidence for a direct BBX31-HY5 interaction, and they primarily regulate different sets of genes in white light. Under high doses of UV-B radiation, BBX31 promotes the accumulation of UV-protective flavonoids and phenolic compounds. It enhances tolerance to UV-B radiation by regulating genes involved in photoprotection and DNA repair in a HY5-dependent manner. Under UV-B radiation, overexpression of BBX31 enhances HY5 transcriptional levels in a UV RESISTANCE LOCUS8-dependent manner, suggesting that BBX31 might regulate HY5 transcription.

The B-box bridge between light and hormones in plants

Plant development is meticulously modulated by interactions between the surrounding environment and the endogenous phytohormones. Light, as an external signal coordinates with the extensive networks of hormones inside the plant to execute its effects on growth and development. Several proteins in plants have been identified for their crucial roles in mediating light regulated development. Among these are the B-box (BBX) family of transcription factors characterized by the presence of zinc-finger B-box domain in their N-terminal region. In Arabidopsis there are 32 BBX proteins that are divided into five structural groups on the basis of the domains present. Several BBX proteins play important roles in seedling photomorphogenesis, neighbourhood detection and photoperiodic regulation of flowering. There is increasing evidence that besides light signaling BBX proteins also play integral roles in several hormone signaling pathways in plants. Here we attempt to comprehensively integrate the roles of multiple BBX proteins in various light and hormone signaling pathways. We further discuss the role of the BBX proteins in mediating crosstalk between the two signaling pathways to harmonize plant growth and development. Finally, we try to analyse the conservation of BBX genes across species and discuss the role of BBX proteins in regulating economically important traits in crop plants.

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.

A Rice B-Box Protein, OsBBX14, Finely Regulates Anthocyanin Biosynthesis in Rice

Anthocyanins are responsible pigments for giving attractive colors of plant organs and nutraceutical benefits of grains. Anthocyanin biosynthesis is known to be regulated by transcription factors and other regulatory proteins. In rice (Oryza sativa), the R2R3 MYB transcription factor (TF) OsC1 and a bHLH TF, OsB2, were previously reported to control anthocyanin biosynthesis in vegetative tissues and seeds, respectively; however, the regulatory mechanisms of the anthocyanin biosynthesis by TFs remain largely unknown. In this study, we identified OsBBX14, a homolog of Arabidopsis thaliana B-box domain protein 22 (AtBBX22), and investigated its function. The transcript level of OsBBX14 was high in pigmented rice seeds and gradually increased as the seeds matured. The ectopic expression of OsBBX14 in Arabidopsis resulted in a dramatic increase in anthocyanin accumulation in its seedlings. Using a steroid receptor-based inducible activation system, OsBBX14 and OsHY5 were found to directly activate OsC1 or OsB2 in an independent or collaborative manner. Yeast two hybrid revealed that the second B-box domain of OsBBX14 physically interacts with the bZIP domain of OsHY5. These results suggest that the anthocyanin biosynthesis in rice is induced and finely tuned by OsBBX14 in collaboration with OsHY5.

Unraveling the induction of phytoene synthase 2 expression by salt stress and abscisic acid in Daucus carota

Phytoene synthase (PSY) is the first committed enzyme of the carotenoid biosynthesis pathway and the most important point of regulation. Carotenoids are precursors of abscisic acid (ABA), which mediates abiotic stress tolerance responses in plants. ABA activates the synthesis of its own precursors through induction of PSY expression. Carrot, a species that accumulates very high amounts of carotenoids in its reserve root, has two PSY paralog genes that are expressed differentially in the root. Here, we determined that DcPSY2 expression is induced by salt stress and ABA. A DcPSY2 promoter fragment was obtained and characterized. Bioinformatic analysis showed the presence of three ABA responsive elements (ABREs). Through overexpressing pPSY2:GFP in Nicotiana tabacum we determined that all three ABREs are necessary for the ABA response. In the carrot transcriptome, we identified three ABRE binding protein (DcAREB) transcription factor candidates that localized in the nucleus, but only one, DcAREB3, was induced under ABA treatment in carrot roots. We found that AREB transcription factors bind to the carrot DcPSY2 promoter and transactivate the expression of reporter genes. We conclude that DcPSY2 is involved in ABA-mediated salt stress tolerance in carrot through the binding of AREB transcription factors to its promoter.

Two B-Box Proteins Regulate Photomorphogenesis by Oppositely Modulating HY5 through their Diverse C-Terminal Domains

The Arabidopsis (Arabidopsis thaliana) BBX family comprises several positive and negative regulators of photomorphogenesis. BBX24, a member of BBX structural group IV, acts as a negative regulator of photomorphogenesis, whereas another member from the same group, BBX21, is a positive regulator. The molecular basis for the functional diversity shown by these related BBX family members is unknown. Using domain-swap lines, we show that the C-terminal regions of BBX24 and BBX21 specify their function. Because both BBX21 and BBX24 work in close association with HY5, we hypothesized that these proteins differentially regulate the levels or activity of HY5 to fulfill their opposite roles. We show that BBX21 can regulate HY5 post-transcriptionally and the two proteins can coordinate to promote photomorphogenesis. By contrast, BBX24 interferes with the binding of HY5 to the promoter of an anthocyanin biosynthetic gene, possibly by heterodimerizing with HY5 and preventing it from binding DNA. Our finding that both BBX21 and BBX24 regulate HY5 activity post-transcriptionally, in opposite ways, suggests that closely related B-box proteins execute contrasting functions through differential regulation of HY5.

The wheat TabZIP2 transcription factor is activated by the nutrient starvation-responsive SnRK3/CIPK protein kinase

The understanding of roles of bZIP factors in biological processes during plant development and under abiotic stresses requires the detailed mechanistic knowledge of behaviour of TFs. Basic leucine zipper (bZIP) transcription factors (TFs) play key roles in the regulation of grain development and plant responses to abiotic stresses. We investigated the role and molecular mechanisms of function of the TabZIP2 gene isolated from drought-stressed wheat plants. Molecular characterisation of TabZIP2 and derived protein included analyses of gene expression and its target promoter, and the influence of interacting partners on the target promoter activation. Two interacting partners of TabZIP2, the 14-3-3 protein, TaWIN1 and the bZIP transcription factor TaABI5L, were identified in a Y2H screen. We established that under elevated ABA levels the activity of TabZIP2 was negatively regulated by the TaWIN1 protein and positively regulated by the SnRK3/CIPK protein kinase WPK4, reported previously to be responsive to nutrient starvation. The physical interaction between the TaWIN1 and the WPK4 was detected. We also compared the influence of homo- and hetero-dimerisation of TabZIP2 and TaABI5L on DNA binding. TabZIP2 gene functional analyses were performed using drought-inducible overexpression of TabZIP2 in transgenic wheat. Transgenic plants grown under moderate drought during flowering, were smaller than control plants, and had fewer spikes and seeds per plant. However, a single seed weight was increased compared to single seed weights of control plants in three of four evaluated transgenic lines. The observed phenotypes of transgenic plants and the regulation of TabZIP2 activity by nutrient starvation-responsive WPK4, suggest that the TabZIP2 could be the part of a signalling pathway, which controls the rearrangement of carbohydrate and nutrient flows in plant organs in response to drought.

The B-Box Domain Protein BBX21 Promotes Photomorphogenesis

B-box-containing (BBX) proteins play critical roles in a variety of cellular and developmental processes in plants. BBX21 (also known as SALT TOLERANCE HOMOLOG2), which contains two B-box domains in tandem at the N terminus, has been previously demonstrated as a key component involved in the COP1-HY5 signaling hub. However, the exact molecular and physiological roles of B-box domains in BBX21 are largely unclear. Here, we found that structurally disruption of the second B-box domain, but not the first one, in BBX21 completely abolishes its biological and physiological activity in conferring hyperphotomorphogenetic phenotype in Arabidopsis (Arabidopsis thaliana). Intact B-box domains in BBX21 are not required for interaction with COP1 and its degradation by COP1 via the 26S proteasome system. However, disruption of the second B-box of BBX21 nearly impairs its ability for binding of T/G-box within the HY5 promoter both in vitro and in vivo, as well as controlling HY5 and HY5-regulated gene expression in Arabidopsis seedlings. Taken together, this study provides a mechanistic framework in which BBX21 directly binds to the T/G-box present in the HY5 promoter possibly through its second B-box domain, which in turn controls HY5 and HY5-regulated gene expression to promote photomorphogenesis.

The Elongator complex regulates hypocotyl growth in darkness and during photomorphogenesis

The Elongator complex (hereafter Elongator) promotes RNA polymerase II-mediated transcript elongation through epigenetic activities such as histone acetylation. Elongator regulates growth, development, immune response and sensitivity to drought and abscisic acid. We demonstrate that elo mutants exhibit defective hypocotyl elongation but have a normal apical hook in darkness and are hyposensitive to light during photomorphogenesis. These elo phenotypes are supported by transcriptome changes, including downregulation of circadian clock components, positive regulators of skoto- or photomorphogenesis, hormonal pathways and cell wall biogenesis-related factors. The downregulated genes LHY, HFR1 and HYH are selectively targeted by Elongator for histone H3K14 acetylation in darkness. The role of Elongator in early seedling development in darkness and light is supported by hypocotyl phenotypes of mutants defective in components of the gene network regulated by Elongator, and by double mutants between elo and mutants in light or darkness signaling components. A model is proposed in which Elongator represses the plant immune response and promotes hypocotyl elongation and photomorphogenesis via transcriptional control of positive photomorphogenesis regulators and a growth-regulatory network that converges on genes involved in cell wall biogenesis and hormone signaling.This article has an associated First Person interview with the first author of the paper.

Opposite roles of group IV BBX proteins: Exploring missing links between structural and functional diversity

BBX proteins are a family of zinc finger transcription factors that are versatile regulators of plant development. The 32 BBX proteins in Arabidopsis are subdivided into five structural groups based on their domain structure. Members of group IV play important and diverse roles in light-regulated development. The N-terminal B-box domains mediate DNA binding and transcriptional regulation. The C-terminal region determines the functional diversity of the structurally similar group IV members as reported in our recent study investigating the basis of functional diversification between BBX21 and BBX24. We also found that multi-layered regulation of HY5 by the BBX proteins leads to a diverse repertoire of developmental effects. Here we provide a comprehensive structure-function analysis of the group IV BBX proteins.

BnaA.bZIP1 Negatively Regulates a Novel Small Peptide Gene, BnaC.SP6, Involved in Pollen Activity

Small peptides secreted to the extracellular matrix control many aspects of the plant's physiological activities which were identified in Arabidopsis thaliana, called ATSPs. Here, we isolated and characterized the small peptide gene Bna.SP6 from Brassica napus. The BnaC.SP6 promoter was cloned and identified. Promoter deletion analysis suggested that the -447 to -375 and -210 to -135 regions are crucial for the silique septum and pollen expression of BnaC.SP6, respectively. Furthermore, the minimal promoter region of p158 (-210 to -52) was sufficient for driving gene expression specifically in pollen and highly conserved in Brassica species. In addition, BnaA.bZIP1 was predominantly expressed in anthers where BnaC.SP6 was also expressed, and was localized to the nuclei. BnaA.bZIP1 possessed transcriptional activation activity in yeast and protoplast system. It could specifically bind to the C-box in p158 in vitro, and negatively regulate p158 activity in vivo. BnaA.bZIP1 functions as a transcriptional repressor of BnaC.SP6 in pollen activity. These results provide novel insight into the transcriptional regulation of BnaC.SP6 in pollen activity and the pollen/anther-specific promoter regions of BnaC.SP6 may have their potential agricultural application for new male sterility line generation.

Molecular mechanisms and ecological function of far-red light signalling

Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1^COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed.

COP1 regulates plant growth and development in response to light at the post-translational level

Photoreceptors perceive different wavelengths of light and transduce light signals downstream via a range of proteins. COP1, an E3 ubiquitin ligase, regulates light signaling by mediating the ubiquitination and subsequent proteasomal degradation of photoreceptors such as phytochromes and cryptochromes, as well as various development-related proteins including other light-responsive proteins. COP1 is itself regulated by direct interactions with several signaling molecules that modulate its activity. The control of photomorphogenesis by COP1 is also regulated by its localization to the cytoplasm in response to light. COP1 thus acts as a tightly regulated switch that determines whether development is skotomorphogenic or photomorphogenic. In this review, we discuss the effects of COP1 on the abundance and activity of various development-related proteins, including photoreceptors, and summarize the regulatory mechanisms that influence COP1 activity and stability in plants.

B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.)

BACKGROUND

The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in pear.

RESULTS

In the present study, a total of 25 BBX genes were identified in pear (Pyrus bretschneideri Rehd.). Subsequently, phylogenetic relationship, gene structure, gene duplication, transcriptome data and qRT-PCR were conducted on these BBX gene members. The transcript analysis revealed that twelve PbBBX genes (48%) were specifically expressed in pear pollen tubes. Furthermore, qRT-PCR analysis indicated that both PbBBX4 and PbBBX13 have potential role in pear fruit development, while PbBBX5 should be involved in the senescence of pear pollen tube.

CONCLUSIONS

This study provided a genome-wide survey of BBX gene family in pear, and highlighted its roles in both pear fruits and pollen tubes. The results will be useful in improving our understanding of the complexity of BBX gene family and functional characteristics of its members in future study.

The G-Protein β Subunit AGB1 Promotes Hypocotyl Elongation through Inhibiting Transcription Activation Function of BBX21 in Arabidopsis

Hypocotyl development in Arabidopsis thaliana is regulated by light and endogenous hormonal cues, making it an ideal model to study the interplay between light and endogenous growth regulators. BBX21, a B-box (BBX)-like zinc-finger transcription factor, integrates light and abscisic acid signals to regulate hypocotyl elongation in Arabidopsis. Heterotrimeric G-proteins are pivotal regulators of plant development. The short hypocotyl phenotype of the G-protein β-subunit (AGB1) mutant (agb1-2) has been previously identified, but the precise role of AGB1 in hypocotyl elongation remains enigmatic. Here, we show that AGB1 directly interacts with BBX21, and the short hypocotyl phenotype of agb1-2 is partially suppressed in agb1-2bbx21-1 double mutant. BBX21 functions in the downstream of AGB1 and overexpression of BBX21 in agb1-2 causes a more pronounced reduction in hypocotyl length, indicating that AGB1 plays an oppositional role in relation to BBX21 during hypocotyl development. Furthermore, we demonstrate that the C-terminal region of BBX21 is important for both its intracellular localization and its transcriptional activation activity that is inhibited by interaction with AGB1. ChIP assays showed that BBX21 specifically associates with its own promoter and with those of BBX22, HY5, and GA2ox1. which is not altered in agb1-2. These data suggest that the AGB1-BBX21 interaction only affects the transcriptional activation activity of BBX21 but has no effect on its DNA binding ability. Taken together, our data demonstrate that AGB1 positively promotes hypocotyl elongation through repressing BBX21 activity.

Light signaling differentially regulates the expression of group IV of the B-box zinc finger family

Light is an important external signal that affects plant growth and development, such as photomorphogenesis. Transcriptional regulation defines a central regulatory mechanism in photomorphogenesis. The B-box zinc finger family consists of 32 proteins in Arabidopsis thaliana. Previous studies show that group IV of the B-box family (BBX18 to BBX25) plays either positive or negative roles in regulating photomorphogenesis. We investigated the expression patterns of BBX18 to BBX25 and the results demonstrate that the transcriptional levels of these genes are differentially regulated by the light signaling pathway.

A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis

Light signaling plays an essential role in controlling higher plants' early developmental process termed as photomorphogenesis. Transcriptional regulation is a vital mechanism that is orchestrated by transcription factors and other regulatory proteins working in concert to finely tune gene expression. Although many transcription factors/regulators have been characterized in the light-signaling pathway, their interregulation remains largely unknown. Here, we show that PHYTOCHROME-INTERACTING FACTOR3 (PIF3) and PIF1 transcription factors directly bind to the regulatory regions of ELONGATED HYPOCOTYL5 (HY5) and a B-box gene BBX23 and activate their expression in Arabidopsis (Arabidopsis thaliana). We found that BBX23 and its close homolog gene BBX22 play a redundant role in regulating hypocotyl growth, and that plants overexpressing BBX23 display reduced hypocotyl elongation under red, far-red, and blue light conditions. Intriguingly, BBX23 transcription is inhibited by light, whereas its protein is degraded in darkness. Furthermore, we demonstrate that HY5 physically interacts with BBX23, and these two proteins coordinately regulate the expression of both light-induced and light-repressed genes. BBX23 is also recruited to the promoter sequences of the light-responsive genes in a partial HY5-dependent manner. Taken together, our study reveals that the transcriptional cascade consisting of PIF1/PIF3, HY5, and BBX23 controls photomorphogenesis, providing a transcriptional regulatory layer by which plants fine-tune their growth in response to changing light environment.

The evening complex coordinates environmental and endogenous signals in Arabidopsis

Plants maximize their fitness by adjusting their growth and development in response to signals such as light and temperature. The circadian clock provides a mechanism for plants to anticipate events such as sunrise and adjust their transcriptional programmes. However, the underlying mechanisms by which plants coordinate environmental signals with endogenous pathways are not fully understood. Using RNA-sequencing and chromatin immunoprecipitation sequencing experiments, we show that the evening complex (EC) of the circadian clock plays a major role in directly coordinating the expression of hundreds of key regulators of photosynthesis, the circadian clock, phytohormone signalling, growth and response to the environment. We find that the ability of the EC to bind targets genome-wide depends on temperature. In addition, co-occurrence of phytochrome B (phyB) at multiple sites where the EC is bound provides a mechanism for integrating environmental information. Hence, our results show that the EC plays a central role in coordinating endogenous and environmental signals in Arabidopsis.

Genome-wide survey of B-box proteins in potato (Solanum tuberosum)-Identification, characterization and expression patterns during diurnal cycle, etiolation and de-etiolation

Plant B-box domain proteins (BBX) mediate many light-influenced developmental processes including seedling photomorphogenesis, seed germination, shade avoidance and photoperiodic regulation of flowering. Despite the wide range of potential functions, the current knowledge regarding BBX proteins in major crop plants is scarce. In this study, we identify and characterize the StBBX gene family in potato, which is composed of 30 members, with regard to structural properties and expression profiles under diurnal cycle, etiolation and de-etiolations. Based on domain organization and phylogenetic relationships, StBBX genes have been classified into five groups. Using real-time quantitative PCR, we found that expression of most of them oscillates following a 24-h rhythm; however, large differences in expression profiles were observed between the genes regarding amplitude and position of the maximal and minimal expression levels in the day/night cycle. On the basis of the time-of-day/time-of-night, we distinguished three expression groups specifically expressed during the light and two during the dark phase. In addition, we showed that the expression of several StBBX genes is under the control of the circadian clock and that some others are specifically associated with the etiolation and de-etiolation conditions. Thus, we concluded that StBBX proteins are likely key players involved in the complex diurnal and circadian networks regulating plant development as a function of light conditions and day duration.

Solanum tuberosum ZPR1 encodes a light-regulated nuclear DNA-binding protein adjusting the circadian expression of StBBX24 to light cycle

ZPR1 proteins belong to the C4-type of zinc finger coordinators known in animal cells to interact with other proteins and participate in cell growth and proliferation. In contrast, the current knowledge regarding plant ZPR1 proteins is very scarce. Here, we identify a novel potato nuclear factor belonging to this family and named StZPR1. StZPR1 is specifically expressed in photosynthetic organs during the light period, and the ZPR1 protein is located in the nuclear chromatin fraction. From modelling and experimental analyses, we reveal the StZPR1 ability to bind the circadian DNA cis motif 'CAACAGCATC', named CIRC and present in the promoter of the clock-controlled double B-box StBBX24 gene, the expression of which peaks in the middle of the day. We found that transgenic lines silenced for StZPR1 expression still display a 24 h period for the oscillation of StBBX24 expression but delayed by 4 h towards the night. Importantly, other BBX genes exhibit altered circadian regulation in these lines. Our data demonstrate that StZPR1 allows fitting of the StBBX24 circadian rhythm to the light period and provide evidence that ZPR1 is a novel clock-associated protein in plants necessary for the accurate rhythmic expression of specific circadian-regulated genes.

Hormonal Regulation in Shade Avoidance

At high vegetation density, shade-intolerant plants sense a reduction in the red (660 nm) to far-red (730 nm) light ratio (R/FR) in addition to a general reduction in light intensity. These light signals trigger a spectrum of morphological changes manifested by growth of stem-like tissue (hypocotyl, petiole, etc.) instead of harvestable organs (leaves, fruits, seeds, etc.)-namely, shade avoidance syndrome (SAS). Common phenotypical changes related to SAS are changes in leaf hyponasty, an increase in hypocotyl and internode elongation and extended petioles. Prolonged shade exposure leads to early flowering, less branching, increased susceptibility to insect herbivory, and decreased seed yield. Thus, shade avoidance significantly impacts on agronomic traits. Many genetic and molecular studies have revealed that phytochromes, cryptochromes and UVR8 (UV-B photoreceptor protein) monitor the changes in light intensity under shade and regulate the stability or activity of phytochrome-interacting factors (PIFs). PIF-governed modulation of the expression of auxin biosynthesis, transporter and signaling genes is the major driver for shade-induced hypocotyl elongation. Besides auxin, gibberellins, brassinosteroids, and ethylene are also required for shade-induced hypocotyl or petiole elongation growth. In leaves, accumulated auxin stimulates cytokinin oxidase expression to break down cytokinins and inhibit leaf growth. In the young buds, shade light promotes the accumulation of abscisic acid to repress branching. Shade light also represses jasmonate- and salicylic acid-induced defense responses to balance resource allocation between growth and defense. Here we will summarize recent findings relating to such hormonal regulation in SAS in Arabidopsis thaliana, Brassica rapa, and certain crops.

The Multifaceted Roles of HY5 in Plant Growth and Development

ELONGATED HYPOCOTYL5 (HY5), a member of the bZIP transcription factor family, inhibits hypocotyl growth and lateral root development, and promotes pigment accumulation in a light-dependent manner in Arabidopsis. Recent research on its role in different processes such as hormone, nutrient, abiotic stress (abscisic acid, salt, cold), and reactive oxygen species signaling pathways clearly places HY5 at the center of a transcriptional network hub. HY5 regulates the transcription of a large number of genes by directly binding to cis-regulatory elements. Recently, HY5 has also been shown to activate its own expression under both visible and UV-B light. Moreover, HY5 acts as a signal that moves from shoot to root to promote nitrate uptake and root growth. Here, we review recent advances on HY5 research in diverse aspects of plant development and highlight still open questions that need to be addressed in the near future for a complete understanding of its function in plant signaling and beyond.

NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana

Recent reports suggest that NF-Y transcription factors are positive regulators of skotomorphogenesis in Arabidopsis thaliana. Three NF-YC genes (NF-YC3, NF-YC4, and NF-YC9) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leucine zipper (bZIP) transcription factors. This included ELONGATED HYPOCOTYL 5 (HY5), which has well-demonstrated roles in photomorphogenesis. Similar to hy5 mutants, we report that nf-yc3 nf-yc4 nf-yc9 triple mutants failed to inhibit hypocotyl elongation in all tested light wavelengths. Surprisingly, nf-yc3 nf-yc4 nf-yc9 hy5 mutants had synergistic defects in light perception, suggesting that NF-Ys represent a parallel light signaling pathway. As with other photomorphogenic transcription factors, nf-yc3 nf-yc4 nf-yc9 triple mutants also partially suppressed the short hypocotyl and dwarf rosette phenotypes of CONSTITUTIVE PHOTOMORPHOGENIC 1 (cop1) mutants. Thus, our data strongly suggest that NF-Y transcription factors have important roles as positive regulators of photomorphogenesis, and in conjunction with other recent reports, implies that the NF-Y are multifaceted regulators of early seedling development.

Light perception is critically important for the fitness of plants in both natural and agricultural settings. Plants not only use light for photosynthesis, but also as a cue for proper development. As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit. When blue and red wavelengths are the dominant sources of light, plants will undergo photomorphogenesis. Photomorphogenesis describes a number of developmental responses initiated by light in a seedling, and includes shortened stems and establishing the ability to photosynthesize. The genes regulating photomorphogenesis have been studied extensively, but a complete picture remains elusive. Here we describe the finding that NUCLEAR FACTOR-Y (NF-Y) genes are positive regulators of photomorphogenesis—i.e., in plants where NF-Y genes are mutated, they display some characteristics of dark grown plants, even though they are in the light. Our data suggests that the roles of NF-Y genes in light perception do not fit in easily with those of other described pathways. Thus, studying these genes promises to help develop a more complete picture of how light drives plant development.

SPA proteins: SPAnning the gap between visible light and gene expression

In this review we focus on the role of SPA proteins in light signalling and discuss different aspects, including molecular mechanisms, specificity, and evolution. The ability of plants to perceive and respond to their environment is key to their survival under ever-changing conditions. The abiotic factor light is of particular importance for plants. Light provides plants energy for carbon fixation through photosynthesis, but also is a source of information for the adaptation of growth and development to the environment. Cryptochromes and phytochromes are major photoreceptors involved in control of developmental decisions in response to light cues, including seed germination, seedling de-etiolation, and induction of flowering. The SPA protein family acts in complex with the E3 ubiquitin ligase COP1 to target positive regulators of light responses for degradation by the 26S proteasome to suppress photomorphogenic development in darkness. Light-activated cryptochromes and phytochromes both repress the function of COP1, allowing accumulation of positive photomorphogenic factors in light. In this review, we highlight the role of the SPA proteins in this process and discuss recent advances in understanding how SPAs link light-activation of photoreceptors and downstream signaling.

BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation

BBX21 (also known as SALT TOLERANCE HOMOLOG 2), a B-box (BBX)-containing protein, has been previously identified as a positive regulator of light signaling; however, the precise role of BBX21 in regulating seedling photomorphogenesis remains largely unclear. In this study, we report that CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) interacts with BBX21 in vivo and is able to ubiquitinate BBX21 in vitro. Thus, BBX21 is targeted for 26S proteasome-mediated degradation in dark-grown Arabidopsis seedlings in a COP1-dependent manner. Moreover, we show that BBX21 binds to the T/G-box in the ELONGATED HYPOCOTYL 5 (HY5) promoter and directly activates HY5 expression in the light. Transgenic seedlings overexpressing BBX21 exhibit dramatically shortened hypocotyls in the light, and this phenotype is dependent on a functional HY5. Taken together, our data suggest a molecular base underlying BBX21-mediated seedling photomorphogenesis, indicating that BBX21 is a pivotal component involved in the COP1-HY5 regulatory hub.

The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis

Plant growth is controlled by integration of hormonal and light-signaling pathways. BZS1 is a B-box zinc finger protein previously characterized as a negative regulator in the brassinosteroid (BR)-signaling pathway and a positive regulator in the light-signaling pathway. However, the mechanisms by which BZS1/BBX20 integrates light and hormonal pathways are not fully understood. Here, using a quantitative proteomic workflow, we identified several BZS1-associated proteins, including light-signaling components COP1 and HY5. Direct interactions of BZS1 with COP1 and HY5 were verified by yeast two-hybrid and co-immunoprecipitation assays. Overexpression of BZS1 causes a dwarf phenotype that is suppressed by the hy5 mutation, while overexpression of BZS1 fused with the SRDX transcription repressor domain (BZS1-SRDX) causes a long-hypocotyl phenotype similar to hy5, indicating that BZS1's function requires HY5. BZS1 positively regulates HY5 expression, whereas HY5 negatively regulates BZS1 protein level, forming a feedback loop that potentially contributes to signaling dynamics. In contrast to BR, strigolactone (SL) increases BZS1 level, whereas the SL responses of hypocotyl elongation, chlorophyll and HY5 accumulation are diminished in the BZS1-SRDX seedlings, indicating that BZS1 is involved in these SL responses. These results demonstrate that BZS1 interacts with HY5 and plays a central role in integrating light and multiple hormone signals for photomorphogenesis in Arabidopsis.

OsBBX14 delays heading date by repressing florigen gene expression under long and short-day conditions in rice

B-box (BBX) proteins are zinc finger proteins containing B-box domains, which have roles in Arabidopsis growth and development. However, little is known concerning rice BBXs. Herein, we identified a rice BBX protein, Oryza sativa BBX14 (OsBBX14). OsBBX14 is highly expressed in flag leaf blades. OsBBX14 expression shows a diurnal rhythm under photoperiodic conditions and subsequent continuous white light. OsBBX14 is located in the nucleus and has transcriptional activation potential. OsBBX14-overexpression (OsBBX14-OX) lines exhibited delayed heading date under long-day (LD) and short-day (SD) conditions, whereas RNAi lines of OsBBX14 lines had similar heading dates to the WT. The florigen genes, Hd3a and RFT1, were downregulated in the OsBBX14-OX lines under LD and SD conditions. Under LD conditions, Hd1 was expressed higher in the OsBBX14-OX lines than in the wild type (WT), and the rhythmic expression of circadian clock genes, OsLHY and OsPRR1, was changed in OsBBX14-OX lines. Thus, OsBBX14 acts as a floral repressor by promoting Hd1 expression under LD conditions, probably because of crosstalk with the circadian clock. Under SD conditions, Ehd1 expression was reduced in OsBBX14-OX lines, but Hd1 and circadian clock gene expressions were unaffected, indicating that OsBBX14 acts as a repressor of Ehd1. Our findings suggested that OsBBX14 regulates heading date differently under LD and SD conditions.

Regulatory modules controlling early shade avoidance response in maize seedlings

BACKGROUND

Optimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still lacking in monocot crops.

RESULTS

In this study, the genome-wide early responses in maize seedlings to the simulated shade (low red/far-red ratio) and also to far-red light treatment were transcriptionally profiled. The two processes were predominantly mediated by phytochrome B and phytochrome A, respectively. Clustering of differentially transcribed genes (DTGs) along with functional enrichment analysis identified important biological processes regulated in response to both treatments. Co-expression network analysis identified two transcription factor modules as potentially pivotal regulators of SAR and de-etiolation, respectively. A comprehensive cross-species comparison of orthologous DTG pairs between maize and Arabidopsis in SAR was also conducted, with emphasis on regulatory circuits controlling accelerated flowering and elongated growth, two physiological hallmarks of SAR. Moreover, it was found that the genome-wide distribution of DTGs in SAR and de-etiolation both biased toward the maize1 subgenome, and this was associated with differential retention of various cis-elements between the two subgenomes.

CONCLUSIONS

The results provide the first transcriptional picture for the early dynamics of maize phytochrome signaling. Candidate genes with regulatory functions involved in maize shade avoidance response have been identified, offering a starting point for further functional genomics investigation of maize adaptation to heavily shaded field conditions.

Regulatory modules controlling early shade avoidance response in maize seedlings

Background

Optimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still lacking in monocot crops.

Results

In this study, the genome-wide early responses in maize seedlings to the simulated shade (low red/far-red ratio) and also to far-red light treatment were transcriptionally profiled. The two processes were predominantly mediated by phytochrome B and phytochrome A, respectively. Clustering of differentially transcribed genes (DTGs) along with functional enrichment analysis identified important biological processes regulated in response to both treatments. Co-expression network analysis identified two transcription factor modules as potentially pivotal regulators of SAR and de-etiolation, respectively. A comprehensive cross-species comparison of orthologous DTG pairs between maize and Arabidopsis in SAR was also conducted, with emphasis on regulatory circuits controlling accelerated flowering and elongated growth, two physiological hallmarks of SAR. Moreover, it was found that the genome-wide distribution of DTGs in SAR and de-etiolation both biased toward the maize1 subgenome, and this was associated with differential retention of various cis-elements between the two subgenomes.

Conclusions

The results provide the first transcriptional picture for the early dynamics of maize phytochrome signaling. Candidate genes with regulatory functions involved in maize shade avoidance response have been identified, offering a starting point for further functional genomics investigation of maize adaptation to heavily shaded field conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2593-6) contains supplementary material, which is available to authorized users.

DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis

When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling.

The Myb-domain protein ULTRAPETALA1 INTERACTING FACTOR 1 controls floral meristem activities in Arabidopsis

Higher plants continuously and iteratively produce new above-ground organs in the form of leaves, stems and flowers. These organs arise from shoot apical meristems whose homeostasis depends on coordination between self-renewal of stem cells and their differentiation into organ founder cells. This coordination is stringently controlled by the central transcription factor WUSCHEL (WUS), which is both necessary and sufficient for stem cell specification in Arabidopsis thaliana ULTRAPETALA1 (ULT1) was previously identified as a plant-specific, negative regulator of WUS expression. However, molecular mechanisms underlying this regulation remain unknown. ULT1 protein contains a SAND putative DNA-binding domain and a B-box, previously proposed as a protein interaction domain in eukaryotes. Here, we characterise a novel partner of ULT1, named ULT1 INTERACTING FACTOR 1 (UIF1), which contains a Myb domain and an EAR motif. UIF1 and ULT1 function in the same pathway for regulation of organ number in the flower. Moreover, UIF1 displays DNA-binding activity and specifically binds to WUS regulatory elements. We thus provide genetic and molecular evidence that UIF1 and ULT1 work together in floral meristem homeostasis, probably by direct repression of WUS expression.

Comparative Analysis and Identification of miRNAs and Their Target Genes Responsive to Salt Stress in Diploid and Tetraploid Paulownia fortunei Seedlings

Salt stress is a global environmental problem that affects plant growth and development. Paulownia fortunei is an adaptable and fast-growing deciduous tree native to China that is environmentally and economically important. MicroRNAs (miRNAs) play important regulatory roles in growth, development, and stress responses in plants. MiRNAs that respond to biotic stresses have been identified; however, how miRNAs in P. fortunei respond to salt stress has not yet been reported. To identify salt-stress-responsive miRNAs and predict their target genes, four small RNA and four degradome libraries were constructed from NaCl-treated and NaCl-free leaves of P. fortunei seedlings. The results indicated that salt stress had different physiological effects on diploid and tetraploid P. fortunei. We detected 53 conserved miRNAs belonging to 17 miRNA families and 134 novel miRNAs in P. fortunei. Comparing their expression levels in diploid and tetraploid P. fortunei, we found 10 conserved and 10 novel miRNAs that were significantly differentially expressed under salt treatment, among them eight were identified as miRNAs probably associated with higher salt tolerance in tetraploid P. fortunei than in diploid P. fortunei. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to predict the functions of the target genes of the conserved and novel miRNAs. The expressions of 10 differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report on P. fortunei miRNAs and their target genes under salt stress. The results provided information at the physiological and molecular levels for further research into the response mechanisms of P. fortunei to salt stress.

Plant Responses to Vegetation Proximity: A Whole Life Avoiding Shade

In high density of vegetation, plants detect neighbors by perceiving changes in light quality through phytochrome photoreceptors. Close vegetation proximity might result in competition for resources, such as light. To face this challenge, plants have evolved two alternative strategies: to either tolerate or avoid shade. Shade-avoiding species generally adapt their development by inducing hypocotyl, stem, and petiole elongation, apical dominance and flowering, and decreasing leaf expansion and yield, a set of responses collectively known as the shade avoidance syndrome (SAS). The SAS responses have been mostly studied at the seedling stage, centered on the increase of hypocotyl elongation. After compiling the main findings about SAS responses in seedlings, this review is focused on the response to shade at adult stages of development, such as petioles of adult leaves, and the little information available on the SAS responses in reproductive tissues. We discuss these responses based on the knowledge about the molecular mechanisms and components with a role in regulating the SAS response of the hypocotyls of Arabidopsis thaliana. The transcriptional networks involved in this process, as well as the communication among the tissues that perceive the shade and the ones that respond to this stimulus will also be briefly commented.

Identification and functional characterization of the BBX24 promoter and gene from chrysanthemum in Arabidopsis

The B-box (BBX) family is a subgroup of zinc finger transcription factors that regulate flowering time, light-regulated morphogenesis, and abiotic stress in Arabidopsis. Overexpression of CmBBX24, a zinc finger transcription factor gene in chrysanthemum, results in abiotic stress tolerance. We have investigated and characterized the promoter of CmBBX24, isolating a 2.7-kb CmBBX24 promoter sequence and annotating a number of abiotic stress-related cis-regulatory elements, such as DRE, MYB, MYC, as well as cis-elements which respond to plant hormones, such as GARE, ABRE, and CARE. We also observed a number of cis-elements related to light, such as TBOX and GBOX, and some tissue-specific cis-elements, such as those for guard cells (TAAAG). Expression of the CmBBX24 promoter produced a clear response in leaves and a lower response in roots, based on β-glucuronidase histochemical staining and fluorometric analysis. The CmBBX24 promoter was induced by abiotic stresses (mannitol, cold temperature), hormones (gibberellic acid, abscisic acid), and different light treatments (white, blue, red); activation was measured by fluorometric analysis in the leaves and roots. The deletion of fragments from the 5'-end of the promoter led to different responses under various stress conditions. Some CmBBX24 promoter segments were found to be more important than others for regulating all stresses, while other segments were relatively more specific to stress type. D0-, D1-, D2-, D3-, and D4-proCmBBX24::CmBBX24 transgenic Arabidopsis lines developed for further study were found to be more tolerant to the low temperature and drought stresses than the controls. We therefore speculate that CmBBX24 is of prime importance in the regulation of abiotic stress in Arabidopsis and that the CmBBX24 promoter is inductive in abiotic stress conditions. Consequently, we suggest that CmBBX24 is a potential candidate for the use in breeding programs of important ornamental plants.

Plasticity to simulated shade is associated with altitude in structured populations of Arabidopsis thaliana

Plants compete for photosynthesis light and induce a shade avoidance syndrome (SAS) that confers an important advantage in asymmetric competition for light at high canopy densities. Shade plasticity was studied in a greenhouse experiment cultivating Arabidopsis thaliana plants from 15 populations spread across an altitudinal gradient in the northeast area of Spain that contain a high genetic variation into a reduced geographical range. Plants were exposed to sunlight or simulated shade to identify the range of shade plasticity. Fourteen vegetative, flowering and reproductive traits were measured throughout the life cycle. Shade plasticity in flowering time and dry mass was significantly associated with the altitude of population origin. Plants from coastal populations showed higher shade plasticity indexes than those from mountains. The altitudinal variation in flowering leaf plasticity adjusted negatively with average and minimum temperatures, whereas dry mass plasticity was better explained by negative regressions with the average, maximum and minimum temperatures, and by a positive regression with average precipitation of the population origin. The lack of an altitudinal gradient for the widest number of traits suggests that shade light could be a driver explaining the distribution pattern of individuals in smaller geographical scales than those explored here.

Transcriptional regulation of the paper mulberry under cold stress as revealed by a comprehensive analysis of transcription factors

BACKGROUND

Several studies have focused on cold tolerance in multiple regulated levels. However, a genome-scale molecular analysis of the regulated network under the control of transcription factors (TFs) is still lacking, especially for trees. To comprehensively identify the TFs that regulate cold stress response in the paper mulberry and understand their regulatory interactions, transcriptomic data was used to assess changes in gene expression induced by exposure to cold.

RESULTS

Results indicated that 794 TFs, belonging to 47 families and comprising more than 59% of the total TFs of this plant, were involved in the cold stress response. They were clustered into three groups, namely early, intermediate and late responsive groups which contained 95, 550 and 149 TFs, respectively. Among of these differentially expressed TFs, one bHLH, two ERFs and three CAMTAs were considered to be the key TFs functioning in the primary signal transduction. After that, at the intermediate stage of cold stress, there were mainly two biological processes that were regulated by TFs, namely cold stress resistance (including 5 bHLH, 14 ERFs, one HSF, 4 MYBs, 3 NACs, 11 WRKYs and so on) and growth and development of lateral organ or apical meristem (including ARR-B, B3, 5 bHLHs, 2 C2H2, 4 CO-like, 2 ERF, 3 HD-ZIP, 3 YABBYs, G2-like, GATA, GRAS and TCP). In late responsive group, 3 ARR-B, C3H, 6 CO-like, 2 G2-like, 2 HSFs, 2 NACs and TCP. Most of them presented the up-regulated expression at 12 or 24 hours after cold stress implied their important roles for the new growth homeostasis under cold stress.

CONCLUSIONS

Our study identified the key TFs that function in the regulatory cascades mediating the activation of downstream genes during cold tress tolerance in the paper mulberry. Based on the analysis, we found that the AP2/ERF, bHLH, MYB, NAC and WRKY families might play the central and significant roles during cold stress response in the paper mulberry just as in other species. Meanwhile, many other TF families previously reported as involving in regulation of growth and development, including ARF, DBB, G2-like, GRF, GRAS, LBD, WOX and YAABY exhibited their important potential function in growth regulation under cold stress.

A novel wheat bZIP transcription factor, TabZIP60, confers multiple abiotic stress tolerances in transgenic Arabidopsis

The basic region/leucine zipper (bZIP) transcription factors (TFs) play vital roles in the response to abiotic stress. However, little is known about the function of bZIP genes in wheat abiotic stress. In this study, we report the isolation and functional characterization of the TabZIP60 gene. Three homologous genome sequences of TabZIP60 were isolated from hexaploid wheat and mapped to the wheat homoeologous group 6. A subcellular localization analysis indicated that TabZIP60 is a nuclear-localized protein that activates transcription. Furthermore, TabZIP60 gene transcripts were strongly induced by polyethylene glycol, salt, cold and exogenous abscisic acid (ABA) treatments. Further analysis showed that the overexpression of TabZIP60 in Arabidopsis resulted in significantly improved tolerances to drought, salt, freezing stresses and increased plant sensitivity to ABA in seedling growth. Meanwhile, the TabZIP60 was capable of binding ABA-responsive cis-elements that are present in promoters of many known ABA-responsive genes. A subsequent analysis showed that the overexpression of TabZIP60 led to enhanced expression levels of some stress-responsive genes and changes in several physiological parameters. Taken together, these results suggest that TabZIP60 enhances multiple abiotic stresses through the ABA signaling pathway and that modifications of its expression may improve multiple stress tolerances in crop plants.

The Transcriptional Regulator BBX19 Promotes Hypocotyl Growth by Facilitating COP1-Mediated EARLY FLOWERING3 Degradation in Arabidopsis

Hypocotyl elongation is a highly coordinated physiological response regulated by myriad internal and external cues. Here, we show that BBX19, a transcriptional regulator with two B-box motifs, is a positive regulator of growth; diminished BBX19 expression by RNA interference reduces hypocotyl length, and its constitutive expression promotes growth. This function of BBX19 is dependent on the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), EARLY FLOWERING3 (ELF3), and PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5. BBX19 is nucleus-colocalized and interacts physically with COP1 and ELF3, a component of the evening complex that represses the expression of PIF4 and PIF5. Moreover, ELF3 protein abundance inversely correlates with BBX19 expression levels in a COP1-dependent manner. By contrast, PIF expression, coinciding with the initiation of hypocotyl growth in the early evening, is positively correlated with the BBX19 transcript abundance. These results collectively establish BBX19 as an adaptor that binds to and recruits ELF3 for degradation by COP1 and, as such, dynamically gates the formation of the evening complex, resulting in derepression of PIF4/5. This finding refines our perspective on how plants grow by providing a molecular link between COP1, ELF3, and PIF4/5 as an underlying mechanism of photomorphogenic development in Arabidopsis thaliana.

The transcriptional regulator BBX24 impairs DELLA activity to promote shade avoidance in Arabidopsis thaliana

In response to canopy shade, plant vegetative structures elongate to gain access to light. However, the mechanism that allows a plastic transcriptional response to canopy shade light is not fully elucidated. Here we propose that the activity of PIF4, a key transcription factor in the shade signalling network, is modulated by the interplay between the BBX24 transcriptional regulator and DELLA proteins, which are negative regulators of the gibberellin (GA) signalling pathway. We show that GA-related targets are enriched among genes responsive to BBX24 under shade and that the shade-response defect in bbx24 mutants is rescued by a GA treatment that promotes DELLA degradation. BBX24 physically interacts with DELLA proteins and alleviates DELLA-mediated repression of PIF4 activity. The proposed molecular mechanism provides reversible regulation of the activity of a key transcription factor that may prove especially relevant under fluctuating light conditions.

Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential

Several transcription factors (TFs) coordinate to regulate expression of specific genes at the transcriptional level. In Arabidopsis thaliana it is estimated that approximately 10% of all genes encode TFs or TF-like proteins. It is important to identify target genes that are directly regulated by TFs in order to understand the complete picture of a plant’s transcriptome profile. Here, we investigate the role of the LONG HYPOCOTYL5 (HY5) transcription factor that acts as a regulator of photomorphogenesis. We used an in vitro genomic DNA binding assay coupled with immunoprecipitation and next-generation sequencing (gDB-seq) instead of the in vivo chromatin immunoprecipitation (ChIP)-based methods. The results demonstrate that the HY5-binding motif predicted here was similar to the motif reported previously and that in vitro HY5-binding loci largely overlapped with the HY5-targeted candidate genes identified in previous ChIP-chip analysis. By combining these results with microarray analysis, we identified hundreds of HY5-binding genes that were differentially expressed in hy5. We also observed delayed induction of some transcripts of HY5-binding genes in hy5 mutants in response to blue-light exposure after dark treatment. Thus, an in vitro gDNA-binding assay coupled with sequencing is a convenient and powerful method to bridge the gap between identifying TF binding potential and establishing function.

HsfB2b-mediated repression of PRR7 directs abiotic stress responses of the circadian clock

The circadian clock perceives environmental signals to reset to local time, but the underlying molecular mechanisms are not well understood. Here we present data revealing that a member of the heat shock factor (Hsf) family is involved in the input pathway to the plant circadian clock. Using the yeast one-hybrid approach, we isolated several Hsfs, including Heat Shock Factor B2b (HsfB2b), a transcriptional repressor that binds the promoter of Pseudo Response Regulator 7 (PRR7) at a conserved binding site. The constitutive expression of HsfB2b leads to severely reduced levels of the PRR7 transcript and late flowering and elongated hypocotyls. HsfB2b function is important during heat and salt stress because HsfB2b overexpression sustains circadian rhythms, and the hsfB2b mutant has a short circadian period under these conditions. HsfB2b is also involved in the regulation of hypocotyl growth under warm, short days. Our findings highlight the role of the circadian clock as an integrator of ambient abiotic stress signals important for the growth and fitness of plants.

The shade avoidance syndrome in Arabidopsis: the antagonistic role of phytochrome a and B differentiates vegetation proximity and canopy shade

Light limitation caused by dense vegetation is one of the greatest threats to plant survival in natural environments. Plants detect such neighboring vegetation as a reduction in the red to far-red ratio (R:FR) of the incoming light. The low R:FR signal, perceived by phytochromes, initiates a set of responses collectively known as the shade avoidance syndrome, intended to reduce the degree of current or future shade from neighbors by overtopping such competitors or inducing flowering to ensure seed production. At the seedling stage these responses include increased hypocotyl elongation. We have systematically analyzed the Arabidopsis seedling response and the contribution of phyA and phyB to perception of decreased R:FR, at three different levels of photosynthetically active radiation. Our results show that the shade avoidance syndrome, induced by phyB deactivation, is gradually antagonized by phyA, operating through the so-called FR-High Irradiance Response, in response to high FR levels in a range that simulates plant canopy shade. The data indicate that the R:FR signal distinguishes between the presence of proximal, but non-shading, neighbors and direct foliar shade, via a intrafamily photosensory attenuation mechanism that acts to suppress excessive reversion toward skotomorphogenic development under prolonged direct vegetation shade.

UV-B-responsive association of the Arabidopsis bZIP transcription factor ELONGATED HYPOCOTYL5 with target genes, including its own promoter

In plants subjected to UV-B radiation, responses are activated that minimize damage caused by UV-B. The bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) acts downstream of the UV-B photoreceptor UV RESISTANCE LOCUS8 (UVR8) and promotes UV-B-induced photomorphogenesis and acclimation. Expression of HY5 is induced by UV-B; however, the transcription factor(s) that regulate HY5 transcription in response to UV-B and the impact of UV-B on the association of HY5 with its target promoters are currently unclear. Here, we show that HY5 binding to the promoters of UV-B-responsive genes is enhanced by UV-B in a UVR8-dependent manner in Arabidopsis thaliana. In agreement, overexpression of REPRESSOR OF UV-B PHOTOMORPHOGENESIS2, a negative regulator of UVR8 function, blocks UV-B-responsive HY5 enrichment at target promoters. Moreover, we have identified a T/G-box in the HY5 promoter that is required for its UV-B responsiveness. We show that HY5 and its homolog HYH bind to the T/G(HY5)-box cis-acting element and that they act redundantly in the induction of HY5 expression upon UV-B exposure. Therefore, HY5 is enriched at target promoters in response to UV-B in a UVR8 photoreceptor-dependent manner, and HY5 and HYH interact directly with a T/G-box cis-acting element of the HY5 promoter, mediating the transcriptional activation of HY5 in response to UV-B.

BBX19 interacts with CONSTANS to repress FLOWERING LOCUS T transcription, defining a flowering time checkpoint in Arabidopsis

The timely transition of vegetative to reproductive development is coordinated through quantitative regulation of floral pathway genes in response to physiological and environmental cues. Here, we show that the circadian-controlled expression of the Arabidopsis thaliana floral transition regulators FLOWERING LOCUS T (FT) and CONSTANS (CO) is antiphasic to that of BBX19, a transcription factor with two B-Box motifs. Diminished expression of BBX19 by RNA interference accelerates flowering, and constitutive expression of BBX19 delays flowering under inductive photoperiods. This delay is not accompanied by the alteration of CO expression levels but rather by a reduction of transcript levels of FT and the FT-regulated genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1, LEAFY, and FRUITFUL. Similar to CO, BBX19 is expressed in vasculature. BBX19 and CO colocalize in the nucleus and interact physically in vivo. In transient assays, coinfiltration of 10-fold more CO overcomes the BBX19-mediated repression of FT activation. Substitution of the conserved Cys-25 to Ser in the BBX19 Box1 motif abolishes the BBX19-CO interaction and eliminates the negative regulation of flowering time, while the analogous C76S substitution in the Box2 motif is ineffective. Together, these results implicate BBX19 as a circadian clock output that depletes the active CO pool to accurately monitor daylength and precisely time FT expression.

Global transcriptomics identification and analysis of transcriptional factors in different tissues of the paper mulberry

BACKGROUND

The paper mulberry (Broussonetia papyifera) is one of the multifunctional tree species in agroforestry system and is also commonly utilized in traditional medicine in China and other Asian countries. To identify the transcription factors (TFs) and comprehensively understand their regulatory roles in the growth of the paper mulberry, a global transcriptomics TF prediction and the differential expression analysis among root, shoot and leaf were performed by using RNA-seq.

RESULTS

Results indicate that there is 1, 337 TFs encoded by the paper mulberry and they belong to the 55 well-characterized TF families. Based on the phylogenetic analysis, the TFs exist extensively in all organisms are more conservative than those exclusively exist in plant and the paper mulberry has the closest relationship with the mulberry. According to the results of differential expression analysis, there are 627 TFs which exhibit the differential expression profiles in root, shoot and leaf. ARR-Bs, ARFs, NACs and bHLHs together with other root-specific and highly expressed TFs might account for the developed lateral root and unconspicuous taproot in the paper mulberry. Meanwhile, five TCPs highly expressed in shoot of the paper mulberry might negatively regulate the expression of 12 LBDs in shoot. Besides, LBDs, which could directly or indirectly cooperate with ARFs, bHLHs and NACs, seem to be the center knot involving in the regulation of the shoot development in the paper mulberry.

CONCLUSIONS

Our study provides the comprehensive transcriptomics identification of TFs in the paper mulberry without genome reference. A large number of lateral organ growth regulation related TFs exhibiting the tissue differential expression may entitle the paper mulberry the developed lateral roots, more branches and rapid growth. It will increase our knowledge of the structure and composition of TFs in tree plant and it will substantially contribute to the improving of this tree.