SALT TOLERANCE HOMOLOG2, a B-box protein in Arabidopsis that activates transcription and positively regulates light-mediated development

CONSTANS and ASYMMETRIC LEAVES 1 complex is involved in the induction of FLOWERING LOCUS T in photoperiodic flowering in Arabidopsis

Plants monitor changes in day length to coordinate flowering with favorable seasons to increase their fitness. The day-length specific induction of FLOWERING LOCUS T (FT) regulated by CONSTANS (CO) is the crucial aspect of photoperiodic flowering in Arabidopsis thaliana. Recent studies have elucidated some mechanisms of CO-dependent FT induction. Here, we demonstrate another mechanism of CO-dependent FT regulation. Our results indicate that CO protein partially regulates FT transcription by forming a complex with ASYMMETRIC LEAVES 1 (AS1) protein, which regulates leaf development partly by controlling gibberellin (GA) levels. We identified AS1 as a CO-interacting protein in yeast and verified their interaction in vitro and in planta. We also showed that the temporal and spatial expression pattern of AS1 overlapped with that of CO. In addition, as1 mutants showed GA-independent delayed flowering under different light/dark conditions. FT expression levels in the as1 mutants and the SUC2:CO-HA/as1 line under long-day and 12-h light/12-h dark conditions were reduced compared with wild-type plants and the SUC2:HA-CO line, respectively. Moreover, AS1 bound directly to the specific regions of the FT promoter in vivo. These results indicate that CO forms a functional complex with AS1 to regulate FT expression and that AS1 plays different roles in two regulatory pathways, both of which concomitantly regulate the precise timing of flowering.

Functional profiling identifies genes involved in organ-specific branches of the PIF3 regulatory network in Arabidopsis

The phytochrome (phy)-interacting basic helix-loop-helix transcription factors (PIFs) constitutively sustain the etiolated state of dark-germinated seedlings by actively repressing deetiolation in darkness. This action is rapidly reversed upon light exposure by phy-induced proteolytic degradation of the PIFs. Here, we combined a microarray-based approach with a functional profiling strategy and identified four PIF3-regulated genes misexpressed in the dark (MIDAs) that are novel regulators of seedling deetiolation. We provide evidence that each one of these four MIDA genes regulates a specific facet of etiolation (hook maintenance, cotyledon appression, or hypocotyl elongation), indicating that there is branching in the signaling that PIF3 relays. Furthermore, combining inferred MIDA gene function from mutant analyses with their expression profiles in response to light-induced degradation of PIF3 provides evidence consistent with a model where the action of the PIF3/MIDA regulatory network enables an initial fast response to the light and subsequently prevents an overresponse to the initial light trigger, thus optimizing the seedling deetiolation process. Collectively, the data suggest that at least part of the phy/PIF system acts through these four MIDAs to initiate and optimize seedling deetiolation, and that this mechanism might allow the implementation of spatial (i.e., organ-specific) and temporal responses during the photomorphogenic program.

Light-responsive double B-box containing transcription factors are conserved in Physcomitrella patens

In the model seed plant Arabidopsis thaliana, a sub-family of B-box containing transcriptional factors (BBXs), which is classified in the BBX-IV group based on the domain structure, contains two tandem B-box domains and plays crucial roles in early photomorphogenesis under the control of blue light receptors, cry1 and cry2. The results of an examination of light responsiveness of representative Physcomitrella BBX-IV genes and their heterologous expression in Arabidopsis suggested that the light signaling-related characteristics of the BBX-IV subfamily are evolutionarily conserved in a moss, which is a basal lineage of land plants.

BBX32, an Arabidopsis B-Box protein, functions in light signaling by suppressing HY5-regulated gene expression and interacting with STH2/BBX21

A B-box zinc finger protein, B-BOX32 (BBX32), was identified as playing a role in determining hypocotyl length during a large-scale functional genomics study in Arabidopsis (Arabidopsis thaliana). Further analysis revealed that seedlings overexpressing BBX32 display elongated hypocotyls in red, far-red, and blue light, along with reduced cotyledon expansion in red light. Through comparative analysis of mutant and overexpression line phenotypes, including global expression profiling and growth curve studies, we demonstrate that BBX32 acts antagonistically to ELONGATED HYPOCOTYL5 (HY5). We further show that BBX32 interacts with SALT TOLERANCE HOMOLOG2/BBX21, another B-box protein previously shown to interact with HY5. Based on these data, we propose that BBX32 functions downstream of multiple photoreceptors as a modulator of light responses. As such, BBX32 potentially has a native role in mediating gene repression to maintain dark adaptation.

Nuclear localization and interaction with COP1 are required for STO/BBX24 function during photomorphogenesis

Arabidopsis (Arabidopsis thaliana) SALT TOLERANCE/B-BOX ZINC FINGER PROTEIN24 (STO/BBX24) is a negative regulator of the light signal transduction that localizes to the nucleus of plant cells and interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) in the yeast (Saccharomyces cerevisiae) two-hybrid system. The protein contains two B-box zinc-finger motives at the N terminus and a conserved motif at the C-terminal part required for the interaction with COP1. BBX24 accumulates during deetiolation of young seedlings in the first hours of exposure to light. However, this accumulation is transient and decreases after prolonged light irradiation. Here, we identified the amino acidic residues necessary for the nuclear import of the protein. In addition, we created mutated forms of the protein, and analyzed them by overexpression in the bbx24-1 mutant background. Our results indicate that the degradation of BBX24 occurs, or at least is initiated in the nucleus, and this nuclear localization is a prerequisite to fulfill its function in light signaling. Moreover, mutations in the region responsible for the interaction with COP1 revealed that a physical interaction of the proteins is also required for degradation of BBX24 in the light and for normal photomorphogenesis.

CONSTANS and the evolutionary origin of photoperiodic timing of flowering

A network of promoting and inhibiting pathways that respond to environmental and internal signals controls the flowering transition. The outcome of this regulatory network establishes, for any particular plant, the correct time of the year to flower. The photoperiod pathway channels inputs from light, day length, and the circadian clock to promote the floral transition. CONSTANS (CO) is a central regulator of this pathway, triggering the production of the mobile florigen hormone FT (FLOWERING LOCUS T) that induces flower differentiation. Because plant reproductive fitness is directly related to its capacity to flower at a precise time, the photoperiod pathway is present in all known plant species. Recent findings have stretched the evolutionary span of this photophase signal to unicellular algae, which show unexpected conserved characteristics with modern plant photoperiodic responses. In this review, a comparative description of the photoperiodic systems in algae and plants will be presented and a general role for the CO family of transcriptional activators proposed.

A high-throughput screening system for Arabidopsis transcription factors and its application to Med25-dependent transcriptional regulation

The activities of transcription factors (TFs) require interactions with specific DNA sequences and other regulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD-TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid (Y1H) and yeast-two-hybrid (Y2H) methods. The efficiency of the system was validated by examining two well-characterized TF-DNA and TF-protein interactions: the CHE-CCA1 promoter interaction by Y1H and NPR1-TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key regulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 expression through these three TFs. These results demonstrate that this high-throughput Y1H/Y2H screening system is an efficient tool for studying transcriptional regulation networks in Arabidopsis. This system will be available for other Arabidopsis researchers, and thus it provides a vital resource for the Arabidopsis community.

Function of B-BOX under shade

Plants are capable of perceiving changes in the light environment and finely adjust their growth and development. Reductions of red to far-red ratio (R:FR) generated by an increase of the plant canopy above the plant are sensed by the phytochrome system triggering the shade-avoidance syndrome (SAS) that includes elongation of vegetative structures, reduction of branching and acceleration of flowering. Albeit the SAS is a strategy of major adaptative significance in plant communities, involving massive changes in gene expression, our knowledge of the SAS signaling network is still fragmented. By a selection and characterization of a T-DNA mutant with a long hypocotyl under shade, we identified BBX21, a protein with two B-box domains involved in the SAS. BBX21 belongs to a small eight member family of B-box containing proteins with both opposite and additive functions in the SAS signaling. BBX21 down-regulates the gene expression of auxin, brassinosteroid and ethylene signaling pathway components under shade. Furthermore BBX21 is a transcription factor that interacts genetically with COP1. We propose a model in which a dynamic balance of positive and negative B-box transcriptional regulators acts as a gas-and-brake mechanism into the COP1 signaling to regulate the expression of SAS.

DBB1a, involved in gibberellin homeostasis, functions as a negative regulator of blue light-mediated hypocotyl elongation in Arabidopsis

Double B-box 1a (DBB1a) belongs to the zinc-finger family proteins in Arabidopsis thaliana. Transcriptional analysis uncovered that the DBB1a gene expression was blue light-dependently regulated, and the transcript level of DBB1a in cry1cry2 was decreased but not in phyAphyB compared to wild type under blue light conditions. Transgenic plants containing pDBB1a:GUS (β-glucuronidase) displayed GUS activity in the vascular system of leaves and petioles. Green fluorescent protein (GFP)-fused DDB1a (DBB1a-GFP) protein was found in the nucleus in transient transformation assays with onion epidermal cells as well as in stable transgenic Arabidopsis plants. To investigate the function of DBB1a, we generated DBB1a over-expressing and under-expressing transgenic Arabidopsis plants. Analysis of hypocotyl growth of these lines indicated that DBB1a promoted hypocotyl elongation under blue light condition. The phenotype of transgenic plants with DBB1a over-expression could be impaired by a gibberellin (GA)-biosynthesis inhibitor. Moreover, the expression analysis of GA metabolic and catabolic genes in DBB1a transgenic lines indicated that the DBB1a suppressed GA2-oxidase1 (GA2ox1) and GA2-oxidase8 (GA2ox8) expression, but induced GA3β-hydroxygenase1 (GA3ox1) and GA20-oxidase1 (GA20ox1) expression under blue light. Taken together, we concluded that DBB1a promotes hypocotyl elongation under blue light condition through an increase in bioactive GA levels in Arabidopsis.

AtBBX21 and COP1 genetically interact in the regulation of shade avoidance

Plants grown at high densities perceive the reduction in the ratio of red (R) to far-red (FR) light as a warning of competition. This light signal triggers morphological responses such as hypocotyl and stem elongation, and acceleration of flowering, which are known collectively as the shade-avoidance syndrome (SAS). Mutations in the photomorphogenic repressor COP1 suppress the SAS, but how COP1 modulates these responses is uncertain. We identified a new mutant with altered responses to natural shade, named lhus (long hypocotyl under shade). lhus seedlings have longer hypocotyls than wild-type under a low R:FR ratio, but not under sunlight or darkness. The lhus phenotype is due to a mutation affecting a B-box zinc finger transcription factor encoded by At1g75540, a gene previously reported as AtBBX21 that interacts with COP1 to control de-etiolation. Mutations in genes encoding other members of this protein family also result in impaired SAS regulation. Under short-term canopy shade, LHUS/BBX21 acts as positive regulator of SAS genes such as PAR1, HFR1, PIL1 and ATHB2. In contrast, global expression analysis of wild-type and lhus/bbx21 seedlings revealed that a large number of genes involved in hormonal signalling pathways are negatively regulated by LHUS/BBX21 in response to long-term canopy shade, and this observation fits well with the phenotype of lhus/bbx21 seedlings grown under a low R:FR ratio. Moreover, the bbx21 bbx22 double mutation restored the SAS in the cop1 background. We propose that LHUS/BBX21 and other B-box-containing proteins, such as BBX22, act downstream of COP1, and play a central role in early and long-term adjustment of the SAS in natural environments.

Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana

Karrikins are a class of seed germination stimulants identified in smoke from wildfires. Microarray analysis of imbibed Arabidopsis thaliana seeds was performed to identify transcriptional responses to KAR(1) before germination. A small set of genes that are regulated by KAR(1), even when germination is prevented by the absence of gibberellin biosynthesis or light, were identified. Light-induced genes, putative HY5-binding targets, and ABRE-like promoter motifs were overrepresented among KAR(1)-up-regulated genes. KAR(1) transiently induced the light signal transduction transcription factor genes HY5 and HYH. Germination of afterripened Arabidopsis seed was triggered at lower fluences of red light when treated with KAR(1). Light-dependent cotyledon expansion and inhibition of hypocotyl elongation were enhanced in the presence of germination-active karrikins. HY5 is important for the Arabidopsis hypocotyl elongation, but not seed germination, response to karrikins. These results reveal a role for karrikins in priming light responses in the emerging seedling, and suggest that the influence of karrikins on postfire ecology may not be limited to germination recruitment.

Feedback-regulation of strigolactone biosynthetic genes and strigolactone-regulated genes in Arabidopsis

Strigolactones (SLs) have recently been found to regulate shoot branching, but the functions of SLs at other stages of development and the regulation of SL-related gene expression are mostly unknown in Arabidopsis. In this study, we performed real-time reverse transcription-PCR (RT-PCR) and microarray analysis using wild-type plants and SL-deficient/insensitive mutants to understand the molecular mechanisms underlying SL biosynthesis and signaling. We found that there is responsiveness to SL in the gene expression of Arabidopsis seedlings, which includes feedback regulation of two carotenoid cleavage dioxygenase genes. Microarray analysis revealed that exogenously applied SL regulated the expression of several genes, including light signaling-related genes and auxin-inducible genes. We also found that MORE AXILLARY GROWTH (MAX)2 plays an important role in the expression of SL-regulated genes. Our data support previous studies indicating that SL might function at the seedling stage. Analysis of SL-responsive and MAX2 downstream gene candidates provides new opportunities to broaden our understanding of SL signaling.

Arabidopsis radical-induced cell death1 is involved in UV-B signaling

The Arabidopsis radical-induced cell death1 (rcd1) mutant is sensitive to ozone fumigation and apoplastic superoxide, but tolerant to methyl viologen. In the present article, we report that the rcd1 mutant is also tolerant to supplementary UV-B radiation. The rcd1-1 mutant exhibits less accumulation of TT dimers, increased hypocotyl growth inhibition and higher accumulation of flavonoids under supplemental UV-B radiation. Moreover, the expression of HY5 (elongated hypocotyl5) is increased in the mutant after UV-B treatment. Gene expression downstream of UV-B signaling reveals that COP1 (constitutively photomorphogenic1)-regulated genes have an elevated expression in rcd1-1 mutant under UV-B radiation, while expression of UVR8 (UV resistance locus 8)-regulated and HY5-independent genes are not changed. Interestingly, the expression of RCD1 genes is not significantly changed by UV-B radiation. Previous study has shown that STO protein is interacting with RCD1 in vitro. Here, we found the mRNA level of STO (salt tolerance) is greatly increased in rcd1-1 mutant after UV-B radiation. However, UV-B-induced HY5 and CHS expression is partially inhibited in sto mutant. Based on the above results, it is deduced that the RCD1, working together with STO, is involved in Arabidopsis UV-B signaling.

Light regulation of gibberellin biosynthesis in pea is mediated through the COP1/HY5 pathway

Light regulation of gibberellin (GA) biosynthesis occurs in several species, but the signaling pathway through which this occurs has not been clearly established. We have isolated a new pea (Pisum sativum) mutant, long1, with a light-dependent elongated phenotype that is particularly pronounced in the epicotyl and first internode. The long1 mutation impairs signaling from phytochrome and cryptochrome photoreceptors and interacts genetically with a mutation in LIP1, the pea ortholog of Arabidopsis thaliana COP1. Mutant long1 seedlings show a dramatic impairment in the light regulation of active GA levels and the expression of several GA biosynthetic genes, most notably the GA catabolism gene GA2ox2. The long1 mutant carries a nonsense mutation in a gene orthologous to the ASTRAY gene from Lotus japonicus, a divergent ortholog of the Arabidopsis bZIP transcription factor gene HY5. Our results show that LONG1 has a central role in mediating the effects of light on GA biosynthesis in pea and demonstrate the importance of this regulation for appropriate photomorphogenic development. By contrast, LONG1 has no effect on GA responsiveness, implying that interactions between LONG1 and GA signaling are not a significant component of the molecular framework for light-GA interactions in pea.

LZF1/SALT TOLERANCE HOMOLOG3, an Arabidopsis B-box protein involved in light-dependent development and gene expression, undergoes COP1-mediated ubiquitination

B-box containing proteins play an important role in light signaling in plants. Here, we identify LIGHT-REGULATED ZINC FINGER1/SALT TOLERANCE HOMOLOG3 (STH3), a B-box encoding gene that genetically interacts with two key regulators of light signaling, ELONGATED HYPOCOTYL5 (HY5) and CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1). STH3 physically interacts with HY5 in vivo and shows a COP1-dependent localization to nuclear speckles when coexpressed with COP1 in plant cells. A T-DNA insertion mutant, sth3, is hyposensitive to high fluence blue, red, and far-red light and has elongated hypocotyls under short days. Analyses of double mutants between sth3, sth2, and hy5 suggest that they have partially overlapping functions. Interestingly, functional assays in protoplasts suggest that STH3 can activate transcription both independently and together with STH2 through the G-box promoter element. Furthermore, sth3 suppresses the cop1 hypocotyl phenotype in the dark as well as the anthocyanin accumulation in the light. Finally, COP1 ubiquitinates STH3 in vitro, suggesting that STH3 is regulated by COP1. In conclusion, we have identified STH3 as a positive regulator of photomorphogenesis acting in concert with STH2 and HY5, while also being a target of COP1-mediated ubiquitination.

CRY1 inhibits COP1-mediated degradation of BIT1, a MYB transcription factor, to activate blue light-dependent gene expression in Arabidopsis

Cryptochromes (CRY) are one of the two major classes of photoreceptors that perceive light stimuli in the UV-A to blue light region and they are involved in multiple aspects of plant growth and development. However, knowledge regarding their signaling transduction components and mechanisms remains limited. Here, we report that a MYB transcription factor Blue Insensitive Trait 1 (BIT1), plays an important role in controlling blue light responses. Hypocotyl growth responses indicate that BIT1 functions as a positive element in blue light signaling, since BIT1 antisense and knock-out lines show a reduced light response in blue light. BIT1 controls blue light-dependent expression of various genes such as PsbS, a member of the light-harvesting complex gene family. A transactivation assay showed that BIT1 regulates promoter activity of PsbS in a blue light-dependent manner and that it requires CRY1 for activation of the PsbS promoter. BIT1 undergoes degradation in darkness and CRY1 functions to stabilize BIT1 in a blue light-dependent manner. In contrast, COP1 binds to BIT1 and mediates its degradation. We propose that the PsbS promoter is activated in blue light via the blue light-dependent stabilization of BIT1 by CRY1, while in darkness BIT1 is degraded by COP1-mediated proteolysis.

STH2 has 2 B there: An insight into the role of B-box containing proteins in Arabidopsis

Recently we reported the identification of a novel B-box transcription factor SALT TOLERANCE HOMOLOG 2 (STH2) that interacts genetically with two key regulators of the light-signaling pathway, HY5 and COP1.1 We also provided phenotypic and genetic characterization of the sth2 mutant suggesting that STH2 plays a positive role in regulating photomorphogenesis both independently or together with HY5. Functional assays in protoplasts revealed that STH2 could act as a transcriptional activator. To our knowledge this is the first report of a B-box domain containing protein playing a direct role in activating transcription in plants. Here we discuss the possible position of STH2 in the transcriptional network and comment on the role of the B-box domain in plants.

Branching out in new directions: the control of root architecture by lateral root formation

Plant roots are required for the acquisition of water and nutrients, for responses to abiotic and biotic signals in the soil, and to anchor the plant in the ground. Controlling plant root architecture is a fundamental part of plant development and evolution, enabling a plant to respond to changing environmental conditions and allowing plants to survive in different ecological niches. Variations in the size, shape and surface area of plant root systems are brought about largely by variations in root branching. Much is known about how root branching is controlled both by intracellular signalling pathays and by environmental signals. Here, we will review this knowledge, with particular emphasis on recent advances in the field that open new and exciting areas of research.