Phytochrome signalling is mediated through nucleoside diphosphate kinase 2

A Possible Role for NDPK2 in the Regulation of Auxin-mediated Responses for Plant Growth and Development

Auxin plays many crucial roles in the course of plant growth and development, such as hook opening, leaf expansion and inhibition of mesocotyl elongation. Although its mechanism of action has not been clarified at the molecular level, recent studies have indicated that auxin triggers the induction of a number of genes known as primary auxin-responsive genes. Hence, the identification of the regulatory components in auxin-mediated cellular responses would help to elucidate the mechanism of the action of this hormone in plant growth and development. NDPK2 encodes a nucleoside diphosphate kinase 2 (NDPK2) in Arabidopsis. We aim to elucidate the possible role of NDPK2 in auxin-related cellular processes, in view of the finding that a ndpk2 mutant displays developmental defects associated with auxin. Interestingly, the ndpk2 mutant exhibits defects in cotyledon development and increased sensitivity to an inhibitor of polar auxin transport (naphthylphthalamic acid; NPA). Consistent with this phenotype, the transcript levels of specific auxin-responsive genes were reduced in the ndpk2 mutant plants treated with auxin. The amount of auxin transported from the shoot apex to the shoot/root transition zone of ndpk2 mutant plants was increased, compared with that in the wild-type plants. These results collectively suggest that NDPK2 appears to participate in auxin-regulated processes, partly through the modulation of auxin transport.

Integration of light signaling with photoperiodic flowering and circadian rhythm

Plants become photosynthetic through de-etiolation, a developmental process regulated by red/far-red light-absorbing phytochromes and blue/ultraviolet A light-absorbing cryptochromes. Genetic screens have identified in the last decade many far-red light signaling mutants and several red and blue light signaling mutants, suggesting the existence of distinct red, far-red, or blue light signaling pathways downstream of phytochromes and cryptochromes. However, genetic screens have also identified mutants with defective de-etiolation responses under multiple wavelengths. Thus, the optimal de-etiolation responses of a plant depend on coordination among the different light signaling pathways. This review intends to discuss several recently identified signaling components that have a potential role to integrate red, far-red, and blue light signalings. This review also highlights the recent discoveries on proteolytic degradation in the desensitization of light signal transmission, and the tight connection of light signaling with photoperiodic flowering and circadian rhythm. Studies on the controlling mechanisms of de-etiolation, photoperiodic flowering, and circadian rhythm have been the fascinating topics in Arabidopsis research. The knowledge obtained from Arabidopsis can be readily applied to food crops and ornamental species, and can be contributed to our general understanding of signal perception and transduction in all organisms.

Repression of light signaling by Arabidopsis SPA1 involves post-translational regulation of HFR1 protein accumulation

Arabidopsis uses two major classes of photoreceptors to mediate seedling de-etiolation. The cryptochromes (cry1 and cry2) absorb blue/ultraviolet-A light, whereas the phytochromes (phyA-phyE) predominantly regulate responses to red/far-red light. Arabidopsis COP1 represses light signaling by acting as an E3 ubiquitin ligase in the nucleus, and is responsible for targeted degradation of a number of photomorphogenesis-promoting factors, including HY5, LAF1, phyA, and HFR1. Distinct light signaling pathways initiated by multiple photoreceptors (including both phytochromes and cryptochromes) eventually converge on COP1, causing its inactivation and nuclear depletion. Arabidopsis SPA1, which encodes a protein structurally related to COP1, also represses light signaling under various light conditions. In this study, we present genetic evidence supporting that HFR1, which encodes a photomorphogenesis-promoting bHLH transcription factor, acts downstream of SPA1 and is required for different subsets of branch pathways of light signaling controlled by SPA1 under different light conditions. We show that SPA1 physically interacts with HFR1 in a yeast two-hybrid assay and an in vitro co-immunoprecipitation assay. We demonstrate that higher levels of HFR1 protein accumulate in the spa1 mutant background under various light conditions, including far-red, red, blue, and white light, whereas a marginal increase in HFR1 transcript level is only seen in dark- and far-red light-grown spa1-100 mutants. Together, our data suggest that repression of light signaling by Arabidopsis SPA1 likely involves post-translational regulation of HFR1 protein accumulation.

Phytochrome phosphorylation in plant light signaling

Reversible protein phosphorylation is a switching mechanism used in eukaryotes to regulate various cellular signalings. In plant light signaling, sophisticated photosensory receptor systems operate to modulate growth and development. The photoreceptors include phytochromes, cryptochromes and phototropins. Despite considerable progresses in defining the photosensory roles of these photoreceptors, the primary biochemical mechanisms by which the photoreceptor molecules transduce the perceived light signals into cellular responses remain to be elucidated. The signal-transducing photoreceptors in plants are all phosphoproteins and/or protein kinases, suggesting that light-dependent protein phosphorylation and dephosphorylation play important roles in the function of the photoreceptors. This review focuses on the role of phytochromes' reversible phosphorylation involved in the light signal transduction in plants.

Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer

Environmental light information such as quality, intensity, and duration in red (approximately 660 nm) and far-red (approximately 730 nm) wavelengths is perceived by phytochrome photoreceptors in plants, critically influencing almost all developmental strategies from germination to flowering. Phytochromes interconvert between red light-absorbing Pr and biologically functional far-red light-absorbing Pfr forms. To ensure optimal photoresponses in plants, the flux of light signal from Pfr-phytochromes should be tightly controlled. Phytochromes are phosphorylated at specific serine residues. We found that a type 5 protein phosphatase (PAPP5) specifically dephosphorylates biologically active Pfr-phytochromes and enhances phytochrome-mediated photoresponses. Depending on the specific serine residues dephosphorylated by PAPP5, phytochrome stability and affinity for a downstream signal transducer, NDPK2, were enhanced. Thus, phytochrome photoreceptors have developed an elaborate biochemical tuning mechanism for modulating the flux of light signal, employing variable phosphorylation states controlled by phosphorylation and PAPP5-mediated dephosphorylation as a mean to control phytochrome stability and affinity for downstream transducers.

Crystal structure of nucleoside diphosphate kinase required for coleoptile elongation in rice (Oryza sativa L.)

Nucleoside diphosphate kinase (NDK) is a ubiquitous enzyme found in all organisms and cell types, and catalyzes the transfer of the phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. The enzyme is involved in and required for coleoptile elongation in rice as the level of the rice NDK (rNDK) changes during seed germination and the early stages of seedling growth. The expression of rice NDK gene is up-regulated in the growing coleoptiles when the anaerobic stress persists. The rNDK structure determined at 2.5 A resolution consists of a four-stranded anti-parallel beta-sheet, of which the surfaces are partially covered with six alpha-helices; its overall and active site structures are similar to those of homologous enzymes except the major conformation variations of residue 132-138 regions, involving significant structural contacts. The model contains 148 residues of 149 residues in total and averaged 19 water molecules per monomer for 12 molecules in an asymmetric unit. A mold of 12 superimposed molecules shows that the alphaA-alpha2 area has greater variations and higher temperature factors, indicating the flexibility for a substrate entrance. Hexameric molecular packing in both crystal and solution implies that rNDK functions as hexamers. This rNDK structure, which is the first NDK structure from a higher plant system, provides the structural information essential to understand the functional significance of this enzyme during growth and development in both rice and other plants.

Proteome analysis of sugar beet leaves under drought stress

Drought is one of the major factors limiting the yield of sugar beet (Beta vulgaris L.). The identification of candidate genes for marker-assisted selection (MAS) could greatly improve the efficiency of breeding for increased drought tolerance. Drought-induced changes in the proteome could highlight important genes. Two genotypes of sugar beet (7112 and 7219-P.69) differing in genetic background were cultivated in the field. A line-source sprinkler irrigation system was used to apply irrigated and water deficit treatments beginning at the four-leaf stage. At 157 days after sowing, leaf samples were collected from well-watered and drought-stressed plants for protein extraction and to measure shoot biomass and leaf relative water content. Changes induced in leaf proteins were studied by two-dimensional gel electrophoresis and quantitatively analyzed using image analysis software. Out of more than 500 protein spots reproducibly detected and analyzed, 79 spots showed significant changes under drought. Some proteins showed genotype-specific patterns of up- or downregulation in response to drought. Twenty protein spots were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), leading to identification of Rubisco and 11 other proteins involved in redox regulation, oxidative stress, signal transduction, and chaperone activities. Some of these proteins could contribute a physiological advantage under drought, making them potential targets for MAS.

Signaling mechanisms of higher plant photoreceptors: a structure-function perspective

Higher plants monitor changes in the ambient light environment using three major classes of photoreceptors: the red/far-red-absorbing phytochromes, the blue/UV-A-absorbing cryptochromes, and phototropins. These photoreceptors mediate various photoresponses, ranging from seed germination, to seedling de-etiolation, stem elongation, leaf expansion, floral initiation, phototropic bending of organs, intracellular movement of chloroplast, and stomata opening. Here I briefly review the distinct and overlapping physiological functions of these photoreceptors and highlight recent progress that provided significant insights into their signaling mechanisms, particularly from a structure-function perspective. This review focuses on the early photochemical and biochemical events that lead to photoreceptor activation and signaling initiation.

A new type of mutation in phytochrome A causes enhanced light sensitivity and alters the degradation and subcellular partitioning of the photoreceptor

A specific light program consisting of multiple treatments with alternating red and far-red light pulses was used to isolate mutants in phytochrome A-dependent signal transduction pathways in Arabidopsis. Because of their phenotype, the mutants were called eid for empfindlicher im dunkelroten Licht, which means hypersensitive in far-red light. One of the isolated mutants, eid4, is a novel semi-dominant allele of the phytochrome A gene that carries a missense mutation in the chromophore-binding domain. The mutation did not change the photochemical properties of the photoreceptor, but it leads to an increased stability under light conditions that induce its rapid degradation. Fusion proteins with the green fluorescent protein exhibited clear alterations in subcellular localization of the mutated photoreceptor: The fusion protein was impaired in the formation of sequestered areas of phytochrome in the cytosol, which can explain its reduced light-dependent degradation. In contrast, the mutation stabilizes nuclear speckles (NUS) that appear late under continuous far-red light, whereas the formation of early, transiently appearing NUS remained more or less unaltered.

Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling

In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the signaling of both stress and light. However, little is known about the structural elements involved in their function. Of the three NDPKs (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in phytochrome-mediated signal transduction. In this study, we found that the binding of dNDP or NTP to NDPK2 strengthens the interaction significantly between activated phytochrome and NDPK2. To better understand the structural basis of the phytochrome-NDPK2 interaction, we determined the X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide binding caused a slight conformational change in NDPK2 that was confined to helices alphaA and alpha2. This suggests that the presence of nucleotide in the active site and/or the evoked conformational change contributes to the recognition of NDPK2 by activated phytochrome. In vitro binding assays showed that only NDPK2 interacted specifically with the phytochrome and the C-terminal regulatory domain of phytochrome is involved in the interaction. A domain swap experiment between NDPK1 and NDPK2 showed that the variable C-terminal region of NDPK2 is important for the activation by phytochrome. The structure of Arabidopsis NDPK1 and NDPK2 showed that the isoforms share common electrostatic surfaces at the nucleotide-binding site, but the variable C-terminal regions have distinct electrostatic charge distributions. These findings suggest that the binding of nucleotide to NDPK2 plays a regulatory role in phytochrome signaling and that the C-terminal extension of NDPK2 provides a potential binding surface for the specific interaction with phytochromes.

NDPK2 as a signal transducer in the phytochrome-mediated light signaling

Nucleoside-diphosphate kinase (NDPK) 2 in Arabidopsis has been identified as a phytochrome-interacting protein by using the C-terminal domain of phytochrome A (PhyA) as the bait in yeast two-hybrid screening. The far-red light-absorbing form of phytochrome (Pfr) A stimulates NDPK2 gamma-phosphate exchange activity in vitro. To better understand the multiple functions of NDPK and its role in phytochrome-mediated signaling, we characterized the interaction between phytochrome and NDPK2. Domain studies revealed that PER-ARNT-SIM domain A in the C-terminal domain of phytochrome is the binding site for NDPK2. Additionally, phytochrome recognizes both the NDPK2 C-terminal fragment and the NDPK2 hexameric structure to fulfill its binding. To illustrate the mechanism of how the Pfr form of phytochrome stimulates NDPK2, His-197-surrounding residue mutants were made and tested. Results suggested that the H-bonding with His-197 inside the nucleotide-binding pocket is critical for NDPK2 functioning. The pH dependence profiles of NDPK2 indicated that mutants with different activities from the wild type have different pK(a) values of His-197 and that NDPK2 hyperactive mutants possess lower pK(a) values. Because a lower pK(a) value of His-197 accelerates NDPK2 autophosphorylation and the phospho-transfer between the phosphorylated NDPK2 and its kinase substrate, we concluded that the Pfr form of phytochrome stimulates NDPK2 by lowering the pK(a) value of His-197.

PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana

The first decision made by an angiosperm seed, whether to germinate or not, is based on integration of various environmental signals such as water and light. The phytochromes (Phys) act as red and far-red light (Pfr) photoreceptors to mediate light signaling through yet uncharacterized pathways. We report here that the PIF3-like 5 (PIL5) protein, a basic helix-loop-helix transcription factor, is a key negative regulator of phytochrome-mediated seed germination. PIL5 preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB). Analyses of a pil5 mutant in conjunction with phyA and phyB mutants, a pif3 pil5 double mutant, and PIL5 overexpression lines indicate that PIL5 is a negative factor in Phy-mediated promotion of seed germination, inhibition of hypocotyl negative gravitropism, and inhibition of hypocotyl elongation. Our data identify PIL5 as the first Phy-interacting protein that regulates seed germination.

The nuclear localization signal and the C-terminal region of FHY1 are required for transmission of phytochrome A signals

Plants use the family of phytochrome photoreceptors to sense their light environment in the red/far-red region of the spectrum. Phytochrome A (phyA) is the primary photoreceptor that regulates germination and early seedling development. This phytochrome mediates seedling de-etiolation for the developmental transition from heterotrophic to photoauxotrophic growth. High intensity far-red light provides a way to specifically assess the role of phyA in this process and was used to isolate phyA-signaling intermediates. fhy1 and pat3 (renamed fhy1-3) are independently isolated alleles of a gene encoding a phyA signal transduction component. FHY1 is a small 24 kDa protein that shows no homology to known functional motifs, besides a small conserved septin-related domain at the C-terminus, a putative nuclear localization signal (NLS) and a putative nuclear exclusion signal (NES). Here we demonstrate that the septin-related domain is important for FHY1 to transmit phyA signals. Moreover, the putative NLS and NES of FHY1 are indeed involved in its nuclear localization and exclusion. Nuclear localization of FHY1 is needed for it to execute responses downstream of phyA. Together with the results from global expression analysis, our findings point to an important role of FHY1 in phyA signaling through its nuclear translocation and induction of gene expression.

Structure and mutational analysis of a plant mitochondrial nucleoside diphosphate kinase. Identification of residues involved in serine phosphorylation and oligomerization

We report the first crystal structure of a plant (Pisum sativum L. cv Oregon sugarpod) mitochondrial nucleoside diphosphate kinase. Similar to other eukaryotic nucleoside diphosphate kinases, the plant enzyme is a hexamer; the six monomers in the asymmetric unit are arranged as trimers of dimers. Different functions of the kinase have been correlated with the oligomeric structure and the phosphorylation of Ser residues. We show that the occurrence of Ser autophosphorylation depends on enzymatic activity. The mutation of the strictly conserved Ser-119 to Ala reduced the Ser phosphorylation to about one-half of that observed in wild type with only a modest change of enzyme activity. We also show that mutating another strictly conserved Ser, Ser-69, to Ala reduces the enzyme activity to 6% and 14% of wild-type using dCDP and dTDP as acceptors, respectively. Changes in the oligomerization pattern of the S69A mutant were observed by cross-linking experiments. A reduction in trimer formation and a change in the dimer interaction could be detected with a concomitant increase of tetramers. We conclude that the S69 mutant is involved in the stabilization of the oligomeric state of this plant nucleoside diphosphate kinase.

Targeted knockout in Physcomitrella reveals direct actions of phytochrome in the cytoplasm

The plant photoreceptor phytochrome plays an important role in the nucleus as a regulator of transcription. Numerous studies imply, however, that phytochromes in both higher and lower plants mediate physiological reactions within the cytoplasm. In particular, the tip cells of moss protonemal filaments use phytochrome to sense light direction, requiring a signaling system that transmits the directional information directly to the microfilaments that direct tip growth. In this work we describe four canonical phytochrome genes in the model moss species Physcomitrella patens, each of which was successfully targeted via homologous recombination and the distinct physiological functions of each gene product thereby identified. One homolog in particular mediates positive phototropism, polarotropism, and chloroplast movement in polarized light. This photoreceptor thus interacts with a cytoplasmic signal/response system. This is our first step in elucidating the cytoplasmic signaling function of phytochrome at the molecular level.

Phenotypic characterization of a photomorphogenic mutant

Light is arguably the most important abiotic factor controlling plant growth and development throughout their life cycle. Plants have evolved sophisticated light-sensing mechanisms to monitor fluctuations in light quality, intensity, direction and periodicity (day length). In Arabidopsis, three families of photoreceptors have been identified by molecular genetic studies. The UV-A/blue light receptors cryptochromes and the red/far-red receptors phytochromes control an overlapping set of responses including photoperiodic flowering induction and de-etiolation. Phototropins are the primary photoreceptors for a set of specific responses to UV-A/blue light such as phototropism, chloroplast movement and stomatal opening. Mutants affecting a photoreceptor have a characteristic phenotype. It is therefore possible to determine the specific developmental responses and the photoreceptor pathway(s) affected in a mutant by performing an appropriate set of photobiological and genetic experiments. In this paper, we outline the principal and easiest experiments that can be performed to obtain a first indication about the nature of the photobiological defect in a given mutant.

Quantification of uridine 5'-diphosphate (UDP)-glucose by high-performance liquid chromatography and its application to a nonradioactive assay for nucleoside diphosphate kinase using UDP-glucose pyrophosphorylase as a coupling enzyme

We describe a method for the detection and quantification of nucleoside diphosphate kinase (NDPK). NDPK catalyzes the transfer of the gamma-phosphate of cytidine 5'-triphosphate on uridine 5'-diphosphate (UDP) to produce uridine 5'-triphosphate (UTP). The method uses a nonradioactive coupled enzyme assay in which UTP produced by NDPK is utilized by UDP-glucose pyrophosphorylase. This latter enzyme synthesizes UDP-glucose and inorganic phosphate in the presence of glucose 1-phosphate. UDP-glucose is detected at 260 nm after separation of the reaction mixture by high-performance liquid chromatography (HPLC) on a strong anion-exchange column. The assay is reliable, specific, and linear with respect to time and enzyme amount. Using 15 min incubation time, the method allows detection of NDPK activity below 10 pmol/min. It can be used to analyze kinetic behavior and to quantify NDPK from a wide variety of animal, microbial, and plant sources. It also provides an alternative to radiometric assays and an improvement on pyruvate kinase-linked spectrophotometric assays, which can be hampered by pigments present in crude extracts. Furthermore, we show that the HPLC method developed here can be directly used to assay enzymes for which UDP-glucose is a product.

Degradation of Phytochrome Interacting Factor 3 in Phytochrome-Mediated Light Signaling

Plant photoreceptors regulate various developmental processes. Among the photoreceptors, phytochromes, red and far-red light receptors, regulate light responses through many signaling components, including phytochrome-interacting proteins. The functional relationships among phytochromes and their interacting proteins, however, have not been clearly established. Here, we sought to identify a functional relationship between phytochromes and phytochrome interacting factor 3 (PIF3). We demonstrate that PIF3 is polyubiquitinated rapidly and subsequently degraded in PHYA and PHYB-mediated light signaling. We also show that the degradation of PIF3 is mediated by the 26S proteasome. Our data indicate that light-stimulated phytochromes cause the degradation of their interacting protein, PIF3, by the 26S proteasome.

A dominant mutation in the pea PHYA gene confers enhanced responses to light and impairs the light-dependent degradation of phytochrome A

Phytochrome A (phyA) is an important photoreceptor controlling many processes throughout the plant life cycle. It is unique within the phytochrome family for its ability to mediate photomorphogenic responses to continuous far-red light and for the strong photocontrol of its transcript level and protein stability. Here we describe a dominant mutant of garden pea (Pisum sativum) that displays dramatically enhanced responses to light, early photoperiod-independent flowering, and impaired photodestruction of phyA. The mutant carries a single base substitution in the PHYA gene that is genetically inseparable from the mutant phenotype. This substitution is predicted to direct the replacement of a conserved Ala in an N-terminal region of PHYA that is highly divergent between phyA and other phytochromes. This result identifies a region of the phyA photoreceptor molecule that may play an important role in its fate after photoconversion.

A Dominant Mutation in the Pea PHYA Gene Confers Enhanced Responses to Light and Impairs the Light-Dependent Degradation of Phytochrome A

Phytochrome A (phyA) is an important photoreceptor controlling many processes throughout the plant life cycle. It is unique within the phytochrome family for its ability to mediate photomorphogenic responses to continuous far-red light and for the strong photocontrol of its transcript level and protein stability. Here we describe a dominant mutant of garden pea (Pisum sativum) that displays dramatically enhanced responses to light, early photoperiod-independent flowering, and impaired photodestruction of phyA. The mutant carries a single base substitution in the PHYA gene that is genetically inseparable from the mutant phenotype. This substitution is predicted to direct the replacement of a conserved Ala in an N-terminal region of PHYA that is highly divergent between phyA and other phytochromes. This result identifies a region of the phyA photoreceptor molecule that may play an important role in its fate after photoconversion.

SwoHp, a nucleoside diphosphate kinase, is essential in Aspergillus nidulans

The temperature-sensitive swoH1 mutant of Aspergillus nidulans was previously identified in a screen for mutants with defects in polar growth. In the present work, we found that the swoH1 mutant swelled, lysed, and did not produce conidia during extended incubation at the restrictive temperature. When shifted from the permissive to the restrictive temperature, swoH1 showed the temperature-sensitive swelling phenotype only after 8 h at the higher temperature. The swoH gene was mapped to chromosome II and cloned by complementation of the temperature-sensitive phenotype. The sequence showed that swoH encodes a homologue of nucleoside diphosphate kinases (NDKs) from other organisms. Deletion experiments showed that the swoH gene is essential. A hemagglutinin-SwoHp fusion complemented the mutant phenotype, and the purified fusion protein possessed phosphate transferase activity in thin-layer chromatography assays. Sequencing of the mutant allele showed a predicted V83F change. Structural modeling suggested that the swoH1 mutation would lead to perturbation of the NDK active site. Crude cell extracts from the swoH1 mutant grown at the permissive temperature had approximately 20% of the NDK activity seen in the wild type and did not show any decrease in activity when assayed at higher temperatures. Though the data are not conclusive, the lack of temperature-sensitive NDK activity in the swoH1 mutant raises the intriguing possibility that the SwoH NDK is required for growth at elevated temperatures rather than for polarity maintenance.

Plant mitochondrial nucleoside diphosphate kinase is attached to the membrane through interaction with the adenine nucleotide translocator

This study shows that the plant mitochondrial nucleoside diphosphate kinase (mNDPK) localizes to both the intermembrane space and to the mitochondrial inner membrane. We show that mNDPK is very firmly attached to the membrane. Co-immunoprecipitation experiments identified the adenine nucleotide translocator as an interaction partner. This is the first report showing a direct association between these two proteins, although previous studies have shown metabolic cooperation between them. Possible consequences for mitochondrial energy metabolism are discussed.

LAF3, a novel factor required for normal phytochrome A signaling

Phytochrome A (phyA) is the photolabile plant light receptor that mediates broad spectrum very low-fluence responses and high irradiance responses to continuous far-red light (FRc). An Arabidopsis mutant laf3-1 (long after far-red 3) was recovered from a screen for transposon-tagged mutants that exhibit reduced inhibition of hypocotyl elongation in FRc. The laf phenotype correlated well with a strongly attenuated disappearance of XTR7 transcript in FRc. The effects of laf3-1 on phyA-controlled CAB, CHS, and PET H expression were more subtle, and the mutation had no clear effects on PET E and ASN1 transcript levels in FRc. The use of two alternative transcription initiation sites in the LAF3 gene generates two isoforms that differ only at their N termini. Transcripts encoding both isoforms were induced during germination and were present at slightly higher levels in de-etiolated seedlings than in those grown in darkness. No significant differential regulation of the two isoforms was observed upon exposure to either FRc or continuous red light. Transcripts encoding the shorter isoform (LAF3ISF2) always appear to be more abundant than those encoding the longer isoform (LAF3ISF1). However, both isoforms were capable of full complementation of the laf3-1 hypocotyl phenotype in FRc. When fused to a yellow fluorescent protein, both isoforms localize to the perinuclear region, suggesting that LAF3 encodes a product that might regulate nucleo-cytoplasmic trafficking of an intermediate(s) involved in phyA signal transduction.

A genomic analysis of the shade avoidance response in Arabidopsis

Plants respond to the proximity of neighboring vegetation by elongating to prevent shading. Red-depleted light reflected from neighboring vegetation triggers a shade avoidance response leading to a dramatic change in plant architecture. These changes in light quality are detected by the phytochrome family of photoreceptors. We analyzed global changes in gene expression over time in wild-type, phyB mutant, and phyA phyB double mutant seedlings of Arabidopsis in response to simulated shade. Using pattern fitting software, we identified 301 genes as shade responsive with patterns of expression corresponding to one of various physiological response modes. A requirement for a consistent pattern of expression across 12 chips in this way allowed more subtle changes in gene expression to be considered meaningful. A number of previously characterized genes involved in light and hormone signaling were identified as shade responsive, as well as several putative, novel shade-specific signal transduction factors. In addition, changes in expression of genes in a range of pathways associated with elongation growth and stress responses were observed. The majority of shade-responsive genes demonstrated antagonistic regulation by phyA and phyB in response to shade following the pattern of many physiological responses. An analysis of promoter elements of genes regulated in this way identified conserved promoter motifs potentially important in shade regulation.

Arabidopsis NDK1 is a Component of ROS Signaling by Interacting with Three Catalases

Plants sense various environmental stimuli and have specific signaling pathways to respond to these cues. We focused on light responsive components and found that NDKs were phosphorylated specifically after red light irradiation in Pisum sativum [Tanaka et al. (1998) J. Photochem. Photobiol. B 45: 113] and after blue light irradiation in Neurospora crassa [Oda and Hasunuma (1997) Mol. Gen. Genet. 256: 593, Ogura et al. (2001) J. Biol. Chem. 276: 21228]. We performed yeast two-hybrid screening using AtNDK1, the counterpart of NDK-P1 (Pisum sativum NDK1) in Arabidopsis, as bait, and isolated catalase3 (AtCat3). Interactions between AtNDK1-AtCAT1 and AtNDK1-AtCAT2 were also detected with the two-hybrid system. Non-denaturing two-dimensional gel electrophoresis of crude extracts from plants revealed that catalase and NDK activities co-migrated in the same area of the gel. Transgenic plants expressing AtNDK1 under control of the CaMV 35S promoter exhibited tolerance to paraquat and high ability to eliminate exogenous H2O2. These results indicate that AtNDK1 has a role in ROS response.

Light perception in plant disease defence signalling

Light is a predominant factor in the control of plant growth, development and stress responses. Many biotic stress responses in plants are therefore specifically adjusted by the prevailing light conditions. The plant cell is equipped with sophisticated light-sensing mechanisms that are localised inside and outside of the chloroplast and the nucleus. Recent progress has provided models of how the signalling pathways that are involved in light perception and in defence could operate and interact to form a plant defence network. Such a signalling network includes systems to sense light and regulate gene expression. Photo-produced H(2)O(2) and other reactive oxygen species in the cell also play an essential role in this regulatory network, controlling biotic and abiotic stress responses.

Mutations in the huge Arabidopsis gene BIG affect a range of hormone and light responses

In independent genetic screens, for shade-avoidance response and cytokinin sensitivity, we identified two Arabidopsis mutants, attenuated shade avoidance 1 (asa1) and umbrella1 (umb1), which have very similar pleiotropic phenotypes. asa1 and umb1 are allelic to tir3-1, and are caused by mutations in BIG, which is required for normal auxin efflux. They have a compact rosette, fewer lateral roots, delayed flowering, more secondary inflorescence, smaller seeds and, in the Laer-0 background, much shorter internodes between adjacent flowers, suggesting an interaction between BIG and ERECTA. These mutants have organ-specific defects in response to cytokinins, ethylene, N-1-naphthylphthalamic acid (NPA) and gibberellin (GA). The phenotype of the asa1 ga1-3 double mutant is consistent with defects in GA signalling. There are subtle effects in responses to auxins, abscisic acid and brassinolide. Elongation growth associated with shade avoidance in phyA phyB null mutants is suppressed by asa1 in all organs other than the hypocotyl. Therefore, we here provide evidence that BIG is a key player not just in auxin signalling, but in a multitude of light and hormone pathways.

Light, phytochrome signalling and photomorphogenesis in Arabidopsis

The phytochromes is a family of plant photoreceptors that control growth and development in response to environmental cues. Red and far-red light are the most efficient wavebands to induce conformational changes of phytochromes and consequently modify their kinetics, nuclear/cytoplasmic partitioning, ability to phosphorylate substrates, and physical interaction with proteins that bind DNA. Many players in phytochrome signalling have been identified and a complex, highly regulated network is envisaged. Here we describe the connection between different features of the phytochrome signalling network and the versatile relationship between light signals and physiological outputs shown by phytochromes.

FIN5 positively regulates far-red light responses in Arabidopsis thaliana

We report the characterization of a semi-dominant mutation fin5-1 (far-red insensitive 5-1) of Arabidopsis, which was isolated from genetic screening of phytochrome A (phyA) signaling components. Plants with the fin5-1 mutation exhibited a long hypocotyl phenotype when grown under far-red (FR) light, but not under red light. Physiological analyses implied that FIN5 might be differentially involved in diverse responses that are regulated by phyA under continuous FR light. Anthocyanin accumulation, gravitropic response of hypocotyl growth, and FR light-preconditioned blocking of greening were also impaired in the fin5-1 mutant, whereas photoperiodic floral induction was not, if at all, significantly affected. Moreover, light-regulated expression of the CHS, PORA and PsbS genes was attenuated in fin5-1 mutant plants, while the light-induced expression of CAB was normal. The mutation exhibited semi-dominance regarding control of hypocotyl growth in FR light. We suggest that FIN5 defines a novel branch in the network of phyA signaling in Arabidopsis.

Signaling activities among the Arabidopsis phyB/D/E-type phytochromes: a major role for the central region of the apoprotein

The Arabidopsis phyB, phyD, and phyE phytochromes regulate plant developmental and growth responses to continuous red light (R) and to the ratio of R to far-red (FR) light. The activities of these three photoreceptors in the control of seedling growth have been compared using a transgenic assay based upon induction of R-hypersensitivity of hypocotyl elongation by overexpression of the apoproteins from the 35S promoter. 35S-phyB, 35S-phyD, and 35S-phyE lines expressing similar levels of the respective phytochromes were isolated. Under pulses of R, phyB is very active in inducing a dwarf hypocotyl phenotype, whereas phyD and phyE are inactive. Under high-fluence continuous R, phyD shows a gain in activity whereas phyE does not. These results demonstrate significant differences in the inherent regulatory activities of these receptor apoproteins. To localize the sequence determinants of these functional differences, chimeric proteins were constructed by shuffling amino-terminal, central, and carboxy-terminal regions of phyB and phyD. Overexpression analysis of the phyB/D chimeras shows that it is the central region of these proteins that is most critical in determining their respective activities.

The Arabidopsis COG1 gene encodes a Dof domain transcription factor and negatively regulates phytochrome signaling

Light is a critical environmental factor that influences almost all developmental aspects of plants, including seed germination, seedling morphogenesis, and transition to reproductive growth. Plants have therefore developed an intricate network of mechanisms to perceive and process environmental light information. To further characterize the molecular basis of light-signaling processes in plants, we screened an activation tagging pool of Arabidopsis for altered photoresponses. A dominant mutation, cog1-D, attenuated various red (R) and far-red (FR) light-dependent photoresponses. The mutation was caused by overexpression of a gene encoding a member of the Dof family of transcription factors. The photoresponses in Arabidopsis were inversely correlated with the expression levels of COG1 mRNA. When the COG1 gene was overexpressed in transgenic plants, the plants exhibited hyposensitive responses to R and FR light in a manner inversely dependent on COG1 mRNA levels. On the other hand, transgenic lines expressing antisense COG1 were hypersensitive to R and FR light. Expression of the COG1 gene is light inducible and requires phytochrome A (phyA) for FR light-induced expression and phytochrome B (phyB) for R light-induced expression. Thus, the COG1 gene functions as a negative regulator in both the phyA- and phyB-signaling pathways. We suggest that these phytochromes positively regulate the expression of COG1, a negative regulator, as a mechanism for fine tuning the light-signaling pathway.

Dissecting the phytochrome A-dependent signaling network in higher plants

Plants monitor their ambient light environment using a network of photoreceptors. In Arabidopsis, phytochrome A (phyA) is the primary photoreceptor responsible for perceiving and mediating various responses to far-red light. Several breakthroughs in understanding the signaling network mediating phyA-activated responses have been made in recent years. Here, we highlight several key advances: the demonstration that light regulates nuclear translocation of phyA and its associated kinase activity; the revelation of a transcriptional cascade controlling phyA-regulated gene expression; the detection of a direct interaction between phyA and a transcription factor; and the identification and characterization of many phyA-specific signaling intermediates, some of them suggesting the involvement of the ubiquitin-proteasome pathway.

Changes in photoperiod or temperature alter the functional relationships between phytochromes and reveal roles for phyD and phyE

The phytochromes are one of the means via which plants obtain information about their immediate environment and the changing seasons. Phytochromes have important roles in developmental events such as the switch to flowering, the timing of which can be crucial for the reproductive success of the plant. Analysis of phyB mutants has revealed that phyB plays a major role in this process. We have recently shown, however, that the flowering phenotype of the phyB monogenic mutant is temperature dependent. A modest reduction in temperature to 16 degrees C was sufficient to abolish the phyB mutant early-flowering phenotype present at 22 degrees C. Using mutants null for one or more phytochrome species, we have now shown that phyA, phyD, and phyE, play greater roles with respect to phyB in the control of flowering under cooler conditions. This change in the relative contributions of individual phytochromes appears to be important for maintaining control of flowering in response to modest alterations in ambient temperature. We demonstrate that changes in ambient temperature or photoperiod can alter the hierarchy and/or the functional relationships between phytochrome species. These experiments reveal new roles for phyD and phyE and provide valuable insights into how the phytochromes help to maintain development in the natural environment.

Phytochrome controlled signalling cascades in higher plants

Plants can sense the changes in the environmental light conditions with highly specialized photoreceptors. Phytochromes are sensitive to red and far-red light and have a dual role in the life of plants. These photoreceptors play an important role in plant growth and development from germination to seed maturation and they are also involved in synchronizing the circadian clock with light/dark cycles. Biochemical, cell biological and genetic studies have been carried out to elucidate the molecular mechanism by which phytochromes transduce light signals. A major step in this process seems to be the light-dependent nuclear import of phytochromes. In the nuclei phytochromes interact with transcription factors and regulate the expression of numerous genes, resulting in complex physiological and developmental responses to light. This review focuses on the recently obtained results leading to the identification of some factors and processes involved in phytochrome signalling.

Putative functions of nucleoside diphosphate kinase in plants and fungi

The putative functions of NDP (nucleoside diaphosphate) kinases from various organisms focusing to fungi and plants are described. The biochemical reactions catalyzed by NDP kinase are as follows. (i) Phosphotransferring activity from mainly ATP to cognate NDPs generating nucleoside triphosphates (NTPs). (ii) Autophosphorylation activity from ATP and GTP. (iii) Protein kinase (phosphotransferring) activity phosphorylating such as myelin basic protein. NDP kinase could function to provide NTPs as a housekeeping enzyme. However, recent works proved possible functions of the NDP kinases in the processes of signal transduction in various organisms, as described below. 1) By use of the extracts of the mycelia of a filamentous fungus Neurospora crassa blue-light irradiation could increase the phosphorylation of a 15-kDa protein, which was purified and identified to be NDP kinase (NDK-1). By use of the etiolated seedlings of Pisum sativum cv Alaska and Oryza sativa red-light irradiation of intact plants increased the phosphorylation of NDP kinase. However, successive irradiation by red-far-red reversed the reaction, indicating that phytochrome-mediated light signals are transduced to the phosphorylation of NDP kinase. 2) NDP kinase localizing in mitochondria is encoded by nuclear genome and different from those localized in cytoplasm. NDP kinase in mitochondria formed a complex with succinyl CoA synthetase. 3) In Spinicia oleraceae two different NDP kinases were detected in the chloroplast, and in Pisum sativum two forms of NDP kinase originated from single species of mRNA could be detected in the choloroplast. However, the function of NDP kinases in the choloroplast is not yet known. 4) In Neurospora crassa a Pro72His mutation in NDP kinase (ndk-1Pro72His) deficient in the autophosphorylation and protein kinase activity resulted in lacking the light-induced polarity of perithecia. In wild-type directional light irradiation parallel to the solid medium resulted in the formation of the perithecial beak at the top of perithecia, which was designated as "light-induced polarity of perithecia." In wild-type in darkness the beak was formed at random places on perithecia, and in ndkPro72His mutant the perithecial beak was formed at random places even under directional light illumination. The introduction of genomic DNA and cDNA for ndk-1 demonstrated that the wild-type DNAs suppressed the mutant phenotype. With all these results except for the demonstration in Neurospora, most of the phenomena are elusive and should be solved in the molecular levels concerning with NDP kinases.

NDP kinase 2 interacts with two oxidative stress-activated MAPKs to regulate cellular redox state and enhances multiple stress tolerance in transgenic plants

NDP kinases (NDPKs) are multifunctional proteins that regulate a variety of eukaryotic cellular activities, including cell proliferation, development, and differentiation. However, much less is known about the functional significance of NDPKs in plants. We show here that NDPK is associated with H(2)O(2)-mediated mitogen-activated protein kinase signaling in plants. H(2)O(2) stress strongly induces the expression of the NDPK2 gene in Arabidopsis thaliana (AtNDPK2). Proteins from transgenic plants overexpressing AtNDPK2 showed high levels of autophosphorylation and NDPK activity, and they have lower levels of reactive oxygen species (ROS) than wild-type plants. Mutants lacking AtNDPK2 had higher levels of ROS than wild type. H(2)O(2) treatment induced the phosphorylation of two endogenous proteins whose molecular weights suggested they are AtMPK3 and AtMPK6, two H(2)O(2)-activated A. thaliana mitogen-activated protein kinases. In the absence of H(2)O(2) treatment, phosphorylation of these proteins was slightly elevated in plants overexpressing AtNDPK2 but markedly decreased in the AtNDPK2 deletion mutant. Yeast two-hybrid and in vitro protein pull-down assays revealed that AtNDPK2 specifically interacts with AtMPK3 and AtMPK6. Furthermore, AtNDPK2 also enhances the myelin basic protein phosphorylation activity of AtMPK3 in vitro. Finally, constitutive overexpression of AtNDPK2 in Arabidopsis plants conferred an enhanced tolerance to multiple environmental stresses that elicit ROS accumulation in situ. Thus, AtNDPK2 appears to play a previously uncharacterized regulatory role in H(2)O(2)-mediated MAPK signaling in plants.

Phytochrome-mediated signal transduction pathways in plants

Phytochromes are photoreceptors that regulate plant growth and development in response to the solar radiation environment. Recent studies reveal how phytochrome-mediated light signals can be transduced to the cells for their responses. The possible signal transduction pathways of phytochromes include: (a) direct regulation of gene transcription and (b) typical kinase-involved signaling pathways and its regulation by phosphorylation, dephosphorylation, and proteolytic degradation. This review highlights some of the recent findings.

Phytochrome-mediated photoperception and signal transduction in higher plants

Light provides a major source of information from the environment during plant growth and development. Light perception is mediated through the action of several photoreceptors, including the phytochromes. Recent results demonstrate that light responses involve the regulation of several thousand genes. Some of the key events controlling this gene expression are the translocation of the phytochrome photoreceptors into the nucleus followed by their binding to transcription factors. Coupled with these events, the degradation of positively acting intermediates appears to be an important process whereby photomorphogenesis is repressed in darkness. This review summarizes our current knowledge of these processes.

Light-signalling pathways leading to the co-ordinated expression of HEMA1 and Lhcb during chloroplast development in Arabidopsis thaliana

During de-etiolation, the co-ordinated synthesis of chlorophyll and the chlorophyll a/b-binding proteins is critical to the development of functional light-harvesting complexes. To understand how this co-ordination is achieved, we have made a detailed study of the light-regulated signalling pathways mediating the expression of the HEMA1 and Lhcb genes encoding glutamyl-tRNA reductase, the first committed enzyme of 5-aminolaevulinic acid formation, and chlorophyll a/b-binding proteins, respectively. To do this, we have screened 7 photoreceptor and 12 light-signalling mutants of Arabidopsis thaliana L. for induction of HEMA1 and Lhcb expression in continuous red, far-red and blue light and following a red pulse. We have categorised these mutants into two groups. The phyA, phyB, phyAphyB, cry1, cry2, cop1, det1, poc1, eid1, and far1 mutations lead to diverse effects on the light regulation of HEMA1, but affect Lhcb expression to a similar degree. The hy1, hy2, hy5, fin219, fhy1, fhy3, spa1, ndpk2, and pat1 mutants also affect light regulation of both HEMA1 and Lhcb expression, but with differences in the relative magnitude of the two responses. The fhy1 and fhy3 mutants show the most significant differences in light regulation between the two genes, with both showing a strong inhibition of HEMA1 expression under continuous red light. These results demonstrate that co-ordinated regulation of HEMA1 and Lhcb is largely achieved through parallel light regulation mediated by shared phytochrome- and cryptochrome-signalling pathways. However, glutamyl-tRNA reductase is also required for the synthesis of other tetrapyrroles and this dual role may account for the observed differences in these light-signalling pathways.

Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis

The Z-box is one of the light-responsive elements (LREs) found in the promoters of light inducible genes. We have studied the light responsive characteristics of Z-box containing synthetic as well as native promoters. We show that promoters with Z-box as a single LRE or paired with another LRE can respond to a broad spectrum of light. The response is primarily mediated by phyA, phyB and CRY1 photoreceptors at their respective wavelengths of light. We have demonstrated that CAB1 and Z-GATA containing promoters are down-regulated in hy5 mutants in the light. On the other hand, a promoter with Z-box alone is down-regulated in hy5 mutants both in dark and in light conditions, suggesting involvement of a similar regulatory system in the regulation of the promoter in two distinct developmental pathways: skotomorphogenesis and photomorphogenesis. Furthermore, similar to the CAB1 promoter, a Z-GATA containing promoter is derepressed in cop1 mutants in the dark. DNA-protein interaction studies reveal the presence of a DNA-binding activity that is specific to Z-box. These results provide insights into the regulation of the Z-box LRE mediated by various light signaling components.

Characterization of a strong dominant phytochrome A mutation unique to phytochrome A signal propagation

Here, we report the isolation and characterization of a strong dominant-negative phytochrome A (phyA) mutation (phyA-300D) in Arabidopsis. This mutation carries a single amino acid substitution at residue 631, from valine to methionine (V631M), in the core region within the C-terminal half of PHYA. This PHYA core region contains two protein-interactive motifs, PAS1 and PAS2. Val-631 is located within the PAS1 motif. The phyA-V631M mutant protein is photochemically active and accumulates to a level similar to wild type in dark-grown seedlings. Overexpression of PHYA-V631M in a wild-type background results in a dominant-negative interference with endogenous wild-type phyA, whereas PHYA-V631M in a phyA null mutant background is inactive. To investigate the specificity of this mutation within the phytochrome family, the corresponding amino acid substitution (V664M) was created in the PHYTOCHROME B (PHYB) polypeptide. We found that the phyB-V664M mutant protein is physiologically active in phyB mutant and causes no interfering effect in a wild-type background. Together, our results reveal a unique feature in phyA signal propagation through the C-terminal core region.

Nm23-H1 metastasis suppressor phosphorylation of kinase suppressor of Ras via a histidine protein kinase pathway

The metastasis-suppressive activity of Nm23-H1 was previously correlated with its in vitro histidine protein kinase activity, but physiological substrates have not been identified. We hypothesized that proteins that interact with histidine kinases throughout evolution may represent partners for Nm23-H1 and focused on the interaction of Arabidopsis "two-component" histidine kinase ERS with CTR1. A mammalian homolog of CTR1 was previously reported to be c-Raf; we now report that CTR1 also exhibits homology to the kinase suppressor of Ras (KSR), a scaffold protein for the mitogen-activated protein kinase (MAPK) cascade. Nm23-H1 co-immunoprecipitated KSR from lysates of transiently transfected 293T cells and at endogenous protein expression levels in MDA-MB-435 breast carcinoma cells. Autophosphorylated recombinant Nm23-H1 phosphorylated KSR in vitro. Phosphoamino acid analysis identified serine as the major target, and two peaks of Nm23-H1 phosphorylation were identified upon high performance liquid chromatography analysis of KSR tryptic peptides. Using site-directed mutagenesis, we found that Nm23-H1 phosphorylated KSR serine 392, a 14-3-3-binding site, as well as serine 434 when serine 392 was mutated. Phosphorylated MAPK but not total MAPK levels were reduced in an nm23-H1 transfectant of MDA-MB-435 cells. The data identify a complex in vitro histidine-to-serine protein kinase pathway, which may contribute to signal transduction and metastasis.

The cell biology of phytochrome signalling

Phytochrome signal transduction has in the past often been viewed as being a nonspatially separated linear chain of events. However, through a combination of molecular, genetic and cell biological approaches, it is becoming increasingly evident that phytochrome signalling constitutes a highly ordered multidimensional network of events. The discovery that some phytochromes and signalling intermediates show light-dependent nucleo-cytoplasmic partitioning has not only led to the suggestion that early signalling events take place in the nucleus, but also that subcellular localization patterns most probably represent an important signalling control point. Moreover, detailed characterization of signalling intermediates has demonstrated that various branches of the signalling network are spatially separated and take place in different cellular compartments including the nucleus, cytosol, and chloroplasts. In addition, proteasome-mediated degradation of signalling intermediates most probably act in concert with subcellular partitioning events as an integrated checkpoint. An emerging view from this is that phytochrome signalling is separated into several subcellular organelles and that these are interconnected in order to execute accurate responses to changes in the light environment. By integrating the available data, both at the cellular and subcellular level, we should be able to construct a solid foundation for further dissection of phytochrome signal transduction in plants. Contents Summary 553 I. Introduction 554 II. Nucleus vs cytoplasm 556 III. The nucleus 562 IV. The cytoplasm 571 V. Interactions with other signalling pathways 577 VI. Conclusions and the future 582 Acknowledgements 583 References 583.

HFR1, a phytochrome A-signalling component, acts in a separate pathway from HY5, downstream of COP1 in Arabidopsis thaliana

HFR1, a basic helix-loop-helix protein, is known to be required for a subset of phytochrome A (phyA)-dependent photoresponses. To investigate the role of HFR1 in light signalling, we have examined the genetic interaction between HFR1 and HY5, a positive regulator of light signalling, and COP1, a repressor of photomorphogenesis. Double mutant analysis suggests that HFR1 mediates phyA-dependent inhibition of hypocotyl elongation independently of HY5. HFR1 was shown to be necessary for a subset of cop1-triggered photomorphogenic phenotypes in the dark, including inhibition of hypocotyl elongation, gravitropic hypocotyl growth, and expression of the light-inducible genes CAB and RBCS. Phenotypic analysis of the triple mutant cop1hy5hfr1 indicated that both HFR1 and HY5 are required for cop1-mediated photomorphogenic seedling development in darkness, consistent with their additive roles in phyA-dependent signalling. Taken together, these results suggest that HFR1 might act downstream of COP1, in a separate pathway from HY5, to mediate photomorphogenesis in Arabidopsis.

PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis

Plants sense and respond to red and far-red light using the phytochrome (phy) family of photoreceptors. However, the mechanism of light signal transduction is not well defined. Here, we report the identification of a new mutant Arabidopsis locus, srl2 (short under red-light 2), which confers selective hypersensitivity to continuous red, but not far-red, light. This hypersensitivity is eliminated in srl2phyB, but not srl2phyA, double mutants, indicating that this locus functions selectively and negatively in phyB signaling. The SRL2 gene encodes a bHLH factor, designated PIF4 (phytochrome-interacting factor 4), which binds selectively to the biologically active Pfr form of phyB, but has little affinity for phyA. Despite its hypersensitive morphological phenotype, the srl2 mutant displays no perturbation of light-induced expression of marker genes for chloroplast development. These data suggest that PIF4 may function specifically in a branch of the phyB signaling network that regulates a subset of genes involved in cell expansion. Consistent with this proposal, PIF4 localizes to the nucleus and can bind to a G-box DNA sequence motif found in various light-regulated promoters.