Phytochrome structure and signaling mechanisms

Structure and function of plant photoreceptors

Signaling photoreceptors use the information contained in the absorption of a photon to modulate biological activity in plants and a wide range of organisms. The fundamental-and as yet imperfectly answered-question is, how is this achieved at the molecular level? We adopt the perspective of biophysicists interested in light-dependent signal transduction in nature and the three-dimensional structures that underpin signaling. Six classes of photoreceptors are known: light-oxygen-voltage (LOV) sensors, xanthopsins, phytochromes, blue-light sensors using flavin adenine dinucleotide (BLUF), cryptochromes, and rhodopsins. All are water-soluble proteins except rhodopsins, which are integral membrane proteins; all are based on a modular architecture except cryptochromes and rhodopsins; and each displays a distinct, light-dependent chemical process based on the photochemistry of their nonprotein chromophore, such as isomerization about a double bond (xanthopsins, phytochromes, and rhodopsins), formation or rupture of a covalent bond (LOV sensors), or electron transfer (BLUF sensors and cryptochromes).

Evolutionary studies illuminate the structural-functional model of plant phytochromes

A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red-induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful.

A complex photoreceptor system mediates the regulation by light of the conidiation genes con-10 and con-6 in Neurospora crassa

Genes con-10 and con-6 in Neurospora crassa are activated during conidiation or after illumination of vegetative mycelia. Light activation requires the white-collar complex (WCC), a transcription factor complex composed of the photoreceptor WC-1 and its partner WC-2. We have characterized the photoactivation of con-10 and con-6, and we have identified 300bp required for photoactivation in the con-10 promoter. A complex stimulus-response relationship for con-10 and con-6 photoactivation suggested the activity of a complex photoreceptor system. The WCC is the key element for con-10 activation by light, but we suggest that other photoreceptors, the cryptochrome CRY-1, the rhodopsin NOP-1, and the phytochrome PHY-2, modify the activity of the WCC for con-10 photoactivation, presumably through a repressor. In addition we show that the regulatory protein VE-1 is required for full photocarotenogenesis. We propose that these proteins may modulate the WCC in a gene-specific way.

Photosynthetic redox imbalance governs leaf sectoring in the Arabidopsis thaliana variegation mutants immutans, spotty, var1, and var2

We hypothesized that chloroplast energy imbalance sensed through alterations in the redox state of the photosynthetic electron transport chain, measured as excitation pressure, governs the extent of variegation in the immutans mutant of Arabidopsis thaliana. To test this hypothesis, we developed a nondestructive imaging technique and used it to quantify the extent of variegation in vivo as a function of growth temperature and irradiance. The extent of variegation was positively correlated (R(2) = 0.750) with an increase in excitation pressure irrespective of whether high light, low temperature, or continuous illumination was used to induce increased excitation pressure. Similar trends were observed with the variegated mutants spotty, var1, and var2. Measurements of greening of etiolated wild-type and immutans cotyledons indicated that the absence of IMMUTANS increased excitation pressure twofold during the first 6 to 12 h of greening, which led to impaired biogenesis of thylakoid membranes. In contrast with IMMUTANS, the expression of its mitochondrial analog, AOX1a, was transiently upregulated in the wild type but permanently upregulated in immutans, indicating that the effects of excitation pressure during greening were also detectable in mitochondria. We conclude that mutations involving components of the photosynthetic electron transport chain, such as those present in immutans, spotty, var1, and var2, predispose Arabidopsis chloroplasts to photooxidation under high excitation pressure, resulting in the variegated phenotype.

Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings

Light signals perceived by the phytochromes induce the transition from skotomorphogenic to photomorphogenic development (deetiolation) in dark-germinated seedlings. Evidence that a quadruple mutant (pifq) lacking four phytochrome-interacting bHLH transcription factors (PIF1, 3, 4, and 5) is constitutively photomorphogenic in darkness establishes that these factors sustain the skotomorphogenic state. Moreover, photoactivated phytochromes bind to and induce rapid degradation of the PIFs, indicating that the photoreceptor reverses their constitutive activity upon light exposure, initiating photomorphogenesis. Here, to define the modes of transcriptional regulation and cellular development imposed by the PIFs, we performed expression profile and cytological analyses of pifq mutant and wild-type seedlings. Dark-grown mutant seedlings display cellular development that extensively phenocopies wild-type seedlings grown in light. Similarly, 80% of the gene expression changes elicited by the absence of the PIFs in dark-grown pifq seedlings are normally induced by prolonged light in wild-type seedlings. By comparing rapidly light-responsive genes in wild-type seedlings with those responding in darkness in the pifq mutant, we identified a subset, enriched in transcription factor-encoding genes, that are potential primary targets of PIF transcriptional regulation. Collectively, these data suggest that the transcriptional response elicited by light-induced PIF proteolysis is a major component of the mechanism by which the phytochromes pleiotropically regulate deetiolation and that at least some of the rapidly light-responsive genes may comprise a transcriptional network directly regulated by the PIF proteins.

Homogeneity of phytochrome Cph1 vibronic absorption revealed by resonance Raman intensity analysis

Phytochromes are an important class of red/far-red responsive photoreceptors that act as light-activated biological switches, ultimately driving growth and development in plants, bacteria, and fungi. The composition of the red-absorbing ground-state has been widely debated due to the presence of a shoulder feature on the blue edge of electronic absorption spectra, which many have attributed to the presence of multiple ground-state conformers. Here we use resonance Raman intensity analysis to calculate the vibronic absorption profile of cyanobacterial phytochrome Cph1 and show that this shoulder feature is due simply to vibronic transitions from a single species, thus reflecting a homogeneous ground-state population.

A non-hydrolyzable ATP derivative generates a stable complex in a light-inducible two-component system

Isothermal calorimetry (ITC) measurements yielded the binding constants during complex formation of light-inducible histidine kinases (HK) and their cognate CheY-type response regulators (RR). HK-RR interactions represent the core function of the bacterial two-component system, which is also present in many bacterial phytochromes. Here, we have studied the recombinant forms of phytochromes CphA and CphB from the cyanobacterium Tolypothrix PCC7601 and their cognate RRs RcpA and RcpB. The interaction between the two reaction partners (HK and RR) was studied in the presence and absence of ATP. A complex formation was observable in the presence of ATP, but specific interactions were only found when a non-hydrolyzable ATP derivative was added to the mixture. Also, the incubation of the HK domain alone (expressed as a recombinant protein) with the RR did not yield specific interactions, indicating that the HK domain is only active as a component of the full-length phytochrome. Considering also previous studies on the same proteins (Hübschmann, T., Jorissen, H. J. M. M., Börner, T., Gärtner, W., and de Marsac, N. (2001) Eur. J. Biochem. 268, 3383-3389) we now conclude that the HK domains of these phytochromes are active only when the chromophore domain is in its Pr form. The formerly documented phosphate transfer between the HK domain and the RR takes place via a transiently formed protein-protein complex, which becomes detectable by ITC in the presence of a non-hydrolyzable ATP derivative. This finding is of interest also in relation to the function of some (blue light-sensitive) photoreceptors that carry the HK domain and the RR fused together in one single protein.

Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a "flip-and-rotate" model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.

Cyanochromes are blue/green light photoreversible photoreceptors defined by a stable double cysteine linkage to a phycoviolobilin-type chromophore

Phytochromes are a collection of bilin-containing photoreceptors that regulate a diverse array of processes in microorganisms and plants through photoconversion between two stable states, a red light-absorbing Pr form, and a far red light-absorbing Pfr form. Recently, a novel set of phytochrome-like chromoproteins was discovered in cyanobacteria, designated here as cyanochromes, that instead photoconvert between stable blue and green light-absorbing forms Pb and Pg, respectively. Here, we show that the distinctive absorption properties of cyanochromes are facilitated through the binding of phycocyanobilin via two stable cysteine-based thioether linkages within the cGMP phosphodiesterase/adenyl cyclase/FhlA domain. Absorption, resonance Raman and infrared spectroscopy, and molecular modeling of the Te-PixJ GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA) domain assembled with phycocyanobilin are consistent with attachments to the C3(1) carbon of the ethylidene side chain and the C4 or C5 carbons in the A-B methine bridge to generate a double thioether-linked phycoviolobilin-type chromophore. These spectroscopic methods combined with NMR data show that the bilin is fully protonated in the Pb and Pg states and that numerous conformation changes occur during Pb --> Pg photoconversion. Also identified were a number of photochromically inactive mutants with strong yellow or red fluorescence that may be useful for fluorescence-based cell biological assays. Phylogenetic analyses detected cyanochromes capable of different signaling outputs in a wide range of cyanobacterial species. One unusual case is the Synechocystis cyanochrome Etr1 that also binds ethylene, suggesting that it works as a hybrid receptor to simultaneously integrate light and hormone signals.

Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: reconciling structural and spectroscopic data by QM/MM calculations

A quantum mechanics (QM)/molecular mechanics (MM) hybrid method was applied to the Pr state of the cyanobacterial phytochrome Cph1 to calculate the Raman spectra of the bound PCB cofactor. Two QM/MM models were derived from the atomic coordinates of the crystal structure. The models differed in the protonation site of His(260) in the chromophore-binding pocket such that either the delta-nitrogen (M-HSD) or the epsilon-nitrogen (M-HSE) carried a hydrogen. The optimized structures of the two models display small differences specifically in the orientation of His(260) with respect to the PCB cofactor and the hydrogen bond network at the cofactor-binding site. For both models, the calculated Raman spectra of the cofactor reveal a good overall agreement with the experimental resonance Raman (RR) spectra obtained from Cph1 in the crystalline state and in solution, including Cph1 adducts with isotopically labeled PCB. However, a distinctly better reproduction of important details in the experimental spectra is provided by the M-HSD model, which therefore may represent an improved structure of the cofactor site. Thus, QM/MM calculations of chromoproteins may allow for refining crystal structure models in the chromophore-binding pocket guided by the comparison with experimental RR spectra. Analysis of the calculated and experimental spectra also allowed us to identify and assign the modes that sensitively respond to chromophore-protein interactions. The most pronounced effect was noted for the stretching mode of the methine bridge A-B adjacent to the covalent attachment site of PCB. Due a distinct narrowing of the A-B methine bridge bond angle, this mode undergoes a large frequency upshift as compared with the spectrum obtained by QM calculations for the chromophore in vacuo. This protein-induced distortion of the PCB geometry is the main origin of a previous erroneous interpretation of the RR spectra based on QM calculations of the isolated cofactor.

The histidine kinase-related domain of Arabidopsis phytochrome a controls the spectral sensitivity and the subcellular distribution of the photoreceptor

Phytochrome A (phyA) is the primary photoreceptor for sensing extremely low amounts of light and for mediating various far-red light-induced responses in higher plants. Translocation from the cytosol to the nucleus is an essential step in phyA signal transduction. EID1 (for EMPFINDLICHER IM DUNKELROTEN LICHT1) is an F-box protein that functions as a negative regulator in far-red light signaling downstream of the phyA in Arabidopsis (Arabidopsis thaliana). To identify factors involved in EID1-dependent light signal transduction, pools of ethylmethylsulfonate-treated eid1-3 seeds were screened for seedlings that suppress the hypersensitive phenotype of the mutant. The phenotype of the suppressor mutant presented here is caused by a missense mutation in the PHYA gene that leads to an amino acid transition in its histidine kinase-related domain. The novel phyA-402 allele alters the spectral sensitivity and the persistence of far-red light-induced high-irradiance responses. The strong eid1-3 suppressor phenotype of phyA-402 contrasts with the moderate phenotype observed when phyA-402 is introgressed into the wild-type background, which indicates that the mutation mainly alters functions in an EID1-dependent signaling cascade. The mutation specifically inhibits nuclear accumulation of the photoreceptor molecule upon red light irradiation, even though it still interacts with FHY1 (for far-red long hypocotyl 1) and FHL (for FHY1-like protein), two factors that are essential for nuclear accumulation of phyA. Degradation of the mutated phyA is unaltered even under light conditions that inhibit its nuclear accumulation, indicating that phyA degradation may occur mostly in the cytoplasm.

OsHAL3 mediates a new pathway in the light-regulated growth of rice

Plants show distinct morphologies in different light conditions through a process called photomorphogenesis. A predominant feature of photomorphogenesis is the reduced growth of seedlings under light conditions compared with darkness. For this adaptive event, the most well-known molecular mechanism involves photoreceptor-mediated inhibition of cell elongation. However, it is not known whether additional pathways exist. Here, we describe a newly discovered pathway of light-modulated plant growth mediated by the halotolerance protein HAL3, a flavin mononucleotide (FMN)-binding protein involved in cell division. We found that light, especially blue light, suppresses growth of rice seedlings by reducing the activity of Oryza sativa (Os) HAL3. Both in vitro and in vivo studies showed that OsHAL3 is structurally inactivated by light through photo-oxidation and by direct interaction with photons. In addition, the transcriptional expression of OsHAL3 is synergistically regulated by different light conditions. Further investigation suggested that OsHAL3 promotes cell division by recruiting a ubiquitin system, rather than by its 4'-phosphopantothenoylcysteine (PPC) decarboxylase activity. Our results uncover a new mechanism for light-regulated plant growth, namely, light not only inhibits cell elongation but also suppresses cell division through HAL3 and E3 ubiquitin ligase. This study thus brings new insights into our understanding of plant photomorphogenesis.

Analysis of the phytochrome gene family in Ceratodon purpureus by gene targeting reveals the primary phytochrome responsible for photo- and polarotropism

Using gene targeting by homologous recombination in Ceratodon purpureus, we were able to knock out four phytochrome photoreceptor genes independently and to analyze their function with respect to red light dependent phototropism, polarotropism, and chlorophyll content. The strongest phenotype was found in knock-out lines of a newly described phytochrome gene termed CpPHY4 lacking photo- and polarotropic responses at moderate fluence rates. Eliminating the atypical phytochrome gene CpPHY1, which is the only known phytochrome-like gene containing a putative C-terminal tyrosine kinase-like domain, affects red light-induced chlorophyll accumulation. This result was surprising, since no light dependent function was ever allocated to this unusual gene.

Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome

Visibly fluorescent proteins (FPs) from jellyfish and corals have revolutionized many areas of molecular and cell biology, but the use of FPs in intact animals, such as mice, has been handicapped by poor penetration of excitation light. We now show that a bacteriophytochrome from Deinococcus radiodurans, incorporating biliverdin as the chromophore, can be engineered into monomeric, infrared-fluorescent proteins (IFPs), with excitation and emission maxima of 684 and 708 nm, respectively; extinction coefficient >90,000 M(-1) cm(-1); and quantum yield of 0.07. IFPs express well in mammalian cells and mice and spontaneously incorporate biliverdin, which is ubiquitous as the initial intermediate in heme catabolism but has negligible fluorescence by itself. Because their wavelengths penetrate tissue well, IFPs are suitable for whole-body imaging. The IFPs developed here provide a scaffold for further engineering.

Light is a key factor in triggering sexual reproduction in the pennate diatom Haslea ostrearia

Sexual reproduction is an obligatory phase in the life cycle of most diatoms, as cell size decreases with successive vegetative divisions and the maximal cell size is only restored by a specialized cell, the auxospore, which follows zygote formation as a result of sexual reproduction. While in pennate diatoms the induction of sexual reproduction depends primarily on cell-cell interactions, the importance of different external factors for the induction of sexual reproduction is less well known. Here, we investigated the effects of light on sexualization in the marine benthic pennate diatom Haslea ostrearia (Gaillon) R. Simonsen. Compatible clones were crossed and exposed to different combinations of light levels, qualities, and photoperiods. Light was found to be a key factor for sexualization, and to a certain extent, to control auxosporulation in H. ostrearia. The light conditions most favorable for sexual reproduction were low irradiances (<50 micromolphotons m(-2) s(-1)) and short photoperiods (6-10 h), conditions that prevail during winter, and to a lesser extent, the higher irradiances and longer photoperiods that correspond to the spring and fall, when blooms of this organism form in the natural environment. Auxospore formation was very rare in continuous light, and maximum in presence of red radiation, while it was never observed in darkness or in radiation other than red.

Protein identification and mRNA analysis of phytochrome-regulated genes in Arabidopsis under red light

Phytochromes are a family of plant photoreceptors that mediate physiological and developmental responses to red and far-red light. According to the affymetrix ATH1 microarray, phytochrome A (phyA) and phytochrome B (phyB) together play a key role in transducing the Rc signals to light-responsive genes. In order to select those red light-responsive genes associated with phyA or phyB, a proteomic approach based on two-dimensional gel electrophoresis (2-DE) was used to compare the protein expression patterns of the phyAphyB double mutant and the wild type of Arabidopsis thaliana (col-4) which grew under constant red light conditions for 7 d. Thirty-two protein spots which exhibited differences in protein abundance were identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry. The expression of ten genes corresponding to ten protein spots was analyzed by a semiquantitative reverse transcription-polymerase chain reaction. Two of the ten genes were confirmed by quantitative PCR (Q-PCR). The results showed that phytochromes may exert their function by regulating mRNA or protein expressions. Proteomic analysis may provide a novel pathway for identifying phytochrome-dependent genes.

PIF3 is a repressor of chloroplast development

The phytochrome-interacting factor PIF3 has been proposed to act as a positive regulator of chloroplast development. Here, we show that the pif3 mutant has a phenotype that is similar to the pif1 mutant, lacking the repressor of chloroplast development PIF1, and that a pif1pif3 double mutant has an additive phenotype in all respects. The pif mutants showed elevated protochlorophyllide levels in the dark, and etioplasts of pif mutants contained smaller prolamellar bodies and more prothylakoid membranes than corresponding wild-type seedlings, similar to previous reports of constitutive photomorphogenic mutants. Consistent with this observation, pif1, pif3, and pif1pif3 showed reduced hypocotyl elongation and increased cotyledon opening in the dark. Transfer of 4-d-old dark-grown seedlings to white light resulted in more chlorophyll synthesis in pif mutants over the first 2 h, and analysis of gene expression in dark-grown pif mutants indicated that key tetrapyrrole regulatory genes such as HEMA1 encoding the rate-limiting step in tetrapyrrole synthesis were already elevated 2 d after germination. Circadian regulation of HEMA1 in the dark also showed reduced amplitude and a shorter, variable period in the pif mutants, whereas expression of the core clock components TOC1, CCA1, and LHY was largely unaffected. Expression of both PIF1 and PIF3 was circadian regulated in dark-grown seedlings. PIF1 and PIF3 are proposed to be negative regulators that function to integrate light and circadian control in the regulation of chloroplast development.

Phytochrome A requires jasmonate for photodestruction

The plant photoreceptor phytochrome is organised in a small gene family with phytochrome A (phyA) being unique, because it is specifically degraded upon activation by light. This so called photodestruction is thought to be important for dynamic aspects of sensing such as measuring day length or shading by competitors. Signal-triggered proteolytic degradation has emerged as central element of signal crosstalk in plants during recent years, but many of the molecular players are still unknown. We therefore analyzed a jasmonate (JA)-deficient rice mutant, hebiba, that in several aspects resembles a mutant affected in photomorphogenesis. In this mutant, the photodestruction of phyA is delayed as shown by in vivo spectroscopy and Western blot analysis. Application of methyl-JA (MeJA) can rescue the delayed phyA photodestruction in the mutant in a time- and dose-dependent manner. Light regulation of phyA transcripts thought to be under control of stable phytochrome B (phyB) is still functional. The delayed photodestruction is accompanied by an elevated sensitivity of phytochrome-dependent growth responses to red and far-red light.

Distinct classes of red/far-red photochemistry within the phytochrome superfamily

Phytochromes are a widespread family of photosensory proteins first discovered in plants, which measure the ratio of red to far-red light to control many aspects of growth and development. Phytochromes interconvert between red-absorbing P(r) and far-red-absorbing P(fr) states via photoisomerization of a covalently-bound linear tetrapyrrole (bilin) chromophore located in a conserved photosensory core. From recent crystal structures of this core region, it has been inferred that the chromophore structures of P(r) and P(fr) are conserved in most phytochromes. Using circular dichroism spectroscopy and ab initio calculations, we establish that the P(fr) states of the biliverdin-containing bacteriophytochromes DrBphP and PaBphP are structurally dissimilar from those of the phytobilin-containing cyanobacterial phytochrome Cph1. This conclusion is further supported by chromophore substitution experiments using semisynthetic bilin monoamides, which indicate that the propionate side chains perform different functional roles in the 2 classes of phytochromes. We propose that different directions of bilin D-ring rotation account for these distinct classes of red/far-red photochemistry.

Molecular dynamics simulations of the chromophore binding site of Deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore

The conformational flexibility of the tetrapyrrolic phytochromobilin (PPhiB) chromophore of the bacteriophytochrome Deinococcus radiodurans (DrCBD) in the Pr state has been investigated by molecular dynamics simulations. Because these simulations require accurate force field parameters for the prosthetic group, in the present work we developed new empirical force field parameters for the PPhiB molecule that are compatible with the CHARMM22 force field for proteins. For this reason, the new force field parameters for the nonbonded (partial atomic charges) and bonded (bonds, angles, dihedrals, improper) energy terms were derived by reproducing ab initio target data following the methodology used in the development of the CHARMM22 force field. This new set of parameters was employed to analyze structural and dynamical features of PPhiB inside DrCBD. The 45 ns all-atom molecular dynamics (MD) simulation reveals the existence of two stable conformational states of the chromophore characterized by distinct torsional angles around the C-C bond at the methine bridge connecting rings A and B of the tetrapyrrole. This result supports experimental observations derived from NMR and resonance Raman spectroscopy. Furthermore, statistical analysis of H-bonding events allowed us to identify (a) important H-bonds between the propionic side chains of the chromophore and the apoprotein which may be relevant for the signal transduction step during the photoinduced cycle and (b) a network of eight water molecules which remain in the vicinity of the chromophore during the entire 45 ns production run.

Tightening the knot in phytochrome by single-molecule atomic force microscopy

A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We used protein engineering and atomic force microscopy to explore the single-molecule mechanics of the figure-eight knot in the chromophore-binding domain of the red/far-red photoreceptor, phytochrome. Under load, apo phytochrome unfolds at forces of approximately 47 pN, whereas phytochrome carrying its covalently bound tetrapyrrole chromophore unfolds at approximately 73 pN. These forces are not unusual in mechanical protein unfolding, and thus the presence of the knot does not automatically indicate a superstable protein. Our experiments reveal a stable intermediate along the mechanical unfolding pathway, reflecting the sequential unfolding of two distinct subdomains in phytochrome, potentially the GAF and PAS domains. For the first time (to the best of our knowledge), our experiments allow a direct determination of knot size under load. In the unfolded chain, the tightened knot is reduced to 17 amino acids, resulting in apparent shortening of the polypeptide chain by 6.2 nm. Steered molecular-dynamics simulations corroborate this number. Finally, we find that covalent phytochrome dimers created for these experiments retain characteristic photoreversibility, unexpectedly arguing against a dramatic rearrangement of the native GAF dimer interface upon photoconversion.

Dynamic intracomplex heterogeneity of phytochrome

Low temperature single-molecule fluorescence emission spectroscopy on individual phytochromes from Agrobacterium tumefaciens corroborates findings from ensemble spectroscopy concerning intercomplex heterogeneity. Furthermore, time-dependent intracomplex heterogeneity has been observed.

Blue light induces degradation of the negative regulator phytochrome interacting factor 1 to promote photomorphogenic development of Arabidopsis seedlings

Phytochrome interacting factors (PIFs) are nuclear basic helix-loop-helix (bHLH) transcription factors that negatively regulate photomorphogenesis both in the dark and in the light in Arabidopsis. The phytochrome (phy) family of photoreceptors induces the rapid phosphorylation and degradation of PIFs in response to both red and far-red light conditions to promote photomorphogenesis. Although phys have been shown to function under blue light conditions, the roles of PIFs under blue light have not been investigated in detail. Here we show that PIF1 negatively regulates photomorphogenesis at the seedling stage under blue light conditions. pif1 seedlings displayed more open cotyledons and slightly reduced hypocotyl length compared to wild type under diurnal (12 hr light/12 hr dark) blue light conditions. Double-mutant analyses demonstrated that pif1phyA, pif1phyB, pif1cry1, and pif1cry2 have enhanced cotyledon opening compared to the single photoreceptor mutants under diurnal blue light conditions. Blue light induced the rapid phosphorylation, polyubiquitination, and degradation of PIF1 through the ubi/26S proteasomal pathway. PIF1 interacted with phyA and phyB in a blue light-dependent manner, and the interactions with phys are necessary for the blue light-induced degradation of PIF1. phyA played a dominant role under pulses of blue light, while phyA, phyB, and phyD induced the degradation of PIF1 in an additive manner under prolonged continuous blue light conditions. Interestingly, the absence of cry1 and cry2 enhanced the degradation of PIF1 under blue light conditions. Taken together, these data suggest that PIF1 functions as a negative regulator of photomorphogenesis under blue light conditions and that blue light-activated phys induce the degradation of PIF1 through the ubi/26S proteasomal pathway to promote photomorphogenesis.

Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor

Phytochromes are dimeric chromoproteins that regulate plant responses to red (R) and far-red (FR) light. The Arabidopsis thaliana genome encodes five phytochrome apoproteins: type I phyA mediates responses to FR, and type II phyB-phyE mediate shade avoidance and classical R/FR-reversible responses. In this study, we describe the complete in vivo complement of homodimeric and heterodimeric type II phytochromes. Unexpectedly, phyC and phyE do not homodimerize and are present in seedlings only as heterodimers with phyB and phyD. Roles in light regulation of hypocotyl length, leaf area, and flowering time are demonstrated for heterodimeric phytochromes containing phyC or phyE. Heterodimers of phyC and chromophoreless phyB are inactive, indicating that phyC subunits require spectrally intact dimer partners to be active themselves. Consistent with the obligate heterodimerization of phyC and phyE, phyC is made unstable by removal of its phyB binding partner, and overexpression of phyE results in accumulation of phyE monomers. Following a pulse of red light, phyA, phyB, phyC, and phyD interact in vivo with the PHYTOCHROME INTERACTING FACTOR3 basic helix-loop-helix transcription factor, and this interaction is FR reversible. Therefore, most or all of the type I and type II phytochromes, including heterodimeric forms, appear to function through PIF-mediated pathways. These findings link an unanticipated diversity of plant R/FR photoreceptor structures to established phytochrome signaling mechanisms.

Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness

BACKGROUND

An important contributing factor to the success of terrestrial flowering plants in colonizing the land was the evolution of a developmental strategy, termed skotomorphogenesis, whereby postgerminative seedlings emerging from buried seed grow vigorously upward in the subterranean darkness toward the soil surface.

RESULTS

Here we provide genetic evidence that a central component of the mechanism underlying this strategy is the collective repression of premature photomorphogenic development in dark-grown seedlings by several members of the phytochrome (phy)-interacting factor (PIF) subfamily of bHLH transcription factors (PIF1, PIF3, PIF4, and PIF5). Conversely, evidence presented here and elsewhere collectively indicates that a significant component of the mechanism by which light initiates photomorphogenesis upon first exposure of dark-grown seedlings to irradiation involves reversal of this repression by rapid reduction in the abundance of these PIF proteins, through degradation induced by direct interaction of the photoactivated phy molecule with the transcription factors.

CONCLUSIONS

We conclude that bHLH transcription factors PIF1, PIF3, PIF4, and PIF5 act as constitutive repressors of photomorphogenesis in the dark, action that is rapidly abrogated upon light exposure by phy-induced proteolytic degradation of these PIFs, allowing the initiation of photomorphogenesis to occur.

The dynamics of photosynthesis

Despite recent elucidation of the three-dimensional structure of major photosynthetic complexes, our understanding of light energy conversion in plant chloroplasts and microalgae under physiological conditions requires exploring the dynamics of photosynthesis. The photosynthetic apparatus is a flexible molecular machine that can acclimate to metabolic and light fluctuations in a matter of seconds and minutes. On a longer time scale, changes in environmental cues trigger acclimation responses that elicit intracellular signaling between the nucleo-cytosol and chloroplast resulting in modification of the biogenesis of the photosynthetic machinery. Here we attempt to integrate well-established knowledge on the functional flexibility of light-harvesting and electron transfer processes, which has greatly benefited from genetic approaches, with data derived from the wealth of recent transcriptomic and proteomic studies of acclimation responses in photosynthetic eukaroytes.

Crystallization and preliminary X-ray studies of the chromophore-binding domain of cyanobacteriochrome AnPixJ from Anabaena sp. PCC 7120

Cyanobacteriochromes form a recently defined superfamily of tetrapyrrole-based photoreceptors that are distantly related to conventional red/far-red photoreceptor phytochromes. Among these molecules, AnPixJ from Anabaena sp. PCC 7120 is a novel photoreceptor that shows reversible photoconversion between green-absorbing and red-absorbing forms, which is in contrast to the properties of conventional phytochromes. In order to better understand the structural basis of this unique photoconversion mechanism, the chromophore-binding domain of AnPixJ (AnPixJ-GAF2) was heterologously overproduced and purified, and crystallization of both forms was attempted. Blue crystals of the red-absorbing form of AnPixJ-GAF2 were successfully obtained; they belonged to space group P4(3)2(1)2 and contained one monomer per asymmetric unit. Diffraction data were collected to a resolution of 1.8 A using synchrotron-radiation beamline BL-5A at the Photon Factory.

Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis

PHYTOCHROME INTERACTING FACTOR 3-LIKE5 (PIL5) is a basic helix-loop-helix transcription factor that inhibits seed germination by regulating the expression of gibberellin (GA)- and abscisic acid (ABA)-related genes either directly or indirectly. It is not yet known, however, whether PIL5 regulates seed germination solely through GA and ABA. Here, we used Chromatin immunoprecipitation-chip (ChIP-chip) analysis to identify 748 novel PIL5 binding sites in the Arabidopsis thaliana genome. Consistent with the molecular function of PIL5 as a transcription regulator, most of the identified binding sites are located in gene promoter regions. Binding site analysis shows that PIL5 binds to its target sites mainly through the G-box motif in vivo. Microarray analysis reveals that phytochromes regulate a large number of genes mainly through PIL5 during seed germination. Comparison between the ChIP-chip and microarray data indicates that PIL5 regulates 166 genes by directly binding to their promoters. Many of the identified genes encode transcription regulators involved in hormone signaling, while some encode enzymes involved in cell wall modification. Interestingly, PIL5 directly regulates many transcription regulators of hormone signaling and indirectly regulates many genes involved in hormone metabolism. Taken together, our data indicate that PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds.

Ultrafast excited-state isomerization in phytochrome revealed by femtosecond stimulated Raman spectroscopy

Photochemical interconversion between the red-absorbing (P(r)) and the far-red-absorbing (P(fr)) forms of the photosensory protein phytochrome initiates signal transduction in bacteria and higher plants. The P(r)-to-P(fr) transition commences with a rapid Z-to-E photoisomerization at the C(15)=C(16) methine bridge of the bilin prosthetic group. Here, we use femtosecond stimulated Raman spectroscopy to probe the structural changes of the phycocyanobilin chromophore within phytochrome Cph1 on the ultrafast time scale. The enhanced intensity of the C(15)-H hydrogen out-of-plane (HOOP) mode, together with the appearance of red-shifted C=C stretch and N-H in-plane rocking modes within 500 fs, reveal that initial distortion of the C(15)=C(16) bond occurs in the electronically excited I* intermediate. From I*, 85% of the excited population relaxes back to P(r) in 3 ps, whereas the rest goes on to the Lumi-R photoproduct consistent with the 15% photochemical quantum yield. The C(15)-H HOOP and skeletal modes evolve to a Lumi-R-like pattern after 3 ps, thereby indicating that the C(15)=C(16) Z-to-E isomerization occurs on the excited-state surface.

Residues clustered in the light-sensing knot of phytochrome B are necessary for conformer-specific binding to signaling partner PIF3

The bHLH transcription factor, PHYTOCHROME INTERACTING FACTOR 3 (PIF3), interacts specifically with the photoactivated, Pfr, form of Arabidopsis phytochrome B (phyB). This interaction induces PIF3 phosphorylation and degradation in vivo and modulates phyB-mediated seedling deetiolation in response to red light. To identify missense mutations in the phyB N-terminal domain that disrupt this interaction, we developed a yeast reverse-hybrid screen. Fifteen individual mutations identified in this screen, or in previous genetic screens for Arabidopsis mutants showing reduced sensitivity to red light, were shown to also disrupt light-induced binding of phyB to PIF3 in in vitro co-immunoprecipitation assays. These phyB missense mutants fall into two general classes: Class I (eleven mutants) containing those defective in light signal perception, due to aberrant chromophore attachment or photoconversion, and Class II (four mutants) containing those normal in signal perception, but defective in the capacity to transduce this signal to PIF3. By generating a homology model for the three-dimensional structure of the Arabidopsis phyB chromophore-binding region, based on the crystal structure of Deinococcus radiodurans phytochrome, we predict that three of the four Class II mutated phyB residues are solvent exposed in a cleft between the presumptive PAS and GAF domains. This deduction suggests that these residues could be directly required for the physical interaction of phyB with PIF3. Because these three residues are also necessary for phyB-imposed inhibition of hypocotyl elongation in response to red light, they are functionally necessary for signal transfer from photoactivated phyB, not only to PIF3 and other related bHLH transcription factors tested here, but also to other downstream signaling components involved in regulating seedling deetiolation.

Plants monitor their environment for informational light signals that are used to direct adaptive morphogenic responses. The phytochrome (phy) family of photoreceptors are central to this process. Upon photoperception, phy molecules rapidly translocate to the nucleus where they interact with basic helix-loop-helix transcription factors, termed PIFs (phy-Interacting Factors), and induce gene-expression changes that control morphogenic responses. The molecular determinants in the phy protein responsible for direct intermolecular signal transfer from the activated photoreceptor to transduction partners are undefined. Using random mutagenesis of Arabidopsis phyB, coupled with a reverse-hybrid protein-interaction screen, we identified missense mutations in the N-terminal domain that abrogate the binding of the photoreceptor molecule to PIF3. A subset of these mutated phyB molecules retain the capacity for light-signal perception but are defective in the capacity to transduce that signal to PIF3 and other related PIFs. The mutated residues in these molecules are predicted to cluster at the surface of the protein in a structure termed the “light-sensing knot.” These residues are necessary for phyB-regulated growth in the living plant, establishing that the protein region identified appears to function as a component of the molecular interface responsible for direct signal transfer to transduction partners in the cell.

On the primary event of phytochrome: quantum chemical comparison of photoreactions at C4, C10 and C15

Phytochromes are widespread photoreceptors responsive to red and far-red light that exist in two photochromic forms Pr (inactive) and Pfr (active). The Pr --> Pfr conversion proceeds through a series of events initiated by Z-->E photoisomerization of the tetrapyrrole chromophore, believed to occur at C15 of the methine bridge between rings C and D. Recent crystal structures show that ring D in Pr is less tightly packed by the protein than rings A, B and C, which should favor the C15 reaction over reactions at C4 (AB methine bridge) and C10 (BC). In the present work, quantum chemical methods are used to establish the intrinsic reactivity of the chromophore towards all three possible Z-->E isomerization events in the absence of steric effects and specific interactions with the protein. Using a level of theory that reproduces spectroscopic data with an accuracy of approximately 0.2 eV, it is demonstrated that isolated conditions allow the C10 photoreaction to substantially dominate. This finding suggests that the different degrees of ring-packing observed in the protein are crucial not only to facilitate a reaction at C15, but also to prevent an intrinsically more favorable reaction at C10 from taking place.

A novel protein phosphatase indirectly regulates phytochrome-interacting factor 3 via phytochrome

Light signal transduction in plants involves an intricate series of pathways which is finely regulated by interactions between specific signalling proteins, as well as by protein modifications such as phosphorylation and ubiquitination. The identification of novel phytochrome-interacting proteins and the precise signalling mechanisms that they mediate is still ongoing. In our present study, we show that the newly identified putative phytochrome-associated protein, PAPP2C (phytochrome-associated protein phosphatase type 2C), interacts in the nucleus with phyA (phytochrome A) and phyB, both in vitro and in vivo. Moreover, the phosphatase activity of PAPP2C and its association with phytochromes were found to be enhanced by red light, indicating that it plays a role in mediating phytochrome signalling. In particular, PAPP2C specifically binds to the N-terminal PHY domain of the phytochromes. We thus speculate that this interaction reflects a unique regulatory function of this phosphatase toward established phytochrome-associated proteins. We also show that PAPP2C effectively dephosphorylates phytochromes in vitro. Interestingly, PAPP2C indirectly mediates the dephosphorylation of PIF3 (phytochrome-interacting factor 3) in vitro. Taken together, we suggest that PAPP2C functions as a regulator of PIF3 by dephosphorylating phytochromes in the nucleus.

A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks

Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su and Lagarias, 2007). In the present study, comparative transcription profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole-genome transcription profiles of dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to but quantitatively greater than those of wild-type seedlings grown under 15 or 50 micromol m(-2) m(-1) continuous red light (Rc). Among the 2977 genes statistically significant two-fold (SSTF) regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways, and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-regulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway(s) strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.

Environmental effects on spatial and temporal patterns of leaf and root growth

Leaves and roots live in dramatically different habitats, but are parts of the same organism. Automated image processing of time-lapse records of these organs has led to understanding of spatial and temporal patterns of growth on time scales from minutes to weeks. Growth zones in roots and leaves show distinct patterns during a diel cycle (24 h period). In dicot leaves under nonstressful conditions these patterns are characterized by endogenous rhythms, sometimes superimposed upon morphogenesis driven by environmental variation. In roots and monocot leaves the growth patterns depend more strongly on environmental fluctuations. Because the impact of spatial variations and temporal fluctuations of above- and belowground environmental parameters must be processed by the plant body as an entire system whose individual modules interact on different levels, growth reactions of individual modules are often highly nonlinear. A mechanistic understanding of plant resource use efficiency and performance in a dynamically fluctuating environment therefore requires an accurate analysis of leaf and root growth patterns in conjunction with knowledge of major intraplant communication systems and metabolic pathways.

Light controls shoot meristem organogenic activity and leaf primordia growth during bud burst in Rosa sp

Light controls bud burst in many plants, which subsequently affects their architecture. Nevertheless, very little is known about this photomorphogenic process. This study ascertains the effects of light on bud burst and on two of its components, i.e. growth of preformed leaves and meristem organogenesis in six cultivars from three Rosa species (R. hybrida L., R. chinensis L., R. wichurana L.). Defoliated plants were severed above the third basal bud and exposed, either to darkness or to different intensities of white light, to blue, red or to FR, at constant temperature. Bud bursting was inhibited in darkness in the six cultivars of Rosa, but not in Arabidopsis, tomato and poplar plants under the same condition. In all Rosa cultivars, bud burst, growth of preformed leaves and meristem organogenesis were triggered by blue and red lights, and extended by increasing light intensities. FR was inhibitory of bud burst. Partial shading experiments demonstrated that bud and not stem was the active site for light perception in bud burst.