Regulation of photoperiodic flowering by Arabidopsis photoreceptors

Photoperiodism is a day-length-dependent seasonal change of physiological or developmental activities that is widely found in plants and animals. Photoperiodic flowering in plants is regulated by photosensory receptors including the red/far-red light-receptor phytochromes and the blue/UV-A light-receptor cryptochromes. However, the molecular mechanisms underlying the specific roles of individual photoreceptors have remained poorly understood. Here, we report a study of the day-length-dependent response of cryptochrome 2 (cry2) and phytochrome A (phyA) and their role as day-length sensors in Arabidopsis. The protein abundance of cry2 and phyA showed a diurnal rhythm in plants grown in short-day but not in plants grown in long-day. The short-day-specific diurnal rhythm of cry2 is determined primarily by blue light-dependent cry2 turnover. Consistent with a proposition that cry2 and phyA are the major day-length sensors in Arabidopsis, we show that phyA mediates far-red light promotion of flowering with modes of action similar to that of cry2. Based on these results and a finding that the photoperiodic responsiveness of plants depends on light quality, a model is proposed to explain how individual phytochromes and cryptochromes work together to confer photoperiodic responsiveness in Arabidopsis.

Blue light activates calcium-permeable channels in Arabidopsis mesophyll cells via the phototropin signaling pathway

Light is a central regulator of plant growth and development. Among the processes triggered by blue and UV-A light, phototropism, stomatal movement, and chloroplast orientation rely on the activation of blue-light receptors known as phototropins. So far, these photoreceptors constitute a class of light receptor kinases unique to the plant kingdom. In Arabidopsis thaliana, the two members phot1 and phot2 have been shown to display partially overlapping functions. Up to now little is known about the signaling cascade, which links these phototropins to the physiological responses downstream of blue-light perception. Here, we show that on illumination with blue light, but not red light, voltage-dependent and calcium-permeable channels activate in the plasma membrane of mesophyll cells. Blue-light stimulation in the presence of the photosynthetic electron transport inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethylurea, indicates that blue-light receptors rather than photosynthesis control channel activity. Sensitivity toward the protein kinase inhibitor K252a further pointed to the possible involvement of light receptor kinases. In support of this hypothesis, in the photoreceptor mutant phot1-5, blue-light induction of calcium currents was dramatically reduced and was eliminated in the double mutant phot1-5 phot2-1. By contrast, in cry1-304 cry2-1, an Arabidopsis mutant lacking another class of plant blue-light receptors, the channel remained sensitive to blue light. We thus conclude that blue light triggers calcium fluxes via the phototropin-activated calcium-permeable channel.

Arabidopsis ICX1 is a negative regulator of several pathways regulating flavonoid biosynthesis genes

Flavonoid biosynthesis gene expression is controlled by a range of endogenous and environmental signals. The Arabidopsis icx1 (increased chalcone synthase expression 1) mutant has elevated induction of CHS (CHALCONE SYNTHASE) and other flavonoid biosynthesis genes in response to several stimuli. We show that ICX1 is a negative regulator of the cryptochrome 1, phytochrome A, ultraviolet (UV)-B, low temperature, sucrose, and cytokinin induction of CHS expression and/or anthocyanin accumulation, demonstrating that these pathways are regulated either directly or indirectly by at least one common component. Expression analysis of CHS and other genes (LTP, CAB, and rbcS) indicates that ICX1 functions in both seedlings and mature leaf tissue and acts principally in the epidermis, consistent with the alterations in epidermal development seen in icx1. The mutant was unaltered in the synergistic interactions between UV-B, blue, and UV-A light that regulate CHS and we propose a model of action of ICX1 in these responses.

A thermosensory pathway controlling flowering time in Arabidopsis thaliana

Onset of flowering is controlled by environmental signals such as light and temperature. Molecular-genetic studies in Arabidopsis thaliana have focused on daily light duration, or photoperiod, and transient exposure to winter-like temperatures, or vernalization. Yet ambient growth temperature, which is strongly affected by current changes in global climate, has been largely ignored. Here, we show that genes of the autonomous pathway, previously thought only to act independently of the environment as regulators of the floral repressor FLC (ref. 1), are centrally involved in mediating the effects of ambient temperature. In contrast to wild-type plants and those mutant in other pathways, autonomous-pathway mutants flower at the same time regardless of ambient temperature. In contrast, the exaggerated temperature response of cryptochrome-2 mutants is caused by temperature-dependent redundancy with the phytochrome A photoreceptor. As with vernalization and photoperiod, ambient temperature ultimately affects expression of the floral pathway integrator FT.

The phototropin family as photoreceptors for blue light-induced chloroplast relocation

Blue light-induced chloroplast accumulation and avoidance relocation movements are controlled by the blue light photoreceptor phototropin. The Arabidopsis thaliana genome has two phototropin genes encoding phot1 and phot2. Each of these photoreceptors contains two LOV (light oxygen and voltage) domains and a kinase domain. The LOV domains absorb blue light though an associated flavin mononucleotide chromophore, while the kinase domain is thought to be associated with signal transduction. The phototropins control not only chloroplast relocation movement, but also blue light-induced phototropic responses, leaf expansion and stomatal opening. Here I review the role of phototropin as a photoreceptor for chloroplast photorelocation movement.

Mouse dexamethasone-induced RAS protein 1 gene is expressed in a circadian rhythmic manner in the suprachiasmatic nucleus

We identified the Dexamethasone-induced RAS protein 1 (Dexras1) gene as a cycling gene in the suprachiasmatic nucleus (SCN). Investigation of the whole brain using in situ hybridization demonstrated the localization of the expression of the gene in the SCN, thalamus, piriform cortex and hippocampus. However, rhythmic expression of the gene was observed only in the SCN. The rhythmic change in gene expression during 1 day was approximately five-fold, and the maximum expression was observed during subjective night. Real-time PCR using the SCN, paraventricular nucleus and cortex confirmed these results. Next, we analyzed the expression of the Dexras1 gene in the SCN of cryptochrome (Cry) 1 and 2 double knockout mice. We found that the rhythmic expression disappeared. The results indicate that Dexras1 rhythmicity and levels are dependent upon CRYs. This is the first time that the G protein, which may be involved in the input pathway, has been isolated as a cycling gene in the SCN.

The LOV domain family: photoresponsive signaling modules coupled to diverse output domains

For single-cell and multicellular systems to survive, they must accurately sense and respond to their cellular and extracellular environment. Light is a nearly ubiquitous environmental factor, and many species have evolved the capability to respond to this extracellular stimulus. Numerous photoreceptors underlie the activation of light-sensitive signal transduction cascades controlling these responses. Here, we review the properties of the light, oxygen, or voltage (LOV) family of blue-light photoreceptor domains, a subset of the Per-ARNT-Sim (PAS) superfamily. These flavin-binding domains, first identified in the higher-plant phototropins, are now shown to be present in plants, fungi, and bacteria. Notably, LOV domains are coupled to a wide array of other domains, including kinases, phosphodiesterases, F-box domains, STAS domains, and zinc fingers, which suggests that the absorption of blue light by LOV domains regulates the activity of these structurally and functionally diverse domains. LOV domains contain a conserved molecular volume extending from the flavin cofactor, which is the locus for light-driven structural change, to the molecular surface. We discuss the role of this conserved volume of structure in LOV-regulated processes.

Intramolecular proton transfers and structural changes during the photocycle of the LOV2 domain of phototropin 1

The phototropins are a family of membrane-associated flavoproteins that function as the primary blue light receptors regulating phototropism, chloroplast movements, stomatal opening, and leaf expansion in plants. Phot1, a member of this family, contains two FMN-binding domains, LOV1 and LOV2, within the N-terminal region and a C-terminal serine-threonine protein kinase domain. Light irradiation of oat phot1 LOV2 produces a cysteinyl adduct (Cys-39) at the flavin C(4a) position, which decays thermally back to the dark state. We measured pH and isotope effects on the photocycle. Between pH 3.7 and 9.5, adduct formation showed minimal pH dependence, and adduct decay showed only slight pH dependence, indicating that the pK values of mechanistically relevant groups are outside this range. LOV2 showed a nearly 5-fold slowing of adduct formation in D(2)O relative to H(2)O, indicating that the rate-limiting step involves proton transfer(s). Light-induced changes in the far UV CD spectrum of LOV2 revealed putative protein structural perturbations. The light minus dark CD difference spectrum resembles an inverted alpha-helix spectrum, suggesting that alpha-helicity is reversibly lost upon light irradiation. Decay kinetics for CD spectral changes in the far UV region occur at the same rate as those in the visible region, indicating synchronous relaxation of protein and chromophore structures.

Rhythmic histone acetylation underlies transcription in the mammalian circadian clock

In the mouse circadian clock, a transcriptional feedback loop is at the centre of the clockwork mechanism. Clock and Bmal1 are essential transcription factors that drive the expression of three period genes (Per1-3) and two cryptochrome genes (Cry1 and Cry2). The Cry proteins feedback to inhibit Clock/Bmal1-mediated transcription by a mechanism that does not alter Clock/Bmal1 binding to DNA. Here we show that transcriptional regulation of the core clock mechanism in mouse liver is accompanied by rhythms in H3 histone acetylation, and that H3 acetylation is a potential target of the inhibitory action of Cry. The promoter regions of the Per1, Per2 and Cry1 genes exhibit circadian rhythms in H3 acetylation and RNA polymerase II binding that are synchronous with the corresponding steady-state messenger RNA rhythms. The histone acetyltransferase p300 precipitates together with Clock in vivo in a time-dependent manner. Moreover, the Cry proteins inhibit a p300-induced increase in Clock/Bmal1-mediated transcription. The delayed timing of the Cry1 mRNA rhythm, relative to the Per rhythms, is due to the coordinated activities of Rev-Erbalpha and Clock/Bmal1, and defines a new mechanism for circadian phase control.

Light signalling in cryptochrome-deficient mice

The mammalian master clock driving circadian rhythmicity in physiology, metabolism, and behaviour resides within the suprachiasmatic nuclei (SCN) of the anterior hypothalamus and is composed of intertwined negative and positive autoregulatory transcription-translation feedback loops. The Cryptochrome 1 and 2 gene products act in the negative feedback loop and are indispensable for molecular core oscillator function, as evident from the arrhythmic wheel running behaviour and absence of cyclic clock gene expression in mCry1/mCry2 double mutant mice in constant darkness. Recently, we have measured real-time multi-unit electrode activity recordings in hypothalamic slices from mCry-deficient mice kept in constant darkness and observed a complete lack of circadian oscillations in firing patterns. This proves that CRY proteins, and thus an intact circadian clock, are prerequisite for circadian rhythmicity in membrane excitability in SCN neurons. Strikingly, when mCry-deficient mice are housed in normal light-dark cycles, a single non-circadian peak in neuronal activity can be detected in SCN slices prepared two hours after the beginning of the day. This light-induced increase in electric activity of the SCN suggests that deletion of the mCry genes converts the core oscillator in an hour-glass-like timekeeper and may explain why in normal day-night cycles mCry-deficient mice show apparently normal behaviour.

The role of phosphorylation and degradation of hPER protein oscillation in normal human fibroblasts

The circadian expression in Drosophila of clock gene products, such as PER and TIM, is thought to be important for driving overt rhythms. The constitutive expression of per by the heat-shock or rhodopsin promoters restores rhythmicity of the null allele of per, suggesting that per mRNA cycling may not be required for protein cycling or for locomotor rhythms. Furthermore, the constitutive expression of tim mRNA also supports protein cycling and behavioural rhythms in tim mutant flies. Other reports have also shown that eliminating the oscillations of PER and TIM proteins by their over-expression abrogated circadian rhythmicity. These data indicate that the circadian rhythmic expression of PER and TIM proteins is also important like their rhythmic mRNA expression in Drosophila. To compare the molecular mechanism of circadian clocks in divergent species, we report here cloning circadian mRNA and protein expression profiling of human clock genes in normal human fibroblasts. Circadian oscillations of hPer1, hPer2, hPer3, hBMAL1 and hCry2 mRNA expression were observed in serum-stimulated normal human fibroblasts. The serum shock of human fibroblasts also caused daily oscillations in the amount and size of human PER proteins as was shown using our novel antibodies. Inhibitor studies indicate that phosphorylation and degradation of PER proteins is an important process in the human molecular clock.

Cryptochromes and inner retinal non-visual irradiance detection

Nearly all circadian clocks have free-running periods that differ significantly from 24 hours. To maintain synchrony with the 24 h day, the mammalian circadian clock is reset by light. Unlike other animals, mammalian circadian entrainment occurs exclusively via the eyes and optic nerves. Remarkably, the classical photoreceptors--the rods and cones--are not necessary for photic entrainment. Instead, a subset of inner retinal ganglion cells are directly photoresponsive and transmit photic information specifically to brain centres involved in irradiance detection, including the master circadian pacemaker in the suprachiasmatic nucleus of the hypothalamus. The photopigment(s) responsible for inner retinal phototransduction are unknown. Several lines of evidence constrain candidate photopigments. First, near-total vitamin A depletion does not diminish retinohypothalamic signalling. Second, loss of cryptochrome function in retinal-degenerate mice substantially decreases photic signalling to the suprachiasmatic nucleus, and markedly decreases pupillary light responses. Third, vitamin A depletion of cryptochrome mutant mice leads to loss of photic signalling to the suprachiasmatic nucleus. These findings suggest a model where either classical photopigments or inner retinal photopigments are sufficient for non-visual irradiance detection.

Contrary to other non-photic cues, acute melatonin injection does not induce immediate changes of clock gene mRNA expression in the rat suprachiasmatic nuclei

The suprachiasmatic nuclei (SCN) contain the main clock of the mammalian circadian system. The endogenous oscillation machinery involves interactive positive and negative transcriptional and posttranslational feedback loops involving the clock genes Per1, Per2, Per3, Clock, Bmal1, Cry1 and Cry2. The SCN endogenous oscillation is entrained to 24 h by the light/dark cycle. Light induced regulation of Per1 and Per2 mRNA expression have been suggested to take part in the clock resetting. However, other factors have chronobiotic and synchronizing effects on SCN activity. Especially, the nocturnal pineal gland hormone, melatonin, which is involved in the regulation of both circadian and seasonal rhythms, is known to feedback on the SCN. Melatonin applied on SCN slices immediately phase-shifts their neuronal electrical activity, while daily injections of melatonin to free running rodents resynchronize their locomotor activity to 24 h. To determine whether melatonin feedback control on SCN activity implicates transcriptional regulation of the clock genes, we monitored the expression pattern of Per 1, 2, 3, Bmal1, Cry1 and AVP mRNAs after a single melatonin injection at the end of the subjective day. Results showed that melatonin injection affected none of the mRNA expression pattern during the first circadian night. Per1, Per3, Bmal1 and AVP expression patterns were, however, significantly but differentially affected, during the second subjective night after the melatonin injection. The present results strongly suggest that the immediate phase shifting effect of melatonin on the SCN molecular loop implicates rather post-translational than transcriptional mechanisms.

Circadian profile and photic regulation of clock genes in the suprachiasmatic nucleus of a diurnal mammal Arvicanthis ansorgei

The molecular mechanisms of the mammalian circadian clock located in the suprachiasmatic nucleus have been essentially studied in nocturnal species. Currently, it is not clear if the clockwork and the synchronizing mechanisms are similar between diurnal and nocturnal species. Here we investigated in a day-active rodent Arvicanthis ansorgei, some of the molecular mechanisms that participate in the generation of circadian rhythmicity and processing of photic signals. In situ hybridization was used to characterize circadian profiles of expression of Per1, Per2, Cry2 and Bmal1 in the suprachiasmatic nucleus of A. ansorgei housed in constant dim red light. All the clock genes studied showed a circadian expression. Per1 and Per2 mRNA increased during the subjective day and decreased during the subjective night. Also, Bmal1 exhibited a circadian expression, but in anti-phase to that of Per1. The expression of Cry2 displayed a circadian pattern, increasing during the late subjective day and decreasing during the late subjective night. We also obtained the phase responses to light for wheel-running rhythm and clock gene expression. At a behavioral level, light was able to induce phase shifts only during the subjective night, like in other diurnal and nocturnal species. At a molecular level, light pulse exposure during the night led to an up-regulation of Per1 and Per2 concomitant with a down-regulation of Cry2 in the suprachiasmatic nucleus of A. ansorgei. In contrast, Bmal1 expression was not affected by light pulses at the circadian times investigated. This study demonstrates that light exposure during the subjective night has opposite effects on the expression of the clock genes Per1 and Per2 compared with that of Cry2. These differential effects can participate in photic resetting of the circadian clock. Our data also indicate that the molecular mechanisms underlying circadian rhythmicity and photic synchronization share clear similarities between diurnal and nocturnal mammals.

Cryptochrome structure and signal transduction

Cryptochromes are photosensory receptors mediating light regulation of growth and development in plants. Since the isolation of the Arabidopsis CRY1 gene in 1993, cryptochromes have been found in every multicellular eukaryote examined. Most plant cryptochromes have a chromophore-binding domain that shares similar structure with DNA photolyase, and a carboxyl terminal extension that contains a DQXVP-acidic-STAES (DAS) domain conserved from moss, to fern, to angiosperm. In Arabidopsis, cryptochromes are nuclear proteins that mediate light control of stem elongation, leaf expansion, photoperiodic flowering, and the circadian clock. Cryptochromes may act by interacting with proteins such as phytochromes, COP1, and clock proteins, or/and chromatin and DNA. Recent studies suggest that cryptochromes undergo a blue light-dependent phosphorylation that affects the conformation, intermolecular interactions, physiological activities, and protein abundance of the photoreceptors.

Identification of a new cryptochrome class. Structure, function, and evolution

Cryptochrome flavoproteins, which share sequence homology with light-dependent DNA repair photolyases, function as photoreceptors in plants and circadian clock components in animals. Here, we coupled sequencing of an Arabidopsis cryptochrome gene with phylogenetic, structural, and functional analyses to identify a new cryptochrome class (cryptochrome DASH) in bacteria and plants, suggesting that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. The cryptochrome crystallographic structure, reported here for Synechocystis cryptochrome DASH, reveals commonalities with photolyases in DNA binding and redox-dependent function, despite distinct active-site and interaction surface features. Whole genome transcriptional profiling together with experimental confirmation of DNA binding indicated that Synechocystis cryptochrome DASH functions as a transcriptional repressor.

Photoperiod differentially regulates clock genes' expression in the suprachiasmatic nucleus of Syrian hamster

The suprachiasmatic nuclei (SCN) contain the master circadian pacemaker in mammals. Generation and maintenance of circadian oscillations involve clock genes which interact to form transcriptional/translational loops and constitute the molecular basis of the clock. There is some evidence that the SCN clock can integrate variations in day length, i.e. photoperiod. However, the effects of photoperiod on clock-gene expression remain largely unknown. We here report the expression pattern of Period (Per) 1, Per2, Per3, Cryptochrome (Cry) 1, Cry2, Bmal1 and Clock genes in the SCN of Syrian hamsters when kept under long (LP) and short (SP) photoperiods. Our data show that photoperiod differentially affects the expression of all clock genes studied. Among the components of the negative limb of the feedback loop, Per1, Per2, Per3, Cry2 but not Cry1 genes show a shortened duration of their peak expression under SP compared with LP. Moreover, mRNA expression of Per1, Per3 and Cry1 are phase advanced in SP compared with LP. Per3 shows an mRNA peak of higher amplitude under SP conditions whereas Per1 and Per2 peak amplitudes are unaffected by photoperiod changes. Bmal1 expression is phase advanced without a change of duration in SP compared with LP. Furthermore, the expression of Clock is rhythmic under SP whereas no rhythm is observed under LP. These results, which provide further evidence that the core clock mechanisms of the SCN integrate photoperiod, are discussed in the context of the existing molecular model.

Ab initio quantum chemical investigation of the first steps of the photocycle of phototropin: a model study

Phototropin is a blue light-activated photoreceptor that plays a dominant role in the phototropism of plants. The protein contains two subunits that bind flavin mononucleotide (FMN), which are responsible for the initial steps of the light-induced reaction. It has been proposed that the photoexcited flavin molecule adds a cysteine residue of the protein backbone, thus activating autophosphorylation of the enzyme. In this study, the electronic properties of several FMN-related compounds in different charge and spin states are characterized by means of ab initio quantum mechanical calculations. The model compounds serve as idealized model chromophores for phototropism. Reaction energies are estimated for simple model reactions, roughly representing the addition of a cysteine residue to the flavin molecule. Excitation energies were calculated with the help of time-dependent density functional theory. On the basis of these calculations we propose the following mechanism for the addition reaction: (1) after photoexcitation of FMN out of the singlet ground state S0, excited singlet state(s) are populated; these relax to the lowest excited singlet state S1, and subsequently by intersystem crossing FMN in the lowest triplet state, T1 is formed; (2) the triplet easily removes the neutral hydrogen atom from the H-S group of the cysteine residue; and (3) the resulting thio radical is added.

Characterization of cry1, cry2, and cry9 genes in Bacillus thuringiensis isolates from China

Bacillus thuringiensis isolates from different ecological regions and sources of China were analyzed to study the distribution and diversity of cry genes and to detect the presence of novel cry genes. Strains containing cry1-type genes were the most abundant and represent 237 of the 310 B. thuringiensis isolates (76.5%). About 70 and 15.5% of the isolates contained a cry2 gene or cry9 gene, respectively, while 10.0% of the strains did not contain a cry1, cry2, or cry9 gene. Among the cry1 containing isolates, cry1A (67.7%), cry1I (60.6%), cry1C (43.9%), and cry1D (39.4%) genes were the most abundant. Forty-three different cry1 gene profiles were detected in this collection. Several cry1 genes were associated at a high frequency, such as the cry1C-cry1D and cry1A-cry1I gene combination. The cry1A and cry2 amplicons were digested with selected restriction enzymes to examine sequence diversity. Based on this RFLP analysis, one novel cry1A-type gene was observed.

Vibrational spectroscopy of an algal Phot-LOV1 domain probes the molecular changes associated with blue-light reception

The LOV1 domain of the blue light Phot1-receptor (phototropin homolog) from Chlamydomonas reinhardtii has been studied by vibrational spectroscopy. The FMN modes of the dark state of LOV1 were identified by preresonance Raman spectroscopy and assigned to molecular vibrations. By comparing the blue-light-induced FTIR difference spectrum with the preresonance Raman spectrum, most of the differences are due to FMN modes. Thus, we exclude large backbone changes of the protein that might occur during the phototransformation of the dark state LOV1-447 into the putative signaling state LOV1-390. Still, the presence of smaller amide difference bands cannot be excluded but may be masked by overlapping FMN modes. The band at 2567 cm(-1) is assigned to the S-H stretching vibration of C57, the residue that forms the transient thio-adduct with the chromophore FMN. The occurrence of this band is evidence that C57 is protonated in the dark state of LOV1. This result challenges conclusions from the homologous LOV2 domain from oat that the thiolate of the corresponding cysteine is the reactive species.

A role for cryptochromes in sleep regulation

BACKGROUND

The cryptochrome 1 and 2 genes (cry1 and cry2) are necessary for the generation of circadian rhythms, as mice lacking both of these genes (cry1,2-/-) lack circadian rhythms. We studied sleep in cry1,2-/- mice under baseline conditions as well as under conditions of constant darkness and enforced wakefulness to determine whether cryptochromes influence sleep regulatory processes.

RESULTS

Under all three conditions, cry1,2-/- mice exhibit the hallmarks of high non-REM sleep (NREMS) drive (i.e., increases in NREMS time, NREMS consolidation, and EEG delta power during NREMS). This unexpected phenotype was associated with elevated brain mRNA levels of period 1 and 2 (per1,2), and albumin d-binding protein (dbp), which are known to be transcriptionally inhibited by CRY1,2. To further examine the relationship between circadian genes and sleep homeostasis, we examined wild type mice and rats following sleep deprivation and found increased levels of per1,2 mRNA and decreased levels of dbp mRNA specifically in the cerebral cortex; these changes subsided with recovery sleep. The expression of per3, cry1,2, clock, npas2, bmal1, and casein-kinase-1epsilon did not change with sleep deprivation.

CONCLUSIONS

These results indicate that mice lacking cryptochromes are not simply a genetic model of circadian arrhythmicity in rodents and functionally implicate cryptochromes in the homeostatic regulation of sleep.