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PubMed2002

Photolyase/cryptochrome blue-light photoreceptors use photon energy to repair DNA and reset the circadian clock.

Blue light governs a number of cellular responses in bacteria, plants, and animals, including photoreactivation, plant development, and circadian photoentrainment. These activities are mediated by a family of highly conserved flavoproteins, the photolyase/cryptochrome family. Photolyase binds to UV photoproducts in DNA and repairs them in a process called photoreactivation in which blue light is used to initiate a cyclic electron transfer to break bonds and restore the integrity of DNA. Cryptochrome, which has a high degree of sequence identity to photolyase, works as the main circadian photoreceptor and as a component of the molecular clock in animals, including mammals, and regulates growth and development in plants.

Amino Acid Sequence↗
PubMed2002

Zebrafish CRY represses transcription mediated by CLOCK-BMAL heterodimer without inhibiting its binding to DNA.

BACKGROUND: CLOCK and BMAL1 proteins, members of the basic helix-loop-helix PAS (PER-ARNT-SIM) superfamily of transcription factors which bind to the E-box DNA motif, are required for the high-level expression of the circadian clock genes period (per) and cryptochrome (cry). CRY inhibits transcriptional activity of the CLOCK-BMAL1 heterodimer, generating a negative-feedback loop that is the core element of the circadian oscillator. RESULTS: We show that zebrafish CRY (zCRY1a) neither disrupts the association between zfCLOCK and zfBMAL nor inhibits binding of the zfCLOCK-zfBMAL heterodimer to an E-box-bearing DNA fragment. Instead it binds to the heterodimer to form a stable zCRY1a-zfCLOCK-zfBMAL-E-box complex. Another zebrafish CRY protein, zCRY4, does not have transcriptional inhibitor activity, whereas zCRY1a has strong activity. zCRY4 does not associate with zfCLOCK and zfBMAL. We also show that the presence of a chemical reductant in the reaction mixture is crucial for efficient binding of the CLOCK-BMAL heterodimer to E-box bearing DNA, which is indicative of the reduction/oxidation (redox)-sensitive character of the heterodimer. CONCLUSIONS: Our findings suggest that CRY represses CLOCK-BMAL-mediated transcription by interacting directly with the zfCLOCK-zfBMAL-E-box complex.

ARNTL Transcription Factors↗
PubMed1995

Mutations throughout an Arabidopsis blue-light photoreceptor impair blue-light-responsive anthocyanin accumulation and inhibition of hypocotyl elongation.

This paper reports the characterization of novel mutations within the Arabidopsis thaliana HY4 gene, which has previously been shown to encode a protein (CRY1) with characteristics of a blue-light photoreceptor. Several point mutations were identified within the amino-terminal domain of CRY1--this region of CRY1 has high homology to photolyase and is likely to be involved in blue-light-mediated electron transfer. Mutations were found within the region of homology to the known chromophore binding domains of photolyase. Point mutations within the 200 amino acid carboxy-terminal extension distinguishing CRY1 from photolyase, likewise disrupt function of the protein. CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition of hypocotyl elongation and we now report that anthocyanin accumulation in germinating seedlings is an additional phenotype under the control of this photoreceptor--this is shown to be mediated in part by modulation of mRNA levels of chalcone synthase, one of the anthocyanin biosynthetic enzymes. The effect of the novel mutations on both inhibition of hypocotyl elongation and anthocyanin biosynthesis have been evaluated, and it is demonstrated that mutations with less severe effects on hypocotyl elongation show a similarly reduced effect on anthocyanin biosynthesis. These results are consistent with the cryptochrome photoreceptor mediating multiple regulatory pathways by the same primary mode of action.

Amino Acid Sequence↗
PubMed1998

UV-B-induced photomorphogenesis in Arabidopsis thaliana.

Relatively little is known about the types of photomorphogenic responses and signal transduction pathways that plants employ in response to ultraviolet-B (UV-B, 290-320 nm) radiation. In wild-type Arabidopsis seedlings, hypocotyl growth inhibition and cotyledon expansion were both reproducibly promoted by continuous UV-B. The fluence rate response of hypocotyl elongation was examined and showed a biphasic response. Whereas photomorphogenic responses were observed at low doses, higher fluences resulted in damage symptoms. In support of our theory that photomorphogenesis, but not damage, occurs at low doses of UV-B, photomorphogenic responses of UV-B sensitive mutants were indistinguishable from wild-type plants at the low dose. This allowed us to examine UV-B-induced photomorphogenesis in photoreceptor deficient plants and constitutive photomorphogenic mutants. The cry1 cryptochrome structural gene mutant, and phytochrome deficient hy1, phyA and phyB mutant seedlings resembled wild-type seedlings, while phyA/phyB double mutants were less sensitive to the photomorphogenic effects of UV-B. These results suggest that either phyA or phyB is required for UV-B-induced photomorphogenesis. The constitutive photomorphogenic mutants cop1 and det1 did not show significant inhibition of hypocotyl growth in response to UV-B, while det2 was strongly affected by UV-B irradiation. This suggests that COP1 and DET1 work downstream of the UV-B signaling pathway.

Arabidopsis↗
PubMed2006

The BMAL1 C terminus regulates the circadian transcription feedback loop.

The circadian clock is driven by cell-autonomous transcription/translation feedback loops. The BMAL1 transcription factor is an indispensable component of the positive arm of this molecular oscillator in mammals. Here, we present a molecular genetic screening assay for mutant circadian clock proteins that is based on real-time circadian rhythm monitoring in cultured fibroblasts. By using this assay, we identified a domain in the extreme C terminus of BMAL1 that plays an essential role in the rhythmic control of E-box-mediated circadian transcription. Remarkably, the last 43 aa of BMAL1 are required for transcriptional activation, as well as for association with the circadian transcriptional repressor CRYPTOCHROME 1 (CRY1), depending on the coexistence of CLOCK protein. C-terminally truncated BMAL1 mutant proteins still associate with mPER2 (another protein of the negative feedback loop), suggesting that an additional repression mechanism may converge on the N terminus. Taken together, these results suggest that the C-terminal region of BMAL1 is involved in determining the balance between circadian transcriptional activation and suppression.

ARNTL Transcription Factors↗
PubMed2006

A single chromoprotein with triple chromophores acts as both a phytochrome and a phototropin.

Plants sense their environmental light conditions by using three photoreceptors that absorb in the UV, blue/near UV, and red/far-red spectral ranges. These photoreceptors have specific chromophore components corresponding to their absorption spectra. Phytochrome, a red/far-red light receptor, has phytochromobilin as its chromophore, whereas the blue/near UV photoreceptors cryptochrome and phototropin have a pair of flavin derivatives. Plants use these various photoreceptors to assess the surrounding light environment. Phytochrome 3 (PHY3) is a red light receptor found in some ferns, which preferentially grow under weak light. PHY3 is composed of a phytochrome chromophore-binding domain in its N-terminal portion and an almost full-length phototropin in its C-terminal half. This unusual domain organization implies that two different light-sensing systems coexist in this single photoreceptor, although these light-sensing systems usually reside in independent photoreceptors. Here, we show that PHY3 acts as a dual-channel photoreceptor that possesses both the red light-sensing system of phytochrome and the blue light-sensing system of phototropin. Furthermore, red- and blue-light signals perceived by PHY3 are processed synergistically within this single chromoprotein. These unusual properties might confer an enhanced light sensitivity on PHY3, allowing ferns to grow under a low-light canopy.

Adiantum↗
PubMed1999

BAS1: A gene regulating brassinosteroid levels and light responsiveness in Arabidopsis.

The Arabidopsis bas1-D mutation suppresses the long hypocotyl phenotype caused by mutations in the photoreceptor phytochrome B (phyB). The adult phenotype of bas1-D phyB-4 double mutants mimics that of brassinosteroid biosynthetic and response mutants. bas1-D phyB-4 has reduced levels of brassinosteroids and accumulates 26-hydroxybrassinolide in feeding experiments. The basis for the mutant phenotype is the enhanced expression of a cytochrome P450 (CYP72B1). bas1-D suppresses a phyB-null allele, but not a phyA-null mutation, and partially suppresses a cryptochrome-null mutation. Seedlings with reduced BAS1 expression are hyperresponsive to brassinosteroids in a light-dependent manner and display reduced sensitivity to light under a variety of conditions. Thus, BAS1 represents one of the control points between multiple photoreceptor systems and brassinosteroid signal transduction.

Arabidopsis↗
PubMed2006

Molecular analysis of clock gene expression in the avian brain.

Birds are equipped with a complex circadian pacemaking system that regulates the rhythmicity of physiology and behavior. As with all organisms, transcriptional and translational feedback loops of clock genes represent the basic molecular mechanism of rhythm generation in birds. To investigate avian clock gene expression, partial cDNA sequences of six mammalian clock gene homologs (Bmal1, Clock, Per2, Per3, Cry1, and Cry2) and a novel avian cryptochrome gene (Cry4) were cloned from the house sparrow, a model system in circadian research. Expression patterns were analyzed by semi-quantitative RT-PCR and RNase protection assays using total RNA extracted from adult male house sparrow brains. With the exception of Cry4, pronounced rhythmic mRNA expression of all the clock genes analyzed was encountered, with mRNA levels varying considerably between the various genes. Although some basic features of the molecular circadian feedback loop appear to be similar between mammals and birds, the precise phase relationships of the clock gene mRNA rhythms relative to each other and to the light zeitgeber differ significantly between the house sparrow and mammals. Our results point to the existence of differences in the organization of avian and mammalian circadian clock mechanisms.

ARNTL Transcription Factors↗
PubMed2001

Further characterization of the phenotype of mCry1/mCry2-deficient mice.

Mice lacking cryptochromes (mCry1/mCry2-/-) were kept in a 16h light, 8h dark, light-dark (16:8 LD) cycle and were given additional pulses of light of different brightness, starting 2h after dark onset and lasting for 1h. The suppression of wheel running during these light pulses (i.e., masking) was compared to that of wild types. No evidence of any decrement in the masking response to light was detected. As well as studying masking, minor bouts of activity occurring in the main light portion of a light-dark cycle were quantified. One possible explanation of such predark activity is that some damped endogenous process is spared in mCry1/mCry2 double-knockout mice.

Animals↗
PubMed2004

Input signals to the plant circadian clock.

Eukaryotes and some prokaryotes have adapted to the 24 h day/night cycle by evolving circadian clocks, which now control very many aspects of metabolism, physiology and behaviour. Circadian clocks in plants are entrained by light and temperature signals from the environment. The relative timing of internal and external events depends upon a complex interplay of interacting rhythmic controls and environmental signals, including changes in the period of the clock. Several of the phytochrome and cryptochrome photoreceptors responsible have been identified. This review concentrates on the resulting patterns of entrainment and on the multiple proposed mechanisms of light input to the circadian oscillator components.

Biological Clocks↗
PubMed2006

Dual role of the CLOCK/BMAL1 circadian complex in transcriptional regulation.

The basic helix-loop-helix (bHLH) -PAS domain containing transcription factors CLOCK and BMAL1 are two major components of the circadian molecular oscillator. It is known that the CLOCK/BMAL1 complex positively regulates the activity of E-box containing promoters. Here we demonstrate that the CLOCK/BMAL1 complex can also suppress the activity of some promoters upon its interaction with CRYPTOCHROME (CRY). Such a dual function of the circadian transcriptional complex provides a mechanistic explanation for the unpredicted pattern of circadian gene expression in the tissues of Bmal1 null mice. We speculate that the switch from transcriptional activation to transcriptional repression may provide a highly efficient mechanism for circadian control of gene expression. We also show that CLOCK/BMAL1 can interfere with promoter regulation by other, non-circadian, transcription factors including N-MYC and ETS, leading to attenuation or abrogation of transcription of CLOCK/BMAL1-controlled stress-induced genes. We propose that, based upon these results, both circadian repression and activation of the transcription of different target genes are required for circadian responses to various external stimuli, including genotoxic stress induced by anticancer treatment.

ARNTL Transcription Factors↗
PubMed2002

Disruption of mCry2 restores circadian rhythmicity in mPer2 mutant mice.

Many biochemical, physiological, and behavioral processes display daily rhythms generated by an internal timekeeping mechanism referred to as the circadian clock. The core oscillator driving this clock is located in the ventral part of the hypothalamus, the so called suprachiasmatic nuclei (SCN). At the molecular level, this oscillator is thought to be composed of interlocking autoregulatory feedback loops involving a set of clock genes. Among the components driving the mammalian circadian clock are the Period 1 and 2 (mPer1 and mPer2) and Cryptochrome 1 and 2 (mCry1 and mCry2) genes. A mutation in the mPer2 gene leads to a gradual loss of circadian rhythmicity in mice kept in constant darkness (DD). Here we show that inactivation of the mCry2 gene in mPer2 mutant mice restores circadian rhythmicity and normal clock gene expression patterns. Thus, mCry2 can act as a nonallelic suppressor of mPer2, which points to direct or indirect interactions of PER2 and CRY2 proteins. In marked contrast, inactivation of mCry1 in mPer2 mutant mice does not restore circadian rhythmicity but instead results in complete behavioral arrhythmicity in DD, indicating different effects of mCry1 and mCry2 in the clock mechanism

Animals↗
PubMed2003

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.

Acyltransferases↗
PubMed2001

The enhancement of phototropin-induced phototropic curvature in Arabidopsis occurs via a photoreversible phytochrome A-dependent modulation of auxin responsiveness.

The induction of phototropism in etiolated (dark-grown) seedlings exposed to an unidirectional pulse or extended irradiation with low fluence rate blue light (BL) requires the action of the phototropin (nph1) BL receptor. Although cryptochromes and phytochromes are not required for phototropic induction, these photoreceptors do modulate the magnitude of curvature resulting from phototropin activation. Modulatory increases in the magnitude of phototropic curvature have been termed "enhancement." Here, we show that phototropic enhancement is primarily a phytochrome A (phyA)-dependent red/far-red-reversible low fluence response. This phyA-dependent response is genetically separable from the basal phototropin-dependent response, as demonstrated by its retention under extended irradiation conditions in the nph4 mutant background, which normally lacks the basal BL-induced response. It is interesting that the nph4 mutants fail to exhibit the basal phototropin-dependent and phyA-dependent enhancement responses under limiting light conditions. Given that NPH4 encodes a transcriptional activator, auxin response factor 7 (ARF7), we hypothesize that the ultimate target(s) of phyA action during the phototropic enhancement response is a rate-limiting ARF-containing transcriptional complex in which the constituent ARFs can vary in identity or activity depending upon the irradiation condition.

Arabidopsis↗
PubMed2001

shl, a New set of Arabidopsis mutants with exaggerated developmental responses to available red, far-red, and blue light.

The interaction of light perception with development is the subject of intensive genetic analysis in the model plant Arabidopsis. We performed genetic screens in low white light-a threshold condition in which photomorphogenetic signaling pathways are only partially active-for ethyl methane sulfonate-generated mutants with altered developmental phenotypes. Recessive mutants with exaggerated developmental responses were obtained in eight complementation groups designated shl for seedlings hyperresponsive to light. shl1, shl2, shl5, and shl3 shl4 (double mutant) seedlings showed limited or no phenotypic effects in darkness, but showed significantly enhanced inhibition of hypocotyl elongation in low-white, red, far-red, blue, and green light across a range of fluences. These results reflect developmental hyper-responsiveness to signals generated by both phytochrome and cryptochrome photoreceptors. The shl11 mutant retained significant phenotypic effects on hypocotyl length in both the phyA mutant and phyB mutant backgrounds but may be dependent on CRY1 for phenotypic expression in blue light. The shl2 phenotype was partially dependent on PHYB, PHYA, and CRY1 in red, far-red, and blue light, respectively. shl2 and, in particular, shl1 were partially dependent on HY5 activity for their light-hyperresponsive phenotypes. The SHL genes act (genetically) as light-dependent negative regulators of photomorphogenesis, possibly in a downstream signaling or developmental pathway that is shared by CRY1, PHYA, and PHYB and other photoreceptors (CRY2, PHYC, PHYD, and PHYE).

Arabidopsis↗
PubMed2001

Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways.

An expressed sequence tag-based microarray was used to profile genome expression underlying light control of Arabidopsis development. Qualitatively similar gene expression profiles were observed among seedlings grown in different light qualities, including far-red, red, and blue light, which are mediated primarily by phytochrome A, phytochrome B, and the cryptochromes, respectively. Furthermore, light/dark transitions also triggered similar differential genome expression profiles. Most light treatments also resulted in distinct expression profiles in small fractions of the expressed sequence tags examined. The similarly regulated genes in all light conditions were estimated to account for approximately one-third of the genome, with three-fifths upregulated and two-fifths downregulated by light. Analysis of those light-regulated genes revealed more than 26 cellular pathways that are regulated coordinately by light. Thus, light controls Arabidopsis development through coordinately regulating metabolic and regulatory pathways.

Arabidopsis↗
PubMed2003

Mutant analyses define multiple roles for phytochrome C in Arabidopsis photomorphogenesis.

The analysis of Arabidopsis mutants deficient in the A, B, D, and E phytochromes has revealed that each of these phytochrome isoforms has both distinct and overlapping roles throughout plant photomorphogenesis. Although overexpression studies of phytochrome C (phyC) have suggested photomorphogenic roles for this receptor, conclusive evidence of function has been lacking as a result of the absence of mutants in the PHYC locus. Here, we describe the isolation of a T-DNA insertion mutant of phyC (phyC-1), the subsequent creation of mutant lines deficient in multiple phytochrome combinations, and the physiological characterization of these lines. In addition to operating as a weak red light sensor, phyC may perform a significant role in the modulation of other photoreceptors. phyA and phyC appear to act redundantly to modulate the phyB-mediated inhibition of hypocotyl elongation in red light and to function together to regulate rosette leaf morphology. In addition, phyC performs a significant role in the modulation of blue light sensing. Several of these phenotypes are supported by the parallel analysis of a quadruple mutant deficient in phytochromes A, B, D, and E, which thus contains only active phyC. Together, these data suggest that phyC has multiple functions throughout plant development that may include working as a coactivator with other phytochromes and the cryptochrome blue light receptors.

Arabidopsis↗
PubMed1997

Effects of synergistic signaling by phytochrome A and cryptochrome1 on circadian clock-regulated catalase expression.

Persistent oscillation in constant conditions is a defining characteristic of circadian rhythms. However, in plants transferred into extended dark conditions, circadian rhythms in mRNA abundance commonly damp in amplitude over two or three cycles to a steady state level of relatively constant, low mRNA abundance. In Arabidopsis, catalase CAT3 mRNA oscillations damp rapidly in extended dark conditions, but unlike catalase CAT2 and the chlorophyll a/b binding protein gene CAB, in which the circadian oscillations damp to low steady state mRNA abundance, CAT3 mRNA oscillations damp to high steady state levels of mRNA abundance. Mutational disruption of either phytochrome- or cryptochrome-mediated light perception prevents damping of the oscillations in CAT3 mRNA abundance and reveals strong circadian oscillations that persist for multiple cycles in extended dark conditions. Damping of CAT3 mRNA oscillations specifically requires phytochrome A but not phytochrome B and also requires the cryptochrome1 blue light receptor. Therefore, we conclude that synergistic signaling mediated through both phytochrome A and cryptochrome1 is required for damping of circadian CAT3 mRNA oscillations in extended dark conditions.

Arabidopsis↗