Tomato contains homologues of Arabidopsis cryptochromes 1 and 2

Cryptochromes are blue light photoreceptors found in both plants and animals. They probably evolved from photolyases, which are blue/UV-light-absorbing photoreceptors involved in DNA repair. In seed plants, two different cryptochrome (CRY) genes have been found in Arabidopsis and one in Sinapis, while three genes have been found in the fern Adiantum. We report the characterisation of tomato CRY genes CRY1 and CRY2. They map to chromosomes 4 and 9, respectively, show relatively constitutive expression and encode proteins of 679 and 635 amino acids, respectively. These proteins show higher similarity to their Arabidopsis counterparts than to each other, suggesting that duplication between CRY1 and CRY2 is an ancient event in the evolution of seed plants. The seed plant cryptochromes form a group distinct from the fern cryptochromes, implying that only one gene was present in the common ancestor between these two groups of plants. Most intron positions in CRY genes from plants and ferns are highly conserved. Tomato cry1 and cry2 proteins carry C-terminal domains 210 and 160 amino acids long, respectively. Several conserved motifs are found in these domains, some of which are common to both types of cryptochromes, while others are cryptochrome-type-specific.     

Cryptochrome nucleocytoplasmic distribution and gene expression are regulated by light quality in the fern Adiantum capillus-veneris

Numerous cellular responses are reportedly regulated by blue light in gametophytes of lower plants; however, the molecular mechanisms of these responses are not known. Here, we report the isolation of two blue light photoreceptor genes, designated cryptochrome genes 4 and 5 (CRY4 and CRY5), from the fern Adiantum capillus-veneris. Because previously we identified three cryptochrome genes, this fern cryptochrome gene family of five members is the largest identified to date in plants. The deduced amino acid sequences of the five genes show remarkable similarities with previously identified cryptochromes as well as class I photolyases. Like the other plant cryptochromes, none of the cryptochromes of this fern possesses photolyase activity. RNA gel blot analysis and competitive polymerase chain reaction analysis indicate that the expression of the newly identified CRY4 and CRY5 genes is regulated by light and is under phytochrome control. The intracellular distribution of reporter beta-glucuronidase (GUS)-CRY fusion proteins indicates that GUS-CRY3 and GUS-CRY4 localize in fern gametophyte nuclei. The nuclear localization of GUS-CRY3 is regulated in a light-dependent manner. Together with our physiological knowledge, these results suggest that CRY3, CRY4, or both might be the photoreceptor that mediates inhibition of spore germination by blue light.     

Tomato and barley contain duplicated copies of cryptochrome 1

The cryptochrome family of blue‐light photoreceptors is involved in the control of plant photomorphogenesis and photoperiodic responses. Two cryptochromes have been described in Arabidopsis and tomato. To investigate the composition of the cryptochrome gene family in angiosperms, we used a ‘garden PCR’ approach, amplifying DNA from different plant species with the same pair of degenerated oligonucleotides representing conserved sequences from the flavin‐binding domain. Different numbers of Cry‐homologous sequences were found in different species: two each in Arabidopsis (Dicots, Brassicaceae), melon (Dicots, Cucurbitaceae) and banana tree (Monocots, Musaceae); three each in tomato (Dicots, Solanaceae) and barley (Monocots, Graminaceae). These sequences contain open reading frames (OFRs) with high homology to cryptochromes, but not photolyases, and are transcribed into RNA. In each case, a Cry1‐ and a Cry2‐like sequence was recognizable. The third gene of tomato and barley seems to have arisen from recent, independent duplications of Cry1, and was thus named Cry1b. The tomato Cry1b gene encodes a protein of 583 amino acids (the shortest of the three tomato cryptochromes), with a high similarity to Cry1. The C‐terminus of Cry1b is truncated before the conserved Ser‐Thr‐Ala‐Glu‐Ser‐Ser‐Ser (STAESSS) motif found in both Cry1a and Cry2. The Cry1b mRNA is expressed throughout the tomato plant, reaching maximal levels of expression in the flower (like Cry1a and Cry2). We conclude that tomato and barley contain at least one additional expressed member of the Cry1 gene family.     

Blue light-dependent interaction of CRY2 with SPA1 regulates COP1 activity and floral initiation in Arabidopsis

Cryptochromes are blue light receptors that mediate light regulation of gene expression in all major evolution lineages, but the molecular mechanism underlying cryptochrome signal transduction remains not fully understood. It has been reported that cryptochromes suppress activity of the multifunctional E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) to regulate gene expression in response to blue light. But how plant cryptochromes mediate light suppression of COP1 activity remains unclear. We report here that Arabidopsis CRY2 (cryptochrome 2) undergoes blue light-dependent interaction with the COP1-interacting protein SUPPRESSOR OF PHYTOCHROME A 1 (SPA1). We demonstrate that SPA1 acts genetically downstream from CRY2 to mediate blue light suppression of the COP1-dependent proteolysis of the flowering-time regulator CONSTANS (CO). We further show that blue light-dependent CRY2-SPA1 interaction stimulates CRY2-COP1 interaction. These results reveal for the first time a wavelength-specific mechanism by which a cryptochrome photoreceptor mediates light regulation of protein degradation to modulate developmental timing in Arabidopsis.     

Magnetic intensity affects cryptochrome-dependent responses in Arabidopsis thaliana

Cryptochromes are blue-light absorbing photoreceptors found in many organisms where they have been involved in numerous growth, developmental, and circadian responses. In Arabidopsis thaliana, two cryptochromes, CRY1 and CRY2, mediate several blue-light-dependent responses including hypocotyl growth inhibition. Our study shows that an increase in the intensity of the ambient magnetic field from 33–44 to 500 μT enhanced growth inhibition in A. thaliana under blue light, when cryptochromes are the mediating photoreceptor, but not under red light when the mediating receptors are phytochromes, or in total darkness. Hypocotyl growth of Arabidopsis mutants lacking cryptochromes was unaffected by the increase in magnetic intensity. Additional cryptochrome-dependent responses, such as blue-light-dependent anthocyanin accumulation and blue-light-dependent degradation of CRY2 protein, were also enhanced at the higher magnetic intensity. These findings show that higher plants are sensitive to the magnetic field in responses that are linked to cryptochrome-dependent signaling pathways. Because cryptochromes form radical pairs after photoexcitation, our results can best be explained by the radical-pair model. Recent evidence indicates that the magnetic compass of birds involves a radical pair mechanism, and cryptochrome is a likely candidate for the avian magnetoreception molecule. Our findings thus suggest intriguing parallels in magnetoreception of animals and plants that appear to be based on common physical properties of photoexcited cryptochromes.     

Molecular evolution of cryptochrome genes and the evolutionary manner of photoreceptor genes in <Emphasis Type="Italic">Cardamine nipponica</Emphasis> (Brassicaceae)

Various photoreceptors in plants are used to monitor important environmental light signals and regulate plant development. Despite their functional importance, recent studies have demonstrated that red/far-red absorbing phytochromes or blue/UV-A absorbing cryptochromes are involved in local adaptation within a species’ range. In the present study, to exemplify the intraspecific photoreceptor evolutionary pattern, the genetic structures of cryptochrome genes (CRY1 and CRY2) in Cardamine nipponica (Brassicaceae), of which PHYE, a gene coding one of the phytochromes, was found to be involved in local adaptation between central and northern Japanese populations. Although clear genetic differentiations between central and northern Japan were detected (CRY1: F _ST = 0.63, CRY2: F _ST = 0.53), overall nucleotide diversity was very low (CRY1: π _Total = 0.0014, CRY2: π _Total = 0.0013), and the polymorphism patterns were neutral (CRY1: Tajima’s D = 0.084, P = 0.32, CRY2: D = −0.014, P = 0.39). Therefore, the involvement of cryptochromes in the adaptation to local environments is difficult to postulate. Consequently, this study along with our previous findings suggest that intraspecific photoreceptor gene polymorphisms in C. nipponica were mostly suppressed by purifying selection due to their functional importance as photoreceptors, while some of the photoreceptors may play substantial roles in adaptation to local environments.     

CHARACTERIZATION OF A DINOFLAGELLATE CRYPTOCHROME BLUE‐LIGHT RECEPTOR WITH A POSSIBLE ROLE IN CIRCADIAN CONTROL OF THE CELL CYCLE1

Karenia brevis (C. C. Davis) G. Hansen et Moestrup is a dinoflagellate responsible for red tides in the Gulf of Mexico. The signaling pathways regulating its cell cycle are of interest because they are the key to the formation of toxic blooms that cause mass marine animal die‐offs and human illness. Karenia brevis displays phased cell division, in which cells enter S phase at precise times relative to the onset of light. Here, we demonstrate that a circadian rhythm underlies this behavior and that light quality affects the rate of cell‐cycle progression: in blue light, K. brevis entered the S phase early relative to its behavior in white light of similar intensity, whereas in red light, K. brevis was not affected. A data base of 25,000 K. brevis expressed sequence tags (ESTs) revealed several sequences with similarity to cryptochrome blue‐light receptors, but none related to known red‐light receptors. We characterized the K. brevis cryptochrome (Kb CRY) and modeled its three‐dimensional protein structure. Phylogenetic analysis of the photolyase/CRY gene family showed that Kb CRY is a member of the cryptochrome DASH (CRY DASH) clade. Western blotting with an antibody designed to bind a conserved peptide within Kb CRY identified a single band at ～55 kDa. Immunolocalization showed that Kb CRY, like CRY DASH in Arabidopsis, is localized to the chloroplast. This is the first blue‐light receptor to be characterized in a dinoflagellate. As the Kb CRY appears to be the only blue‐light receptor expressed, it is a likely candidate for circadian entrainment of the cell cycle.     

Four distinct photoreceptors contribute to light-induced side branch formation in the moss <Emphasis Type="Italic">Physcomitrella patens</Emphasis>

Side branch formation in the moss, Physcomitrella patens, has been shown to be light dependent with cryptochrome 1a and 1b (Ppcry1a and Ppcry1b), being the blue light receptors for this response (Imaizumi et al. in Plant Cell 14:373, 2002). In this study, detailed photobiological analyses were performed, which revealed that this response involves multiple photoreceptors including cryptochromes. For light induction of branches, blue light of a fluence rate higher than 6 μmol m⁻² s⁻¹ for period longer than 3 h is required. The number of branches increased with the increase in fluence rate and in the irradiation period. The number of branches also increased when red light was applied together with the blue light, although red light alone had a very few effect. By partially irradiating a cell, both receptive sites for blue and red light were found to be located around the nucleus. Further, both red and blue light determine the positions of branches being dependent upon the vibration plane of polarized light. Red light control of branch position was nullified by simultaneous far-red light irradiation. A blue light effect on branch position was not found in lines with disrupted phototropin genes. Thus, dichroic phytochrome and phototropin, possibly on the plasma membrane, regulate branch position. These results indicate that at least four distinct photoreceptor systems, namely, cryptochromes and red light receptor around or in the nucleus, dichroic phytochrome and phototropin around the cell periphery, are involved in the light induction of side branches in the moss Physcomitrella patens.     

A Spectroscopic View of Some Recent Advances in the Study of Blue Light Photoreception*

The blue to UV-A region of the spectrum, spanning the region of about 320–520 nm, strongly influences the growth and development of plants and fungi. Photomorphogenesis in plants is, to a great extent, controlled by phytochrome, but there are unique contributions of the blue region, which cannot be duplicated by any amount of red light. Phototropism is, with few exceptions, a purely blue light response. In fungi, the blue region dominates the photocontrol of growth and development, though some red light effects have been reported. Many blue light action spectra fit the definition of cryptochrome, a pigment class defined by its UV-A and blue peaks. The action spectrum, if measured to sufficient resolution, displays several minor maxima or shoulders in the blue region which call to mind the vibrational levels of carotenoids and flavins. Recent molecular genetic studies, as well as photobiological work, have shown that some cryptochromes are related to the DNA repair enzyme photolyase, while others appear genetically and spectroscopically distinct. In this review, we have applied established criteria from photobiology, in particular, comparison of action spectra with absorption spectra, to these recent results. It is apparent that photolyase homologs such as CRY1 can explain the blue light portion of the action spectrum for hypocotyl elongation, assuming participation of the oxidized flavin. In fungi, the photoreceptor question remains open. Identification of the nph1 gene in Arabidopsis may soon lead to a photoreceptor for higher plant phototropism. Also, we present a possible solution to the most recent version of the long-standing flavin-carotenoid controversy, the zeaxanthin hypothesis for higher plant phototropism. In conclusion, there appear to be at least three classes of cryptochromes.     

Composition and phylogenetic analysis of wheat cryptochrome gene family

Cryptochrome (CRY) gene family encodes photoreceptors mediating developmental responses to blue light throughout the life of plants. We report here the characterization of CRY gene family in hexaploid wheat. Degenerate PCR amplification of the regions encoding the conserved flavin-binding domain of CRY proteins yielded seven bands, resulting from amplification of CRY1a, CRY1b and CRY2 homologous genes. Assignment of individual amplicons to subgenomes was accomplished by comparing their sequence compositions with those from the ancestor species of wheat. ESTs coding for CRY-DASH like proteins were identified in wheat EST database in GenBank. Southern blot showed that TaCRY1a, TaCRY1b and TaCRY2 are single copy genes. We mapped TaCRY1a and TaCRY2 to chromosomes of homoeologous group 6, TaCRY1b to group 2, and TaCRY-DASH to group 7. Phylogenetic analysis showed that CRY subfamily diversification occurred before the divergence of monocots and dicots. The regulatory and functional changes of CRY members within subfamily are discussed.     

A study of the blue-light-dependent phosphorylation, degradation, and photobody formation of Arabidopsis CRY2

Arabidopsis cryptochrome 2 (CRY2) is a blue-light receptor mediating blue-light inhibition of hypocotyl elongation and photoperiodic promotion of floral initiation. CRY2 is a constitutive nuclear protein that undergoes blue-light-dependent phosphorylation, ubiquitination, photobody formation, and degradation in the nucleus, but the relationship between these blue-light-dependent events remains unclear. It has been proposed that CRY2 phosphorylation triggers a conformational change responsible for the subsequent ubiquitination and photobody formation, leading to CRY2 function and/or degradation. We tested this hypothesis by a structure-function study, using mutant CRY2-GFP fusion proteins expressed in transgenic Arabidopsis. We show that changes of lysine residues of the NLS (Nuclear Localization Signal) sequence of CRY2 to arginine residues partially impair the nuclear importation of the CRY2K541R and CRY2K554/5R mutant proteins, resulting in reduced phosphorylation, physiological activities, and degradation in response to blue light. In contrast to the wild-type CRY2 protein that forms photobodies exclusively in the nucleus, the CRY2K541R and CRY2K554/5R mutant proteins form protein bodies in both the nucleus and cytosol in response to blue light. These results suggest that photoexcited CRY2 molecules can aggregate to form photobody-like structure without the nucleus-dependent protein modifications or the association with the nuclear CRY2-interacting proteins. Taken together, the observation that CRY2 forms photobodies markedly faster than CRY2 phosphorylation in response to blue light, we hypothesize that the photoexcited cryptochromes form oligomers, preceding other biochemical changes of CRY2, to facilitate photobody formation, signal amplification, and propagation, as well as desensitization by degradation.     

The moss genes <Emphasis Type="Italic">PpSKI1</Emphasis> and <Emphasis Type="Italic">PpSKI2</Emphasis> encode nuclear SnRK1 interacting proteins with homologues in vascular plants

The yeast Snf1, animal AMPK, and plant SnRK1 protein kinases constitute a family of related proteins that have been proposed to serve as metabolic sensors of the eukaryotic cell. We have previously reported the characterization of two redundant SnRK1 encoding genes (PpSNF1a and PpSNF1b) in the moss Physcomitrella patens. Phenotypic analysis of the snf1a snf1b double knockout mutant suggested that SnRK1 is important for the plant’s ability to recognize and adapt to conditions of limited energy supply, and also suggested a possible role of SnRK1 in the control of plant development. We have now used a yeast two-hybrid system to screen for PpSnf1a interacting proteins. Two new moss genes were found, PpSKI1 and PpSKI2, which encode highly similar proteins with homologues in vascular plants. Fusions of the two encoded proteins to the green fluorescent protein localize to the nucleus. Knockout mutants for either gene have an excess of gametophores under low light conditions, and exhibit reduced gametophore stem lengths. Possible functions of the new proteins and their connection to the SnRK1 kinase are discussed.     

An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles

Cryptochromes (CRYs) are blue/UV-A photoreceptors related to the DNA repair enzyme DNA photolyase. They have been found in plants, animals and most recently in the cyanobacterium Synechocystis. Closely related to the Synechocystis cryptochrome is the Arabidopsis gene At5g24850. Here, we show that the encoded protein of At5g24850 binds flavin adenine dinucleotide (FAD). It has no photolyase activity, and is likely to function as a photoreceptor. We have named it At-cry3 to distinguish it from the other Arbabidopsis cryptochrome homologues At-cry1 and At-cry2. At-cry3 carries an N-terminal sequence, which mediates import into chloroplasts and mitochondria. Furthermore, we show that At-cry3 binds DNA. DNA binding was also demonstrated for the Synechocystis cryptochrome, indicating that both photoreceptors could have similar modes of action. Based on the finding of a new cryptochrome class in bacteria and plants, it has been suggested that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. However, our phylogenetic analyses are also consistent with an alternative explanation that the presence of cryptochromes in the plant nuclear genome is the result of dual horizontal gene transfer. That is, CRY1 and CRY2 genes may originate from an endosymbiotic ancestor of modern-day alpha-proteobacteria, while the CRY3 gene may originate from an endosymbiotic ancestor of modern-day cyanobacteria.     

Nuclear localization of the Arabidopsis blue light receptor cryptochrome 2

The cryptochrome blue light photoreceptor family of Arabidopsis thaliana consists of two members, CRY1 and CRY2 (PHH1). CRY2 contains a putative nuclear localization signal (NLS) within its C-terminal region. We examined whether CRY2 is localized in the nucleus and whether the C-terminal region of CRY2 is involved in nuclear targeting. Total cellular and nuclear protein extracts from Arabidopsis were subjected to immunoblot analysis with CRY2-specific antibodies. Strong CRY2 signals were obtained in the nuclear fraction. Fusion proteins consisting of the green fluorescent protein (GFP) and different fragments of CRY2 were expressed in parsley protoplasts and the localization of the fusion proteins was determined by fluorescence and confocal laser scanning microscopy. GFP-fusions containing the entire CRY2 protein or its C-terminal region were found exclusively in the nucleus. We conclude from these results that CRY2 is localized in the nucleus and that nuclear localization is mediated by the C-terminal region of CRY2.