Cryptochromes (from the

Greek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...

κρυπτός χρώμα, "hidden colour") are a class of flavoproteins found in plants and

animal Animals are multicellular, eukaryotic organisms in the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, are Motilit ...

s that are sensitive to blue light. They are involved in the

circadian rhythm A circadian rhythm (), or circadian cycle, is a natural, internal process that regulates the sleep–wake cycle and repeats roughly every 24 hours. It can refer to any process that originates within an organism (i.e., endogenous) and responds to ...

s and the sensing of magnetic fields in a number of species. The name ''cryptochrome'' was proposed as a ''

portmanteau A portmanteau word, or portmanteau (, ) is a blend of wordschromatic'' nature of the photoreceptor, and the '' cryptogamic'' organisms on which many blue-light studies were carried out. The two

gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

s ''Cry1'' and ''Cry2'' code the two cryptochrome

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

s CRY1 and CRY2. In

insects Insects (from Latin ') are pancrustacean hexapod invertebrates of the class Insecta. They are the largest group within the arthropod phylum. Insects have a chitinous exoskeleton, a three-part body (head, thorax and abdomen), three pairs ...

and plants, CRY1 regulates the circadian clock in a light-dependent fashion, whereas in mammals, CRY1 and CRY2 act as light-independent inhibitors of

CLOCK A clock or a timepiece is a device used to measure and indicate time. The clock is one of the oldest human inventions, meeting the need to measure intervals of time shorter than the natural units such as the day, the lunar month and t ...

- BMAL1 components of the circadian clock. In plants, blue-light photoreception can be used to cue developmental signals. Besides

chlorophylls Chlorophyll (also chlorophyl) is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words , ("pale green") and , ("leaf"). Chlorophyll allow plants to a ...

, cryptochromes are the only proteins known to form photoinduced radical-pairs '' in vivo''. These appear to enable some animals to detect magnetic fields. Cryptochromes have been the focus of several current efforts in

optogenetics Optogenetics is a biological technique to control the activity of neurons or other cell types with light. This is achieved by expression of light-sensitive ion channels, pumps or enzymes specifically in the target cells. On the level of indiv ...

. Employing transfection, initial studies on yeast have capitalized on the potential of Cry2 heterodimerization to control cellular processes, including

gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. ...

, by light.

Discovery

Although

Charles Darwin Charles Robert Darwin ( ; 12 February 1809 – 19 April 1882) was an English natural history#Before 1900, naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all speci ...

first documented plant responses to blue light in the 1880s, it was not until the 1980s that research began to identify the pigment responsible. In 1980, researchers discovered that the HY4 gene of the plant '' Arabidopsis thaliana'' was necessary for the plant's blue light sensitivity, and, when the gene was sequenced in 1993, it showed high sequence homology with photolyase, a DNA repair protein activated by blue light. By 1995, it became clear that the products of the HY4 gene and its two human homologs did not exhibit photolyase activity and were instead a new class of blue light photoreceptor hypothesized to be circadian photopigments. In 1996 and 1998, ''Cry'' homologs were identified in ''

Drosophila ''Drosophila'' () is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many s ...

'' and mice, respectively.

Evolutionary history and structure

Cryptochromes (CRY1, CRY2) are evolutionarily old and highly conserved proteins that belong to the flavoproteins superfamily that exists in all kingdoms of life. All members of this superfamily have the characteristics of an N-terminal photolyase homology (PHR) domain. The PHR domain can bind to the flavin adenine dinucleotide (FAD) cofactor and a light-harvesting chromophore. Cryptochromes are derived from and closely related to photolyases, which are bacterial enzymes that are activated by light and involved in the repair of UV-induced DNA damage. In eukaryotes, cryptochromes no longer retain this original enzymatic activity. The structure of cryptochrome involves a fold very similar to that of photolyase, with a single molecule of FAD noncovalently bound to the protein. These proteins have variable lengths and surfaces on the C-terminal end, due to the changes in genome and appearance that result from the lack of DNA repair enzymes. The Ramachandran plot shows that the

secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...

of the CRY1 protein is primarily a right-handed alpha helix with little to no steric overlap. The structure of CRY1 is almost entirely made up of alpha helices, with several loops and few beta sheets. The molecule is arranged as an orthogonal bundle.

Function

Phototropism

In plants, cryptochromes mediate

phototropism Phototropism is the growth of an organism in response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi. The cells on the plant that are farthest from the light contain a hor ...

, or directional growth toward a light source, in response to blue light. This response is now known to have its own set of photoreceptors, the phototropins. Unlike phytochromes and phototropins, cryptochromes are not kinases. Their flavin chromophore is reduced by light and transported into the cell nucleus, where it affects the turgor pressure and causes subsequent stem elongation. To be specific, ''Cry2'' is responsible for blue-light-mediated

cotyledon A cotyledon (; ; ; , gen. (), ) is a significant part of the embryo within the seed of a plant, and is defined as "the embryonic leaf in seed-bearing plants, one or more of which are the first to appear from a germinating seed." The num ...

and leaf expansion. ''Cry2'' overexpression in transgenic plants increases blue-light-stimulated cotyledon expansion, which results in many broad leaves and no flowers rather than a few primary leaves with a flower. A double loss-of-function mutation in Arabidopsis thaliana Early Flowering 3 (elf3) and Cry2 genes delays flowering under continuous light and was shown to accelerate it during long and short days, which suggests that Arabidopsis CRY2 may play a role in accelerating flowering time during continuous light.

Photomorphogenesis

Cryptochromes receptors cause plants to respond to blue light via photomorphogenesis. They help control seed and seedling development, as well as the switch from the vegetative to the flowering stage of development. In Arabidopsis, it has been shown that cryptochromes controls plant growth during sub-optimal blue-light conditions.

Light capture

Despite much research on the topic, cryptochrome photoreception and phototransduction in ''

'' and ''Arabidopsis thaliana'' is still poorly understood. Cryptochromes are known to possess two chromophores: pterin (in the form of

5,10-methenyltetrahydrofolic acid 5,10-Methenyltetrahydrofolate (5,10-CH=THF) is a form of tetrahydrofolate that is an intermediate in metabolism. 5,10-CH=THF is a coenzyme that accepts and donates methenyl (CH=) groups. It is produced from 5,10-methylenetetrahydrofolate by eith ...

(MTHF)) and flavin (in the form of FAD). Both may absorb a

photon A photon () is an elementary particle that is a quantum of the electromagnetic field, including electromagnetic radiation such as light and radio waves, and the force carrier for the electromagnetic force. Photons are Massless particle, massless ...

, and in ''Arabidopsis'', pterin appears to absorb at a wavelength of 380 nm and flavin at 450 nm. Past studies have supported a model by which energy captured by pterin is transferred to flavin. Under this model of phototransduction, FAD would then be reduced to FADH, which probably mediates the phosphorylation of a certain domain in cryptochrome. This could then trigger a

signal transduction Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular ...

chain, possibly affecting gene regulation in the cell nucleus. A new hypothesis proposes that in plant cryptochromes, the transduction of the light signal into a chemical signal that might be sensed by partner molecules could be triggered by a photo-induced negative charge within the protein - on the FAD cofactor or on the neighbouring aspartic acid. This negative charge would electrostatically repel the protein-bound

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molecule and thereby also the protein C-terminal domain, which covers the

binding pocket prior to photon absorption. The resulting change in protein conformation could lead to phosphorylation of previously inaccessible phosphorylation sites on the C-terminus and the given phosphorylated segment could then liberate the transcription factor HY5 by competing for the same binding site at the negative regulator of photomorphogenesis COP1. A different mechanism may function in ''Drosophila''. The true ground state of the flavin cofactor in ''Drosophila'' CRY is still debated, with some models indicating that the FAD is in an oxidized form, while others support a model in which the flavin cofactor exists in anion radical form, •. Recently, researchers have observed that oxidized FAD is readily reduced to • by light. Furthermore, mutations that blocked photoreduction had no effect on light-induced degradation of CRY, while mutations that altered the stability of • destroyed CRY photoreceptor function. These observations provide support for a ground state of •. Researchers have also recently proposed a model in which is excited to its doublet or quartet state by absorption of a photon, which then leads to a conformational change in the CRY protein. Also the ring eyes of the

demosponge Demosponges (Demospongiae) are the most diverse class in the phylum Porifera. They include 76.2% of all species of sponges with nearly 8,800 species worldwide (World Porifera Database). They are sponges with a soft body that covers a hard ...

larva of ''Amphimedon queenslandica'' express a blue-light-sensitive cryptochrome (Aq-Cry2), which might mediate phototaxis. In contrast, the eyes of most animals use photo-sensitive

opsin Animal opsins are G-protein-coupled receptors and a group of proteins made light-sensitive via a chromophore, typically retinal. When bound to retinal, opsins become Retinylidene proteins, but are usually still called opsins regardless. Most pro ...

s expressed in photoreceptor cells, which communicate information about light from the environment to the nervous system. However, ''A. queenslandica'' lacks a nervous system, like other

sponge Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate throug ...

s. And it does not have an

in its fully sequenced

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

either, despite having many other G-protein-coupled receptors (GPCRs). Therefore, the sponge's unique eyes must have evolved a different mechanism to detect light and mediate phototaxis, possibly with cryptochromes or other proteins.

Iris function

The iris of chicken embryos senses short-wavelength light via a cryptochrome, rather than opsins.

Circadian rhythm

Studies in animals and plants suggest that cryptochromes play a pivotal role in the generation and maintenance of circadian rhythms. Similarly, cryptochromes play an important role in the entrainment of circadian rhythms in plants. In ''Drosophila'', cryptochrome (dCRY) acts as a blue-light photoreceptor that directly modulates light input into the circadian clock, while in mammals, cryptochromes (CRY1 and CRY2) act as transcription repressors within the circadian clockwork. Some insects, including the monarch butterfly, have both a mammal-like and a ''Drosophila''-like version of cryptochrome, providing evidence for an ancestral clock mechanism involving both light-sensing and transcriptional-repression roles for cryptochrome. ''Cry'' mutants have altered circadian rhythms, showing that ''Cry'' affects the circadian pacemaker. ''Drosophila'' with mutated ''Cry'' exhibit little to no mRNA cycling. A point mutation in ''cry^b,'' which is required for flavin association in CRY protein, results in no PER or TIM protein cycling in either DD or LD. In addition, mice lacking ''Cry1'' or ''Cry2'' genes exhibit differentially altered free running periods, but are still capable of photoentrainment. However, mice that lack both ''Cry1'' and ''Cry2'' are arrhythmic in both LD and DD and always have high Per1 mRNA levels. These results suggest that cryptochromes play a photoreceptive role, as well as acting as negative regulators of Per gene expression in mice.

In ''Drosophila''

In ''Drosophila'', cryptochrome functions as a blue light photoreceptor. Exposure to blue light induces a conformation similar to that of the always-active CRY mutant with a C-terminal deletion (CRYΔ). The half-life of this conformation is 15 minutes in the dark and facilitates the binding of CRY to other clock gene products, PER and TIM, in a light-dependent manner. Once bound by dCRY, dTIM is committed to degradation by the ubiquitin- proteasome system. Although light pulses do not entrain, full photoperiod LD cycles can still drive cycling in the ventral- lateral neurons in the ''Drosophila'' brain. These data along with other results suggest that CRY is the cell-autonomous photoreceptor for body clocks in ''Drosophila'' and may play a role in nonparametric entrainment (entrainment by short discrete light pulses). However, the lateral neurons receive light information through both the blue light CRY pathway and the

rhodopsin Rhodopsin, also known as visual purple, is a protein encoded by the RHO gene and a G-protein-coupled receptor (GPCR). It is the opsin of the rod cells in the retina and a light-sensitive receptor protein that triggers visual phototransduct ...

pathway. Therefore, CRY is involved in light perception and is an input to the circadian clock, however it is not the only input for light information, as a sustained rhythm has been shown in the absence of the CRY pathway, in which it is believed that the rhodopsin pathway is providing some light input. Recently, it has also been shown that there is a CRY-mediated light response that is independent of the classical circadian CRY-TIM interaction. This mechanism is believed to require a flavin

redox Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate (chemistry), substrate change. Oxidation is the loss of Electron, electrons or an increase in the oxidation state, while reduction ...

-based mechanism that is dependent on potassium channel conductance. This CRY-mediated light response has been shown to increase

action potential An action potential occurs when the membrane potential of a specific cell location rapidly rises and falls. This depolarization then causes adjacent locations to similarly depolarize. Action potentials occur in several types of animal cells, ...

firing within seconds of a light response in

-knockout ''Drosophila''. Cryptochrome, like many genes involved in circadian rhythm, shows circadian cycling in

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...

and protein levels. In ''Drosophila'', ''Cry'' mRNA concentrations cycle under a light-dark cycle (LD), with high levels in light and low levels in the dark. This cycling persists in constant darkness (DD), but with decreased amplitude. The transcription of the ''Cry'' gene also cycles with a similar trend. CRY protein levels, however, cycle in a different manner than ''Cry'' transcription and mRNA levels. In LD, CRY protein has low levels in light and high levels in dark, and, in DD, CRY levels increase continuously throughout the subjective day and night. Thus, CRY expression is regulated by the clock at the transcriptional level and by light at the

translational Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...

and posttranslational level. Overexpression of ''Cry'' also affects circadian light responses. In ''Drosophila'', ''Cry'' overexpression increases flies' sensitivity to low-intensity light. This light regulation of CRY protein levels suggests that CRY has a circadian role upstream of other clock genes and components.

In mammals

Cryptochrome is one of the four groups of mammalian clock genes/proteins that generate a transcription-translation negative-feedback loop (TTFL), along with Period (PER), CLOCK, and BMAL1. In this loop, CLOCK and BMAL1 proteins are transcriptional activators, which together bind to the promoters of the ''Cry'' and ''Per'' genes and activate their transcription. The CRY and PER proteins then bind to each other, enter the nucleus, and inhibit CLOCK-BMAL1-activated transcription. In mice, ''Cry1'' expression displays circadian rhythms in the suprachiasmatic nucleus, a brain region involved in the generation of circadian rhythms, with mRNA levels peaking during the light phase and reaching a minimum in the dark. These daily oscillations in expression are maintained in constant darkness. While CRY has been well established as a TIM homolog in mammals, the role of CRY as a photoreceptor in mammals has been controversial. Early papers indicated that CRY has both light-independent and -dependent functions. A study in 2000 indicated that mice without rhodopsin but with cryptochrome still respond to light; however, in mice without either rhodopsin or cryptochrome, ''

c-Fos Protein c-Fos is a proto-oncogene that is the human homolog of the retroviral oncogene v-fos. It is encoded in humans by the ''FOS'' gene. It was first discovered in rat fibroblasts as the transforming gene of the FBJ MSV (Finkel–Biskis–Jin ...

'' transcription, a mediator of light sensitivity, significantly drops. In recent years, data have supported melanopsin as the main circadian photoreceptor, in particular melanopsin cells that mediate entrainment and communication between the

eye Eyes are organs of the visual system. They provide living organisms with vision, the ability to receive and process visual detail, as well as enabling several photo response functions that are independent of vision. Eyes detect light and conv ...

and the suprachiasmatic nucleus (SCN). One of the main difficulties in confirming or denying CRY as a mammalian photoreceptor is that when the gene is knocked out the animal goes arrhythmic, so it is hard to measure its capacity as purely a photoreceptor. However, some recent studies indicate that human CRY may mediate light response in peripheral tissues. Normal mammalian circadian rhythm relies critically on delayed expression of ''Cry1'' following activation of the ''Cry1'' promoter. Whereas rhythms in ''Per2'' promoter activation and ''Per2'' mRNA levels have almost the same phase, ''Cry1'' mRNA production is delayed by approximately four hours relative to ''Cry1'' promoter activation. This delay is independent of CRY1 or CRY2 levels and is mediated by a combination of E/E'-box and D-box elements in the promoter and RevErbA/ ROR binding elements (RREs) in the gene's first intron. Transfection of arrhythmic ''Cry1''^−/− ''Cry2''^−/− double-knockout cells with only the ''Cry1'' promoter (causing constitutive ''Cry1'' expression) is not sufficient to rescue rhythmicity. Transfection of these cells with both the promoter and the first intron is required for restoration of circadian rhythms in these cells.

Magnetoreception

Magnetoreception is a sense which allows an organism to detect a magnetic field to perceive direction, altitude or location. Experimental data suggests that cryptochromes in the photoreceptor neurons of birds' eyes are involved in magnetic orientation during migration. Cryptochromes are also thought to be essential for the light-dependent ability of ''

'' to sense magnetic fields. Magnetic fields were once reported to affect cryptochromes also in ''Arabidopsis thaliana'' plants: growth behavior seemed to be affected by magnetic fields in the presence of blue (but not red) light. Nevertheless, these results have later turned out to be irreproducible under strictly controlled conditions in another laboratory, suggesting that plant cryptochromes do not respond to magnetic fields. Quantum Magnetoreception in Birds

Cryptochrome forms a pair of radicals with correlated spins when exposed to blue light. Radical pairs can also be generated by the light-independent dark reoxidation of the flavin cofactor by molecular oxygen through the formation of a spin-correlated FADH-superoxide radical pairs. Magnetoreception is hypothesized to function through the surrounding magnetic field's effect on the correlation (parallel or anti-parallel) of these radicals, which affects the lifetime of the activated form of cryptochrome. Activation of cryptochrome may affect the light-sensitivity of

retina The retina (from la, rete "net") is the innermost, light-sensitive layer of tissue of the eye of most vertebrates and some molluscs. The optics of the eye create a focused two-dimensional image of the visual world on the retina, which then ...

l neurons, with the overall result that the animal can sense the magnetic field. Animal cryptochromes and closely related animal (6-4) photolyases contain a longer chain of electron-transferring tryptophans than other proteins of the cryptochrome-photolyase superfamily (a tryptophan tetrad instead of a triad). The longer chain leads to a better separation and over 1000× longer lifetimes of the photoinduced flavin-tryptophan radical pairs than in proteins with a triad of tryptophans. The absence of spin-selective recombination of these radical pairs on the nanosecond to microsecond timescales seems to be incompatible with the suggestion that magnetoreception by cryptochromes is based on the forward light reaction.

References

External links

*
Cryptochrome circadian clock in Monarch Butterflies
, by Steven M. Reppert, Department of Neurobiology, University of Massachusetts
Cryptochrome and Magnetic Sensing
''Theoretical and Computational Biophysics Group'' at the University of Illinois at Urbana-Champaign
2IJG
at the

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, c ...

; 3-D structure of ''Arabidopsis'' cryptochrome 3, obtained by X-ray crystallography.
Animated model of murine circadian pathway, including role of Cry
* {{Flavoproteins Physiology Biological pigments Sensory receptors Plant cognition