#cryptochrome

BAZI HAYVANLAR MANYETİK ALANI NASIL ALGILAR? | MANYETİK ALGI KURAMLARI

Dünyamızın bir manyetik alanı var, bunu çoğumuz biliyoruz. Bu manyetik alanı algılayan kuşlar olduğunu ve bu sayede yönlerini bulabildiklerini de biliyoruz. İyi de biz algılayamazken kuşlar, arılar ve balıklar gibi daha pek çok başka hayvan türü bu manyetik alanı nasıl algılayabiliyor? Manyetik algıya sebep olan şey ne? Gelin videonun devamında hep beraber öğrenelim. (intro)            …

Abstract

Cryptochromes are photolyase-like blue light receptors originally discovered in Arabidopsis but later found in other plants, microbes, and animals. Arabidopsis has two cryptochromes, CRY1 and CRY2, which mediate primarily blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation, respectively. In addition, cryptochromes also regulate over a dozen other light responses, including circadian rhythms, tropic growth, stomata opening, guard cell development, root development, bacterial and viral pathogen responses, abiotic stress responses, cell cycles, programmed cell death, apical dominance, fruit and ovule development, seed dormancy, and magnetoreception. Cryptochromes have two domains, the N-terminal PHR (Photolyase-Homologous Region) domain that bind the chromophore FAD (flavin adenine dinucleotide), and the CCE (CRY C-terminal Extension) domain that appears intrinsically unstructured but critical to the function and regulation of cryptochromes. Most cryptochromes accumulate in the nucleus, and they undergo blue light-dependent phosphorylation or ubiquitination. It is hypothesized that photons excite electrons of the flavin molecule, resulting in redox reaction or circular electron shuttle and conformational changes of the photoreceptors. The photoexcited cryptochrome are phosphorylated to adopt an open conformation, which interacts with signaling partner proteins to alter gene expression at both transcriptional and posttranslational levels and consequently the metabolic and developmental programs of plants.

INTRODUCTION

Plants possess two types of photoreceptors: photosynthetic pigments that harvest light energy for photosynthesis, and photosensory receptors that mediate non-photosynthetic light responses. Plant photosensory receptors are presently best studied in Arabidopsis. The Arabidopsis genome encodes apoproteins of at least a dozen photoreceptors: five red/far-red light receptors phytochromes (phyA, phyB, phyC, phyD, and phyE), and seven blue light receptors, including two cryptochromes (CRY1 and CRY2), two phototropins (phot1 and phot2), and three LOV/F-box/Kelch-domain proteins (ZTL, FKF, and LKP2). Cryptochromes are photolyase-like flavoproteins that mediate blue-light regulation of gene expression and photomorphogenic responses in Arabidopsis and other organisms (Cashmore, 1997; Lin and Shalitin, 2003; Sancar, 2003). In this chapter, we will discuss the function, structure, photochemistry, and signal transduction mechanisms of Arabidopsis cryptochromes. Readers are encouraged to read other chapters in this book for the related topics, such as photomorphogenesis (Nemhauser and Chory, 2002), phytochromes (Wang and Deng, 2002), phototropins (Liscum, 2002), and the circadian clock (McClung et al., 2002).

The term cryptochrome was first coined three decades ago for the then “cryptic” photoreceptors mediating various UV-A/ blue responses in cryptogams, which is an obsolete taxonomic term for plants that do not reproduce by seed, such as algae, fungi, mosses, and ferns (Gressel, 1979). Earlier physiological and photochemical experiments suggested that flavin might be the chromophore of the then unidentified cryptochromes (Briggs and Huala, 1999). In 1980, the Arabidopsis mutant hy4 was identified, which showed elongated hypocotyls when grown in blue light but not in other wavelengths of light or in the dark (Koornneef et al., 1980), suggesting that the gene is involved in blue light sensing . Over a decade later, Ahmad and Cashmore isolated another allele of the hy4 mutant from an Arabidopsis T-DNA insertion population generated by Ken Feldman and cloned the HY4 gene (Ahmad and Cashmore, 1993). The HY4 gene encodes a protein that resembles a DNA photolyase. Because DNA photolyase is a flavoprotein that catalyzes blue/UV-A light-dependent repair of lesions (cyclobutane pyrimidine dimers) in UV-damaged DNA (Sancar, 1990), HY4 was immediately suspected to be the long sought-after cryptochrome. It was subsequently found that the HY4 protein binds to flavin adenine dinucleotide (FAD) and that it lacks DNA-repairing photolyase activity (Lin et al., 1995b; Malhotra et al., 1995). These results, together with the finding that transgenic tobacco seedlings expressing the Arabidopsis HY4 cDNA were hypersensitive to blue and UV-A light but not to red or far-red light, argued strongly that HY4 is a cryptochrome and so it was renamed cryptochrome 1 or CRY1 (Lin et al., 1995a). The second member of the CRY gene family in Arabidopsis, CRY2, was isolated by screening Arabidopsis cDNA libraries with the CRY1 cDNA probes (Hoffman et al., 1996; Lin et al., 1996b). Studies of the cry2 mutants demonstrated that CRY2 primarily regulates the photoperiodic promotion of floral initiation (Guo et al., 1998; El-Assal et al., 2001). The third member of the Arabidopsis CRY family, CRY3, is a CRY-DASH protein that can be detected in chloroplasts and mitochondria (Kleine et al., 2003). CRY-DASH proteins do not have conventional photolyase activity, but they bind DNA or RNA directly. Although some CRY-DASH have been shown to possess cryptochrome activity in regulating transcription or development (Hitomi et al., 2000; Brudler et al., 2003; Worthington et al., 2003; Veluchamy and Rollins, 2008), it was also found that CRY-DASH proteins, including Arabidopsis CRY3, catalyze repair of the cyclobutane pyrimidine dimers of single-stranded DNA in vitro (Huang et al., 2006; Selby and Sancar, 2006; Klar et al., 2007; Pokorny et al., 2008). Therefore, Arabidopsis CRY3 and other CRY-DASH proteins may act as single-stranded DNA photolyases or dual-activity photoreceptors that have both photolyase and cryptochrome activities.

Since the discovery of the first cryptochrome in Arabidopsis, this type of photoreceptor has been widely found in organisms ranging from bacteria to human (Cashmore, 2003; Partch and Sancar, 2005b). All cryptochromes share sequence similarity at their N-terminal PHR domains with DNA photolyases, and they act as photoreceptors not only in plants, but also in bacteria, insects, coral, zebrafish, chicken, and mammals (Emery et al., 1998; Stanewsky et al., 1998; Ceriani et al., 1999; Selby et al., 2000; Cermakian et al., 2002; Van Gelder et al., 2003; Tu et al., 2004; Tamai et al., 2007; Hoang et al., 2008b; Zhu et al., 2008b; Hendrischk et al., 2009). Based on phylogenetic analyses, the photolyase/cryptochrome superfamily was divided into five subfamilies: CPD (cyclobutane pyrimidine dimer) photolyase (photolyase without further qualification refers to CPD photolyase), 6–4 photolyase, plant cryptochromes, animal cryptochromes, and CRY-DASH (Partch and Sancar, 2005a). CPD photolyases and 6–4 photolyases repair cyclobutane pyrimidine dimers and pyrimidine (6–4) pyrimidone photoproducts, respectively (Sancar, 2000; Sancar, 2003). Arabidopsis possesses both CPD photolyase and 6–4 DNA photolyase (Ahmad et al., 1997; Nakajima et al., 1998), in addition to CRY1, CRY2, and CRY-DASH (CRY3). Animal cryptochromes are further divided into two classes, based on both phylogenetic analysis of sequences and their light responsiveness. Animal type I cryptochromes, such as Drosophila dCRY and monarch butterfly CRY1, act as photoreceptors, whereas animal type II cryptochromes, such as mouse cryptochromes, human cryptochromes, and monarch butterfly CRY2, act as light-independent transcription repressors (Zhu et al., 2005; Yuan et al., 2007). Some insects, such as monarch butterfly and mosquito, have both types of cryptochromes, whereas others, such as Drosophila, has only one (Yuan et al., 2007). Different cryptochromes have been shown to act as the essential components of the circadian clock in mammals (Thresher et al., 1998; van der Horst et al., 1999; Vitaterna et al., 1999), the dual-function photolyase/ transcription-regulator in bacteria, fungus, or algae (Hitomi et al., 2000; Bayram et al., 2008; Coesel et al., 2009), and the light-dependent magnetoreceptors in plants, birds, and insects (Ahmad et al., 2007; Liedvogel et al., 2007; Gegear et al., 2008; Liedvogel and Mouritsen, 2009; Gegear et al., 2010). Studies of the last 17 years indicate that cryptochromes are probably the most widely spread photoreceptors in nature that play various biological functions across all three major evolutionary lineages, from bacteria, plants, to animals.

The nomenclature of Arabidopsis cryptochromes was previously suggested in 1998 to follow that of the phytochromes, such that the wild-type genes, mutant genes, apoproteins, and holoproteins of cryptochromes were referred to as CRY, cry, CRY, and cry, respectively (Quail et al., 1994; Lin et al., 1998). However, because a clear distinction between apocryptochromes and holocryptochromes is often difficult and not used by researchers of cryptochromes in other organisms, the capital and un-italicized symbol, CRY, is now used more frequently (and in this chapter) to describe cryptochrome proteins regardless whether they are apoproteins or holoproteins (Yu et al., 2007b; Yu et al., 2007a).

CRYPTOCHROME FUNCTIONS