Abstract
Plant Cryptochromes (CRYs) are photolyase-like flavoproteins that have been reported in all evolutionary lineages. As UV-A/blue light photoreceptors, CRYs play a vital role in plant growth and development. In the present study, a total of 94 CRY1 and 68 CRY2 candidate genes were retrieved from 58 and 50 plant genomes, respectively. Phylogenetic analysis indicates that CRY genes could be divided into three groups (dicotyledons, monocots, and spore plants). A comprehensive review of the CRY gene family suggests that the CRY genes are relatively conservative and stable during evolution.
Similar content being viewed by others
Abbreviations
- CRY:
-
Cryptochrome
- PHR:
-
photolyase homologous region
- FAD:
-
flavin adenine dinucleotide
- COP1:
-
Constitutive photomorphogenesis 1
- PHOT:
-
phototropin
- PHY:
-
phytochrome
- TTFL:
-
transcription/translation feedback loop
References
Ahmad M, Cashmore AR (1993) HY4 gene of a. thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature 366:162–166. https://doi.org/10.1038/366162a0
Ahmad M, Cashmore AR (1996) Seeing blue: the discovery of cryptochrome. Plant Mol Biol 30:851–861. https://doi.org/10.1007/bf00020798
Bailey TL et al (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208. https://doi.org/10.1093/nar/gkp335
Barrero JM, Downie AB, Xu Q, Gubler F (2014) A role for barley CRYPTOCHROME1 in light regulation of grain dormancy and germination. Plant Cell 26:1094–1104. https://doi.org/10.1105/tpc.113.121830
Bayram O, Biesemann C, Krappmann S, Galland P, Braus GH (2008) More than a repair enzyme: Aspergillus nidulans photolyase-like CryA is a regulator of sexual development. Mol Biol Cell 19:3254–3262. https://doi.org/10.1091/mbc.E08-01-0061
Biasini M et al (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258. https://doi.org/10.1093/nar/gku340
Blazquez M, Koornneef M, Putterill J (2001) Flowering on time: genes that regulate the floral transition. Workshop on the molecular basis of flowering time control. EMBO Rep 2:1078–1082. https://doi.org/10.1093/embo-reports/kve254
Briggs WR, Christie JM (2002) Phototropins 1 and 2: versatile plant blue-light receptors. Trends Plant Sci 7:204–210
Brudler R et al (2003) Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell 11:59–67
Cashmore AR, Jarillo JA, Wu YJ, Liu D (1999) Cryptochromes: blue light receptors for plants and animals. Science 284:760–765
Chatterjee M, Sharma P, Khurana JP (2006) Cryptochrome 1 from Brassica napus is up-regulated by blue light and controls hypocotyl/stem growth and anthocyanin accumulation. Plant Physiol 141:61–74. https://doi.org/10.1104/pp.105.076323
Fankhauser C, Ulm R (2011) Light-regulated interactions with SPA proteins underlie cryptochrome-mediated gene expression. Genes Dev 25:1004–1009. https://doi.org/10.1101/gad.2053911
Giliberto L et al (2005) Manipulation of the blue light photoreceptor cryptochrome 2 in tomato affects vegetative development, flowering time, and fruit antioxidant content. Plant Physiol 137:199–208. https://doi.org/10.1104/pp.104.051987
Goodstein DM et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186. https://doi.org/10.1093/nar/gkr944
Guex N, Peitsch MC, Schwede T (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis 30(Suppl 1):S162–S173. https://doi.org/10.1002/elps.200900140
Guo H, Duong H, Ma N, Lin C (1999) The Arabidopsis blue light receptor cryptochrome 2 is a nuclear protein regulated by a blue light-dependent post-transcriptional mechanism. Plant J 19:279–287. https://doi.org/10.1046/j.1365-313x.1999.00525.x
He SB, Wang WX, Zhang JY, Xu F, Lian HL, Li L, Yang HQ (2015) The CNT1 domain of Arabidopsis CRY1 alone is sufficient to mediate blue light inhibition of hypocotyl elongation. Mol Plant 8:822–825. https://doi.org/10.1016/j.molp.2015.02.008
Hirose F, Shinomura T, Tanabata T, Shimada H, Takano M (2006) Involvement of rice cryptochromes in de-etiolation responses and flowering. Plant Cell Physiol 47:915–925. https://doi.org/10.1093/pcp/pcj064
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518–522. https://doi.org/10.1093/molbev/msx281
Hsu DS et al (1996) Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins. Biochemistry 35:13871–13877. https://doi.org/10.1021/bi962209o
Imaizumi T, Kadota A, Hasebe M, Wada M (2002) Cryptochrome light signals control development to suppress auxin sensitivity in the moss Physcomitrella patens. Plant Cell 14:373–386. https://doi.org/10.1105/tpc.010388
Imaizumi T, Kanegae T, Wada M (2000) Cryptochrome nucleocytoplasmic distribution and gene expression are regulated by light quality in the fern Adiantum capillus-veneris. Plant Cell 12:81–96. https://doi.org/10.1105/tpc.12.1.81
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14:587–589. https://doi.org/10.1038/nmeth.4285
Kleine T, Lockhart P, Batschauer A (2003) An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles. Plant J 35:93–103
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Lin C (2002) Blue light receptors and signal transduction. Plant Cell 14(Suppl):S207–S225
Lin C, Ahmad M, Gordon D, Cashmore AR (1995) Expression of an Arabidopsis cryptochrome gene in transgenic tobacco results in hypersensitivity to blue, UV-A, and green light. Proc Natl Acad Sci U S A 92:8423–8427. https://doi.org/10.1073/pnas.92.18.8423
Lin C, Shalitin D (2003) Cryptochrome structure and signal transduction. Annu Rev Plant Biol 54:469–496. https://doi.org/10.1146/annurev.arplant.54.110901.160901
Lin C, Todo T (2005) The cryptochromes Genome Biol 6:220. https://doi.org/10.1186/gb-2005-6-5-220
Lin C, Yang H, Guo H, Mockler T, Chen J, Cashmore AR (1998) Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2 Proc Natl Acad Sci U S a 95:2686-2690. https://doi.org/10.1073/pnas.95.5.2686
Liu HT, Liu B, Zhao CX, Pepper M (2011) Lin CT. The action mechanisms of plant cryptochromes Trends Plant Sci 16:684–691. https://doi.org/10.1016/j.tplants.2011.09.002
Liu HT, Yu XH, Li KW, Klejnot J, Yang HY, Lisiero D, Lin CT (2008) Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322:1535–1539. https://doi.org/10.1126/science.1163927
Liu YW, Li X, Li KW, Liu HT, Lin CT (2013) Multiple bHLH proteins form heterodimers to mediate CRY2-dependent regulation of flowering-time in Arabidopsis. PLoS Genet 9. https://doi.org/10.1371/journal.pgen.1003861
Malhotra K, Kim ST, Batschauer A, Dawut L, Sancar A (1995) Putative blue-light photoreceptors from Arabidopsis thaliana and Sinapis alba with a high degree of sequence homology to DNA photolyase contain the two photolyase cofactors but lack DNA repair activity. Biochemistry 34:6892–6899
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/molbev/msu300
Partch CL, Clarkson MW, Ozgur S, Lee AL, Sancar A (2005) Role of structural plasticity in signal transduction by the cryptochrome blue-light photoreceptor. Biochemistry 44:3795–3805. https://doi.org/10.1021/bi047545g
Quail PH (2002) Photosensory perception and signalling in plant cells: new paradigms? Curr Opin Cell Biol 14:180–188. https://doi.org/10.1016/S0955-0674(02)00309-5
Rizzini L et al (2011) Perception of UV-B by the Arabidopsis UVR8 protein. Science 332:103–106. https://doi.org/10.1126/science.1200660
Rosensweig C et al (2018) An evolutionary hotspot defines functional differences between CRYPTOCHROMES. Nat Commun 9. https://doi.org/10.1038/s41467-018-03503-6
Sancar A (2004) Regulation of the mammalian circadian clock by cryptochrome. J Biol Chem 279:34079–34082. https://doi.org/10.1074/jbc.R400016200
Valverde F, Mouradov A, Soppe W, Ravenscroft D, Samach A, Coupland G (2004) Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 303:1003–1006. https://doi.org/10.1126/science.1091761
Wang HC, Minh BQ, Susko E, Roger AJ (2018a) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate Phylogenomic estimation. Syst Biol 67:216–235. https://doi.org/10.1093/sysbio/syx068
Wang W et al (2018b) Photoexcited CRYPTOCHROME1 interacts with dephosphorylated BES1 to regulate Brassinosteroid signaling and Photomorphogenesis in Arabidopsis. Plant Cell 30:1989–2005. https://doi.org/10.1105/tpc.17.00994
Yang HQ, Wu YJ, Tang RH, Liu D, Liu Y, Cashmore AR (2000) The C termini of Arabidopsis cryptochromes mediate a constitutive light response. Cell 103:815–827. https://doi.org/10.1016/s0092-8674(00)00184-7
Yu X et al (2007) Derepression of the NC80 motif is critical for the photoactivation of Arabidopsis CRY2. Proc Natl Acad Sci U S A 104:7289–7294. https://doi.org/10.1073/pnas.0701912104
Zhang Q et al (2008) Association of the circadian rhythmic expression of GmCRY1a with a latitudinal cline in photoperiodic flowering of soybean. Proc Natl Acad Sci U S A 105:21028–21033. https://doi.org/10.1073/pnas.0810585105
Zhang YC, Gong SF, Li QH, Sang Y, Yang HQ (2006) Functional and signaling mechanism analysis of rice CRYPTOCHROME 1. Plant J 46:971–983. https://doi.org/10.1111/j.1365-313X.2006.02753.x
Zuo ZC, Liu HT, Liu B, Liu XM, Lin CT (2011) Blue light-dependent interaction of CRY2 with SPA1 regulates COP1 activity and floral initiation in Arabidopsis. Curr Biol 21:841–847. https://doi.org/10.1016/j.cub.2011.03.048
Acknowledgments
This work was supported by NSFC (31600228 to S.C.; U1605212, 31761130074 to Y.Q.), fund from Fujian Agriculture and Forestry University Forestry peak discipline construction project (71201800739 to S.C.) and a Guangxi Distinguished Experts Fellowship and a Newton Advanced Fellowship (NA160391) to Y.Q.
Author information
Authors and Affiliations
Contributions
S.C., S.H, H.L. designed the study, performed the experiments and wrote manuscript. J.Z., M.A., Q.W., H.C., and A.H. assisted with the data interpretation and manuscript writing. Y. Y. and Y. Q. conceived the study and revised the manuscript.
Corresponding authors
Ethics declarations
Conflict of Interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Additional information
Communicated by: Yuval Cohen
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Cao, S., He, S., Lv, H. et al. Genome-Wide Analysis of the Cryptochrome Gene Family in Plants. Tropical Plant Biol. 13, 117–126 (2020). https://doi.org/10.1007/s12042-019-09249-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12042-019-09249-9