Signaling ánh sáng như một bộ tích hợp tế bào đối với nhiều yếu tố môi trường ở thực vật

Abdellatif IM, Yuan S, Yoshihara S, Suzaki T, Ezura H, Miura K (2023) Stimulation of tomato drought tolerance by PHYTOCHROME A and B1B2 mutations. Int J Mol Sci 24:1560 Al-Sady B, Ni WM, Kircher S, Schafer E, Quail PH (2006) Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation. Mol Cell 23:439–446 Bai MY, Fan M, Oh E, Wang ZY (2012) A triple helix-loop-helix/basic helix-loop-helix cascade controls cell elongation downstream of multiple hormonal and environmental signaling pathways in Arabidopsis. Plant Cell 24:4917–4929 Bajracharya A, Xi J, Grace KF, Bayer EE, Grant CA, Clutton CH, Qiu Y (2022) PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosensory growth requires the mediator subunit MED14. Plant Physiol 190:2706–2721 Balasubramanian S, Sridevi S, Janne L, Detlef W (2006) Potent induction of arabidopsis thaliana flowering by elevated growth temperature. PLoS Genet 2:e106 Ballesteros ML, Bolle C, Lois LM, Moore JM, Vielle-Calzada JP, Grossniklaus U, Chua NH (2001) LAF1, a MYB transcription activator for phytochrome a signaling. Genes Dev 15:2613–2625 Balogh E, Kalapos B, Ahres M, Boldizsár Á, Gierczik K, Gulyás Z, Gyugos M, Szalai G, Novák A, Kocsy G (2022) Far-red light coordinates the diurnal changes in the transcripts related to nitrate reduction, glutathione metabolism and antioxidant enzymes in barley. Int J Mol Sci 23:7479 Barros-Galvão T, Dave A, Gilday AD, Harvey D, Vaistij FE, Graham IA (2020) ABA INSENSITIVE4 promotes rather than represses PHYA-dependent seed germination in Arabidopsis thaliana. New Phytol 226:953 Bernula P, Pettkó-Szandtner A, Hajdu A, Kozma-Bognár L, Josse EM, Ádám É, Nagy F, Viczián A (2021) Sumoylation of phytochrome interacting factor 3 promotes photomorphogenesis in Arabidopsis thaliana. New Phytol 229:2050–2061 Blanco Touriñán N (2020) New mechanisms of DELLA protein regulation and activity in Arabidopsis (Doctoral dissertation, Universitat Politècnica de València). Brown BA, Jenkins GI (2008) UV-B signaling pathways with different fluence-rate response profiles are distinguished in mature Arabidopsis leaf tissue by requirement for UVR8, HY5, and HYH. Plant Physiol 146:576 Bursch K, Toledo-Ortiz G, Pireyre M, Lohr M, Braatz C, Johansson H (2020) Identification of BBX proteins as rate-limiting cofactors of HY5. Nat Plants 6:921–928 Cai Y, Liu Y, Fan Y, Li X, Yang M, Xu D, Wang H, Deng XW, Li J (2023) MYB112 connects light and circadian clock signals to promote hypocotyl elongation in Arabidopsis. Plant Cell 19:koad170 Casal JJ, Balasubramanian S (2019) Thermomorphogenesis. Annu Rev Plant Biol 70:321–346 Castillon A, Shen H, Huq E (2007) Phytochrome interacting factors: central players in phytochrome-mediated light signaling networks. Trends Plant Sci 12:514–521 Catalá R, Medina J, Salinas J (2011) Integration of low temperature and light signaling during cold acclimation response in Arabidopsis. Proc Natl Acad Sci 108:16475–16480 Černý M, Habánová H, Berka M, Luklová M, Brzobohatý B (2018) Hydrogen peroxide: its role in plant biology and crosstalk with signalling networks. Int J Mol Sci 19:2812 Çevik V, Kidd BN, Zhang P, Hill C, Kiddle S, Denby KJ (2012) MEDIATOR 25 acts as an integrative hub for the regulation of jasmonate- responsive gene expression in Arabidopsis. Plant Physiol 160:541–555 Chaiwanon J, Wang W, Zhu JY, Oh E, Wang ZY (2016) Information integration and communication in plant growth regulation. Cell 164(6):1257–1268 Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N (1998) Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10:673–683 Chen H, Shen Y, Tang X, Yu L, Wang J, Guo L, Zhang Y, Zhang H, Feng S, Strickland E, Zheng N (2006) Arabidopsis CULLIN4 forms an E3 ubiquitin ligase with RBX1 and the CDD complex in mediating light control of development. Plant Cell 18:1991–2004 Chen R, Jiang H, Li L, Zhai Q, Qi L, Zhou W, Liu X, Li H, Zheng W, Sun J, Li C (2012) The Arabidopsis Mediator subunit MED 25 differentially regulates jasmonate and abscisic acid Signalling through interacting with the MYC2 and ABI5 transcription factors. Plant Cell 24:2898–2916 Cheng MC, Kathare PK, Paik I, Huq E (2021) Phytochrome signaling networks. Annu Rev Plant Biol 72:217–244 Choi WG, Toyota M, Kim SH, Hilleary R, Gilroy S (2014) Salt stress-induced Ca2+ waves are associated with rapid, long-distance root-to-shoot signalling in plants. Proc Natl Acad Sci USA 111:6497–6502 Choudhury S, Panda P, Sahoo L, Panda SK (2013) Reactive oxygen species signaling in plants under abiotic stress. Plant Signal Behav 8:e23681 Christie JM (2007) Phototropin blue-light receptors. Annu Rev Plant Biol 58:21–45 Christie JM, Yang H, Richter GL, Sullivan S, Thomson CE, Lin J, Titapiwatanakun B, Ennis M, Kaiserli E, Lee OR, Adamec J (2011) phot1 inhibition of ABCB19 primes lateral auxin fluxes in the shoot apex required for phototropism. PLoS Biol 9(6):e1001076 Christie JM, Blackwood L, Petersen J, Sullivan S (2015) Plant flavoprotein photoreceptors. Plant Cell Physiol 56:401–413 Chung Y, Maharjan PM, Lee O, Fujioka S, Jang S, Kim B, Takatsuto S, Tsujimoto M, Kim H, Cho S, Park T (2011) Auxin stimulates DWARF4 expression and brassinosteroid biosynthesis in Arabidopsis. Plant J 66:564–578 Cockburn W, Whitelam GC, Broad A, Smith J (1996) The participation of phytochrome in the signal transduction pathway of salt stress responses in Mesembryanthemum crystallinum L. J Exp Bot 47:647–653 Cordeiro AM, Figueiredo DD, Tepperman J, Borba AR, Lourenço T, Abreu IA, Ouwerkerk PB, Quail PH, Oliveira MM, Saibo NJ (2016) Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B. Biochim Et Biophys Acta Gene Regul Mech 1859:393–404 Cordeiro AM, Andrade L, Monteiro CC, Leitão G, Wigge PA, Saibo NJ (2022) Phytochrome-interacting factors: a promising tool to improve crop productivity. J Exp Bot 73:3881–3897 Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163–177 D’Amico-Damião V, Cruz FJ, Gavassi MA, Santos DM, Melo HC, Carvalho RF (2015) Photomorphogenic modulation of water stress in tomato (Solanum lycopersicum L.): the role of phytochromes A, B1, and B2. J Hortic Sci Biotechnol 90:25–30 de Wit M, Galvão VC, Fankhauser C (2016) Light-mediated hormonal regulation of plant growth and development. Annu Rev Plant Biol 67:513–537 Deng XW, Quail PH (1999) Signalling in light-controlled development. Semi Cell Dev Biol 10:121–129 Deng XW, Caspar T, Quail PH (1991) Copl: a regulatory locus involved in light-controlled development and gene expression in Arabidopsis. Genes Dev 5:1172–1182 Deng XW, Matsui M, Wei N, Wagner D, Chu AM, Feldmann KA, Quail PH (1992) COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a Gβ homologous domain. Cell 71:791–801 Dieterle M, Buche C, Schafer E, Kretsch T (2003) Characterization of a novel non-constitutive photomorphogenic cop1 allele. Plant Physiol 133:1557–1564 Dixit SK, Gupta A, Fatima U, Senthil-Kumar M (2019) AtGBF3 confers tolerance to Arabidopsis thaliana against combined drought and Pseudomonas syringae stress. Environ Exp Bot 168:103881 Dong J, Dafang T, Zhaoxu G, Renbo Y, Kunlun L, Hang H, William T, Xing WD, Haodong C (2014) Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark. Plant Cell 26:3630–3645 Dong X, Yan Y, Jiang B, Shi Y, Jia Y, Cheng J, Shi Y, Kang J, Li H, Zhang D, Qi L (2020) The cold response regulator CBF1 promotes Arabidopsis hypocotyl growth at ambient temperatures. EMBO J 39:e103630 Duan L, Dietrich D, Ng CH, Chan PM, Bhalerao R, Bennett MJ, Dinneny JR (2013) Endodermal ABA signaling promotes lateral root quiescence during salt stress in Arabidopsis seedlings. Plant Cell 25:324–341 El-Esawi M, Arthaut LD, Jourdan N, d’Harlingue A, Link J, Martino CF, Ahmad M (2017) Blue-light induced biosynthesis of ROS contributes to the signaling mechanism of Arabidopsis cryptochrome. Sci Rep 7:13875 Facella P, Daddiego L, Giuliano G, Perrotta G (2012) Gibberellin and auxin influence the diurnal transcription pattern of photoreceptor genes via CRY1a in tomato. PLoS ONE 2012:e30121 Fang F, Lin L, Zhang Q, Lu M, Skvortsova MY, Podolec R, Zhang Q, Pi J, Zhang C, Ulm R (2022) Yin R (2022) Mechanisms of UV-B light-induced photoreceptor UVR8 nuclear localization dynamics. New Phytol 236:1824–1837 Farquharson KL (2016) Decoding the molecular network that drives hypocotyl elongation. Plant Cell 28:1994–1995 Fei C, Chen L, Yang T, Zou W, Lin H, Xi D (2019) The role of phytochromes in Nicotiana tabacum against Chilli veinal mottle virus. Plant Physiol Biochem 139:4707 Fiorucci AS, Michaud O, Schmid-Siegert E, Trevisan M, Allenbach Petrolati L, Çaka Ince Y, Fankhauser C (2022) Shade suppresses wound-induced leaf repositioning through a mechanism involving Phytochrome Kinase Substrate (PKS) genes. PLoS Genet 18:e1010213 Franklin KA, Larner VS, Whitelam GC (2005) The signal transducing photoreceptors of plants. Int J Dev Biol 49:653–664 Frigerio M, Alabadí D, Pérez-Gómez J, García-Cárcel L et al (2006) Transcriptional regulation of gibberellin metabolism genes by auxin signaling in Arabidopsis. Plant Physiol 142:553–563 Fujii Y, Tanaka H, Konno N, Ogasawara Y, Hamashima N, Tamura S, Hasegawa S, Hayasaki Y, Okajima K, Kodama Y (2017) Phototropin perceives temperature based on the lifetime of its photoactivated state. Proc Natl Acad Sci USA 114:9206–9211 Gallé Á, Czékus Z, Tóth L, Galgóczy L, Poór P (2021) Pest and disease management by red light. Plant Cell Environ 44:3197–3210 Gangappa SN, Botto JF (2016) The multifaceted roles of HY5 in plant growth and development. Mol Plant 9:1353–1365 Gangappa SN, Kumar SV (2017) DET1 and HY5 control PIF4-mediated thermosensory elongation growth through distinct mechanisms. Cell Rep 18:344–351 Gao Y, Jiang W, Dai Y, Xiao N, Zhang C, Li H, Lu Y, Wu M, Tao X, Deng D, Chen J (2015) A maize phytochrome-interacting factor 3 improves drought and salt stress tolerance in rice. Plant Mol Biol 87:413–428 Gao Y, Wu M, Zhang M, Jiang W, Ren X, Liang E, Zhang D, Zhang C, Xiao N, Li Y, Dai Y (2018) A maize phytochrome-interacting factors protein ZmPIF1 enhances drought tolerance by inducing stomatal closure and improves grain yield in Oryza sativa. Plant Biotechnol J 16:1375–1387 Gautam JK, Giri MK, Singh D, Chattopadhyay S, Nandi AK (2021) MYC2 influences salicylic acid biosynthesis and defense against bacterial pathogens in Arabidopsis thaliana. Physiol Plant 173:2248–2261 Geng Y, Wu R, Wee CW, Xie F, Wei X, Chan PMY, Tham C, Duan L, Dinneny JR (2013) A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis. Plant Cell 25:2132–2154 Genoud T, Buchala AJ, Chua NH, Métraux JP (2002) Phytochrome signalling modulates the SA-perceptive pathway in Arabidopsis. Plant J 31:87–95 Giustozzi M, Freytes SN, Jaskolowski A, Lichy M, Mateos J, Falcone Ferreyra ML, Rosano GL, Cerdán P, Casati P (2022) Arabidopsis mediator subunit 17 connects transcription with DNA repair after UV-B exposure. Plant J 110:1047–1067 Gruszka D (2013) The brassinosteroid signaling pathway- New key players and interconnections with other signaling networks crucial for plant development and stress tolerance. Int J Mol Sci 14:8740–8774 Gyugos M, Ahres M, Gulyás Z, Szalai G, Darkó É, Végh B, Boldizsár Á, Mednyánszky Z, Kar RK, Dey N, Simon-Sarkadi L (2019) Role of light-intensity-dependent changes in thiol and amino acid metabolism in the adaptation of wheat to drought. J Agron Crop Sci 205:562–570 Gyula P, Eberhard S, Ferenc N (2003) Light perception and signalling in higher plants. Curr Opin Plan Biol 6:446–452 Ha JH, Kim JH, Kim SG, Sim HJ, Lee G, Halitschke R, Baldwin IT, Kim JI, Park CM (2018) Shoot phytochrome B modulates reactive oxygen species homeostasis in roots via abscisic acid signaling in Arabidopsis. Plant J 94:790–798 Hardtke CS, Osterlund GK et al (2000) HY5 stability and activity in Arabidopsis is regulated by phosphorylation in its COP1 binding domain. EMBO J 19:4997–5006 Harmon AC, Michael G, Jeffrey FH (2000) CDPKs–a kinase for every Ca2+ signal? Trends Plant Sci 5:154–159 Harter K, Frohnmeyer H, Kircher S, Kunkel T, Mühlbauer S, Schäfer E (1994) Light induces rapid changes of the phosphorylation pattern in the cytosol of evacuolated parsley protoplasts. Proc Nat Acad Sci 91:5038–5042 He Y, Li Y, Cui L, Xie L, Zheng C, Zhou G, Zhou J, Xie X (2016) Phytochrome B negatively affects cold tolerance by regulating OsDREB1 gene expression through phytochrome interacting factor-like protein OsPIL16 in rice. Front Plant Sci 7:1963 Hoang QT, Han YJ, Kim JI (2019) Plant phytochromes and their phosphorylation. Int J Mol Sci 20:3450 Holalu SV (2014) Phytochrome B controls shoot architecture by regulating phytochrome interacting factors and phytohormones. Texas A&M University Hsieh HL, Okamoto H (2014) Molecular interaction of jasmonate and phytochrome a signalling. J Exp Bot 65:2847–2857 Hua J (2009) From freezing to scorching, transcriptional responses to temperature variations in plants. Curr Opin Plant Biol 12:568–573 Huang Z, Tang R, Yi X, Xu W, Zhu P, Jiang CZ (2022) Overexpressing phytochrome interacting F actor 8 of Myrothamnus flabellifolia enhanced drought and salt tolerance in Arabidopsis. Int J Mol Sci 23:8155 Huang J, Qiu ZY, He J, Xu HS, Wang K, Du HY, Gao D, Zhao WN, Sun QG, Wang YS, Wen PZ (2023) Phytochrome B mediates dim-light-reduced insect resistance by promoting the ethylene pathway in rice. Plant Physiol 191:1272–1287 Indorf M, Cordero J, Neuhaus G, Rodríguez-Franco M (2007) Salt tolerance (STO), a stress-related protein, has a major role in light signalling. Plant J 51:563–574 Inoue SI, Matsushita T, Tomokiyo Y, Matsumoto M, Nakayama KI, Kinoshita T, Shimazaki KI (2011) Functional analyses of the activation loop of phototropin2 in Arabidopsis. Plant Physiol 156:117–128 Ito S, Young HS, Takato I (2012) LOV domain-containing F-box proteins: light-dependent protein degradation modules in Arabidopsis. Mol Plant 5:573–582 Jaeger KE, Wigge PA (2007) FT protein acts as a long-range signal in Arabidopsis. Curr Biol 17:1050–1054 Jang IC, Henriques R, Chua NH (2013) Three transcription factors, HFR1, LAF1 and HY5, regulate largely independent signaling pathways downstream of phytochrome A. Plant Cell Physiol 54:907–916 Jia KP, Luo Q, He SB, Lu XD, Yang HQ (2014) Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome and phytochrome signaling pathways in Arabidopsis. Mol Plant 7:528–540 Jia X, Song M, Wang S, Liu T, Wang L, Guo L, Su L, Shi Y, Zheng X, Yang J (2023) Arabidopsis phytochromes A and B synergistically repress SPA1 under blue light. J Integr Plant Biol 65:888–894 Jiang B, Shi Y, Zhang X, Xin X, Qi L, Guo H, Li J, Yang S (2017) PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis. Proc Natl Acad Sci 114:E6695-6702 Jiang B, Shi Y, Peng Y, Jia Y, Yan Y, Dong X, Li H, Dong J, Li J, Gong Z, Thomashow MF (2020a) Cold-induced CBF–PIF3 interaction enhances freezing tolerance by stabilizing the phyB thermosensor in Arabidopsis. Mol Plant 13:894–906 Jiang J, Xiao Y, Chen H, Hu W, Zeng L, Ke H, Ditengou FA, Devisetty U, Palme K, Maloof J, Dehesh K (2020b) Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate growth. Plant Physiol 183(3):1268–1280 Jiao Y, Lau OS, Deng XW (2007) Light-regulated transcriptional networks in higher plants. Nat Rev Genet 8:217–223 Josse EM, Halliday KJ (2008) Skotomorphogenesis: the dark side of light signalling. Curr Biol 18:R1144-1146 Jung JH, Domijan M, Klose C, Biswas S, Ezer D, Gao M, Khattak AK, Box MS, Charoensawan V, Cortijo S, Kumar M (2016) Phytochromes function as thermosensors in Arabidopsis. Science 354:886–889 Jung JH, Li Z, Chen H, Yang S, Li D, Priatama RA, Kumar V, Xuan YH (2023) Mutation of phytochrome B promotes resistance to sheath blight and saline–alkaline stress via increasing ammonium uptake in rice. Plant J 113:277–290 Kang JH, Kim D, Yoon HI, Son JE (2023) Growth, morphology, and photosynthetic activity of Chinese cabbage and lettuce grown under polyethylene and spectrum conversion films. Hortic Environ Biotechnol 14:1–1 Karnachuk RA, Tishchenko SY, Golovatskaya IF (2001) Endogenous phytohormones and regulation of morphogenesis of arabidopsis thalianaby blue light. Russ J Plant Physiol 48:226–230 Kazan K, Manners JM (2011) The interplay between light and jasmonate signalling during defence and development. J Exp Bot 62:4087–4100 Keller MM, Jaillais Y, Pedmale UV, Moreno JE, Chory J, Ballaré CL (2011) Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades. Plant J 67:195–207 Kidokoro S, Maruyama K, Nakashima K, Imura Y, Narusaka Y, Shinwari ZK, Osakabe Y, Fujita Y, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2009) The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis. Plant Physiol 151:2046–2057 Kim YM, Woo JC, Song PS, Soh MS (2002) HFR1, a phytochrome A-signalling component, acts in a separate pathway from HY5, downstream of COP1 in Arabidopsis thaliana. Plant J 30:711–719 Kim C, Kim SJ, Jeong J, Park E, Oh E, Park YI, Lim PO, Choi G (2020) High ambient temperature accelerates leaf senescence via phytochrome-interacting factor 4 and 5 in Arabidopsis. Mol Cells 43:645 Kim JY, Lee SJ, Min WK, Cha S, Song JT, Seo HS (2022) COP1 controls salt stress tolerance by modulating sucrose content. Plant Signal Behav 17:2096784 Kinoshita T, Emi T, Tominaga M, Sakamoto K, Shigenaga A, Doi M, Shimazaki KI (2003) Blue-light-and phosphorylation-dependent binding of a 14–3–3 protein to phototropins in stomatal guard cells of broad bean. Plant Physiol 133:1453–1463 Kirchler T, Briesemeister S, Singer M, Schutze K, Keinath M, Kohlbacher O, Vicente-Carbajosa J, Teige M, Harter K, Chaban C (2010) The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. Eur J Cell Biol 89:175–183 Koini MA, Alvey L, Allen T, Tilley CA, Harberd NP, Whitelam GC, Franklin KA (2009) High temperature-mediated adaptations in plant architecture require the bHLH transcription factor PIF4. Curr Biol 19:408–413 Kudo M, Kidokoro S, Yoshida T, Mizoi J, Todaka D, Fernie AR, Shinozaki K, Yamaguchi-Shinozaki K (2017) Double overexpression of DREB and PIF transcription factors improves drought stress tolerance and cell elongation in transgenic plants. Plant Biotechnol J 15:458–471 Küpers JJ, Oskam L, Pierik R (2020) Photoreceptors regulate plant developmental plasticity through auxin. Plants 9:940 Kusnetsov VV, Doroshenko AS, Kudryakova NV, Danilova MN (2020) Role of phytohormones and light in de-etiolation. Russ J Plant Physiol 67:971–984 Kwon CT, Song G, Kim SH, Han J, Yoo SC, An G, Kang K, Paek NC (2018) Functional deficiency of phytochrome B improves salt tolerance in rice. Environ Exp Bot 148:100–108 Lang J, Genot B, Hirt H, Colcombet J (2017) Constitutive activity of the Arabidopsis MAP Kinase 3 confers resistance to Pseudomonas syringae and drives robust immune responses. Plant Signal Behav 12:e1356533 Lau OS, Deng XW (2010) Plant hormone signaling lightens up: integrators of light and hormones. Curr Opin Plant Biol 13:571–577 Lau OS, Xing D (2012) The photomorphogenic repressors COP1 and DET1: 20 years later. Trends Plant Sci 17:584–593 Lee CM, Thomashow MF (2012) Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. Proc Natl Acad Sci 109:15054–15059 Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19:731–749 Lee BD, Cha JY, Kim MR, Shin GI, Paek NC, Kim WY (2019) Light-dependent suppression of COP1 multimeric complex formation is determined by the blue-light receptor FKF1 in Arabidopsis. Biochem Biophys Res Commun 508:191–197 Legris M, Klose C, Costigliolo C, Burgie E, Neme M, Hiltbrunner A, Wigge PA, Schafer E, Vierstra RD, Casal JJ (2016) Phytochrome B integrates light and temperature signals in Arabidopsis. Science 354:897–900 Legris M, Nieto C, Sellaro R, Prat S, Casal JJ (2017) Perception and signalling of light and temperature cues in plants. Plant J 90:683–697 Leivar P, Monte E (2014) PIFs: systems integrators in plant development. Plant Cell 26:56–78 Leivar P, Quail PH (2011) PIFs: pivotal components in a cellular signaling hub. Trends Plant Sci 16:19–28 Leivar P, Monte E, Al-Sady B, Carle C, Storer A, Alonso JM, Ecker JR, Quail PH (2008) The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. Plant Cell 20:337–352 Li G, Siddiqui H, Teng Y, Lin R, Wan XY, Li J, Lau OS, Ouyang X, Dai M, Wan J, Devlin PF (2011) Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol 13:616–622 Li QF, Wang C, Jiang L, Li S, Sun SS, He JX (2012) An interaction between BZR1 and DELLAs mediates direct signaling crosstalk between brassinosteroids and gibberellins in Arabidopsis. Sci Signal 5:72 Li Y, Shi Y, Li M, Fu D, Wu S, Li J, Gong Z, Liu H, Yang S (2021) The CRY2–COP1–HY5–BBX7/8 module regulates blue light-dependent cold acclimation in Arabidopsis. Plant Cell 33:3555–3573 Lian H, Xu P, He S, Wu J, Pan J, Wang W, Xu F, Wang S, Pan J, Huang J, Yang HQ (2018) Photoexcited CRYPTOCHROME 1 interacts directly with G-protein β subunit AGB1 to regulate the DNA-binding activity of HY5 and photomorphogenesis in Arabidopsis. Mol Plant 11:1248–1263 Liang T, Mei S, Shi C, Yang Y, Peng Y, Ma L, Wang F, Li X, Huang X, Yin Y, Liu H (2018) UVR8 interacts with BES1 and BIM1 to regulate transcription and photomorphogenesis in Arabidopsis. Dev Cell 44:512–523 Lin C, Shalitin D (2003) Cryptochrome structure and signal transduction. Annu Rev Plant Biol 54:469–496 Liu CC, Ahammed GJ, Wang GT, Xu CJ, Chen KS, Zhou YH, Yu JQ (2018a) Tomato CRY1a plays a critical role in the regulation of phytohormone homeostasis, plant development, and carotenoid metabolism in fruits. Plant Cell Environ 41:354–366 Liu K, Li Y, Chen X, Li L, Liu K, Zhao H, Wang Y, Han S (2018b) ERF72 interacts with ARF6 and BZR1 to regulate hypocotyl elongation in Arabidopsis. J Exp Bot 69:3933–3347 Liu Z, Guo C, Wu R, Wang J, Zhou Y, Yu X, Zhang Y, Zhao Z, Liu H, Sun S, Hu M (2022) Identification of the regulators of epidermis development under drought-and salt-stressed conditions by single-cell RNA-seq. Int J Mol Sci 23:2759 Liu H, Li L, Fu X, Li Y, Chen T, Qin W, Yan X, Wu Z, Xie L, Kayani SL, Hassani D (2023a) AaMYB108 is the core factor integrating light and jasmonic acid signaling to regulate artemisinin biosynthesis in Artemisia annua. New Phytol 237:2224–2237 Liu S, Zhang Y, Pan X, Li B, Yang Q, Yang C, Zhang J, Wu F, Yang A, Li Y (2023b) PIF1, a phytochrome-interacting factor negatively regulates drought tolerance and carotenoids biosynthesis in tobacco. Int J Biol Macromol 6:125693 Liu X, Jiang W, Li Y, Nie H, Cui L, Li R, Tan L, Peng L, Li C, Luo J, Li M (2023c) FERONIA coordinates plant growth and salt tolerance via the phosphorylation of phyB. Nat Plants 9:645–660 Ljung K, Nemhauser JL, Perata P (2015) New mechanistic links between sugar and hormone signaling networks. Curr Opin Plant Biol 25:130–137 Lozano-Duran R, Zipfel C (2015) Trade-off between growth and immunity: role of brassinosteroids. Trends Plant Sci 20:12–19 Lu XD, Zhou CM, Xu PB, Luo Q, Lian HL, Yang HQ (2015) Red-light-dependent interaction of phyB with SPA1 promotes COP1–SPA1 dissociation and photomorphogenic development in Arabidopsis. Mol Plant 8:467–478 Ma L, Gao Y, Qu L, Chen Z, Li J, Zhao H, Deng XW (2002) Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14:2383–2398 Ma L, Han R, Yang Y, Liu X, Li H, Zhao X, Li J, Fu H, Huo Y, Sun L, Yan Y (2023) Phytochromes enhance SOS2-mediated PIF1 and PIF3 phosphorylation and degradation to promote Arabidopsis salt tolerance. Plant Cell 29:koad117 Major IT, Guo Q, Zhai J, Kapali G, Kramer DM, Howe GA (2020) A phytochrome B-independent pathway restricts growth at high levels of jasmonate defense. Plant Physiol 183:733–749 Mallappa C, Yadav V, Negi P, Chattopadhyay S (2006) A bzip transcription factor, G-box binding factor 1, regulates blue light mediated photomorphogenic growth in Arabidopsis. J Biol Chem 31:22190–22199 Manivannan A, Soundararajan P, Park YG, Jeong BR (2021) Physiological and proteomic insights into red and blue light-mediated enhancement of in vitro growth in Scrophularia kakudensis—a potential medicinal plant. Front Plant Sci 11:607007 Mao Z, He S, Xu F, Wei X, Jiang L, Liu Y, Wang W, Li T, Xu P, Du S, Li L (2020) Photoexcited CRY1 and phyB interact directly with ARF6 and ARF8 to regulate their DNA-binding activity and auxin-induced hypocotyl elongation in Arabidopsis. New Phytol 225:848–865 Mawphlang OIL, Eros VK (2017) Photoreceptor mediated plant growth responses: implications for photoreceptor engineering toward improved performance in crops. Fron Plant Sci 8:1181 McNellis TW, von Arnim AG, Araki T, Komeda Y, Misera S, Deng XW (1994) Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains. Plant Cell 6:487–500 Mo W, Tang W, Du Y, Jing Y, Bu Q, Lin R (2020) Phytochrome-interacting factor-like14 and slender rice1 interaction controls seedling growth under salt stress. Plant Physiol 184:506–517 Motchoulski A, Liscum E (1999) Arabidopsis NPH3: a NPH1 photoreceptor-interacting protein essential for phototropism. Science 286:961–964 Nagy F, Schäfer E (2002) Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants. Annu Rev Plant Biol 53:329–355 Nam TG, Lim YJ, Eom SH (2018) Flavonoid accumulation in common buckwheat (Fagopyrum esculentum) sprout tissues in response to light. Hortic Environ Biotechnol 59:19–27 Neff MM, Fanhauser C, Chory J (2000) Light: an indicator of time and place. Genes Dev 14:257–271 Nie N, Huo J, Sun S, Zuo Z, Chen Y, Liu Q, He S, Gao S, Zhang H, Zhao N, Zhai H (2023) Genome-wide characterization of the PIFs family in sweet potato and functional identification of IbPIF3.1 under drought and fusarium wilt stresses. Int J Mol Sci 24:40920 Oh E, Yamaguchi S, Kamiya Y, Bae G, Chung WI, Choi G (2006) Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Plant J 47:124–139 Oh E, Yamaguchi S, Hu J, Yusuke J, Jung B, Paik I, Lee HS, Sun TP, Kamiya Y, Choi G (2007) PIL5, a phytochrome-interacting bHLH protein, regulates gibberellin responsiveness by binding directly to the GAI and RGA promoters in Arabidopsis seeds. Plant Cell 19:1192–1208 Oh E, Zhu JY, Wang ZY (2012) Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat Cell Biol 14:802–809 Oh E, Zhu JY, Bai MY, Arenhart RA, Sun Y, Wang ZY (2014) Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. Elife 3:e03031 Ohgishi M, Saji K, Okada K, Sakai T (2004) Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis. Proc Nat Acad Sci 101:2223–2228 Osterlund MT, Hardtke CS, Wei N, Deng XW (2000) Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405:462–466 OuYang F, Mao JF, Wang J, Zhang S, Li Y (2015) Transcriptome analysis reveals that red and blue light regulate growth and phytohormone metabolism in Norway spruce [Picea abies (L.) Karst.]. PLoS ONE 10:e0127896 Paik I, Huq E (2019) Rapid Examination of phytochrome–phytochrome interacting factor (PIF) interaction by in vitro coimmunoprecipitation assay. In: Phytochromes: methods and protocols. Springer Nature, Switzerland AG, pp 21–28 Paik I, Kathare PK, Kim JI, Huq E (2017) Expanding roles of PIFs in signal integration from multiple processes. Molec Plant 10:1035-1046. https://doi.org/10.1016/j.molp.2017.07.002 Pandey N, Ranjan A, Pant P, Tripathi RK, Ateek F, Pandey HP, Patre UV, Sawant SV (2013) CAMTA 1 regulates drought responses in Arabidopsis thaliana. BMC Genom 14:1–5 Park DH, Lim PO, Kim JS, Cho DS, Hong SH, Nam HG (2003) The Arabidopsis COG1 gene encodes a Dof domain transcription factor and negatively regulates phytochrome signaling. Plant J 34:161–171 Pasrija R, Thakur JK (2012) Analysis of differential expression of mediator subunit genes in Arabidopsis. Plant Signal Behav 7:1676–1686 Pearce S, Kippes N, Chen A, Debernardi JM, Dubcovsky J (2016) RNA-seq studies using wheat phytochrome B and phytochrome C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways. BMC Plant Biol 16:141 Peng J, Wang M, Wang X, Qi L, Guo C, Li H, Li C, Yan Y, Zhou Y, Terzaghi W, Li Z (2022) COP1 positively regulates ABA signaling during Arabidopsis seedling growth in darkness by mediating ABA-induced ABI5 accumulation. Plant Cell 34:2286–2308 Perochon A, Aldon D, Galaud JP, Ranty B (2011) Calmodulin and calmodulin-like proteins in plant calcium signaling. Biochimie 93:2048–2053 Pham V, Xiaosa X, Enamul H (2018) Molecular bases for the constitutive photomorphogenic phenotypes in Arabidopsis. Development 145:dev169870 Piskurewicz U, Sentandreu M, Iwasaki M, Glauser G, Lopez-Molina L (2023) The Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB. Nat Commun 14:1202 Podolec R, Ulm R (2018) Photoreceptor-mediated regulation of the COP1/SPA E3 ubiquitin ligase. Curr Opin Plant Biol 45:18–25 Ponnu J, Hoecker U (2022) Signaling mechanisms by Arabidopsis cryptochromes. Front Plant Sci 13:844714 Qiu JR, Xiang XY, Wang JT, Xu WX, Chen J, Xiao Y, Jiang CZ, Huang Z (2020) MfPIF1 of resurrection plant Myrothamnus flabellifolia plays a positive regulatory role in responding to drought and salinity stresses in Arabidopsis. Int J Mol Sci 21:3011 Quail PH (2002) Phytochrome photgosensory signalling networks. Nat Rev Mol Cell Biol 3:85–93 Quint M, Delker C, Franklin KA, Wigge PA, Halliday KJ, Van Zanten M (2016) Molecular and genetic control of plant thermomorphogenesis. Nat Plants 2:1–9 Ranty B, Aldon D, Cotelle V, Galaud JP, Thuleau P, Mazars C (2016) Calcium sensors as key hubs in plant responses to biotic and abiotic stresses. Front Plant Sci 7:1–7 Rizzini L, Favory JJ, Cloix C, Faggionato D et al (2011) Perception of UV-B by the Arabidopsis UVR8 protein. Science 332:103–106 Roberts D, Pedmale UV, Morrow J, Sachdev S, Lechner E, Tang X, Zheng N, Hannink M, Genschik P, Liscum E (2011) Modulation of phototropic responsiveness in Arabidopsis through ubiquitination of phototropin 1 by the CUL3-ring E3 ubiquitin ligase CRL3(NPH3). Plant Cell 23:3627–3640 Rojas CC, Bianchimano L, Oh J, Montepaone SR, Tarkowska D, Minguet EG, Schön J, Hourquet MG, Flugel T, Blazquez MA, Choi G (2022) Organ-specific COP1 control of BES1 stability adjusts plant growth patterns under shade or warmth. Dev Cell 57:2009–2025 Sarvepalli K, Nath U (2011) Hyperactivation of the TCP4 transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation. Plant J 67:595–607 Sassi M, Lu Y, Zhang Y, Wang J, Dhonukshe P, Blilou I, Dai M, Li J, Gong X, Jaillais Y, Yu X (2012) COP1 mediates the coordination of root and shoot growth by light through modulation of PIN1- and PIN2-dependent auxin transport in Arabidopsis. Development 139:3402–3412 Scheres B, Van-der-Putten WH (2017) The plant perceptron connects environment to development. Nature 543:337–345 Senapati D, Kushwaha R, Dutta S, Maurya JP, Biswas S, Sreeramaiah NG, Chattopadhyay S (2019) COP 1 regulates the stability of CAM 7 to promote photomorphogenic growth. Plant Direct 3:e00144 Seo HS, Yang JY, Ishikawa M, Bolle C, Ballesteros ML, Chua NH (2003) LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1. Nature 423:995–999 Shao K, Zhang X, Li X, Hao Y, Huang X, Ma M, Zhang M, Yu F, Liu H, Zhang P (2020) The oligomeric structures of plant cryptochromes. Nat Struct Mol Biol 27:480–488 Shapulatov U, van Zanten M, van Hoogdalem M, Meisenburg M, van Hall A, Kappers I, Fasano C, Facella P, Loh CC, Perrella G, van der Krol A (2023) The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis. Plant Physiol 192:582–600 Sharma P, Chatterjee M, Burman N, Khurana JP (2014) Cryptochrome 1 regulates growth and development in B rassica through alteration in the expression of genes involved in light, phytohormone and stress signalling. Plant Cell Environ 37:961–977 Sheerin DJ, Menon C et al (2015) Light-activated phytochrome A and B interact with members of the SPA family to promote photomorphogenesis in Arabidopsis by reorganizing the COP1/SPA complex. Plant Cell 27:189–201 Shen H, Moon J, Huq E (2005) PIF1 is regulated by light-mediated degradation through the ubiquitin-26S proteasome pathway to optimize photomorphogenesis of seedlings in Arabidopsis. Plant J 44:1023–1035 Shimizu-Sato S, Huq E, Tepperman JM, Quail PH (2002) A light-switchable gene promoter system. Nat Biotechnol 20:1041–1044 Song Z, Bian Y, Liu J, Sun Y, Xu D (2020a) B-box proteins: Pivotal players in light-mediated development in plants. J Integr Plant Biol 62:1293–1309 Song Z, Yan T, Liu J, Bian Y, Heng Y, Lin F, Jiang Y, Wang Deng X, Xu D (2020b) BBX28/BBX29, HY5 and BBX30/31 form a feedback loop to fine-tune photomorphogenic development. Plant J 104:377–390 Spoel SH, Dong X (2008) Making sense of hormone crosstalk during plant immune response. Cell Host Microbe 3:348–351 Srivastava AK, Dutta S, Chattopadhyay S (2019) MYC2 regulates ARR16, a component of cytokinin signaling pathways, in Arabidopsis seedling development. Plant Direct 3:e00177 Sullivan S, Waksman T, Paliogianni D, Henderson L, Lütkemeyer M, Suetsugu N, Christie JM (2021) Regulation of plant phototropic growth by NPH3/RPT2-like substrate phosphorylation and 14-3-3 binding. Nat Commun 12:6129 Sun Y, Fan XY, Cao DM, Tang W, He K, Zhu JY, He JX, Bai MY, Zhu S, Oh E, Patil S, Kim TW, Ji H, Wong WH, Rhee SY, Wang ZY (2010) Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Dev Cell 19:765–777 Suri SS, Dhindsa RS (2008) A heat-activated MAP kinase (HAMK) as a mediator of heat shock response in tobacco cells. Plant Cell Environ 31:218–226 Teige M, Scheikl E, Eulgem T, Doczi R, Ichimura K, Shinozaki K, Dangl JL, Hirt H (2004) The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell 15:141–152 Todaka D, Nakashima K, Maruyama K, Kidokoro S, Osakabe Y, Ito Y, Matsukura S, Fujita Y, Yoshiwara K, Ohme-Takagi M, Kojima M (2012) Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress. Proc Natl Acad Sci 109:15947–15952 Tokutomi S, Matsuoka D, Zikihara K (2008) Molecular structure and regulation of phototropin kinase by blue light. Biochim Biophys Acta Proteins Proteom 1784:133–142 Toldi D, Gyugos M, Darkó É, Szalai G, Gulyás Z, Gierczik K, Székely A, Boldizsár Á, Galiba G, Müller M, Simon-Sarkadi L (2019) Light intensity and spectrum affect metabolism of glutathione and amino acids at transcriptional level. PLoS ONE 14:e0227271 Unterholzner SJ, Rozhon W, Papacek M, Ciomas J, Lange T, Kugler KG, Mayer KF, Sieberer T, Poppenberger B (2015) Brassinosteroids are master regulators of gibberellin biosynthesis in Arabidopsis. Plant Cell 27:2261–2272 Vernoux T, Brunoud G, Farcot E, Morin V, Van Den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guedon Y, Armitage L, Picard F, Guyomarc’h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J (2011) The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol Syst Biol 7:508 Wang Q, Lin C (2020) Mechanisms of cryptochrome-mediated photoresponses in plants. Annu Rev Plant Biol 71:103–129 Wang H, Ma L, Habashi J, Li J, Zhao H, Deng XW (2002) Analysis of far-red light-regulated genome expression profiles of phytochrome a pathway mutants in Arabidopsis. Plant J 32:723–733 Wang ZY, Bai MY, Oh E, Zhu JY (2012) Brassinosteroid signalling network and regulation of photomorphogenesis. Annu Rev Genet 46:701–724 Wang L, Qin L, Liu W, Zhang D, Wang Y (2014a) A novel ethylene-responsive factor from Tamarix hispida, ThERF1, is a GCC-box- and DRE-motif binding protein that negatively modulates abiotic stress tolerance in Arabidopsis. Physiol Plant 152:84–97 Wang W, Bai MY, Wang ZY (2014b) The brassinosteroid signalling network-a paradigm of signal integration. Curr Opin Plant Biol 21:147–153 Wang X, Wang Q, Han YJ, Liu Q, Gu L, Yang Z, Su J, Liu B, Zuo Z, He W, Wang J (2017) A CRY–BIC negative-feedback circuitry regulating blue light sensitivity of Arabidopsis. Plant J 92:426–436 Wang S, Li L, Xu P, Lian H, Wang W, Xu F, Mao Z, Zhang T, Yang H (2018a) CRY1 interacts directly with HBI1 to regulate its transcriptional activity and photomorphogenesis in Arabidopsis. J Exp Bot 16:3867–3881 Wang W, Lu X, Li L, Lian H, Mao Z, Xu P, Guo T, Xu F, Du S, Cao X, Wang S (2018b) Photoexcited CRYPTOCHROME1 interacts with dephosphorylated BES1 to regulate brassinosteroid signaling and photomorphogenesis in Arabidopsis. Plant Cell 30:1989–2005 Wang F, Chen X, Dong S, Jiang X, Wang L, Yu J, Zhou Y (2020) Crosstalk of PIF4 and DELLA modulates CBF transcript and hormone homeostasis in cold response in tomato. Plant Biotechnol J 18:1041–1055 Wang D, Dawadi B, Qu J, Ye J (2022a) Light-engineering technology for enhancing plant disease resistance. Front Plant Sci 12:805614 Wang F, Wang X, Zhang Y, Yan J, Ahammed GJ, Bu X, Sun X, Liu Y, Xu T, Qi H, Qi M (2022b) SlFHY3 and SlHY5 act compliantly to enhance cold tolerance through the integration of myo-inositol and light signaling in tomato. New Phytol 233:2127–2143 Wang XR, Wang YH, Jia M, Zhang RR, Liu H, Xu ZS (2022c) Xiong AS (2022) The phytochrome-interacting factor DcPIF3 of carrot plays a positive role in drought stress by increasing endogenous ABA level in Arabidopsis. Plant Sci 322:111367 Ward JM, Cufr CA, Denzel MA, Neff MM (2005) The Dof transcription factor OBP3 modulates phytochrome and cryptochrome signaling in Arabidopsis. Plant Cell 17:475–485 Webb AA, Seki M, Satake A, Caldana C (2019) Continuous dynamic adjustment of the plant circadian oscillator. Nat Communi 10:550 Weinl S, Jörg K (2009) The CBL–CIPK Ca2+ decoding signalling network: function and perspectives. New Phytol 184:517–528 Weisshaar B, Armstrong GA, Block A et al (1991) Light-inducible and constitutively expressed DNA-binding proteins recognizing a plant promoter element with functional relevance in light responsiveness. EMBO J 10:1777–1786 Weng H, Yoo CY, Gosney MJ, Hasegawa PM, Mickelbart MV (2012) Poplar GTL1 is a Ca2+/calmodulin-binding transcription factor that functions in plant water use efficiency and drought tolerance. PLoS ONE 7:e32925 Wu L, Yang HQ (2010) CRYPTOCHROME 1 is implicated in promoting R protein-mediated plant resistance to Pseudomonas syringae in Arabidopsis. Mol Plant 3:539–548 Xiang S, Wu S, Jing Y, Chen L, Yu D (2022) Phytochrome B regulates jasmonic acid-mediated defense response against Botrytis cinerea in Arabidopsis. Plant Divers 44:109–115 Xie XZ, Xue YJ, Zhou JJ, Zhang B, Chang H, Takano M (2011) Phytochromes regulate SA and JA signaling pathways in rice and are required for developmentally controlled resistance to Magnaporthe grisea. Mol Plant 4:688–696 Xu D (2020) COP1 and BBXs-HY5-mediated light signal transduction in plants. New Phytol 228:1748–1753 Xu D, Xing WD (2020) CBF-phyB-PIF module links light and low temperature signaling. Trends Plant Sci 25:952–954 Xu F, He S, Zhang J, Mao Z, Wang W, Li T, Hua J, Du S, Xu P, Li L, Lian H (2018) Photoactivated CRY1 and phyB interact directly with AUX/IAA proteins to inhibit auxin signaling in Arabidopsis. Mol Plant 11:523–541 Xu D, Liu X, Guo C, Lin L, Yin R (2023a) The B-box transcription factor 4 regulates seedling photomorphogenesis and flowering in tomato. Scientia Hortic 309:111692 Xu P, Hu J, Chen H, Cai W (2023b) SMAX1 interacts with DELLA protein to inhibit seed germination under weak light conditions via gibberellin biosynthesis in Arabidopsis. Cell Rep 42:112740 Xuan Y, Zhou S, Wang L, Cheng Y, Zhao L (2010) Nitric oxide functions as a signal and acts upstream of AtCaM3 in thermotolerance in Arabidopsis seedlings. Plant Physiol 153:1895–1906 Yadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S (2005) A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth. Plant Cell 17:1953–1966 Yadukrishnan P, Rahul PV, Ravindran N, Bursch K, Johansson H, Datta S (2020) Constitutively photomorphogenic1 promotes ABA-mediated inhibition of post-germination seedling establishment. Plant J 103(2):481–496 Yan Y, Li C, Dong X, Li H, Zhang D, Zhou Y, Jiang B, Peng J, Qin X, Cheng J, Wang X (2020) MYB30 is a key negative regulator of Arabidopsis photomorphogenic development that promotes PIF4 and PIF5 protein accumulation in the light. Plant Cell 32:2196–2215 Yan B, Yang Z, He G, Jing Y, Dong H, Ju L, Zhang Y, Zhu Y, Zhou Y, Sun J (2021) The blue light receptor CRY1 interacts with GID1 and DELLA proteins to repress gibberellin signaling and plant growth. Plant Commun 2:100245 Yang HQ, Tang RH, Cashmore AR (2001) The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1. Plant Cell 13:2573–2587 Yang YX, Wang MM, Yin YL, Onac E, Zhou GF, Peng S, Xia XJ, Shi K, Yu JQ, Zhou YH (2015) RNA-seq analysis reveals the role of red light in resistance against Pseudomonas syringae pv. tomato DC3000 in tomato plants. Bmc Genom 16:1–6 Yang T, Lv R, Li J, Lin H, Xi D (2018a) Phytochrome A and B negatively regulate salt stress tolerance of Nicotiana tobacum via ABA–jasmonic acid synergistic cross-talk. Plant Cell Physiol 59:2381–2393 Yang Y, Liang T, Zhang L, Shao K, Gu X, Shang R, Shi N, Li X, Zhang P, Liu H (2018b) UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. Nat Plants 4:98–107 Yang C, Huang S, Zeng Y, Liu C, Ma Q, Pruneda-Paz J, Kay SA, Li L (2021a) Two bHLH transcription factors, bHLH48 and bHLH60, associate with phytochrome interacting factor 7 to regulate hypocotyl elongation in Arabidopsis. Cell Rep 35:5 Yang X, Lu M, Wang Y, Wang Y, Liu Z, Chen S (2021b) Response mechanism of plants to drought stress. Horticulturae 7:1–36 Yang Y, Guang Y, Wang F, Chen Y, Yang W, Xiao X, Luo S, Zhou Y (2021c) Characterization of phytochrome-interacting factor genes in pepper and functional analysis of CaPIF8 in cold and salt stress. Front Plant Sci 12:746517 Yang J, Qu X, Li T, Gao Y, Du H, Zheng L, Ji M, Zhang P, Zhang Y, Hu J, Liu L (2023) HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis. J Integr Plant Biol 65:45–63 Yoo JH, Park CY, Kim JC, Do Heo W, Cheong MS, Park HC, Kim MC, Moon BC, Choi MS, Kang YH, Lee JH (2005) Direct interaction of a divergent CaM isoform and the transcription factor, MYB2, enhances salt tolerance in Arabidopsis. J Biol Chem 280:3697–3706 Yoo CY, Pasoreck EK, Wang H, Cao J, Blaha GM, Weigel D, Chen M (2019) Phytochrome activates the plastid-encoded RNA polymerase for chloroplast biogenesis via nucleus-to-plastid signaling. Nat Commun 10:2629 Yuan DP, Yang S, Feng L, Chu J, Dong H, Sun J, Chen H, Li Z, Yamamoto N, Zheng A, Li S (2023) Red-light receptor phytochrome B inhibits BZR1-NAC028-CAD8B signaling to negatively regulate rice resistance to sheath blight. Plant Cell Environ 46:1249–1263 Zeng Y, Wang J, Huang S, Xie Y, Zhu T, Liu L, Li L (2023) HSP90s are required for hypocotyl elongation during skotomorphogenesis and thermomorphogenesis via the COP1–ELF3–PIF4 pathway in Arabidopsis. New Phytol 2023:1–13 Zhang L, Jiang X, Liu Q, Ahammed GJ, Lin R, Wang L, Shao S, Yu J, Zhou Y (2020) The HY5 and MYB15 transcription factors positively regulate cold tolerance in tomato via the CBF pathway. Plant Cell Environ 43:2712–2726 Zhang BO, Zhu ZZ, Qu D, Wang BC, Hao NN, Yang YZ, Yang HJ, Zhao ZY (2021) MdBBX21, a B-box protein, positively regulates light-induced anthocyanin accumulation in apple peel. Front Plant Sci 12:774446 Zhang Q, Lin L, Fang F, Cui B, Zhu C, Luo S, Yin R (2023) Dissecting the functions of COP1 in the UVR8 pathway with a COP1 variant in Arabidopsis. Plant J 13:478–492 Zhao H, Zhang Y, Zheng Y (2022a) Integration of ABA, GA, and light signaling in seed germination through the regulation of ABI5. Front Plant Sci 13:1000803 Zhao J, Yang G, Jiang L, Zhang S, Miao L, Xu P, Chen H, Chen L, Mao Z, Guo T, Kou S (2022b) Phytochromes A and B mediate light stabilization of BIN2 to regulate brassinosteroid signaling and photomorphogenesis in Arabidopsis. Front Plant Sci 13:865019 Zhao J, Bo K, Pan Y, Li Y, Yu D, Li C, Chang J, Wu S, Wang Z, Zhang X, Gu X (2023) Phytochrome-interacting factor PIF3 integrates phytochrome B and UVB signaling pathways to regulate gibberellin-and auxin-dependent growth in cucumber hypocotyls. J Exp Bot 18:rerad181 Zheng B, Deng Y, Mu J, Ji Z, Xiang T, Niu QW, Chua NH, Zuo J (2006) Cytokinin affects circadian-clock oscillation in a phytochrome B-and Arabidopsis response regulator 4-dependent manner. Physiol Plant 127:277–292 Zheng X, Wu S, Zhai H, Zhou P, Song M, Su L, Xi Y, Li Z, Cai Y, Meng F, Yang L (2013) Arabidopsis phytochrome B promotes SPA1 nuclear accumulation to repress photomorphogenesis under far-red light. Plant Cell 25:115–133 Zheng PF, Yang YY, Zhang S, You CX, Zhang ZL, Hao YJ (2021) Identification and functional characterization of MdPIF3 in response to cold and drought stress in Malus domestica. Plant Cell Tissue Organ Cult 144:435–447 Zhong S, Shi H, Xue C, Wang L, Xi Y, Li J, Quail PH, Deng XW, Guo H (2012) A molecular framework of light-controlled phytohormone action in Arabidopsis. Curr Biol 22:1530–1535 Zhong M, Zeng B, Tang D, Yang J, Qu L, Yan J, Wang X, Li X, Liu X, Zhao X (2021) The blue light receptor CRY1 interacts with GID1 and DELLA proteins to repress GA signaling during photomorphogenesis in Arabidopsis. Mol Plant 14:1328–1342 Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273 Zhu D, Maier A, Lee JH, Laubinger S, Saijo Y, Wang H, Qu LJ, Hoecker U, Deng XW (2008) Biochemical characterization of Arabidopsis complexes containing constitutively photomorphogenic1 and suppressor of PHYA proteins in light control of plant development. Plant Cell 20:2307–2323 Zoltowski BD, Takato I (2014) Structure and function of the ZTL/FKF1/LKP2 group proteins in Arabidopsis. The Enzymes 35:213–239