Abstract
The calmodulin-binding transcription activator (CAMTA) is a family of transcriptional factors containing a cluster of calmodulin-binding proteins that can activate gene regulation in response to stresses. The presence of this family of genes has been reported earlier, though, the comprehensive analyses of rice CAMTA (OsCAMTA) genes, their promoter regions, and the proteins were not deliberated till date. The present report revealed the existence of seven CAMTA genes along with their alternate transcripts in five chromosomes of rice (Oryza sativa) genome. Phylogenetic trees classified seven CAMTA genes into three clades indicating the evolutionary conservation in gene structure and their association with other plant species. The in silico study was carried out considering 2 kilobases (kb) promoter regions of seven OsCAMTA genes regarding the distribution of transcription factor binding sites (TFbs) of major and plant-specific transcription factors whereas OsCAMTA7a was identified with highest number of TFbs, while OsCAMTA4 had the lowest. Comparative modelling, i.e., homology modelling, and molecular docking of the CAMTA proteins contributed the thoughtful comprehension of protein 3D structures and protein–protein interaction with probable partners. Gene ontology annotation identified the involvement of the proteins in biological processes, molecular functions, and localization in cellular components. Differential gene expression study gave an insight on functional multiplicity to showcase OsCAMTA3b as most upregulated stress-responsive gene. Summarization of the present findings can be interpreted that OsCAMTA gene duplication, variation in TFbs available in the promoters, and interactions of OsCAMTA proteins with their binding partners might be linked to tolerance against multiple biotic and abiotic cues.
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Alves MS, Dadalto SP, Gonçalves AB, De Souza GB, Barros VA, Fietto LG (2014) Transcription factor functional protein-protein interactions in plant defense responses. Proteomes 2(1):85–106. https://doi.org/10.3390/proteomes2010085
Ambawat S, Sharma P, Yadav NR, Yadav RC (2013) MYB transcription factor genes as regulators for plant responses: an overview. Physiol Mol Biol Plants 19(3):307–321. https://doi.org/10.1007/s12298-013-0179-1
Bähler M, Rhoads A (2002) Calmodulin signaling via the IQ motif. FEBS Lett 513(1):107–113. https://doi.org/10.1016/S0014-5793(01)03239-2
Baum G, Lev-Yadun S, Fridmann Y, Arazi T, Katsnelson H, Zik M, Fromm H (1996) Calmodulin binding to glutamate decarboxylase is required for regulation of glutamate and GABA metabolism and normal development in plants. EMBO J 15(12):2988–2996. https://doi.org/10.1002/j.1460-2075.1996.tb00662.x
Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T (2017) Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology. Sci Rep 7(1):1–15. https://doi.org/10.1038/s41598-017-09654-8
Boonburapong B, Buaboocha T (2007) Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins. BMC Plant Biol 7(1):1–17. https://doi.org/10.1186/1471-2229-7-4
Chang AT, Liu Y, Ayyanathan K, Benner C, Jiang Y, Prokop JW, Paz H, Wang D, Li HR, Fu XD, Rauscher FJ (2015) An evolutionarily conserved DNA architecture determines target specificity of the TWIST family bHLH transcription factors. Genes Dev 29(6):603–616. https://doi.org/10.1101/gad.242842.114
Chen L, Song Y, Li S, Zhang L, Zou C, Yu D (2012) The role of WRKY transcription factors in plant abiotic stresses. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1819(2):120–128. https://doi.org/10.1016/j.bbagrm.2011.09.002
Chinpongpanich A, Limruengroj K, Limpaseni T, Buaboocha T (2012) Expression analysis of calmodulin and calmodulin-like genes from rice, Oryza sativa L. BMC research notes 5(1):1–12. https://doi.org/10.1186/2F1756-0500-5-625
Choi MS, Kim MC, Yoo JH, Moon BC, Koo SC, Park BO, Lee JH, Koo YD, Han HJ, Lee SY, Chung WS (2005) Isolation of a calmodulin-binding transcription factor from rice (Oryza sativa L.). Journal of Biological Chemistry 280(49):40820–40831. https://doi.org/10.1074/jbc.M504616200
Chow CN, Zheng HQ, Wu NY, Chien CH, Huang HD, Lee TY, Chiang-Hsieh YF, Hou PF, Yang TY, Chang WC (2016) PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. Nucleic acids research 44(D1):D1154-D1160. https://doi.org/10.1093/nar/gkv1035
Chung JS, Koo SC, Jin BJ, Baek D, Yeom SI, Chun HJ, Choi MS, Cho HM, Lee SH, Jung WH, Choi CW (2020) Rice CaM-binding transcription factor (OsCBT) mediates defense signaling via transcriptional reprogramming. Plant Biotechnology Reports 14(3). https://doi.org/10.1007/s11816-020-00603-y
Conesa A, Götz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics. https://doi.org/10.1155/2008/619832
Das A, Pramanik K, Sharma R, Gantait S, Banerjee J (2019) In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes. PLoS ONE 14(2):e0211887. https://doi.org/10.1371/journal.pone.0211887
DeFalco TA, Bender KW, Snedden WA (2010) Breaking the code: Ca2+ sensors in plant signalling. Biochemical Journal 425(1):27–40. https://doi.org/10.1042/BJ20091147
Doherty CJ, Van Buskirk HA, Myers SJ, Thomashow MF (2009) Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. Plant Cell 21(3):972–984. https://doi.org/10.1105/tpc.108.063958
Dombrecht B, Xue GP, Sprague SJ, Kirkegaard JA, Ross JJ, Reid JB, Fitt GP, Sewelam N, Schenk PM, Manners JM, Kazan K (2007) MYC2 differentially modulates diverse jasmonate-dependent functions in Arabidopsis. Plant Cell 19(7):2225–2245. https://doi.org/10.1105/tpc.106.048017
Du L, Ali GS, Simons KA, Hou J, Yang T, Reddy A, Poovaiah B (2009) Ca 2+/calmodulin regulates salicylic-acid-mediated plant immunity. Nature 457(7233):1154–1158. https://doi.org/10.1038/nature07612
Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci 5(5):199–206. https://doi.org/10.1016/s1360-1385(00)01600-9
Finkler A, Ashery-Padan R, Fromm H (2007) CAMTAs: calmodulin-binding transcription activators from plants to human. FEBS Lett 581(21):3893–3898. https://doi.org/10.1016/j.febslet.2007.07.051
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic acids research 39(suppl_2):W29-W37. https://doi.org/10.1093/nar/gkr367
Fuller JC, Burgoyne NJ, Jackson RM (2009) Predicting druggable binding sites at the protein–protein interface. Drug Discovery Today 14(3–4):155–161. https://doi.org/10.1016/j.drudis.2008.10.009
Galon Y, Finkler A, Fromm H (2010) Calcium-regulated transcription in plants. Mol Plant 3(4):53–669. https://doi.org/10.1093/mp/ssq019
Gao F, Robe K, Gaymard F, Izquierdo E, Dubos C (2019) The transcriptional control of iron homeostasis in plants: a tale of bHLH transcription factors? Frontiers in plant science 10(6). https://doi.org/10.3389/fpls.2019.00006
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server The proteomics protocols handbook. Springer571–607. https://doi.org/10.1385/1-59259-890-0:571
Han G, Lu C, Guo J, Qiao Z, Sui N, Qiu N, Wang B (2020) C2H2 zinc finger proteins: master regulators of abiotic stress responses in plants. Frontiers in plant science 11(115). https://doi.org/10.3389/fpls.2020.00115
Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier C, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic acids research 35(suppl_2):W585-W587. https://doi.org/10.1093/nar/gkm259
Hosoda K, Imamura A, Katoh E, Hatta T, Tachiki M, Yamada H, Mizuno T, Yamazaki T (2002) Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. Plant Cell 14(9):2015–2029. https://doi.org/10.1105/tpc.002733
Islam T, Madhubala D, Mukhopadhyay R, Mukherjee A (2021) Transcriptomic and functional proteomics analyses to unveil the common and unique pathway(s) of neuritogenesis induced by Russell’s viper venom nerve growth factor in rat pheochromocytoma neuronal cells. Expert Rev Proteomics 18(6):463–481. https://doi.org/10.1080/14789450.2021.1941892
Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7(3):106–111. https://doi.org/10.1016/s1360-1385(01)02223-3
Jenuth JP (2000) The NCBI bioinformatics methods and protocols. Springer 301-312https://doi.org/10.1385/1-59259-192-2:301
Jiménez-García B, Pons C, Fernández-Recio J (2013) pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring. Bioinformatics 29(13):1698–1699. https://doi.org/10.1093/bioinformatics/btt262
Kaewneramit T, Buaboocha T, Sangchai P, Wutipraditkul N (2019) OsCaM1–1 overexpression in the transgenic rice mitigated salt-induced oxidative damage. Biologia plantarum 63:335–42. https://doi.org/10.32615/bp.2019.039
Kakar KU, Nawaz Z, Cui Z, Cao P, Jin J, Shu Q, Ren X (2018) Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses. Sci Rep 8(1):1–14. https://doi.org/10.1038/s41598-018-28148-9
Kankainen M, Holm L (2004) POBO, transcription factor binding site verification with bootstrapping. Nucleic Acids Res 32(Web Server issue):W222–229. https://doi.org/10.1093/nar/gkh463
Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17(3):287–291. https://doi.org/10.1038/7036
Khan SA, Li MZ, Wang SM, Yin HJ (2018) Revisiting the role of plant transcription factors in the battle against abiotic stress. Int J Mol Sci 19(6):634. https://doi.org/10.3390/ijms19061634
Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL Repository and associated resources. Nucleic acids research 37(suppl_1):D387-D392. https://doi.org/10.1093/nar/gkn750
Kim Y, Park S, Gilmour SJ, Thomashow MF (2013) Roles of CAMTA transcription factors and salicylic acid in configuring the low-temperature transcriptome and freezing tolerance of A rabidopsis. Plant J 75(3):364–376. https://doi.org/10.1111/tpj.12205
Koo SC, Choi MS, Chun HJ, Shin DB, Park BS, Kim YH, Park HM, Seo HS, Song JT, Kang K, Yun DJ (2009) The calmodulin-binding transcription factor OsCBT suppresses defense responses to pathogens in rice. Mol Cells 27(5):563–570. https://doi.org/10.1007/s10059-009-0081-4
Kranz HD, Denekamp M, Greco R, Jin H, Leyva A, Meissner RC, Petroni K, Urzainqui A, Bevan M, Martin C, Smeekens S (1998) Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J 16(2):263–276. https://doi.org/10.1046/j.1365-313x.1998.00278.x
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD (2007) Clustal W and Clustal X version 2.0. bioinformatics 23(21): 2947–2948. https://doi.org/10.1093/bioinformatics/btm404
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J App Cryst 26:283–291. https://doi.org/10.1107/S0021889892009944
Li C, Ng CKY, Fan LM (2015) MYB transcription factors, active players in abiotic stress signaling. Environ Exp Bot 114:80–91. https://doi.org/10.1016/j.envexpbot.2014.06.014
Lindemose S, O’Shea C, Jensen MK, Skriver K (2013) Structure, function and networks of transcription factors involved in abiotic stress responses. Int J Mol Sci 14(3):842–5878. https://doi.org/10.3390/ijms14035842
Ling L, Zhang W, An Y, Du B, Wang D, Guo C (2020) Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses. Funct Integr Genomics 20(4):537–550. https://doi.org/10.1007/s10142-020-00733-0
Liu D, Chen X, Liu J, Ye J, Guo Z (2012) The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance. J Exp Bot 63(10):3899–3911. https://doi.org/10.1093/jxb/ers079
Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, Lahrmann U, Zhao Q, Zheng Y, Zhao Y, Xue Y (2015) IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics 31(20):3359–3361. https://doi.org/10.1093/bioinformatics/btv362
Liu XQ, Bai XQ, Qian Q, Wang XJ, Chen MS, Chu CC (2005) OsWRKY03, a rice transcriptional activator that functions in defense signaling pathway upstream of OsNPR1. Cell Res 15(8):593–603. https://doi.org/10.1038/sj.cr.7290329
Lu J, Ju H, Zhou G, Zhu C, Erb M, Wang X, Wang P, Lou Y (2011) An EAR-motif-containing ERF transcription factor affects herbivore-induced signaling, defense and resistance in rice. Plant J 68(4):583–596. https://doi.org/10.1111/j.1365-313X.2011.04709.x
Mengiste T, Chen X, Salmeron J, Dietrich R (2003) The BOTRYTIS SUSCEPTIBLE1 gene encodes an R2R3MYB transcription factor protein that is required for biotic and abiotic stress responses in Arabidopsis. Plant Cell 15(11):2551–2565. https://doi.org/10.1105/tpc.014167
Nan H, Gao LZ (2019) Genome-wide analysis of WRKY genes and their response to hormone and mechanic stresses in carrot. Frontiers in Genetics 10(363). https://doi.org/10.3389/fgene.2019.00363
Najeeb S, Ali J, Mahender A, Pang YL, Zilhas J, Murugaiyan V, Vemireddy LR, Li Z (2020) Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination-and early seedling vigor-related traits in rice (Oryza sativa L.). Molecular Breeding 40(1):1–25. https://doi.org/10.1007/s11032-019-1090-4
Nie H, Zhao C, Wu G, Wu Y, Chen Y, Tang D (2012) SR1, a calmodulin-binding transcription factor, modulates plant defense and ethylene-induced senescence by directly regulating NDR1 and EIN3. Plant Physiol 158(4):1847–1859. https://doi.org/10.1104/pp.111.192310
Nim S, Jeon J, Corbi-Verge C, Seo MH, Ivarsson Y, Moffat J, Tarasova N, Kim PM (2016) Pooled screening for antiproliferative inhibitors of protein-protein interactions. Nat Chem Biol 12(4):275–281. https://doi.org/10.1038/nchembio.2026
Ogo Y, Itai RN, Nakanishi H, Inoue H, Kobayashi T, Suzuki M, Takahashi M, Mori S, Nishizawa NK (2006) Isolation and characterization of IRO2, a novel iron-regulated bHLH transcription factor in graminaceous plants. J Exp Bot 57(11):2867–2878. https://doi.org/10.1093/jxb/erl054
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 Genomics 14(1):1–23. https://doi.org/10.1186/1471-2164-14-216
Pant P, Iqbal Z, Pandey BK, Sawant SV (2018) Genome-wide comparative and evolutionary analysis of calmodulin-binding transcription activator (CAMTA) family in Gossypium species. Sci Rep 8(1):1–17. https://doi.org/10.1038/s41598-018-23846-w
Patra N, Hariharan S, Gain H, Maiti MK, Das A, Banerjee J (2021) TypiCal but DeliCate Ca++re: dissecting the essence of calcium signaling network as a robust response coordinator of versatile abiotic and biotic stimuli in plants. Front Plant Sci 12:2349. https://doi.org/10.3389/fpls.2021.752246
Peterson LX, Togawa Y, Esquivel-Rodriguez J, Terashi G, Christoffer C, Roy A, Shin WH, Kihara D (2018) Modeling the assembly order of multimeric heteroprotein complexes. PLoS Comput Biol 14(1):e1005937. https://doi.org/10.1371/journal.pcbi.1005937
Phean-O-Pas S, Punteeranurak P, Buaboocha T (2005) Calcium signaling-mediated and differential induction of calmodulin gene expression by stress in Oryza sativa L. BMB Rep 38(4):432–439. https://doi.org/10.5483/bmbrep.2005.38.4.432
Prasad K, Abdel-Hameed AAE, Xing D, Reddy ASN (2016) Global gene expression analysis using RNA-seq uncovered a new role for SR1/CAMTA3 transcription factor in salt stress. Sci Rep 6:27021. https://doi.org/10.1038/srep27021
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A (2012) The Pfam protein families database. Nucleic Acids Res 40(D1):D290–D301. https://doi.org/10.1093/nar/gkr1065
Qiu D, Xiao J, Ding X, Xiong M, Cai M, Cao Y, Li X, Xu C, Wang S (2007) OsWRKY13 mediates rice disease resistance by regulating defense-related genes in salicylate-and jasmonate-dependent signaling. Mol Plant Microbe Interact 20(5):492–499. https://doi.org/10.1094/mpmi-20-5-0492
Qiu Y, Xi J, Du L, Suttle JC, Poovaiah BW (2012) Coupling calcium/calmodulin-mediated signaling and herbivore-induced plant response through calmodulin-binding transcription factor AtSR1/CAMTA3. Plant Mol Biol 79(1):89–99. https://doi.org/10.1007/s11103-012-9896-z
Rahman H, Yang J, Xu YP, Munyampundu JP, Cai XZ (2016) Phylogeny of plant CAMTAs and role of AtCAMTAs in nonhost resistance to Xanthomonas oryzae pv. oryzae. Frontiers in plant science 7:177. https://doi.org/10.3389/fpls.2016.00177
Rasheed F, Markgren J, Hedenqvist M, Johansson E (2020) Modeling to understand plant protein structure-function relationships—implications for seed storage proteins. Molecules 25(4):873. https://doi.org/10.3390/molecules25040873
Reddy A, Reddy VS, Golovkin M (2000) A calmodulin binding protein from Arabidopsis is induced by ethylene and contains a DNA-binding motif. Biochem Biophys Res Commun 279(3):762–769. https://doi.org/10.1006/bbrc.2000.4032
Fujita Y, Nakashima K, Yoshida T, Fujita M, Shinozaki K, Yamaguchi‐Shinozaki K (2013) Role of abscisic acid signaling in drought tolerance and preharvest sprouting under climate change. Climate change and plant abiotic stress tolerance 521-554https://doi.org/10.1002/9783527675265.ch20
Rushton PJ, Somssich IE (1998) Transcriptional control of plant genes responsive to pathogens. Curr Opin Plant Biol 1(4):311–315. https://doi.org/10.1016/1369-5266(88)80052-9
Saeng-ngam S, Takpirom W, Buaboocha T, Chadchawan S (2012) The role of the OsCam1-1 salt stress sensor in ABA accumulation and salt tolerance in rice. Journal of Plant Biology 55(3):198–208. https://doi.org/10.1007/s12374-011-0154-8
Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, Yamada Y (2013) Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol 54(2):e6–e6. https://doi.org/10.1016/S1369-5266(99)00047-3
Sarwar MW, Riaz A, Nahid N, Al Qahtani A, Ahmed N, Nawaz-Ul-Rehman MS, Younus A, Mubin M (2019) Homology modeling and docking analysis of ßC1 protein encoded by cotton leaf curl Multan betasatellite with different plant flavonoids. Heliyon 5(3):e01303. https://doi.org/10.1016/j.heliyon.2019.e01303
Sasaki T, Burr B (2000) International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3(2):138–142. https://doi.org/10.1016/s1369-5266(99)00047-3
Shkolnik D, Finkler A, Pasmanik-Chor M, Fromm H (2019) CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 6: a key regulator of Na+ homeostasis during germination. Plant Physiol 180(2):1101–1118. https://doi.org/10.1104/pp.19.00119
Shi J, Du X (2020) Identification, characterization and expression analysis of calmodulin and calmodulin-like proteins in Solanum pennellii. Sci Rep 10(1):1–17. https://doi.org/10.1038/s41598-020-64178-y
Singh KB, Foley RC, Oñate-Sánchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5(5):430–436. https://doi.org/10.1016/S1369-5266(02)00289-3
Takahashi Y, Ito T (2011) Structure and function of CDPK: a sensor responder of calcium. In Coding and decoding of calcium signals in plants. Springer, Berlin, Heidelberg. 129–146. https://doi.org/10.1007/978-3-642-20829-4_9.
Tripathi P, Rabara RC, Rushton PJ (2014) A systems biology perspective on the role of WRKY transcription factors in drought responses in plants. Planta 239(2):255–266. https://doi.org/10.1007/s00425-013-1985-y
Tsuda K, Somssich IE (2015) Transcriptional networks in plant immunity. New Phytol 206(3):932–947. https://doi.org/10.1111/nph.13286
Vannini C, Campa M, Iriti M, Genga A, Faoro F, Carravieri S, Rotino GL, Rossoni M, Spinardi A, Bracale M (2007) Evaluation of transgenic tomato plants ectopically expressing the rice Osmyb4 gene. Plant Sci 173(2):231–239. https://doi.org/10.1016/j.plantsci.2007.05.007
Viola IL, Reinheimer R, Ripoll R, Manassero NG, Gonzalez DH (2012) Determinants of the DNA binding specificity of class I and class II TCP transcription factors. J Biol Chem 287(1):347–356. https://doi.org/10.1074/jbc.M111.256271
Wang J, Hu Z, Zhao T, Yang Y, Chen T, Yang M, Yu W, Zhang B (2015) Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum). BMC Genomics 16(1):1–14. https://doi.org/10.1186/s12864-015-1249-2
Wei M, Xu X, Li C (2017) Identification and expression of CAMTA genes in Populus trichocarpa under biotic and abiotic stress. Sci Rep 7(1):1–10. https://doi.org/10.1038/s41598-017-18219-8
Wu H C, Luo D L, Vignols F, Jinn T L (2012) Heat shock‐induced biphasic Ca2+ signature and OsCaM1‐1 nuclear localization mediate downstream signalling in acquisition of thermotolerance in rice (Oryza sativa L.). Plant, cell & environment 35(9):1543–1557. https://doi.org/10.1111/j.1365-3040.2012.02508.x
Yang J, Zhang Y (2015) I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 43(W1):W174–W181. https://doi.org/10.1093/nar/gkv342
Yang T, Peng H, Whitaker B, Conway W (2012) Characterization of a calcium/calmodulin-regulated SR. CAMTA Gene. https://doi.org/10.1186/1471-2229-12-19
Yang T, Peng H, Whitaker BD, Jurick WM (2013) Differential expression of calcium/calmodulin-regulated SlSRs in response to abiotic and biotic stresses in tomato fruit. Physiol Plant 148(3):445–455. https://doi.org/10.1111/ppl.12027
Yang T, Poovaiah B (2000) Molecular and biochemical evidence for the involvement of calcium/calmodulin in auxin action. J Biol Chem 275(5):3137–3143. https://doi.org/10.1074/jbc.275.5.3137
Yang T, Poovaiah B (2002) A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants. J Biol Chem 277(47):45049–45058. https://doi.org/10.1074/jbc.M207941200
Yang Y, Sun T, Xu L, Pi E, Wang S, Wang H, Shen C (2015) Genome-wide identification of CAMTA gene family members in Medicago truncatula and their expression during root nodule symbiosis and hormone treatments. Front Plant Sci 6:459. https://doi.org/10.3389/fpls.2015.00459
Yang F, Dong FS, Hu FH, Liu YW, Chai JF, Zhao H, Lv MY, Zhou S (2020) Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.). BMC genetics 21(1):1–10. https://doi.org/10.1186/s12863-020-00916-5
Yin J, Wang L, Zhao J, Li Y, Huang R, Jiang X, Zhou X, Zhu X, He Y, He Y, Liu Y (2020) Genome-wide characterization of the C2H2 zinc-finger genes in Cucumis sativus and functional analyses of four CsZFPs in response to stresses. BMC plant biology 20(1):1–22. https://doi.org/10.1186/s12870-020-02575-1
Yoon Y, Seo DH, Shin H, Kim HJ, Kim CM, Jang G (2020) The role of stress-responsive transcription factors in modulating abiotic stress tolerance in plants. Agronomy 10(6):788. https://doi.org/10.3390/agronomy10060788
Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics 64(3):643–651. https://doi.org/10.1002/prot21018
Yuenyong W, Chinpongpanich A, Comai L, Chadchawan S, Buaboocha T (2018) Downstream components of the calmodulin signaling pathway in the rice salt stress response revealed by transcriptome profiling and target identification. BMC plant biology 18(1):pp.1–23. https://doi.org/10.1186/2Fs12870-018-1538-4
Zeng H, Xu L, Singh A, Wang H, Du L, Poovaiah BW (2015) Involvement of calmodulin and calmodulin-like proteins in plant responses to abiotic stresses. Front Plant Sci 6:600. https://doi.org/10.3389/fpls.2015.00600
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This publication was supported by SERB, DST, Govt. of India (File no. ECR/2018/000328) and Indian Institute of Technology Kharagpur as well as SRIC, IIT Kharagpur.
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HG, AD, and JB conceptualized the idea of these research analysis and article. HG has done the required analysis and prepared the draft manuscript. AD, SBD, and JB reviewed and edited the manuscript. DN and DK helped in making some of the analysis. All authors contributed to the article and approved the submitted version.
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10142_2022_828_MOESM2_ESM.pptx
Schematic representation of functional domains of eighteen OsCAMTAs. Gene structure of total eighteen OsCAMTAs. Supplementary file2 (PPTX 364 KB)
10142_2022_828_MOESM4_ESM.pdf
Enlistment of OsCAMTAs with OsCaM/ OsCML proteins based on docking scores and Gibbs free energy from FireDock and pyDockWEB software. Top ΔG scores for docked models of every individual CAMTA protein. Structure analysis or validation scores of non-docked CAMTA with ERRAT score and PROCHECK values. Structure analysis which showed gross changes on analysis of non-docked structures. Supplementary file4 (PDF 147 KB)
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Gain, H., Nandi, D., Kumari, D. et al. Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure. Funct Integr Genomics 22, 193–214 (2022). https://doi.org/10.1007/s10142-022-00828-w
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DOI: https://doi.org/10.1007/s10142-022-00828-w