Identification of Calmodulin-binding Transcription Factor CAMTA Gene Family and Its Expression Analysis Under Low-temperature Stress in Tomato (Solanum lycopersicum)
WANG Bao-Qiang, ZHU Xiao-Lin, WEI Xiao-Hong*, JIN Bao-Xia, WANG Xian, WANG Wang-Tian
College of Life Science and Technology, Gansu Agricultural University/Gansu Provincial Key Laboratory of Crop Genetic & Germplasm Enhancement/Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
Abstract：Plant calmodulin-binding transcription factor (CAMTA) plays important roles in hormone signal transduction, developmental regulation, and low-temperature stress. In this study, the genome-wide identification of CAMTA genes were carried out in tomato (Solanum lycopersicum), the pivotal information of the family members was comprehensively analyzed by bioinformatics technology, and qRT-PCR was used to analyse the expression pattern of them under low-temperature stress. The results showed that there were 18 CAMTA gene family members were identified in tomato genome, which were distributed on 9 chromosomes and existed in one pair of segmental duplication gene. Based on phylogenetic analysis, the SlCAMTA members were clustered into 6 groups. There are 49 cis-acting elements related to plant hormone, stress, light response and tissue-specific expression were identified in the promoter region. Protein-protein interaction network showed that some of SlCAMTA proteins were closely related to Arabidopsis reported proteins. Most of the SlCAMTAs were expressed in various tissues, and more than half of the CAMTA genes had molecular functions and constituted the basic components of cells. Especially, SlCAMTA10 participated in 11 plant biological processes. Under low-temperature stress, 14 SlCAMTAs were significantly up-regulated expression, and the expression level of SlCAMTA02 reached the highest at 12 h (396.53), which was 396 times as compared with the control. Accordingly, this study provides a reference for further excavation of the gene function in tomato CAMTA family and the response mechanism to low-temperature tolerance.
王宝强, 朱晓林, 魏小红, 金宝霞, 王贤, 王旺田. 番茄钙调蛋白结合转录因子CAMTA家族基因的鉴定及其低温胁迫下表达模式的分析[J]. 农业生物技术学报, 2021, 29(5): 871-884.
WANG Bao-Qiang, ZHU Xiao-Lin, WEI Xiao-Hong, JIN Bao-Xia, WANG Xian, WANG Wang-Tian. Identification of Calmodulin-binding Transcription Factor CAMTA Gene Family and Its Expression Analysis Under Low-temperature Stress in Tomato (Solanum lycopersicum). 农业生物技术学报, 2021, 29(5): 871-884.
[1] 胡秋涛, 侯丹, 赵钟毓, 等. 2020. 毛竹PP2C基因家族鉴定与表达分析[J]. 农业生物技术学报, 28(10): 1776-1787. (Hu Q T, Hou D, Zhao Z Y, et al.2020, Identification and expression analysis of PP2C gene family in Phyllostachys edulis[J]. Journal of Agricultural Biotechnology, 28(10): 1776-1787.) [2] 曾后清, 王国平, 王慧中, 等. 2015. 植物钙调素结合转录因子CAMTA/SR功能的研究进展[J]. 植物生理学报, 51(05): 633-641. (Zeng H Q, Wang G P, Wang H Z, et al.Functions of calmodulin-binding transcription activators (CAMTAs) in plants[J]. Plant Physiology Journal,2015, 51(05): 633-641.) [3] 张高原, 魏兵强. 2020. 甜瓜WRKY基因家族鉴定及其响应低温胁迫的表达分析[J]. 农业生物技术学报, 28(10): 1761-1775. (Zhang G Y, Wei B Q.Identification of WRKY gene family and their expression analysis under low-temperature stress in melon(Cucumis melo)[J]. Journal of Agricultural Biotechnology, 28(10): 1761-1775.) [4] 张南南, 黄咏虹, 綦鹏, 等. 2020. 割手密CDPK基因家族的鉴定及表达分析[J]. 农业生物技术学报, 28(12): 2151-2164. (Zhang N N, Huang Y H, Qi P, et al.2020. Identification and expression analysis of CDPK gene family in Saccharum spontaneum[J]. Journal of Agricultural Biotechnology, 28(12): 2151-2164.) [5] Banerjee A, Roychoudhury A.2017. Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress[J]. Protoplasma, 254(1): 3-16. [6] Bouche N, Scharlat A, Snedden W, et al.2002. A novel family of calmodulin-binding transcription activators in multicellular organisms[J]. Journal Biological Chemistry, 277(24): 21851-21861. [7] Büyük İlker, İlhan Emre, Şener Dilara, et al.2019. Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress[J]. Molecular Biology Reports, 46(3): 2721-2732. [8] Del Campo E M, Casano L M, Barreno E.2013. Evolutionary implications of intron-exon distribution and the properties and sequences of the RPL10A gene in eukaryotes[J]. Molecular Phylogenetics & Evolution, 66(3): 857-867. [9] Doherty C J, Van Buskirk H A, Myers S J, et al.2009. Roles for Arabidopsis CAMTA transcripti-on factors in cold-regulated gene expression and freezing tolerance[J]. Plant Cell, 21(3): 972-984. [10] Fujita M, Fujita Y, Noutoshi Y, et al.2006. Crosstalk between abiotic and biotic stress responses: A current view from the points of convergence in the stress signaling networks[J]. Current Opinion in Plant Biology, 9(4): 436-442. [11] Garcion C, Guilleminot J, Kroj T, et al.2006. AKRP and EMB506 are two ankyrin repeat proteins essential for plastid differentiation and plant development in Arabidopsis[J]. Plant Journal, 48(6): 895-906. [12] Gorlova O, Fedorov A, Logothetis C, et al.2014. Genes with a large intronic burden show greater evolutionary conservation on the protein level[J]. BMC Evolutionary Biology, 14(1): 50. [13] Iqbal Z, Shariq I M, Singh S P, et al.2020. Ca2+/calmodulin complex triggers CAMTA transcriptional machinery under stress in plants: Signaling cascade and molecular regulation[J]. Frontier Plant Science, 11: 598327. [14] Kim M C, Chung W S, Yun D J, et al.2009. Calcium and calmodulin-mediated regulation of gene expression in plants[J]. Molecular Plant, 2(1): 13-21. [15] Kim Y S, An C, Park S, et al.2017. CAMTA-mediated regulation of salicylic acid immunity pathway genes in Arabidopsis exposed to low temperature and pathogen infection, Plant Cell, 29(10): 2465-2477. [16] Lynch M, Conery J S.2003. The evolutionary demography of duplicate genes[J]. Journal of Structural & Functional Genomics, 3(1-4): 35-44. [17] Lynch M, Conery J S.2000. The evolutionary fate and consequences of duplicate genes[J]. Science, 290(5954): 1151-1155. [18] Mitsis T, Efthimiadou A, Bacopoulou F, et al.2020. Transcription factors and evolution: An integral part of gene expression[J]. World Academy of Sciences Journal, 2: 3-8. [19] Nie H Z, Zhao C Z, Wu G H, et al.2012. SR1, a calmodulin-binding transcription factor, modulates plant defense and ethylene-induced senescence by directly regulating NDR1 and EIN3[J]. Plant Physiology, 158(4): 1847-1859. [20] Noman M, Jameel A, Qiang W D, et al.2019. Overexpression of GmCAMTA12 enhanced drought tolerance in arabidopsis and soybean[J]. International Journal of Molecular Sciences, 20(19): 4849. [21] Pant P, Iqbal Z, Pandey B K, et al.2018. Genome-wide comparative and evolutionary analysis of calmodulin-binding transcription activator (CAMTA) family in Gossypium species[J]. Scientific Reports, 8(1): 5573. [22] Reddy Anireddy S N, Ali Gul S, Celesnik H, et al.2011. Coping with stresses: Roles of calcium and calcium/calmodulin-regulated gene expression[J]. Plant Cell, 23(6): 2010-2032. [23] Schweighofer A, Hirt H, Meskiene I.2004. Plant PP2C phosphatases: Emerging functions in stress signaling[J]. Trends in Plant Science, 9(5): 236-243. [24] Shkolnik D, Finkler A, Pasmanik-Chor M, et al.2019. CALMODULIN-BINDING TRANSCRIPTION ACTIV ATOR 6: A key regulator of Na+ homeostasis during germination[J]. Plant Physiology, 180(2): 1101-1118. [25] Soto G, Alleva K, Mazzella M A, et al.2008. AtTIP1;3 and AtTIP5;1, the only highly expressed Arabidopsis pollen-specific aquaporins, transport water and urea[J]. FEBS Letters, 582(29): 4077-82. [26] Suyama M, Torrents D, Bork P.2006. PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments[J]. Nucleic Acids Research, 34(Web Server issue): W609-W612. [27] Tanaka K M, Takahasi K R. Takano-Shimizu T.2009. Enhanced fixation and preservation of a newly arisen duplicate gene by masking deleterious loss-of-function mutations[J]. Genetical Research, 91(04): 267-280. [28] Wei M, Xu X M, Li C H.2017. Identification and expression of CAMTA genes in Populus trichocarpa under biotic and abiotic stress[J]. Scientific Reports, 7(1): 17910. [29] Whalley H J, Sargeant A W, Steele J F, et al.2011. Transcriptomic analysis reveals calcium regulation of specific promoter motifs in Arabidopsis[J]. Plant Cell, 23(11): 4079-4095. [30] Yamniuk A P, Vogel H J.2004. Calmodulin's flexibility allows for promiscuity in its interactions with target proteins and peptides[J]. Molecular Biotechnology, 27(1): 33-57. [31] Yang Y J, Sun T, Xu L Q, et al.2015. Genome-wide identification of CAMTA gene family members in Medicago truncatula and their expression during root nodule symbiosis and hormone treatments[J]. Frontiers in Plant Science, 6(459): 459. [32] Zhang T Z, Hu Y, Jiang W K, et al.2015. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement[J]. Nature Biotechnology, 33(5): 531-537.
