|
|
|
| Identification and Expression Analysis of CDPK Gene Family in Pecan (Carya illinoinensis) and Chinese Hickory (Carya cathayensis) |
| ZHAO Juan1,2, ZHU Kai-Kai1,2, FAN Ping-Hua1,2, TAN Peng-Peng1,2, PENG Fang-Ren1,2,*, LI Yong-Rong3 |
1 Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China;
2 College of Forestry, Nanjing Forestry University, Nanjing 210037, China;
3 Nanjing Green Universe Pecan Science and Technology Co. Ltd., Nanjing 211500, China |
|
|
|
|
Abstract Calcium-dependent protein kinase (CDPK) is a specific type of Ser/Thr protein kinase to plants, which plays an important role in plant growth, development and stress signal transduction. In order to explore the function of CDPK genes in the growth and development of pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis), bioinformatics methods were applied to identify the members of CDPK gene family from pecan and Chinese hickory genome. MEGA7.0 software was used to carry on the multiple sequence alignment, classification and phylogenetic tree construction. The gene structures and conserved motifs of CDPK family were also analyzed. The results showed that 28 (CILCDPK1~28) and 25 (CCACDPK1~25) CDPK members were successfully identified in pecan and Chinese hickory, respectively. In order to explore the homologous evolutionary relationship between the two plants and other species, a phylogenetic tree was constructed using CDPKs in pecan, Chinese hickory, Arabidopsis and rice (Oryza sativa). The phylogenetic tree showed that all CDPK proteins could be divided into 4 subgroups. Cis-acting element analysis showed that all CDPK genes contained hormone-response elements, and abscisic acid-response elements were the most abundant. Transcriptome data analysis of pecan and Chinese hickory showed that 3 CILCDPKs and 2 CCACDPKs might play an important role in the 3 key stages of embryonic development. In addition, 3 CDPK genes showed high expression during pecan grafting and healing, which might play important roles in callus and vascular tissue formation of pecan. qPCR analysis showed that CILCDPK1/3/6/11/13/19/25 were up-regulated under drought stress. The present study provides a reference basis for exploring the mechanism of CDPK gene family in plant growth and development and drought stress response.
|
|
Received: 18 May 2021
|
|
|
|
Corresponding Authors:
*frpeng@njfu.edu.cn
|
|
|
|
[1] 韩艳丽, 李静, 操庆国, 等. 2017.梨树CDPK基因家族进化和表达分析[J]. 西北农业学报, 26(07): 1026-1032.
(Han Y L, Li J, Cao G Q, et al.2017. Evolution and expression analysis of CDPK gene family in pear[J]. Acta Agriculturae Boreali-occidentalis Sinica, 26(07): 1026-1032.)
[2] 刘贯山, 陈珈. 2003. 钙依赖蛋白激酶(CDPKs)在植物钙信号转导中的作用[J]. 植物学通报, 20(2): 160-167.
(Liu G S, Chen J.2003. The role of calcium dependent protein kinases (CDPKs) in plant calcium signal transduction[J]. Chinese Bulletin of Botany, 20(2): 160-167.)
[3] 莫正海, 何海洋, 陈文静, 等. 2017. 薄壳山核桃嫁接愈合过程中差异蛋白质的分析[J]. 南京林业大学学报(自然科学版), 41(06): 19-25.
(Mo Z H, He H Y, Chen W J, et al.2017. Analysis of the differential proteins in the graft healing process of pecan (Carya illinoinensis)[J]. Journal of Nanjing Forestry University (Naturnal Sciences Edition), 41(06): 19-25.)
[4] 莫正海, 李风达, 苏文川, 等. 2019. 薄壳山核桃嫁接愈合过程中CiMYB46基因的克隆与表达分析[J]. 南京林业大学学报(自然科学版), 43(05): 156-162.
(Mo Z H, Li F D, Su W C, et al.2019. Cloning and expression analysis of CiMYB46 in the graft healing process of Carya illinoinensis[J]. Journal of Nanjing Forestry University (Naturnal Sciences Edition), 43(05): 156-162.)
[5] 彭方仁, 李永荣, 郝明灼, 等. 2012. 我国薄壳山核桃生产现状与产业化发展策略[J]. 林业科技开发, 26(04): 1-4.
(Peng F R, Li Y R, Hao M Z, et al.2012. Production status and industrialization development strategy of pecan in China[J]. Development of Forestry Science and Technology, 26(04): 1-4.)
[6] 许园园, 李晓刚, 李慧, 等. 2015. 梨CDPK基因家族全基因组序列鉴定分析[J]. 江苏农业学报, 31(03): 659-666.
(Xu Y Y, Li X G, Li H, et al.2015. Identification and analysis of the whole genome of pear CDPK gene family[J]. Jiangsu Journal of Agricultural Sciences, 31(03): 659-666.)
[7] Bolling B W, Chen C Y, McKay D L, et al.2011. Tree nut phytochemicals: Composition, antioxidant capacity, bioactivity, impact factors. A systematic review of almonds, Brazils, cashews, hazelnuts, macadamias, pecans, pine nuts, pistachios and walnuts[J]. Nutrition Research Reviews, 24(2): 244-275.
[8] Cheng S H, Willmann M R, Chen H C, et al.2002. Calcium signaling through protein kinases. The Arabidopsis calcium-dependent protein kinase gene family[J]. Plant Physiology, 129(2): 469-485.
[9] Delormel T Y, Boudsocq M.2019. Properties and functions of calcium-dependent protein kinases and their relatives in Arabidopsis thaliana[J]. New Phytologist, 224(2): 585-604.
[10] Dubrovina A S, Kiselev K V, Khristenko V S.2013. Expression of calcium-dependent protein kinasc (CDPK) genes under abiotic stress conditions in wild-growing grapevine Vitis amurensis[J]. Journal Plant Physiology, 170(17): 1491-1500.
[11] Gutermuth T, Lassig R, Portes M T, et al.2013. Pollen tube growth regulation by free anions depends on the interaction between the anion channel SLAH3 and calcium-dependent protein kinases CPK2 and CPK20[J]. Plant Cell, 25(11): 4525-4543.
[12] Hadas K, Galit L M, Gil A.2010. Alternative splicing and evolution: Diversification, exon definition and function[J]. Nature Reviews Genetics, 11(5): 345-355.
[13] Harmon A C, Michael G, Gubrium E, et al.2001. The CDPK superfamily of protein kinases[J]. New Phytologist, 151(1): 175-183.
[14] Harper J F, Sussman M R, Schaller G E, et al.1991. A calcium-dependent protein kinase with a regulatory domain similar to calmodulin[J]. Science, 252(5008): 951-954.
[15] Hilbig J, Policarpi P B, Grinevicius V M A S, et al.2018. Aqueous extract from pecan nut [Carya illinoinensis (Wangenh) C. Koch] shell show activity against breast cancer cell line MCF-7 and Ehrlich ascites tumor in Balb-c mice[J]. Journal of Ethnopharmacology, 211: 256-266.
[16] Hrabak E M, Chan C W M, Gribskov M, et al.2003. The Arabidopsis CDPK-SnRK superfamily of protein kinases[J]. Plant Physiology, 132(2): 666-680.
[17] Huang Y J, Xiao L H, Zhang Z R, et al.2019. The genomes of pecan and Chinese hickory provide insights into carya evolution and nut nutrition[J]. Gigascience, 8(5): giz036.
[18] Jin Y, Ye N, Zhu F, et al.2017. Calcium-dependent protein kinase CPK28 targets the methionine adenosyltransferases for degradation by the 26S proteasome and affects ethylene biosynthesis and lignin deposition in Arabidopsis[J]. The Plant Journal, 90(2): 304-318.
[19] Keren H, Lev-Maor G, Ast G.2010. Properties and functions of calcium-dependent protein kinases and their relatives in Arabidopsis thaliana[J]. New Phytologist, 11(5): 345-355.
[20] Kong X P, Lv W, Jiang S S, et al.2013. Genome-wide identification and expression analysis of calcium-dependent protein kinase in maize[J]. BMC Genomics, 14: 433.
[21] Liu W, Li W, He Q L, et al.2014. Genome-wide survey and expression analysis of calcium-dependent protein kinase in Gosspium raimondii[J]. PLOS ONE, 9(6): e98189.
[22] Manik S M N, Shi S J, Mao J J, et al.2015. The calcium sensor CBL-CIPK is involved in plant's response to abiotic stresses[J]. International Journal of Genomics, 493191. DOI: 10.1155/2015/493191.
[23] Matschi S, Hake K, Herde M, et al.2015. The calcium-dependent protein kinase CPK28 regulates development by inducing growth phase-specific, spatially restricted alterations in jasmonic acid levels independent of defense responses in Arabidopsis[J]. Plant Cell, 27(3): 591-606.
[24] Matschi S, Werner S, Schulze W X, et al.2013. Function of calcium-dependent protein kinase CPK28 of Arabidopsis thalianain plant stem elongation and vascular development[J]. The Plant Journal, 73(6): 883-896.
[25] Miraliakbari H, Shahidi F.2008. Antioxidant activity of minor components of tree nut oils[J]. Food Chemistry, 111(2): 421-427.
[26] Mori I C, Murata Y, Yang Y Z, et al.2006. CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion-and Ca2+-permeable channels and stomatalclosure[J]. PLOS Biology, 4(10): e327.
[27] Myers C, Romanowsky S M, Barron Y D, et al.2009. Calcium-dependent protein kinases regulate polarized tip growth in pollen tubes[J]. The Plant Journal, 59(4): 528-539.
[28] Nemoto K, Ramadan A, Arimura G I, et al.2017. Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation[J]. Nature Communications, 8(1): 1004.
[29] Romeis T, Ludwig A A, Martin R, et al.2001. Calcium-dependent protein kinases play an essential role in a plant defense response[J]. EMBO Journal, 20(20): 5556-5567.
[30] Romeis T, Piedaras P, Jones J D.2000. Resistance gene-dependent activation of a calcium-dependent protein kinase in the plant defense response[J]. Plant Cell, 12(5): 803-816.
[31] Sanders D, Brownlee C, Harper J F.1999. Communicating with calcium[J]. Plant Cell, 11(4): 691-706.
[32] Shi S J, Li S G, Asim M, et al.2018. The Arabidopsis calcium-dependent protein kinases (CDPKs) and their roles in plant growth regulation and abiotic stress responses[J]. International Journal of Molecular Sciences, 19(7):1900.
[33] Singh A, Sagar S, Biswas D K.2017. Calcium dependent protein kinase, a versatile player in plant stress management and development[J]. Critical Reviews in Plant Sciences, 36(5-6): 336-352.
[34] Trapnell C, Williams B A, Pertea G, et al.2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nature Biotechnolnol, 28(5): 511-515.
[35] Valliyodan B, Nguyen H T.2006. Understanding regulatory networks and engineering for enhanced drought tolerance in plants[J]. Current Opinion in Plant Biology, 9(2): 189-195.
[36] Venkatachalam M, Kshirsagar H H, Seeram N P, et al.2007. Biochemical composition and immunological comparison of select pecan [Carya illinoinensis (Wangenh.) K. Koch] cultivars[J]. Journal of Agricultural and Food Chemistry, 55(24): 9899-9907.
[37] Wang J P, Xu Y P, Munyampundu J P, et al.2015. Calcium-dependent protein kinase (CDPK) and CDPK-related kinase (CRK) gene families in tomato: Genome-wide identification and functional analyses in disease resistance[J]. Molecular Genetics and Genomics, 291(2): 661-676.
[38] Wei S Y, Hu W, Deng X M, et al.2014. A rice calcium-dependent protein kinase OsCPK9 positively regulates drought stress tolerance and spikelet fertility[J]. BMC Plant Biology, 14: 133.
[39] Witte C P, Keinath N,Dubiella U, et al.2010. Tobacco calcium-dependet protein kinases are differentially phosphorylated in vivo as part of a kinase cascade that regulates stress response[J]. Journal Biological Chemistry, 285(13): 9740-9748.
[40] Xiao X H, Yang M, Sui J L, et al.2016. The calcium-dependent protein kinase (CDPK) and CDPK-related kinase gene families in Hevea brasiliensis-comparison with five other plant species in structure, evolution, and expression[J]. FEBS Open Bio, 7(1): 4-24.
[41] Xiong L M, Schumaker K S, Zhu J K.2002. Cell Signaling during cold, drought, and salt tress[J]. Plant Cell, 14(suppl): 165-183.
[42] Xu Q F, Dunbrack R L Jr.2012. Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB[J]. Bioinformatics, 28(21): 2763-2772.
[43] Yamaguchi-Shinozaki K, Shinozaki K.2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses[J]. Annual Review of Plant Biology, 57: 781-803.
[44] Zhang K, Han Y T, Zhao F L, et al.2015. Genome-wide identification and expression analysis of the CDPK gene family in grape, Vitis spp.[J]. BMC Plant Biology, 15: 164.
[45] Zhu J K.2002. Salt and drought stress signal transduction in plants[J]. Annual Review of Plant Biology, 53: 247-73.
[46] Zhu K K, Fan P H, Mo Z H, et al.2020. Identification, expression and co-expression analysis of R2R3-MYB family genes involved in graft union formation in pecan (Carya illinoinensis)[J]. Forests, 11(9): 917.
[47] Zou J J, Li X D, Ratnasekera D, et al.2015. Arabidopsis CALCIUM-DEPENDENT PROTEIN KINASE8 and CATALASE3 function in abscisic acid-mediated signaling and H2O2 homeostasis in stomatal guardcells under drought stress[J]. Plant Cell, 27(5): 1445-1460.
[48] Zuo R, Hu R, Chai G H, et al.2013. Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa)[J]. Molecular Biology Reporter, 40(3): 2645-2662. |
|
|
|
