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Genome-wide analysis of the calcium-dependent protein kinase gene family in Gossypium raimondii |
LI Li-bei, YU Ding-wei, ZHAO Feng-li, PANG Chao-you, SONG Mei-zhen, WEI Heng-ling, FAN Shu-li, YU Shu-xun |
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, P.R.China |
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摘要 Plant calcium-dependent protein kinases (CDPKs) play important roles in diverse physiological processes by regulating the downstream components of calcium signaling. To date, only a few species of the plant CDPK gene family have been functionally identified. In addition, there has been no systematic analysis of the CDPK family in cotton. Here, 41 putative cotton CDPK (GrCDPK) genes were identified via bioinformatics analysis of the entire genome of Gossypium raimondii and were classified into four groups based on evolutionary relatedness. Gene structure analysis indicated that most of these GrCDPK genes share a similar intron-exon structure (7 or 8 exons), strongly supporting their close evolutionary relationships. Chromosomal distributions and phylogenetics analysis showed that 13 pairs of GrCDPK genes arose via segmental duplication events. Furthermore, using microarray data of upland cotton (G. hirsutum L.), comparative profiles analysis of these GhCDPKs indicated that some of the encoding genes might be involved in the responses to multiple abiotic stresses and play important regulatory roles during cotton fiber development. This study is the first genome-wide analysis of the CDPK family in cotton, and it will provide valuable information for the further functional characterization of cotton CDPK genes.
Abstract Plant calcium-dependent protein kinases (CDPKs) play important roles in diverse physiological processes by regulating the downstream components of calcium signaling. To date, only a few species of the plant CDPK gene family have been functionally identified. In addition, there has been no systematic analysis of the CDPK family in cotton. Here, 41 putative cotton CDPK (GrCDPK) genes were identified via bioinformatics analysis of the entire genome of Gossypium raimondii and were classified into four groups based on evolutionary relatedness. Gene structure analysis indicated that most of these GrCDPK genes share a similar intron-exon structure (7 or 8 exons), strongly supporting their close evolutionary relationships. Chromosomal distributions and phylogenetics analysis showed that 13 pairs of GrCDPK genes arose via segmental duplication events. Furthermore, using microarray data of upland cotton (G. hirsutum L.), comparative profiles analysis of these GhCDPKs indicated that some of the encoding genes might be involved in the responses to multiple abiotic stresses and play important regulatory roles during cotton fiber development. This study is the first genome-wide analysis of the CDPK family in cotton, and it will provide valuable information for the further functional characterization of cotton CDPK genes.
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Received: 10 February 2014
Accepted: 08 January 2015
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Fund: This work was supported by the National High-Tech R&D Program of China (2013AA102601). |
Corresponding Authors:
FAN Shu-li, Tel: +86-372-2562249, E-mail: fansl@cricaas.com.cn;YU Shu-xun, Tel: +86-372-2562201, Fax: +86-372-2562256,E-mail: yu@cricaas.com.cn
E-mail: fansl@cricaas.com.cn;yu@cricaas.com.cn
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About author: * These authors contributed equally to this study. |
Cite this article:
LI Li-bei, YU Ding-wei, ZHAO Feng-li, PANG Chao-you, SONG Mei-zhen, WEI Heng-ling, FAN Shu-li, YU Shu-xun.
2015.
Genome-wide analysis of the calcium-dependent protein kinase gene family in Gossypium raimondii. Journal of Integrative Agriculture, 14(1): 29-41.
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Abbasi F, Onodera H, Toki S, Tanaka H, Komatsu S. 2004.OsCDPK13, a calcium-dependent protein kinase gene fromrice, is induced by cold and gibberellin in rice leaf sheath.Plant Molecular Biology, 55, 541-552Asano T, Kunieda N, Omura Y, Ibe H, Kawasaki T, Takano M,Sato M, Furuhashi H, Mujin T, Takaiwa F, Wu C, Tada Y,Satozawa T, Sakamoto M, Shimada H. 2002. Rice SPK,a calmodulin-like domain protein kinase, is required forstorage product accumulation during seed development:Phosphorylation of sucrose synthase is a possible factor.The Plant Cell, 14, 619-628Asano T, Tanaka N, Yang G, Hayashi N, Komatsu S. 2005.Genome-wide identification of the rice calcium-dependentprotein kinase and its closely related kinase gene families:Comprehensive analysis of the CDPKs gene family in rice.Plant Cell Physiology, 46, 356-366de Castro E, Sigrist C J, Gattiker A, Bulliard V, Langendijk-Genevaux P S, Gasteiger E, Bairoch A, Hulo N. 2006. ScanProsite: Detection of PROSITE signature matchesand ProRule-associated functional and structural residuesin proteins. Nucleic Acids Research, 34, W362-W365.Cheng S H, Willmann M R, Chen H C, Sheen J. 2002. Calciumsignaling through protein kinases. The Arabidopsis calciumdependentprotein kinase gene family. Plant Physiology,129, 469-485Choi H I, Park H J, Park J H, Kim S, Im M Y, Seo H H, KimY W, Hwang I, Kim S Y. 2005. Arabidopsis calciumdependentprotein kinase AtCPK32 interacts with ABF4, atranscriptional regulator of abscisic acid-responsive geneexpression, and modulates its activity. Plant Physioogy,139, 1750-1761Chothia C, Gough J, Vogel C, Teichmann S A. 2003. Evolutionof the protein repertoire. Science, 300, 1701-1703Curran B, Jonas D, Grundmann H, Pitt T, Dowson C G. 2004.Development of a multilocus sequence typing scheme forthe opportunistic pathogen Pseudomonas aeruginosa.Journal of Clinical Microbiology, 42, 5644-5649Finn R D, Clements J, Eddy S R. 2011. HMMER web server:Interactive sequence similarity searching. Nucleic AcidsResearch, 39, W29-W37.Gargantini P R, Gonzalez-Rizzo S, Chinchilla D, Raices M,Giammaria V, Ulloa R M, Frugier F, Crespi M D. 2006.A CDPK isoform participates in the regulation of nodulenumber in Medicago truncatula. The Plant Journal, 48,843-856Gu Z, Cavalcanti A, Chen F C, Bouman P, Li W H. 2002.Extent of gene duplication in the genomes of Drosophila,nematode, and yeast. Molecular Biology Evolution, 19,256-262Harmon A C. 2003. Calcium-regulated protein kinases of plants.Gravitational and Space Biology Bulletin, 16, 83-90Harper J F, Breton G, Harmon A. 2004. Decoding Ca(2+)signals through plant protein kinases. Annual Review ofPlant Biology, 55, 263-288He H, Dong Q, Shao Y, Jiang H, Zhu S, Cheng B, Xiang Y. 2012.Genome-wide survey and characterization of the WRKYgene family in Populus trichocarpa. Plant Cell Reports,31, 1199-1217Hetherington A M, Brownlee C. 2004. The generation ofCa(2+) signals in plants. Annual Review of Plant Biology,55, 401-427Hrabak E M, Chan C W, Gribskov M, Harper J F, Choi J H,Halford N, Kudla J, Luan S, Nimmo H G, Sussman M R,Thomas M, Walker-Simmons K, Zhu J K, Harmon A C.2003. The Arabidopsis CDPK-SnRK superfamily of proteinkinases. Plant Physiology, 132, 666-680Hrabak E M, Dickmann L J, Satterlee J S, Sussman M R. 1996.Characterization of eight new members of the calmodulinlikedomain protein kinase gene family from Arabidopsisthaliana. Plant Molecular Biology, 31, 405-412Huang Q S, Wang H Y, Gao P, Wang G Y, Xia G X. 2008.Cloning and characterization of a calcium dependent proteinkinase gene associated with cotton fiber development. PlantCell Reports, 27, 1869-1875Hurst L D. 2002. The Ka/Ks ratio: Diagnosing the form ofsequence evolution. Trends in Genetics, 18, 486.Johnson D R, Bhatnagar R S, Knoll L J, Gordon J I. 1994.Genetic and biochemical studies of protein N-myristoylation.Annual Review Biochemistry, 63, 869-914Kerr M K. 2003. Linear models for microarray data analysis:Hidden similarities and differences. Journal of ComputationalBiology, 10, 891-901Komatsu S, Yang G, Khan M, Onodera H, Toki S, YamaguchiM. 2007. Over-expression of calcium-dependent proteinkinase 13 and calreticulin interacting protein 1 confers coldtolerance on rice plants. Molecular Genetic and Genomics,277, 713-723Kong X, Lv W, Jiang S, Zhang D, Cai G, Pan J, Li D. 2013.Genome-wide identification and expression analysisof calcium-dependent protein kinase in maize. BMCGenomics, 14, 433.Larkin M A, Blackshields G, Brown N P, Chenna R, McGettiganP A, McWilliam H, Valentin F, Wallace I M, Wilm A, LopezR, Thompson J D, Gibson T J, Higgins D G. 2007. ClustalW and Clustal X version 2.0. Bioinformatics, 23, 2947-2948de Las Rivas B, Marcobal A, Munoz R. 2004. Allelic diversityand population structure in Oenococcus oeni as determinedfrom sequence analysis of housekeeping genes. Appliedand Environmental Microbiology, 70, 7210-7219Lecourieux D, Ranjeva R, Pugin A. 2006. Calcium in plantdefence-signalling pathways. New Phytologist, 171, 249-269Long M, Rosenberg C, Gilbert W. 1995. Intron phasecorrelations and the evolution of the intron/exon structureof genes. Proceeding of the National Academy of Sciencesof the United States of America, 92, 12495-12499Lu S X, Hrabak E M. 2013. The myristoylated amino-terminus ofan Arabidopsis calcium-dependent protein kinase mediatesplasma membrane localization. Plant Molecular Biology,82, 267-278Ma S Y, Wu W H. 2007. AtCPK23 functions in Arabidopsisresponses to drought and salt stresses. Plant MolecularBiology, 65, 511-518Munemasa S, Hossain M A, Nakamura Y, Mori I C, Murata Y.2011. The Arabidopsis calcium-dependent protein kinase,CPK6, functions as a positive regulator of methyl jasmonatesignaling in guard cells. Plant Physiology, 155, 553-561Ohno S, Wolf U, Atkin N B. 1968. Evolution from fish tomammals by gene duplication. Hereditas, 59, 169-187Paterson A H, Wendel J F, Gundlach H, Guo H, Jenkins J, JinD, Llewellyn D, Showmaker K C, Shu S, Udall J, Yoo M J,Byers R, Chen W, Doron-Faigenboim A, Duke M V, GongL, Grimwood J, Grover C, Grupp K, Hu G, et al. 2012.Repeated polyploidization of Gossypium genomes and theevolution of spinnable cotton fibres. Nature, 492, 423-427Ray S, Agarwal P, Arora R, Kapoor S, Tyagi A K. 2007.Expression analysis of calcium-dependent protein kinasegene family during reproductive development and abioticstress conditions in rice (Oryza sativa L. ssp. indica).Molecular Genetics and Genomics, 278, 493-505 Romeis T, Piedras P, Jones J D. 2000. Resistance genedependentactivation of a calcium-dependent protein kinasein the plant defense response. The Plant Cell, 12, 803-816Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K. 2000. Overexpressionof a single Ca2+-dependent protein kinaseconfers both cold and salt/drought tolerance on rice plants.The Plant Journal, 23, 319-327Suyama M, Torrents D, Bork P. 2006. PAL2NAL: Robustconversion of protein sequence alignments into thecorresponding codon alignments. Nucleic Acids Research,34, W609-W612.Szczegielniak J, Borkiewicz L, Szurmak B, Lewandowska-Gnatowska E, Statkiewicz M, Klimecka M, Ciesla J,Muszynska G. 2012. Maize calcium-dependent proteinkinase (ZmCPK11): Local and systemic response towounding, regulation by touch and components ofjasmonate signaling. Physiologia Plantarum, 146, 1-14Tamura K, Peterson D, Peterson N, Stecher G, Nei M, KumarS. 2011. MEGA5: Molecular evolutionary genetics analysisusing maximum likelihood, evolutionary distance, andmaximum parsimony methods. Molecular Biology Evolution,28, 2731-2739Towler D A, Gordon J I, Adams S P, Glaser L. 1988. The biologyand enzymology of eukaryotic protein acylation. AnnualReview Biochemistry, 57, 69-99Wan B, Lin Y, Mou T. 2007. Expression of rice Ca(2+)-dependent protein kinases (CDPKs) genes under differentenvironmental stresses. FEBS Letters, 581, 1179-1189Wang H, Mei W, Qin Y, Zhu Y. 2011. 1-Aminocyclopropane-1-carboxylic acid synthase 2 is phosphorylated by calciumdependentprotein kinase 1 during cotton fiber elongationActa Biochimica et Biophysica Sinica, 43, 654-661Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, CongL, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, GouC, Zheng Z, Yin Y, Zhang X, Liu K, et al. 2012. The draftgenome of a diploid cotton Gossypium raimondii. NatureGenetics, 44, 1098-1103Wei K, Wang Y, Xie D. 2013. Identification and expressionprofile analysis of the protein kinase gene superfamily inmaize development. Molecular Breeding, 33, 155-172Wernimont A K, Amani M, Qiu W, Pizarro J C, Artz J D, Lin YH, Lew J, Hutchinson A, Hui R. 2011. Structures of parasiticCDPK domains point to a common mechanism of activation.Proteins, 79, 803-820Wernimont A K, Artz J D, Finerty Jr P, Lin Y H, Amani M, Allali-Hassani A, Senisterra G, Vedadi M, Tempel W, MackenzieF, Chau I, Lourido S, Sibley L D, Hui R. 2010. Structuresof apicomplexan calcium-dependent protein kinases revealmechanism of activation by calcium. Nature StructuralMolecular Biology, 17, 596-601Yang S, Zhang X, Yue J X, Tian D, Chen J Q. 2008. Recentduplications dominate NBS-encoding gene expansion intwo woody species. Molecular Genetics and Genomics,280, 187-198Ye S, Wang L, Xie W, Wan B, Li X, Lin Y. 2009. Expressionprofile of calcium-dependent protein kinase (CDPKs)genes during the whole lifespan and under phytohormonetreatment conditions in rice (Oryza sativa L. ssp. indica).Plant Molecular Biology, 70, 311-325Yuan X, Deng K, Zhao X, Wu X, Qin Y, Tang D, Liu X. 2007.A calcium-dependent protein kinase is involved in planthormone signal transduction in Arabidopsis. Journal of PlantPhysiology and Molecular Biology, 33, 227.Zhu S Y, Yu X C, Wang X J, Zhao R, Li Y, Fan R C, Shang Y,Du S Y, Wang X F, Wu F Q, Xu Y H, Zhang X Y, Zhang DP. 2007. Two calcium-dependent protein kinases, CPK4and CPK11, regulate abscisic acid signal transduction inArabidopsis. The Plant Cell, 19, 3019-3036Zhu Y N, Shi D Q, Ruan M B, Zhang L L, Meng Z H, Liu J,Yang W C. 2013. Transcriptome analysis reveals crosstalkof responsive genes to multiple abiotic stresses in cotton(Gossypium hirsutum L.). PLOS ONE, 8, e80218.Zuo R, Hu R, Chai G, Xu M, Qi G, Kong Y, Zhou G. 2013.Genome-wide identification, classification, and expressionanalysis of CDPK and its closely related gene families inpoplar (Populus trichocarpa). Molecular Biology Reports,40, 2645-2662 |
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