陆地棉KFB基因家族全基因组鉴定与表达分析
|
摘要
【目的】KFB(Kelch containing F-box protein)是普遍存在于各种生物体中含有F-box结构域的一类家族蛋白,参与众多生物过程。本研究旨在开展陆地棉KFB家族基因鉴定和表达分析。【方法】利用生物信息学方法从陆地棉(TM-1)基因组中鉴定KFB家族成员,与已知的拟南芥、水稻、大豆等KFB蛋白序列构建系统进化树;进一步针对第Ⅱ亚族进行基因结构、染色体定位和表达分析。【结果】从陆地棉基因组共鉴定出150个KFB家族成员,进化分析表明这些基因可分为7个亚族。陆地棉KFB第Ⅱ亚族24个基因分布在14条染色体上,有9对直系同源基因;该亚族基因结构简单,半数基因只有1个外显子;qRT-PCR结果表明,该亚族基因具有较为广泛的组织表达模式,但在不同组织的表达存在差异。【结论】这些结果显示陆地棉KFB第Ⅱ亚族基因在进化过程中出现了功能分化。
[Objective] The KFB(Kelch containing F-box protein) family, involving in many physiological pathways, is a subfamily of the biggest F-box protein family in all organisms. In the study, we aims to identify the KFB family members in the upland cotton genome and analyze their expression patterns. [Method] The KFB genes were identified from the whole genome of upland cotton(Gossypium hirsutum L. acc. TM-1) by bioinformatics methods. A phylogenetic analysis was conducted based on the alignment of the KFB proteins from upland cotton, Arabidopsis, rice and soybean, and the gene structure, chromosomal localization, and expression of subgroup Ⅱ in this family. [Result] A total of 150 KFB genes were identified from the whole genome of upland cotton and were then divided into seven subgroups based on phylogenetic analyses. In subgroup Ⅱ, 24 genes distributed on fourteen chromosomes, and nine pairs were orthologous genes. Structures of half genes in this subfamily were simple, including only one exon, respectively. According to the results of qRT-PCR, this subfamily had a wide range of tissue expression patterns, but the expression level of these genes varied from different tissues. [Conclusion] The results indicate that the functions of subgroup Ⅱ in KFB family have been differentiated during the process of evolution.
[Objective] The KFB(Kelch containing F-box protein) family, involving in many physiological pathways, is a subfamily of the biggest F-box protein family in all organisms. In the study, we aims to identify the KFB family members in the upland cotton genome and analyze their expression patterns. [Method] The KFB genes were identified from the whole genome of upland cotton(Gossypium hirsutum L. acc. TM-1) by bioinformatics methods. A phylogenetic analysis was conducted based on the alignment of the KFB proteins from upland cotton, Arabidopsis, rice and soybean, and the gene structure, chromosomal localization, and expression of subgroup Ⅱ in this family. [Result] A total of 150 KFB genes were identified from the whole genome of upland cotton and were then divided into seven subgroups based on phylogenetic analyses. In subgroup Ⅱ, 24 genes distributed on fourteen chromosomes, and nine pairs were orthologous genes. Structures of half genes in this subfamily were simple, including only one exon, respectively. According to the results of qRT-PCR, this subfamily had a wide range of tissue expression patterns, but the expression level of these genes varied from different tissues. [Conclusion] The results indicate that the functions of subgroup Ⅱ in KFB family have been differentiated during the process of evolution.
引文
[1]Kipreos E T,Pagano M.The F-box protein family[J].Genome Biology,1999,1(5):1-7.
[2]Andrade M A,Gonzalez-Guzman M,Serrano R,et al.A combination of the F-box motif and kelch repeats defines a large Arabidopsis family of F-box proteins[J].Plant Molecular Biology,2001,46(5):603-614.
[3]Hassan M,Zainal Z,Ismail I.Plant kelch containing F-box proteins:structure,evolution and functions[J].RSC Advances,2015,5(53):42808-42814.
[4]Sekine Y,Hatanaka R,Watanabe T,et al.The kelch repeat protein KLHDC10 regulates oxidative stress-induced ASK1 activation by suppressing PP5[J].Molecular Cell,2012,48(5):692-704.
[5]Franciosini A,Lombardi B,Iafrate S,et al.The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 protein forms an SCF ubiquitin ligase and regulates hypocotyl elongation[J].Molecular Plant,2013,6(5):1616-1629.
[6]Adams J,Kelso R,Cooley L.The kelch repeat superfamily of proteins:propellers of cell function[J].Trends in Cell Biology,2000,10(1):17-24.
[7]Prag S,Adams J C.Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals[J/OL].BMC Bioinformatics,2003,4(40):42[2016-10-27].http://link.springer.com/article/10.1186/1471-2105-4-42.DOI:10.1186/1471-2105-4-42.
[8]Kim J,Geng R,Gallenstein R A,et al.The F-box protein ZEITLUPE controls stability and nucleocytoplasmic partitioning of GIGANTEA[J].Development,2013,140(19):4060-4069.
[9]Imaizumi T,Tran H G,Swartz T E,et al.FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis[J].Nature,2003,426(6964):302-306.
[10]Imaizumi T,Schultz T F,Harmon F G,et al.FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANSin Arabidopsis[J].Science,2005,309(5732):293-297.
[11]Zhang X B,Gou M Y,Guo C R,et al.Down-regulation of kelch domain-containing F-Box protein in Arabidopsis enhances the production of(Poly)phenols and tolerance to ultraviolet radiation[J].Plant Physiology,2014,167(2):337-350.
[12]Li M,Tang D,Wang K J,et al.Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice[J].Plant Biotechnology Journal,2011,9(9):1002-1013.
[13]Han S K,Delaney T P.Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance[J].Plant Cell,2002,14(7):1469-1482.
[14]Lorenzo O,Chico J M,Sánchezserrano J J,et al.JAS-MONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis[J].Plant Cell,2004,16(7):1938-1950.
[15]Chen R G,Guo W L,Yin Y X,et al.A novel F-Box protein Ca F-Box is involved in responses to plant hormones and abiotic stress in pepper(Capsicum annuum L.)[J].International Journal of Molecular Sciences,2014,15(2):2413-2430.
[16]于海川,吴娇,崔百明,等.棉花中两个新的F-box蛋白基因的克隆与表达分析[J].棉花学报,2008,20(2):99-104.Yu Haichuan,Wu Jiao,Cui Baiming,et al.Cloning and expression analysis of tuo new genes encoding F-box proteins in cotton(Gossypium hirsutum L.)[J].Cotton Science,2008,20(2):99-104.
[17]王娟,倪志勇,吕萌,等.棉花纤维伸长期与次生壁增厚期蛋白质组比较[J].作物学报,2010,36(11):2004-2010.Wang Juan,Ni Zhiyong,LüMeng,et al.Comparison of proteome in cotton fiber cell between elongation and secondary wall thickening stages[J].Acta Agronomica Sinica,2010,36(11):2004-2010.
[18]卫江辉,范术丽,宋美珍,等.棉花一个新F-box基因的克隆与表达分析[J].棉花学报,2011,23(3):212-218.Wei Jianghui,Fan Shuli,Song Meizhen,et al.Cloning and expression analysis of Gh FBO in Gossypium hirsutum L.[J].Cotton Science,2011,23(3):212-218.
[19]Li Fuguang,Fan Guangyi,Lu Cairui,et al.Genome sequence of cultivated upland cotton(Gossypium hirsutum TM-1)provides insights into genome evolution[J].Nature Biotechnology,2015,33(5):524-532.
[20]Zhang Tianzhen,Hu Yan,Jiang Wenkai,et al.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement[J].Nature Biotechnology,2015,33(5):531-537.
[21]Initiative A G.Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J].Nature,2000,408(6814):796-815.
[22]Yu J,Wang J,Lin W,et al.The genomes of Oryza sativa:a history of duplications[J/OL].PLo S Biology,2005,3(2):e38[2016-10-27].http://dx.doi.org/10.1371/journal.pbio.0030038.DOI:10.1371/journal.pbio.0030038.
[23]Gupta S,Garg V,Kant C,et al.Genome-wide survey and expression analysis of F-box genes in chickpea[J].BMC Genomics,2015,16(1):1-15.
[24]Tamura K,Stecher G,Peterson D,et al.Mega 6:molecular evolutionary genetics analysis version 6.0[J].Molecular biology and evolution,2013,30(12):2725-2729.
[25]Yu C S,Cheng C W,Su W C,et al.Cello2go:a web server for protein subcellular localization prediction with functional gene on tology annotation[J/OL].PLo S ONE,2014,9(6):e99368[2016-10-27].http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0099368.PDF.DOI:10.1371/journal.pone.0099368.
[26]Bailey T L,Boden M,Buske F A,et al.MEME SUITE:tools for motif discovery and searching[J].Nucleic Acids Research,2009,37(Suppl 2):W202-W208.
[27]Map Inspect software[CP/OL].(2012-10-10)[2016-10-27].http://www.plantbreeding.wur.nl/UK/soft-ware_mapinspect.htm.
[28]Guo A Y,Zhu Q H,Chen X,et al.GSDS:a gene structure display server[J].Hereditas,2007,29(8):1023-1026.
[29]张军,王芙蓉,张传云,等.高产、抗病转基因抗虫棉新品种鲁棉研37号[J].山东农业科学,2009,4(11):117-118.Zhang Jun,Wang Furong,Zhang Chuanyun,et al.New transgenic Bt cotton variety SCRC 37 with high yield and disease resistance[J].Shandong Agricultural Sceience,2009,4(11):117-118.
[30]Li X B,Fan X P,Wang X L,et al.The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation[J].Plant Cell,2005,17(3):859-875.
[31]Sun Y,Zhou X,Ma H.Genome-wide analysis of kelch repeat-containing f-box family[J].Journal of Integrative Plant Biology,2007,49(6):940-952.
[32]Kim W Y,Fujiwara S,Suh S S,et al.ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light[J].Nature,2007,449(7160):356-360.
[33]Yasuhara M,Mitsui S,Hirano H,et al.Identification of ASKand clock-associated proteins as molecular partners of LKP2(LOV kelch protein 2)in Arabidopsis[J].Journal of Experimental Botany,2004,55(405):2015-2027.
[34]Baudry A,Ito S,Song Y H,et al.F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression[J].Plant Cell,2010,22(3):606-622.
[35]Miyazaki Y,Takase T,Kiyosue T.ZEITLUPE positively regulates hypocotyl elongation at warm temperature under light in Arabidopsis thaliana[J/OL].Plant Signaling&Behavior,2015,10(5):e998540(2014-12-04)[2016-10-27].http://dx.doi.org/10.1080/15592324.2014.998540.
[36]Ito S,Song Y H,Imaizumi T.LOV domain-containing f-box proteins:light-dependent protein degradation modules in Arabidopsis[J].Molecular Plant,2012,5(3):573-582.
[37]Han S H,Yoo S C,Lee B D,et al.Rice FLAVIN-BINDING,KELCH REPEAT,F-BOX 1(Os FKF1)promotes flowering independent of photoperiod[J].Plant,Cell&Environment,2015,38(12):2527-2540.
[38]Chen Y,Xu Y,Luo W,et al.The F-box protein Os FBK12 targets Os SAMS1 for degradation and affects pleiotropic phenotypes,including leaf senescence,in rice[J].Plant Physiology,2013,163(4):1673-1685.
[39]Tian S,Qian Q,Ding T,et al.A novel gene IBF1 is required for the inhibition of brown pigment deposition in rice hull furrows[J].Theoretical&Applied Genetics,2012,125(2):381-390.
[40]Jia Y,Gu H,Wang X,et al.Molecular cloning and characterization of an F-box family gene Car F-box1 from chickpea(Cicer arietinum L.)[J].Molecular Biology Reports,2012,39(3):2337-2345.
[41]Li F,Zhang X M,Hu R B,et al.Identification and molecular characterization of FKF1 and GI homologous genes in soybean[J/OL].Plo S ONE,2013,8(11):e79036[2016-10-27].http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0079036.PDF.
[42]Chai C L,Wang Y Q,Joshi T,et al.Soybean transcription factor ORFeome associated with drought resistance:a valuable resource to accelerate research on abiotic stress resistance[J/OL].BMC Genomics,2015,16(1):596[2016-10-27].http://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1743-6?.DOI:10.1186/s12864-015-1743-6.
[2]Andrade M A,Gonzalez-Guzman M,Serrano R,et al.A combination of the F-box motif and kelch repeats defines a large Arabidopsis family of F-box proteins[J].Plant Molecular Biology,2001,46(5):603-614.
[3]Hassan M,Zainal Z,Ismail I.Plant kelch containing F-box proteins:structure,evolution and functions[J].RSC Advances,2015,5(53):42808-42814.
[4]Sekine Y,Hatanaka R,Watanabe T,et al.The kelch repeat protein KLHDC10 regulates oxidative stress-induced ASK1 activation by suppressing PP5[J].Molecular Cell,2012,48(5):692-704.
[5]Franciosini A,Lombardi B,Iafrate S,et al.The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 protein forms an SCF ubiquitin ligase and regulates hypocotyl elongation[J].Molecular Plant,2013,6(5):1616-1629.
[6]Adams J,Kelso R,Cooley L.The kelch repeat superfamily of proteins:propellers of cell function[J].Trends in Cell Biology,2000,10(1):17-24.
[7]Prag S,Adams J C.Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals[J/OL].BMC Bioinformatics,2003,4(40):42[2016-10-27].http://link.springer.com/article/10.1186/1471-2105-4-42.DOI:10.1186/1471-2105-4-42.
[8]Kim J,Geng R,Gallenstein R A,et al.The F-box protein ZEITLUPE controls stability and nucleocytoplasmic partitioning of GIGANTEA[J].Development,2013,140(19):4060-4069.
[9]Imaizumi T,Tran H G,Swartz T E,et al.FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis[J].Nature,2003,426(6964):302-306.
[10]Imaizumi T,Schultz T F,Harmon F G,et al.FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANSin Arabidopsis[J].Science,2005,309(5732):293-297.
[11]Zhang X B,Gou M Y,Guo C R,et al.Down-regulation of kelch domain-containing F-Box protein in Arabidopsis enhances the production of(Poly)phenols and tolerance to ultraviolet radiation[J].Plant Physiology,2014,167(2):337-350.
[12]Li M,Tang D,Wang K J,et al.Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice[J].Plant Biotechnology Journal,2011,9(9):1002-1013.
[13]Han S K,Delaney T P.Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance[J].Plant Cell,2002,14(7):1469-1482.
[14]Lorenzo O,Chico J M,Sánchezserrano J J,et al.JAS-MONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis[J].Plant Cell,2004,16(7):1938-1950.
[15]Chen R G,Guo W L,Yin Y X,et al.A novel F-Box protein Ca F-Box is involved in responses to plant hormones and abiotic stress in pepper(Capsicum annuum L.)[J].International Journal of Molecular Sciences,2014,15(2):2413-2430.
[16]于海川,吴娇,崔百明,等.棉花中两个新的F-box蛋白基因的克隆与表达分析[J].棉花学报,2008,20(2):99-104.Yu Haichuan,Wu Jiao,Cui Baiming,et al.Cloning and expression analysis of tuo new genes encoding F-box proteins in cotton(Gossypium hirsutum L.)[J].Cotton Science,2008,20(2):99-104.
[17]王娟,倪志勇,吕萌,等.棉花纤维伸长期与次生壁增厚期蛋白质组比较[J].作物学报,2010,36(11):2004-2010.Wang Juan,Ni Zhiyong,LüMeng,et al.Comparison of proteome in cotton fiber cell between elongation and secondary wall thickening stages[J].Acta Agronomica Sinica,2010,36(11):2004-2010.
[18]卫江辉,范术丽,宋美珍,等.棉花一个新F-box基因的克隆与表达分析[J].棉花学报,2011,23(3):212-218.Wei Jianghui,Fan Shuli,Song Meizhen,et al.Cloning and expression analysis of Gh FBO in Gossypium hirsutum L.[J].Cotton Science,2011,23(3):212-218.
[19]Li Fuguang,Fan Guangyi,Lu Cairui,et al.Genome sequence of cultivated upland cotton(Gossypium hirsutum TM-1)provides insights into genome evolution[J].Nature Biotechnology,2015,33(5):524-532.
[20]Zhang Tianzhen,Hu Yan,Jiang Wenkai,et al.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement[J].Nature Biotechnology,2015,33(5):531-537.
[21]Initiative A G.Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J].Nature,2000,408(6814):796-815.
[22]Yu J,Wang J,Lin W,et al.The genomes of Oryza sativa:a history of duplications[J/OL].PLo S Biology,2005,3(2):e38[2016-10-27].http://dx.doi.org/10.1371/journal.pbio.0030038.DOI:10.1371/journal.pbio.0030038.
[23]Gupta S,Garg V,Kant C,et al.Genome-wide survey and expression analysis of F-box genes in chickpea[J].BMC Genomics,2015,16(1):1-15.
[24]Tamura K,Stecher G,Peterson D,et al.Mega 6:molecular evolutionary genetics analysis version 6.0[J].Molecular biology and evolution,2013,30(12):2725-2729.
[25]Yu C S,Cheng C W,Su W C,et al.Cello2go:a web server for protein subcellular localization prediction with functional gene on tology annotation[J/OL].PLo S ONE,2014,9(6):e99368[2016-10-27].http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0099368.PDF.DOI:10.1371/journal.pone.0099368.
[26]Bailey T L,Boden M,Buske F A,et al.MEME SUITE:tools for motif discovery and searching[J].Nucleic Acids Research,2009,37(Suppl 2):W202-W208.
[27]Map Inspect software[CP/OL].(2012-10-10)[2016-10-27].http://www.plantbreeding.wur.nl/UK/soft-ware_mapinspect.htm.
[28]Guo A Y,Zhu Q H,Chen X,et al.GSDS:a gene structure display server[J].Hereditas,2007,29(8):1023-1026.
[29]张军,王芙蓉,张传云,等.高产、抗病转基因抗虫棉新品种鲁棉研37号[J].山东农业科学,2009,4(11):117-118.Zhang Jun,Wang Furong,Zhang Chuanyun,et al.New transgenic Bt cotton variety SCRC 37 with high yield and disease resistance[J].Shandong Agricultural Sceience,2009,4(11):117-118.
[30]Li X B,Fan X P,Wang X L,et al.The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation[J].Plant Cell,2005,17(3):859-875.
[31]Sun Y,Zhou X,Ma H.Genome-wide analysis of kelch repeat-containing f-box family[J].Journal of Integrative Plant Biology,2007,49(6):940-952.
[32]Kim W Y,Fujiwara S,Suh S S,et al.ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light[J].Nature,2007,449(7160):356-360.
[33]Yasuhara M,Mitsui S,Hirano H,et al.Identification of ASKand clock-associated proteins as molecular partners of LKP2(LOV kelch protein 2)in Arabidopsis[J].Journal of Experimental Botany,2004,55(405):2015-2027.
[34]Baudry A,Ito S,Song Y H,et al.F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression[J].Plant Cell,2010,22(3):606-622.
[35]Miyazaki Y,Takase T,Kiyosue T.ZEITLUPE positively regulates hypocotyl elongation at warm temperature under light in Arabidopsis thaliana[J/OL].Plant Signaling&Behavior,2015,10(5):e998540(2014-12-04)[2016-10-27].http://dx.doi.org/10.1080/15592324.2014.998540.
[36]Ito S,Song Y H,Imaizumi T.LOV domain-containing f-box proteins:light-dependent protein degradation modules in Arabidopsis[J].Molecular Plant,2012,5(3):573-582.
[37]Han S H,Yoo S C,Lee B D,et al.Rice FLAVIN-BINDING,KELCH REPEAT,F-BOX 1(Os FKF1)promotes flowering independent of photoperiod[J].Plant,Cell&Environment,2015,38(12):2527-2540.
[38]Chen Y,Xu Y,Luo W,et al.The F-box protein Os FBK12 targets Os SAMS1 for degradation and affects pleiotropic phenotypes,including leaf senescence,in rice[J].Plant Physiology,2013,163(4):1673-1685.
[39]Tian S,Qian Q,Ding T,et al.A novel gene IBF1 is required for the inhibition of brown pigment deposition in rice hull furrows[J].Theoretical&Applied Genetics,2012,125(2):381-390.
[40]Jia Y,Gu H,Wang X,et al.Molecular cloning and characterization of an F-box family gene Car F-box1 from chickpea(Cicer arietinum L.)[J].Molecular Biology Reports,2012,39(3):2337-2345.
[41]Li F,Zhang X M,Hu R B,et al.Identification and molecular characterization of FKF1 and GI homologous genes in soybean[J/OL].Plo S ONE,2013,8(11):e79036[2016-10-27].http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0079036.PDF.
[42]Chai C L,Wang Y Q,Joshi T,et al.Soybean transcription factor ORFeome associated with drought resistance:a valuable resource to accelerate research on abiotic stress resistance[J/OL].BMC Genomics,2015,16(1):596[2016-10-27].http://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1743-6?.DOI:10.1186/s12864-015-1743-6.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |