大豆KUP/HAK/KT钾转运体基因家族的鉴定与表达分析
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摘要
该研究基于已公布的大豆基因组序列信息,对大豆KUP/HAK/KT钾转运体基因家族进行了全基因组鉴定,并对该家族成员的基因特征、蛋白结构、染色体定位、基因复制和表达模式等进行了全面分析,为进一步了解该家族基因的功能及培育钾高效大豆品种提供理论支撑。结果表明:(1)在大豆基因组中共鉴定30个KUP/HAK/KT基因(简写为GmHAK01~GmHAK30),这些基因分布在大豆的15条染色体上,串联复制和片段复制可能导致了GmHAKs基因在大豆基因组中的扩增。(2)大豆GmHAKs蛋白间序列一致性很高,均具有12~14个跨膜区,且都定位于质膜上。(3)进化分析表明大豆GmHAKs可聚为4个进化簇ClusterⅠ~Ⅳ,其中ClusterⅡ的成员数目最多(16个),ClusterⅣ的成员数目最少(1个)。(4)所有GmHAKs基因均包含内含子和外显子,其内含子数目在7~9个之间,且同一亚家族的GmHAKs基因大部分具有相似的内含子-外显子分布模式。(5)表达模式分析表明,大豆GmHAKs的表达大致可分为两类:一类是一些组织特异性表达的基因,包括了ClusterⅠ和ClusterⅣ的全部成员,ClusterⅡ的部分成员,他们在根(GmHAK30和GmHAK04)、花(GmHAK03和GmHAK15)、荚(GmHAK10)或种子(GmHAK25)中表达量很高;另外一类是一些非组织特异性表达的基因,包括了ClusterⅢ的全部成员和ClusterⅡ的部分成员,这些基因(GmHAK05、GmHAK17和GmHAK28等)在所有被检测的组织中均有较高的表达;KUP/HAK/KT家族基因表达模式在不同进化簇的差异化结果表明,其在进化过程可能受到了选择的作用。以上研究结果为今后研究KUP/HAK/KT家族基因功能及定向改良大豆的钾吸收物性提供了重要的基因信息,也为大豆钾高效品种的选育提供了理论基础。
In this study,we performed the genome-wide identification of the KUP/HAK/KT family genes in soybean based on soybean genome sequence information.We also analyzed the gene character,protein structure,chromosome location,gene duplication and expression pattern of the family members.Our results showed that:(1)30 KUP/HAK/KTtransporter genes(GmHAK01-GmHAK30)had been identi-fied in soybean genome,which were distributed on 15 chromosomes of soybean;The segmental duplication and tandem duplication were the contributors to the expansion of GmHAKs genes in soybean genome.(2)The sequence identity of GmHAKs was very high,and all of them had 12-14 transmembrane regions,and were located on the plasma membrane.(3)Phylogenetic analysis indicated that the GmHAKs in soybean can be classified into 4clusters:ClusterⅠ-Ⅳ,and the number of ClusterⅡmembers was the most(16),and the number of ClusterⅣmembers was the least(1).(4)Gene structure analysis revealed that all GmHAKs genes had intron and exon.The intron number was between 7-9,and GmHAKs genes in the same subfamily exhibited similar exon-intron pattern.(5)Expression pattern analysis showed that the expression of GmHAKs can be roughly divided into two categories:one is the expression of some tissue-specific genes,including all members of ClusterⅠand Cluster Ⅳ,part members of ClusterⅡ.These genes expressed highly in root(GmHAK30and GmHAK04),or flower(GmHAK03and GmHAK15),or pod(GmHAK10),or seed(GmHAK25);The other is the expression of some non-tissue specific genes,including all members of Cluster Ⅲ,part members of ClusterⅡ,these genes(GmHAK05,GmHAK17 and GmHAK28)were highly expressed in all the examined tissues.The differential gene expression patterns of KUP/HAK/KT gene family in different evolutionary clusters suggested that it may be affected by selection in the process of evolution.The above results not only provide the important gene information for studying the KUP/HAK/KT gene function and the characteristics of potassium absorption in soybean,but also provides theoretical basis for the breeding of soybean varieties with high potassium efficiency.
In this study,we performed the genome-wide identification of the KUP/HAK/KT family genes in soybean based on soybean genome sequence information.We also analyzed the gene character,protein structure,chromosome location,gene duplication and expression pattern of the family members.Our results showed that:(1)30 KUP/HAK/KTtransporter genes(GmHAK01-GmHAK30)had been identi-fied in soybean genome,which were distributed on 15 chromosomes of soybean;The segmental duplication and tandem duplication were the contributors to the expansion of GmHAKs genes in soybean genome.(2)The sequence identity of GmHAKs was very high,and all of them had 12-14 transmembrane regions,and were located on the plasma membrane.(3)Phylogenetic analysis indicated that the GmHAKs in soybean can be classified into 4clusters:ClusterⅠ-Ⅳ,and the number of ClusterⅡmembers was the most(16),and the number of ClusterⅣmembers was the least(1).(4)Gene structure analysis revealed that all GmHAKs genes had intron and exon.The intron number was between 7-9,and GmHAKs genes in the same subfamily exhibited similar exon-intron pattern.(5)Expression pattern analysis showed that the expression of GmHAKs can be roughly divided into two categories:one is the expression of some tissue-specific genes,including all members of ClusterⅠand Cluster Ⅳ,part members of ClusterⅡ.These genes expressed highly in root(GmHAK30and GmHAK04),or flower(GmHAK03and GmHAK15),or pod(GmHAK10),or seed(GmHAK25);The other is the expression of some non-tissue specific genes,including all members of Cluster Ⅲ,part members of ClusterⅡ,these genes(GmHAK05,GmHAK17 and GmHAK28)were highly expressed in all the examined tissues.The differential gene expression patterns of KUP/HAK/KT gene family in different evolutionary clusters suggested that it may be affected by selection in the process of evolution.The above results not only provide the important gene information for studying the KUP/HAK/KT gene function and the characteristics of potassium absorption in soybean,but also provides theoretical basis for the breeding of soybean varieties with high potassium efficiency.
引文
[1]VRY A A,SENTENAC H.Molecular mechanisms and regulation of K+transport in higher plants[J].Annual Review of Plant Biology,2003,54:575-603.
[2]GRABOV A.Plant KT/KUP/HAK potassium transporters:single family-multiple functions[J].Annals of Botany,2007,99(6):1 035-1 041.
[3]ASHLEY M K,GRANT M,GRABOV A.Plant responses to potassium deficiencies:a role for potassium transport proteins[J].Journal of Experimental Botany,2006,57(2):425-436.
[4]MAATHUIS F J M,SANDERS D.Regulation of K+absorption in plant root cells by external K+:interplay of different plasma membrane K+transporters[J].Journal of Experimental Botany,1997,48:451-458.
[5]MAATHUIS F J,SANDERS D.Mechanism of high-affinity potassium uptake in roots of Arabidopsis thaliana[J].Proceedings of the National Academy of Sciences,1994,91(20):9 272-9 276.
[6]GUPTA M,QIU X,WANG L,et al.KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice(Oryza sativa)[J].Molecular Genetics and Genomics,2008,280(5):437-452.
[7]VRY A A,NIEVESCORDONES M,DALY M,et al.Molecular biology of K+transport across the plant cell membrane:what do we learn from comparison between plant species?[J].Journal of Plant Physiology,2014,171(9):748-769.
[8]AHN S J,SHIN R,SCHACHTMAN D P.Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+uptake[J].Plant Physiology,2004,134(3):1 135-1 145.
[9]MSER P,THOMINE S,SCHROEDER J I,et al.Phylogenetic relationships within cation transporter families of Arabidopsis[J].Plant Physiology,2001,126(4):1 646-1 667.
[10]ZHANG Z,ZHANG J,CHEN Y,et al.Genome-wide analysis and identification of HAK potassium transporter gene family in maize(Zea mays L.)[J].Molecular Biology Reports,2012,39(8):8 465-8 473.
[11]YANG Z,GAO Q,SUN C,et al.Molecular evolution and functional divergence of HAK potassium transporter gene family in rice(Oryza sativa L.)[J].Journal of Genetics and Genomics,2009,36(3):161-172.
[12]HE C,CUI K,DUAN A,et al.Genome-wide and molecular evolution analysis of the Poplar KT/HAK/KUP potassium transporter gene family[J].Ecology and Evolution,2012,2(8):1 996-2 004.
[13]SONG Z Z,MA R J,YU M L.Genome-wide analysis and identification of KT/HAK/KUP potassium transporter gene family in peach(Prunus persica)[J].Genetics and Molecular Research:GMR,2015,14(1):774-787.
[14]郭兆奎,杨谦,姚泉洪,等.转拟南芥AtKup1基因高含钾量烟草获得[J].中国生物工程杂志,2005,25(12):24-28.GUO Z K,YANG Q,YAO Q H,et al.Transgenic tobacco with Arabidopsis thaliana AtKup1gene has high potassium content in leaves[J].Progress in Biotechnology,2005,25(12):24-28.
[15]闫春娟,宋书宏,王文斌,等.大豆钾营养研究进展[J].大豆科学,2009,28(5):926-930.YAN C J,SONG S H,WANG W B,et al.Advances of potassium nutrition in soybean[J].Soybean Science,2009,28(5):926-930.
[16]GOODSTEIN D M,SHU S,HOWSON R,et al.Phytozome:a comparative platform for green plant genomics[J].Nucleic Acids Research,2011,40:1 178-1 186.
[17]SONNHAMMER E L,EDDY S R,DURBIN R.Pfam:a comprehensive database of protein domain families based on seed alignments[J].Proteins,1997,28(3):405-420.
[18]HALL T A.BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT[J].Nucleic Acids Symposium,1999,41:95-98.
[19]KROGH A,LARSSON B,VON H G,et al.Predicting transmembrane protein topology with a hidden Markov model:application to complete genomes[J].Journal of Molecular Biology,2001,305(3):567-580.
[20]HORTON P,PARK K J,OBAYASHI T,et al.WoLF PSORT:protein localization predictor[J].Nucleic Acids Research,2007,35:585-587.
[21]KUMAR S,NEI M,DUDLEY J,et al.MEGA:a biologistcentric software for evolutionary analysis of DNA and protein sequences[J].Briefings in Bioinformatics,2008,9(4):299-306.
[22]YANG S,ZHANG X,YUE J X,et al.Recent duplications dominate NBS-encoding gene expansion in two woody species[J].Molecular Genetics and Genomics,2008,280(3):187-198.
[23]JIANG H,WU Q,JIN J,et al.Genome-wide identification and expression profiling of ankyrin-repeat gene family in maize[J].Development Genes and Evolution,2013,223(5):303-318.
[24]SAEED A I,BHAGABATI N K,BRAISTED J C,et al.TM4 Microarray Software Suite[J].Methods in Enzymology,2006,411(2):134-193.
[25]JIANG C,WANG Y,LU J,et al.Advances of study on the K-efficiency in different plant genotypes[J].Journal of Huazhong Agricultural,2004,23(4):483-487.
[26]ADAMS K L,WENDEL J F.Polyploidy and genome evolution in plants[J].Current Opinion in Plant Biology,2005,8(2):135-141.
[27]SATO Y,NANATANI K,HAMAMOTO S,et al.Defining membrane spanning domains and crucial membrane-localized acidic amino acid residues for K+transport of a Kup/HAK/KT-type Escherichia coli potassium transporter[J].The Journal of Biochemistry,2014,155(5):315-323.
[28]ELUMALAI R P,NAGPAL P,REED J W.A mutation in the Arabidopsis KT2/KUP2potassium transporter gene affects shoot cell expansion[J].Plant Cell,2002,14(1):119-131.
[29]宋毓峰,张良,董连红,等.植物KUP/HAK/KT家族钾转运体研究进展[J].中国农业科技导报,2013,15(6):92-98.SONG Y F,ZHANG L,DONG L H,et al.Research progress on KUP/HAK/KT potassium transporter family in plant[J].Journal of Agricultural Science and Technology,2013,15(6):92-98.
[30]GIERTH M,SCHROEDER J I.The potassium transporter AtHAK5functions in K+deprivation-induced high-affinity K+uptake and AKT1K+channel contribution to K+uptake kinetics in Arabidopsis roots[J].Plant Physiology,2005,137(3):1 105-1 114.
[31]WANG Y H,GARVIN D F,KOCHIAN L V.Rapid induction of regulatory and transporter genes in response to phosphorus,potassium,and iron deficiencies in tomato roots.Evidence for cross talk and root/rhizosphere-mediated signals[J].Plant Physiology,2002,130(3):1 361-1 370.
[32]SANTA-MARA G E,RUBIO F,DUBCOVSKY J,et al.The HAK1gene of barley is a member of a large gene family and encodes a high-affinity potassium transporter[J].Plant Cell,1997,9(12):2 281-2 289.
[33]BAUELOS M A,GARCIADEBLAS B,CUBERO B,et al.Inventory and functional characterization of the HAK potassium transporters of rice[J].2002,Plant Physiology,130(2):784-795.
[34]KIM E J,KWAK J M,UOZUMI N,et al.AtKUP1:an Arabidopsis gene encoding high-affinity potassium transport activity[J].Plant Cell,1998,10(1):51-62.
[35]MAATHUIS F J M.The role of monovalent cation transporters in plant responses to salinity[J].Journal of Experimental Botany,2006,57(5):1 137-1 147.
[36]TAKAHASHI R,NISHIO T,ICHIZEN N,et al.High-affinity K+transporter PhaHAK5is expressed only in saltsensitive reed plants and shows Na+permeability under NaCl stress[J].Plant Cell Reports,2007,26(9):1 673-1 679.
[2]GRABOV A.Plant KT/KUP/HAK potassium transporters:single family-multiple functions[J].Annals of Botany,2007,99(6):1 035-1 041.
[3]ASHLEY M K,GRANT M,GRABOV A.Plant responses to potassium deficiencies:a role for potassium transport proteins[J].Journal of Experimental Botany,2006,57(2):425-436.
[4]MAATHUIS F J M,SANDERS D.Regulation of K+absorption in plant root cells by external K+:interplay of different plasma membrane K+transporters[J].Journal of Experimental Botany,1997,48:451-458.
[5]MAATHUIS F J,SANDERS D.Mechanism of high-affinity potassium uptake in roots of Arabidopsis thaliana[J].Proceedings of the National Academy of Sciences,1994,91(20):9 272-9 276.
[6]GUPTA M,QIU X,WANG L,et al.KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice(Oryza sativa)[J].Molecular Genetics and Genomics,2008,280(5):437-452.
[7]VRY A A,NIEVESCORDONES M,DALY M,et al.Molecular biology of K+transport across the plant cell membrane:what do we learn from comparison between plant species?[J].Journal of Plant Physiology,2014,171(9):748-769.
[8]AHN S J,SHIN R,SCHACHTMAN D P.Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+uptake[J].Plant Physiology,2004,134(3):1 135-1 145.
[9]MSER P,THOMINE S,SCHROEDER J I,et al.Phylogenetic relationships within cation transporter families of Arabidopsis[J].Plant Physiology,2001,126(4):1 646-1 667.
[10]ZHANG Z,ZHANG J,CHEN Y,et al.Genome-wide analysis and identification of HAK potassium transporter gene family in maize(Zea mays L.)[J].Molecular Biology Reports,2012,39(8):8 465-8 473.
[11]YANG Z,GAO Q,SUN C,et al.Molecular evolution and functional divergence of HAK potassium transporter gene family in rice(Oryza sativa L.)[J].Journal of Genetics and Genomics,2009,36(3):161-172.
[12]HE C,CUI K,DUAN A,et al.Genome-wide and molecular evolution analysis of the Poplar KT/HAK/KUP potassium transporter gene family[J].Ecology and Evolution,2012,2(8):1 996-2 004.
[13]SONG Z Z,MA R J,YU M L.Genome-wide analysis and identification of KT/HAK/KUP potassium transporter gene family in peach(Prunus persica)[J].Genetics and Molecular Research:GMR,2015,14(1):774-787.
[14]郭兆奎,杨谦,姚泉洪,等.转拟南芥AtKup1基因高含钾量烟草获得[J].中国生物工程杂志,2005,25(12):24-28.GUO Z K,YANG Q,YAO Q H,et al.Transgenic tobacco with Arabidopsis thaliana AtKup1gene has high potassium content in leaves[J].Progress in Biotechnology,2005,25(12):24-28.
[15]闫春娟,宋书宏,王文斌,等.大豆钾营养研究进展[J].大豆科学,2009,28(5):926-930.YAN C J,SONG S H,WANG W B,et al.Advances of potassium nutrition in soybean[J].Soybean Science,2009,28(5):926-930.
[16]GOODSTEIN D M,SHU S,HOWSON R,et al.Phytozome:a comparative platform for green plant genomics[J].Nucleic Acids Research,2011,40:1 178-1 186.
[17]SONNHAMMER E L,EDDY S R,DURBIN R.Pfam:a comprehensive database of protein domain families based on seed alignments[J].Proteins,1997,28(3):405-420.
[18]HALL T A.BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT[J].Nucleic Acids Symposium,1999,41:95-98.
[19]KROGH A,LARSSON B,VON H G,et al.Predicting transmembrane protein topology with a hidden Markov model:application to complete genomes[J].Journal of Molecular Biology,2001,305(3):567-580.
[20]HORTON P,PARK K J,OBAYASHI T,et al.WoLF PSORT:protein localization predictor[J].Nucleic Acids Research,2007,35:585-587.
[21]KUMAR S,NEI M,DUDLEY J,et al.MEGA:a biologistcentric software for evolutionary analysis of DNA and protein sequences[J].Briefings in Bioinformatics,2008,9(4):299-306.
[22]YANG S,ZHANG X,YUE J X,et al.Recent duplications dominate NBS-encoding gene expansion in two woody species[J].Molecular Genetics and Genomics,2008,280(3):187-198.
[23]JIANG H,WU Q,JIN J,et al.Genome-wide identification and expression profiling of ankyrin-repeat gene family in maize[J].Development Genes and Evolution,2013,223(5):303-318.
[24]SAEED A I,BHAGABATI N K,BRAISTED J C,et al.TM4 Microarray Software Suite[J].Methods in Enzymology,2006,411(2):134-193.
[25]JIANG C,WANG Y,LU J,et al.Advances of study on the K-efficiency in different plant genotypes[J].Journal of Huazhong Agricultural,2004,23(4):483-487.
[26]ADAMS K L,WENDEL J F.Polyploidy and genome evolution in plants[J].Current Opinion in Plant Biology,2005,8(2):135-141.
[27]SATO Y,NANATANI K,HAMAMOTO S,et al.Defining membrane spanning domains and crucial membrane-localized acidic amino acid residues for K+transport of a Kup/HAK/KT-type Escherichia coli potassium transporter[J].The Journal of Biochemistry,2014,155(5):315-323.
[28]ELUMALAI R P,NAGPAL P,REED J W.A mutation in the Arabidopsis KT2/KUP2potassium transporter gene affects shoot cell expansion[J].Plant Cell,2002,14(1):119-131.
[29]宋毓峰,张良,董连红,等.植物KUP/HAK/KT家族钾转运体研究进展[J].中国农业科技导报,2013,15(6):92-98.SONG Y F,ZHANG L,DONG L H,et al.Research progress on KUP/HAK/KT potassium transporter family in plant[J].Journal of Agricultural Science and Technology,2013,15(6):92-98.
[30]GIERTH M,SCHROEDER J I.The potassium transporter AtHAK5functions in K+deprivation-induced high-affinity K+uptake and AKT1K+channel contribution to K+uptake kinetics in Arabidopsis roots[J].Plant Physiology,2005,137(3):1 105-1 114.
[31]WANG Y H,GARVIN D F,KOCHIAN L V.Rapid induction of regulatory and transporter genes in response to phosphorus,potassium,and iron deficiencies in tomato roots.Evidence for cross talk and root/rhizosphere-mediated signals[J].Plant Physiology,2002,130(3):1 361-1 370.
[32]SANTA-MARA G E,RUBIO F,DUBCOVSKY J,et al.The HAK1gene of barley is a member of a large gene family and encodes a high-affinity potassium transporter[J].Plant Cell,1997,9(12):2 281-2 289.
[33]BAUELOS M A,GARCIADEBLAS B,CUBERO B,et al.Inventory and functional characterization of the HAK potassium transporters of rice[J].2002,Plant Physiology,130(2):784-795.
[34]KIM E J,KWAK J M,UOZUMI N,et al.AtKUP1:an Arabidopsis gene encoding high-affinity potassium transport activity[J].Plant Cell,1998,10(1):51-62.
[35]MAATHUIS F J M.The role of monovalent cation transporters in plant responses to salinity[J].Journal of Experimental Botany,2006,57(5):1 137-1 147.
[36]TAKAHASHI R,NISHIO T,ICHIZEN N,et al.High-affinity K+transporter PhaHAK5is expressed only in saltsensitive reed plants and shows Na+permeability under NaCl stress[J].Plant Cell Reports,2007,26(9):1 673-1 679.