大豆蔗糖合成酶家族成员的全基因组鉴定及表达分析
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摘要
该研究基于已公布的大豆基因组序列,旨在对大豆蔗糖合成酶(SUS)家族成员进行全基因组鉴定及表达分析,以探讨大豆SUS家族基因的生物学功能,为GmSUS基因的利用及大豆高产育种奠定理论基础。结果表明:(1)在大豆基因组中共鉴定到12个蔗糖合成酶基因(GmSUS1~GmSUS12)。(2)GmSUS蛋白之间序列一致性很高,均具有植物SUS家族蛋白特有的蔗糖合成结构域和糖基转移结构域;除GmSUS5外,其他GmSUS蛋白N端均具有一个保守的丝氨酸(Ser)磷酸化位点。(3)系统进化分析显示,GmSUS蛋白主要聚为3组(SUSⅠ~SUSⅢ),且位于同1组的GmSUS基因大部分具有相似的内含子/外显子分布模式。(4)12个GmSUS基因不均匀地分布在大豆的10条染色体上,片段复制可能导致了GmSUS基因在大豆基因组中的扩增。(5)表达特性分析表明,大豆SUS家族成员具有不同的组织表达模式,GmSUS8在大豆种子中表达量很高,GmSUS1、GmSUS7和GmSUS5在大豆根瘤中表达量很高,GmSUS3、GmSUS11和GmSUS12在所有被检测的组织均具有较高的表达。
In order to understand the biological function of soybean SUS family genes,and provides basic information for breeding of high yield varieties and functional utilization of GmSUSgenes in soybean,in this study,we performed the genome-wide identification and expression analysis of sucrose synthase(SUS)gene family based on published soybean genome sequence.Our results showed that:(1)a total of 12 putative SUS genes(GmSUS1-GmSUS12)were identified in soybean genome.(2)The sequence identity of GmSUS proteins was very high,and all of them had the sucrose synthase domain and glycosyl transferase domain.In addition to GmSUS5,other GmSUS proteins had a conserved serine phosphorylation site at their N terminal.(3)A phylogenetic analysis showed that GmSUS proteins in soybean could be classifiedinto three groups(SUSI-SUSⅢ),and GmSUSgenes in the same group exhibited similar intron/exon pattern.(4)12 GmSUSgenes were unevenly located on 10 chromosomes of soybean,and tandem duplication was the contributor to the expansion of GmSUSgenes in soybean genome.(5)Expression pattern analysis indicated that GmSUSgenes exhibited differential tissue expression patterns.GmSUS8 was highly expressed in seed;GmSUS1,GmSUS7 and GmSUS5 were highly expressed in nodule;GmSUS3,GmSUS11 and GmSUS12 were highly expressed in all examined tissues.
In order to understand the biological function of soybean SUS family genes,and provides basic information for breeding of high yield varieties and functional utilization of GmSUSgenes in soybean,in this study,we performed the genome-wide identification and expression analysis of sucrose synthase(SUS)gene family based on published soybean genome sequence.Our results showed that:(1)a total of 12 putative SUS genes(GmSUS1-GmSUS12)were identified in soybean genome.(2)The sequence identity of GmSUS proteins was very high,and all of them had the sucrose synthase domain and glycosyl transferase domain.In addition to GmSUS5,other GmSUS proteins had a conserved serine phosphorylation site at their N terminal.(3)A phylogenetic analysis showed that GmSUS proteins in soybean could be classifiedinto three groups(SUSI-SUSⅢ),and GmSUSgenes in the same group exhibited similar intron/exon pattern.(4)12 GmSUSgenes were unevenly located on 10 chromosomes of soybean,and tandem duplication was the contributor to the expansion of GmSUSgenes in soybean genome.(5)Expression pattern analysis indicated that GmSUSgenes exhibited differential tissue expression patterns.GmSUS8 was highly expressed in seed;GmSUS1,GmSUS7 and GmSUS5 were highly expressed in nodule;GmSUS3,GmSUS11 and GmSUS12 were highly expressed in all examined tissues.
引文
[1]LUTFIYYA L L,XU N,D'ORDINE R L,et al.Phylogenetic and expression analysis of sucrose phosphate synthase isozymes in plants[J].Journal of Plant Physiology,2007,164(7):923-933.
[2]LI J,BAROJAFERNANDEZ E,BAHAJI A,et al.Enhancing sucrose synthase activity results in increased levels of starch and ADP-glucose in maize(Zea mays L.)seed endosperms[J].Plant and Cell Physiology,2013,54(2):282-294.
[3]卢合全,沈法富,刘凌霄,等.植物蔗糖合成酶功能与分子生物学研究进展[J].中国农学通报,2005,21(7):34-37.LU H Q,SHEN F F,LIU L X,et al.Recent advances in study on plant sucrose synthase[J].Chinese Agricultural Science Bulletin,2005,21(7):34-37.
[4]BAI W Q,XIAO Y H,ZHAO J,et al.Gibberellin overproduction promotes sucrose synthase expression and secondary cell wall deposition in cotton fibers[J].Plos One,2014,9(5):e96537.
[5]YU W P.Complete structures of three rice sucrose synthase isogenes and differential regulation of their expressions[J].Bioscience,Biotechnology,and Biochemistry,1996,60(2):233-239.
[6]GORDON A J,MINCHIN F R,JAMES C L,et al.Sucrose synthase in legume nodules is essential for nitrogen fixation[J].Plant Physiology,1999,120(3):867-878.
[7]XIAO X,TANG C,FANG Y,et al.Structure and expression profile of the sucrose synthase gene family in the rubber tree:indicative of roles in stress response and sucrose utilization in the laticifers[J].Febs Journal,2014,281(1):291-305.
[8]DUNCAN K A,HARDIN S C,HUBER S C.The three maize sucrose synthase isoforms differ in distribution,localization,and phosphorylation[J].Plant&Cell Physiology,2006,47(7):959-971.
[9]BARBER L,SMITH A M,WANG T L,et al.Multiple,distinct isoforms of sucrose synthase in pea[J].Plant Physiology,2001,127(2):655-664.
[10]BAUD S,VAULTIER M N,ROCHAT C.Structure and expression profile of the sucrose synthase multigene family in Arabidopsis[J].Journal of Experimental Botany,2004,55(396):397-409.
[11]HIROSE T,SCOFIELD G N,TERAO T.An expression analysis profile for the entire sucrose synthase gene family in rice[J].Plant Science,2008,174(5):534-543.
[12]ZHANG C,YU M,MA R,et al.Structure,expression profile,and evolution of the sucrose synthase gene family in peach(Prunus persica)[J].Acta Physiologiae Plantarum,2015,37(4):1-15.
[13]ZOU C,LU C,SHANG H,et al.Genome-wide analysis of the Sus gene family in cotton[J].Journal of Integrative Plant Biology,2013,55(7):643-653.
[14]BARRERO-SICILIA C,HERNANDO-AMADO S,GONZALEZMELENDI P,et al.Structure,expression profile and subcellular localisation of four different sucrose synthase genes from barley[J].Planta,2011,234(2):391-403.
[15]ZHANG D,XU B,YANG X,et al.The sucrose synthase gene family in Populus:structure,expression,and evolution[J].Tree Genetics&Genomes,2011,7(3):443-456.
[16]ZHU X,WANG M,LI X,et al.Genome-Wide analysis of the sucrose synthase gene family in grape(Vitis vinifera):structure,evolution,and expression profiles[J].Genes,2017,8(4),111;doi:10.3390/genes8040111.
[17]ISLAM M Z,HU X M,JIN L F,et al.Genome-Wide identification and expression profile analysis of citrus sucrose synthase genes:investigation of possible roles in the regulation of sugar accumulation[J].PloS One,2014,9(11):e113623.
[18]BRILL E,THOURNOUT M V,WHITE R G,et al.A novel isoform of sucrose synthase is targeted to the cell wall during secondary cell wall synthesis in cotton fiber[J].Plant Physiology,2011,157(1):40-54.
[19]黄圣,何鹏,田莉莉,等.棉花蔗糖合成酶基因家族在纤维发育期时空表达模式分析[J].棉花学报,2015,27(4):317-328.HUANG S,HE P,TIAN L L,et al.Expression profiles of the cotton Sus gene family during fiber development[J].Cotton Science,2015,27(4):317-328.
[20]BAROJAFERNANDEZ E,MUNOZ F J,MONTERO M,et al.Enhancing sucrose synthase activity in transgenic potato(Solanum tuberosum L.)tubers results in increased levels of starch,ADPglucose and UDPglucose and total yield[J].Plant&Cell Physiology,2009,50(9):1 651-1 662.
[21]XU S M,BRILL E,LLEWELLYN D J,et al.Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion,reduces seed abortion,and enhances fiber production[J].Molecular Plant,2012,5(2):430-441.
[22]GOODSTEIN D M,SHU S,HOWSON R,et al.Phytozome:a comparative platform for green plant genomics[J].Nucleic Acids Research,2011,40(D1):D1 178-D1 186.
[23]SONNHAMMER E L,EDDY S R,DURBIN R.Pfam:a comprehensive database of protein domain families based on seed alignments[J].Proteins-structure Function&Bioinformatics,1997,28(3):405-420.
[24]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.
[25]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.
[26]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.
[27]SAEED A I,BHAGABATI N K,BRAISTED J C,et al.TM4 microarray software suite[J].Methods in Enzymology,2006,411(2):134-193.
[28]HUBER S C,HUBER J L,LIAO P C,et al.Phosphorylation of serine-15of maize leaf sucrose synthase.Occurrence in vivo and possible regulatory significance[J].Plant Physiology,1996,112(2):793-802.
[29]HARDIN S C,HUBER S C.Proteasome activity and the post-translational control of sucrose synthase stability in maize leaves[J].Plant Physiology&Biochemistry,2004,42(3):197-208.
[30]ZHANG J,JIE A,CHEN Y,et al.Haplotype analysis of sucrose synthase gene family in three Saccharumspecies[J].BMCGenomics,2013,14:314.
[31]CHEN A,HE S,LI F,et al.Analyses of the sucrose synthase gene family in cotton:structure,phylogeny and expression patterns[J].BMC Plant Biology,2012,12:85.
[32]KIM K D,El B M,Abernathy B,et al.A comparative epigenomic analysis of polyploidy-derived genes in soybean and common bean[J].Plant Physiology,2015,168(4):1433-1447.
[33]BLANC G,BARAKAT A,GUYOT R,et al.Extensive duplication and reshuffling in the Arabidopsis genome[J].Plant Cell,2000,12(7):1 093-1 101.
[34]WANG X,SHI X,HAO B,et al.Duplication and DNA segmental loss in the rice genome:implications for diploidization[J].New Phytologist,2005,165(3):937-946.
[35]SCHMUTZ J,CANNON S B,SCHLUETER J,et al.Genome sequence of the palaeopolyploid soybean[J].Nature,2010,463(7278):178-183.
[36]HAAGENSON D M,KLOTZ K L,MCGRATH J M.Sugarbeet sucrose synthase genes differ in organ-specific and developmental expression[J].Journal of Plant Physiology,2006,163(1):102-106.
[37]TANG H,BOWERS J E,WANG X,et al.Synteny and collinearity in plant genomes[J].Science,2008,320(5 875):486-488.
[38]LI F,HAO C,YAN L,et al.Gene structure,phylogeny and expression profile of the sucrose synthase gene family in cacao(Theobroma cacao L.)[J].Journal of Genetics,2015,94(3):461-472.
[39]HU L,LIU S.Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers[J].Genetics&Molecular Biology,2011,34(4):624-633.
[40]LECHARNY A,BOUDET N,GY I,et al.Introns in,introns out in plant gene families:agenomic approach of the dynamics of gene structure[J].Journal of Structural&Functional Genomics,2003,3(1-4):111-116.
[41]GHASSEN A,YORDAN M,JEAN-MARIE J,et al.Characterization and expression profile analysis of a sucrose synthase gene from common bean(Phaseolus vulgaris L.)during seed development[J].Molecular Biology Reports,2012,39(2):1 133-1 143.
[42]YONGLING R,DANNYJ L,LIU Q,et al.Expression of sucrose synthase in the developing endosperm is essential for early seed development in cotton[J].Functional Plant Biology,2008,35(5):382-393.
[43]CRAIG J,BARRATT P,TATGE H,et al.Mutations at the rug4locus alter the carbon and nitrogen metabolism of pea plants through an effect on sucrose synthase[J].Plant Journal,1999,17(4):353-362.
[44]PHANG T H,SHAO G,LAM H M.Salt tolerance mechanisms in soybean[J].Journal of Integrative Plant Biology,2008,50(10):1 196-1 212.
[45]MANAVALAN L P,GUTTIKONDA S K,PHAN TRAN L S,et al.Physiological and molecular approaches to improve drought resistance in soybean[J].Plant&Cell Physiology,2009,50(7):1 260-1 276.
[46]王萍,宋海星,马淑英,等.花期低温对大豆荚和籽粒形成的影响[J].中国油料作物学报,2000,22(2):31-33.WANG P,SONG H X,MA S Y,et al.Effects of low temperature at blooming on podding and seed filling in soybean varieties[J].Chinese Journal of Oil Crop Sciences,2000,22(2):31-33.
[2]LI J,BAROJAFERNANDEZ E,BAHAJI A,et al.Enhancing sucrose synthase activity results in increased levels of starch and ADP-glucose in maize(Zea mays L.)seed endosperms[J].Plant and Cell Physiology,2013,54(2):282-294.
[3]卢合全,沈法富,刘凌霄,等.植物蔗糖合成酶功能与分子生物学研究进展[J].中国农学通报,2005,21(7):34-37.LU H Q,SHEN F F,LIU L X,et al.Recent advances in study on plant sucrose synthase[J].Chinese Agricultural Science Bulletin,2005,21(7):34-37.
[4]BAI W Q,XIAO Y H,ZHAO J,et al.Gibberellin overproduction promotes sucrose synthase expression and secondary cell wall deposition in cotton fibers[J].Plos One,2014,9(5):e96537.
[5]YU W P.Complete structures of three rice sucrose synthase isogenes and differential regulation of their expressions[J].Bioscience,Biotechnology,and Biochemistry,1996,60(2):233-239.
[6]GORDON A J,MINCHIN F R,JAMES C L,et al.Sucrose synthase in legume nodules is essential for nitrogen fixation[J].Plant Physiology,1999,120(3):867-878.
[7]XIAO X,TANG C,FANG Y,et al.Structure and expression profile of the sucrose synthase gene family in the rubber tree:indicative of roles in stress response and sucrose utilization in the laticifers[J].Febs Journal,2014,281(1):291-305.
[8]DUNCAN K A,HARDIN S C,HUBER S C.The three maize sucrose synthase isoforms differ in distribution,localization,and phosphorylation[J].Plant&Cell Physiology,2006,47(7):959-971.
[9]BARBER L,SMITH A M,WANG T L,et al.Multiple,distinct isoforms of sucrose synthase in pea[J].Plant Physiology,2001,127(2):655-664.
[10]BAUD S,VAULTIER M N,ROCHAT C.Structure and expression profile of the sucrose synthase multigene family in Arabidopsis[J].Journal of Experimental Botany,2004,55(396):397-409.
[11]HIROSE T,SCOFIELD G N,TERAO T.An expression analysis profile for the entire sucrose synthase gene family in rice[J].Plant Science,2008,174(5):534-543.
[12]ZHANG C,YU M,MA R,et al.Structure,expression profile,and evolution of the sucrose synthase gene family in peach(Prunus persica)[J].Acta Physiologiae Plantarum,2015,37(4):1-15.
[13]ZOU C,LU C,SHANG H,et al.Genome-wide analysis of the Sus gene family in cotton[J].Journal of Integrative Plant Biology,2013,55(7):643-653.
[14]BARRERO-SICILIA C,HERNANDO-AMADO S,GONZALEZMELENDI P,et al.Structure,expression profile and subcellular localisation of four different sucrose synthase genes from barley[J].Planta,2011,234(2):391-403.
[15]ZHANG D,XU B,YANG X,et al.The sucrose synthase gene family in Populus:structure,expression,and evolution[J].Tree Genetics&Genomes,2011,7(3):443-456.
[16]ZHU X,WANG M,LI X,et al.Genome-Wide analysis of the sucrose synthase gene family in grape(Vitis vinifera):structure,evolution,and expression profiles[J].Genes,2017,8(4),111;doi:10.3390/genes8040111.
[17]ISLAM M Z,HU X M,JIN L F,et al.Genome-Wide identification and expression profile analysis of citrus sucrose synthase genes:investigation of possible roles in the regulation of sugar accumulation[J].PloS One,2014,9(11):e113623.
[18]BRILL E,THOURNOUT M V,WHITE R G,et al.A novel isoform of sucrose synthase is targeted to the cell wall during secondary cell wall synthesis in cotton fiber[J].Plant Physiology,2011,157(1):40-54.
[19]黄圣,何鹏,田莉莉,等.棉花蔗糖合成酶基因家族在纤维发育期时空表达模式分析[J].棉花学报,2015,27(4):317-328.HUANG S,HE P,TIAN L L,et al.Expression profiles of the cotton Sus gene family during fiber development[J].Cotton Science,2015,27(4):317-328.
[20]BAROJAFERNANDEZ E,MUNOZ F J,MONTERO M,et al.Enhancing sucrose synthase activity in transgenic potato(Solanum tuberosum L.)tubers results in increased levels of starch,ADPglucose and UDPglucose and total yield[J].Plant&Cell Physiology,2009,50(9):1 651-1 662.
[21]XU S M,BRILL E,LLEWELLYN D J,et al.Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion,reduces seed abortion,and enhances fiber production[J].Molecular Plant,2012,5(2):430-441.
[22]GOODSTEIN D M,SHU S,HOWSON R,et al.Phytozome:a comparative platform for green plant genomics[J].Nucleic Acids Research,2011,40(D1):D1 178-D1 186.
[23]SONNHAMMER E L,EDDY S R,DURBIN R.Pfam:a comprehensive database of protein domain families based on seed alignments[J].Proteins-structure Function&Bioinformatics,1997,28(3):405-420.
[24]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.
[25]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.
[26]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.
[27]SAEED A I,BHAGABATI N K,BRAISTED J C,et al.TM4 microarray software suite[J].Methods in Enzymology,2006,411(2):134-193.
[28]HUBER S C,HUBER J L,LIAO P C,et al.Phosphorylation of serine-15of maize leaf sucrose synthase.Occurrence in vivo and possible regulatory significance[J].Plant Physiology,1996,112(2):793-802.
[29]HARDIN S C,HUBER S C.Proteasome activity and the post-translational control of sucrose synthase stability in maize leaves[J].Plant Physiology&Biochemistry,2004,42(3):197-208.
[30]ZHANG J,JIE A,CHEN Y,et al.Haplotype analysis of sucrose synthase gene family in three Saccharumspecies[J].BMCGenomics,2013,14:314.
[31]CHEN A,HE S,LI F,et al.Analyses of the sucrose synthase gene family in cotton:structure,phylogeny and expression patterns[J].BMC Plant Biology,2012,12:85.
[32]KIM K D,El B M,Abernathy B,et al.A comparative epigenomic analysis of polyploidy-derived genes in soybean and common bean[J].Plant Physiology,2015,168(4):1433-1447.
[33]BLANC G,BARAKAT A,GUYOT R,et al.Extensive duplication and reshuffling in the Arabidopsis genome[J].Plant Cell,2000,12(7):1 093-1 101.
[34]WANG X,SHI X,HAO B,et al.Duplication and DNA segmental loss in the rice genome:implications for diploidization[J].New Phytologist,2005,165(3):937-946.
[35]SCHMUTZ J,CANNON S B,SCHLUETER J,et al.Genome sequence of the palaeopolyploid soybean[J].Nature,2010,463(7278):178-183.
[36]HAAGENSON D M,KLOTZ K L,MCGRATH J M.Sugarbeet sucrose synthase genes differ in organ-specific and developmental expression[J].Journal of Plant Physiology,2006,163(1):102-106.
[37]TANG H,BOWERS J E,WANG X,et al.Synteny and collinearity in plant genomes[J].Science,2008,320(5 875):486-488.
[38]LI F,HAO C,YAN L,et al.Gene structure,phylogeny and expression profile of the sucrose synthase gene family in cacao(Theobroma cacao L.)[J].Journal of Genetics,2015,94(3):461-472.
[39]HU L,LIU S.Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers[J].Genetics&Molecular Biology,2011,34(4):624-633.
[40]LECHARNY A,BOUDET N,GY I,et al.Introns in,introns out in plant gene families:agenomic approach of the dynamics of gene structure[J].Journal of Structural&Functional Genomics,2003,3(1-4):111-116.
[41]GHASSEN A,YORDAN M,JEAN-MARIE J,et al.Characterization and expression profile analysis of a sucrose synthase gene from common bean(Phaseolus vulgaris L.)during seed development[J].Molecular Biology Reports,2012,39(2):1 133-1 143.
[42]YONGLING R,DANNYJ L,LIU Q,et al.Expression of sucrose synthase in the developing endosperm is essential for early seed development in cotton[J].Functional Plant Biology,2008,35(5):382-393.
[43]CRAIG J,BARRATT P,TATGE H,et al.Mutations at the rug4locus alter the carbon and nitrogen metabolism of pea plants through an effect on sucrose synthase[J].Plant Journal,1999,17(4):353-362.
[44]PHANG T H,SHAO G,LAM H M.Salt tolerance mechanisms in soybean[J].Journal of Integrative Plant Biology,2008,50(10):1 196-1 212.
[45]MANAVALAN L P,GUTTIKONDA S K,PHAN TRAN L S,et al.Physiological and molecular approaches to improve drought resistance in soybean[J].Plant&Cell Physiology,2009,50(7):1 260-1 276.
[46]王萍,宋海星,马淑英,等.花期低温对大豆荚和籽粒形成的影响[J].中国油料作物学报,2000,22(2):31-33.WANG P,SONG H X,MA S Y,et al.Effects of low temperature at blooming on podding and seed filling in soybean varieties[J].Chinese Journal of Oil Crop Sciences,2000,22(2):31-33.