铁皮石斛Csl基因家族生物信息学及表达分析
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摘要
通过分析铁皮石斛类纤维素合成酶(cellulase synthase-like, Csl)的氨基酸序列特征,挖掘与多糖合成相关的Csl基因,从而为参与多糖代谢的铁皮石斛Csl蛋白的后续研究提供有力参考。本研究在生物信息学层面,对铁皮石斛21条完整Csl蛋白序列的理化性质、导肽、信号肽、疏水性/亲水性、跨膜结构域、蛋白质高级结构及功能域等进行预测分析,并与拟南芥的Csl蛋白进行了同源比对并构建系统进化树。结果表明,CslD2a/b/c、CslD4、CslG3b为酸性蛋白,其余为碱性蛋白;Leu、Ser、Ala、Phe、Val和Ille等氨基酸是铁皮石斛Csl蛋白的主要氨基酸;铁皮石斛Csl蛋白具有明显的疏水区和亲水区,都存在跨膜结构。蛋白质二级结构的主要元件是α-螺旋、无规则卷曲和延伸链。与拟南芥的进化分析显示,铁皮石斛Csl蛋白基因被分为3大分支,CslA和CslC归为一支,CslB/E/G/H归为一支,CslD归为一支。本研究系统分析了铁皮石斛Csl蛋白的序列特征,可为今后深入研究该蛋白在铁皮石斛多糖代谢上的功能提供参考。
The Csl genes related to polysaccharide synthesis were mined by analyzing the amino acid sequence characteristics of cellulase synthase like(Csl) of Dendrobium candidum, so as to provide a powerful reference for the followup study of Dendrobium candidum Csl proteins involved in polysaccharide metabolism. In this study, bioinformatics methods were used to perform the prediction of physicochemical character, leader peptide, signal peptide, hydrophobicity/hydrophilicity, transmembrane domain, protein advanced structure and functional domains of 21 Dc Csl protein sequences. Homology analysis and phylogenetic trees of Csl proteins between D. catenatum and Arabidopsis thaliana were carried out. The result showed that Csl D2 a/b/c, Csl D4 and Csl G3 b were acidic proteins and the rest were alkaline proteins. Leu, Ser, Ala, Phe, Val and Ille were the main amino acids of Dc Csl proteins, which displayapparent hydrophobic region and hydrophilicity region with transmembrane structures. The main secondary structure of Dc Csl proteins were the α-helix, random coil and extension chain. Phylogenetic analysis showed that the Dc Csl family of D. catenatum was divided into three major branches: the first branch was Csl A and Csl C, the second was Csl B/E/G/H and the third was Csl D. In a word, This study systematically analyzed the sequence characteristics of Dc Csl proteins, which could provide a valuable reference for further study on the function of Dc Csl family polysaccharide metabolism in D. catenatum.
The Csl genes related to polysaccharide synthesis were mined by analyzing the amino acid sequence characteristics of cellulase synthase like(Csl) of Dendrobium candidum, so as to provide a powerful reference for the followup study of Dendrobium candidum Csl proteins involved in polysaccharide metabolism. In this study, bioinformatics methods were used to perform the prediction of physicochemical character, leader peptide, signal peptide, hydrophobicity/hydrophilicity, transmembrane domain, protein advanced structure and functional domains of 21 Dc Csl protein sequences. Homology analysis and phylogenetic trees of Csl proteins between D. catenatum and Arabidopsis thaliana were carried out. The result showed that Csl D2 a/b/c, Csl D4 and Csl G3 b were acidic proteins and the rest were alkaline proteins. Leu, Ser, Ala, Phe, Val and Ille were the main amino acids of Dc Csl proteins, which displayapparent hydrophobic region and hydrophilicity region with transmembrane structures. The main secondary structure of Dc Csl proteins were the α-helix, random coil and extension chain. Phylogenetic analysis showed that the Dc Csl family of D. catenatum was divided into three major branches: the first branch was Csl A and Csl C, the second was Csl B/E/G/H and the third was Csl D. In a word, This study systematically analyzed the sequence characteristics of Dc Csl proteins, which could provide a valuable reference for further study on the function of Dc Csl family polysaccharide metabolism in D. catenatum.
引文
B ernal A.J.,Jensen J.K.,Harholt J.,S?rensen S.,Moller I.Blaukopf C.,Johansen B.,de Lotto R.,Pauly M.,Scheller H.V.,and Willats W.G.,2007,Disruption of At CSLD5 results in reduced growth,reduced xylan and homogalacturonan synthase activity and altered xylan occurrence in Arabidopsis,Plant J.,52(5):791-802
Bernal A.J.,Yoo C.M.,Mutwil M.,Jensen J.K.,Hou G.,Blaukopf C.S?rensen I.,Blancaflor E.B.,Scheller H.V.,and Willats W.G.2008,Functional analysis of the cellulose synthase-likegenes CSLD1,CSLD2,and CSLD4 in tip-growing Arabidopsis cells,Plant Physiol.,148(3):1238-1253
Burton R.A.,Collins H.M.,Kibble N.A.,Smith J.A.,Shirley N.J.,Jobling S.A.,Henderson M.,Sinqh R.R.,Wison S.M.,Bird A.R.,Topping D.L.,Bacic A.,and Fincher G.B.,2011,Overexpression of specific HvCslF cellulose synthase-like genes in transgenic barley increases the levels of cell wall(1,3;1,4)-β-D-glucans and alters their fine structure,Plant Biotechnol.J.,9(2):117-135
Burton R.A.,Wilson S.M.,Hrmova M.,Harvey A.J.,Shirley N.J.,Medhurst A.,Stone B.A.,Newbigin E.J.,Bacic A.,and Fincher G.B.,2006,Cellulose synthase-like CslF genes mediate the synthesis of cell wall(1,3;1,4)-β-d-glucans,Science,311(5769):1940-1942
Dhugga K.S.,Barreiro R.,Whitten B.,Stecca K.,Hazebroek J.,Randhawa G.S.,Dolan M.,Kinney A.J.,Tomes D.,Nichols S.,and Anderson P.,2004,Guar seed beta-mannan synthase is a member of the cellulose synthase super gene family,Science,303(5656):363-366
Doblin M.S.,Pettolino F.A.,Wilson S.M.,Campbell R.,Burton R.A.,Fincher G.B.,Newbigin E.D.,and Bacic A.,2009,Abarley cellulose synthase-like CSLH gene mediates(1,3;1,4)-beta-D-glucan synthesis in transgenic Arabidopsis,Proc.Natl.Acad.Sci.USA,106(14):5996-6001
Dubos C.,Stracke R.,Grotewold E.,Weisshaar B.,Martin C.,and Lepiniec L.,2010,MYB transcription factors in Arabidopsis,Trends Plant Sci.,15(10):573-581
Fincher G.B.,2009,Revolutionary times in our understanding of cell wall biosynthesis and remodeling in the grasses,Plant Physiol.,149(1):27-37
Goubet F.,Barton C.J.,Mortimer J.C.,Yu X.L.,Zhang Z.N.,Miles G.P.,Richens J.,Liepman A.H.,Seffen K.,and Dupree P.,2009,Cell wall glucomannan in Arabidopsis is synthesised by CSLA glycosyltransferases,and influences the progression of embryogenesis,Plant J.,60(3):527-538
Hazen S.P.,Scott-Craig J.S.,and Walton J.D.,2002,Cellulose synthase-like genes of rice,Plant Physiol.,128(2):336-340
He C.,Zhang J.X.,Liu X.C.,Zeng S.J.,Wu K.L.,Yu Z.M.,Wang X.J.,Teixeira da Silva J.A.,Lin Z.J.,and Duan J.,2015,Identification of genes involved in biosynthesis of mannan polysaccharides in Dendrobium officinale by RNA-seq analysis,Plant Mol.Biol.,88(3):219-231
He C.M.,W u K.L.,Zhang J.X.,Liu X.C.,Zeng S.J.,Yu Z.M.,Zhang X.H.,Teixeira da Silva J.A.,Deng R.F.,Tan J.W.,Luo J.P.,and Duan J.,2017,Cytochemical localization of polysaccharides in Dendrobium officinale and the involvement of DoCSLA6 in the synthesis of mannan polysaccharides,Front.Plant Sci.,8(1599):173
Li M.,Xiong G.Y.,Li R.,Cui J.J.,Tang D.,Zhang B.C.,Pauly M.,Cheng Z.K.,and Zhou Y.H.,2009,Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth,Plant J.,60(6):1055-1069
Li Y.H.,Qian Q.,Zhou Y.H.,Yan M.X.,Sun L.,Zhang M.,Fu ZM.,Wang Y.H.,Han B.,Pang X.M.,Chen M.S.,and Li J.Y.2003,BRITTLE CULM1,which encodes a COBRA-like protein,affects the mechanical properties of rice plants,Plan Cell,15(9):2020-2031
Liepman A.H.,Wilkerson C.G.,and Keegstra K.,2005,Expression of cellulose synthase-like(Csl)genes in insect cells reveals that CslA family members encode mannan synthases,Proc Natl.Acad.Sci.USA,102(6):2221-2226
Meng Y.J.,Yu D.L.,Xue J.,Lu J.J.,Feng S.G.,Shen C.J.,and Wang H.Z.,2016,A transcriptome-wide,organ-specific regulatory map of Dendrobium officinale,an important traditional Chinese orchid herb,Sci.Rep.,6:18864
Nobles D.R.,and Brown R.M.,2004,The pivotal role of cyanobacteria in the evolution of cellulose synthases and cellulose synthase-like proteins,Cellulose,11(3-4):437-448
Richmond T.A.,and Somerville C.R.,2000,The cellulose synthase superfamily,Plant Physiol.,124(2):495-498
Suzuki S.,Li L.,Sun Y.H.,and Chiang V.L.,2006,The cellulose synthase gene superfamily and biochemical functions of xylemspecific cellulose synthaselike genes in Populus trichocarpa Plant Physiol.,142(3):1233-1245
Verhertbruggen Y.,Yin L.,Oikawa A.,and Scheller H.V.,2011Mannan synthase activity in the CSLD family,Plant Signal Behav.,6(10):1620-1623
Williamson R.E.,Burn J.E.,and Hocart C.H.,2002,Towards the mechanism of cellulose synthesis,TrendsPlant Sci.,7(10):461-467
Yin L.,Verhertbruggen Y.,Oikawa A.,Manisseri C.,Knierim B.,Prak L.,Jensen J.K.,Knox J.P.,Auer M.,Willats W.G.,and Scheller H.V.,2011,The cooporative activities of CSLD2,CSLD3,and CSLD5 are required for normal Arabidopsis development,Mol.Plant,4(6):1024-1037
Yin Y.B.,Huang J.L.,and Xu Y.,2009,The cellulose synthase superfamily in fully sequenced plants and algae,BMC Plant Biol.,9(1):99
Zhang G.Q.,Xu Q.,Bian C.,Tsai W.C.,Yeh C.M.,Liu K.W.,Yoshida K.,Zhang L.S.,Chang S.B.,Chen F.,Shi Y.,Su Y.Y.,Zhang Y.Q.,Chen L.J.,Yin Y.Y.,Lin M.,Huang H.X.,Deng H.,Wang Z.W.,Zhu S.L.,Zhao X.,Deng C.Niu S.C.,Huang J.,Wang M.Liu G.H.,Yang H.J.,Xiao X.J.,Hsiao Y.Y.,Wu W.L.,Chen Y.Y.,Mitsuda N.,Ohme-Takagi M.,Luo Y.B.,Peer Y.V.,and Liu Z.J.,2016,The Dendrobium catenatum Lindl.genome sequence provides insights into polysaccharide synthase,floral development and adaptive evolution,Sci.Rep.,6(19029):19029
Zhang J.X.,He C.M.,Wu K.L.,Teixeira da Silva J.A.,Zeng S.J.,Zhang X.H.,Yu Z.M.,Xia H.Q.,and Duan J.,2016,Transcriptome analysis of Dendrobium officinale and its application to the identification of genes associated with polysaccharide synthesis,Front.Plant Sci.,7:5
Zhang J.Y.,Guo Y.,Si J.P.,Sun X.B.,Sun G.B.,and Liu J.J.,2017,A polysaccharide of Dendrobium officinale ameliorates H2O2-Induced apoptosis in H9c2 cardiomyocytes via PI3K/AKTand MAPK Pathways,Int.J.Biol.Macromol.,104:1-10
Bernal A.J.,Yoo C.M.,Mutwil M.,Jensen J.K.,Hou G.,Blaukopf C.S?rensen I.,Blancaflor E.B.,Scheller H.V.,and Willats W.G.2008,Functional analysis of the cellulose synthase-likegenes CSLD1,CSLD2,and CSLD4 in tip-growing Arabidopsis cells,Plant Physiol.,148(3):1238-1253
Burton R.A.,Collins H.M.,Kibble N.A.,Smith J.A.,Shirley N.J.,Jobling S.A.,Henderson M.,Sinqh R.R.,Wison S.M.,Bird A.R.,Topping D.L.,Bacic A.,and Fincher G.B.,2011,Overexpression of specific HvCslF cellulose synthase-like genes in transgenic barley increases the levels of cell wall(1,3;1,4)-β-D-glucans and alters their fine structure,Plant Biotechnol.J.,9(2):117-135
Burton R.A.,Wilson S.M.,Hrmova M.,Harvey A.J.,Shirley N.J.,Medhurst A.,Stone B.A.,Newbigin E.J.,Bacic A.,and Fincher G.B.,2006,Cellulose synthase-like CslF genes mediate the synthesis of cell wall(1,3;1,4)-β-d-glucans,Science,311(5769):1940-1942
Dhugga K.S.,Barreiro R.,Whitten B.,Stecca K.,Hazebroek J.,Randhawa G.S.,Dolan M.,Kinney A.J.,Tomes D.,Nichols S.,and Anderson P.,2004,Guar seed beta-mannan synthase is a member of the cellulose synthase super gene family,Science,303(5656):363-366
Doblin M.S.,Pettolino F.A.,Wilson S.M.,Campbell R.,Burton R.A.,Fincher G.B.,Newbigin E.D.,and Bacic A.,2009,Abarley cellulose synthase-like CSLH gene mediates(1,3;1,4)-beta-D-glucan synthesis in transgenic Arabidopsis,Proc.Natl.Acad.Sci.USA,106(14):5996-6001
Dubos C.,Stracke R.,Grotewold E.,Weisshaar B.,Martin C.,and Lepiniec L.,2010,MYB transcription factors in Arabidopsis,Trends Plant Sci.,15(10):573-581
Fincher G.B.,2009,Revolutionary times in our understanding of cell wall biosynthesis and remodeling in the grasses,Plant Physiol.,149(1):27-37
Goubet F.,Barton C.J.,Mortimer J.C.,Yu X.L.,Zhang Z.N.,Miles G.P.,Richens J.,Liepman A.H.,Seffen K.,and Dupree P.,2009,Cell wall glucomannan in Arabidopsis is synthesised by CSLA glycosyltransferases,and influences the progression of embryogenesis,Plant J.,60(3):527-538
Hazen S.P.,Scott-Craig J.S.,and Walton J.D.,2002,Cellulose synthase-like genes of rice,Plant Physiol.,128(2):336-340
He C.,Zhang J.X.,Liu X.C.,Zeng S.J.,Wu K.L.,Yu Z.M.,Wang X.J.,Teixeira da Silva J.A.,Lin Z.J.,and Duan J.,2015,Identification of genes involved in biosynthesis of mannan polysaccharides in Dendrobium officinale by RNA-seq analysis,Plant Mol.Biol.,88(3):219-231
He C.M.,W u K.L.,Zhang J.X.,Liu X.C.,Zeng S.J.,Yu Z.M.,Zhang X.H.,Teixeira da Silva J.A.,Deng R.F.,Tan J.W.,Luo J.P.,and Duan J.,2017,Cytochemical localization of polysaccharides in Dendrobium officinale and the involvement of DoCSLA6 in the synthesis of mannan polysaccharides,Front.Plant Sci.,8(1599):173
Li M.,Xiong G.Y.,Li R.,Cui J.J.,Tang D.,Zhang B.C.,Pauly M.,Cheng Z.K.,and Zhou Y.H.,2009,Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth,Plant J.,60(6):1055-1069
Li Y.H.,Qian Q.,Zhou Y.H.,Yan M.X.,Sun L.,Zhang M.,Fu ZM.,Wang Y.H.,Han B.,Pang X.M.,Chen M.S.,and Li J.Y.2003,BRITTLE CULM1,which encodes a COBRA-like protein,affects the mechanical properties of rice plants,Plan Cell,15(9):2020-2031
Liepman A.H.,Wilkerson C.G.,and Keegstra K.,2005,Expression of cellulose synthase-like(Csl)genes in insect cells reveals that CslA family members encode mannan synthases,Proc Natl.Acad.Sci.USA,102(6):2221-2226
Meng Y.J.,Yu D.L.,Xue J.,Lu J.J.,Feng S.G.,Shen C.J.,and Wang H.Z.,2016,A transcriptome-wide,organ-specific regulatory map of Dendrobium officinale,an important traditional Chinese orchid herb,Sci.Rep.,6:18864
Nobles D.R.,and Brown R.M.,2004,The pivotal role of cyanobacteria in the evolution of cellulose synthases and cellulose synthase-like proteins,Cellulose,11(3-4):437-448
Richmond T.A.,and Somerville C.R.,2000,The cellulose synthase superfamily,Plant Physiol.,124(2):495-498
Suzuki S.,Li L.,Sun Y.H.,and Chiang V.L.,2006,The cellulose synthase gene superfamily and biochemical functions of xylemspecific cellulose synthaselike genes in Populus trichocarpa Plant Physiol.,142(3):1233-1245
Verhertbruggen Y.,Yin L.,Oikawa A.,and Scheller H.V.,2011Mannan synthase activity in the CSLD family,Plant Signal Behav.,6(10):1620-1623
Williamson R.E.,Burn J.E.,and Hocart C.H.,2002,Towards the mechanism of cellulose synthesis,TrendsPlant Sci.,7(10):461-467
Yin L.,Verhertbruggen Y.,Oikawa A.,Manisseri C.,Knierim B.,Prak L.,Jensen J.K.,Knox J.P.,Auer M.,Willats W.G.,and Scheller H.V.,2011,The cooporative activities of CSLD2,CSLD3,and CSLD5 are required for normal Arabidopsis development,Mol.Plant,4(6):1024-1037
Yin Y.B.,Huang J.L.,and Xu Y.,2009,The cellulose synthase superfamily in fully sequenced plants and algae,BMC Plant Biol.,9(1):99
Zhang G.Q.,Xu Q.,Bian C.,Tsai W.C.,Yeh C.M.,Liu K.W.,Yoshida K.,Zhang L.S.,Chang S.B.,Chen F.,Shi Y.,Su Y.Y.,Zhang Y.Q.,Chen L.J.,Yin Y.Y.,Lin M.,Huang H.X.,Deng H.,Wang Z.W.,Zhu S.L.,Zhao X.,Deng C.Niu S.C.,Huang J.,Wang M.Liu G.H.,Yang H.J.,Xiao X.J.,Hsiao Y.Y.,Wu W.L.,Chen Y.Y.,Mitsuda N.,Ohme-Takagi M.,Luo Y.B.,Peer Y.V.,and Liu Z.J.,2016,The Dendrobium catenatum Lindl.genome sequence provides insights into polysaccharide synthase,floral development and adaptive evolution,Sci.Rep.,6(19029):19029
Zhang J.X.,He C.M.,Wu K.L.,Teixeira da Silva J.A.,Zeng S.J.,Zhang X.H.,Yu Z.M.,Xia H.Q.,and Duan J.,2016,Transcriptome analysis of Dendrobium officinale and its application to the identification of genes associated with polysaccharide synthesis,Front.Plant Sci.,7:5
Zhang J.Y.,Guo Y.,Si J.P.,Sun X.B.,Sun G.B.,and Liu J.J.,2017,A polysaccharide of Dendrobium officinale ameliorates H2O2-Induced apoptosis in H9c2 cardiomyocytes via PI3K/AKTand MAPK Pathways,Int.J.Biol.Macromol.,104:1-10