被子植物中核糖体失活蛋白基因家族分子进化研究
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摘要
利用34种具有全基因组数据的代表植物,通过生物信息分析方法,深入挖掘和分析不同植物类群基因组中RIPs基因家族的成员构成,推测其可能的扩增方式和功能分化,并探讨了该基因家族在植物中的总体进化趋势.采用BLAST和HMMsearch两种检索方法共鉴定出79个RIPs基因家族成员;通过序列比对和系统进化树的构建,发现RIPs在单双子叶中存在双起源,RIPs在两者分化之前就已存在.它们可能为适应复杂的环境而出现在早期陆生植物中,随后在长期进化过程中不断发生谱系的扩张和拷贝丢失,最后通过功能分化在不同植物中保留下来,其在被子植物进化的过程中有物种特异性的重复.
The genome-wide identification of the ribosome-inactivating protein family genes in 34 representative plant species with the genome data were performed.The different taxa was analyzed,the possible way of amplifications and the functional differentiation wereestimated,and the general evolution trend of the RIP gene family in plants was discussed.A total of 79 RIP gene family members were identified by BLAST and HMMSearch method.Through the sequence alignment and construction of the phylogenetic tree,it was found that RIPs had dual origins in the monocotyledons,and RIPs existed before the differentiation of the dicotyledons and monocotyledons.It is obtained that they maybe appeared in the early terrestrial plants in order to adapt the complex environment,then expansion of the spectrum and loss of the copies are happening during the long term evolution,finally survived in different plants through the functional differentiation.
The genome-wide identification of the ribosome-inactivating protein family genes in 34 representative plant species with the genome data were performed.The different taxa was analyzed,the possible way of amplifications and the functional differentiation wereestimated,and the general evolution trend of the RIP gene family in plants was discussed.A total of 79 RIP gene family members were identified by BLAST and HMMSearch method.Through the sequence alignment and construction of the phylogenetic tree,it was found that RIPs had dual origins in the monocotyledons,and RIPs existed before the differentiation of the dicotyledons and monocotyledons.It is obtained that they maybe appeared in the early terrestrial plants in order to adapt the complex environment,then expansion of the spectrum and loss of the copies are happening during the long term evolution,finally survived in different plants through the functional differentiation.
引文
[1]GIRBES T,FERRERAS J M,ARIAS F J,et al.Description,distribution,activity and phylogenetic relationship of ribosome-inactivating proteins in plants,fungi and bacteria[J].Mini Reviews in Medicinal Chemistry,2004,4(5):461-476.
[2]DI MARO A,CITORES L,RUSSO R,et al.Sequence comparison and phylogenetic analysis by the Maximum Likelihood method of ribosome-inactivating proteins from angiosperms[J].Plant Molecular Biology,2014,85(6):575-588.
[3]LOSS-MORAIS G,TURCHETTO-ZOLET A C,ETGES M,et al.Analysis of castor bean ribosome-inactivating proteins and their gene expression during seed development[J].Genetics and Molecular Biology,2013,36(1):74-86.
[4]STIRPE F,BARBIERI L,BATTELLI M G,et al.Ribosome-inactivating proteins from plants:Present status and future prospects[J].Nature Biotechnology,1992,10(4):405-412.
[5]STIRPE F.Ribosome-inactivating proteins[J].Toxicon,2004,44(4):371-383.
[6]LAMB F I,ROBERTS L M,LORD J M.Nucleotide sequence of cloned cDNA coding for preproricin[J].European Journal of Biochemistry,1985,148(2):265-270.
[7]FRIGERIO L,ROBERTS L M.The enemy within:Ricin and plant cells[J].Journal of Experimental Botany,1998,49(326):1473-1480.
[8]BARBIERI L,BATTELLI M G,STIRPE F.Ribosome-inactivating proteins from plants[J].Biochimica et Biophysica Acta Reviews on Biomembranes,1993,1154(3):237-282.
[9]NIELSEN K,BOSTON R S.Ribosome-inactivating proteins:A plant perspective[J].Annu Rev Plant Physiol Plant Mol Biol,2001,52(52):785-816.
[10]林娟,颜钫,唐琳,等,麻疯树核糖体失活蛋白的分离纯化和作用机制研究[J].高技术通讯,2002,12(11):36-40.LIN Juan,YAN Fang,TANG Lin,et al.Isolation,purification and mechaism of ribosome inactivating protein from jatropha curcas[J].High Technology Letters,2002,12(11):36-40.
[11]董槁,刘望夷.核糖体失活蛋白-RNA N-糖苷酶[J].细胞生物学杂志,1990,42(2):58-63.DONG Gao,LIU Wangyi.Ribosome inactivating protein-RNA N-glycosidase activity[J].Chinese Journal of Cell Biology,1900,42(2):58-63.
[12]ZHU F,ZHANG P,MENG Y F,et al.Alpha-momorcharin,a RIP produced by bitter melon,enhances defense response in tobacco plants against diverse plant viruses and shows antifungal activity in vitro[J].Planta,2013,237(1):77-88.
[13]JOHNSON L S,EDDY S R,PORTUGALY E.Hidden markov model speed heuristic and iterative HMM search procedure[J].BMC Bioinformatics,2010,11(1):431-438.
[14]CHENG Lin,YUAN Hongyu,REN Ren,et al.Genome-wide identification,classification and expression analyses of amino acid transporter gene family in Glycine max[J].Frontiers in Plant Science,2016,7(320):515-528.
[15]ZHANG Zaibao,ZHAO Yilin,FENG Xiaobing,et al.Genomic,molecular evolution,and expression analysis of NOX genes in soybean(Glycine max)[J].Genomics,2018,doi:10.1016/j.ygeno.2018.03.18.
[16]TAMURA K,STECHER G,PETERSON D,et al.MEGA6:Molecular evolutionary genetics analysis version 6.0[J].Mol Biol Evol,2013,30:2725-2729.
[17]STAMATAKIS A.RAxML-VI-HPC:Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models[J].Bioinformatics,2006,22(21):2688-2690.
[18]LESHIN J,DANIELSEN M,CREDLE J J,et al.Characterization of ricin toxin family members from Ricinus communis[J].Toxicon,2010,55(2):658-661.
[19]DANG L,VAN DAMME E J.Toxic proteins in plants[J].Phytochemistry,2015,117:51-64.
[20]AKKOUH O,NG T B,CHEUNG R C F,et al.Biological activities of ribosome-inactivating proteins and their possible applications as antimicrobial,anticancer,and anti-pest agents and in neuroscience research[J].Applied Microbiology and Biotechnology,2015,99(23):9847-9863.
[21]LI Y,YANG L,PATHAK M,et al.Fine genetic mapping of cp:A recessive gene for compact(dwarf)plant architecture in cucumber,Cucumis sativus L[J].Theoretical and Applied Genetics,2011,123(6):973-983.
[22]TENAILLON M I,CHARCOSSET A.A European perspective on maize history[J].Comptes Rendus Biologies,2011,334(3):221-228.
[23]VISION T J,BROWN D G,TANKSLEY S D.The origins of genomic duplications in Arabidopsis[J].Science,2000,2905:2114-2117.
[24]TANG H,BOWERS J E,WANG X,et al.Synteny and collinearity in plant genomes[J].Science,2008,320:486-488.
[25]LYONS E,PEDERSEN B,KANE J,et al.Finding and comparing syntenic regions among arabidopsis and the outgroups papaya,poplar,and grape:Co Ge with rosids[J].Plant Physiology,2008,148:1772-1781.
[26]TANG H,WANG X,BOWERS J E,et al.Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps[J].Genome Research,2008,18:1944-1954.
[27]BOWERS J E,CHAPMAN B A,RONG J,et al.Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events[J].Nature,2003,422:433-438.
[28]WANG X,WANG H,WANG J,et al.The genome of the mesopolyploid crop species Brassica rapa[J].Nature Genetics,2011,43:1035-1039.
[29]SWIGONOVZ,LAI J,MA J,et al.Close split of sorghum and maize genome progenitors[J].Genome Reserch,2004,14:1916-1923.
[30]DING M,CHEN Z J.Epigenetic perspectives on the evolution and domestication of polyploid plant and crops[J].Curr Opin Plant Biol,2018,42(1):37-48.
[31]OHNO S.Evolution by gene duplication[M].New York:Springer Verlag,1970.
[32]张丽丽,乔利,梁丽宁,等.SCP-2基因的表达调控研究进展[J].信阳师范学院学报(自然科学版),2016,29(2):299-303.ZHANG Lili,QIAO Li,LIANG Lining,et al.Review of research on transcriptional regulations of sterol carrier protein-2[J].Journal of Xinyang Normal University(Natural Science Edition),2016,29(2):299-303.
[33]柯丹霞,李祥永.结瘤信号途径中相关调控蛋白的研究进展[J].信阳师范学院学报(自然科学版),2015,28(4):621-626.KE Danxia,LI Xiangyong.Research progress of key regulation proteins in nodulatoin pathway[J].Journal of Xinyang Normal University(Natural Science Edition),2015,28(4):621-626.
[34]HE X,ZHANG J.Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution[J].Genetics,2005,169:1157-1164.
[35]PAPP B,PAL C,HURST L D.Dosage sensitivity and the evolution of gene families in yeast[J].Nature,2003,424:194-197.
[36]WANG L,CAO C,MA Q,et al.RNA-seq analyses of multiple meristems of soybean:novel and alternative transcripts,evolutionary and functional implications[J].BMC Plant Biology,2014,14(1):169-188.
[37]JITENDER G,RAHUL B,HUANG G Q,et al.Rice auxin influx carrier OsAUX1facilitates root hair elongation in response to low external phosphate[J].Nature Communications,2018,9(1):1408-1415.
[38]LIN Feng,YANG Tianyuan,ZHANG Zhaoliang,et al.Identification and characterization of cationic amino acid transporters(CATs)in tea plant(Camellia sinensis)[J].Plant Growth Regul,2018(5):1-13.
[2]DI MARO A,CITORES L,RUSSO R,et al.Sequence comparison and phylogenetic analysis by the Maximum Likelihood method of ribosome-inactivating proteins from angiosperms[J].Plant Molecular Biology,2014,85(6):575-588.
[3]LOSS-MORAIS G,TURCHETTO-ZOLET A C,ETGES M,et al.Analysis of castor bean ribosome-inactivating proteins and their gene expression during seed development[J].Genetics and Molecular Biology,2013,36(1):74-86.
[4]STIRPE F,BARBIERI L,BATTELLI M G,et al.Ribosome-inactivating proteins from plants:Present status and future prospects[J].Nature Biotechnology,1992,10(4):405-412.
[5]STIRPE F.Ribosome-inactivating proteins[J].Toxicon,2004,44(4):371-383.
[6]LAMB F I,ROBERTS L M,LORD J M.Nucleotide sequence of cloned cDNA coding for preproricin[J].European Journal of Biochemistry,1985,148(2):265-270.
[7]FRIGERIO L,ROBERTS L M.The enemy within:Ricin and plant cells[J].Journal of Experimental Botany,1998,49(326):1473-1480.
[8]BARBIERI L,BATTELLI M G,STIRPE F.Ribosome-inactivating proteins from plants[J].Biochimica et Biophysica Acta Reviews on Biomembranes,1993,1154(3):237-282.
[9]NIELSEN K,BOSTON R S.Ribosome-inactivating proteins:A plant perspective[J].Annu Rev Plant Physiol Plant Mol Biol,2001,52(52):785-816.
[10]林娟,颜钫,唐琳,等,麻疯树核糖体失活蛋白的分离纯化和作用机制研究[J].高技术通讯,2002,12(11):36-40.LIN Juan,YAN Fang,TANG Lin,et al.Isolation,purification and mechaism of ribosome inactivating protein from jatropha curcas[J].High Technology Letters,2002,12(11):36-40.
[11]董槁,刘望夷.核糖体失活蛋白-RNA N-糖苷酶[J].细胞生物学杂志,1990,42(2):58-63.DONG Gao,LIU Wangyi.Ribosome inactivating protein-RNA N-glycosidase activity[J].Chinese Journal of Cell Biology,1900,42(2):58-63.
[12]ZHU F,ZHANG P,MENG Y F,et al.Alpha-momorcharin,a RIP produced by bitter melon,enhances defense response in tobacco plants against diverse plant viruses and shows antifungal activity in vitro[J].Planta,2013,237(1):77-88.
[13]JOHNSON L S,EDDY S R,PORTUGALY E.Hidden markov model speed heuristic and iterative HMM search procedure[J].BMC Bioinformatics,2010,11(1):431-438.
[14]CHENG Lin,YUAN Hongyu,REN Ren,et al.Genome-wide identification,classification and expression analyses of amino acid transporter gene family in Glycine max[J].Frontiers in Plant Science,2016,7(320):515-528.
[15]ZHANG Zaibao,ZHAO Yilin,FENG Xiaobing,et al.Genomic,molecular evolution,and expression analysis of NOX genes in soybean(Glycine max)[J].Genomics,2018,doi:10.1016/j.ygeno.2018.03.18.
[16]TAMURA K,STECHER G,PETERSON D,et al.MEGA6:Molecular evolutionary genetics analysis version 6.0[J].Mol Biol Evol,2013,30:2725-2729.
[17]STAMATAKIS A.RAxML-VI-HPC:Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models[J].Bioinformatics,2006,22(21):2688-2690.
[18]LESHIN J,DANIELSEN M,CREDLE J J,et al.Characterization of ricin toxin family members from Ricinus communis[J].Toxicon,2010,55(2):658-661.
[19]DANG L,VAN DAMME E J.Toxic proteins in plants[J].Phytochemistry,2015,117:51-64.
[20]AKKOUH O,NG T B,CHEUNG R C F,et al.Biological activities of ribosome-inactivating proteins and their possible applications as antimicrobial,anticancer,and anti-pest agents and in neuroscience research[J].Applied Microbiology and Biotechnology,2015,99(23):9847-9863.
[21]LI Y,YANG L,PATHAK M,et al.Fine genetic mapping of cp:A recessive gene for compact(dwarf)plant architecture in cucumber,Cucumis sativus L[J].Theoretical and Applied Genetics,2011,123(6):973-983.
[22]TENAILLON M I,CHARCOSSET A.A European perspective on maize history[J].Comptes Rendus Biologies,2011,334(3):221-228.
[23]VISION T J,BROWN D G,TANKSLEY S D.The origins of genomic duplications in Arabidopsis[J].Science,2000,2905:2114-2117.
[24]TANG H,BOWERS J E,WANG X,et al.Synteny and collinearity in plant genomes[J].Science,2008,320:486-488.
[25]LYONS E,PEDERSEN B,KANE J,et al.Finding and comparing syntenic regions among arabidopsis and the outgroups papaya,poplar,and grape:Co Ge with rosids[J].Plant Physiology,2008,148:1772-1781.
[26]TANG H,WANG X,BOWERS J E,et al.Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps[J].Genome Research,2008,18:1944-1954.
[27]BOWERS J E,CHAPMAN B A,RONG J,et al.Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events[J].Nature,2003,422:433-438.
[28]WANG X,WANG H,WANG J,et al.The genome of the mesopolyploid crop species Brassica rapa[J].Nature Genetics,2011,43:1035-1039.
[29]SWIGONOVZ,LAI J,MA J,et al.Close split of sorghum and maize genome progenitors[J].Genome Reserch,2004,14:1916-1923.
[30]DING M,CHEN Z J.Epigenetic perspectives on the evolution and domestication of polyploid plant and crops[J].Curr Opin Plant Biol,2018,42(1):37-48.
[31]OHNO S.Evolution by gene duplication[M].New York:Springer Verlag,1970.
[32]张丽丽,乔利,梁丽宁,等.SCP-2基因的表达调控研究进展[J].信阳师范学院学报(自然科学版),2016,29(2):299-303.ZHANG Lili,QIAO Li,LIANG Lining,et al.Review of research on transcriptional regulations of sterol carrier protein-2[J].Journal of Xinyang Normal University(Natural Science Edition),2016,29(2):299-303.
[33]柯丹霞,李祥永.结瘤信号途径中相关调控蛋白的研究进展[J].信阳师范学院学报(自然科学版),2015,28(4):621-626.KE Danxia,LI Xiangyong.Research progress of key regulation proteins in nodulatoin pathway[J].Journal of Xinyang Normal University(Natural Science Edition),2015,28(4):621-626.
[34]HE X,ZHANG J.Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution[J].Genetics,2005,169:1157-1164.
[35]PAPP B,PAL C,HURST L D.Dosage sensitivity and the evolution of gene families in yeast[J].Nature,2003,424:194-197.
[36]WANG L,CAO C,MA Q,et al.RNA-seq analyses of multiple meristems of soybean:novel and alternative transcripts,evolutionary and functional implications[J].BMC Plant Biology,2014,14(1):169-188.
[37]JITENDER G,RAHUL B,HUANG G Q,et al.Rice auxin influx carrier OsAUX1facilitates root hair elongation in response to low external phosphate[J].Nature Communications,2018,9(1):1408-1415.
[38]LIN Feng,YANG Tianyuan,ZHANG Zhaoliang,et al.Identification and characterization of cationic amino acid transporters(CATs)in tea plant(Camellia sinensis)[J].Plant Growth Regul,2018(5):1-13.