中国莲P_(1B)-ATPase亚家族成员的生物信息学分析
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摘要
P_(1B)-ATPase是在生物中广泛存在的一类可通过水解ATP跨膜运送重金属离子的蛋白,属于P型ATPase家族的一个亚类,在植物对重金属离子的转运过程中扮演着重要角色。以拟南芥和水稻中已知的P_(1B)-ATPase蛋白为对照,对中国莲P_(1B)-ATPase蛋白亚家族成员进行序列比对、系统发育、保守基序、跨膜结构、二级结构、三级结构和亚细胞定位等生物信息学分析。结果表明,中国莲存在4个P_(1B)-ATPase蛋白,分别命名为NnHMA1、NnHMA2、NnHMA3、NnHMA4,其中NnHMA1属于Zn~(2+)/Co~(2+)/Cd~(2+)/Pb~(2+)P_(1B)-ATPase (Zn亚类),NnHMA2、NnHMA3、NnHMA4属于Cu+/Ag+P_(1B)-ATPase(Cu亚类),它们均定位于质膜上,属于跨膜蛋白,有5～8个跨膜结构,含有DKTGT、TGE、C/SPx、HP等保守基序;二级结构和三级结构在组成和结构上具有较高的相似性和保守性,以α-螺旋、无规卷曲元件为主,其他元件包括延伸链和β-转角等。研究结果展示了中国莲P_(1B)-ATPase蛋白亚家族成员的序列基本信息和结构特点,为深入研究中国莲P_(1B)-ATPase蛋白及其编码基因的功能提供了理论基础。
引文
[1]Lin Y F,Aarts M G. The molecular mechanism of zinc and cadmium stress response in plants[J]. Cellular and Molecular Life Sciences,2012,69(19):3187-3206.
[2]Lutts S,Lefèvre I. How can we take advantage of halophyte properties to cope with heavy metal toxicity in salt-affected areas?[J].Annals of Botany,2015,115(3):509-528.
[3]Dalcorso G,Farinati S,Maistri S,et al. How plants cope with cadmium:staking all on metabolism and gene expression[J]. Journal of Integrative Plant Biology,2008,50(10):1268-1280.
[4]孙维锋,肖迪.水体重金属污染现状及治理技术[J].能源与节能,2012(2):49-50.
[5]Halim M,Conte P,Piccolo A. Potential availability of heavy metals to phytoextraction from contaminated soils induced by exogenous humic substances[J]. Chemosphere,2003,52(1):265-275.
[6]刘伸伸,张震,何金铃,等.水生植物对氮磷及重金属污染水体的净化作用[J].浙江农林大学学报,2016,33(5):910-919.
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[8]张玉秀,张媛雅,孙涛,等.植物重金属转运蛋白P1B-ATPase结构和功能研究进展[J].生物工程学报,2010,26(6):715-725.
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[10]Bublitz M,Morth J P,Nissen P. P-type ATPases at a glance[J].Journal of Cell Science,2011,124(15):2515-2519.
[11]Wang K T,Sitsel O,Meloni G,et al. Structure and mechanism of Zn2+-transporting P-type ATPases[J]. Nature,2014,514(7523):518-522.
[12]Hussain D,Haydon M J,Wang Y,et al. P-type ATPase heavy metal transporters with roles in essential zinc homeostasis in Arabidopsis[J]. Plant Cell,2004,16(5):1327-1339.
[13]Puig S,Andrés-Colás N,García-Molina A,et al. Copper and iron homeostasis in Arabidopsis:responses to metal deficiencies,interactions and biotechnological applications[J]. Plant Cell and Environment,2007,30(3):271-290.
[14]Lee S,Kim Y Y,Lee Y,et al. Rice P1B-type heavy-metal ATPase,Os HMA9,is a metal efflux protein[J]. Plant Physiology,2007,145(3):831-842.
[15]Williams L E,Mills R F. P1B-ATPases-an ancient family of transition metal pumps with diverse functions in plants[J]. Trends in Plant Science,2005,10(10):491-502.
[16]Bernal M,Testillano P S,Alfonso M,et al. Identification and subcellular localization of the soybean copper P1B-ATPase Gm HMA8 transporter[J]. Journal of Structural Biology,2007,158(1):46-58.
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[18]Bernard C,Roosens N,Czernic P,et al. A novel CPx-ATPase from the cadmium hyperaccumulator Thlaspi caerulescens[J]. FEBS Letters,2004,569(1/2/3):140-148.
[19]Papoyan A,Kochian L V. Identification of Thlaspi caerulescens genes that may be involved in heavy metal hyperaccumulation and tolerance characterization of a novel heavy metal transporting ATPase[J].Plant Physiology,2004,136(3):3814-3823.
[20]Courbot M,Willems G,Motte P,et al. A major quantitative trait locus for cadmium tolerance in Arabidopsis halleri colocalizes with HMA4,a gene encoding a heavy metal ATPase[J]. Plant Physiology,2007,144(2):1052-1065.
[21]Wang K,Deng J,Damaris R N,et al. LOTUS-DB:an integrative and interactive database for Nelumbo nucifera study[J]. Database,2015,2015:bavo23.
[22]袁丁,李红,郝文芳,等.毛果杨全基因组硝酸根转运蛋白家族(NRT2s)序列分析[J].西北林学院学报,2012,27(5):80-86.
[23]龙凌云.灰杨再生体系的建立和Pc HMA3的克隆及生物信息学分析[D].杨凌:西北农林科技大学,2012:42-43.
[24]Kubala M. ATP-binding to P-type ATPases as revealed by biochemical,spectroscopic,and crystallographic experiments[J].Proteins-Structure Function and Bioinformatics,2006,64(1):1-12.
[25]Hirayama T,Kieber J J,Hirayama N,et al. RESPONSIVE-TOANTAGONIST1,a Menkes/Wilson disease-related Copper transporter,is required for ethylene signaling in Arabidopsis[J].Cell,1999,97(3):383-393.
[26]Cobbett C S,Hussain D,Haydon M J. Structural and functional relationships between type 1(B)heavy metal-transporting P-type ATPases in Arabidopsis[J]. The New Phytologist,2003,159(2):315-321.
[27]Baxter I,Tchieu J,Sussman M R,et al. Genomic comparison of Ptype ATPase ion pumps in Arabidopsis and rice[J]. Plant Physiology,2003,132(2):618-628.
[28]Pedersen C N,Axelsen K B,Harper J F,et al. Evolution of plant Ptype ATPases[J]. Frontiers in Plant Science,2012,3:31.
[29]易华伟,唐晓峰.基于氨基酸序列和模拟结构预测蛋白质稳定性的研究进展[J].生物技术通报,2017,33(4):83-89.
[30]孔繁良.基于二级结构的蛋白质三级结构预测[D].济南:济南大学,2016.
[31]Geourjon C,Deléage G. SOPMA:significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments[J]. Computer Applications in the Biosciences,1995,11(6):681-684.
[32]Verret F,Gravot A,Auroy P,et al. Heavy metal transport by At HMA4 involves the N-terminal degenerated metal binding domain and the C-terminal His11 stretch[J]. FEBS Letters,2005,579(6):1515-1522.
[33]Gravot A,Lieutaud A,Verret F,et al. At HMA3,a plant P1BATPase,functions as a Cd/Pb transporter in yeast[J]. FEBS Letters,2004,561(1/2/3):22-28.
[34]Toyoshima C,Nomura H,Sugita Y. Structural basis of ion pumping by Ca2+-ATPase of the sarcoplasmic reticulum[J]. FEBS Letters,2003,555(1):106-110.
[35]Efremov R G,Kosinsky Y A,Nolde D E,et al. Molecular modelling of the nucleotide-binding domain of Wilson's disease protein:location of the ATP-binding site,domain dynamics and potential effects of the major disease mutations[J]. Biochemical Journal,2004,382(1):293-305.
[36]Mills R F,Francini A,da Rocha P,et al. The plant P1B-type ATPase At HMA4 transports Zn and Cd and plays a role in detoxification of transition metals supplied at elevated levels[J].FEBS Letters,2005,579(3):783-791.
[37]薛庆中,陈辰,陈晓龙,等. DNA和蛋白质序列数据分析工具[M]. 3版.北京:科学出版社,2012:71-113.
[2]Lutts S,Lefèvre I. How can we take advantage of halophyte properties to cope with heavy metal toxicity in salt-affected areas?[J].Annals of Botany,2015,115(3):509-528.
[3]Dalcorso G,Farinati S,Maistri S,et al. How plants cope with cadmium:staking all on metabolism and gene expression[J]. Journal of Integrative Plant Biology,2008,50(10):1268-1280.
[4]孙维锋,肖迪.水体重金属污染现状及治理技术[J].能源与节能,2012(2):49-50.
[5]Halim M,Conte P,Piccolo A. Potential availability of heavy metals to phytoextraction from contaminated soils induced by exogenous humic substances[J]. Chemosphere,2003,52(1):265-275.
[6]刘伸伸,张震,何金铃,等.水生植物对氮磷及重金属污染水体的净化作用[J].浙江农林大学学报,2016,33(5):910-919.
[7]Argüello J M,Eren E,González-Guerrero M. The structure and function of heavy metal transport P1B-ATPases[J]. BioMetals,2007,20(3/4):233-248.
[8]张玉秀,张媛雅,孙涛,等.植物重金属转运蛋白P1B-ATPase结构和功能研究进展[J].生物工程学报,2010,26(6):715-725.
[9]Axelsen K B,Palmgren M G. Inventory of the superfamily of P-type ion pumps in Arabidopsis[J]. Plant Physiology,2001,126(2):696-706.
[10]Bublitz M,Morth J P,Nissen P. P-type ATPases at a glance[J].Journal of Cell Science,2011,124(15):2515-2519.
[11]Wang K T,Sitsel O,Meloni G,et al. Structure and mechanism of Zn2+-transporting P-type ATPases[J]. Nature,2014,514(7523):518-522.
[12]Hussain D,Haydon M J,Wang Y,et al. P-type ATPase heavy metal transporters with roles in essential zinc homeostasis in Arabidopsis[J]. Plant Cell,2004,16(5):1327-1339.
[13]Puig S,Andrés-Colás N,García-Molina A,et al. Copper and iron homeostasis in Arabidopsis:responses to metal deficiencies,interactions and biotechnological applications[J]. Plant Cell and Environment,2007,30(3):271-290.
[14]Lee S,Kim Y Y,Lee Y,et al. Rice P1B-type heavy-metal ATPase,Os HMA9,is a metal efflux protein[J]. Plant Physiology,2007,145(3):831-842.
[15]Williams L E,Mills R F. P1B-ATPases-an ancient family of transition metal pumps with diverse functions in plants[J]. Trends in Plant Science,2005,10(10):491-502.
[16]Bernal M,Testillano P S,Alfonso M,et al. Identification and subcellular localization of the soybean copper P1B-ATPase Gm HMA8 transporter[J]. Journal of Structural Biology,2007,158(1):46-58.
[17] Southron J L,Basu U,Taylor G J. Complementation of Saccharomyces cerevisiae ccc2 mutant by a putative P1B-ATPase from Brassica napus supports a copper-transporting function[J].FEBS Letters,2004,566(1/2/3):218-222.
[18]Bernard C,Roosens N,Czernic P,et al. A novel CPx-ATPase from the cadmium hyperaccumulator Thlaspi caerulescens[J]. FEBS Letters,2004,569(1/2/3):140-148.
[19]Papoyan A,Kochian L V. Identification of Thlaspi caerulescens genes that may be involved in heavy metal hyperaccumulation and tolerance characterization of a novel heavy metal transporting ATPase[J].Plant Physiology,2004,136(3):3814-3823.
[20]Courbot M,Willems G,Motte P,et al. A major quantitative trait locus for cadmium tolerance in Arabidopsis halleri colocalizes with HMA4,a gene encoding a heavy metal ATPase[J]. Plant Physiology,2007,144(2):1052-1065.
[21]Wang K,Deng J,Damaris R N,et al. LOTUS-DB:an integrative and interactive database for Nelumbo nucifera study[J]. Database,2015,2015:bavo23.
[22]袁丁,李红,郝文芳,等.毛果杨全基因组硝酸根转运蛋白家族(NRT2s)序列分析[J].西北林学院学报,2012,27(5):80-86.
[23]龙凌云.灰杨再生体系的建立和Pc HMA3的克隆及生物信息学分析[D].杨凌:西北农林科技大学,2012:42-43.
[24]Kubala M. ATP-binding to P-type ATPases as revealed by biochemical,spectroscopic,and crystallographic experiments[J].Proteins-Structure Function and Bioinformatics,2006,64(1):1-12.
[25]Hirayama T,Kieber J J,Hirayama N,et al. RESPONSIVE-TOANTAGONIST1,a Menkes/Wilson disease-related Copper transporter,is required for ethylene signaling in Arabidopsis[J].Cell,1999,97(3):383-393.
[26]Cobbett C S,Hussain D,Haydon M J. Structural and functional relationships between type 1(B)heavy metal-transporting P-type ATPases in Arabidopsis[J]. The New Phytologist,2003,159(2):315-321.
[27]Baxter I,Tchieu J,Sussman M R,et al. Genomic comparison of Ptype ATPase ion pumps in Arabidopsis and rice[J]. Plant Physiology,2003,132(2):618-628.
[28]Pedersen C N,Axelsen K B,Harper J F,et al. Evolution of plant Ptype ATPases[J]. Frontiers in Plant Science,2012,3:31.
[29]易华伟,唐晓峰.基于氨基酸序列和模拟结构预测蛋白质稳定性的研究进展[J].生物技术通报,2017,33(4):83-89.
[30]孔繁良.基于二级结构的蛋白质三级结构预测[D].济南:济南大学,2016.
[31]Geourjon C,Deléage G. SOPMA:significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments[J]. Computer Applications in the Biosciences,1995,11(6):681-684.
[32]Verret F,Gravot A,Auroy P,et al. Heavy metal transport by At HMA4 involves the N-terminal degenerated metal binding domain and the C-terminal His11 stretch[J]. FEBS Letters,2005,579(6):1515-1522.
[33]Gravot A,Lieutaud A,Verret F,et al. At HMA3,a plant P1BATPase,functions as a Cd/Pb transporter in yeast[J]. FEBS Letters,2004,561(1/2/3):22-28.
[34]Toyoshima C,Nomura H,Sugita Y. Structural basis of ion pumping by Ca2+-ATPase of the sarcoplasmic reticulum[J]. FEBS Letters,2003,555(1):106-110.
[35]Efremov R G,Kosinsky Y A,Nolde D E,et al. Molecular modelling of the nucleotide-binding domain of Wilson's disease protein:location of the ATP-binding site,domain dynamics and potential effects of the major disease mutations[J]. Biochemical Journal,2004,382(1):293-305.
[36]Mills R F,Francini A,da Rocha P,et al. The plant P1B-type ATPase At HMA4 transports Zn and Cd and plays a role in detoxification of transition metals supplied at elevated levels[J].FEBS Letters,2005,579(3):783-791.
[37]薛庆中,陈辰,陈晓龙,等. DNA和蛋白质序列数据分析工具[M]. 3版.北京:科学出版社,2012:71-113.