基于线粒体基因组的鼠兔高海拔适应机制探讨
|
摘要
鼠兔隶属于兔型目,大多生活在海拔较高的地区,是研究哺乳动物对高寒缺氧环境适应机制的理想模型。线粒体通过氧化磷酸化产生能量,在机体的氧气利用和能量代谢中发挥重要作用。本研究测定了柯氏鼠兔线粒体全基因,然后分析了5种分布于较高海拔的鼠兔与6种较低海拔的兔科物种的线粒体基因组,并探讨了鼠兔高海拔适应时线粒体基因的作用。研究表明相比于较低海拔物种,鼠兔积累了更多的非同义突变,并且在鼠兔的线粒体编码基因的NADH2、NADH4L、NADH4、NADH5、NADH6、Cytb上均检测到正选择信号。ND2、ND4和ND5亚基的正选择位点位于非跨膜区,鼠兔的ND4L、ND6亚基的正选择位点位于TM区,但并不在与质子转运相关的关键区域。NADH脱氢酶亚基可能通过氨基酸变异干扰了质子转运过程的有效性。Cytb上的正选择信号位于跨膜螺旋H,氨基酸的变异可能影响到泛醇的结合与转移,进而改变了能量代谢。
Pikas belong to the Order of Lagomorpha, which live in the region of high altitude, are considered the ideal animal model for cold and hypoxia adaptation studies. Mitochondria, which produces energy by oxidative phosphorylation, plays an important role in oxygen utilization and energy metabolism of the body. In this study, we determined the complete gene of the O. koslowi mitochondrial, analyzed the mitochondrial genome between 5 kinds of pikas distributed in the higher altitudes and 6 species of Leporidae in lower-elevation areas, and then discussed the roles of mitochondrial genome of pikas in the adaption to high altitude. The research indicated that the pikas accumulated more nonsynonymous mutation. The positive selection signals were detected in the NADH2, NADH4 L, NADH4, NADH5, NADH6 and Cytb genes of mitochondrial genome in the pikas. The positive selection sites of ND2, ND4 and ND5 were located in the non-transmembrane regions. The positive selection sites of ND4 L and ND6 were seated in the TM regions, these sites were not at the critical section related to the proton transport. The mutation of amino acid in NADH dehydrogenase subu nits may interference the validity of the process of proton transport. The positive selection signal of Cytb is located in the transmembrane helix H. The mutation of amino acid could affect the combination and transfer of panthenol, and then changes the energy metabolism.
Pikas belong to the Order of Lagomorpha, which live in the region of high altitude, are considered the ideal animal model for cold and hypoxia adaptation studies. Mitochondria, which produces energy by oxidative phosphorylation, plays an important role in oxygen utilization and energy metabolism of the body. In this study, we determined the complete gene of the O. koslowi mitochondrial, analyzed the mitochondrial genome between 5 kinds of pikas distributed in the higher altitudes and 6 species of Leporidae in lower-elevation areas, and then discussed the roles of mitochondrial genome of pikas in the adaption to high altitude. The research indicated that the pikas accumulated more nonsynonymous mutation. The positive selection signals were detected in the NADH2, NADH4 L, NADH4, NADH5, NADH6 and Cytb genes of mitochondrial genome in the pikas. The positive selection sites of ND2, ND4 and ND5 were located in the non-transmembrane regions. The positive selection sites of ND4 L and ND6 were seated in the TM regions, these sites were not at the critical section related to the proton transport. The mutation of amino acid in NADH dehydrogenase subu nits may interference the validity of the process of proton transport. The positive selection signal of Cytb is located in the transmembrane helix H. The mutation of amino acid could affect the combination and transfer of panthenol, and then changes the energy metabolism.
引文
Al meida D.,Ma ldonado E.,Vasconcelos V.,and Antunes A.,2015,Adaptation of the mitochondrial genome in Cephalopods:enhancing proton translocation channels and the subunit interactions,PLoS One,10(8):1-29
Bonfield J.K.,Smith K.F.,and Staden R.,1995,A new DNAsequence assembly program,Nucleic Acids Res.,23(24):4992-4999
Chen C.P.,and Rost B.,2002,State-of-the-art in membrane protein prediction,Applied Bioinformatics,1(1):21
Chen T.F.,Bai Z.Z.,Hou B.,Gao Y.,and Ge R.L.,2005,Cloning and analysis of the coding cDNA sequence of myoglobin of Ochotona curzoniae lived in Qinghai-Tibet Plateau,Gaoyuan Yixue Zazhi(Journal of High Altitude Medicine),15(4):4-7(陈婷方,白振忠,侯冰,高艳,格日力,2005,青藏高原高原鼠兔肌红蛋白(MGB)基因编码区的克隆与分析,高原医学杂志,15(4):4-7)
Fonseca R.R.D.,Johnson W.E.,O'Brien S.J.,Ramos M.J.,and Antunes A.,2008,The adaptive evolution of the mammalian mitochondrial genome,BMC Genomics,9(1):1-22
Dowling D.K.,Friberg U.,and Lindell J.,2008,Evolutionary implications of non-neutral mitochondrial genetic variation,Trends in Ecology and Evolution,23(10):546-554
Efremov R.G.,and Sazanov L.A.,2011,Structure of the membrane domain of respiratory complex I,Nature,476(7361):414-420
Gu P.,Liu W.,Yao Y.F.,Ni Q.Y.,Zhang M.W.,Li D.Y.,and Xu H.L.,2014,Evidence of adaptive evolution of alpine pheasants to high-altitude environment from mitogenomic perspective,Mitochondrial DNA,27(1):455
Hassanin A.,Ropiq uet A.,Couloux A.,and Cruaud C.,2009,Evolution of the mitochondrial genome in mammals living at high altitude:New insights from a study of the Tribe Caprini(Bovidae,Antilopinae),Journal of Molecular Evolution,68(4):293-310
Lanier H.C.,and Olson L.E.,2009,Inferring divergence times within pikas(Ochotona spp.)using mtDNA and relaxed moleculalr dating techniques,Molecular Phylogenetics and Evolution,53(1):1-12
Li N.,Yang W.Z.,and Fu J.Z.,2015,High-altitude adaptation of genus Phrynocephalus based on mitochondrial genome,Sichuan Dongwu(Sichuan Journal of Zoology),34(6):810-816(李娜,杨伟钊,傅金钟,2015,基于线粒体基因组的沙蜥高海拔适应研究,四川动物,34(6):810-816)
Li W.D.,Zhang H.B.,and Liu Z.H.,2000,On the status of Ochotona koslowi in the East Kunlun Mountains of China,Dongwuxue Zazhi(Chinese Journal of Zoology),35(6):28-31(李维东,张会斌,刘志虎,2000,柯氏鼠兔在东昆仑山的生存现状,动物学杂志,35(6):28-31)
Luo Y.J.,Gao W.X.,Gao Y.Q.,Tang S.,Huang Q.Y.,Tan X.L.,Chen J.,and Huang T.S.,2008,Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation,Mitochondrion,8(6):352-357
Luo Y.J.,Yang X.H.,and Gao Y.Q.,2013,Mitochondrial DNAresponse to high altitude:A new perspective on high-altitude adaptation,Mitochondrial DNA,24(4):313-319
Ning T.,Xiao H.,Li J.,Hua S.,and Zhang Y.P.,2010,Adaptive evolution of the mitochondrial ND6 gene in the domestic horse,Genetics and Molecular Research,9(1):144-150
Ronquist F.,Teslenko M.,and Ayres D.L.,2012,Mr Bayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space,System Biology,61(3):539-542
Sazanov L.A.,2015,A giant molecular proton pump:structure and mechanism of respiratory complex I,Nature Reviews Molecualr Cell Biology,16(6):375-388
Schwede T.,Kopp J.,Guex N.,and Peitsch M.C.,2003,SWISS-MODEL:an automated protein homology-modeling server,Nucleic Acids Res.,31(13):3381-3385
Stamatakis A.,2006,RAxML-VI-HPC:maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models,Bioinformatics,22(21):2688-2690
Wang A.F.,Yonezawa T.,Liu B.,Ma T.,Shen X.,Su J.P.,Guo S.C.,Hasegawa M.,and Liu J.Q.,2011,Domestication relaxed selective constraints on the yak mitochondrial genome,Molecular Biology Evolution,28(5):1553-1556
Wang X.H.,Yu M.T.,and Liu S.M.,1995,Studies on haptoglobin genetic polymorphism of the pika,Gaoyuan Yixue Zazhi(Journal of High Altitude Medicine),(1):19-22(王修海,余满堂,刘世民,1995,高原鼠兔结合珠蛋白遗传多样性研究,高原医学杂志,(1):19-22)
Wang Y.,Shen Y.J.,Feng C.G.,Zhao K.,Song A.B.,Zhang Y.P.,Yang L.D.,and He S.P.,2016,Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude,Sci.Rep.,6:29690
Wu M.,Gu J.K.,Guo R.Y.,Huang Y.S.,and Yang M.J.,2016,Structure of mammalian respiratory supercomplex I1II-I2IV1,Cell,167(6):1598-1609
Xia D.,Yu C.A.,Kim H.,Xia J.Z.,Kachurin A.M.,Zhang L.,Yu L.,and Deisenhofer J.,1997,Crystal structure of the Cytochrome bc1 complex from bovine heart mitochondria,Science,277(5322):60-66
Yang Z.,and Nielsen R.,1998,Synonymous and nonsynonymous rate variation in nuclear genes of mammals,Molecular Evolution,46(4):409-418
Yang Z.H.,2007,PAML 4:phylogenetic analysis by maximum likelihood,Molecular Biology and Evolution,24(8):1586-1591
Yu L.,Wang X.P.,Ting N.,and Zhang Y.P.,2011,Mitogenomic analysis of Chinese snub-nosed monkeys:Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation,Mitochondrion,11(3):497-503
Zhao X.Q.,Qi D.L.,and Yang J.,eds.,2008,Reaseach of molecular evolution and adaptation of representative native animals in Qinghai-Tibetan plateau,Science Press,Beijing,China,pp.152-189(赵新全,祁得林,杨洁,主编,2008,青藏高原代表性土著动物分子进化与适应研究,科学出版社,中国,北京,pp.152-189)
Zhou T.C.,2015,Studies on the evolutionary molecular mechanism of adaptation of animals native to the plateau for Galliformes,Rodentia and Lagomorpha,Dissertation for Ph.D.,Yunnan University,Supervisor:Zhang Y.P.,pp.37(周太成,2015,高原土著动物适应性进化分子机制探讨-以鸡形目,啮齿目和兔形目为例,博士学位论文,云南大学,导师:张亚平,pp.37)
Zhu J.P.,Vinothkumar K.R.,and Hirst J.,2016,Structure of mammalian respiratory complex I,Nature,536(18):354-370
Bonfield J.K.,Smith K.F.,and Staden R.,1995,A new DNAsequence assembly program,Nucleic Acids Res.,23(24):4992-4999
Chen C.P.,and Rost B.,2002,State-of-the-art in membrane protein prediction,Applied Bioinformatics,1(1):21
Chen T.F.,Bai Z.Z.,Hou B.,Gao Y.,and Ge R.L.,2005,Cloning and analysis of the coding cDNA sequence of myoglobin of Ochotona curzoniae lived in Qinghai-Tibet Plateau,Gaoyuan Yixue Zazhi(Journal of High Altitude Medicine),15(4):4-7(陈婷方,白振忠,侯冰,高艳,格日力,2005,青藏高原高原鼠兔肌红蛋白(MGB)基因编码区的克隆与分析,高原医学杂志,15(4):4-7)
Fonseca R.R.D.,Johnson W.E.,O'Brien S.J.,Ramos M.J.,and Antunes A.,2008,The adaptive evolution of the mammalian mitochondrial genome,BMC Genomics,9(1):1-22
Dowling D.K.,Friberg U.,and Lindell J.,2008,Evolutionary implications of non-neutral mitochondrial genetic variation,Trends in Ecology and Evolution,23(10):546-554
Efremov R.G.,and Sazanov L.A.,2011,Structure of the membrane domain of respiratory complex I,Nature,476(7361):414-420
Gu P.,Liu W.,Yao Y.F.,Ni Q.Y.,Zhang M.W.,Li D.Y.,and Xu H.L.,2014,Evidence of adaptive evolution of alpine pheasants to high-altitude environment from mitogenomic perspective,Mitochondrial DNA,27(1):455
Hassanin A.,Ropiq uet A.,Couloux A.,and Cruaud C.,2009,Evolution of the mitochondrial genome in mammals living at high altitude:New insights from a study of the Tribe Caprini(Bovidae,Antilopinae),Journal of Molecular Evolution,68(4):293-310
Lanier H.C.,and Olson L.E.,2009,Inferring divergence times within pikas(Ochotona spp.)using mtDNA and relaxed moleculalr dating techniques,Molecular Phylogenetics and Evolution,53(1):1-12
Li N.,Yang W.Z.,and Fu J.Z.,2015,High-altitude adaptation of genus Phrynocephalus based on mitochondrial genome,Sichuan Dongwu(Sichuan Journal of Zoology),34(6):810-816(李娜,杨伟钊,傅金钟,2015,基于线粒体基因组的沙蜥高海拔适应研究,四川动物,34(6):810-816)
Li W.D.,Zhang H.B.,and Liu Z.H.,2000,On the status of Ochotona koslowi in the East Kunlun Mountains of China,Dongwuxue Zazhi(Chinese Journal of Zoology),35(6):28-31(李维东,张会斌,刘志虎,2000,柯氏鼠兔在东昆仑山的生存现状,动物学杂志,35(6):28-31)
Luo Y.J.,Gao W.X.,Gao Y.Q.,Tang S.,Huang Q.Y.,Tan X.L.,Chen J.,and Huang T.S.,2008,Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation,Mitochondrion,8(6):352-357
Luo Y.J.,Yang X.H.,and Gao Y.Q.,2013,Mitochondrial DNAresponse to high altitude:A new perspective on high-altitude adaptation,Mitochondrial DNA,24(4):313-319
Ning T.,Xiao H.,Li J.,Hua S.,and Zhang Y.P.,2010,Adaptive evolution of the mitochondrial ND6 gene in the domestic horse,Genetics and Molecular Research,9(1):144-150
Ronquist F.,Teslenko M.,and Ayres D.L.,2012,Mr Bayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space,System Biology,61(3):539-542
Sazanov L.A.,2015,A giant molecular proton pump:structure and mechanism of respiratory complex I,Nature Reviews Molecualr Cell Biology,16(6):375-388
Schwede T.,Kopp J.,Guex N.,and Peitsch M.C.,2003,SWISS-MODEL:an automated protein homology-modeling server,Nucleic Acids Res.,31(13):3381-3385
Stamatakis A.,2006,RAxML-VI-HPC:maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models,Bioinformatics,22(21):2688-2690
Wang A.F.,Yonezawa T.,Liu B.,Ma T.,Shen X.,Su J.P.,Guo S.C.,Hasegawa M.,and Liu J.Q.,2011,Domestication relaxed selective constraints on the yak mitochondrial genome,Molecular Biology Evolution,28(5):1553-1556
Wang X.H.,Yu M.T.,and Liu S.M.,1995,Studies on haptoglobin genetic polymorphism of the pika,Gaoyuan Yixue Zazhi(Journal of High Altitude Medicine),(1):19-22(王修海,余满堂,刘世民,1995,高原鼠兔结合珠蛋白遗传多样性研究,高原医学杂志,(1):19-22)
Wang Y.,Shen Y.J.,Feng C.G.,Zhao K.,Song A.B.,Zhang Y.P.,Yang L.D.,and He S.P.,2016,Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude,Sci.Rep.,6:29690
Wu M.,Gu J.K.,Guo R.Y.,Huang Y.S.,and Yang M.J.,2016,Structure of mammalian respiratory supercomplex I1II-I2IV1,Cell,167(6):1598-1609
Xia D.,Yu C.A.,Kim H.,Xia J.Z.,Kachurin A.M.,Zhang L.,Yu L.,and Deisenhofer J.,1997,Crystal structure of the Cytochrome bc1 complex from bovine heart mitochondria,Science,277(5322):60-66
Yang Z.,and Nielsen R.,1998,Synonymous and nonsynonymous rate variation in nuclear genes of mammals,Molecular Evolution,46(4):409-418
Yang Z.H.,2007,PAML 4:phylogenetic analysis by maximum likelihood,Molecular Biology and Evolution,24(8):1586-1591
Yu L.,Wang X.P.,Ting N.,and Zhang Y.P.,2011,Mitogenomic analysis of Chinese snub-nosed monkeys:Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation,Mitochondrion,11(3):497-503
Zhao X.Q.,Qi D.L.,and Yang J.,eds.,2008,Reaseach of molecular evolution and adaptation of representative native animals in Qinghai-Tibetan plateau,Science Press,Beijing,China,pp.152-189(赵新全,祁得林,杨洁,主编,2008,青藏高原代表性土著动物分子进化与适应研究,科学出版社,中国,北京,pp.152-189)
Zhou T.C.,2015,Studies on the evolutionary molecular mechanism of adaptation of animals native to the plateau for Galliformes,Rodentia and Lagomorpha,Dissertation for Ph.D.,Yunnan University,Supervisor:Zhang Y.P.,pp.37(周太成,2015,高原土著动物适应性进化分子机制探讨-以鸡形目,啮齿目和兔形目为例,博士学位论文,云南大学,导师:张亚平,pp.37)
Zhu J.P.,Vinothkumar K.R.,and Hirst J.,2016,Structure of mammalian respiratory complex I,Nature,536(18):354-370
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |