盘基网柄菌DdLIS1蛋白生物信息学分析
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摘要
LIS1蛋白是一种与人类无脑回疾病以及细胞癌变相关的重要蛋白。对盘基网柄菌DdLIS1进行生物信息学分析,探究盘基网柄菌能否作为研究人类无脑回疾病及细胞癌变机制的模型。现从NCBI中的Genank找到盘基网柄菌DdLIS1的氨基酸序列,随后进行blastp找到模式生物中相似序列,利用理化性分析网站ProtScale、ProtParam分析DdLIS1的理化性质,通过NCBI中的保守结构域库(CDD)分析DdLIS1的保守结构域,使用MEGA6.0并选用邻位连接法构建系统进化树,分别使用PredictProtein、SWISS-MODEL网站预测Dd LIS1蛋白的二级结构、三维结构。结果得出DdLIS1蛋白全长为419,属于亲水性蛋白,有7个保守结构域,属于WD40家族,与人类和小鼠的氨基酸序列相似性为72%。二级结构中β折叠所占比例最高,为49.40%,α螺旋、随机卷曲分别占该蛋白7.16%、43.44%,与三级结构一致。以上结果说明DdLIS1与LIS1高度相似,有助于盘基网柄菌能够作为研究人类无脑回疾病以及细胞癌变机制的模型。
LIS1 protein is an important protein related to human lissencephaly disease and cell canceration. This study carried out the bioinformatics analysis of DdLIS1, and explored whether Dictyostelium discoideum could be used as a model for the study of human lissencephaly disease and cell canceration. The amino acid sequence of Dictyostelium discoideum DdLIS1 was obtained from Genank in NCBI. Then, the similar sequences of model organisms were found by blastp. Physicochemical properties of DdLIS1 were analyzed by the websites of ProtScale and ProtParam. The conserved domain database(CDD) in NCBI was used to analyze the conserved domain of DdLIS1. The phylogenetic tree was constructed by the orthotopic linkage method of MEGA6.0. PredictProtein and SWISS-MODEL were respectively used to predict the secondary and the tertiary structure of DdLIS1. The results showed that the full length of DdLIS1 protein was 419, which belonged to the hydrophilic protein and had seven conserved domains belonging to the WD40 family. The similarity of DdLIS1 with LIS1 of Homo sapiens and Mus musculus was 72%. In DdLIS1, the proportion of β-fold in the secondary structure was the highest, 49.40%,α-helix and the random curl respectively accounted for 7.16% and 43.44%, which was consistent with the tertiary structure. These results indicate that DdLIS1 might be highly similar to LIS1, and it could be beneficial to study the human lissencephaly disease and cell canceration.
LIS1 protein is an important protein related to human lissencephaly disease and cell canceration. This study carried out the bioinformatics analysis of DdLIS1, and explored whether Dictyostelium discoideum could be used as a model for the study of human lissencephaly disease and cell canceration. The amino acid sequence of Dictyostelium discoideum DdLIS1 was obtained from Genank in NCBI. Then, the similar sequences of model organisms were found by blastp. Physicochemical properties of DdLIS1 were analyzed by the websites of ProtScale and ProtParam. The conserved domain database(CDD) in NCBI was used to analyze the conserved domain of DdLIS1. The phylogenetic tree was constructed by the orthotopic linkage method of MEGA6.0. PredictProtein and SWISS-MODEL were respectively used to predict the secondary and the tertiary structure of DdLIS1. The results showed that the full length of DdLIS1 protein was 419, which belonged to the hydrophilic protein and had seven conserved domains belonging to the WD40 family. The similarity of DdLIS1 with LIS1 of Homo sapiens and Mus musculus was 72%. In DdLIS1, the proportion of β-fold in the secondary structure was the highest, 49.40%,α-helix and the random curl respectively accounted for 7.16% and 43.44%, which was consistent with the tertiary structure. These results indicate that DdLIS1 might be highly similar to LIS1, and it could be beneficial to study the human lissencephaly disease and cell canceration.
引文
Arnold K.,Bordoli L.,Kopp J.,and Schwede T.,2006,The SWISS-MODEL workspace:a web-based environment for protein structure homology modeling,Bioinformatics,22(2):195-201
Baumbach J.,Murthy A.,McClintock M.A.,Dix C.I.,Zalyte R.,Hoang H.T.,and Bullock S.L.,2017,Lissencephaly-1 is a context-dependent regulator of the human dynein complex,Elife,6:e21768
Cai Y.Q.,2010,Characterization of NudCL and Twa1,centrosome-associated proteins in Lis1/Dynein pathway,Dissertation for Ph.D.,School of Medicine,Zhejiang University,Supervisor:Zhou T.H.,pp.93(蔡雨奇,2010,Lis1/Dynein通路上中心体相关蛋白NudCL和Twa1的功能研究,博士学位论文,浙江大学医学院,导师:周天华,pp.93)
Dong C.C.,Xu H.L.,Zhang R.,Tanaka N.,Takeichi M.,and Meng W.X.,2017,CAMSAP3 accumulates in the pericentrosomal area and accompanies microtubules release from the centrosome via katanin,J.Cell Sci.,130(10):1709-1715
Doxsey S.,Zimmerman W.,and Mikule K.,2005,Centrosome control of the cell cycle,Trends Cell Biol.,15(6):303-311
Glotzer M.,2001,Animal cell cytokinesis,Annual Review of Cell and Developmental Biology,17(1):351-386
Iefremova V.,Manikakis G.,Krefft O.,Jabali A.,Weynans K.,Wilkens R.,Marsoner F.,Br覿ndl B.,Müller F.J.,Koch P.,and Ladewig J.,2017,An organoid-based model of cortical development identifies non-cell-autonomous defects in Wnt signaling contributing to Miller-Dieker syndrome,Cell Report,19(1):50-59
Krapp A.,Gulli M.P.,and Simanis V.,2004,SIN and the art of splitting the fission yeast cell,Current Biology,14(17):R722-R730
Kuwayama H.,and Kubohara Y.,2016,Differentiation-inducing factor 2 modulates chemotaxis via the histidine kinase DhkC-dependent pathway in Dictyostelium discoideum,FEBS Letters,590(6):760-768
Lockrow J.P.,Holden K.R.,Dwivedi A.,Matheus M.G.,and Lyons M.J.,2012,LIS1 duplication:expanding the phenotype,Journal of Child Neurology,27(6):791-795
Meyer I.,Kuhnert O.,and Grf R.,2011,Functional analyses of lissencephaly-related proteins in Dictyostelium,Seminars in Cell&Developmental Biology,22(1):89-96
Moore K.D.,Chen R.,Cilluffo M.,Golden J.A.,and Phelps P.E.,2012,Lis1 reduction causes tangential migratory errors in mouse spinal cord,The Journal of Comparative Neurology,520(6):1198-1211
Ou Y.,and Rattner J.B.,2004,The centrosome in higher organisms:structure,composition,and duplication,International Review of Cytology,238:119-182
Pandey J.P.,and Smith D.S.,2011,A Cdk5-dependent switch regulates Lis1/Ndel1/dynein-driven organelle transport in adult axons,Journal of Neuroscience,31(47):17207-17219
Rehberg M.,Kleylein-Sohn J.,Faix J.,Ho T.H.,Schulz I.,and Gr覿f R.,2005,Dictyostelium LIS1 is a centrosomal protein required for microtubule/cell cortex interactions,nucleus/centrosome linkage,and actin dynamics,Mol.Biol.Cell,16(6):2759-2771
Sun C.F.,Xu M.F.,Xing Z.,Wu Z.L.,Li Y.P.,Li T.,and Zhao M.J.,2009,Expression and function on embryonic development of lissencephaly-1 genes in zebrafish,Acta Biochimica Biophysica Sinica,41(8):677-688
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,MEGA6:molecular evolutionary genetics analysis version 6.0,Molecular Biology and Evolution,30(12):2725-2729
Taylor-Mulneix D.L.,Bendor L.,Linz B.,Rivera I.,Ryman V.E.,Dewan K.K.,Wanger S.M.,Wilson E.F.,Hilburger L.J.,Cuff L.E.,West C.M.,and Harvill E.T.,2017,Bordetella bronchiseptica exploits the complex life cycle of Dictyostelium discoideum as an amplifying transmission vector,PLoS Biology,15(4):e2000420
Vallee R.B.,and Tsai J.W.,2006,The cellular roles of the lissencephaly gene LIS1,and what they tell us about brain development,Genes&Development,20(11):1384-1393
Williams R.S.B.,Boeckeler K.,Grf R.,Müller-Taubenberger A.,Li Z.R.,Isberg R.R.,Wessels D.,Soll D.R.,Alexander H.,and Alexander S.,2006,Towards a molecular understanding of human diseases using Dictyostelium discoideum,Trends in Molecular Medicine,12(9):415-424
Wynshaw-Boris A.,2007,Lissencephaly and LIS1:insights into the molecular mechanisms of neuronal migration and development,Clinical Genetics,72(4):296-304
Xue D.M.,and Liu D.D.,2015,Advances on the developmental mechanism of Dictyostelium discoideum,Shengwu Jishu(Biotechnology),25(5):500-504(薛德明,刘丹丹,2015,盘基网柄菌发育机制研究进展,生物技术,25(5):500-504)
Zhai Z.H.,Wang X.Z.,and Ding M.X.,eds.,2008,Cell biology,The third edition,Higher Education Press,Beijing,China,pp.274,296-299(翟中和,王喜忠,丁明孝,主编,2008,细胞生物学,第3版,高等教育出版社,中国,北京,pp.274,296-299)
Zhou W.,Tang J.F.,Gan Z.,Jian J.C.,Wu Z.H.,and Ding Y.,2015,Cloning and bioinformatics analysis of quinolone resistance gene from Vibrio alginolyticus,Shengwu Jishu(Biotechnology),25(5):414-419(周维,汤菊芬,甘桢,简纪常,吴灶和,丁燏,2015,溶藻弧菌耐药基因qnr的克隆及生物信息学分析,生物技术,25(5):414-419)
Zimdahl B.,Ito T.,Blevins A.,Bajaj J.,Konuma T.,Weeks J.,Koechlein C.S.,Kwon H.Y.,Arami O.,Rizzieri D.,Broome H.E.,Chuah C.,Oehler V.G.,Sasik R.,Hardiman G.,and Reya T.,2014,Lis1 regulates asymmetric division in hematopoietic stem cells and in leukemia,Nature Genetics,46(3):245-252
Zuloaga D.G.,Carbone D.L.,Hiroi R.,Chong D.L.,and Handa R.J.,2011,Dexamethasone induces apoptosis in the developing rat amygdala in an age-,region-,and sex-specific manner,Neuroscience,199:535-547
Baumbach J.,Murthy A.,McClintock M.A.,Dix C.I.,Zalyte R.,Hoang H.T.,and Bullock S.L.,2017,Lissencephaly-1 is a context-dependent regulator of the human dynein complex,Elife,6:e21768
Cai Y.Q.,2010,Characterization of NudCL and Twa1,centrosome-associated proteins in Lis1/Dynein pathway,Dissertation for Ph.D.,School of Medicine,Zhejiang University,Supervisor:Zhou T.H.,pp.93(蔡雨奇,2010,Lis1/Dynein通路上中心体相关蛋白NudCL和Twa1的功能研究,博士学位论文,浙江大学医学院,导师:周天华,pp.93)
Dong C.C.,Xu H.L.,Zhang R.,Tanaka N.,Takeichi M.,and Meng W.X.,2017,CAMSAP3 accumulates in the pericentrosomal area and accompanies microtubules release from the centrosome via katanin,J.Cell Sci.,130(10):1709-1715
Doxsey S.,Zimmerman W.,and Mikule K.,2005,Centrosome control of the cell cycle,Trends Cell Biol.,15(6):303-311
Glotzer M.,2001,Animal cell cytokinesis,Annual Review of Cell and Developmental Biology,17(1):351-386
Iefremova V.,Manikakis G.,Krefft O.,Jabali A.,Weynans K.,Wilkens R.,Marsoner F.,Br覿ndl B.,Müller F.J.,Koch P.,and Ladewig J.,2017,An organoid-based model of cortical development identifies non-cell-autonomous defects in Wnt signaling contributing to Miller-Dieker syndrome,Cell Report,19(1):50-59
Krapp A.,Gulli M.P.,and Simanis V.,2004,SIN and the art of splitting the fission yeast cell,Current Biology,14(17):R722-R730
Kuwayama H.,and Kubohara Y.,2016,Differentiation-inducing factor 2 modulates chemotaxis via the histidine kinase DhkC-dependent pathway in Dictyostelium discoideum,FEBS Letters,590(6):760-768
Lockrow J.P.,Holden K.R.,Dwivedi A.,Matheus M.G.,and Lyons M.J.,2012,LIS1 duplication:expanding the phenotype,Journal of Child Neurology,27(6):791-795
Meyer I.,Kuhnert O.,and Grf R.,2011,Functional analyses of lissencephaly-related proteins in Dictyostelium,Seminars in Cell&Developmental Biology,22(1):89-96
Moore K.D.,Chen R.,Cilluffo M.,Golden J.A.,and Phelps P.E.,2012,Lis1 reduction causes tangential migratory errors in mouse spinal cord,The Journal of Comparative Neurology,520(6):1198-1211
Ou Y.,and Rattner J.B.,2004,The centrosome in higher organisms:structure,composition,and duplication,International Review of Cytology,238:119-182
Pandey J.P.,and Smith D.S.,2011,A Cdk5-dependent switch regulates Lis1/Ndel1/dynein-driven organelle transport in adult axons,Journal of Neuroscience,31(47):17207-17219
Rehberg M.,Kleylein-Sohn J.,Faix J.,Ho T.H.,Schulz I.,and Gr覿f R.,2005,Dictyostelium LIS1 is a centrosomal protein required for microtubule/cell cortex interactions,nucleus/centrosome linkage,and actin dynamics,Mol.Biol.Cell,16(6):2759-2771
Sun C.F.,Xu M.F.,Xing Z.,Wu Z.L.,Li Y.P.,Li T.,and Zhao M.J.,2009,Expression and function on embryonic development of lissencephaly-1 genes in zebrafish,Acta Biochimica Biophysica Sinica,41(8):677-688
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,MEGA6:molecular evolutionary genetics analysis version 6.0,Molecular Biology and Evolution,30(12):2725-2729
Taylor-Mulneix D.L.,Bendor L.,Linz B.,Rivera I.,Ryman V.E.,Dewan K.K.,Wanger S.M.,Wilson E.F.,Hilburger L.J.,Cuff L.E.,West C.M.,and Harvill E.T.,2017,Bordetella bronchiseptica exploits the complex life cycle of Dictyostelium discoideum as an amplifying transmission vector,PLoS Biology,15(4):e2000420
Vallee R.B.,and Tsai J.W.,2006,The cellular roles of the lissencephaly gene LIS1,and what they tell us about brain development,Genes&Development,20(11):1384-1393
Williams R.S.B.,Boeckeler K.,Grf R.,Müller-Taubenberger A.,Li Z.R.,Isberg R.R.,Wessels D.,Soll D.R.,Alexander H.,and Alexander S.,2006,Towards a molecular understanding of human diseases using Dictyostelium discoideum,Trends in Molecular Medicine,12(9):415-424
Wynshaw-Boris A.,2007,Lissencephaly and LIS1:insights into the molecular mechanisms of neuronal migration and development,Clinical Genetics,72(4):296-304
Xue D.M.,and Liu D.D.,2015,Advances on the developmental mechanism of Dictyostelium discoideum,Shengwu Jishu(Biotechnology),25(5):500-504(薛德明,刘丹丹,2015,盘基网柄菌发育机制研究进展,生物技术,25(5):500-504)
Zhai Z.H.,Wang X.Z.,and Ding M.X.,eds.,2008,Cell biology,The third edition,Higher Education Press,Beijing,China,pp.274,296-299(翟中和,王喜忠,丁明孝,主编,2008,细胞生物学,第3版,高等教育出版社,中国,北京,pp.274,296-299)
Zhou W.,Tang J.F.,Gan Z.,Jian J.C.,Wu Z.H.,and Ding Y.,2015,Cloning and bioinformatics analysis of quinolone resistance gene from Vibrio alginolyticus,Shengwu Jishu(Biotechnology),25(5):414-419(周维,汤菊芬,甘桢,简纪常,吴灶和,丁燏,2015,溶藻弧菌耐药基因qnr的克隆及生物信息学分析,生物技术,25(5):414-419)
Zimdahl B.,Ito T.,Blevins A.,Bajaj J.,Konuma T.,Weeks J.,Koechlein C.S.,Kwon H.Y.,Arami O.,Rizzieri D.,Broome H.E.,Chuah C.,Oehler V.G.,Sasik R.,Hardiman G.,and Reya T.,2014,Lis1 regulates asymmetric division in hematopoietic stem cells and in leukemia,Nature Genetics,46(3):245-252
Zuloaga D.G.,Carbone D.L.,Hiroi R.,Chong D.L.,and Handa R.J.,2011,Dexamethasone induces apoptosis in the developing rat amygdala in an age-,region-,and sex-specific manner,Neuroscience,199:535-547