甘草NRAMP基因家族的鉴定和生物信息学分析
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摘要
为研究甘草自然抗性相关巨噬细胞蛋白(NRAMP)家族成员的结构和功能,利用生物信息学方法,从甘草全基因组数据库中筛选并鉴定甘草NRAMP家族基因序列,并对该家族成员做进化分析、基因结构分析、保守结构域和保守基序分析、二级结构和三维结构分析。结果显示,从甘草基因组中共鉴定出11个NRAMP基因家族成员,通过进化分析发现,亲缘关系近的NRAMP家族成员基因结构和保守基序都更为相似,甘草和大豆的NRAMP家族成员间亲缘关系更接近。甘草大部分NRAMP家族成员的氨基酸数量差异不大,介于300～549个,且亚细胞定位在细胞膜上,而2个分子质量较大的成员GurNRAMP7和GurNRAMP8亚细胞定位在叶绿体上,各个成员的跨膜结构数量不尽相同。各个基因在染色体上的分布较为分散,只有NRAMP9、NRAMP10、NRAMP11定位在同一条染色体上。α-螺旋是甘草NRAMP家族成员中最主要的二级结构,但各个成员含有的α-螺旋数量不完全一样。
In order to study the structure and function of NRAMP(Natural sesistance-associated macrophage protein) family members,the bioinformatics methods were used to obtain the NRAMP gene sequences of Glycyrrhiza uralensis from the genomic database,and the phylogenetic relationship,gene structure,conserved domain,conserved motif,secondary structure and tertiary structure were analyzed.The results showed 11 NRAMP family members were identified from the Glycyrrhiza uralensis genome.The gene structures and conserved motifs of NRAMPs were more similar among the members with closer evolutionary relationship.The relationship of GurNRAMP family members was closer to soybean than other plants.The amino acid residues of most NRAMP proteins were similar in number,ranging from 300 to 549,and the subcellular localization of them was on cell membrane.Particularly,GurNRAMP7 and GurNRAMP8 had larger molecular weight and different subcellular localization,which were in chloroplast.The number of transmembrane regions of each NRAMP protein was different.The distribution of most NRAMP genes on chromosomes was dispersive while NRAMP9,NRAMP10 and NRAMP11 were located on one chromosome.The primary secondary structure of all the proteins was α-helix,but the number in each member was not the same.
In order to study the structure and function of NRAMP(Natural sesistance-associated macrophage protein) family members,the bioinformatics methods were used to obtain the NRAMP gene sequences of Glycyrrhiza uralensis from the genomic database,and the phylogenetic relationship,gene structure,conserved domain,conserved motif,secondary structure and tertiary structure were analyzed.The results showed 11 NRAMP family members were identified from the Glycyrrhiza uralensis genome.The gene structures and conserved motifs of NRAMPs were more similar among the members with closer evolutionary relationship.The relationship of GurNRAMP family members was closer to soybean than other plants.The amino acid residues of most NRAMP proteins were similar in number,ranging from 300 to 549,and the subcellular localization of them was on cell membrane.Particularly,GurNRAMP7 and GurNRAMP8 had larger molecular weight and different subcellular localization,which were in chloroplast.The number of transmembrane regions of each NRAMP protein was different.The distribution of most NRAMP genes on chromosomes was dispersive while NRAMP9,NRAMP10 and NRAMP11 were located on one chromosome.The primary secondary structure of all the proteins was α-helix,but the number in each member was not the same.
引文
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[13] MOCHIDA K,SAKURAI T,SEKI H,et al.Draft genome assembly and annotation of Glycyrrhiza uralensis,a medicinal legume[J].Plant Journal,2017,89(2):181-194.
[14] 钟静,吴小明,胡颖.大豆FLAs蛋白理化性质和结构特征的生物信息学分析[J].河南农业科学,2017,46(3):34-40.
[15] LARKIN M A,BLACKSHIELDS G,BROWN N P,et al.Clustal W and Clustal X version 2.0[J].Bioinforma-tics,2007,23(21):2947-2948.
[16] CANNON S B,MITRA A,BAUMGARTEN A,et al.The roles of segmental and tandem geneduplication in the evolution of large gene families in Arabidopsis thaliana[J].BMC Plant Biology,2004,4(1):10.
[17] 胡润芳,林国强,张广庆,等.大豆Nramp基因家族的序列特征与亲缘关系分析[J].分子植物育种,2011,9(2):245-250.
[2] HOSSEINZADEH H,NASSIRI-ASL M.Pharmacological effects of Glycyrrhiza spp.and its bioactive constituents:Update and review[J].Phytotherapy Research,2015,29(12):1868-1886.
[3] 赵连华,杨银慧,胡一晨,等.我国中药材中重金属污染现状分析及对策研究[J].中草药,2014,45(9):1199-1206.
[4] CELLIER M,PRIVé G,BELOUCHI A,et al.Nramp defines a family of membrane proteins[J].Proceedings of the National Academy of Sciences of the United States of America,1995,92(22):10089-10093.
[5] MANI A,SANKARANARAYANAN K.In silico analysis of natural resistance-associated macrophage protein(NRAMP) family of transporters in rice[J].Protein Journal,2018,37(3):237-247.
[6] 戚金亮,韩振海,印莉萍.Nramp基因家族及其功能[J].微生物学报,2003,43(2):293-297.
[7] VIDAL S M,MALO D,VOGAN K,et al.Natural resistance to infection with intracellular parasites:Isolation of a candidate for Bcg[J].Cell,1993,73(3):469-485.
[8] GOVONI G,GROS P.Macrophage NRAMP1 and its role in resistance to microbial infections[J].Inflammation Research,1998,47(7):277-284.
[9] XIONG H C,KOBAYASHI T,KAKEI Y,et al.AhNRAMP1 iron transporter is involved in iron acquisition in peanut[J].Journal of Experimental Botany,2012,63(12):4437-4446.
[10] THOMINE S,LELIèVRE F,DEBARBIEUX E,et al.AtNRAMP3,a multispecific vacuolar metal transporter involved in plant responses to iron deficiency[J].Plant Journal,2003,34(5):685-695.
[11] LANQUAR V,RAMOS M S,LELIèVRE F A,et al.Export of vacuolar manganese by AtNRAMP3 and AtNRAMP4 is required for optimal photosynthesis and growth under manganese deficiency[J].Plant Physiology,2010,152(4):1986-1999.
[12] POTTIER M,OOMEN R,PICCO C,et al.Identification of mutations allowing natural resistance associated macrophage proteins(NRAMP) to discriminate against cadmium[J].Plant Journal,2015,83(4):625-637.
[13] MOCHIDA K,SAKURAI T,SEKI H,et al.Draft genome assembly and annotation of Glycyrrhiza uralensis,a medicinal legume[J].Plant Journal,2017,89(2):181-194.
[14] 钟静,吴小明,胡颖.大豆FLAs蛋白理化性质和结构特征的生物信息学分析[J].河南农业科学,2017,46(3):34-40.
[15] LARKIN M A,BLACKSHIELDS G,BROWN N P,et al.Clustal W and Clustal X version 2.0[J].Bioinforma-tics,2007,23(21):2947-2948.
[16] CANNON S B,MITRA A,BAUMGARTEN A,et al.The roles of segmental and tandem geneduplication in the evolution of large gene families in Arabidopsis thaliana[J].BMC Plant Biology,2004,4(1):10.
[17] 胡润芳,林国强,张广庆,等.大豆Nramp基因家族的序列特征与亲缘关系分析[J].分子植物育种,2011,9(2):245-250.