[1]陈超,端木慧子,朱丹,等.大豆CML家族基因的生物信息学分析[J].大豆科学,2015,34(06):957-963.[doi:10.11861/j.issn.1000-9841.2015.06.0957]
　CHEN Chao,DUANMU Hui-zi,ZHU Dan,et al.Bioinformatics Analysis of GmCML Genes in Soybean Genome[J].Soybean Science,2015,34(06):957-963.[doi:10.11861/j.issn.1000-9841.2015.06.0957]
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大豆CML家族基因的生物信息学分析

《大豆科学》[ISSN:1000-9841/CN:23-1227/S] 卷: 第34卷 期数: 2015年06期 页码: 957-963 栏目: 出版日期: 2015-12-25
Title:
Bioinformatics Analysis of GmCML Genes in Soybean Genome
作者:
陈超; 端木慧子; 朱丹; 刘艾林; 肖佳雷; 朱延明
东北农业大学 农业生物功能基因重点实验室，黑龙江 哈尔滨 150030
Author(s):
CHEN Chao;  DUANMU Hui-zi;  ZHU Dan;  LIU Ai-lin;  XIAO Jia-lei;  ZHU Yan-ming
Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China
关键词:
大豆; CMLs; EF-hand; 生物信息学; 进化分析
Keywords:
Soybean;  CMLs;  EF-hand;  Bioinformatics;  Evolution analysis
DOI:
10.11861/j.issn.1000-9841.2015.06.0957
文献标志码:
A
摘要:
CMLs蛋白是一类具有Ca2+结合的EF-hand保守结构域蛋白，广泛参与钙依赖的信号传导途径，在植物生长发育及生物胁迫与非生物胁迫响应中起着重要的作用。通过NCBI和植物基因组注释数据库等筛选并获得了68个大豆GmCML蛋白；分析了所有蛋白的基本特性；通过与拟南芥CMLs基因的进化树分析表明，GmCML家族基因属于8个亚类；对GmCML家族基因进行了染色体定位与重复基因进化关系分析，发现其具有较高的进化速率；序列比对发现GmCML类蛋白含有2~4个保守的EF-hand结构域；利用芯片数据对野生大豆在碱胁迫下的叶和根中的CMLs基因表达模式进行了分析，得到26个GsCML基因在碱胁迫下有显著的差异表达，且在根和叶中的差异表达模式不同，表明这些基因参与植物碱胁迫应答，且具组织表达特异性。
Abstract:
CMLs is a kind of calcium-binding proteins with conserved EF-hand motifs, play an important role in calcium-dependent signaling pathway and play a key role in response to plant development and abiotic and bioticstresses.In this study, we identified and characterized 68 soybean CML through plant genome annotation and NCBI database. Phylogenetic analysis suggested that these GmCML genes could be classified into eight groups,combining with Arabidopsis CMLs. Furthermore, physical locations and gene duplications showed a higher evolution rate of GmCML Sequence alignment confirmed that this family proteins contain 2- 4 conserved EF-hand motifs.Expression profiles of all CML-transcripts from bicarbonate stress treated G.soja showed that there were 26 differently expressed GmCMLs. The transcript pattern in leaves and in roots was different.These results suggest that those genes may play important roles in plant environmental stress responses and adaptation, with different function in leaf and root.

参考文献/References:

［1］Day I S, Reddy V S, Shad G A, et al.Analysis of EF-hand-containing proteins in Arabidopsis［J］.Genome Biology, 2002, 3(10):1-24.

［2］Hashimoto K, Kudla J.Calcium decoding mechanisms in plants［J］.Biochimie, 2011,93: 2054-2059
［3］Reddy A S. Calcium: Silver bullet in signaling［J］.Plant Science，2001,160:381-404.
［4］Kretsinger R H, Nockolds C E. Carp muscle calcium-binding protein.II.Structure determination and general description［J］.The Journal of Biological Chemistry, 1973,248: 3313-3326
［5］Perochon A, Aldon D, Galaud J P, et al.Calmodulin and calmodulin-like proteins in plant calcium signaling［J］.Biochimie, 2011, 93: 2048-2053.
［6］Boonburapong B, Buaboocha T.Genome-wide identification and analyses of the rice calmodulin and related potential calciumsensor proteins［J］.BMC Plant Biology, 2007, 7: 4
［7］McCormack E, Braam J. Calmodulins and related potential calcium sensors of Arabidopsis［J］.New Phytologist, 2003,159: 585-598
［8］Delk N A, Johnson K A, Chowdhury N I, et al.CML24, regulated in expression by diverse stimuli, encodes a potential Ca2+sensor that functions in responses to abscisicacid, daylength, and ion stress［J］. Plant Physiology, 2005,139: 240-253.［9］Dobney S, Chiasson D, Lam P, et al.The calmodulin-related calcium sensor CML42 plays a role in trichome branching［J］. Journal of Biological Chemistry, 2009,284: 31647-31657
［10］Magnan F, Ranty B, Charpenteau M,et al.Mutations in AtCML9, a calmodulin-like protein from Arabidopsis thaliana, alter plant responses to abiotic stress and abscisic acid［J］.Plant Journal, 2008, 56: 575-589
［11］Larkin M A, Blackshields G, Brown N P, et al.Higgins DG:Clustal W and Clustal X version 2.0［J］. Bioinformatics, 2007,23:2947-2948.
［12］Tamura K, Peterson D, Peterson N,et al.Kumar S:MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance, and maximum parsimony methods［J］.Molecular Biology and Evolution, 2011,28:2731-2739.
［13］Yang S, Zhang X, Yue J X,et al.Recent duplications dominate NBS-encoding gene expansion in two woody species［J］. Molecular Genetics and Genomics, 2008,280:187-198.
［14］Gu Z, Cavalcanti A, Chen F C, et al. Extent of gene duplicationin the genomes of drosophila, nematode, and yeast［J］.Molecular Biology and Evolution, 2002,19:256-262
［15］Ge Y, Li Y, Zhu Y M,et al.Global Transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3?treatment［J］.BMC Plant Biology, 2010, 10:153.
［16］Ge Y, Li Y, Lyu D K, et al.Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors［J］.Functional & Integrative Genomics, 2011, 11:369-379.
［17］McCormack E, Braam J. Calmodulins and related potential calcium sensors of Arabidopsis［J］.New Phytologist, 2003, 159: 585-598
［18］Boonburapong B, Buaboocha T. Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins［J］.BMC Plant Biology, 2007, 7:4.
［19］孙红正,葛颂.重复基因的进化－回顾与进展［J］.植物学报,2010, 45(1): 13-22.(Sun H Z, Ge S.The evolution of the duplicated genes -review and progress［J］Chinese Bulletin of Botany,2010,45(1):13-22)
［20］Thomas A D, Kyle W B, Wayne A S.Breaking the code: Ca2+sensors in plant signaling［J］. Biochemical Journal, 2010, 425: 27-40.

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备注/Memo

基金项目：转基因生物新品种培育重大专项(2011ZX08004-002)；国家自然科学基金(31171578)；黑龙江省高校科技创新团队建设计划(2011TD055)；国家基础科学人才培养基金(J1210069)。

第一作者简介：陈超（1988-），男，硕士，主要从事植物分子生物学与基因工程研究。E-mail:chenchaochenchao09@163.com。
通讯作者：朱延明（1955-），男，教授，博导，主要从事植物分子生物学与基因工程研究。E-mail:ymzhu2001@neau.edu.cn。

更新日期/Last Update: 2016-01-05