Genome-Wide Identification, Evolution, and Co-expression Network Analysis of Mitogen-Activated Protein Kinase Kinase Kinases in Brachypodium distachyon.
Genome-Wide Identification, Evolution, and Co-expression Network Analysis of Mitogen-Activated Protein Kinase Kinase Kinases in Brachypodium distachyon.
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二穗短柄草中有丝分裂原激活蛋白激酶激酶的全基因组鉴定、进化和共表达网络分析
DOI：
10.3389/fpls.2016.01400
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发表时间：
2016
影响因子：
5.6
通讯作者：
Nie X
中科院分区：
文献类型：
--
作者：
Feng K;Liu F;Zou J;Xing G;Deng P;Song W;Tong W;Nie X
丝裂原活化蛋白激酶（Mitogen-activated protein kinase， MAPK）级联是所有真核生物中保守的通用信号转导模块，在植物生长发育和多种胁迫响应中起着至关重要的作用。本研究利用生物信息学方法鉴定了短柄茅73个MAPKKK基因编码的86个MAPKKK蛋白。对拟南芥、水稻和短茅的MAPKKK家族进行系统发育分析，将其划分为3个亚家族，其中MEKK亚家族28个，Raf亚家族52个，ZIK亚家族6个。激酶结构域的保守蛋白基序、外显子-内含子组织和剪接内含子阶段支持从系统发育分析中推断的进化关系。基因重复分析表明，染色体片段重复发生在水稻和短柄茅分化之前，而3对串联重复基因都发生在它们分化之后。我们进一步证明了MAPKKKs在强烈的净化选择下进化，这意味着它们的保守性。剪接转录本表达分析表明，剪接体翻译最长蛋白倾向于被采用。此外，bdmapkkk基因在不同器官和发育阶段以及高温、病毒和干旱胁迫下的表达分析表明，MAPKKK基因参与了多种信号通路。节律分析表明，短柄藓有41个MAPKKK基因在至少一种条件下循环表达，其中7个MAPKKK基因在所有条件下都表达，启动子分析表明这些基因具有许多参与昼夜节律和光反应的顺式调控元件。最后，利用144个芯片和RNA-seq数据集构建了MAPK、MAPKK和MAPKKK在短柄植物中的共表达网络，并预测了10个潜在的MAPK级联通路。综上所述，本研究为短柄植物MAPKKK家族的进化和功能表征提供了重要信息，这将有助于BdMAPKKK基因的功能分析，也将有助于更好地理解短柄植物及其他植物的MAPK信号通路。
Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development, and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes in Brachypodium. Phylogenetic analysis of MAPKKK family from Arabidopsis, rice, and Brachypodium has classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf, and 6 to ZIK subfamily, respectively. Conserved protein motif, exon-intron organization, and splicing intron phase in kinase domains supported the evolutionary relationships inferred from the phylogenetic analysis. And gene duplication analysis suggested the chromosomal segment duplication happened before the divergence of the rice and Brachypodium, while all of three tandem duplicated gene pairs happened after their divergence. We further demonstrated that the MAPKKKs have evolved under strong purifying selection, implying the conservation of them. The splicing transcripts expression analysis showed that the splicesome translating longest protein tended to be adopted. Furthermore, the expression analysis of BdMAPKKKs in different organs and development stages as well as heat, virus and drought stresses revealed that the MAPKKK genes were involved in various signaling pathways. And the circadian analysis suggested there were 41 MAPKKK genes in Brachypodium showing cycled expression in at least one condition, of which seven MAPKKK genes expressed in all conditions and the promoter analysis indicated these genes possessed many cis-acting regulatory elements involved in circadian and light response. Finally, the co-expression network of MAPK, MAPKK, and MAPKKK in Brachypodium was constructed using 144 microarray and RNA-seq datasets, and ten potential MAPK cascades pathway were predicted. To conclude, our study provided the important information for evolutionary and functional characterization of MAPKKK family in Brachypodium, which will facilitate the functional analysis of BdMAPKKK genes, and also will facilitate better understanding the MAPK signal pathway in Brachypodium and beyond.
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影响因子：
3.7
作者：
Chen L;Hu W;Tan S;Wang M;Ma Z;Zhou S;Deng X;Zhang Y;Huang C;Yang G;He G
通讯作者：
He G
DOI：
10.1073/pnas.0907205106
发表时间：
2009-12-01
影响因子：
11.1
作者：
Jammes, Fabien;Song, Charlotte;Kwak, June M.
通讯作者：
Kwak, June M.
影响因子：
5.6
作者：
Çakır B;Kılıçkaya O
通讯作者：
Kılıçkaya O
DOI：
10.1073/pnas.011405198
发表时间：
2001-01-02
影响因子：
11.1
作者：
Frye, CA;Tang, DZ;Innes, RW
通讯作者：
Innes, RW
影响因子：
7.2
作者：
Huang, Yadong;Li, Chun Yao;Gibson, Susan I.
通讯作者：
Gibson, Susan I.