Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis.
Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis.
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DOI：
10.1186/1471-2164-9-550
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发表时间：
2008-11-20
期刊：
影响因子：
4.4
通讯作者：
Zhong, Yuan
中科院分区：
文献类型：
--
作者：
Xue, Tongtong;Wang, Dong;Zhang, Shizhong;Ehlting, Juergen;Ni, Fei;Jakab, Stephen;Zheng, Chengchao;Zhong, Yuan
来自各种生物体的蛋白磷酸酶2c （pp2c）被认为是参与各种环境应激反应和发育过程的蛋白激酶途径的负调节因子。目前还没有关于植物中PP2C基因家族的全基因组综述。综合计算分析，在拟南芥（Arabidopsis thaliana, atpp2c）和水稻（Oryza sativa, ospp2c）中分别鉴定出80个和78个PP2C基因，这表明PP2C基因家族是植物中鉴定出的最大家族之一。系统发育分析将拟南芥和水稻的pp2c分别划分为13个亚家族和11个亚家族，基因结构和蛋白基序分析也支持了这一结论。通过对拟南芥和水稻中PP2C基因的比较分析，确定了共同和谱系特异性亚家族以及潜在的“基因生与死”事件。基因重复分析表明，ospp2c和atpp2c扩增的主要原因是全基因组和染色体片段重复，但串联或局部重复在拟南芥中的发生频率低于水稻。一些蛋白基序在PP2C蛋白中广泛存在，而其他一些基序仅针对一两个亚家族。表达模式分析表明：1)两个物种中大部分PP2C基因在多个组织中发挥功能作用；2)多种刺激诱导A亚家族大部分基因的表达表明其主要参与胁迫耐受，尤其是ABA应答；3)D亚家族成员的表达模式表明它们可能在ABA介导的信号通路中构成正调控因子。通过两种方法对推测的上游调控元件的分析进一步支持了A亚家族在ABA信号传导中的功能，并为双子叶和单子叶植物共享和不同的转录调控机制提供了见解。本研究对拟南芥和水稻PP2C家族的全基因组比较综述提供了PP2C基因在双子叶和单子叶中的功能和调控机制，以及PP2C基因在双子叶和单子叶中的进化和分化的见解。生物信息学分析表明，来自不同亚家族的植物PP2C蛋白参与不同的信号通路。我们的研究结果为进一步研究不同PP2C亚家族的功能分化奠定了坚实的基础。
The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes. A genome-wide overview of the PP2C gene family in plants is not yet available. A comprehensive computational analysis identified 80 and 78 PP2C genes in Arabidopsis thaliana (AtPP2Cs) and Oryza sativa (OsPP2Cs), respectively, which denotes the PP2C gene family as one of the largest families identified in plants. Phylogenic analysis divided PP2Cs in Arabidopsis and rice into 13 and 11 subfamilies, respectively, which are supported by the analyses of gene structures and protein motifs. Comparative analysis between the PP2C genes in Arabidopsis and rice identified common and lineage-specific subfamilies and potential 'gene birth-and-death' events. Gene duplication analysis reveals that whole genome and chromosomal segment duplications mainly contributed to the expansion of both OsPP2Cs and AtPP2Cs, but tandem or local duplication occurred less frequently in Arabidopsis than rice. Some protein motifs are widespread among the PP2C proteins, whereas some other motifs are specific to only one or two subfamilies. Expression pattern analysis suggests that 1) most PP2C genes play functional roles in multiple tissues in both species, 2) the induced expression of most genes in subfamily A by diverse stimuli indicates their primary role in stress tolerance, especially ABA response, and 3) the expression pattern of subfamily D members suggests that they may constitute positive regulators in ABA-mediated signaling pathways. The analyses of putative upstream regulatory elements by two approaches further support the functions of subfamily A in ABA signaling, and provide insights into the shared and different transcriptional regulation machineries in dicots and monocots. This comparative genome-wide overview of the PP2C family in Arabidopsis and rice provides insights into the functions and regulatory mechanisms, as well as the evolution and divergence of the PP2C genes in dicots and monocots. Bioinformatics analyses suggest that plant PP2C proteins from different subfamilies participate in distinct signaling pathways. Our results have established a solid foundation for future studies on the functional divergence in different PP2C subfamilies.
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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
11.6
作者：
Leonhardt, N;Kwak, JM;Schroeder, JI
通讯作者：
Schroeder, JI
影响因子：
4.4
作者：
Gómez-Porras JL;Riaño-Pachón DM;Dreyer I;Mayer JE;Mueller-Roeber B
通讯作者：
Mueller-Roeber B
DOI：
10.1073/pnas.1932072100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Kent, WJ;Baertsch, R;Haussler, D
通讯作者：
Haussler, D
影响因子：
4.8
作者：
Gaits, F;Shiozaki, K;Russell, P
通讯作者：
Russell, P