Genome-wide identification and evolutionary analyses of the PP2C gene family with their expression profiling in response to multiple stresses in Brachypodium distachyon.
Genome-wide identification and evolutionary analyses of the PP2C gene family with their expression profiling in response to multiple stresses in Brachypodium distachyon.
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DOI：
10.1186/s12864-016-2526-4
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发表时间：
2016-03-03
期刊：
影响因子：
4.4
通讯作者：
Chu Z
中科院分区：
文献类型：
--
作者：
Cao J;Jiang M;Li P;Chu Z
2C型蛋白磷酸酶（PP 2Cs）在植物逆境信号转导中起重要作用，负调控阿坝反应和MAPK级联途径。二穗短柄草是研究温带禾本科、谷类和生物燃料作物功能基因组学的新模式植物。迄今为止，在B.二穗子还没有被研究过。本研究对86个B. B.鉴定了二穗子。基于结构域的PP 2C蛋白的分析表明，它们都含有磷酸酶结构域，具有11个保守的签名基序。虽然不是所有的磷酸酶结构域的BdPP 2C成员包括所有的11个图案，三级结构分析表明，四个残基有助于镁/锰离子（Mg 2 +/Mn 2+）的协调是保守的，除了两个非典型的成员。染色体定位分析表明，BdPP 2C基因大多位于CpG低密度区。B的系统树和同线区组分析。二穗草、拟南芥和水稻的PP 2C基因在遗传学上可分为13个亚群（A-M），BdPP 2C与OsPP 2C的亲缘关系比AtPP 2C近。节段性重复尤其有助于BdPP 2C基因家族的扩展，并且所有重复的BdPP 2C主要由纯化选择进化而来。实时定量逆转录PCR（qRT-PCR）分析表明BdPP 2Cs在不同组织中广泛表达。我们还发现，几乎所有的成员都表现出上调响应非生物胁迫，如冷，热，PEG和NaCl处理，但下调生物胁迫，如Ph 14，Guy 11和F0968感染。在本研究中，首次在一个新的模式单子叶植物中，对PP 2C基因家族的全基因组鉴定和蛋白质结构域的表征、系统发育关系、基因和蛋白质结构、染色体定位和表达模式进行了全面分析，B。二穗子本研究结果为其他物种PP 2C基因家族的全基因组鉴定提供了参考，也为进一步研究B中PP 2C基因的功能奠定了基础。二穗子本文的在线版本（doi：10.1186/s12864-016-2526-4）包含补充材料，可供授权用户使用。
The type-2C protein phosphatases (PP2Cs), negatively regulating ABA responses and MAPK cascade pathways, play important roles in stress signal transduction in plants. Brachypodium distachyon is a new model plant for exploring the functional genomics of temperate grasses, cereals and biofuel crops. To date, genome-wide identification and analysis of the PP2C gene family in B. distachyon have not been investigated. In this study, 86 PP2C genes in B. distachyon were identified. Domain-based analyses of PP2C proteins showed that they all contained the phosphatase domains featured as 11 conserved signature motifs. Although not all phosphatase domains of BdPP2C members included all 11 motifs, tertiary structure analysis showed that four residues contributing to magnesium/manganese ions (Mg2+/Mn2+) coordination were conserved, except for two noncanonical members. The analysis of their chromosomal localizations showed that most of the BdPP2C genes were located within the low CpG density region. Phylogenetic tree and synteny blocks analyses among B. distachyon, Arabidopsis thaliana and Oryza sativa revealed that all PP2C members from the three species can be phylogenetically categorized into 13 subgroups (A–M) and BdPP2Cs were evolutionarily more closely related to OsPP2Cs than to AtPP2Cs. Segmental duplications contributed particularly to the expansion of the BdPP2C gene family and all duplicated BdPP2Cs evolved mainly from purifying selection. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis showed that BdPP2Cs were broadly expressed in disparate tissues. We also found that almost all members displayed up-regulation in response to abiotic stresses such as cold, heat, PEG and NaCl treatments, but down-regulation to biotic stresses such as Ph14, Guy11 and F0968 infection. In the present study, a comprehensive analysis of genome-wide identification and characterization of protein domains, phylogenetic relationship, gene and protein structure, chromosome location and expression pattern of the PP2C gene family was carried out for the first time in a new model monocot, i.e., B. distachyon. Our results provide a reference for genome-wide identification of the PP2C gene family of other species and also provide a foundation for future functional research on PP2C genes in B. distachyon. The online version of this article (doi:10.1186/s12864-016-2526-4) contains supplementary material, which is available to authorized users.