Cao Jianmei, Jiang Min, Li Peng, Chu Zhaoqing
Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China.
BMC Genomics. 2016 Mar 3;17:175. doi: 10.1186/s12864-016-2526-4.
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 (Mg(2+)/Mn(2+)) 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.
2C型蛋白磷酸酶（PP2C）负调控脱落酸应答和丝裂原活化蛋白激酶（MAPK）级联途径，在植物胁迫信号转导中发挥重要作用。短柄草是探索温带禾本科植物、谷类作物和生物燃料作物功能基因组学的新型模式植物。迄今为止，尚未对短柄草中PP2C基因家族进行全基因组鉴定和分析。
本研究在短柄草中鉴定出86个PP2C基因。基于结构域对PP2C蛋白进行分析，结果表明它们均含有具有11个保守特征基序的磷酸酶结构域。虽然并非所有短柄草PP2C成员的磷酸酶结构域都包含全部11个基序，但三级结构分析表明，除两个非典型成员外，参与镁/锰离子（Mg(2+)/Mn(2+)）配位且保守的四个残基均存在。对其染色体定位进行分析，结果表明大多数短柄草PP2C基因位于低CpG密度区域。对短柄草、拟南芥和水稻进行系统发育树和共线性分析，结果表明来自这三个物种的所有PP2C成员在系统发育上可分为13个亚组（A - M），且短柄草PP2C在进化上与水稻PP2C的关系比与拟南芥PP2C的关系更为密切。片段重复对短柄草PP2C基因家族的扩增贡献尤为显著，所有重复的短柄草PP2C主要通过纯化选择进化而来。实时定量逆转录PCR（qRT-PCR）分析表明，短柄草PP2C在不同组织中广泛表达。我们还发现，几乎所有成员在受到冷、热、聚乙二醇（PEG）和氯化钠（NaCl）处理等非生物胁迫时表达上调，但在受到诸如Ph14、Guy11和F0968感染等生物胁迫时表达下调。
在本研究中，首次在新型单子叶模式植物即短柄草中，对PP2C基因家族进行全基因组鉴定，并对其蛋白结构域、系统发育关系、基因和蛋白质结构、染色体定位及表达模式进行了综合分析。我们的研究结果为其他物种PP2C基因家族的全基因组鉴定提供了参考，也为短柄草中PP2C基因的后续功能研究奠定了基础。
