Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.).
Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.).
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SNP 对水稻蛋白质磷酸化状态的影响 (Oryza sativa L.)
DOI：
10.3390/ijms17111738
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发表时间：
2016-11-11
影响因子：
5.6
通讯作者：
He H
中科院分区：
文献类型：
--
作者：
Lin S;Chen L;Tao H;Huang J;Xu C;Li L;Ma S;Tian T;Liu W;Xue L;Ai Y;He H
单核苷酸多态性（single nucleotide polymorphisms，SNPs）在功能基因组学和遗传学研究中有着广泛的应用。高质量的水稻基因组序列的获得，为研究水稻全基因组的SNP和蛋白质组提供了重要的资源。然而，SNPs对水稻蛋白质磷酸化状态的影响尚未完全了解。本文首先基于水稻新基因组Ver. 7.0的方法，系统分析了非同义SNPs（nsSNPs）对蛋白质磷酸化状态的潜在影响。Ver. 7.0水稻基因组中，nsSNPs占9.9%。水稻蛋白质组中共有2，508，261个磷酸化位点。有趣的是，我们观察到150，197（39.1%）个nsSNPs可以影响蛋白质磷酸化状态，其中52.2%可能导致相邻磷酸化位点的蛋白激酶（PK）类型的变化。我们建立了一个数据库SNP_rice，存款保存最新的水稻SNP资源和SNP信息。学术研究人员可在http://bioinformatics.fafu.edu.cn上免费获得该报告。作为一个案例研究，我们检测到5个nsSNPs可能影响异源三聚体G蛋白磷酸化状态的水稻，表明遗传多态性通过影响异源三聚体G蛋白的磷酸化状态来影响信号转导。本研究结果可为今后的实验鉴定提供有用的资源，并为更好的水稻育种提供有趣的信息。
Single nucleotide polymorphisms (SNPs) are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs) on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1%) nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK) types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at http://bioinformatics.fafu.edu.cn. As a case study, we detected five nsSNPs that potentially influenced heterotrimeric G proteins phosphorylation status in rice, indicating that genetic polymorphisms showed impact on the signal transduction by influencing the phosphorylation status of heterotrimeric G proteins. The results in this work could be a useful resource for future experimental identification and provide interesting information for better rice breeding.