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Int. J. Mol. Sci. 2016, 17(11), 1738; doi:10.3390/ijms17111738

Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.)

1
College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
College of Environmental and Biological Engineering, Putian University, Putian 351100, China
*
Authors to whom correspondence should be addressed.
Academic Editor: Marcello Iriti
Received: 26 July 2016 / Revised: 4 October 2016 / Accepted: 11 October 2016 / Published: 11 November 2016
(This article belongs to the Section Molecular Botany)
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Abstract

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. View Full-Text
Keywords: rice (Oryza sativa L.); single nucleotide polymorphisms (SNPs); protein phosphorylation; impact rice (Oryza sativa L.); single nucleotide polymorphisms (SNPs); protein phosphorylation; impact
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Lin, S.; Chen, L.; Tao, H.; Huang, J.; Xu, C.; Li, L.; Ma, S.; Tian, T.; Liu, W.; Xue, L.; Ai, Y.; He, H. Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.). Int. J. Mol. Sci. 2016, 17, 1738.

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