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

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 . 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.

Interactive Effects of Elevated [CO2] and Water Stress on Physiological Traits and Gene Expression during Vegetative Growth in Four Durum Wheat Genotypes

“…This fact could indicate that a stimulation of plant growth may be associated with a lower investment of resources (mainly N) in Rubisco protein, especially under elevated [CO 2 ], thus leading to a higher nitrogen efficiency (Pang et al, 2014; Carmo-Silva et al, 2015). The negative correlation between transcript levels of CAT and chlorophyll content highlighted that the up-regulation of CAT expression was a response to the high H 2 O 2 levels generated under stress conditions (Luna et al, 2005), which could promote chlorophyll degradation (Upadhyaya et al, 2007). Interestingly, transcript levels of CAT were positively correlated with g s , although a negative correlation should be expected since greater g s leads to lower photorespiration rates and consequently lower H 2 O 2 generation (Luna et al, 2005).…”

Differences in the genomic diversity, structure, and inbreeding patterns in wild and managed populations of Agave potatorum Zucc. used in the production of Tobalá mezcal in Southern Mexico

“…We found that the highest number of outlier loci with possible selection signals were related to molecular processes, of which we think the most noteworthy was related to protein phosphorylation, which plays an essential role in signal transduction and has a vital role in the life cycle of plants [88][89][90][91]. We also detected outlier loci related to protein kinase activity.…”