Comparative analysis of RNA-binding proteomes under Arabidopsis thaliana-Pst DC3000-PAMP interaction by orthogonal organic phase separation

Abstract

RNA-binding proteins (RBPs) are pivotal participants in post-transcriptional gene regulation. They interact with RNA directly to perform several post-transcriptional RNA regulatory functions or direct metabolic processes. Despite the essential importance, the understanding of plant RBPs is elementary, which derives mainly from other kingdoms via bioinformatic extrapolation or mRNA-binding proteins captured through UV crosslinked method. Recently, orthogonal organic phase separation (OOPS) method for RBP identification has been used in mammals and Escherichia coli. And plentiful RBPs were enriched without molecular tagging or capture of polyadenylated RNA in an unbiased way. In our study, OOPS was conducted on Arabidopsis and 468 RBPs were discovered including 244 putative RBPs. There were 17 peroxidases in 232 RBPs with enzymatic activities. In addition, Arabidopsis thaliana-Pst DC3000-chitinpentaose interaction system was chosen to explore whether OOPS can be used to dig specific RBPs under special physiological conditions. Eighty-four differential RBPs in this system were found and some of them involved in reactive oxygen species (ROS) metabolic pathway. These results showed OOPS can be applied to plants successfully and would be a useful method to identify RBPomes and specific RBPs.