LC-MS Based Draft Map of the Arabidopsis thaliana Nuclear Proteome and Protein Import in Pattern Triggered Immunity

An LC-MS based discovery proteomics approach was used to measure the nuclear proteome fractions of Arabidopsis thaliana cell culture. An enrichment score based on the relative abundance of cytoplasmic, mitochondrial and golgi markers in the nuclear protein fraction allowed us to curate the nuclear proteome producing high quality catalogs of around 3,000 nuclear proteins under untreated and both PTI conditions (flg22 and nlp20). The measurements also covered low abundant proteins including more than 100 transcription factors and transcriptional co-activators. Here we sought to gain a broader impression of protein import to the nucleus upon stimulus with flg22 and nlp20. Furthermore, the abundance of 93 proteins changed significantly in the nucleus following elicitation of immunity. These results suggest promiscuous ribosome assembly and retrograde signaling from the mitochondrion to the nucleus including Prohibitins and Cytochrome C, in the two forms of PTI.