446 / 2019-02-19 02:11:31

Digging deep into the proteome, phosphoproteome and transcriptome of Arabidopsis

Proteomics, Phosphorylation, Co-expression

全体主题 > Systems Biology

Recent years have seen a surge in publications quantifying transcript and/or protein abundance across different tissues in a range of organisms. Many of these studies are of considerable depth, however only few of them extracted both mRNA and protein from matched samples. Here, we used state of the art mass spectrometry and RNA-sequencing to profile 30 matched Arabidopsis tissues collected from adult plants, seedlings or cell culture.
We generated an extensive atlas of transcript, protein and phosphorylation site abundance and on average identified 17,603 +/- 1,317 transcripts and 14,430 +/- 911 unambiguous proteins. More than 90 % of all proteins were covered by three or more peptides, providing a robust basis for both protein identification and quantification. In addition, we detected 8,577 proteins (31 %) with at least one phosphorylated amino acid, totalling 43,903 phosphorylation sites with tissue-resolved quantitative information. To our knowledge, this dataset represents the most comprehensive atlas of transcript, protein and phosphorylation site abundance in Arabidopsis thaliana to date. Using this resource we compared transcript and protein abundance, built co-expression networks, investigated protein complexes and examined kinase and phosphatase expression patterns to gain more knowledge about the players in hormone-mediated signalling and development.