20.10.2020

Exploring the Arabidopsis proteome.

IPB proteomics experts recently succeeded in performing deep proteome analytics of Arabidopsis thaliana and gained numerous insights. For this purpose, a comprehensive extraction of tissue proteins with multi-step fractionation and subsequent MS analysis was performed. As a result of this deep sampling approach, about 10,000 proteins per tissue and almost 16,000 proteins over the entire life cycle of the plant could be defined and quantified. The resulting data set was then subjected to cluster analysis. This correlation analysis of protein abundance uncovered potentially new tissue- and development-specific expression patterns of entire signaling modules regulating the transcriptional processes of photosynthesis, seed development, senescence and abscission. Important insights were also gained in the field of plant immunity. In the deep proteomics approach designed for this purpose, Arabidopsis seedlings were first treated with the flg22 elicitor and then subjected to targeted proteome analysis as well as phytohormone and transcript measurements.

Although proteome biology is receiving increasing interest in recent years, in plants it proves especially difficult to realize due to their complex protein composition. In fact, to date, only a handful of true deep proteomics studies have been performed for maize, tomato and wheat. Last year, however, marked a milestone in Arabidopsis proteomics. In 2019, Zhang et al. published an outstanding paper on tissue-specific proteome remodeling in unprecedented resolution and detail. In 2020, Mergner et al. presented a tissue-specific expression atlas for Arabidopsis with 18,210 proteins and 43,903 phosphorylation sites in 30 tissues. The work of the IPB scientists around Wolfgang Hoehenwarter constitutes the third publication of this kind. Both the raw and meta data of this study is made available to the general public and will be a valuable resource to plant biologists.

Reference:
Mona Bassal, Mohammad Abukhalaf, Petra Majovsky, Domenika Thieme, Tobias Herr, Mohamed Ayash, Naheed Tabassum, Mhd Rami Al Shweiki, Carsten Proksch, Ali Hmedat, Jörg Ziegler, Justin Lee, Steffen Neumann & Wolfgang Hoehenwarter. Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity. Mol. Plant 2020, doi: 10.1016/j.molp.2020.09.024.