Location, location, location: exploration of the spatial proteome of plants

The development of organelles is an important hallmark of evolution. Organelles offer unique micro-environments in the cell where a broader range of proteins can function, and provide an additional layer of regulation by separating or concentrating proteins. Hence, many cellular processes involve movement of proteins between organelles and subcellular localization of proteins can often be linked to their functions. The systematic assessment of the localization of proteins is therefore insightful, but also technically challenging.

In plants specifically, the presence of a rigid cell wall and organelles such as chloroplasts and large vacuoles add to the challenges. Hence, knowledge about the spatial proteome of plants is lacking compared to other eukaryotes, which complicates the assignment of functions to genes. To address this problem, we used our expertise on both plant biology and proteomics to adapt pre-existing methods from the broader spatial proteomics field for use in plants.

We were not only able to obtain spatial data on the widely used model plant Arabidopsis thaliana, but also on the less well known evolutionary model Marchantia polymorpha, one of the first plants to grow on land. Furthermore, we compared the spatial proteome of cultured cells, organs and whole organisms to study the differences of the spatial proteome. Additionally, we used a cross-linking approach to study protein complexes in their spatial context. Lastly, we show that these approaches not only offer static maps of protein subcellular localization, but can also be used to detect proteins that move between organelles in different conditions or genetic backgrounds. As an example we treated Arabidopsis roots with the protein trafficking disrupting drug Brefeldin-a, identified the translocating proteins and confirmed a number of those translocations in planta.

Summarizing, we will present not only an extensive resource of protein subcellular localization and complex formation in plants, but also a strategy to identify translocating proteins during a great variety of processes at the subcellular level.