gejaeGeert De Jaeger leads the Functional Interactomics Group.
The field of functional interactomics aims to map system-wide molecular interactions and analyze their function. This is of pivotal importance, as biological structures and functions are generally accomplished by networks of short- and long-term molecular interactions.     
As a technology-driven team, our research focuses on the continuous development and optimization of interactomics tools for plant research, more specifically for the discovery of protein-protein interactions and interactions between proteins and nucleic acids. At the core of our technology lies affinity purification coupled to mass spectrometry (AP-MS). The advantage of this approach is that interactions are mapped in situ, enabling proteome-wide investigation of interactions that occur inside plant cells.

We implement these interactomics tools to gain insight on how cell growth1 and proliferation2 are regulated in plants, and as such discover new avenues for the engineering of plant growth. Many important signaling pathways impinge on the growth and proliferation of cells in plants. However, signaling pathways involving key growth regulators such as nutrients remain to a large extent elusive in plants. To broaden our knowledge in these nutrient signaling pathways, we are studying protein complexes comprising the antagonistic target of rapamycin (TOR) and SNF1-related (SnRK1) kinases, two master regulators that integrate nutrient signaling with plant growth. ​ 

1. Van Leene, J. et al. Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. Nature Plants in press (2019).

2. Van Leene, J. et al. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol 6, 397 (2010).

Chromatin Complex Isolation iconThe TOR kinase is a central regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions.

Although the TOR pathway is conserved across eukaryotes, plants developed unique adaptations to this pathway to cope with their autotrophic and sessile nature. Overall, compared to other eukaryotic model species, the current knowledge of TOR signaling in plants is still scarce. Only few TOR pathway components are known and no phosphoproteome or interactome screens targeted to the TOR kinase have been performed.

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TAP iconWe offer the plant research community and companies access to our protein complex purification platform1,2,3.

Purifications under research service agreement are performed based on well-established protocols for complex purification from either the Arabidopsis cell suspension cultures PSB-D/L, seedlings or isolated plant tissues. We have recently been able to show that our complex purification technology performs equally well in crop species such as corn4,5 and rice6. We have extensive experience with tandem affinity purification (TAP) for the isolation of stable protein complexes at high purity, whereas for more short-term interactions, we apply pull-downs using GFP-containing tags, or a more efficient protocol based on the Protein A/G moiety present in our TAP tags. More recently, we have developed an approach to enrich for unstable protein interactions by means of protein cross-linking.

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