Protein-Protein Interaction Analysis in Plant Systems

Proteins rarely act in isolation; they assemble into dynamic complexes that underpin cellular processes such as signal transduction, metabolism and stress responses. In plant systems, the identification and characterisation of protein–protein interactions (PPIs) are central to understanding development, adaptation to environmental challenges and agricultural traits. Techniques to probe PPIs span from genetic and biochemical strategies to in vivo imaging, each offering distinct advantages. The yeast two‐hybrid system enables high‐throughput screening of binary interactions, whereas affinity purification coupled with mass spectrometry reveals complex networks in native contexts. Optical methods such as bimolecular fluorescence complementation (BiFC) and Förster resonance energy transfer (FRET) provide spatial and temporal resolution of interactions in living cells. Recent advances in co‐fractionation mass spectrometry have further mapped stable protein assemblies across multiple species, elucidating conserved complexes and novel assemblies that are crucial for processes such as vernalization, defence and metabolic regulation. Together, these approaches have expanded the plant interactome, linking protein connectivity to phenotypic outcomes and offering targets for crop improvement.

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Protein-Protein Interaction Analysis in Plant Systems publication trend

The graph below shows the total number of articles in protein-protein interaction analysis in plant systems across all publications each year (not limited to Nature Index journals).

Technical terms

Affinity purification mass spectrometry: A method that isolates protein complexes via tag‐based capture followed by mass spectrometric identification of interacting partners.

Bimolecular fluorescence complementation (BiFC): A technique in which two non-fluorescent fragments of a fluorescent protein are fused to candidate interactors and reconstitute fluorescence upon interaction.

Förster resonance energy transfer (FRET): A sensitive optical approach that measures energy transfer between two fluorophores in close proximity, indicating an interaction event.

Co-fractionation mass spectrometry: A strategy that separates native protein complexes by chromatography or centrifugation and profiles their composition by mass spectrometry.

Yeast two-hybrid (Y2H): A genetic system in yeast that detects binary protein interactions via transcriptional activation of a reporter gene.

References

1. Investigating the dynamics of protein–protein interactions in plants. The Plant Journal (2023).
2. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. Cell (2020).