Molecular & Cell Biology

Physical interactions

The Rhee lab and former Frommer lab use high-throughput approaches to identify pairwise physical interactions among proteins, with a focus on membrane proteins and those involved in signaling. Over 65,000 interactions have been identified thus far. The team uses a screen called the mating-based protein complementation assay, or split ubiquitin system. Ubiquitin is a small protein. Candidate proteins are fused onto a version of ubiquitin that is split in half. When the two candidates interact, the two halves of the ubiquitin reassemble, triggering a process that liberates a transcription factor—a protein that switches a gene on—which then goes to the nucleus. When genes are turned on in the nucleus, the researchers are alerted to the successful interaction.

The Wang lab is dissecting protein-protein interactions and protein modifications using mass spectrometry, with a focus on proteins involved in signal transduction and gene expression in the cytosol and nucleus. Among their discoveries, a complete chain of protein interactions links the cell surface-localized brassinosterod receptor BRI1 to the nuclear transcription factor BZR1 and its thousands of target gene promoters; a module of interacting transcription regulators integrates multiple environmental and endogenous signals including light, temperature, pathogen signal, brassinosteroid, auxin, gibberellin, and sugar. 

Protein Localization

The Ehrhardt lab has developed a system for generating N-terminal fusions of GFP with random endogenous genes in the Arabidopsis genome, and used it to characterize the localizations and dynamics of 120 GFP-protein fusions. (Cutler et al, PNAS, 1999). See the website.

Gametophyte Gene Expression Data

The Evans lab is generating RNA-seq data to describe the transcriptome of the maize male and female gametophytes. In collaboration with John Fowler and Scott Givan this data is being mapped to the maize genome for identification of genes specific to the male and/or female gametophytes. This data can be visualized by the community on the project genome browser at