You’ve probably heard the term “genome” before, which refers to the set of genes in an organism.  Biology has a lot of buzzwords for describing what’s going on inside cells, and one of the recent ones is “interactome”. The word “interactome” refers to all of the interactions that are occurring between proteins, the large molecules that do most of the work inside your cells. Proteins are built from their corresponding gene’s instructions, and they drive cellular processes by interacting with each other. For example, when a receptor protein on the cell membrane is triggered—such as by recognizing an invading virus—it temporarily binds to another type of protein, which interacts with yet another protein and so on, until the cell’s immune response is fully activated and self-defense proteins are released to deal with the invaders.  This series of protein interactions is called a “signaling cascade”.

As you might have guessed, if one of the proteins in a signaling cascade isn’t interacting properly, it leads to problems which can be the basis of diseases, such as Alzheimer’s disease, ALS, or cancer. As a result, it is very important to understand how proteins interact, especially when mutations can lead to human diseases. Unfortunately, a single protein can have dozens or even hundreds of binding partners. To make matters worse, it is thought that proteins have cell-specific interactions, which means that a given protein may interact with one set of proteins in one type of cell, and a different set of proteins in another cell type. However, current techniques for studying a protein’s binding partners use whole brains or brain structures consisting of many different types of cells and cannot distinguish among them.

A recent paper¹ published in the Griffith lab addresses this problem by taking advantage of the genetics tools developed in Drosophila melanogaster. They created a fly line with a mutation in the gene for the protein of interest, and then used a binary expression system (UAS/GAL4) to reintroduce normal versions of the protein into specific subsets of cells. The authors then followed up with current techniques for studying the protein’s interactions, but they knew that the binding partners were specific to the cells they were interested in.

To demonstrate their new technique, the authors studied a protein called CASK. In mammals, CASK is important for signaling between neurons and is implicated in two human developmental disorders. In flies, CASK is present in almost all neurons, and CASK mutants have problems with locomotion and learning. Researchers already knew that different types of neurons were responsible for each of these behaviors, and thought that CASK may have different interactions based on the type of cell. To test this hypothesis, the authors used a fly line with a non-functioning mutation in the CASK gene, and then reintroduced normal versions of the protein in three different types of neurons.  They were then able to use current identification techniques (check out this link on mass spectrometry, if you’re interested) to determine which proteins had bound to CASK in each of the three lines and compare them to each other (as well as to a fly line where they had reintroduced CASK in all neurons). They found that while there were many proteins that interacted with CASK in all of the neuron subtypes, each group also had a set of unique interactions.

So what’s the bottom line?  How can the findings in this paper help us? Because abnormal protein interactions are the basis of many human diseases, the only way to treat them is to determine which proteins are involved and understand their function. Only then we would know how to fix the problem. Unfortunately, while many of those interactions are specific to certain types of cells, current techniques require researchers to investigate the protein’s binding partners from many cell types.  This creates unnecessary complexity because only specific populations of neurons are affected in some diseases. For example, in Parkinson’s disease, a type of cell known as dopaminergic neurons are most seriously affected. Researchers are studying proteins known to be involved in the disease, but may benefit from being able to limit the interactions to those that occur within dopaminergic neurons. Using fruit flies, the Griffith lab developed a technique for uncovering cell-specific differences in a protein’s interactions. In the future, researchers will be able to use Drosophila as a model organism for studying cell-specific protein interactions involved in human disease, and this technique may even be modified for use in mammalian systems.

1. Mukherjee K., Bethany L. Christmann & Leslie C. Griffith (2014). Neuron-specific protein interactions of Drosophila CASK-β are revealed by mass spectrometry, Frontiers in Molecular Neuroscience, 7 DOI: http://dx.doi.org/10.3389/fnmol.2014.00058