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Extracellular Interaction Networks are Revealed in Study Published in Cell, Co-authored by Prof. Karl Johnson

Professor Karl Johnson

Karl Johnson, associate professor of biology and neuroscience, is a member of the research team that has developed a new high-throughput assay to identify the interactions between extracellular proteins. The study, “An Extracellular Interactome of Immunoglobulin and LRR Proteins Reveals Receptor-Ligand Networks,” was published in the July 3 issue of Cell.

 “It’s been a huge challenge for biologists to understand how cells talk to each other,” explains Johnson. “The goal of the project was to characterize the proteins at the cell surface and to understand what proteins interact with each other to communicate information between cells.”

“Cells have a nearly impenetrable plasma membrane which makes it hard for another cell to ‘talk’ to it. The way cells ‘listen’ is to put proteins in their membranes – receptor proteins – which allow cells to detect information in the form of proteins outside the cell,” Johnson says.

The study reports the complete interactome of three extracellular protein families in Drosophilia melanoganster – immunoglobulin superfamily (IgSF), fibronectin type III (FnlIl) and leucine rich repeat (LRR) classes of proteins.  These protein families, the study notes, are “known to mediate important homeostatic functions and neural wiring.”

“Cell surface receptors and secreted ligands mediate cellular adhesions of all types; serve as immune neural receptors; connect the extracellular matrix to the cytoskeleton; determine cell shape, polarity and mobility; relay extracellular signals to cytoplasm; and regulate processes that can lead to disease,” note the authors in the discussion section of the paper.

The team screened 20,000 different candidate interactions, resulting in the identification of 106 interactions between extracellular proteins, 83 of which were new discoveries. Since the screens were done in vitro, the team also verified the interactions in a living Drosophila embryo to ensure that the interactions would be verified in the organism.

These “real world” tests involved the live dissection of fly embryos, and the probing of these fly embryos with tagged receptor proteins to examine the distribution pattern of the ligand. Then, fly embryos with mutations in the ligand were examined to determine if the receptor binding sites were lost. It was in this phase of testing that Johnson participated most heavily. In each case, the interaction was validated suggesting a low false positive rate.

The team consisted of Engin Özkan (Howard Hughes Medical Institute), Robert A. Carrillio (California Institute of Technology), Catharine L. Eastman (Howard Hughes Medical Institute), Richard Weiszmann (Lawrence Berkeley National Laboratory), Deepa Waghray (Howard Hughes Medical Institute), Karl G. Johnson (Pomona College), Kai Zinn (California Institute of Technology), Susan E. Celniker (Lawrence Berkeley Laboratory) and K. Christopher Garcia (Howard Hughes Medical Institute).

According to Daniel Leahy, of Johns Hopkins University School of Medicine, whose review of the study appears in the same issue of Cell, “Özkan et al have clearly uncovered a bounty of interactions that will keep biologists busy for a long time to come…. It is conceivable that the [Extracellular Interactome Assay] could be applied to much larger subsets of extracellular proteins, including, one hopes, all or most secreted proteins in key organisms…. The current study of Drosophilia proteins demonstrates that discovery of treasure troves of extracellular interactions awaits.”

Prof. Johnson is the Sarah and Harbert S. Rempel Professor Neuroscience and an associate professor of biology at Pomona College.

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