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bioRxiv · 10.1101/462309

High resolution protein-protein interaction mapping using all-versus-all sequencing (AVA-seq)

Andrews, S. S.·Ramadan, S.·Al-Thani, N. M.·Ahmed, I.·Mohamoud, Y. A.·Malek, J.
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Abstract

Two-hybrid systems test for protein-protein interactions and can provide important information for genes with unknown function. Despite their success, two-hybrid systems have remained mostly untouched by improvements from next-generation DNA sequencing. Here we present a method for all-versus-all protein interaction mapping (AVA-seq) that utilizes next-generation sequencing to remove multiple bottlenecks of the two-hybrid process. The method allows for high resolution protein-protein interaction mapping of a small set of proteins, or the potential for lower-resolution mapping of entire proteomes. Features of the system include open-reading frame selection to improve efficiency, high bacterial transformation efficiency, a convergent fusion vector to allow paired-end sequencing of interactors, and the use of protein fragments rather than full-length genes to better resolve specific protein contact points. We demonstrate the systems strengths and limitations on a set of proteins known to interact in humans and provide a framework for future large-scale projects.

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Andrews, S. S., Ramadan, S., Al-Thani, N. M., Ahmed, I., Mohamoud, Y. A., Malek, J.. 2018-11-05. High resolution protein-protein interaction mapping using all-versus-all sequencing (AVA-seq). https://doi.org/10.1101/462309

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