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Nat Biotechnol. 2018 Aug;36(7):638-644. doi: 10.1038/nbt.4150. Epub 2018 Jun 11.

Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions.

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Department of Cellular & Molecular Physiology, Yale University, New Haven, Connecticut, USA.
Systems Biology Institute, Yale University, West Haven, Connecticut, USA.
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.
Biology Department, Southern Connecticut State University, New Haven, Connecticut, USA.
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
Department of Computer Science, Yale University, New Haven, Connecticut, USA.
Agilent Laboratories, Agilent Technologies, Santa Clara, California, USA.


Post-translational phosphorylation is essential to human cellular processes, but the transient, heterogeneous nature of this modification complicates its study in native systems. We developed an approach to interrogate phosphorylation and its role in protein-protein interactions on a proteome-wide scale. We genetically encoded phosphoserine in recoded E. coli and generated a peptide-based heterologous representation of the human serine phosphoproteome. We designed a single-plasmid library encoding >100,000 human phosphopeptides and confirmed the site-specific incorporation of phosphoserine in >36,000 of these peptides. We then integrated our phosphopeptide library into an approach known as Hi-P to enable proteome-level screens for serine-phosphorylation-dependent human protein interactions. Using Hi-P, we found hundreds of known and potentially new phosphoserine-dependent interactors with 14-3-3 proteins and WW domains. These phosphosites retained important binding characteristics of the native human phosphoproteome, as determined by motif analysis and pull-downs using full-length phosphoproteins. This technology can be used to interrogate user-defined phosphoproteomes in any organism, tissue, or disease of interest.

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