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Open Access Research article

Cotranslational protein-RNA associations predict protein-protein interactions

Caia DS Duncan and Juan Mata*

Author Affiliations

Department of Biochemistry, University of Cambridge, Cambridge, UK

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BMC Genomics 2014, 15:298  doi:10.1186/1471-2164-15-298

Published: 22 April 2014

Abstract

Background

Most cellular proteins function as part of stable protein complexes. We recently showed that around 38% of proteins associate with mRNAs that encode interacting proteins, reflecting the cotranslational formation of the complex between the bait protein and the nascent peptides encoded by the interacting mRNAs. Here we hypothesise that these cotranslational protein-mRNA associations can be used to predict protein-protein interactions.

Results

We found that the fission yeast Exo2 protein, which encodes an exonuclease of the XRN1 family, coimmunoprecipitates with the eti1 mRNA, which codes for a protein of unknown function and uninformative sequence. Based on this protein-mRNA association, we predicted that the Exo2 and Eti1 protein are part of the same complex, and confirmed this hypothesis by coimmunoprecipitation and colocalization of the proteins. Similarly, we show that the cotranslational interaction between the Sty1 MAP kinase and the cip2 mRNA, which encodes an RNA-binding protein, predicts a complex between Sty1 and Cip2.

Conclusions

Our results demonstrate that cotranslational protein-mRNA associations can be used to identify new components of protein complexes.