PT - JOURNAL ARTICLE AU - Stalder, Luzia AU - Banaei-Esfahani, Amir AU - Ciuffa, Rodolfo AU - Payne, Joshua L AU - Aebersold, Ruedi TI - SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution AID - 10.1101/2020.09.08.287334 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.09.08.287334 4099 - http://biorxiv.org/content/early/2020/09/08/2020.09.08.287334.short 4100 - http://biorxiv.org/content/early/2020/09/08/2020.09.08.287334.full AB - Understanding the conservation and evolution of protein complexes is of critical value to decode their function in physiological and pathological processes. One prominent proposal posits gene duplication as a potential mechanism for protein complex evolution. In this study we take advantage of large-scale proteome expression datasets to systematically investigate the role of paralogues, and specifically self-interacting paralogues, in shaping the evolutionary trajectories of protein complexes. First, we show that protein co-expression derived from quantitative proteomic matrices is a good indicator for complex membership and is conserved across species. Second, we suggest that paralogues are commonly strongly co-expressed and that for the subset of paralogues that show diverging co-expression patterns, the divergent co-expression patterns reflect both sequence and functional divergence. Finally, on this basis, we show that homomeric paralogues known to be part of protein complexes display a unique co-expression pattern distribution, with a subset of them being highly diverging. These findings support the idea that homomeric paralogues can avoid cross-interference by diversifying their expression patterns, and corroborates the role of this mechanism as a force shaping protein complex evolution and specialization.Competing Interest StatementThe authors have declared no competing interest.