SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution [article]

Luzia Stalder, Amir Banaei-Esfahani, Rodolfo Ciuffa, Joshua L. Payne, Ruedi Aebersold
2020 bioRxiv   pre-print
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.
more » ... irst, 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.
doi:10.1101/2020.09.08.287334 fatcat:ytmtfsw5s5fkpcgh6cdedn5msq