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

Luzia Stalder, Amir Banaei-Esfahani, Rodolfo Ciuffa, Joshua L Payne, Ruedi Aebersold
doi: https://doi.org/10.1101/2020.09.08.287334
Luzia Stalder
1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
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  • For correspondence: luzia.stalder@unine.ch aebersold@imsb.biol.ethz.ch
Amir Banaei-Esfahani
1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
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Rodolfo Ciuffa
1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
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Joshua L Payne
2Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
3Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Ruedi Aebersold
1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
4Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
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  • For correspondence: luzia.stalder@unine.ch aebersold@imsb.biol.ethz.ch
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Abstract

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 Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 08, 2020.
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SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution
Luzia Stalder, Amir Banaei-Esfahani, Rodolfo Ciuffa, Joshua L Payne, Ruedi Aebersold
bioRxiv 2020.09.08.287334; doi: https://doi.org/10.1101/2020.09.08.287334
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SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution
Luzia Stalder, Amir Banaei-Esfahani, Rodolfo Ciuffa, Joshua L Payne, Ruedi Aebersold
bioRxiv 2020.09.08.287334; doi: https://doi.org/10.1101/2020.09.08.287334

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