Altered assembly paths mitigate interference among paralogous complexes

Chi-Wei Yeh, Kuan-Lun Hsu, Shu-Ting Lin, Wei-Chieh Huang, Kun-Hai Yeh, Chien-Fu Jeff Liu, Li-Chin Wang, Ting-Ting Li, Shu-Chuan Chen, Chen-Hsin Yu, Jun-Yi Leu, Chen-Hsiang Yeang and Hsueh-Chi S. Yen ()
Additional contact information
Chi-Wei Yeh: Academia Sinica
Kuan-Lun Hsu: Academia Sinica
Shu-Ting Lin: Academia Sinica
Wei-Chieh Huang: Academia Sinica
Kun-Hai Yeh: Academia Sinica
Chien-Fu Jeff Liu: Academia Sinica
Li-Chin Wang: Academia Sinica
Ting-Ting Li: Academia Sinica
Shu-Chuan Chen: Academia Sinica
Chen-Hsin Yu: Academia Sinica
Jun-Yi Leu: Academia Sinica
Chen-Hsiang Yeang: National Taiwan University and Academia Sinica
Hsueh-Chi S. Yen: Academia Sinica

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: Abstract Protein complexes are fundamental to all cellular processes, so understanding their evolutionary history and assembly processes is important. Gene duplication followed by divergence is considered a primary mechanism for diversifying protein complexes. Nonetheless, to what extent assembly of present-day paralogous complexes has been constrained by their long evolutionary pathways and how cross-complex interference is avoided remain unanswered questions. Subunits of protein complexes are often stabilized upon complex formation, whereas unincorporated subunits are degraded. How such cooperative stability influences protein complex assembly also remains unclear. Here, we demonstrate that subcomplexes determined by cooperative stabilization interactions serve as building blocks for protein complex assembly. We further develop a protein stability-guided method to compare the assembly processes of paralogous complexes in cellulo. Our findings support that oligomeric state and the structural organization of paralogous complexes can be maintained even if their assembly processes are rearranged. Our results indicate that divergent assembly processes by paralogous complexes not only enable the complexes to evolve new functions, but also reinforce their segregation by establishing incompatibility against deleterious hybrid assemblies.

Date: 2024
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DOI: 10.1038/s41467-024-51286-w

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