Co-translational assembly orchestrates competing biogenesis pathways

Julian D. Langer,Vladimir Benes,Anja Becker,Nayara Trevisan Doimo de Azevedo,Eva Kaindl,Natalie Romanov,Janina Baumbach,Filipa Pereira,Maximilian Seidel,Martin Beck,Gerhard Hummer,Jonathan J. M. Landry,Claudia M. Fusco,Erin M. Schuman,Kiran Raosaheb Patil

doi:10.1038/s41467-022-28878-5

Abstract

During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examine structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally test candidate structural motifs and identify several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs may act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assemble co-translationally in only some but not all of the relevant biogenesis pathways. Our results highlight the regulatory complexity of assembly pathways.

Highlights

During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner
Co-translational assembly can tolerate higher levels of such competitive binders because it increases the dwell-time of synthesis intermediates at the ribosome in which surfaces that potentially engage in promiscuous interactions are not yet exposed
Co-translational assembly may increase the on-rate of a newly synthesized component to a partial complex retained in the vicinity of the ribosome, such that the rate of assembly will be limited by the translation speed instead of the slow diffusion of low abundance species

Summary

Introduction

During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiledcoils, and short linear motifs may act as co-translational assembly domains Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Phenylalanine-Glycine (FG)-rich repeats contained in so-called FG-Nups that function as a velcro[14] and short linear motifs (SLiMs) within so-called linker Nups that facilitate interactions within and across subcomplexes[15,16] Structured motifs such as beta-propeller complementation[17–19] and coiledcoil interactions[16,20,21] are observed in multiple instances. It remains unclear how such promiscuous interactions are suppressed or discriminated in vivo

Methods

Results

Conclusion