Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Abstract

Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (∼23%) than the other two, COPI (∼9%) and COPII (∼8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of evolutionary adaptability in the three routes.

Membrane fission by protein crowding

“…Our data highlight the potential of bulky, IDP-containing proteins to generate an imbalance of steric pressure that can contribute strongly to membrane fission. Importantly, many proteins involved in membrane traffic contain large IDP domains (73), including auxilin (76), intersectin (72), and amphiphysin (77). Several of these proteins assemble with dynamin at the necks of late-stage endocytic buds.…”

“…We began by testing the prediction that larger proteins should drive fission more efficiently. Interestingly, many endocytic proteins have bulky IDP domains with large hydrodynamic radii (72,73). Specifically, the intrinsically disordered C-terminal domain of epsin1 consists of 432 amino acids and has a projected area on the membrane surface of ∼70 nm 2 (37), approximately five times larger than the membrane footprint of the ENTH domain alone (42) (Fig.…”

BAR scaffolds drive membrane fission by crowding disordered domains

“…Our work reveals a synergistic relationship between structured protein assemblies and disordered pressure generators, which can be harnessed to drive membrane fission. It is increasingly recognized that structural disorder is prevalent in membrane trafficking, and that disordered domains are often coupled to structured domains within the same protein molecules (Pietrosemoli et al, 2013). While previous work has focused primarily on structure-function relationships revealed by studying individual protein domains, these findings highlight the importance of examining the collective contributions from both structure and disorder to understand how proteins shape membranes in diverse cellular contexts.…”

A multivalent fuzzy interface drives reversible COPII coat assembly

“…Our findings of coat assembly driven by interactions involving intrinsically disordered regions are also likely to apply to other vesicle trafficking steps. Each of the major coat complexes have significant disordered regions within their subunits (30), and the flexible nature of the clathrin light chain is important in coat assembly (31). Our approach and the findings that we present here provide a 30 conceptual framework to now discover and investigate how such elements in disordered regions of other coat complexes are used for dynamic assembly and disassembly.…”