The TRAPP complexes: oligomeric exchange factors that activate the small GTPases Rab1 and Rab11

Abstract

The Transport Protein Particle (TRAPP) complexes are highly conserved multisubunit complexes that act as nucleotide exchange factors (GEFs) for Rab GTPases. They act in both protein secretion and autophagy and have also been proposed to have a role in other processes such as cytokinesis and ciliogenesis. There are two TRAPP complexes in metazoans: TRAPPII, which activates Rab11; and TRAPPIII, which activates Rab1. Both complexes share a core of small subunits that form the active site for the exchange of GDP for GTP. In addition, each TRAPP complex has distinct large subunits that determine the specificity of each complex towards its substrate Rab and are essential for activity in vivo. Crystal structures have revealed the organisation of the TRAPP core and the mechanism of Rab1 activation, whilst recent cryo-EM structures have unveiled the arrangement of the specific subunits around the core to form each complex. Combining these findings with functional experiments has allowed the proposal of mechanisms for how the specificity of each complex towards their cognate Rab is determined and for the arrangement of these large complexes on the membrane.

Keywords: Golgi apparatus; Rab GTPase; autophagy; exchange factor; membrane traffic; recycling endosome.

Fig. 1

The TRAPP complexes participate in key cellular processes. (A) The Rab activation cycle between GDP to GTP is facilitated by guanine exchange factors (GEFs), and GTPase activating proteins (GAPS). The conformational change between these two forms promotes the interaction of the GTP‐bound form with effector proteins. Rabs are linked to the membrane via a flexible C‐terminal hypervariable domain that is prenylated at the C‐terminus. In the cytosol, GDP‐bound Rabs are in a complex with chaperone proteins known as GDP dissociation inhibitors (GDIs), which hide the hydrophobic C‐terminal prenyl groups from the polar environment of the cytosol. (B) Rab1 and Rab11 are master regulators of different steps of the secretory pathway, and Rab1 also regulates autophagy. TRAPPII activates Rab11 whilst TRAPPIII acts on Rab1.

Fig. 2

Architecture of the metazoan and yeast TRAPP complexes. (A) The TRAPP subunits. In vertebrates, TRAPPC6 has two isoforms (6A and 6B). Also shown is essentiality for human cell lines, and yeast viability [36, 75]. (B) Subunit composition of the TRAPP complexes. (C) Cryo‐EM density maps for TRAPP complexes from Saccharomyces cerevisiae and Drosophila, coloured to highlight the TRAPP‐specific subunits. Drosophila TRAPPIII (EMD‐12056, with Rab1 (pink) modelled into the map) and TRAPPII (EMD‐12066). Saccharomyces cerevisiae TRAPPIII (EMD‐22928) and TRAPPII (EMD‐26270).

Fig. 3

Structural models of the TRAPP complexes. Orthogonal views of the 3D models of Drosophila melanogaster TRAPPIII (7B6R), Saccharomyces cerevisiae TRAPPIII (7KMT), and S. cerevisiae TRAPPII (7U05). The subunits are depicted as ribbons, with the colour code for the core subunits applicable to all three models. (A and B) TRAPPIII‐specific subunits TRAPPC8 (N‐terminal model) and Trs85 (C8) are yellow, TRAPPC11 (N‐terminal model) is blue. (C) TRAPPII‐specific subunits Trs120 (C9) and Trs130 (C10) are light yellow and light blue, respectively. Trs65 is beige.

Fig. 4

The specific subunits as nucleotide exchange regulators. (A) Ribbon model of the TRAPP core‐Ypt1 interface [88]. Ypt1 is purple, except for switch regions I and II (orange) and the P loop (yellow). The C‐terminus of Bet3a (C3a) is highlighted in green. (B) The secondary structure of Rab GTPases. (C) Rab1 modelled into Drosophila TRAPPIII. The inset shows the proximity between TRAPPC8 (yellow) and the α‐helices 3 (dark blue) and 4 (light blue) of Rab1. The Rab1 switch region I is yellow, interswitch green, switch region II orange, and α‐helix 5 red. (D) Movement of TRAPPC8 and TRAPPC11 relative to the core. Superposition of the two extreme positions of the particles from cryo‐EM analysis. (E) The TRAPPII‐Ypt32 complex (7E8T). (Bet5 (C1): light green, Trs20 (C2): orange, Tca17 (C2L): magenta, Bet3a (C3a): purple, Bet3b (C3b): dark green, Trs23 (C4): light brown, Trs31 (C5): grey, Trs33 (C6): red, Trs120 (C9): light yellow, Trs130 (C11): light blue, Ypt32: pink). Inset 1: Surface representation of the Trs120 (C9) IgD1 loop pushing the Ypt32 α‐helices 4 (dark blue) and 5 (light blue). Inset 2: Surface representation of the TRAPP core‐Ypt32 interface. The HVD (red) lies in the Trs31 (C5) pocket.

Fig. 5

Models of TRAPP complexes on membranes. The C‐terminal hypervariable domain (HVD) of the Rabs stretches from their C‐terminal lipid anchors to the Rab binding site on the TRAPP core. The location of the complexes on the bilayer is hypothetical based on binding sites for the Rabs and their HVDs, and assuming that the N‐terminal regions of the specific subunits mediate membrane contact.