The TRAPP complex: insights into its architecture and function

Abstract

Vesicle-mediated transport is a process carried out by virtually every cell and is required for the proper targeting and secretion of proteins. As such, there are numerous players involved to ensure that the proteins are properly localized. Overall, transport requires vesicle budding, recognition of the vesicle by the target membrane and fusion of the vesicle with the target membrane resulting in delivery of its contents. The initial interaction between the vesicle and the target membrane has been referred to as tethering. Because this is the first contact between the two membranes, tethering is critical to ensuring that specificity is achieved. It is therefore not surprising that there are numerous 'tethering factors' involved ranging from multisubunit complexes, coiled-coil proteins and Rab guanosine triphosphatases. Of the multisubunit tethering complexes, one of the best studied at the molecular level is the evolutionarily conserved TRAPP complex. There are two forms of this complex: TRAPP I and TRAPP II. In yeast, these complexes function in a number of processes including endoplasmic reticulum-to-Golgi transport (TRAPP I) and an ill-defined step at the trans Golgi (TRAPP II). Because the complex was first reported in 1998 (1), there has been a decade of studies that have clarified some aspects of its function but have also raised further questions. In this review, we will discuss recent advances in our understanding of yeast and mammalian TRAPP at the structural and functional levels and its role in disease while trying to resolve some apparent discrepancies and highlighting areas for future study.

Figure 1

The structure of yeast and mammalian TRAPP subcomplexes. A) The structure of a subcomplex of yeast TRAPP containing two copies of Bet3p and one each of Bet5p, Trs23p and Trs31p in complex with the GTPase Ypt1p was solved to 3.7 Å resolution (18). The TRAPP subunit models are shown in the absence of Ypt1p that would be on the surface facing the reader. B) The structure of two subcomplexes of mammalian TRAPP were solved to 2.4 Å resolution (TRAPPC1–TRAPPC3–TRAPPC4–TRAPPC6a, slate color) and 2.1 Å resolution (TRAPPC2–TRAPPC3–TRAPPC5, pink color) (9). The main differences between the yeast and the mammalian complexes are the presence of a PDZL domain on TRAPPC4 and an insertion in the β3‐α4 loop of TRAPPC5, resulting in a protrusion at the TRAPPC4–TRAPPC5 interface (circled in panels A and B). C) The TRAPPC5–TRAPPC4 interface is superimposed onto the Trs31p–Trs23p interface with the protruding region of TRAPPC5 colored in yellow. Panels (A–C) were rendered in PyMol. D) A multi‐sequence alignment of TRAPPC5/Trs31p orthologues. The red and blue letters indicate the amino acids that are 100 and >70% conserved in nine representative orthologues. Secondary structural elements are indicated above the alignment. The ‘SVPK’ insertion in the β3‐α4 loop of TRAPPC5 is highlighted in yellow. Aligned sequences are H. sapi. (Homo sapiens), M. musc. (Mus musculus), G. gall. (Gallus gallus), D. reri. (Dario rerio), X. laev. (Xenopus laevis), D. mela. (Drosophila melanogaster), C. eleg. (Caenorhabditis elegans), S. pomb. (Schizosaccharomyces pombe) and S. cere. (Saccharomyces cerevisiae).

Figure 3

Conservation of residues in TRAPP I required for Ypt1p contact. The amino acid sequences at the contact patches between Ypt1p and TRAPP I are highly conserved between yeast and humans. Shown are sequence alignments for the three relevant TRAPP I subunits using BLAST of A) yeast Trs23p with human TRAPPC4, B) yeast Bet5p with human TRAPPC1 and C) yeast Bet3p with human TRAPPC3.

Figure 2

The TRAPP I–Ypt1p interface. Ypt1p–TRAPP I contact regions span three TRAPP I subunits as revealed by the Ypt1p–TRAPP I complex recently reported by Cai et al. (18). A) Ribbon diagram of the Ypt1p–TRAPP I complex. B) A 90° rotated view relative to that shown in A). The orientation is similar to that shown in Cai et al. C) A close‐up view showing the important putative interactions between TRAPP I and Ypt1. To demonstrate the incompatibility between the C‐terminal region (wedge) of Bet3p‐A with the presence of nucleotide on Ypt1p when in complex with TRAPP, a GTP analog (GppNHp) was docked to the Ypt1p–TRAPP I complex based on its position in the structure of Ypt1p‐GTP (PDB ID 1YZN). Note how residues from the C‐terminus of Bet3p‐A occupy a similar position to that of the phosphate groups of the nucleotide. Figure prepared with Molscript.