The GOLD domain, a novel protein module involved in Golgi function and secretion

Abstract

Background: Members of the p24 (p24/gp25L/emp24/Erp) family of proteins have been shown to be critical components of the coated vesicles that are involved in the transportation of cargo molecules from the endoplasmic reticulum to the Golgi complex. The p24 proteins form hetero-oligomeric complexes and are believed to function as receptors for specific secretory cargo.

Results: Using sensitive sequence-profile analysis methods, we identified a novel beta-strand-rich domain, the GOLD (Golgi dynamics) domain, in the p24 proteins and several other proteins with roles in Golgi dynamics and secretion. This domain is predicted to mediate diverse protein-protein interactions. Other than in the p24 proteins, the GOLD domain is always found combined with lipid- or membrane-association domains such as the pleckstrin homology (PH), Sec14p and FYVE domains.

Conclusions: The identification of the GOLD domain could aid in directed investigation of the role of the p24 proteins in the secretion process. The newly detected group of GOLD-domain proteins, which might simultaneously bind membranes and other proteins, point to the existence of a novel class of adaptors that could have a role in the assembly of membrane-associated complexes or in regulating assembly of cargo into membranous vesicles.

Figure 1

A multiple alignment of the GOLD domain was constructed using T-Coffee [32] and realigning the sequences by parsing high-scoring pairs from PSI-BLAST search results. The PHD-secondary structure [15] is shown above the alignment, with E representing a β strand (upper-case letters indicate predictions with > 82% accuracy, and lower-case letters denote predictions with > 72% accuracy). A search with the lumenal region of Caenorhabditis elegans p24-family member K08E4.6 (region 20-191) recovers RALBP from Todarodes pacificus, the squid ortholog of SEC14L2 (E = 7 × 10^-3, iteration 1). A reciprocal search with RALBP_Todarodes pacificus (region 189-343) recovers GCP60 (E = 2 × 10^-10, iteration 1), FYCO1 (8 × 10^-4, iteration 1), SPAC23H4.01c (10^-3, iteration 2), KIAA0420 (10^-3, iteration 2) and K08E4.6 (7 × 10^-3, iteration 2). The 80% consensus shown below the alignment was derived using the following amino-acid classes: h, hydrophobic (ALICVMYFW, yellow shading); l, the aliphatic subset of the hydrophobic class (ALIVMC, yellow shading); a, aromatic (FHWY, yellow shading); s, small (ACDGNPSTV, green letters); u and p are the tiny subsets of the small class (u, GAS, green shading) and polar (p, CDEHKNQRST, blue letters). Y denotes a conserved tyrosine residue. The limits of the domains are indicated by the residue positions on each side. The numbers within the alignment indicate poorly conserved inserts that are not shown. The different families are shown on the right. A, p24 family; B, Osh3p family; C, CG9528 family (Sec14-like proteins with an amino-terminal PRELI/MSF1p' domain); D, Sec14-like proteins; E,GCP60 family; and F, FYCO1. The sequences are denoted by their gene name followed by the species abbreviation and GenBank Identifier. Ce, Caenorhabditis elegans; Dm, Drosophila melanogaster; Hs, Homo sapiens; Sc, Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe; Top, Todarodes pacificus.

Figure 2

A phylogenetic tree of the GOLD-domain-containing proteins is shown along with the various architectures, drawn approximately to scale, and the phyletic distributions of individual architectural classes. The RELL bootstrap values for the major branches are shown at their base. The thickness of a given branch is approximately proportional to the number of proteins contained within it. PH, pleckstrin-homology domain; OxB, oxysterol-binding domain; Aco, acyl-CoA-binding domain; Sec14, domain found in Sec14 proteins; RUN (for RPIP8, UNC-14 and NESCA) and FYVE (for Fab1p, YOTB, Vac1p and EEA1).

Figure 3

A multiple alignment of the PRELI/MSF1p' domain was constructed using T-Coffee [32] and realigning the sequences by parsing high-scoring pairs from PSI-BLAST search results. The PHD-secondary structure [15] is shown above the alignment with E representing a β strand (upper-case is for predictions with > 82% accuracy; lower-case denotes predictions with > 72% accuracy). The 100% consensus shown below the alignment was derived using the following amino-acid classes: h, hydrophobic (ALICVMYFW, yellow shading); l, the aliphatic subset of the hydrophobic class (ALIVMC, yellow shading); a, aromatic (FHWY, yellow shading); c, charged (DEHKR, pink letters); s, small (ACDGNPSTV, green letters) and p, polar (CDEHKNQRST, blue letters). The limits of the domains are indicated by the residue positions on each side (except for the unfinished genome of Cryptosporidium parvum). The numbers within the alignment are poorly conserved inserts that are not shown. The different families are shown on the right. The PRELI and Kisir subgroups contain stand-alone versions of the domain, whereas the CG9528 family comprises Sec14-like proteins with an amino-terminal PRELI and a carboxy-terminal GOLD domain. The sequences are denoted by their gene name followed by the species abbreviation and GenBank Identifier. At, Arabidopsis thaliana; Ce, Caenorhabditis elegans; Cpar, Cryptosporidium parvum; Dm, Drosophila melanogaster; Hs, Homo sapiens; Mm, Mus musculus; Sc, Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe.