Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z

Abstract

Distant homology relationships among proteins with many transmembrane regions (TMs) are difficult to detect as they are clouded by the TMs' hydrophobic compositional bias and mutational divergence in connecting loops. In the case of several GPI lipid anchor biosynthesis pathway components, the hidden evolutionary signal can be revealed with dissectHMMER, a sequence similarity search tool focusing on fold-critical, high complexity sequence segments. We find that a sequence module with 10 TMs in PIG-W, described as acyl transferase, is homologous to PIG-U, a transamidase subunit without characterized molecular function, and to mannosyltransferases PIG-B, PIG-M, PIG-V and PIG-Z. We conclude that this new, membrane-embedded domain named BindGPILA functions as the unit for recognizing, binding and stabilizing the GPI lipid anchor in a modification-competent form as this appears the only functional aspect shared among all proteins. Thus, PIG-U's likely molecular function is shuttling/presenting the anchor in a productive conformation to the transamidase complex.

Keywords: GPI biosynthesis; GPI lipid anchor; GPI mannosyltransferase; GPI transamidase complex; dissectHMMER; glycosylphosphatidylinositol; inositol acylase; transmembrane protein function.

Figure 1.

The GPI lipid anchor biosynthesis pathway – overview. The various steps of the pathway (from the N-acetylglucosaminyltransferase complex with PIG-A etc. to the step of leaving the ER where further anchor remodeling happens) are schematically depicted. All reactions and translocations are shown in white and black except for the six steps involving PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z that are highlighted in colors. Please note that PIG-U is a subunit of the transamidase complex and not all proteins, for example PIG-Z, are available in all organisms.

Figure 2.

Scheme of the sequence architecture of PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z. The figure shows the schematic architecture of the transmembrane domains from PIGB, PIGM, PIGU, PGW, PIGV and PIGZ. The TMs colored in blue forms the membrane embedded sequence domain, BindGPILA, comprising of 10 TMs. The extracellular loops are shown by curved loops and the length of the loop shows the distance between two TMs. The conserved catalytic motif, which is present in the first extracellular loop between the first and second TM, are labelled in red.