A comprehensive comparison of transmembrane domains reveals organelle-specific properties.
Bottom Line: The various membranes of eukaryotic cells differ in composition, but it is at present unclear if this results in differences in physical properties.In addition, TMDs from post-ER organelles show striking asymmetries in amino acid compositions across the bilayer that is linked to residue size and varies between organelles.The pervasive presence of organelle-specific features among the TMDs of a particular organelle has implications for TMD prediction, regulation of protein activity by location, and sorting of proteins and lipids in the secretory pathway.
Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.Show MeSH
Mentions: Although the trend for longer TMDs in post-Golgi compartments is broadly similar in fungi and vertebrates, there also appear to be some differences. The TMD lengths imply that the fungal plasma membrane is even thicker than that of vertebrates, and also the membranes of the TGN/endosomal system are similar in thickness to the plasma membrane in vertebrates, but in fungi their thickness is intermediate between those of the Golgi and plasma membrane. The TGN/endosomal route is followed by proteins taken in from the plasma membrane or traveling from the Golgi to the vacuole or lysosome (Bonifacino and Traub, 2003; Bowers and Stevens, 2005). We did not include these lytic compartments in the analysis above because only a few bitopic proteins are known for each. However, when the methods used above are applied to these small datasets, the vertebrate lysosomal proteins appear similar to plasma membrane proteins, with longer TMDs and a preference for smaller residues in the exoplasmic half of the bilayer (Figure S4). In contrast, the fungal vacuolar proteins have shorter TMD lengths and an increased abundance of bulky aromatic residues compared to lysosomal TMDs (Figure S4). These differences cannot be viewed as definitive given the small numbers of reference proteins, but they are at least consistent with all post-Golgi membranes in vertebrates being equally thickened compared to the Golgi and ER, whereas in fungi the plasma membrane is particularly thick and the other post-Golgi membranes are intermediate in thickness compared to the Golgi.
Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.