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A comprehensive comparison of transmembrane domains reveals organelle-specific properties.

Sharpe HJ, Stevens TJ, Munro S - Cell (2010)

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.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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A Comparison of the TMDs from the Fungal Vacuole and Vertebrate Lysosome, Related to Figure 7(A) Positional analysis of mean hydrophobicity relative to the cytosolic ends of TMDs.(B) Distribution of relative TMD lengths.(C) Positional analysis of amino acid volume.(D) Abundance of aromatic residues (phenylalanine, tryptophan and tyrosine) along TMDs. Error bars in (A) and (C) indicate the standard error of the mean.
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figs4: A Comparison of the TMDs from the Fungal Vacuole and Vertebrate Lysosome, Related to Figure 7(A) Positional analysis of mean hydrophobicity relative to the cytosolic ends of TMDs.(B) Distribution of relative TMD lengths.(C) Positional analysis of amino acid volume.(D) Abundance of aromatic residues (phenylalanine, tryptophan and tyrosine) along TMDs. Error bars in (A) and (C) indicate the standard error of the mean.

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.


A comprehensive comparison of transmembrane domains reveals organelle-specific properties.

Sharpe HJ, Stevens TJ, Munro S - Cell (2010)

A Comparison of the TMDs from the Fungal Vacuole and Vertebrate Lysosome, Related to Figure 7(A) Positional analysis of mean hydrophobicity relative to the cytosolic ends of TMDs.(B) Distribution of relative TMD lengths.(C) Positional analysis of amino acid volume.(D) Abundance of aromatic residues (phenylalanine, tryptophan and tyrosine) along TMDs. Error bars in (A) and (C) indicate the standard error of the mean.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2928124&req=5

figs4: A Comparison of the TMDs from the Fungal Vacuole and Vertebrate Lysosome, Related to Figure 7(A) Positional analysis of mean hydrophobicity relative to the cytosolic ends of TMDs.(B) Distribution of relative TMD lengths.(C) Positional analysis of amino acid volume.(D) Abundance of aromatic residues (phenylalanine, tryptophan and tyrosine) along TMDs. Error bars in (A) and (C) indicate the standard error of the mean.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

Show MeSH