Limits...
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.

Show MeSH
Overview of the Methodology for TMD Analysis(A) Schematic of a typical single-pass or bitopic protein embedded in a lipid bilayer.(B) Bitopic proteins of known topology and location from S. cerevisiae and H. sapiens were identified by literature and database searches. Orthologous proteins were identified using BLAST and aligned with the reference proteins. The starts of the TMDs were identified by a hydrophobicity scanning algorithm and used to align the TMDs at their cytosolic edges.(C) The number of proteins from the indicated organelles that were used in the analyses of TMDs (PM, plasma membrane). Redundancy reduction was such that TMDs and flanking sequences have <30% identity. Reference proteins are listed in Table S1 and Table S2.See also Figure S1.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2928124&req=5

fig1: Overview of the Methodology for TMD Analysis(A) Schematic of a typical single-pass or bitopic protein embedded in a lipid bilayer.(B) Bitopic proteins of known topology and location from S. cerevisiae and H. sapiens were identified by literature and database searches. Orthologous proteins were identified using BLAST and aligned with the reference proteins. The starts of the TMDs were identified by a hydrophobicity scanning algorithm and used to align the TMDs at their cytosolic edges.(C) The number of proteins from the indicated organelles that were used in the analyses of TMDs (PM, plasma membrane). Redundancy reduction was such that TMDs and flanking sequences have <30% identity. Reference proteins are listed in Table S1 and Table S2.See also Figure S1.

Mentions: To reliably compare TMDs that span different membranes, we curated a dataset of proteins with an experimentally determined topology and location and a single TMD (bitopic proteins, Figure 1A). Bitopic proteins represent ∼40% of all membrane proteins in eukaryotic genomes, and their TMDs are those likely to have the most residues exposed to the lipid bilayer (Almén et al., 2009; Krogh et al., 2001). We assembled datasets of all single TMD proteins from what are probably the best characterized eukaryotic genomes, Saccharomyces cerevisiae and Homo sapiens. We then used literature searches and cross-referencing between databases to identify those proteins with a known organelle of residence and topology (Table S1 and Table S2). For the Golgi apparatus we pooled all the proteins from the various cisternae of the Golgi stack into a single “Golgi” set, with a separate set for those proteins that cycle between the trans-Golgi network (TGN) and endosomes. Only a few mammalian Golgi proteins have been accurately located within the Golgi stack, but for yeast, where this is more easily done, we found that the proteins of the early part of the stack were strikingly similar in TMD properties to those from the later part of the stack (see below), indicating that this pooling probably does not mask significant complexity.


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

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

Overview of the Methodology for TMD Analysis(A) Schematic of a typical single-pass or bitopic protein embedded in a lipid bilayer.(B) Bitopic proteins of known topology and location from S. cerevisiae and H. sapiens were identified by literature and database searches. Orthologous proteins were identified using BLAST and aligned with the reference proteins. The starts of the TMDs were identified by a hydrophobicity scanning algorithm and used to align the TMDs at their cytosolic edges.(C) The number of proteins from the indicated organelles that were used in the analyses of TMDs (PM, plasma membrane). Redundancy reduction was such that TMDs and flanking sequences have <30% identity. Reference proteins are listed in Table S1 and Table S2.See also Figure S1.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Overview of the Methodology for TMD Analysis(A) Schematic of a typical single-pass or bitopic protein embedded in a lipid bilayer.(B) Bitopic proteins of known topology and location from S. cerevisiae and H. sapiens were identified by literature and database searches. Orthologous proteins were identified using BLAST and aligned with the reference proteins. The starts of the TMDs were identified by a hydrophobicity scanning algorithm and used to align the TMDs at their cytosolic edges.(C) The number of proteins from the indicated organelles that were used in the analyses of TMDs (PM, plasma membrane). Redundancy reduction was such that TMDs and flanking sequences have <30% identity. Reference proteins are listed in Table S1 and Table S2.See also Figure S1.
Mentions: To reliably compare TMDs that span different membranes, we curated a dataset of proteins with an experimentally determined topology and location and a single TMD (bitopic proteins, Figure 1A). Bitopic proteins represent ∼40% of all membrane proteins in eukaryotic genomes, and their TMDs are those likely to have the most residues exposed to the lipid bilayer (Almén et al., 2009; Krogh et al., 2001). We assembled datasets of all single TMD proteins from what are probably the best characterized eukaryotic genomes, Saccharomyces cerevisiae and Homo sapiens. We then used literature searches and cross-referencing between databases to identify those proteins with a known organelle of residence and topology (Table S1 and Table S2). For the Golgi apparatus we pooled all the proteins from the various cisternae of the Golgi stack into a single “Golgi” set, with a separate set for those proteins that cycle between the trans-Golgi network (TGN) and endosomes. Only a few mammalian Golgi proteins have been accurately located within the Golgi stack, but for yeast, where this is more easily done, we found that the proteins of the early part of the stack were strikingly similar in TMD properties to those from the later part of the stack (see below), indicating that this pooling probably does not mask significant complexity.

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