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Janezic EM, Lauer SML, Williams RG, Chungyoun M, Lee KS, Navaluna E, Lau HT, Ong SE, Hague C. N-glycosylation of α 1D-adrenergic receptor N-terminal domain is required for correct trafficking, function, and biogenesis. Sci Rep 2020; 10:7209. [PMID: 32350295 PMCID: PMC7190626 DOI: 10.1038/s41598-020-64102-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/09/2020] [Indexed: 01/21/2023] Open
Abstract
G protein-coupled receptor (GPCR) biogenesis, trafficking, and function are regulated by post-translational modifications, including N-glycosylation of asparagine residues. α1D-adrenergic receptors (α1D-ARs) - key regulators of central and autonomic nervous system function - contain two putative N-glycosylation sites within the large N-terminal domain at N65 and N82. However, determining the glycosylation state of this receptor has proven challenging. Towards understanding the role of these putative glycosylation sites, site-directed mutagenesis and lectin affinity purification identified N65 and N82 as bona fide acceptors for N-glycans. Surprisingly, we also report that simultaneously mutating N65 and N82 causes early termination of α1D-AR between transmembrane domain 2 and 3. Label-free dynamic mass redistribution and cell surface trafficking assays revealed that single and double glycosylation deficient mutants display limited function with impaired plasma membrane expression. Confocal microscopy imaging analysis and SNAP-tag sucrose density fractionation assays revealed the dual glycosylation mutant α1D-AR is widely distributed throughout the cytosol and nucleus. Based on these novel findings, we propose α1D-AR transmembrane domain 2 acts as an ER localization signal during active protein biogenesis, and that α1D-AR N-terminal glycosylation is required for complete translation of nascent, functional receptor.
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Affiliation(s)
- Eric M Janezic
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Sophia My-Linh Lauer
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Robert George Williams
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Michael Chungyoun
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Kyung-Soon Lee
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Edelmar Navaluna
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Ho-Tak Lau
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Shao-En Ong
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA
| | - Chris Hague
- Department of Pharmacology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98185, USA.
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2
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Tinti E, Geay F, Lopes Rodrigues M, Kestemont P, Perpète EA, Michaux C. Molecular cloning and 3D model of a fatty-acid elongase in a carnivorous freshwater teleost, the European perch ( Perca fluviatilis). 3 Biotech 2019; 9:242. [PMID: 31168435 PMCID: PMC6542919 DOI: 10.1007/s13205-019-1773-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/20/2019] [Indexed: 01/30/2023] Open
Abstract
The European perch (Perca fluviatilis) is a carnivorous freshwater fish able to metabolise polyunsaturated fatty acids (PUFA) into highly unsaturated fatty acids (HUFA). This makes it a potential candidate for sustainable aquaculture development. In this study, special attention is given to the fatty-acid elongase (ELOVL) family, one of the two enzymatic systems implied in the HUFA biosynthesis. Structural information on European perch enzyme converting PUFA into HUFA is obtained by both molecular cloning and in silico characterization of an ELOVL5-like elongase from P. fluviatilis (pfELOVL). The full-length cDNA sequence consists of a 885-base pair Open Reading Frame coding for a 294-amino acid protein. Phylogenetic analysis and sequence alignment with fish elongases predict the pfELOVL clusters within the ELOVL5 sub-group. The amino-acid sequence displays the typical ELOVL features: several transmembrane α helices (TMH), an endoplasmic reticulum (ER) retention signal, and four "conserved boxes" involved in the catalytic site. In addition, the topology analysis predicts a 7-TMH structure addressed in the ER membrane. A 3D model of the protein embedded in an ER-like membrane environment is also provided using de novo modelling and molecular dynamics. From docking studies, two putative enzyme-substrate-binding modes, including H bonds and CH-π interactions, emphasize the role of specific residues in the "conserved boxes".
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Affiliation(s)
- Emmanuel Tinti
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
- Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
| | | | - Maximilien Lopes Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
- Namur Institute of Structures Matter, University of Namur, Namur, Belgium
| | - Patrick Kestemont
- Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
- Research Unit in Environmental and Evolutionary Biology, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Eric A. Perpète
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
- Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
- Namur Institute of Structures Matter, University of Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
- Namur Institute of Structures Matter, University of Namur, Namur, Belgium
- Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
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3
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Vitrac H, Dowhan W, Bogdanov M. Effects of mixed proximal and distal topogenic signals on the topological sensitivity of a membrane protein to the lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1291-1300. [PMID: 28432030 DOI: 10.1016/j.bbamem.2017.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
The final topology of membrane proteins is thought to be dictated primarily by the encoding sequence. However, according to the Charge Balance Rule the topogenic signals within nascent membrane proteins are interpreted in agreement with the Positive Inside Rule as influenced by the protein phospholipid environment. The role of long-range protein-lipid interactions in establishing a final uniform or dual topology is unknown. In order to address this role, we determined the positional dependence of the potency of charged residues as topological signals within Escherichia coli sucrose permease (CscB) in cells in which the zwitterionic phospholipid phosphatidylethanolamine (PE), acting as topological determinant, was either eliminated or tightly titrated. Although the position of a single or paired oppositely charged amino acid residues within an extramembrane domain (EMD), either proximal, central or distal to a transmembrane domain (TMD) end, does not appear to be important, the oppositely charged residues exert their topogenic effects separately only in the absence of PE. Thus, the Charge Balance Rule can be executed in a retrograde manner from any cytoplasmic EMD or any residue within an EMD most likely outside of the translocon. Moreover, CscB is inserted into the membrane in two opposite orientations at different ratios with the native orientation proportional to the mol % of PE. The results demonstrate how the cooperative contribution of lipid-protein interactions affects the potency of charged residues as topological signals, providing a molecular mechanism for the realization of single, equal or different amounts of oppositely oriented protein within the same membrane.
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Affiliation(s)
- Heidi Vitrac
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center McGovern Medical School, Houston, TX 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center McGovern Medical School, Houston, TX 77030, USA
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science Center McGovern Medical School, Houston, TX 77030, USA.
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4
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Vitrac H, MacLean DM, Karlstaedt A, Taegtmeyer H, Jayaraman V, Bogdanov M, Dowhan W. Dynamic Lipid-dependent Modulation of Protein Topology by Post-translational Phosphorylation. J Biol Chem 2016; 292:1613-1624. [PMID: 27974465 DOI: 10.1074/jbc.m116.765719] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/13/2016] [Indexed: 01/01/2023] Open
Abstract
Membrane protein topology and folding are governed by structural principles and topogenic signals that are recognized and decoded by the protein insertion and translocation machineries at the time of initial membrane insertion and folding. We previously demonstrated that the lipid environment is also a determinant of initial protein topology, which is dynamically responsive to post-assembly changes in membrane lipid composition. However, the effect on protein topology of post-assembly phosphorylation of amino acids localized within initially cytoplasmically oriented extramembrane domains has never been investigated. Here, we show in a controlled in vitro system that phosphorylation of a membrane protein can trigger a change in topological arrangement. The rate of change occurred on a scale of seconds, comparable with the rates observed upon changes in the protein lipid environment. The rate and extent of topological rearrangement were dependent on the charges of extramembrane domains and the lipid bilayer surface. Using model membranes mimicking the lipid compositions of eukaryotic organelles, we determined that anionic lipids, cholesterol, sphingomyelin, and membrane fluidity play critical roles in these processes. Our results demonstrate how post-translational modifications may influence membrane protein topology in a lipid-dependent manner, both along the organelle trafficking pathway and at their final destination. The results provide further evidence that membrane protein topology is dynamic, integrating for the first time the effect of changes in lipid composition and regulators of cellular processes. The discovery of a new topology regulatory mechanism opens additional avenues for understanding unexplored structure-function relationships and the development of optimized topology prediction tools.
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Affiliation(s)
- Heidi Vitrac
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
| | - David M MacLean
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Anja Karlstaedt
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Heinrich Taegtmeyer
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Vasanthi Jayaraman
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Mikhail Bogdanov
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - William Dowhan
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
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5
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Bogdanov M, Dowhan W, Vitrac H. Lipids and topological rules governing membrane protein assembly. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:1475-88. [PMID: 24341994 PMCID: PMC4057987 DOI: 10.1016/j.bbamcr.2013.12.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/03/2013] [Accepted: 12/08/2013] [Indexed: 10/25/2022]
Abstract
Membrane protein folding and topogenesis are tuned to a given lipid profile since lipids and proteins have co-evolved to follow a set of interdependent rules governing final protein topological organization. Transmembrane domain (TMD) topology is determined via a dynamic process in which topogenic signals in the nascent protein are recognized and interpreted initially by the translocon followed by a given lipid profile in accordance with the Positive Inside Rule. The net zero charged phospholipid phosphatidylethanolamine and other neutral lipids dampen the translocation potential of negatively charged residues in favor of the cytoplasmic retention potential of positively charged residues (Charge Balance Rule). This explains why positively charged residues are more potent topological signals than negatively charged residues. Dynamic changes in orientation of TMDs during or after membrane insertion are attributed to non-sequential cooperative and collective lipid-protein charge interactions as well as long-term interactions within a protein. The proportion of dual topological conformers of a membrane protein varies in a dose responsive manner with changes in the membrane lipid composition not only in vivo but also in vitro and therefore is determined by the membrane lipid composition. Switching between two opposite TMD topologies can occur in either direction in vivo and also in liposomes (designated as fliposomes) independent of any other cellular factors. Such lipid-dependent post-insertional reversibility of TMD orientation indicates a thermodynamically driven process that can occur at any time and in any cell membrane driven by changes in the lipid composition. This dynamic view of protein topological organization influenced by the lipid environment reveals previously unrecognized possibilities for cellular regulation and understanding of disease states resulting from mis-folded proteins. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA.
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA.
| | - Heidi Vitrac
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA
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6
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Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. J Am Chem Soc 2013; 135:2291-7. [PMID: 23298280 PMCID: PMC3573731 DOI: 10.1021/ja310777k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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For the vast majority of membrane proteins, insertion
into a membrane
is not direct, but rather is catalyzed by a protein-conducting channel,
the translocon. This channel provides a lateral exit into the bilayer
while simultaneously offering a pathway into the aqueous lumen. The
determinants of a nascent protein’s choice between these two
pathways are not comprehensively understood, although both energetic
and kinetic factors have been observed. To elucidate the specific
roles of some of these factors, we have carried out extensive all-atom
molecular dynamics simulations of different nascent transmembrane
segments embedded in a ribosome-bound bacterial translocon, SecY.
Simulations on the μs time scale reveal a spontaneous motion
of the substrate segment into the membrane or back into the channel,
depending on its hydrophobicity. Potential of mean force (PMF) calculations
confirm that the observed motion is the result of local free-energy
differences between channel and membrane. Based on these and other
PMFs, the time-dependent probability of membrane insertion is determined
and is shown to mimic a two-state partition scheme with an apparent
free energy that is compressed relative to the molecular-level PMFs.
It is concluded that insertion kinetics underlies the experimentally
observed thermodynamic partitioning process.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30363, USA
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7
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Lipid-protein interactions as determinants of membrane protein structure and function. Biochem Soc Trans 2011; 39:767-74. [PMID: 21599647 DOI: 10.1042/bst0390767] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To determine how the lipid environment affects membrane protein structure and function, strains of Escherichia coli were developed in which normal phospholipid composition can be altered or foreign lipids can be introduced. The properties of LacY (lactose permease) were investigated as a function of lipid environment. Assembly of LacY in membranes lacking PE (phosphatidylethanolamine) results in misorientation of the N-terminal six-TM (transmembrane domain) helical bundle with loss of energy-dependent uphill transport and retention of energy-independent downhill transport. Post-assembly introduction of PE results in nearly native orientation of TMs and restoration of uphill transport. Foreign lipids with no net charge can substitute for PE in supporting native LacY topology, but restoration of uphill transport is dependent on native topology and the proper folding of a solvent-exposed domain. Increasing the positive charge density of the cytoplasmically exposed surface of LacY counters TM misorientation in the absence of neutral lipids, demonstrating that charge interactions between these domains and the surface of the membrane bilayer are determinants of TM orientation. Therefore membrane protein organization or reorganization is determined either during initial assembly or post-insertionally through direct interactions between the protein and the lipid environment, which affects the topogenic potency of opposing charged residues as topological signals independent of the translocon.
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8
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Vitrac H, Bogdanov M, Heacock P, Dowhan W. Lipids and topological rules of membrane protein assembly: balance between long and short range lipid-protein interactions. J Biol Chem 2011; 286:15182-94. [PMID: 21454589 DOI: 10.1074/jbc.m110.214387] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The N-terminal six-transmembrane domain (TM) bundle of lactose permease of Escherichia coli is uniformly inverted when assembled in membranes lacking phosphatidylethanolamine (PE). Inversion is dependent on the net charge of cytoplasmically exposed protein domains containing positive and negative residues, net charge of the membrane surface, and low hydrophobicity of TM VII acting as a molecular hinge between the two halves of lactose permease (Bogdanov, M., Xie, J., Heacock, P., and Dowhan, W. (2008) J. Cell Biol. 182, 925-935). Net neutral lipids suppress the membrane translocation potential of negatively charged amino acids, thus increasing the cytoplasmic retention potential of positively charged amino acids. Herein, TM organization of sucrose permease (CscB) and phenylalanine permease (PheP) as a function of membrane lipid composition was investigated to extend these principles to other proteins. For CscB, topological dependence on PE only becomes evident after a significant increase in the net negative charge of the cytoplasmic surface of the N-terminal TM bundle. High negative charge is required to overcome the thermodynamic block to inversion due to the high hydrophobicity of TM VII. Increasing the positive charge of the cytoplasmic surface of the N-terminal TM hairpin of PheP, which is misoriented in PE-lacking cells, favors native orientation in the absence of PE. PheP and CscB also display co-existing dual topologies dependent on changes in the charge balance between protein domains and the membrane lipids. Therefore, the topology of both permeases is dependent on PE. However, CscB topology is governed by thermodynamic balance between opposing lipid-dependent electrostatic and hydrophobic interactions.
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Affiliation(s)
- Heidi Vitrac
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, USA
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9
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Free-energy cost for translocon-assisted insertion of membrane proteins. Proc Natl Acad Sci U S A 2011; 108:3596-601. [PMID: 21317362 DOI: 10.1073/pnas.1012758108] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nascent membrane proteins typically insert in a sequential fashion into the membrane via a protein-conducting channel, the Sec translocon. How this process occurs is still unclear, although a thermodynamic partitioning between the channel and the membrane environment has been proposed. Experiment- and simulation-based scales for the insertion free energy of various amino acids are, however, at variance, the former appearing to lie in a narrower range than the latter. Membrane insertion of arginine, for instance, requires 14-17 kcal/mol according to molecular dynamics simulations, but only 2-3 kcal/mol according to experiment. We suggest that this disagreement is resolved by assuming a two-stage insertion process wherein the first step, the insertion into the translocon, is energized by protein synthesis and, therefore, has an effectively zero free-energy cost; the second step, the insertion into the membrane, invokes the translocon as an intermediary between the fully hydrated and the fully inserted locations. Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a background polyleucine helix. Indeed, the insertion penalty for arginine as well as the insertion gain for leucine from the translocon to the membrane is found to be significantly reduced compared to direct insertion from water, resulting in the same compression as observed in the experiment-based scale.
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Schlegel S, Klepsch M, Gialama D, Wickström D, Slotboom DJ, de Gier JW. Revolutionizing membrane protein overexpression in bacteria. Microb Biotechnol 2009; 3:403-11. [PMID: 21255339 PMCID: PMC3815807 DOI: 10.1111/j.1751-7915.2009.00148.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The bacterium Escherichia coli is the most widely used expression host for overexpression trials of membrane proteins. Usually, different strains, culture conditions and expression regimes are screened for to identify the optimal overexpression strategy. However, yields are often not satisfactory, especially for eukaryotic membrane proteins. This has initiated a revolution of membrane protein overexpression in bacteria. Recent studies have shown that it is feasible to (i) engineer or select for E. coli strains with strongly improved membrane protein overexpression characteristics, (ii) use bacteria other than E. coli for the expression of membrane proteins, (iii) engineer or select for membrane protein variants that retain functionality but express better than the wild‐type protein, and (iv) express membrane proteins using E. coli‐based cell‐free systems.
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Affiliation(s)
- Susan Schlegel
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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Abstract
The topology of polytopic membrane proteins is determined by topogenic sequences in the protein, protein-translocon interactions, and interactions during folding within the protein and between the protein and the lipid environment. Orientation of transmembrane domains is dependent on membrane phospholipid composition during initial assembly as well as on changes in lipid composition postassembly. The membrane translocation potential of negative amino acids working in opposition to the positive-inside rule is largely dampened by the normal presence of phosphatidylethanolamine, thus explaining the dominance of positive residues as retention signals. Phosphatidylethanolamine provides the appropriate charge density that permits the membrane surface to maintain a charge balance between membrane translocation and retention signals and also allows the presence of negative residues in the cytoplasmic face of proteins for other purposes.
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Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas-Houston Medical School, Houston, TX 77030, USA.
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