Structure and function of bacterial outer membrane proteins: barrels in a nutshell

The outer membrane protects Gram‐negative bacteria against a harsh environment. At the same time, the embedded proteins fulfil a number of tasks that are crucial to the bacterial cell, such as solute and protein translocation, as well as signal transduction. Unlike membrane proteins from all other sources, integral outer membrane proteins do not consist of transmembrane α‐helices, but instead fold into antiparallel β‐barrels. Over recent years, the atomic structures of several outer membrane proteins, belonging to six families, have been determined. They include the OmpA membrane domain, the OmpX protein, phospholipase A, general porins (OmpF, PhoE), substrate‐specific porins (LamB, ScrY) and the TonB‐dependent iron siderophore transporters FhuA and FepA. These crystallographic studies have yielded invaluable insight into and decisively advanced the understanding of the functions of these intriguing proteins. Our review is aimed at discussing their common principles and peculiarities as well as open questions associated with them.

[1]  P. Phale,et al.  Brownian dynamics simulation of ion flow through porin channels. , 1999, Journal of molecular biology.

[2]  J. Gouaux,et al.  Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore , 1996, Science.

[3]  C. Ferran,et al.  Plasmid-mediated sucrose metabolism in Escherichia coli: characterization of scrY, the structural gene for a phosphoenolpyruvate-dependent sucrose phosphotransferase system outer membrane porin , 1991, Journal of bacteriology.

[4]  V. Braun Energy-coupled transport and signal transduction through the gram-negative outer membrane via TonB-ExbB-ExbD-dependent receptor proteins. , 1995, FEMS microbiology reviews.

[5]  V. Braun,et al.  Identification of a New Site for Ferrichrome Transport by Comparison of the FhuA Proteins of Escherichia coli,Salmonella paratyphi B, Salmonella typhimurium, and Pantoea agglomerans , 1998, Journal of bacteriology.

[6]  G. Rummel,et al.  Structural and Functional Characterization of OmpF Porin Mutants Selected for Larger Pore Size , 1996, The Journal of Biological Chemistry.

[7]  J. Tommassen,et al.  Demonstration of a folded monomeric form of porin PhoE of Escherichia coli in vivo , 1996, Journal of bacteriology.

[8]  J. Lakey,et al.  Voltage-gating of Escherichia coli porin: a cystine-scanning mutagenesis study of loop 3. , 1998, Journal of molecular biology.

[9]  R. Morona,et al.  Escherichia coli K-12 outer membrane protein (OmpA) as a bacteriophage receptor: analysis of mutant genes expressing altered proteins , 1984, Journal of bacteriology.

[10]  J. Deisenhofer,et al.  Crystal structure of the outer membrane active transporter FepA from Escherichia coli , 1999, Nature Structural Biology.

[11]  R. Koebnik In vivo membrane assembly of split variants of the E.coli outer membrane protein OmpA. , 1996, The EMBO journal.

[12]  G. Schulz,et al.  Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus. , 1994, Journal of molecular biology.

[13]  V. Koronakis,et al.  Structure of TolC, the outer membrane component of the bacterial type I efflux system, derived from two‐dimensional crystals , 1997, Molecular microbiology.

[14]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[15]  M. Karplus,et al.  Computer simulations of the OmpF porin from the outer membrane of Escherichia coli. , 1997, Biophysical journal.

[16]  V. Braun,et al.  The β‐barrel domain of FhuAΔ5‐160 is sufficient for TonB‐dependent FhuA activities of Escherichia coli , 1999, Molecular microbiology.

[17]  Scott J. Hultgren,et al.  Bacterial Adhesins: Common Themes and Variations in Architecture and Assembly , 1999, Journal of bacteriology.

[18]  R. Benz,et al.  Pore formation by LamB of Escherichia coli in lipid bilayer membranes , 1986, Journal of bacteriology.

[19]  A. Delcour,et al.  E.coli PhoE porin has an opposite voltage‐dependence to the homologous OmpF , 1998, The EMBO journal.

[20]  Y. Stierhof,et al.  An outer membrane protein (OmpA) of Escherichia coli K-12 undergoes a conformational change during export. , 1986, The Journal of biological chemistry.

[21]  N. Dekker Outer‐membrane phospholipase A: known structure, unknown biological function , 2000, Molecular microbiology.

[22]  J. Tommassen,et al.  Topology of outer membrane pore protein PhoE of Escherichia coli. Identification of cell surface-exposed amino acids with the aid of monoclonal antibodies. , 1986, The Journal of biological chemistry.

[23]  R. Liddington,et al.  Crystal structure of the anthrax toxin protective antigen , 1997, Nature.

[24]  R. Koebnik,et al.  Proposal for a peptidoglycan‐associating alpha‐helical motif in the C‐terminal regions of some bacterial cell‐surface proteins , 1995, Molecular microbiology.

[25]  H. Engelhardt,et al.  Significance of positively charged amino acids for the function of the acidovorax delafieldii porin omp34 , 1995 .

[26]  H. Verheij,et al.  Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine. , 1991, European journal of biochemistry.

[27]  G. Schulz,et al.  Structure of the outer membrane protein A transmembrane domain , 1998, Nature Structural Biology.

[28]  J. Rosenbusch,et al.  Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution , 1995, Science.

[29]  G. Schulz,et al.  Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide‐protein interactions , 1997, Protein science : a publication of the Protein Society.

[30]  J. Tommassen,et al.  Role of the constriction loop in the gating of outer membrane porin PhoE of Escherichia coli , 1997, FEBS letters.

[31]  E. Bremer,et al.  Single amino acid substitutions affecting the substrate specificity of the Escherichia coli K-12 nucleoside-specific Tsx channel. , 1993, The Journal of biological chemistry.

[32]  C. Houssin,et al.  Fast and slow kinetics of porin channels from Escherichia coli reconstituted into giant liposomes and studied by patch‐clamp , 1992, FEBS letters.

[33]  J. Tommassen,et al.  Carboxy-terminal phenylalanine is essential for the correct assembly of a bacterial outer membrane protein. , 1991, Journal of molecular biology.

[34]  Kay Diederichs,et al.  Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose , 1998, Nature Structural Biology.

[35]  J. Rosenbusch,et al.  Voltage sensing in the PhoE and OmpF outer membrane porins of Escherichia coli: role of charged residues. , 1997, Journal of molecular biology.

[36]  A. Lesk,et al.  Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis. , 1994, Journal of molecular biology.

[37]  K. Diederichs,et al.  Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. , 1998, Science.

[38]  M. A. Payne,et al.  Ligand-specific opening of a gated-porin channel in the outer membrane of living bacteria. , 1997, Science.

[39]  R. Freudl Insertion of peptides into cell-surface-exposed areas of the Escherichia coli OmpA protein does not interfere with export and membrane assembly. , 1989, Gene.

[40]  L. Regan Protein Structure: Born to be beta , 1994, Current Biology.

[41]  R. Benz,et al.  Conversion of the FhuA transport protein into a diffusion channel through the outer membrane of Escherichia coli. , 1993, The EMBO journal.

[42]  J. Liu,et al.  Formation of a gated channel by a ligand-specific transport protein in the bacterial outer membrane. , 1992, Science.

[43]  R. Koebnik,et al.  Sugar Transport through Maltoporin of Escherichia coli , 2000, The Journal of Biological Chemistry.

[44]  P. Black,et al.  Bacterial long-chain fatty acid transport. Identification of amino acid residues within the outer membrane protein FadL required for activity. , 1993, The Journal of biological chemistry.

[45]  F. Jähnig,et al.  Kinetics of Folding and Membrane Insertion of a β-Barrel Membrane Protein (*) , 1995, The Journal of Biological Chemistry.

[46]  Luc Moulinier,et al.  Transmembrane Signaling across the Ligand-Gated FhuA Receptor Crystal Structures of Free and Ferrichrome-Bound States Reveal Allosteric Changes , 1998, Cell.

[47]  R. Koebnik Membrane assembly of the Escherichia coli outer membrane protein OmpA: exploring sequence constraints on transmembrane beta-strands. , 1999, Journal of molecular biology.

[48]  R. Dutzler,et al.  Crystal structures of various maltooligosaccharides bound to maltoporin reveal a specific sugar translocation pathway. , 1996, Structure.

[49]  H. Berendsen,et al.  A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. , 1998, Biophysical journal.

[50]  S. Cowan,et al.  Prediction of membrane‐spanning β‐strands and its application to maltoporin , 1993, Protein science : a publication of the Protein Society.

[51]  R. Koebnik,et al.  Membrane assembly of circularly permuted variants of the E. coli outer membrane protein OmpA. , 1995, Journal of molecular biology.

[52]  Arne Elofsson,et al.  Architecture of β‐barrel membrane proteins: Analysis of trimeric porins , 1998 .

[53]  J. Vanderleyden,et al.  The C‐terminal sequence conservation between OmpA‐related outer membrane proteins and MotB suggests a common function in both Gram‐positive and Gram‐negative bacteria, possibly in the interaction of these domains with peptidoglycan , 1994, Molecular microbiology.

[54]  G. Schulz,et al.  Molecular architecture and electrostatic properties of a bacterial porin. , 1991, Science.

[55]  M. Achtman,et al.  Two‐dimensional structure of the Opc invasin from Neisseria meningitidis , 1997, Molecular microbiology.

[56]  A. Pugsley The complete general secretory pathway in gram-negative bacteria. , 1993, Microbiological reviews.

[57]  R. Dutzler,et al.  Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin. , 1997, Journal of molecular biology.

[58]  J. Tommassen,et al.  Molecular basis of porin selectivity: membrane experiments with OmpC-PhoE and OmpF-PhoE hybrid proteins of Escherichia coli K-12. , 1989, Biochimica et biophysica acta.

[59]  J. Tommassen,et al.  Pore functioning of outer membrane protein PhoE of Escherichia coli: mutagenesis of the constriction loop L3. , 1997, Protein engineering.

[60]  M. Montal Protein folds in channel structure. , 1996, Current opinion in structural biology.

[61]  J. Rosenbusch,et al.  Dimerization Regulates the Enzymatic Activity of Escherichia coli Outer Membrane Phospholipase A* , 1997, The Journal of Biological Chemistry.

[62]  J. Tommassen,et al.  One single lysine residue is responsible for the special interaction between polyphosphate and the outer membrane porin PhoE of Escherichia coli. , 1989, The Journal of biological chemistry.

[63]  M. T. Brown,et al.  Omptin: an Escherichia coli outer membrane proteinase that activates plasminogen. , 1994, Methods in enzymology.

[64]  G. Schulz,et al.  The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. , 1999, Structure.

[65]  P. Boulanger,et al.  FhuA, a transporter of the Escherichia coli outer membrane, is converted into a channel upon binding of bacteriophage T5. , 1996, The EMBO journal.

[66]  U. Henning,et al.  Cell envelope and shape of Escherichia coli: multiple mutants missing the outer membrane lipoprotein and other major outer membrane proteins , 1978, Journal of bacteriology.

[67]  H. Nikaido,et al.  Specificity of diffusion channels produced by lambda phage receptor protein of Escherichia coli. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[68]  J. Tommassen,et al.  Escherichia coli outer membrane phospholipase A: role of two serines in enzymatic activity. , 1996, Biochemistry.

[69]  A. Delcour Function and modulation of bacterial porins: insights from electrophysiology. , 1997, FEMS microbiology letters.

[70]  N. Orange,et al.  Ionophore properties of OmpA of Escherichia coli. , 1993, Biochimica et biophysica acta.

[71]  H. Nikaido,et al.  Stoichiometry of maltodextrin-binding sites in LamB, an outer membrane protein from Escherichia coli , 1991, Journal of bacteriology.

[72]  J. Rosenbusch,et al.  Stability of trimeric OmpF porin: the contributions of the latching loop L2. , 1998, Biochemistry.

[73]  J. Lengeler,et al.  Site-Directed Mutagenesis of Loop L3 of Sucrose Porin ScrY Leads to Changes in Substrate Selectivity , 1999, Journal of bacteriology.

[74]  K. H. Kalk,et al.  Structural evidence for dimerization-regulated activation of an integral membrane phospholipase , 1999, Nature.

[75]  J. Tommassen,et al.  Molecular characterization of enterobacterial pldA genes encoding outer membrane phospholipase A , 1994, Journal of bacteriology.

[76]  B. Pullman,et al.  Membrane Proteins: Structures, Interactions and Models , 1992 .

[77]  G. von Heijne,et al.  Positively and negatively charged residues have different effects on the position in the membrane of a model transmembrane helix. , 1998, Journal of molecular biology.

[78]  P. Phale,et al.  Voltage gating of Escherichia coli porin channels: role of the constriction loop. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[79]  A. Delcour,et al.  The spontaneous gating activity of OmpC porin is affected by mutations of a putative hydrogen bond network or of a salt bridge between the L3 loop and the barrel. , 1998, Protein engineering.

[80]  H. Verheij,et al.  Inactivation of Escherichia coli outer‐membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride , 1991 .

[81]  C. Mannella The 'ins' and 'outs' of mitochondrial membrane channels. , 1992, Trends in biochemical sciences.

[82]  O. Tapia,et al.  L3 loop-mediated mechanisms of pore closing in porin: a molecular dynamics perturbation approach. , 1995, Protein engineering.

[83]  T. Meyer,et al.  Characterization of the Neisseria Iga beta-core. The essential unit for outer membrane targeting and extracellular protein secretion. , 1993, Journal of molecular biology.

[84]  M. Hofnung,et al.  A cluster of charged and aromatic residues in the C-terminal portion of maltoporin participates in sugar binding and uptake , 1998, Molecular and General Genetics MGG.

[85]  Hiroshi Nikaido,et al.  OmpA protein of Escherichia coli outer membrane occurs in open and closed channel forms. , 1994, The Journal of biological chemistry.

[86]  J. Lakey,et al.  Voltage gating is a fundamental feature of porin and toxin β‐barrel membrane channels , 1998, FEBS letters.

[87]  G. Schulz,et al.  Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside. , 1997, Journal of molecular biology.

[88]  L. Dekker,et al.  Regulated Binding of the Protein Kinase C Substrate GAP-43 to the V0/C2 Region of Protein Kinase C-δ* , 1997, The Journal of Biological Chemistry.

[89]  R. Koebnik Structural and Functional Roles of the Surface-Exposed Loops of the β-Barrel Membrane Protein OmpA fromEscherichia coli , 1999, Journal of bacteriology.

[90]  G. Rummel,et al.  Crystal structures explain functional properties of two E. coli porins , 1992, Nature.

[91]  J. Lakey,et al.  The bacterial porin superfamily: sequence alignment and structure prediction , 1991, Molecular microbiology.

[92]  D. Tsernoglou,et al.  Structure of the Aeromonas toxin proaerolysin in its water-soluble and membrane-channel states , 1994, Nature.

[93]  J. Fierer,et al.  Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica , 1994, Infection and immunity.

[94]  L. Tamm,et al.  Folding intermediates of a beta-barrel membrane protein. Kinetic evidence for a multi-step membrane insertion mechanism. , 1996, Biochemistry.

[95]  R. Macnab,et al.  The Bacterial Flagellum: Reversible Rotary Propellor and Type III Export Apparatus , 1999, Journal of bacteriology.