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The β-Barrel Assembly Machinery Complex

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The BAM Complex

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1329))

Abstract

The outer membranes of gram-negative bacteria contain integral membrane proteins, most of which are of β-barrel structure, and critical for bacterial survival. These β-barrel proteins rely on the β-barrel assembly machinery (BAM) complex for their integration into the outer membrane as folded species. The central and essential subunit of the BAM complex, BamA, is a β-barrel protein conserved in all gram-negative bacteria and also found in eukaryotic organelles derived from bacterial endosymbionts. In Escherichia coli, BamA docks with four peripheral lipoproteins, BamB, BamC, BamD and BamE, partner subunits that add to the function of the BAM complex in outer membrane protein biogenesis. By way of introduction to this volume, we provide an overview of the work that has illuminated the mechanism by which the BAM complex drives β-barrel assembly. The protocols and methodologies associated with these studies as well as the challenges encountered and their elegant solutions are discussed in subsequent chapters.

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References

  1. Cronan JE (2003) Bacterial membrane lipids: where do we stand? Annu Rev Microbiol 57(1):203–224

    Article  CAS  PubMed  Google Scholar 

  2. Nikaido H (2003) Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67(4):593–656

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Okuda S, Tokuda H (2011) Lipoprotein sorting in bacteria. Annu Rev Microbiol 65(1):239–259

    Article  CAS  PubMed  Google Scholar 

  4. Silhavy TJ, Kahne D, Walker S (2010) The bacterial cell envelope. Cold Spring Harb Perspect Biol 2:a000414

    Google Scholar 

  5. Dong C, Beis K, Nesper J et al (2006) Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Nature 444(7116):226–229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Chandran V, Fronzes R, Duquerroy S et al (2009) Structure of the outer membrane complex of a type IV secretion system. Nature 462(7276):1011–1015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Wimley WC (2003) The versatile β-barrel membrane protein. Curr Opin Struct Biol 13(4):404–411

    Article  CAS  PubMed  Google Scholar 

  8. Nakamura K, Mizushima S (1976) Effects of heating in dodecyl sulfate solution on the conformation and electrophoretic mobility of isolated major outer membrane proteins from Escherichia coli K-12. J Biochem (Tokyo) 80(6):1411–1422

    CAS  Google Scholar 

  9. Fairman JW, Noinaj N, Buchanan SK (2011) The structural biology of β-barrel membrane proteins: a summary of recent reports. Curr Opin Struct Biol 21(4):523–531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Domene C, Bond PJ, Deol SS et al (2003) Lipid/protein interactions and the membrane/water interfacial region. J Am Chem Soc 125(49):14966–14967

    Article  CAS  PubMed  Google Scholar 

  11. Selkrig J, Leyton DL, Webb CT et al (2014) Assembly of β-barrel proteins into bacterial outer membranes. Biochim Biophys Acta 1843(8):1542–1550

    Article  CAS  PubMed  Google Scholar 

  12. Naveed H, Liang J (2013) Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins. Curr Pharm Des 20:1268–1273

    Article  Google Scholar 

  13. Celik N, Webb CT, Leyton DL et al (2012) A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. PLoS One 7(8), e43245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Bitto E, McKay DB (2003) The periplasmic molecular chaperone protein SurA binds a peptide motif that is characteristic of integral outer membrane proteins. J Biol Chem 278(49):49316–49322

    Article  CAS  PubMed  Google Scholar 

  15. Robert V, Volokhina EB, Senf F et al (2006) Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif. PLoS Biol 4(11), e377

    Article  PubMed  PubMed Central  Google Scholar 

  16. Driessen AJM, Nouwen N (2008) Protein translocation across the bacterial cytoplasmic membrane. Annu Rev Biochem 77(1):643–667

    Article  CAS  PubMed  Google Scholar 

  17. Knowles TJ, Scott-Tucker A, Overduin M et al (2009) Membrane protein architects: the role of the BAM complex in outer membrane protein assembly. Nat Rev Micro 7(3):206–214

    Article  CAS  Google Scholar 

  18. de Cock H, Struyvé M, Kleerebezem M et al (1997) Role of the carboxy-terminal phenylalanine in the biogenesis of outer membrane protein PhoE of Escherichia coli K-12. J Mol Biol 269(4):473–478

    Article  PubMed  Google Scholar 

  19. Struyvé M, Moons M, Tommassen J (1991) Carboxy-terminal phenylalanine is essential for the correct assembly of a bacterial outer membrane protein. J Mol Biol 218(1):141–148

    Article  PubMed  Google Scholar 

  20. Gawarzewski I, DiMaio F, Winterer E et al (2014) Crystal structure of the transport unit of the autotransporter adhesin involved in diffuse adherence from Escherichia coli. J Struct Biol 187(1):20–29

    Article  CAS  PubMed  Google Scholar 

  21. Gessmann D, Chung YH, Danoff EJ et al (2014) Outer membrane β-barrel protein folding is physically controlled by periplasmic lipid head groups and BamA. Proc Natl Acad Sci U S A 111(16):5878–5883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Paramasivam N, Habeck M, Linke D (2012) Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not? BMC Genomics 13(1):510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Volokhina EB, Grijpstra J, Beckers F et al (2013) Species-specificity of the BamA component of the bacterial outer membrane protein-assembly machinery. PLoS One 8(12), e85799

    Article  PubMed  PubMed Central  Google Scholar 

  24. Rizzitello AE, Harper JR, Silhavy TJ (2001) Genetic evidence for parallel pathways of chaperone activity in the periplasm of Escherichia coli. J Bacteriol 183(23):6794–6800

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Sklar JG, Wu T, Kahne D et al (2007) Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli. Genes Dev 21(19):2473–2484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Schäfer U, Beck K, Müller M (1999) Skp, a molecular chaperone of Gram-negative bacteria, is required for the formation of soluble periplasmic intermediates of outer membrane proteins. J Biol Chem 274(35):24567–24574

    Article  PubMed  Google Scholar 

  27. Vertommen D, Ruiz N, Leverrier P et al (2009) Characterization of the role of the Escherichia coli periplasmic chaperone SurA using differential proteomics. Proteomics 9(9):2432–2443

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Harms N, Koningstein G, Dontje W et al (2001) The early interaction of the outer membrane protein PhoE with the periplasmic chaperone Skp occurs at the cytoplasmic membrane. J Biol Chem 276(22):18804–18811

    Article  CAS  PubMed  Google Scholar 

  29. Ureta AR, Endres RG, Wingreen NS et al (2007) Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment. J Bacteriol 189(2):446–454

    Article  CAS  PubMed  Google Scholar 

  30. Ruiz-Perez F, Henderson IR, Nataro JP (2010) Interaction of FkpA, a peptidyl-prolyl cis/trans isomerase with EspP autotransporter protein. Gut Microbes 1(5):339–344

    Article  PubMed  PubMed Central  Google Scholar 

  31. Qu J, Mayer C, Behrens S et al (2007) The trimeric periplasmic chaperone Skp of Escherichia coli forms 1:1 complexes with outer membrane proteins via hydrophobic and electrostatic interactions. J Mol Biol 374(1):91–105

    Article  CAS  PubMed  Google Scholar 

  32. Hagan CL, Kim S, Kahne D (2010) Reconstitution of outer membrane protein assembly from purified components. Science 328(5980):890–892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hagan CL, Kahne D (2011) The reconstituted Escherichia coli Bam complex catalyzes multiple rounds of β-barrel assembly. Biochemistry (Mosc) 50(35):7444–7446

    Article  CAS  Google Scholar 

  34. Xu X, Wang S, Hu Y-X et al (2007) The periplasmic bacterial molecular chaperone SurA adapts its structure to bind peptides in different conformations to assert a sequence preference for aromatic residues. J Mol Biol 373(2):367–381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Walton TA, Sandoval CM, Fowler CA et al (2009) The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains. Proc Natl Acad Sci U S A 106(6):1772–1777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Burmann BM, Hiller S (2012) Solution NMR studies of membrane-protein-chaperone complexes. Chima (Aarau) 66(10):759–763

    Article  CAS  Google Scholar 

  37. Ge X, Wang R, Ma J et al (2014) DegP primarily functions as a protease for the biogenesis of β-barrel outer membrane proteins in the Gram-negative bacterium Escherichia coli. FEBS J 281(4):1226–1240

    Article  CAS  PubMed  Google Scholar 

  38. CastilloKeller M, Misra R (2003) Protease-deficient DegP suppresses lethal effects of a mutant OmpC protein by its capture. J Bacteriol 185(1):148–154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Webb CT, Heinz E, Lithgow T (2012) Evolution of the β-barrel assembly machinery. Trends Microbiol 20(12):612–620

    Article  CAS  PubMed  Google Scholar 

  40. Voulhoux R, Bos MP, Geurtsen J et al (2003) Role of a highly conserved bacterial protein in outer membrane protein assembly. Science 299(5604):262–265

    Article  CAS  PubMed  Google Scholar 

  41. Genevrois S, Steeghs L, Roholl P et al (2003) The Omp85 protein of Neisseria meningitidis is required for lipid export to the outer membrane. EMBO J 22(8):1780–1789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Heinz E, Lithgow T (2014) A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence and evolution. Front Microbiol 5:370

    Article  PubMed  PubMed Central  Google Scholar 

  43. Clantin B, Delattre A-S, Rucktooa P et al (2007) Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily. Science 317(5840):957–961

    Article  CAS  PubMed  Google Scholar 

  44. Gruss F, Zähringer F, Jakob RP et al (2013) The structural basis of autotransporter translocation by TamA. Nat Struct Mol Biol 20(11):1318–1320

    Article  CAS  PubMed  Google Scholar 

  45. Noinaj N, Kuszak AJ, Gumbart JC et al (2013) Structural insight into the biogenesis of β-barrel membrane proteins. Nature 501(7467):385–390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Fan E, Fiedler S, Jacob-Dubuisson F et al (2012) Two-partner secretion of Gram-negative bacteria: a single β-barrel protein enables transport across the outer membrane. J Biol Chem 287(4):2591–2599

    Article  CAS  PubMed  Google Scholar 

  47. Guédin S, Willery E, Tommassen J et al (2000) Novel topological features of FhaC, the outer membrane transporter involved in the secretion of the Bordetella pertussis filamentous hemagglutinin. J Biol Chem 275(39):30202–30210

    Article  PubMed  Google Scholar 

  48. Rigel NW, Ricci DP, Silhavy TJ (2013) Conformation-specific labeling of BamA and suppressor analysis suggest a cyclic mechanism for β-barrel assembly in Escherichia coli. Proc Natl Acad Sci U S A 110(13):5151–5156

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Delattre A-S, Clantin B, Saint N et al (2010) Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily. FEBS J 277(22):4755–4765

    Article  CAS  PubMed  Google Scholar 

  50. Leonard-Rivera M, Misra R (2012) Conserved residues of the putative L6 loop of Escherichia coli BamA play a critical role in the assembly of β-barrel outer membrane proteins, including that of BamA itself. J Bacteriol 194(17):4662–4668

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Ni D, Wang Y, Yang X et al (2014) Structural and functional analysis of the β-barrel domain of BamA from Escherichia coli. FASEB J 28(6):2677–2685

    Article  CAS  PubMed  Google Scholar 

  52. Noinaj N, Kuszak AJ, Balusek C et al (2014) Lateral opening and exit pore formation are required for BamA function. Structure 22(7):1055–1062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Selkrig J, Mosbahi K, Webb CT et al (2012) Discovery of an archetypal protein transport system in bacterial outer membranes. Nat Struct Mol Biol 19(5):506–510

    Article  CAS  PubMed  Google Scholar 

  54. Kim S, Malinverni JC, Sliz P et al (2007) Structure and function of an essential component of the outer membrane protein assembly machine. Science 317(5840):961–964

    Article  CAS  PubMed  Google Scholar 

  55. Knowles TJ, Jeeves M, Bobat S et al (2008) Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes. Mol Microbiol 68(5):1216–1227

    Article  CAS  PubMed  Google Scholar 

  56. Gatzeva-Topalova PZ, Warner LR, Pardi A et al (2010) Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane. Structure 18(11):1492–1501

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Gatzeva-Topalova PZ, Warner LR, Pardi A et al (2008) Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane. Structure 18(11):1492–1501

    Article  Google Scholar 

  58. Gatzeva-Topalova PZ, Walton TA, Sousa MC (2008) Crystal structure of YaeT: conformational flexibility and substrate recognition. Structure 16(12):1873–1881

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Bennion D, Charlson ES, Coon E et al (2010) Dissection of β-barrel outer membrane protein assembly pathways through characterizing BamA POTRA 1 mutants of Escherichia coli. Mol Microbiol 77(5):1153–1171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Anwari K, Webb CT, Poggio S et al (2012) The evolution of new lipoprotein subunits of the bacterial outer membrane BAM complex. Mol Microbiol 84(5):832–844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Volokhina EB, Beckers F, Tommassen J et al (2009) The β-barrel outer membrane protein assembly complex of Neisseria meningitidis. J Bacteriol 191(22):7074–7085

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Gatsos X, Perry AJ, Anwari K et al (2008) Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev 32(6):995–1009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Stenberg F, Chovanec P, Maslen SL et al (2005) Protein complexes of the Escherichia coli cell envelope. J Biol Chem 280(41):34409–34419

    Article  CAS  PubMed  Google Scholar 

  64. Wu T, Malinverni J, Ruiz N et al (2005) Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli. Cell 121(2):235–245

    Article  CAS  PubMed  Google Scholar 

  65. Malinverni JC, Werner J, Kim S et al (2006) YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli. Mol Microbiol 61(1):151–164

    Article  CAS  PubMed  Google Scholar 

  66. Vuong P, Bennion D, Mantei J et al (2008) Analysis of YfgL and YaeT interactions through bioinformatics, mutagenesis, and biochemistry. J Bacteriol 190(5):1507–1517

    Article  CAS  PubMed  Google Scholar 

  67. Webb CT, Selkrig J, Perry AJ et al (2012) Dynamic association of BAM complex modules includes surface exposure of the lipoprotein BamC. J Mol Biol 422(4):545–555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Ricci DP, Hagan CL, Kahne D et al (2012) Activation of the Escherichia coli β-barrel assembly machine (Bam) is required for essential components to interact properly with substrate. Proc Natl Acad Sci U S A 109(9):3487–3491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Noinaj N, Fairman JW, Buchanan SK (2011) The crystal structure of BamB suggests interactions with BamA and its role within the BAM complex. J Mol Biol 407(2):248–260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Dong C, Yang X, Hou H-F et al (2012) Structure of Escherichia coli BamB and its interaction with POTRA domains of BamA. Acta Crystallogr D Biol Crystallogr 68(9):1134–1139

    Article  CAS  PubMed  Google Scholar 

  71. Charlson ES, Werner JN, Misra R (2006) Differential effects of yfgL mutation on Escherichia coli outer membrane proteins and lipopolysaccharide. J Bacteriol 188(20):7186–7194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Ruiz N, Falcone B, Kahne D et al (2005) Chemical conditionality: a genetic strategy to probe organelle assembly. Cell 121(2):307–317

    Article  CAS  PubMed  Google Scholar 

  73. Heuck A, Schleiffer A, Clausen T (2011) Augmenting β-augmentation: structural basis of how BamB binds BamA and may support folding of outer membrane proteins. J Mol Biol 406(5):659–666

    Article  CAS  PubMed  Google Scholar 

  74. Jansen KB, Baker SL, Sousa MC (2012) Crystal structure of BamB from Pseudomonas aeruginosa and functional evaluation of its conserved structural features. PLoS One 7(11), e49749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Ieva R, Tian P, Peterson JH et al (2011) Sequential and spatially restricted interactions of assembly factors with an autotransporter β domain. Proc Natl Acad Sci U S A 108(31):E383–E391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Hagan CL, Westwood DB, Kahne D (2013) Bam lipoproteins assemble BamA in vitro. Biochemistry (Mosc) 52(35):6108–6113

    Article  CAS  Google Scholar 

  77. Misra R, Stikeleather R, Gabriele R (2014) In vivo roles of BamA, BamB and BamD in the biogenesis of BamA, a core protein of the β-barrel assembly machine of Escherichia coli. J Mol Biol. doi:10.1016/j.jmb.2014.1004.1021

    PubMed  PubMed Central  Google Scholar 

  78. Sklar JG, Wu T, Gronenberg LS et al (2007) Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli. Proc Natl Acad Sci U S A 104(15):6400–6405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Albrecht R, Zeth K (2011) Structural basis of outer membrane protein biogenesis in bacteria. J Biol Chem 286(31):27792–27803

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Kim KH, Aulakh S, Paetzel M (2011) Crystal structure of β-barrel assembly machinery BamCD protein complex. J Biol Chem 286(45):39116–39121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Sandoval CM, Baker SL, Jansen K et al (2011) Crystal structure of BamD: an essential component of the β-barrel assembly machinery of Gram-negative bacteria. J Mol Biol 409(3):348–357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Dong C, Hou H-F, Yang X et al (2012) Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly. Acta Crystallogr D Biol Crystallogr 68(2):95–101

    Article  CAS  PubMed  Google Scholar 

  83. D’Andrea LD, Regan L (2003) TPR proteins: the versatile helix. Trends Biochem Sci 28(12):655–662

    Article  PubMed  Google Scholar 

  84. Leyton DL, Sevastsyanovich YR, Browning DF et al (2011) Size and conformation limits to secretion of disulfide-bonded loops in autotransporter proteins. J Biol Chem 286(49):42283–42291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Knowles TJ, Browning DF, Jeeves M et al (2011) Structure and function of BamE within the outer membrane and the β-barrel assembly machine. EMBO Rep 12(2):123–128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Rigel NW, Schwalm J, Ricci DP et al (2012) BamE modulates the Escherichia coli beta-barrel assembly machine component BamA. J Bacteriol 194(5):1002–1008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank Chaille Webb, Victoria Hewitt, and Christopher Stubenrauch for constructive comments on the manuscript. We acknowledge support from the Australian Research Council (ARC) for research funding through the Super Science Fellowship grant FS110200015 (to T.L.) and NHMRC Program Grant 606788 (to T.L.). D.L.L. is an ARC Super Science Fellow, M.J.B. is an NHMRC Biomedical Research Fellow and T.L. is an ARC Australian Laureate Fellow.

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Correspondence to Denisse L. Leyton or Trevor Lithgow .

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Leyton, D.L., Belousoff, M.J., Lithgow, T. (2015). The β-Barrel Assembly Machinery Complex. In: Buchanan, S., Noinaj, N. (eds) The BAM Complex. Methods in Molecular Biology, vol 1329. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2871-2_1

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  • DOI: https://doi.org/10.1007/978-1-4939-2871-2_1

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