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Folding Engineering Strategies for Efficient Membrane Protein Production in E. coli

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Therapeutic Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 899))

Abstract

Membrane proteins are notoriously difficult to produce at the high levels required for structural and biochemical characterization. Among the various expression systems used to date, the enteric bacterium Escherichia coli remains one of the best characterized and most versatile. However, membrane protein overexpression in E. coli is often accompanied by toxicity and low yields of functional product. Here, we briefly review the involvement of signal recognition particle, trigger factor, and YidC in α-helical membrane protein biogenesis and describe a set of strains, vectors, and chaperone co-expression plasmids that can lead to significant gains in the production of recombinant membrane proteins in E. coli. Methods to quantify membrane proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis are also provided.

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References

  1. Wallin E, von Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7:1029–1038

    Article  PubMed  CAS  Google Scholar 

  2. Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AG, Tate CG, Schertler GF (2008) Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454:486–491

    Article  PubMed  CAS  Google Scholar 

  3. Bilwes AM, Alex LA, Crane BR, Simon MI (1999) Structure of CheA, a signal-transducing histidine kinase. Cell 96:131–141

    Article  PubMed  CAS  Google Scholar 

  4. Neutze R, Pebay-Peyroula E, Edman K, Royant A, Navarro J, Landau EM (2002) Bacteriorhodopsin: a high-resolution structural view of vectorial proton transport. Biochim Biophys Acta 1565:144–167

    Article  PubMed  CAS  Google Scholar 

  5. Capaldi RA, Aggeler R (2002) Mechanism of the F(1)F(0)-type ATP synthase, a biological rotary motor. Trends Biochem Sci 27:154–160

    Article  PubMed  CAS  Google Scholar 

  6. Olesen C, Picard M, Winther AM, Gyrup C, Morth JP, Oxvig C, Moller JV, Nissen P (2007) The structural basis of calcium transport by the calcium pump. Nature 450:1036–1042

    Article  PubMed  CAS  Google Scholar 

  7. Gonen T, Walz T (2006) The structure of aquaporins. Q Rev Biophys 39:361–396

    Article  PubMed  CAS  Google Scholar 

  8. Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1:727–730

    Article  PubMed  CAS  Google Scholar 

  9. McCusker EC, Bane SE, O’Malley MA, Robinson AS (2007) Heterologous GPCR expression: a bottleneck to obtaining crystal structures. Biotechnol Prog 23:540–547

    Article  PubMed  CAS  Google Scholar 

  10. Curnow P (2009) Membrane proteins in nanotechnology. Biochem Soc Trans 37:643–652

    Article  PubMed  CAS  Google Scholar 

  11. Soong RK, Bachand GD, Neves HP, Olkhovets AG, Craighead HG, Montemagno CD (2000) Powering an inorganic nanodevice with a biomolecular motor. Science (New York, NY) 290:1555–1558

    Article  CAS  Google Scholar 

  12. Choi HJ, Montemagno CD (2005) Artificial organelle: ATP synthesis from cellular mimetic polymersomes. Nano Lett 5:2538–2542

    Article  PubMed  CAS  Google Scholar 

  13. Luo TJ, Soong R, Lan E, Dunn B, Montemagno C (2005) Photo-induced proton gradients and ATP biosynthesis produced by vesicles encapsulated in a silica matrix. Nat Mater 4:220–224

    Article  PubMed  CAS  Google Scholar 

  14. Nakamura C, Hasegawa M, Yasuda Y, Miyake J (2000) Self-assembling photosynthetic reaction centers on electrodes for current generation. Appl Biochem Biotechnol 84–86:401–408

    Article  PubMed  Google Scholar 

  15. Zhang L, Zeng T, Cooper K, Claus RO (2003) High-performance photovoltaic behavior of oriented purple membrane polymer composite films. Biophys J 84:2502–2507

    Article  PubMed  CAS  Google Scholar 

  16. Mo X, Krebs MP, Yu SM (2006) Directed synthesis and assembly of nanoparticles using purple membrane. Small 2:526–529

    Article  PubMed  CAS  Google Scholar 

  17. Gu LQ, Braha O, Conlan S, Cheley S, Bayley H (1999) Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter. Nature 398:686–690

    Article  PubMed  CAS  Google Scholar 

  18. Kang XF, Cheley S, Guan X, Bayley H (2006) Stochastic detection of enantiomers. J Am Chem Soc 128:10684–10685

    Article  PubMed  CAS  Google Scholar 

  19. Cheley S, Gu LQ, Bayley H (2002) Stochastic sensing of nanomolar inositol 1,4,5-trisphosphate with an engineered pore. Chem Biol 9:829–838

    Article  PubMed  CAS  Google Scholar 

  20. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93:13770–13773

    Article  PubMed  CAS  Google Scholar 

  21. Kang XF, Cheley S, Rice-Ficht AC, Bayley H (2007) A storable encapsulated bilayer chip containing a single protein nanopore. J Am Chem Soc 129:4701–4705

    Article  PubMed  CAS  Google Scholar 

  22. Baneyx F (1999) Recombinant protein expression in Escherichia coli. Curr Opin Biotechnol 10:411–421

    Article  PubMed  CAS  Google Scholar 

  23. Wagner S, Bader ML, Drew D, de Gier JW (2006) Rationalizing membrane protein overexpression. Trends Biotechnol 24:364–371

    Article  PubMed  CAS  Google Scholar 

  24. Weiner JH, Li L (2008) Proteome of the Escherichia coli envelope and technological challenges in membrane proteome analysis. Biochim Biophys Acta 1778:1698–1713

    Article  PubMed  CAS  Google Scholar 

  25. Ulbrandt ND, Newitt JA, Bernstein HD (1997) The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins. Cell 88:187–196

    Article  PubMed  CAS  Google Scholar 

  26. Yuan J, Zweers JC, van Dijl JM, Dalbey RE (2009) Protein transport across and into cell membranes in bacteria and archaea. Cell Mol Life Sci 67:179–199

    Article  PubMed  Google Scholar 

  27. Schierle CF, Berkmen M, Huber D, Kumamoto C, Boyd D, Beckwith J (2003) The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway. J Bacteriol 185:5706–5713

    Article  PubMed  CAS  Google Scholar 

  28. Bowers CW, Lau F, Silhavy TJ (2003) Secretion of LamB-LacZ by the signal recognition particle pathway of Escherichia coli. J Bacteriol 185:5697–5705

    Article  PubMed  CAS  Google Scholar 

  29. Brown S, Fournier MJ (1984) The 4.5S RNA gene of Escherichia coli is essential for cell growth. J Mol Biol 178:533–550

    Article  PubMed  CAS  Google Scholar 

  30. Phillips GJ, Silhavy TJ (1992) The E. coli ffh gene is necessary for viability and efficient protein export. Nature 359:744–746

    Article  PubMed  CAS  Google Scholar 

  31. Luirink J, Sinning I (2004) SRP-mediated protein targeting: structure and function revisited. Biochim Biophys Acta 1694:17–35

    PubMed  CAS  Google Scholar 

  32. Pool MR, Stumm J, Fulga TA, Sinning I, Dobberstein B (2002) Distinct modes of signal recognition particle interaction with the ribosome. Science (New York, NY) 297:1345–1348

    Article  CAS  Google Scholar 

  33. Ullers RS, Houben EN, Raine A, ten Hagen-Jongman CM, Ehrenberg M, Brunner J, Oudega B, Harms N, Luirink J (2003) Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome. J Cell Biol 161:679–684

    Article  PubMed  CAS  Google Scholar 

  34. Gu SQ, Peske F, Wieden HJ, Rodnina MV, Wintermeyer W (2003) The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome. RNA 9:566–573

    Article  PubMed  CAS  Google Scholar 

  35. Luirink J, ten Hagen-Jongman CM, van der Weijden CC, Oudega B, High S, Dobberstein B, Kusters R (1994) An alternative protein targeting pathway in Escherichia coli: studies on the role of FtsY. EMBO J 13:2289–2296

    PubMed  CAS  Google Scholar 

  36. de Leeuw E, Poland D, Mol O, Sinning I, ten Hagen-Jongman CM, Oudega B, Luirink J (1997) Membrane association of FtsY, the E. coli SRP receptor. FEBS Lett 416:225–229

    Article  PubMed  Google Scholar 

  37. Bibi E (2011) Early targeting events during membrane protein biogenesis in Escherichia coli. Biochim Biophys Acta 1801:841–850

    Google Scholar 

  38. Luirink J, Samuelsson T, de Gier JW (2001) YidC/Oxa1p/Alb3: evolutionarily conserved mediators of membrane protein assembly. FEBS Lett 501:1–5

    Article  PubMed  CAS  Google Scholar 

  39. Jiang F, Yi L, Moore M, Chen M, Rohl T, Van Wijk KJ, De Gier JW, Henry R, Dalbey RE (2002) Chloroplast YidC homolog Albino3 can functionally complement the bacterial YidC depletion strain and promote membrane ­insertion of both bacterial and chloroplast thylakoid proteins. J Biol Chem 277:19281–19288

    Article  PubMed  CAS  Google Scholar 

  40. van Bloois E, Nagamori S, Koningstein G, Ullers RS, Preuss M, Oudega B, Harms N, Kaback HR, Herrmann JM, Luirink J (2005) The Sec-independent function of Escherichia coli YidC is evolutionary-conserved and essential. J Biol Chem 280:12996–13003

    Article  PubMed  Google Scholar 

  41. Xie K, Dalbey RE (2008) Inserting proteins into the bacterial cytoplasmic membrane using the Sec and YidC translocases. Nat Rev Microbiol 6:234–244

    PubMed  CAS  Google Scholar 

  42. Nagamori S, Smirnova IN, Kaback HR (2004) Role of YidC in folding of polytopic membrane proteins. J Cell Biol 165:53–62

    Article  PubMed  CAS  Google Scholar 

  43. Kol S, Nouwen N, Driessen AJ (2008) Mechanisms of YidC-mediated insertion and assembly of multimeric membrane protein complexes. J Biol Chem 283:31269–31273

    Article  PubMed  CAS  Google Scholar 

  44. Houben EN, ten Hagen-Jongman CM, Brunner J, Oudega B, Luirink J (2004) The two membrane segments of leader peptidase partition one by one into the lipid bilayer via a Sec/YidC interface. EMBO Rep 5:970–975

    Article  PubMed  CAS  Google Scholar 

  45. Beck K, Eisner G, Trescher D, Dalbey RE, Brunner J, Muller M (2001) YidC, an assembly site for polytopic Escherichia coli membrane proteins located in immediate proximity to the SecYE translocon and lipids. EMBO Rep 2:709–714

    Article  PubMed  CAS  Google Scholar 

  46. van der Laan M, Bechtluft P, Kol S, Nouwen N, Driessen AJ (2004) F1F0 ATP synthase subunit c is a substrate of the novel YidC pathway for membrane protein biogenesis. J Cell Biol 165:213–222

    Article  PubMed  Google Scholar 

  47. Samuelson JC, Jiang F, Yi L, Chen M, de Gier JW, Kuhn A, Dalbey RE (2001) Function of YidC for the insertion of M13 procoat protein in Escherichia coli: translocation of mutants that show differences in their membrane potential dependence and Sec requirement. J Biol Chem 276:34847–34852

    Article  PubMed  CAS  Google Scholar 

  48. Maier T, Ferbitz L, Deuerling E, Ban N (2005) A cradle for new proteins: trigger factor at the ribosome. Curr Opin Struct Biol 15:204–212

    Article  PubMed  CAS  Google Scholar 

  49. Hoffmann A, Bukau B, Kramer G (2010) Structure and function of the molecular chaperone trigger factor. Biochim Biophys Acta 1803:650–661

    Article  PubMed  CAS  Google Scholar 

  50. Kramer G, Rauch T, Rist W, Vordewulbecke S, Patzell H, Schulze-Specking A, Ban N, Deuerling E, Bukau B (2002) L23 functions as a chaperone docking site on the ribosome. Nature 419:171–174

    Article  PubMed  CAS  Google Scholar 

  51. Hoffmann A, Merz F, Rutkowska A, Zachmann-Brand B, Deuerling E, Bukau B (2006) Trigger factor forms a protective shield for nascent polypeptides at the ribosome. J Biol Chem 281:6539–6545

    Article  PubMed  CAS  Google Scholar 

  52. Patzelt H, Kramer G, Rauch T, Schonfeld HJ, Bukau B, Deuerling E (2002) Three-state equilibrium of Escherichia coli trigger factor. Biol Chem 383:1611–1619

    Article  PubMed  Google Scholar 

  53. Buskiewicz I, Deuerling E, Gu SQ, Jockel J, Rodnina MV, Bukau B, Wintermeyer W (2004) Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor. Proc Natl Acad Sci USA 101:7902–7906

    Article  PubMed  CAS  Google Scholar 

  54. Buskiewicz I, Deuerling E, Gu S-Q, Jöckel J, Rodnina MV, Bukau B, Wintermeyer W (2004) Trigger factor binds to ribosome-signal recognition particle (SRP) complexes and is excluded by binding of the SRP receptor. Proc Natl Acad Sci USA 101:7902–7906

    Article  PubMed  CAS  Google Scholar 

  55. Deuerling E, Patzelt H, Vorderwulbecke S, Rauch T, Kramer G, Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B (2003) Trigger factor and DnaK possess overlapping substrate pools and binding specificities. Mol Microbiol 47:1317–1328

    Article  PubMed  CAS  Google Scholar 

  56. Baneyx F, Nannenga BL (2010) Chaperones: a story of thrift unfolds. Nat Chem Biol 6:880–881

    Article  PubMed  CAS  Google Scholar 

  57. Sharma SK, De los Rios P, Christen P, Lustig A, Goloubinoff P (2010) The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase. Nat Chem Biol 6:914–920

    Article  PubMed  CAS  Google Scholar 

  58. Mujacic M, Cooper KW, Baneyx F (1999) Cold-inducible cloning vectors for low-temperature protein expression in Escherichia coli: application to the production of a toxic and proteolytically sensitive fusion protein. Gene 238:325–332

    Article  PubMed  CAS  Google Scholar 

  59. Wagner S, Klepsch MM, Schlegel S, Appel A, Draheim R, Tarry M, Hogbom M, van Wijk KJ, Slotboom DJ, Persson JO, de Gier JW (2008) Tuning Escherichia coli for membrane protein overexpression. Proc Natl Acad Sci USA 105:14371–14376

    Article  PubMed  CAS  Google Scholar 

  60. Guzman LM, Belin D, Carson MJ, Beckwith J (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177:4121–4130

    PubMed  CAS  Google Scholar 

  61. Ren H, Yu D, Ge B, Cook B, Xu Z, Zhang S (2009) High-level production, solubilization and purification of synthetic human GPCR chemokine receptors CCR5, CCR3, CXCR4 and CX3CR1. PLoS One 4:e4509

    Article  PubMed  Google Scholar 

  62. Hassan KA, Xu Z, Watkins RE, Brennan RG, Skurray RA, Brown MH (2009) Optimized production and analysis of the staphylococcal multidrug efflux protein QacA. Protein Expr Purif 64:118–124

    Article  PubMed  CAS  Google Scholar 

  63. Romantsov T, Battle AR, Hendel JL, Martinac B, Wood JM (2010) Protein localization in Escherichia coli cells: comparison of the cytoplasmic membrane proteins ProP, LacY, ProW, AqpZ, MscS, and MscL. J Bacteriol 192:912–924

    Article  PubMed  CAS  Google Scholar 

  64. Nannenga BL, Baneyx F (2011) Reprogramming chaperone pathways to improve membrane protein expression in Escherichia coli. Protein Sci 20:1411–1420

    Google Scholar 

  65. Puertas JM, Nannenga BL, Dornfeld KT, Betton JM, Baneyx F (2010) Enhancing the secretory yields of leech carboxypeptidase inhibitor in Escherichia coli: influence of trigger factor and signal recognition particle. Protein Expr Purif 74:122–128

    Article  PubMed  CAS  Google Scholar 

  66. Kramer G, Rauch T, Rist W, Vorderwulbecke S, Patzelt H, Schulze-Specking A, Ban N, Deuerling E, Bukau B (2002) L23 protein functions as a chaperone docking site on the ribosome. Nature 419:171–174

    Article  PubMed  CAS  Google Scholar 

  67. Menetret JF, Schaletzky J, Clemons WM Jr, Osborne AR, Skanland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW (2007) Ribosome binding of a single copy of the SecY complex: implications for protein translocation. Mol Cell 28:1083–1092

    Article  PubMed  CAS  Google Scholar 

  68. Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N (2011) The crystal structure of the signal recognition particle in complex with its receptor. Science (New York, NY) 331:881–886

    Article  CAS  Google Scholar 

  69. Palmeros B, Wild J, Szybalski W, Le Borgne S, Hernandez-Chavez G, Gosset G, Valle F, Bolivar F (2000) A family of removable cassettes designed to obtain antibiotic-resistance-free genomic modifications of Escherichia coli and other bacteria. Gene 247:255–264

    Article  PubMed  CAS  Google Scholar 

  70. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97:6640–6645

    Article  PubMed  CAS  Google Scholar 

  71. Baneyx F, Palumbo JL (2003) Improving heterologous protein folding via molecular chaperone and foldase co-expression. Methods Mol Biol 205:171–197

    PubMed  CAS  Google Scholar 

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Acknowledgments

BLN gratefully acknowledges NSF-IGERT fellowship support from the University of Washington Center for Nanotechnology. This work was supported by NSF award BBBE-0854511.

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Correspondence to François Baneyx .

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Nannenga, B.L., Baneyx, F. (2012). Folding Engineering Strategies for Efficient Membrane Protein Production in E. coli . In: Voynov, V., Caravella, J. (eds) Therapeutic Proteins. Methods in Molecular Biology, vol 899. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-921-1_12

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  • DOI: https://doi.org/10.1007/978-1-61779-921-1_12

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