Skip to main content

High-Throughput Protein Production of Membrane Proteins in Saccharomyces cerevisiae

  • Protocol
  • First Online:
High-Throughput Protein Production and Purification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2025))

Abstract

This chapter outlines a protocol to assess viability for large-scale protein production and purification for selected targets from an initial medium-throughput cloning strategy. Thus, one can assess a broad number of potential candidate proteins, mutants, or expression variants using an empirically minimalistic approach. In addition, a key output from this protocol is utilization of Saccharomyces cerevisiae as a means for the efficient screening and production of purified proteins. The primary focus in this protocol is overexpression of polytopic integral membrane proteins though methods can be equally applied to soluble proteins. The protocol starts with outlining high-throughput (sans robotics) cloning of expression proteins into a dual-tag yeast expression plasmid. These membrane proteins are then screened for expression level, detergent solubilization, initial purity, and chromatography characteristics. Both small- and large-scale expression methods are discussed along with fermentation.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 239.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Newstead S, Kim H, von Heijne G, Iwata S, Drew D (2007) High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 104(35):13936–13941. https://doi.org/10.1073/pnas.0704546104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Drew D, Newstead S, Sonoda Y, Kim H, von Heijne G, Iwata S (2008) GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae. Nat Protoc 3(5):784–798. https://doi.org/10.1038/nprot.2008.44

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O’Connell JD 3rd, Miercke LJ, Giacomini KM, Sali A, Stroud RM (2009) Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol 385(3):820–830. https://doi.org/10.1016/j.jmb.2008.11.021

    Article  CAS  PubMed  Google Scholar 

  4. Hays FA, Roe-Zurz Z, Stroud RM (2010) Overexpression and purification of integral membrane proteins in yeast. Methods Enzymol 470:695–707. https://doi.org/10.1016/S0076-6879(10)70029-X

    Article  CAS  PubMed  Google Scholar 

  5. Flot D, Mairs T, Giraud T, Guijarro M, Lesourd M, Rey V, van Brussel D, Morawe C, Borel C, Hignette O, Chavanne J, Nurizzo D, McSweeney S, Mitchell E (2010) The ID23-2 structural biology microfocus beamline at the ESRF. J Synchrotron Radiat 17(1):107–118. https://doi.org/10.1107/S0909049509041168

    Article  CAS  PubMed  Google Scholar 

  6. Grochulski P, Cygler M, Yates B (2016) Designing a synchrotron micro-focusing beamline for macromolecular crystallography. Postepy Biochem 62(3):395–400

    PubMed  Google Scholar 

  7. Batyuk A, Galli L, Ishchenko A, Han GW, Gati C, Popov PA, Lee MY, Stauch B, White TA, Barty A, Aquila A, Hunter MS, Liang M, Boutet S, Pu M, Liu ZJ, Nelson G, James D, Li C, Zhao Y, Spence JC, Liu W, Fromme P, Katritch V, Weierstall U, Stevens RC, Cherezov V (2016) Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. Sci Adv 2(9):e1600292. https://doi.org/10.1126/sciadv.1600292

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Liao M, Cao E, Julius D, Cheng Y (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504(7478):107–112. https://doi.org/10.1038/nature12822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kuhlbrandt W (2014) Biochemistry. The resolution revolution. Science 343(6178):1443–1444. https://doi.org/10.1126/science.1251652

    Article  PubMed  Google Scholar 

  10. Newby ZE, O’Connell JD 3rd, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM (2009) A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nat Protoc 4(5):619–637. https://doi.org/10.1038/nprot.2009.27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Moraes I, Evans G, Sanchez-Weatherby J, Newstead S, Stewart PD (2014) Membrane protein structure determination – the next generation. Biochim Biophys Acta 1838(1 Pt A):78–87. https://doi.org/10.1016/j.bbamem.2013.07.010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chae PS, Rasmussen SG, Rana RR, Gotfryd K, Chandra R, Goren MA, Kruse AC, Nurva S, Loland CJ, Pierre Y, Drew D, Popot JL, Picot D, Fox BG, Guan L, Gether U, Byrne B, Kobilka B, Gellman SH (2010) Maltose-neopentyl glycol (MNG) amphiphiles for solubilization, stabilization and crystallization of membrane proteins. Nat Methods 7(12):1003–1008. https://doi.org/10.1038/nmeth.1526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Orwick-Rydmark M, Arnold T, Linke D (2016) The use of detergents to purify membrane proteins. Curr Protoc Protein Sci 84:4.8.1–4.8.35. https://doi.org/10.1002/0471140864.ps0408s84

    Article  Google Scholar 

  14. Saez NJ, Nozach H, Blemont M, Vincentelli R (2014) High throughput quantitative expression screening and purification applied to recombinant disulfide-rich venom proteins produced in E. coli. J Vis Exp 89:e51464. https://doi.org/10.3791/51464

    Article  Google Scholar 

  15. Saez NJ, Vincentelli R (2014) High-throughput expression screening and purification of recombinant proteins in E. coli. Methods Mol Biol 1091:33–53. https://doi.org/10.1007/978-1-62703-691-7_3

    Article  CAS  PubMed  Google Scholar 

  16. Rosano GL, Ceccarelli EA (2014) Recombinant protein expression in microbial systems. Front Microbiol 5:341. https://doi.org/10.3389/fmicb.2014.00341

    Article  PubMed  PubMed Central  Google Scholar 

  17. Rosano GL, Ceccarelli EA (2014) Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 5:172. https://doi.org/10.3389/fmicb.2014.00172

    Article  PubMed  PubMed Central  Google Scholar 

  18. Coolbaugh MJ, Wood DW (2014) Purification of E. coli proteins using a self-cleaving chitin-binding affinity tag. Methods Mol Biol 1177:47–58. https://doi.org/10.1007/978-1-4939-1034-2_4

    Article  CAS  PubMed  Google Scholar 

  19. Wood DW (2014) New trends and affinity tag designs for recombinant protein purification. Curr Opin Struct Biol 26:54–61. https://doi.org/10.1016/j.sbi.2014.04.006

    Article  CAS  PubMed  Google Scholar 

  20. Munro S, Pelham HR (1984) Use of peptide tagging to detect proteins expressed from cloned genes: deletion mapping functional domains of Drosophila hsp 70. EMBO J 3(13):3087–3093

    Article  CAS  Google Scholar 

  21. Peng B, Williams TC, Henry M, Nielsen LK, Vickers CE (2015) Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microb Cell Factories 14:91. https://doi.org/10.1186/s12934-015-0278-5

    Article  CAS  Google Scholar 

  22. Clark KM, Fedoriw N, Robinson K, Connelly SM, Randles J, Malkowski MG, DeTitta GT, Dumont ME (2010) Purification of transmembrane proteins from Saccharomyces cerevisiae for X-ray crystallography. Protein Expr Purif 71(2):207–223. https://doi.org/10.1016/j.pep.2009.12.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Ahmad M, Hirz M, Pichler H, Schwab H (2014) Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production. Appl Microbiol Biotechnol 98(12):5301–5317. https://doi.org/10.1007/s00253-014-5732-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Zhang Z, Moo-Young M, Chisti Y (1996) Plasmid stability in recombinant Saccharomyces cerevisiae. Biotechnol Adv 14(4):401–435

    Article  CAS  Google Scholar 

  25. Dragosits M, Frascotti G, Bernard-Granger L, Vazquez F, Giuliani M, Baumann K, Rodriguez-Carmona E, Tokkanen J, Parrilli E, Wiebe MG, Kunert R, Maurer M, Gasser B, Sauer M, Branduardi P, Pakula T, Saloheimo M, Penttila M, Ferrer P, Luisa Tutino M, Villaverde A, Porro D, Mattanovich D (2011) Influence of growth temperature on the production of antibody Fab fragments in different microbes: a host comparative analysis. Biotechnol Prog 27(1):38–46. https://doi.org/10.1002/btpr.524

    Article  CAS  PubMed  Google Scholar 

  26. Andre N, Cherouati N, Prual C, Steffan T, Zeder-Lutz G, Magnin T, Pattus F, Michel H, Wagner R, Reinhart C (2006) Enhancing functional production of G protein-coupled receptors in Pichia pastoris to levels required for structural studies via a single expression screen. Protein Sci 15(5):1115–1126. https://doi.org/10.1110/ps.062098206

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Figler RA, Omote H, Nakamoto RK, Al-Shawi MK (2000) Use of chemical chaperones in the yeast Saccharomyces cerevisiae to enhance heterologous membrane protein expression: high-yield expression and purification of human P-glycoprotein. Arch Biochem Biophys 376(1):34–46. https://doi.org/10.1006/abbi.2000.1712

    Article  CAS  PubMed  Google Scholar 

  28. Lanza AM, Curran KA, Rey LG, Alper HS (2014) A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae. BMC Syst Biol 8:33. https://doi.org/10.1186/1752-0509-8-33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Mellitzer A, Ruth C, Gustafsson C, Welch M, Birner-Grunberger R, Weis R, Purkarthofer T, Glieder A (2014) Synergistic modular promoter and gene optimization to push cellulase secretion by Pichia pastoris beyond existing benchmarks. J Biotechnol 191:187–195. https://doi.org/10.1016/j.jbiotec.2014.08.035

    Article  CAS  PubMed  Google Scholar 

  30. Mauro VP, Chappell SA (2014) A critical analysis of codon optimization in human therapeutics. Trends Mol Med 20(11):604–613. https://doi.org/10.1016/j.molmed.2014.09.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Gruswitz F, Frishman M, Goldstein BM, Wedekind JE (2005) Coupling of MBP fusion protein cleavage with sparse matrix crystallization screens to overcome problematic protein solubility. BioTechniques 39(4):476. 478, 480. Epub 2005/10/21

    Article  CAS  Google Scholar 

  32. Aslanidis C, de Jong PJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18(20):6069–6074. Epub 1990/10/25

    Article  CAS  Google Scholar 

  33. Parker JL, Newstead S (2014) Method to increase the yield of eukaryotic membrane protein expression in Saccharomyces cerevisiae for structural and functional studies. Protein Sci 23(9):1309–1314. Epub 2014/06/21. https://doi.org/10.1002/pro.2507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lin SY, Sun XH, Hsiao YH, Chang SE, Li GS, Hu NJ (2016) Fluorophore Absorption Size Exclusion Chromatography (FA-SEC): an alternative method for high-throughput detergent screening of membrane proteins. PLoS One 11(6):e0157923. Epub 2016/06/23. https://doi.org/10.1371/journal.pone.0157923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Joska TM, Mashruwala A, Boyd JM, Belden WJ (2014) A universal cloning method based on yeast homologous recombination that is simple, efficient, and versatile. J Microbiol Methods 100:46–51. Epub 2014/01/15. https://doi.org/10.1016/j.mimet.2013.11.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Weir M, Keeney JB (2014) PCR mutagenesis and gap repair in yeast. Methods Mol Biol 1205:29–35Epub 2014/09/13. https://doi.org/10.1007/978-1-4939-1363-3_3

    Article  CAS  PubMed  Google Scholar 

  37. Casini A, Storch M, Baldwin GS, Ellis T (2015) Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol 16(9):568–576Epub 2015/06/18. https://doi.org/10.1038/nrm4014

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors would like to acknowledge Jennifer Washburn, Zygy Roe-Žurž, Hannah Schmitz, and Dr. Robert M. Stroud for their support in previous development and implementation of methods outlined in this chapter. The Hays lab is supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number R01GM118599.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Franklin A. Hays .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Johnson, J.M., Hays, F.A. (2019). High-Throughput Protein Production of Membrane Proteins in Saccharomyces cerevisiae. In: Vincentelli, R. (eds) High-Throughput Protein Production and Purification. Methods in Molecular Biology, vol 2025. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9624-7_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9624-7_11

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9623-0

  • Online ISBN: 978-1-4939-9624-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics