Skip to main content

Genetic Enzyme Screening System: A Method for High-Throughput Functional Screening of Novel Enzymes from Metagenomic Libraries

  • Protocol
  • First Online:
Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

This protocol describes a single-cell high-throughput genetic enzyme screening system (GESS) in which GFP fluorescence is used to detect the production of phenolic compounds from a given substrate by metagenomic enzyme activity. One of the important features of this single-cell genetic circuit is that it can be used to screen more than 200 different types of enzymes that produce phenolic compounds from phenyl group-containing substrates. The highly sensitive and quantitative nature of the GESS, combined with flow cytometry techniques, will facilitate rapid finding and directed evolution of valuable new enzymes such as glycosidases, cellulases, and lipases from metagenomic and other genetic libraries.

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

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

Similar content being viewed by others

References

  1. Kumar A, Singh S (2013) Directed evolution: tailoring biocatalysts for industrial applications. Crit Rev Biotechnol 33(4):365–378

    Article  CAS  PubMed  Google Scholar 

  2. Jemli S, Ayadi-Zouari D, Hlima HB, Bejar S (2014) Biocatalysts: application and engineering for industrial purposes. Crit Rev Biotechnol 1–13

    Google Scholar 

  3. Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3(6):510–516

    Article  CAS  PubMed  Google Scholar 

  4. Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77(4):1153–1161

    Article  CAS  PubMed  Google Scholar 

  5. Iqbal HA, Feng Z, Brady SF (2012) Biocatalysts and small molecule products from metagenomic studies. Curr Opin Chem Biol 16(1):109–116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Ferrer M, Beloqui A, Timmis KN, Golyshin PN (2008) Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 16(1–2):109–123

    PubMed  Google Scholar 

  7. Steele HL, Jaeger K-E, Daniel R, Streit WR (2008) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 16(1–2):25–37

    PubMed  Google Scholar 

  8. Uchiyama T, Abe T, Ikemura T, Watanabe K (2004) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23(1):88–93

    Article  PubMed  Google Scholar 

  9. van Sint Fiet S, van Beilen JB, Witholt B (2006) Selection of biocatalysts for chemical synthesis. Proc Natl Acad Sci U S A 103(6):1693–1698

    Article  PubMed  PubMed Central  Google Scholar 

  10. Dietrich JA, McKee AE, Keasling JD (2010) High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem 79:563–590

    Article  CAS  PubMed  Google Scholar 

  11. Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefèvre F, Doré J, Blottière HM (2010) Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. PLoS One 5(9):e13092

    Article  PubMed  PubMed Central  Google Scholar 

  12. Jacquiod S, Demanèche S, Franqueville L, Ausec L, Xu Z, Delmont TO, Dunon V, Cagnon C, Mandic-Mulec I, Vogel TM (2014) Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library. J Biotechnol 190:18–29

    Article  CAS  PubMed  Google Scholar 

  13. Choi S-L, Rha E, Lee SJ, Kim H, Kwon K, Jeong Y-S, Rhee YH, Song JJ, Kim H-S, Lee S-G (2013) Toward a generalized and high-throughput enzyme screening system based on artificial genetic circuits. ACS Synth Biol 3(3):163–171

    Article  PubMed  Google Scholar 

  14. Shingler V, Bartilson M, Moore T (1993) Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J Bacteriol 175(6):1596–1604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ng LC, O’Neill E, Shingler V (1996) Genetic evidence for interdomain regulation of the phenol-responsive 54-dependent activator DmpR. J Biol Chem 271(29):17281–17286

    Article  CAS  PubMed  Google Scholar 

  16. Jeong Y-S, Choi S-L, Kyeong H-H, Kim J-H, Kim E-J, Pan J-G, Rha E, Song JJ, Lee S-G, Kim H-S (2012) High-throughput screening system based on phenolics-responsive transcription activator for directed evolution of organophosphate-degrading enzymes. Protein Eng Des Sel 25(11):725–731

    Article  CAS  PubMed  Google Scholar 

  17. LESUISSE E, Schanck K, Colson C (1993) Purification and preliminary characterization of the extracellular lipase of Bacillus subtilis 168, an extremely basic pH‐tolerant enzyme. Eur J Biochem 216(1):155–160

    Article  CAS  PubMed  Google Scholar 

  18. Salameh M, Wiegel J (2007) Lipases from extremophiles and potential for industrial applications. Adv Appl Microbiol 61:253–283

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

This research was supported by grants from the Intelligent Synthetic Biology Center of Global Frontier Project (2011–0031944) and the KRIBB Research Initiative Program.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Seung-Goo Lee .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer-Verlag Berlin Heidelberg

About this protocol

Cite this protocol

Kim, H., Kwon, K.K., Rha, E., Lee, SG. (2015). Genetic Enzyme Screening System: A Method for High-Throughput Functional Screening of Novel Enzymes from Metagenomic Libraries. In: McGenity, T., Timmis, K., Nogales, B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_65

Download citation

  • DOI: https://doi.org/10.1007/8623_2015_65

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-53113-6

  • Online ISBN: 978-3-662-53115-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics