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Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes

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Microbial Environmental Genomics (MEG)

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1399))

Abstract

Activity-based metagenomics is one of the most efficient approaches to boost the discovery of novel biocatalysts from the huge reservoir of uncultivated bacteria. In this chapter, we describe a highly generic procedure of metagenomic library construction and high-throughput screening for carbohydrate-active enzymes. Applicable to any bacterial ecosystem, it enables the swift identification of functional enzymes that are highly efficient, alone or acting in synergy, to break down polysaccharides and oligosaccharides.

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References

  1. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  2. André I, Potocki-Véronèse G, Barbe S, Moulis C, Remaud-Siméon M (2014) CAZyme discovery and design for sweet dreams. Curr Opin Chem Biol 19:17–24

    Article  PubMed  Google Scholar 

  3. Li L-L, McCorkle SR, Monchy S, Taghavi S, van der Lelie D (2009) Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels 2:10

    Article  PubMed  PubMed Central  Google Scholar 

  4. Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Martins Dos Santos VAP, Yakimov MM, Timmis KN, Golyshin PN (2005) Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem Biol 12:895–904

    Article  PubMed  CAS  Google Scholar 

  5. Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 20:1605–1612

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  6. Ladevèze S, Tarquis L, Cecchini DA, Bercovici J, André I, Topham CM, Morel S, Laville E, Monsan P, Lombard V, Henrissat B, Potocki-Véronèse G (2013) Role of glycoside phosphorylases in mannose foraging by human gut bacteria. J Biol Chem 288:32370–32383

    Article  PubMed  PubMed Central  Google Scholar 

  7. Ekkers DM, Cretoiu MS, Kielak AM, van Elsas JD (2012) The great screen anomaly—a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 93:1005–1020

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  8. Taupp M, Mewis K, Hallam SJ (2011) The art and design of functional metagenomic screens. Curr Opin Biotechnol 22:465–472

    Article  PubMed  CAS  Google Scholar 

  9. Bastien G, Arnal G, Bozonnet S, Laguerre S, Ferreira F, Fauré R, Henrissat B, Lefèvre F, Robe P, Bouchez O, Noirot C, Dumon C, O’Donohue M (2013) Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics. Biotechnol Biofuels 6:78

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  10. Atteia O, Dubois JP, Webster R (1994) Geostatistical analysis of soil contamination in the Swiss Jura. Environ Pollut (Barking Essex) 86:315–327

    Article  CAS  Google Scholar 

  11. Courtois S, Frostegård A, Göransson P, Depret G, Jeannin P, Simonet P (2001) Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ Microbiol 3:431–439

    Article  PubMed  CAS  Google Scholar 

  12. Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perriere G, Simonet P, Nalin R (2004) Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Appl Environ Microbiol 70:5522–5527

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  13. Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Doré J, Henrissat B, Remaud-Siméon M, Monsan P, Potocki-Véronèse G (2013) Functional metagenomics reveals novel pathways of prebiotic breakdown by Human gut bacteria. PLoS One 8:e72766

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  14. Moreira D, López-Garcı́a P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10:31–38

    Article  PubMed  CAS  Google Scholar 

  15. Oliver MA, Webster R (2010) Combining nested and linear sampling for determining the scale and form of spatial variation of regionalized variables. Geogr Anal 18:227–242

    Article  Google Scholar 

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Acknowledgements

This research was funded by the European Union project MetaExplore, the French Research Agency (Agence Nationale de la Recherche) ANR project Metasoil, and the INRA metaprogramme M2E (project Metascreen).

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Authors and Affiliations

  1. INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France

    Lisa Ufarté, Sophie Bozonnet, Elisabeth Laville, Davide A. Cecchini, Sandra Pizzut-Serin & Gabrielle Potocki Veronese

  2. UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, 31400, Toulouse, France

    Lisa Ufarté, Sophie Bozonnet, Elisabeth Laville, Davide A. Cecchini, Sandra Pizzut-Serin & Gabrielle Potocki Veronese

  3. UMR5504, CNRS, 31400, Toulouse, France

    Lisa Ufarté, Sophie Bozonnet, Elisabeth Laville, Davide A. Cecchini, Sandra Pizzut-Serin & Gabrielle Potocki Veronese

  4. Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully, France

    Samuel Jacquiod, Sandrine Demanèche, Pascal Simonet & Laure Franqueville

Authors
  1. Lisa Ufarté
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  2. Sophie Bozonnet
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  3. Elisabeth Laville
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  4. Davide A. Cecchini
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  5. Sandra Pizzut-Serin
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  6. Samuel Jacquiod
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  7. Sandrine Demanèche
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  8. Pascal Simonet
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  9. Laure Franqueville
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  10. Gabrielle Potocki Veronese
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Corresponding author

Correspondence to Gabrielle Potocki Veronese .

Editor information

Editors and Affiliations

  1. "Tree-Microbe Interactions" (IAM), UMR1136 INRA/University of Lorraine, Nancy, France

    Francis Martin

  2. "Tree-Microbe Interactions" (IAM);, UMR1136 INRA/University of Lorraine, Champenoux, France

    Stephane Uroz

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© 2016 Springer Science+Business Media New York

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Ufarté, L. et al. (2016). Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes. In: Martin, F., Uroz, S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 1399. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3369-3_15

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  • DOI: https://doi.org/10.1007/978-1-4939-3369-3_15

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3367-9

  • Online ISBN: 978-1-4939-3369-3

  • eBook Packages: Springer Protocols

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