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Novel Tools for the Functional Expression of Metagenomic DNA

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Metagenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1539))

Abstract

Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus. Different broad-host-range shuttle vectors are described that allow activity-based screening of metagenomic DNA in these bacteria. Furthermore, we describe the newly developed transfer-and-expression system TREX which comprises genetic elements essential to allow for expression of large clusters of functionally coupled genes in different microbial species.

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Acknowledgments

Part of this work was funded by the Bioeconomy Science Center which is financially supported by the Ministry of Innovation, Research and Science of North-Rhine Westphalia, Germany, within the framework of the NRW Strategieprojekt BioSC (No. 313/323 - 400 - 00213), and by the Deutsche Forschungsgemeinschaft within CEPLAS—Cluster of Excellence on Plant Sciences (EXC 1028).

We thank Alexander Bollinger (Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Germany) for his contribution regarding handling of B. glumae PG1.

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Authors and Affiliations

  1. Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany

    Nadine Katzke, Andreas Knapp, Anita Loeschcke, Thomas Drepper & Karl-Erich Jaeger

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  1. Nadine Katzke
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  2. Andreas Knapp
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  3. Anita Loeschcke
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  4. Thomas Drepper
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  5. Karl-Erich Jaeger
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Correspondence to Karl-Erich Jaeger .

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Editors and Affiliations

  1. Mikrobiologie & Biotechnologie Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany

    Wolfgang R. Streit

  2. Göttingen Genomics Laboratory Department of Genomic and Applied Microbiology Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany

    Rolf Daniel

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Katzke, N., Knapp, A., Loeschcke, A., Drepper, T., Jaeger, KE. (2017). Novel Tools for the Functional Expression of Metagenomic DNA. In: Streit, W., Daniel, R. (eds) Metagenomics. Methods in Molecular Biology, vol 1539. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6691-2_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6691-2_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6689-9

  • Online ISBN: 978-1-4939-6691-2

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