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Functional Screening of Metagenomic Libraries: Enzymes Acting on Greasy Molecules as Study Case

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Hydrocarbon and Lipid Microbiology Protocols

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

Abstract

Greasy molecules such as aromatic and aliphatic hydrocarbons are ubiquitous and chemically heterogeneous microbial substrates that occur in the biosphere through human activities as well as natural inputs. Organic compounds consisting of one, two, or more fused aromatic rings are due to their toxicity considered as pollutants of a great concern; however, they are also important chemical building blocks of relevance for biology, chemistry, and materials sciences. Biological approaches are known to provide exquisite ecologically friendly methods, as compared to chemical ones, for their biodegradation or bioconversions. For that, ubiquitous yet specialized hydrocarbonoclastic bacteria and polycyclic aromatic hydrocarbons (PAH) degrading bacteria of the genera Alcanivorax, Marinobacter, Oleispira, Thalassolitus, Oleiphilus, Cycloclasticus, and Neptunomonas to name some, have developed a complex arsenal of catabolic genes involved in greasy oil component degradation. Oxidoreductases and hydrolases are the first enzymes initiating on their catabolism. The rapid evolution of next generation sequencing methods had a big impact on the identification of genes for metabolism of greasy molecules. But sequencing allows only the identification of enzymes with certain sequence similarity to those previously deposited in databases without functional information. Functional screening of expression libraries from pure cultures or microbial consortia is an alternative approach that solves the problem of sequence similarity and also ensures proper function assignation. Here we describe available screening methods to identify enzymes capable of acting towards greasy molecules that include not only oil components such as alkanes and PAH but also other types of greasy molecules of biotechnological relevance to produce fine chemicals and precursors in chemical industries.

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Acknowledgments

The authors gratefully acknowledge the financial support provided by the European Community project MAMBA (FP7-KBBE-2008-226977), MAGIC-PAH (FP7-KBBE-2009-245226), ULIXES (FP7-KBBE-2010-266473), KILL-SPILL (FP7-KBBE-2012-312139), and MicroB3 (FP7-OCEAN.2011-2-287589). We thank EU Horizon 2020 Program for the support of the Project INMARE H2020-BG-2014-2634486. This work was further funded by grants BIO2011-25012, PCIN-2014-107, and BIO2014-54494-R from the Spanish Ministry of Economy and Competitiveness. The present investigation was also funded by the Spanish Ministry of Economy and Competitiveness within the ERA NET IB2, grant number ERA-IB-14-030. The authors gratefully acknowledge the financial support provided by the European Regional Development Fund (ERDF).

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Authors and Affiliations

  1. Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain

    Mónica Martínez-Martínez & Manuel Ferrer

  2. School of Biological Sciences, University of Bangor, Gwynedd, LL57 2UW, UK

    Peter N. Golyshin

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  1. Mónica Martínez-Martínez
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  2. Peter N. Golyshin
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  3. Manuel Ferrer
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Correspondence to Mónica Martínez-Martínez or Manuel Ferrer .

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Editors and Affiliations

  1. School of Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

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Martínez-Martínez, M., Golyshin, P.N., Ferrer, M. (2015). Functional Screening of Metagenomic Libraries: Enzymes Acting on Greasy Molecules as Study Case. 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_104

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  • DOI: https://doi.org/10.1007/8623_2015_104

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