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Metagenome-derived haloalkane dehalogenases with novel catalytic properties

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Abstract

Haloalkane dehalogenases (HLDs) are environmentally relevant enzymes cleaving a carbon-halogen bond in a wide range of halogenated pollutants. PCR with degenerate primers and genome-walking was used for the retrieval of four HLD-encoding genes from groundwater-derived environmental DNA. Using specific primers and the environmental DNA as a template, we succeeded in generating additional amplicons, resulting altogether in three clusters of sequences with each cluster comprising 8–13 closely related putative HLD-encoding genes. A phylogenetic analysis of the translated genes revealed that three HLDs are members of the HLD-I subfamily, whereas one gene encodes an enzyme from the subfamily HLD-II. Two metagenome-derived HLDs, eHLD-B and eHLD-C, each from a different subfamily, were heterologously produced in active form, purified and characterized in terms of their thermostability, pH and temperature optimum, quaternary structure, substrate specificity towards 30 halogenated compounds, and enantioselectivity. eHLD-B and eHLD-C showed striking differences in their activities, substrate preferences, and tolerance to temperature. Profound differences were also determined in the enantiopreference and enantioselectivity of these enzymes towards selected substrates. Comparing our data with those of known HLDs revealed that eHLD-C exhibits a unique combination of high thermostability, high activity, and an unusually broad pH optimum, which covers the entire range of pH 5.5–8.9. Moreover, a so far unreported high thermostability for HLDs was determined for this enzyme at pH values lower than 6.0. Thus, eHLD-C represents an attractive and novel biocatalyst for biotechnological applications.

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Acknowledgements

We would like to thank Envisan—GEM a.s. (Prague, Czech Republic) for the groundwater samples and their analyses. This work was supported by the Czech Science Foundation (grants P504/10/0137 and 16-07965S). We also acknowledge support for the long-term conceptual advancement of the Institute of Microbiology (RVO61388971). The research infrastructure for this project was supported by the following grants from the Czech Ministry of Education: LO1214, LM2015051, LM2015047, and LM2015055. Antonin Kunka acknowledges the Brno Municipality for funding a Ph.D. Talent Scholarship.

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  1. Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic

    Michael Kotik

  2. Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic

    Pavel Vanacek, Antonin Kunka, Zbynek Prokop & Jiri Damborsky

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Kotik, M., Vanacek, P., Kunka, A. et al. Metagenome-derived haloalkane dehalogenases with novel catalytic properties. Appl Microbiol Biotechnol 101, 6385–6397 (2017). https://doi.org/10.1007/s00253-017-8393-3

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