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From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules

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Abstract

Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development.

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Acknowledgments

We thank Anja Stieler and Victoria Michael for their skillful technical assistance. In addition, we thank Boyke Bunk for his bioinformatic support and Petra Henke for her critical review of the manuscript. This work was supported by the EU Framework Program 7: MICROME Collaborative Project [222886-2] and Marie Curie IOF Program (CoGniSePlanctomyces).

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  1. Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124, Braunschweig, Germany

    Olga Jeske, Mareike Jogler, Jörn Petersen, Johannes Sikorski & Christian Jogler

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  1. Olga Jeske
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Correspondence to Christian Jogler.

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Olga Jeske and Mareike Jogler contributed equally to this paper.

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Jeske, O., Jogler, M., Petersen, J. et al. From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules. Antonie van Leeuwenhoek 104, 551–567 (2013). https://doi.org/10.1007/s10482-013-0007-1

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