Metagenomic Survey of Potential Symbiotic Bacteria and Polyketide Synthase Genes in an Indonesian Marine Sponge

  • Nia M. Kurnia Graduate School of Pharmacy, Pancasila University, Jakarta
  • Agustinus R. Uria Laboratory of Marine Biotechnology, Research Center for Marine and Fisheries Product Processing and Biotechnology, Ministry of Marine Affairs and Fisheries, Jalan KS Tubun Petamburan VI, Jakarta 10260
  • Yudi Kusnadi Laboratory of Marine Biotechnology, Research Center for Marine and Fisheries Product Processing and Biotechnology, Ministry of Marine Affairs and Fisheries, Jalan KS Tubun Petamburan VI, Jakarta 10260
  • Lidia Dinawati Faculty of Fisheries and Marine Science, University of Riau, Pekanbaru
  • Dewi S. Zilda Laboratory of Marine Biotechnology, Research Center for Marine and Fisheries Product Processing and Biotechnology, Ministry of Marine Affairs and Fisheries, Jalan KS Tubun Petamburan VI, Jakarta 10260
  • Tri A. Hadi Research Center for Oceanography, Indonesian Institute of Sciences (LIPI)
  • Siswa Setyahadi Center for Bioindustrial Technology, Agency for the Assessment and Application of Technology (BPPT)
  • Feliatra Felix Faculty of Fisheries and Marine Science, University of Riau, Pekanbaru
Keywords: “Candidatus Entotheonella sp.”, marine sponge, microbiome, polyketide synthase, Rhabdastrella sp.

Abstract

There has been emerging evidence that the bacteria associated with marine sponges are the key producers of many complex bioactive compounds. The as-yet uncultured candidate bacterial genus “Candidatus Entotheonella” of the marine sponge Theonella swinhoei from Japan have recently been recognized as the source of numerous pharmacologically relevant polyketides and modified peptides, as previously reported by the Piel group (Wilson et al. 2014). This work reported the presence of “Candidatus Entotheonella sp.” in the highly complex microbiome of an Indonesian marine sponge from Kapoposang Island, SouthSulawesi. We further identified the Kapoposang sponge specimen used in this work as Rhabdastrella sp. based on the integrated morphological, histological, and cytochrome oxidase subunit I (COI) gene analyses. To detect the polyketide biosynthetic machinery called type I polyketide synthase (PKS) in this Indonesian Rhabdastrella sp., we amplified and cloned the ketosynthase-encoding DNA regions of approximately 700 bp from the uncultured sponge's microbiome. Further sequencing and analysis of several randomly chosen clones indicated that all of them are mostly likely involved in the biosynthesis of methyl-branched fatty acids. However, employing a PKS-targeting primer designed in this work led to the isolation of four positive clones. BlastX search and subsequent phylogenetic analysis showed that one of the positive clones, designed as RGK32, displayed high homology with ketosynthase domains of many type I PKS systems and may belong to the subclass cis-AT PKS group.

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Published
2018-03-23