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Diversity of polyketide synthase genes from bacteria associated with the marine sponge Pseudoceratina clavata : culture‐dependent and culture‐independent approaches
Author(s) -
Kim Tae Kyung,
Fuerst John A.
Publication year - 2006
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2006.01040.x
Subject(s) - fosmid , biology , metagenomics , sponge , polyketide synthase , 16s ribosomal rna , polyketide , phylogenetic tree , gene , phylum , gene cluster , microbiology and biotechnology , genetics , computational biology , biosynthesis , botany
Summary Diverse ketosynthase (KS) genes were retrieved from the microbial community associated with the Great Barrier Reef sponge Pseudoceratina clavata . Bacterial isolation and metagenomic approaches were employed. Phylogenetic analysis of 16S rRNA of culturable sponge‐associated bacterial communities comprised eight groups over four phyla. Ten KS domains were amplified from four genera of isolates and phylogenetics demonstrated that these KS domains were located in three clusters (actinobacterial, cyanobacterial and trans ‐AT type). Metagenomic DNA of the sponge microbial community was extracted to explore community KS genes by two approaches: direct amplification of KS domains and construction of fosmid libraries for KS domain screening. Five KS domains were retrieved from polymerase chain reaction (PCR) amplification using sponge metagenome DNA as template and five fosmid clones containing KS domains found using multiplex PCR screening. Analysis of selected polyketide synthase (PKS) from one fosmid showed that the PKS consists of two modules. Open reading frames located up‐ and downstream of the PKS displayed similarity with membrane synthesis‐related proteins such as cardiolipin synthase. Metagenome approaches did not detect KS domains found in sponge isolates. All KS domains from both metagenome approaches formed a single cluster with KS domains originating from metagenomes derived from other sponge species from other geographical regions.