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Applied and Environmental Microbiology, March 2006, p. 2118-2125, Vol. 72, No. 3
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.3.2118-2125.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Discovery of a New Source of Rifamycin Antibiotics in Marine Sponge Actinobacteria by Phylogenetic Prediction

Tae Kyung Kim,1 Amitha K. Hewavitharana,2 P. Nicholas Shaw,2 and John A. Fuerst1*

School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia,1 School of Pharmacy, University of Queensland, Brisbane, Queensland 4072, Australia2

Received 7 October 2005/ Accepted 31 December 2005

Phylogenetic analysis of the ketosynthase (KS) gene sequences of marine sponge-derived Salinispora strains of actinobacteria indicated that the polyketide synthase (PKS) gene sequence most closely related to that of Salinispora was the rifamycin B synthase of Amycolatopsis mediterranei. This result was not expected from taxonomic species tree phylogenetics using 16S rRNA sequences. From the PKS sequence data generated from our sponge-derived Salinispora strains, we predicted that such strains might synthesize rifamycin-like compounds. Liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis was applied to one sponge-derived Salinispora strain to test the hypothesis of rifamycin synthesis. The analysis reported here demonstrates that this Salinispora isolate does produce compounds of the rifamycin class, including rifamycin B and rifamycin SV. A rifamycin-specific KS primer set was designed, and that primer set increased the number of rifamycin-positive strains detected by PCR screening relative to the number detectable using a conserved KS-specific set. Thus, the Salinispora group of actinobacteria represents a potential new source of rifamycins outside the genus Amycolatopsis and the first recorded source of rifamycins from marine bacteria.

* Corresponding author. Mailing address: School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia. Phone: 617 3365-4643. Fax: 617 3365-4699. E-mail: j.fuerst{at}mailbox.uq.edu.au.

Applied and Environmental Microbiology, March 2006, p. 2118-2125, Vol. 72, No. 3
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.3.2118-2125.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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