title: Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogenetic prediction.
abstract: 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.
authors.affiliation: School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Tae Kyung
authors.initials: TK
authors.lastname: Kim
authors.forename: Amitha K
authors.initials: AK
authors.lastname: Hewavitharana
authors.forename: P Nicholas
authors.initials: PN
authors.lastname: Shaw
authors.forename: John A
authors.initials: JA
authors.lastname: Fuerst
mesh_terms: D000192:Actinomycetales / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D000818:Animals; D000900:Anti-Bacterial Agents / Q000378:metabolism*; D004275:DNA, Ribosomal / Q000032:analysis; D008969:Molecular Sequence Data; D010802:Phylogeny; D048630:Polyketide Synthases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D011161:Porifera / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012294:Rifamycins / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D000900:Anti-Bacterial Agents; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012294:Rifamycins; D048630:Polyketide Synthases