Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogenetic prediction.
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.
Kim
Tae Kyung
TK
School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
Hewavitharana
Amitha K
AK
Shaw
P Nicholas
PN
Fuerst
John A
JA
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
D000900:Anti-Bacterial Agents; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012294:Rifamycins; D048630:Polyketide Synthases