Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699

Chem Biol. 1998 Feb;5(2):69-79. doi: 10.1016/s1074-5521(98)90141-7.


Background: The ansamycin class of antibiotics are produced by various Actinomycetes. Their carbon framework arises from the polyketide pathway via a polyketide synthase (PKS) that uses an unusual starter unit. Rifamycin (rif), produced by Amycolatopsis mediterranei, is the archetype ansamycin and it is medically important. Although its basic precursors (3-amino-5-hydroxy benzoic acid AHBA, and acetic and propionic acids) had been established, and several biosynthetic intermediates had been identified, very little was known about the origin of AHBA nor had the PKS and the various genes and enzymes that modify the initial intermediate been characterized.

Results: A set of 34 genes clustered around the rifK gene encoding AHBA synthase were defined by sequencing all but 5 kilobases (kb) of a 95 kb contiguous region of DNA from A. mediterranei. The involvement of some of the genes in the biosynthesis of rifamycin B was examined. At least five genes were shown to be essential for the synthesis of AHBA, five genes were determined to encode the modular type I PKS that uses AHBA as the starter unit, and 20 or more genes appear to govern modification of the polyketide-derived framework, and rifamycin resistance and export. Putative regulatory genes were also identified. Disruption of the PKS genes at the end of rifA abolished rifamycin B production and resulted in the formation of P8/1-OG, a known shunt product of rifamycin biosynthesis, whereas disruption of the orf6 and orf9 genes, which may encode deoxysugar biosynthesis enzymes, had no apparent effect.

Conclusions: Rifamycin production in A. mediterranei is governed by a single gene cluster consisting of structural, resistance and export, and regulatory genes. The genes characterized here could be modified to produce novel forms of the rifamycins that may be effective against rifamycin-resistant microorganisms.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Actinobacteria / chemistry*
  • Amino Acid Sequence
  • Aminobenzoates / metabolism
  • Anti-Bacterial Agents / biosynthesis
  • Gene Expression Regulation, Bacterial / genetics
  • Genes, Bacterial / genetics
  • Hydro-Lyases / genetics
  • Hydroxybenzoates
  • Lactams, Macrocyclic
  • Molecular Sequence Data
  • Molecular Structure
  • Multienzyme Complexes / chemistry*
  • Multienzyme Complexes / genetics
  • Open Reading Frames / genetics
  • Rifamycins / biosynthesis*
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid


  • Aminobenzoates
  • Anti-Bacterial Agents
  • Hydroxybenzoates
  • Lactams, Macrocyclic
  • Multienzyme Complexes
  • Rifamycins
  • 3-amino-5-hydroxybenzoic acid
  • 3-amino-5-hydroxybenzoic acid synthase
  • Hydro-Lyases

Associated data

  • GENBANK/U33059