Daptomycin biosynthesis in Streptomyces roseosporus: cloning and analysis of the gene cluster and revision of peptide stereochemistry

Microbiology (Reading). 2005 May;151(Pt 5):1507-1523. doi: 10.1099/mic.0.27757-0.

Abstract

Daptomycin is a 13 amino acid, cyclic lipopeptide produced by a non-ribosomal peptide synthetase (NRPS) mechanism in Streptomyces roseosporus. A 128 kb region of S. roseosporus DNA was cloned and verified by heterologous expression in Streptomyces lividans to contain the daptomycin biosynthetic gene cluster (dpt). The cloned region was completely sequenced and three genes (dptA, dptBC, dptD) encoding the three subunits of an NRPS were identified. The catalytic domains in the subunits, predicted to couple five, six or two amino acids, respectively, included a novel activation domain and amino-acid-binding pocket for incorporating the unusual amino acid l-kynurenine (Kyn), three types of condensation domains and an extra epimerase domain (E-domain) in the second module. Novel genes (dptE, dptF) whose products likely work in conjunction with a unique condensation domain to acylate the first amino acid, as well as other genes (dptI, dptJ) probably involved in supply of the non-proteinogenic amino acids l-3-methylglutamic acid and Kyn, were located next to the NRPS genes. The unexpected E-domain suggested that daptomycin would have d-Asn, rather than l-Asn, as originally assigned, and this was confirmed by comparing stereospecific synthetic peptides and the natural product both chemically and microbiologically.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Anti-Bacterial Agents / biosynthesis*
  • Anti-Bacterial Agents / chemistry
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Cloning, Molecular*
  • Conserved Sequence
  • Daptomycin / biosynthesis*
  • Molecular Sequence Data
  • Multigene Family*
  • Open Reading Frames
  • Peptide Synthases* / chemistry
  • Peptide Synthases* / genetics
  • Peptide Synthases* / metabolism
  • Peptides, Cyclic / biosynthesis
  • Peptides, Cyclic / chemistry
  • Protein Subunits / chemistry
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • Sequence Analysis, DNA
  • Stereoisomerism
  • Streptomyces / enzymology*
  • Streptomyces / genetics
  • Streptomyces / metabolism
  • Streptomyces lividans / enzymology
  • Streptomyces lividans / genetics
  • Streptomyces lividans / metabolism

Substances

  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Peptides, Cyclic
  • Protein Subunits
  • Peptide Synthases
  • non-ribosomal peptide synthase
  • Daptomycin

Associated data

  • GENBANK/AY787762