The complete genomic sequence of Streptomyces spectabilis NRRL-2792 and identification of secondary metabolite biosynthetic gene clusters

  • Arkadeep Sinha
  • Silvia Phillips-Salemka
  • Tanu-Adhikari Niraula
  • Kevin A. Short
  • Narayan P. NiraulaEmail author
Natural Products - Original Paper


This is the first report of a fully annotated genomic sequence of Streptomyces spectabilis NRRL-2792, isolated and identified by The Upjohn Company in 1961. The genome was assembled into a single scaffold for annotation and analysis. The chromosome is linear, 9.5 Mb in size which is one of the largest Streptomyces genomes yet described, has a G+C content of 72%, and encodes for approximately 7943 genes. Antibiotic Secondary Metabolite Analysis Shell (antiSMASH) and Basic Local Alignment Search Tool (BLAST) bioinformatics analyses identified six complete secondary metabolite biosynthetic gene clusters for ectoine, melanin, albaflavenone, spectinomycin, 2-methylisoborneol and coelichelin. Additionally, biosynthetic clusters were identified that shared ≥ 90% gene content with complestatin, hopene, neoaureothin, or undecylprodigiosin. Thirty-one other likely secondary metabolite gene clusters were identified by antiSMASH. BLAST identified two subsets of undecylprodigiosin biosynthetic genes at polar opposites of the chromosome; their duplication was subsequently confirmed by primer walking.


Antibiotics DNA sequencing Secondary metabolites Streptomyces 



We appreciate the review and suggestions of Michael J. White and Richard H. Baltz.

Supplementary material

10295_2019_2172_MOESM1_ESM.docx (532 kb)
Supplementary material 1 (DOCX 531 kb)


  1. 1.
    Bachmann BO, Van Lanen SG, Baltz RH (2014) Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? J Ind Microbiol Biotechnol 41:175–184CrossRefGoogle Scholar
  2. 2.
    Baltz RH (2017) Molecular beacons to identify gifted microbes for genome mining. J Antibiot (Tokyo) 70:639–646. CrossRefGoogle Scholar
  3. 3.
    Baltz RH (2017) Gifted microbes for genome mining and natural product discovery. J Ind Microbiol Biotechnol 44:573–588CrossRefGoogle Scholar
  4. 4.
    Baltz RH (2018) Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities. J Ind Microbiol Biotechnol. Google Scholar
  5. 5.
    Blin K, Wolf T, Chevrette MG et al (2017) antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 45:W36–W41CrossRefGoogle Scholar
  6. 6.
    Cerdeno AM, Bibb MJ, Challis GL (2001) Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes. Chem Biol 8:817–829CrossRefGoogle Scholar
  7. 7.
    Chater KF (2016) Recent advances in understanding Streptomyces. F1000Research 5:2795. CrossRefGoogle Scholar
  8. 8.
    Feitelson JS, Malpartida F, Hopwood DA (1985) Genetic and biochemical characterization of the red gene cluster of Streptomyces coelicolor A3(2). J Gen Microbiol 131:2431–2441. Google Scholar
  9. 9.
    Gomez-Escribano JP, Castro JF, Razmilic V, Chandra G, Andrews B, Asenjo JA, Bibb MJ (2015) The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genom 16:485. CrossRefGoogle Scholar
  10. 10.
    Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Practical Streptomyces genetics. The John Innes Foundation, NorwichGoogle Scholar
  11. 11.
    Isaka M, Jaturapat A, Kramyu J, Tanticharoen M, Thebtaranonth Y (2002) Potent in vitro antimalarial activity of metacycloprodigiosin isolated from Streptomyces spectabilis BCC 4785. Antimicrob Agents Chemother 46:1112–1113CrossRefGoogle Scholar
  12. 12.
    Liu R, Cui CB, Duan L, Gu QQ, Zhu WM (2005) Potent in vitro anticancer activity of metacycloprodigiosin and undecylprodigiosin from a sponge-derived actinomycete Saccharopolyspora sp. nov. Arch Pharm Res 28:1341–1344CrossRefGoogle Scholar
  13. 13.
    Mason DJ, Dietz A, Smith RM (1961) Actinospectacin, a new antibiotic. I. Discovery and biological properties. Antibiot Chemother 1:118–122Google Scholar
  14. 14.
    Short KA, Hoogerheide JG, Williams RG, Grode SH, Ceglarek JA (1997) Identification and characterization of metacycloprodigiosin, a pigmented secondary metabolite of the spectinomycin producer Streptomyces spectabilis. In: American Society for Microbiology, Miami Beach, FL, 5/4/1997-5/8/1997Google Scholar
  15. 15.
    Sydor PK, Barry SM, Odulate OM, Barona-Gomez F, Haynes SW, Corre C, Song L, Challis GL (2011) Regio- and stereodivergent antibiotic oxidative carbocyclizations catalysed by Rieske oxygenase-like enzymes. Nat Chem 3:388–392. CrossRefGoogle Scholar
  16. 16.
    Williamson NR, Fineran PC, Leeper FJ, Salmond GP (2006) The biosynthesis and regulation of bacterial prodiginines. Nat Rev Microbiol 4:887–899. CrossRefGoogle Scholar
  17. 17.
    Withall DM, Haynes SW, Challis GL (2015) Stereochemistry and mechanism of undecylprodigiosin oxidative carbocyclization to streptorubin B by the rieske oxygenase RedG. J Am Chem Soc 137:7889–7897. CrossRefGoogle Scholar

Copyright information

© Society for Industrial Microbiology and Biotechnology 2019

Authors and Affiliations

  1. 1.Bioprocess Development GroupPfizerKalamazooUSA

Personalised recommendations