Bioprocess and Biosystems Engineering

, Volume 36, Issue 11, pp 1621–1630 | Cite as

Transcriptomic study for screening genes involved in the oxidative bioconversions of Streptomyces avermitilis

  • Hyo-Jeong Kim
  • Kwon-Young Choi
  • Da-Hye Jung
  • Joon-Young Jung
  • EunOk Jung
  • Yung-Hun Yang
  • Byung-Gee Kim
  • Min-Kyu Oh
Original Paper


Streptomyces avermitilis is a well known organism producing avermectin antibiotics, and has been utilized as an industrial host for oxidation bioconversion processes. Recently, gene screening strategies related to bioconversions have received much focus, as attempts are made to optimize oxidation and biodegradation pathways to maximize yield and productivity. Here, we have demonstrated the oxidative metabolisms of three molecules, daidzein, p-coumaric acid and mevastatin, where S. avermitilis converted each substrate to 3′,4′,7-trihydroxyisoflavone, caffeic acid and hydroxyl-mevastatin to yield 9.3, 32.5 and 15.0 %, respectively. Microarray technology was exploited to investigate genome-wide analysis of gene expression changes, which were induced upon the addition of each substrate. Cytochrome P450 hydroxylases (pteC, cyp28 and olmB), diooxygenases (xylE, cdo1 and putatives) and LuxAB-like oxygenase were identified. One of them, cyp28, was indeed a gene encoding P450 hydroxylase responsible for the oxidative reaction of daidzein. Furthermore, possible electron transfer chain (fdrC → pteE → pteC) supporting cytochrome P450 dependent hydroxylation of daidzein has been suggested based on the interpretation of expression profiles. The result provided a potential application of transcriptomic study on uncovering enzymes involved in oxidative bioconversions of S. avermitilis.


Streptomyces avermitilis Transcriptomics Daidzein Biotransformation 

Supplementary material

449_2013_935_MOESM1_ESM.doc (556 kb)
Supplementary material 1 (DOC 556 kb)


  1. 1.
    Paradkar A, Trefzer A, Chakraburtty R, Stassi D (2003) Streptomyces genetics: a genomic perspective. Crit Rev Biotechnol 23:1–27CrossRefGoogle Scholar
  2. 2.
    Chen M, Wang G, Dai S, Xie L, Li X (2009) Polyketide antibiotics produced by polyketide synthase in streptomyces–a review. Wei Sheng Wu Xue Bao = Acta Microbiol Sinica 49:1555–1563Google Scholar
  3. 3.
    Horvath I, Lovrekovich I, Varga JM (1964) Antibiotics produced by Streptomyces. 3. A new antibiotic K 178; biological studies. Z Allg Mikrobiol 61:236–241CrossRefGoogle Scholar
  4. 4.
    Kim YS, Kim HM, Chang C, Hwang IC, Oh H, Ahn JS, Kim KD, Hwang BK, Kim BS (2007) Biological evaluation of neopeptins isolated from a Streptomyces strain. Pest Manag Sci 63:1208–1214CrossRefGoogle Scholar
  5. 5.
    Rassi H, Ghasemi SF (2008) Production of novel chemotherapeutic drugs by Streptomycetes. Lik Sprava 7–8:40–47Google Scholar
  6. 6.
    Zhan J (2009) Biosynthesis of bacterial aromatic polyketides. Curr Top Med Chem 9:1610–1958CrossRefGoogle Scholar
  7. 7.
    Ikeda H, Kotaki H, Omura S (1987) Genetic studies of avermectin biosynthesis in Streptomyces avermitilis. J Bacteriol 169:5615–5621Google Scholar
  8. 8.
    MacNeil DJ, Gewain KM, Ruby CL, Dezeny G, Gibbons PH, MacNeil T (1992) Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector. Gene 111:61–68CrossRefGoogle Scholar
  9. 9.
    Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21:526–531CrossRefGoogle Scholar
  10. 10.
    Ikeda H, Omura S (1995) Control of avermectin biosynthesis in Streptomyces avermitilis for the selective production of a useful component. J Antibiot (Tokyo) 48:549–562CrossRefGoogle Scholar
  11. 11.
    Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, Kikuchi H, Shiba T, Sakaki Y, Hattori M (2001) Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci USA 98:12215–12220CrossRefGoogle Scholar
  12. 12.
    Quaderer R, Omura S, Ikeda H, Cane DE (2006) Pentalenolactone biosynthesis. Molecular cloning and assignment of biochemical function to PtlI, a cytochrome P450 of Streptomyces avermitilis. J Am Chem Soc 128:13036–13037CrossRefGoogle Scholar
  13. 13.
    Lamb DC, Ikeda H, Nelson DR, Ishikawa J, Skaug T, Jackson C, Omura S, Waterman MR, Kelly SL (2003) Cytochrome p450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2). Biochem Biophys Res Commun 307:610–619CrossRefGoogle Scholar
  14. 14.
    Pandey BP, Roh C, Choi KY, Lee N, Kim EJ, Ko S, Kim T, Yun H, Kim BG (2010) Regioselective hydroxylation of daidzein using P450 (CYP105D7) from Streptomyces avermitilis MA4680. Biotechnol Bioeng 105:697–704Google Scholar
  15. 15.
    Roh C, Seo SH, Choi KY, Cha M, Pandey BP, Kim JH, Park JS, Kim DH, Chang IS, Kim BG (2009) Regioselective hydroxylation of isoflavones by Streptomyces avermitilis MA-4680. J Biosci Bioeng 108:41–46CrossRefGoogle Scholar
  16. 16.
    Bugg TD, Ahmad M, Hardiman EM, Rahmanpour R (2011) Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep 28:1883–1896CrossRefGoogle Scholar
  17. 17.
    Crawford DL, Pometto AL 3rd, Crawford RL (1984) Production of useful modified lignin polymers by bioconversion of lignocellulose with Streptomyces. Biotechnol Adv 2:217–232CrossRefGoogle Scholar
  18. 18.
    Davis JR, Sello JK (2010) Regulation of genes in Streptomyces bacteria required for catabolism of lignin-derived aromatic compounds. Appl Microbiol Biotechnol 86:921–929CrossRefGoogle Scholar
  19. 19.
    Iwagami SG, Yang K, Davies J (2000) Characterization of the protocatechuic acid catabolic gene cluster from Streptomyces sp. strain 2065. Appl Environ Microbiol 66:1499–1508CrossRefGoogle Scholar
  20. 20.
    Stanier RY (1950) The bacterial oxidation of aromatic compounds. IV. Studies on the mechanism of enzymatic degradation of protocatechuic acid. J Bacteriol 59:527–532Google Scholar
  21. 21.
    Rivas FJ (2006) Polycyclic aromatic hydrocarbons sorbed on soils: a short review of chemical oxidation based treatments. J Hazard Mater 138:234–251CrossRefGoogle Scholar
  22. 22.
    Artham T, Doble M (2008) Biodegradation of aliphatic and aromatic polycarbonates. Macromol Biosci 8:14–24CrossRefGoogle Scholar
  23. 23.
    Murray M (1999) Mechanisms and significance of inhibitory drug interactions involving cytochrome P450 enzymes. Int J Mol Med 3:227–238Google Scholar
  24. 24.
    Chen W, He F, Zhang X, Chen Z, Wen Y, Li J (2010) Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome. BMC Microbiol 10:198CrossRefGoogle Scholar
  25. 25.
    Yun J, Ryu S (2005) Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb Cell Fact 4:8CrossRefGoogle Scholar
  26. 26.
    Chigu NL, Hirosue S, Nakamura C, Teramoto H, Ichinose H, Wariishi H (2010) Cytochrome P450 monooxygenases involved in anthracene metabolism by the white-rot basidiomycete Phanerochaete chrysosporium. Appl Microbiol Biotechnol 87:1907–1916CrossRefGoogle Scholar
  27. 27.
    Syed K, Doddapaneni H, Subramanian V, Lam YW, Yadav JS (2010) Genome-to-function characterization of novel fungal P450 monooxygenases oxidizing polycyclic aromatic hydrocarbons (PAHs). Biochem Biophys Res Commun 399:492–497CrossRefGoogle Scholar
  28. 28.
    Watanabe I, Nara F, Serizawa N (1995) Cloning, characterization and expression of the gene encoding cytochrome P-450sca-2 from Streptomyces carbophilus involved in production of pravastatin, a specific HMG-CoA reductase inhibitor. Gene 163:81–85CrossRefGoogle Scholar
  29. 29.
    Shepherd MD, Kharel MK, Bosserman MA, Rohr J (2010) In: Coico R, Kowalik T, Quarles J, Stevenson B, Taylor R (eds) Current protocols in microbiology. J. Wiley & Sons, NJGoogle Scholar
  30. 30.
    Kulling SE, Honig DM, Metzler M (2001) Oxidative metabolism of the soy isoflavones daidzein and genistein in humans in vitro and in vivo. J Agric Food Chem 49:3024–3033CrossRefGoogle Scholar
  31. 31.
    Choi KY, Jung E, Jung DH, An BR, Pandey BP, Yun H, Sung C, Park HY, Kim BG (2012) Engineering of daidzein 3′-hydroxylase P450 enzyme into catalytically self-sufficient cytochrome P450. Microb Cell Fact 11:81CrossRefGoogle Scholar
  32. 32.
    Kumar RP, Ravindranath SD, Vaidyanathan CS, Rao NA (1972) Mechanism of hydroxylation of aromatic compounds. II. Evidence for the involvement of superoxide anions in enzymatic hydroxylations. Biochem Biophys Res Commun 49:1422–1426CrossRefGoogle Scholar
  33. 33.
    Mitoma C, Posner HS, Reitz HC, Udenfriend S (1956) Enzymatic hydroxylation of aromatic compounds. Arch Biochem Biophys 61:431–441CrossRefGoogle Scholar
  34. 34.
    Ullrich R, Hofrichter M (2007) Enzymatic hydroxylation of aromatic compounds. Cell Mol Life Sci 64:271–293CrossRefGoogle Scholar
  35. 35.
    Choi KY, Jung E, Jung DH, Pandey BP, Yun H, Park HY, Kazlauskas RJ, Kim BG (2012) Cloning, expression and characterization of CYP102D1, a self-sufficient P450 monooxygenase from Streptomyces avermitilis. FEBS J 279:1650–1662CrossRefGoogle Scholar
  36. 36.
    Sevrioukova IF, Li H, Zhang H, Peterson JA, Poulos TL (1999) Structure of a cytochrome P450-redox partner electron-transfer complex. Proc Natl Acad Sci USA 96:1863–1868CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Hyo-Jeong Kim
    • 1
  • Kwon-Young Choi
    • 2
  • Da-Hye Jung
    • 2
  • Joon-Young Jung
    • 1
  • EunOk Jung
    • 2
  • Yung-Hun Yang
    • 3
  • Byung-Gee Kim
    • 2
  • Min-Kyu Oh
    • 1
  1. 1.Department of Chemical and Biological EngineeringKorea UniversitySeoulSouth Korea
  2. 2.School of Chemical and Biological Engineering, Institute of BioengineeringSeoul National UniversitySeoulSouth Korea
  3. 3.Department of Microbial Engineering, College of EngineeringKonkuk UniversitySeoulSouth Korea

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