Skip to main content
SpringerLink
Log in

Cloning and characterization of decaprenyl diphosphate synthase from three different fungi

  • Applied genetics and molecular biotechnology
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Coenzyme Q (CoQ) is composed of a benzoquinone moiety and an isoprenoid side chain of varying lengths. The length of the side chain is controlled by polyprenyl diphosphate synthase. In this study, dps1 genes encoding decaprenyl diphosphate synthase were cloned from three fungi: Bulleromyces albus, Saitoella complicata, and Rhodotorula minuta. The predicted Dps1 proteins contained seven conserved domains found in typical polyprenyl diphosphate synthases and were 528, 440, and 537 amino acids in length in B. albus, S. complicata, and R. minuta, respectively. Escherichia coli expressing the fungal dps1 genes produced CoQ10 in addition to endogenous CoQ8. Two of the three fungal dps1 genes (from S. complicata and R. minuta) were able to replace the function of ispB in an E. coli mutant strain. In vitro enzymatic activities were also detected in recombinant strains. The three dps1 genes were able to complement a Schizosaccharomyces pombe dps1, dlp1 double mutant. Recombinant S. pombe produced mainly CoQ10, indicating that the introduced genes were independently functional and did not require dlp1. The cloning of dps1 genes from various fungi has the potential to enhance production of CoQ10 in other organisms.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  • Allan CM, Awad AM, Johnson JS, Shirasaki DI, Wang C, Blaby-Haas CE, Merchant SS, Loo JA, Clarke CF (2015) Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae. J Biol Chem 290:7517–7534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Asai KI, Fujisaki S, Nishimura Y, Nishino T, Okada K, Nakagawa T, Kawamukai M, Matsuda H (1994) The identification of Escherichia coli ispB (cel) gene encoding the octaprenyl diphosphate synthase. Biochem Biophys Res Commun 202:340–345

    Article  CAS  PubMed  Google Scholar 

  • Ashby MN, Edwards PA (1990) Elucidation of the deficiency in two yeast coenzyme Q mutants. Characterization of the structural gene encoding hexaprenyl pyrophosphate synthetase. J Biol Chem 265:13157–13164

    CAS  PubMed  Google Scholar 

  • Aussel L, Pierrel F, Loiseau L, Lombard M, Fontecave M, Barras F (2014) Biosynthesis and physiology of coenzyme Q in bacteria. Biochim Biophys Acta 1837:1004–1011

    Article  CAS  PubMed  Google Scholar 

  • Ayer A, Macdonald P, Stocker R (2015) CoQ(10) function and role in heart failure and ischemic heart disease. Annu Rev Nutr 35:175–213

    Article  CAS  PubMed  Google Scholar 

  • Bader M, Muse W, Ballou DP, Gassner C, Bardwell JCA (1999) Oxidative protein folding is driven by the electron transport system. Cell 98:217–227

    Article  CAS  PubMed  Google Scholar 

  • Chan HC, Feng X, Ko TP, Huang CH, Hu Y, Zheng Y, Bogue S, Nakano C, Hoshino T, Zhang L, Lv P, Liu W, Crick DC, Liang PH, Wang AH, Oldfield E, Guo RT (2014) Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis. J Am Chem Soc 136:2892–2896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cluis CP, Burja AM, Martin VJ (2007) Current prospects for the production of coenzyme Q10 in microbes. Trends Biotechnol 25:514–521

    Article  CAS  PubMed  Google Scholar 

  • Cui TZ, Kaino T, Kawamukai M (2010) A subunit of decaprenyl diphosphate synthase stabilizes octaprenyl diphosphate synthase in Escherichia coli by forming a high-molecular weight complex. FEBS Lett 584:652–656

    Article  CAS  PubMed  Google Scholar 

  • Ferella M, Montalvetti A, Rohloff P, Miranda K, Fang J, Reina S, Kawamukai M, Bua J, Nilsson D, Pravia C, Katzin A, Cassera MB, Aslund L, Andersson B, Docampo R, Bontempi EJ (2006) A solanesyl-diphosphate synthase localizes in glycosomes of Trypanosoma cruzi. J Biol Chem 281:39339–39348

    Article  CAS  PubMed  Google Scholar 

  • Hayashi K, Ogiyama Y, Yokomi K, Nakagawa T, Kaino T, Kawamukai M (2014) Functional conservation of coenzyme Q biosynthetic genes among yeasts, plants, and humans. PLoS One 9:e99038

    Article  PubMed  PubMed Central  Google Scholar 

  • Hirooka K, Bamba T, E-i F, Kobayashi A (2003) Cloning and kinetic characterization of Arabidopsis thaliana solanesyl diphosphate syntahse. Biochem J 370:679–686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267–272

    Article  CAS  PubMed  Google Scholar 

  • Ikenaka Y, Nanba, H, Takano, M, Yajima, K, Yamada, Y, Takahashi, S (2003) DNA coding for decarbamylase improved in thermostability and use thereof. Japan Patent 3438890

  • Jun L, Saiki R, Tatsumi K, Nakagawa T, Kawamukai M (2004) Identification and subcellular localization of two solanesyl diphosphate synthases from Arabidopsis thaliana. Plant Cell Physiol 45:1882–1888

    Article  CAS  PubMed  Google Scholar 

  • Kainou T, Okada K, Suzuki K, Nakagawa T, Matsuda H, Kawamukai M (2001) Dimer formation of octaprenyl diphosphate synthase (IspB) is essential for chain length determination of ubiquinone. J Biol Chem 276:7876–7883

    Article  CAS  PubMed  Google Scholar 

  • Kawamukai M (2002) Biosynthesis, bioproduction and novel roles of ubiquinone. J Biosci Bioeng 94:511–517

    Article  CAS  PubMed  Google Scholar 

  • Kawamukai M (2009) Biosynthesis and bioproduction of coenzyme Q10 by yeasts and other organisms. Biotechnol Appl Biochem 53:217–226

    Article  CAS  PubMed  Google Scholar 

  • Kawamukai M (2016) Biosynthesis of coenzyme Q in eukaryotes. Biosci Biotechnol Biochem 80:23–33

    CAS  Google Scholar 

  • Lee JK, Her G, Kim SY, Seo JH (2004) Cloning and functional expression of the dps gene encoding decaprenyl diphosphate synthase from Agrobacterium tumefaciens. Biotechnol Prog 20:51–56

    Article  CAS  PubMed  Google Scholar 

  • López-Martín JM, Salviati L, Trevisson E, Montini G, Dimauro S, Quinzii C, Hirano M, Rodriguez-Hernandez A, Cordero MD, Sanchez-Alcazar JA, Santos-Ocana C, Navas P (2007) Missense mutation of the COQ2 gene causes defects of bioenergetics and de novo pyrimidine synthesis. Hum Mol Genet 16:1091–1097

    Article  PubMed  PubMed Central  Google Scholar 

  • Matsuo Y, Kishimoto H, Horiuchi T, Tanae K, Kawamukai M (2010) Simple and effective gap-repair cloning using short tracts of flanking homology in fission yeast. Biosci Biotechnol Biochem 74:685–689

    Article  CAS  PubMed  Google Scholar 

  • Matsuo Y, Nishino K, Mizuno K, Akihiro T, Toda T, Matsuo Y, Kaino T, Kawamukai M (2013) Polypeptone induces dramatic cell lysis in ura4 deletion mutants of fission yeast. PLoS One 8:e59887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moriyama D, Hosono K, Fujii M, Washida M, Nanba H, Kaino T, Kawamukai M (2015) Production of CoQ10 in fission yeast by expression of genes responsible for CoQ10 biosynthesis. Biosci Biotechnol Biochem 79:1026–1033

    Article  CAS  PubMed  Google Scholar 

  • Nishida H, Hamamoto M, Sugiyama J (2011) Draft genome sequencing of the enigmatic yeast Saitoella complicata. J Gen Appl Microbiol 57:243–246

    Article  CAS  PubMed  Google Scholar 

  • Okada K, Kainou T, Matsuda H, Kawamukai M (1998a) Biological significance of the side chain length of ubiquinone in Saccharomyces cerevisiae. FEBS Lett 431:241–244

    Article  CAS  PubMed  Google Scholar 

  • Okada K, Kainou T, Tanaka K, Nakagawa T, Matsuda H, Kawamukai M (1998b) Molecular cloning and mutational analysis of the ddsA gene encoding decaprenyl diphosphate synthase from Gluconobacter suboxydans. Eur J Biochem 255:52–59

    Article  CAS  PubMed  Google Scholar 

  • Okada K, Kamiya Y, Zhu X, Suzuki K, Tanaka K, Nakagawa T, Matsuda H, Kawamukai M (1997a) Cloning of the sdsA gene encoding solanesyl diphosphate synthase from Rhodobacter capsulatus and its functional expression in Escherichia coli and Saccharomyces cerevisiae. J Bacteriol 179:5992–5998

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Okada K, Minehira M, Zhu X, Suzuki K, Nakagawa T, Matsuda H, Kawamukai M (1997b) The ispB gene encoding octaprenyl diphosphate synthase is essential for growth of Escherichia coli. J Bacteriol 179:3058–3060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Okada K, Ohara K, Yazaki K, Nozaki K, Uchida N, Kawamukai M, Nojiri H, Yamane H (2004) The AtPPT1 gene encoding 4-hydroxybenzoate polyprenyl diphosphate transferase in ubiquinone biosynthesis is required for embryo development in Arabidopsis thaliana. Plant Mol Biol 55:567–577

    Article  CAS  PubMed  Google Scholar 

  • Okada K, Suzuki K, Kamiya Y, Zhu X, Fujisaki S, Nishimura Y, Nishino T, Nakagawa T, Kawamukai M, Matsuda H (1996) Polyprenyl diphosphate synthase essentially defines the length of the side chain of ubiquinone. Biochim Biophys Acta 1302:217–223

    Article  PubMed  Google Scholar 

  • Park YC, Kim SJ, Choi JH, Lee WH, Park KM, Kawamukai M, Ryu YW, Seo JH (2005) Batch and fed-batch production of coenzyme Q10 in recombinant Escherichia coli containing the decaprenyl diphosphate synthase gene from Gluconobacter suboxydans. Appl Microbiol Biotechnol 67:192–196

    Article  CAS  PubMed  Google Scholar 

  • Quinzii CM, Emmanuele V, Hirano M (2014) Clinical presentations of coenzyme q10 deficiency syndrome. Mol Syndromol 5:141–146

    CAS  PubMed  PubMed Central  Google Scholar 

  • Saiki R, Nagata A, Kainou T, Matsuda H, Kawamukai M (2005) Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans. FEBS J 272:5606–5622

    Article  CAS  PubMed  Google Scholar 

  • Saiki R, Nagata A, Uchida N, Kainou T, Matsuda H, Kawamukai M (2003a) Fission yeast decaprenyl diphosphate synthase consists of Dps1 and the newly characterized Dlp1 protein in a novel heterotetrameric structure. Eur J Biochem 270:4113–4121

    Article  CAS  PubMed  Google Scholar 

  • Saiki R, Ogiyama Y, Kainou T, Nishi T, Matsuda H, Kawamukai M (2003b) Pleiotropic phenotypes of fission yeast defective in ubiquinone-10 production. A study from the abc1Sp (coq8Sp) mutant. Biofactors 18:229–235

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a lablatory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Seo MJ, Im EM, Hur JH, Nam JY, Hyun CG, Pyun YR, Kim SO (2006) Production of coenzyme Q10 by recombinant E. coli harboring the decaprenyl diphosphate synthase gene from Sinorhizobium meliloti. J Microbiol Biotechnol 16:933–938

    CAS  Google Scholar 

  • Shimizu N, Koyama T, Ogura K (1998) Molecular cloning, expression, and characterization of the genes encoding the two essential protein components of Micrococcus luteus B-P 26 hexaprenyl diphosphate synthase. J Bacteriol 180:1578–1581

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sun HY, Ko TP, Kuo CJ, Guo RT, Chou CC, Liang PH, Wang AH (2005) Homodimeric hexaprenyl pyrophosphate synthase from the thermoacidophilic crenarchaeon Sulfolobus solfataricus displays asymmetric subunit structures. J Bacteriol 187:8137–8148

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suzuki K, Okada K, Kamiya Y, Zhu X, Tanaka K, Nakagawa T, Kawamukai M, Matsuda H (1997) Analysis of the decaprenyl diphosphate synthase (dps) gene in fission yeast suggests a role of ubiquinone as an antioxidant. J Biochem (Tokyo) 121:496–505

    Article  CAS  Google Scholar 

  • Suzuki K, Ueda M, Yuasa M, Nakagawa T, Kawamukai M, Matsuda H (1994) Evidence that Escherichia coli ubiA product is a functional homolog of yeast COQ2, and the regulation of ubiA gene expression. Biosci Biotech Biochem 58:1814–1819

    Article  CAS  Google Scholar 

  • Takahashi S, Ogiyama Y, Kusano H, Shimada H, Kawamukai M, Kadowaki K (2006) Metabolic engineering of coenzyme Q by modification of isoprenoid side chain in plant. FEBS Lett 580:955–959

    Article  CAS  PubMed  Google Scholar 

  • Tonhosolo R, D’Alexandri FL, Genta FA, Wunderlich G, Gozzo FC, Eberlin MN, Peres VJ, Kimura EA, Katzin AM (2005) Identification, molecular cloning and functional characterization of an octaprenyl pyrophosphate synthase in intra-erythrocytic stages of Plasmodium falciparum. Biochem J 392:117–126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tran UC, Clarke CF (2007) Endogenous synthesis of coenzyme Q in eukaryotes. Mitochondrion 7(Suppl 1):S62–S71

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vinothkumar KR, Zhu J, Hirst J (2014) Architecture of mammalian respiratory complex I. Nature 515:80–84

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zahiri HS, Noghabi KA, Shin YC (2006) Biochemical characterization of the decaprenyl diphosphate synthase of Rhodobacter sphaeroides for coenzyme Q10 production. Appl Microbiol Biotechnol 73:796–806

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Li ZX (2013) In vitro and in vivo characterization of a novel insect decaprenyl diphosphate synthase: a two-major step catalytic mechanism is proposed. Biochem Biophys Res Commun 442:105–111

    Article  CAS  PubMed  Google Scholar 

  • Zhang M, Luo J, Ogiyama Y, Saiki R, Kawamukai M (2008) Heteromer formation of a long-chain prenyl diphosphate synthase from fission yeast Dps1 and budding yeast Coq1. FEBS J 275:3653–3668

    Article  CAS  PubMed  Google Scholar 

  • Zhu X, Yuasa M, Okada K, Suzuki K, Nakagawa T, Kawamukai M, Matsuda H (1995) Production of ubiquinone in Escherichia coli by expression of various genes responsible for ubiquinone biosynthesis. J Ferment Bioeng 79:493–495

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Kaneka Corporation, 1-8, Miyamae-cho, Takasago-cho, Takasago, Hyogo, 676-8688, Japan

    Daisuke Moriyama, Kazuyoshi Yajima, Yasuhiro Ikenaka, Junzo Hasegawa, Motohisa Washida & Hirokazu Nanba

  2. Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, 690-8504, Japan

    Daisuke Moriyama, Tomohiro Kaino, Ryota Yanai & Makoto Kawamukai

Authors
  1. Daisuke Moriyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tomohiro Kaino
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kazuyoshi Yajima
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ryota Yanai
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yasuhiro Ikenaka
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Junzo Hasegawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Motohisa Washida
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hirokazu Nanba
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Makoto Kawamukai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Makoto Kawamukai.

Ethics declarations

Funding

This study was partly supported by a Grant-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (no. 24380056, 15K07360).

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Daisuke Moriyama and Tomohiro Kaino contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Moriyama, D., Kaino, T., Yajima, K. et al. Cloning and characterization of decaprenyl diphosphate synthase from three different fungi. Appl Microbiol Biotechnol 101, 1559–1571 (2017). https://doi.org/10.1007/s00253-016-7963-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-016-7963-0

Keywords

Search

Navigation