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Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F420 biosynthesis

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Abstract

The hydride carrier coenzyme F420 contains the unusual chromophore 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO). Microbes that generate F420 produce this FO moiety using a pyrimidine intermediate from riboflavin biosynthesis and the 4-hydroxyphenylpyruvate precursor of tyrosine. The fbiC gene, cloned from Mycobacterium smegmatis, encodes the bifunctional FO synthase. Expression of this protein in Escherichia coli caused the host cells to produce FO during growth, and activated cell-free extracts catalyze FO biosynthesis in vitro. FO synthase in the methanogenic euryarchaeon Methanocaldococcus jannaschii comprises two proteins encoded by cofG (MJ0446) and cofH (MJ1431). Both subunits were required for FO biosynthesis in vivo and in vitro. Cyanobacterial genomes encode homologs of both genes, which are used to produce the coenzyme for FO-dependent DNA photolyases. A molecular phylogeny of the paralogous cofG and cofH genes is consistent with the genes being vertically inherited within the euryarchaeal, cyanobacterial, and actinomycetal lineages. Ancestors of the cyanobacteria and actinomycetes must have acquired the two genes, which subsequently fused in actinomycetes. Both CofG and CofH have putative radical S-adenosylmethionine binding motifs, and pre-incubation with S-adenosylmethionine, Fe2+, sulfide, and dithionite stimulates FO production. Therefore a radical reaction mechanism is proposed for the biosynthesis of FO.

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Abbreviations

AdoMet (SAM) :

S-adenosyl-l-methionine

Compound 6 :

5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione

FO :

7,8-Didemethyl-8-hydroxy-5-deazariboflavin

HPP :

4-Hydroxyphenylpyruvate

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    PubMed  Google Scholar 

  • Ashton WT, Brown RD (1980) Synthesis of 8-demethyl-8-hydroxy-5-deazariboflavins. J Heterocyclic Chem 17:1709–1712

    CAS  Google Scholar 

  • Bacher A (1986) Heavy riboflavin synthase from Bacillus subtilis. Methods Enzymol 122:192–199

    CAS  PubMed  Google Scholar 

  • Bacher A, Eberhardt S, Fischer M, Kis K, Richter G (2000) Biosynthesis of vitamin B2 (riboflavin). Annu Rev Nutr 20:153–167

    Article  CAS  PubMed  Google Scholar 

  • Blasi F, Fragomele F, Covelli I (1969) Thyroidal phenylpyruvate tautomerase. Isolation and characterization. J Biol Chem 244:4864–4870

    CAS  PubMed  Google Scholar 

  • Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1017–1140

    Google Scholar 

  • Cahnmann HJ, Funakoshi K (1970) Model reactions for the biosynthesis of thyroxine. Nonenzymic formation of 3,5,3’-triiodothyronine from 4-hydroxy-3-iodophenylpyruvic acid, 3,5-diiodotyrosine, and oxygen. Biochemistry 9:90–98

    CAS  PubMed  Google Scholar 

  • Cheek J, Broderick JB (2001) Adenosylmethionine-dependent iron-sulfur enzymes: versatile clusters in a radical new role. J Biol Inorg Chem 6:209–226

    Article  CAS  PubMed  Google Scholar 

  • Cheeseman P, Toms-Wood A, Wolfe RS (1972) Isolation and properties of a fluorescent compound, factor 420, from Methanobacterium strain M.o.H. J Bacteriol 112:527–531

    CAS  PubMed  Google Scholar 

  • Choi K-P, Bair TB, Bae Y-M, Daniels L (2001) Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F420 biosynthesis by Mycobacterium bovis BCG. J Bacteriol 183:7058–7066

    Article  CAS  PubMed  Google Scholar 

  • Choi KP, Kendrick N, Daniels L (2002) Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F420 and FO biosynthesis. J Bacteriol 184:2420–2428

    Article  CAS  PubMed  Google Scholar 

  • Cousins FB (1960) The prosthetic group of a chromoprotein from Mycobacteria. Biochim Biophys Acta 40:532–534

    Article  CAS  PubMed  Google Scholar 

  • De Wit LEA, Eker APM (1987) 8-Hydroxy-5-deazaflavin-dependent electron transfer in the extreme halophile Halobacterium cutirubrum. FEMS Microbiol Lett 48:121–125

    Article  Google Scholar 

  • Duin EC, Lafferty ME, Crouse BR, Allen RM, Sanyal I, Flint DH, Johnson MK (1997) [2Fe-2S] to [4Fe-4S] cluster conversion in Escherichia coli biotin synthase. Biochemistry 36:11811–11820

    Article  CAS  PubMed  Google Scholar 

  • Eberhardt S, Korn S, Lottspeich F, Bacher A (1997) Biosynthesis of riboflavin: an unusual riboflavin synthase of Methanobacterium thermoautotrophicum. J Bacteriol 179:2938–2943

    CAS  PubMed  Google Scholar 

  • Eirich LD, Vogels GD, Wolfe RS (1978) Proposed structure for coenzyme F420 from Methanobacterium. Biochemistry 17:4583–4593

    CAS  PubMed  Google Scholar 

  • Eisenreich W, Schwarzkopf B, Bacher A (1991) Biosynthesis of nucleotides, flavins, and deazaflavins in Methanobacterium thermoautotrophicum. J Biol Chem 266:9622–9631

    CAS  PubMed  Google Scholar 

  • Eker AP, Kooiman P, Hessels JK, Yasui A (1990) DNA photoreactivating enzyme from the cyanobacterium Anacystis nidulans. J Biol Chem 265:8009–8015

    PubMed  Google Scholar 

  • Felsenstein J (2001) PHYLIP (phylogeny inference package). In, 3.6a2.1 edn. Department of Genetics, University of Washington, Seattle

  • Finley KT (1974) The addition and substitution chemistry of quionines. In: Patai S (ed) The chemistry of the quinonoid compounds. Wiley, London, pp 877–1144

  • Frey PA (2001) Radical mechanisms of enzymatic catalysis. Annu Rev Biochem 70:121–148

    Article  CAS  PubMed  Google Scholar 

  • Goyal RN, Kumar A, Jain N, Gupta P (1999) Electrochemical oxidation of 6-hydroxy-2,4,5-triaminopyrimidine at pyrolytic graphite electrode. Indian J Chem 38A:1015–1023

    CAS  Google Scholar 

  • Graham DE, White RH (2002) Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat Prod Rep 19:133–147

    Article  CAS  PubMed  Google Scholar 

  • Graham DE, Xu H, White RH (2002) Identification of coenzyme M biosynthetic phosphosulfolactate synthase. A new family of sulfonate-biosynthesizing enzymes. J Biol Chem 277:13421–13429

    CAS  PubMed  Google Scholar 

  • Graupner M, White RH (2003) Methanococcus jannaschii coenzyme F420 analogs contain a terminal a-linked glutamate. J Bacteriol 185:4662–4665

    Article  CAS  PubMed  Google Scholar 

  • Graupner M, Xu H, White RH (2002) The pyrimidine nucleotide reductase step in riboflavin and F420 biosynthesis in archaea proceeds by the eukaryotic route to riboflavin. J Bacteriol 184:1952–1957

    Article  CAS  PubMed  Google Scholar 

  • Haase I, Mörtl S, Köhler P, Bacher A, Fischer M (2003) Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii. Eur J Biochem 270:1025–1032

    Article  PubMed  Google Scholar 

  • Hemmerich P, Massey V, Fenner H (1977) Flavin and 5-deazaflavin: a chemical evaluation of ‘modified’ flavoproteins with respect to the mechanisms of redox biocatalysis. FEBS Lett 84:5–21

    Article  CAS  PubMed  Google Scholar 

  • Hu XE, Yang HW, Wang XJ, Bai RS (2002) Electrohydrogenation of 4-amino-5-nitrosodimethyluracil with a foamed nickel cathode. J Appl Electrochem 32:321–328

    Article  CAS  Google Scholar 

  • Huang X, Holden HM, Raushel FM (2001) Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu Rev Biochem 70:149–180

    Article  CAS  PubMed  Google Scholar 

  • Isabelle D, Simpson DR, Daniels L (2002) Large-scale production of coenzyme F420-5,6 by using Mycobacterium smegmatis. Appl Environ Microbiol 68:5750–5755

    CAS  PubMed  Google Scholar 

  • Kaneko T, Nakamura Y, Wolk CP, Kuritz T, Sasamoto S, Watanabe A et al. (2001) Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res 8:205–213; 227–253

    CAS  PubMed  Google Scholar 

  • Kern R, Keller PJ, Schmidt G, Bacher A (1983) Isolation and structural identification of a chromophoric coenzyme F420 fragment from culture fluid of Methanobacterium thermoautotrophicum. Arch Microbiol 136:191–193

    CAS  Google Scholar 

  • Kulzer R, Pils T, Kappl R, H¸ttermann J, Knappe J (1998) Reconstitution and characterization of the polynuclear iron-sulfur cluster in pyruvate formate-lyase-activating enzyme. Molecular properties of the holoenzyme form. J Biol Chem 273:4897–4903

    Article  CAS  PubMed  Google Scholar 

  • Larsen MH (2000) Some common methods in mycobacterial genetics. In: Hatfull GF, Jacobs WRJ (eds) Molecular genetics of mycobacteria. ASM Press, Washington, DC, p 316

  • Li H, Graupner M, Xu H, White RH (2003) CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42:9771–9778

    Article  CAS  PubMed  Google Scholar 

  • Lin X-L, White RH (1986) Occurrence of coenzyme F420 and its γ-monoglutamyl derivative in nonmethanogenic archaebacteria. J Bacteriol 168:444–448

    CAS  PubMed  Google Scholar 

  • McCready S, Marcello L (2003) Repair of UV damage in Halobacterium salinarum. Biochem Soc Trans 31:694–698

    CAS  PubMed  Google Scholar 

  • Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory, Plainview, New York

  • Plaut GWE, Harvey RA (1971) The enzymatic synthesis of riboflavin. Methods Enzymol 18B:515–538

    Google Scholar 

  • Reuke B, Korn S, Eisenreich W, Bacher A (1992) Biosynthetic precursors of deazaflavins. J Bacteriol 174:4042–4049

    CAS  PubMed  Google Scholar 

  • Seo HS, Koo YJ, Lim JY, Song JT, Kim CH, Kim JK, Lee JS, Choi YD (2000) Characterization of a bifunctional enzyme fusion of trehalose-6-phosphate synthetase and trehalose-6-phosphate phosphatase of Escherichia coli. Appl Environ Microbiol 66:2484–2490

    Article  CAS  PubMed  Google Scholar 

  • Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV et al. (2002) The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci USA 99:4644–4649

    Article  CAS  PubMed  Google Scholar 

  • Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE (2001) Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res 29:1097–1106

    CAS  PubMed  Google Scholar 

  • Tabor S, Richardson CC (1985) A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci USA 82:1074–1078

    CAS  PubMed  Google Scholar 

  • Taylor EC, Jr., Loux HM, Falco E, Hitchings GH (1955) Pyrimidopteridines by oxidative self-condensation of aminopyrimidines. J Am Chem Soc 77:2243–2248

    CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    PubMed  Google Scholar 

  • Van QL, Schwarzkopf B, Bacher A, Keller PJ, Lee S, Floss HG (1985) Biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, the chromophoric moiety of coenzyme F420. J Am Chem Soc 107:8300–8301

    Google Scholar 

  • Walsh C (1986) Naturally occurring 5-deazaflavin coenzymes: biological redox roles. Acc Chem Res 19:216–221

    CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by a U.S. National Science Foundation grant awarded to D.E.G. in 2002 and NSF Grant MCB 0231319 to R.H.W.

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  1. David E. Graham

    Present address: Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712–0165, USA

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  1. Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia , 24061–0308, USA

    David E. Graham, Huimin Xu & Robert H. White

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Correspondence to Robert H. White.

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Graham, D.E., Xu, H. & White, R.H. Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F420 biosynthesis. Arch Microbiol 180, 455–464 (2003). https://doi.org/10.1007/s00203-003-0614-8

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