Biochemistry, physiology and molecular biology of glycyl radical enzymes

FEMS Microbiology Reviews

Volumn 22, Issue 5, 1998, Pages 543-551

  Sawers, Gary ^a  

^a JOHN INNES CENTRE   (United Kingdom)

Author keywords

Anaerobic gene regulation; Enzyme interconversion; Glycyl radical; Iron sulfur protein; Redox control

Indexed keywords

ENZYME; IRON SULFUR PROTEIN; LYASE; OXIDOREDUCTASE; RADICAL; SYNTHETASE;

ANAEROBIC BACTERIUM; ARCHAEBACTERIUM; DNA SEQUENCE; GENE CONTROL; GENOME; MOLECULAR BIOLOGY; NONHUMAN; REVIEW;

EID: 0032457890     PISSN: 01686445     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6445(98)00020-5     Document Type: Review

References (49)

1. [1] Kalnitzky, G. and Werkman, C.H. (1943) The anaerobic dissimilation of pyruvate by a cell-free extract of Escherichia coli. Arch. Biochem. Biophys. 2, 113-124.
2. [2] Knappe, J., Neugebauer, F.A., Blaschkowski, H.P. and Gänzler, M. (1984) Post-translational activation introduces a free radical into pyruvate formate-lyase. Proc. Natl. Acad. Sci. USA 81, 1332-1335.
3. [3] Wagner, A.F.V., Frey, M., Neugebauer, F.A., Schäfer, W. and Knappe, J. (1992) The free radical in pyruvate formate-lyase is located on glycine-734. Proc. Natl. Acad. Sci. USA 89, 996-1000.
4. [4] Sun, X., Harder, J., Krook, M., Jörnvall, H., Sjöberg, B.-M. and Reichard, P. (1993) A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene. Proc. Natl. Acad. Sci. USA 90, 577-581.
5. [5] Heßlinger, C., Fairhurst, S.A. and Sawers, G. (1998) Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate. Mol. Microbiol. 27, 477-492.
6. [6] Leuthner, B., Leutwein, C., Schulz, H., Hörth, P., Haehnel, W., Schiltz, E., Schägger, H. and Heider, J. (1998) Biochemical and genetic characterisation of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol. Microbiol. 28, 615-628.
7. [7] Blattner, F.R., Plunkett III, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462.
8. [8] Klenk, H.P., Clayton, R.A., Tomb, J.F., White, O., Nelson, K.E., Ketchum, K.A. et al. (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370.
9. [9] Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T. et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: functional analysis and comparative genetics. J. Bacteriol. 179, 7135-7155.
10. [10] Knappe, J. and Sawers, G. (1990) A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli. FEMS Microbiol. Rev. 75, 383-398.
11. [11] Kessler, D. and Knappe, J. (1996) Anaerobic Dissimilation of Pyruvate, in Escherichia coli and Salmonella: cellular and Molecular Biology, Vol. 1 (Neidhardt, F.C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaechter, M. and Umbarger, H.E., Eds.), pp. 199-205. American Society for Microbiology, Washington, DC.
12. [12] Reichard, P. (1997) The evolution of ribonucleotide reduction. Trends. Biochem. 22, 81-85.
13. [13] Buckel, W. and Golding, B. (1998) Radicals in the catalysis of enzymes from anaerobic microorganisms. FEMS Microbiol. Rev., submitted for publication.
14. [14] Sun, X., Eliasson, R., Pontis, E., Andersson, J., Buist, G., Sjöberg, B.-M. and Reichard, P. (1995) Generation of the glycyl radical of the anaerobic Escherichia coli ribonucleotide reductase requires a specific activating enzyme. J. Biol. Chem. 270, 2443-2446.
15. [15] Ollagnier, S., Mulliez, E., Gaillard, J., Eliasson, R., Fontecave, M. and Reichard, P. (1996) The anaerobic Escherichia coli ribonucleotide reductase. J. Biol. Chem. 271, 9410-9416.
16. [16] Broderick, J.B., Duderstadt, R.E., Fernandez, D.C., Wojtuszewski, K., Henshaw, T.F. and Johnson, M.K. (1997) Pyruvate formate-lyase activating enzyme is an iron sulfur protein. J. Am. Chem. Soc. 119, 7396-7397.
17. [17] Külzer, R., Pils, T., Kappl, R., Hüttermann, J. and Knappe, J. (1998) Reconstitution and characterization of the polynuclear iron sulfur cluster in pyruvate formate-lyase-activating enzyme. J. Biol. Chem. 273, 4897-4903.
18. [18] Frey, M., Rothe, M., Wagner, A.F.V. and Knappe, J. (1994) Adenosylmethionine-dependent synthesis of the glycyl radical in pyruvate formate-lyase by abstraction of the glycine pro-S hydrogen atom. J. Biol. Chem. 269, 12432-12437.
19. [19] Ollagnier, S., Mulliez, E., Schmidt, P.P., Eliasson, R., Gaillard, J., Deronzier, C., Bergman, T., Gräslund, A., Reichard, P. and Fontecave, M. (1997) Activation of the anaerobic ribonucleotide reductase from Escherichia coli: the essential role of the iron sulfur center for S-adenosylmethionine reduction. J. Biol. Chem. 272, 24216-24223.
20. [20] Mulliez, E., Ollagnier, S., Fontecave, M., Eliasson, R. and Reichard, P. (1995) Formate is the hydrogen donor for the anaerobic ribonucleotide reductase from Escherichia coli. Proc. Natl. Acad. Sci. USA 92, 8759-8762.
21. [21] Mulliez, E., Fontecave, M., Gaillard, J. and Reichard, P. (1993) An iron sulfur center and a free radical in the active anaerobic ribonucleotide reductase of Escherichia coli. J. Biol. Chem. 268, 2296-2299.
22. [22] Unkrig, V., Neugebauer, F.A. and Knappe, J. (1989) The free radical of pyruvate formate-lyase. Characterisation by EPR spectroscopy and involvement in catalysis as studied with the substrate-analogue hypophosphite. Eur. J. Biochem. 184, 723-728.
23. [23] Parast, C., Wong. K.K., Kozarich, J.W., Peisach, J. and Magliozzo, R.S. (1995) Electron paramagnetic resonance evidence for a cysteine-based radical in pyruvate formate-lyase inactivated with mercaptopyruvate. Biochemistry 34, 5712-5717.
24. [24] Knappe, J., Elbert, S., Frey, M. and Wagner, A.F.V. (1993) Pyruvate formate-lyase mechanism involving the protein-based glycyl radical. Biochem. Soc. Trans. 21, 731-734.
25. [25] King, D.S. and Reichard, P. (1995) Mass spectroscopic determination of the radical scission site in the anaerobic ribonucleotide reductase of Escherichia coli. Biochem. Biophys. Res. Commun. 206, 731-735.
26. [26] Kessler, D., Herth, W. and Knappe, J. (1992) Ultrastructure and pyruvate formate-lyase radical quenching property of the multienzymic AdhE protein of Escherichia coli. J. Biol. Chem. 267, 18073-18079.
27. [27] Eliasson, R., Pontis, E., Fontecave, M., Gerez, C., Harder, J., Jörnvall, H., Krook, M. and Reichard, P. (1992) Characterization of components of the anaerobic ribonucleotide reductase system from Escherichia coli. J. Biol. Chem. 267, 25541-25547.
28. [28] Thauer, R.K., Kirschniawy, F.S. and Jungermann, K.A. (1972) Properties and function of the pyruvate formate-lyase reaction in clostridiae. Eur. J. Biochem. 27, 282-290.
29. [29] Weidner, G. and Sawers, G. (1996) Molecular characterization of the genes encoding pyruvate formate-lyase and its activating enzyme of Clostridium pasteurianum. J. Bacteriol. 178, 2440-2444.
30. [30] Yamamoto, Y., Sato, Y., Takahashi-Abbe, S., Abbe, K., Yamada, T. and Kizaki, H. (1996) Cloning and sequence analysis of the pfl gene encoding pyruvate formate-lyase from Streptococcus mutans. Infect. Immun. 64, 385-391.
31. [31] Sawers, G., Heßlinger, C., Muller, N. and Kaiser, M. (1998) The glycyl radical enzyme TdcE can replace pyruvate formate-lyase in glucose fermentation. J. Bacteriol., submitted for publication.
32. [32] Goss, T.J., Schweizer, H.P. and Datta, P. (1988) Molecular characterization of the tdc operon of Escherichia coli K-12. J. Bacteriol. 170, 5352-5359.
33. [33] Altenschmidt, U. and Fuchs, G. (1991) Anaerobic degradation of toluene in denitrifying Pseudomonas sp.: indication for toluene methylhydroxylation and benzoyl-CoA as central aromatic intermediate. Arch. Microbiol. 156, 152-158.
34. [34] Biegert, T., Fuchs, G. and Heider, J. (1996) Evidence that anaerobic oxidation of toluene in the denitrifying bacterium Thauera aromatica is initiated by formation of benzylsuccinate from toluene and fumarate. Eur. J. Biochem. 238, 661-668.
35. [35] Rödel, W., Plaga, W., Frank, R. and Knappe, J. (1988) Primary structures of Escherichia coli pyruvate formate-lyase and pyruvate formate-lyase-activating enzyme deduced from the DNA nucleotide sequence. Eur. J. Biochem. 177, 153-158.
36. [36] Sawers, G. and Böck, A. (1988) Anaerobic regulation of pyruvate formate-lyase from Escherichia coli K-12. J. Bacteriol. 170, 5330-5336.
37. [37] Sawers, G. and Böck, A. (1989) Novel transcriptional control of the pyruvate formate-lyase gene: upstream regulatory sequences and multiple promoters regulate anaerobic expression. J. Bacteriol. 171, 2485-2498.
38. [38] Sawers, G. (1993) Specific transcriptional requirements for positive regulation of the anaerobically inducible pfl operon by ArcA and FNR. Mol. Microbiol. 10, 737-747.
39. [39] Suppmann, B. and Sawers, G. (1994) Isolation and characterization of hypophosphite-resistant mutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter. Mol. Microbiol. 11, 965-982.
40. [40] Sawers, G. and Suppmann, B. (1992) Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins. J. Bacteriol. 174, 3474-3478.
41. [41] Drapal, N. and Sawers, G. (1995) Purification of ArcA and analysis of its specific interaction with the pfl promoter-regulatory region. Mol. Microbiol. 16, 597-607.
42. [42] Kaiser, M. and Sawers, G. (1995) FNR activates transcription from the P6 promoter of the pfl operon in vitro. Mol. Microbiol. 18, 331-342.
43. [43] Sauter, M. and Sawers, R.G. (1990) Transcriptional analysis of the gene encoding pyruvate formate-lyase-activating enzyme of Escherichia coli. Mol. Microbiol. 4, 355-363.
44. [44] Ganduri, Y.L., Sadda, S.R., Datta, M.W., Jambukeswaran, R.K. and Datta, P. (1993) TdcA, a transcriptional activator of the tdcABC operon of Escherichia coli, is a member of the LysR family of proteins. Mol. Gen. Genet. 240, 395-402.
45. [45] Schweizer, H.P. and Datta, P. (1989) Identification and DNA sequence of tdcR, a positive regulatory gene of the tdc operon of Escherichia coli. Mol. Gen. Genet. 218, 516-522.
46. [46] Wu, Y., Patil, R.V. and Datta, P. (1992) Catabolite gene activator protein and integration host factor act in concert to regulate tdc operon expression in Escherichia coli. J. Bacteriol. 174, 6918-6927.
47. [47] Chattopadhyay, S., Wu, Y. and Datta, P. (1997) Involvement of Fnr and ArcA in anaerobic expression of the tdc operon of Escherichia coli. J. Bacteriol. 179, 4868-4873.
48. [48] Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D. et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
49. [49] Green, J. and Baldwin, M.L. (1997) HlyX, the FNR homologue of Actinobacillus pleuropneumoniae, is a [4Fe 4S]-containing oxygen-responsive transcription regulator that anaerobically activates FNR-dependent Class I promoters via an enhanced AR1 contact. Mol. Microbiol. 24, 593-605.