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Gene Review

fnr  -  oxygen-sensing anaerobic growth regulon...

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK1330, JW1328, nirA, nirR, ossA
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Disease relevance of fnr


High impact information on fnr


Chemical compound and disease context of fnr

  • The nucleotide sequence of a 1.64 kb fragment of E. coli DNA containing the fnr gene (regulatory gene for fumarate and nitrate reduction) was determined using the dideoxy chain termination method [9].
  • Mutations in the Escherichia coli fnr and tgt genes: control of molybdate reductase activity and the cytochrome d complex by fnr [10].
  • Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS [11].
  • RNA was isolated from cultures of Escherichia coli strain MG1655 and derivatives defective in fnr, narXL, or narXL with narP, during aerobic growth, or anaerobic growth in the presence or absence of nitrate or nitrite, in non-repressing media in which both strain MG1655 and an fnr deletion mutant grew at similar rates [12].
  • A library of Escherichia coli fnr mutants has been screened to identify FNR (regulator of fumarate and nitrate reduction) variants that are defective repressors, but competent activators [13].

Biological context of fnr

  • It was not possible to assign specific metabolic lesions to the fnr mutants nor to the remaining classes, which all exhibited pleiotropic phenotypes [14].
  • Succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli is negatively regulated by the arcA and fnr gene products during anaerobic cell growth conditions [15].
  • Nucleotide sequence of the fnr gene and primary structure of the Enr protein of Escherichia coli [9].
  • A library of random mutations in the Escherichia coli fnr gene has been screened to identify positive control mutants of FNR that are defective in transcription activation at Class I promoters [16].
  • Two distinct regulatory domains have been delineated in the 5' region of the operon which respond respectively to positive induction by the fnr gene product under anaerobic conditions and to positive induction by the narL gene product in the presence of nitrate (S.F. Li, T. Rabi, and J.A. DeMoss, J. Bacteriol. 164:25-32) [17].

Anatomical context of fnr


Associations of fnr with chemical compounds

  • Introduction of an fnr+ gene into UV14 restored anaerobic repression of sodA::lacZ and restored the ability of the cells to reduce nitrate [20].
  • The fnr gene was initially defined by the isolation of some pleiotropic mutants which characteristically lacked the ability to use fumarate and nitrate as reducible substrates for supporting anaerobic growth and several other anaerobic respiratory functions [21].
  • The N-terminal sequence of FNR (Mr 30,000) was identical to that predicted from the fnr gene starting with the initiating methionine residue and including a four-cysteine cluster (16)Cys-X3-Cys-X2-Cys-X5-Cys(29) [22].
  • The results indicate that lower conversion of pyruvate to acetyl-CoA is the main reason for high fluxes through lactate dehydrogenase (LDH) in cultures of the arcA, fnr double mutant strain [23].
  • The results suggest that fnr is involved in anaerobic control of components of the cytochrome d complex and of the redox system that transfers electrons to molybdate [10].

Other interactions of fnr

  • Anaerobic, but not aerobic, expression of phi (hmp-lacZ)1 was stimulated three- to four-fold by an fnr mutation; an apparent Fnr-binding site is present in the hmp promoter [24].
  • These increases were totally dependent on a functional fnr gene and were shown by S1 mapping experiments to be due to transcriptional read-through from the Fnr-dependent nirB promoter [25].
  • The expression of fnr-lacZ was relatively unaffected by iron limitation suggesting that Fnr levels in the cell do not change in response to iron [26].
  • LacZ operon fusions were constructed and were inserted in single copies into strain MC4100 and into its fnr, arcA or hemA carrying derivatives [27].
  • Expression of narL does not require the fnr gene product, a pleiotropic activator that is required for full expression of narC, frd, and tor [28].

Analytical, diagnostic and therapeutic context of fnr

  • After error-prone PCR mutagenesis of the gonococcal fnr gene, we identified four mutant fnr derivatives carrying the same S18F substitution, and we showed that the mutant FNR could activate transcription from a range of class I and class II FNR-dependent promoters in E. coli [29].
  • In the same way, using the anti-trimethylamine-N-oxide reductase serum, rocket immunoelectrophoresis analyses were able to show that the inducible apoenzyme is not regulated by the fnr gene product and that molybdate does not seem necessary for the synthesis or stabilisation of this enzyme [30].


  1. A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. Constantinidou, C., Hobman, J.L., Griffiths, L., Patel, M.D., Penn, C.W., Cole, J.A., Overton, T.W. J. Biol. Chem. (2006) [Pubmed]
  2. Molecular genetic analysis of FNR-dependent promoters. Eiglmeier, K., Honoré, N., Iuchi, S., Lin, E.C., Cole, S.T. Mol. Microbiol. (1989) [Pubmed]
  3. Actinobacillus pleuropneumoniae hlyX gene homology with the fnr gene of Escherichia coli. MacInnes, J.I., Kim, J.E., Lian, C.J., Soltes, G.A. J. Bacteriol. (1990) [Pubmed]
  4. Two-component regulatory proteins ResD-ResE are required for transcriptional activation of fnr upon oxygen limitation in Bacillus subtilis. Nakano, M.M., Zuber, P., Glaser, P., Danchin, A., Hulett, F.M. J. Bacteriol. (1996) [Pubmed]
  5. Anaerobic control of denitrification in Pseudomonas stutzeri escapes mutagenesis of an fnr-like gene. Cuypers, H., Zumft, W.G. J. Bacteriol. (1993) [Pubmed]
  6. Anaerobic transcription activation in Bacillus subtilis: identification of distinct FNR-dependent and -independent regulatory mechanisms. Cruz Ramos, H., Boursier, L., Moszer, I., Kunst, F., Danchin, A., Glaser, P. EMBO J. (1995) [Pubmed]
  7. Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes. Melville, S.B., Gunsalus, R.P. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  8. crnA encodes a nitrate transporter in Aspergillus nidulans. Unkles, S.E., Hawker, K.L., Grieve, C., Campbell, E.I., Montague, P., Kinghorn, J.R. Proc. Natl. Acad. Sci. U.S.A. (1991) [Pubmed]
  9. Nucleotide sequence of the fnr gene and primary structure of the Enr protein of Escherichia coli. Shaw, D.J., Guest, J.R. Nucleic Acids Res. (1982) [Pubmed]
  10. Mutations in the Escherichia coli fnr and tgt genes: control of molybdate reductase activity and the cytochrome d complex by fnr. Frey, B., Jänel, G., Michelsen, U., Kersten, H. J. Bacteriol. (1989) [Pubmed]
  11. Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS. Membrillo-Hernández, J., Lin, E.C. J. Bacteriol. (1999) [Pubmed]
  12. Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology. Overton, T.W., Griffiths, L., Patel, M.D., Hobman, J.L., Penn, C.W., Cole, J.A., Constantinidou, C. Biochem. Soc. Trans. (2006) [Pubmed]
  13. Identification of a surface of FNR overlapping activating region 1 that is required for repression of gene expression. Green, J., Marshall, F.A. J. Biol. Chem. (1999) [Pubmed]
  14. Mutants of Escherichia coli K12 unable to use fumarate as an anaerobic electron acceptor. Lambden, P.R., Guest, J.R. J. Gen. Microbiol. (1976) [Pubmed]
  15. Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli. Shen, J., Gunsalus, R.P. Mol. Microbiol. (1997) [Pubmed]
  16. Transcription activation at class I FNR-dependent promoters: identification of the activating surface of FNR and the corresponding contact site in the C-terminal domain of the RNA polymerase alpha subunit. Williams, S.M., Savery, N.J., Busby, S.J., Wing, H.J. Nucleic Acids Res. (1997) [Pubmed]
  17. Promoter region of the nar operon of Escherichia coli: nucleotide sequence and transcription initiation signals. Li, S.F., DeMoss, J.A. J. Bacteriol. (1987) [Pubmed]
  18. Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. Cotter, P.A., Chepuri, V., Gennis, R.B., Gunsalus, R.P. J. Bacteriol. (1990) [Pubmed]
  19. The blue copper-containing nitrite reductase from Alcaligenes xylosoxidans: cloning of the nirA gene and characterization of the recombinant enzyme. Prudêncio, M., Eady, R.R., Sawers, G. J. Bacteriol. (1999) [Pubmed]
  20. Characterization of regulatory mutations causing anaerobic derepression of the sodA gene in Escherichia coli K12: cooperation between cis- and trans-acting regulatory loci. Beaumont, M.D., Hassan, H.M. J. Gen. Microbiol. (1993) [Pubmed]
  21. FNR and its role in oxygen-regulated gene expression in Escherichia coli. Spiro, S., Guest, J.R. FEMS Microbiol. Rev. (1990) [Pubmed]
  22. Isolation of intact FNR protein (Mr 30,000) of Escherichia coli. Trageser, M., Spiro, S., Duchêne, A., Kojro, E., Fahrenholz, F., Guest, J.R., Unden, G. Mol. Microbiol. (1990) [Pubmed]
  23. Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions. Shalel-Levanon, S., San, K.Y., Bennett, G.N. Biotechnol. Bioeng. (2005) [Pubmed]
  24. Nitric oxide, nitrite, and Fnr regulation of hmp (flavohemoglobin) gene expression in Escherichia coli K-12. Poole, R.K., Anjum, M.F., Membrillo-Hernández, J., Kim, S.O., Hughes, M.N., Stewart, V. J. Bacteriol. (1996) [Pubmed]
  25. Transcriptional control of the cysG gene of Escherichia coli K-12 during aerobic and anaerobic growth. Peakman, T., Busby, S., Cole, J. Eur. J. Biochem. (1990) [Pubmed]
  26. The effect of iron limitation on expression of the aerobic and anaerobic electron transport pathway genes in Escherichia coli. Cotter, P.A., Darie, S., Gunsalus, R.P. FEMS Microbiol. Lett. (1992) [Pubmed]
  27. Regulation of the isofunctional genes ubiD and ubiX of the ubiquinone biosynthetic pathway of Escherichia coli. Zhang, H., Javor, G.T. FEMS Microbiol. Lett. (2003) [Pubmed]
  28. The narL gene product activates the nitrate reductase operon and represses the fumarate reductase and trimethylamine N-oxide reductase operons in Escherichia coli. Iuchi, S., Lin, E.C. Proc. Natl. Acad. Sci. U.S.A. (1987) [Pubmed]
  29. Transcription activation at Escherichia coli FNR-dependent promoters by the gonococcal FNR protein: effects of a novel S18F substitution and comparisons with the corresponding substitution in E. coli FNR. Overton, T., Reid, E.G., Foxall, R., Smith, H., Busby, S.J., Cole, J.A. J. Bacteriol. (2003) [Pubmed]
  30. The inducible trimethylamine-N-oxide reductase of Escherichia coli K12: biochemical and immunological studies. Silvestro, A., Pommier, J., Giordano, G. Biochim. Biophys. Acta (1988) [Pubmed]
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