Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1989 Apr;8(4):1279–1286. doi: 10.1002/j.1460-2075.1989.tb03502.x

fixK, a gene homologous with fnr and crp from Escherichia coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti.

J Batut 1, M L Daveran-Mingot 1, M David 1, J Jacobs 1, A M Garnerone 1, D Kahn 1
PMCID: PMC400945  PMID: 2663474

Abstract

Nitrogen fixation genes are shown to undergo a complex positive and negative regulation in Rhizobium meliloti. Activation of fixN by fixLJ is shown to require a third regulatory gene, fixK. As fixK is activated by fixLJ, we propose a cascade model for fixN regulation such that fixLJ activates fixN via fixK. In addition fixK negatively regulates expression of the nif-specific activator nifA as well as its own expression by autoregulation. Thus nifA and fixK are subject to a mixed regulation, positive (by fixLJ) and negative (by fixK). The sequence of fixK shows homology with the Escherichia coli regulators fnr and crp, which makes fixK the third characterized member of this family of prokaryotic regulators.

Full text

PDF
1279

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aiba H. Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own gene. Cell. 1983 Jan;32(1):141–149. doi: 10.1016/0092-8674(83)90504-4. [DOI] [PubMed] [Google Scholar]
  2. Buikema W. J., Szeto W. W., Lemley P. V., Orme-Johnson W. H., Ausubel F. M. Nitrogen fixation specific regulatory genes of Klebsiella pneumoniae and Rhizobium meliloti share homology with the general nitrogen regulatory gene ntrC of K. pneumoniae. Nucleic Acids Res. 1985 Jun 25;13(12):4539–4555. doi: 10.1093/nar/13.12.4539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chippaux M., Bonnefoy-Orth V., Ratouchniak J., Pascal M. C. Operon fusions in the nitrate reductase operon and study of the control gene nir R in Escherichia coli. Mol Gen Genet. 1981;182(3):477–479. doi: 10.1007/BF00293938. [DOI] [PubMed] [Google Scholar]
  4. Cossart P., Gicquel-Sanzey B. Regulation of expression of the crp gene of Escherichia coli K-12: in vivo study. J Bacteriol. 1985 Jan;161(1):454–457. doi: 10.1128/jb.161.1.454-457.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. David M., Daveran M. L., Batut J., Dedieu A., Domergue O., Ghai J., Hertig C., Boistard P., Kahn D. Cascade regulation of nif gene expression in Rhizobium meliloti. Cell. 1988 Aug 26;54(5):671–683. doi: 10.1016/s0092-8674(88)80012-6. [DOI] [PubMed] [Google Scholar]
  6. David M., Domergue O., Pognonec P., Kahn D. Transcription patterns of Rhizobium meliloti symbiotic plasmid pSym: identification of nifA-independent fix genes. J Bacteriol. 1987 May;169(5):2239–2244. doi: 10.1128/jb.169.5.2239-2244.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dayhoff M. O., Barker W. C., Hunt L. T. Establishing homologies in protein sequences. Methods Enzymol. 1983;91:524–545. doi: 10.1016/s0076-6879(83)91049-2. [DOI] [PubMed] [Google Scholar]
  8. De Vos G. F., Walker G. C., Signer E. R. Genetic manipulations in Rhizobium meliloti utilizing two new transposon Tn5 derivatives. Mol Gen Genet. 1986 Sep;204(3):485–491. doi: 10.1007/BF00331029. [DOI] [PubMed] [Google Scholar]
  9. Ditta G., Virts E., Palomares A., Kim C. H. The nifA gene of Rhizobium meliloti is oxygen regulated. J Bacteriol. 1987 Jul;169(7):3217–3223. doi: 10.1128/jb.169.7.3217-3223.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dixon R. A. The genetic complexity of nitrogen fixation. The ninth Fleming lecture. J Gen Microbiol. 1984 Nov;130(11):2745–2755. doi: 10.1099/00221287-130-11-2745. [DOI] [PubMed] [Google Scholar]
  11. Dodd I. B., Egan J. B. Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins. J Mol Biol. 1987 Apr 5;194(3):557–564. doi: 10.1016/0022-2836(87)90681-4. [DOI] [PubMed] [Google Scholar]
  12. Ebright R. H., Cossart P., Gicquel-Sanzey B., Beckwith J. Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature. 1984 Sep 20;311(5983):232–235. doi: 10.1038/311232a0. [DOI] [PubMed] [Google Scholar]
  13. Griffiths L., Cole J. A. Lack of redox control of the anaerobically-induced nirB+ gene of Escherichia coli K-12. Arch Microbiol. 1987 May;147(4):364–369. doi: 10.1007/BF00406134. [DOI] [PubMed] [Google Scholar]
  14. Gussin G. N., Ronson C. W., Ausubel F. M. Regulation of nitrogen fixation genes. Annu Rev Genet. 1986;20:567–591. doi: 10.1146/annurev.ge.20.120186.003031. [DOI] [PubMed] [Google Scholar]
  15. Jayaraman P. S., Gaston K. L., Cole J. A., Busby S. J. The nirB promoter of Escherichia coli: location of nucleotide sequences essential for regulation by oxygen, the FNR protein and nitrite. Mol Microbiol. 1988 Jul;2(4):527–530. doi: 10.1111/j.1365-2958.1988.tb00059.x. [DOI] [PubMed] [Google Scholar]
  16. Kahn D., David M., Domergue O., Daveran M. L., Ghai J., Hirsch P. R., Batut J. Rhizobium meliloti fixGHI sequence predicts involvement of a specific cation pump in symbiotic nitrogen fixation. J Bacteriol. 1989 Feb;171(2):929–939. doi: 10.1128/jb.171.2.929-939.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Leong S. A., Williams P. H., Ditta G. S. Analysis of the 5' regulatory region of the gene for delta-aminolevulinic acid synthetase of Rhizobium meliloti. Nucleic Acids Res. 1985 Aug 26;13(16):5965–5976. doi: 10.1093/nar/13.16.5965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Martin M. O., Long S. R. Generalized transduction in Rhizobium meliloti. J Bacteriol. 1984 Jul;159(1):125–129. doi: 10.1128/jb.159.1.125-129.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  20. Renalier M. H., Batut J., Ghai J., Terzaghi B., Gherardi M., David M., Garnerone A. M., Vasse J., Truchet G., Huguet T. A new symbiotic cluster on the pSym megaplasmid of Rhizobium meliloti 2011 carries a functional fix gene repeat and a nod locus. J Bacteriol. 1987 May;169(5):2231–2238. doi: 10.1128/jb.169.5.2231-2238.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ronson C. W., Nixon B. T., Ausubel F. M. Conserved domains in bacterial regulatory proteins that respond to environmental stimuli. Cell. 1987 Jun 5;49(5):579–581. doi: 10.1016/0092-8674(87)90530-7. [DOI] [PubMed] [Google Scholar]
  22. Rossen L., Shearman C. A., Johnston A. W., Downie J. A. The nodD gene of Rhizobium leguminosarum is autoregulatory and in the presence of plant exudate induces the nodA,B,C genes. EMBO J. 1985 Dec 16;4(13A):3369–3373. doi: 10.1002/j.1460-2075.1985.tb04092.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Shaw D. J., Rice D. W., Guest J. R. Homology between CAP and Fnr, a regulator of anaerobic respiration in Escherichia coli. J Mol Biol. 1983 May 15;166(2):241–247. doi: 10.1016/s0022-2836(83)80011-4. [DOI] [PubMed] [Google Scholar]
  24. Spiro S., Guest J. R. Activation of the lac operon of Escherichia coli by a mutant FNR protein. Mol Microbiol. 1987 Jul;1(1):53–58. doi: 10.1111/j.1365-2958.1987.tb00526.x. [DOI] [PubMed] [Google Scholar]
  25. Spiro S., Guest J. R. Inactivation of the FNR protein of Escherichia coli by targeted mutagenesis in the N-terminal region. Mol Microbiol. 1988 Nov;2(6):701–707. doi: 10.1111/j.1365-2958.1988.tb00080.x. [DOI] [PubMed] [Google Scholar]
  26. Spiro S., Guest J. R. Regulation and over-expression of the fnr gene of Escherichia coli. J Gen Microbiol. 1987 Dec;133(12):3279–3288. doi: 10.1099/00221287-133-12-3279. [DOI] [PubMed] [Google Scholar]
  27. Stormo G. D., Schneider T. D., Gold L., Ehrenfeucht A. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res. 1982 May 11;10(9):2997–3011. doi: 10.1093/nar/10.9.2997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Szeto W. W., Nixon B. T., Ronson C. W., Ausubel F. M. Identification and characterization of the Rhizobium meliloti ntrC gene: R. meliloti has separate regulatory pathways for activation of nitrogen fixation genes in free-living and symbiotic cells. J Bacteriol. 1987 Apr;169(4):1423–1432. doi: 10.1128/jb.169.4.1423-1432.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Szeto W. W., Zimmerman J. L., Sundaresan V., Ausubel F. M. A Rhizobium meliloti symbiotic regulatory gene. Cell. 1984 Apr;36(4):1035–1043. doi: 10.1016/0092-8674(84)90053-9. [DOI] [PubMed] [Google Scholar]
  30. Unden G., Guest J. R. Isolation and characterization of the Fnr protein, the transcriptional regulator of anaerobic electron transport in Escherichia coli. Eur J Biochem. 1985 Jan 2;146(1):193–199. doi: 10.1111/j.1432-1033.1985.tb08638.x. [DOI] [PubMed] [Google Scholar]
  31. Virts E. L., Stanfield S. W., Helinski D. R., Ditta G. S. Common regulatory elements control symbiotic and microaerobic induction of nifA in Rhizobium meliloti. Proc Natl Acad Sci U S A. 1988 May;85(9):3062–3065. doi: 10.1073/pnas.85.9.3062. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Weber G., Reiländer H., Pühler A. Mapping and expression of a regulatory nitrogen fixation gene (fixD) of Rhizobium meliloti. EMBO J. 1985 Nov;4(11):2751–2756. doi: 10.1002/j.1460-2075.1985.tb03999.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Weber I. T., Steitz T. A. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution. J Mol Biol. 1987 Nov 20;198(2):311–326. doi: 10.1016/0022-2836(87)90315-9. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES