Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the −24/−12 promoter element

References

1. Arsene F., Kaminski P. A., Elmerich C. 1996; Modulation of NifA activity by PII in Azospirillum brasilense: evidence for a regulatory role of the NifA N-terminal domain. J Bacteriol 178:4830–4838
   [Google Scholar]
2. Austin S., Henderson N., Dixon R. 1990; Characterization of the Klebsiella pneumoniae nitrogen-fixation regulatory protein NifA and NifL ‘in vitro’. Eur J Biochem 187:353–360 [CrossRef]
   [Google Scholar]
3. Austin S., Buck M., Cannon W., Eydmann T., Dixon R. 1994; Purification and in vitro activities of the native nitrogen fixation control proteins NifA and NifL. J Bacteriol 176:3460–3465
   [Google Scholar]
4. Baldani J. I., Baldani V. L. D., Seldin L., Dobereiner J. 1986; Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a root-associated nitrogen-fixing bacterium. Int J Syst Bacteriol 36:86–93 [CrossRef]
   [Google Scholar]
5. Batut J., Daveran-Mingot M.-L., David M., Jacob J., Garnerone A. M., Kahn D. 1989; fixK, a gene homologous with fnr and crp from Escherichia coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti. EMBO J 8:1279–1286
   [Google Scholar]
6. Bauer E., Kaspar T., Fischer H.-M., Hennecke H. 1998; Expression of the fixR-nifA operon in Bradyrhizobium japonicum depends on a new response regulator, RegR. J Bacteriol 180:3853–3863
   [Google Scholar]
7. Benelli E. M., Souza E. M., Funayama S., Rigo L., Pedrosa F. O. 1997; Evidence for two possible glnB-type genes in Herbaspirillum seropedicae. J Bacteriol 179:4623–4626
   [Google Scholar]
8. Boddey R. M., Oliveira O. C., Urquiaga S., Reis V. M., Olivares F. L., Baldani V. L. D., Döbereiner J. 1995; Biological nitrogen fixation associated with sugar cane and rice: contributions and prospects for improvement. Plant Soil 174:195–209 [CrossRef]
   [Google Scholar]
9. Buchanan-Wollaston V., Cannon M. C., Beynon J. C., Cannon F. C. 1981; Role of the nifA gene product in the regulation of nif expression in Klebsiella pneumoniae. Nature 294:776–778 [CrossRef]
   [Google Scholar]
10. Buck M., Cannon W. 1989; Mutations in the RNA polymerase recognition sequence of the Klebsiella pneumoniae nifH promoter permitting transcriptional activation in the absence of NifA binding to upstream activator sequences. Nucleic Acids Res 7:2597–2612
    [Google Scholar]
11. Buck M., Cannon W. 1992; Activator-independent formation of a closed complex between σ⁵⁴-holoenzyme and nifH and nifU of Klebsiella pneumoniae. Mol Microbiol 6:1625–1630 [CrossRef]
    [Google Scholar]
12. David M., Daveran M. L., Batut J., Dedieu A., Domergue O., Gai J., Hertig C., Boistard P., Kahn D. 1988; Cascade regulation of nif gene expression in Rhizobium meliloti. Cell 54:671–683 [CrossRef]
    [Google Scholar]
13. Dixon R. 1988; Genetic regulation of nitrogen fixation. In The Nitrogen and Sulphur CyclesSociety for General Microbiology symposium no. 42 pp. 417–438Edited by Cole J. A., Ferguson S. J. Cambridge: Cambridge University Press;
    [Google Scholar]
14. Dixon R., Kennedy C., Kondorosi A., Krishnapillai V., Merrick M. 1977; Complementation analysis of Klebsiella pneumoniae mutants defective in nitrogen fixation. Mol Gen Genet 157:189–198 [CrossRef]
    [Google Scholar]
15. Figurski D. H., Helinski D. R. 1979; Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci U S A 76:1648–1652 [CrossRef]
    [Google Scholar]
16. Fischer H.-M., Hennecke H. 1987; Direct response of Bradyrhizobium japonicum nifA-mediated nif gene regulation to cellular oxygen status. Mol Gen Genet 209:621–626 [CrossRef]
    [Google Scholar]
17. Kaminski P. A., Elmerich C. 1998; The control of Azorhizobium caulinodans nifA expression by oxygen, ammonia and by the HF-I-like protein, NrfA. Mol Microbiol 28:603–613 [CrossRef]
    [Google Scholar]
18. Kennedy C., Robson R. L. 1983; Activation of nif gene expression in Azotobacter by the nifA gene product of Klebsiella pneumoniae. Nature 301:626–628 [CrossRef]
    [Google Scholar]
19. Knauf V. C., Nester E. W. 1982; Wide host range cloning vectors: a cosmid bank of an Agrobacterium Ti plasmid. Plasmid 8:45–54 [CrossRef]
    [Google Scholar]
20. Krol A. J. M., Hontelez J. G. J., Roozendaal B., Kammen A. 1982; On the operon structure of the nitrogenase of Rhizobium leguminosarum and Azotobacter vinelandii. Nucleic Acids Res 10:4147–4157 [CrossRef]
    [Google Scholar]
21. Liang Y. Y., Kaminski P. A., Elmerich C. 1991; Identification of a nifA-like regulator gene of Azospirillum brasilense Sp7 expressed under conditions of nitrogen fixation and in the presence of air and ammonia. Mol Microbiol 5:2735–2744 [CrossRef]
    [Google Scholar]
22. Loroch A. I., Nguyen B. G., Ludwig R. A. 1995; Interactive regulation of Azorhizobium nifA transcription via overlapping promoters. J Bacteriol 177:7210–7221
    [Google Scholar]
23. MacNeil D. 1981; General method, using Mu-Mud1 dilysogens, to determine the direction of transcription of and generate deletions in the glnA region of Escherichia coli. J Bacteriol 146:260–268
    [Google Scholar]
24. Merrick M. 1983; Nitrogen control of the nif regulon in Klebsiella pneumoniae: involvement of the ntrA gene and analogies between ntrC and nifA. EMBO J 2:39–44
    [Google Scholar]
25. Merrick M., Edwards R. A. 1995; Nitrogen control in bacteria. Microbiol Rev 59:604–622
    [Google Scholar]
26. Miller J. H. 1972 Experiments in Molecular Genetics Cold Spring Harbor, N Y: Cold Spring Harbor Laboratory;
    [Google Scholar]
27. Moret E., Buck M. 1988; NifA-dependent in vivo protection demonstrates that the upstream activating sequence of nif promoters is a protein-binding site. Proc Natl Acad Sci U S A 85:9401–9405 [CrossRef]
    [Google Scholar]
28. Moret E., Buck M. 1989; studies on the interaction of RNA polymerase-σ⁵⁴ with Klebsiella pneumoniae and Rhizobium meliloti nifH promoters: the role of NifA in the formation of an open promoter complex. J Mol Biol 210:65–77 [CrossRef]
    [Google Scholar]
29. Nees D. W., Stein P. A., Ludwig R. A. 1988; The Azorhizobium caulinodans nifA gene: identification of upstream activating sequences including a new element, the ‘anaerobox’. Nucleic Acids Res 16:9839–9853 [CrossRef]
    [Google Scholar]
30. Pedrosa F. O., Yates M. G. 1984; Regulation of nitrogen fixation (nif) genes of Azospirillum brasilense by nifA and ntr (gln) type gene products. FEMS Microbiol Lett 23:95–101 [CrossRef]
    [Google Scholar]
31. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
32. Sasse-Dwight S., Gralla J. D. 1991; Footprinting protein–DNA complexes in vivo. Methods Enzymol 208:146–168
    [Google Scholar]
33. Simon R., Priefer U., Pühler A. 1983; A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Biotechnology 1:784–791 [CrossRef]
    [Google Scholar]
34. Simon R., Quandt J., Klipp W. 1989; New derivatives of transposon Tn5 suitable for mobilization of replicons, generation of operon fusions and induction of genes in Gram-negative bacteria. Gene 80:161–169 [CrossRef]
    [Google Scholar]
35. Souza E. M., Funayama S., Rigo L. U., Yates M. G., Pedrosa F. O. 1991a; Sequence and structural organization of a nifA-like gene and part of a nifB-like gene of Herbaspirillum seropedicae strain Z78. J Gen Microbiol 137:1511–1522 [CrossRef]
    [Google Scholar]
36. Souza E. M., Funayama S., Rigo L. U., Pedrosa F. O. 1991b; Cloning and characterization of the nifA gene from Herbaspirillum seropedicae. Can J Microbiol 37:425–429 [CrossRef]
    [Google Scholar]
37. Souza E. M., Drummond M., Pedrosa F. O., Rigo L. U., Yates M. G. 1999; Control of Herbaspirillum seropedicae NifA activity by ammonium ions and oxygen. J Bacteriol 181:681–684
    [Google Scholar]
38. Spaniak H. P., Okker R. J. H., Wijffelman C. A., Pees E., Lugtenberg B. J. J. 1987; Promoters in the nodulation region of the Rhizobium leguminosarum Sym plasmid pRL1JI. Plant Mol Biol 9:27–39 [CrossRef]
    [Google Scholar]
39. Stigter J., Schneider M., de Bruijn F. J. 1992; Azorhizobium caulinodans nitrogen fixation (nif/fix) gene regulation: mutagenesis of the nifA −24/−12 promoter element, characterization of a ntrA (rpoN) gene, and derivation of a model. Mol Plant–Microbe Interact 6:238–252
    [Google Scholar]
40. Young J. P. W. 1992; Phylogenetic classification of nitrogen-fixing organisms. In Biological Nitrogen Fixation pp. 43–88Edited by Stacey G., Burris R. H., Evans H. J. New York: Chapman & Hall;
    [Google Scholar]
41. de Zamaroczy M., Paquelin A., Elmerich C. 1993; Functional organization of the glnB-glnA cluster of Azospirillum brasilense. J Bacteriol 175:2507–2515
    [Google Scholar]