Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1986 May 27;14(10):4207–4227. doi: 10.1093/nar/14.10.4207

Activation of the Bradyrhizobium japonicum nifH and nifDK operons is dependent on promoter-upstream DNA sequences.

A Alvarez-Morales, M Betancourt-Alvarez, K Kaluza, H Hennecke
PMCID: PMC339856  PMID: 3086837

Abstract

Previous analysis of B. japonicum nifH'- and nifD'-'lacZ translational fusions showed that these promoters could be activated by the K. pneumoniae nifA plus the E. coli ntrA gene products. To study the functions of the DNA 5' to these promoters, plasmids carrying deletions in this region were constructed and analyzed in vivo in a heterologous system consisting of an E. coli (NtrA+) background with a plasmid that constitutively expresses the K. pneumoniae nifA gene. Activation of the B. japonicum promoters was completely dependent on sequences located between positions -165 and -100, relative to the start of transcription. Some of the nifD deletion-fusions were mobilized to the wild-type B. japonicum and the exconjugants tested in an ex planta micro-aerobic system, and also used to infect soybean seedlings. The time course of derepression was followed by assaying beta-galactosidase activity from samples withdrawn from the microaerobic cultures or from root-nodule extracts. The results conclusively show that in the homologous system the sequences upstream of the promoter are required to achieve wild-type activity.

Full text

PDF

Selected References

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

  1. Alvarez-Morales A., Dixon R., Merrick M. Positive and negative control of the glnA ntrBC regulon in Klebsiella pneumoniae. EMBO J. 1984 Mar;3(3):501–507. doi: 10.1002/j.1460-2075.1984.tb01837.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alvarez-Morales A., Hennecke H. Expression of Rhizobium japonicum nifH and nifDK operons can be activated by the Klebsiella pneumonia nifA protein but not by the product of ntrC. Mol Gen Genet. 1985;199(2):306–314. doi: 10.1007/BF00330273. [DOI] [PubMed] [Google Scholar]
  3. Better M., Ditta G., Helinski D. R. Deletion analysis of Rhizobium meliloti symbiotic promoters. EMBO J. 1985 Oct;4(10):2419–2424. doi: 10.1002/j.1460-2075.1985.tb03950.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Better M., Lewis B., Corbin D., Ditta G., Helinski D. R. Structural relationships among Rhizobium meliloti symbiotic promoters. Cell. 1983 Dec;35(2 Pt 1):479–485. doi: 10.1016/0092-8674(83)90181-2. [DOI] [PubMed] [Google Scholar]
  5. Beynon J., Cannon M., Buchanan-Wollaston V., Cannon F. The nif promoters of Klebsiella pneumoniae have a characteristic primary structure. Cell. 1983 Sep;34(2):665–671. doi: 10.1016/0092-8674(83)90399-9. [DOI] [PubMed] [Google Scholar]
  6. Brent R., Ptashne M. A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell. 1985 Dec;43(3 Pt 2):729–736. doi: 10.1016/0092-8674(85)90246-6. [DOI] [PubMed] [Google Scholar]
  7. Brigle K. E., Newton W. E., Dean D. R. Complete nucleotide sequence of the Azotobacter vinelandii nitrogenase structural gene cluster. Gene. 1985;37(1-3):37–44. doi: 10.1016/0378-1119(85)90255-0. [DOI] [PubMed] [Google Scholar]
  8. Brown S. E., Ausubel F. M. Mutations affecting regulation of the Klebsiella pneumoniae nifH (nitrogenase reductase) promotor. J Bacteriol. 1984 Jan;157(1):143–147. doi: 10.1128/jb.157.1.143-147.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Buchanan-Wollaston V., Cannon M. C., Beynon J. L., Cannon F. C. Role of the nifA gene product in the regulation of nif expression in Klebsiella pneumoniae. Nature. 1981 Dec 24;294(5843):776–778. doi: 10.1038/294776a0. [DOI] [PubMed] [Google Scholar]
  10. Buchanan-Wollaston V., Cannon M. C., Cannon F. C. The use of cloned nif (nitrogen fixation) DNA to investigate transcriptional regulation of nif expression in Klebsiella pneumoniae. Mol Gen Genet. 1981;184(1):102–106. doi: 10.1007/BF00271203. [DOI] [PubMed] [Google Scholar]
  11. Buck M., Khan H., Dixon R. Site-directed mutagenesis of the Klebsiella pneumoniae nifL and nifH promoters and in vivo analysis of promoter activity. Nucleic Acids Res. 1985 Nov 11;13(21):7621–7638. doi: 10.1093/nar/13.21.7621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Bueno R., Pahel G., Magasanik B. Role of glnB and glnD gene products in regulation of the glnALG operon of Escherichia coli. J Bacteriol. 1985 Nov;164(2):816–822. doi: 10.1128/jb.164.2.816-822.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Casadaban M. J., Martinez-Arias A., Shapira S. K., Chou J. Beta-galactosidase gene fusions for analyzing gene expression in escherichia coli and yeast. Methods Enzymol. 1983;100:293–308. doi: 10.1016/0076-6879(83)00063-4. [DOI] [PubMed] [Google Scholar]
  15. Dean D. R., Brigle K. E. Azotobacter vinelandii nifD- and nifE-encoded polypeptides share structural homology. Proc Natl Acad Sci U S A. 1985 Sep;82(17):5720–5723. doi: 10.1073/pnas.82.17.5720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ditta G., Stanfield S., Corbin D., Helinski D. R. Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7347–7351. doi: 10.1073/pnas.77.12.7347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Dixon R., Eady R. R., Espin G., Hill S., Iaccarino M., Kahn D., Merrick M. Analysis of regulation of Klebsiella pneumoniae nitrogen fixation (nif) gene cluster with gene fusions. Nature. 1980 Jul 10;286(5769):128–132. doi: 10.1038/286128a0. [DOI] [PubMed] [Google Scholar]
  19. Dixon R., Kennedy C., Kondorosi A., Krishnapillai V., Merrick M. Complementation analysis of Klebsiella pneumoniae mutants defective in nitrogen fixation. Mol Gen Genet. 1977 Nov 29;157(2):189–198. doi: 10.1007/BF00267397. [DOI] [PubMed] [Google Scholar]
  20. Dixon R. Tandem promoters determine regulation of the Klebsiella pneumoniae glutamine synthetase (glnA) gene. Nucleic Acids Res. 1984 Oct 25;12(20):7811–7830. doi: 10.1093/nar/12.20.7811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Downie J. A., Ma Q. S., Knight C. D., Hombrecher G., Johnston A. W. Cloning of the symbiotic region of Rhizobium leguminosarum: the nodulation genes are between the nitrogenase genes and a nifA-like gene. EMBO J. 1983;2(6):947–952. doi: 10.1002/j.1460-2075.1983.tb01526.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Drummond M., Clements J., Merrick M., Dixon R. Positive control and autogenous regulation of the nifLA promoter in Klebsiella pneumoniae. Nature. 1983 Jan 27;301(5898):302–307. doi: 10.1038/301302a0. [DOI] [PubMed] [Google Scholar]
  23. Drummond M., Whitty P., Wootton J. Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins. EMBO J. 1986 Feb;5(2):441–447. doi: 10.1002/j.1460-2075.1986.tb04230.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Dynan W. S., Tjian R. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. 1985 Aug 29-Sep 4Nature. 316(6031):774–778. doi: 10.1038/316774a0. [DOI] [PubMed] [Google Scholar]
  25. Figurski D. H., Helinski D. R. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1648–1652. doi: 10.1073/pnas.76.4.1648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Filser M., Merrick M., Cannon F. Cloning and characterisation of nifLA regulatory mutations from Klebsiella pneumoniae. Mol Gen Genet. 1983;191(3):485–491. doi: 10.1007/BF00425767. [DOI] [PubMed] [Google Scholar]
  27. Fuhrmann M., Hennecke H. Rhizobium japonicum nitrogenase Fe protein gene (nifH). J Bacteriol. 1984 Jun;158(3):1005–1011. doi: 10.1128/jb.158.3.1005-1011.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Gicquel-Sanzey B., Cossart P. Homologies between different procaryotic DNA-binding regulatory proteins and between their sites of action. EMBO J. 1982;1(5):591–595. doi: 10.1002/j.1460-2075.1982.tb01213.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Giniger E., Varnum S. M., Ptashne M. Specific DNA binding of GAL4, a positive regulatory protein of yeast. Cell. 1985 Apr;40(4):767–774. doi: 10.1016/0092-8674(85)90336-8. [DOI] [PubMed] [Google Scholar]
  30. Guarente L. Yeast promoters: positive and negative elements. Cell. 1984 Apr;36(4):799–800. doi: 10.1016/0092-8674(84)90028-x. [DOI] [PubMed] [Google Scholar]
  31. Hawkes T., Merrick M., Dixon R. Interaction of purified NtrC protein with nitrogen regulated promoters from Klebsiella pneumoniae. Mol Gen Genet. 1985;201(3):492–498. doi: 10.1007/BF00331345. [DOI] [PubMed] [Google Scholar]
  32. Hill S., Kennedy C., Kavanagh E., Goldberg R. B., Hanau R. Nitrogen fixation gene (nifL) involved in oxygen regulation of nitrogenase synthesis in K. pneumoniae. Nature. 1981 Apr 2;290(5805):424–426. doi: 10.1038/290424a0. [DOI] [PubMed] [Google Scholar]
  33. Hirschman J., Wong P. K., Sei K., Keener J., Kustu S. Products of nitrogen regulatory genes ntrA and ntrC of enteric bacteria activate glnA transcription in vitro: evidence that the ntrA product is a sigma factor. Proc Natl Acad Sci U S A. 1985 Nov;82(22):7525–7529. doi: 10.1073/pnas.82.22.7525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Hunt T. P., Magasanik B. Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG, and glnL. Proc Natl Acad Sci U S A. 1985 Dec;82(24):8453–8457. doi: 10.1073/pnas.82.24.8453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Kennedy C., Robson R. L. Activation of nif gene expression in Azotobacter by the nifA gene product of Klebsiella pneumoniae. Nature. 1983 Feb 17;301(5901):626–628. doi: 10.1038/301626a0. [DOI] [PubMed] [Google Scholar]
  36. MacFarlane S. A., Merrick M. The nucleotide sequence of the nitrogen regulation gene ntrB and the glnA-ntrBC intergenic region of Klebsiella pneumoniae. Nucleic Acids Res. 1985 Nov 11;13(21):7591–7606. doi: 10.1093/nar/13.21.7591. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. MacNeil T., Roberts G. P., MacNeil D., Tyler B. The products of glnL and glnG are bifunctional regulatory proteins. Mol Gen Genet. 1982;188(2):325–333. doi: 10.1007/BF00332696. [DOI] [PubMed] [Google Scholar]
  38. Magasanik B. Genetic control of nitrogen assimilation in bacteria. Annu Rev Genet. 1982;16:135–168. doi: 10.1146/annurev.ge.16.120182.001031. [DOI] [PubMed] [Google Scholar]
  39. Merrick M. J., Gibbins J. R. The nucleotide sequence of the nitrogen-regulation gene ntrA of Klebsiella pneumoniae and comparison with conserved features in bacterial RNA polymerase sigma factors. Nucleic Acids Res. 1985 Nov 11;13(21):7607–7620. doi: 10.1093/nar/13.21.7607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Merrick M. J. Nitrogen control of the nif regulon in Klebsiella pneumoniae: involvement of the ntrA gene and analogies between ntrC and nifA. EMBO J. 1983;2(1):39–44. doi: 10.1002/j.1460-2075.1983.tb01377.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Merrick M. J., Stewart W. D. Studies on the regulation and function of the Klebsiella pneumoniae ntrA gene. Gene. 1985;35(3):297–303. doi: 10.1016/0378-1119(85)90008-3. [DOI] [PubMed] [Google Scholar]
  42. Ow D. W., Ausubel F. M. Regulation of nitrogen metabolism genes by nifA gene product in Klebsiella pneumoniae. Nature. 1983 Jan 27;301(5898):307–313. doi: 10.1038/301307a0. [DOI] [PubMed] [Google Scholar]
  43. Quinto C., De La Vega H., Flores M., Leemans J., Cevallos M. A., Pardo M. A., Azpiroz R., De Lourdes Girard M., Calva E., Palacios R. Nitrogenase reductase: A functional multigene family in Rhizobium phaseoli. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1170–1174. doi: 10.1073/pnas.82.4.1170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Regensburger B., Hennecke H. RNA polymerase from Rhizobium japonicum. Arch Microbiol. 1983 Aug;135(2):103–109. doi: 10.1007/BF00408017. [DOI] [PubMed] [Google Scholar]
  45. Roberts G. P., Brill W. J. Gene-product relationships of the nif regulon of Klebsiella pneumoniae. J Bacteriol. 1980 Oct;144(1):210–216. doi: 10.1128/jb.144.1.210-216.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Rossen L., Ma Q. S., Mudd E. A., Johnston A. W., Downie J. A. Identification and DNA sequence of fixZ, a nifB-like gene from Rhizobium leguminosarum. Nucleic Acids Res. 1984 Sep 25;12(18):7123–7134. doi: 10.1093/nar/12.18.7123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Schofield P. R., Watson J. M. Conservation of nif- and species-specific domains within repeated promoter sequences from fast-growing Rhizobium species. Nucleic Acids Res. 1985 May 24;13(10):3407–3418. doi: 10.1093/nar/13.10.3407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Scott K. F., Rolfe B. G., Shine J. Biological nitrogen fixation: primary structure of the Klebsiella pneumoniae nifH and nifD genes. J Mol Appl Genet. 1981;1(1):71–81. [PubMed] [Google Scholar]
  49. Scott K. F., Rolfe B. G., Shine J. Nitrogenase structural genes are unlinked in the nonlegume symbiont Parasponia rhizobium. DNA. 1983;2(2):141–148. doi: 10.1089/dna.1983.2.141. [DOI] [PubMed] [Google Scholar]
  50. Sibold L., Elmerich C. Constitutive expression of nitrogen fixation (nif) genes of Klebsiella pneumoniae due to a DNA duplication. EMBO J. 1982;1(12):1551–1558. doi: 10.1002/j.1460-2075.1982.tb01354.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Staden R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res. 1982 May 11;10(9):2951–2961. doi: 10.1093/nar/10.9.2951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Sundaresan V., Ow D. W., Ausubel F. M. Activation of Klebsiella pneumoniae and Rhizobium meliloti nitrogenase promoters by gln (ntr) regulatory proteins. Proc Natl Acad Sci U S A. 1983 Jul;80(13):4030–4034. doi: 10.1073/pnas.80.13.4030. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. 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]
  54. Travers A. A., Lamond A. I., Mace H. A., Berman M. L. RNA polymerase interactions with the upstream region of the E. coli tyrT promoter. Cell. 1983 Nov;35(1):265–273. doi: 10.1016/0092-8674(83)90229-5. [DOI] [PubMed] [Google Scholar]
  55. 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]
  56. Weinman J. J., Fellows F. F., Gresshoff P. M., Shine J., Scott K. F. Structural analysis of the genes encoding the molybdenum-iron protein of nitrogenase in the Parasponia rhizobium strain ANU289. Nucleic Acids Res. 1984 Nov 26;12(22):8329–8344. doi: 10.1093/nar/12.22.8329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Yun A. C., Szalay A. A. Structural genes of dinitrogenase and dinitrogenase reductase are transcribed from two separate promoters in the broad host range cowpea Rhizobium strain IRc78. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7358–7362. doi: 10.1073/pnas.81.23.7358. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Zimmerman J. L., Szeto W. W., Ausubel F. M. Molecular characterization of Tn5-induced symbiotic (Fix-) mutants of Rhizobium meliloti. J Bacteriol. 1983 Dec;156(3):1025–1034. doi: 10.1128/jb.156.3.1025-1034.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES