Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1985 May 24;13(10):3407–3418. doi: 10.1093/nar/13.10.3407

Conservation of nif- and species-specific domains within repeated promoter sequences from fast-growing Rhizobium species.

P R Schofield, J M Watson
PMCID: PMC341248  PMID: 3892479

Abstract

In the fast-growing Rhizobium species, repeated DNA sequences, which include the promoter region of the nif HDK operon have been described. These repeated sequences are promoters which specifically activate transcription in the endosymbiotic state. Hybridization analysis of these sequences from R. trifolii has revealed that they may be involved in the species-specific activation of the various genes whose transcription they promote. Comparative analysis of various copies of these repeated sequences, from R. trifolii (the clover symbiont) and R. meliloti (the alfalfa symbiont), reveals the presence of domains of intra- and interspecific conservation within the promoter regions. We suggest that these promoter elements represent sites which are involved in the species-specific and general, nif-specific activation of Rhizobium symbiotic genes.

Full text

PDF
3408

Selected References

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

  1. Abraham J., Mascarenhas D., Fischer R., Benedik M., Campbell A., Echols H. DNA sequence of regulatory region for integration gene of bacteriophage lambda. Proc Natl Acad Sci U S A. 1980 May;77(5):2477–2481. doi: 10.1073/pnas.77.5.2477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Adams T. H., Chelm B. K. The nifH and nifDK promoter regions from Rhizobium japonicum share structural homologies with each other and with nitrogen-regulated promoters from other organisms. J Mol Appl Genet. 1984;2(4):392–405. [PubMed] [Google Scholar]
  3. Ausubel F. M. Regulation of nitrogen fixation genes. Cell. 1984 May;37(1):5–6. doi: 10.1016/0092-8674(84)90294-0. [DOI] [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. Bitoun R., Berman J., Zilberstein A., Holland D., Cohen J. B., Givol D., Zamir A. Promoter mutations that allow nifA-independent expression of the nitrogen fixation nifHDKY operon. Proc Natl Acad Sci U S A. 1983 Oct;80(19):5812–5816. doi: 10.1073/pnas.80.19.5812. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. 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]
  9. Christensen A. H., Schubert K. R. Identification of a Rhizobium trifolii plasmid coding for nitrogen fixation and nodulation genes and its interaction with pJB5JI, a Rhizobium leguminosarum plasmid. J Bacteriol. 1983 Nov;156(2):592–599. doi: 10.1128/jb.156.2.592-599.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Hirsch A. M., Bang M., Ausubel F. M. Ultrastructural analysis of ineffective alfalfa nodules formed by nif::Tn5 mutants of Rhizobium meliloti. J Bacteriol. 1983 Jul;155(1):367–380. doi: 10.1128/jb.155.1.367-380.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. KLECZKOWSKA J. A study of phage-resistant mutants of Rhizobium trifolii. J Gen Microbiol. 1950 Sep;4(3):298–310. doi: 10.1099/00221287-4-3-298. [DOI] [PubMed] [Google Scholar]
  13. Kleczkowska J., Nutman P. S., Bond G. Note on the Ability of Certain Strains of Rhizobi from Peas and Clover to Infect Each Other's Host Plants. J Bacteriol. 1944 Dec;48(6):673–675. doi: 10.1128/jb.48.6.673-675.1944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lamond A. I., Travers A. A. Requirement for an upstream element for optimal transcription of a bacterial tRNA gene. Nature. 1983 Sep 15;305(5931):248–250. doi: 10.1038/305248a0. [DOI] [PubMed] [Google Scholar]
  15. Landick R., Vaughn V., Lau E. T., VanBogelen R. A., Erickson J. W., Neidhardt F. C. Nucleotide sequence of the heat shock regulatory gene of E. coli suggests its protein product may be a transcription factor. Cell. 1984 Aug;38(1):175–182. doi: 10.1016/0092-8674(84)90538-5. [DOI] [PubMed] [Google Scholar]
  16. Losick R., Pero J. Cascades of Sigma factors. Cell. 1981 Sep;25(3):582–584. doi: 10.1016/0092-8674(81)90164-1. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Miyada C. G., Soberón X., Itakura K., Wilcox G. The use of synthetic oligodeoxyribonucleotides to produce specific deletions in the araBAD promoter of Escherichia coli B/r. Gene. 1982 Feb;17(2):167–177. doi: 10.1016/0378-1119(82)90070-1. [DOI] [PubMed] [Google Scholar]
  19. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Ow D. W., Sundaresan V., Rothstein D. M., Brown S. E., Ausubel F. M. Promoters regulated by the glnG (ntrC) and nifA gene products share a heptameric consensus sequence in the -15 region. Proc Natl Acad Sci U S A. 1983 May;80(9):2524–2528. doi: 10.1073/pnas.80.9.2524. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Riedel G. E., Brown S. E., Ausubel F. M. Nitrogen fixation by Klebsiella pneumoniae is inhibited by certain multicopy hybrid nif plasmids. J Bacteriol. 1983 Jan;153(1):45–56. doi: 10.1128/jb.153.1.45-56.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Scott K. F., Rolfe B. G., Shine J. Biological nitrogen fixation: primary structure of the Rhizobium trifolii iron protein gene. DNA. 1983;2(2):149–155. doi: 10.1089/dna.1983.2.149. [DOI] [PubMed] [Google Scholar]
  26. Sundaresan V., Jones J. D., Ow D. W., Ausubel F. M. Klebsiella pneumoniae nifA product activates the Rhizobium meliloti nitrogenase promoter. Nature. 1983 Feb 24;301(5902):728–732. doi: 10.1038/301728a0. [DOI] [PubMed] [Google Scholar]
  27. 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]
  28. 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]
  29. Taylor W. E., Straus D. B., Grossman A. D., Burton Z. F., Gross C. A., Burgess R. R. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Cell. 1984 Sep;38(2):371–381. doi: 10.1016/0092-8674(84)90492-6. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. Westpheling J., Ranes M., Losick R. RNA polymerase heterogeneity in Streptomyces coelicolor. Nature. 1985 Jan 3;313(5997):22–27. doi: 10.1038/313022a0. [DOI] [PubMed] [Google Scholar]
  32. 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