Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1984 Nov 26;12(22):8329–8344. doi: 10.1093/nar/12.22.8329

Structural analysis of the genes encoding the molybdenum-iron protein of nitrogenase in the Parasponia rhizobium strain ANU289.

J J Weinman, F F Fellows, P M Gresshoff, J Shine, K F Scott
PMCID: PMC320364  PMID: 6095197

Abstract

The genes encoding the Molybdenum-Iron protein component of nitrogenase (nifD and nifK) have been identified and fully characterised in the Parasponia Rhizobium strain ANU289. The two genes are contiguous and are separated from the gene encoding the Fe-protein component of nitrogenase (nifH) by 21 kb of DNA. We present the entire DNA sequence of the nifD and nifK genes, thus completing the characterisation of the primary structure of the nitrogenase genes in this Rhizobium strain. Comparison of the sequence preceding the transcription initiation point of nifDK with that preceding nifH reveals a consensus promoter sequence 5'-PyTGGCAPyG-4 bp-TTGC(T/A)-10 bp-3'. This consensus promoter is found preceding nif genes in both fast-growing and slow-growing Rhizobium strains and shows a structural similarity to that preceding the coordinately-regulated nif operons in the asymbiotic organism Klebsiella pneumoniae.

Full text

PDF
8344

Images in this article

8332Image
on p.8332
8338Image
on p.8338

Selected References

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

  1. 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]
  2. 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]
  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. Bergersen F. J., Turner G. L. Activity of nitrogenase and glutamine synthetase in relation to availability of oxygen in continuous cultures of a strain of cowpea Rhizobium sp. supplied with excess ammonium. Biochim Biophys Acta. 1978 Feb 1;538(3):406–416. doi: 10.1016/0304-4165(78)90402-6. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. 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]
  7. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  8. Borer P. N., Dengler B., Tinoco I., Jr, Uhlenbeck O. C. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. doi: 10.1016/0022-2836(74)90357-x. [DOI] [PubMed] [Google Scholar]
  9. Brown C. M., Dilworth M. J. Ammonia assimilation by rhizobium cultures and bacteroids. J Gen Microbiol. 1975 Jan;86(1):39–48. doi: 10.1099/00221287-86-1-39. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. 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]
  12. 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]
  13. Chou P. Y., Fasman G. D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148. doi: 10.1002/9780470122921.ch2. [DOI] [PubMed] [Google Scholar]
  14. Corbin D., Barran L., Ditta G. Organization and expression of Rhizobium meliloti nitrogen fixation genes. Proc Natl Acad Sci U S A. 1983 May;80(10):3005–3009. doi: 10.1073/pnas.80.10.3005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. Hase T., Wakabayashi S., Nakano T., Zumft W. G., Matsubara H. Structural homologies between the amino acid sequence of Clostridium pasteurianum MoFe protein and the DNA sequences of nifD and K genes of phylogenetically diverse bacteria. FEBS Lett. 1984 Jan 23;166(1):39–43. doi: 10.1016/0014-5793(84)80040-x. [DOI] [PubMed] [Google Scholar]
  20. Inouye S., Ebina Y., Nakazawa A., Nakazawa T. Nucleotide sequence surrounding transcription initiation site of xylABC operon on TOL plasmid of Pseudomonas putida. Proc Natl Acad Sci U S A. 1984 Mar;81(6):1688–1691. doi: 10.1073/pnas.81.6.1688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lammers P. J., Haselkorn R. Sequence of the nifD gene coding for the alpha subunit of dinitrogenase from the cyanobacterium Anabaena. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4723–4727. doi: 10.1073/pnas.80.15.4723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Liu C. P., Tucker P. W., Mushinski J. F., Blattner F. R. Mapping of heavy chain genes for mouse immunoglobulins M and D. Science. 1980 Sep 19;209(4463):1348–1353. doi: 10.1126/science.6774414. [DOI] [PubMed] [Google Scholar]
  23. Lundell D. J., Howard J. B. Isolation and sequences of the cysteinyl tryptic peptides from the MoFe-protein of Azotobacter vinelandii nitrogenase. J Biol Chem. 1981 Jun 25;256(12):6385–6391. [PubMed] [Google Scholar]
  24. Mazur B. J., Chui C. F. Sequence of the gene coding for the beta-subunit of dinitrogenase from the blue-green alga Anabaena. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6782–6786. doi: 10.1073/pnas.79.22.6782. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mazur B. J., Chui C. F. Sequence of the gene coding for the beta-subunit of dinitrogenase from the blue-green alga Anabaena. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6782–6786. doi: 10.1073/pnas.79.22.6782. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
  27. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  28. Nelson M. J., Levy M. A., Orme-Johnson W. H. Metal and sulfur composition of iron-molybdenum cofactor of nitrogenase. Proc Natl Acad Sci U S A. 1983 Jan;80(1):147–150. doi: 10.1073/pnas.80.1.147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. doi: 10.1016/0378-1119(83)90040-9. [DOI] [PubMed] [Google Scholar]
  30. O'Farrell P. H., Kutter E., Nakanishi M. A restriction map of the bacteriophage T4 genome. Mol Gen Genet. 1980;179(2):421–435. doi: 10.1007/BF00425473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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]
  32. Quiviger B., Franche C., Lutfalla G., Rice D., Haselkorn R., Elmerich C. Cloning of a nitrogen fixation (nif) gene cluster of Azospirillum brasilense. Biochimie. 1982 Jul;64(7):495–502. doi: 10.1016/s0300-9084(82)80165-x. [DOI] [PubMed] [Google Scholar]
  33. Roberts G. P., Brill W. J. Genetics and regulation of nitrogen fixation. Annu Rev Microbiol. 1981;35:207–235. doi: 10.1146/annurev.mi.35.100181.001231. [DOI] [PubMed] [Google Scholar]
  34. 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]
  35. Ruvkun G. B., Ausubel F. M. A general method for site-directed mutagenesis in prokaryotes. Nature. 1981 Jan 1;289(5793):85–88. doi: 10.1038/289085a0. [DOI] [PubMed] [Google Scholar]
  36. Ruvkun G. B., Ausubel F. M. Interspecies homology of nitrogenase genes. Proc Natl Acad Sci U S A. 1980 Jan;77(1):191–195. doi: 10.1073/pnas.77.1.191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ruvkun G. B., Sundaresan V., Ausubel F. M. Directed transposon Tn5 mutagenesis and complementation analysis of Rhizobium meliloti symbiotic nitrogen fixation genes. Cell. 1982 Jun;29(2):551–559. doi: 10.1016/0092-8674(82)90171-4. [DOI] [PubMed] [Google Scholar]
  38. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Schetgens T. M., Bakkeren G., van Dun C., Hontelez J. G., van den Bos R. C., van Kammen A. Molecular cloning and functional characterization of Rhizobium leguminosarum structural nif-genes by site-directed transposon mutagenesis and expression in Escherichia coli minicells. J Mol Appl Genet. 1984;2(4):406–421. [PubMed] [Google Scholar]
  40. Scott K. F., Hughes J. E., Gresshoff P. M., Beringer J. E., Rolfe B. G., Shine J. Molecular cloning of Rhizobium trifolii genes involved in symbiotic nitrogen fixation. J Mol Appl Genet. 1982;1(4):315–326. [PubMed] [Google Scholar]
  41. 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]
  42. 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]
  43. 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]
  44. Shine J., Dalgarno L. Determinant of cistron specificity in bacterial ribosomes. Nature. 1975 Mar 6;254(5495):34–38. doi: 10.1038/254034a0. [DOI] [PubMed] [Google Scholar]
  45. Siebenlist U., Simpson R. B., Gilbert W. E. coli RNA polymerase interacts homologously with two different promoters. Cell. 1980 Jun;20(2):269–281. doi: 10.1016/0092-8674(80)90613-3. [DOI] [PubMed] [Google Scholar]
  46. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  47. 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]
  48. 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]
  49. Török I., Kondorosi A. Nucleotide sequence of the R.meliloti nitrogenase reductase (nifH) gene. Nucleic Acids Res. 1981 Nov 11;9(21):5711–5723. doi: 10.1093/nar/9.21.5711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. 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