Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1988 Apr;170(4):1475–1487. doi: 10.1128/jb.170.4.1475-1487.1988

Nucleotide sequence and genetic analysis of the nifB-nifQ region from Azotobacter vinelandii.

R D Joerger 1, P E Bishop 1
PMCID: PMC210991  PMID: 2450865

Abstract

A 3.8-kilobase-pair EcoRI fragment which corrects the mutations carried by the NifB- Azotobacter vinelandii strains CA30 and UW45 was cloned, and its nucleotide sequence was determined. Four complete open reading frames (ORFs) and two partial ORFs were found. The translation product of the first partial ORF is the carboxy-terminal end of a protein homologous to the nifA gene product from Klebsiella pneumoniae. A 285-base-pair sequence containing a potential nif promoter and nif regulatory sites separates this nifA gene from the first complete ORF which encodes a protein homologous to nifB gene products from K. pneumoniae and Rhizobium species. The Tn5 insertion in strain CA30 and the nif-45 mutation of strain UW45 are located within this nifB gene. The ORF downstream from nifB predicts an amino acid sequence with a cysteine residue pattern that is characteristic of ferredoxins. No similarities were found between the translation product of the third complete ORF and those of nif genes from other organisms. At the carboxy-terminal end of the predicted translation product of the fourth complete ORF, 30 of 60 amino acid residues were identical with the sequence of the nifQ gene product from K. pneumoniae. The partial ORF located at the end of the fragment encodes the N-terminal part of a potential protein with an unknown function. Northern (RNA) blot analysis indicated that transcripts from the region containing the four complete ORFs were NH4+ repressible and that the transcription products were identical in cells derepressed under conditions of Mo sufficiency or Mo deficiency or in the presence of vanadium. In contrast to the NifB- strain CA30, which is Nif- under all conditions, mutants that carry mutations affecting the C-terminal end of nifB or genes located immediately downstream from nifB, grew under all N2-fixing conditions. However, in the presence of Mo, most of the strains required 1,000 times the amount of molybdate that is sufficient for maximal growth of the wild-type strain CA under N2-fixing conditions. Growth data from strain CA37, which carries a Kanr insertion in nifQ, indicate that nifQ in A. vinelandii is not required for N2 fixation in the presence of V2O5 or under Mo-deficient conditions. Growth studies and acetylene reduction assays performed on two nifEN deletion strains showed that nifE and nifN are required for N2 fixation under Mo sufficiency, as previously observed (K. E. Brigle, M. C. Weiss, W. E. Newton, and D. R. Dean, J. Bacteriol. 169:1547-1553, 1987), but not under conditions of Mo deficiency or in the presence of 50 nM V2O5.

Full text

PDF
1477

Images in this article

1482Image
on p.1482

Selected References

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

  1. Beynon J., Ally A., Cannon M., Cannon F., Jacobson M., Cash V., Dean D. Comparative organization of nitrogen fixation-specific genes from Azotobacter vinelandii and Klebsiella pneumoniae: DNA sequence of the nifUSV genes. J Bacteriol. 1987 Sep;169(9):4024–4029. doi: 10.1128/jb.169.9.4024-4029.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. Bishop P. E., Brill W. J. Genetic analysis of Azotobacter vinelandii mutant strains unable to fix nitrogen. J Bacteriol. 1977 May;130(2):954–956. doi: 10.1128/jb.130.2.954-956.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bishop P. E., Hawkins M. E., Eady R. R. Nitrogen fixation in molybdenum-deficient continuous culture by a strain of Azotobacter vinelandii carrying a deletion of the structural genes for nitrogenase (nifHDK). Biochem J. 1986 Sep 1;238(2):437–442. doi: 10.1042/bj2380437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bishop P. E., Jarlenski D. M., Hetherington D. R. Evidence for an alternative nitrogen fixation system in Azotobacter vinelandii. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7342–7346. doi: 10.1073/pnas.77.12.7342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bishop P. E., Jarlenski D. M., Hetherington D. R. Expression of an alternative nitrogen fixation system in Azotobacter vinelandii. J Bacteriol. 1982 Jun;150(3):1244–1251. doi: 10.1128/jb.150.3.1244-1251.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bishop P. E., Premakumar R., Dean D. R., Jacobson M. R., Chisnell J. R., Rizzo T. M., Kopczynski J. Nitrogen Fixation by Azotobacter vinelandii Strains Having Deletions in Structural Genes for Nitrogenase. Science. 1986 Apr 4;232(4746):92–94. doi: 10.1126/science.232.4746.92. [DOI] [PubMed] [Google Scholar]
  8. Bolivar F. Construction and characterization of new cloning vehicles. III. Derivatives of plasmid pBR322 carrying unique Eco RI sites for selection of Eco RI generated recombinant DNA molecules. Gene. 1978 Oct;4(2):121–136. doi: 10.1016/0378-1119(78)90025-2. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Brigle K. E., Weiss M. C., Newton W. E., Dean D. R. Products of the iron-molybdenum cofactor-specific biosynthetic genes, nifE and nifN, are structurally homologous to the products of the nitrogenase molybdenum-iron protein genes, nifD and nifK. J Bacteriol. 1987 Apr;169(4):1547–1553. doi: 10.1128/jb.169.4.1547-1553.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Buikema W. J., Klingensmith J. A., Gibbons S. L., Ausubel F. M. Conservation of structure and location of Rhizobium meliloti and Klebsiella pneumoniae nifB genes. J Bacteriol. 1987 Mar;169(3):1120–1126. doi: 10.1128/jb.169.3.1120-1126.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Cannon M., Hill S., Kavanaugh E., Cannon F. A molecular genetic study of nif expression in Klebsiella pneumoniae at the level of transcription, translation and nitrogenase activity. Mol Gen Genet. 1985;198(2):198–206. doi: 10.1007/BF00382996. [DOI] [PubMed] [Google Scholar]
  14. Carlomagno M. S., Riccio A., Bruni C. B. Convergently functional, Rho-independent terminator in Salmonella typhimurium. J Bacteriol. 1985 Jul;163(1):362–368. doi: 10.1128/jb.163.1.362-368.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Chisnell J. R., Premakumar R., Bishop P. E. Purification of a second alternative nitrogenase from a nifHDK deletion strain of Azotobacter vinelandii. J Bacteriol. 1988 Jan;170(1):27–33. doi: 10.1128/jb.170.1.27-33.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Conrad B., Mount D. W. Microcomputer programs for DNA sequence analysis. Nucleic Acids Res. 1982 Jan 11;10(1):31–38. doi: 10.1093/nar/10.1.31. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. DE WITT C. W., ROWE J. A. N,O-Diacetylneuraminic acid and N-acetylneuraminic acid in Escherichia coli. Nature. 1959 Aug 1;184(Suppl 6):381–382. doi: 10.1038/184381b0. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Eady R. R., Robson R. L., Richardson T. H., Miller R. W., Hawkins M. The vanadium nitrogenase of Azotobacter chroococcum. Purification and properties of the VFe protein. Biochem J. 1987 May 15;244(1):197–207. doi: 10.1042/bj2440197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Earl C. D., Ronson C. W., Ausubel F. M. Genetic and structural analysis of the Rhizobium meliloti fixA, fixB, fixC, and fixX genes. J Bacteriol. 1987 Mar;169(3):1127–1136. doi: 10.1128/jb.169.3.1127-1136.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Fickett J. W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 1982 Sep 11;10(17):5303–5318. doi: 10.1093/nar/10.17.5303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Fisher R. J., Brill W. J. Mutants of Azotobacter vinelandii unable to fix nitrogen. Biochim Biophys Acta. 1969 Jun 17;184(1):99–105. doi: 10.1016/0304-4165(69)90103-2. [DOI] [PubMed] [Google Scholar]
  25. Frischauf A. M., Lehrach H., Poustka A., Murray N. Lambda replacement vectors carrying polylinker sequences. J Mol Biol. 1983 Nov 15;170(4):827–842. doi: 10.1016/s0022-2836(83)80190-9. [DOI] [PubMed] [Google Scholar]
  26. Graves M. C., Mullenbach G. T., Rabinowitz J. C. Cloning and nucleotide sequence determination of the Clostridium pasteurianum ferredoxin gene. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1653–1657. doi: 10.1073/pnas.82.6.1653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Gribskov M., Devereux J., Burgess R. R. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):539–549. doi: 10.1093/nar/12.1part2.539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Hales B. J., Case E. E., Morningstar J. E., Dzeda M. F., Mauterer L. A. Isolation of a new vanadium-containing nitrogenase from Azotobacter vinelandii. Biochemistry. 1986 Nov 18;25(23):7251–7255. doi: 10.1021/bi00371a001. [DOI] [PubMed] [Google Scholar]
  29. Hales B. J., Langosch D. J., Case E. E. Isolation and characterization of a second nitrogenase Fe-protein from Azotobacter vinelandii. J Biol Chem. 1986 Nov 15;261(32):15301–15306. [PubMed] [Google Scholar]
  30. Holmes D. S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981 Jun;114(1):193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
  31. Holmes W. M., Platt T., Rosenberg M. Termination of transcription in E. coli. Cell. 1983 Apr;32(4):1029–1032. doi: 10.1016/0092-8674(83)90287-8. [DOI] [PubMed] [Google Scholar]
  32. Howard J. B., Lorsbach T. W., Ghosh D., Melis K., Stout C. D. Structure of Azotobacter vinelandii 7Fe ferredoxin. Amino acid sequence and electron density maps of residues. J Biol Chem. 1983 Jan 10;258(1):508–522. [PubMed] [Google Scholar]
  33. Howard K. S., McLean P. A., Hansen F. B., Lemley P. V., Koblan K. S., Orme-Johnson W. H. Klebsiella pneumoniae nifM gene product is required for stabilization and activation of nitrogenase iron protein in Escherichia coli. J Biol Chem. 1986 Jan 15;261(2):772–778. [PubMed] [Google Scholar]
  34. Hu N., Messing J. The making of strand-specific M13 probes. Gene. 1982 Mar;17(3):271–277. doi: 10.1016/0378-1119(82)90143-3. [DOI] [PubMed] [Google Scholar]
  35. Imperial J., Ugalde R. A., Shah V. K., Brill W. J. Mol- mutants of Klebsiella pneumoniae requiring high levels of molybdate for nitrogenase activity. J Bacteriol. 1985 Sep;163(3):1285–1287. doi: 10.1128/jb.163.3.1285-1287.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Imperial J., Ugalde R. A., Shah V. K., Brill W. J. Role of the nifQ gene product in the incorporation of molybdenum into nitrogenase in Klebsiella pneumoniae. J Bacteriol. 1984 Apr;158(1):187–194. doi: 10.1128/jb.158.1.187-194.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Jacobson M. R., Premakumar R., Bishop P. E. Transcriptional regulation of nitrogen fixation by molybdenum in Azotobacter vinelandii. J Bacteriol. 1986 Aug;167(2):480–486. doi: 10.1128/jb.167.2.480-486.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Joerger R. D., Premakumar R., Bishop P. E. Tn5-induced mutants of Azotobacter vinelandii affected in nitrogen fixation under Mo-deficient and Mo-sufficient conditions. J Bacteriol. 1986 Nov;168(2):673–682. doi: 10.1128/jb.168.2.673-682.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Johnston R. E., Mackenzie J. M., Jr, Dougherty W. G. Assembly of overlapping DNA sequences by a program written in BASIC for 64K CP/M and MS-DOS IBM-compatible microcomputers. Nucleic Acids Res. 1986 Jan 10;14(1):517–527. doi: 10.1093/nar/14.1.517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Jorgensen R. A., Rothstein S. J., Reznikoff W. S. A restriction enzyme cleavage map of Tn5 and location of a region encoding neomycin resistance. Mol Gen Genet. 1979;177(1):65–72. doi: 10.1007/BF00267254. [DOI] [PubMed] [Google Scholar]
  41. Krol A. J., Hontelez J. G., Roozendaal B., van Kammen A. On the operon structure of the nitrogenase genes of Rhizobium leguminosarum and Azotobacter vinelandii. Nucleic Acids Res. 1982 Jul 24;10(14):4147–4157. doi: 10.1093/nar/10.14.4147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. LOWRY O. H., ROSEBROUGH N. J., FARR A. L., RANDALL R. J. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951 Nov;193(1):265–275. [PubMed] [Google Scholar]
  43. Mandel M., Higa A. Calcium-dependent bacteriophage DNA infection. J Mol Biol. 1970 Oct 14;53(1):159–162. doi: 10.1016/0022-2836(70)90051-3. [DOI] [PubMed] [Google Scholar]
  44. McMaster G. K., Carmichael G. G. Analysis of single- and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4835–4838. doi: 10.1073/pnas.74.11.4835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. 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]
  46. Mount D. W., Conrad B. Microcomputer programs for graphic analysis of nucleic acid and protein sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):811–817. doi: 10.1093/nar/12.1part2.811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Noti J. D., Folkerts O., Turken A. N., Szalay A. A. Organization and characterization of genes essential for symbiotic nitrogen fixation from Bradyrhizobium japonicum I110. J Bacteriol. 1986 Sep;167(3):774–783. doi: 10.1128/jb.167.3.774-783.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Orme-Johnson W. H. Molecular basis of biological nitrogen fixation. Annu Rev Biophys Biophys Chem. 1985;14:419–459. doi: 10.1146/annurev.bb.14.060185.002223. [DOI] [PubMed] [Google Scholar]
  49. Page W. J., von Tigerstrom M. Optimal conditions for transformation of Azotobacter vinelandii. J Bacteriol. 1979 Sep;139(3):1058–1061. doi: 10.1128/jb.139.3.1058-1061.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Robinson A. C., Burgess B. K., Dean D. R. Activity, reconstitution, and accumulation of nitrogenase components in Azotobacter vinelandii mutant strains containing defined deletions within the nitrogenase structural gene cluster. J Bacteriol. 1986 Apr;166(1):180–186. doi: 10.1128/jb.166.1.180-186.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Robinson A. C., Dean D. R., Burgess B. K. Iron-molybdenum cofactor biosynthesis in Azotobacter vinelandii requires the iron protein of nitrogenase. J Biol Chem. 1987 Oct 15;262(29):14327–14332. [PubMed] [Google Scholar]
  52. Robson R., Woodley P., Jones R. Second gene (nifH*) coding for a nitrogenase iron protein in Azotobacter chroococcum is adjacent to a gene coding for a ferredoxin-like protein. EMBO J. 1986 Jun;5(6):1159–1163. doi: 10.1002/j.1460-2075.1986.tb04341.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. 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]
  54. Shah V. K., Davis I. C., Gordon J. K., Orme-Johnson W. H., Brill W. J. Nitrogenase. 3. Nitrogenaseless mutants of Azotobacter vinelandii: activities, cross-reactions and EPR spectra. Biochim Biophys Acta. 1973 Jan 18;292(1):246–255. doi: 10.1016/0005-2728(73)90269-7. [DOI] [PubMed] [Google Scholar]
  55. Shah V. K., Imperial J., Ugalde R. A., Ludden P. W., Brill W. J. In vitro synthesis of the iron-molybdenum cofactor of nitrogenase. Proc Natl Acad Sci U S A. 1986 Mar;83(6):1636–1640. doi: 10.1073/pnas.83.6.1636. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Tanaka M., Haniu M., Yasunobu K. T., Evans M. C., Rao K. K. Amino acid sequence of ferredoxin from a photosynthetic green bacterium, Chlorobium limicola. Biochemistry. 1974 Jul 2;13(14):2953–2959. doi: 10.1021/bi00711a026. [DOI] [PubMed] [Google Scholar]
  57. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  58. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES