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. 1986 Feb;5(2):441–447. doi: 10.1002/j.1460-2075.1986.tb04230.x

Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins.

M Drummond, P Whitty, J Wootton
PMCID: PMC1166750  PMID: 3011408

Abstract

We have determined the nucleotide sequences of two genes from Klebsiella pneumoniae, nifA, the nif-specific activator of transcription and ntrC, the bifunctional regulatory protein involved in 'nitrogen control'. These sequences differ significantly from those previously published. In particular, nifA extends 40 codons beyond the stop codon reported earlier. This extension encodes a putative DNA-binding domain strongly homologous to the Rhizobium meliloti nifA protein and to some extent to the ntrC protein. In all three proteins this domain is linked by a segment of variable length to a strongly conserved central domain of 240 residues. A short segment having the properties of an interdomain linker joins the central region to an N-terminal domain, which is weakly related in the case of the two nifA proteins. This homology is not shared by the N-terminal domain of ntrC, which is clearly but unexpectedly related to the N-terminal domains of a diverse set of procaryotic pleiotropic control proteins, including ompR, dye and nusA from Escherichia coli and spoOA and spoOF from Bacillus subtilis.

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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. Argos P., Siezen R. J. Structural homology of lens crystallins. A method to detect protein structural homology from primary sequences. Eur J Biochem. 1983 Mar 1;131(1):143–148. doi: 10.1111/j.1432-1033.1983.tb07241.x. [DOI] [PubMed] [Google Scholar]
  3. Ausubel F. M., Cannon F. C. Molecular genetic analysis of Klebsiella pneumoniae nitrogen-fixation (nif) genes. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 2):487–499. doi: 10.1101/sqb.1981.045.01.064. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. Dente L., Cesareni G., Cortese R. pEMBL: a new family of single stranded plasmids. Nucleic Acids Res. 1983 Mar 25;11(6):1645–1655. doi: 10.1093/nar/11.6.1645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. Drury L. S., Buxton R. S. DNA sequence analysis of the dye gene of Escherichia coli reveals amino acid homology between the dye and OmpR proteins. J Biol Chem. 1985 Apr 10;260(7):4236–4242. [PubMed] [Google Scholar]
  16. Eisenberg D., Weiss R. M., Terwilliger T. C. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature. 1982 Sep 23;299(5881):371–374. doi: 10.1038/299371a0. [DOI] [PubMed] [Google Scholar]
  17. Espin G., Alvarez-Morales A., Cannon F., Dixon R., Merrick M. Cloning of the glnA, ntrB and ntrC genes of Klebsiella pneumoniae and studies of their role in regulation of the nitrogen fixation (nif) gene cluster. Mol Gen Genet. 1982;186(4):518–524. doi: 10.1007/BF00337959. [DOI] [PubMed] [Google Scholar]
  18. Ferrari F. A., Trach K., LeCoq D., Spence J., Ferrari E., Hoch J. A. Characterization of the spo0A locus and its deduced product. Proc Natl Acad Sci U S A. 1985 May;82(9):2647–2651. doi: 10.1073/pnas.82.9.2647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ferro-Luzzi Ames G., Nikaido K. Nitrogen regulation in Salmonella typhimurium. Identification of an ntrC protein-binding site and definition of a consensus binding sequence. EMBO J. 1985 Feb;4(2):539–547. doi: 10.1002/j.1460-2075.1985.tb03662.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Fitch W. M. Random sequences. J Mol Biol. 1983 Jan 15;163(2):171–176. doi: 10.1016/0022-2836(83)90002-5. [DOI] [PubMed] [Google Scholar]
  21. Friedman D. I., Olson E. R. Evidence that a nucleotide sequence, "boxA," is involved in the action of the NusA protein. Cell. 1983 Aug;34(1):143–149. doi: 10.1016/0092-8674(83)90144-7. [DOI] [PubMed] [Google Scholar]
  22. Gaffney D., Skurray R., Willetts N. Regulation of the F conjugation genes studied by hybridization and tra-lacZ fusion. J Mol Biol. 1983 Jul 25;168(1):103–122. doi: 10.1016/s0022-2836(83)80325-8. [DOI] [PubMed] [Google Scholar]
  23. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  24. Greenblatt J., Li J. Interaction of the sigma factor and the nusA gene protein of E. coli with RNA polymerase in the initiation-termination cycle of transcription. Cell. 1981 May;24(2):421–428. doi: 10.1016/0092-8674(81)90332-9. [DOI] [PubMed] [Google Scholar]
  25. Hall M. N., Silhavy T. J. Genetic analysis of the ompB locus in Escherichia coli K-12. J Mol Biol. 1981 Sep 5;151(1):1–15. doi: 10.1016/0022-2836(81)90218-7. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. 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]
  28. Hoch J. A., Trach K., Kawamura F., Saito H. Identification of the transcriptional suppressor sof-1 as an alteration in the spo0A protein. J Bacteriol. 1985 Feb;161(2):552–555. doi: 10.1128/jb.161.2.552-555.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Hochschild A., Irwin N., Ptashne M. Repressor structure and the mechanism of positive control. Cell. 1983 Feb;32(2):319–325. doi: 10.1016/0092-8674(83)90451-8. [DOI] [PubMed] [Google Scholar]
  30. Ishii S., Ihara M., Maekawa T., Nakamura Y., Uchida H., Imamoto F. The nucleotide sequence of the cloned nusA gene and its flanking region of Escherichia coli. Nucleic Acids Res. 1984 Apr 11;12(7):3333–3342. doi: 10.1093/nar/12.7.3333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kubota Y., Takahashi S., Nishikawa K., Ooi T. Homology in protein sequences expressed by correlation coefficients. J Theor Biol. 1981 Jul 21;91(2):347–361. doi: 10.1016/0022-5193(81)90237-x. [DOI] [PubMed] [Google Scholar]
  32. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
  33. Leonardo J. M., Goldberg R. B. Regulation of nitrogen metabolism in glutamine auxotrophs of Klebsiella pneumoniae. J Bacteriol. 1980 Apr;142(1):99–110. doi: 10.1128/jb.142.1.99-110.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. Mills D. R., Kramer F. R. Structure-independent nucleotide sequence analysis. Proc Natl Acad Sci U S A. 1979 May;76(5):2232–2235. doi: 10.1073/pnas.76.5.2232. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Ollington J. F., Haldenwang W. G., Huynh T. V., Losick R. Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome. J Bacteriol. 1981 Aug;147(2):432–442. doi: 10.1128/jb.147.2.432-442.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  42. Pahel G., Rothstein D. M., Magasanik B. Complex glnA-glnL-glnG operon of Escherichia coli. J Bacteriol. 1982 Apr;150(1):202–213. doi: 10.1128/jb.150.1.202-213.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Reitzer L. J., Magasanik B. Isolation of the nitrogen assimilation regulator NR(I), the product of the glnG gene of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Sep;80(18):5554–5558. doi: 10.1073/pnas.80.18.5554. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Rhaese H. J., Hoch J. A., Groscurth R. Studies on the control of development: isolation of Bacillus subtilis mutants blocked early in sporulation and defective in synthesis of highly phosphorylated nucleotides. Proc Natl Acad Sci U S A. 1977 Mar;74(3):1125–1129. doi: 10.1073/pnas.74.3.1125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Riedel G. E., Ausubel F. M., Cannon F. C. Physical map of chromosomal nitrogen fixation (nif) genes of Klebsiella pneumoniae. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2866–2870. doi: 10.1073/pnas.76.6.2866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Rossmann M. G., Argos P. Protein folding. Annu Rev Biochem. 1981;50:497–532. doi: 10.1146/annurev.bi.50.070181.002433. [DOI] [PubMed] [Google Scholar]
  47. 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]
  48. 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]
  49. Staden R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):505–519. doi: 10.1093/nar/12.1part2.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Stormo G. D., Schneider T. D., Gold L. M. Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 1982 May 11;10(9):2971–2996. doi: 10.1093/nar/10.9.2971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Trach K. A., Chapman J. W., Piggot P. J., Hoch J. A. Deduced product of the stage 0 sporulation gene spo0F shares homology with the Spo0A, OmpR, and SfrA proteins. Proc Natl Acad Sci U S A. 1985 Nov;82(21):7260–7264. doi: 10.1073/pnas.82.21.7260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Ueno-Nishio S., Mango S., Reitzer L. J., Magasanik B. Identification and regulation of the glnL operator-promoter of the complex glnALG operon of Escherichia coli. J Bacteriol. 1984 Oct;160(1):379–384. doi: 10.1128/jb.160.1.379-384.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Wei G. R., Kustu S. Glutamine auxotrophs with mutations in a nitrogen regulatory gene, ntrC, that is near glnA. Mol Gen Genet. 1981;183(2):392–399. doi: 10.1007/BF00270646. [DOI] [PubMed] [Google Scholar]
  54. Wurtzel E. T., Chou M. Y., Inouye M. Osmoregulation of gene expression. I. DNA sequence of the ompR gene of the ompB operon of Escherichia coli and characterization of its gene product. J Biol Chem. 1982 Nov 25;257(22):13685–13691. [PubMed] [Google Scholar]
  55. de Bruijn F. J., Ausubel F. M. The cloning and transposon Tn5 mutagenesis of the glnA region of Klebsiella pneumoniae: identification of glnR, a gene involved in the regulation of the nif and hut operons. Mol Gen Genet. 1981;183(2):289–297. doi: 10.1007/BF00270631. [DOI] [PubMed] [Google Scholar]

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