Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1986 Oct;83(20):7850–7854. doi: 10.1073/pnas.83.20.7850

Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC.

B T Nixon, C W Ronson, F M Ausubel
PMCID: PMC386820  PMID: 3020561

Abstract

We report that the ntrB and ntrC proteins of Bradyrhizobium sp. [Parasponia] strain RP501 share homology with other regulatory proteins. There is extensive conservation of C-terminal regions between products of RP501 ntrB; Klebsiella pneumoniae ntrB; Escherichia coli envZ, cpxA, and phoR; Agrobacterium tumefaciens virA; and, to a lesser extent, E. coli cheA. There is also extensive conservation of N-terminal regions between products of RP501 ntrC; K. pneumoniae ntrC; E. coli ompR, sfrA, phoB, cheY and cheB; Salmonella typhimurium cheB and cheY; Bacillus subtilis spoOA and spoOF; and A. tumefaciens virG. We propose that these regulatory genes comprise two-component regulatory systems that evolved from a common ancestral system that involved transduction of information about the status of the environment by one protein domain (the C-terminal regions conserved among ntrB, envZ, etc.) to a second one (the N-terminal region conserved among ntrC, ompR, etc.). The ntrC-set protein then acts upon a specific responding mechanism, typically as a transcriptional activator but also as an effector of the maturation of outer membrane proteins or as a modulator of the direction of flagella rotation.

Full text

PDF
7850

Images in this article

7852Image
on p.7852
7852Image
on p.7852

Selected References

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

  1. Albin R., Silverman P. M. Identification of the Escherichia coli K-12 cpxA locus as a single gene: construction and analysis of biologically-active cpxA gene fusions. Mol Gen Genet. 1984;197(2):272–279. doi: 10.1007/BF00330973. [DOI] [PubMed] [Google Scholar]
  2. Albin R., Weber R., Silverman P. M. The Cpx proteins of Escherichia coli K12. Immunologic detection of the chromosomal cpxA gene product. J Biol Chem. 1986 Apr 5;261(10):4698–4705. [PubMed] [Google Scholar]
  3. Backman K., Chen Y. M., Magasanik B. Physical and genetic characterization of the glnA--glnG region of the Escherichia coli chromosome. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3743–3747. doi: 10.1073/pnas.78.6.3743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Bollinger J., Park C., Harayama S., Hazelbauer G. L. Structure of the Trg protein: Homologies with and differences from other sensory transducers of Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jun;81(11):3287–3291. doi: 10.1073/pnas.81.11.3287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Boyd A., Kendall K., Simon M. I. Structure of the serine chemoreceptor in Escherichia coli. Nature. 1983 Feb 17;301(5901):623–626. doi: 10.1038/301623a0. [DOI] [PubMed] [Google Scholar]
  7. 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]
  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. Chen Y. M., Backman K., Magasanik B. Characterization of a gene, glnL, the product of which is involved in the regulation of nitrogen utilization in Escherichia coli. J Bacteriol. 1982 Apr;150(1):214–220. doi: 10.1128/jb.150.1.214-220.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Clegg D. O., Koshland D. E., Jr The role of a signaling protein in bacterial sensing: behavioral effects of increased gene expression. Proc Natl Acad Sci U S A. 1984 Aug;81(16):5056–5060. doi: 10.1073/pnas.81.16.5056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Comeau D. E., Ikenaka K., Tsung K. L., Inouye M. Primary characterization of the protein products of the Escherichia coli ompB locus: structure and regulation of synthesis of the OmpR and EnvZ proteins. J Bacteriol. 1985 Nov;164(2):578–584. doi: 10.1128/jb.164.2.578-584.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cuozzo M., Silverman P. M. Characterization of the F plasmid TraJ protein synthesized in F' and Hfr strains of Escherichia coli K-12. J Biol Chem. 1986 Apr 15;261(11):5175–5179. [PubMed] [Google Scholar]
  13. Das A., Stachel S., Ebert P., Allenza P., Montoya A., Nester E. Promoters of Agrobacterium tumefaciens Ti-plasmid virulence genes. Nucleic Acids Res. 1986 Feb 11;14(3):1355–1364. doi: 10.1093/nar/14.3.1355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dayhoff M. O., Barker W. C., Hunt L. T. Establishing homologies in protein sequences. Methods Enzymol. 1983;91:524–545. doi: 10.1016/s0076-6879(83)91049-2. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. 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]
  17. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [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. Hall M. N., Silhavy T. J. The ompB locus and the regulation of the major outer membrane porin proteins of Escherichia coli K12. J Mol Biol. 1981 Feb 15;146(1):23–43. doi: 10.1016/0022-2836(81)90364-8. [DOI] [PubMed] [Google Scholar]
  20. Hall M. N., Silhavy T. J. Transcriptional regulation of Escherichia coli K-12 major outer membrane protein 1b. J Bacteriol. 1979 Nov;140(2):342–350. doi: 10.1128/jb.140.2.342-350.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hayashi H., Koiwai O., Kozuka M. Studies on bacterial chemotaxis. II. Effect of cheB and cheZ mutations on the methylation of methyl-accepting chemotaxis protein of Escherichia coli. J Biochem. 1979 May;85(5):1213–1223. [PubMed] [Google Scholar]
  22. 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]
  23. Hohn B., Collins J. A small cosmid for efficient cloning of large DNA fragments. Gene. 1980 Nov;11(3-4):291–298. doi: 10.1016/0378-1119(80)90069-4. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Inouye S., Nakazawa A., Nakazawa T. Determination of the transcription initiation site and identification of the protein product of the regulatory gene xylR for xyl operons on the TOL plasmid. J Bacteriol. 1985 Sep;163(3):863–869. doi: 10.1128/jb.163.3.863-869.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kehry M. R., Doak T. G., Dahlquist F. W. Stimulus-induced changes in methylesterase activity during chemotaxis in Escherichia coli. J Biol Chem. 1984 Oct 10;259(19):11828–11835. [PubMed] [Google Scholar]
  27. Krikos A., Mutoh N., Boyd A., Simon M. I. Sensory transducers of E. coli are composed of discrete structural and functional domains. Cell. 1983 Jun;33(2):615–622. doi: 10.1016/0092-8674(83)90442-7. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. 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]
  30. Makino K., Shinagawa H., Amemura M., Nakata A. Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12. J Mol Biol. 1986 Jul 5;190(1):37–44. doi: 10.1016/0022-2836(86)90073-2. [DOI] [PubMed] [Google Scholar]
  31. McEwen J., Sambucetti L., Silverman P. M. Synthesis of outer membrane proteins in cpxA cpxB mutants of Escherichia coli K-12. J Bacteriol. 1983 Apr;154(1):375–382. doi: 10.1128/jb.154.1.375-382.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. 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]
  33. Mutoh N., Simon M. I. Nucleotide sequence corresponding to five chemotaxis genes in Escherichia coli. J Bacteriol. 1986 Jan;165(1):161–166. doi: 10.1128/jb.165.1.161-166.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Nara F., Matsuyama S., Mizuno T., Mizushima S. Molecular analysis of mutant ompR genes exhibiting different phenotypes as to osmoregulation of the ompF and ompC genes of Escherichia coli. Mol Gen Genet. 1986 Feb;202(2):194–199. doi: 10.1007/BF00331636. [DOI] [PubMed] [Google Scholar]
  35. Ninfa A. J., Magasanik B. Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5909–5913. doi: 10.1073/pnas.83.16.5909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. 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]
  37. Pahel G., Zelenetz A. D., Tyler B. M. gltB gene and regulation of nitrogen metabolism by glutamine synthetase in Escherichia coli. J Bacteriol. 1978 Jan;133(1):139–148. doi: 10.1128/jb.133.1.139-148.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Parkinson J. S., Parker S. R., Talbert P. B., Houts S. E. Interactions between chemotaxis genes and flagellar genes in Escherichia coli. J Bacteriol. 1983 Jul;155(1):265–274. doi: 10.1128/jb.155.1.265-274.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Poncz M., Solowiejczyk D., Ballantine M., Schwartz E., Surrey S. "Nonrandom" DNA sequence analysis in bacteriophage M13 by the dideoxy chain-termination method. Proc Natl Acad Sci U S A. 1982 Jul;79(14):4298–4302. doi: 10.1073/pnas.79.14.4298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Reitzer L. J., Magasanik B. Expression of glnA in Escherichia coli is regulated at tandem promoters. Proc Natl Acad Sci U S A. 1985 Apr;82(7):1979–1983. doi: 10.1073/pnas.82.7.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Reitzer L. J., Magasanik B. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell. 1986 Jun 20;45(6):785–792. doi: 10.1016/0092-8674(86)90553-2. [DOI] [PubMed] [Google Scholar]
  42. Simms S. A., Keane M. G., Stock J. Multiple forms of the CheB methylesterase in bacterial chemosensing. J Biol Chem. 1985 Aug 25;260(18):10161–10168. [PubMed] [Google Scholar]
  43. Springer M. S., Goy M. F., Adler J. Protein methylation in behavioural control mechanisms and in signal transduction. Nature. 1979 Jul 26;280(5720):279–284. doi: 10.1038/280279a0. [DOI] [PubMed] [Google Scholar]
  44. Stock A., Koshland D. E., Jr, Stock J. Homologies between the Salmonella typhimurium CheY protein and proteins involved in the regulation of chemotaxis, membrane protein synthesis, and sporulation. Proc Natl Acad Sci U S A. 1985 Dec;82(23):7989–7993. doi: 10.1073/pnas.82.23.7989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Stock J. B., Koshland D. E., Jr A protein methylesterase involved in bacterial sensing. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3659–3663. doi: 10.1073/pnas.75.8.3659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. 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]
  47. 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 Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES