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. 1986 Aug;167(2):639–646. doi: 10.1128/jb.167.2.639-646.1986

crp genes of Shigella flexneri, Salmonella typhimurium, and Escherichia coli.

P Cossart, E A Groisman, M C Serre, M J Casadaban, B Gicquel-Sanzey
PMCID: PMC212937  PMID: 3525518

Abstract

The complete nucleotide sequences of the Salmonella typhimurium LT2 and Shigella flexneri 2B crp genes were determined and compared with those of the Escherichia coli K-12 crp gene. The Shigella flexneri gene was almost like the E. coli crp gene, with only four silent base pair changes. The S. typhimurium and E. coli crp genes presented a higher degree of divergence in their nucleotide sequence with 77 changes, but the corresponding amino acid sequences presented only one amino acid difference. The nucleotide sequences of the crp genes diverged to the same extent as in the other genes, trp, ompA, metJ, and araC, which are structural or regulatory genes. An analysis of the amino acid divergence, however, revealed that the catabolite gene activator protein, the crp gene product, is the most conserved protein observed so far. Comparison of codon usage in S. typhimurium and E. coli for all genes sequenced in both organisms showed that their patterns were similar. Comparison of the regulatory regions of the S. typhimurium and E. coli crp genes showed that the most conserved sequences were those known to be essential for the expression of E. coli crp.

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Selected References

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

  1. Aiba H. Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own gene. Cell. 1983 Jan;32(1):141–149. doi: 10.1016/0092-8674(83)90504-4. [DOI] [PubMed] [Google Scholar]
  2. Aiba H., Fujimoto S., Ozaki N. Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. Nucleic Acids Res. 1982 Feb 25;10(4):1345–1361. doi: 10.1093/nar/10.4.1345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Beck E., Bremer E. Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12. Nucleic Acids Res. 1980 Jul 11;8(13):3011–3027. doi: 10.1093/nar/8.13.3011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Braun G., Cole S. T. The nucleotide sequence coding for major outer membrane protein OmpA of Shigella dysenteriae. Nucleic Acids Res. 1982 Apr 10;10(7):2367–2378. doi: 10.1093/nar/10.7.2367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brenner D. J., Fanning G. R., Johnson K. E., Citarella R. V., Falkow S. Polynucleotide sequence relationships among members of Enterobacteriaceae. J Bacteriol. 1969 May;98(2):637–650. doi: 10.1128/jb.98.2.637-650.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Clarke P., Lin H. C., Wilcox G. The nucleotide sequence of the araC regulatory gene in Salmonella typhimurium LT2. Gene. 1982 May;18(2):157–163. doi: 10.1016/0378-1119(82)90113-5. [DOI] [PubMed] [Google Scholar]
  9. Cossart P., Gicquel-Sanzey B. Cloning and sequence of the crp gene of Escherichia coli K 12. Nucleic Acids Res. 1982 Feb 25;10(4):1363–1378. doi: 10.1093/nar/10.4.1363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cossart P., Gicquel-Sanzey B. Regulation of expression of the crp gene of Escherichia coli K-12: in vivo study. J Bacteriol. 1985 Jan;161(1):454–457. doi: 10.1128/jb.161.1.454-457.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Crawford I. P., Nichols B. P., Yanofsky C. Nucleotide sequence of the trpB gene in Escherichia coli and Salmonella typhimurium. J Mol Biol. 1980 Oct 5;142(4):489–502. doi: 10.1016/0022-2836(80)90259-4. [DOI] [PubMed] [Google Scholar]
  12. Crawford I. P., Stauffer G. V. Regulation of tryptophan biosynthesis. Annu Rev Biochem. 1980;49:163–195. doi: 10.1146/annurev.bi.49.070180.001115. [DOI] [PubMed] [Google Scholar]
  13. Csonka L. N., Howe M. M., Ingraham J. L., Pierson L. S., 3rd, Turnbough C. L., Jr Infection of Salmonella typhimurium with coliphage Mu d1 (Apr lac): construction of pyr::lac gene fusions. J Bacteriol. 1981 Jan;145(1):299–305. doi: 10.1128/jb.145.1.299-305.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Ebright R. H., Cossart P., Gicquel-Sanzey B., Beckwith J. Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7274–7278. doi: 10.1073/pnas.81.23.7274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ebright R. H., Cossart P., Gicquel-Sanzey B., Beckwith J. Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature. 1984 Sep 20;311(5983):232–235. doi: 10.1038/311232a0. [DOI] [PubMed] [Google Scholar]
  16. Farabaugh P. J. Sequence of the lacI gene. Nature. 1978 Aug 24;274(5673):765–769. doi: 10.1038/274765a0. [DOI] [PubMed] [Google Scholar]
  17. Freudl R., Cole S. T. Cloning and molecular characterization of the ompA gene from Salmonella typhimurium. Eur J Biochem. 1983 Aug 15;134(3):497–502. doi: 10.1111/j.1432-1033.1983.tb07594.x. [DOI] [PubMed] [Google Scholar]
  18. Garges S., Adhya S. Sites of allosteric shift in the structure of the cyclic AMP receptor protein. Cell. 1985 Jul;41(3):745–751. doi: 10.1016/s0092-8674(85)80055-6. [DOI] [PubMed] [Google Scholar]
  19. Grantham R., Gautier C., Gouy M., Jacobzone M., Mercier R. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 1981 Jan 10;9(1):r43–r74. doi: 10.1093/nar/9.1.213-b. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Groisman E. A., Castilho B. A., Casadaban M. J. In vivo DNA cloning and adjacent gene fusing with a mini-Mu-lac bacteriophage containing a plasmid replicon. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1480–1483. doi: 10.1073/pnas.81.5.1480. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Horwitz A. H., Heffernan L., Morandi C., Lee J. H., Timko J., Wilcox G. DNA sequence of the araBAD-araC controlling region in Salmonella typhimurium LT2. Gene. 1981 Sep;14(4):309–319. doi: 10.1016/0378-1119(81)90163-3. [DOI] [PubMed] [Google Scholar]
  22. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 1981 Feb 15;146(1):1–21. doi: 10.1016/0022-2836(81)90363-6. [DOI] [PubMed] [Google Scholar]
  23. Konigsberg W., Godson G. N. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Feb;80(3):687–691. doi: 10.1073/pnas.80.3.687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lee N. L., Gielow W. O., Wallace R. G. Mechanism of araC autoregulation and the domains of two overlapping promoters, Pc and PBAD, in the L-arabinose regulatory region of Escherichia coli. Proc Natl Acad Sci U S A. 1981 Feb;78(2):752–756. doi: 10.1073/pnas.78.2.752. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. McKay D. B., Weber I. T., Steitz T. A. Structure of catabolite gene activator protein at 2.9-A resolution. Incorporation of amino acid sequence and interactions with cyclic AMP. J Biol Chem. 1982 Aug 25;257(16):9518–9524. [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. Milkman R., Crawford I. P. Clustered third-base substitutions among wild strains of Escherichia coli. Science. 1983 Jul 22;221(4608):378–380. doi: 10.1126/science.6346486. [DOI] [PubMed] [Google Scholar]
  29. Miyada C. G., Horwitz A. H., Cass L. G., Timko J., Wilcox G. DNA sequence of the araC regulatory gene from Escherichia coli B/r. Nucleic Acids Res. 1980 Nov 25;8(22):5267–5274. doi: 10.1093/nar/8.22.5267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Movva N. R., Nakamura K., Inouye M. Regulatory region of the gene for the ompA protein, a major outer membrane protein of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3845–3849. doi: 10.1073/pnas.77.7.3845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nichols B. P., Miozzari G. F., van Cleemput M., Bennett G. N., Yanofsky C. Nucleotide sequences of the trpG regions of Escherichia coli, Shigella dysenteriae, Salmonella typhimurium and Serratia marcescens. J Mol Biol. 1980 Oct 5;142(4):503–517. doi: 10.1016/0022-2836(80)90260-0. [DOI] [PubMed] [Google Scholar]
  32. Nichols B. P., Yanofsky C. Nucleotide sequences of trpA of Salmonella typhimurium and Escherichia coli: an evolutionary comparison. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5244–5248. doi: 10.1073/pnas.76.10.5244. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ogden S., Haggerty D., Stoner C. M., Kolodrubetz D., Schleif R. The Escherichia coli L-arabinose operon: binding sites of the regulatory proteins and a mechanism of positive and negative regulation. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3346–3350. doi: 10.1073/pnas.77.6.3346. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Postle K., Good R. F. A bidirectional rho-independent transcription terminator between the E. coli tonB gene and an opposing gene. Cell. 1985 Jun;41(2):577–585. doi: 10.1016/s0092-8674(85)80030-1. [DOI] [PubMed] [Google Scholar]
  35. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  36. 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]
  37. Rothman-Denes L. B., Hesse J. E., Epstein W. Role of cyclic adenosine 3',5'-monophosphate in the in vivo expression of the galactose operon of Escherichia coli. J Bacteriol. 1973 Jun;114(3):1040–1044. doi: 10.1128/jb.114.3.1040-1044.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sabourin D., Beckwith J. Deletion of the Escherichia coli crp gene. J Bacteriol. 1975 Apr;122(1):338–340. doi: 10.1128/jb.122.1.338-340.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Saint-Girons I., Duchange N., Cohen G. N., Zakin M. M. Structure and autoregulation of the metJ regulatory gene in Escherichia coli. J Biol Chem. 1984 Nov 25;259(22):14282–14285. [PubMed] [Google Scholar]
  40. 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]
  41. Singleton C. K., Roeder W. D., Bogosian G., Somerville R. L., Weith H. L. DNA sequence of the E. coli trpR gene and prediction of the amino acid sequence of Trp repressor. Nucleic Acids Res. 1980 Apr 11;8(7):1551–1560. doi: 10.1093/nar/8.7.1551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Smiley B. L., Lupski J. R., Svec P. S., McMacken R., Godson G. N. Sequences of the Escherichia coli dnaG primase gene and regulation of its expression. Proc Natl Acad Sci U S A. 1982 Aug;79(15):4550–4554. doi: 10.1073/pnas.79.15.4550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Smith A. A., Greene R. C., Kirby T. W., Hindenach B. R. Isolation and characterization of the product of the methionine-regulatory gene metJ of Escherichia coli K-12. Proc Natl Acad Sci U S A. 1985 Sep;82(18):6104–6108. doi: 10.1073/pnas.82.18.6104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. 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]
  45. Stoner C. M., Schleif R. Is the amino acid but not the nucleotide sequence of the Escherichia coli araC gene conserved? J Mol Biol. 1982 Feb 5;154(4):649–652. doi: 10.1016/s0022-2836(82)80020-x. [DOI] [PubMed] [Google Scholar]
  46. Urbanowski M. L., Stauffer G. V. Nucleotide sequence and biochemical characterization of the metJ gene from Salmonella typhimurium LT2. Nucleic Acids Res. 1985 Feb 11;13(3):673–685. doi: 10.1093/nar/13.3.673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Wallace R. G., Lee N., Fowler A. V. The araC gene of Escherichia coli: transcriptional and translational start-points and complete nucleotide sequence. Gene. 1980 Dec;12(3-4):179–190. doi: 10.1016/0378-1119(80)90100-6. [DOI] [PubMed] [Google Scholar]
  48. Weber I. T., Takio K., Titani K., Steitz T. A. The cAMP-binding domains of the regulatory subunit of cAMP-dependent protein kinase and the catabolite gene activator protein are homologous. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7679–7683. doi: 10.1073/pnas.79.24.7679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Yanofsky C., vanCleemput M. Nucleotide sequence of trpE of Salmonella typhimurium and its homology with the corresponding sequence of Escherichia coli. J Mol Biol. 1982 Mar 5;155(3):235–246. doi: 10.1016/0022-2836(82)90003-1. [DOI] [PubMed] [Google Scholar]

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