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. 1988 Sep;85(18):6602–6606. doi: 10.1073/pnas.85.18.6602

A large family of bacterial activator proteins.

S Henikoff 1, G W Haughn 1, J M Calvo 1, J C Wallace 1
PMCID: PMC282025  PMID: 3413113

Abstract

At least nine different bacterial proteins belong to the LysR family. The gene sequence for one of these proteins is presented here. Six others (Escherichia coli LysR, IlvY, CysB; Salmonella typhimurium MetR; Rhizobium NodD; and Enterobacter cloacae AmpR) are known to activate other genes. Based on sequence alignments, each member of this family is predicted to have a helix-turn-helix DNA binding motif near its amino terminus. The combined evidence indicates that all nine proteins are related by common ancestry, are similarly folded, and are not detectably related to other known bacterial regulatory proteins. The DNA database searching procedure and other methods used in this study should be useful in detecting other groups of related proteins.

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Selected References

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

  1. Amemura M., Makino K., Shinagawa H., Nakata A. Nucleotide sequence of the phoM region of Escherichia coli: four open reading frames may constitute an operon. J Bacteriol. 1986 Oct;168(1):294–302. doi: 10.1128/jb.168.1.294-302.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Appelbaum E. R., Thompson D. V., Idler K., Chartrain N. Rhizobium japonicum USDA 191 has two nodD genes that differ in primary structure and function. J Bacteriol. 1988 Jan;170(1):12–20. doi: 10.1128/jb.170.1.12-20.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Barton G. J., Sternberg M. J. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol. 1987 Nov 20;198(2):327–337. doi: 10.1016/0022-2836(87)90316-0. [DOI] [PubMed] [Google Scholar]
  4. Bielińska A., Hulanicka D. Effect of DNA gyrase inhibitors and urea on the expression of cysB, the regulatory gene of the cysteine regulon. J Gen Microbiol. 1986 Sep;132(9):2571–2576. doi: 10.1099/00221287-132-9-2571. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Dodd I. B., Egan J. B. Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins. J Mol Biol. 1987 Apr 5;194(3):557–564. doi: 10.1016/0022-2836(87)90681-4. [DOI] [PubMed] [Google Scholar]
  7. Downie J. A., Johnston A. W. Nodulation of legumes by Rhizobium: the recognized root? Cell. 1986 Oct 24;47(2):153–154. doi: 10.1016/0092-8674(86)90436-8. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. 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]
  11. Egelhoff T. T., Fisher R. F., Jacobs T. W., Mulligan J. T., Long S. R. Nucleotide sequence of Rhizobium meliloti 1021 nodulation genes: nodD is read divergently from nodABC. DNA. 1985 Jun;4(3):241–248. doi: 10.1089/dna.1985.4.241. [DOI] [PubMed] [Google Scholar]
  12. Feng D. F., Doolittle R. F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987;25(4):351–360. doi: 10.1007/BF02603120. [DOI] [PubMed] [Google Scholar]
  13. Goldberg E. B., Arbel T., Chen J., Karpel R., Mackie G. A., Schuldiner S., Padan E. Characterization of a Na+/H+ antiporter gene of Escherichia coli. Proc Natl Acad Sci U S A. 1987 May;84(9):2615–2619. doi: 10.1073/pnas.84.9.2615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Haughn G. W., Squires C. H., De Felice M., Largo C. T., Calvo J. M. Unusual organization of the ilvIH promoter of Escherichia coli. J Bacteriol. 1985 Jul;163(1):186–198. doi: 10.1128/jb.163.1.186-198.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Haughn G. W., Wessler S. R., Gemmill R. M., Calvo J. M. High A + T content conserved in DNA sequences upstream of leuABCD in Escherichia coli and Salmonella typhimurium. J Bacteriol. 1986 Jun;166(3):1113–1117. doi: 10.1128/jb.166.3.1113-1117.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Heffron F., McCarthy B. J., Ohtsubo H., Ohtsubo E. DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3. Cell. 1979 Dec;18(4):1153–1163. doi: 10.1016/0092-8674(79)90228-9. [DOI] [PubMed] [Google Scholar]
  17. Henikoff S., Wallace J. C. Detection of protein similarities using nucleotide sequence databases. Nucleic Acids Res. 1988 Jul 11;16(13):6191–6204. doi: 10.1093/nar/16.13.6191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Honoré N., Nicolas M. H., Cole S. T. Inducible cephalosporinase production in clinical isolates of Enterobacter cloacae is controlled by a regulatory gene that has been deleted from Escherichia coli. EMBO J. 1986 Dec 20;5(13):3709–3714. doi: 10.1002/j.1460-2075.1986.tb04704.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Horvath B., Bachem C. W., Schell J., Kondorosi A. Host-specific regulation of nodulation genes in Rhizobium is mediated by a plant-signal, interacting with the nodD gene product. EMBO J. 1987 Apr;6(4):841–848. doi: 10.1002/j.1460-2075.1987.tb04829.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kredich N. M. Regulation of L-cysteine biosynthesis in Salmonella typhimurium. I. Effects of growth of varying sulfur sources and O-acetyl-L-serine on gene expression. J Biol Chem. 1971 Jun 10;246(11):3474–3484. [PubMed] [Google Scholar]
  21. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  22. Mackie G. A. Structure of the DNA distal to the gene for ribosomal protein S20 in Escherichia coli K12: presence of a strong terminator and an IS1 element. Nucleic Acids Res. 1986 Sep 11;14(17):6965–6981. doi: 10.1093/nar/14.17.6965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Maizel J. V., Jr, Lenk R. P. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665–7669. doi: 10.1073/pnas.78.12.7665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ostrowski J., Jagura-Burdzy G., Kredich N. M. DNA sequences of the cysB regions of Salmonella typhimurium and Escherichia coli. J Biol Chem. 1987 May 5;262(13):5999–6005. [PubMed] [Google Scholar]
  25. 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]
  26. Patthy L. Detecting homology of distantly related proteins with consensus sequences. J Mol Biol. 1987 Dec 20;198(4):567–577. doi: 10.1016/0022-2836(87)90200-2. [DOI] [PubMed] [Google Scholar]
  27. Plamann L. S., Stauffer G. V. Nucleotide sequence of the Salmonella typhimurium metR gene and the metR-metE control region. J Bacteriol. 1987 Sep;169(9):3932–3937. doi: 10.1128/jb.169.9.3932-3937.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Schachman H. K., Pauza C. D., Navre M., Karels M. J., Wu L., Yang Y. R. Location of amino acid alterations in mutants of aspartate transcarbamoylase: Structural aspects of interallelic complementation. Proc Natl Acad Sci U S A. 1984 Jan;81(1):115–119. doi: 10.1073/pnas.81.1.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Schevitz R. W., Otwinowski Z., Joachimiak A., Lawson C. L., Sigler P. B. The three-dimensional structure of trp repressor. 1985 Oct 31-Nov 6Nature. 317(6040):782–786. doi: 10.1038/317782a0. [DOI] [PubMed] [Google Scholar]
  30. Schofield P. R., Watson J. M. DNA sequence of Rhizobium trifolii nodulation genes reveals a reiterated and potentially regulatory sequence preceding nodABC and nodFE. Nucleic Acids Res. 1986 Apr 11;14(7):2891–2903. doi: 10.1093/nar/14.7.2891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Scott K. F. Conserved nodulation genes from the non-legume symbiont Bradyrhizobium sp. (Parasponia). Nucleic Acids Res. 1986 Apr 11;14(7):2905–2919. doi: 10.1093/nar/14.7.2905. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Shearman C. A., Rossen L., Johnston A. W., Downie J. A. The Rhizobium leguminosarum nodulation gene nodF encodes a polypeptide similar to acyl-carrier protein and is regulated by nodD plus a factor in pea root exudate. EMBO J. 1986 Apr;5(4):647–652. doi: 10.1002/j.1460-2075.1986.tb04262.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Stokes H. W., Hall B. G. Sequence of the ebgR gene of Escherichia coli: evidence that the EBG and LAC operons are descended from a common ancestor. Mol Biol Evol. 1985 Nov;2(6):478–483. doi: 10.1093/oxfordjournals.molbev.a040373. [DOI] [PubMed] [Google Scholar]
  34. 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]
  35. Stragier P., Patte J. C. Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. III. Nucleotide sequence and regulation of the lysR gene. J Mol Biol. 1983 Aug 5;168(2):333–350. doi: 10.1016/s0022-2836(83)80022-9. [DOI] [PubMed] [Google Scholar]
  36. Streber W. R., Timmis K. N., Zenk M. H. Analysis, cloning, and high-level expression of 2,4-dichlorophenoxyacetate monooxygenase gene tfdA of Alcaligenes eutrophus JMP134. J Bacteriol. 1987 Jul;169(7):2950–2955. doi: 10.1128/jb.169.7.2950-2955.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Urbanowski M. L., Stauffer G. V. Regulation of the metR gene of Salmonella typhimurium. J Bacteriol. 1987 Dec;169(12):5841–5844. doi: 10.1128/jb.169.12.5841-5844.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Valentin-Hansen P., Larsen J. E., Højrup P., Short S. A., Barbier C. S. Nucleotide sequence of the CytR regulatory gene of E. coli K-12. Nucleic Acids Res. 1986 Mar 11;14(5):2215–2228. doi: 10.1093/nar/14.5.2215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Wek R. C., Hatfield G. W. Nucleotide sequence and in vivo expression of the ilvY and ilvC genes in Escherichia coli K12. Transcription from divergent overlapping promoters. J Biol Chem. 1986 Feb 15;261(5):2441–2450. [PubMed] [Google Scholar]
  40. Welinder K. G. Covalent structure of the glycoprotein horseradish peroxidase (EC 1.11.1.7). FEBS Lett. 1976 Dec 15;72(1):19–23. doi: 10.1016/0014-5793(76)80804-6. [DOI] [PubMed] [Google Scholar]
  41. Winans S. C., Ebert P. R., Stachel S. E., Gordon M. P., Nester E. W. A gene essential for Agrobacterium virulence is homologous to a family of positive regulatory loci. Proc Natl Acad Sci U S A. 1986 Nov;83(21):8278–8282. doi: 10.1073/pnas.83.21.8278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Wu J., Anderton-Loviny T., Smith C. A., Hartley B. S. Structure of wild-type and mutant repressors and of the control region of the rbt operon of Klebsiella aerogenes. EMBO J. 1985 May;4(5):1339–1344. doi: 10.1002/j.1460-2075.1985.tb03782.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. 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]

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