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. 1984 Mar 26;12(6):2605–2618. doi: 10.1093/nar/12.6.2605

Conserved features of coordinately regulated E. coli promoters.

A A Travers
PMCID: PMC318693  PMID: 6369249

Abstract

E. coli promoters which are coordinately regulated in response to amino acid limitation contain conserved nucleotide sequences immediately 3' to -10 region. These sequences contain predominantly either GC or AT residues depending on whether the response is respectively negative or positive. Certain classes of promoters also contain conserved sequences upstream of the primary promoter. In tRNA genes these sequences could act as a secondary polymerase binding site.

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Selected References

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  1. Bencini D. A., Houghton J. E., Hoover T. A., Foltermann K. F., Wild J. R., O'Donovan G. A. The DNA sequence of argI from Escherichia coli K12. Nucleic Acids Res. 1983 Dec 10;11(23):8509–8518. doi: 10.1093/nar/11.23.8509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Berman M. L., Beckwith J. Fusions of the lac operon to the transfer RNA gene tyrT of Escherichia coli. J Mol Biol. 1979 May 25;130(3):285–301. doi: 10.1016/0022-2836(79)90542-4. [DOI] [PubMed] [Google Scholar]
  3. Bossi L. The hisR locus of Salmonella: nucleotide sequence and expression. Mol Gen Genet. 1983;192(1-2):163–170. doi: 10.1007/BF00327662. [DOI] [PubMed] [Google Scholar]
  4. Brückner R., Matzura H. In vivo synthesis of a polycistronic messenger RNA for the ribosomal proteins L11, L1, L10 and L7/12 in Escherichia coli. Mol Gen Genet. 1981;183(2):277–282. doi: 10.1007/BF00270629. [DOI] [PubMed] [Google Scholar]
  5. Burton Z. F., Gross C. A., Watanabe K. K., Burgess R. R. The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12. Cell. 1983 Feb;32(2):335–349. doi: 10.1016/0092-8674(83)90453-1. [DOI] [PubMed] [Google Scholar]
  6. Byström A. S., Hjalmarsson K. J., Wikström P. M., Björk G. R. The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide. EMBO J. 1983;2(6):899–905. doi: 10.1002/j.1460-2075.1983.tb01519.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cassan M., Ronceray J., Patte J. C. Nucleotide sequence of the promoter region of the E. coli lysC gene. Nucleic Acids Res. 1983 Sep 24;11(18):6157–6166. doi: 10.1093/nar/11.18.6157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Csordás-Tóth E., Boros I., Venetianer P. Structure of the promoter region for the rrnB gene in Escherichia coli. Nucleic Acids Res. 1979 Dec 20;7(8):2189–2197. doi: 10.1093/nar/7.8.2189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cunin R., Eckhardt T., Piette J., Boyen A., Piérard A., Glansdorff N. Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12. Nucleic Acids Res. 1983 Aug 11;11(15):5007–5019. doi: 10.1093/nar/11.15.5007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dennis P. P., Nomura M. Stringent control of the transcriptional activities of ribosomal protein genes in E. coli. Nature. 1975 Jun 5;255(5508):460–465. doi: 10.1038/255460a0. [DOI] [PubMed] [Google Scholar]
  11. Duchange N., Zakin M. M., Ferrara P., Saint-Girons I., Park I., Tran S. V., Py M. C., Cohen G. N. Structure of the metJBLF cluster in Escherichia coli K12. Sequence of the metB structural gene and of the 5'- and 3'-flanking regions of the metBL operon. J Biol Chem. 1983 Dec 25;258(24):14868–14871. [PubMed] [Google Scholar]
  12. Duester G., Elford R. M., Holmes W. M. Fusion of the Escherichia coli tRNALeu1 promoter to the galK gene: analysis of sequences necessary for growth-rate-dependent regulation. Cell. 1982 Oct;30(3):855–864. doi: 10.1016/0092-8674(82)90290-2. [DOI] [PubMed] [Google Scholar]
  13. Gallant J. A. Stringent control in E. coli. Annu Rev Genet. 1979;13:393–415. doi: 10.1146/annurev.ge.13.120179.002141. [DOI] [PubMed] [Google Scholar]
  14. Gourse R. L., Stark M. J., Dahlberg A. E. Regions of DNA involved in the stringent control of plasmid-encoded rRNA in vivo. Cell. 1983 Apr;32(4):1347–1354. doi: 10.1016/0092-8674(83)90315-x. [DOI] [PubMed] [Google Scholar]
  15. Hansen F. G., Hansen E. B., Atlung T. The nucleotide sequence of the dnaA gene promoter and of the adjacent rpmH gene, coding for the ribosomal protein L34, of Escherichia coli. EMBO J. 1982;1(9):1043–1048. doi: 10.1002/j.1460-2075.1982.tb01294.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Haziza C., Stragier P., Patte J. C. Nucleotide sequence of the asd gene of Escherichia coli: absence of a typical attenuation signal. EMBO J. 1982;1(3):379–384. doi: 10.1002/j.1460-2075.1982.tb01178.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hirota Y., Mordoh J., Jacob F. On the process of cellular division in Escherichia coli. 3. Thermosensitive mutants of Escherichia coli altered in the process of DNA initiation. J Mol Biol. 1970 Nov 14;53(3):369–387. doi: 10.1016/0022-2836(70)90072-0. [DOI] [PubMed] [Google Scholar]
  19. Ishii S., Kuroki K., Imamoto F. tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jan;81(2):409–413. doi: 10.1073/pnas.81.2.409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lamond A. I., Travers A. A. Requirement for an upstream element for optimal transcription of a bacterial tRNA gene. Nature. 1983 Sep 15;305(5931):248–250. doi: 10.1038/305248a0. [DOI] [PubMed] [Google Scholar]
  21. Little R., Ryals J., Bremer H. Physiological characterization of Escherichia coli rpoB mutants with abnormal control of ribosome synthesis. J Bacteriol. 1983 Sep;155(3):1162–1170. doi: 10.1128/jb.155.3.1162-1170.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Little R., Ryals J., Bremer H. rpoB mutation in Escherichia coli alters control of ribosome synthesis by guanosine tetraphosphate. J Bacteriol. 1983 May;154(2):787–792. doi: 10.1128/jb.154.2.787-792.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. MAALOE O., HANAWALT P. C. Thymine deficiency and the normal DNA replication cycle. I. J Mol Biol. 1961 Apr;3:144–155. doi: 10.1016/s0022-2836(61)80041-7. [DOI] [PubMed] [Google Scholar]
  24. Maher D. L., Dennis P. P. In vivo transcription of E. coli genes coding for rRNA, ribosomal proteins and subunits of RNA polymerase: influence of the stringent control system. Mol Gen Genet. 1977 Oct 20;155(2):203–211. doi: 10.1007/BF00393161. [DOI] [PubMed] [Google Scholar]
  25. Mayaux J. F., Fayat G., Fromant M., Springer M., Grunberg-Manago M., Blanquet S. Structural and transcriptional evidence for related thrS and infC expression. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6152–6156. doi: 10.1073/pnas.80.20.6152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Miura A., Krueger J. H., Itoh S., de Boer H. A., Nomura M. Growth-rate-dependent regulation of ribosome synthesis in E. coli: expression of the lacZ and galK genes fused to ribosomal promoters. Cell. 1981 Sep;25(3):773–782. doi: 10.1016/0092-8674(81)90185-9. [DOI] [PubMed] [Google Scholar]
  27. Nene V., Glass R. E. Relaxed mutants of Escherichia coli RNA polymerase. FEBS Lett. 1983 Mar 21;153(2):307–310. doi: 10.1016/0014-5793(83)80630-9. [DOI] [PubMed] [Google Scholar]
  28. Ogasawara N., Moriya S., Yoshikawa H. Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome. Nucleic Acids Res. 1983 Sep 24;11(18):6301–6318. doi: 10.1093/nar/11.18.6301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Oppenheim D. S., Bennett G. N., Yanofsky C. Escherichia coli RNA polymerase and trp repressor interaction with the promoter-operator region of the tryptophan operon of Salmonella typhimurium. J Mol Biol. 1980 Dec 5;144(2):133–142. doi: 10.1016/0022-2836(80)90029-7. [DOI] [PubMed] [Google Scholar]
  30. Sarmientos P., Cashel M. Carbon starvation and growth rate-dependent regulation of the Escherichia coli ribosomal RNA promoters: differential control of dual promoters. Proc Natl Acad Sci U S A. 1983 Nov;80(22):7010–7013. doi: 10.1073/pnas.80.22.7010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sarmientos P., Sylvester J. E., Contente S., Cashel M. Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids. Cell. 1983 Apr;32(4):1337–1346. doi: 10.1016/0092-8674(83)90314-8. [DOI] [PubMed] [Google Scholar]
  32. Schwartz I., Klotsky R. A., Elseviers D., Gallagher P. J., Krauskopf M., Siddiqui M. A., Wong J. F., Roe B. A. Molecular cloning and sequencing of pheU, a gene for Escherichia coli tRNAPhe. Nucleic Acids Res. 1983 Jul 11;11(13):4379–4389. doi: 10.1093/nar/11.13.4379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Stewart G. C., Bott K. F. DNA sequence of the tandem ribosomal RNA promoter for B. subtilis operon rrnB. Nucleic Acids Res. 1983 Sep 24;11(18):6289–6300. doi: 10.1093/nar/11.18.6289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Stewart G. C., Wilson F. E., Bott K. F. Detailed physical mapping of the ribosomal RNA genes of Bacillus subtilis. Gene. 1982 Sep;19(2):153–162. doi: 10.1016/0378-1119(82)90001-4. [DOI] [PubMed] [Google Scholar]
  35. Travers A. A. A tRNATyr promoter with an altered in vitro response to ppgpp. J Mol Biol. 1980 Jul 25;141(1):91–97. doi: 10.1016/s0022-2836(80)80030-1. [DOI] [PubMed] [Google Scholar]
  36. Travers A. A., Lamond A. I., Mace H. A., Berman M. L. RNA polymerase interactions with the upstream region of the E. coli tyrT promoter. Cell. 1983 Nov;35(1):265–273. doi: 10.1016/0092-8674(83)90229-5. [DOI] [PubMed] [Google Scholar]
  37. Travers A. A. Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J Bacteriol. 1980 Feb;141(2):973–976. doi: 10.1128/jb.141.2.973-976.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Zurawski G., Gunsalus R. P., Brown K. D., Yanofsky C. Structure and regulation of aroH, the structural gene for the tryptophan-repressible 3-deoxy-D-arabino-heptulosonic acid-7-phosphate synthetase of Escherichia coli. J Mol Biol. 1981 Jan 5;145(1):47–73. doi: 10.1016/0022-2836(81)90334-x. [DOI] [PubMed] [Google Scholar]
  39. de Boer H. A., Gilbert S. F., Nomura M. DNA sequences of promoter regions for rRNA operons rrnE and rrnA in E. coli. Cell. 1979 May;17(1):201–209. doi: 10.1016/0092-8674(79)90308-8. [DOI] [PubMed] [Google Scholar]

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