Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Mar 11;15(5):2343–2361. doi: 10.1093/nar/15.5.2343

Analysis of E. coli promoter sequences.

C B Harley, R P Reynolds
PMCID: PMC340638  PMID: 3550697

Abstract

We have compiled and analyzed 263 promoters with known transcriptional start points for E. coli genes. Promoter elements (-35 hexamer, -10 hexamer, and spacing between these regions) were aligned by a program which selects the arrangement consistent with the start point and statistically most homologous to a reference list of promoters. The initial reference list was that of Hawley and McClure (Nucl. Acids Res. 11, 2237-2255, 1983). Alignment of the complete list was used for reference until successive analyses did not alter the structure of the list. In the final compilation, all bases in the -35 (TTGACA) and -10 (TATAAT) hexamers were highly conserved, 92% of promoters had inter-region spacing of 17 +/- 1 bp, and 75% of the uniquely defined start points initiated 7 +/- 1 bases downstream of the -10 region. The consensus sequence of promoters with inter-region spacing of 16, 17 or 18 bp did not differ. This compilation and analysis should be useful for studies of promoter structure and function and for programs which identify potential promoter sequences.

Full text

PDF
2343

Selected References

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

  1. Adachi T., Mizuuchi K., Menzel R., Gellert M. DNA sequence and transcription of the region upstream of the E. coli gyrB gene. Nucleic Acids Res. 1984 Aug 24;12(16):6389–6395. doi: 10.1093/nar/12.16.6389. [DOI] [PMC free article] [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. Aiba H., Kawamukai M., Ishihama A. Cloning and promoter analysis of the Escherichia coli adenylate cyclase gene. Nucleic Acids Res. 1983 Jun 11;11(11):3451–3465. doi: 10.1093/nar/11.11.3451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Aoyama T., Takanami M. Essential structure of E. coli promoter II. Effect of the sequences around the RNA start point on promoter function. Nucleic Acids Res. 1985 Jun 11;13(11):4085–4096. doi: 10.1093/nar/13.11.4085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Aoyama T., Takanami M., Ohtsuka E., Taniyama Y., Marumoto R., Sato H., Ikehara M. Essential structure of E. coli promoter: effect of spacer length between the two consensus sequences on promoter function. Nucleic Acids Res. 1983 Sep 10;11(17):5855–5864. doi: 10.1093/nar/11.17.5855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  7. Bertrand K. P., Postle K., Wray L. V., Jr, Reznikoff W. S. Overlapping divergent promoters control expression of Tn10 tetracycline resistance. Gene. 1983 Aug;23(2):149–156. doi: 10.1016/0378-1119(83)90046-x. [DOI] [PubMed] [Google Scholar]
  8. Bindereif A., Neilands J. B. Promoter mapping and transcriptional regulation of the iron assimilation system of plasmid ColV-K30 in Escherichia coli K-12. J Bacteriol. 1985 Jun;162(3):1039–1046. doi: 10.1128/jb.162.3.1039-1046.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Boros I., Csordás-Tóth E., Kiss A., Kiss I., Török I., Udvardy A., Udvardy K., Venetianer P. Identification of two new promoters probably involved in the transcription of a ribosomal RNA gene of Escherichia coli. Biochim Biophys Acta. 1983 Mar 10;739(2):173–180. doi: 10.1016/0167-4781(83)90027-1. [DOI] [PubMed] [Google Scholar]
  10. Brosius J., Erfle M., Storella J. Spacing of the -10 and -35 regions in the tac promoter. Effect on its in vivo activity. J Biol Chem. 1985 Mar 25;260(6):3539–3541. [PubMed] [Google Scholar]
  11. Busby S., Truelle N., Spassky A., Dreyfus M., Buc H. The selection and characterisation of two novel mutations in the overlapping promoters of the Escherichia coli galactose operon. Gene. 1984 May;28(2):201–209. doi: 10.1016/0378-1119(84)90257-9. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Chan P. T., Lebowitz J., Bastia D. Nucleotide sequence determination of a strong promoter of the colicin E 1 plasmid. Analysis of restriction sites protected by RNA polymerase interactions before and after limited transcription. Nucleic Acids Res. 1979 Nov 10;7(5):1247–1262. doi: 10.1093/nar/7.5.1247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Chan P. T., Lebowitz J. The coupled use of 'footprinting' and exonuclease III methodology for RNA polymerase binding and initiation. Application for the analysis of three tandem promoters at the control region of colicin El. Nucleic Acids Res. 1983 Feb 25;11(4):1099–1116. doi: 10.1093/nar/11.4.1099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Chase J. W., Merrill B. M., Williams K. R. F sex factor encodes a single-stranded DNA binding protein (SSB) with extensive sequence homology to Escherichia coli SSB. Proc Natl Acad Sci U S A. 1983 Sep;80(18):5480–5484. doi: 10.1073/pnas.80.18.5480. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Chen S. T., Clowes R. C. Two improved promoter sequences for the beta-lactamase expression arising from a single base-pair substitution. Nucleic Acids Res. 1984 Apr 11;12(7):3219–3234. doi: 10.1093/nar/12.7.3219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Churchward G., Linder P., Caro L. The nucleotide sequence of replication and maintenance functions encoded by plasmid pSC101. Nucleic Acids Res. 1983 Aug 25;11(16):5645–5659. doi: 10.1093/nar/11.16.5645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Cowing D. W., Bardwell J. C., Craig E. A., Woolford C., Hendrix R. W., Gross C. A. Consensus sequence for Escherichia coli heat shock gene promoters. Proc Natl Acad Sci U S A. 1985 May;82(9):2679–2683. doi: 10.1073/pnas.82.9.2679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. 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]
  21. Daldal F. Molecular cloning of the gene for phosphofructokinase-2 of Escherichia coli and the nature of a mutation, pfkB1, causing a high level of the enzyme. J Mol Biol. 1983 Aug 5;168(2):285–305. doi: 10.1016/s0022-2836(83)80019-9. [DOI] [PubMed] [Google Scholar]
  22. Daldal F. Nucleotide sequence of gene pfkB encoding the minor phosphofructokinase of Escherichia coli K-12. Gene. 1984 Jun;28(3):337–342. doi: 10.1016/0378-1119(84)90151-3. [DOI] [PubMed] [Google Scholar]
  23. Dean G. E., Macnab R. M., Stader J., Matsumura P., Burks C. Gene sequence and predicted amino acid sequence of the motA protein, a membrane-associated protein required for flagellar rotation in Escherichia coli. J Bacteriol. 1984 Sep;159(3):991–999. doi: 10.1128/jb.159.3.991-999.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Demple B., Sedgwick B., Robins P., Totty N., Waterfield M. D., Lindahl T. Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis. Proc Natl Acad Sci U S A. 1985 May;82(9):2688–2692. doi: 10.1073/pnas.82.9.2688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Deuschle U., Kammerer W., Gentz R., Bujard H. Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J. 1986 Nov;5(11):2987–2994. doi: 10.1002/j.1460-2075.1986.tb04596.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Easton A. M., Kushner S. R. Transcription of the uvrD gene of Escherichia coli is controlled by the lexA repressor and by attenuation. Nucleic Acids Res. 1983 Dec 20;11(24):8625–8640. doi: 10.1093/nar/11.24.8625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Eisenbeis S. J., Parker J. The nucleotide sequence of the promoter region of hisS, the structural gene for histidyl-tRNA synthetase. Gene. 1982 May;18(2):107–114. doi: 10.1016/0378-1119(82)90108-1. [DOI] [PubMed] [Google Scholar]
  29. Fowler T., Taylor L., Thompson R. The control region of the F plasmid transfer operon: DNA sequence of the traJ and traY genes and characterisation of the traY leads to Z promoter. Gene. 1983 Dec;26(1):79–89. doi: 10.1016/0378-1119(83)90038-0. [DOI] [PubMed] [Google Scholar]
  30. Freedman R., Gibson B., Donovan D., Biemann K., Eisenbeis S., Parker J., Schimmel P. Primary structure of histidine-tRNA synthetase and characterization of hisS transcripts. J Biol Chem. 1985 Aug 25;260(18):10063–10068. [PubMed] [Google Scholar]
  31. Gay N. J., Tybulewicz V. L., Walker J. E. Insertion of transposon Tn7 into the Escherichia coli glmS transcriptional terminator. Biochem J. 1986 Feb 15;234(1):111–117. doi: 10.1042/bj2340111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Goosen N., van Heuvel M., Moolenaar G. F., van de Putte P. Regulation of Mu transposition. II. The escherichia coli HimD protein positively controls two repressor promoters and the early promoter of bacteriophage Mu. Gene. 1984 Dec;32(3):419–426. doi: 10.1016/0378-1119(84)90017-9. [DOI] [PubMed] [Google Scholar]
  33. Gragerov A. I., Smirnov OYu, Mekhedov S. L., Nikiforov V. G., Chuvpilo S. A., Korobko V. G. DNA rearrangements generating artificial promoters. FEBS Lett. 1984 Jun 25;172(1):64–66. doi: 10.1016/0014-5793(84)80874-1. [DOI] [PubMed] [Google Scholar]
  34. Grindley J. N., Nakada D. The nucleotide sequence of the replication origin of plasmid NTP1. Nucleic Acids Res. 1981 Sep 11;9(17):4355–4366. doi: 10.1093/nar/9.17.4355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Grisolia V., Riccio A., Bruni C. B. Structure and function of the internal promoter (hisBp) of the Escherichia coli K-12 histidine operon. J Bacteriol. 1983 Sep;155(3):1288–1296. doi: 10.1128/jb.155.3.1288-1296.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Gutierrez C., Raibaud O. Point mutations that reduce the expression of malPQ, a positively controlled operon of Escherichia coli. J Mol Biol. 1984 Jul 25;177(1):69–86. doi: 10.1016/0022-2836(84)90058-5. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Harr R., Häggström M., Gustafsson P. Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res. 1983 May 11;11(9):2943–2957. doi: 10.1093/nar/11.9.2943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. 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]
  40. 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]
  41. Horwitz A. H., Miyada C. G., Wilcox G. Functional limits of the araIc promoter suggest an additional regulatory site for araBAD expression. J Bacteriol. 1984 Apr;158(1):141–147. doi: 10.1128/jb.158.1.141-147.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Hsu L. M., Zagorski J., Fournier M. J. Cloning and sequence analysis of the Escherichia coli 4.5 S RNA gene. J Mol Biol. 1984 Sep 25;178(3):509–531. doi: 10.1016/0022-2836(84)90236-5. [DOI] [PubMed] [Google Scholar]
  43. Hudson G. S., Davidson B. E. Nucleotide sequence and transcription of the phenylalanine and tyrosine operons of Escherichia coli K12. J Mol Biol. 1984 Dec 25;180(4):1023–1051. doi: 10.1016/0022-2836(84)90269-9. [DOI] [PubMed] [Google Scholar]
  44. Hull E. P., Spencer M. E., Wood D., Guest J. R. Nucleotide sequence of the promoter region of the citrate synthase gene (gltA) of Escherichia coli. FEBS Lett. 1983 Jun 13;156(2):366–370. doi: 10.1016/0014-5793(83)80530-4. [DOI] [PubMed] [Google Scholar]
  45. Inokuchi K., Furukawa H., Nakamura K., Mizushima S. Characterization by deletion mutagenesis in vitro of the promoter region of ompF, a positively regulated gene of Escherichia coli. J Mol Biol. 1984 Sep 25;178(3):653–668. doi: 10.1016/0022-2836(84)90243-2. [DOI] [PubMed] [Google Scholar]
  46. Inouye S., Inouye M. Up-promoter mutations in the lpp gene of Escherichia coli. Nucleic Acids Res. 1985 May 10;13(9):3101–3110. doi: 10.1093/nar/13.9.3101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Ishiguro N., Sato G. Nucleotide sequence of the gene determining plasmid-mediated citrate utilization. J Bacteriol. 1985 Dec;164(3):977–982. doi: 10.1128/jb.164.3.977-982.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. 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]
  49. 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]
  50. Izui K., Miwa T., Kajitani M., Fujita N., Sabe H., Ishihama A., Katsuki H. Promoter analysis of the phosphoenolpyruvate carboxylase gene of Escherichia coli. Nucleic Acids Res. 1985 Jan 11;13(1):59–71. doi: 10.1093/nar/13.1.59. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Jones H. M., Brajkovich C. M., Gunsalus R. P. In vivo 5' terminus and length of the mRNA for the proton-translocating ATPase (unc) operon of Escherichia coli. J Bacteriol. 1983 Sep;155(3):1279–1287. doi: 10.1128/jb.155.3.1279-1287.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Jones H. M., Gunsalus R. P. Transcription of the Escherichia coli fumarate reductase genes (frdABCD) and their coordinate regulation by oxygen, nitrate, and fumarate. J Bacteriol. 1985 Dec;164(3):1100–1109. doi: 10.1128/jb.164.3.1100-1109.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Kamio Y., Lin C. K., Regue M., Wu H. C. Characterization of the ileS-lsp operon in Escherichia coli. Identification of an open reading frame upstream of the ileS gene and potential promoter(s) for the ileS-lsp operon. J Biol Chem. 1985 May 10;260(9):5616–5620. [PubMed] [Google Scholar]
  54. Kammerer W., Deuschle U., Gentz R., Bujard H. Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. EMBO J. 1986 Nov;5(11):2995–3000. doi: 10.1002/j.1460-2075.1986.tb04597.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Landick R., Vaughn V., Lau E. T., VanBogelen R. A., Erickson J. W., Neidhardt F. C. Nucleotide sequence of the heat shock regulatory gene of E. coli suggests its protein product may be a transcription factor. Cell. 1984 Aug;38(1):175–182. doi: 10.1016/0092-8674(84)90538-5. [DOI] [PubMed] [Google Scholar]
  56. Larsen J. N., Jensen K. F. Nucleotide sequence of the pyrD gene of Escherichia coli and characterization of the flavoprotein dihydroorotate dehydrogenase. Eur J Biochem. 1985 Aug 15;151(1):59–65. doi: 10.1111/j.1432-1033.1985.tb09068.x. [DOI] [PubMed] [Google Scholar]
  57. Linder P., Churchward G., Caro L. Plasmid pSC101 replication mutants generated by insertion of the transposon Tn1000. J Mol Biol. 1983 Oct 25;170(2):287–303. doi: 10.1016/s0022-2836(83)80149-1. [DOI] [PubMed] [Google Scholar]
  58. Lund P. A., Ford S. J., Brown N. L. Transcriptional regulation of the mercury-resistance genes of transposon Tn501. J Gen Microbiol. 1986 Feb;132(2):465–480. doi: 10.1099/00221287-132-2-465. [DOI] [PubMed] [Google Scholar]
  59. Machida C., Machida Y., Ohtsubo E. Both inverted repeat sequences located at the ends of IS1 provide promoter functions. J Mol Biol. 1984 Aug 5;177(2):247–267. doi: 10.1016/0022-2836(84)90455-8. [DOI] [PubMed] [Google Scholar]
  60. Maki H., Horiuchi T., Sekiguchi M. Structure and expression of the dnaQ mutator and the RNase H genes of Escherichia coli: overlap of the promoter regions. Proc Natl Acad Sci U S A. 1983 Dec;80(23):7137–7141. doi: 10.1073/pnas.80.23.7137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Mandecki W., Reznikoff W. S. A lac promoter with a changed distance between -10 and -35 regions. Nucleic Acids Res. 1982 Feb 11;10(3):903–912. doi: 10.1093/nar/10.3.903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. March P. E., Inouye M. Characterization of the lep operon of Escherichia coli. Identification of the promoter and the gene upstream of the signal peptidase I gene. J Biol Chem. 1985 Jun 25;260(12):7206–7213. [PubMed] [Google Scholar]
  63. Matsuyama S., Mizushima S. Construction and characterization of a deletion mutant lacking micF, a proposed regulatory gene for OmpF synthesis in Escherichia coli. J Bacteriol. 1985 Jun;162(3):1196–1202. doi: 10.1128/jb.162.3.1196-1202.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. McClure W. R. Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem. 1985;54:171–204. doi: 10.1146/annurev.bi.54.070185.001131. [DOI] [PubMed] [Google Scholar]
  65. Michaeli S., Mevarech M., Ron E. Z. Regulatory region of the metA gene of Escherichia coli K-12. J Bacteriol. 1984 Dec;160(3):1158–1162. doi: 10.1128/jb.160.3.1158-1162.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Miles J. S., Guest J. R. Complete nucleotide sequence of the fumarase gene fumA, of Escherichia coli. Nucleic Acids Res. 1984 Apr 25;12(8):3631–3642. doi: 10.1093/nar/12.8.3631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Miles J. S., Guest J. R. Nucleotide sequence and transcriptional start point of the phosphomannose isomerase gene (manA) of Escherichia coli. Gene. 1984 Dec;32(1-2):41–48. doi: 10.1016/0378-1119(84)90030-1. [DOI] [PubMed] [Google Scholar]
  68. Misra T. K., Brown N. L., Fritzinger D. C., Pridmore R. D., Barnes W. M., Haberstroh L., Silver S. Mercuric ion-resistance operons of plasmid R100 and transposon Tn501: the beginning of the operon including the regulatory region and the first two structural genes. Proc Natl Acad Sci U S A. 1984 Oct;81(19):5975–5979. doi: 10.1073/pnas.81.19.5975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Mizuno T., Chou M. Y., Inouye M. A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc Natl Acad Sci U S A. 1984 Apr;81(7):1966–1970. doi: 10.1073/pnas.81.7.1966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Moore S. K., Garvin R. T., James E. Nucleotide sequence of the argF regulatory region of Escherichia coli K-12. Gene. 1981 Dec;16(1-3):119–132. doi: 10.1016/0378-1119(81)90068-8. [DOI] [PubMed] [Google Scholar]
  71. Movva R. N., Green P., Nakamura K., Inouye M. Interaction of cAMP receptor protein with the ompA gene, a gene for a major outer membrane protein of Escherichia coli. FEBS Lett. 1981 Jun 15;128(2):186–190. doi: 10.1016/0014-5793(81)80077-4. [DOI] [PubMed] [Google Scholar]
  72. Mulligan M. E., Brosius J., McClure W. R. Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter. J Biol Chem. 1985 Mar 25;260(6):3529–3538. [PubMed] [Google Scholar]
  73. Mulligan M. E., Hawley D. K., Entriken R., McClure W. R. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789–800. doi: 10.1093/nar/12.1part2.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Nakabeppu Y., Kondo H., Kawabata S., Iwanaga S., Sekiguchi M. Purification and structure of the intact Ada regulatory protein of Escherichia coli K12, O6-methylguanine-DNA methyltransferase. J Biol Chem. 1985 Jun 25;260(12):7281–7288. [PubMed] [Google Scholar]
  75. Nasoff M. S., Baker H. V., 2nd, Wolf R. E., Jr DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase. Gene. 1984 Mar;27(3):253–264. doi: 10.1016/0378-1119(84)90070-2. [DOI] [PubMed] [Google Scholar]
  76. Nomura T., Fujita N., Ishihama A. Promoter selectivity of E. coli RNA polymerase: analysis of the promoter system of convergently-transcribed dnaQ-rnh genes. Nucleic Acids Res. 1985 Nov 11;13(21):7647–7661. doi: 10.1093/nar/13.21.7647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Ohmori H., Kimura M., Nagata T., Sakakibara Y. Structural analysis of the dnaA and dnaN genes of Escherichia coli. Gene. 1984 May;28(2):159–170. doi: 10.1016/0378-1119(84)90253-1. [DOI] [PubMed] [Google Scholar]
  78. Olsson O., Bergström S., Normark S. Identification of a novel ampC beta-lactamase promoter in a clinical isolate of Escherichia coli. EMBO J. 1982;1(11):1411–1416. doi: 10.1002/j.1460-2075.1982.tb01331.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Pannekoek H., Maat J., van den Berg E., Noordermeer I. Structure of a promotor on plasmid pMB9 derived from plasmid pSC101. Nucleic Acids Res. 1980 Apr 11;8(7):1535–1550. doi: 10.1093/nar/8.7.1535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. Parker R. C. The 5'-terminal ribonucleotide of an in vitro ColE1 transcript is not complementary to the DNA template. Gene. 1983 Dec;26(2-3):127–136. doi: 10.1016/0378-1119(83)90182-8. [DOI] [PubMed] [Google Scholar]
  81. Piette J., Cunin R., Boyen A., Charlier D., Crabeel M., Van Vliet F., Glansdorff N., Squires C., Squires C. L. The regulatory region of the divergent argECBH operon in Escherichia coli K-12. Nucleic Acids Res. 1982 Dec 20;10(24):8031–8048. doi: 10.1093/nar/10.24.8031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Piette J., Nyunoya H., Lusty C. J., Cunin R., Weyens G., Crabeel M., Charlier D., Glansdorff N., Piérard A. DNA sequence of the carA gene and the control region of carAB: tandem promoters, respectively controlled by arginine and the pyrimidines, regulate the synthesis of carbamoyl-phosphate synthetase in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4134–4138. doi: 10.1073/pnas.81.13.4134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Plamann M. D., Stauffer G. V. Characterization of the Escherichia coli gene for serine hydroxymethyltransferase. Gene. 1983 Apr;22(1):9–18. doi: 10.1016/0378-1119(83)90059-8. [DOI] [PubMed] [Google Scholar]
  84. Postle K., Good R. F. DNA sequence of the Escherichia coli tonB gene. Proc Natl Acad Sci U S A. 1983 Sep;80(17):5235–5239. doi: 10.1073/pnas.80.17.5235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Poulsen P., Bonekamp F., Jensen K. F. Structure of the Escherichia coli pyrE operon and control of pyrE expression by a UTP modulated intercistronic attentuation. EMBO J. 1984 Aug;3(8):1783–1790. doi: 10.1002/j.1460-2075.1984.tb02046.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Poulsen P., Jensen K. F., Valentin-Hansen P., Carlsson P., Lundberg L. G. Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region. Eur J Biochem. 1983 Sep 15;135(2):223–229. doi: 10.1111/j.1432-1033.1983.tb07641.x. [DOI] [PubMed] [Google Scholar]
  87. Pribnow D. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc Natl Acad Sci U S A. 1975 Mar;72(3):784–788. doi: 10.1073/pnas.72.3.784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Prosen D. E., Cech C. L. Bacteriophage T7 E promoter: identification and measurement of kinetics of association with Escherichia coli RNA polymerase. Biochemistry. 1985 Apr 23;24(9):2219–2227. doi: 10.1021/bi00330a016. [DOI] [PubMed] [Google Scholar]
  89. Raibaud O., Gutierrez C., Schwartz M. Essential and nonessential sequences in malPp, a positively controlled promoter in Escherichia coli. J Bacteriol. 1985 Mar;161(3):1201–1208. doi: 10.1128/jb.161.3.1201-1208.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  90. Richaud C., Richaud F., Martin C., Haziza C., Patte J. C. Regulation of expression and nucleotide sequence of the Escherichia coli dapD gene. J Biol Chem. 1984 Dec 10;259(23):14824–14828. [PubMed] [Google Scholar]
  91. Rodriguez R. L., West R. W., Heyneker H. L., Bolivar F., Boyer H. W. Characterizing wild-type and mutant promoters of the tetracycline resistance gene in pBR313. Nucleic Acids Res. 1979 Jul 25;6(10):3267–3287. doi: 10.1093/nar/6.10.3267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. 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]
  93. Russell D. R., Bennett G. N. Construction and analysis of in vivo activity of E. coli promoter hybrids and promoter mutants that alter the -35 to -10 spacing. Gene. 1982 Dec;20(2):231–243. doi: 10.1016/0378-1119(82)90042-7. [DOI] [PubMed] [Google Scholar]
  94. Saint Girons I., Margarita D. Evidence for an internal promoter in the Escherichia coli threonine operon. J Bacteriol. 1985 Jan;161(1):461–462. doi: 10.1128/jb.161.1.461-462.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Saint-Girons I., Duchange N., Zakin M. M., Park I., Margarita D., Ferrara P., Cohen G. N. Nucleotide sequence of metF, the E. coli structural gene for 5-10 methylene tetrahydrofolate reductase and of its control region. Nucleic Acids Res. 1983 Oct 11;11(19):6723–6732. doi: 10.1093/nar/11.19.6723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Sakamoto H., Kimura N., Shimura Y. Processing of transcription products of the gene encoding the RNA component of RNase P. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6187–6191. doi: 10.1073/pnas.80.20.6187. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. Sancar A., Williams K. R., Chase J. W., Rupp W. D. Sequences of the ssb gene and protein. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4274–4278. doi: 10.1073/pnas.78.7.4274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Sasatsu M., Misra T. K., Chu L., Laddaga R., Silver S. Cloning and DNA sequence of a plasmid-determined citrate utilization system in Escherichia coli. J Bacteriol. 1985 Dec;164(3):983–993. doi: 10.1128/jb.164.3.983-993.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  99. Schaller H., Gray C., Herrmann K. Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd. Proc Natl Acad Sci U S A. 1975 Feb;72(2):737–741. doi: 10.1073/pnas.72.2.737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Schollmeier K., Hillen W. Transposon Tn10 contains two structural genes with opposite polarity between tetA and IS10R. J Bacteriol. 1984 Nov;160(2):499–503. doi: 10.1128/jb.160.2.499-503.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  101. 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]
  102. Seeburg P. H., Nüsslein C., Schaller H. Interaction of RNA polymerase with promoters from bacteriophage fd. Eur J Biochem. 1977 Mar 15;74(1):107–113. doi: 10.1111/j.1432-1033.1977.tb11372.x. [DOI] [PubMed] [Google Scholar]
  103. Selzer G., Som T., Itoh T., Tomizawa J. The origin of replication of plasmid p15A and comparative studies on the nucleotide sequences around the origin of related plasmids. Cell. 1983 Jan;32(1):119–129. doi: 10.1016/0092-8674(83)90502-0. [DOI] [PubMed] [Google Scholar]
  104. Siebenlist U., Simpson R. B., Gilbert W. E. coli RNA polymerase interacts homologously with two different promoters. Cell. 1980 Jun;20(2):269–281. doi: 10.1016/0092-8674(80)90613-3. [DOI] [PubMed] [Google Scholar]
  105. Smith C. A., Shingler V., Thomas C. M. The trfA and trfB promoter regions of broad host range plasmid RK2 share common potential regulatory sequences. Nucleic Acids Res. 1984 Apr 25;12(8):3619–3630. doi: 10.1093/nar/12.8.3619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Smith G. P. Unequal crossover and the evolution of multigene families. Cold Spring Harb Symp Quant Biol. 1974;38:507–513. doi: 10.1101/sqb.1974.038.01.055. [DOI] [PubMed] [Google Scholar]
  107. Spencer M. E., Guest J. R. Transcription analysis of the sucAB, aceEF and lpd genes of Escherichia coli. Mol Gen Genet. 1985;200(1):145–154. doi: 10.1007/BF00383328. [DOI] [PubMed] [Google Scholar]
  108. 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]
  109. Stefano J. E., Gralla J. D. Spacer mutations in the lac ps promoter. Proc Natl Acad Sci U S A. 1982 Feb;79(4):1069–1072. doi: 10.1073/pnas.79.4.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Stoner C., Schleif R. The araE low affinity L-arabinose transport promoter. Cloning, sequence, transcription start site and DNA binding sites of regulatory proteins. J Mol Biol. 1983 Dec 25;171(4):369–381. doi: 10.1016/0022-2836(83)90035-9. [DOI] [PubMed] [Google Scholar]
  111. Tachibana H., Ishihama A. Correlation between the rate of productive transcription initiation and the strand-melting property of Escherichia coli promoters. Nucleic Acids Res. 1985 Dec 20;13(24):9031–9042. doi: 10.1093/nar/13.24.9031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Takanami M., Sugimoto K., Sugisaki H., Okamoto T. Sequence of promoter for coat protein gene of bacteriophage fd. Nature. 1976 Mar 25;260(5549):297–302. doi: 10.1038/260297a0. [DOI] [PubMed] [Google Scholar]
  113. Tamura F., Nishimura S., Ohki M. The E. coli divE mutation, which differentially inhibits synthesis of certain proteins, is in tRNASer1. EMBO J. 1984 May;3(5):1103–1107. doi: 10.1002/j.1460-2075.1984.tb01936.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Taylor W. E., Straus D. B., Grossman A. D., Burton Z. F., Gross C. A., Burgess R. R. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Cell. 1984 Sep;38(2):371–381. doi: 10.1016/0092-8674(84)90492-6. [DOI] [PubMed] [Google Scholar]
  115. Thompson R., Taylor L., Kelly K., Everett R., Willetts N. The F plasmid origin of transfer: DNA sequence of wild-type and mutant origins and location of origin-specific nicks. EMBO J. 1984 May;3(5):1175–1180. doi: 10.1002/j.1460-2075.1984.tb01947.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. 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]
  117. Turnbough C. L., Jr, Hicks K. L., Donahue J. P. Attenuation control of pyrBI operon expression in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1983 Jan;80(2):368–372. doi: 10.1073/pnas.80.2.368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  118. 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]
  119. Valentin-Hansen P., Hammer K., Løve Larsen J. E., Svendsen I. The internal regulated promoter of the deo operon of Escherichia coli K-12. Nucleic Acids Res. 1984 Jul 11;12(13):5211–5224. doi: 10.1093/nar/12.13.5211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Vidal-Ingigliardi D., Raibaud O. A convenient technique to compare the efficiency of promoters in Escherichia coli. Nucleic Acids Res. 1985 Aug 26;13(16):5919–5926. doi: 10.1093/nar/13.16.5919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  121. Walker J. E., Gay N. J., Saraste M., Eberle A. N. DNA sequence around the Escherichia coli unc operon. Completion of the sequence of a 17 kilobase segment containing asnA, oriC, unc, glmS and phoS. Biochem J. 1984 Dec 15;224(3):799–815. doi: 10.1042/bj2240799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  122. Wallace B. J., Kushner S. R. Genetic and physical analysis of the thioredoxin (trxA) gene of Escherichia coli K-12. Gene. 1984 Dec;32(3):399–408. doi: 10.1016/0378-1119(84)90015-5. [DOI] [PubMed] [Google Scholar]
  123. Womble D. D., Sampathkumar P., Easton A. M., Luckow V. A., Rownd R. H. Transcription of the replication control region of the IncFII R-plasmid NR1 in vitro and in vivo. J Mol Biol. 1985 Feb 5;181(3):395–410. doi: 10.1016/0022-2836(85)90228-1. [DOI] [PubMed] [Google Scholar]
  124. Wood D., Darlison M. G., Wilde R. J., Guest J. R. Nucleotide sequence encoding the flavoprotein and hydrophobic subunits of the succinate dehydrogenase of Escherichia coli. Biochem J. 1984 Sep 1;222(2):519–534. doi: 10.1042/bj2220519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  125. 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]
  126. Youderian P., Bouvier S., Susskind M. M. Sequence determinants of promoter activity. Cell. 1982 Oct;30(3):843–853. doi: 10.1016/0092-8674(82)90289-6. [DOI] [PubMed] [Google Scholar]
  127. van Sluis C. A., Moolenaar G. F., Backendorf C. Regulation of the uvrC gene of Escherichia coli K12: localization and characterization of a damage-inducible promoter. EMBO J. 1983;2(12):2313–2318. doi: 10.1002/j.1460-2075.1983.tb01739.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. van den Elzen P. J., Maat J., Walters H. H., Veltkamp E., Nijkamp H. J. The nucleotide sequence of the bacteriocin promoters of plasmids Clo DF13 and Co1 E1: role of lexA repressor and cAMP in the regulation of promoter activity. Nucleic Acids Res. 1982 Mar 25;10(6):1913–1928. doi: 10.1093/nar/10.6.1913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. von Hippel P. H., Bear D. G., Morgan W. D., McSwiggen J. A. Protein-nucleic acid interactions in transcription: a molecular analysis. Annu Rev Biochem. 1984;53:389–446. doi: 10.1146/annurev.bi.53.070184.002133. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES