Skip to main content
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1991 Aug;173(16):5181–5187. doi: 10.1128/jb.173.16.5181-5187.1991

Identification of the promoter region of the ribosome-releasing factor cistron (frr).

I Shimizu 1, A Kaji 1
PMCID: PMC208211  PMID: 1860827

Abstract

Previous studies of the structure and expression of the ribosome-releasing factor (RRF) cistron (frr) have suggested that an efficient promoter region is located in the RRF cistron. We report here on the nucleotide sequence and in vivo function of the RRF promoter. The transcriptional start site was determined by primer extension to be 58 bp upstream of the translational initiation codon of frr. The location of the RRF promoter region was confirmed by means of (i) deletion analysis of the 5' proximal sequences of frr fused to the chloramphenicol acetyltransferase reporter gene, (ii) analysis of RRF produced in vivo from the deletion derivatives of frr cloned into pUC19, and (iii) gel retardation analysis with Escherichia coli RNA polymerase. The -35 and -10 regions were TTacCc and TATAcT, respectively. The strength of the RRF promoter was similar to that of the lac promoter, as determined by in vivo expression of chloramphenicol acetyltransferase activity. However, the RRF promoter was not affected by the intracellular cyclic AMP level despite the presence of a cyclic AMP receptor protein binding site downstream of the RRF promoter.

Full text

PDF
5181

Images in this article

Selected References

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

  1. Adhya S., Gottesman M. Control of transcription termination. Annu Rev Biochem. 1978;47:967–996. doi: 10.1146/annurev.bi.47.070178.004535. [DOI] [PubMed] [Google Scholar]
  2. Alt-Moerbe J., Rak B., Schröder J. A 3.6-kbp segment from the vir region of Ti plasmids contains genes responsible for border-sequence-directed production of T region circles in E. coli. EMBO J. 1986 Jun;5(6):1129–1135. doi: 10.1002/j.1460-2075.1986.tb04337.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Beckwith J., Grodzicker T., Arditti R. Evidence for two sites in the lac promoter region. J Mol Biol. 1972 Aug 14;69(1):155–160. doi: 10.1016/0022-2836(72)90031-9. [DOI] [PubMed] [Google Scholar]
  4. Bendiak D. S., Friesen J. D. Organization of genes in the four minute region of the Escherichia coli chromosome: evidence that rpsB and tsf are co-transcribed. Mol Gen Genet. 1981;181(3):356–362. doi: 10.1007/BF00425611. [DOI] [PubMed] [Google Scholar]
  5. Betenbaugh M. J., Dhurjati P. Effects of promoter induction and copy number amplification on cloned gene expression and growth of recombinant cell cultures. Ann N Y Acad Sci. 1990;589:111–120. doi: 10.1111/j.1749-6632.1990.tb24238.x. [DOI] [PubMed] [Google Scholar]
  6. Beutel B. A., Record M. T., Jr E. coli promoter spacer regions contain nonrandom sequences which correlate to spacer length. Nucleic Acids Res. 1990 Jun 25;18(12):3597–3603. doi: 10.1093/nar/18.12.3597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. 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]
  9. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  10. Brosius J., Cate R. L., Perlmutter A. P. Precise location of two promoters for the beta-lactamase gene of pBR322. S1 mapping of ribonucleic acid isolated from Escherichia coli or synthesized in vitro. J Biol Chem. 1982 Aug 10;257(15):9205–9210. [PubMed] [Google Scholar]
  11. Brosius J. Plasmid vectors for the selection of promoters. Gene. 1984 Feb;27(2):151–160. doi: 10.1016/0378-1119(84)90136-7. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Chan B., Spassky A., Busby S. The organization of open complexes between Escherichia coli RNA polymerase and DNA fragments carrying promoters either with or without consensus -35 region sequences. Biochem J. 1990 Aug 15;270(1):141–148. doi: 10.1042/bj2700141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Chen J. D., Morrison D. A. Construction and properties of a new insertion vector, pJDC9, that is protected by transcriptional terminators and useful for cloning of DNA from Streptococcus pneumoniae. Gene. 1988 Apr 15;64(1):155–164. doi: 10.1016/0378-1119(88)90489-1. [DOI] [PubMed] [Google Scholar]
  15. Clarke L., Carbon J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell. 1976 Sep;9(1):91–99. doi: 10.1016/0092-8674(76)90055-6. [DOI] [PubMed] [Google Scholar]
  16. Clewell D. B., Helinski D. R. Supercoiled circular DNA-protein complex in Escherichia coli: purification and induced conversion to an opern circular DNA form. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1159–1166. doi: 10.1073/pnas.62.4.1159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Dickson R. C., Abelson J., Barnes W. M., Reznikoff W. S. Genetic regulation: the Lac control region. Science. 1975 Jan 10;187(4171):27–35. doi: 10.1126/science.1088926. [DOI] [PubMed] [Google Scholar]
  18. Elliott T., Geiduschek E. P. Defining a bacteriophage T4 late promoter: absence of a "-35" region. Cell. 1984 Jan;36(1):211–219. doi: 10.1016/0092-8674(84)90091-6. [DOI] [PubMed] [Google Scholar]
  19. Emmer M., deCrombrugghe B., Pastan I., Perlman R. Cyclic AMP receptor protein of E. coli: its role in the synthesis of inducible enzymes. Proc Natl Acad Sci U S A. 1970 Jun;66(2):480–487. doi: 10.1073/pnas.66.2.480. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Garner M. M., Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 1981 Jul 10;9(13):3047–3060. doi: 10.1093/nar/9.13.3047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Gilman M. Z., Chamberlin M. J. Developmental and genetic regulation of Bacillus subtilis genes transcribed by sigma 28-RNA polymerase. Cell. 1983 Nov;35(1):285–293. doi: 10.1016/0092-8674(83)90231-3. [DOI] [PubMed] [Google Scholar]
  22. Harley C. B., Reynolds R. P. Analysis of E. coli promoter sequences. Nucleic Acids Res. 1987 Mar 11;15(5):2343–2361. doi: 10.1093/nar/15.5.2343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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]
  24. Hirashima A., Kaji A. Factor dependent breakdown of polysomes. Biochem Biophys Res Commun. 1970 Nov 25;41(4):877–883. doi: 10.1016/0006-291x(70)90165-8. [DOI] [PubMed] [Google Scholar]
  25. Horii T., Ogawa T., Ogawa H. Nucleotide sequence of the lexA gene of E. coli. Cell. 1981 Mar;23(3):689–697. doi: 10.1016/0092-8674(81)90432-3. [DOI] [PubMed] [Google Scholar]
  26. Ichikawa S., Kaji A. Molecular cloning and expression of ribosome releasing factor. J Biol Chem. 1989 Nov 25;264(33):20054–20059. [PubMed] [Google Scholar]
  27. Ichikawa S., Ryoji M., Siegfried Z., Kaji A. Localization of the ribosome-releasing factor gene in the Escherichia coli chromosome. J Bacteriol. 1989 Jul;171(7):3689–3695. doi: 10.1128/jb.171.7.3689-3695.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Keilty S., Rosenberg M. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J Biol Chem. 1987 May 5;262(13):6389–6395. [PubMed] [Google Scholar]
  29. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. Lee J. S., An G., Friesen J. D., Isono K. Cloning and the nucleotide sequence of the genes for Escherichia coli ribosomal proteins L28 (rpmB) and L33 (rpmG). Mol Gen Genet. 1981;184(2):218–223. doi: 10.1007/BF00272908. [DOI] [PubMed] [Google Scholar]
  32. Reed R. E., Baer M. F., Guerrier-Takada C., Donis-Keller H., Altman S. Nucleotide sequence of the gene encoding the RNA subunit (M1 RNA) of ribonuclease P from Escherichia coli. Cell. 1982 Sep;30(2):627–636. doi: 10.1016/0092-8674(82)90259-8. [DOI] [PubMed] [Google Scholar]
  33. 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]
  34. Ryoji M., Karpen J. W., Kaji A. Further characterization of ribosome releasing factor and evidence that it prevents ribosomes from reading through a termination codon. J Biol Chem. 1981 Jun 10;256(11):5798–5801. [PubMed] [Google Scholar]
  35. 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]
  36. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. 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]
  38. Stueber D., Bujard H. Transcription from efficient promoters can interfere with plasmid replication and diminish expression of plasmid specified genes. EMBO J. 1982;1(11):1399–1404. doi: 10.1002/j.1460-2075.1982.tb01329.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. 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]
  40. 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]
  41. Yamamoto T., Yokota T., Kaji A. Requirement of cyclic adenosine 3',5'-monophosphate for the thermosensitive effects of Rts1 in a cyclic adenosine 3',5'-monophosphate-less mutant of Escherichia coli. J Bacteriol. 1977 Oct;132(1):80–89. doi: 10.1128/jb.132.1.80-89.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. 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]
  43. de Crombrugghe B., Busby S., Buc H. Cyclic AMP receptor protein: role in transcription activation. Science. 1984 May 25;224(4651):831–838. doi: 10.1126/science.6372090. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES