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. 1989 Jul;171(7):3689–3695. doi: 10.1128/jb.171.7.3689-3695.1989

Localization of the ribosome-releasing factor gene in the Escherichia coli chromosome.

S Ichikawa 1, M Ryoji 1, Z Siegfried 1, A Kaji 1
PMCID: PMC210112  PMID: 2661533

Abstract

The ribosome-releasing factor (RRF) gene was localized at a position between 2 and 6 min on the Escherichia coli chromosome by measuring the gene-dosage-dependent production of RRF in various E. coli F' merozygotes. This position was confirmed and refined by using a nucleotide probe corresponding to a 16-amino-acid sequence in RRF. It was found that the RRF gene was contained in pLC 6-32 of the Clark-Carbon Gene Bank. Restriction enzyme mapping of E. coli genomic DNA with the above probe led us to conclude that the RRF gene is situated in the 4-min region, somewhere downstream (clockwise) of the elongation factor Ts gene, tsf. A pLC 6-32-derived DNA fragment which carries the RRF gene was found to contain a partial sequence of tsf. The exact location of the translational initiation site of the RRF gene was determined to be 1.1 kilobases downstream from the translational termination site of tsf. The RRF gene is designated frr.

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Selected References

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  1. An G., Bendiak D. S., Mamelak L. A., Friesen J. D. Organization and nucleotide sequence of a new ribosomal operon in Escherichia coli containing the genes for ribosomal protein S2 and elongation factor Ts. Nucleic Acids Res. 1981 Aug 25;9(16):4163–4172. doi: 10.1093/nar/9.16.4163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arai K., Kawakita M., Kaziro Y., Kondo T., Ui N. Studies on the polypeptide elongation factors from E. coli. 3. Molecular characteristics of EF-Tu-guanosine diphosphate, EP-Ts, and EF-Tu-Ts complex. J Biochem. 1973 May;73(5):1095–1105. doi: 10.1093/oxfordjournals.jbchem.a130164. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. Berg C. M., Curtiss R., 3rd Transposition derivatives of an Hfr strain of Escherichia coli K-12. Genetics. 1967 Jul;56(3):503–525. doi: 10.1093/genetics/56.3.503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. CLARK A. J., MARGULIES A. D. ISOLATION AND CHARACTERIZATION OF RECOMBINATION-DEFICIENT MUTANTS OF ESCHERICHIA COLI K12. Proc Natl Acad Sci U S A. 1965 Feb;53:451–459. doi: 10.1073/pnas.53.2.451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Caskey C. T., Tompkins R., Scolnick E., Caryk T., Nirenberg M. Sequential translation of trinucleotide codons for the initiation and termination of protein synthesis. Science. 1968 Oct 4;162(3849):135–138. doi: 10.1126/science.162.3849.135. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Friesen J. D., Parker J., Watson R. J., Bendiak D., Reeh S. V., Pedersen S., Fiil N. P. A transducing bacteriophage lambda carrying the structural gene for elongation factor Ts. Mol Gen Genet. 1976 Oct 18;148(1):93–98. doi: 10.1007/BF00268549. [DOI] [PubMed] [Google Scholar]
  9. Furano A. V. Direct demonstration of duplicate tuf genes in enteric bacteria. Proc Natl Acad Sci U S A. 1978 Jul;75(7):3104–3108. doi: 10.1073/pnas.75.7.3104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Grosjean H., Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene. 1982 Jun;18(3):199–209. doi: 10.1016/0378-1119(82)90157-3. [DOI] [PubMed] [Google Scholar]
  11. Harris J. D., Martinez I. I., Calendar R. A gene from Escherichia coli affecting the sigma subunit of RNA polymerase. Proc Natl Acad Sci U S A. 1977 May;74(5):1836–1840. doi: 10.1073/pnas.74.5.1836. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hayward R. S., Fyfe S. Over-synthesis and instability of sigma protein in a merodiploid strain of Escherichia coli. Mol Gen Genet. 1978 Feb 7;159(1):89–99. doi: 10.1007/BF00401752. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Hirashima A., Kaji A. Factor-dependent release of ribosomes from messenger RNA. Requirement for two heat-stable factors. J Mol Biol. 1972 Mar 14;65(1):43–58. doi: 10.1016/0022-2836(72)90490-1. [DOI] [PubMed] [Google Scholar]
  15. Hirashima A., Kaji A. Purification and properties of ribosome-releasing factor. Biochemistry. 1972 Oct 24;11(22):4037–4044. doi: 10.1021/bi00772a005. [DOI] [PubMed] [Google Scholar]
  16. Howard-Flanders P., Theriot L. Mutants of Escherichia coli K-12 defective in DNA repair and in genetic recombination. Genetics. 1966 Jun;53(6):1137–1150. doi: 10.1093/genetics/53.6.1137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Icho T., Sparrow C. P., Raetz C. R. Molecular cloning and sequencing of the gene for CDP-diglyceride synthetase of Escherichia coli. J Biol Chem. 1985 Oct 5;260(22):12078–12083. [PubMed] [Google Scholar]
  18. Ikemura T., Ozeki H. Gross map location of Escherichia coli transfer RNA genes. J Mol Biol. 1977 Dec 5;117(2):419–446. doi: 10.1016/0022-2836(77)90136-x. [DOI] [PubMed] [Google Scholar]
  19. Jaskunas S. R., Lindahl L., Nomura M. Identification of two copies of the gene for the elongation factor EF-Tu in E. coli. Nature. 1975 Oct 9;257(5526):458–462. doi: 10.1038/257458a0. [DOI] [PubMed] [Google Scholar]
  20. Jaye M., de la Salle H., Schamber F., Balland A., Kohli V., Findeli A., Tolstoshev P., Lecocq J. P. Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX. Nucleic Acids Res. 1983 Apr 25;11(8):2325–2335. doi: 10.1093/nar/11.8.2325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  22. Kuwano M., Schlessinger D. G factor mutants of Escherichia coli: map location and properties. Biochem Biophys Res Commun. 1971 Feb 5;42(3):441–444. doi: 10.1016/0006-291x(71)90390-1. [DOI] [PubMed] [Google Scholar]
  23. Lathe R., Buc H., Lecocq J. P., Bautz E. K. Prokaryotic histone-like protein interacting with RNA polymerase. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3548–3552. doi: 10.1073/pnas.77.6.3548. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lee C. C., Kohara Y., Akiyama K., Smith C. L., Craigen W. J., Caskey C. T. Rapid and precise mapping of the Escherichia coli release factor genes by two physical approaches. J Bacteriol. 1988 Oct;170(10):4537–4541. doi: 10.1128/jb.170.10.4537-4541.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Low K. B. Escherichia coli K-12 F-prime factors, old and new. Bacteriol Rev. 1972 Dec;36(4):587–607. doi: 10.1128/br.36.4.587-607.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Nakamura Y., Osawa T., Yura T. Chromosomal location of a structural gene for the RNA polymerase sigma factor in Escherichia coli. Proc Natl Acad Sci U S A. 1977 May;74(5):1831–1835. doi: 10.1073/pnas.74.5.1831. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. O'Farrell P. Z., Goodman H. M., O'Farrell P. H. High resolution two-dimensional electrophoresis of basic as well as acidic proteins. Cell. 1977 Dec;12(4):1133–1141. doi: 10.1016/0092-8674(77)90176-3. [DOI] [PubMed] [Google Scholar]
  28. Ogawa K., Kaji A. Requirement for ribosome-releasing factor for the release of ribosomes at the termination codon. Eur J Biochem. 1975 Oct 15;58(2):411–419. doi: 10.1111/j.1432-1033.1975.tb02388.x. [DOI] [PubMed] [Google Scholar]
  29. Pedersen S., Reeh S. V. Analysis of the proteins synthesized in ultraviolet light-irradiated Escherichia coli following infection with the bacteriophages lambdadrifd 18 and lambdadfus-3. Mol Gen Genet. 1976 Mar 30;144(3):339–343. doi: 10.1007/BF00341733. [DOI] [PubMed] [Google Scholar]
  30. Plumbridge J. A., Howe J. G., Springer M., Touati-Schwartz D., Hershey J. W., Grunberg-Manago M. Cloning and mapping of a gene for translational initiation factor IF2 in Escherichia coli. Proc Natl Acad Sci U S A. 1982 Aug;79(16):5033–5037. doi: 10.1073/pnas.79.16.5033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ryoji M., Berland R., Kaji A. Reinitiation of translation from the triplet next to the amber termination codon in the absence of ribosome-releasing factor. Proc Natl Acad Sci U S A. 1981 Oct;78(10):5973–5977. doi: 10.1073/pnas.78.10.5973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. 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]
  33. Ryoji M., Yamane T., Gordon M., Kaji A. Two modes of amber codon read-through in vitro. Arch Biochem Biophys. 1985 May 1;238(2):636–641. doi: 10.1016/0003-9861(85)90209-7. [DOI] [PubMed] [Google Scholar]
  34. Sands J. F., Cummings H. S., Sacerdot C., Dondon L., Grunberg-Manago M., Hershey J. W. Cloning and mapping of infA, the gene for protein synthesis initiation factor IF1. Nucleic Acids Res. 1987 Jul 10;15(13):5157–5168. doi: 10.1093/nar/15.13.5157. [DOI] [PMC free article] [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. Springer M., Graffe M., Grunberg-Manago M. Characterization of an E. coli mutant with a thermolabile initiation factor IF3 activity. Mol Gen Genet. 1977 Feb 28;151(1):17–26. doi: 10.1007/BF00446908. [DOI] [PubMed] [Google Scholar]
  37. Yamamoto M., Strycharz W. A., Nomura M. Identification of genes for elongation factor Ts and ribosomal protein S2 in E. coli. Cell. 1976 May;8(1):129–138. doi: 10.1016/0092-8674(76)90194-x. [DOI] [PubMed] [Google Scholar]

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