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. 1990 Jun;125(2):237–248. doi: 10.1093/genetics/125.2.237

The Riia Gene of Bacteriophage T4. I. Its DNA Sequence and Discovery of a New Open Reading Frame between Genes 60 and Riia

P Daegelen 1, E Brody 1
PMCID: PMC1204014  PMID: 2379817

Abstract

We have determined the DNA sequence of the rIIA gene and have discovered a small open reading frame, rIIA.1, between genes 60 and rIIA. The predicted molecular weights of these proteins are 82,840 for rIIA and 8,124 for rIIA.1. The rIIA protein has a repeated motif which suggests that the gene has evolved by duplication. It also has a motif which suggests that it belongs to a group of ompR-like proteins that control regulation of gene expression in response to changes in the external environment. We have sequenced three different missense mutants whose mutations lie in the Ala segment of the rIIA genetic map. All three changes are found within the first 35 bp of the rIIA coding sequence. The region of control of protein synthesis is identical in the rIIA gene and in gene 44 of T4. We relate this finding to the high sensitivity of both RNAs to translational repression by the T4 regA gene product.

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Selected References

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  1. CRICK F. H., BARNETT L., BRENNER S., WATTS-TOBIN R. J. General nature of the genetic code for proteins. Nature. 1961 Dec 30;192:1227–1232. doi: 10.1038/1921227a0. [DOI] [PubMed] [Google Scholar]
  2. Casadaban M. J., Cohen S. N. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179–207. doi: 10.1016/0022-2836(80)90283-1. [DOI] [PubMed] [Google Scholar]
  3. Daegelen P., Brody E. Early bacteriophage T4 transcription. A diffusible product controls rIIA and rIIB RNA synthesis. J Mol Biol. 1976 May 5;103(1):127–142. doi: 10.1016/0022-2836(76)90055-3. [DOI] [PubMed] [Google Scholar]
  4. Daegelen P., Brody E. The rIIA gene of bacteriophage T4. II. Regulation of its messenger RNA synthesis. Genetics. 1990 Jun;125(2):249–260. doi: 10.1093/genetics/125.2.249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dardel F., Bensoussan P. DNAid: a Macintosh full screen editor featuring a built-in regular expression interpreter for the search of specific patterns in biological sequences using finite state automata. Comput Appl Biosci. 1988 Nov;4(4):483–486. doi: 10.1093/bioinformatics/4.4.483. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dretzen G., Bellard M., Sassone-Corsi P., Chambon P. A reliable method for the recovery of DNA fragments from agarose and acrylamide gels. Anal Biochem. 1981 Apr;112(2):295–298. doi: 10.1016/0003-2697(81)90296-7. [DOI] [PubMed] [Google Scholar]
  9. Engelman D. M., Steitz T. A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem. 1986;15:321–353. doi: 10.1146/annurev.bb.15.060186.001541. [DOI] [PubMed] [Google Scholar]
  10. Huang W. M. The 52-protein subunit of T4 DNA topoisomerase is homologous to the gyrA-protein of gyrase. Nucleic Acids Res. 1986 Sep 25;14(18):7379–7390. [PMC free article] [PubMed] [Google Scholar]
  11. Ikenaka K., Tsung K., Comeau D. E., Inouye M. A dominant mutation in Escherichia coli OmpR lies within a domain which is highly conserved in a large family of bacterial regulatory proteins. Mol Gen Genet. 1988 Mar;211(3):538–540. doi: 10.1007/BF00425713. [DOI] [PubMed] [Google Scholar]
  12. Karam J. D., Bowles M. G. Mutation to overproduction of bacteriophage T4 gene products. J Virol. 1974 Feb;13(2):428–438. doi: 10.1128/jvi.13.2.428-438.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Manoil C., Sinha N., Alberts B. Intracellular DNA-protein complexes from bacteriophage T4-infected cells isolated by a rapid two-step procedure. Characterization and identification of the protein components. J Biol Chem. 1977 Apr 25;252(8):2734–2741. [PubMed] [Google Scholar]
  15. Matz K., Schmandt M., Gussin G. N. The rex gene of bacteriophage lambda is really two genes. Genetics. 1982 Nov;102(3):319–327. doi: 10.1093/genetics/102.3.319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. McPheeters D. S., Christensen A., Young E. T., Stormo G., Gold L. Translational regulation of expression of the bacteriophage T4 lysozyme gene. Nucleic Acids Res. 1986 Jul 25;14(14):5813–5826. doi: 10.1093/nar/14.14.5813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  18. Miller E. S., Karam J., Dawson M., Trojanowska M., Gauss P., Gold L. Translational repression: biological activity of plasmid-encoded bacteriophage T4 RegA protein. J Mol Biol. 1987 Apr 5;194(3):397–410. doi: 10.1016/0022-2836(87)90670-x. [DOI] [PubMed] [Google Scholar]
  19. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
  20. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. doi: 10.1016/0378-1119(83)90040-9. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Pribnow D., Sigurdson D. C., Gold L., Singer B. S., Napoli C., Brosius J., Dull T. J., Noller H. F. rII cistrons of bacteriophage T4. DNA sequence around the intercistronic divide and positions of genetic landmarks. J Mol Biol. 1981 Jul 5;149(3):337–376. doi: 10.1016/0022-2836(81)90477-0. [DOI] [PubMed] [Google Scholar]
  23. Rand K. N., Gait M. J. Sequence and cloning of bacteriophage T4 gene 63 encoding RNA ligase and tail fibre attachment activities. EMBO J. 1984 Feb;3(2):397–402. doi: 10.1002/j.1460-2075.1984.tb01819.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ripley L. S., Dubins J. S., deBoer J. G., DeMarini D. M., Bogerd A. M., Kreuzer K. N. Hotspot sites for acridine-induced frameshift mutations in bacteriophage T4 correspond to sites of action of the T4 type II topoisomerase. J Mol Biol. 1988 Apr 20;200(4):665–680. doi: 10.1016/0022-2836(88)90479-2. [DOI] [PubMed] [Google Scholar]
  25. Risler J. L., Delorme M. O., Delacroix H., Henaut A. Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix. J Mol Biol. 1988 Dec 20;204(4):1019–1029. doi: 10.1016/0022-2836(88)90058-7. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Sekiguchi M. Studies on the physiological defect in rII mutants of bacteriophage T4. J Mol Biol. 1966 Apr;16(2):503–522. doi: 10.1016/s0022-2836(66)80188-2. [DOI] [PubMed] [Google Scholar]
  28. Selzer G., Belin D., Bolle A., Van Houwe G., Mattson T., Epstein R. In vivo expression of the rII region of bacteriophage T4 present in chimeric plasmids. Mol Gen Genet. 1981;183(3):505–513. doi: 10.1007/BF00268772. [DOI] [PubMed] [Google Scholar]
  29. Selzer G., Bolle A., Krisch B., Epstein R. Construction and properties of recombinant plasmids containing the rII genes of bacteriophage T4. Mol Gen Genet. 1978 Feb 27;159(3):301–309. doi: 10.1007/BF00268267. [DOI] [PubMed] [Google Scholar]
  30. Shinedling S., Gayle M., Pribnow D., Gold L. Mutations affecting translation of the bacteriophage T4 rIIB gene cloned in Escherichia coli. Mol Gen Genet. 1987 May;207(2-3):224–232. doi: 10.1007/BF00331582. [DOI] [PubMed] [Google Scholar]
  31. Shinedling S., Singer B. S., Gayle M., Pribnow D., Jarvis E., Edgar B., Gold L. Sequences and studies of bacteriophage T4 rII mutants. J Mol Biol. 1987 Jun 5;195(3):471–480. doi: 10.1016/0022-2836(87)90176-8. [DOI] [PubMed] [Google Scholar]
  32. Shinedling S., Walker L. T., Gold L. Cloning the complete rIIB gene of bacteriophage T4 and some observations concerning its middle promoters. J Virol. 1986 Nov;60(2):787–792. doi: 10.1128/jvi.60.2.787-792.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Sugino A., Drake J. W. Modulation of mutation rates in bacteriophage T4 by a base-pair change a dozen nucleotides removed. J Mol Biol. 1984 Jun 25;176(2):239–249. doi: 10.1016/0022-2836(84)90422-4. [DOI] [PubMed] [Google Scholar]
  34. Takacs B. J., Rosenbusch J. P. Modification of Escherichia coli membranes in the prereplicative phase of phage T4 infection. Specificity of association and quantitation of bound phage proteins. J Biol Chem. 1975 Mar 25;250(6):2339–2350. [PubMed] [Google Scholar]
  35. Uzan M., Favre R., Brody E. A nuclease that cuts specifically in the ribosome binding site of some T4 mRNAs. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8895–8899. doi: 10.1073/pnas.85.23.8895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Uzan M., d'Aubenton-Carafa Y., Favre R., de Franciscis V., Brody E. The T4 mot protein functions as part of a pre-replicative DNA-protein complex. J Biol Chem. 1985 Jan 10;260(1):633–639. [PubMed] [Google Scholar]
  37. Webster K. R., Adari H. Y., Spicer E. K. Bacteriophage T4 regA protein binds to the Shine-Dalgarno region of gene 44 mRNA. Nucleic Acids Res. 1989 Dec 11;17(23):10047–10068. doi: 10.1093/nar/17.23.10047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Weintraub S. B., Frankel F. R. Identification of the T4rIIB gene product as a membrane protein. J Mol Biol. 1972 Oct 14;70(3):589–615. doi: 10.1016/0022-2836(72)90561-x. [DOI] [PubMed] [Google Scholar]
  39. Winter R. B., Morrissey L., Gauss P., Gold L., Hsu T., Karam J. Bacteriophage T4 regA protein binds to mRNAs and prevents translation initiation. Proc Natl Acad Sci U S A. 1987 Nov;84(22):7822–7826. doi: 10.1073/pnas.84.22.7822. [DOI] [PMC free article] [PubMed] [Google Scholar]

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