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. 1986 Dec 9;14(23):9311–9327. doi: 10.1093/nar/14.23.9311

The region of phage T4 genes 34, 33 and 59: primary structures and organization on the genome.

S Hahn, U Kruse, W Rüger
PMCID: PMC311960  PMID: 3797242

Abstract

The product of gene 33 is essential for the regulation of late transcription and gene product 59 is required in recombination, DNA repair and replication. The exact functions of both proteins are not known. Restriction fragments spanning the genomic area of genes 33 and 59 have been cloned into phage M13 and a 4.9 kb nucleotide sequence has been determined. Translation of the DNA sequence predicted that gp33 contains 112 amino acids with a mol.wt. of 12.816 kd while gp59 is composed of 217 amino acids adding up to a mol.wt. of 25.967 kd. The genomic area studied here also contains 3 open reading frames of genes not identified to date and it is thought to include the NH2-terminal part of g34. One of the open reading frames seems to code for the 10 kd protein, probably involved in the regulation of transcription of bacteriophage T4. This protein is predicted to consist of 89 amino acid residues with a mol.wt. of 10.376 kd. Gene 33 and the gene for the 10 kd protein were cloned separately on high expression vectors resulting in over-production of the two proteins.

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Selected References

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  1. Beckendorf S. K., Wilson J. H. A recombination gradient in bacteriophage T4 gene 34. Virology. 1972 Nov;50(2):315–321. doi: 10.1016/0042-6822(72)90382-0. [DOI] [PubMed] [Google Scholar]
  2. 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]
  3. Burton Z., Burgess R. R., Lin J., Moore D., Holder S., Gross C. A. The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res. 1981 Jun 25;9(12):2889–2903. doi: 10.1093/nar/9.12.2889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Capaldi R. A., Vanderkooi G. The low polarity of many membrane proteins. Proc Natl Acad Sci U S A. 1972 Apr;69(4):930–932. doi: 10.1073/pnas.69.4.930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
  6. Christensen A. C., Young E. T. T4 late transcripts are initiated near a conserved DNA sequence. Nature. 1982 Sep 23;299(5881):369–371. doi: 10.1038/299369a0. [DOI] [PubMed] [Google Scholar]
  7. Costanzo M., Brzustowicz L., Hannett N., Pero J. Bacteriophage SPO1 genes 33 and 34. Location and primary structure of genes encoding regulatory subunits of Bacillus subtilis RNA polymerase. J Mol Biol. 1984 Dec 15;180(3):533–547. doi: 10.1016/0022-2836(84)90026-3. [DOI] [PubMed] [Google Scholar]
  8. Costanzo M., Pero J. Structure of a Bacillus subtilis bacteriophage SPO1 gene encoding RNA polymerase sigma factor. Proc Natl Acad Sci U S A. 1983 Mar;80(5):1236–1240. doi: 10.1073/pnas.80.5.1236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. DeLange R. J., Williams L. C., Searcy D. G. A histone-like protein (HTa) from Thermoplasma acidophilum. II. Complete amino acid sequence. J Biol Chem. 1981 Jan 25;256(2):905–911. [PubMed] [Google Scholar]
  11. 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]
  12. Escarmís C., Salas M. Nucleotide sequence of the early genes 3 and 4 of bacteriophage phi 29. Nucleic Acids Res. 1982 Oct 11;10(19):5785–5798. doi: 10.1093/nar/10.19.5785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fukada K., Abelson J. DNA sequence of a T4 transfer RNA gene cluster. J Mol Biol. 1980 May 25;139(3):377–391. doi: 10.1016/0022-2836(80)90136-9. [DOI] [PubMed] [Google Scholar]
  14. Gentz R., Langner A., Chang A. C., Cohen S. N., Bujard H. Cloning and analysis of strong promoters is made possible by the downstream placement of a RNA termination signal. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4936–4940. doi: 10.1073/pnas.78.8.4936. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gitt M. A., Wang L. F., Doi R. H. A strong sequence homology exists between the major RNA polymerase sigma factors of Bacillus subtilis and Escherichia coli. J Biol Chem. 1985 Jun 25;260(12):7178–7185. [PubMed] [Google Scholar]
  16. Gold L., Pribnow D., Schneider T., Shinedling S., Singer B. S., Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. doi: 10.1146/annurev.mi.35.100181.002053. [DOI] [PubMed] [Google Scholar]
  17. Gram H., Liebig H. D., Hack A., Niggemann E., Rüger W. A physical map of bacteriophage T4 including the positions of strong promoters and terminators recognized in vitro. Mol Gen Genet. 1984;194(1-2):232–240. doi: 10.1007/BF00383522. [DOI] [PubMed] [Google Scholar]
  18. Gram H., Rüger W. Genes 55, alpha gt, 47 and 46 of bacteriophage T4: the genomic organization as deduced by sequence analysis. EMBO J. 1985 Jan;4(1):257–264. doi: 10.1002/j.1460-2075.1985.tb02344.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gribskov M., Burgess R. R. Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. Nucleic Acids Res. 1986 Aug 26;14(16):6745–6763. doi: 10.1093/nar/14.16.6745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Harrison C. A., Turner D. H., Hinkle D. C. Laser crosslinking of E. coli RNA polymerase and T7 DNA. Nucleic Acids Res. 1982 Apr 10;10(7):2399–2414. doi: 10.1093/nar/10.7.2399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hattori M., Sakaki Y. Dideoxy sequencing method using denatured plasmid templates. Anal Biochem. 1986 Feb 1;152(2):232–238. doi: 10.1016/0003-2697(86)90403-3. [DOI] [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. Hercules K., Wiberg J. S. Specific suppression of mutations in genes 46 and 47 by das, a new class of mutations in bacteriophage T4D. J Virol. 1971 Nov;8(5):603–612. doi: 10.1128/jvi.8.5.603-612.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Hercules K., Wiberg J. S. Specific suppression of mutations in genes 46 and 47 by das, a new class of mutations in bacteriophage T4D. J Virol. 1971 Nov;8(5):603–612. doi: 10.1128/jvi.8.5.603-612.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Hockensmith J. W., Kubasek W. L., Vorachek W. R., von Hippel P. H. Laser cross-linking of nucleic acids to proteins. Methodology and first applications to the phage T4 DNA replication system. J Biol Chem. 1986 Mar 15;261(8):3512–3518. [PubMed] [Google Scholar]
  27. Joyce C. M., Kelley W. S., Grindley N. D. Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I. J Biol Chem. 1982 Feb 25;257(4):1958–1964. [PubMed] [Google Scholar]
  28. Krisch H. M., Allet B. Nucleotide sequences involved in bacteriophage T4 gene 32 translational self-regulation. Proc Natl Acad Sci U S A. 1982 Aug;79(16):4937–4941. doi: 10.1073/pnas.79.16.4937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kröger M., Hobom G. A chain of interlinked genes in the ninR region of bacteriophage lambda. Gene. 1982 Nov;20(1):25–38. doi: 10.1016/0378-1119(82)90084-1. [DOI] [PubMed] [Google Scholar]
  30. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
  34. Malik S., Dimitrov M., Goldfarb A. Initiation of transcription by bacteriophage T4-modified RNA polymerase independently of host sigma factor. J Mol Biol. 1985 Sep 5;185(1):83–91. doi: 10.1016/0022-2836(85)90184-6. [DOI] [PubMed] [Google Scholar]
  35. Mattson T., Van Houwe G., Bolle A., Selzer G., Epstein R. Genetic identification of cloned fragments of bacteriophage T4 DNA and complementation by some clones containing early T4 genes. Mol Gen Genet. 1977 Sep 9;154(3):319–326. doi: 10.1007/BF00571289. [DOI] [PubMed] [Google Scholar]
  36. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Mickelson C., Wiberg J. S. Membrane-associated DNase activity controlled by genes 46 and 47 of bacteriophage T4D and elevated DNase activity associated with the T4 das mutation. J Virol. 1981 Oct;40(1):65–77. doi: 10.1128/jvi.40.1.65-77.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. 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]
  39. Pulitzer J. F., Colombo M., Ciaramella M. New control elements of bacteriophage T4 pre-replicative transcription. J Mol Biol. 1985 Mar 20;182(2):249–263. doi: 10.1016/0022-2836(85)90343-2. [DOI] [PubMed] [Google Scholar]
  40. Putterman D. G., Casadevall A., Boyle P. D., Yang H. L., Frangione B., Day L. A. Major coat protein and single-stranded DNA-binding protein of filamentous virus Pf3. Proc Natl Acad Sci U S A. 1984 Feb;81(3):699–703. doi: 10.1073/pnas.81.3.699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Rawlings N., Ashman K., Wittmann-Liebold B. Computerised version of the Chou and Fasman protein secondary structure predictive method. Int J Pept Protein Res. 1983 Nov;22(5):515–524. doi: 10.1111/j.1399-3011.1983.tb02124.x. [DOI] [PubMed] [Google Scholar]
  43. Remaut E., Stanssens P., Fiers W. Plasmid vectors for high-efficiency expression controlled by the PL promoter of coliphage lambda. Gene. 1981 Oct;15(1):81–93. doi: 10.1016/0378-1119(81)90106-2. [DOI] [PubMed] [Google Scholar]
  44. Revel H. R. Molecular cloning of the T4 genome: organization and expression of the tail fiber gene cluster 34--38. Mol Gen Genet. 1981;182(3):445–455. doi: 10.1007/BF00293934. [DOI] [PubMed] [Google Scholar]
  45. Robson B., Suzuki E. Conformational properties of amino acid residues in globular proteins. J Mol Biol. 1976 Nov 5;107(3):327–356. doi: 10.1016/s0022-2836(76)80008-3. [DOI] [PubMed] [Google Scholar]
  46. 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]
  47. Rüger W. Transcription of bacteriophage T4 DNA in vitro: selective initiation with dinucleotides. Eur J Biochem. 1978 Jul 17;88(1):109–117. doi: 10.1111/j.1432-1033.1978.tb12427.x. [DOI] [PubMed] [Google Scholar]
  48. 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]
  49. Shah D. B. Replication and recombination of gene 59 mutant of bacteriophage T4D. J Virol. 1975 Jan;17(1):175–182. doi: 10.1128/jvi.17.1.175-182.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. 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]
  51. Shortle D., DiMaio D., Nathans D. Directed mutagenesis. Annu Rev Genet. 1981;15:265–294. doi: 10.1146/annurev.ge.15.120181.001405. [DOI] [PubMed] [Google Scholar]
  52. Sinha N. D., Biernat J., McManus J., Köster H. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res. 1984 Jun 11;12(11):4539–4557. doi: 10.1093/nar/12.11.4539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Stevens A. New small polypeptides associated with DNA-dependent RNA polymerase of Escherichia coli after infection with bacteriophage T4. Proc Natl Acad Sci U S A. 1972 Mar;69(3):603–607. doi: 10.1073/pnas.69.3.603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Stevens A., Rhoton J. C. Characterization of an inhibitor causing potassium chloride sensitivity of an RNA polymerase from T4 phage-infected Escherichia coli. Biochemistry. 1975 Nov 18;14(23):5074–5079. doi: 10.1021/bi00694a007. [DOI] [PubMed] [Google Scholar]
  55. Stragier P., Bouvier J., Bonamy C., Szulmajster J. A developmental gene product of Bacillus subtilis homologous to the sigma factor of Escherichia coli. Nature. 1984 Nov 22;312(5992):376–378. doi: 10.1038/312376a0. [DOI] [PubMed] [Google Scholar]
  56. Tabor S., Richardson C. C. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1074–1078. doi: 10.1073/pnas.82.4.1074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Tomaschewski J., Gram H., Crabb J. W., Rüger W. T4-induced alpha- and beta-glucosyltransferase: cloning of the genes and a comparison of their products based on sequencing data. Nucleic Acids Res. 1985 Nov 11;13(21):7551–7568. doi: 10.1093/nar/13.21.7551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Vanderslice R. W., Yegian C. D. The identification of late bacteriophage T4 proteins on sodium dodecyl sulfate polyacrylamide gels. Virology. 1974 Jul;60(1):265–275. doi: 10.1016/0042-6822(74)90384-5. [DOI] [PubMed] [Google Scholar]
  59. Walz A., Pirrotta V., Ineichen K. Lambda repressor regulates the switch between PR and Prm promoters. Nature. 1976 Aug 19;262(5570):665–669. doi: 10.1038/262665a0. [DOI] [PubMed] [Google Scholar]
  60. Ward S., Dickson R. C. Assembly of bacteriophage T4 tail fibers. 3. Genetic control of the major tail fiber polypeptides. J Mol Biol. 1971 Dec 28;62(3):479–492. doi: 10.1016/0022-2836(71)90149-5. [DOI] [PubMed] [Google Scholar]
  61. Wood W. B., Revel H. R. The genome of bacteriophage T4. Bacteriol Rev. 1976 Dec;40(4):847–868. doi: 10.1128/br.40.4.847-868.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Wu R., Wu J. L., Yeh Y. C. Role of gene 59 of bacteriophage T4 in repair of UV-irradiated and alkylated DNA in vivo. J Virol. 1975 Jul;16(1):5–16. doi: 10.1128/jvi.16.1.5-16.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. 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]

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