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J Bacteriol. 1993 April; 175(8): 2393–2399.
PMCID: PMC204528

Sites and gene products involved in lambdoid phage DNA packaging.

Abstract

21 is a temperate lambdoid coliphage, and the genes that encode the head proteins of lambda and 21 are descended from a common ancestral bacteriophage. The sequencing of terminase genes 1 and 2 of 21 was completed, along with that of a segment at the right end of 21 DNA that includes the R4 sequence. The R4 sequence, a site that is likely involved in termination of DNA packaging, was found to be very similar to the R4 sequences of lambda and phi 80, suggesting that R4 is a recognition site that is not phage specific. DNA packaging by 21 is dependent on a host protein, integration host factor. A series of mutations in gene 1 (her mutations), which allow integration host factor-independent DNA packaging by 21, were found to be missense changes that affect predicted alpha-helixes in gp1. gp2, the large terminase subunit, is predicted to contain an ATP-binding domain and, perhaps, a second domain important for the cos-cutting activity of terminase. orf1, an open reading frame analogous in position to FI, a lambda gene involved in DNA packaging, shares some sequence identity with FI. orf1 was inactivated with nonsense and insertion mutations; these mutations were found not to affect phage growth. 21 was also not able to complement a lambda FI mutant.

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Selected References

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  • Baldwin RL, Barrand P, Fritsch A, Goldthwait DA, Jacob F. Cohesive sites on the deoxyribonucleic acids from several temperate coliphages. J Mol Biol. 1966 Jun;17(2):343–357. [PubMed]
  • Bear SE, Court DL, Friedman DI. An accessory role for Escherichia coli integration host factor: characterization of a lambda mutant dependent upon integration host factor for DNA packaging. J Virol. 1984 Dec;52(3):966–972. [PMC free article] [PubMed]
  • Becker A, Gold M. Prediction of an ATP reactive center in the small subunit, gpNu1, of the phage lambda terminase enzyme. J Mol Biol. 1988 Jan 5;199(1):219–222. [PubMed]
  • Becker A, Murialdo H. Bacteriophage lambda DNA: the beginning of the end. J Bacteriol. 1990 Jun;172(6):2819–2824. [PMC free article] [PubMed]
  • Becker A, Murialdo H, Lucko H, Morell J. Bacteriophage lambda DNA packaging. The product of the FI gene promotes the incorporation of the prohead to the DNA-terminase complex. J Mol Biol. 1988 Feb 20;199(4):597–607. [PubMed]
  • Berg JM. Potential metal-binding domains in nucleic acid binding proteins. Science. 1986 Apr 25;232(4749):485–487. [PubMed]
  • Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. [PMC free article] [PubMed]
  • Blasco MA, Lázaro JM, Bernad A, Blanco L, Salas M. Phi 29 DNA polymerase active site. Mutants in conserved residues Tyr254 and Tyr390 are affected in dNTP binding. J Biol Chem. 1992 Sep 25;267(27):19427–19434. [PubMed]
  • CAMPBELL A. Sensitive mutants of bacteriophage lambda. Virology. 1961 May;14:22–32. [PubMed]
  • Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148. [PubMed]
  • Cue D, Feiss M. Genetic analysis of mutations affecting terminase, the bacteriophage lambda DNA packaging enzyme, that suppress mutations in cosB, the terminase binding site. J Mol Biol. 1992 Nov 5;228(1):72–87. [PubMed]
  • Davidson A, Gold M. A novel in vitro DNA packaging system demonstrating a direct role for the bacteriophage lambda FI gene product. Virology. 1987 Dec;161(2):305–314. [PubMed]
  • Davidson AR, Gold M. Mutations abolishing the endonuclease activity of bacteriophage lambda terminase lie in two distinct regions of the A gene, one of which may encode a "leucine zipper" DNA-binding domain. Virology. 1992 Jul;189(1):21–30. [PubMed]
  • Delarue M, Poch O, Tordo N, Moras D, Argos P. An attempt to unify the structure of polymerases. Protein Eng. 1990 May;3(6):461–467. [PubMed]
  • 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. [PMC free article] [PubMed]
  • Feiss M, Fisher R, Siegele DA, Widner W. Bacteriophage lambda and 21 packaging specificities. Prog Clin Biol Res. 1981;64:213–222. [PubMed]
  • Feiss M, Frackman S, Momany T. Partial FI gene-independence of lambda-21 hybrid phages specifying chimeric terminases. Virology. 1988 Nov;167(1):323–325. [PubMed]
  • Feiss M, Frackman S, Sippy J. Essential interaction between lambdoid phage 21 terminase and the Escherichia coli integrative host factor. J Mol Biol. 1985 May 25;183(2):239–246. [PubMed]
  • Feiss M, Widner W, Miller G, Johnson G, Christiansen S. Structure of the bacteriophage lambda cohesive end site: location of the sites of terminase binding (cosB) and nicking (cosN). Gene. 1983 Oct;24(2-3):207–218. [PubMed]
  • Frackman S, Siegele DA, Feiss M. The terminase of bacteriophage lambda. Functional domains for cosB binding and multimer assembly. J Mol Biol. 1985 May 25;183(2):225–238. [PubMed]
  • Guo P, Peterson C, Anderson D. Initiation events in in-vitro packaging of bacteriophage phi 29 DNA-gp3. J Mol Biol. 1987 Sep 20;197(2):219–228. [PubMed]
  • Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. [PubMed]
  • Higgins RR, Lucko HJ, Becker A. Mechanism of cos DNA cleavage by bacteriophage lambda terminase: multiple roles of ATP. Cell. 1988 Sep 9;54(6):765–775. [PubMed]
  • Hohn B. DNA sequences necessary for packaging of bacteriophage lambda DNA. Proc Natl Acad Sci U S A. 1983 Dec;80(24):7456–7460. [PubMed]
  • Kleina LG, Miller JH. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J Mol Biol. 1990 Mar 20;212(2):295–318. [PubMed]
  • Kunkel TA. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. [PubMed]
  • Kypr J, Mrázek J. Lambda phage protein Nu 1 contains the conserved DNA binding fold of repressors. J Mol Biol. 1986 Sep 5;191(1):139–140. [PubMed]
  • Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. [PubMed]
  • Miller G, Feiss M. Sequence of the left end of phage 21 DNA. J Mol Biol. 1985 May 25;183(2):246–249. [PubMed]
  • Miwa T, Matsubara K. Lambda phage DNA sequences affecting the packaging process. Gene. 1983 Oct;24(2-3):199–206. [PubMed]
  • Murgola EJ, Prather NE, Pagel FT, Mims BH, Hijazi KA. Missense and nonsense suppressors derived from a glycine tRNA by nucleotide insertion and deletion in vivo. Mol Gen Genet. 1984;193(1):76–81. [PubMed]
  • Murialdo H, Fife WL, Becher A, Feiss M, Yochem J. Bacteriophage lambda DNA maturation. The functional relationships among the products of genes Nul, A and FI. J Mol Biol. 1981 Jan 15;145(2):375–404. [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PubMed]
  • Shibata H, Fujisawa H, Minagawa T. Characterization of the bacteriophage T3 DNA packaging reaction in vitro in a defined system. J Mol Biol. 1987 Aug 20;196(4):845–851. [PubMed]
  • Shinder G, Gold M. The Nul subunit of bacteriophage lambda terminase binds to specific sites in cos DNA. J Virol. 1988 Feb;62(2):387–392. [PMC free article] [PubMed]
  • Siegele DA, Frackman S, Sippy J, Momany T, Howard TM, Tilly K, Georgopoulos C, Feiss M. The head genes of bacteriophage 21. Virology. 1983 Sep;129(2):484–489. [PubMed]
  • Vieira J, Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. [PubMed]
  • Walker JE, Saraste M, Runswick MJ, Gay NJ. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. [PubMed]
  • Wu WF, Christiansen S, Feiss M. Domains for protein-protein interactions at the N and C termini of the large subunit of bacteriophage lambda terminase. Genetics. 1988 Jul;119(3):477–484. [PubMed]
  • Xin WN, Feiss M. The interaction of Escherichia coli integration host factor with the cohesive end sites of phages lambda and 21. Nucleic Acids Res. 1988 Mar 25;16(5):2015–2030. [PMC free article] [PubMed]
  • 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. [PubMed]

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