Skip to main content
NCBI home page
The EMBO Journal logoLink to The EMBO Journal
. 1993 Nov;12(11):4453–4459. doi: 10.1002/j.1460-2075.1993.tb06131.x

RNA-mediated specificity of DNA packaging into hybrid lambda/phi 29 proheads.

J M Valpuesta 1, L E Donate 1, C Mier 1, L Herranz 1, J L Carrascosa 1
PMCID: PMC413745  PMID: 8223455

Abstract

A small RNA (pRNA, 174 nt) is known to be essential for DNA packaging in bacteriophage phi 29. However, in an in vitro DNA packaging system based on hybrid lambda/phi 29 proheads (made up of head proteins from phage lambda and connectors from phage phi 29), the specificity of DNA packaging is lost, and different RNA molecules fulfil the requirements for DNA packaging, albeit with less efficiency than phi 29 pRNA. Competition assays with RNAs from different sources have shown that phi 29 connectors bind preferentially pRNA. An increase in the efficiency of phi 29 DNA packaging into hybrid proheads induced by phi 29 pRNA is observed because, when phi 29 pRNA is incubated with hybrid proheads, phi 29 DNA is packaged more efficiently than other DNAs of similar length. Furthermore, when hybrid proheads carrying phi 29 pRNA are incubated with a mixture of DNAs from different sources, phi 29 DNA is selectively packaged, thus indicating that phi 29 pRNA determines the specificity of DNA packaging.

Full text

PDF
4453

Images in this article

4456Image
on p.4456

Selected References

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

  1. Bailey S., Wichitwechkarn J., Johnson D., Reilly B. E., Anderson D. L., Bodley J. W. Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging. J Biol Chem. 1990 Dec 25;265(36):22365–22370. [PubMed] [Google Scholar]
  2. Bazinet C., King J. The DNA translocating vertex of dsDNA bacteriophage. Annu Rev Microbiol. 1985;39:109–129. doi: 10.1146/annurev.mi.39.100185.000545. [DOI] [PubMed] [Google Scholar]
  3. Black L. W. DNA packaging in dsDNA bacteriophages. Annu Rev Microbiol. 1989;43:267–292. doi: 10.1146/annurev.mi.43.100189.001411. [DOI] [PubMed] [Google Scholar]
  4. Buchwald M., Murialdo H., Siminovitch L. The morphogenesis of bacteriophage lambda. II. Identification of the principal structural proteins. Virology. 1970 Oct;42(2):390–400. doi: 10.1016/0042-6822(70)90282-5. [DOI] [PubMed] [Google Scholar]
  5. Camacho A., Jiménez F., De La Torre J., Carrascosa J. L., Mellado R. P., Vásquez C., Viñuela E., Salas M. Assembly of Bacillus subtilis phage phi29. 1. Mutants in the cistrons coding for the structural proteins. Eur J Biochem. 1977 Feb 15;73(1):39–55. doi: 10.1111/j.1432-1033.1977.tb11290.x. [DOI] [PubMed] [Google Scholar]
  6. Carazo J. M., Donate L. E., Herranz L., Secilla J. P., Carrascosa J. L. Three-dimensional reconstruction of the connector of bacteriophage phi 29 at 1.8 nm resolution. J Mol Biol. 1986 Dec 20;192(4):853–867. doi: 10.1016/0022-2836(86)90033-1. [DOI] [PubMed] [Google Scholar]
  7. Carazo J. M., Santisteban A., Carrascosa J. L. Three-dimensional reconstruction of bacteriophage phi 29 neck particles at 2 X 2 nm resolution. J Mol Biol. 1985 May 5;183(1):79–88. doi: 10.1016/0022-2836(85)90282-7. [DOI] [PubMed] [Google Scholar]
  8. Carrascosa J. L., Carazo J. M., Ibañez C., Santisteban A. Structure of phage phi 29 connector protein assembled in vivo. Virology. 1985 Mar;141(2):190–200. doi: 10.1016/0042-6822(85)90251-x. [DOI] [PubMed] [Google Scholar]
  9. Chow S., Daub E., Murialdo H. The overproduction of DNA terminase of coliphage lambda. Gene. 1987;60(2-3):277–289. doi: 10.1016/0378-1119(87)90236-8. [DOI] [PubMed] [Google Scholar]
  10. Donate L. E., Carrascosa J. L. Characterization of a versatile in vitro DNA-packaging system based on hybrid lambda/phi 29 proheads. Virology. 1991 Jun;182(2):534–544. doi: 10.1016/0042-6822(91)90594-2. [DOI] [PubMed] [Google Scholar]
  11. Donate L. E., Herranz L., Secilla J. P., Carazo J. M., Fujisawa H., Carrascosa J. L. Bacteriophage T3 connector: three-dimensional structure and comparison with other viral head-tail connecting regions. J Mol Biol. 1988 May 5;201(1):91–100. doi: 10.1016/0022-2836(88)90441-x. [DOI] [PubMed] [Google Scholar]
  12. Donate L. E., Murialdo H., Carrascosa J. L. Production of lambda-phi 29 phage chimeras. Virology. 1990 Dec;179(2):936–940. doi: 10.1016/0042-6822(90)90172-n. [DOI] [PubMed] [Google Scholar]
  13. Donate L. E., Valpuesta J. M., Rocher A., Méndez E., Rojo F., Salas M., Carrascosa J. L. Role of the amino-terminal domain of bacteriophage phi 29 connector in DNA binding and packaging. J Biol Chem. 1992 May 25;267(15):10919–10924. [PubMed] [Google Scholar]
  14. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Driedonks R. A., Engel A., tenHeggeler B., van Driel Gene 20 product of bacteriophage T4 its purification and structure. J Mol Biol. 1981 Nov 15;152(4):641–662. doi: 10.1016/0022-2836(81)90121-2. [DOI] [PubMed] [Google Scholar]
  16. Earnshaw W. C., Casjens S. R. DNA packaging by the double-stranded DNA bacteriophages. Cell. 1980 Sep;21(2):319–331. doi: 10.1016/0092-8674(80)90468-7. [DOI] [PubMed] [Google Scholar]
  17. Escarmís C., Salas M. Nucleotide sequence at the termini of the DNA of Bacillus subtilis phage phi 29. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1446–1450. doi: 10.1073/pnas.78.3.1446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. García J. A., Méndez E., Salas M. Cloning, nucleotide sequence and high level expression of the gene coding for the connector protein of Bacillus subtilis phage phi 29. Gene. 1984 Oct;30(1-3):87–98. doi: 10.1016/0378-1119(84)90108-2. [DOI] [PubMed] [Google Scholar]
  19. Grimes S., Anderson D. Cleaving the prohead RNA of bacteriophage phi 29 alters the in vitro packaging of restriction fragments of DNA-gp3. J Mol Biol. 1989 Sep 5;209(1):101–108. doi: 10.1016/0022-2836(89)90173-3. [DOI] [PubMed] [Google Scholar]
  20. Grimes S., Anderson D. RNA dependence of the bacteriophage phi 29 DNA packaging ATPase. J Mol Biol. 1990 Oct 20;215(4):559–566. doi: 10.1016/s0022-2836(05)80168-8. [DOI] [PubMed] [Google Scholar]
  21. Guo P. X., Bailey S., Bodley J. W., Anderson D. Characterization of the small RNA of the bacteriophage phi 29 DNA packaging machine. Nucleic Acids Res. 1987 Sep 11;15(17):7081–7090. doi: 10.1093/nar/15.17.7081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Guo P. X., Erickson S., Anderson D. A small viral RNA is required for in vitro packaging of bacteriophage phi 29 DNA. Science. 1987 May 8;236(4802):690–694. doi: 10.1126/science.3107124. [DOI] [PubMed] [Google Scholar]
  23. Guo P. X., Rajagopal B. S., Anderson D., Erickson S., Lee C. S. sRNA of phage phi 29 of Bacillus subtilis mediates DNA packaging of phi 29 proheads assembled in Escherichia coli. Virology. 1991 Nov;185(1):395–400. doi: 10.1016/0042-6822(91)90787-c. [DOI] [PubMed] [Google Scholar]
  24. Guo P., Grimes S., Anderson D. A defined system for in vitro packaging of DNA-gp3 of the Bacillus subtilis bacteriophage phi 29. Proc Natl Acad Sci U S A. 1986 May;83(10):3505–3509. doi: 10.1073/pnas.83.10.3505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. 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. doi: 10.1016/0022-2836(87)90120-3. [DOI] [PubMed] [Google Scholar]
  26. Hendrix R. W. Symmetry mismatch and DNA packaging in large bacteriophages. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4779–4783. doi: 10.1073/pnas.75.10.4779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Herranz L., Bordas J., Towns-Andrews E., Mendez E., Usobiaga P., Carrascosa J. L. Conformational changes in bacteriophage phi 29 connector prevents DNA-binding activity. J Mol Biol. 1990 May 20;213(2):263–273. doi: 10.1016/s0022-2836(05)80189-5. [DOI] [PubMed] [Google Scholar]
  28. Herranz L., Salas M., Carrascosa J. L. Interaction of the bacteriophage phi 29 connector protein with the viral DNA. Virology. 1986 Nov;155(1):289–292. doi: 10.1016/0042-6822(86)90191-1. [DOI] [PubMed] [Google Scholar]
  29. Hsiao C. L., Black L. W. Head morphogenesis of bacteriophage T4. II. The role of gene 40 in initiating prehead assembly. Virology. 1978 Nov;91(1):15–25. doi: 10.1016/0042-6822(78)90351-3. [DOI] [PubMed] [Google Scholar]
  30. Ibáez C., García J. A., Carrascosa J. L., Salas M. Overproduction and purification of the connector protein of Bacillus subtilis phage phi 29. Nucleic Acids Res. 1984 Mar 12;12(5):2351–2365. doi: 10.1093/nar/12.5.2351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kenan D. J., Query C. C., Keene J. D. RNA recognition: towards identifying determinants of specificity. Trends Biochem Sci. 1991 Jun;16(6):214–220. doi: 10.1016/0968-0004(91)90088-d. [DOI] [PubMed] [Google Scholar]
  32. Kochan J., Murialdo H. Early intermediates in bacteriophage lambda prohead assembly. II. Identification of biologically active intermediates. Virology. 1983 Nov;131(1):100–115. doi: 10.1016/0042-6822(83)90537-8. [DOI] [PubMed] [Google Scholar]
  33. Lesk A. M., Chothia C. Mechanisms of domain closure in proteins. J Mol Biol. 1984 Mar 25;174(1):175–191. doi: 10.1016/0022-2836(84)90371-1. [DOI] [PubMed] [Google Scholar]
  34. Ley V., Almendral J. M., Carbonero P., Beloso A., Viñuela E., Talavera A. Molecular cloning of African swine fever virus DNA. Virology. 1984 Mar;133(2):249–257. doi: 10.1016/0042-6822(84)90392-1. [DOI] [PubMed] [Google Scholar]
  35. Murialdo H., Becker A. Head morphogenesis of complex double-stranded deoxyribonucleic acid bacteriophages. Microbiol Rev. 1978 Sep;42(3):529–576. doi: 10.1128/mr.42.3.529-576.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Murialdo H., Siminovitch L. The morphogenesis of bacteriophage lambda. IV. Identification of gene products and control of the expression of the morphogenetic information. Virology. 1972 Jun;48(3):785–823. doi: 10.1016/0042-6822(72)90162-6. [DOI] [PubMed] [Google Scholar]
  37. Nakasu S., Fujisawa H., Minagawa T. Purification of characterization of gene 8 product of bacteriophage T3. Virology. 1985 Jun;143(2):422–434. doi: 10.1016/0042-6822(85)90382-4. [DOI] [PubMed] [Google Scholar]
  38. Peñalva M. A., Salas M. Initiation of phage phi 29 DNA replication in vitro: formation of a covalent complex between the terminal protein, p3, and 5'-dAMP. Proc Natl Acad Sci U S A. 1982 Sep;79(18):5522–5526. doi: 10.1073/pnas.79.18.5522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Pérez-Martín J., Espinosa M. The RepA repressor can act as a transcriptional activator by inducing DNA bends. EMBO J. 1991 Jun;10(6):1375–1382. doi: 10.1002/j.1460-2075.1991.tb07657.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Raj A. S., Raj A. Y., Schmieger H. Phage genes involved in the formation generalized transducing particles in Salmonella--Phage P22. Mol Gen Genet. 1974;135(2):175–184. doi: 10.1007/BF00264784. [DOI] [PubMed] [Google Scholar]
  41. Turnquist S., Simon M., Egelman E., Anderson D. Supercoiled DNA wraps around the bacteriophage phi 29 head-tail connector. Proc Natl Acad Sci U S A. 1992 Nov 1;89(21):10479–10483. doi: 10.1073/pnas.89.21.10479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Valpuesta J. M., Fujisawa H., Marco S., Carazo J. M., Carrascosa J. L. Three-dimensional structure of T3 connector purified from overexpressing bacteria. J Mol Biol. 1992 Mar 5;224(1):103–112. doi: 10.1016/0022-2836(92)90579-9. [DOI] [PubMed] [Google Scholar]
  43. Valpuesta J. M., Serrano M., Donate L. E., Herranz L., Carrascosa J. L. DNA conformational change induced by the bacteriophage phi 29 connector. Nucleic Acids Res. 1992 Nov 11;20(21):5549–5554. doi: 10.1093/nar/20.21.5549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wichitwechkarn J., Johnson D., Anderson D. Mutant prohead RNAs in the in vitro packaging of bacteriophage phi 29 DNA-gp3. J Mol Biol. 1992 Feb 20;223(4):991–998. doi: 10.1016/0022-2836(92)90257-k. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES