The ø29 DNA Packaging Motor

Seeking the Mechanism
  • Dwight Anderson
  • Shelley Grimes
Part of the Molecular Biology Intelligence Unit book series (MBIU)

Abstract

The Bacillus subtilis bacteriophage ø29 research team in Minneapolis has marveled at (and reveled in) the intricacies of ø29 assembly for more than 30 years. Here we highlight the current state of knowledge of ø29 DNA packaging. We describe the in vitro packaging system and focus on recent advances that address the mechanism of the packaging motor. Among advances, the head-tail connector has been visualized in proheads and the packaging motor resolved in partially packaged particles by electron microscopy, the structure of the connector has been solved by X-ray crystallography, and the force-velocity relationship of the motor has been established in single molecule studies. A challenge in the future is to determine the structure and interaction of motor components as well as the conformational changes in these components during energy transduction that define the mechanism of DNA translocation.

The compaction of ø29 DNA by more than 100-fold in length during packaging into the prohead is remarkable in that it overcomes the entropic, electrostatic and bending energies of DNA. The ø29 packaging motor is a multisubunit protein-RNA complex at the prohead portal vertex. The motor, driven by ATP hydrolysis, is force-generating and highly processive, and it opposes a strong internal force that builds up within the capsid as DNA is compressed. The motor can work against loads of 57 picoNewtons on average, making it one of the strongest molecular motors yet reported. We aim to identify and characterize the intermediates during the assembly and function of the motor and to determine the structure of each component of the motor at atomic resolution.

A brief overview of the ø29 DNA packaging system follows, and accordingly citation of published work is highly selective. For more detail, refer to a recent comprehensive review of ø29 DNA packaging.1 Also, a comparison of all the bacteriophage DNA packaging systems under study has been addressed (Jardine and Anderson, in press).

Keywords

Connector Channel Single Molecule Study Ratchet Mechanism Head Fiber Packaging Motor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Grimes S, Jardine PJ, Anderson D. Bacteriophage ø29 DNA packaging. Adv Virus Res 2002; 58:255–294.PubMedCrossRefGoogle Scholar
  2. 2.
    Rajagopal BS, Reilly BE, Anderson DL. Bacillus subtilis mutants defective in bacteriophage ø29 head assembly. J Bacteriol 1993; 175:2357–2362.PubMedGoogle Scholar
  3. 3.
    Tao Y, Olson NH, Xu W et al. Assembly of a tailed bacterial virus and its genome release studied in three dimensions. Cell 1998; 95:431–437.PubMedCrossRefGoogle Scholar
  4. 4.
    Guo P, Erickson S, Xu W et al. Regulation of the phage ø29 pro head shape and size by the portal vertex. Virology 1991; 183:366–373.PubMedCrossRefGoogle Scholar
  5. 5.
    Simpson AA, Tao Y, Leiman PG et al. Structure of the bacteriophage ø29 DNA packaging motor. Nature 2000; 408:745–750.PubMedCrossRefGoogle Scholar
  6. 6.
    Guasch A, Pous J, Ibarra B et al. Detailed architecture of a DNA translocating machine: The high-resolution structure of the bacteriophage ø29 connector particle. J Mol Biol 2002; 315:663–676.PubMedCrossRefGoogle Scholar
  7. 7.
    Guasch A, Pous J, Ibarra B et al. (Note to ref. 6) Detailed architecture of a DNA translocating machine: The high-resolution structure of the bacteriophage ø29 connector particle. J Mol Biol 2002; 321:379–380.CrossRefGoogle Scholar
  8. 8.
    Simpson AA, Leiman PG, Tao Y et al. Structure determination of the head-tail connector of bac teriophage ø29. Acta Cryst 2001; D57:1260–1269.Google Scholar
  9. 9.
    Guo P, Erickson S, Anderson DL. A small viral RNA is required for in vitro packaging of bacte riophage ø29 DNA. Science 1987; 236:690–694.PubMedCrossRefGoogle Scholar
  10. 10.
    Wichitwechkarn J, Bailey S, Bodley JW et al. Prohead RNA of bacteriophage ø29: Size, stoichiometry, and biological activity. Nucl Acids Res 1989; 17:3459–3468.PubMedCrossRefGoogle Scholar
  11. 11.
    Guo P, Bailey S, Bodley JW et al. Characterization of the small RNA of the bacteriophage ø29 DNA packaging machine. Nucl Acids Res 1987; 15:7081–7090.PubMedCrossRefGoogle Scholar
  12. 12.
    Wichitwechkarn J, Johnson D, Anderson D. Mutant prohead RNAs in the in vitro packaging of bacteriophage ø29 DNA-gp3. J Mol Biol 1992; 223:991–998.PubMedCrossRefGoogle Scholar
  13. 13.
    Reid RJD, Bodley JW, Anderson D. Identification of bacteriophage ø29 prohead RNA domains necessary for in vitro DNA-gp3 packaging. J Biol Chem 1994; 269:9084–9089.PubMedGoogle Scholar
  14. 14.
    Reid RJD, Zhang F, Benson S et al. Probing the structure of bacteriophage ø29 prohead RNA with specific mutations. J Biol Chem 1994; 269:18656–18661.PubMedGoogle Scholar
  15. 15.
    Zhang C, Lee CS, Guo P. The proximate 5′ and 3′ ends of the 120-base viral RNA (pRNA) are crucial for the packaging of bacteriophage ø29. Virol 1994; 201:77–85.CrossRefGoogle Scholar
  16. 16.
    Zhang C, Tellinghuisen T, Guo P. Use of circular permutation to assess six bulges and four loops of DNA-packaging pRNA of bacteriophage ø29. RNA 1997; 3:315–323.PubMedGoogle Scholar
  17. 17.
    Zhang F, Lemieux S, Wu X et al. Function of hexameric RNA in packaging of bacteriophage ø29 DNA in vitro. Mol Cell 1998; 2:141–147.PubMedCrossRefGoogle Scholar
  18. 18.
    Guo P, Zhang C, Chen C et al. Inter-RNA interaction of phage ø29 pRNA to form a hexameric complex for viral DNA transportation. Mol Cell 1998; 2:149–155.PubMedCrossRefGoogle Scholar
  19. 19.
    Chen C, Sheng S, Shao Z et al. A dimer as a building block in assembling RNA. J Biol Chem 2000; 275:17510–17516.PubMedCrossRefGoogle Scholar
  20. 20.
    Morais MC, Tao Y, Olson NH et al. Cryo-EM image reconstruction of symmetry mismatches in bacteriophage ø29. J Struct Biol 2001; 135:38–46.PubMedCrossRefGoogle Scholar
  21. 21.
    Ibarra B, Caston JR, Llorca O et al. Topology of the components of the DNA packaging machinery in the phage ø29 prohead. J Mol Biol 2000; 298:807–815.PubMedCrossRefGoogle Scholar
  22. 22.
    Guo P, Peterson C, Anderson D. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gpl6 of bacteriophage ø29. J Mol Biol 1987; 197:229–236.PubMedCrossRefGoogle Scholar
  23. 23.
    Grimes S, Anderson D. RNA dependence of the bacteriophage ø29 DNA packaging ATPase. J Mol Biol 1990; 215:559–566.PubMedCrossRefGoogle Scholar
  24. 24.
    Bjornsti MA, Reilly BE, Anderson DL. Bacteriophage ø29 proteins required for in vitro DNA-gp3 packaging. J Virol 1984; 50:766–772.PubMedGoogle Scholar
  25. 25.
    Chen C, Guo P. Sequential action of six virus-encoded DNA-packaging RNAs during phage ø29 genomic DNA translation. J Virol 1997; 71:3864–3871.PubMedGoogle Scholar
  26. 26.
    Meijer WJJ, Horcajadas JA, Salas M. ø29 Family of Phages. Microbiol and Mol Biol Rev 2001; 65:261–287.CrossRefGoogle Scholar
  27. 27.
    Grimes S, Anderson D. The bacteriophage ø29 packaging proteins supercoil the DNA ends. J Mol Biol 1997; 266:901–914.PubMedCrossRefGoogle Scholar
  28. 28.
    Grimes S, Anderson D. In vitro packaging of bacteriophage ø29 DNA restriction fragments and the role of the terminal protein gp3. J Mol Biol 1989; 209:91–100.PubMedCrossRefGoogle Scholar
  29. 29.
    Bjornsti MA, Reilly BE, Anderson DL. Morphogenesis of bacteriophage ø29 of Bacillus subtilis: Oriented and quantized in vitro packaging of DNA-gp3. J Virol 1983; 45:383–396.PubMedGoogle Scholar
  30. 30.
    Turnquist S, Simon M, Egelman E et al. Supercoiled DNA wraps around the bacteriophage ø29 head-tail connector. Proc Natl Acad Sci USA 1992; 89:10479–10483.PubMedCrossRefGoogle Scholar
  31. 31.
    Hendrix RW. Symmetry mismatch and DNA packaging in large bacteriophages. Proc Natl Acad Sci USA 1978; 75:4779–4783.PubMedCrossRefGoogle Scholar
  32. 32.
    Muller DJ, Engel A, Carrascosa JL et al. The bacteriophage ø29 head-tail connector imaged at high resolution with the atomic force microscope in buffer solution. EMBO J 1997; 16:2547–2553.PubMedCrossRefGoogle Scholar
  33. 33.
    Kinosita Jr K, Yasuda R, Noji H et al. F1-ATPase: A rotary motor made of a single molecule. Cell 1998; 93:21–24.PubMedCrossRefGoogle Scholar
  34. 34.
    Silverman MR, Simon MI. Flagellar rotation and the mechanism of bacterial motility. Nature 1974; 249:73–74.PubMedCrossRefGoogle Scholar
  35. 35.
    Vale RD, Milligan RA. The way things move: Looking under the hood of molecular motor proteins. Science 2000; 288:88–95.PubMedCrossRefGoogle Scholar
  36. 36.
    Smith DE, Tans SJ, Smith SJ et al. The bacteriophage ø29 portal motor can package DNA against a large internal force. Nature 2001; 413:748–752.PubMedCrossRefGoogle Scholar
  37. 37.
    Earnshaw WC, Casjens SR. DNA packaging by the double-stranded DNA bacteriophages. Cell 1980; 21:319–331.PubMedCrossRefGoogle Scholar
  38. 38.
    Alberts B, Miaki-Lye R. Unscrambling the puzzle of biological machines: The importance of the details. Cell 1992; 68:415–420.PubMedCrossRefGoogle Scholar

Copyright information

© Eurekah.com and Kluwer Academic/Plenum Publishers 2005

Authors and Affiliations

  • Dwight Anderson
    • 1
  • Shelley Grimes
    • 2
  1. 1.Department of Oral Science and Department of MicrobiologyUniversity of MinnesotaMinneapolisUSA
  2. 2.Department of Oral ScienceUniversity of MinnesotaMinneapolisUSA

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