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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

DNA Packaging

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Disease relevance of DNA Packaging

  • The packaging enzyme and the mature capsid protein (gp23*) both appear to arise from processing of gp23, the former as a minor product of a specific gp23 structure in the prohead, acting in DNA packaging as a DNA-dependent ATPase, and a headful-dependent terminase [1].
  • The first structure reveals a complex assembly in the interior of the capsid, which involves the scaffolding, and the core complex, which plays an important role in DNA packaging and is located in one of the phage vertices [2].
  • Escherichia coli integration host factor and D108 transposase proteins exerted an inhibitory effect on circular DNA substrates but had little effect on linear DNA packaging [3].
  • In contrast to the well-established DNA packaging mechanism of Bacillus subtilis phage Ø29, that involves a molecular motor formed by the connector and a viral ATPase, nothing is known about its DNA injection into the cell [4].
  • Structural characterization of the UL25 DNA-packaging protein from herpes simplex virus type 1 [5].

High impact information on DNA Packaging

  • We report here that positive charge on one of the four lysine side chains in the latter region has a direct effect on DNA packaging, because when this charge is absent, elongated particles are produced with lengths that can be correlated with the residual positive charge in the C-terminal region of the coat protein subunit [6].
  • DNA packaging into chromatin presents a strong barrier to RNA polymerase II transcription [7].
  • Although we show that gp6 in the connector has a fold similar to that of the isolated portal protein, we observe conformational changes in the region of gp6 exposed to the DNA-packaging ATPase and to gp15 [8].
  • 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 [9].
  • These data therefore suggest that the formation of novel DNA structures by the pac1 motif confers added specificity on recognition of DNA packaging sequences by the U(L)28-encoded component of the herpesvirus cleavage and packaging machinery [10].

Chemical compound and disease context of DNA Packaging


Biological context of DNA Packaging

  • Mutants in specific amino acids of the NH2-terminal domain, obtained by directed mutagenesis techniques, showed that the Ala1-Arg2-Lys3-Arg4 region of the connector is absolutely necessary for DNA packaging into the proheads as well as for efficient DNA binding [16].
  • Dimerization of pRNA was promoted by a variety of cations including spermidine, whereas procapsid binding and DNA packaging required specific divalent cations, including Mg(2+), Ca(2+), and Mn(2+) [17].
  • Mutation resulting in changes of the D hairpin loop and its connecting residues within the prohead binding site of pRNA and DNA packaging studies demonstrated that some alteration of secondary structure in this helix was permissible [18].
  • These machines appear to mediate diverse, complex and essential processes such as intron excision, RNA modification and editing, protein targeting, DNA packaging, etc [19].
  • A set of 40 genes, termed the 'core genes', is commonly found in all herpesviruses; their products include four capsid proteins, six DNA replication proteins, seven DNA packaging/cleavage proteins, four envelope glycoproteins, as well as several others [20].

Anatomical context of DNA Packaging


Associations of DNA Packaging with chemical compounds

  • To reveal intermediates in lambda DNA packaging, infected cells were osmotically ruptured and the cell lysates were deposited on electron microscope grids by sedimentation through a sucrose/formalin cushion [22].
  • However, cycloheximide is an inhibitor of mammalian protein synthesis and inhibits DNA synthesis only indirectly, probably through a consequent deficiency of DNA-packaging proteins [23].
  • This increase is (i) caused by an increase in the solid support-free mu (muo) of the procapsid, not a decrease in its radius, and (ii) not prevented by either genetically or chemically (use of proflavine) blocking DNA packaging [24].
  • Thus, this study for the first time identified and characterized a catalytic glutamate residue that is involved in the energy transduction mechanism of a viral DNA packaging machine [11].
  • From these results, we concluded that the prohead binding domain is composed of two subdomains: Region I is a "core" domain, and its binding to the prohead is crucial for DNA packaging, and Region II is an "anchor" domain stabilizing the binding by Region I [25].

Gene context of DNA Packaging

  • The properties of the UL17 and UL25 proteins are consistent with the idea that the two proteins are important in stabilizing capsid-DNA structures rather than having a direct role in DNA packaging [26].
  • These lysozyme-hypersensitive polymerases behave without lysozyme similarly to wild-type polymerase with lysozyme: both remain longer at the promoter before establishing a lysozyme-resistant elongation complex and both increase the length of pausing when elongation complexes encounter an eight-base recognition sequence involved in DNA packaging [27].
  • In DR they are each adjacent to DNA packaging motifs, pac1 and pac2, described for herpes simplex virus and human cytomegalovirus, in the arrangement pac1-imperfect repeat-7.2 kb-perfect repeat-pac2 [28].
  • Here we demonstrate that, in rho(-) yeast strains, Hmi1p stimulates the synthesis of long concatemeric mitochondrial DNA molecules associated with a reduction in the number of nucleoids used for mitochondrial DNA packaging [29].
  • We were able to coimmunoprecipitate capsid proteins sedimenting between 60 and 110S with antibodies against Rep proteins, suggesting that they exist in common complexes possibly involved in AAV DNA packaging [30].

Analytical, diagnostic and therapeutic context of DNA Packaging

  • Sequence analysis of this molecule, named pGIL01, showed the presence of at least 30 ORFs, five of which displayed similarity with proteins involved in phage systems: a B-type family DNA polymerase, a LexA-like repressor, two potential muramidases and a DNA-packaging protein (distantly related to the P9 protein of the tectiviral phage PRD1) [31].


  1. Evidence that a phage T4 DNA packaging enzyme is a processed form of the major capsid gene product. Rao, V.B., Black, L.W. Cell (1985) [Pubmed]
  2. Maturation of phage T7 involves structural modification of both shell and inner core components. Agirrezabala, X., Martín-Benito, J., Castón, J.R., Miranda, R., Valpuesta, J.M., Carrascosa, J.L. EMBO J. (2005) [Pubmed]
  3. In vitro maturation and encapsidation of the DNA of transposable Mu-like phage D108. Burns, C.M., Chan, H.L., DuBow, M.S. Proc. Natl. Acad. Sci. U.S.A. (1990) [Pubmed]
  4. The push-pull mechanism of bacteriophage Ø29 DNA injection. González-Huici, V., Salas, M., Hermoso, J.M. Mol. Microbiol. (2004) [Pubmed]
  5. Structural characterization of the UL25 DNA-packaging protein from herpes simplex virus type 1. Bowman, B.R., Welschhans, R.L., Jayaram, H., Stow, N.D., Preston, V.G., Quiocho, F.A. J. Virol. (2006) [Pubmed]
  6. Interactions between DNA and coat protein in the structure and assembly of filamentous bacteriophage fd. Hunter, G.J., Rowitch, D.H., Perham, R.N. Nature (1987) [Pubmed]
  7. How does Pol II overcome the nucleosome barrier? Adelman, K., Lis, J.T. Mol. Cell (2002) [Pubmed]
  8. Structure of a viral DNA gatekeeper at 10 A resolution by cryo-electron microscopy. Orlova, E.V., Gowen, B., Dröge, A., Stiege, A., Weise, F., Lurz, R., van Heel, M., Tavares, P. EMBO J. (2003) [Pubmed]
  9. RNA-mediated specificity of DNA packaging into hybrid lambda/phi 29 proheads. Valpuesta, J.M., Donate, L.E., Mier, C., Herranz, L., Carrascosa, J.L. EMBO J. (1993) [Pubmed]
  10. Herpes simplex virus DNA packaging sequences adopt novel structures that are specifically recognized by a component of the cleavage and packaging machinery. Adelman, K., Salmon, B., Baines, J.D. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  11. Defining the ATPase center of bacteriophage T4 DNA packaging machine: requirement for a catalytic glutamate residue in the large terminase protein gp17. Goetzinger, K.R., Rao, V.B. J. Mol. Biol. (2003) [Pubmed]
  12. Inhibition of herpes simplex virus replication by WAY-150138: assembly of capsids depleted of the portal and terminase proteins involved in DNA encapsidation. Newcomb, W.W., Brown, J.C. J. Virol. (2002) [Pubmed]
  13. Model for DNA packaging into bacteriophage T4 heads. Black, L.W., Silverman, D.J. J. Virol. (1978) [Pubmed]
  14. Maturation of the head of bacteriophage T4: 9-aminoacridine blocks a late step in DNA packaging. Wagner, J.A., Laemmli, U.K. Virology (1979) [Pubmed]
  15. Differences in DNA packaging genes and sensitivity to benzimidazole ribonucleosides between human cytomegalovirus strains AD169 and Towne. Krosky, P.M., Ptak, R.G., Underwood, M.R., Biron, K.K., Townsend, L.B., Drach, J.C. Antivir. Chem. Chemother. (2000) [Pubmed]
  16. Role of the amino-terminal domain of bacteriophage phi 29 connector in DNA binding and packaging. Donate, L.E., Valpuesta, J.M., Rocher, A., Méndez, E., Rojo, F., Salas, M., Carrascosa, J.L. J. Biol. Chem. (1992) [Pubmed]
  17. A dimer as a building block in assembling RNA. A hexamer that gears bacterial virus phi29 DNA-translocating machinery. Chen, C., Sheng, S., Shao, Z., Guo, P. J. Biol. Chem. (2000) [Pubmed]
  18. Probing the structure of bacteriophage phi 29 prohead RNA with specific mutations. Reid, R.J., Zhang, F., Benson, S., Anderson, D. J. Biol. Chem. (1994) [Pubmed]
  19. RNA-modifying machines in archaea. Omer, A.D., Ziesche, S., Decatur, W.A., Fournier, M.J., Dennis, P.P. Mol. Microbiol. (2003) [Pubmed]
  20. Herpes simplex virus gene products: the accessories reflect her lifestyle well. Nishiyama, Y. Rev. Med. Virol. (2004) [Pubmed]
  21. The testis-specific high-mobility-group protein, a phosphorylation-dependent DNA-packaging factor of elongating and condensing spermatids. Alami-Ouahabi, N., Veilleux, S., Meistrich, M.L., Boissonneault, G. Mol. Cell. Biol. (1996) [Pubmed]
  22. Visualization of the intracellular development of bacteriophage lambda, with special reference to DNA packaging. Yamagishi, H., Okamoto, M. Proc. Natl. Acad. Sci. U.S.A. (1978) [Pubmed]
  23. Evidence for double replication of chromosomal DNA segments as a general consequence of DNA replication inhibition. Woodcock, D.M., Cooper, I.A. Cancer Res. (1981) [Pubmed]
  24. Heterogeneity of the procapsid of bacteriophage T3. Serwer, P., Watson, R.H., Hayes, S.J. J. Virol. (1985) [Pubmed]
  25. Analysis of the fine structure of the prohead binding domain of the packaging protein of bacteriophage T3 using a hexapeptide, an analog of a prohead binding site. Morita, M., Tasaka, M., Fujisawa, H. Virology (1995) [Pubmed]
  26. Herpes simplex virus type 1 DNA-packaging protein UL17 is required for efficient binding of UL25 to capsids. Thurlow, J.K., Murphy, M., Stow, N.D., Preston, V.G. J. Virol. (2006) [Pubmed]
  27. Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection. Zhang, X., Studier, F.W. J. Mol. Biol. (2004) [Pubmed]
  28. Characterization of human telomeric repeat sequences from human herpesvirus 6 and relationship to replication. Gompels, U.A., Macaulay, H.A. J. Gen. Virol. (1995) [Pubmed]
  29. Helicase Hmi1 stimulates the synthesis of concatemeric mitochondrial DNA molecules in yeast Saccharomyces cerevisiae. Sedman, T., Jõers, P., Kuusk, S., Sedman, J. Curr. Genet. (2005) [Pubmed]
  30. Intermediates of adeno-associated virus type 2 assembly: identification of soluble complexes containing Rep and Cap proteins. Wistuba, A., Weger, S., Kern, A., Kleinschmidt, J.A. J. Virol. (1995) [Pubmed]
  31. pGIL01, a linear tectiviral plasmid prophage originating from Bacillus thuringiensis serovar israelensis. Verheust, C., Jensen, G., Mahillon, J. Microbiology (Reading, Engl.) (2003) [Pubmed]
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