dna packaging

Summary

Summary: The folding of an organism's DNA molecule into a compact, orderly structure that fits within the limited space of a CELL or VIRUS PARTICLE.

Top Publications

  1. Zhang W, Arcos R. Interaction of the adenovirus major core protein precursor, pVII, with the viral DNA packaging machinery. Virology. 2005;334:194-202 pubmed
    Adenovirus is one of the well-studied double-stranded DNA viruses. However, the mechanisms of its DNA packaging and virion assembly are still not fully understood...
  2. Bowman B, Welschhans R, Jayaram H, Stow N, Preston V, Quiocho F. Structural characterization of the UL25 DNA-packaging protein from herpes simplex virus type 1. J Virol. 2006;80:2309-17 pubmed
    ..The herpes simplex virus type 1 UL25 protein is incorporated into the capsid during DNA packaging, and previous studies of a null mutant have demonstrated that its function is essential at the late stages of ..
  3. Bernal R, Hafenstein S, Esmeralda R, Fane B, Rossmann M. The phiX174 protein J mediates DNA packaging and viral attachment to host cells. J Mol Biol. 2004;337:1109-22 pubmed
    ..particles containing the smaller DNA-binding protein cannot be generated due to procapsid instability during DNA packaging. However, chimeric alpha3 and G4 phages, containing the phiX174 DNA-binding protein in place of the endogenous ..
  4. Uchiyama A, Fane B. Identification of an interacting coat-external scaffolding protein domain required for both the initiation of phiX174 procapsid morphogenesis and the completion of DNA packaging. J Virol. 2005;79:6751-6 pubmed
    ..external scaffolding protein inhibits two morphogenetic steps: the initiation of procapsid formation and DNA packaging. phiX174 mutants that can efficiently utilize the chimeric protein were isolated and characterized...
  5. Lee T, Zhang H, Liang D, Guo P. Strand and nucleotide-dependent ATPase activity of gp16 of bacterial virus phi29 DNA packaging motor. Virology. 2008;380:69-74 pubmed publisher
    ..The results suggest that pRNA accelerates gp16 ATPase activity more significantly than genomic dsDNA, albeit both pRNA and genomic DNA are involved in the contact with gp16 during DNA packaging.
  6. Nadal M, Mas P, Mas P, Blanco A, Arnan C, Sol M, et al. Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain. Proc Natl Acad Sci U S A. 2010;107:16078-83 pubmed publisher
    ..We also show that the nuclease function can be inactivated by raltegravir, a recently approved anti-AIDS drug that targets the HIV integrase...
  7. Alam T, Rao V. The ATPase domain of the large terminase protein, gp17, from bacteriophage T4 binds DNA: implications to the DNA packaging mechanism. J Mol Biol. 2008;376:1272-81 pubmed publisher
    ..The small terminase protein, gp16, inhibited DNA binding, which was further accentuated by ATP. The presence of a DNA binding site in the ATPase domain and its binding properties implicate a role in the DNA packaging mechanism.
  8. Tao P, Mahalingam M, Marasa B, Zhang Z, Chopra A, Rao V. In vitro and in vivo delivery of genes and proteins using the bacteriophage T4 DNA packaging machine. Proc Natl Acad Sci U S A. 2013;110:5846-51 pubmed publisher
    The bacteriophage T4 DNA packaging machine consists of a molecular motor assembled at the portal vertex of an icosahedral head...
  9. Hynes A, Mercer R, Watton D, Buckley C, Lang A. DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA. Mol Microbiol. 2012;85:314-25 pubmed publisher
    ..This subpopulation's role in producing and releasing the RcGTA particles explains the lack of observed cell lysis in cultures. ..

More Information

Publications62

  1. Kottadiel V, Rao V, Chemla Y. The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4. Proc Natl Acad Sci U S A. 2012;109:20000-5 pubmed publisher
    ..These results lead to a four-state mechanochemical model that provides insights into the mechanisms of translocation of an intricately branched concatemeric viral genome...
  2. Karhu N, Ziedaite G, Bamford D, Bamford J. Efficient DNA packaging of bacteriophage PRD1 requires the unique vertex protein P6. J Virol. 2007;81:2970-9 pubmed
    ..A packaging model for bacteriophage PRD1, based on previous results and those obtained in this study, is presented...
  3. Jing P, Haque F, Vonderheide A, Montemagno C, Guo P. Robust properties of membrane-embedded connector channel of bacterial virus phi29 DNA packaging motor. Mol Biosyst. 2010;6:1844-52 pubmed publisher
    ..Herein, we demonstrate the robust characteristics of the connector of the bacteriophage phi29 DNA packaging motor by single pore electrophysiological assays...
  4. Forrey C, Muthukumar M. Langevin dynamics simulations of genome packing in bacteriophage. Biophys J. 2006;91:25-41 pubmed
    ..Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general. ..
  5. de Frutos M, Brasiles S, Tavares P, Raspaud E. Effect of spermine and DNase on DNA release from bacteriophage T5. Eur Phys J E Soft Matter. 2005;17:429-34 pubmed
    ..We discuss the results in terms of free energy minimization and we demonstrate that the presence of a DNA condensate outside the phage generates an additional force pulling passively on the DNA remaining inside the capsid. ..
  6. Zhao W, Morais M, Anderson D, Jardine P, Grimes S. Role of the CCA bulge of prohead RNA of bacteriophage ø29 in DNA packaging. J Mol Biol. 2008;383:520-8 pubmed publisher
    The oligomeric ring of prohead RNA (pRNA) is an essential component of the ATP-driven DNA packaging motor of bacteriophage ø29...
  7. Ubeda C, Olivarez N, Barry P, Wang H, Kong X, Matthews A, et al. Specificity of staphylococcal phage and SaPI DNA packaging as revealed by integrase and terminase mutations. Mol Microbiol. 2009;72:98-108 pubmed
    ..TerS, however, determines DNA packaging specificity but not the choice of large versus small capsids...
  8. Maluf N, Yang Q, Catalano C. Self-association properties of the bacteriophage lambda terminase holoenzyme: implications for the DNA packaging motor. J Mol Biol. 2005;347:523-42 pubmed
    ..Both the heterotrimer and the higher-order species possess site-specific cos cleavage activity, as well as DNA packaging activity; however, the heterotrimer is dependent upon Escherichia coli integration host factor (IHF) for these ..
  9. Black L, Rao V. Structure, assembly, and DNA packaging of the bacteriophage T4 head. Adv Virus Res. 2012;82:119-53 pubmed publisher
    ..Extensive mutagenesis, combined with atomic structures of the DNA packaging/terminase proteins gp16 and gp17, elucidated the ATPase and nuclease functional motifs involved in DNA ..
  10. Lee T, Schwartz C, Guo P. Construction of bacteriophage phi29 DNA packaging motor and its applications in nanotechnology and therapy. Ann Biomed Eng. 2009;37:2064-81 pubmed publisher
    ..The novelty and ingenious design of the bacterial virus phi29 DNA packaging motor and its parts inspired the synthesis of this motor and its components as biomimetics...
  11. Zhang H, Schwartz C, De Donatis G, Guo P. "Push through one-way valve" mechanism of viral DNA packaging. Adv Virus Res. 2012;83:415-65 pubmed publisher
    ..Viral DNA packaging motors are mainly composed of the connector channel and two DNA packaging enzymes...
  12. Fuller D, Raymer D, Kottadiel V, Rao V, Smith D. Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proc Natl Acad Sci U S A. 2007;104:16868-73 pubmed
    Terminase enzyme complexes, which facilitate ATP-driven DNA packaging in phages and in many eukaryotic viruses, constitute a wide and potentially diverse family of molecular motors about which little dynamic or mechanistic information is ..
  13. Hegde S, Padilla Sanchez V, Draper B, Rao V. Portal-large terminase interactions of the bacteriophage T4 DNA packaging machine implicate a molecular lever mechanism for coupling ATPase to DNA translocation. J Virol. 2012;86:4046-57 pubmed publisher
    b>DNA packaging by double-stranded DNA bacteriophages and herpesviruses is driven by a powerful molecular machine assembled at the portal vertex of the empty prohead...
  14. Toropova K, Huffman J, Homa F, Conway J. The herpes simplex virus 1 UL17 protein is the second constituent of the capsid vertex-specific component required for DNA packaging and retention. J Virol. 2011;85:7513-22 pubmed publisher
    The herpes simplex virus (HSV) UL17 and UL25 minor capsid proteins are essential for DNA packaging. They are thought to comprise a molecule arrayed in five copies around each of the capsid vertices...
  15. Lee T, Guo P. Interaction of gp16 with pRNA and DNA for genome packaging by the motor of bacterial virus phi29. J Mol Biol. 2006;356:589-99 pubmed
    ..The C18C19A20 bulge that is essential for DNA packaging was found to be dispensable for gp16 binding...
  16. Dixit A, Ray K, Thomas J, Black L. The C-terminal domain of the bacteriophage T4 terminase docks on the prohead portal clip region during DNA packaging. Virology. 2013;446:293-302 pubmed publisher
    ..Such a terminase-portal orientation fits better to a proposed "DNA crunching" compression packaging motor and to portal determined DNA headful cutting...
  17. Johnson J, Chiu W. DNA packaging and delivery machines in tailed bacteriophages. Curr Opin Struct Biol. 2007;17:237-43 pubmed
    ..epsilon15, P22 and phi29, were determined at resolutions sufficient to visualize details of the machinery for DNA packaging and delivery, as well as the organization of the double-stranded DNA within the particles...
  18. Grigoryev S, Woodcock C. Chromatin organization - the 30 nm fiber. Exp Cell Res. 2012;318:1448-55 pubmed publisher
    ..Interactions between neighboring fibers in highly compact chromatin lead to extensive interdigitation of nucleosomes and the inability to resolve individual fibers in compact chromatin in situ. ..
  19. Shen X, Li M, Zeng Y, Hu X, Tan Y, Rao X, et al. Functional identification of the DNA packaging terminase from Pseudomonas aeruginosa phage PaP3. Arch Virol. 2012;157:2133-41 pubmed publisher
    Terminase proteins are responsible for DNA recognition and initiation of DNA packaging in phages...
  20. Xiang Y, Morais M, Battisti A, Grimes S, Jardine P, Anderson D, et al. Structural changes of bacteriophage phi29 upon DNA packaging and release. EMBO J. 2006;25:5229-39 pubmed
    ..Gene product 3, bound to the 5' ends of the genome, appears to be positioned within the expanded connector, which may potentiate the release of DNA-packaging machine components, creating a binding site for attachment of the tail. ..
  21. Alam T, Draper B, Kondabagil K, Rentas F, Ghosh Kumar M, Sun S, et al. The headful packaging nuclease of bacteriophage T4. Mol Microbiol. 2008;69:1180-90 pubmed publisher
    ..These results lead to hypotheses concerning how phage headful nucleases cut the viral genomes before and after, but not during, DNA packaging.
  22. Guo Y, Blocker F, Xiao F, Guo P. Construction and 3-D computer modeling of connector arrays with tetragonal to decagonal transition induced by pRNA of phi29 DNA-packaging motor. J Nanosci Nanotechnol. 2005;5:856-63 pubmed
    ..Both the connector array and the decagon are ideal candidates to be used as templates to build patterned suprastructures in nanotechnology...
  23. Petrov A, Harvey S. Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4. J Struct Biol. 2011;174:137-46 pubmed publisher
    ..In all cases packaging in a specific conformation occurs as a result of interplay between bending stresses experienced by the confined polymer and interactions between the strands. ..
  24. Fuller D, Raymer D, Rickgauer J, Robertson R, Catalano C, Anderson D, et al. Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations. J Mol Biol. 2007;373:1113-22 pubmed
  25. Sun S, Kondabagil K, Draper B, Alam T, Bowman V, Zhang Z, et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell. 2008;135:1251-62 pubmed publisher
    ..We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4...
  26. Yang Q, Maluf N, Catalano C. Packaging of a unit-length viral genome: the role of nucleotides and the gpD decoration protein in stable nucleocapsid assembly in bacteriophage lambda. J Mol Biol. 2008;383:1037-48 pubmed publisher
    ..In most instances, a capsid expansion process accompanies DNA packaging, which significantly increases the volume of the capsid to accommodate the full-length viral genome...
  27. Atz R, Ma S, Gao J, Anderson D, Grimes S. Alanine scanning and Fe-BABE probing of the bacteriophage ø29 prohead RNA-connector interaction. J Mol Biol. 2007;369:239-48 pubmed
    The DNA packaging motor of the Bacillus subtilis bacteriophage ø29 prohead is comprised in part of an oligomeric ring of 174 base RNA molecules (pRNA) positioned near the N termini of subunits of the dodecameric head-tail connector...
  28. Jacobson J, Yang K, Baines J, Homa F. Linker insertion mutations in the herpes simplex virus type 1 UL28 gene: effects on UL28 interaction with UL15 and UL33 and identification of a second-site mutation in the UL15 gene that suppresses a lethal UL28 mutation. J Virol. 2006;80:12312-23 pubmed
    ..The isolation of an intergenic suppressor mutant provides direct genetic evidence of an association between the UL28 and UL15 proteins and demonstrates that this association is essential for DNA cleavage and packaging. ..
  29. Oliveira L, Henriques A, Tavares P. Modulation of the viral ATPase activity by the portal protein correlates with DNA packaging efficiency. J Biol Chem. 2006;281:21914-23 pubmed
    b>DNA packaging in tailed bacteriophages and herpesviruses requires assembly of a complex molecular machine at a specific vertex of a preformed procapsid...
  30. Zhao Z, Khisamutdinov E, Schwartz C, Guo P. Mechanism of one-way traffic of hexameric phi29 DNA packaging motor with four electropositive relaying layers facilitating antiparallel revolution. ACS Nano. 2013;7:4082-92 pubmed publisher
    ..The viral DNA packaging motor has been believed to be a rotational machine...
  31. Smith D. Single-molecule studies of viral DNA packaging. Curr Opin Virol. 2011;1:134-41 pubmed publisher
    ..Single-molecule fluorescence methods have also been used to measure packaging kinetics and motor conformations. Here we review recent discoveries made using these new techniques. ..
  32. Kala S, Cumby N, Sadowski P, Hyder B, Kanelis V, Davidson A, et al. HNH proteins are a widespread component of phage DNA packaging machines. Proc Natl Acad Sci U S A. 2014;111:6022-7 pubmed publisher
    ..Bioinformatic analysis reveals that the role of HNH proteins in terminase function is widespread among long-tailed phages and is uniquely required for the activity of the Terminase_1 family of large terminase proteins. ..
  33. Schwartz C, De Donatis G, Zhang H, Fang H, Guo P. Revolution rather than rotation of AAA+ hexameric phi29 nanomotor for viral dsDNA packaging without coiling. Virology. 2013;443:28-39 pubmed publisher
    ..Here we report a revolution rather than rotation mechanism for the bacteriophage phi29 DNA packaging motor. The phi29 motor contains six copies of the ATPase (Schwartz et al...
  34. Feiss M, Rao V. The bacteriophage DNA packaging machine. Adv Exp Med Biol. 2012;726:489-509 pubmed publisher
    ..The phage packaging machine has emerged as an excellent model for understanding the molecular machines, given the mechanistic parallels between terminases, helicases, and numerous motor proteins. ..
  35. Nurmemmedov E, Castelnovo M, Medina E, Catalano C, Evilevitch A. Challenging packaging limits and infectivity of phage ?. J Mol Biol. 2012;415:263-73 pubmed publisher
    ..Further, we demonstrated that the phage production rate is modulated by the presence of multivalent ionic species. The biological consequences of these findings are discussed...
  36. de Frutos M, Letellier L, Raspaud E. DNA ejection from bacteriophage T5: analysis of the kinetics and energetics. Biophys J. 2005;88:1364-70 pubmed
    ..Both effects contribute to shorten or to lengthen the pause time between the different stages explaining why the T5 DNA ejection is so slow compared to other types of phage. ..
  37. Morais M, Koti J, Bowman V, Reyes Aldrete E, Anderson D, Rossmann M. Defining molecular and domain boundaries in the bacteriophage phi29 DNA packaging motor. Structure. 2008;16:1267-74 pubmed publisher
    Cryo-electron microscopy (cryo-EM) studies of the bacteriophage phi29 DNA packaging motor have delineated the relative positions and molecular boundaries of the 12-fold symmetric head-tail connector, the 5-fold symmetric prohead RNA (..
  38. Chang J, Weigele P, King J, Chiu W, Jiang W. Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure. 2006;14:1073-82 pubmed
    ..The coaxially packed DNA genome is encapsidated by the icosahedral shell. This complete structure unifies various biochemical, genetic, and crystallographic data of its components from the past several decades...
  39. Fang Y, Shu D, Xiao F, Guo P, Qin P. Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging. Biochem Biophys Res Commun. 2008;372:589-94 pubmed publisher
    The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double-stranded DNA genome into a pre-formed protein capsid...
  40. Kitamura A, Jardine P, Anderson D, Grimes S, Matsuo H. Analysis of intermolecular base pair formation of prohead RNA of the phage phi29 DNA packaging motor using NMR spectroscopy. Nucleic Acids Res. 2008;36:839-48 pubmed
    The bacteriophage ø29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers...
  41. Tolstorukov M, Virnik K, Adhya S, Zhurkin V. A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res. 2005;33:3907-18 pubmed
  42. Kondabagil K, Rao V. A critical coiled coil motif in the small terminase, gp16, from bacteriophage T4: insights into DNA packaging initiation and assembly of packaging motor. J Mol Biol. 2006;358:67-82 pubmed publisher
    Double-stranded DNA packaging in bacteriophages is driven by one of the most powerful force-generating molecular motors reported to date...
  43. Wu K, Guimet D, Hearing P. The adenovirus L4-33K protein regulates both late gene expression patterns and viral DNA packaging. J Virol. 2013;87:6739-47 pubmed publisher
    ..The L4-33K mutant virus produces only empty capsids, indicating a defect in viral DNA packaging. We demonstrate that L4-33K does not preferentially bind to viral packaging sequences in vivo, and mutation of ..
  44. Lander G, Tang L, Casjens S, Gilcrease E, Prevelige P, Poliakov A, et al. The structure of an infectious P22 virion shows the signal for headful DNA packaging. Science. 2006;312:1791-5 pubmed
    ..We propose that the tight dsDNA spooling activates the switch that signals the headful chromosome packing density to the particle exterior. ..
  45. Shu D, Zhang H, Jin J, Guo P. Counting of six pRNAs of phi29 DNA-packaging motor with customized single-molecule dual-view system. EMBO J. 2007;26:527-37 pubmed
    ..The stalled motors were restarted to observe the motion of DNA packaging in real time...
  46. Sweet C, Ball K, Morley P, Guilfoyle K, Kirby M. Mutations in the temperature-sensitive murine cytomegalovirus (MCMV) mutants tsm5 and tsm30: a study of genes involved in immune evasion, DNA packaging and processing, and DNA replication. J Med Virol. 2007;79:285-99 pubmed
    ..Sequencing of the herpesvirus conserved cis-acting elements, pac1 and pac2, and genes involved in DNA packaging and cleavage located in the central core region of the genome identified few point mutations...
  47. Baines J. Herpes simplex virus capsid assembly and DNA packaging: a present and future antiviral drug target. Trends Microbiol. 2011;19:606-13 pubmed publisher
    ..The goal of this review is to outline these intranuclear assembly steps and illustrate potential and existing antiviral strategies that exploit them...
  48. Ko S, Chen Y, Shu D, Guo P, Mao C. Reversible switching of pRNA activity on the DNA packaging motor of bacteriophage phi29. J Am Chem Soc. 2008;130:17684-7 pubmed publisher
    ..of the biological activity of an RNA molecule, packaging RNA (pRNA), which is a central component of the DNA packaging motor of bacteriophage phi29...
  49. Xiao F, Cai Y, Wang J, Green D, Cheng R, Demeler B, et al. Adjustable ellipsoid nanoparticles assembled from re-engineered connectors of the bacteriophage phi29 DNA packaging motor. ACS Nano. 2009;3:2163-70 pubmed publisher
    ..containing 84 subunits or 7 dodecamers of the re-engineered core protein of the bacteriophage phi29 DNA packaging motor was constructed. Homogeneous nanoparticles were obtained with simple one-step purification...
  50. Casjens S. The DNA-packaging nanomotor of tailed bacteriophages. Nat Rev Microbiol. 2011;9:647-57 pubmed publisher
  51. Fang H, Jing P, Haque F, Guo P. Role of channel lysines and the "push through a one-way valve" mechanism of the viral DNA packaging motor. Biophys J. 2012;102:127-35 pubmed publisher
    ..The results support our recent findings regarding the dsDNA packaging mechanism known as the "push through a one-way valve". ..
  52. Campbell C, Kolesar J, Kaufman B. Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number. Biochim Biophys Acta. 2012;1819:921-9 pubmed publisher
    ..This article is part of a Special Issue entitled: Mitochondrial Gene Expression. ..
  53. Beilstein F, Higgs M, Stow N. Mutational analysis of the herpes simplex virus type 1 DNA packaging protein UL33. J Virol. 2009;83:8938-45 pubmed publisher
    ..These data indicate that the ability of UL33 to interact with UL28 is probably necessary, but not sufficient, to support viral growth and DNA packaging.