bacillus phages

Summary

Summary: Viruses whose host is Bacillus. Frequently encountered Bacillus phages include bacteriophage phi 29 and bacteriophage phi 105.

Top Publications

  1. Illana B, Blanco L, Salas M. Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1. Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication. J Mol Biol. 1996;264:453-64 pubmed
    ..As in other TP-containing genomes, a sliding-back mechanism is proposed to account for the maintenance of the DNA length at the GA-1 DNA ends. ..
  2. Moll W, Guo P. Translocation of nicked but not gapped DNA by the packaging motor of bacteriophage phi29. J Mol Biol. 2005;351:100-7 pubmed
    ..Thus the phi29 DNA packaging machinery tolerated nicks, but stopped at gaps. The packaging motor did not require a nick-free DNA backbone, but the presence of both DNA strands, for uninterrupted packaging. ..
  3. Koti J, Morais M, Rajagopal R, Owen B, McMurray C, Anderson D. DNA packaging motor assembly intermediate of bacteriophage phi29. J Mol Biol. 2008;381:1114-32 pubmed publisher
    ..The complex was capable of supercoiling DNA-gp3 as observed previously for gp16 alone; therefore, the binding of gp16 to the prohead, rather than first to DNA-gp3, represents an alternative packaging motor assembly pathway...
  4. Freire R, Serrano M, Salas M, Hermoso J. Activation of replication origins in phi29-related phages requires the recognition of initiation proteins to specific nucleoprotein complexes. J Biol Chem. 1996;271:31000-7 pubmed
    ..The results obtained indicate that the activation requires not only the formation of a specific nucleoprotein complex but also its specific recognition by the proteins involved in the initiation of DNA replication. ..
  5. Lee J, Shin H, Son B, Ryu S. Complete genome sequence of Bacillus cereus bacteriophage BCP78. J Virol. 2012;86:637-8 pubmed publisher
    ..Here we announce the complete genome sequence of BCP78, which may be useful for understanding its inhibition mechanism against B. cereus, and describe major findings from the genome annotation...
  6. Geng J, Fang H, Haque F, Zhang L, Guo P. Three reversible and controllable discrete steps of channel gating of a viral DNA packaging motor. Biomaterials. 2011;32:8234-42 pubmed publisher
    ..The step-wise conformational change of the channel was also reversible and controllable, making it an ideal nano-valve for constructing a nanomachine with potential applications in nanobiotechnology and nanomedicine. ..
  7. Pérez Arnaiz P, Lázaro J, Salas M, de Vega M. Involvement of phi29 DNA polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication. Nucleic Acids Res. 2006;34:3107-15 pubmed
    ..The results presented here lead us to propose phi29 DNA polymerase thumb as the main subdomain responsible for the coordination of polymerization and exonuclease activities. ..
  8. Serrano Heras G, Ruíz Masó J, del Solar G, Espinosa M, Bravo A, Salas M. Protein p56 from the Bacillus subtilis phage phi29 inhibits DNA-binding ability of uracil-DNA glycosylase. Nucleic Acids Res. 2007;35:5393-401 pubmed
    ..These results suggest that protein p56 could be a novel naturally occurring DNA mimicry. ..
  9. Morais M, Choi K, Koti J, Chipman P, Anderson D, Rossmann M. Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29. Mol Cell. 2005;18:149-59 pubmed
    ..7 A, respectively. Thus, phi29 joins the growing number of phages that utilize the HK97 capsid structure, suggesting that this protein fold may be as prevalent in capsids of dsDNA phages as the jelly roll fold is in eukaryotic viruses. ..

More Information

Publications96

  1. Xiao F, Zhang H, Guo P. Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging. Nucleic Acids Res. 2008;36:6620-32 pubmed publisher
    ..This new mechanism was tested by redesigning two artificial RNAs that formed hexamer and packaged DNA. The results confirmed the stoichiometry of pRNA on the motor was the common multiple of two and three, thus, a hexamer. ..
  2. Cai Y, Xiao F, Guo P. The effect of N- or C-terminal alterations of the connector of bacteriophage phi29 DNA packaging motor on procapsid assembly, pRNA binding, and DNA packaging. Nanomedicine. 2008;4:8-18 pubmed publisher
  3. Bourassa N, Major F. Implication of the prohead RNA in phage phi29 DNA packaging. Biochimie. 2002;84:945-51 pubmed
    ..This article presents and debates current knowledge about the prohead RNA structures, mechanisms, and roles in DNA encapsidation. A new dimer structure is presented, and its specific role in DNA encapsidation is discussed. ..
  4. Gonzalez Huici V, Salas M, Hermoso J. The push-pull mechanism of bacteriophage Ø29 DNA injection. Mol Microbiol. 2004;52:529-40 pubmed
    ..Both steps are energy-dependent, as treatment of cells with azide overrides the whole mechanism, leading to a deregulated, passive entry of DNA. ..
  5. Guo P. Structure and function of phi29 hexameric RNA that drives the viral DNA packaging motor: review. Prog Nucleic Acid Res Mol Biol. 2002;72:415-72 pubmed
    ..This article reviews the structure and function of this pRNA and focuses on novel methods and unique approaches that lead to the illumination of its structure and function. ..
  6. Veesler D, Blangy S, Spinelli S, Tavares P, Campanacci V, Cambillau C. Crystal structure of Bacillus subtilis SPP1 phage gp22 shares fold similarity with a domain of lactococcal phage p2 RBP. Protein Sci. 2010;19:1439-43 pubmed publisher
    ..35 A resolution. We found that gp22 is a monomer in solution and possesses a significant structural similarity with lactococcal phage p2 ORF 18 N-terminal "shoulder" domain...
  7. Thomas J, Hardies S, Rolando M, Hayes S, Lieman K, Carroll C, et al. Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305phi8-36. Virology. 2007;368:405-21 pubmed
    ..Phage 0305phi8-36 has twice the virion protein coding sequence of T4. Based on its genomic isolation, 0305phi8-36 is a resource for future studies of vertical gene transmission. ..
  8. Stewart C, Gaslightwala I, Hinata K, Krolikowski K, Needleman D, Peng A, et al. Genes and regulatory sites of the "host-takeover module" in the terminal redundancy of Bacillus subtilis bacteriophage SPO1. Virology. 1998;246:329-40 pubmed
    ..Transcription-termination and RNase III cleavage sites were found at appropriate locations. ..
  9. 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 data also imply that, with the exception of the C18C19A20 bulge, the main role of the 5'/3' helical double-stranded region of pRNA is not for procapsid binding but for binding to gp16. ..
  10. Reid R, Bodley J, Anderson D. Identification of bacteriophage phi 29 prohead RNA domains necessary for in vitro DNA-gp3 packaging. J Biol Chem. 1994;269:9084-9 pubmed
  11. Hugel T, Michaelis J, Hetherington C, Jardine P, Grimes S, Walter J, et al. Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids. PLoS Biol. 2007;5:e59 pubmed
    ..From our data, we can exclude connector rotation with greater than 99% probability and therefore answer a long-standing mechanistic question. ..
  12. 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
    ..Interestingly, this pRNA bound to prohead and packaged DNA as well as the wild-type 120-nt pRNA. ..
  13. Serna Rico A, Muñoz Espín D, Villar L, Salas M, Meijer W. The integral membrane protein p16.7 organizes in vivo phi29 DNA replication through interaction with both the terminal protein and ssDNA. EMBO J. 2003;22:2297-306 pubmed
    ..These and previous results indicate that p16.7 encompasses four distinct modules. An integrated model of the structural and functional domains of p16.7 in relation to the organization of in vivo phi29 DNA replication is presented. ..
  14. Kamtekar S, Berman A, Wang J, Lázaro J, de Vega M, Blanco L, et al. The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition. EMBO J. 2006;25:1335-43 pubmed
    ..The model indicates that terminal protein should dissociate from polymerase after the incorporation of approximately six nucleotides. ..
  15. Raghunathan A, Ferguson H, Bornarth C, Song W, Driscoll M, Lasken R. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol. 2005;71:3342-7 pubmed
    ..A 662-bp segment of the 16S rRNA gene could be accurately sequenced from the amplified DNA. MDA methods enable new strategies for studying non-culturable microorganisms. ..
  16. Grimes S, Jardine P, Anderson D. Bacteriophage phi 29 DNA packaging. Adv Virus Res. 2002;58:255-94 pubmed
  17. Landthaler M, Shen B, Stoddard B, Shub D. I-BasI and I-HmuI: two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities. J Mol Biol. 2006;358:1137-51 pubmed
    ..which are each encoded by a group I intron inserted into homologous sites within the DNA polymerase genes of Bacillus phages SPO1 and Bastille, respectively...
  18. Pérez Lago L, Salas M, Camacho A. A precise DNA bend angle is essential for the function of the phage phi29 transcriptional regulator. Nucleic Acids Res. 2005;33:126-34 pubmed
    ..The functionality of the p4 binding sites and the contribution of p4-mediated promoter restructuring in transcription regulation is discussed. ..
  19. 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
    ..They suggest an assembly pathway for the packaging motor and a mechanism for DNA translocation into empty proheads. ..
  20. Peterson C, Simon M, Hodges J, Mertens P, Higgins L, Egelman E, et al. Composition and mass of the bacteriophage phi29 prohead and virion. J Struct Biol. 2001;135:18-25 pubmed publisher
    ..2 MDa. The data complement studies relating the structure of phi29 components to dynamic functions in morphogenesis and infection...
  21. Calles B, Salas M, Rojo F. The phi29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex. EMBO J. 2002;21:6185-94 pubmed
    ..Therefore, at this DNA region, stable polymerization of protein p6 relies on p4-specified signals in addition to the structural features of the DNA. Protein p4 would define the phase and boundaries of the p6-DNA complex...
  22. Fang Y, Cai Q, Qin P. The procapsid binding domain of phi29 packaging RNA has a modular architecture and requires 2'-hydroxyl groups in packaging RNA interaction. Biochemistry. 2005;44:9348-58 pubmed
    ..The functional constructs developed here will aid biophysical and biochemical investigations of pRNA structure and function, as well as developments of pRNA-based technology for nanoscience and gene therapy. ..
  23. Xu S, Gupta Y. Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease. Nucleic Acids Res. 2013;41:378-90 pubmed publisher
    ..In addition, the engineered ZF nickase is useful for evaluation of off-target sites in vitro before performing cell-based gene modification. ..
  24. Schuch R, Fischetti V. Detailed genomic analysis of the Wbeta and gamma phages infecting Bacillus anthracis: implications for evolution of environmental fitness and antibiotic resistance. J Bacteriol. 2006;188:3037-51 pubmed
    ..anthracis life cycle. Initial findings suggest that lysogeny of B. anthracis promotes ecological adaptation, rather than virulence, as with other gram-positive pathogens. ..
  25. Dean F, Nelson J, Giesler T, Lasken R. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 2001;11:1095-9 pubmed
    ..Amplified products can also be used for in vitro cloning, library construction, and other molecular biology applications. ..
  26. Shu Y, Shu D, Haque F, Guo P. Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells. Nat Protoc. 2013;8:1635-59 pubmed publisher
    ..The time required for completing one round of this protocol is 3-4 weeks when including in vitro functional assays, or 2-3 months when including in vivo studies. ..
  27. Str msten N, Benson S, Burnett R, Bamford D, Bamford J. The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J Bacteriol. 2003;185:6985-9 pubmed
    ..1-kbp linear plasmid, pBClin15. We show that pBClin15 closely resembles Bam35 and demonstrate conversion of Bam35 to a prophage. This state is common, as several B. thuringiensis strains release Bam35-related viruses...
  28. Truniger V, Lázaro J, Salas M. Two positively charged residues of phi29 DNA polymerase, conserved in protein-primed DNA polymerases, are involved in stabilisation of the incoming nucleotide. J Mol Biol. 2004;335:481-94 pubmed
  29. Guo S, Huang F, Guo P. Construction of folate-conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells. Gene Ther. 2006;13:814-20 pubmed
  30. Grimes S, Ma S, Gao J, Atz R, Jardine P. Role of ?29 connector channel loops in late-stage DNA packaging. J Mol Biol. 2011;410:50-9 pubmed publisher
    ..Instead, they appear to have an essential function near the end of packaging, acting to retain the packaged DNA in the head in preparation for motor detachment and subsequent tail assembly and virion completion...
  31. Hutchison C, Smith H, Pfannkoch C, Venter J. Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci U S A. 2005;102:17332-6 pubmed
    ..These include environmental DNA samples that have proven difficult to clone and synthetic genes encoding toxic products. The method may also speed genome sequencing by eliminating the need for biological cloning...
  32. Mencía M, Gella P, Camacho A, de Vega M, Salas M. Terminal protein-primed amplification of heterologous DNA with a minimal replication system based on phage Phi29. Proc Natl Acad Sci U S A. 2011;108:18655-60 pubmed publisher
    ..Amplification factors of 30-fold have been obtained. Possible applications of DNAs produced by this method are discussed...
  33. Serrano Heras G, Bravo A, Salas M. Phage phi29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase. Proc Natl Acad Sci U S A. 2008;105:19044-9 pubmed publisher
    ..Thus, our data support a model in which protein p56 ensures an efficient viral DNA replication, preventing the deleterious effect caused by UDG when it eliminates uracil residues present in the phi29 genome...
  34. Isidro A, Henriques A, Tavares P. The portal protein plays essential roles at different steps of the SPP1 DNA packaging process. Virology. 2004;322:253-63 pubmed
    ..The similarity between the architecture of portal oligomers and between the DNA packaging strategies of viruses using portals strongly suggests that the portal protein plays the same roles in a large number of viruses...
  35. Auzat I, Dr ge A, Weise F, Lurz R, Tavares P. Origin and function of the two major tail proteins of bacteriophage SPP1. Mol Microbiol. 2008;70:557-69 pubmed publisher
    ..The carboxyl-terminal extension is an elaboration present in some tailed bacteriophages. Different extensions were found to combine in a mosaic fashion with the MTP essential module in a subset of Siphoviridae genomes...
  36. Asensio J, P rez Lago L, L zaro J, Gonz lez C, Serrano Heras G, Salas M. Novel dimeric structure of phage ?29-encoded protein p56: insights into uracil-DNA glycosylase inhibition. Nucleic Acids Res. 2011;39:9779-88 pubmed publisher
  37. Pérez Lago L, Salas M, Camacho A. Homologies and divergences in the transcription regulatory system of two related Bacillus subtilis phages. J Bacteriol. 2005;187:6403-9 pubmed
  38. Baptista C, Santos M, São José C. Phage SPP1 reversible adsorption to Bacillus subtilis cell wall teichoic acids accelerates virus recognition of membrane receptor YueB. J Bacteriol. 2008;190:4989-96 pubmed publisher
    ..Our results support a model in which fast SPP1 adsorption to and desorption from teichoic acids allows SPP1 to scan the bacterial surface for rapid YueB recognition...
  39. Ding F, Lu C, Zhao W, Rajashankar K, Anderson D, Jardine P, et al. Structure and assembly of the essential RNA ring component of a viral DNA packaging motor. Proc Natl Acad Sci U S A. 2011;108:7357-62 pubmed publisher
    ..Construction of structure-based designer pRNAs with little sequence similarity to the wild-type pRNA were shown to fully support the packaging of 29 DNA...
  40. Veesler D, Blangy S, Lichi re J, Ortiz Lombard a M, Tavares P, Campanacci V, et al. Crystal structure of Bacillus subtilis SPP1 phage gp23.1, a putative chaperone. Protein Sci. 2010;19:1812-6 pubmed publisher
    ..The gp23.1 hexamer does not fit well in the unassigned SPP1 tail-tip EM density and we hypothesize that this protein might act as a chaperone...
  41. Fouts D, Rasko D, Cer R, Jiang L, Fedorova N, Shvartsbeyn A, et al. Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry. J Bacteriol. 2006;188:3402-8 pubmed
    ..The genomes of these two phages were identical except at three variable loci, which showed heterogeneity within individual lysates and among Cherry, Wbeta, Fah, and four Gamma bacteriophage sequences...
  42. Berthet N, Reinhardt A, Leclercq I, van Ooyen S, Batejat C, Dickinson P, et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Mol Biol. 2008;9:77 pubmed publisher
    ..We adapted the QuantiTect Whole Transcriptome Kit (Qiagen) to our purposes and designated the method as Whole Transcriptome Amplification (WTA)...
  43. Serrano Heras G, Salas M, Bravo A. In vivo assembly of phage phi 29 replication protein p1 into membrane-associated multimeric structures. J Biol Chem. 2003;278:40771-7 pubmed
    ..We propose that a phage structure assembled on the cell membrane provides a specific site for 29 DNA replication...
  44. Aathavan K, Politzer A, Kaplan A, Moffitt J, Chemla Y, Grimes S, et al. Substrate interactions and promiscuity in a viral DNA packaging motor. Nature. 2009;461:669-73 pubmed publisher
    ..Such promiscuous, nonspecific contacts may reflect common translocase-substrate interactions for both the nucleic acid and protein translocases of the ASCE superfamily...
  45. Paez J, Lin M, Beroukhim R, Lee J, Zhao X, Richter D, et al. Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res. 2004;32:e71 pubmed
    ..These results suggest that phi29MDA yields high fidelity, near-complete genome representation suitable for high resolution genetic analysis...
  46. Longás E, de Vega M, Lázaro J, Salas M. Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity. Nucleic Acids Res. 2006;34:6051-63 pubmed
    ..Such exceptional behaviour is discussed in the light of the recently solved structure of the DNA polymerase/TP complex of the related bacteriophage phi29...
  47. Johnson J, Chiu W. DNA packaging and delivery machines in tailed bacteriophages. Curr Opin Struct Biol. 2007;17:237-43 pubmed
  48. Westers H, Dorenbos R, van Dijl J, Kabel J, Flanagan T, Devine K, et al. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol. 2003;20:2076-90 pubmed
    ..We show that genome engineering is a feasible strategy for functional analysis of large gene clusters, and that removal of dispensable genomic regions may pave the way toward an optimized Bacillus cell factory...
  49. Shu D, Huang L, Hoeprich S, Guo P. Construction of phi29 DNA-packaging RNA monomers, dimers, and trimers with variable sizes and shapes as potential parts for nanodevices. J Nanosci Nanotechnol. 2003;3:295-302 pubmed
    ..Other conditions, including the salt requirement for the formation of monomers, dimers, and trimers, have been investigated. RNA monomers, dimers, and trimers with variable lengths are potential parts for nanodevices...
  50. Zhang H, Shu D, Huang F, Guo P. Instrumentation and metrology for single RNA counting in biological complexes or nanoparticles by a single-molecule dual-view system. RNA. 2007;13:1793-802 pubmed
    ..The dual-viewing system for excitation and recording at different wavelengths simultaneously will enable the differentiation of different complexes with different labels or relative motion of each labeled component in motion machines...
  51. Pérez Arnaiz P, Longás E, Villar L, Lázaro J, Salas M, de Vega M. Involvement of phage phi29 DNA polymerase and terminal protein subdomains in conferring specificity during initiation of protein-primed DNA replication. Nucleic Acids Res. 2007;35:7061-73 pubmed
    ..The sequential events occurring during initiation of bacteriophage protein-primed DNA replication are proposed...
  52. 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
  53. Morais M, Tao Y, Olson N, Grimes S, Jardine P, Anderson D, et al. Cryoelectron-microscopy image reconstruction of symmetry mismatches in bacteriophage phi29. J Struct Biol. 2001;135:38-46 pubmed
  54. 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...
  55. Rodríguez I, Lázaro J, Salas M, de Vega M. phi29 DNA polymerase-terminal protein interaction. Involvement of residues specifically conserved among protein-primed DNA polymerases. J Mol Biol. 2004;337:829-41 pubmed
  56. Stewart C, Casjens S, Cresawn S, Houtz J, Smith A, Ford M, et al. The genome of Bacillus subtilis bacteriophage SPO1. J Mol Biol. 2009;388:48-70 pubmed publisher
    ..There is a correlation between genes in rapid evolutionary flux through these genomes and genes that are small...
  57. 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
    ..The fingerprint of DNA translocation in this system has provided a new tool for future biophysical and physicochemical characterizations of DNA transportation, motion, and packaging...
  58. Lee T, Zhang H, Chang C, Savran C, Guo P. Engineering of the fluorescent-energy-conversion arm of phi29 DNA packaging motor for single-molecule studies. Small. 2009;5:2453-9 pubmed publisher
    ..The activity of the re-engineered motor with eGFP-gp16 is also observed directly with a bright-field microscope via its ability to transport a 2-microm-sized cargo bound to the DNA...
  59. Ravantti J, Gaidelyte A, Bamford D, Bamford J. Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrates a viral lineage. Virology. 2003;313:401-14 pubmed
    ..This and other observations made here support the idea that a common early ancestor for Bam35, PRD1, and adenoviruses existed...
  60. Haque F, Lunn J, Fang H, Smithrud D, Guo P. Real-time sensing and discrimination of single chemicals using the channel of phi29 DNA packaging nanomotor. ACS Nano. 2012;6:3251-61 pubmed publisher
    ..The results demonstrated that this channel system could be further developed into very sensitive sensing devices...
  61. Guasch A, Pous J, Ibarra B, Gomis Ruth F, Valpuesta J, Sousa N, et al. Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle. J Mol Biol. 2002;315:663-76 pubmed
    ..The structure suggests a translocation mechanism in which the longitudinal displacement of the DNA along its axis is coupled to connector spinning...
  62. Pask R, Rance H, Barratt B, Nutland S, Smyth D, Sebastian M, et al. Investigating the utility of combining phi29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray genotyping. BMC Biotechnol. 2004;4:15 pubmed
    ..As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates...
  63. Davison S, Couture Tosi E, Candela T, Mock M, Fouet A. Identification of the Bacillus anthracis (gamma) phage receptor. J Bacteriol. 2005;187:6742-9 pubmed
    ..B. thuringiensis 97-27, a strain which, by sequence analysis, is predicted to harbor a GamR-like protein, is resistant to the phage but nevertheless displays phage binding...
  64. 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
    ..Heat-denaturation analysis confirmed that the stoichiometry of pRNA is the common multiple of 2 and 3. EM imaging of procapsid/pRNA complexes clearly revealed six ferritin particles that were conjugated to each pRNA ring...
  65. Badia D, Camacho A, Pérez Lago L, Escandón C, Salas M, Coll M. The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA. Mol Cell. 2006;22:73-81 pubmed
    ..The two N-hooks enter the major groove of the double helix, establishing base-specific contacts. A high DNA curvature allows p4 N-hooks to reach two major groove areas three helical turns apart, like a bow and its string...
  66. Smith D, Tans S, Smith S, Grimes S, Anderson D, Bustamante C. The bacteriophage straight phi29 portal motor can package DNA against a large internal force. Nature. 2001;413:748-52 pubmed
    ..Our data suggest that this force may be available for initiating the ejection of the DNA from the capsid during infection...
  67. Zhang H, Endrizzi J, Shu Y, Haque F, Sauter C, Shlyakhtenko L, et al. Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA. RNA. 2013;19:1226-37 pubmed publisher
  68. Tavares P, Lurz R, Stiege A, Ruckert B, Trautner T. Sequential headful packaging and fate of the cleaved DNA ends in bacteriophage SPP1. J Mol Biol. 1996;264:954-67 pubmed
    ..Upon ejection this extremity is the first to move along the tail tube to exit from the virion through the region where the tail spike was attached...
  69. Moffitt J, Chemla Y, Aathavan K, Grimes S, Jardine P, Anderson D, et al. Intersubunit coordination in a homomeric ring ATPase. Nature. 2009;457:446-50 pubmed publisher
    ..Furthermore, a step size that is a non-integer number of base pairs demands new models for motor-DNA interactions...
  70. Reif R, Haque F, Guo P. Fluorogenic RNA nanoparticles for monitoring RNA folding and degradation in real time in living cells. Nucleic Acid Ther. 2012;22:428-37 pubmed publisher
    ..We show that the half-life (t½) of the electroporated MG aptamer containing RNA nanoparticle was 4.3 hours after electroporation into cells...
  71. 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
    ..The application of viral DNA packaging motors is also discussed...
  72. Sato M, Ohtsuka M, Ohmi Y. Usefulness of repeated GenomiPhi, a phi29 DNA polymerase-based rolling circle amplification kit, for generation of large amounts of plasmid DNA. Biomol Eng. 2005;22:129-32 pubmed
    ..We demonstrated that repeated RCA (at least three times) is useful for high-fidelity amplification of large amounts of plasmid DNA...
  73. Minakhin L, Semenova E, Liu J, Vasilov A, Severinova E, Gabisonia T, et al. Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah. J Mol Biol. 2005;354:1-15 pubmed
    ..sigma(Fah) is negatively regulated by host SpoIIAB, an anti-sigma factor that controls sporulation. Thus, sigma(Fah) may link phage gene expression to sporulation of the host...
  74. Serrano Heras G, Salas M, Bravo A. A uracil-DNA glycosylase inhibitor encoded by a non-uracil containing viral DNA. J Biol Chem. 2006;281:7068-74 pubmed
    ..Protein p56 is the first example of a UDG inhibitor encoded by a non-uracil-containing viral DNA...
  75. Sozhamannan S, McKinstry M, Lentz S, Jalasvuori M, Mcafee F, Smith A, et al. Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity. Appl Environ Microbiol. 2008;74:6792-6 pubmed publisher
    ..Spontaneous AP50c-resistant B. anthracis mutants exhibit a mucoid colony phenotype...
  76. Loessner M, Maier S, Daubek Puza H, Wendlinger G, Scherer S. Three Bacillus cereus bacteriophage endolysins are unrelated but reveal high homology to cell wall hydrolases from different bacilli. J Bacteriol. 1997;179:2845-51 pubmed
    ..We speculate that the close relationship of the phage enzymes and cell wall autolysins is based upon horizontal gene transfer among different Bacillus phages and their hosts.
  77. Ravishankar R, Bidya Sagar M, Roy S, Purnapatre K, Handa P, Varshney U, et al. X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG. Nucleic Acids Res. 1998;26:4880-7 pubmed
    ..Ec UDG could serve as a prototype for UDGs from pathogenic prokaryotes, and provide a framework for possible drug development against such pathogens with emphasis on features of the molecule that differ from those in the human enzyme...
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    ..The results suggest that this bulge is not involved in procapsid binding but may interact with other DNA-packaging components. A computer model showing the location of the CCA bulge was presented...
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    ..Furthermore, its specificity was comparable to the gamma-phage test. PlyGB is applicable in conventional methods instead of antibodies and could be a potent tool for detection of B. anthracis...
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    ..anthracis. Our observations provide new insight into the mechanism of specific binding of lysin to B. anthracis, and may be useful in establishing new methods for detection of B. anthracis...
  82. Huang L, Guo P. Use of PEG to acquire highly soluble DNA-packaging enzyme gp16 of bacterial virus phi29 for stoichiometry quantification. J Virol Methods. 2003;109:235-44 pubmed
    ..This result leads to a subsequent finding that the stoichiometry of gp16 for phi29 DNA-packaging was about 11+/-2. These findings will facilitate the study on this novel motor that involves three pRNA dimers and a 12-subunit connector...
  83. 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
    ..This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor...
  84. Liao W, Song S, Sun F, Jia Y, Zeng W, Pang Y. Isolation, characterization and genome sequencing of phage MZTP02 from Bacillus thuringiensis MZ1. Arch Virol. 2008;153:1855-65 pubmed publisher
    ..coli exonuclease III to digest the genome DNA. A TMP phylogenetic tree was constructed based on amino acid sequences from ten phages...
  85. Serwer P, Hayes S, Thomas J, Hardies S. Propagating the missing bacteriophages: a large bacteriophage in a new class. Virol J. 2007;4:21 pubmed
    ..Bacteriophage 0305phi8-36 is in a new genomic class, based on genes for both structural components and DNA packaging ATPase. Thus, knowledge of environmental virus diversity is expanded with prospect of greater future expansion...
  86. Kong M, Kim M, Ryu S. Complete genome sequence of Bacillus cereus bacteriophage PBC1. J Virol. 2012;86:6379-80 pubmed publisher
    ..PBC1 showed a very low degree of homology to previously reported phages, implying that it is novel. Here we report the complete genome sequence of PBC1 and describe major findings from our analysis...
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    ..Our results provide the first examples of H-N-H endonuclease-mediated intron homing and the first demonstration of intron homing initiated by a nicking endonuclease...