Novel bacteriophages containing a genome of another bacteriophage within their genomes

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Swanson, Maud M ^a   Reavy, Brian ^a   Makarova, Kira S ^b   Cock, Peter J ^a   Hopkins, David W ^a,c   Torrance, Lesley ^a   Koonin, Eugene V ^b   Taliansky, Michael ^a  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c HERIOT WATT UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA;

ANTARCTICA; ARTICLE; BACILLUS CEREUS; BACILLUS THURINGIENSIS; BACTERIOPHAGE; BACTERIOPHAGE BCEA1; BACTERIOPHAGE SPAA1; GENE CLUSTER; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROPHAGE; SOIL; STAPHYLOCOCCUS; STAPHYLOCOCCUS PASTEURI;

BACILLUS PHAGES; BACILLUS SUBTILIS; BACTERIOPHAGES; GENES, VIRAL; GENOME, VIRAL; HOST SPECIFICITY; OPEN READING FRAMES; PHYLOGENY; SIPHOVIRIDAE; SPOROSARCINA; VIRAL PROTEINS; VIRION;

BACILLUS (BACTERIUM); BACILLUS CEREUS; BACILLUS THURINGIENSIS; BACILLUS THURINGIENSIS SEROVAR KURSTAKI; BACILLUS THURINGIENSIS SEROVAR MONTERREY; BACTERIA (MICROORGANISMS); SIPHOVIRIDAE;

EID: 84863992182     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040683     Document Type: Article

References (62)

1. Suttle CA, (2005) Viruses in the sea. Nature 437: 356-61.
2. Edwards RA, Rohwer F, (2005) Viral metagenomics. Nat Rev Microbiol 3: 504-10.
3. Casas V, Rohwer F, (2007) Phage metagenomics. Meth Enzymol 421: 259-68.
4. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. (2006) The marine viromes of four oceanic regions. PLoS Biol 4: e368.
5. Suttle CA, (2007) Marine viruses-major players in the global ecosystem. Nat Rev Microbiol 5: 801-812.
6. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-632.
7. Kristensen DM, Mushegian AR, Dolja VV, Koonin EV, (2010) New dimensions of the virus world discovered through metagenomics. Trends Microbiol 18: 11-19.
8. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, eds. (2011) Ninth Report of the International Committee on Taxonomy of Viruses. San Diego: Elsevier (Eds). (.
9. Breitbart M, Rohwer F, (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13: 278-284.
10. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, et al. (2007) Metagenomic and small-subunit RNA analyses reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73: 7059-7066.
11. Ashelford KE, Day MJ, Fry JC, (2003) Elevated Abundance of Bacteriophage Infecting Bacteria in Soil. Appl Environ Microbiol 69: 285-289.
12. Williamson KE, Radosevich M, Wommack KE, (2005) Abundance and Diversity of Viruses in Six Delaware Soils. Appl Environ Microbiol 71: 3119-3125.
13. Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, et al. (2007) The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples. PLoS One 3: e1456.
14. Brussow H, Kutter E, (2005) Phage ecology. In: Kutter E, Sulakvelidse A, editors. pp. 129-163 editors. Bacteriophages: Biology and Applications. Washington, DC: CRC Press.
15. Wommack KE, Colwell RR, (2000) Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64: 69-114.
16. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, et al. (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 99: 14350-14355.
17. Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, et al. (2004) Diversity and population structure of a nearshore marine sediment viral community. Proc R Soc Lond B. Biol Sci 271: 565-574.
18. Frost LS, Leplae R, Summers AO, Toussaint A, (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 9: 722-732.
19. McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, et al. (2010) High frequency of horizontal gene transfer in the oceans. Science 330: 50.
20. Sobecky PA, Hazen TH, (2009) Horizontal gene transfer and mobile genetic elements in marine systems. Methods Mol Biol 532: 435-453.
21. Fuhrman JA, (1999) Marine viruses: biogeochemical and ecological effects. Nature 399: 541-548.
22. Haaber J, Middelboe M, (2009) Viral lysis of Phaeocystis pouchetii: Implications for algal population dynamics and heterotrophic C, N, and P cycling. ISME J 3: 430-441.
23. Rohwer F, Thurber RV, (2009) Viruses manipulate the marine environment. Nature 459: 207-212.
24. McGrath S, van Sinderen D, (2007) Bacteriophage: Genetics and Molecular Biology. Norfolk, England: Caister Academic Press.
25. Ackermann H-W, (2007) 5550 Phages examined in the electron microscope. Arch Virol 152: 277-243.
26. Calendar R, (2006) The bacteriophages. Oxford University Press.
27. Kutter E, Sulakvelidze A, (2005) Bacteriophages: biology and applications. Boca Raton, Florida: CRC Press.
28. Hendrix RW, Lawrence JG, Hatfull GF, Casiens S, (2000) The origins and ongoing evolution of viruses. Trends Microbiol 8: 504-508.
29. Hatfull GF, Cresawn SG, Hendrix RW, (2008) Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. Res Microbiol 159: 332-339.
30. Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, et al. (2011) Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PLoS One 6: e16329.
31. Liao W, Song S, Sun F, Jia Y, Zeng W, et al. (2008) Isolation, characterization and genome sequencing of phage MZTP02 from Bacillus thuringiensis MZ1. Arch Virol 153: 1855-1865.
32. Lukashin AV, Borodovsky M, (1998) GeneMark.hmm: new solutions for gene finding. Nuc Acids Res 26: 1107-1115.
33. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402.
34. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37 (Database issue), D205-210.
35. Klumpp J, Calendar R, Loessner MJ, (2010) Complete nucleotide sequence and molecular characterization of Bacillus phage TP21 and its relatedness to other phages with the same name. Viruses 2: 961-971.
36. Katsura I, (1990) Mechanism of length determination in bacteriophage lambda tails. Adv Biophys 26: 1-18.
37. Xu J, Hendrix RW, Duda RL, (2004) Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol. Cell 16 11-21.
38. Theis C, Reeder J, Giegerich R, (2008) KnotInFrame: prediction of -1 ribosomal frameshift events. Nucleic Acids Re 36: 6013-6020.
39. Casjens SR, Gilcrease EB, Winn-Stapley DA, Schiklmaier P, Schmieger H, et al. (2005) The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J Bacteriol 187: 1091-1104.
40. Omelchenko MV, Makarov KS, Wolf YI, Rogozin IB, Koonin EV, (2003) Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol 4: R55.
41. Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, et al. (2006) Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry. J. Bacteriol 188: 3402-3408.
42. Romero P, López R, García E, (2004) Genomic organization and molecular analysis of the inducible prophage EJ-1, a mosaic myovirus from an atypical pneumococcus. Virology 322: 239-252.
43. Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, et al. (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423: 87-91.
44. Wang Y, Zhang X, (2010) Genome analysis of deep-sea thermophilic phage D6E. Appl Environ Microbiol 76: 7861-7866.
45. Chesneau O, Morvan A, Grimont F, Labischinski H, El Solh N, (1993) Staphylococcus pasteuri sp. nov., isolation from human, animal, and food specimens. Int J Syst Bacteriol 43: 237-244.
46. He J, Shao X, Zheng H, Li M, Wang J, et al. (2010) Complete genome sequence of Bacillus thuringiensis mutant strain BMB171. J Bacteriol 192: 4074-4075.
47. Ravin NV, (2011) N15: The linear phage-plasmid. Plasmid 65: 102-109.
48. Verheust C, Jensen G, Mahilon J, (2003) pGIL01, a linear tectiviral plasmid prophage originating from Bacillus thuringiensis serovar israelensis. Microbiology 149: 2083-2092.
49. Christie GE, Calendar R, (1990) Interactions between satellite bacteriophage P4 and its helpers. Ann Rev Genet 24: 465-90.
50. Briani F, Dehò G, Forti F, Ghisotti D, (2001) The plasmid status of satellite bacteriophage P4. Plasmid 45: 1-17.
51. Shore D, Deho G, Tsipis J, Goldstein R, (1978) Determination of capsid size by satellite bacteriophage P4. Proc Natl Acad Sci (USA) 75: 400-404.
52. Pruss G, Goldstein RN, Calendar R, (1974) In vitro packaging of satellite phage P4 DNA. Proc Natl Acad Sci (USA) 71: 2367-2371.
53. Thurber R, (2009) Current insights into phage biodiversity and biogeography. Curr Opin Microbiol 12: 582-587.
54. Elberling B, Gregorich EG, Hopkins DW, Sparrow AD, Novis P, et al. (2006) Distribution and dynamics of soil organic matter in an Antarctic dry valley. Soil Biol Biochem 38: 3095-3106.
55. Hopkins DW, Sparrow AD, Elberling B, Gregorich EG, Novis PM, et al. (2006) Carbon, nitrogen and temperature controls on microbial activity in soils from an Antarctic dry valley. Soil Biol Biochem 38: 3130-3140.
56. Chevreux B, Wetter T, Suhai S, (1999) Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99: 45-56.
57. Milne I, Bayer M, Cardle L, Shaw P, Stephen G, et al. (2010) Tablet- next generation sequence assembly visualization. Bioinformatics 26: 401-402.
58. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
59. Adachi J, Hasegawa M, (1992) MOLPHY: programs for molecular phylogenetics. In Computer Science Monographs 27; Institute of Statistical Mathematics.
60. Fitch WM, Margoliash E, (1967) Construction of phylogenetic trees. Science 155: 279-284.
61. Pritchard L, White JA, Birch PRJ, Toth IK, (2006) GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 22: 616-617.
62. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.