Complete genome sequence of the lytic Pseudomonas fluorescens phage IBB-PF7A

Virology Journal

Volumn 8, Issue , 2011, Pages

  Sillankorva, Sanna ^a,b   Kluskens, Leon D ^a   Lingohr, Erika J ^c   Kropinski, Andrew M ^c,d   Neubauer, Peter ^e   Azeredo, Joana ^a  

^a UNIVERSITY OF MINHO   (Portugal)

^b UNIVERSITY OF OULU   (Finland)

^c PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^d UNIVERSITY OF GUELPH   (Canada)

^e TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CYSTEINE; DOUBLE STRANDED DNA; GLYCINE; NUCLEOTIDE; PROTEIN; VIRUS PROTEIN;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIOLYSIS; BACTERIOPHAGE; BACTERIUM ISOLATE; COLIPHAGE; CONTROLLED STUDY; GENE SEQUENCE; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PSEUDOMONAS FLUORESCENS; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; PHYSIOLOGY; PSEUDOMONAS PHAGE; VIROLOGY; VIRUS GENOME;

BACTERIA (MICROORGANISMS); PODOVIRIDAE; PSEUDOMONAS FLUORESCENS; PSEUDOMONAS PHAGE GH-1; PSEUDOMONAS PUTIDA;

BASE SEQUENCE; GENE EXPRESSION REGULATION, VIRAL; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; PSEUDOMONAS FLUORESCENS; PSEUDOMONAS PHAGES; VIRAL PROTEINS;

EID: 79953083799     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-8-142     Document Type: Article

References (28)

1. Bacteriophages. MH Adams, New York: Interscience Publishers 1959
2. A theory of modular evolution for bacteriophages. D Botstein, Ann N Y Acad Sci 1980 354 484 490 10.1111/j.1749-6632.1980.tb27987.x 6452848
3. Comparative molecular biology of lambdoid phages. A Campbell, Annu Rev Microbiol 1994 48 193 222 10.1146/annurev.mi.48.100194.001205 7826005 (Pubitemid 24334096)
4. Bacteriophage P22 portal protein is part of the gauge that regulates packing density of intravirion DNA. S Casjens E Wyckoff M Hayden, Journal of Molecular Biology 1992 224 1055 1074 10.1016/0022-2836(92)90469-Z 1569567
5. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. H Brüssow F Desiere, Mol Microbiol 2001 39 213 222 11136444 (Pubitemid 32113496)
6. Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory. S Lucchini F Desiere H Brüssow, J Virol 1999 73 8647 8656 10482618 (Pubitemid 29441729)
7. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. R Lavigne D Seto P Mahadevan HW Ackermann AM Kropinski, Research in Microbiology 2008 159 406 414 10.1016/j.resmic.2008.03.005 18555669
8. The T7 Group. IJ Molineux, The bacteriophages Oxford: Oxford University Press, Calendar RL, 2005
9. Isolation and characterization of a T7-like lytic phage for Pseudomonas fluorescens. S Sillankorva P Neubauer J Azeredo, Bmc Biotechnology 2008 8 80 10.1186/1472-6750-8-80 18954452
10. Pseudomonas fluorescens biofilms subjected to phage IBB-PF7A. S Sillankorva P Neubauer J Azeredo, Bmc Biotechnology 2008 8 79 10.1186/1472-6750-8-79 18954451
11. Phage control of dual species biofilms of Pseudomonas fluorescens and Staphylococcus lentus. S Sillankorva P Neubauer J Azeredo, Biofouling 2008
12. The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida - evidence for close relationship to the T7 group. IV Kovalyova AM Kropinski, Virology 2003 311 305 315 10.1016/S0042-6822(03)00124-7 12842620 (Pubitemid 36808773)
13. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. JJ Dunn FW Studier, Journal of Molecular Biology 1983 166 477 535 10.1016/S0022-2836(83)80282-4 6864790 (Pubitemid 13027896)
14. Genomic Analysis of Pseudomonas aeruginosa Phages LKD16 and LKA1: Establishment of the KMV Subgroup within the T7 Supergroup. P-J Ceyssens R Lavigne W Mattheus A Chibeu K Hertveldt J Mast J Robben G Volckaert, Journal of Bacteriology 2008 188 6924 6931 10.1128/JB.00831-06 (Pubitemid 44497905)
15. The genome of bacteriophage KMV, a T7-like virus infecting Pseudomonas aeruginosa. R Lavigne MV Burkal'tseva J Robben NN Sykilinda LP Kurochkina B Grymonprez B Jonckx VN Krylov VV Mesyanzhinov G Volckaert, Virology 2008 312 49 59 10.1016/S0042-6822(03)00123-5 (Pubitemid 36918459)
16. In silico identification of genes in bacteriophage DNA. AM Kropinski M Borodovsky TJ Carver AM Cerdẽo-Trraga A Darling A Lomsadze P Mahadevan P Stothard D Seto G Van Domselaar DS Wishart, Methods Mol Biol 2009 502 89
17. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. N Zafar R Mazumder D Seto, BMC Bioinformatics 2002 24 3 12
18. Mauve: multiple alignment of conserved genomic sequence with rearrangements. AC Darling B Mau FR Blattner NT Perna, Genome Res 2004 14 1394 1403 10.1101/gr.2289704 15231754 (Pubitemid 39029237)
19. Programmed ribosomal frameshifting: Much ado about knotting! SL Alam JF Atkins RF Gesteland, Proceedings of the National Academy of Sciences of the United States of America 1999 96 14177 14179 10.1073/pnas.96.25.14177 10588670 (Pubitemid 30000615)
20. Programmed translational frameshifting. PJ Farabaugh, Annual Review of Genetics 1996 30 507 528 10.1146/annurev.genet.30.1.507 8982463 (Pubitemid 27014476)
21. An 'integrated model' of programmed ribosomal frameshifting. JW Harger A Meskauskas JD Dinman, Trends in Biochemical Sciences 2002 27 448 454 10.1016/S0968-0004(02)02149-7 12217519 (Pubitemid 35246253)
22. pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. J Reeder P Steffen R Giegerich, Nucleic Acids Research 2007 35 320 W324 10.1093/nar/gkm258 17478505
23. Transcription-independent DNA translocation of bacteriophage T7 DNA into Escherichia coli. LR Garcia IJ Molineux, Journal of Bacteriology 1996 178 6921 6929 8955315 (Pubitemid 26404970)
24. Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon a three base-pair region located 10 to 12 base-pairs upstream from the start site. JF Klement MB Moorefield E Jorgensen JE Brown S Risman WT McAllister, Molecular Biology 1990 215 21 29 10.1016/S0022-2836(05)80091-9 (Pubitemid 20301301)
25. Molecular Cloning: A Laboratory Manual. J Sambrook DW Russell, New York: Cold Spring Harbor Laboratory Press, Cold Spring Harbor 2001
26. The Staden package, 1998. R Staden KF Beal JK Bonfield, Methods Mol Biol 2000 132 130
27. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. TM Lowe SR Eddy, Nucleic Acids Res 1997 1 25 955 964 10.1093/nar/25.5.955 (Pubitemid 27298263)
28. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. R Lavigne WD Sun G Volckaert, Bioinformatics 2004 20 629 U99 10.1093/bioinformatics/btg456 15033869