Sequencing and Characterization of Pseudomonas aeruginosa phage JG004

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  Garbe, Julia ^a,b   Bunk, Boyke ^a   Rohde, Manfred ^c   Schobert, Max ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^b Department of Clinical Sciences   (Sweden)

^c HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; PHOSPHOGLUCOMUTASE; PHOSPHOMANNOMUTASE; TRANSFER RNA; VIRUS DNA;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIOPHAGE JG004; DNA REPLICATION; ENZYME ACTIVITY; GENE SEQUENCE; NONHUMAN; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS PHAGE; TRANSMISSION ELECTRON MICROSCOPY; TRANSPOSON; BACTERIOLYSIS; BACTERIOPHAGE; CHEMISTRY; DNA SEQUENCE; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; ULTRASTRUCTURE; VIROLOGY; VIRUS GENOME;

BACTERIA (MICROORGANISMS); MYOVIRIDAE; PSEUDOMONAS AERUGINOSA;

BACTERIOLYSIS; DNA, VIRAL; GENOME, VIRAL; HUMANS; MOLECULAR SEQUENCE DATA; MYOVIRIDAE; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS PHAGES; SEQUENCE ANALYSIS, DNA;

EID: 79955820125     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-102     Document Type: Article

References (58)

1. Pseudomonas aeruginosa - a phenomenon of bacterial resistance. T Strateva D Yordanov, J Med Microbiol 2009 58 1133 1148 10.1099/jmm.0.009142-0 19528173
2. Has the era of untreatable infections arrived? DM Livermore, J Antimicrob Chemother 2009 64 Suppl 1 29 36 19675016
3. Phage therapy: facts and fiction. M Skurnik E Strauch, Int J Med Microbiol 2006 296 5 14 17024745 (Pubitemid 43089713)
4. Bacteriophage therapy. WC Summers, Annu Rev Microbiol 2001 55 437 451 10.1146/annurev.micro.55.1.437 11544363 (Pubitemid 32978113)
5. High abundance of viruses found in aquatic environments. O Bergh KY Børsheim G Bratbak M Heldal, Nature 1989 340 467 468 10.1038/340467a0 2755508
6. Global phage diversity. F Rohwer, Cell 2003 113 141 10.1016/S0092- 8674(03)00276-9 12705861 (Pubitemid 36514964)
7. Here a virus, there a virus, everywhere the same virus? M Breitbart F Rohwer, Trends Microbiol 2005 13 278 284 10.1016/j.tim.2005.04.003 15936660 (Pubitemid 40779816)
8. Comparative genomics and evolution of the tailed-bacteriophages. SR Casjens, Curr Opin Microbiol 2005 8 451 458 10.1016/j.mib.2005.06.014 16019256 (Pubitemid 41021907)
9. HW Ackermann: 5500 Phages examined in the electron microscope. Arch Virol 2007 152 227 243 10.1007/s00705-006-0849-1 17051420
10. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. T Kwan J Liu M DuBow P Gros J Pelletier, Proc Natl Acad Sci USA 2005 102 5174 5179 10.1073/pnas.0501140102 15788529
11. Genomes of "phiKMV-like viruses" of Pseudomonas aeruginosa contain localized single-strand interruptions. LA Kulakov KV N MG Shlyapnikov VV Kochetkov A Del Casale CCR Allen MJ Larkin PJ Ceyssens R Lavigne, Virology 2009 391 1 4 10.1016/j.virol.2009.06.024 19592061
12. Survey of Pseudomonas aeruginosa and its phages: de novo peptide sequencing as a novel tool to assess the diversity of worldwide collected viruses. PJ Ceyssens JP Noben HW Ackermann J Verhaegen D De Vos JP Pirnay M Merabishvili M Vaneechoutte A Chibeu G Volckaert R Lavigne, Environ Microbiol 2009 11 1303 1313 10.1111/j.1462-2920.2008.01862.x 19207572
13. Blood kinetics of four intraperitoneally administered therapeutic candidate bacteriophages in healthy and neutropenic mice. J Uchiyama Y Maeda I Takemura R Chess-Williams H Wakiguchi S Matsuzaki, Microbiol Immunol 2009 53 301 304 10.1111/j.1348-0421.2009.00125.x 19457172
14. Isolation of Pseudomonas aeruginosa specific phages with broad activity spectra. P Knezevic R Kostanjsek D Obreht O Petrovic, Curr Microbiol 2009 59 173 180 10.1007/s00284-009-9417-8 19472004
15. Characterization of a T7-like lytic bacteriophage of Klebsiella pneumoniae B5055: a potential therapeutic agent. V Verma K Harjai S Chhibber, Curr Microbiol 2009 59 274 281 10.1007/s00284-009-9430-y 19484297
16. The Pseudomonas aeruginosa algC gene encodes phosphoglucomutase, required for the synthesis of a complete lipopolysaccharide core. MJ Coyne KS Russell CL Coyle JB Goldberg, J Bacteriol 1994 176 3500 3507 7515870 (Pubitemid 24189649)
17. Mechanism of conversion to mucoidy in Pseudomonas aeruginosa infecting cystic fibrosis patients. DW Martin MJ Schurr MH Mudd JR Govan BW Holloway V Deretic, Proc Natl Acad Sci USA 1993 90 8377 8381 10.1073/pnas.90.18.8377 8378309 (Pubitemid 23277671)
18. Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. JR Govan V Deretic, Microbiol Rev 1996 60 539 574 8840786 (Pubitemid 26303478)
19. Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. MJ Loessner RB Inman P Lauer R Calendar, Mol Microbiol 2000 35 324 340 10.1046/j.1365-2958.2000.01720.x 10652093 (Pubitemid 30055229)
20. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. TM Lowe SR Eddy, Nucleic Acids Res 1997 25 955 964 10.1093/nar/25.5.955 9023104 (Pubitemid 27298263)
21. Transfer RNA genes and their significance to codon usage in the Pseudomonas aeruginosa lamboid bacteriophage D3. AM Kropinski MJ Sibbald, Can J Microbiol 1999 45 791 796 10526403
22. Sequence alignment kernel for recognition of promoter regions. L Gordon AY Chervonenkis AJ Gammerman IA Shahmuradov VV Solovyev, Bioinformatics 2003 19 1964 1971 10.1093/bioinformatics/btg265 14555630 (Pubitemid 37322341)
23. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. CL Kingsford K Ayanbule SL Salzberg, Genome Biol 2007 8 22 10.1186/gb-2007-8-2-r22 17313685
24. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. TL Bailey C Elkan, Proc Int Conf Intell Syst Mol Biol 1994 2 28 36 7584402
25. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. CK Stover XQ Pham AL Erwin SD Mizoguchi P Warrener MJ Hickey FS Brinkman WO Hufnagle DJ Kowalik M Lagrou RL Garber L Goltry E Tolentino S Westbrock-Wadman Y Yuan LL Brody SN Coulter KR Folger A Kas K Larbig R Lim K Smith D Spencer GK Wong Z Wu IT Paulsen J Reizer MH Saier RE Hancock S Lory MV Olson, Nature 2000 406 959 964 10.1038/35023079 10984043
26. Heuristic approach to deriving models for gene finding. J Besemer M Borodovsky, Nucleic Acids Res 1999 27 3911 3920 10.1093/nar/27.19.3911 10481031 (Pubitemid 29454440)
27. Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections. L Debarbieux D Leduc D Maura E Morello A Criscuolo O Grossi V Balloy L Touqui, J Infect Dis 2010 201 1096 1101 10.1086/651135 20196657
28. The bacteriophage DNA packaging motor. VB Rao M Feiss, Annu Rev Genet 2008 42 647 681 10.1146/annurev.genet.42.110807.091545 18687036
29. Tail length determination in bacteriophage T4. NK Abuladze M Gingery J Tsai FA Eiserling, Virology 1994 199 301 310 10.1006/viro.1994.1128 8122363 (Pubitemid 24168968)
30. Phages will out: strategies of host cell lysis. I Young I Wang WD Roof, Trends Microbiol 2000 8 120 128 10.1016/S0966-842X(00)01705-4 10707065 (Pubitemid 30155487)
31. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. ES Miller JF Heidelberg JA Eisen WC Nelson AS Durkin A Ciecko TV Feldblyum O White IT Paulsen WC Nierman J Lee B Szczypinski CM Fraser, J Bacteriol 2003 185 5220 5233 10.1128/JB.185.17. 5220-5233.2003 12923095 (Pubitemid 37025119)
32. Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: establishment of the phiKMV subgroup within the T7 supergroup. PJ Ceyssens R Lavigne W Mattheus A Chibeu K Hertveldt J Mast J Robben G Volckaert, J Bacteriol 2006 188 6924 6931 10.1128/JB.00831-06 16980495 (Pubitemid 44497905)
33. Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. PR Weigele WH Pope ML Pedulla JM Houtz AL Smith JF Conway J King GF Hatfull JG Lawrence RW Hendrix, Environ Microbiol 2007 9 1675 1695 10.1111/j.1462-2920.2007.01285.x 17564603 (Pubitemid 46905404)
34. The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains. NH Mann MRJ Clokie A Millard A Cook WH Wilson PJ Wheatley A Letarov HM Krisch, J Bacteriol 2005 187 3188 3200 10.1128/JB.187.9.3188-3200.2005 15838046 (Pubitemid 40571612)
35. REDOR NMR characterization of DNA packaging in bacteriophage T4. TY Yu J Schaefer, J Mol Biol 2008 382 1031 1042 10.1016/j.jmb.2008.07.077 18703073
36. Mauve: multiple alignment of conserved genomic sequence with rearrangements. ACE Darling B Mau FR Blattner NT Perna, Genome Res 2004 14 1394 1403 10.1101/gr.2289704 15231754 (Pubitemid 39029237)
37. Classification of Myoviridae bacteriophages using protein sequence similarity. R Lavigne P Darius EJ Summer D Seto P Mahadevan AS Nilsson HW Ackermann AM Kropinski, BMC Microbiol 2009 9 224 10.1186/1471-2180-9-224 19857251
38. Comparative analysis of the widespread and conserved PB1-like viruses infecting Pseudomonas aeruginosa. P Ceyssens K Miroshnikov W Mattheus V Krylov J Robben J Noben S Vanderschraeghe N Sykilinda A Kropinski G Volckaert V Mesyanzhinov R Lavigne, Environ Microbiol 2009 11 2874 2883 10.1111/j.1462-2920. 2009.02030.x 19678828
39. The purification, crystallization and preliminary structural characterization of glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme of the dTDP-L-rhamnose synthesis pathway from Pseudomonas aeruginosa. W Blankenfeldt MF Giraud G Leonard R Rahim C Creuzenet JS Lam JH Naismith, Acta Crystallogr D Biol Crystallogr 2000 56 1501 1504 10.1107/S0907444900010040 11053865
40. Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa. J King D Kocíncová E Westman J Lam, Innate immun 2009 15 261 312 10.1177/1753425909106436 19710102
41. Differential lipopolysaccharide core capping leads to quantitative and correlated modifications of mechanical and structural properties in Pseudomonas aeruginosa biofilms. P Lau T Lindhout T Beveridge J Dutcher J Lam, J Bacteriol 2009 191 6618 6631 10.1128/JB.00698-09 19717596
42. Functional characterization of MigA and WapR: putative rhamnosyltransferases involved in outer core oligosaccharide biosynthesis of Pseudomonas aeruginosa. KKH Poon EL Westman E Vinogradov S Jin JS Lam, J Bacteriol 2008 190 1857 1865 10.1128/JB.01546-07 18178733 (Pubitemid 351355308)
43. Transcriptome analysis of agmatine and putrescine catabolism in Pseudomonas aeruginosa PAO1. HT Chou DH Kwon M Hegazy CD Lu, J Bacteriol 2008 190 1966 1967 10.1128/JB.01804-07 18192388
44. A novel two-component system controls the expression of Pseudomonas aeruginosa flmbrial cup genes. HD Kulasekara I Ventre BR Kulasekara A Lazdunski A Filloux S Lory, Mol Microbiol 2005 55 368 380 15659157 (Pubitemid 40179374)
45. Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. GA O'Toole R Kolter, Mol Microbiol 1998 28 449 461 10.1046/j.1365-2958.1998.00797.x 9632250 (Pubitemid 28218392)
46. Characterization of JG024, a Pseudomonas aeruginosa PB1-like broad host range phage under simulated infection conditions. J Garbe A Wesche B Bunk M Kazmierczak K Selezska C Rohde J Sikorski M Rohde D Jahn M Schobert, BMC Microbiol 2010 10 301 10.1186/1471-2180-10-301 21110836
47. Bacteriophage phiYeO3-12, specific for Yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7. M Pajunen S Kiljunen M Skurnik, J Bacteriol 2000 182 5114 5120 10.1128/JB.182.18.5114-5120.2000 10960095
48. Differentiation of Two Abortive Mechanisms by Using Monoclonal Antibodies Directed toward Lactococcal Bacteriophage Capsid Proteins. S Moineau E Durmaz S Pandian TR Klaenhammer, Appl Environ Microbiol 1993 59 208 212 16348844 (Pubitemid 23028392)
49. Database resources of the National Center for Biotechnology. DL Wheeler DM Church S Federhen AE Lash TL Madden JU Pontius GD Schuler LM Schriml E Sequeira TA Tatusova L Wagner, Nucleic Acids Res 2003 31 28 33 10.1093/nar/gkg033 12519941 (Pubitemid 36150327)
50. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
51. Clustal W and Clustal X version 2.0. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins, Bioinformatics 2007 23 2947 2948 10.1093/bioinformatics/btm404 17846036 (Pubitemid 350162903)
52. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. A Grote K Hiller M Scheer R Münch B Nörtemann DC Hempel D Jahn, Nucleic Acids Res 2005 33 526 531 10.1093/nar/gki376 15980527
53. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. R Münch K Hiller A Grote M Scheer J Klein M Schobert D Jahn, Bioinformatics 2005 21 4187 4189 10.1093/bioinformatics/bti635 16109747 (Pubitemid 41672111)
54. Pleiotrophy of p-uorophenylalanine-resistant and antibiotic hypersensitive mutants of Pseudomonas aeruginosa. NW Dunn BW Holloway, Genet Res 1971 18 185 197 10.1017/S0016672300012593 4258431
55. Common virulence factors for bacterial pathogenicity in plants and animals. LG Rahme EJ Stevens SF Wolfort J Shao RG Tompkins FM Ausubel, Science 1995 268 1899 1902 10.1126/science.7604262 7604262
56. Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants. M Klausen A Heydorn P Ragas L Lambertsen A Aaes- Jørgensen S Molin T Tolker-Nielsen, Mol Microbiol 2003 48 1511 1524 10.1046/j.1365-2958.2003.03525.x 12791135 (Pubitemid 36751058)
57. Pseudomonas aeruginosa O-antigen chain length is determined before ligation to lipid A core. C Daniels C Griffiths B Cowles JS Lam, Environ Microbiol 2002 4 883 897 10.1046/j.1462-2920.2002.00288.x 12534470 (Pubitemid 36064178)
58. Functional characterization of WaaL, a ligase associated with linking O-antigen polysaccharide to the core of Pseudomonas aeruginosa lipopolysaccharide. PD Abeyrathne C Daniels KKH Poon MJ Matewish JS Lam, J Bacteriol 2005 187 3002 3012 10.1128/JB.187.9.3002-3012.2005 15838026 (Pubitemid 40571592)