First genome sequences of Achromobacter phages reveal new members of the N4 family
Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, Rohde C (2014)
Virology Journal 11(1): 14.
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Autor*in
Wittmann, JohannesUniBi;
Dreiseikelmann, BrigitteUniBi;
Rohde, Manfred;
Meier-Kolthoff, Jan P.;
Bunk, Boyke;
Rohde, Christine
Abstract / Bemerkung
Background: Multi-resistant Achromobacter xylosoxidans has been recognized as an emerging pathogen causing nosocomially acquired infections during the last years. Phages as natural opponents could be an alternative to fight such infections. Bacteriophages against this opportunistic pathogen were isolated in a recent study. This study shows a molecular analysis of two podoviruses and reveals first insights into the genomic structure of Achromobacter phages so far. Methods: Growth curve experiments and adsorption kinetics were performed for both phages. Adsorption and propagation in cells were visualized by electron microscopy. Both phage genomes were sequenced with the PacBio RS II system based on single molecule, real-time (SMRT) technology and annotated with several bioinformatic tools. To further elucidate the evolutionary relationships between the phage genomes, a phylogenomic analysis was conducted using the genome Blast Distance Phylogeny approach (GBDP). Results: In this study, we present the first detailed analysis of genome sequences of two Achromobacter phages so far. Phages JWAlpha and JWDelta were isolated from two different waste water treatment plants in Germany. Both phages belong to the Podoviridae and contain linear, double-stranded DNA with a length of 72329 bp and 73659 bp, respectively. 92 and 89 putative open reading frames were identified for JWAlpha and JWDelta, respectively, by bioinformatic analysis with several tools. The genomes have nearly the same organization and could be divided into different clusters for transcription, replication, host interaction, head and tail structure and lysis. Detailed annotation via protein comparisons with BLASTP revealed strong similarities to N4-like phages. Conclusions: Analysis of the genomes of Achromobacter phages JWAlpha and JWDelta and comparisons of different gene clusters with other phages revealed that they might be strongly related to other N4-like phages, especially of the Escherichia group. Although all these phages show a highly conserved genomic structure and partially strong similarities at the amino acid level, some differences could be identified. Those differences, e.g. the existence of specific genes for replication or host interaction in some N4-like phages, seem to be interesting targets for further examination of function and specific mechanisms, which might enlighten the mechanism of phage establishment in the host cell after infection.
Stichworte
GBDP;
Podoviridae;
N4likevirus;
N4-like phage;
Achromobacter xylosoxidans;
Lar-like protein;
Genome
Erscheinungsjahr
2014
Zeitschriftentitel
Virology Journal
Band
11
Ausgabe
1
Art.-Nr.
14
ISSN
1743-422X
Page URI
https://pub.uni-bielefeld.de/record/2677421
Zitieren
Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, Rohde C. First genome sequences of Achromobacter phages reveal new members of the N4 family. Virology Journal. 2014;11(1): 14.
Wittmann, J., Dreiseikelmann, B., Rohde, M., Meier-Kolthoff, J. P., Bunk, B., & Rohde, C. (2014). First genome sequences of Achromobacter phages reveal new members of the N4 family. Virology Journal, 11(1), 14. doi:10.1186/1743-422X-11-14
Wittmann, Johannes, Dreiseikelmann, Brigitte, Rohde, Manfred, Meier-Kolthoff, Jan P., Bunk, Boyke, and Rohde, Christine. 2014. “First genome sequences of Achromobacter phages reveal new members of the N4 family”. Virology Journal 11 (1): 14.
Wittmann, J., Dreiseikelmann, B., Rohde, M., Meier-Kolthoff, J. P., Bunk, B., and Rohde, C. (2014). First genome sequences of Achromobacter phages reveal new members of the N4 family. Virology Journal 11:14.
Wittmann, J., et al., 2014. First genome sequences of Achromobacter phages reveal new members of the N4 family. Virology Journal, 11(1): 14.
J. Wittmann, et al., “First genome sequences of Achromobacter phages reveal new members of the N4 family”, Virology Journal, vol. 11, 2014, : 14.
Wittmann, J., Dreiseikelmann, B., Rohde, M., Meier-Kolthoff, J.P., Bunk, B., Rohde, C.: First genome sequences of Achromobacter phages reveal new members of the N4 family. Virology Journal. 11, : 14 (2014).
Wittmann, Johannes, Dreiseikelmann, Brigitte, Rohde, Manfred, Meier-Kolthoff, Jan P., Bunk, Boyke, and Rohde, Christine. “First genome sequences of Achromobacter phages reveal new members of the N4 family”. Virology Journal 11.1 (2014): 14.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
UNIPROT
180 Einträge gefunden, die diesen Artikel zitieren von denen 10 angezeigt werden
Uncharacterized protein (UNIPROT: V9VCT7)
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Uncharacterized protein (UNIPROT: V9VEJ4)
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Uncharacterized protein (UNIPROT: V9VG44)
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Uncharacterized protein (UNIPROT: V9VHN0)
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Uncharacterized protein (UNIPROT: V9SKN4)
Organism: Achromobacter phage JWDelta
Download in FASTA format
Organism: Achromobacter phage JWDelta
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Uncharacterized protein (UNIPROT: V9SI71)
Organism: Achromobacter phage JWDelta
Download in FASTA format
Organism: Achromobacter phage JWDelta
Download in FASTA format
Uncharacterized protein (UNIPROT: V9SJ62)
Organism: Achromobacter phage JWDelta
Download in FASTA format
Organism: Achromobacter phage JWDelta
Download in FASTA format
Uncharacterized protein (UNIPROT: V9VCY6)
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Uncharacterized protein (UNIPROT: V9VFX8)
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Organism: Achromobacter phage JWAlpha
Download in FASTA format
Uncharacterized protein (UNIPROT: V9VEL9)
Organism: Achromobacter phage JWAlpha
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Organism: Achromobacter phage JWAlpha
Download in FASTA format
EMBL
2 Einträge gefunden, die diesen Artikel zitieren
Achromobacter phage JWAlpha, complete genome. (EMBL: KF787095)
Sequence length: 72329
Download in FASTA format
Sequence length: 72329
Download in FASTA format
Achromobacter phage JWDelta, complete genome. (EMBL: KF787094)
Sequence length: 73659
Download in FASTA format
Sequence length: 73659
Download in FASTA format
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Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8.
Strnad H, Ridl J, Paces J, Kolar M, Vlcek C, Paces V., J. Bacteriol. 193(3), 2010
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Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O., BMC Genomics 9(), 2008
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Schattner P, Brooks AN, Lowe TM., Nucleic Acids Res. 33(Web Server issue), 2005
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Bailly-Bechet M, Vergassola M, Rocha E., Genome Res. 17(10), 2007
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De Paepe M, Taddei F., PLoS Biol. 4(7), 2006
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Sullivan MJ, Petty NK, Beatson SA., Bioinformatics 27(7), 2011
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Transcriptional map of bacteriophage N4: location and polarity of N4 RNAs
AUTHOR UNKNOWN, 1981
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Virion-associated RNA polymerase required for bacteriophage N4 development.
Falco SC, Laan KV, Rothman-Denes LB., Proc. Natl. Acad. Sci. U.S.A. 74(2), 1977
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DNA-dependent RNA polymerase from bacteriophage N4 virions. Purification and characterization.
Falco SC, Zehring W, Rothman-Denes LB., J. Biol. Chem. 255(9), 1980
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The phage N4 virion RNA polymerase catalytic domain is related to single-subunit RNA polymerases.
Kazmierczak KM, Davydova EK, Mustaev AA, Rothman-Denes LB., EMBO J. 21(21), 2002
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N4 RNA polymerase II, a heterodimeric RNA polymerase with homology to the single-subunit family of RNA polymerases.
Willis SH, Kazmierczak KM, Carter RH, Rothman-Denes LB., J. Bacteriol. 184(18), 2002
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Novel virulent and broad-host-range Erwinia amylovora bacteriophages reveal a high degree of mosaicism and a relationship to Enterobacteriaceae phages.
Born Y, Fieseler L, Marazzi J, Lurz R, Duffy B, Loessner MJ., Appl. Environ. Microbiol. 77(17), 2011
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Shutoff of host macromolecular synthesis after T-even bacteriophage infection
AUTHOR UNKNOWN, 1979
AUTHOR UNKNOWN, 1979
A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19.
Lavigne R, Lecoutere E, Wagemans J, Cenens W, Aertsen A, Schoofs L, Landuyt B, Paeshuyse J, Scheer M, Schobert M, Ceyssens PJ., MBio 4(2), 2013
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T4 DNA injection. II. Protection of entering DNA from host exonuclease V.
Silverstein JL, Goldberg EB., Virology 72(1), 1976
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Active protection by bacteriophages T3 and T7 against E. coli B- and K-specific restriction of their DNA.
Kruger DH, Schroeder C, Hansen S, Rosenthal HA., Mol. Gen. Genet. 153(1), 1977
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Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA.
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Handa N, Kobayashi I., J. Bacteriol. 187(21), 2005
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The roles of the bacteriophage T4 r genes in lysis inhibition and fine-structure genetics: a new perspective.
Paddison P, Abedon ST, Dressman HK, Gailbreath K, Tracy J, Mosser E, Neitzel J, Guttman B, Kutter E., Genetics 148(4), 1998
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Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W., Microbiol. Mol. Biol. Rev. 67(1), 2003
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Schleifer KH, Kandler O., Bacteriol Rev 36(4), 1972
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Schleifer KH, Kandler O., Bacteriol Rev 36(4), 1972
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Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Krogh A, Larsson B, von Heijne G, Sonnhammer EL., J. Mol. Biol. 305(3), 2001
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Phages will out: strategies of host cell lysis.
Young I, Wang I, Roof WD., Trends Microbiol. 8(3), 2000
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The final step in the phage infection cycle: the Rz and Rz1 lysis proteins link the inner and outer membranes.
Berry J, Summer EJ, Struck DK, Young R., Mol. Microbiol. 70(2), 2008
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Zhang N, Young R., Mol. Gen. Genet. 262(4-5), 1999
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The endolysins of bacteriophages CMP1 and CN77 are specific for the lysis of Clavibacter michiganensis strains.
Wittmann J, Eichenlaub R, Dreiseikelmann B., Microbiology (Reading, Engl.) 156(Pt 8), 2010
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Wittmann J, Eichenlaub R, Dreiseikelmann B., Microbiology (Reading, Engl.) 156(Pt 8), 2010
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Whole-genome prokaryotic phylogeny.
Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC., Bioinformatics 21(10), 2004
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Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC., Bioinformatics 21(10), 2004
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Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.
Auch AF, Henz SR, Holland BR, Goker M., BMC Bioinformatics 7(), 2006
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Auch AF, Henz SR, Holland BR, Goker M., BMC Bioinformatics 7(), 2006
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Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M., BMC Bioinformatics 14(), 2013
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Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
Desper R, Gascuel O., J. Comput. Biol. 9(5), 2002
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Desper R, Gascuel O., J. Comput. Biol. 9(5), 2002
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An empirical test of the midpoint rooting method
AUTHOR UNKNOWN, 2007
AUTHOR UNKNOWN, 2007
BLAST+: architecture and applications.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL., BMC Bioinformatics 10(), 2009
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Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL., BMC Bioinformatics 10(), 2009
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Isolation and characterization of a novel indigenous intestinal N4-related coliphage vB_EcoP_G7C.
Kulikov E, Kropinski AM, Golomidova A, Lingohr E, Govorun V, Serebryakova M, Prokhorov N, Letarova M, Manykin A, Strotskaya A, Letarov A., Virology 426(2), 2012
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Complete genome sequence of the bacteriophages ECBP1 and ECBP2 isolated from two different Escherichia coli strains.
Nho SW, Ha MA, Kim KS, Kim TH, Jang HB, Cha IS, Park SB, Kim YK, Jung TS., J. Virol. 86(22), 2012
PMID: 23087106
Nho SW, Ha MA, Kim KS, Kim TH, Jang HB, Cha IS, Park SB, Kim YK, Jung TS., J. Virol. 86(22), 2012
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Complete genome sequence of IME11, a new N4-like bacteriophage.
Fan H, Fan H, An X, Huang Y, Zhang Z, Mi Z, Tong Y., J. Virol. 86(24), 2012
PMID: 23166261
Fan H, Fan H, An X, Huang Y, Zhang Z, Mi Z, Tong Y., J. Virol. 86(24), 2012
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The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80.
Gan HM, Sieo CC, Tang SG, Omar AR, Ho YW., Virol. J. 10(), 2013
PMID: 24134834
Gan HM, Sieo CC, Tang SG, Omar AR, Ho YW., Virol. J. 10(), 2013
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Complete genome of Pseudomonas aeruginosa phage PA26.
Kim MS, Cha KE, Myung H., J. Virol. 86(18), 2012
PMID: 22923802
Kim MS, Cha KE, Myung H., J. Virol. 86(18), 2012
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Bacteriophages of freshwater Brevundimonas vesicularis isolates.
Beilstein F, Dreiseikelmann B., Res. Microbiol. 157(3), 2005
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Beilstein F, Dreiseikelmann B., Res. Microbiol. 157(3), 2005
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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Thorvaldsdottir H, Robinson JT, Mesirov JP., Brief. Bioinformatics 14(2), 2012
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Thorvaldsdottir H, Robinson JT, Mesirov JP., Brief. Bioinformatics 14(2), 2012
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Artemis: sequence visualization and annotation.
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B., Bioinformatics 16(10), 2000
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Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B., Bioinformatics 16(10), 2000
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Genomic and molecular analysis of phage CMP1 from Clavibacter michiganensis subspecies michiganensis.
Wittmann J, Gartemann KH, Eichenlaub R, Dreiseikelmann B., Bacteriophage 1(1), 2011
PMID: 21687530
Wittmann J, Gartemann KH, Eichenlaub R, Dreiseikelmann B., Bacteriophage 1(1), 2011
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Regulation of glutamine synthetase. XII. Electron microscopy of the enzyme from Escherichia coli.
Valentine RC, Shapiro BM, Stadtman ER., Biochemistry 7(6), 1968
PMID: 4873173
Valentine RC, Shapiro BM, Stadtman ER., Biochemistry 7(6), 1968
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A low-viscosity epoxy resin embedding medium for electron microscopy.
Spurr AR., J. Ultrastruct. Res. 26(1), 1969
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Spurr AR., J. Ultrastruct. Res. 26(1), 1969
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Highly parallelized inference of large genome-based phylogenies
AUTHOR UNKNOWN, 2013
AUTHOR UNKNOWN, 2013
AUTHOR UNKNOWN, 2003
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