메뉴 건너뛰기




Volumn 86, Issue 3, 2012, Pages 1844-1852

Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse φKZ-related phages

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; EXONUCLEASE; PEPTIDOGLYCAN; VIRUS PROTEIN;

EID: 84857071796     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.06330-11     Document Type: Article
Times cited : (59)

References (54)
  • 1
    • 84873061648 scopus 로고    scopus 로고
    • Reference deleted
    • Reference deleted.
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 4
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: application to sequence homology searches
    • Bailey TL, Gribskov M. 1998. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14:48 -54.
    • (1998) Bioinformatics , vol.14 , pp. 48-54
    • Bailey, T.L.1    Gribskov, M.2
  • 5
    • 34948860729 scopus 로고    scopus 로고
    • Causes for the intriguing presence of tRNAs in phages
    • Bailly-Bechet M, Vergassola M, Rocha E. 2007. Causes for the intriguing presence of tRNAs in phages. Genome Res. 17:1486 -1495.
    • (2007) Genome Res , vol.17 , pp. 1486-1495
    • Bailly-Bechet, M.1    Vergassola, M.2    Rocha, E.3
  • 7
    • 0033214628 scopus 로고    scopus 로고
    • Heuristic approach to deriving models for gene finding
    • Besemer J, Borodovsky M. 1999. Heuristic approach to deriving models for gene finding. Nucleic Acids Res. 27:3911-3920.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3911-3920
    • Besemer, J.1    Borodovsky, M.2
  • 9
    • 34547897398 scopus 로고    scopus 로고
    • Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophagesφKZ and EL
    • Briers Y, et al. 2007. Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophagesφKZ and EL. Mol. Microbiol. 65:1334 -1344.
    • (2007) Mol. Microbiol. , vol.65 , pp. 1334-1344
    • Briers, Y.1
  • 10
    • 49449108717 scopus 로고    scopus 로고
    • The structural peptidoglycan hydrolase gp181 of bacteriophage φKZ
    • Briers Y, et al. 2008. The structural peptidoglycan hydrolase gp181 of bacteriophage φKZ. Biochem. Biophys. Res. Commun. 374:747-751.
    • (2008) Biochem. Biophys. Res. Commun. , vol.374 , pp. 747-751
    • Briers, Y.1
  • 11
    • 34247602006 scopus 로고    scopus 로고
    • Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery
    • Comeau A, Bertrand C, Letarov A, Tétart F, Krisch H. 2007. Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Virology 362:384 -396.
    • (2007) Virology , vol.362 , pp. 384-396
    • Comeau, A.1    Bertrand, C.2    Letarov, A.3    Tétart, F.4    Krisch, H.5
  • 13
    • 0032893184 scopus 로고    scopus 로고
    • TransTerm, the translational signal database, extended to include full coding sequenced and untranslated regions
    • Dalphin ME, Stockwell PA, Tate WP, Brown CM. 1999. TransTerm, the translational signal database, extended to include full coding sequenced and untranslated regions. Nucleic Acids Res. 27:293-294.
    • (1999) Nucleic Acids Res , vol.27 , pp. 293-294
    • Dalphin, M.E.1    Stockwell, P.A.2    Tate, W.P.3    Brown, C.M.4
  • 14
    • 0012315109 scopus 로고
    • Transactions in T4-infected Escherichia coli
    • Karam JD (ed.), ASM Press, Washington DC
    • Drake JW, Kreuzer KN. 1994. Transactions in T4-infected Escherichia coli, p. 11-13. InKaram JD (ed.), Molecular biology of bacteriophage T4. ASM Press, Washington, DC.
    • (1994) Molecular biology of bacteriophage T4 , pp. 11-13
    • Drake, J.W.1    Kreuzer, K.N.2
  • 15
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 16
    • 0034680628 scopus 로고    scopus 로고
    • The crystal structure of UUCG tetraloop
    • Ennifar E, et al. 2000. The crystal structure of UUCG tetraloop. J. Mol. Biol. 304:35- 42.
    • (2000) J. Mol. Biol. , vol.304 , pp. 35-42
    • Ennifar, E.1
  • 17
    • 33748165572 scopus 로고    scopus 로고
    • A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes
    • Filée J, Bapteste E, Susko E, Krisch HM. 2006. A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes. Mol. Biol. Evol. 23:1688 -1696.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1688-1696
    • Filée, J.1    Bapteste, E.2    Susko, E.3    Krisch, H.M.4
  • 18
    • 34548405106 scopus 로고    scopus 로고
    • Cryo-EM study of the Pseudomonas bacteriophage φKZ
    • Fokine A, et al. 2007. Cryo-EM study of the Pseudomonas bacteriophage φKZ. Structure 15:1099 -1104.
    • (2007) Structure , vol.15 , pp. 1099-1104
    • Fokine, A.1
  • 20
    • 0035369086 scopus 로고    scopus 로고
    • Structure of the replicating complex of a pol α family DNA polymerase
    • Franklin MC, Wang J, Steitz TA. 2001. Structure of the replicating complex of a pol α family DNA polymerase. Cell 105:657- 667.
    • (2001) Cell , vol.105 , pp. 657-667
    • Franklin, M.C.1    Wang, J.2    Steitz, T.A.3
  • 21
    • 58149191274 scopus 로고    scopus 로고
    • Rfam: updates to the RNA families database
    • Gardner PP, et al. 2009. Rfam: updates to the RNA families database. Nucleic Acids Res. 37:D136-D140.
    • (2009) Nucleic Acids Res , vol.37
    • Gardner, P.P.1
  • 22
    • 37349114483 scopus 로고    scopus 로고
    • Comparative genomics of Bacillus thuringiensis phage 0305φ8-36: defining patterns of descent in a novel ancient phage lineage
    • Hardies SC, Thomas JA, Serwer P. 2007. Comparative genomics of Bacillus thuringiensis phage 0305φ8-36: defining patterns of descent in a novel ancient phage lineage. Virol. J. 4:97.
    • (2007) Virol. J. , vol.4 , pp. 97
    • Hardies, S.C.1    Thomas, J.A.2    Serwer, P.3
  • 23
    • 27744600407 scopus 로고    scopus 로고
    • Genome comparison of Pseudomonas aeruginosa large phages
    • Hertveldt K, et al. 2005. Genome comparison of Pseudomonas aeruginosa large phages. J. Mol. Biol. 354:536 -545.
    • (2005) J. Mol. Biol. , vol.354 , pp. 536-545
    • Hertveldt, K.1
  • 24
    • 0023134569 scopus 로고
    • Genetic mapping of the amino-terminal domain of bacteriophage T4 DNA polymerase
    • Hughes MB, Yee MA, Dawson M, Karam J. 1987. Genetic mapping of the amino-terminal domain of bacteriophage T4 DNA polymerase. Genetics 115:393- 403.
    • (1987) Genetics , vol.115 , pp. 393-403
    • Hughes, M.B.1    Yee, M.A.2    Dawson, M.3    Karam, J.4
  • 25
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: extension and analysis of the basic method
    • Hughey R, Krogh A. 1996. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci. 12: 95-107.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 26
    • 58149181382 scopus 로고    scopus 로고
    • Transterm: a database to aid the analysis of regulatory sequences in mRNAs
    • Jacobs GH, et al. 2009. Transterm: a database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Res. 37:D72-D76.
    • (2009) Nucleic Acids Res , vol.37
    • Jacobs, G.H.1
  • 27
    • 0041341888 scopus 로고    scopus 로고
    • Prediction of lipoprotein signal peptides in Gramnegative bacteria
    • Juncker AS, et al. 2003. Prediction of lipoprotein signal peptides in Gramnegative bacteria. Protein Sci. 12:1652-1662.
    • (2003) Protein Sci , vol.12 , pp. 1652-1662
    • Juncker, A.S.1
  • 28
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus K, Barrett C, Hughey R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14:846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 29
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh A, Larsson B, Von Heijne G, Sonnhammer ELL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.L.4
  • 30
    • 70350437756 scopus 로고    scopus 로고
    • A rational scheme for the nomenclature of prokaryotic viruses
    • Kropinski AM, Prangishvilli D, Lavigne R. 2009. A rational scheme for the nomenclature of prokaryotic viruses. Environ. Microbiol. 11: 2775-2777.
    • (2009) Environ. Microbiol. , vol.11 , pp. 2775-2777
    • Kropinski, A.M.1    Prangishvilli, D.2    Lavigne, R.3
  • 32
    • 0021222313 scopus 로고
    • Pseudomonas bacteriophage φKZ contains an inner body in its capsid
    • Krylov VN, et al. 1984. Pseudomonas bacteriophage φKZ contains an inner body in its capsid. Can. J. Microbiol. 30:758 -762.
    • (1984) Can. J. Microbiol. , vol.30 , pp. 758-762
    • Krylov, V.N.1
  • 33
    • 34848906889 scopus 로고    scopus 로고
    • "phiKZ-like viruses", a proposed new genus of myovirus bacteriophages
    • Krylov VN, Dela Cruz DM, Hertveldt K, Ackermann H-W. 2007. "phiKZ-like viruses", a proposed new genus of myovirus bacteriophages. Arch. Virol. 152:1955-1959.
    • (2007) Arch. Virol. , vol.152 , pp. 1955-1959
    • Krylov, V.N.1    Dela Cruz, D.M.2    Hertveldt, K.3    Ackermann, H.-W.4
  • 34
    • 1842559901 scopus 로고    scopus 로고
    • PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes
    • Lavigne R, Sun WD, Volckaert G. 2004. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 20:629-635.
    • (2004) Bioinformatics , vol.20 , pp. 629-635
    • Lavigne, R.1    Sun, W.D.2    Volckaert, G.3
  • 35
    • 70449380104 scopus 로고    scopus 로고
    • Classification of Myoviridae bacteriophages using protein sequence similarity
    • Lavigne R, et al. 2009. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 9:224.
    • (2009) BMC Microbiol , vol.9 , pp. 224
    • Lavigne, R.1
  • 36
    • 67649229159 scopus 로고    scopus 로고
    • Identification and comparative analysis of the structural proteomes of φKZ and EL, two giant Pseudomonas aeruginosa bacteriophages
    • Lecoutere E, et al. 2009. Identification and comparative analysis of the structural proteomes of φKZ and EL, two giant Pseudomonas aeruginosa bacteriophages. Proteomics 9:3215-3219.
    • (2009) Proteomics , vol.9 , pp. 3215-3219
    • Lecoutere, E.1
  • 37
    • 22544471225 scopus 로고    scopus 로고
    • Bacteriophage endolysins- current state of research and applications
    • Loessner MJ. 2005. Bacteriophage endolysins- current state of research and applications. Curr. Opin. Microbiol. 8:480-487.
    • (2005) Curr. Opin. Microbiol. , vol.8 , pp. 480-487
    • Loessner, M.J.1
  • 38
    • 0030854739 scopus 로고    scopus 로고
    • tRNA-scan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR. 1997. tRNA-scan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 39
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: new solutions for gene finding
    • Lukashin A, Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26:1107-1115.
    • (1998) Nucleic Acids Res , vol.26 , pp. 1107-1115
    • Lukashin, A.1    Borodovsky, M.2
  • 40
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas A, Van Dyke M, Stock J. 1991. Predicting coiled coils from protein sequences. Science 252:1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 41
    • 3242876311 scopus 로고    scopus 로고
    • BLAST: at the core of a powerful and diverse set of sequence analysis tools
    • McGinnis S, Madden TL. 2004. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32:W20-W25.
    • (2004) Nucleic Acids Res , vol.32
    • McGinnis, S.1    Madden, T.L.2
  • 42
    • 0036018291 scopus 로고    scopus 로고
    • The genome of bacteriophage φKZ of Pseudomonas aeruginosa
    • Mesyanzhinov VV, et al. 2002. The genome of bacteriophage φKZ of Pseudomonas aeruginosa. J. Mol. Biol. 317:1-19.
    • (2002) J. Mol. Biol. , vol.317 , pp. 1-19
    • Mesyanzhinov, V.V.1
  • 43
    • 79952258759 scopus 로고    scopus 로고
    • The Pseudomonas aeruginosa generalized transducing phage φPA3 is a new member of the φKZ-like group of 'jumbo' phages, and infects model laboratory strains and clinical isolates form cystic fibrosis patients
    • Monson R, Foulds I, Foweraker J, Welch M, Salmond GPC. 2011. The Pseudomonas aeruginosa generalized transducing phage φPA3 is a new member of the φKZ-like group of 'jumbo' phages, and infects model laboratory strains and clinical isolates form cystic fibrosis patients. Microbiology 157:859-867.
    • (2011) Microbiology , vol.157 , pp. 859-867
    • Monson, R.1    Foulds, I.2    Foweraker, J.3    Welch, M.4    Salmond, G.P.C.5
  • 44
    • 0024769281 scopus 로고
    • Functional relationships and structural determinants of two bacteriophage T4 lysozymes: a soluble (gene e) and a baseplate-associated (gene 5) protein
    • Mosig G, Lin GW, Franklin J, Fan WH. 1989. Functional relationships and structural determinants of two bacteriophage T4 lysozymes: a soluble (gene e) and a baseplate-associated (gene 5) protein. New Biol. 1:171-179.
    • (1989) New Biol , vol.1 , pp. 171-179
    • Mosig, G.1    Lin, G.W.2    Franklin, J.3    Fan, W.H.4
  • 45
    • 33751070265 scopus 로고    scopus 로고
    • Thermus thermophilus bacteriophage phiYS40 genome and proteomic characterization of virions
    • Naryshkina T, et al. 2006. Thermus thermophilus bacteriophage phiYS40 genome and proteomic characterization of virions. J. Mol. Biol. 364: 667-677.
    • (2006) J. Mol. Biol. , vol.364 , pp. 667-677
    • Naryshkina, T.1
  • 46
    • 7944222972 scopus 로고    scopus 로고
    • Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus
    • Savino C, et al. 2004. Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus. Structure 12:2001-2008.
    • (2004) Structure , vol.12 , pp. 2001-2008
    • Savino, C.1
  • 47
    • 33750609702 scopus 로고    scopus 로고
    • Comparison of new giant bacteriophages OBP and Lu11 of soil pseudomonads with bacteriophages of φKZ-supergroup of Pseudomonas aeruginosa
    • [In Russian]
    • Shaburova OV, et al. 2006.Comparison of new giant bacteriophages OBP and Lu11 of soil pseudomonads with bacteriophages of φKZ-supergroup of Pseudomonas aeruginosa. Genetika 42:1065-1074. [In Russian].
    • (2006) Genetika , vol.42 , pp. 1065-1074
    • Shaburova, O.V.1
  • 48
    • 0033384536 scopus 로고    scopus 로고
    • Finding prokaryotic genes by the "frame-by-frame" algorithm: targeting gene starts and overlapping genes
    • Shmatkov AM, Melikyan AA, Chernousko FL, Borodovsky M. 1999. Finding prokaryotic genes by the "frame-by-frame" algorithm: targeting gene starts and overlapping genes. Bioinformatics 15:874-886.
    • (1999) Bioinformatics , vol.15 , pp. 874-886
    • Shmatkov, A.M.1    Melikyan, A.A.2    Chernousko, F.L.3    Borodovsky, M.4
  • 49
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 50
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33:W244-W248.
    • (2005) Nucleic Acids Res , vol.33
    • Söding, J.1    Biegert, A.2    Lupas, A.N.3
  • 51
    • 35548995474 scopus 로고    scopus 로고
    • Complete genomic sequence and mass spectrometric analysis of highly diverse atypical Bacillus thuringiensis phage 0305phi8-36
    • Thomas JA, et al. 2007. Complete genomic sequence and mass spectrometric analysis of highly diverse atypical Bacillus thuringiensis phage 0305phi8-36. Virology 368:405- 421.
    • (2007) Virology , vol.368 , pp. 405-421
    • Thomas, J.A.1
  • 52
    • 44649113056 scopus 로고    scopus 로고
    • Characterization of Pseudomonas chlororaphis myovirus 201φ2-1 via genomic sequencing, mass spectrometry, and electron microscopy
    • Thomas JA, et al. 2008. Characterization of Pseudomonas chlororaphis myovirus 201φ2-1 via genomic sequencing, mass spectrometry, and electron microscopy. Virology 376:330 -338.
    • (2008) Virology , vol.376 , pp. 330-338
    • Thomas, J.A.1
  • 53
    • 0031587827 scopus 로고    scopus 로고
    • Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69
    • Wang J, et al. 1997. Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69. Cell 89:1087-1099.
    • (1997) Cell , vol.89 , pp. 1087-1099
    • Wang, J.1
  • 54
    • 2342634418 scopus 로고    scopus 로고
    • A signal-arrestrelease sequence mediates export and control of the phage P1 endolysin
    • Xu M, Struck D, Deaton J, Wang I-N, Young R. 2004. A signal-arrestrelease sequence mediates export and control of the phage P1 endolysin. Proc. Natl. Acad. Sci. U. S. A. 101:6415- 6420.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 6415-6420
    • Xu, M.1    Struck, D.2    Deaton, J.3    Wang, I.-N.4    Young, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.