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Volumn 83, Issue 21, 2009, Pages 11233-11243

Gene mapping and phylogenetic analysis of the complete genome from 30 single-stranded RNA male-specific coliphages (family Leviviridae)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC RNA; RNA DIRECTED RNA POLYMERASE; SINGLE STRANDED RNA;

EID: 70350320585     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.01308-09     Document Type: Article
Times cited : (29)

References (44)
  • 1
    • 0035581083 scopus 로고    scopus 로고
    • Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs
    • Beier, H., and M. Grimm. 2001. Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs. Nucleic Acids Res. 29:4767-4782. (Pubitemid 33133548)
    • (2001) Nucleic Acids Research , vol.29 , Issue.23 , pp. 4767-4782
    • Beier, H.1    Grimm, M.2
  • 2
    • 0035137890 scopus 로고    scopus 로고
    • Endless possibilities: Translation termination and stop codon recognition
    • Bertram, G., S. Innes, O. Minella, J. P. Richardson, and I. Stansfield. 2001. Endless possibilities: translation termination and stop codon recognition. Microbiology 147:255-269. (Pubitemid 32156802)
    • (2001) Microbiology , vol.147 , Issue.2 , pp. 255-269
    • Bertram, G.1    Innes, S.2    Minella, O.3    Richardson, J.P.4    Stansfield, I.5
  • 4
    • 0035089952 scopus 로고    scopus 로고
    • Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae)
    • Bollback, J. P., and J. P. Huelsenbeck. 2001. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae). J. Mol. Evol. 52:117-128.
    • (2001) J. Mol. Evol. , vol.52 , pp. 117-128
    • Bollback, J.P.1    Huelsenbeck, J.P.2
  • 5
    • 70350313911 scopus 로고    scopus 로고
    • Levivirus
    • Buchen-Osmond, C. (ed.). version 4. ICTVdB Management, Columbia University, New York, NY
    • Buchen-Osmond, C. (ed.). 2006. Levivirus. In ICTVdB - the Universal Virus Database, version 4. ICTVdB Management, Columbia University, New York, NY.
    • (2006) ICTVdB - The Universal Virus Database
  • 6
    • 0001174747 scopus 로고
    • Genetic analysis of a "double male" strain of Escherichia coli K-12
    • Clark, A. J. 1963. Genetic analysis of a "double male" strain of Escherichia coli K-12. Genetics 48:105-120.
    • (1963) Genetics , vol.48 , pp. 105-120
    • Clark, A.J.1
  • 7
    • 0005665629 scopus 로고
    • The adsorption of bacteriophage R17
    • Crawford, E. M., and R. G. Gesteland. 1964. The adsorption of bacteriophage R17. Virology 22:165-167.
    • (1964) Virology , vol.22 , pp. 165-167
    • Crawford, E.M.1    Gesteland, R.G.2
  • 8
    • 0019482556 scopus 로고
    • UGA suppression by normal tRNATrp in Escherichia coli: Codon context effects
    • Engelberg-Kulka, H. 1981. UGA suppression by normal tRNATrp in Escherichia coli: codon context effects. Nucleic Acids Res. 9:983-991.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 983-991
    • Engelberg-Kulka, H.1
  • 11
    • 67349214184 scopus 로고    scopus 로고
    • A reverse transcription-PCR assay to distinguish the four genogroups of male-specific (F+) RNA coliphages
    • Friedman, S. D., E. M. Cooper, L. Casanova, M. D. Sobsey, and F. J. Genthner. 2009. A reverse transcription-PCR assay to distinguish the four genogroups of male-specific (F+) RNA coliphages. J. Virol. Methods 159:47-52.
    • (2009) J. Virol. Methods , vol.159 , pp. 47-52
    • Friedman, S.D.1    Cooper, E.M.2    Casanova, L.3    Sobsey, M.D.4    Genthner, F.J.5
  • 12
    • 0001856441 scopus 로고
    • Distribution of coliphages in the environment: General considerations
    • S. M. Goyal, C. P. Gerba, and G. Bitton (ed.), John Wiley & Sons, Inc., New York, NY
    • Furuse, K. 1987. Distribution of coliphages in the environment: general considerations, p. 87-124. In S. M. Goyal, C. P. Gerba, and G. Bitton (ed.), Phage ecology. John Wiley & Sons, Inc., New York, NY.
    • (1987) Phage Ecology , pp. 87-124
    • Furuse, K.1
  • 13
    • 0029971613 scopus 로고    scopus 로고
    • RNA phage KU1 has an insertion of 18 nucleotides in the start codon of its lysis gene
    • DOI 10.1006/viro.1996.0174
    • Groeneveld, H., F. Oudot, and J. van Duin. 1996. RNA phage KU1 has an insertion of 18 nucleotides in the start codon of its lysis gene. Virology 218:141-147. (Pubitemid 26133094)
    • (1996) Virology , vol.218 , Issue.1 , pp. 141-147
    • Groeneveld, H.1    Oudot, F.2    Van Duin, J.3
  • 14
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
    • (1999) Nucleic Acids Symp. Ser. , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 16
    • 23844439948 scopus 로고    scopus 로고
    • Eukaryotic translational coupling in UAAUG stop-start codons for the bicistronic RNA translation of the non-long terminal repeat retrotransposon SART1
    • Kojima, K. K., T. Matsumoto, and H. Fujiwara. 2005. Eukaryotic translational coupling in UAAUG stop-start codons for the bicistronic RNA translation of the non-long terminal repeat retrotransposon SART1. Mol. Cell. Biol. 25:7675-7686.
    • (2005) Mol. Cell. Biol. , vol.25 , pp. 7675-7686
    • Kojima, K.K.1    Matsumoto, T.2    Fujiwara, H.3
  • 18
    • 0032889281 scopus 로고    scopus 로고
    • Full-length human immunodeficiency virus type 1 genomes from subtype c-infected seroconverters in India, with evidence of intersubtype recombination
    • Lole, K. S., R. C. Bollinger, R. S. Paranjape, D. Gadkari, S. S. Kulkarni, N. G. Novak, R. Ingersoll, H. W. Sheppard, and S. C. Ray. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype c-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73:152-160.
    • (1999) J. Virol. , vol.73 , pp. 152-160
    • Lole, K.S.1    Bollinger, R.C.2    Paranjape, R.S.3    Gadkari, D.4    Kulkarni, S.S.5    Novak, N.G.6    Ingersoll, R.7    Sheppard, H.W.8    Ray, S.C.9
  • 19
    • 0242677606 scopus 로고    scopus 로고
    • Microarrays for genotyping human group a rotavirus by multiplex capture and type-specific primer extension
    • Lovmar, L., C. Fock, F. Espinoza, F. Bucardo, A. C. Syvanen, and K. Bondeson. 2003. Microarrays for genotyping human group A rotavirus by multiplex capture and type-specific primer extension. J. Clin. Microbiol. 41:5153-5158.
    • (2003) J. Clin. Microbiol. , vol.41 , pp. 5153-5158
    • Lovmar, L.1    Fock, C.2    Espinoza, F.3    Bucardo, F.4    Syvanen, A.C.5    Bondeson, K.6
  • 20
    • 0036786891 scopus 로고    scopus 로고
    • Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures
    • Ma, J., A. Campbell, and S. Karlin. 2002. Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J. Bacteriol. 184:5733-5745.
    • (2002) J. Bacteriol. , vol.184 , pp. 5733-5745
    • Ma, J.1    Campbell, A.2    Karlin, S.3
  • 21
    • 0030950412 scopus 로고    scopus 로고
    • Evolution subverting essentiality: Dispensability of the cell attachment Arg-Gly-Asp motif in multiply passaged foot-and-mouth disease virus
    • Martínez, M. A., N. Verdaguer, M. G. Mateu, and E. Domingo. 1997. Evolution subverting essentiality: dispensability of the cell attachment Arg-Gly-Asp motif in multiply passaged foot-and-mouth disease virus. Proc. Natl. Acad. Sci. USA 94:6798-6802.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 6798-6802
    • Martínez, M.A.1    Verdaguer, N.2    Mateu, M.G.3    Domingo, E.4
  • 23
    • 0034779875 scopus 로고    scopus 로고
    • Impact of the six nucleotides downstream of the stop codon on translation termination
    • DOI 10.1093/embo-reports/kve176
    • Namy, O., I. Hatin, and J. P. Rousset. 2001. Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep. 2:787-793. (Pubitemid 32982746)
    • (2001) EMBO Reports , vol.2 , Issue.9 , pp. 787-793
    • Namy, O.1    Hatin, I.2    Rousset, J.-P.3
  • 24
    • 0032855287 scopus 로고    scopus 로고
    • 3 (vitronectin receptor) is a candidate receptor for the virulent echovirus 9 strain Barty
    • 3 (vitronectin receptor) is a candidate receptor for the virulent echovirus 9 strain Barty. Gen. Virol. 80:2311-2313.
    • (1999) Gen. Virol. , vol.80 , pp. 2311-2313
    • Nelsen-Salz, B.1    Eggers, H.J.2    Zimmermann, H.3
  • 25
    • 31344437879 scopus 로고    scopus 로고
    • Analysis of six new genes encoding lysis proteins and coat proteins in Escherichia coli group A RNA phages
    • Nishihara, T., S. Fujisaki, Y. Nishimura, Y. Minami, and T. Yubisui. 2006. Analysis of six new genes encoding lysis proteins and coat proteins in Escherichia coli group A RNA phages. Microbiol. Immunol. 50:61-66.
    • (2006) Microbiol. Immunol. , vol.50 , pp. 61-66
    • Nishihara, T.1    Fujisaki, S.2    Nishimura, Y.3    Minami, Y.4    Yubisui, T.5
  • 26
    • 0015578110 scopus 로고
    • Host range and properties of the Pseudomonas aeruginosa R factor R1822
    • Olsen, R. H., and P. Shipley. 1973. Host range and properties of the Pseudomonas aeruginosa R factor R1822. J. Bacteriol. 113:772-780.
    • (1973) J. Bacteriol. , vol.113 , pp. 772-780
    • Olsen, R.H.1    Shipley, P.2
  • 27
    • 0028852550 scopus 로고
    • Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: Kinship to coliphages and conservation of regulatory RNA structures
    • Olsthoorn, R. C. L., G. Garde, T. Dayhuff, J. F. Atkins, and J. van Duin. 1995. Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures. Virology 206:611-625.
    • (1995) Virology , vol.206 , pp. 611-625
    • Olsthoorn, R.C.L.1    Garde, G.2    Dayhuff, T.3    Atkins, J.F.4    Van Duin, J.5
  • 28
    • 0002671573 scopus 로고
    • Attachment, ejection and penetration stages of the RNA phage infectious process
    • N. D. Zinder (ed.), Cold Spring Harbor Laboratory Press, New York, NY
    • Paranchych, W. 1975. Attachment, ejection and penetration stages of the RNA phage infectious process, p. 85-111. In N. D. Zinder (ed.), RNA phages. Cold Spring Harbor Laboratory Press, New York, NY.
    • (1975) RNA Phages , pp. 85-111
    • Paranchych, W.1
  • 29
    • 33748507575 scopus 로고    scopus 로고
    • Complete genome sequence of the broad host range single-stranded RNA phage PRR1 places it in the Levivirus genus with characteristics shared with alloleviviruses
    • Ruokoranta, T. M., A. M. Grahn, J. J. Ravantti, M. M. Poranen, and D. H. Bamford. 2006. Complete genome sequence of the broad host range single-stranded RNA phage PRR1 places it in the Levivirus genus with characteristics shared with alloleviviruses. J. Virol. 80:9326-9330.
    • (2006) J. Virol. , vol.80 , pp. 9326-9330
    • Ruokoranta, T.M.1    Grahn, A.M.2    Ravantti, J.J.3    Poranen, M.M.4    Bamford, D.H.5
  • 30
    • 0027321823 scopus 로고
    • Identification and characterization of E. coli ribosomal binding sites by free energy computation
    • Schurr, T., E. Nadir, and H. Margalit. 1993. Identification and characterization of E. coli ribosomal binding sites by free energy computation. Nucleic Acids Res. 21:4019-4023.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 4019-4023
    • Schurr, T.1    Nadir, E.2    Margalit, H.3
  • 31
    • 0025464674 scopus 로고
    • Analysis of leaky viral translation termination codons in vivo by transient expression of improved beta-glucuronidase vectors
    • Skuzeski, J. M., L. M. Nichols, and R. F. Gesteland. 1990. Analysis of leaky viral translation termination codons in vivo by transient expression of improved beta-glucuronidase vectors. Plant Mol. Biol. 15:65-79.
    • (1990) Plant Mol. Biol. , vol.15 , pp. 65-79
    • Skuzeski, J.M.1    Nichols, L.M.2    Gesteland, R.F.3
  • 32
    • 33144478150 scopus 로고    scopus 로고
    • Sequence variation among group III F-specific RNA coliphages from water samples and swine lagoons
    • Stewart, J. R., J. Vinjé, S. J. G. Oudejans, and G. I. Scott. 2006. Sequence variation among group III F-specific RNA coliphages from water samples and swine lagoons. Appl. Environ. Microbiol. 72:1226-1230.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 1226-1230
    • Stewart, J.R.1    Vinjé, J.2    Oudejans, S.J.G.3    Scott, G.I.4
  • 33
    • 29944441133 scopus 로고    scopus 로고
    • Genotyping of F-RNA coliphages isolated from wastewater and river water samples
    • Sundram, A., N. Jumanial, and M. M. Ehlers. 2006. Genotyping of F-RNA coliphages isolated from wastewater and river water samples. Water SA 32:65-70. (Pubitemid 43042706)
    • (2006) Water SA , vol.32 , Issue.1 , pp. 65-70
    • Sundram, A.1    Jumanla, N.2    Ehlers, M.M.3
  • 34
    • 0035079190 scopus 로고    scopus 로고
    • RGD tripeptide of bluetongue virus VP7 protein is responsible for core attachment to Culicoides cell
    • Tan, B. H., E. Nason, N. Staeuber, W. Jiang, K. Monastryrskaya, and P. Roy. 2001. RGD tripeptide of bluetongue virus VP7 protein is responsible for core attachment to Culicoides cell. J. Virol. 75:3937-3947.
    • (2001) J. Virol. , vol.75 , pp. 3937-3947
    • Tan, B.H.1    Nason, E.2    Staeuber, N.3    Jiang, W.4    Monastryrskaya, K.5    Roy, P.6
  • 36
    • 0000694197 scopus 로고
    • The single-stranded RNA bacteriophages
    • C. H. Fraenkel and R. R. Wagner (ed.), Plenum Press, New York, NY
    • van Duin, J. 1988. The single-stranded RNA bacteriophages, p. 117-167. In C. H. Fraenkel and R. R. Wagner (ed.), The bacteriophages. The viruses. Plenum Press, New York, NY.
    • (1988) The Bacteriophages. The Viruses , pp. 117-167
    • Van Duin, J.1
  • 37
    • 0009328416 scopus 로고    scopus 로고
    • Single-stranded RNA phages (Leviviridae)
    • A. Granoff and R. Webster (ed.), Academic Press, London, United Kingdom
    • van Duin, J. 1999. Single-stranded RNA phages (Leviviridae), p. 1663-1668. In A. Granoff and R. Webster (ed.), Encyclopedia of virology. Academic Press, London, United Kingdom.
    • (1999) Encyclopedia of Virology , pp. 1663-1668
    • Van Duin, J.1
  • 38
    • 0009431550 scopus 로고    scopus 로고
    • Family Leviviridae
    • M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. S. Mayo, D. J. McGeoch, C. R. Pringle, and R. B. Wickner (ed.), Academic Press, San Diego, CA
    • van Duin, J. 2000. Family Leviviridae, p. 645-646. In M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. S. Mayo, D. J. McGeoch, C. R. Pringle, and R. B. Wickner (ed.), Virus taxonomy. Seventh report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA.
    • (2000) Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses , pp. 645-646
    • Van Duin, J.1
  • 39
    • 33748509219 scopus 로고    scopus 로고
    • Single-stranded RNA phages
    • R. L. Calendar and S. T. Abedon (ed.), Oxford University Press, New York, NY
    • van Duin, J., and N. Tsareva. 2006. Single-stranded RNA phages, p. 175-196. In R. L. Calendar and S. T. Abedon (ed.), The bacteriophages. Oxford University Press, New York, NY.
    • (2006) The Bacteriophages , pp. 175-196
    • Van Duin, J.1    Tsareva, N.2
  • 40
    • 33947201672 scopus 로고    scopus 로고
    • Different rates of (non-) synonymous mutations in astrovirus genes; correlation with gene function
    • van Hemert, F. J., V. V. Lukashow, and B. Berkhout. 2007. Different rates of (non-) synonymous mutations in astrovirus genes; correlation with gene function. Virol. J. 4:25-37.
    • (2007) Virol. J. , vol.4 , pp. 25-37
    • Van Hemert, F.J.1    Lukashow, V.V.2    Berkhout, B.3
  • 41
    • 8144224232 scopus 로고    scopus 로고
    • Molecular detection and genotyping of male-specific coliphages by reverse transcription-PCR and reverse line blot hybridization
    • Vinjé, J., S. J. G. Oudejans, J. R. Stewart, M. D. Sobsey, and S. C. Long. 2004. Molecular detection and genotyping of male-specific coliphages by reverse transcription-PCR and reverse line blot hybridization. Appl. Environ. Microbiol. 70:5996-6004.
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 5996-6004
    • Vinjé, J.1    Oudejans, S.J.G.2    Stewart, J.R.3    Sobsey, M.D.4    Long, S.C.5
  • 42
    • 0012130048 scopus 로고
    • Proteins of the RNA phages
    • N. D. Zinder (ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Weber, K., and W. Konigsberg. 1975. Proteins of the RNA phages, p. 51-84. In N. D. Zinder (ed.), RNA phages. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1975) RNA Phages , pp. 51-84
    • Weber, K.1    Konigsberg, W.2
  • 43
    • 0015848560 scopus 로고
    • A single UGA codon functions as a natural termination signal in the coliphage Q.β coat protein cistron
    • Weiner, A. M., and K. Weber. 1973. A single UGA codon functions as a natural termination signal in the coliphage Q.β coat protein cistron. J. Mol. Biol. 80:837-855.
    • (1973) J. Mol. Biol. , vol.80 , pp. 837-855
    • Weiner, A.M.1    Weber, K.2


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