This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Rohwer, F.
Right arrow Articles by Edwards, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rohwer, F.
Right arrow Articles by Edwards, R.

 Previous Article  |  Next Article 

Journal of Bacteriology, August 2002, p. 4529-4535, Vol. 184, No. 16
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.16.4529-4535.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage

Forest Rohwer1 and Rob Edwards2*

Department of Biology, San Diego State University, San Diego, California 92182-4614,1 University of Tennessee Health Sciences Center, Memphis, Tennessee 381632

Received 30 January 2002/ Accepted 6 May 2002

There are ~1031 phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage biodiversity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the "Phage Proteomic Tree," which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage biodiversity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage.

* Corresponding author. Mailing address: University of Tennessee Health Sciences Center, MSB 101, 858 Madison Ave., Memphis, TN 38163. Phone: (901) 448-8101. Fax: (901) 448-8462. E-mail: redwards{at}utmem.edu.

Journal of Bacteriology, August 2002, p. 4529-4535, Vol. 184, No. 16
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.16.4529-4535.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Ventura, M., Turroni, F., Lima-Mendez, G., Foroni, E., Zomer, A., Duranti, S., Giubellini, V., Bottacini, F., Horvath, P., Barrangou, R., Sela, D. A., Mills, D. A., van Sinderen, D. (2009). Comparative Analyses of Prophage-Like Elements Present in Bifidobacterial Genomes. Appl. Environ. Microbiol. 75: 6929-6936 [Abstract] [Full Text]  
  • Brussow, H. (2009). The not so universal tree of life or the place of viruses in the living world. Phil Trans R Soc B 364: 2263-2274 [Abstract] [Full Text]  
  • Domelier, A.-S., van der Mee-Marquet, N., Sizaret, P.-Y., Hery-Arnaud, G., Lartigue, M.-F., Mereghetti, L., Quentin, R. (2009). Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features. J. Bacteriol. 191: 4776-4785 [Abstract] [Full Text]  
  • Dassa, B., London, N., Stoddard, B. L., Schueler-Furman, O., Pietrokovski, S. (2009). Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucleic Acids Res 37: 2560-2573 [Abstract] [Full Text]  
  • Helton, R. R., Wommack, K. E. (2009). Seasonal Dynamics and Metagenomic Characterization of Estuarine Viriobenthos Assemblages by Randomly Amplified Polymorphic DNA PCR. Appl. Environ. Microbiol. 75: 2259-2265 [Abstract] [Full Text]  
  • Lehman, S. M., Kropinski, A. M., Castle, A. J., Svircev, A. M. (2009). Complete Genome of the Broad-Host-Range Erwinia amylovora Phage {Phi}Ea21-4 and Its Relationship to Salmonella Phage Felix O1. Appl. Environ. Microbiol. 75: 2139-2147 [Abstract] [Full Text]  
  • Pell, L. G., Kanelis, V., Donaldson, L. W., Lynne Howell, P., Davidson, A. R. (2009). The phage {lambda} major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system. Proc. Natl. Acad. Sci. USA 106: 4160-4165 [Abstract] [Full Text]  
  • Winget, D. M., Wommack, K. E. (2008). Randomly Amplified Polymorphic DNA PCR as a Tool for Assessment of Marine Viral Richness. Appl. Environ. Microbiol. 74: 2612-2618 [Abstract] [Full Text]  
  • Lima-Mendez, G., Van Helden, J., Toussaint, A., Leplae, R. (2008). Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes. Mol Biol Evol 25: 762-777 [Abstract] [Full Text]  
  • Yoshida, T., Nagasaki, K., Takashima, Y., Shirai, Y., Tomaru, Y., Takao, Y., Sakamoto, S., Hiroishi, S., Ogata, H. (2008). Ma-LMM01 Infecting Toxic Microcystis aeruginosa Illuminates Diverse Cyanophage Genome Strategies. J. Bacteriol. 190: 1762-1772 [Abstract] [Full Text]  
  • Bench, S. R., Hanson, T. E., Williamson, K. E., Ghosh, D., Radosovich, M., Wang, K., Wommack, K. E. (2007). Metagenomic Characterization of Chesapeake Bay Virioplankton. Appl. Environ. Microbiol. 73: 7629-7641 [Abstract] [Full Text]  
  • Ventura, M., Zomer, A., Canchaya, C., O'Connell-Motherway, M., Kuipers, O., Turroni, F., Ribbera, A., Foroni, E., Buist, G., Wegmann, U., Shearman, C., Gasson, M. J., Fitzgerald, G. F., Kok, J., van Sinderen, D. (2007). Comparative Analyses of Prophage-Like Elements Present in Two Lactococcus lactis Strains. Appl. Environ. Microbiol. 73: 7771-7780 [Abstract] [Full Text]  
  • Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., Robeson, M., Edwards, R. A., Felts, B., Rayhawk, S., Knight, R., Rohwer, F., Jackson, R. B. (2007). Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil. Appl. Environ. Microbiol. 73: 7059-7066 [Abstract] [Full Text]  
  • Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G. F., Chater, K. F., van Sinderen, D. (2007). Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum. Microbiol. Mol. Biol. Rev. 71: 495-548 [Abstract] [Full Text]  
  • Heo, Y.-J., Chung, I.-Y., Choi, K. B., Lau, G. W., Cho, Y.-H. (2007). Genome sequence comparison and superinfection between two related Pseudomonas aeruginosa phages, D3112 and MP22. Microbiology 153: 2885-2895 [Abstract] [Full Text]  
  • Atterbury, R. J., Van Bergen, M. A. P., Ortiz, F., Lovell, M. A., Harris, J. A., De Boer, A., Wagenaar, J. A., Allen, V. M., Barrow, P. A. (2007). Bacteriophage Therapy To Reduce Salmonella Colonization of Broiler Chickens. Appl. Environ. Microbiol. 73: 4543-4549 [Abstract] [Full Text]  
  • Daniel, A., Bonnen, P. E., Fischetti, V. A. (2007). First Complete Genome Sequence of Two Staphylococcus epidermidis Bacteriophages. J. Bacteriol. 189: 2086-2100 [Abstract] [Full Text]  
  • Fouts, D. E. (2006). Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res 34: 5839-5851 [Abstract] [Full Text]  
  • Ceyssens, P.-J., Lavigne, R., Mattheus, W., Chibeu, A., Hertveldt, K., Mast, J., Robben, J., Volckaert, G. (2006). Genomic Analysis of Pseudomonas aeruginosa Phages LKD16 and LKA1: Establishment of the {phi}KMV Subgroup within the T7 Supergroup.. J. Bacteriol. 188: 6924-6931 [Abstract] [Full Text]  
  • Baker, A. C., Goddard, V. J., Davy, J., Schroeder, D. C., Adams, D. G., Wilson, W. H. (2006). Identification of a Diagnostic Marker To Detect Freshwater Cyanophages of Filamentous Cyanobacteria. Appl. Environ. Microbiol. 72: 5713-5719 [Abstract] [Full Text]  
  • Fortier, L.-C., Bransi, A., Moineau, S. (2006). Genome Sequence and Global Gene Expression of Q54, a New Phage Species Linking the 936 and c2 Phage Species of Lactococcus lactis.. J. Bacteriol. 188: 6101-6114 [Abstract] [Full Text]  
  • Sandaa, R.-A., Larsen, A. (2006). Seasonal Variations in Virus-Host Populations in Norwegian Coastal Waters: Focusing on the Cyanophage Community Infecting Marine Synechococcus spp.. Appl. Environ. Microbiol. 72: 4610-4618 [Abstract] [Full Text]  
  • Deveau, H., Labrie, S. J., Chopin, M.-C., Moineau, S. (2006). Biodiversity and classification of lactococcal phages.. Appl. Environ. Microbiol. 72: 4338-4346 [Abstract] [Full Text]  
  • Ventura, M., Canchaya, C., Bernini, V., Altermann, E., Barrangou, R., McGrath, S., Claesson, M. J., Li, Y., Leahy, S., Walker, C. D., Zink, R., Neviani, E., Steele, J., Broadbent, J., Klaenhammer, T. R., Fitzgerald, G. F., O'Toole, P. W., van Sinderen, D. (2006). Comparative Genomics and Transcriptional Analysis of Prophages Identified in the Genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei.. Appl. Environ. Microbiol. 72: 3130-3146 [Abstract] [Full Text]  
  • Fouts, D. E., Rasko, D. A., Cer, R. Z., Jiang, L., Fedorova, N. B., Shvartsbeyn, A., Vamathevan, J. J., Tallon, L., Althoff, R., Arbogast, T. S., Fadrosh, D. W., Read, T. D., Gill, S. R. (2006). Sequencing Bacillus anthracis Typing Phages Gamma and Cherry Reveals a Common Ancestry. J. Bacteriol. 188: 3402-3408 [Abstract] [Full Text]  
  • Rokyta, D. R., Burch, C. L., Caudle, S. B., Wichman, H. A. (2006). Horizontal Gene Transfer and the Evolution of Microvirid Coliphage Genomes. J. Bacteriol. 188: 1134-1142 [Abstract] [Full Text]  
  • Lavigne, R., Noben, J.-P., Hertveldt, K., Ceyssens, P.-J., Briers, Y., Dumont, D., Roucourt, B., Krylov, V. N., Mesyanzhinov, V. V., Robben, J., Volckaert, G. (2006). The structural proteome of Pseudomonas aeruginosa bacteriophage {phi}KMV. Microbiology 152: 529-534 [Abstract] [Full Text]  
  • Summer, E. J., Gonzalez, C. F., Bomer, M., Carlile, T., Embry, A., Kucherka, A. M., Lee, J., Mebane, L., Morrison, W. C., Mark, L., King, M. D., LiPuma, J. J., Vidaver, A. K., Young, R. (2006). Divergence and Mosaicism among Virulent Soil Phages of the Burkholderia cepacia Complex. J. Bacteriol. 188: 255-268 [Abstract] [Full Text]  
  • Ventura, M., Lee, J.-H., Canchaya, C., Zink, R., Leahy, S., Moreno-Munoz, J. A., O'Connell-Motherway, M., Higgins, D., Fitzgerald, G. F., O'Sullivan, D. J., van Sinderen, D. (2005). Prophage-Like Elements in Bifidobacteria: Insights from Genomics, Transcription, Integration, Distribution, and Phylogenetic Analysis. Appl. Environ. Microbiol. 71: 8692-8705 [Abstract] [Full Text]  
  • Chen, Z., Schneider, T. D. (2005). Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases. Nucleic Acids Res 33: 6172-6187 [Abstract] [Full Text]  
  • Levesque, C., Duplessis, M., Labonte, J., Labrie, S., Fremaux, C., Tremblay, D., Moineau, S. (2005). Genomic Organization and Molecular Analysis of Virulent Bacteriophage 2972 Infecting an Exopolysaccharide-Producing Streptococcus thermophilus Strain. Appl. Environ. Microbiol. 71: 4057-4068 [Abstract] [Full Text]  
  • Paul, J. H., Williamson, S. J., Long, A., Authement, R. N., John, D., Segall, A. M., Rohwer, F. L., Androlewicz, M., Patterson, S. (2005). Complete Genome Sequence of {phi}HSIC, a Pseudotemperate Marine Phage of Listonella pelagia. Appl. Environ. Microbiol. 71: 3311-3320 [Abstract] [Full Text]  
  • Kwan, T., Liu, J., DuBow, M., Gros, P., Pelletier, J. (2005). The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc. Natl. Acad. Sci. USA 102: 5174-5179 [Abstract] [Full Text]  
  • Nelson, D. (2004). Phage Taxonomy: We Agree To Disagree. J. Bacteriol. 186: 7029-7031 [Full Text]  
  • Chibani-Chennoufi, S., Dillmann, M.-L., Marvin-Guy, L., Rami-Shojaei, S., Brussow, H. (2004). Lactobacillus plantarum Bacteriophage LP65: a New Member of the SPO1-Like Genus of the Family Myoviridae. J. Bacteriol. 186: 7069-7083 [Abstract] [Full Text]  
  • Brussow, H., Canchaya, C., Hardt, W.-D. (2004). Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion. Microbiol. Mol. Biol. Rev. 68: 560-602 [Abstract] [Full Text]  
  • Lindell, D., Sullivan, M. B., Johnson, Z. I., Tolonen, A. C., Rohwer, F., Chisholm, S. W. (2004). Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc. Natl. Acad. Sci. USA 101: 11013-11018 [Abstract] [Full Text]  
  • Liu, J., Mushegian, A. (2004). Displacements of Prohead Protease Genes in the Late Operons of Double-Stranded-DNA Bacteriophages. J. Bacteriol. 186: 4369-4375 [Abstract] [Full Text]  
  • O'Flaherty, S., Coffey, A., Edwards, R., Meaney, W., Fitzgerald, G. F., Ross, R. P. (2004). Genome of Staphylococcal Phage K: a New Lineage of Myoviridae Infecting Gram-Positive Bacteria with a Low G+C Content. J. Bacteriol. 186: 2862-2871 [Abstract] [Full Text]  
  • Liu, M., Gingery, M., Doulatov, S. R., Liu, Y., Hodes, A., Baker, S., Davis, P., Simmonds, M., Churcher, C., Mungall, K., Quail, M. A., Preston, A., Harvill, E. T., Maskell, D. J., Eiserling, F. A., Parkhill, J., Miller, J. F. (2004). Genomic and Genetic Analysis of Bordetella Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes. J. Bacteriol. 186: 1503-1517 [Abstract] [Full Text]  
  • Dorigo, U., Jacquet, S., Humbert, J.-F. (2004). Cyanophage Diversity, Inferred from g20 Gene Analyses, in the Largest Natural Lake in France, Lake Bourget. Appl. Environ. Microbiol. 70: 1017-1022 [Abstract] [Full Text]  
  • Wang, P. W., Chu, L., Guttman, D. S. (2004). Complete Sequence and Evolutionary Genomic Analysis of the Pseudomonas aeruginosa Transposable Bacteriophage D3112. J. Bacteriol. 186: 400-410 [Abstract] [Full Text]  
  • Leplae, R., Hebrant, A., Wodak, S. J., Toussaint, A. (2004). ACLAME: A CLAssification of Mobile genetic Elements. Nucleic Acids Res 32: D45-49 [Abstract] [Full Text]  
  • Seguritan, V., Feng, I-W., Rohwer, F., Swift, M., Segall, A. M. (2003). Genome Sequences of Two Closely Related Vibrio parahaemolyticus Phages, VP16T and VP16C. J. Bacteriol. 185: 6434-6447 [Abstract] [Full Text]  
  • Canchaya, C., Proux, C., Fournous, G., Bruttin, A., Brussow, H. (2003). Prophage Genomics. Microbiol. Mol. Biol. Rev. 67: 238-276 [Abstract] [Full Text]  
  • Nelson, D., Schuch, R., Zhu, S., Tscherne, D. M., Fischetti, V. A. (2003). Genomic Sequence of C1, the First Streptococcal Phage. J. Bacteriol. 185: 3325-3332 [Abstract] [Full Text]  
  • Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D., Azam, F., Rohwer, F. (2002). Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. USA 99: 14250-14255 [Abstract] [Full Text]  
  • Bhattacharyya, A., Stilwagen, S., Reznik, G., Feil, H., Feil, W. S., Anderson, I., Bernal, A., D'Souza, M., Ivanova, N., Kapatral, V., Larsen, N., Los, T., Lykidis, A., Selkov, E. Jr., Walunas, T. L., Purcell, A., Edwards, R. A., Hawkins, T., Haselkorn, R., Overbeek, R., Kyrpides, N. C., Predki, P. F. (2002). Draft Sequencing and Comparative Genomics of Xylella fastidiosa Strains Reveal Novel Biological Insights. Genome Res 12: 1556-1563 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»