Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform

PLoS Genetics

Volumn 2, Issue 6, 2006, Pages 0835-0847

  Hatfull, Graham F ^a   Pedulla, Marisa L ^a,f   Jacobs Sera, Deborah ^a   Cichon, Pauline M ^a   Foley, Amy ^b   Ford, Michael E ^a,g   Gonda, Rebecca M ^a   Houtz, Jennifer M ^a   Hryckowian, Andrew J ^a   Kelchner, Vanessa A ^a,h   Namburi, Swathi ^a   Pajcini, Kostandin V ^a,i   Popovich, Mark G ^c   Schleicher, Donald T ^a   Simanek, Brian Z ^a,j   Smith, Alexis L ^a   Zdanowicz, Gina M ^a,k   Kumar, Vanaja ^d   Peebles, Craig L ^a   Jacobs Jr , William R ^e   Lawrence, Jeffrey G ^a   Hendrix, Roger W ^a   more..

^a UNIVERSITY OF PITTSBURGH   (United States)

^b Hampton High School   (United States)

^c Lincoln High School   (United States)

^d NATIONAL INSTITUTE FOR RESEARCH IN TUBERCULOSIS   (India)

^e ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^f MONTANA TECH OF THE UNIVERSITY OF MONTANA   (United States)

^g WEILL CORNELL MEDICAL COLLEGE   (United States)

^h BRISTOL MYERS SQUIBB   (United States)

ⁱ STANFORD UNIVERSITY   (United States)

^j WILLIAMS COLLEGE   (United States)

^k UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MESSENGER RNA; PROTEOME; TRANSFER RNA; VIRUS DNA; VIRUS PROTEIN; VIRUS RNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE; BACTERIUM ISOLATION; BIOSPHERE; CONTROLLED STUDY; GENE SEQUENCE; GENETIC VARIABILITY; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; EDUCATION; GENETICS; MOLECULAR GENETICS; MYCOBACTERIOPHAGE; VIROLOGY; VIRUS GENE; VIRUS GENOME;

DNA, VIRAL; GENES, VIRAL; GENOME, VIRAL; GENOMICS; MOLECULAR SEQUENCE DATA; MYCOBACTERIOPHAGES; PROTEOME; RNA, MESSENGER; RNA, TRANSFER; RNA, VIRAL; VIRAL PROTEINS; VIROLOGY;

EID: 33745698561     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020092     Document Type: Article

References (63)

1. Suttle CA (2005) Viruses in the sea. Nature 437: 356-361.
2. Wommack KE, Colwell RR (2000) Virioplankton: Viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64: 69-114.
3. Hambly E, Suttle CA (2005) The viriosphere, diversity, and genetic exchange within phage communities. Curr Opin Microbiol 8: 444-450.
4. Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399: 541-548.
5. Wilhelm SW, Suttle CA (1999) Viruses and nutrient cycles in the sea. Bioscience 49: 781-788.
6. Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, et al. (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113: 171-182.
7. Hendrix RW (2002) Bacteriophages: Evolution of the majority. Theor Popul Biol 61: 471-480.
8. Brussow H, Hendrix RW (2002) Phage genomics: Small is beautiful. Cell 108: 13-16.
9. Hendrix RW (2003) Bacteriophage genomics. Curr Opin Microbiol 6: 506-511.
10. Hendrix RW, Hatfull GF, Smith MC (2003) Bacteriophages with tails: Chasing their origins and evolution. Res Microbiol 154: 253-257.
11. Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage. Proc Natl Acad Sci U S A 96: 2192-2197.
12. Hendrix RW (1999) The long evolutionary reach of viruses. Curr Biol 9: 914-917.
13. Bamford DH, Burnett RM, Stuart DI (2002) Evolution of viral structure. Theor Popul Biol 61: 461-470.
14. Brussow H (2001) Phages of dairy bacteria. Annu Rev Microbiol 55: 283-303.
15. Casjens SR (2005) Comparative genomics and evolution of the tailed-bacteriophages. Curr Opin Microbiol 8: 451-458.
16. Kwan T, Liu J, Dubow M, Gros P, Pelletier J (2006) Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. J Bacteriol 188: 1184-1187.
17. 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 U S A 102: 5174-5179.
18. Maniloff J, Ackermann HW (1998) Taxonomy of bacterial viruses: Establishment of tailed virus genera and the order Caudovirales. Arch Virol 143: 2051-2063.
19. Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev Microbiol 3: 504-510.
20. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, et al. (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99: 14250-14255.
21. Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, et al. (2004) Diversity and population structure of a nearshore marine sediment viral community. Proc R Soc Ser B 271: 565-574.
22. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 6220-6223.
23. Cann AJ, Fandrich SE, Heaphy S (2005) Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 30: 151-156.
24. Hatfull GF (2004) Mycobacteriophages and tuberculosis. In: Eisenach K, Cole ST, Jacobs WR Jr, McMurray D, editors. Tuberculosis. Washington (D.C.): ASM Press.
25. Hatfull GF (2004) Mycobacteriophages. In: Calendar R, editor. The bacteriophages. New York: Oxford University Press. pp. 602-620.
26. Hatfull GF (1994) Mycobacteriophage L5: A toolbox for tuberculosis. ASM News 60: 255-260.
27. McNerney R (1999) TB: The return of the phage. A review of fifty years of mycobacteriophage research. Int J Tuberc Lung Dis 3: 179-184.
28. Hatfull GF, Sarkis GJ (1993) DNA sequence, structure and gene expression of mycobacteriophage L5: A phage system for mycobacterial genetics. Mol Microbiol 7: 395-405.
29. Mediavilla J, Jain S, Kriakov J, Ford ME, Duda RL, et al. (2000) Genome organization and characterization of mycobacteriophage Bxb1. Mol Microbiol 38: 955-970.
30. Ford ME, Sarkis GJ, Belanger AE, Hendrix RW, Hatfull GF (1998) Genome structure of mycobacteriophage D29: Implications for phage evolution. J Mol Biol 279: 143-164.
31. Ford ME, Stenstrom C, Hendrix RW, Hatfull GF (1998) Mycobacteriophage TM4: Genome structure and gene expression. Tuber Lung Dis 79: 63-73.
32. Juhala RJ, Ford ME, Duda RL, Youlton A, Hatfull GF, et al. (2000) Genomic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages. J Mol Biol 299: 27-51.
33. Katsura I, Hendrix RW (1984) Length determination in bacteriophage lambda tails. Cell 39: 691-698.
34. Brussow H, Desiere F (2001) Comparative phage genomics and the evolution of Siphoviridae: Insights from dairy phages. Mol Microbiol 39: 213-222.
35. Liu M, Gingery M, Doulatov SR, Liu Y, Hodes A, et al. (2004) Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes. J Bacteriol 186: 1503-1517.
36. Liu M, Deora R, Doulatov SR, Gingery M, Eiserling FA, et al. (2002) Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295: 2091-2094.
37. Jensen EC, Schrader HS, Rieland B, Thompson TL, Lee KW, et al. (1998) Prevalence of broad-host-range lytic bacteriophages of Sphaerotilus natans, Escherichia coli, and Pseudomonas aeruginosa. Appl Environ Microbiol 64: 575-580.
38. Hendrix RW, Lawrence JG, Hatfull GF, Casjens S (2000) The origins and ongoing evolution of viruses. Trends Microbiol 8: 504-508.
39. Lawrence JG, Hendrix RW, Casjens S (2001) Where are the pseudogenes in bacterial genomes? Trends Microbiol 9: 535-540.
40. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
41. Brussow H, Canchaya C, Hardt WD (2004) Phages and the evolution of bacterial pathogens: From genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 68: 560-602.
42. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brussow H (2003) Phage as agents of lateral gene transfer. Curr Opin Microbiol 6: 417-424.
43. Boyd EF, Davis BM, Hochhut B (2001) Bacteriophage-bacteriophage interactions in the evolution of pathogenic bacteria. Trends Microbiol 9: 137-144.
44. Casjens S (2003) Prophages and bacterial genomics: What have we learned so far? Mol Microbiol 49: 277-300.
45. Wagner PL, Waldor MK (2002) Bacteriophage control of bacterial virulence. Infect Immun 70: 3985-3993.
46. Mekalanos JJ, Rubin EJ, Waldor MK (1997) Cholera: Molecular basis for emergence and pathogenesis. FEMS Immunol Med Microbiol 18: 241-248.
47. Garcia M, Pimentel M, Moniz-Pereira J (2002) Expression of mycobacteriophage Ms6 lysis genes is driven by two sigma(70)-like promoters and is dependent on a transcription termination signal present in the leader RNA. J Bacteriol 184: 3034-3043.
48. Desplats C, Krisch HM (2003) The diversity and evolution of the T4-type bacteriophages. Res Microbiol 154: 259-267.
49. Tetart F, Desplats C, Krisch HM (1998) Genome plasticity in the distal tail fiber locus of the T-even bacteriophage: Recombination between conserved motifs swaps adhesin specificity. J Mol Biol 282: 543-556.
50. Huson DH (1998) SplitsTree: Analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
51. Rohwer F, Edwards R (2002) The Phage Proteomic Tree: A genome-based taxonomy for phage. J Bacteriol 184: 4529-4535.
52. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631-637.
53. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4: 41.
54. Lapatto D (2004) Survey of Undergraduate Research Experiences (SURE): First findings. Cell Biol Educ 3: 270-277.
55. Seymour E, Hunter A-B, Laursen SL, DeAntoni T (2004) Establishing the benefits of undergraduate research for undergraduates in the sciences: First findings from a three-year study. Sci Educ 88: 493-594.
56. Summer EJ, Gonzalez CF, Carlisle T, Mebane LM, Cass AM, et al. (2004) Burkholderia cenocepacia phage BcepMu and a family of Mu-like phages encoding potential pathogenesis factors. J Mol Biol 340: 49-65.
57. Pfund C, Maidl Pribbenow C, Branchaw J, Miller Lauffer S, Handelsman J (2006) Professional skills. The merits of training mentors. Science 311: 473-474.
58. Gordon D, Abajian C, Green P (1998) Consed: A graphical tool for sequence finishing. Genome Res 8: 195-202.
59. Borodovsky M, McIninch J (1993) Recognition of genes in DNA sequence with ambiguities. Biosystems 30: 161-171.
60. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636-4641.
61. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
62. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11-16.
63. Sonnhammer EL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: GC1-GC10.