Mycobacteriophage marvin: A new singleton phage with an unusual genome organization

Journal of Virology

Volumn 86, Issue 9, 2012, Pages 4762-4775

  Mageeney, Catherine ^a   Pope, Welkin H ^b   Harrison, Melinda ^a   Moran, Deborah ^a   Cross, Trevor ^a   Jacobs Sera, Deborah ^b   Hendrix, Roger W ^b   Dunbar, David ^a   Hatfull, Graham F ^b  

^a Cabrini University   (United States)

^b UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARTICLE; CONTROLLED STUDY; DNA METHYLATION; DNA PURIFICATION; ELECTRON MICROSCOPY; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; MARVIN GENOME; MYCOBACTERIOPHAGE; MYCOBACTERIUM SMEGMATIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; VIRUS GENOME;

DNA, VIRAL; GENE ORDER; GENOME, VIRAL; MOLECULAR SEQUENCE ANNOTATION; MYCOBACTERIOPHAGES; MYCOBACTERIUM SMEGMATIS; SEQUENCE ANALYSIS, DNA; VIRAL PROTEINS; VIRION;

MYCOBACTERIUM SMEGMATIS;

EID: 84861307161     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.00075-12     Document Type: Article

References (59)

1. Anne J, et al. 1995. Analysis of the open reading frames of the main capsid proteins of actinophage VWB. Arch. Virol. 140:1033-1047.
2. Baudoux AC, et al. 9 January 2012. Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. Environ. Microbiol. doi:10.1111/j.1462-2920.2011.02685.x.
3. Belfort M, Roberts RJ. 1997. Homing endonucleases: keeping the house in order. Nucleic Acids Res. 25:3379-3388.
4. Borodovsky M, McIninch J. 1993. Recognition of genes in DNA sequence with ambiguities. Biosystems 30:161-171.
5. Brussow H, Hendrix RW. 2002. Phage genomics: small is beautiful. Cell 108:13-16.
6. Casjens SR. 2005. Comparative genomics and evolution of the tailedbacteriophages. Curr. Opin. Microbiol. 8:451-458.
7. Catalao MJ, Gil F, Moniz-Pereira J, Pimentel M. 2010. The mycobacteriophage Ms6 encodes a chaperone-like protein involved in the endolysin delivery to the peptidoglycan. Mol. Microbiol. 77:672-686.
8. Champe SP, Eddleman HL. 1967. Poypeptides associated with morphogenetic defects in bacteriophage T4, p 55-70. In Colter JS, ParanchychW (ed), The molecular biology of viruses. Academic Press, New York, NY.
9. Chang JR, Poliakov A, Prevelige PE, Mobley JA, Dokland T. 2008. Incorporation of scaffolding protein gpO in bacteriophages P2 and P4. Virology 370:352-361.
10. Cresawn SG, et al. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12:395.
11. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27: 4636-4641.
12. Derbyshire V, Belfort M. 1998. Lightning strikes twice: intron-intein coincidence. Proc. Natl. Acad. Sci. U. S. A. 95:1356-1357.
13. Fineran PC, et al. 2009. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl. Acad. Sci. U. S. A. 106:894-899.
14. 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.
15. Ford ME, Stenstrom C, Hendrix RW, Hatfull GF. 1998. Mycobacteriophage TM4: genome structure and gene expression. Tuber. Lung Dis. 79:63-73.
16. Gil F, et al. 2008. The lytic cassette of mycobacteriophage Ms6 encodes an enzyme with lipolytic activity. Microbiology 154:1364-1371.
17. Gomathi NS, et al. 2007. In silico analysis of mycobacteriophage Che12 genome: characterization of genes required to lysogenise Mycobacterium tuberculosis. Comput. Biol. Chem. 31:82-91.
18. Hatfull GF. 2006. Mycobacteriophages, p 602-620. In Calendar R (ed), The bacteriophages. Oxford University Press, New York, NY.
19. Hatfull GF, et al. 2010. Comparative genome analysis of 60 mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J. Mol. Biol. 397:119-143.
20. Hatfull GF. 2010. Mycobacteriophages: genes and genomes. Annu. Rev. Microbiol. 64:331-356.
21. Hatfull GF, Hendrix RW. 2011. Bacteriophages and their genomes. Curr. Opin. Virol. 1:298-303.
22. Hatfull GF, et al. 2006. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2:e92.
23. Hatfull GF, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program, KwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students, and Phage Hunters Integrating Research and Education Program. 2012. The complete genome sequences of 138 mycobacteriophages. J. Virol. 86:2382-2384.
24. 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.
25. Hendrix RW. 2003. Bacteriophage genomics. Curr. Opin. Microbiol. 6:506-511.
26. Hendrix RW. 2009. Jumbo bacteriophages. Curr. Top. Microbiol. Immunol. 328:229-240.
27. Hendrix RW, Casjens S. 2006. Bacteriophage lambda and its genetic neighborhood, p 409-447. In Calendar R (ed), The bacteriophages. Oxford University Press, Oxford, United Kingdom.
28. Hendrix RW, Casjens SR. 1974. Protein cleavage in bacteriophage lambda tail assembly. Virology 61:156-159.
29. Hendrix RW, Hatfull GF, Smith MC. 2003. Bacteriophages with tails: chasing their origins and evolution. Res. Microbiol. 154:253-257.
30. Hendrix RW, Lawrence JG, Hatfull GF, Casjens S. 2000. The origins and ongoing evolution of viruses. Trends Microbiol. 8:504-508.
31. 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.
32. Henry M, et al. 2010. In silico analysis of Ardmore, a novel mycobacteriophage isolated from soil. Gene 453:9-23.
33. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L. 2009. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferaselike domains: synthesis of novel metabolites and peptide modifications of proteins. Mol. Biosyst. 5:1636-1660.
34. Katsura I. 1987. Determination of bacteriophage lambda tail length by a protein ruler. Nature 327:73-75.
35. Katsura I, Hendrix RW. 1984. Length determination in bacteriophage lambda tails. Cell 39:691-698.
36. Krumsiek J, Arnold R, Rattei T. 2007. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23:1026-1028.
37. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11-16.
38. Lee E, Harris N, Gibson M, Chetty R, Lewis S. 2009. Apollo: a community resource for genome annotation editing. Bioinformatics 25:1836-1837.
39. 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.
40. Mediavilla J, et al. 2000. Genome organization and characterization of mycobacteriophage Bxb1. Mol. Microbiol. 38:955-970.
41. Morris P, Marinelli LJ, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2008. Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination. J. Bacteriol. 190:2172-2182.
42. Nesbit CE, Levin ME, Donnelly-Wu MK, Hatfull GF. 1995. Transcriptional regulation of repressor synthesis in mycobacteriophage L5. Mol. Microbiol. 17:1045-1056.
43. Payne K, Sun Q, Sacchettini J, Hatfull GF. 2009. Mycobacteriophage lysin B is a novel mycolylarabinogalactan esterase. Mol. Microbiol. 73: 367-381.
44. Pedulla ML, et al. 2003. Origins of highly mosaic mycobacteriophage genomes. Cell 113:171-182.
45. Petrovski S, Seviour RJ, Tillett D. 2011. Genome sequence and characterization of the Tsukamurella bacteriophage TPA2. Appl. Environ. Microbiol. 77:1389-1398.
46. Piuri M, Hatfull GF. 2006. A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. Mol. Microbiol. 62:1569-1585.
47. Pope WH, et al. 2011. Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4. PLoS One 6:e26750.
48. Pope WH, et al. 2011. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PLoS One 6:e16329.
49. Sampson T, et al. 2009. Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. Microbiology 155:2962-2977.
50. Savalia D, et al. 2008. Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage. J. Mol. Biol. 377:774-789.
51. Showe MK, Isobe E, Onorato L. 1976. Bacteriophage T4 prehead proteinase. I. Purification and properties of a bacteriophage enzyme which cleaves the capsid precursor proteins. J. Mol. Biol. 107:35-54.
52. Showe MK, Isobe E, Onorato L. 1976. Bacteriophage T4 prehead proteinase. II. Its cleavage from the product of gene 21 and regulation in phage-infected cells. J. Mol. Biol. 107:55-69.
53. Stein LD, et al. 2002. The generic genome browser: a building block for a model organism system database. Genome Res. 12:1599-1610.
54. Suttle CA. 2007. Marine viruses-major players in the global ecosystem. Nat. Rev. Microbiol. 5:801-812.
55. Tori K, et al. 2009. Splicing of the mycobacteriophage Bethlehem DnaB intein: identification of a new mechanistic class of inteins that contain an obligate block F nucleophile. J. Biol. Chem. 285:2515-2526.
56. Van Dessel W, et al. 2005. Complete genomic nucleotide sequence and analysis of the temperate bacteriophage VWB. Virology 331:325-337.
57. Wommack KE, Colwell RR. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114.
58. Xu J, Hendrix RW, Duda RL. 2004. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol. Cell 16:11-21.
59. Zimmer M, Sattelberger E, Inman RB, Calendar R, Loessner MJ. 2003. Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed (1 translational frameshifting in structural protein synthesis. Mol. Microbiol. 50:303-317.