Bacteriophage evolution differs by host, lifestyle and genome

Nature Microbiology

Volumn 2, Issue , 2017, Pages

  Mavrich, Travis N ^a   Hatfull, Graham F ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIOPHAGE; GENE CLUSTER; GENE FUNCTION; GENE STRUCTURE; GENE TRANSFER; GENETIC DISTANCE; HOST; LIFESTYLE; MOLECULAR EVOLUTION; MOSAICISM; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; VIRAL GENETICS; VIRUS GENOME; GENETIC VARIATION; GENETICS; HORIZONTAL GENE TRANSFER; HUMAN;

BACTERIOPHAGES; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENETIC VARIATION; GENOME, VIRAL; HUMANS; PHYLOGENY;

EID: 85023738635     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/nmicrobiol.2017.112     Document Type: Article

References (47)

1. Canchaya, C., Fournous, G. & Brussow, H. The impact of prophages on bacterial chromosomes. Mol. Microbiol. 53, 9-18 (2004).
2. Bondy-Denomy, J. et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 10, 2854-2866 (2016).
3. Rodriguez-Brito, B. et al. Viral and microbial community dynamics in four aquatic environments. ISME J. 4, 739-751 (2010).
4. Brussow, H., Canchaya, C. & Hardt, W. D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68, 560-602 (2004).
5. Pedulla, M. L. et al. Origins of highly mosaic mycobacteriophage genomes. Cell 113, 171-182 (2003).
6. Lawrence, J. G., Hatfull, G. F. & Hendrix, R. W. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol. 184, 4891-4905 (2002).
7. Hendrix, R. W., Smith, M. C., Burns, R. N., Ford, M. E. & Hatfull, G. F. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc. Natl Acad. Sci. USA 96, 2192-2197 (1999).
8. Pope, W. H. et al. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. elife 4, e06416 (2015).
9. Deng, L. et al. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 513, 242-245 (2014).
10. Roux, S., Hallam, S. J., Woyke, T. & Sullivan, M. B. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife 4, e08490 (2015).
11. Jordan, T. C. et al. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. mBio 5, e01051-13 (2014).
12. Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).
13. Hatfull, G. F. et al. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2, e92 (2006).
14. Cresawn, S. G. et al. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12, 395 (2011).
15. Grazziotin, A. L., Koonin, E. V. & Kristensen, D. M. Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45, D491-D498 (2017).
16. Hatfull, G. F. et al. Comparative genomic analysis of 60 mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J. Mol. Biol. 397, 119-143 (2010).
17. Knowles, B. et al. Lytic to temperate switching of viral communities. Nature 531, 466-470 (2016).
18. Bobay, L. M., Rocha, E. P. & Touchon, M. The adaptation of temperate bacteriophages to their host genomes. Mol. Biol. Evol. 30, 737-751 (2013).
19. Chopin, A., Bolotin, A., Sorokin, A., Ehrlich, S. D. & Chopin, M. Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations. Nucleic Acids Res. 29, 644-651 (2001).
20. Lima-Mendez, G., Van Helden, J., Toussaint, A. & Leplae, R. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 25, 762-777 (2008).
21. Lucks, J. B., Nelson, D. R., Kudla, G. R. & Plotkin, J. B. Genome landscapes and bacteriophage codon usage. PLoS Comput. Biol. 4, e1000001 (2008).
22. Perez Sepulveda, B. et al. Marine phage genomics: the tip of the iceberg. FEMS Microbiol. Lett. 363, fnw158 (2016).
23. Grose, J. H. & Casjens, S. R. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 468-470, 421-443 (2014).
24. Konstantinidis, K. T., Ramette, A. & Tiedje, J. M. The bacterial species definition in the genomic era. Phil. Trans. R. Soc. Lond. B 361, 1929-1940 (2006).
25. Rodriguez-R, L. M. & Konstantinidis, K. T. Bypassing cultivation to identify bacterial species. ASM Microbe Magazine 9, 111-118 (2014).
26. Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43, 6761-6771 (2015).
27. Puigbo, P., Lobkovsky, A. E., Kristensen, D. M., Wolf, Y. I. & Koonin, E. V. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol. 12, 66 (2014).
28. Dedrick, R. M. et al. Prophage-mediated defence against viral attack and viral counter-defence. Nat. Microbiol. 2, 16251 (2017).
29. Hendrix, R. W., Roberts, J. W., Stahl, F. W. & Weisberg, R. A. Lambda II (Cold Spring Harbor Press, 1983).
30. Jacobs-Sera, D. et al. On the nature of mycobacteriophage diversity and host preference. Virology 434, 187-201 (2012).
31. Marinelli, L. J. et al. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. mBio 3, e00279-12 (2012).
32. Cock, P. J. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422-1423 (2009).
33. Huerta-Cepas, J., Dopazo, J. & Gabaldon, T. ETE A python environment for tree exploration. BMC Bioinformatics 11, 24 (2010).
34. McNair, K., Bailey, B. A. & Edwards, R. A. PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 28, 614-618 (2012).
35. Leplae, R., Lima-Mendez, G. & Toussaint, A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res. 38, D57-D61 (2010).
36. Chithambaram, S., Prabhakaran, R. & Xia, X. Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli. Mol. Biol. Evol. 31, 1606-1617 (2014).
37. Klumpp, J. & Loessner, M. J. Listeria phages: genomes, evolution, and application. Bacteriophage 3, e26861 (2013).
38. Sau, K., Gupta, S. K., Sau, S. & Ghosh, T. C. Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy. Virus Res. 113, 123-131 (2005).
39. Marchler-Bauer, A. et al. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30, 281-283 (2002).
40. Dedrick, R. M. et al. Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. Mol. Microbiol. 101, 625-644 (2016).
41. Pope, W. H. et al. Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4. PLoS ONE 6, e26750 (2011).
42. Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl Acad. Sci. USA 102, 2567-2572 (2005).
43. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631-637 (1997).
44. Hatfull, G. F. & Hendrix, R. W. Bacteriophages and their genomes. Curr. Opin. Virol. 1, 298-303 (2011).
45. Loytynoja, A. & Goldman, N. webPRANK a phylogeny-Aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11, 579 (2010).
46. Gouy, M., Guindon, S. & Gascuel, O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221-224 (2010).
47. Csuros, M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26, 1910-1912 (2010).