Comparative transcriptomics analyses reveal the conservation of an ancestral infectious strategy in two bacteriophage genera

ISME Journal

Volumn 11, Issue 9, 2017, Pages 1988-1996

  Blasdel, Bob G ^a   Chevallereau, Anne ^b,c   Monot, Marc ^b   Lavigne, Rob ^a   Debarbieux, Laurent ^b  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b INSTITUT PASTEUR   (France)

^c UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE; COMPARATIVE STUDY; DEGRADATION; DNA; ENZYME; GENE EXPRESSION; GENETIC ANALYSIS; INFECTIVITY; REACTION KINETICS;

PSEUDOMONAS AERUGINOSA;

IRON; TRANSCRIPTOME; VIRAL PROTEIN;

BACTERIOPHAGE; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; PSEUDOMONAS AERUGINOSA; VIROLOGY; VIRUS GENOME;

BACTERIOPHAGES; EVOLUTION, MOLECULAR; GENOME, VIRAL; IRON; PHYLOGENY; PSEUDOMONAS AERUGINOSA; TRANSCRIPTOME; VIRAL PROTEINS;

EID: 85030688711     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2017.63     Document Type: Article

References (32)

1. Bonnain C, Breitbart M, Buck KN. (2016). The Ferrojan horse hypothesis: iron-virus interactions in the ocean. Front Mar Sci 3: 82.
2. Calendar R. (2006). The Bacteriophages. 2nd edn. Oxford University Press: Oxford; New York.
3. Ceyssens PJ, Minakhin L, Van den Bossche A, Yakunina M, Klimuk E, Blasdel B et al. (2014). Development of giant bacteriophage fKZ is independent of the host transcription apparatus. J Virol 88: 10501-10510.
4. Chevallereau A, Blasdel BG, De Smet J, Monot M, Zimmermann M, Kogadeeva M et al. (2016). Nextgeneration '-omics' approaches reveal a massive alteration of host RNA metabolism during bacteriophageinfection of Pseudomonas aeruginosa. PLoS Genet 12: e1006134.
5. De Smet J, Zimmermann M, Kogadeeva M, Ceyssens PJ, Vermaelen W, Blasdel B et al. (2016). High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection. ISME J 10: 1823-1835.
6. Doron S, Fedida A, Hernandez-Prieto MA, Sabehi G, Karunker I, Stazic D et al. (2016). Transcriptome dynamics of a broad host-range cyanophage and its hosts. ISME J 10: 1437-1455.
7. Essoh C, Latino L, Midoux C, Blouin Y, LoukouG, Nguetta SP et al. (2015). Investigation of a large collection of Pseudomonas aeruginosa bacteriophages collected from a single environmental source in Abidjan, Cote d'Ivoire. PLoS One 10: e0130548.
8. Forterre P, Krupovic M, Prangishvili D. (2014). Cellular domains and viral lineages. Trends Microbiol 22: 554-558.
9. Grose JH, Casjens SR. (2014). Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae. Virology 468-470: 421-443.
10. Hantke K. (2001). Iron and metal regulation in bacteria. Curr Opin Microbiol 4: 172-177.
11. Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME et al. (2006). Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet 2: e92.
12. Henry M, Lavigne R, Debarbieux L. (2013). Predicting in vivo efficacy of therapeutic bacteriophages used to treat pulmonary infections. Antimicrob Agents Chemother 57: 5961-5968.
13. Henry M, Bobay LM, Chevallereau A, Saussereau E, Ceyssens PJ, Debarbieux L. (2015). The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae. PLoS One 10: e0117163.
14. Howard-Varona C, Roux S, Dore H, Solonenko NE, Holmfeldt K, Markillie LM et al. (2016). Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus. ISME J 11: 284-295.
15. Koskella B, Brockhurst MA. (2014). Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev 38: 916-931.
16. Kropinski AM, Sulakvelidze A, Konczy P, Poppe C. (2007). Salmonella phages and prophages-genomics and practical aspects. Methods Mol Biol 394: 133-175.
17. Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK, Sullivan MB et al. (2016). Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 161: 1095-1099.
18. 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.
19. Kwan T, Liu J, Dubow M, Gros P, Pelletier J. (2006). Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. J Bacteriol 188: 1184-1187.
20. Love MI, Huber W, Anders S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550.
21. Mahadevan P, King JF, Seto D. (2009). CGUG: in silico proteome and genome parsing tool for the determination of 'core' and unique genes in the analysis of genomes up to ca. 1. 9Mb. BMC Res Notes 2: 168.
22. Marinelli LJ, Fitz-Gibbon S, Hayes C, Bowman C, Inkeles M, Loncaric A et al. (2012). Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. MBio 3: e00279-12.
23. Marston MF, Pierciey FJ Jr, Shepard A, Gearin G, Qi J, Yandava C et al. (2012). Rapid diversification of coevolving marine Synechococcus and a virus. Proc Natl Acad Sci USA 109: 4544-4549.
24. Morello E, Saussereau E, Maura D, Huerre M, Touqui L, Debarbieux L. (2011). Pulmonary bacteriophage therapy on Pseudomonas aeruginosa cystic fibrosis strains: first steps towards treatment and prevention. PLoS One 6: e16963.
25. Ochsner UA, Johnson Z, Vasil ML. (2000). Genetics and regulation of two distinct haem-uptake systems, phu and has, in Pseudomonas aeruginosa. Microbiology 146: 185-198.
26. Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG et al. (2015). Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife 4: e06416.
27. Roux S, Hallam SJ, Woyke T, Sullivan MB. (2015). Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 4: e08490.
28. Saussereau E, Vachier I, Chiron R, Godbert B, Sermet I, Dufour N et al. (2014). Effectiveness of bacteriophages in the sputum of cystic fibrosis patients. Clin Microbiol Infect 20: O983-O990.
29. Takeya K, Amako K. (1966). A rod-shaped Pseudomonas phage. Virology 28: 163-165.
30. Wang I-N, Dykhuizen DE, Slobodkin LB. (1996). The evolution of phage lysis timing. Evolut Ecol 10: 545-558.
31. Williams HT. (2013). Phage-induced diversification improves host evolvability. BMC Evol Biol 13: 17.
32. Winsor GL, Griffiths EJ, Lo R, Dhillon BK, Shay JA, Brinkman FS. (2016). Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Res 44: D646-D653.