Advertisement

Archives of Virology

, Volume 158, Issue 3, pp 601–609 | Cite as

Characterization and whole genome sequences of the Rhodococcus bacteriophages RGL3 and RER2

  • Steve Petrovski
  • Robert J. Seviour
  • Daniel Tillett
Original Article

Abstract

We report here the isolation and genome sequences of two novel phages, lytic for Rhodococcus and Nocardia species. Named RER2 and RGL3, both are members of the family Siphoviridae, and each possesses a novel genome of 46,586 bp and 48,072 bp, respectively. RER2 and RGL3 phages share a modular genome organization, as seen in other sequenced Siphoviridae phage genomes, and appear to share a common evolutionary origin. The genomes of these phages share no similarity with other Rhodococcus or Nocardia phages but are related to Mycobacterium phages. The data presented here extend our understanding of Rhodococcus phage genomics.

Keywords

Nocardia Species Actinobacterial Strain Tape Measure Protein Rhodococcus Species High Amino Acid Sequence Similarity 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This research was supported by an Australian Research Council Linkage Grant (LP0774913), together with Melbourne Water and South East Water, who are thanked for their financial support. S. Petrovski was funded by ARC Linkage and La Trobe University grants.

References

  1. 1.
    Ackermann HW (2003) Bacteriophage observations and evolution. Res Microbiol 154:245–251PubMedCrossRefGoogle Scholar
  2. 2.
    Ackermann HW (2007) 5500 phages examined in the electron microscope. Arch Virol 152:227–243PubMedCrossRefGoogle Scholar
  3. 3.
    Ackermann HW (2012) Bacteriophage electron microscopy. Adv Virus Res 82:1–32PubMedCrossRefGoogle Scholar
  4. 4.
    Bailly-Bechet M, Vergassola M, Rocha E (2007) Causes for the intriguing presence of tRNA’s in phages. Genome Res 17:1486–1495PubMedCrossRefGoogle Scholar
  5. 5.
    Barker ML, Jiang W, Rixon FJ, Chiu W (2005) Common ancestry of herpesvirus and tailed DNA bacteriophages. J Virol 79:14967–14970CrossRefGoogle Scholar
  6. 6.
    Bergh Ø, Børsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467–468PubMedCrossRefGoogle Scholar
  7. 7.
    Brownell GH, Adams JN (1967) Growth and characterization of Nocardiophages for Nocardia canicruria and Nocardia erythropolis mating types. J Gen Microbiol 47:247–256PubMedGoogle Scholar
  8. 8.
    Brownell GH, Enquist LW, Denniston-Thompston K (1980) An analysis of the genome of actinophage φEC. Gene 12:311–314PubMedCrossRefGoogle Scholar
  9. 9.
    Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S, NISC Comparative sequencing program (2003) LAGAN and multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13:721–731PubMedCrossRefGoogle Scholar
  10. 10.
    Brüssow H, Desiere F (2001) Comparative phage genomics and the evolution of Siphovirdae: insights from dairy phages. Mol Microbiol 39:213–222PubMedCrossRefGoogle Scholar
  11. 11.
    Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann M, Brüssow H (2003) Phages as agents of lateral gene transfer. Curr Opin Microbiol 6:417–424PubMedCrossRefGoogle Scholar
  12. 12.
    Canchaya C, Proux C, Fournous G, Bruttin A, Brüssow H (2003) Prophage genomics. Microbiol Mol Biol Rev 67:238–276PubMedCrossRefGoogle Scholar
  13. 13.
    Casjen SR, Thuman-Commike PA (2011) Evolution of mosaically related bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology 411:393–415CrossRefGoogle Scholar
  14. 14.
    de los Reyes FL (2010) Foaming. In: Seviour RJ, Nielsen PH (eds) Microbial ecology of activated sludge. IWA publishing, London, pp 215–259Google Scholar
  15. 15.
    Desiere F, McShan WM, van Sinderen D, Ferretti JJ, Brüssow H (2001) Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic Streptococci: evolutionary implications for prophage–host interactions. Virology 288:325–341PubMedCrossRefGoogle Scholar
  16. 16.
    Gürtler V, Seviour RJ (2010) Systematics of members of the genus Rhodococcus (Zopf 1891) Emend Goodfellow et al. 1989. In: Alvarez HM (ed) Biology of Rhodococcus, vol 16. Springer, Heidelberg, pp 1–28Google Scholar
  17. 17.
    Hiddema R, Curran MD, Ferreira NP, Coetzee JN, Lecatsas G (1985) Characterization of phages derived from strains of Rhodococcus australis and R. equii. Intervirology 23:109–111PubMedCrossRefGoogle Scholar
  18. 18.
    Hatfull GF, Cresawn SG, Hendrix RW (2008) Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. Res Microbiol 159:332–339PubMedCrossRefGoogle Scholar
  19. 19.
    Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, Hoyle NN, Bowman CA, Tantoco AT, Paladin EC, Myers MS, Smith AL, Grace MS, Pham TT, O’Brien MB, Vogelsberger AM, Hryckowian AJ, Wynalek JL, Donis-Keller H, Bogel MW, Peebles CL, Cresawn SG, Hendrix RW (2010) Comparative genomics analysis of 60 mycobacteriophage geneomes: genome clustering, gene acquisition and gene size. J Mol Biol 397:119–143PubMedCrossRefGoogle Scholar
  20. 20.
    Heldwein EE, Lou H, Bender FC, Cohen GH, Eisenberg RJ, Harrison SC (2006) Crystal structure of glycoprotein B from herpes simplex virus 1. Science 313:217–220PubMedCrossRefGoogle Scholar
  21. 21.
    Hendrix RW (2003) Bacteriophage genomics. Curr Opin Microbiol 6:506–511PubMedCrossRefGoogle Scholar
  22. 22.
    Hendrix RW, Lawrence JG, Hatfull GF, Casjens S (2000) The origins and ongoing evolution of viruses. Trends Microbiol 5:504–508CrossRefGoogle Scholar
  23. 23.
    Hendrix RW, Smith MCM, Burns RN, Ford ME (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc Natl Acad Sci USA 96:2192–2197PubMedCrossRefGoogle Scholar
  24. 24.
    Herniou EA, Olszewski JA, Cory JS, O’Reilly DR (2003) The genome sequence and evolution of baculoviruses. Ann Rev Entomol 48:211–234CrossRefGoogle Scholar
  25. 25.
    Mirold S, Rabsch W, Tschäpe H, Hardt WD (2001) Transfer of the Salmonella type III effector sopE between unrelated phage families. J Mol Biol 312:7–16PubMedCrossRefGoogle Scholar
  26. 26.
    Muscatello G, Leadon DP, Klayt M, Ocampo-Sosa A, Lewis DA, Fogarty U, Buckley T, Gilkerson JR, Meijer WG, Vazquez-Boland JA (2007) Rhodococcus equi infections in foal: the science of ‘rattles’. Equine Vet J 39:470–478PubMedCrossRefGoogle Scholar
  27. 27.
    Pereira L, Ali M, Kousoulas K, Huo B, Banks T (1989) Domain structure of herpes simplex virus 1 glycoprotein B: neutralizing epitomes map in regions of continuous and discontinuous residues. Virology 172:11–24PubMedCrossRefGoogle Scholar
  28. 28.
    Petrovski S, Dyson ZA, Quill ES, McIlroy SJ, Tillett D, Seviour RJ (2011) An examination of the mechanisms for stable foam formation in activated sludge systems. Water Res 45:2146–2154PubMedCrossRefGoogle Scholar
  29. 29.
    Petrovski S, Dyson ZA, Seviour RJ, Tillett D (2012) Small but sufficient: the Rhodococcus phage RRH1 has the smallest known Siphoviridae genome at 14.2 kb. J Virol 86:358–363PubMedCrossRefGoogle Scholar
  30. 30.
    Petrovski S, Seviour RJ, Tillett D (2011) Genome sequence and characterization of the Tsukamurella phage TPA2. Appl Environ Microbiol 77:1389–1398PubMedCrossRefGoogle Scholar
  31. 31.
    Petrovski S, Seviour RJ, Tillett D (2011) Genome characterization of the polyvalent lytic bacteriophage GTE2 with the potential for biocontrol of Gordonia, Rhodococcus and Nocardia stabilized foams in activated sludge plants. Appl Environ Microbiol 77:3923–3929PubMedCrossRefGoogle Scholar
  32. 32.
    Petrovski S, Seviour RJ, Tillett D (2011) Prevention of Gordonia and Nocardia stabilized foam formation by using bacteriophage GTE7. Appl Environ Microbiol 77:7864–7867PubMedCrossRefGoogle Scholar
  33. 33.
    Petrovski S, Tillett D, Seviour RJ (2012) Genome sequences and characterization of the Gordonia phages GTE5 and GRU1 and their use as potential biocontrol agents. Appl Environ Microbiol 78:42–47PubMedCrossRefGoogle Scholar
  34. 34.
    Rohwer F (2003) Global phage diversity. Cell 113:141PubMedCrossRefGoogle Scholar
  35. 35.
    Rohwer F, Edwards R (2002) The phage proteomic tree: a genome-based taxonomy of phage. J Bacteriol 184:4529–4535PubMedCrossRefGoogle Scholar
  36. 36.
    Summers EJ, Liu M, Gill JJ, Grant M, Chan-Cortes TN, Ferguson L, Janes C, Lange K, Bertoli M, Moore C, Orchard RC, Cohen ND, Young R (2011) Genomic and functional analysis of Rhodococcus equi phages ReqiPepy6, ReqiPoco6, ReqiPine5 and ReqiDocB7. Appl Environ Microbiol 77:669–683CrossRefGoogle Scholar
  37. 37.
    Sunairi M, Watanabe T, Oda H, Murooka H, Nakajima M (1993) Characterization of the genome of the Rhodococcus rhodochrous bacteriophage NJL. Appl Environ Microbiol 59:97–100Google Scholar
  38. 38.
    Wang I, Smith DL, Young R (2000) Holins: the protein clocks of bacteriophage infections. Annu Rev Microbiol 54:799–825PubMedCrossRefGoogle Scholar
  39. 39.
    Xu J, Hendrix RW, Duda RL (2004) Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol Cell 16:11–21PubMedCrossRefGoogle Scholar
  40. 40.
    Yu M, Souaya J, Julin DA (1998) The 30-kDa C-terminal domain of the RecB protein is critical for the nuclease activity, but not the helicase activity, of the RecBCD enzyme from Escherichia coli. Proc Natl Acad Sci USA 95:981–986PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2012

Authors and Affiliations

  • Steve Petrovski
    • 1
    • 3
  • Robert J. Seviour
    • 1
    • 2
  • Daniel Tillett
    • 1
  1. 1.La Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneAustralia
  2. 2.Department of MicrobiologyLa Trobe UniversityMelbourneAustralia
  3. 3.Peter MacCallum Cancer Centre, Molecular PathologyMelbourneAustralia

Personalised recommendations