1887

Abstract

SH1 is the only reported isolate of a spherical halovirus, a dominant morphotype in hypersaline lakes. The virus lytically infects the haloarchaeon , and carries a 30.9 kb linear dsDNA genome that, in a previous study, was proposed to contain 56 protein-coding genes, probably organized into between four and eight operons. In the present study, these predictions were directly tested by determining the orientations and lengths of virus transcripts using systematic RT-PCR and primer extension. Seven major transcripts were observed that together covered most of the genome. Six transcripts were synthesized from early in infection (1 h post-infection; p.i.) onwards, while transcript T6 was only detected late in infection (5–6 h p.i.). No transcripts were detected in the inverted terminal repeat sequences or at the extreme right end of the genome (ORFs 55–56). Start points for the major transcripts were mapped by primer extension and corresponded closely to the 5′ termini determined by RT-PCR. Between 1 and 4 h p.i., transcripts usually terminated not far beyond the end of their last coding ORF, but late in infection, transcripts from the same promoters often terminated at more distal points, resulting in much of the genome being transcribed from both strands. Since many of these transcripts are complementary, RNA–RNA interactions are likely, and may play a role in regulating viral gene expression. Puromycin blockage of post-infection protein synthesis significantly altered the levels of certain virus transcripts, indicating that protein synthesis is essential for the correct regulation of SH1 gene expression.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2008/019422-0
2008-11-01
2019-10-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/154/11/3599.html?itemId=/content/journal/micro/10.1099/mic.0.2008/019422-0&mimeType=html&fmt=ahah

References

  1. Ackermann, H. W. ( 2007; ). 5500 Phages examined in the electron microscope. Arch Virol 152, 227–243.[CrossRef]
    [Google Scholar]
  2. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. ( 1994; ). Current Protocols in Molecular Biology. New York: John Wiley and Sons.
  3. Azzam, M. E. & Algranati, I. D. ( 1973; ). Mechanism of puromycin action: fate of ribosomes after release of nascent protein chains from polysomes. Proc Natl Acad Sci U S A 70, 3866–3869.[CrossRef]
    [Google Scholar]
  4. Badia, D., Camacho, A., Perez-Lago, L., Escandon, C., Salas, M. & Coll, M. ( 2006; ). The structure of phage φ29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA. Mol Cell 22, 73–81.[CrossRef]
    [Google Scholar]
  5. Baliga, N. S., Bonneau, R., Facciotti, M. T., Pan, M., Glusman, G., Deutsch, E. W., Shannon, P., Chiu, Y., Weng, R. S. & other authors ( 2004; ). Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14, 2221–2234.[CrossRef]
    [Google Scholar]
  6. Bamford, D. H., Ravantti, J. J., Rönnholm, G., Laurinavičius, S., Kukkaro, P., Dyall-Smith, M., Somerharju, P., Kalkkinen, N. & Bamford, J. K. ( 2005; ). Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica. J Virol 79, 9097–9107.[CrossRef]
    [Google Scholar]
  7. Bath, C., Cukalac, T., Porter, K. & Dyall-Smith, M. ( 2006; ). His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 350, 228–239.[CrossRef]
    [Google Scholar]
  8. Beck, C. F. & Warren, R. A. ( 1988; ). Divergent promoters, a common form of gene organization. Microbiol Rev 52, 318–326.
    [Google Scholar]
  9. Benlloch, S., López-López, A., Casamayor, E. O., Øvreås, L., Goddard, V., Daae, F. L., Smerdon, G., Massana, R., Joint, I. & other authors ( 2002; ). Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environ Microbiol 4, 349–360.[CrossRef]
    [Google Scholar]
  10. Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeiffer, F. & Oesterhelt, D. ( 2006; ). The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7, 169 [CrossRef]
    [Google Scholar]
  11. Bouvier, T. & del Giorgio, P. ( 2007; ). Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9, 287–297.[CrossRef]
    [Google Scholar]
  12. Brenneis, M., Hering, O., Lange, C. & Soppa, J. ( 2007; ). Experimental characterization of cis-acting elements important for translation and transcription in halophilic Archaea. PLoS Genet 3, e229 [CrossRef]
    [Google Scholar]
  13. Burns, D. G., Camakaris, H. M., Janssen, P. H. & Dyall-Smith, M. L. ( 2004; ). Combined use of cultivation-dependent and cultivation-independent methods indicates that members of most haloarchaeal groups in an Australian crystallizer pond are cultivable. Appl Environ Microbiol 70, 5258–5265.[CrossRef]
    [Google Scholar]
  14. Camacho, A. & Salas, M. ( 2001; ). Mechanism for the switch of φ6 DNA early to late transcription by regulatory protein p4 and histone-like protein p6. EMBO J 20, 6060–6070.[CrossRef]
    [Google Scholar]
  15. Cline, S. W. & Doolittle, W. F. ( 1992; ). Transformation of members of the genus Haloarcula with shuttle vectors based on Halobacterium halobium and Haloferax volcanii plasmid replicons. J Bacteriol 174, 1076–1080.
    [Google Scholar]
  16. Contursi, P., Cannio, R., Prato, S., She, Q., Rossi, M. & Bartolucci, S. ( 2007; ). Transcriptional analysis of the genetic element pSSVx: differential and temporal regulation of gene expression reveals correlation between transcription and replication. J Bacteriol 189, 6339–6350.[CrossRef]
    [Google Scholar]
  17. Dyall-Smith, M., Tang, S. L. & Bath, C. ( 2003; ). Haloarchaeal viruses: how diverse are they? Res Microbiol 154, 309–313.[CrossRef]
    [Google Scholar]
  18. Falb, M., Pfeiffer, F., Palm, P., Rodewald, K., Hickmann, V., Tittor, J. & Oesterhelt, D. ( 2005; ). Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Genome Res 15, 1336–1343.[CrossRef]
    [Google Scholar]
  19. Fauquet, C. M., Mayo, M. A., Maniloff, J., Desselberger, U. & Ball, L. A. ( 2005; ). Virus Taxonomy, VIIIth Report of the ICTV. London: Elsevier/Academic Press.
  20. Fröls, S., Gordon, P. M., Panlilio, M. A., Schleper, C. & Sensen, C. W. ( 2007; ). Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 365, 48–59.[CrossRef]
    [Google Scholar]
  21. Gropp, F., Palm, P. & Zillig, W. ( 1989; ). Expression and regulation of Halobacterium halobium phage φH genes. Can J Microbiol 35, 182–188.[CrossRef]
    [Google Scholar]
  22. Gropp, F., Grampp, B., Stolt, P., Palm, P. & Zillig, W. ( 1992; ). The immunity-conferring plasmid pφHL from the Halobacterium salinarium phage φH: nucleotide sequence and transcription. Virology 190, 45–54.[CrossRef]
    [Google Scholar]
  23. Guixa-Boixareu, N., Calderón-Paz, J. I., Heldal, M., Bratbak, G. & Pedrós-Alió, C. ( 1996; ). Viral lysis and bacterivory as prokaryotic loss factors along a salinity gradient. Aquat Microb Ecol 11, 215–227.[CrossRef]
    [Google Scholar]
  24. Hendrix, R. W. ( 2002; ). Bacteriophages: evolution of the majority. Theor Popul Biol 61, 471–480.[CrossRef]
    [Google Scholar]
  25. Hendrix, R. W., Smith, M. C., Burns, R. N., Ford, M. E. & Hatfull, G. F. ( 1999; ). Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci U S A 96, 2192–2197.[CrossRef]
    [Google Scholar]
  26. Iro, M., Klein, R., Galos, B., Baranyi, U., Rossler, N. & Witte, A. ( 2007; ). The lysogenic region of virus φCh1: identification of a repressor–operator system and determination of its activity in halophilic Archaea. Extremophiles 11, 383–396.[CrossRef]
    [Google Scholar]
  27. Jäälinoja, H. T., Roine, E., Laurinmäki, P., Kivelä, H. M., Bamford, D. H. & Butcher, S. J. ( 2008; ). Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus. Proc Natl Acad Sci U S A 105, 8008–8013.[CrossRef]
    [Google Scholar]
  28. Juez, G., Rodriguez-Valera, F., Ventosa, A. & Kushner, D. J. ( 1986; ). Haloarcula hispanica spec. nov. and Haloferax gibbonsii spec. nov., two new species of extremely halophilic archaebacteria. Syst Appl Microbiol 8, 75–79.[CrossRef]
    [Google Scholar]
  29. Kessler, A., Brinkman, A. B., van der Oost, J. & Prangishvili, D. ( 2004; ). Transcription of the rod-shaped viruses SIRV1 and SIRV2 of the hyperthermophilic archaeon Sulfolobus. J Bacteriol 186, 7745–7753.[CrossRef]
    [Google Scholar]
  30. Kessler, A., Sezonov, G., Guijarro, J. I., Desnoues, N., Rose, T., Delepierre, M., Bell, S. D. & Prangishvili, D. ( 2006; ). A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters. Nucleic Acids Res 34, 4837–4845.[CrossRef]
    [Google Scholar]
  31. Matsunaga, F., Forterre, P., Ishino, Y. & Myllykallio, H. ( 2001; ). In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc Natl Acad Sci U S A 98, 11152–11157.[CrossRef]
    [Google Scholar]
  32. Meijer, W. J., Horcajadas, J. A. & Salas, M. ( 2001; ). φ29 family of phages. Microbiol Mol Biol Rev 65, 261–287.[CrossRef]
    [Google Scholar]
  33. Ng, W. V., Kennedy, S. P., Mahairas, G. G., Berquist, B., Pan, M., Shukla, H. D., Lasky, S. R., Baliga, N. S., Thorsson, V. & other authors ( 2000; ). Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 97, 12176–12181.[CrossRef]
    [Google Scholar]
  34. Nuttall, S. D. & Dyall-Smith, M. L. ( 1993; ). HF1 and HF2: novel bacteriophages of halophilic archaea. Virology 197, 678–684.[CrossRef]
    [Google Scholar]
  35. Oren, A., Bratbak, G. & Heldal, M. ( 1997; ). Occurrence of virus-like particles in the Dead Sea. Extremophiles 1, 143–149.[CrossRef]
    [Google Scholar]
  36. Porter, K. & Dyall-Smith, M. L. ( 2008; ). Transfection of haloarchaea by the DNAs of spindle and round haloviruses and the use of transposon mutagenesis to identify non-essential regions. Molecular Microbiology (in press).
    [Google Scholar]
  37. Porter, K., Kukkaro, P., Bamford, J. K., Bath, C., Kivelä, H. M., Dyall-Smith, M. L. & Bamford, D. H. ( 2005; ). SH1: a novel, spherical halovirus isolated from an Australian hypersaline lake. Virology 335, 22–33.[CrossRef]
    [Google Scholar]
  38. Prangishvili, D., Forterre, P. & Garrett, R. A. ( 2006; ). Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4, 837–848.[CrossRef]
    [Google Scholar]
  39. Reiter, W. D., Palm, P., Yeats, S. & Zillig, W. ( 1987; ). Gene expression in archaebacteria: physical mapping of constitutive and UV-inducible transcripts from the Sulfolobus virus-like particle SSV1. Mol Gen Genet 209, 270–275.[CrossRef]
    [Google Scholar]
  40. Stolt, P. & Zillig, W. ( 1993; ). Antisense RNA mediates transcriptional processing in an archaebacterium, indicating a novel kind of RNase activity. Mol Microbiol 7, 875–882.[CrossRef]
    [Google Scholar]
  41. Stolt, P. & Zillig, W. ( 1994; ). Transcription of the halophage φH repressor gene is abolished by transcription from an inversely oriented lytic promoter. FEBS Lett 344, 125–128.[CrossRef]
    [Google Scholar]
  42. Weinbauer, M. G. ( 2004; ). Ecology of prokaryotic viruses. FEMS Microbiol Rev 28, 127–181.[CrossRef]
    [Google Scholar]
  43. Woods, W. G., Ngui, K. & Dyall-Smith, M. ( 1999; ). An improved transposon for the halophilic archaeon Haloarcula hispanica. J Bacteriol 181, 7140–7142.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2008/019422-0
Loading
/content/journal/micro/10.1099/mic.0.2008/019422-0
Loading

Data & Media loading...

Supplements

[PDF file](31 KB)

PDF

[PDF file](48 KB)

PDF

[PDF file](12 KB)

PDF

[PDF file](582 KB)

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error