Advertisement

Archives of Virology

, Volume 151, Issue 3, pp 525–535 | Cite as

Preliminary characterisation of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi

  • M. J. Allen
  • D. C. Schroeder
  • W. H. Wilson
Article

Summary.

EhV-86 is a large double stranded DNA virus with a 407,339 base pair circular genome that infects the globally important microalga Emiliania huxleyi. It belongs to a new genus of viruses termed the Coccolithoviridae within the algal virus family Phycodnaviridae. By plotting the EhV-86 genome against itself in a dot-plot analysis we revealed three families of distinctly different repeat sequences throughout its genome, designated Family A, B and C. Family A repeats are non-coding, found immediately upstream of 86 predicted coding sequences (CDSs) and are likely to play a crucial role in controlling the expression of the associated CDSs. Family B repeats are GC rich, coding and correspond to possible calcium binding sites in 22 proline-rich domains found in the protein products of eight predicted EhV-86 CDSs. Family C repeats are AT-rich, non-coding and are likely to form part of the origin of replication. We suggest that these repeat regions are of fundamental importance during virus propagation being involved with transcriptional control (Family A), virus adsorption/release (Family B) and DNA replication (Family C).

Keywords

Calcium Binding Transcriptional Control Repeat Region Preliminary Characterisation Virus Family 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Allen MJ, Schroeder DC, Holden M, Wilson WH (2005) Evolutionary history of Coccolithoviridae. Mol Biol Evol, doi: 10.1093/molbev/msj010Google Scholar
  2. Blum, H, Zillig, W, Mallok, S, Domdey, H, Prangishvili, D 2001The genome of the archaeal virus SIRV1 has features in common with genomes of eukaryal viruses.Virology28169CrossRefPubMedGoogle Scholar
  3. Boehmer, PE, Lehman, IR 1997Herpes simplex virus DNA replication.Annu Rev Biochem66347384CrossRefPubMedGoogle Scholar
  4. Brownlee C, Nimer N, Dong LF, Merrett MJ (1994) Cellular regulation during calcification in Emiliania huxleyi. In: Green JC, Leadbeater BSC (eds) The haptophyte algae. Syst Assoc Special vol 51: 133–148, Clarendon Press, OxfordGoogle Scholar
  5. Chen, Y, Yao, B, Zhu, ZZ, Yi, YZ, Lin, X, Zhang, ZF, Shen, GF 2004A constitutive super-enhancer: homologous region 3 of Bombyx mori nucleopolyhedrovirus.Biochem Biophys Res Commun31810391044PubMedGoogle Scholar
  6. Delaroque, N, Muller, DG, Bothe, G, Pohl, T, Knippers, R, Boland, W 2001The complete DNA sequence of the Ectocarpus siliculosus virus EsV-1 genome.Virology287112132CrossRefPubMedGoogle Scholar
  7. Endo, H, Persson, P, Watanabe, T 2000Molecular cloning of the crustacean DD4 cDNA encoding a Ca2+-binding protein.Biochem Biophys Res Commun276286291PubMedGoogle Scholar
  8. Fliegel, L, Burns, K, MacLennan, DH, Reithmeier, RA, Michalak, M 1989Molecular cloning of the high affinity calcium-binding protein (calreticulin) of skeletal muscle sarcoplasmic reticulum.J Biol Chem2642152221528PubMedGoogle Scholar
  9. Galli, I, Iguchi-Ariga, SM, Ariga, H 1992The AT-rich tract of the SV40 ori core: negative synergism and specific recognition by single stranded and duplex DNA binding proteins.Nucleic Acids Res2033333339PubMedGoogle Scholar
  10. Gompels, UA, Macaulay, HA 1995Characterization of human telomeric repeat sequences from human herpesvirus 6 and relationship to replication.J Gen Virol76451458PubMedGoogle Scholar
  11. Hayakawa, T, Rohrmann, GF, Hashimoto, Y 2000Patterns of genome organization and content in lepidopteran baculoviruses.Virology278112CrossRefPubMedGoogle Scholar
  12. Hill, CW 1999Large genomic sequence repetitions in bacteria: lessons from rRNA operons and Rhs elements.Res Microbiol150665674CrossRefPubMedGoogle Scholar
  13. Huang, Y, Zhang, L 2004Rapid and sensitive dot-matrix methods for genome analysis.Bioinformatics20460466PubMedGoogle Scholar
  14. Huang, Y, Zhang, L 2004Rapid and sensitive dot-matrix methods for genome analysis.Bioinformatics20460466PubMedGoogle Scholar
  15. Klein, M, Lanka, S, Muller, D, Knippers, R 1994Single-stranded regions in the genome of the Ectocarpus siliculosus virus.Virology20210761078CrossRefPubMedGoogle Scholar
  16. La Scola, B, Audic, S, Robert, C, Jungang, L, de Lamballerie, X, Drancourt, M, Birtles, R, Claverie, JM, Raoult, D 2003A giant virus in amoebae.Science29920332033PubMedGoogle Scholar
  17. Martin, JH, Benzer, S, Rudnicka, M, Miller, CA 1993Calphotin: a Drosophila photoreceptor cell calcium-binding protein.Proc Natl Acad Sci USA9015311535PubMedGoogle Scholar
  18. Raoult, D, Audic, S, Robert, C, Abergel, C, Renesto, P, Ogata, H, La Scola, B, Suzan, M, Claverie, JM 2004The 1.2-megabase genome sequence of mimivirus.Science30613441350CrossRefPubMedGoogle Scholar
  19. Ritzi, M, Tillack, K, Gerhardt, J, Ott, E, Humme, S, Kremmer, E, Hammerschmidt, W, Schepers, A 2003Complex protein-DNA dynamics at the latent origin of DNA replication of Epstein-Barr virus.J Cell Sci11639713984CrossRefPubMedGoogle Scholar
  20. Schlesinger, DH, Hay, DI 1986Complete covalent structure of a proline-rich phosphoprotein, PRP-2, an inhibitor of calcium phosphate crystal growth from human parotid saliva.Int J Pept Protein Res27373379PubMedGoogle Scholar
  21. Schuster, AM, Graves, M, Korth, K, Ziegelbein, M, Brumbaugh, J, Grone, D, Meints, RH 1990Transcription and sequence studies of a 4.3-kbp fragment from a ds-DNA eukaryotic algal virus.Virology176515523CrossRefPubMedGoogle Scholar
  22. Stahl, L, Wright, R, Castle, J, Castle, A 1996The unique proline-rich domain of parotid proline-rich proteins functions in secretory sorting.J Cell Sci10916371645PubMedGoogle Scholar
  23. Sugden, B 2002In the beginning: a viral origin exploits the cell.Trends Biochem Sci2713CrossRefPubMedGoogle Scholar
  24. Thompson, JD, Higgins, DG, Gibson, TJ 1994Clustal-W – improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Nucleic Acids Res2246734680PubMedGoogle Scholar
  25. van Etten, JL, Meints, RH 1999Giant viruses infecting algae.Annu Rev Microbiol53447494CrossRefPubMedGoogle Scholar
  26. Van Etten, JL, Graves, MV, Muller, DG, Boland, W, Delaroque, N 2002Phycodnaviridae – large DNA algal viruses.Arch Virol14714791516CrossRefPubMedGoogle Scholar
  27. Vink, C, Beuken, E, Bruggeman, CA 1996Structure of the rat cytomegalovirus genome termini.J Virol7052215229PubMedGoogle Scholar
  28. Westbroek, P, Dejong, EW, Vanderwal, P, Borman, AH, Devrind, JPM, Kok, D, Debruijn, WC, Parker, SB 1984Mechanism of calcification in the marine alga Emiliania huxleyi.Philos Trans Roy Soc Lond Ser B Biol Sci304435444Google Scholar
  29. Wilson, WH, Tarran, GA, Schroeder, D, Cox, M, Oke, J, Malin, G 2002Isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel.J Marine Biol Assoc UK82369377Google Scholar
  30. Wilson, WH, Schroeder, DC, Allen, MJ, Holden, MTG, Parkhill, J, Barrell, BG, Churcher, C, Hamlin, N, Mungall, K, Norbertczak, H, Quail, MA, Price, C, Rabbinowitsch, E, Walker, D, Craigon, M, Roy, D, Ghazal, P 2005Complete genome sequence and lytic phase transcription profile of a coccolithovirus.Science30910901092CrossRefPubMedGoogle Scholar
  31. Wilson WH, Van Etten JL, Schroeder DS, Nagasaki K, Brussaard C, Delaroque N, Bratbak G, Suttle C (2005) Family: Phycodnaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Dusselberger U, Ball LA (eds) Virus taxonomy, VIIIth ICTV Report. Elsevier/Academic Press, London, pp 163–175Google Scholar

Copyright information

© Springer-Verlag/Wien 2005

Authors and Affiliations

  • M. J. Allen
    • 1
  • D. C. Schroeder
    • 2
  • W. H. Wilson
    • 1
    • 2
  1. 1.Plymouth Marine LaboratoryPlymouthU.K.
  2. 2.Marine Biological AssociationPlymouthU.K.

Personalised recommendations