dsRNA viruses RNA / protein tables: Edited by Peter Mertens and Denis Bamford

The dsRNA genome segments and proteins of Pseudomonas phage Phi 6

(genus Cystovirus : family Cystoviridae)

last updated 11/09/2002

dsRNA
(Size, bp)
[5,8,20,23] / Open reading frames (ORFs)
[5,8,20,23] / Proteins
(': protein structure/ function) / Size 'aa' (kDa )
[5,8,20,23] / protein copy number per particle / location / Function
L
(6,374) / Gene 1 / P1
(T=2) / 769
(84.986) / 120
[2. 6] / inner particle shell / Self assembles with proteins P2, P4 and P7 into procapsid particles [9, 29]. Corresponds to the T=2 particle in BTV [11]. Controls procapsid size and organization. Binds minor proteins and RNA. Conserved in dsRNA viruses.
L / Gene 2 / P2 (pol)
[3, 18, 19] / 664
(74.791) / 12
[6] / inner particle / Semi-conservative RNA dependent RNA polymerase [34, 35]. Isolated protein acts on ss and dsRNA templates [18, 19]. Three-dimensional structure homologous to HIV reverse transcriptase and hepatitis C polymerase [3]. Binding sites for nucleic acid, NTPs, Mn and Mg ions known [3].
M
(4,063) / Gene 3 / P3 (spike)
[17] / 648
(69.178) / extends from virion surface [17] and is attached to the integral membrane protein P6 [25] / Binds to the receptor [25] , the pilus IV of Pseudomonas syringae [30, 31]
L / Gene 4 / P4 (NTPase)
[7, 10, 16] / 331
(35.032) / 72
[7] / inner particle at 5 fold axes
[7] / Hexameric NTPase, symmetry mismatched position [7, 10, 16]. Powers the packaging of ssRNA genomic precursors and is involved in transcription [27]. Nucleates the assembly of the procapsid with P1 [29]
S
(2.948) / Gene 5 / P5 (mur)
[4, 12, 21] / 219
(24.018) / between the membrane and NC
[12] / Muralytic enzyme exposed to host peptidoglycan layer after membrane fusion during viral entry. Also used to lyse the host cell late in infection to release the virus [4, 12, 21].
M / Gene 6 / P6 (fus)
[1] / 167
(17.229) / Membrane
[32] / Integral membrane protein that has membrane fusion activity and binds the receptor -binding protein, P3 [1, 25, 32].
L / Gene 7 / P7 (assembly factor) [29] / 160
(17.169) / 60
[15] / inner particle
[15] / Dimeric, stabilizes the procapsid [15]. Increases the assembly rate of the procapsid in vitro [29]
S / Gene 8 / P8 (T=13)
[2] / 148
(15.873) / 600
[2, 29] / second protein layer
[2] / A trimer [29] that forms the T=13 nucleocapsid shell around the dsRNA-containing inner particle (core) [2]. During entry P8 drives the penetration of the nucleocapsid into the cytoplasm [26, 28].
S / Gene 9 / P9 (env)
[13, 32, 33] / 89
(9.482) / Membrane
[32] / Major membrane protein, essential for membrane formation [13, 32, 33]
M / Gene 10 / P10 (lys)
[14] / 42
(4.272) / Membrane
[32] / Needed for cell lysis [14]
S / Gene 12 / P12
(assembly)
[13. 22, 25] / 195
(20.293) / 0 / Non-structural
[32] / Assembly factor active in viral membrane morphogenesis [13, 22, 25].
M / Gene 13 / P13 / 72
(7.649) / Membrane
[8] / Minor, nonessential membrane protein [8, 24]
L / Gene 14 / P14 / 61
(6.810) / 0 / Non- structural
[5] / Nonessential [5].

': ': To facilitate comparisons of proteins across species, genera and families, protein structure / function indicators have been added to protein names, eg (pol) = RNA polymerase; (T=2) = capsid protein organized with icosahedral T=2 symmetry; (T=13) = capsid protein organized with icosahedral T=13 symmetry.

Constructed by Sarah Butcher and Dennis Bamford.

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References.

1. Bamford, D.H., Romantschuk, M. and Somerharju, P.J. (1987) Membrane fusion in prokaryotes: bacteriophage phi6 membrane fuses with the Pseudomonas syringae outer membrane. EMBO J., 6, 1467-1473.

2. Butcher, S.J., Dokland, T., Ojala, P.M., Bamford, D.H. and Fuller, S.D. (1997) Intermediates in the assembly pathway of the double-stranded RNA virus f6. EMBO J., 16, 4477-4487.

3.Butcher, S.J., Grimes, J.M., Makeyev, E.V., Bamford, D.H. and Stuart, D.I. (2001) A mechanism for initiating RNA-dependent RNA polymerization. Nature, 410, 235-40.

4. Caldentey, J. and Bamford, D.H. (1992) The lytic enzyme of the Pseudomonas phage phi 6. Purification and biochemical characterization. Biochim Biophys Acta, 1159, 44-50.

5. Casini, G. and Revel, H.R. (1994) A new small low-abundant nonstructural protein encoded by the L segment of the dsRNA bacteriophage phi 6. Virology, 203, 221-8.

6. Day, L.A. and Mindich, L. (1980) The molecular weight of bacteriophage phi6 and its nucleocapsid. Virology, 103, 376-385.

7.de Haas, F., Paatero, A.O., Mindich, L., Bamford, D.H. and Fuller, S.D. (1999) A symmetry mismatch at the site of RNA packaging in the polymerase complex of dsRNA bacteriophage phi6. J Mol Biol, 294, 357-72.

8. Gottlieb, P., Metzger, S., Romantschuk, M., Carton, J., Strassman, J., Bamford, D.H., Kalkkinen, N. and Mindich, L. (1988a) Nucleotide sequence of the middle dsRNA segment of bacteriophage phi 6: placement of the genes of membrane-associated proteins. Virology, 163, 183-90.

9. Gottlieb, P., Strassman, J., Bamford, D. and Mindich, L. (1988b) Production of a polyhedral particle in Escherichia coli from a cDNA copy of the large genome segment of Phi 6. J. Virol., 62, 181-187.

10. Gottlieb, P., Strassman, J. and Mindich, L. (1992) Protein P4 of the bacteriophage phi 6 procapsid has a nucleoside triphosphate-binding site with associated nucleoside triphosphate phosphohydrolase activity. J. Virol., 66, 6220-2.

11. Grimes, J.M., Burroughs, J.N., Gouet, P., Diprose, J.M., Malby, R., Zientara, S., Mertens, P.P. and Stuart, D.I. (1998) The atomic structure of the bluetongue virus core. Nature, 395, 470-8.

  1. Hantula, J. and Bamford, D.H. (1988) Chemical crosslinking of bacteriophage ø6 nucleocapsid proteins. Virology, 165, 482-488.
  1. Johnson, M.D. and Mindich, L. (1994a) Plasmid-directed assembly of the lipid-containing membrane of bacteriophage phi 6. J Bacteriol, 176, 4124-32.
  1. Johnson, M.D. (3rd) and Mindich, L. (1994b) Isolation and characterization of nonsense mutations in gene 10 of bacteriophage phi 6. J. Virol., 68, 2331-8.
  1. Juuti, J.T. and Bamford, D.H. (1997) Protein P7 of phage phi6 RNA polymerase complex, acquiring of RNA packaging activity by in vitro assembly of the purified protein onto deficient particles. J Mol Biol, 266, 891-900.
  1. Juuti, J.T., Bamford, D.H., Tuma, R. and Thomas, G.J., Jr. (1998) Structure and NTPase activity of the RNA-translocating protein (P4) of bacteriophage phi 6. J Mol Biol, 279, 347-59.
  1. Kenney, J.M., Hantula, J., Fuller, S.D., Mindich, L., Ojala, P.M. and Bamford, D.H. (1992) Bacteriophage phi 6 envelope elucidated by chemical cross-linking, immunodetection, and cryoelectron microscopy. Virology, 190, 635-644.
  1. Makeyev, E.V. and Bamford, D.H. (2000a) The polymerase subunit of a dsRNA virus plays a central role in the regulation of viral RNA metabolism. EMBO J., 19, 6275-6284.

19. Makeyev, E.V. and Bamford, D.H. (2000b) Replicase activity of purified recombinant protein P2 of double- stranded RNA bacteriophage phi6. EMBO J, 19, 124-133.

20. McGraw, T., Mindich, L. and Frangione, B. (1986) Nucleotide sequence of the small double-stranded RNA segment of bacteriophage phi 6: novel mechanism of natural translational control. J. Virol., 58, 142-151.

21. Mindich, L. and Lehman, J.F. (1979) Cell wall lysin as a component of the bacteriophage ø6 virion. J. Virology, 30, 489-496.

22. Mindich, L. and Lehman, J.F. (1983) Characterization of phi6 mutants that are temperature sensitive in the morphogenetic protein P12. Virology,127, 438-445.

23. Mindich, L., Nemhauser, I., Gottlieb, P., Romantschuk, M., Carton, J., Frucht, S., Strassman, J., Bamford, D.H. and Kalkkinen, N. (1988) Nucleotide sequence of the large double-stranded RNA segment of bacteriophage phi 6: genes specifying the viral replicase and transcriptase. J.Virol., 62, 1180-5.

24. Mindich, L., Qiao, X., Onodera, S., Gottlieb, P. and Strassman, J. (1992) Heterologous recombination in the double-stranded RNA bacteriophage phi 6. J. Virol., 66, 2605-10.

25. Mindich, L., Sinclair, J.F. and Cohen, J. (1976) The morphogenesis of bacteriophage phi6: particles formed by nonsense mutants. Virology, 75,224-231.

26. Olkkonen, V.M., Ojala, P.M. and Bamford, D.H. (1991) Generation of infectious nucleocapsids by in vitro assembly of the shell protein on to the polymerase complex of the dsRNA bacteriophage phi 6. J Mol Biol, 218, 569-581.

27. Pirttimaa, M.J., Paatero, A.O., Frilander, M.J. and Bamford, D.H. (2002) Nonspecific nucleoside triphosphatase P4 of double-stranded RNA bacteriophage phi6 is required for single-stranded RNA packaging and transcription. J Virol, 76.

28. Poranen, M.M., Daugelavicius, R., Ojala, P.M., Hess, M.W. and Bamford, D.H. (1999) A novel virus-host cell membrane interaction. Membrane voltage-dependent endocytic-like entry of bacteriophage phi6 nucleocapsid. J Cell Biol, 147, 671-82.

29. Poranen, M.M., Paatero, A.O., Tuma, R. and Bamford, D.H. (2001) Self assembly of a viral molecular machine from purified protein and RNA constituents. Molecular Cell, 7, 845-854.

30. Roine, E., Raineri, D.M., Romantschuk, M., Wilson, M. and Nunn, D.N. (1998) Characterization of type IV pilus genes in Pseudomonas syringae pv. tomato DC3000. Mol Plant Microbe Interact, 11, 1048-56.

31. Romantschuk, M. and Bamford, D.H. (1985) Function of pili in bacteriophage phi6 penetration. J. Gen. Virol., 66, 2461-2469.

32. Sinclair, J.F., Tzagoloff, A., Levine, D. and Mindich, L. (1975) Proteins of the bacteriophage phi6. Virology, 75, 685-695.

33. Stitt, B.L. and Mindich, L. (1983) Morphogenesis of bacteriophage phi6: a presumptive viral membrane precursor. Virology, 127, 446-458.

34. Usala, S.J., Brownstein, B.H. and Haselkorn, R. (1980) Displacement of parental RNA strands during in vitro transcription by bacteriophage phi6 nucleocapsids. Cell, 19, 855-862.

35. Van Etten, J.L., Burbank, D.E., Cuppels, D.A., Lane, L.C. and Vidaver, A.K. (1980) Semiconservative synthesis of single-stranded RNA by bacteriophage phi6 polymerase. J. Virol., 33, 769-773.