The RNAs and Proteins of dsRNA Viruses

 

Edited by Peter. P. C. Mertens, Houssam Attoui and Dennis H. Bamford

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The dsRNA genome segments and proteins of Pseudomonas phage Phi 6  

(genus Cystovirus : family Cystoviridae

 

(available as a Word file)  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.

 

If you have any queries regarding this page please contact Peter Mertens on peter.mertens@bbsrc.ac.uk.

 

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.

  12. Hantula, J. and Bamford, D.H. (1988) Chemical crosslinking of bacteriophage 6 nucleocapsid proteins. Virology, 165, 482-488.

  13. Johnson, M.D. and Mindich, L. (1994a) Plasmid-directed assembly of the lipid-containing membrane of bacteriophage phi 6. J Bacteriol, 176, 4124-32.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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 6 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.

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(The RNAs and Proteins  of dsRNA Viruses:  Edited by Peter. P. C. Mertens, Houssam Attoui and Dennis H. Bamford)