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 segments of Bombyx mori cypovirus type 1 (BmCPV-1) (strain I) 

 

(genus Cypovirus,  family Reoviridae ) 

 

last updated 13/08/2003   (also available as a Word file) 

 

References [in square brackets]. Recent structural analyses [7, 12, 14] 

 

Genome Segment†

Size

 

(bp)

Base pair position of ORFs

Protein1 nomenclature

(': Protein Function)

 

[alternative nomenclature2]

Protein Size

aa

 

(kDa)

Copy Number/

Particle

Protein Location

Accession Numbers

Cognate Proteins‡

Functions and Properties

1

(4190)

40-4038

VP1

1333

(148)

120

virion

AF323781

Orbivirus VP 3(T2)

Orthoreovirus lambda 1

 

Major virus structural protein forms the capsid shell (CSP)3 [14]. Comparable to sub-core protein VP3(T2) of bluetongue virus & Lambda 1 of mammalian orthoreovirus.

2

(3,854)

78-3752

VP2 (Pol)

1225

(136)

unknown

Virion

AF323782

Orthoreovirus lambda 3(Pol)

Orbivirus VP 1(Pol)

Rotavirus VP1 (Pol)

RNA dependent RNA polymerase (Pol),

Polymerase activity significantly stimulated by

S-Adenosyl-l-methionine (Ado Met) or its analogues

3

(3,846)

41-3757

- [VP3]

1239 (138)

unknown

Virion

AF323783

-

-

4

(3,262)

[8]

14-3187

VP3(CaP) [VP4]

1058

(130)

60

virion surface

AF323784

-

Guanylyl transferase, methylases, forms the turret (spike) on the virion surface. Turret protein (TP)3 [14]..

5

(2852)

[3]

71-2713

 

NS1 [NS5]

 

NS2 [NS5a] NS6 [NS5b]

881

(101)

 

(80*)

(23*)

 

0

 

0

0

Non structural

Non structural

Non structural

AB035732

-

Amino acid sequence (at position aa 232) contains an FMDV 2A-like, 'ribosome skip' sequence (NPGP) [13]. This would cause production of some of the protein molecules (total 881aa) as two polypetides of 234aa and 647aa.

6

(1,796)

[4]

44-1726

VP4 [VP6]

561

(64)

unknown

virion

AB030014

-

high leucine content (10%) and leucine zipper motif. ATP/GTP binding protein (virion)

7

(1,501)

[4]

25-1368

NS3

NS4

[VP7]

448

(49.8)

 

(58*)

 

(31*)

 

0

 

0

 

unknown

 

non structural

 

non structural

 

virion

AB030015

-

 

NS3 and NS4 are two non-structural proteins with sizes of 58 and 61 kDa, estimated by SDS PAGE [4].

 

Large Protrusion Protein (LPP)3 [14].

8

(1,328)

[5]

38-1207

VP5 or P44

[NSP8]

390

(44)

unknown

unknown

AB016436

-

Unknown, shows anomalous migration during PAGE, with apparent Mr of 55 K.

9

(1,186)

[6]

75-1034

NS5 [NSP9]

320

(36)

0

Non structural

AF061199

-

dsRNA binding [6].

10

(944)

[9, 10]

42-797

polyhedrin

(Pod)

252

(28.5)

unknown

polyhedra

D37768

-

polyhedron matrix protein (Pod) [1, 2, 11].

Size of genome segments and encoded proteins determined by sequence analysis of the genome segments, except where estimated from electrophoretic migration (indicated by *).

 

': To facilitate comparisons of proteins across species, genera and families, protein structure / function indicators have been added to protein names : RNA polymerase = (Pol), Polyhedrin = (Pod). Guanylyl transferase / transmethylase, 'cap' forming enzyme = (CaP). Other species within the genus may have proteins with significant differences in sizes.

 

1 : Protein nomenclature based on protein migration order during PAGE (McCrae and Mertens 1983).

 

2 : [Alternative nomenclature based on the number of the genome segment from which the protein is translated, (Hagiwara et al 2002)].

 

3 : Structural roles ('capsid shell protein' (CSP), 'turret protein' (TP) and 'large protrusion protein' (LPP)), identified by Zhou et al 2003.

 

If you have any additional data to add to this table, or any suggested corrections, please mail them to: peter.mertens@bbsrc.ac.uk

Constructed using data supplied by Peter Mertens, Hajime Mori, Hong Zhou and Shujing Rao.

 

 

Reference List

  1. Echeverry, F., Bergeron, J., Kaupp, W., Guertin, C., Arella, M. (1997) Sequence analysis and expression of the polyhedrin gene of Choristoneura fumiferana cytoplasmic polyhedrosis virus (CfCPV). Gene. 198, 399-406.

  2. Galinski, M. S., Yu, Y., Heminway, B. R., Beaudreau, G. S. (1994) Analysis of the C-polyhedrin genes from different geographical isolates of a type 5 cytoplasmic polyhedrosis virus. Journal of General Virology 75, 1969-1974.

  3. Hagiwara, K., Kobayashi, J., Tomita, M., Yoshimura, T. (2001) Sequence of genome segment 5 from Bombyx mori cypovirus 1. Archives of Virology, 146, 181-187.

  4. Hagiwara, K., Matsumoto, T. (2000) Sequences of genome segments 6 and 7 of Bombyx mori cypovirus 1, encoding the viral structural proteins V4 and V5, respectively. Journal of General Virology 81, 1143-7.

  5. Hagiwara, K., Tomita, M., Kobayashi, J., Miyajima, S. and Yoshimura, T. (1998) Nucleotide sequence of Bombyx mori cytoplasmic polyhedrosis virus segment 8. Biochemical Biophysical Research Communications 247, 549-553.

  6. Hagiwara, K., Tomita, M., Nakai, K., Kobayashi, J., Miyajima, S. and Yoshimura, T (1998). Determination of the nucleotide sequence of Bombyx mori cytoplasmic polyhedrosis virus segment 9 and its expression in BmN4 cells. Journal of Virology 72, 5762-5768.

  7. Hill, C. L., Booth, T. F., Prasad, B. V. V., Grimes J. M. Mertens P. P. C. Sutton, G. C. and Stuart, D. I. (1999) The structure of a cypovirus and the functional organisation of dsRNA viruses. Nature Structural Biology 6, 565-568.

  8. Ikeda, K., Nagaoka, S., Winkler, S., Kotani, K., Yagi, H., Nakanishi, K., Miyajima, S., Kobayashi, J. and Mori, H. (2001) Molecular characterization of Bombyx mori cytoplasmic polyhedrosis virus genome segment 4. Journal of Virology. 75, 988-995.

  9. Ikeda, K., Nakazawa, H., Alain, R., Belloncik, S. and Mori, H. (1998) Characterizations of natural and induced polyhedrin gene mutants of Bombyx mori cytoplasmic polyhedrosis viruses. Archives of Virology 143, 241-8.

  10. Lavallee, C., Arella, M., Belloncik, S. and Furuichi, Y. (1993) Expression in Escherichia coli of the cloned polyhedrin gene of Bombyx mori cytoplasmic polyhedrosis virus. Protein Expr Purif. 4, 570-579.

  11. Mori, H., Ito, R., Nakazawa, H., Sumida, M., Matsubara, F. and Minobe, Y. (1993) Expression of Bombyx mori cytoplasmic polyhedrosis virus polyhedrin in insect cells by using a baculovirus expression vector, and its assembly into polyhedra. Journal of General Virology 74, 99-102.

  12. Tomita, M., Hasegawa, T., Tsukihara, T., Miyajima, S., Nagao, M. and Sato, M. (1999) Two concentric protein shell structure with spikes of silkworm Bombyxmori cytoplasmic polyhedrosis virus revealed by small-angle neutron scattering using the contrast variation method. J Biochem (Tokyo) 125, 916-922.

  13. Donnelly, M. L, Luke, G., Mehrotra, A., Li, X., Hughes, L.E., Gani, D., Ryan, M.D. (2001) Analysis of the aphthovirus 2A/2B polyprotein 'cleavage' mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal 'skip'. J Gen Virol.82 :1013-25.

  14. Zhou, Z. H., Zhang, H., Jakana, J., JU, X-Y. and Zhang, J-Q (2003) Cytoplasmic polyhedrosis virus structure at 8Å by electron cryomicroscopy: structural basis of capsid stability ans mRNA processing regulation. Structure 11 651-663

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