Table 2.
Bioinformatic prediction of plant virus coat proteins interacting with E. coli GroEL and “Ca. Tremblaya princeps” GroELa
| Genus | Virus name (acronym), accession no. | Binding of intact virus to E. coli GroEL (1) | Virion shape | Properties of coat protein (Mw, pI, charge, and Arg [%]) | No. of E. coli GroES patternsc |
E. coli GroEL binding predictionb | No. of “Ca. Tremblaya princeps” GroES patternsc |
“Ca. Tremblaya princeps” GroEL binding predictionb | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4 | 5 | 6 | 4 | 5 | 6 | |||||||
| Begomovirus | Tomato yellow leaf curl virus (TYLCV), X15656 | Yes | Geminate | 30,285; 10.4; 22.7; 12.9 | 4 | 2 | 2 | Yes | 4 | 3 | 2 | Yes |
| Begomovirus | African cassava mosaic virus (ACMV), AF366902 | Yes | Geminate | 30,129; 10.3; 22.8; 12.5 | 3 | 1 | 0 | Yes | 2 | 2 | 1 | Yes |
| Cucumovirus | Cucumber mosaic virus (CMV), D10538 | Yes | Globular | 24,113; 10.3; 12.2; 13.0 | 2 | 1 | 1 | Yes | 2 | 2 | 1 | Yes |
| Luteovirus | Bean leafroll virus (BLRV), NC 003369 | Yes | Globular | 21,966; 11.2; 22.3; 13 | 3 | 0 | 0 | Yes | 3 | 0 | 0 | Yes |
| Luteovirus | Barley yellow dwarf virus (BYDV), NC 002160 | Yes | Globular | 21,930; 12.1; 23.2; 15.0 | 4 | 2 | 0 | Yes | 1 | 0 | 0 | No |
| Luteovirus | Soybean dwarf virus (SbDV), NC_001747 | Yes | Globular | 22,201; 11.3; 22.3; 13.5 | 3 | 1 | 0 | Yes | 1 | 0 | 0 | No |
| Luteovirus (Enamovirus) | Pea enation mosaic virus (PEMV), NC_003629 | Yes | Globular | 21,104; 11.2; 19.3; 15.6 | 3 | 2 | 1 | Yes | 3 | 1 | 1 | Yes |
| Luteovirus (Polerovirus) | Potato leafroll virus (PLRV), NC_001747 | Yes | Globular | 23,127; 11.6; 24.2; 15.5 | 3 | 2 | 1 | Yes | 1 | 0 | 0 | No |
| Luteovirus (Polerovirus) | Beet western yellows virus (BWYV), NC_003743 | Yes | Globular | 22,459; 11.7; 22.2; 16.0 | 2 | 1 | 0 | Yes | 1 | 1 | 1 | No |
| Potexvirus | Potato virus X (PVX), AF260641 | No | Filamentous | 25,111; 7.0; 0.06; 5.3 | 3 | 2 | 0 | Yes | 3 | 2 | 1 | Yes |
| Potyvirus | Potato virus Y M95491 | No | Filamentous | 29,879; 5.9; 3.5; 7.0 | 1 | 0 | 0 | No | 0 | 0 | 0 | No |
| Tricovirus | Grapevine virus A (GVA), NC_003604 | No | Filamentous | 21,624; 8.4; 1.2; 6.9 | 3 | 2 | 0 | Yes | 3 | 2 | 1 | Yes |
| Ampelovirus (Closteroviridae) | Grapevine leafroll virus 3 (GLRVa 3), NC_004667 | No | Isometric | 4,802.8; 6.78; 0.4; 3.0 | 4 | 2 | 1 | Yes | 4 | 2 | 2 | Yes |
| Llavirus (Bromoviridae) | Prune dwarf virus (PDV), U31310 | Yes | Isometric | 23,922.2; 10.0; 9.0; 6.26 | 4 | 2 | 1 | Yes | 3 | 0 | 0 | Yes |
| Nepovirus (Comoviradae) | Tobacco ringspot virus (TSRV), AF461164 | No | Isometric | 57,177.8; 7.25; 1.78; 6.03 | 6 | 2 | 2 | Yes | 7 | 0 | 0 | Yes |
| Tobamovirus | Tobacco mosaic virus (TMV), NC_001367 | No | Filamentous | 17,620.0; 4.83; 2.04; 9.36 | 2 | 2 | 1 | Yes | 2 | 0 | 0 | Yes |
a
Adapted from reference 1 with permission of H. Czosnek and Springer-Verlag Wien.
b
In the yes/no scoring, “yes” means that the number of GroES patterns is at least 2 and that the number of contacts at each site is at least 4 in the (major) coat protein sequence (40).
c
Pattern match scores are as follows: 4, P_HHH and H_HHH; 5, P_HHH_P and H_HHH_−; or 6, P_HHH_P_H and H_HHH_−_H for E. coli and “Ca. Tremblaya princeps,” respectively (see Materials and Methods for further explanation).