TABLE 2 .
Proteins found to be associated with DENV RNA by antisense-mediated affinity purification of dengue viral ribonucleoprotein complexes followed by mass spectrometrya
| Protein | Gene ID | No. of spectra |
Ratio (DENV:mock) |
Binding in vitro |
Reference | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Expt 1 |
Expt 2 |
Expt 3 |
Total |
|||||||||
| Mock | DENV | Mock | DENV | Mock | DENV | Mock | DENV | |||||
| Cold shock domain- containing protein E1 |
CSDE1 | 0 | 0 | 0 | 4 | 0 | 3 | 0 | 7 | INF | X | 12 |
| Nuclease-sensitive element-binding protein 1 |
YBX1 | 0 | 5 | 0 | 4 | 2 | 5 | 2 | 14 | 7.0 | X | 10 |
| Nucleolin | NCL | 2 | 11 | 3 | 6 | 0 | 2 | 5 | 19 | 3.8 | X | 12 |
| Eukaryotic translation initiation factor 4B |
EIF4B | 0 | 4 | 5 | 10 | 3 | 12 | 8 | 26 | 3.3 | ||
| Heterogeneous nuclear ribonucleoproteins C1/C2 |
HNRNPC | 0 | 0 | 2 | 2 | 0 | 3 | 2 | 5 | 2.5 | X | 33 |
| Putative RNA- binding protein 3 |
RBM3 | 3 | 4 | 2 | 8 | 0 | 0 | 5 | 12 | 2.4 | ||
| Polyadenylate- binding protein 1 |
PABPC1 | 0 | 0 | 3 | 4 | 0 | 3 | 3 | 7 | 2.3 | X | 11 |
| Heterogeneous nuclear ribonucleoproteins A2/B1 |
HNRNPA2B1 | 2 | 5 | 4 | 5 | 0 | 4 | 6 | 14 | 2.3 | X | 10 |
| Actin, alpha skeletal muscle |
ACTA1 | 0 | 0 | 0 | 2 | 4 | 7 | 4 | 9 | 2.3 | ||
| Cellular nucleic acid- binding protein |
CNBP | 3 | 8 | 5 | 5 | 2 | 9 | 10 | 22 | 2.2 | X | 12 |
| Single-stranded DNA-binding protein, mitochondrial |
SSBP1 | 0 | 2 | 2 | 2 | 0 | 0 | 2 | 4 | 2.0 | ||
| Plasminogen activator inhibitor 1 RNA-binding protein |
SERBP1 | 0 | 0 | 4 | 6 | 0 | 2 | 4 | 8 | 2.0 | ||
a
The sum of unique spectra identified in all three experiments was used to calculate a ratio representing the enrichment in infected samples (INF, infinite). Proteins listed are those that were identified by a unique-spectrum count ≥2-fold higher in infected samples than in mock-infected controls in at least two of three independent experiments.