Table 1.
Streptococcus pneumoniae Strains, Plasmids, and Pneumolysin Codon-pair Bias
| S. pneumoniae strain or plasmid | Genotype, description, or codon-pair bias value | Source, reference, or no. of nucleotide changes |
| S. pneumoniae strains | ||
| A66.1 | Serotype 3 S. pneumoniae | [17] |
| A66.1:PM2 | A66.1; synthetically modified pneumolysin via transformation with pPM2, Kmr | This study |
| A66.1:PM4 | A66.1; synthetically modified pneumolysin via transformation with pPM4, Kmr | This study |
| A66.1:Δply | A66.1; Δply via transformation with pΔPLY, Kmr | This study |
| A66.1::ply | A66.1; reconstituted ply via transformation with pPLY, Kmr | This study |
| Plasmids | ||
| pUCminus | Synthetic carrier plasmid | Blue Heron Biotechnology |
| pPM4 | Derivative of pUCminus that contains synthetic construct pPM4 (Figure 1) | This study |
| pPM2 | Derivative of pUCminus that contains synthetic construct pPM2 (Figure 1) | This study |
| pΔPLY | Derivative of pUCminus that contains synthetic construct pΔPLY (Figure 1) | This study |
| pPLY | Derivative of pUCminus that contains the wild-type pneumolysin and Kmr cassette (not shown) | This study |
| Strain (pneumolysin) | ||
| A66.1 (ply) | .095 | … |
| A66:PM2 (ply−.19) | −.194a | 275b |
| A66:PM4 (ply−.47) | −.472a | 360b |
NOTE. Kmr, kanamycin resistance; ply, pneumolysin gene; r, resistance.
a
The negative codon-pair bias value indicates pneumolysin genes encoded with codon pairs that are underrepresented in S. Pneumoniae genes. The more negative the value, the greater the density of underrepresented pairs.
b
All nucleotide changes to ply are silent mutations. The amino acid sequences are identical to those of the A66.1 ply gene.