TABLE 3.
Comparison of the T. pallidum subsp. pallidum Nichols and T. paraluiscuniculi Cuniculi A genomes using WGF and subsequent DNA sequencing of identified diverse regions: major sequence changes (multiple SNPs) and frameshifts
| Affected gene(s) | Detected multiple SNPs or frameshifta | Protein changeb |
|---|---|---|
| TP0126 | Deletion (1 nt) resulting in frameshift at nt 148 (148340) | Truncated hypothetical protein TP0126 (227 aa) |
| TP0131 (tprD) | Insertion (1 nt) resulting in frameshift between nt 438 and 439 (152459-152460) | Two hypothetical proteins, TprD2a and TprD2b (196 and 463 aa, respectively) |
| Multiple SNPs | Nonfunctional tprD2c | |
| TP0132 | Insertion (1 nt) resulting in frameshift between nt 28 and 29 (153123-153124) | Truncated hypothetical protein TP0132 (64 aa) |
| TP0133 | Multiple SNPs and small indels | Hypothetical TP0133-like protein (420 aa); 74.7% aa identity to Nichols TP0133 homolog (410 aa); 10-aa elongation at N terminus |
| TP0136 | Multiple SNPs and small indels | Hypothetical protein (437 aa); 42.7% aa identity to the Nichols homolog TP0136 (495 aa); 74.6% identity the Nichols homolog TP0133 (410 aa); 96.1% identity to the Cuniculi A homolog TP0133 (420 aa) |
| TP0137 | Multiple SNPs and small indels | Hypothetical protein TP0137 (45 aa) |
| TP0309 | Deletion (2 nt) resulting in frameshift at nt 207 and 208 (325811-325812) | Amino acid ABC transporter; periplasmic binding protein; two truncated TP0309 proteins (107 and 288 aa) |
| TP0310 | Insertion (1 nt) resulting in frameshift between nt 375 and 376 (326766-326767) | 49-aa elongation of hypothetical protein TP0310 at C terminus (176 aa) |
| TP0311 | Insertion (1 nt) and deletion (1 nt) between coordinates 326766 and 326767 and at coordinate 326872, respectively | Hypothetical protein TP0311 (47 aa); 29.2% aa identity to the Nichols homolog TP0311 (47 aa) |
| TP0313 (tprE) | Insertion (1 nt) resulting in frameshift between nt 652 and 653 (328636-328637) | Two hypothetical proteins, TprEa and TprEb (260 and 560 aa, respectively) |
| Multiple SNPs | Nonfunctional tprG1; tprG/J hybridd | |
| TP0315 | Multiple SNPs and small indels | Truncated hypothetical protein TP0315 (120 aa) |
| TP0317 (tprG)e | Insertion (1 nt) resulting in frameshift between nt 652 and 653 (334011-334012) | Nonfunctional tprG and tprI; tprG/I hybridc |
| Deletione | ||
| TP0318 | Deletion (2 nt) resulting in frameshift at nt 121 and 122 (334673-334674) | Truncated hypothetical protein TP0318 (40 aa) |
| TP0487e | Insertion (1 nt) resulting in frameshift between 520371-520372 | 10-aa elongation of hypothetical protein TP0487 at N terminus (535 aa) |
| Insertione | ||
| TP0548 | Multiple SNPs and small indels | Hypothetical protein TP0548 (437 aa); 82.8% aa identity to Nichols homolog (434 aa) |
| TP0616 | G668671 → A (M1 → I), missing start codon at coordinates 668669 to 668671 | 29-aa elongation of hypothetical protein TP0616 at N terminus (283 aa) |
| TP0617, TP0618 | Multiple SNPs and small indels | Fusion of genes TP0617 and TP0618 (254 aa) |
| TP0621 (tprJ) | Insertion (1 nt) resulting in frameshift between nt 652 and 653 (674569-674570) | Two hypothetical proteins, TprJa and TprJb (260 and 580 aa, respectively) |
| Multiple SNPs | Nonfunctional tprG2 allele; tprG/J hybridd | |
| TP0922 | Insertion (1 nt) and insertion (2 nt) between coordinates 1001601 and 1001602 and between coordinates 1000784 and 1000785, respectively | Hypothetical protein (350 aa) related to TDE0306 protein encoded in T. denticola genomef |
| TP0968 | Insertion (1 nt) resulting in frameshift between coordinates 1051760 and 1051761 | Possible truncated hypothetical protein TP0968 |
| TP1030e | Insertion (1 nt) resulting in frameshift between nt 138 and 139 (1124188-1124189) | Truncated hypothetical protein TP1030 (51 aa) |
| Insertione | ||
| TP1031 (tprL) | Multiple SNPs | 98-aa elongation of TprL protein at N terminus (possible fusion of the TP1030 and TP1031 genes) |