TABLE 2.
Comparison of the T. pallidum subsp. pallidum Nichols and T. paraluiscuniculi Cuniculi A genomes using WGF and subsequent DNA sequencing of identified diverse regions: prominent insertions and deletions
| XL PCR-amplified region (TPI interval) | Detected indela | Affected IGR or gene(s) | Protein or gene changeb | Putative function, biological relevance, and/or BLAST hitb | GenBank accession no.a |
|---|---|---|---|---|---|
| TPI2 | Insertion (41 bp) (10208-10209) | IGR TP0009-TP0010 | tprA sequence (100% identity; nt 421 to 381), tprB sequence (100% identity; nt 216 to 256) | EF137737 (9630-10791) | |
| TPI8 | Deletion (153 bp) (115478-115630) | TP0104 | 51-aa deletion (aa 541 to 591) at C terminus | UshA (5′ nucleotidase), putative substrate binding sitec | EF057750 (115191-115911) |
| TPI12-13 | Deletion (228 bp) and insertion (1,451 bp) between coordinates 148296 and 150385 (411 nt in this region remained as TP0129 sequence) | TP0127, TP0128 | Genes completely deleted | Hypothetical proteins | EF137743 (145689-159352) |
| TP0129 | Gene partially deleted | Hypothetical protein TP0129, ORF encoding 136 aa remained | |||
| IGR TP0126-TP0129 | Insertion (1,451 bp) of tprK-like sequence with three ORFs encoding 121, 155, and 184 aa | ||||
| Deletion (1,063 bp) between coordinates 153136 and 156388 (2,190 nt in this region remained) | TP0134 | Gene completely deleted | Hypothetical protein | ||
| TP0135 | Gene partially deleted | Hypothetical TP0135-like sequence with two ORFs encoding 228 and 103 aa and additional hypothetical TP0126-like ORF encoding 292 aa | |||
| Deletion (63 bp) (156459-156521) | IGR TP0135-TP0136 | ||||
| Insertion (97 bp) (156750-156751) | IGR TP0135-TP0136 | No BLAST hit | |||
| TPI25A-25B | Deletion (1,660 bp) between coordinates 331139 and 334663 (1,864 nt in this region remained) | TP0316, TP0317 | Genes partially deleted | TprF and TprG proteins; additional ORF encoding 429 aa with 71% aa identity to TprI; nonfunctional tprG and tprI; tprG/tprI hybridd | EF137742 (325013-337122) |
| TPI32B | Insertion (885 bp) (461015-461517)e | TP0433, TP0434 | 14 complete repetitions plus 45 nt of incomplete repetition inserted | Arp protein, fusion of TP0433 and TP0434 genes to arp genef | EF137736 (460718-464495) |
| TPI34 | Deletion (264 bp) (497265-497688)g | TP0470 | Gene partially deleted, 11 tandem repetitions deleted | Conserved hypothetical protein; 88 aa (aa 246 to 333) deleted; no protein domain was identified in the deleted region | EF137740 (496637-498283) |
| TPI38 | Insertion (66 bp) (519663-519664) | TP0487 | 22-aa elongation | Hypothetical TP0487-like protein | EF419245 (519481-521656) |
| TPI41-42A | Deletion (103 bp) (588576-588678) | TP0545, IGR TP0545- TP0546 | 11 aa of signal peptide deleted from TP0545 (mglB-1) | Methylgalactoside ABC transporter; periplasmic galactose-binding protein | EF137738 (587756-594311) |
| Insertion (52 bp) (593023-593024) | IGR TP0548-TP0549 | No BLAST hit | |||
| TPI48 | Deletion (2,609 bp) between coordinates 669739 and 672944 (597 nt in this region remained as TP0618-like sequence) | TP0619, TP0620 | Genes completely deleted | Hypothetical protein TP0619 and TprI | EF137741 (667318-678691) |
| TPI57A | Deletion (21 bp) between coordinates 798596 and 798646 (30 nt in this region remained) | TP0733 | Gene partially deleted, 7 aa deleted | Hypothetical protein | EF419246 (797469-800801) |
| TPI65 | Insertion (30 bp) (936629-936630) | TP0860 | 10-aa elongation | Hypothetical protein | EF419247 (936435-936924) |
| TPI66A | Deletion (12 bp) (944598-944609) | TP0865 | Gene partially deleted, 5 aa deleted | Hypothetical protein | EF419248 (943859-945703) |
| Insertion (18 bp) (944541-944542) | |||||
| Deletion (21 bp) (944086-944106) | |||||
| TPI68 | Insertion (330 bp) between coordinates 1001719 and 1002228 (510 nt in this region remained) | TP0923 | 105-aa elongation | No BLAST hit, hypothetical protein | EF419249 (999546-1002637) |
| TPI71 | Deletion (15 bp) between coordinates 1050290 and 1050319 (15 nt in this region remained) | TP0967 | Gene partially deleted, 5 aa deleted | Hypothetical protein | EF419250 (1049862-1051795) |
| TPI77 | Deletion (18 bp) (1123530-1123547) | TP1029 | Gene partially deleted, 6 aa deleted | Hypothetical protein | EF137739 (1122770-1125482) |
| Insertion (67 bp) (1124102-1124103) | TP1030 | No BLAST hit, hypothetical protein |
a
The numbers in parentheses are the coordinates in the strain Nichols genome.
b
aa, amino acid.
c
See reference 8.
d
See reference 9.
e
Insertion into the chromosomal region containing tandem repetitions (length, 60 nt) (i.e., increased number of tandem repetitions).
f
See reference 19.
g
Deletion in the chromosomal region containing tandem repetitions (length, 24 nt) (i.e., decreased number of tandem repetitions).