TABLE 2.
Evidence for deletion of ETR A in certain PETRA lineage strainsa
| Status | Strain | PCR product of ETR A by AGEb |
ETR A copy no. by CEc | PCR product of mla-1 by AGE |
PCR product of ETR B by AGE |
Copy no. by CE |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| bp | Copy no. | Proto-bp | bp | Proto-bp | bp | Copy no. | Proto-bp | ETR B | QUB11b | |||
| mla PETRA | 0433-00 | NB | NB | NB | 234 | 2 | 235 | 2 | 2 | |||
| 1178-00 | NB | NB | NB | 231 | 2 | 235 | 2 | 2 | ||||
| 2136-00 | NB | NB | NB | 232 | 2 | 235 | 2 | 2 | ||||
| 0545-06 | NB | NB | NB | 233 | 2 | 235 | 2 | 2 | ||||
| 0958-06 | NB | NB | NB | 232 | 2 | 235 | 2 | 2 | ||||
| 0170-08 | NB | NB | NB | 227 | 2 | 235 | 2 | 2 | ||||
| 0469-08 | NB | NB | NB | 176 | 1 | 178 | 1 | 0 | ||||
| 0804-08 | NB | NB | NB | 232 | 2 | 235 | 2 | 2 | ||||
| 0937-08 | NB | NB | NB | 227 | 2 | 235 | 2 | 2 | ||||
| 1158-08 | NB | NB | NB | 233 | 2 | 235 | 2 | 2 | ||||
| PETRA | 1468-00 | 497 | 4 | 495 | 4 | 748 | 753 | 230 | 2 | 235 | 2 | 2 |
| 0428-05 | 637 | 6 | 645 | 6 | 887 | 903 | 230 | 2 | 235 | 2 | 2 | |
| 0339-06 | 500 | 4 | 495 | 4 | 755 | 753 | 232 | 2 | 235 | 2 | 2 | |
| 0382-08 | 491 | 4 | 495 | 4 | 748 | 753 | 229 | 2 | 235 | 2 | 2 | |
| Beijing (PETRA-like) | 0674-06 | 494 | 4 | 495 | 4 | 753 | 753 | 231 | 2 | 235 | 2 | 2 |
| 0653-08 | 488 | 4 | 495 | 4 | 750 | 753 | 229 | 2 | 235 | 2 | 6 | |
| Beijing (classic) | 0419-04 | 494 | 4 | 495 | 4 | 746 | 753 | 228 | 2 | 235 | 2 | 6 |
| 0944-06 | 497 | 4 | 495 | 4 | 746 | 753 | 236 | 2 | 235 | 2 | 6 | |
| Control | BCG P2 | 573 | 5 | 570 | 5 | 840 | 828 | 410 | 5 | 406 | 5 | 3 |
| MT14323 | 421 | 3 | 420 | 3 | 672 | 678 | 232 | 2 | 235 | 2 | 2 | |
The chromosomal region containing ETR A in the putative PPE protein-coding RD Rv1917c gene is deleted in some PETRA lineage strains. PETRA lineage strains lacking locus ETR A (missing locus A [mla] [no amplicons made on PCR with the standard primer pair]) also lack an enlarged region amplified with primers (mla-1) flanking the standard ETR A region primers. Note that the ETR A repeat size for a copy is 75 bp. Locus QUB11b is also found in M. tuberculosis RD Rv1917c, upstream of the ETR A locus. The flanking mla-1 primers enlarge the ETR A region by 258 bp (170 bp upstream and 88 bp downstream according to H37Rv sequence data).
The PCR product of ETR A by agarose gel electrophoresis (AGE) is shown. Abbreviations: bp, base pairs; proto-bp, prototype (expected) base pairs; copy no., MIRU-VNTR copy number; NB, no band.
The PCR product of ETR A by capillary electrophoresis (CE) is shown. NB, no band.