Table 1

Genetic complement for PG remodelling enzymes in 19 mycobacterial species
MTB complex Other mycobacterial pathogens Environmental mycobacterial species
M. tuberculosis H37Rv M. tuberculosis H37Ra M. tuberculosis CDC1551 M. africanum GM041182 M. bovis AF2122/97 M. bovis BCG Pasteur 1173P2 M. avium 104 M. avium subsp. paraTB K-10 M. intracellulare ATCC 13950 M. ulcerans AGY99 M. marinum M M. abscessus ATCC19977 M. smegmatis mc2155 M. vanbaalenii PYR–1 M. sp. MCS M. sp. KMS M. sp. JLS M. gilvum PYR–GCK M. leprae TN
Resuscitation promoting factors
rpfA Rv0867c MRA_0874 MT0890 MAF_08760 Mb0891c BCG_0919c MAV_0996 MAP0805c OCU_08710 MUL_0283 MMAR_4665 MAB_0869c MSMEG_5700 Mvan_5049 Mmcs_4479 Mkms_4566 Mjls_4862 Mflv_1703 ML2151
rpfB Rv1009 MRA_1018 MT1038 MAF_10190 Mb1036 BCG_1066 MAV_1147 MAP0974 OCU_10320 MUL_4651 MMAR_4479 MAB_1130 MSMEG_5439 Mvan_4801 Mmcs_4264 Mmcs_1712 Mkms_4350 Mkms_1758 Mjls_ 4643 Mjls_1689 Mflv_1932 ML0240
rpfC Rv1884c MRA_1895 MT1932 MAF_19060 Mb1916c BCG_1921c MAV_2818 MAP1607c OCU_26380 MUL_2975 MMAR_2772 MAB_4080 ML2030
rpfD Rv2389c MRA_2413 MT2458 MAF_24030 Mb2410c BCG_2403c
rpfE Rv2450c MRA_2476 MT2526 MAF_24670 Mb2477c BCG_2470c MAV_1722 MAP2273c OCU_18020 MUL_3723 MMAR_3776 MAB_1597 MSMEG_4643/MSMEG_4640 Mvan_3962/Mvan_3961 Mmcs_3564/Mmcs_3563 Mkms_3637/Mkms_3636 Mjls_3569/ Mjls_3568 Mflv_2619/Mflv_2620
Penicillin binding proteins
ponA1 Rv0050 MRA_0053 MT0056 MAF_00500 Mb0051 BCG_0081 MAV_0071 MAP0064 OCU_00670 MUL_0068 MMAR_0069 MAB_4901c MSMEG_6900 Mvan_6036 Mmcs_5372 Mkms_5461 Mjls_5748 Mflv_0871 ML2688c
ponA2 Rv3682 MRA_3717 MT3784 MAF_36900 Mb3707 BCG_3741 MAV_0446 MAP0392c OCU_03970 MUL_4257 MMAR_5171 MAB_0408c MSMEG_6201 MSMEG_4384 Mvan_5442 Mvan_1068 Mmcs_4825 Mmcs_1483 Mkms_4911 Mkms_1505 Mjls_5212 Mjls_1480 Mflv_1365 Mflv_5209 ML2308
pbpA Rv0016c MRA_0018 MT0019 MAF_00160 Mb0016c BCG_0046c MAV_0020 MAP0019c OCU_00180 MUL_0020 MMAR_0018 MAB_0035c MSMEG_0031 Mvan_0025 Mmcs_0017 Mkms_0025 Mjls_0017 Mflv_0810 ML0018
pbpB Rv2163c MRA_2178 MT2221 MAF_21760 Mb2187c BCG_2180c MAV_2330 MAP1903c OCU_22960 MUL_3508 MMAR_3200 MAB_2000 MSMEG_4233 Mvan_3529 Mmcs_3262 Mkms_3324 Mjls_3273 Mflv_2982 ML0908
PBP-lipo Rv2864c MRA_2889 MT2933 MAF_28690 Mb2889c BCG_2886c MAV_3723 MAP2936c OCU_35570 MUL_2089 MMAR_1840 MAB_3167c MSMEG_2584 MSMEG_6319 Mvan_2266 Mvan_4630 Mmcs_2047 Mmcs_4955 Mkms_2093 Mkms_5043 Mjls_2030 Mjls_5336 Mflv_4076 Mflv_2080 ML1577c
dacB1 Rv3330 MRA_3372 MT3433 MAF_33460 Mb3363 BCG_3400 MAV_4305 MAP3448 OCU_41630 MUL_1445 MMAR_1192 MAB_3681 MSMEG_1661 Mvan_1562 Mmcs_1216 Mkms_1233 Mjls_1243 Mflv_4869 ML0691
dacB2 Rv2911 MRA_2936 MT2979 MAF_29150 Mb2935 BCG_2932 MAV_3766 MAP2979 OCU_36070 MUL_2045 MMAR_1797 MAB_3234 MSMEG_2433/MSMEG_2432 Mvan_2184/Mvan_2183 Mmcs_1962/Mmcs_1961 Mkms_2008/Mkms_2007 Mjls_1942/Mjls_1941 Mflv_4179/Mflv_4180
Rv3627c Rv3627c MRA_3663 MT3729 MAF_36340 Mb3651c BCG_3685c MAV_0529 MAP0436 OCU_04440 MUL_4203 MMAR_5127 MAB_0519 MSMEG_6113 Mvan_5380 Mmcs_4778 Mkms_4864 Mjls_5164 Mflv_1409 ML0211
MSMEG_1900 MAB_2019 MSMEG_1900 Mvan_4520 Mmcs_0342 Mkms_0352 Mjls_0331 Mflv_2177
Endo-Peptidases
Rv0024 Rv0024 MRA_0027 MT0027 MAF_00240 Mb0024 BCG_0054 MAV_0042 MAP0036 OCU_00360 MUL_0042 MMAR_0043
ripA Rv1477 MRA_1487 MT1524 MAF_15000 Mb1513 BCG_1539 MAV_3301 MAP1203 OCU_31420 MUL_1486 MMAR_2284 MAB_2728c MSMEG_3145 Mvan_3656 Mvan_2747 Mmcs_1440 Mmcs_2451 Mkms_5716 Mkms_1458 Mkms_2496 Mjls_ 2488 Mjls_4564 Mjls_4520 Mflv_5292 Mflv_0895 Mflv_2839 Mflv_3663 ML1812
ripB Rv1478 MRA_1488 MT1525 MAF_15010 Mb1514 BCG_1540 MAV_3300 MAP1204 OCU_31410 MUL_1487 MMAR_2285 MAB_2727c MSMEG_3146 Mvan_2748 Mvan_3652 Mmcs_2452 Mmcs_1447 Mkms_2497 Mkms_1465 Mkms_5687 Mkms_5720 Mjls_ 2489 Mjls_ 4472 Mjls_ 4557 Mjls_ 4529 Mflv_5324 Mflv_5288 Mflv_0902 Mflv_2843 ML1811
ripD Rv1566c MRA_1578 MT1617 MAF_15930 Mb1593c BCG_1619c MAV_3208 MAP1272c OCU_30430 MUL_1557 MMAR_2381 (MAB_2474) (MSMEG_3477) (Mvan_2970) (Mmcs_2672) (Mkms_2717) (Mjls_2702) (Mflv_3253) ML1214
Rv2190c Rv2190c MRA_2205 MT2245 MAF_22010 Mb2213c BCG_2206c MAV_2304 MAP1928c OCU_22720 MUL_3545 MMAR_3234 MAB_1974 MSMEG_4256 Mvan_3552 Mvan_3713 Mmcs_3287 Mmcs_1435 Mkms_3349 Mkms_5661 Mkms_1453 Mjls_3298 Mjls_4528 Mjls_4570 Mflv_2959 Mflv_5385 Mflv_5350 Mflv_2808 Mflv_0888 ML0885
L,D-transpeptidases
ldtMt1 Rv0116c MRA_0123 MT0125 MAF_01170 Mb0120c BCG_0150c MAV_5194 MAP3520c OCU_50160 MUL_4806 MMAR_0316 MAB_3165c MSMEG_3528 Mvan_3019 Mmcs_2729 Mkms_2773 Mjls_2759 Mflv_3298 ML2664
ldtMt2 Rv2518c MRA_2545 MT2594 MAF_25330 Mb2547c BCG_2539c MAV_1661 MAP2322c OCU_17500 MUL_3804 MMAR_3872 MAB_1530 MSMEG_4745 Mvan_4102 Mvan_3651 Mvan_5854 Mmcs_1448 Mmcs_3641 Mkms_5721 Mkms_3714 Mkms_1466 Mjls_3646 Mjls_4532 Mjls_4556 Mflv_2542 Mflv_5287 Mflv_0904 ML0426
ldtMt3 Rv1433 MRA_1442 MT1477 MAF_14550 Mb1468 BCG_1494 MAV_4834 MAP3812c OCU_47330 MMAR_3552 MAB_4775 MSMEG_0674 Mjls_4515 Mflv_1397 ML0569
ldtMt4 Rv0192 MRA_0200 MT0202 MAF_01930 Mb0198 BCG_0229 MAV_4986 MAP3634 OCU_48990 MUL_1085 MMAR_0435 MAB_4537c MSMEG_0233 Mvan_3694 Mvan_0177 Mmcs_0151 Mkms_5680 Mkms_0160 Mjls_4535 Mjls_0141 Mflv_5330 Mflv_2824 Mflv_5369 Mflv_0479
ldtMt5 Rv0483 MRA_0490 MT0501 MAF_04870 Mb0493 BCG_0524 MAV_4666 MAP3976 OCU_45320 MUL_4553 MMAR_0809 MAB_4061c MSMEG_0929 Mvan_0824 Mmcs_0654 Mkms_0667 Mjls_0647 Mflv_0089 ML2446
Amidases
ami1 Rv3717 MRA_3754 MT3820 MAF_37260 Mb3744 BCG_3777 MAV_0385 MAP0318 OCU_03450 MUL_4308 MMAR_5233 MAB_0318c MSMEG_6281 Mvan_5529 Mmcs_4905 Mkms_4994 Mjls_5273 Mflv_1286 ML2331
ami2 Rv3915 MRA_3954 MT4034 MAF_39300 Mb3946 BCG_0021 MAV_5303 MAP4341 OCU_51370 MUL_5068 MMAR_5479 MAB_4942 MSMEG_6935 Mvan_6069 Mmcs_5404 Mkms_5493 Mjls_5780 Mflv_0837 ML2704
ami3 Rv3811 MRA_3851 MT3918 MAF_38260 Mb3841 BCG_3873 MAV_0206 MAP0209c OCU_02160 MUL_4995 MMAR_5375 MAB_0168c MSMEG_6406 Mvan_5652 Mmcs_5022 Mkms_5110 Mjls_5403 Mflv_1157
ami4 Rv3594 MRA_3633 MT3700 MAF_36070 Mb3625 BCG_3659 MAB_4807 MSMEG_5315 Mvan_3376 Mmcs_4180 Mkms_4246 Mjls_4402 Mflv_3152

The names of the various organisms analysed are shown in the columns and gene complement is given in the corresponding rows. Mycobacteria are grouped as M. tuberculosis Cluster (MTBC), other pathogens, environmental species and M. leprae. Genes are sorted by functional groups in rows. The listing of a gene is based on its presence by protein BLAST analysis, either at curated sites or directly at NCBI. For all genes the protein sequence, in FASTA format, was obtained and utilised for phylogeny. Annotations for M. africanum (MAF_) and M. intracellulare (OCU_) were obtained directly from NCBI. BLAST analysis was performed against individual strains at NCBI using M. tuberculosis H37Rv homologues as the query sequence. The cut off was taken at a coverage of >90% and an identity of >40%. MSMEG_1900 was identified at SmegmaList. In the case of ripD, parentheses indicate the 63C-terminal amino acid truncation. Further in-depth information, and confirmation of gene annotation, was obtained by assessment of phylogeny based on protein sequences, Additional file 1 Figure S1-S7. Font differences in the M. tuberculosis H37Rv column indicate genes that have been annotated as essential by two different TraSH analyses – indicated in bold (Sassetti et al. [20]) and/or italicised (Griffin et al. [21]) are those genes identified as essential or required for optimal growth.

Machowski et al.

Machowski et al. BMC Microbiology 2014 14:75   doi:10.1186/1471-2180-14-75

Open Data