Comparative genomics for mycobacterial peptidoglycan remodelling enzymes reveals extensive genetic multiplicity

Machowski, Edith Erika; Senzani, Sibusiso; Ealand, Christopher; Kana, Bavesh Davandra

doi:10.1186/1471-2180-14-75

BMC Microbiology

Table 1 Genetic complement for PG remodelling enzymes in 19 mycobacterial species

From: Comparative genomics for mycobacterial peptidoglycan remodelling enzymes reveals extensive genetic multiplicity

	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. bovisBCG 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. smegmatismc²155	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
ldt _Mt1	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
ldt _Mt2	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
ldt _Mt3	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
ldt _Mt4	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	–
ldt _Mt5	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.

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ISSN: 1471-2180

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