High-throughput comparison of gene fitness among related bacteria

Canals, Rocio; Xia, Xiao-Qin; Fronick, Catrina; Clifton, Sandra W; Ahmer, Brian MM; Andrews-Polymenis, Helene L; Porwollik, Steffen; McClelland, Michael

doi:10.1186/1471-2164-13-212

BMC Genomics

Table 3 Genes displaying prominent differences in selection between Typhimurium and Typhi*

From: High-throughput comparison of gene fitness among related bacteria

S. Typhimurium 14028 gene symbol	Gene name	Gene description	Best hit in S. Typhimurium strain LT2	Best hit in S. Typhi Ty2^a	Best hit in ECO^a	STM1 transposons	STM1 reads	STY1 transposons	STY1 reads	STY2 transposons^b	STY2 reads^b	STY2 transposons^c	STY2 reads^c
						Percentile rank
A. Examples of genes with stronger selection in STM1 than in STY1 and STY2
STM14_0199.RJ	yacC		STM0167	t0172	b0122	12	13	57	70	53	51	59	51
STM14_1028.R	potF	Putrescine ABC transporter putrescine-binding protein	STM0877	t2019	b0854	14	15	47	63	35	24	38	32
STM14_1092		Hypothetical protein		t1967		13	10	61	59	35	42	75	66
STM14_1127	ycbL	Putative metallo-beta- lactamase	STM0997	t1937	b0927	13	13	30	40	27	34	23	36
STM14_1141	xisW	Excisionase	STM1006	t1928		11	9	72	62	53	30	43	24
STM14_1152	dnaC	Putative replication protein	STM1015	t1917		16	16	27	36	34	31	41	32
STM14_1548	yeaM	Putative regulatory protein	STM1279	t1159	b1790	14	17	50	59	36	25	44	38
STM14_1599	celG	Hypothetical protein	STM1317	t1196	b1733	15	17	67	75	54	46	50	48
STM14_1682	orf70	Hypothetical protein	STM1388	t1256	b1675	12	11	32	71	34	27	37	29
STM14_1877 ^d		Putative coiled-coil protein	STM1554	t1468		15	16	39	37	79	81	78	81
STM14_1977 ^d		Putative periplasmic binding protein	STM1633	t1536		13	16	34	27	86	85	86	83
STM14_1978 ^d		Putative ABC transporter permease component	STM1634	t1537		6	7	17	44	87	91	85	90
STM14_2116	hns	Global DNA-binding transcriptional dual regulator H-NS	STM1751	t1662	b1237	5	3	32	29	91	89	35	91
STM14_2119	hnr	Response regulator of RpoS	STM1753	t1664	b1235	1	1	63	58	69	59	48	31
STM14_2120	ychK	Hypothetical protein	STM1754	t1665	b1234	11	11	64	81	64	61	62	46
STM14_2140	chaB	Cation transport regulator	STM1770	t1679	b1217	12	11	30	29	63	60	73	49
STM14_2176	ldcA	L,D-carboxypeptidase A	STM1800	t1077	b1192	14	15	43	37	28	28	39	39
STM14_2186 ^d	gsnB	Putative cytoplasmic protein	STM1809	t1068		18	14	39	30	43	58	59	70
STM14_2278		Hypothetical protein	STM1873	t1004	b1839	14	13	37	57	48	28	54	38
STM14_2685		Putative 1,2-dioxygenase	STM2178	t0677		15	18	32	33	31	29	24	32
STM14_2708.RJ		Putative DNA-binding protein	STM2195	t0660		17	15	51	44	65	36	62	49
STM14_2745		Bicyclomycin/multidrug efflux system		t0634		16	14	65	47	66	43	73	68
STM14_3050	purC	Phosphoribosylaminoimidazole- succinocarboxamide synthase	STM2487	t0372	b2476	11	11	28	32	47	34	34	30
STM14_4596 ^d		Pseudogene	STM3806	t0121		14	12	78	49	53	55	36	51
STM14_4883	cpxP	Periplasmic repressor	STM4060	t3559	b3913	16	16	27	46	38	41	43	34
STM14_5142 ^d		Putative cytoplasmic protein	STM4276	t4182		15	13	46	28	16	49	19	47
STM14_0109	ksgA	Dimethyladenosine transferase	STM0090	t0093	b0051	37	28	5	5	19	13	5	5
STM14_2281	holE	DNA polymerase III subunit theta	STM1876	t1001	b1842	63	70	11	11	9	8	25	15
STM14_2498		Hypothetical protein	STM2011.1n	t0860		51	43	13	12	8	10	14	17
STM14_2665 ^e		Hypothetical protein	STM2161	t0694	b2128	37	53	14	13	8	7	14	11
STM14_3017	eutA	Reactivating factor for ethanolamine ammonia lyase	STM2459	t0399	b2451	26	29	16	16	10	11	16	16
STM14_3267 ^e		Hypothetical protein	STM2666	t2621	b2598	81	84	17	14	9	7	19	13
STM14_4041 ^e	degS	Serine endoprotease	STM3349	t3265	b3235	50	34	14	14	6	7	4	4
STM14_4465	yibP	Hypothetical protein	STM3705	t3814	b3613	63	65	19	18	11	11	10	11
STM14_4747	yifL	Putative outer membrane lipoprotein	STM3946	t3351	b4558	77	65	12	12	22	17	18	16
STM14_5345	treC	Trehalose-6-phosphate hydrolase	STM4453	t4488	b4239	50	49	13	13	10	8	5	9

* Details for all genes can be found in Additional file5: Table S2. See Table2 for notes a, b, and c. Ranks above the 20^th percentile are shown in bold.
^d Knockout mutant has been created in STM[4].
^e Considered essential in STY2[3].

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ISSN: 1471-2164

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