High-resolution mapping of plasmid transcriptomes in different host bacteria

Miyakoshi, Masatoshi; Nishida, Hiromi; Shintani, Masaki; Yamane, Hisakazu; Nojiri, Hideaki

doi:10.1186/1471-2164-10-12

BMC Genomics

Table 1 Transcription units of pCAR1 identified by tiling array analysis at 9-bp resolution.

From: High-resolution mapping of plasmid transcriptomes in different host bacteria

Unit	Direction	Transcription start site	Transcription termination site	Length	Genes or ORFs	KT_SUC sense	KT_SUC antisense	KT_CAR sense	KT_CAR antisense	CA_SUC sense	CA_SUC antisense	CA_CAR sense	CA_CAR antisense
#1	-	4440	3210	1230	tnpA3	2164	428	1879	378	1386	236	2339	386
#2	-	7530	4440	3090	antA-antC	86	86	4410	1399	136	78	4883	1810
#3	-	8830	7440	1390	tnpA2	1153	161	1266	201	929	124	851	100
#4	+	10580	12310	1730	antR	54	45	1271	277	52	25	2902	430
#5	-	14440	13310	1130	ORF21	310	110	486	175	513	187	1325	491
#6	+	18860	19730	870	ORF16	678	124	395	141	465	84	405	72
#7	+	25320	26350	1030	tnpA1	1450	182	1375	219	1045	115	1001	104
#8A	+	26620	40170	13550	ORF9-carE	589	151	4068	646	1444	319	5481	946
#8B	+	27760	40170	12410	carAa-carE	645	159	3919	632	1552	358	5488	929
#9	-	40980	39560	1420	ORF37	576	142	658	252	936	182	875	186
#10	+	41500	42530	1030	tnpA4	1420	193	1320	217	1103	119	943	109
#11	+	43880	44630	750	ORF40	577	372	623	335	987	351	706	211
#12	-	46080	44190	1890	ORF42-41	898	300	903	460	653	234	637	173
#13	+	46110	48370	2260	tnpRaAa	296	183	580	257	168	82	129	76
#14	-	53780	50550	3230	tnpS- ORF47	839	212	780	277	494	109	409	72
#15	+	53890	55400	1510	tnpT	261	94	458	145	143	56	137	46
#16	+	56180	58400	2220	ORF53-54	719	216	582	222	1073	255	789	150
#17	+	60210	64660	4450	klaA- ORF59	356	120	269	105	353	130	368	119
#18	-	68940	64440	4500	ORF61-ORF60	217	101	214	93	246	128	267	101
#19	-	70120	69120	1000	repA	347	67	235	65	362	82	372	85
#20A	+	70060	75580	5520	parW- ORF67a	2441	364	1316	175	1372	255	1257	202
#20B	+	71770	75580	3810	parA- ORF67a	3199	506	1713	231	1924	319	1562	221
#21	+	77490	80400	2910	pmr- ORF72	1163	269	769	184	752	198	728	181
#22	-	81820	79480	2340	ORF74-73	318	174	271	183	388	169	427	150
#23	-	84010	82170	1840	ORF77-75	401	88	301	76	294	78	411	87
#24	+	85720	85870	150	ncRNA1	1301	543	1168	470	403	150	1283	114
#25	-	86510	84550	1960	ORF81-79	249	61	291	72	196	48	262	60
#26	-	90880	87680	3200	ORF89-85	880	158	406	93	1051	211	620	128
#27	-	92880	91500	1380	ORF91	283	93	123	94	207	75	146	80
#28	+	93360	94230	870	ORF92	569	100	357	64	366	86	479	78
#29	-	95580	94380	1200	ORF93	541	187	404	149	482	152	559	169
#30	+	97170	98100	930	ORF95a	848	146	627	121	607	110	587	107
#31	+	102560	110380	7820	ORF100-109	4564	554	1588	169	667	80	443	59
#32	-	117040	113160	3880	ORF115-111	264	76	129	58	302	93	165	70
#33	+	117170	119180	2010	ssb-recT	719	103	249	33	208	34	114	19
#34	-	119470	119330	140	ncRNA2	806	725	656	545	242	254	237	168
#35	+	121840	121950	110	ncRNA3	1847	573	1562	472	581	125	694	129
#36	+	123060	124110	1050	ORF120	458	60	598	62	189	39	400	47
#37	+	127040	140790	13750	traG- ORF131	125	46	73	44	191	70	150	63
#38	+	141370	152460	11090	ORF134-143	252	150	204	188	235	120	187	118
#39	+	153440	155620	2180	ORF145-146	4464	645	2126	311	897	149	801	115
#40	+	155840	161570	5730	traF-trhG	181	134	135	212	180	103	120	107
#41	-	165130	161590	3540	ORF154-150	193	60	180	102	217	63	222	47
#42	+	168730	176860	8130	ORF159-167	1295	263	1296	272	1082	214	1148	181
#43	-	180180	179390	790	tnpRb	283	68	439	113	144	28	223	30
#44	+	180340	185550	5210	ORF170-175	717	165	899	218	492	106	765	153
#45	+	185870	189340	3470	tnpAcC	310	307	1004	536	76	93	853	290
#46	+	190420	192860	2440	ORF179-181	746	489	640	349	664	379	608	308
#47	+	193300	195590	2290	ORF182-184	1451	227	1167	208	1942	330	1537	207

The transcription units of pCAR1 and their median signal intensities on both the sense and antisense strands are indicated; KT_SUC, KT2440(pCAR1) grown on succinate; KT_CAR, KT2440(pCAR1) grown on carbazole; CA_SUC, CA10 grown on succinate; CA_CAR, CA10 grown on carbazole. The positions of the transcription start and stop sites correspond to the pCAR1 nucleotide sequence [GenBank:AB088420].

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ISSN: 1471-2164

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