Table 7.

Influence of antisense activities on the expression and regulation of the genes needed for transcription in C. metallidurans^a.

					Comparisons
					CH34_M_0		CH34_E_0		0_AE104_CH34		M_AE104_CH34		E_AE104_CH34
locus tag	gene	MeanS	MeanAST	S/AS	Q_sense	Q_ast	Q_sense	Q_ast	Q_sense	Q_ast	Q_sense	Q_ast	Q_sense	Q_ast	Description
Rmet_3291	rpoA	783	58.0	13.5	0.43	0.41	1.14	0.95	1.33	0.82	1.84	1.94	1.09	0.85	Q1LI63 DNA-directed RNA polymerase subunit alpha
Rmet_3334	rpoB	401	39.7	10.1	0.63	1.84	1.13	0.97	1.34	0.78	1.30	0.56	1.11	0.94	Q1LI20 DNA-directed RNA polymerase subunit beta
Rmet_3333	rpoC	379	39.7	9.56	0.79	1.84	1.09	0.97	1.28	0.78	1.07	0.56	1.10	0.94	Q1LI21 DNA-directed RNA polymerase subunit beta'
Rmet_0857	rpoZ	2033	126	16.2	1.38	1.21	0.99	1.07	0.90	0.90	0.72	0.62	0.95	0.87	Subunit Omega
Rmet_2032	nusA	562	8.00	70.3	0.50	0.88	0.96	0.83	1.15	0.75	1.91	0.90	1.14	0.70	Q1LLR5 NusA antitermination factor
Rmet_2695	nusB	144	475	0.30	0.51	0.45	1.09	1.01	1.30	0.81	1.65	1.71	1.05	0.91	Q1LJV8 N utilization substance protein B homolog
Rmet_3339	nusG	1280	39.7	32.3	0.45	1.84	1.04	0.97	1.22	0.78	2.32	0.56	1.13	0.94	Q1LI15 Transcription antitermination protein nusG
Rmet_2192	greA	485	36.3	13.4	0.34	5.09	1.00	1.52	1.14	0.76	2.59	0.72	1.12	0.64	Q1LLA5 Transcription elongation factor
Rmet_0859	greB	225	231	0.97	0.54	1.04	1.02	0.98	1.00	1.03	1.41	0.97	0.96	1.10	Q1LQ31 Transcription elongation factor
Rmet_2135	rho	509	230	2.21	0.63	0.87	1.06	1.18	1.08	0.99	1.67	1.25	1.03	0.96	Q1LLG2 Transcription termination factor Rho
Rmet_2606	rpoD1	426	19.3	22.1	0.65	5.00	1.03	0.90	1.18	0.83	1.79	0.24	1.16	0.81	Q1LK43 RNA polymerase sigma factor
Rmet_4661	rpoD2	12.0	6.00	2.00	1.14	1.89	0.86	0.83	0.78	1.33	1.02	1.74	1.10	1.07	Q1LEA3 RNA polymerase sigma factor
Rmet_2115	rpoS	392	136	2.89	1.28	1.55	1.05	1.18	1.11	0.06	0.89	0.83	1.03	0.90	Q1LLI2 RNA polymerase sigma factor
Rmet_0272	rpoH	381	345	1.11	2.48	0.54	1.05	1.03	0.96	0.98	0.83	1.54	0.85	0.87	Q1LRR8 RNA polymerase sigma factor
Rmet_3702	fliA	43.0			0.47		1.05		1.02		0.90	0.76	0.81	1.21	Q1LH02 RNA polymerase sigma factor
Rmet_0303	rpoN	352	81.3	4.33	2.16	0.13	1.05	1.16	0.91	1.17	0.73	7.00	0.90	0.06	Q1LRN7 Sigma-54 (RpoN)
Rmet_2425	rpoE	806	10.3	78.0	1.54	1.16	0.95	0.97	0.95	0.71	0.88	0.78	1.10	0.77	Q1LKM4 RNA polymerase sigma factor
Rmet_1120	rpoI	135	2.00	67.7	0.81	1.67	1.10	0.50	0.83	0.50	1.19	0.60	0.91	2.33	Q1LPC0 Sigma-24 (FecI-like)
Rmet_4499	rpoJ	10.7	1.00	10.7	1.25	3.67	1.31	1.33	1.06	1.33	1.28	0.45	1.07	1.25	Q1LER2 Sigma-24 (FecI-like)
Rmet_4001	rpoK	53.0	2.67	19.9	0.66	0.88	1.07	1.00	0.75	0.88	1.31	1.00	1.06	0.88	Q1LG57 Sigma-24 (FecI-like)
Rmet_3280	rpoL	240	4.00	60.1	1.24	0.92	1.16	0.83	1.23	0.58	0.86	1.00	0.90	1.00	Q1LI74 Sigma-24 (FecI-like)
Rmet_5400	rpoM	9.3	2.33	4.00	1.07	0.29	0.93	0.71	0.93	0.14	1.00	3.00	1.15	0.60	Q1LC67 Sigma-24 (FecI-like)
Rmet_0597	rpoO	28.3	1.33	21.3	0.69	0.75	0.92	0.75	0.82	0.25	1.07	0.00	0.81	0.33	Q1LQU3 Sigma-24 (FecI-like)
Rmet_1648	rpoP	17.0	1.67	10.2	0.94	1.00	0.54		0.90	0.40	1.15	1.00	1.02	2.25	Q1LMU5 Sigma-24 (FecI-like)
Rmet_4686	rpoQ	69.3	4.33	16.0	2.19	3.23	1.15	1.31	0.95	1.31	0.64	1.93	0.66	1.06	Q1LE78 Sigma-24 (FecI-like)
Rmet_0910	rpoR	378	664	0.57	0.64	0.53	0.91	0.97	0.92	0.98	1.26	1.03	0.99	0.99	Q1LPY0 Sigma-24 (FecI-like)
Rmet_6207	cnrH	61.0	3.00	20.3	7.64	361	1.13	5.44							P37978 RNA polymerase sigma factor cnrH

The locus tag, gene name, NPKM values of the sense and antisense transcripts is shown followed by the ration S/AS of both values. Bold-faced are here transcripts with NPKM >100 or S/AS ratios >10, which indicates a low probability of an antisense influence. The comparisons are metal-challenged to non-challenged CH34 cells, EDTA-treated to non-treated CH34 cells, unchallenged, metal- and EDTA- challenged AE104 to CH34 cells. The ratios Q of the sense and antisense NPKM values is shown. Bold if Q >2, italics and bold if Q <0.5. Deviations are in the Supplementary Material. Empty cells indicate missing sense or antisense transcripts, for instance for plasmid-encoded factors in the plasmid-free strain AE104.