Table 8. Open in new tab Influence of...

					Comparisons
Uptake systems systems
Rmet_3052	corA₁	55.0	125	0.44	0.55	*0.02*	1.05	1.04	1.04	0.83	1.77	50.0	1.03	0.92
Rmet_0036	corA₂	66.3	373	0.18	0.81	*0.37*	0.94	0.94	0.92	0.00	0.96	1.46	0.97	0.87
Rmet_3287	corA₃	114	853	0.13	0.92	*0.48*	0.96	1.05	1.20	1.11	1.18	1.39	0.99	0.30
Rmet_2621	zupT	151	61.0	2.48	0.72	0.86	1.63	1.17	1.02	1.19	1.11	1.04	0.78	0.86
Rmet_1533	hoxN	183	5.67	32.3	1.36	0.59	0.98	0.94	0.82	0.82	0.57	1.50	0.71	1.00
Rmet_1973	pitA	280	99.3	2.82	0.34	1.66	1.05	1.01	1.28	0.82	2.44	0.87	1.09	1.26
Rmet_5396	mgtA	12.3	1.67	7.40	1.38	0.60	1.05	*0.20*	0.95	0.00	0.69	2.67	0.97	2.00
Rmet_2211	mgtB	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_0549	zntB	12.7	2.00	6.33	0.58	1.67	0.97	0.83	1.00	1.00	1.05	0.30	0.95	1.40
Rmet_5890	feoB	110	14.3	7.70	1.43	0.81	1.21	0.91	1.04	0.93	0.95	0.77	0.91	0.00
Rmet_5891	feoA	132	14.3	9.19	1.33	0.81	1.24	0.91	0.92	0.93	1.06	0.77	0.84	1.18
Efflux systems
Rmet_4594	zntA	41.7	77.3	0.54	73.2	5.54	*0.40*	1.17	1.23	0.55	*0.25*	*0.34*	1.39	0.79
Rmet_2303	cadA	10.3	50.0	0.21	62.1	1.89	*0.48*	1.01	1.19	0.81	0.08	0.75	1.27	0.87
Rmet_5947	pbrA	8.0	1.67	4.80	30.0	3.00	0.75	0.80
Rmet_5970	czcP	7.7	0.67	11.5	9.74	840	1.13
Rmet_3524	cupA	15.0	47.3	0.32	126	10.0	1.07	0.82	1.00	0.77	*0.42*	2.42	0.94	0.82
Rmet_6119	copF	41.3	10.0	4.13	13.4	8.97	1.00	2.00
Rmet_2211	ctpF	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_2046	rdxI	250	5.67	44.2	*0.41*	1.29	1.00	1.06	1.08	0.59	1.10	0.86	1.08	0.72
Rmet_5979	czcD	13.7	1.33	10.2	27.9	119	*0.46*	1.25
Rmet_0198	dmeF	44.3	1734	0.26	1.32	0.77	0.89	1.02	1.00	0.93	1.05	1.02	0.92	0.93
Rmet_3406	fieF	108	30.7	3.52	2.43	5.37	1.23	0.99	0.98	0.78	0.53	*0.45*	0.94	0.96
Rmet_6211	cnrT	47.3	21.3	2.22	4.86	0.94	1.04	0.78
Rmet_0391	atmA	58.0	42.3	1.37	3.68	*0.47*	1.09	0.90	1.01	0.59	*0.40*	1.68	0.88	1.11

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_ast14

Q_sense

Q_ast

Q_sense

QS_AS

Uptake systems systems

Rmet_3052

corA₁

55.0

125

0.44

0.55

0.02

1.05

1.04

1.04

0.83

1.77

50.0

1.03

0.92

Rmet_0036

corA₂

66.3

373

0.18

0.81

0.37

0.94

0.92

0.00

0.96

1.46

0.97

0.87

Rmet_3287

corA₃

114

853

0.13

0.92

0.48

0.96

1.05

1.20

1.11

1.18

1.39

0.99

0.30

Rmet_2621

zupT

151

61.0

2.48

0.72

0.86

1.63

1.17

1.02

1.19

1.11

1.04

0.78

0.86

Rmet_1533

hoxN

183

5.67

32.3

1.36

0.59

0.98

0.94

0.82

0.57

1.50

0.71

1.00

Rmet_1973

pitA

280

99.3

2.82

0.34

1.66

1.05

1.01

1.28

0.82

2.44

0.87

1.09

1.26

Rmet_5396

mgtA

12.3

1.67

7.40

1.38

0.60

1.05

0.20

0.95

0.00

0.69

2.67

0.97

2.00

Rmet_2211

mgtB

19.7

2.00

9.83

1.05

14.7

1.12

2.17

0.98

1.67

0.98

1.15

0.97

1.23

Rmet_0549

zntB

12.7

2.00

6.33

0.58

1.67

0.97

0.83

1.00

1.05

0.30

0.95

1.40

Rmet_5890

feoB

110

14.3

7.70

1.43

0.81

1.21

0.91

1.04

0.93

0.95

0.77

0.91

0.00

Rmet_5891

feoA

132

14.3

9.19

1.33

0.81

1.24

0.91

0.92

0.93

1.06

0.77

0.84

1.18

Efflux systems

Rmet_4594

zntA

41.7

77.3

0.54

73.2

5.54

0.40

1.17

1.23

0.55

0.25

0.34

1.39

0.79

Rmet_2303

cadA

10.3

50.0

0.21

62.1

1.89

0.48

1.01

1.19

0.81

0.08

0.75

1.27

0.87

Rmet_5947

pbrA

8.0

1.67

4.80

30.0

3.00

0.75

0.80

Rmet_5970

czcP

7.7

0.67

11.5

9.74

840

1.13

Rmet_3524

cupA

15.0

47.3

0.32

126

10.0

1.07

0.82

1.00

0.77

0.42

2.42

0.94

0.82

Rmet_6119

copF

41.3

10.0

4.13

13.4

8.97

1.00

2.00

Rmet_2211

ctpF

19.7

2.00

9.83

1.05

14.7

1.12

2.17

0.98

1.67

0.98

1.15

0.97

1.23

Rmet_2046

rdxI

250

5.67

44.2

0.41

1.29

1.00

1.06

1.08

0.59

1.10

0.86

1.08

0.72

Rmet_5979

czcD

13.7

1.33

10.2

27.9

119

0.46

1.25

Rmet_0198

dmeF

44.3

1734

0.26

1.32

0.77

0.89

1.02

1.00

0.93

1.05

1.02

0.92

0.93

Rmet_3406

fieF

108

30.7

3.52

2.43

5.37

1.23

0.99

0.98

0.78

0.53

0.45

0.94

0.96

Rmet_6211

cnrT

47.3

21.3

2.22

4.86

0.94

1.04

0.78

Rmet_0391

atmA

58.0

42.3

1.37

3.68

0.47

1.09

0.90

1.01

0.59

0.40

1.68

0.88

1.11

					Comparisons
Uptake systems systems
Rmet_3052	corA₁	55.0	125	0.44	0.55	*0.02*	1.05	1.04	1.04	0.83	1.77	50.0	1.03	0.92
Rmet_0036	corA₂	66.3	373	0.18	0.81	*0.37*	0.94	0.94	0.92	0.00	0.96	1.46	0.97	0.87
Rmet_3287	corA₃	114	853	0.13	0.92	*0.48*	0.96	1.05	1.20	1.11	1.18	1.39	0.99	0.30
Rmet_2621	zupT	151	61.0	2.48	0.72	0.86	1.63	1.17	1.02	1.19	1.11	1.04	0.78	0.86
Rmet_1533	hoxN	183	5.67	32.3	1.36	0.59	0.98	0.94	0.82	0.82	0.57	1.50	0.71	1.00
Rmet_1973	pitA	280	99.3	2.82	0.34	1.66	1.05	1.01	1.28	0.82	2.44	0.87	1.09	1.26
Rmet_5396	mgtA	12.3	1.67	7.40	1.38	0.60	1.05	*0.20*	0.95	0.00	0.69	2.67	0.97	2.00
Rmet_2211	mgtB	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_0549	zntB	12.7	2.00	6.33	0.58	1.67	0.97	0.83	1.00	1.00	1.05	0.30	0.95	1.40
Rmet_5890	feoB	110	14.3	7.70	1.43	0.81	1.21	0.91	1.04	0.93	0.95	0.77	0.91	0.00
Rmet_5891	feoA	132	14.3	9.19	1.33	0.81	1.24	0.91	0.92	0.93	1.06	0.77	0.84	1.18
Efflux systems
Rmet_4594	zntA	41.7	77.3	0.54	73.2	5.54	*0.40*	1.17	1.23	0.55	*0.25*	*0.34*	1.39	0.79
Rmet_2303	cadA	10.3	50.0	0.21	62.1	1.89	*0.48*	1.01	1.19	0.81	0.08	0.75	1.27	0.87
Rmet_5947	pbrA	8.0	1.67	4.80	30.0	3.00	0.75	0.80
Rmet_5970	czcP	7.7	0.67	11.5	9.74	840	1.13
Rmet_3524	cupA	15.0	47.3	0.32	126	10.0	1.07	0.82	1.00	0.77	*0.42*	2.42	0.94	0.82
Rmet_6119	copF	41.3	10.0	4.13	13.4	8.97	1.00	2.00
Rmet_2211	ctpF	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_2046	rdxI	250	5.67	44.2	*0.41*	1.29	1.00	1.06	1.08	0.59	1.10	0.86	1.08	0.72
Rmet_5979	czcD	13.7	1.33	10.2	27.9	119	*0.46*	1.25
Rmet_0198	dmeF	44.3	1734	0.26	1.32	0.77	0.89	1.02	1.00	0.93	1.05	1.02	0.92	0.93
Rmet_3406	fieF	108	30.7	3.52	2.43	5.37	1.23	0.99	0.98	0.78	0.53	*0.45*	0.94	0.96
Rmet_6211	cnrT	47.3	21.3	2.22	4.86	0.94	1.04	0.78
Rmet_0391	atmA	58.0	42.3	1.37	3.68	*0.47*	1.09	0.90	1.01	0.59	*0.40*	1.68	0.88	1.11

Table 8.

Open in new tab

Influence of antisense activities on the expression and regulation of the genes for main metal ion uptake and efflux systems 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_ast14	Q_sense	Q_ast	Q_sense	QS_AS
Uptake systems systems
Rmet_3052	corA₁	55.0	125	0.44	0.55	*0.02*	1.05	1.04	1.04	0.83	1.77	50.0	1.03	0.92
Rmet_0036	corA₂	66.3	373	0.18	0.81	*0.37*	0.94	0.94	0.92	0.00	0.96	1.46	0.97	0.87
Rmet_3287	corA₃	114	853	0.13	0.92	*0.48*	0.96	1.05	1.20	1.11	1.18	1.39	0.99	0.30
Rmet_2621	zupT	151	61.0	2.48	0.72	0.86	1.63	1.17	1.02	1.19	1.11	1.04	0.78	0.86
Rmet_1533	hoxN	183	5.67	32.3	1.36	0.59	0.98	0.94	0.82	0.82	0.57	1.50	0.71	1.00
Rmet_1973	pitA	280	99.3	2.82	0.34	1.66	1.05	1.01	1.28	0.82	2.44	0.87	1.09	1.26
Rmet_5396	mgtA	12.3	1.67	7.40	1.38	0.60	1.05	*0.20*	0.95	0.00	0.69	2.67	0.97	2.00
Rmet_2211	mgtB	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_0549	zntB	12.7	2.00	6.33	0.58	1.67	0.97	0.83	1.00	1.00	1.05	0.30	0.95	1.40
Rmet_5890	feoB	110	14.3	7.70	1.43	0.81	1.21	0.91	1.04	0.93	0.95	0.77	0.91	0.00
Rmet_5891	feoA	132	14.3	9.19	1.33	0.81	1.24	0.91	0.92	0.93	1.06	0.77	0.84	1.18
Efflux systems
Rmet_4594	zntA	41.7	77.3	0.54	73.2	5.54	*0.40*	1.17	1.23	0.55	*0.25*	*0.34*	1.39	0.79
Rmet_2303	cadA	10.3	50.0	0.21	62.1	1.89	*0.48*	1.01	1.19	0.81	0.08	0.75	1.27	0.87
Rmet_5947	pbrA	8.0	1.67	4.80	30.0	3.00	0.75	0.80
Rmet_5970	czcP	7.7	0.67	11.5	9.74	840	1.13
Rmet_3524	cupA	15.0	47.3	0.32	126	10.0	1.07	0.82	1.00	0.77	*0.42*	2.42	0.94	0.82
Rmet_6119	copF	41.3	10.0	4.13	13.4	8.97	1.00	2.00
Rmet_2211	ctpF	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_2046	rdxI	250	5.67	44.2	*0.41*	1.29	1.00	1.06	1.08	0.59	1.10	0.86	1.08	0.72
Rmet_5979	czcD	13.7	1.33	10.2	27.9	119	*0.46*	1.25
Rmet_0198	dmeF	44.3	1734	0.26	1.32	0.77	0.89	1.02	1.00	0.93	1.05	1.02	0.92	0.93
Rmet_3406	fieF	108	30.7	3.52	2.43	5.37	1.23	0.99	0.98	0.78	0.53	*0.45*	0.94	0.96
Rmet_6211	cnrT	47.3	21.3	2.22	4.86	0.94	1.04	0.78
Rmet_0391	atmA	58.0	42.3	1.37	3.68	*0.47*	1.09	0.90	1.01	0.59	*0.40*	1.68	0.88	1.11

					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_ast14	Q_sense	Q_ast	Q_sense	QS_AS
Uptake systems systems
Rmet_3052	corA₁	55.0	125	0.44	0.55	*0.02*	1.05	1.04	1.04	0.83	1.77	50.0	1.03	0.92
Rmet_0036	corA₂	66.3	373	0.18	0.81	*0.37*	0.94	0.94	0.92	0.00	0.96	1.46	0.97	0.87
Rmet_3287	corA₃	114	853	0.13	0.92	*0.48*	0.96	1.05	1.20	1.11	1.18	1.39	0.99	0.30
Rmet_2621	zupT	151	61.0	2.48	0.72	0.86	1.63	1.17	1.02	1.19	1.11	1.04	0.78	0.86
Rmet_1533	hoxN	183	5.67	32.3	1.36	0.59	0.98	0.94	0.82	0.82	0.57	1.50	0.71	1.00
Rmet_1973	pitA	280	99.3	2.82	0.34	1.66	1.05	1.01	1.28	0.82	2.44	0.87	1.09	1.26
Rmet_5396	mgtA	12.3	1.67	7.40	1.38	0.60	1.05	*0.20*	0.95	0.00	0.69	2.67	0.97	2.00
Rmet_2211	mgtB	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_0549	zntB	12.7	2.00	6.33	0.58	1.67	0.97	0.83	1.00	1.00	1.05	0.30	0.95	1.40
Rmet_5890	feoB	110	14.3	7.70	1.43	0.81	1.21	0.91	1.04	0.93	0.95	0.77	0.91	0.00
Rmet_5891	feoA	132	14.3	9.19	1.33	0.81	1.24	0.91	0.92	0.93	1.06	0.77	0.84	1.18
Efflux systems
Rmet_4594	zntA	41.7	77.3	0.54	73.2	5.54	*0.40*	1.17	1.23	0.55	*0.25*	*0.34*	1.39	0.79
Rmet_2303	cadA	10.3	50.0	0.21	62.1	1.89	*0.48*	1.01	1.19	0.81	0.08	0.75	1.27	0.87
Rmet_5947	pbrA	8.0	1.67	4.80	30.0	3.00	0.75	0.80
Rmet_5970	czcP	7.7	0.67	11.5	9.74	840	1.13
Rmet_3524	cupA	15.0	47.3	0.32	126	10.0	1.07	0.82	1.00	0.77	*0.42*	2.42	0.94	0.82
Rmet_6119	copF	41.3	10.0	4.13	13.4	8.97	1.00	2.00
Rmet_2211	ctpF	19.7	2.00	9.83	1.05	14.7	1.12	2.17	0.98	1.67	0.98	1.15	0.97	1.23
Rmet_2046	rdxI	250	5.67	44.2	*0.41*	1.29	1.00	1.06	1.08	0.59	1.10	0.86	1.08	0.72
Rmet_5979	czcD	13.7	1.33	10.2	27.9	119	*0.46*	1.25
Rmet_0198	dmeF	44.3	1734	0.26	1.32	0.77	0.89	1.02	1.00	0.93	1.05	1.02	0.92	0.93
Rmet_3406	fieF	108	30.7	3.52	2.43	5.37	1.23	0.99	0.98	0.78	0.53	*0.45*	0.94	0.96
Rmet_6211	cnrT	47.3	21.3	2.22	4.86	0.94	1.04	0.78
Rmet_0391	atmA	58.0	42.3	1.37	3.68	*0.47*	1.09	0.90	1.01	0.59	*0.40*	1.68	0.88	1.11

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 (<10 in italics) 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 M2, “Transport”. Empty cells indicate missing sense or antisense transcripts, for instance for plasmid-encoded factors in the plasmid-free strain AE104.

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