Table 6.
Influence of antisense activities on the expression and regulation of copper resistance genes in C. metalliduransa.
| 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 |
| cup, copF | |||||||||||||||
| Rmet_3523 | cupR | 62.3 | 8.00 | 7.79 | 35.4 | 59.2 | 1.07 | 1.17 | 0.97 | 1.17 | 0.39 | 0.02 | 0.72 | 0.25 | Q1LHI1 Transcriptional regulator, MerR family |
| 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 | Q1LHI0 Heavy metal translocating P-type ATPase |
| Rmet_3525 | cupC | 184 | 334 | 0.55 | 42.9 | 0.77 | 5.00b | 0.79 | 0.92 | 0.86 | 0.60 | 0.79 | 1.06 | Q1LHH9 Heavy metal transport/detoxification protein | |
| Rmet_6119 | copF | 41.3 | 10.0 | 4.13 | 13.5 | 8.97 | 1.00 | 2.00 | Q58AE3 Heavy metal translocating P-type ATPase | ||||||
| cop2, cop1 | |||||||||||||||
| Rmet_5668 | copD2 | 4.3 | 12.3 | 0.35 | 25.5 | 0.16 | 1.40 | 1.16 | 1.00 | 1.46 | 2.62 | 10.3 | 1.07 | 1.19 | Q1LBE9 Copper resistance D |
| Rmet_5669 | copC2 | 1.7 | 4.67 | 0.36 | 37.0 | 0.50 | 1.40 | 0.21 | 2.84 | 0.57 | 1.00 | 0.12 | Q1LBE8 Copper resistance protein CopC | ||
| Rmet_5670 | copB2 | 3.7 | 0.67 | 5.50 | 15.6 | 0.50 | 0.64 | 1.50 | 0.64 | 0.50 | 2.64 | 102 | 1.14 | 1.00 | Q1LBE7 Copper resistance B |
| Rmet_5671 | copA2 | 3.3 | 8.67 | 0.38 | 19.9 | 3.35 | 0.80 | 0.96 | 0.70 | 0.85 | 3.22 | 1.17 | 1.00 | 1.04 | Q1LBE6 Copper-resistance protein CopA |
| Rmet_5672 | copR2 | 9.7 | 5.52 | 0.84 | 0.64 | 1.00 | 1.82 | 1.74 | 1.03 | 0.81 | Q1LBE5 Two component response regulator | ||||
| Rmet_5673 | copS2 | 5.3 | 7.38 | 1.19 | 1.13 | 1.19 | 2.32 | 0.89 | 0.02 | Q1LBE4 Sensor protein | |||||
| Rmet_6110 | copS | 27.7 | 0.67 | 41.5 | 21.2 | 277 | 0.99 | 11.0 | Q58AD4 Sensor protein | ||||||
| Rmet_6111 | copR | 24.0 | 8.00 | 3.00 | 25.9 | 23.1 | 0.96 | Q58AD5 Two component response regulator | |||||||
| Rmet_6112 | copA | 7.0 | 20.7 | 0.34 | 48.1 | 11.0 | 1.18 | 1.18 | Q58AD6 Copper resistance protein CopA | ||||||
| Rmet_6113 | copB | 5.7 | 1.33 | 4.25 | 28.5 | 171 | 0.88 | 2.50 | Q58AD7 CopB protein (Copper resistance B) | ||||||
| Rmet_6114 | copC | 20.3 | 31.0 | 0.66 | 20.4 | 11.1 | 1.20 | 0.09 | Q1LA53 Copper resistance protein CopC | ||||||
| Rmet_6115 | copD | 29.3 | 31.00 | 0.95 | 16.8 | 11.1 | 1.08 | 0.09 | Q58AD9 Copper resistance protein CopD | ||||||
| cus, sil | |||||||||||||||
| Rmet_5030 | cusD | 291 | 1.70 | 1.01 | 0.95 | 1.82 | 11.3 | 0.99 | 0.86 | Q1LD84 Putative uncharacterized protein | |||||
| Rmet_5031 | cusC | 1.7 | 2.00 | 0.83 | 14.0 | 0.17 | 1.00 | 1.00 | 1.00 | 0.67 | 6.33 | 68 | 1.00 | 0.67 | Q1LD83 Putative outer membrane cation efflux protein |
| Rmet_5032 | cusB | 2.0 | 35.0 | 0.06 | 12.2 | 0.13 | 0.83 | 0.14 | 1.00 | 0.57 | 6.92 | 4.86 | 1.40 | 0.93 | Q1LD82 Secretion protein HlyD |
| Rmet_5033 | cusA | 1.7 | 35.0 | 0.05 | 14.2 | 0.13 | 0.80 | 0.14 | 1.00 | 0.57 | 5.99 | 4.86 | 1.50 | 0.93 | Q1LD81 Heavy metal efflux pump CzcA |
| Rmet_5034 | cusF | 2.3 | 35.0 | 0.07 | 21.3 | 1.90 | 0.67 | 1.11 | 0.86 | 0.57 | 5.32 | 0.34 | 1.75 | 1.03 | Q1LD80 Periplasmic protein |
| Rmet_6133 | silD | 129 | 8.67 | 14.85 | 1.84 | 2.38 | 1.06 | 0.08 | Q1LA34 Putative uncharacterized protein | ||||||
| Rmet_6134 | silC | 4.0 | 1.33 | 3.00 | 3.00 | 15.5 | 1.08 | 0.75 | Q58AF2 Outer membrane silver efflux protein | ||||||
| Rmet_6135 | silB | 6.3 | 8.33 | 0.76 | 2.26 | 1.04 | 0.89 | 1.12 | Q58AF3 Silver efflux protein | ||||||
| Rmet_6136 | silA | 36.7 | 3.00 | 12.2 | 1.71 | 0.89 | 0.98 | 0.89 | Q58AF4 Silver efflux protein | ||||||
| gig, rpoQ | |||||||||||||||
| Rmet_4682 | gigT | 5.7 | 5.67 | 1.00 | 3.12 | 2.82 | 1.06 | 1.35 | 0.82 | 2.65 | 0.98 | 1.17 | 0.78 | 0.61 | Q1LE82 DoxX |
| Rmet_4683 | gigB | 3.3 | 5.67 | 0.59 | 3.30 | 0.47 | 1.10 | 0.41 | 1.00 | 2.65 | 1.09 | 7.00 | 0.82 | 2.00 | Q1LE81 Putative uncharacterized protein |
| Rmet_4684 | gigA | 8.7 | 28.3 | 0.31 | 2.42 | 1.72 | 0.81 | 0.98 | 0.92 | 0.53 | 0.97 | 0.38 | 1.05 | 0.71 | Q1LE80 Putative uncharacterized protein |
| Rmet_4685 | gigP | 7.7 | 28.3 | 0.27 | 2.26 | 1.72 | 1.00 | 0.98 | 0.70 | 0.53 | 1.13 | 0.38 | 1.06 | 0.71 | Q1LE79 Putative uncharacterized protein |
| 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_4687 | rsqA | 27.0 | 2.11 | 1.01 | 0.91 | 0.79 | 0.70 | 0.80 | 1.00 | Q1LE77 Putative uncharacterized protein | |||||
| gshA, gshB | |||||||||||||||
| Rmet_0242 | gshA | 329 | 69.3 | 4.75 | 2.67 | 0.17 | 1.07 | 0.13 | 1.05 | 0.11 | 0.62 | 0.75 | 0.87 | 0.86 | Q1LRU8 Glutamate–cysteine ligase GshA |
| Rmet_0243 | gshB | 268 | 69.3 | 3.87 | 2.36 | 0.17 | 1.07 | 0.13 | 1.12 | 0.11 | 0.70 | 0.75 | 0.82 | 0.86 | Q1LRU7 Glutathione synthase |
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.
b Not significant. Plasmid genes on light-gray fields.