Table 5.
Transcriptomic data for the gene-encoded proteins with different changes in the sense-to-antisense ratiosa
| Before the change | After the change | Comparison | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus tag | Gene | Mean | Mean_AST | S/AS | MEAN | Mean_AST | S/AS | Comp | Q_sense | Q_AST | QS_AS |
| Data with QS_AS ratios >50 | |||||||||||
| Rmet_3525 | cupC | 184 ± 37 | 334 ± 45 | 0.55 | 7 912 ± 912 | 255 ± 28 | 31.0 | CM0+ | 42.9 | 0.77 | 56.1 |
| Rmet_0333 | arsR | 47 ± 4 | 3 ± 2 | 14.2 | 17 327 ± 1 563 | 20 ± 3 | 852 | AM0+ | 366 | 6.10 | 60.0 |
| Rmet_0333 | arsR | 61 ± 3 | 5 ± 3 | 13.0 | 20 485 ± 2 242 | 23 ± 2 | 878 | CM0+ | 338 | 5.00 | 67.5 |
| Rmet_0331 | arsC2 | 11 ± 1 | 3 ± 1 | 3.40 | 5 969 ± 277 | 20 ± 3 | 294 | AM0+ | 527 | 6.10 | 86.3 |
| Rmet_3525 | cupC | 145 ± 19 | 306 ± 38 | 0.48 | 6 767 ± 1 554 | 153 ± 17 | 44.3 | AM0+ | 46.6 | 0.50 | 93.2 |
| Rmet_3620 | degP | 28 ± 1 | 105 ± 10 | 0.26 | 3 680 ± 424 | 116 ± 8 | 31.7 | CM0+ | 133 | 1.10 | 121 |
| Rmet_0123 | 6 ± 1 | 102 ± 12 | 0.06 | 132 ± 20 | 1.7 ± 1.1 | 79.0 | AE0+ | 23.2 | 0.02 | 1 417 | |
| Data with QS_AS ratios between 1.2 and 20 (selected data points) | |||||||||||
| Rmet_5319 | zniA | 57 ± 3 | 4 ± 1 | 13.1 | 147 ± 3 | 3 ± 1 | 49 | CE0+ | 2.6 | 0.69 | 3.7 |
| Rmet_5320 | zniB | 116 ± 8 | 29 ± 3 | 3.94 | 291 ± 56 | 44 ± 4 | 6.6 | CE0+ | 2.5 | 1.49 | 1.7 |
| Data with QS_AS ratios <0.25 | |||||||||||
| Rmet_5673 | copS2 | 5 ± 1 | Not found | 39 ± 3 | 43 ± 4 | 0.91 | CM0+ | 7.38 | |||
| Rmet_5321 | zniC | 46 ± 4 | 1 ± 1 | 46.3 | 110 ± 7 | 156 ± 9 | 0.71 | AE0+ | 2.37 | 157 | 0.02 |
| Rmet_1195 | bfrB | 315 ± 5 | 157 ± 20 | 2.01 | 110 ± 9 | 681 ± 93 | 0.16 | AM0− | 0.35b | 4.35 | 0.08 |
| Rmet_1026 | iscU | 545 ± 36 | 2.3 ± 0.6 | 233 | 1 724 ± 72 | 65 ± 9 | 26.5 | AM0+ | 3.17 | 27.9 | 0.11 |
| Rmet_0506 | purK | 125 ± 24 | 0.3 ± 0.6 | 375 | 62 ± 9 | 1.3 ± 0.6 | 46.2 | AM0− | 0.49 b | 4.00 | 0.12 |
| Rmet_0970 | ggt | 235 ± 17 | 2.3 ± 0.6 | 101 | 37 ± 3 | 2.7 ± 1.1 | 14.0 | AM0− | 0.16 b | 1.14 | 0.14 |
| Rmet_1026 | iscU | 506 ± 17 | 4 ± 0 | 127 | 1 728 ± 146 | 63 ± 5 | 27.3 | CM0+ | 3.41 | 15.8 | 0.22 |
| Rmet_1027 | iscA | 556 ± 59 | 4 ± 0 | 139 | 2 015 ± 421 | 63 ± 5 | 31.8 | CM0+ | 3.62 | 15.8 | 0.23 |
aThe published transcriptomic data [58] for genes with strongly increased (>50) or decreased (<0.25) sense-to-antisense RNA ratios in the comparisons CH34 metal-shocked to the control (CM0; CMO+ up- and CM0− down-regulated), same for AE104 (AM0), metal-starved CH34 cells to the control (CE0) and the same for strain AE104 (AE0). The abundances as NPKM values of the RNAs before and after application of the changed condition are listed, Mean for sense RNA, Mean_AST for antisense RNA, S/AS for the ratio of sense-to-antisense RNA plus the changes of the sense, antisense abundances and that of the sense-to-antisense ratios.
bThe ratios Q are given while the associated figures are using the 1/Q values. Down-regulated genes on a gray field.