TABLE 4.
CiaR-regulated genes, distributed over 18 operonsa
| Gene | Product | TPM at 0 min | Log2 fold change at: |
Note | ||
|---|---|---|---|---|---|---|
| 3 min | 10 min | 20 min | ||||
| ccnC | csRNA3 | 155 | 4.4 | 1.2 | 0.0 | Also ComE regulon |
| SPV_0098 | Glycosyltransferase, group 2 family | 218 | −0.5 | 1.0 | 0.3 | |
| ccnE | csRNA5 | 32 | 0.6 | 0.8 | 0.2 | |
| ccnA | csRNA1 | 27 | −2.0 | −1.4 | −1.0 | |
| ccnB | csRNA2 | 2 | −0.6 | 2.8 | −1.5 | |
| ccnD | csRNA4 | 25 | 0.4 | 1.9 | 0.0 | |
| manL | Mannose-specific PTS IIAB components | 3,379 | 0.0 | −3.3 | −1.0 | Also CcpA-binding site |
| manM | Mannose-specific PTS IIC component | 3,296 | 0.1 | −3.1 | −1.1 | |
| manN | Mannose-specific PTS IID component | 4,750 | 0.2 | −3.3 | −1.0 | |
| rimP | Bacterial ribosome SSU maturation protein | 228 | −0.2 | 1.0 | 0.8 | CiaR-binding motif on opposite strand |
| nusA | Transcription termination/antitermination protein | 206 | 0.1 | 1.0 | 0.9 | |
| SPV_0480 | Putative transcription termination protein | 117 | 0.5 | 1.2 | 1.1 | |
| SPV_0481 | L7Ae family ribosomal protein | 103 | 0.6 | 1.4 | 1.4 | |
| infB | Translation initiation factor 2 | 277 | 0.8 | 0.7 | 0.9 | |
| rbfA | Ribosome-binding factor A | 194 | 1.0 | 0.5 | 0.8 | |
| ciaR | Two-component system response regulator | 225 | 0.2 | 3.2 | 0.3 | |
| ciaH | Two-component system sensor histidine kinase | 164 | 0.3 | 3.2 | 0.2 | |
| SPV_0775 | Acetyltransferase | 28 | 0.4 | 4.8 | 1.0 | |
| prsA | Putative parvulin type peptidyl-prolyl isomerase | 267 | 1.3 | 3.9 | 0.6 | Potentially also ComX regulon |
| SPV_0913 | Extracellular protein | 55 | 2.0 | 5.9 | 1.3 | |
| rlmCD | 23S rRNA [uracil(1939)-C(5)]-methyltransferase | 38 | −0.4 | 2.0 | 0.4 | Secondary |
| tarIb | Ribitol-5-phosphate cytidylyltransferase | 308 | 0.6 | 0.4 | 0.2 | |
| tarJb | Ribulose-5-phosphate reductase | 362 | 0.4 | 0.3 | 0.1 | |
| licAb | Choline kinase | 319 | 0.6 | 0.2 | 0.1 | |
| licBb | Choline permease | 397 | 0.6 | 0.0 | −0.1 | |
| licCb | Cholinephosphate cytidylyltransferase | 422 | 0.8 | 0.0 | 0.0 | |
| srf-21 | ncRNA of unknown function | 325 | 0.7 | 3.2 | 0.3 | |
| axe1 | Acetyl xylan esterase 1/cephalosporin-C deacetylase | 58 | 0.8 | 4.2 | 0.2 | Secondary |
| SPV_1769 | Membrane protein | 497 | 0.0 | 1.9 | −0.4 | |
| malQ | 4-Alpha-glucanotransferase (amylomaltase) | 69 | 0.1 | 4.2 | −0.2 | |
| malP | Maltodextrin phosphorylase | 83 | 0.2 | 4.2 | −0.4 | |
| dltX | d-Alanyl-lipoteichoic acid biosynthesis protein | 277 | −0.6 | 1.9 | 0.2 | CiaR-binding motif on opposite strand |
| dltA | d-Alanine-poly(phosphoribitol) ligase subunit 1 | 392 | −0.3 | 1.6 | 0.1 | |
| dltB | d-Alanyl transfer protein | 322 | 0.0 | 1.6 | 0.0 | |
| dltC | d-Alanine-poly(phosphoribitol) ligase subunit 2 | 429 | 0.0 | 1.5 | 0.1 | |
| dltD | Poly(glycerophosphate chain) d-alanine transfer protein | 326 | 0.3 | 1.5 | 0.0 | |
| htrA | Serine protease | 49 | 1.5 | 7.0 | 1.5 | |
| parB | Chromosome partitioning protein | 57 | 0.9 | 6.5 | 1.4 | Secondary |
a
The 18 operons are indicated by the 9 blocks of data in a gray background and the 9 blocks of data in a white background. “Secondary” indicates either read-through after incomplete termination or the influence of an additional TSS. For complete supplemental information, including TSS positions, see Table S5. Boldface data indicate significance (P < 0.001; |log2 FC| > 1; DESeq [91]). PTS, phosphotransferase system; SSU, small subunit.
b
The indicated operon has two different detected TSSs. The TSS at 1159217 (−) is under the control of CiaR.