TABLE 3.
ComX-regulated genes, distributed over 19 operonsa
| Gene | Product | TPM at 0 min | Log2 fold change at: |
Note | ||
|---|---|---|---|---|---|---|
| 3 min | 10 min | 20 min | ||||
| dut | Deoxyuridine 5ʹ-triphosphate nucleotidohydrolase | 78 | 2.7 | 1.5 | −0.2 | |
| SPV_0028 | Hypothetical protein | 94 | 2.6 | 1.6 | −0.2 | |
| radA | DNA repair protein | 96 | 2.5 | 2.4 | −0.1 | |
| SPV_0030 | Carbonic anhydrase | 388 | 0.8 | 1.1 | 0.1 | Secondary |
| srf-01 | ncRNA of unknown function | 71 | 3.7 | 3.3 | 0.9 | Putative pseudogene |
| SPV_2082b | Hypothetical protein | 22 | 6.6 | 6.3 | 2.6 | |
| SPV_0034b | IS1167 transposase | 3 | 3.6 | 3.7 | 1.1 | |
| cibA | Two-peptide bacteriocin peptide | 8 | 12.0 | 12.9 | 7.4 | |
| cibB | Two-peptide bacteriocin peptide | 11 | 10.2 | 11.0 | 5.5 | |
| cibC | CibAB immunity factor | 10 | 10.6 | 12.3 | 6.5 | |
| SPV_2121 | Hypothetical protein | 124 | 4.6 | 4.4 | 0.6 | |
| SPV_0186 | Competence-damage induced protein | 283 | 2.4 | 2.3 | 0.1 | Secondary |
| SPV_0683 | Hypothetical protein | 136 | 4.2 | 4.9 | 0.8 | |
| comEA | Late-competence DNA receptor | 4 | 9.8 | 9.2 | 3.7 | |
| comEC | Late-competence DNA transporter | 3 | 9.5 | 9.8 | 5.0 | |
| SPV_2256 | Hypothetical protein | 156 | 4.0 | 4.8 | 1.4 | Secondary |
| SPV_2257b | ABC transporter ATP-binding protein | 91 | 3.7 | 5.0 | 1.3 | Secondary |
| SPV_0846 | Hypothetical protein | 68 | 3.9 | 5.4 | 1.5 | Secondary |
| coiA | Competence protein | 1 | 8.2 | 7.4 | 1.2 | |
| pepF1 | Oligoendopeptidase F | 252 | 1.3 | 1.2 | 0.0 | Secondary |
| SPV_0867 | O-Methyltransferase family protein | 136 | 1.4 | 1.5 | 0.3 | Secondary |
| radC | DNA repair protein | 3 | 9.8 | 9.8 | 2.6 | |
| dprA | DNA protecting protein | 6 | 10.1 | 8.8 | 4.6 | |
| SPV_2340b | Hypothetical protein | 222 | 2.5 | 2.6 | 0.2 | Secondary |
| pgdA | Peptidoglycan N-acetylglucosamine deacetylase | 397 | 1.4 | 1.7 | 0.1 | Secondary |
| SPV_1308 | Oxidoreductase of aldo/keto reductase family, subgroup 1 | 182 | 0.9 | 1.4 | 0.3 | Secondary |
| cclA | Type IV prepilin peptidase | 2 | 9.3 | 9.0 | 3.7 | |
| ssbB | Single-stranded DNA-binding protein | 9 | 10.7 | 11.9 | 6.8 | |
| cinA | ADP-ribose pyrophosphatase/nicotinamide-nucleotide amidase | 78 | 5.8 | 6.5 | 2.5 | |
| recA | DNA recombination/repair protein | 391 | 3.0 | 3.8 | 0.7 | Secondary |
| dinF | MATE efflux family protein | 288 | 2.2 | 3.8 | 0.4 | Secondary |
| lytA | Autolysin/N-acetylmuramoyl-l-alanine amidase | 703 | 1.4 | 3.2 | 0.4 | Secondary |
| tygc | NA | <1 | 6.7 | 6.8 | 4.2 | |
| rmuC | DNA recombination protein | 314 | 2.1 | 1.8 | −0.3 | |
| yhaM | 3ʹ→5ʹ exoribonuclease | 312 | 1.7 | 1.7 | −0.4 | |
| SPV_1828 | Hypothetical protein | 142 | 6.5 | 6.0 | 1.4 | |
| nadC | Quinolinate phosphoribosyltransferase | 72 | 1.7 | 3.2 | 0.3 | Secondary |
| SPV_1825b | IS630-Spn1 transposase | 162 | 0.5 | 1.7 | 0.0 | Secondary |
| SPV_1824 | ABC transporter, permease | 34 | 0.9 | 2.7 | 0.2 | Secondary |
| comGA | Late-competence protein | 14 | 9.4 | 10.4 | 5.1 | |
| comGB | Late-competence protein | 8 | 9.4 | 10.8 | 5.4 | |
| comGC | Late-competence protein | 6 | 9.3 | 11.2 | 5.3 | |
| comGD | Late-competence protein | 4 | 10.1 | 12.1 | 6.3 | |
| comGE | Late-competence protein | 3 | 10.3 | 12.3 | 6.5 | |
| comGF | Late-competence protein | 2 | 9.9 | 12.2 | 6.5 | |
| comGG | Late-competence protein | 8 | 8.7 | 11.0 | 5.5 | |
| SPV_2427b | S-Adenosylmethionine-dependent methyltransferase | 2 | 10.3 | 13.0 | 7.2 | |
| srf-29 | ncRNA of unknown function | 3 | 9.3 | 8.8 | 3.0 | |
| cbpD | Choline-binding protein D | 6 | 9.9 | 10.0 | 3.8 | |
| SPV_2027 | Cytoplasmic thiamin-binding component of thiamin ABC transporter | 89 | 1.0 | 1.2 | −0.7 | Secondary |
| thiX | Thiamin ABC transporter transmembrane component | 88 | 0.8 | 1.2 | −1.1 | Secondary |
| thiY | Thiamin ABC transporter substrate-binding component | 134 | 0.8 | 0.9 | −1.1 | Secondary |
| thiZ | Thiamin ABC transporter ATPase component | 128 | 0.6 | 1.0 | −1.2 | Secondary |
| comFA | DNA transporter ATPase | 3 | 9.0 | 8.1 | 2.9 | |
| comFC | Phosphoribosyltransferase domain protein | 3 | 8.6 | 8.5 | 2.7 | |
| hpf | Ribosome hibernation promotion factor | 624 | 0.9 | 1.4 | −0.3 | Secondary |
a
The 19 operons are indicated by the 9 blocks of data in a gray background and the 10 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]). NA, data not available.
b
Pseudogene.
c
The tyg TSS was previously found to be ComX regulated (32). An artificial 250-nucleotide transcript starting at this TSS was added to the annotation file to allow differential expression analysis.