TABLE 2.
Genes in H. ducreyi whose expression is most affected by growth in the presence of FCSa
| ORF | Gene | Description | log2(+FCS/-FCS)b | SD |
|---|---|---|---|---|
| HD0344 | nrfA | Nitrate reductase, cytochrome c552 | 3.93 | 0.17 |
| HD0233 | carB | Carbamoyl-phosphate synthase, large subunit | 3.75 | 0.07 |
| HD0235 | carA | Carbamoyl-phosphate synthase, small subunit | 3.72 | 0.14 |
| HD1433 | ompP2A | Outer membrane protein P2 homolog | 3.61 | 0.26 |
| HD1311 | flp2 | flp operon protein Flp2 | 3.56 | 0.21 |
| HD0347 | nrfB | Nitrate reductase, cytochrome c type protein | 3.46 | 0.17 |
| HD1312 | flp1 | flp operon protein Flp1 | 3.33 | 0.18 |
| HD0349 | nrfC | Nitrate reductase, Fe-S protein | 3.26 | 0.31 |
| HD0998 | uraA | Uracil permease | 3.07 | 0.18 |
| HD1310 | flp3 | flp operon protein Flp3 | 3.06 | 0.26 |
| HD0232 | arcB1 | Ornithine carbamoyltransferase | 3.05 | 0.17 |
| HD1985 | Possible DNA transformation protein | 2.84 | 0.10 | |
| HD1306 | rcpB | Rough colony protein B | 2.75 | 0.41 |
| HD0769 | dsrA | Serum resistance protein DsrA | 2.74 | 0.50 |
| HD0427 | comA | Possible competence protein A homolog | 2.52 | 0.45 |
| HD1309 | flp operon protein B | 2.47 | 0.46 | |
| HD1078 | ompP1 | Outer membrane protein P1 | 2.40 | 0.19 |
| HD1326 | hhdB | Hemolysin activation/secretion protein | 2.37 | 0.28 |
| HD1305 | flp operon protein D | 2.36 | 0.20 | |
| HD1304 | tadA | Tight adherence protein A | 2.35 | 0.30 |
| HD1307 | rcpA | Rough colony protein A | 2.34 | 0.36 |
| HD1156 | lspA2 | Large supernatant protein 2 | 2.33 | 1.99 |
| HD0046 | ompA2 | Major outer membrane protein homolog | 2.32 | 0.28 |
| HD0350 | nrfD | Nitrate reductase, transmembrane protein | 2.31 | 0.37 |
| HD1290 | msrB | Peptide methionine sulfoxide reductase MsrB | 2.27 | 0.22 |
| HD1278 | Possible serine protease | 2.27 | 0.24 | |
| HD0073 | napD | Possible NapD protein | 2.18 | 0.15 |
| HD1921 | recG | ATP-dependent DNA helicase RecG | 2.07 | 0.17 |
| HD0072 | napF | Ferredoxin-type protein NapF | 2.03 | 0.21 |
| HD1155 | lspB | Large supernatant protein exporter | 2.01 | 0.18 |
| HD1303 | tadB | Tight adherence protein B | 1.78 | 0.28 |
| HD1221 | ykgE | Conserved putative dehydrogenase subunit | 1.75 | 0.23 |
| HD1302 | tadC | Tight adherence protein C | 1.74 | 0.10 |
| HD1666 | Probable phosphatase | 1.64 | 0.10 | |
| HD1291 | gapA | Glyceraldehyde 3-phosphate dehydrogenase | 1.61 | 0.13 |
| HD1435 | ompP2B | Outer membrane protein P2 homolog | -3.74 | 0.50 |
| HD1512 | Acriflavine resistance protein | -2.81 | 0.05 | |
| HD1163 | ribAB | Riboflavin biosynthesis protein RibA | -2.80 | 0.24 |
| HD1513 | Putative RND efflux membrane fusion protein | -2.67 | 0.30 | |
| HD1161 | ribD | Riboflavin-specific deaminase | -2.28 | 0.21 |
| HD1162 | ribE | Riboflavin synthase, alpha chain | -2.24 | 0.19 |
| HD1109 | Putative oxalate/formate antiporter | -2.18 | 0.19 | |
| HD0282 | fimB | Possible fimbrial structural subunit | -2.16 | 0.17 |
| HD1816 | yfeA | Iron (chelated) ABC transporter | -2.04 | 0.11 |
| HD2025 | hgbA | Hemoglobin-binding protein HgbA | -2.02 | 0.19 |
| HD0648 | tnaB | Tryptophan-specific transport protein | -2.02 | 0.25 |
| HD1024 | yfeD | Iron (chelated) transport system | -2.01 | 0.46 |
| HD1470 | cpxA | Sensor kinase CpxA | -2.00 | 0.05 |
| HD1165 | ribH | 6,7-Dimethyl-8-ribityllumazine synthase | -1.96 | 0.06 |
| HD1179 | ksgA | Dimethyladenosine transferase | -1.91 | 0.11 |
| HD0723 | trmA | tRNA (uracil-5-)-methyltransferase | -1.88 | 0.30 |
| HD1817 | yfeB | Iron (chelated) transporter, ATP-binding protein | -1.81 | 0.11 |
| HD1511 | glmU | Bifunctional GlmU protein | -1.77 | 0.13 |
| HD1025 | yfeC | Iron (chelated) transport system | -1.74 | 0.25 |
| HD1010 | prc | Tail-specific protease | -1.73 | 0.28 |
| HD1469 | cpxR | Transcriptional regulatory protein CpxR | -1.69 | 0.20 |
| HD0454 | waaA | 3-Deoxy-d-manno-octulosonic acid transferase | -1.68 | 0.10 |
| HD1084 | HesB family protein | -1.68 | 0.14 | |
| HD1815 | Putative sulfite reductase | -1.68 | 0.25 | |
| HD1629 | lolB | Outer membrane lipoprotein LolB | -1.68 | 0.23 |
| HD2012 | lipA | Lipoic acid synthetase | -1.63 | 0.19 |
| HD0791 | ccmE | Cytochrome c-type biogenesis protein | -1.62 | 0.27 |
| HD0328 | exbD | Biopolymer transport protein | -1.60 | 0.08 |
| HD1342 | recJ | Single-stranded-DNA-specific exonuclease RecJ | -1.54 | 0.18 |
| HD1191 | Outer membrane protein D15 | -1.54 | 0.16 | |
| HD1628 | ispE | 4-Diphosphocytidyl-2-C-methyl-d-erythritol kinase | -1.54 | 0.08 |
| HD1806 | thiI | Thiamine biosynthesis protein ThiI | -1.54 | 0.20 |
| HD1094 | Possible outer membrane serine protease | -1.52 | 0.10 | |
| HD0329 | exbB | Biopolymer transport protein | -1.49 | 0.12 |
| HD1085 | hscB | Chaperone protein HscB | -1.49 | 0.14 |
a
The table lists the 35 most upregulated genes and the 35 most downregulated genes, not including ORFs described as hypothetical or conserved hypothetical proteins.
b
That is, the median log2 ratio of expression when grown in the presence of FCS relative to expression in the absence of FCS from four experiments (P < 0.05).