Table 3.
S. Typhimurium genes of interest which were downregulated during colonization of the cecal lumen, compared with expression in broth culturesa
| COGs class | Locus tag | Gene | Function or product | Change in expression level (fold) | P value |
|---|---|---|---|---|---|
| Not in COGs | STM2770 | fljA | Phase 1 flagellin repressor | 2.5 | 0.03 |
| STM2304 | pmrD | Polymyxin resistance protein B | 6.02 | 0.005 | |
| Amino acid transport and metabolism | STM | dsdA | d-Serine deaminase | 6.65 | 0.0036 |
| STM3244 | tdcB | Threonine dehydratase | 4.9 | 0.01 | |
| STM3240 | tdcG | l-Serine deaminase | 2.6 | 0.03 | |
| Carbohydrate transport and metabolism | STM2433 | crr | Glucose-specific IIA component | 10.78 | 0.026 |
| STM4231 | lamB | Maltoporin precursor | 4.4 | 0.04 | |
| STM2190 | mglB | Galactose transport protein | 5.6 | 0.001 | |
| STM0684 | nagB | Glucosamine-6-phosphate deaminase | 2.5 | 0.05 | |
| STM0685 | nagE | N-Acetylglucosamine-specific enzyme IIABC | 2.1 | 0.04 | |
| STM2431 | ptsH | Phosphohistidinoprotein-hexose phosphotransferase | 9.00 | 0.014 | |
| Cell cycle | STM3569 | ftsX | Putative cell division protein | 3.3 | 0.008 |
| STN3570 | ftsE | Putative cell division ATPase | 3.3 | 0.03 | |
| STM0960 | ftsK | Cell division protein | 3.5 | 0.02 | |
| Energy production and conversion | STM2320 | nuoJ | NADH dehydrogenase I chain J | 2.3 | 0.03 |
| STM2321 | nuoI | NADH dehydrogenase I chain I | 2.4 | 0.03 | |
| STM2255 | napC | Periplasmic nitrate reductase | 3.0 | 0.02 | |
| STM0440 | cyoD | Cytochrome o ubiquinol oxidase subunit IV | 3.4 | 0.04 | |
| STM4340 | frdD | Fumarate reductase membrane anchor polypeptide | 3.6 | 0.05 | |
| STM2325 | nuoE | NADH dehydrogenase I chain E | 4.1 | 0.03 | |
| STM2324 | nuoF | NADH dehydrogenase I chain F | 3.5 | 0.05 | |
| STM0441 | cyoC | Cytochrome o ubiquinol oxidase subunit III | 6.96 | 0.013 | |
| STM0740 | cydA | Cytochrome d terminal oxidase polypeptide subunit I | 6.33 | 0.0062 | |
| General function | STM4361 | hfq | Host factor I | 10.08 | 0.0005 |
| STM1751 | hns | DNA-binding protein HLP-II | 8.73 | 0.0033 | |
| Cell motility | STM1959 | fliC | Flagellin | 14.89 | 0.00055 |
| STM1171 | flgN | Putative FlgK/FlgL export chaperone | 7.79 | 0.007 | |
| STM1920 | cheW | Chemotaxis docking protein | 7.26 | 0.0027 | |
| STM1183 | flgK | Flagellar hook-associated protein 1 | 2.3 | 0.02 | |
| STM4533 | tsr | Methyl-accepting chemotaxis protein | 3.9 | 0.03 | |
| STM1915 | cheZ | Chemotactic response protein | 4.0 | 0.02 | |
| STM2771 | fljB | Phase 2 flagellin | 4.0 | 0.01 | |
| STM1921 | cheA | Chemotaxis sensory histidine protein kinase | 4.0 | 0.02 | |
| STM1174 | flgB | Flagellar basal body rod protein | 4.2 | 0.05 | |
| STM3577 | tcp | Methyl-accepting transmembrane citrate/phenol | 5.2 | 0.002 | |
| chemoreceptor | |||||
| Replication, recombination, and repair | STM1339 | himA | Integration host factor alpha subunit | 3.9 | 0.013 |
| STM3185 | yqiE | ADP-ribose pyrophosphatase | 3.6 | 0.007 | |
| STM0484 | dnaX | DNA polymerase III tau/gamma subunits | 3.1 | 0.01 | |
| STM4170 | hupA | DNA-binding protein HU-alpha | 6.36 | 0.00079 | |
| Signal transduction mechanisms | STM1916 | cheY | Chemotaxis regulator | 6.62 | 0.01 |
| Transcription | STM0900 | Putative helicase | 12.5 | 0.002 | |
| STM2875 | hilD | Invasion protein regulatory protein | 10.3 | 0.008 | |
| STM1172 | flgM | Anti-FliA factor | 7.71 | 0.011 | |
| STM2867 | hilC | Invasion regulatory protein | 5.89 | 0.014 | |
| STM3245 | tdcA | Transcriptional activator | 3.0 | 0.005 | |
| STM1956 | fliA | Sigma 28 | 3.0 | 0.025 | |
| Translation | STM3728 | rpmB | 50S ribosomal subunit protein L28 | 5.92 | 0.02 |
| STM3440 | rplC | 50S ribosomal subunit protein L3 | 2.1 | 0.04 | |
| STM3437 | rplB | 50S ribosomal subunit protein L2 | 2.22 | 0.02 | |
| STM3425 | rplF | 50S ribosomal subunit protein L6 | 2.6 | 0.02 | |
| STM3414 | rplQ | 50S ribosomal subunit protein L17 | 3.3 | 0.01 | |
| STM3438 | rplW | 50S ribosomal subunit protein L23 | 2.9 | 0.01 | |
| STM3430 | rplN | 50S ribosomal subunit protein L14 | 3.2 | 0.008 | |
| STM3422 | rplP | 50S ribosomal subunit protein L16 | 3.3 | 0.01 | |
| STM4393 | rpsR | 30S ribosomal subunit protein S18 | 2.2 | 0.03 | |
| STM3441 | rpsJ | 30S ribosomal subunit protein S10 | 2.5 | 0.02 | |
| STM0981 | rpsA | 30S ribosomal subunit protein S1 | 3.2 | 0.03 | |
| STM3447 | rpsG | 30S ribosomal subunit protein S7 | 3.6 | 0.03 | |
| STM3448 | rpsL | 30S ribosomal subunit protein S12 | 3.7 | 0.045 | |
| STM3436 | rpsS | 30S ribosomal subunit protein S19 | 3.9 | 0.012 | |
| STM3419 | rpmJ | 50S ribosomal subunit protein X | 3.6 | 0.02 | |
| STM1335 | rpmI | 50S ribosomal subunit protein L35 | 3.9 | 0.01 | |
| Translocation | STM3321 | yhbH | Putative sigma N modulation factor | 16.11 | 0.0049 |
| Function unknown | STM2390 | yfcZ | Putative cytoplasmic protein | 9.52 | 0.0051 |
| STM3995 | yihD | Putative cytoplasmic protein | 6.99 | 0.00041 | |
| STM2697 | Phage tail-like protein | 6.87 | 0.003 | ||
| STM4088 | yiiU | Putative cytoplasmic protein | 6.26 | 0.0017 |
a
Genes selected as genes of interest showed a >2-fold change in expression levels and a P value of <0.05.