Table 1.
List of proteins differentially expressed in ΔldcF.
| Gene name | Locus | Description | Proteomic data | |
|---|---|---|---|---|
| Log 2FC | P value | |||
| Downregulated proteins in ΔldcF | ||||
| cadA | FTN_0504 | Lysine decarboxylase | − 6.135487177 | 6.5901E−12 |
| udp | FTN_0652 | Uridine phosphorylase | − 2.442473795 | 0.000355044 |
| uvrB | FTN_1176 | Excinuclease ABC subunit B | − 2.359970258 | 1.5872E−07 |
| yhiP | FTN_0885 | Proton-dependent oligopeptide transporter (POT) family protein, di- or tripeptide:H + symporter | − 2.233739832 | 1.28816E−08 |
| – | FTN_1453 | Two-component regulator, sensor histidine kinase | − 2.225623368 | 0.000269144 |
| – | FTN_0705 | Abortive infection bacteriophage resistance protein | − 1.909345488 | 0.006797082 |
| – | FTN_0655 | N6-adenine-specific methylase | − 1.645819843 | 0.009836595 |
| – | FTN_1348 | Acetyltransferase | − 1.493386099 | 3.68028E−07 |
| – | FTN_0898 | Amino acid permease | − 1.424644622 | 3.5435E−06 |
| panD | FTN_1354 | Aspartate 1-decarboxylase | − 1.405501066 | 0.006567341 |
| – | FTN_0862 | Hypothetical protein | − 1.276557703 | 0.000969217 |
| ung | FTN_1486 | Uracil-DNA glycosylase | − 1.261354286 | 4.40904E−07 |
| – | FTN_0308 | Membrane protein of unknown function | − 1.255628185 | 0.000806353 |
| – | FTN_1272 | Proton-dependent oligopeptide transporter (POT) family protein, di- or tripeptide:H + symporter | − 1.243209089 | 1.20616E−05 |
| dapD | FTN_1727 | 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase | − 1.185622324 | 0.000977552 |
| – | FTN_1258 | Hypothetical protein | − 1.11437438 | 0.000177817 |
| hsdM | FTN_1152 | Type I restriction-modification system, subunit M (methyltransferase) | − 1.098834276 | 0.000436818 |
| – | FTN_1316 | Hypothetical protein | − 1.075883638 | 0.005337719 |
| – | FTN_1628 | LysR family transcriptional regulator | − 1.010217775 | 0.001268379 |
| hdsR | FTN_0710 | Type I restriction-modification system, subunit R (restriction) | − 0.974133834 | 0.00046316 |
| – | FTN_1212 | Glycosyl transferases group 1 family protein | − 0.967248679 | 7.07496E−06 |
| – | FTN_1397 | Hypothetical protein | − 0.962399859 | 6.53792E−05 |
| – | FTN_0976 | ThiF family protein | − 0.962086728 | 6.76869E−05 |
| waaG | FTN_1218 | Glycosyl transferase, group 1 | − 0.942030987 | 0.000643833 |
| pilE4 | FTN_0389 | Type IV pili, pilus assembly protein | − 0.94007106 | 2.01122E−05 |
| – | FTN_1440 | Hypothetical protein | − 0.935671185 | 0.007635418 |
| ubiC | FTN_0386 | Chorismate pyruvate lyase | − 0.934045712 | 6.57717E−05 |
| – | FTN_0137 | Hypothetical protein | − 0.928404833 | 3.73274E−06 |
| mglA | FTN_1290 | Macrophage growth locus, protein A | − 0.926959218 | 6.24086E−07 |
| – | FTN_1697 | Galactose mutarotase | − 0.901042767 | 0.008192095 |
| – | FTN_1148 | Glycoprotease family protein | − 0.816650922 | 0.005012835 |
| galP1 | FTN_0687 | Major facilitator superfamily galactose-proton symporter | − 0.746905316 | 5.94864E−05 |
| – | FTN_1459 | Short chain dehydrogenase | − 0.723695755 | 0.001285646 |
| – | FTN_1254 | Hypothetical protein | − 0.716291799 | 0.00237079 |
| – | FTN_1266 | ABC transporter membrane protein | − 0.66256701 | 0.001562237 |
| – | FTN_0923 | Hypothetical protein | − 0.654493997 | 0.002785307 |
| yhbG | FTN_0902 | ABC transporter, ATP-binding protein | − 0.652797305 | 3.32447E−05 |
| rpsF | FTN_0951 | 30S ribosomal protein S6 | − 0.641616628 | 5.78051E−05 |
| yrbI | FTN_0905 | 3-Deoxy-d-manno-octulosonate 8-phosphate phosphatase | − 0.627622272 | 0.001032099 |
| – | FTN_1547 | Hypothetical protein | − 0.608477024 | 0.000859667 |
| Upregulated proteins in ΔldcF | ||||
| rimM | FTN_1561 | Ribosome maturation factor rimM | 0.626513088 | 0.000555064 |
| apaH | FTN_0561 | Diadenosine tetraphosphatase | 0.629366731 | 0.000669224 |
| – | FTN_0118 | S49 family serine peptidase | 0.635972422 | 0.006578849 |
| – | FTN_1468 | Putative deoxyribonucleotide triphosphate pyrophosphatase | 0.640919668 | 0.000191944 |
| – | FTN_0089 | Allophanate hydrolase subunit 2 | 0.672742647 | 0.000997506 |
| rnc | FTN_1463 | Ribonuclease 3 | 0.681039745 | 0.001289497 |
| – | FTN_0789 | Putative rhodanese, sulfurtransferase | 0.68404703 | 0.000345296 |
| secF | FTN_1094 | Preprotein translocase subunit SecF | 0.695399198 | 3.15477E−05 |
| murD | FTN_0542 | UDP-N-acetylmuramoylalanine–d-glutamate ligase | 0.715198106 | 5.10756E−05 |
| xthA | FTN_0838 | Exodeoxyribonuclease III | 0.726407142 | 1.90678E−05 |
| sun | FTN_1347 | tRNA and rRNA cytosine-C5-methylases, sun protein | 0.73058117 | 0.00042405 |
| – | FTN_0872 | Small conductance mechanosensitive ion channel (MscS) family protein | 0.78091602 | 2.90828E−05 |
| – | FTN_1387 | Hypothetical protein | 0.812379067 | 0.00883337 |
| ispD | FTN_0623 | 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase | 0.824072741 | 5.66929E−06 |
| – | FTN_0041 | Hypothetical protein | 0.828287322 | 0.002571557 |
| mltA | FTN_1286 | Membrane-bound lytic murein transglycosylase | 0.843953091 | 0.000666109 |
| – | FTN_1080 | Phosphosugar binding protein | 0.857709173 | 0.000844453 |
| – | FTN_1015 | Isochorismatase family protein | 0.860701266 | 0.000470586 |
| pilW | FTN_0307 | Type IV pilus assembly protein | 0.903906623 | 0.004575204 |
| – | FTN_1061 | Acid phosphatase, HAD superfamily protein | 0.951666713 | 0.001807004 |
| pilV | FTN_0413 | Type IV pili, pilus assembly protein | 0.975215693 | 0.001866241 |
| murQ | FTN_1504 | N-acetylmuramic acid 6-phosphate etherase | 0.994710363 | 1.2722E−06 |
| tdh | FTN_0625 | l-Threonine 3-dehydrogenase | 1.02107175 | 2.99619E−05 |
| ruvA | FTN_1025 | Holliday junction ATP-dependent DNA helicase RuvA | 1.125358669 | 5.65196E−07 |
| – | FTN_1506 | Hypothetical protein | 1.20406212 | 0.000656496 |
| putP | FTN_0299 | Proline/Na + symporter | 1.206589507 | 0.001401361 |
| – | FTN_0452 | Hypothetical protein | 1.274923951 | 4.08167E−08 |
| – | FTN_0006 | Hypothetical protein | 1.345660313 | 1.02878E−06 |
| – | FTN_0004 | Aspartate/glutamate transporter | 1.352713527 | 0.003023321 |
| – | FTN_0829 | Hypothetical protein | 1.454738617 | 6.98601E−07 |
| – | FTN_1388 | Oxidoreductase | 1.515433578 | 0.000565317 |
| – | FTN_1267 | ABC transporter ATP-binding protein | 1.74578111 | 3.84443E−09 |
| lptC | FTN_0904 | Lipopolysaccharide export ABC transporter periplasmic protein | 1.999604273 | 1.63282E−05 |
| rnpA | FTN_0075 | Ribonuclease P protein component | 2.366923256 | 0.000708316 |
| – | FTN_0384 | Hypothetical protein | 2.702678582 | 0.002040018 |
| – | FTN_0987 | tRNA-dihydrouridine synthase | 2.830069785 | 5.08771E−06 |
| – | FTN_1386 | Hypothetical protein | 2.845246288 | 4.58158E−09 |
| – | FTN_0722 | l-lysine 2,3-aminomutase | 3.467288507 | 1.01829E−10 |
| – | FTN_1220 | Lipopolysaccharide synthesis sugar transferase | 3.613912551 | 0.000821341 |
| recB | FTN_1357 | ATP-dependent exoDNAse (exonuclease V) beta subunit | 3.825585172 | 1.16584E−11 |
The protein deleted in the mutant was labeled in bold.