Table 2. Differentially expressed genes under C8 stress highlight the acid resistance fitness island.
| b1493 | gadB | 0.000 | 0.015 | 25.3 | AR2 decarboxylase |
| b3509 | hdeB | 0.000 | 0.004 | 21.1 | AR1 chaperone protein |
| b3238 | yhcN | 0.002 | 0.064 | 15.2 | Acid response |
| b3510 | hdeA | 0.000 | 0.000 | 13.7 | AR1 chaperone protein |
| b4439 | micF | 0.003 | 0.078 | 11.9 | Antisense RNA regulator of OmpF porin |
| b3512 | gadE | 0.004 | 0.115 | 10.1 | TA of AR2 |
| b1492 | gadC | 0.000 | 0.013 | 9.3 | AR2 antiporter |
| b3511 | hdeD | 0.001 | 0.053 | 8.7 | AR1 |
| b1480 | sra | 0.001 | 0.009 | 5.1 | SP component of the 30S ribosomal subunit |
| b3508 | yhiD | 0.001 | 0.017 | 4.5 | density-dependent acid resistance |
| b0812 | dps | 0.004 | 0.101 | 4.4 | DNA-binding, iron-collecting, oxidative damage protection/repair |
| b3517 | gadA | 0.003 | 0.108 | 4.4 | AR2 decarboxylase |
| b0485 | ybaS | 0.007 | 0.144 | 4.1 | Glutaminase- acid shock inducible |
| b1531 | marA | 0.002 | 0.067 | 3.9 | Multiple antibiotic resistance TR- organic solvents, oxidative stress |
| b2013 | yeeE | 0.009 | 0.157 | 3.8 | Resistance to the DNA-damage |
| b0287 | yagU | 0.003 | 0.012 | 3.5 | IMP- acid resistance |
| b1165 | ymgA | 0.002 | 0.003 | 3.5 | Biofilm formation- rapid acid treatment |
| b3516 | gadX | 0.001 | 0.014 | 3.5 | AR2 TR |
| b1112 | bhsA | 0.002 | 0.003 | 3.3 | Influencing biofilm through hydrophobicity and SR |
| b2012 | yeeD | 0.010 | 0.106 | 3.0 | Uncharacterized |
| b1164 | ycgZ | 0.006 | 0.107 | 2.9 | Cold shock stimulon |
| b4554 (c4419) | yibT | 0.001 | 0.056 | 2.8 | Uncharacterized |
| b0814 | ompX | 0.004 | 0.017 | 2.8 | Acid-induced OMP |
| b4376 | osmY | 0.001 | 0.023 | 2.8 | Hyperosmotic stress |
| b3405 | ompR | 0.013 | 0.163 | 2.7 | OMP TR |
| b3515 | gadW | 0.026 | 0.219 | 2.6 | AR2 TR |
| b2924 | mscS | 0.001 | 0.028 | 2.4 | IMP mechanosensitive (MS) channel; non-specific transporter |
| b0850 | ybjC | 0.003 | 0.011 | 2.4 | marA/SoxS induced |
| b3024 | ygiW | 0.004 | 0.014 | 2.4 | IMP transporter, SR |
| b0775 (c0855) | bioB | 0.018 | 0.193 | 2.3 | SAM-dependent biotin synthase |
| b2425 | cysP | 0.020 | 0.105 | 2.2 | IMP Sulfate transporter |
| b1661 | cfa | 0.010 | 0.110 | 2.1 | Cyclopropane fatty acid synthase |
| b3160 | yhbW | 0.000 | 0.015 | 2.0 | Monooxygenase |
| b4077 | gltP | 0.024 | 0.213 | 2.0 | Glutamate and aspartate transporter |
| b3458 | livK | 0.005 | 0.090 | −2.0 | leucine transporter |
| b1194 | ycgR | 0.002 | 0.018 | −2.0 | Flagellar motility |
| b1887 | cheW | 0.003 | 0.019 | −2.0 | Flagellar motors |
| b4484 | cpxP | 0.038 | 0.116 | −2.1 | TR, SR of cell envelope |
| b1075 | flgD | 0.009 | 0.032 | −2.2 | Flagella |
| b1941 | fliI | 0.007 | 0.031 | −2.2 | Flagellar export |
| b0455 | ffs | 0.035 | 0.220 | −2.2 | RNA, membrane protein assembly |
| b1942 | fliJ | 0.002 | 0.015 | −2.5 | Flagellar export |
| b1946 | fliN | 0.012 | 0.118 | −2.5 | Flagellar motor |
| b1921 | fliZ | 0.005 | 0.096 | −2.5 | TR flagella |
| b1922 | fliA | 0.000 | 0.000 | −2.6 | Flagella; sigma F factor |
| b1884 | cheR | 0.001 | 0.008 | −2.8 | Chemotaxis sensory transduction system |
| b1072 | flgA | 0.002 | 0.017 | −3.0 | Flagella assembly |
| b1742 (Z2774) | ves | 0.010 | 0.157 | −3.0 | Cold shock stimulon |
| b1939 | fliG | 0.001 | 0.007 | −3.2 | Flagellar motor |
| b1945 | fliM | 0.000 | 0.001 | −3.2 | Flagellar motor |
| b1881 | cheZ | 0.012 | 0.173 | −3.3 | Chemotaxis sensory transduction system |
| b1078 | flgG | 0.024 | 0.223 | −3.3 | Flagellar motor |
| b4355 | tsr | 0.004 | 0.112 | −3.4 | Chemotaxis proteins |
| b1073 | flgB | 0.002 | 0.027 | −3.4 | Flagellar motor |
| b1937 | fliE | 0.005 | 0.045 | −3.5 | Flagella |
| b1076 (Z1714) | flgE | 0.007 | 0.133 | −3.6 | Flagellar motor |
| b0557 (Z1878) | borD | 0.001 | 0.011 | −3.7 | Magnesium stimulon |
| b1938 | fliF | 0.005 | 0.109 | −3.7 | Flagella |
| b1888 | cheA | 0.015 | 0.190 | −3.7 | chemotaxis protein |
| b1947 | fliO | 0.013 | 0.154 | −3.8 | Flagellar export |
| b1925 | fliS | 0.002 | 0.033 | −3.8 | Flagellar export |
| b1882 | cheY | 0.003 | 0.033 | −3.9 | Chemotaxis response regulator |
| b1071 | flgM | 0.001 | 0.018 | −3.9 | Flagella |
| b3525 | yhjH | 0.003 | 0.064 | −3.9 | flagellar motility |
| b1940 (c2357) | fliH | 0.001 | 0.008 | −3.9 | flagella ATPase inhibitor |
| b1074 | flgC | 0.001 | 0.013 | −4.0 | Flagellar motor |
| b1944 | fliL | 0.000 | 0.015 | −4.1 | Flagella |
| b1943 | fliK | 0.001 | 0.003 | −4.3 | Flagellar export |
| b1886 | tar | 0.005 | 0.114 | −4.3 | Aspartate chemoreceptor |
| b1924 | fliD | 0.013 | 0.173 | −4.4 | Flagella |
| b1889 | motB | 0.004 | 0.086 | −4.5 | Flagellar motor |
| b1070 | flgN | 0.000 | 0.000 | −5.1 | Flagellar export |
| b1923 | fliC | 0.003 | 0.095 | −5.4 | Flagella |
| b1076 | flgE | 0.004 | 0.106 | −5.8 | Flagellar motor |
| b1890 | motA | 0.000 | 0.000 | −6.0 | Flagellar motor |
| b1566 | flxA | 0.000 | 0.000 | −6.3 | Prophage |
| b1083 | flgL | 0.002 | 0.083 | −9.3 | Flagella |
| b0929 | ompF | 0.000 | 0.022 | −16.0 | Transport of sugars, ions, and amino acids <600 daltons |
| b0553 | nmpC | 0.002 | 0.069 | −16.3 | OMP porin associated with the peptidoglycan |
Expression ratio for genes significantly perturbed (q<0.05) at least 2-fold are reported as increased abundance (+) or decreased abundance (−). Probes not annotated as MG1655, but homologous to other E. coli strains, are annotated as either CFT073 or EDL933, with the corresponding c-number or Z-number, respectively. The table is sorted by the magnitude of the expression ratio and the function categories are derived from the Ecocyc database [68]. Abbreviations: AR1- acid resistance system 1; AR2- glutamate-dependent acid resistance system 2; OMP- outer membrane protein; IMP- inner membrane protein; TA- transcriptional activator; TR- transcriptional regulator; SP- stationary phase; SR- stress response.