Table 4.
Group and gene name | ID | Product | COGa | Fold upregulation in RM6607Wb |
---|---|---|---|---|
Acid resistance genes | ||||
gadC | Z2216 | Acid sensitivity protein | COG0531E | 99.2 |
yhiM | Z4890 | Hypothetical protein related to acid resistance | NA | 101.1 |
yhiD | Z4920 | Putative Mg2+ transport ATPase | COG1285S | 5.3 |
hdeB | Z4921 | Acid resistance protein | NA | 100.8 |
hdeA | Z4922 | Acid resistance protein | NA | 83.2 |
hdeD | Z4923 | Acid resistance membrane protein | COG3247S | 70.6 |
gadA | Z4930 | Glutamate decarboxylase isozyme | COG0076E | 100.6 |
Heat shock resistance genes | ||||
dnaK | Z0014 | Chaperone Hsp70, autoregulated heat shock protein | COG0443O | 3.0 |
dnaJ | Z0015 | Chaperone with DnaK, heat shock protein | COG0484O | 3.0 |
htpG | Z0590 | Chaperone Hsp90, heat shock protein C 62.5 | COG0326O | 2.7 |
cbpA | Z1418 | Curved DNA-binding protein, functions closely related to DnaJ | COG0484O | 2.8 |
grpE | Z3907 | Heat shock protein GrpE | COG0576O | 2.0 |
groES | Z5747 | Cochaperonin GroES | COG0234O | 3.7 |
groEL | Z5748 | Chaperonin GroEL | COG0459O | 3.5 |
ybbN | Z0645 | Trx-like protein, functions as molecular chaperone | COG3118O | 2.4 |
yrfH | Z4754 | Ribosome-associated heat shock protein Hsp15 | COG1188J | 2.3 |
lon | Z0545 | DNA-binding, ATP-dependent protease La; heat shock K protein | COG0466O | 2.2 |
clpB | Z3886 | Protein disaggregation chaperone | COG0542O | 3.5 |
hslU | Z5478 | ATP-dependent protease ATP-binding subunit | COG1220O | 2.2 |
hslV | Z5479 | ATP-dependent protease peptidase subunit | COG5405O | 2.6 |
Other stress resistance genes | ||||
yecG | Z2948 | Universal stress protein UspC | COG0589T | 2.4 |
treF | Z4932 | Trehalase | COG1626G | 2.6 |
katE | Z2761 | Catalase, hydroperoxidase HPII(III) | COG0753P | 2.3 |
yhjA | Z4931 | Putative cytochrome c peroxidase | COG1858P | 3.2 |
topA | Z2536 | DNA topoisomerase type I, ω protein | COG0550L | 2.4 |
mutS | Z4043 | DNA mismatch repair protein | COG0249L | 2.1 |
exo | Z4115 | Exonuclease IX | COG0258L | 2.6 |
mutM | Z5059 | Formamidopyrimidine-DNA glycosylase | COG0266L | 3.6 |
sms | Z5990 | DNA repair protein RadA | COG1066O | 2.5 |
spy | Z2775 | Periplasmic protein induced by stress response via Cpx and BaeSR system; similar to CpxP | COG3678UNTP | 2.8 |
yiiO | Z5458 | Periplasmic repressor CpxP related to envelope stress | COG3678UNTP | 2.1 |
ykfE | Z0277 | Defense, inactivate vertebrate C-type lysozyme | NA | 3.2 |
The COG category was assigned based on the annotation for E. coli O157:H7 strain EDL933. NA, no category assigned.
The ratio of normalized hybridization intensities of the gene in RM6607W to that in RM6607R. All genes listed here passed the significance test as detailed in Materials and Methods.