Table 4.
Select genes that were differentially-expressed during adherence to HeLa compared to growth in DMEM broth.
| Gene IDa | Predicted protein | Protein accession no.a | Log2 fold-change (LFC) in HeLa vs. DMEM (OD600 = 0.5)b,c | LFC in DMEM vs. LB (OD600 = 0.5)b,c | |||
|---|---|---|---|---|---|---|---|
| DE genes of core gene clusters | E2348/69 | C581-05 | B171 | E110019 | |||
| rbsD | RbsD/FucU transport family protein | YP_002331517.1 | −2.21 | −4.52 | −4.65 | −2.96 | Decreased in all, except increased in C581-05 |
| yliE | Hypothetical protein | YP_002328350.1 | −2.42 | −6.14 | −3.31 | −4.27 | NS |
| slp | Outer membrane protein Slp | YP_002331206.1 | −4.60 | −4.62 | −3.67 | 2.73 | NS |
| yqjB | SecD export N-terminal TM region family protein | YP_002330857.1 | 2.28 | 2.66 | 2.03 | 2.13 | NS |
| hscB | Fe-S protein assembly co-chaperone HscB | YP_002330308.1 | 2.17 | 3.36 | 3.66 | 3.28 | NS |
| nirC | Putative nitrite transporter | YP_002331085.1 | 2.60 | 2.06 | −4.90 | −7.24 | NS |
| DE GENES OF EXCLUSIVE GENE CLUSTERS | |||||||
| E2348/69 | |||||||
| wzy | O-antigen polymerase | YP_002329685.1 | −5.92 | NA | NA | NA | 4.39 |
| rfaS | Lipopolysaccharide core biosynthesis protein | YP_002331339.1 | −6.63 | NA | NA | NA | NS |
| C581-05 | |||||||
| rfaG | Glycosyl transferases group 1 family protein | WP_024235092.1 | NA | −2.14 | NA | NA | NS |
| argR | Arginine repressor, DNA binding domain protein | YP_002559154.1 | NA | −2.37 | NA | NA | NS |
| yopT-like | Cysteine protease, YopT-type domain protein | WP_024235005.1 | NA | −2.75 | NA | NA | NS |
| B171 | |||||||
| mhpR | Mhp operon transcriptional activator | EDX27960.1 | NA | NA | 2.77 | NA | −4.25 |
| eamA | EamA-like transporter family protein | WP_011251361.1 | NA | NA | 2.33 | NA | NS |
| None | Transcriptional regulator, GntR family | EDX31174.1 | NA | NA | −2.26 | NA | −2.30 |
| E110019 | |||||||
| IutA | Ferric aerobactin receptor LutA | EDV87696.1 | NA | NA | NA | 2.56 | NS |
| terA | Tellurium resistance family protein | EDV86455.1 | NA | NA | NA | −2.42 | NS |
| EcE110019_4492 | Sulfatase family protein | EDV86483.1 | NA | NA | NA | −3.82 | NS |
The gene symbol or locus id and the protein accession number are indicated for the top match protein. In some cases a protein match could not be identified for a gene cluster in a particular genome, which likely results from differences in the gene-calling that was used for LS-BSR compared to that used for the GenBank sequences. None indicates there was not a corresponding locus id for the particular genome.
These are LFC values for samples that have been normalized for a single EPEC isolate, and have not been normalized across all EPEC isolates.
NS indicates a value was not significant, while NA indicates a comparison was not applicable.