Table 3.
Select genes that exhibited significant differential expression in DMEM compared to LB at an OD600 = 0.5.
| Gene IDa | Predicted protein function | Protein accession no.a | Log2 fold-change (LFC)b,c | |||
|---|---|---|---|---|---|---|
| E2348/69 | C581-05 | B171 | E110019 | |||
| LEE-ENCODED EFFECTORS, REGULATORS, AND ADHESION | ||||||
| eae | Intimin adherence factor | YP_002331401.1 | NS | NS | 4.57 | 4.82 |
| ler | Transcriptional regulator | YP_002331430.1 | 2.81 | NS | 2.08 | NS |
| grlR | Negative regulator GrlR | YP_002331420.1 | 5.43 | NS | 3.22 | 2.33 |
| grlA | Positive regulator GrlA | YP_002331419.1 | 4.89 | NS | 3.6 | NS |
| espF | LEE-encoded effector EspF | YP_002331392.1 | 5.17 | NS | 4.7 | 3.93 |
| espG | LEE-encoded effector EspG | YP_002331432.1 | 4.71 | 2.67 | 4.07 | 3.11 |
| espH | LEE-encoded effector EspH | YP_002331406.1 | 5.64 | NS | 4.05 | 2.62 |
| espZ | LEE-encoded effector EspZ | YP_002331413.1 | 4.36 | NS | 3.31 | 2.68 |
| map | LEE-encoded effector Map | YP_002331404.1 | 3.87 | NS | 3.83 | 2.97 |
| tir | Translocated intimin receptor Tir | YP_002331403.1 | NS | NS | 4.34 | 3.57 |
| NON-LEE-ENCODED EFFECTORS | ||||||
| espG | T3SS secreted effector EspG-like protein | YP_002330404.1 | 2.56 | NS | NS | NS |
| nleG | T3SS secreted effector NleI/NleG-like protein | YP_002328601.1 | 2.66 | NS | NS | NS |
| nleH | T3SS secreted effector NleH-like protein | YP_002328982.1 | NS | NS | NS | −2.00 |
| nleF | T3SS secreted effector NleF-like protein | YP_002328983.1 | NS | NS | NS | −2.40 |
| EAF PLASMID-ENCODED | ||||||
| bfpA | Major pilin structural unit bundlin | YP_002332157.1 | 4.07 | NS | 3.11 | NA |
| perA | Transcriptional activator of the bfp operon | YP_002332173.1 | 4.67 | NS | 4.01 | NA |
| perB | Transcriptional regulator | YP_002332174.1 | 4.69 | NS | 3.69 | NA |
| perC | Transcriptional regulator | YP_002332175.1 | 4.41 | −2.04 | 3.22 | NA |
| DE GENES OF CORE GENE CLUSTERS | ||||||
| napB | Citrate reductase cytochrome c-type subunit | YP_002329852.1 | −4.11 | −3.93 | 2.14 | 2.15 |
| napH | Quinol dehydrogenase membrane component | YP_002329853.1 | −3.45 | −3.56 | 2.48 | 3.02 |
| napG | Quinol dehydrogenase periplasmic component | YP_002329854.1 | −3.4 | −3.66 | 2.27 | 2.69 |
| rbsD | D-ribose pyranase | YP_002331517.1 | −5.15 | 2.46 | −5.4 | −5.27 |
| cirA | Colicin I receptor | YP_002329807.1 | 4.16 | 5.82 | 3.62 | 4.62 |
| dppF | Dipeptide transporter ATP-binding subunit | YP_002331254.1 | 4.55 | 3.62 | 2.15 | 2.84 |
| espG | LEE-encoded effector EspG | YP_002331432.1 | 4.71 | 2.67 | 4.07 | 3.11 |
| narK | Nitrate/nitrite transporter | YP_002328887.1 | −8.07 | −6.81 | −2.67 | −4.32 |
| fucI | L-fucose isomerase | YP_002330550.1 | −4.09 | −2.45 | −3.22 | −2.96 |
| ygeV | DNA-binding transcriptional regulator | YP_002330601.1 | −3.29 | −2.42 | −4.43 | −2.95 |
| ygfJ | Hypothetical protein | YP_002330609.1 | −5.57 | −3.17 | −2.32 | −2.53 |
| nanT | Sialic acid transporter | YP_002330964.1 | −3.39 | −2.67 | −2.12 | −2.67 |
| yjfO | Biofilm stress and motility protein A | YP_002331964.1 | −4.79 | −2.21 | −4.28 | −3.59 |
| DE GENES OF EXCLUSIVE GENE CLUSTERS | ||||||
| E2348/69 | ||||||
| espC | Serine protease | YP_002330403.1 | 5.4 | NA | NA | NA |
| wzx | O-antigen flippase | YP_002329687.1 | 5.2 | NA | NA | NA |
| E2348C_2104 | Lipoprotein | YP_002329618.1 | 2.68 | NA | NA | NA |
| C581-05 | ||||||
| idnD | L-idonate 5-dehydrogenase | WP_024223218.1 | NA | −2.02 | NA | NA |
| tctA | Tripartite tricarboxylate transporter TctA family protein | YP_543360.1 | NA | −2.05 | NA | NA |
| purR | Cytochrome C peroxidase | WP_024223889.1 | NA | −2.09 | NA | NA |
| B171 | ||||||
| EcB171_5053 | Glycosyl hydrolase 108 family protein | EDX28171.1 | NA | NA | 3.56 | NA |
| bor | Lipoprotein Bor | EDX30251.1 | NA | NA | −2.24 | NA |
| EcB171_3359 | Transcriptional regulator, GntR family | EDX31174.1 | NA | NA | −2.3 | NA |
| E110019 | ||||||
| imm | Colicin-E2 immunity protein | EDV85355.1 | NA | NA | NA | 2.04 |
| EcE110019_3691 | Transcriptional regulator, C terminal family protein | EDV86975.1 | NA | NA | NA | 2.03 |
| stbB | Plasmid stability family protein | WP_000361389.1 | NA | NA | NA | −2.17 |
a
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 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.
b
These are LFC values for samples that have been normalized for a single EPEC isolate, and have not been normalized across all EPEC isolates.
c
NS indicates a value was not significant, while NA indicates a comparison was not applicable.