TABLE 4.
Genea | Function | Fold inductionb |
Fold differencec | |
---|---|---|---|---|
RegASMS | RegACR | |||
Housekeeping and stress genes | ||||
thrABC | Threonine biosynthesis | 2.13 | 2.19 | 1.03 |
tdcAB | Threonine metabolism | −3.21 | −3.11 | 0.97 |
glpADFKQT | Glycerol metabolism | −3.08 | −2.54 | 0.82 |
treBC | Trelahose metabolism | −2.78 | −3.0 | 1.08 |
lamB, malETK | Maltose metabolism | −2.81 | −2.84 | 1.01 |
stpA | Global gene repressor | 2.48 | 1.85 | 0.75 |
dnaK | Heat shock protein 70 | −2.48 | −1.88 | 1.32 |
ompFW | Outer membrane protein | −1.92 | −2.26 | 1.31 |
cspA | Cold shock protein A | −2.49 | −2.58 | 0.97 |
Motility genes | ||||
flgABCKLMN | Motility | −3.18 to −9.38 | −3.15 to −9.29 | 0.9 to 1.11 |
flhB | Flagellum biosynthesis protein | −2.07 | −2.07 | 1.0 |
fliADEFGHJMOSZ | Flagellum cap protein | −2.12 to −6.35 | −2.28 to −7.1 | 0.93 to 1.12 |
Virulence genes | ||||
aap | Dispersin | 78 | 88.18 | 1.13 |
aatABDP | Aat transport system | 10.64 | 12.9 | 1.21 |
ROD_41031 to ROD_41051 | ABC transporter membrane protein; putative HlyD (Shewanella woodyi) | 3.11 | 3.97 | 1.28 |
sfpA | Porin protein SfpA (pseudogene) | 6.36 | 7.37 | 1.16 |
fimA | Major subunit of the type I fimbriae (pilin) | −3.82 | −5.43 | 1.42 |
kfcCEFH | Kfc fimbrial operon | 5.26 | 5.25 | 0.99 |
adcA | AdcA autotransporter | 5.65 | 6.59 | 1.17 |
pagC | PagC homologue | 2.85 | 3.96 | 1.39 |
regB | Regulator protein | 42.34 | 45.79 | 1.08 |
LEE PAI genes | ||||
espG | R1/R2; T3SSd effector protein | NS | 2.28 | −2.21 |
LEE4: espABDF, escF, sepL, and ROD29711 | LEE4 operon; effector protein | 1.45 | 3.32 | 2.29 |
Tir operon: eae, cesT, tir, and map | Tir operon; intimin | NS to 2.01 | 2.92 to 5.01 | 2.02 to 2.49 |
LEE3: cesF, sepQ, and miscellaneous | Chaperone | 1.64 | 3.44 | 2.09 |
LEE2: cesD, espJ, escZ, sepD, and miscellaneous | LEE2 operon; effector protein | 1.46 | 2.9 | 1.97 |
grlAR | Global regulators of LEE | 2.34 | 9.67 | 4.13 |
LEE1: escSTU, orf345, and ler | LEE1 operon; structural protein | 1.86 | 4.61 | 2.41 |
espN1, espM2, espS, espT, espX7, espI (nleA), and nleG1 | Effector proteins | NS to 1.59 | 2.04 to 4.76 | 2.04 to 4.03 |
ORF and gene names and functions are as annotated in the C. rodentium genome in GenBank (accession number FN543502). In some cases, the annotation and function have been determined with reference to BLAST searches and EcoCyc (http://www.ecocyc.org). ORFs are shown in numerical order and grouped by functional category.
RegASMS or RegACR activation or repression (−) of the target, relative to the pACYC184 empty-vector control condition, for assays conducted in LB broth with 45 mM bicarbonate. Data were included only where the average magnitude of the change exceeded 2-fold for either condition and the adjusted P value for all assays was <0.05. NS, transcription was insufficient to generate a signal on the array. Note that for gene groups, the change presented is an average of all induction levels; individual levels varied.
The fold difference between RegASMS and RegACR induction or repression levels, calculated as the fold change in transcription induced/repressed by RegACR divided by the fold change induced/repressed by RegASMS. Where RegASMS induction was not calculated, the value was derived by direct comparison of the RegASMS and RegACR data generated by the Agilent Feature Extraction software.
T3SS, type 3 secretion system.