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. 2015 Mar 17;83(4):1384–1395. doi: 10.1128/IAI.02697-14

TABLE 4.

C. rodentium genes regulated by RegASMS and RegACR

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
a

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.

b

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.

c

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.

d

T3SS, type 3 secretion system.