Table 2 Down-regulated genes in K3 strain
From: Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant
Functional class and gene namea,b,c,d,e,f | Operonb,c,d,e,g | Known or predicted function | Fold change |
|---|---|---|---|
Transport and binding protein | |||
dctA | Â | C4-dicarboxylate transport protein | -2.03 |
fadL | Â | Long-chain fatty acid transporter | -1.69 |
proV | proVWX | Glycine betaine transporter subunit | -2.30 |
Energy metabolism | |||
fucI b | f uc P IK UR | L-fucose isomerase | -1.59 |
glpD c | Â | Aerobic glycerol-3-phosphate dehydrogenase | -3.56 |
glpE b | glpEGR | Thiosulfate sulfurtransferase | -2.04 |
glpT | glpTQ | sn-glycerol-3-phosphate transporter | -2.54 |
glpX | glp FK X | Fructose 1,6-bisphosphatase II | -1.51 |
grxA e | Â | Glutaredoxin 1 | -2.19 |
trxB b,e | Â | Thioredoxin reductase, FAD/NAD(P)-binding | -1.88 |
trxC b,e | Â | Thioredoxin 2 | -1.87 |
Protein fate | |||
c1935 f | Â | Chaperone protein (F9 fimbriae) | -3.72 |
dnaK | dnaKJ | Molecular chaperone | -3.23 |
grpE | Â | Heat shock protein | -1.68 |
hscB | hscBA-fdx-iscX | Co-chaperone with HscA | -1.81 |
hslO | Â | Hsp33-like chaperonin | -1.59 |
hslV | hslVU | ATP-dependent protease peptidase subunit | -2.68 |
htpG b | Â | Heat shock protein 90 | -1.91 |
ibpA | ibpAB | Heat shock chaperone | -2.63 |
slpA d | Â | FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) | -1.60 |
ydhJ | ydhIJK | Undecaprenyl pyrophosphate phosphatase | -2.05 |
Protein synthesis | |||
dinD | Â | DNA-damage-inducible protein | -1.90 |
lexA | lexA-dinF | Regulator for SOS regulon | -2.14 |
nrdA | nrdAB | Ribonucleotide-diphosphate reductase alpha subunit | -1.58 |
recN | Â | DNA repair protein/recombination and repair protein | -2.80 |
rplR | rplNXE-rpsNH- rpl F R - rpsE - rpmD - rplO -secY-rpmJ | 50S ribosomal protein L18 | -1.59 |
rplW | rpsJ- rpl CD WB - rpsS - rplV -rpsC- rplP - rpmC - rpsQ | 50S ribosomal protein L23 | -1.91 |
umuD | umuDC | DNA polymerase V, subunit D | -1.72 |
Purines, pyrimidines, nucleosides and nucleotides | |||
carA b | carAB | Carbamoyl-phosphate synthase small subunit | -2.02 |
guaB | guaBA | Inositol-5-monophosphate dehydrogenase | -2.33 |
purH b | purHD | Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase | -3.01 |
purl | Â | Phosphoribosylformyl-glycineamide synthetase | -3.33 |
purM | purMN | Phosphoribosylaminoimidazole synthetase | -2.62 |
pyrL | pyrLB I | Orotate phosphoribosyltransferase | -1.96 |
Cell envelope | |||
bcsZ | bcs AB Z C | Endo-1,4-D-glucanase | -1.58 |
eptA | Â | Predicted metal dependent hydrolase | -1.68 |
rfaJ | rfa QGPSBI J YZ-waaU | Lipopolysaccharide 1,2-glucosyltransferase | -1.68 |
rffC | rfe-rff A CD E GH MT-wzxE-wzyE-wzzE | Lipopolysaccharide biosynthesis protein/TDP-fucosamine acetyltransferase | -1.66 |
yeiU | yei R U | Undecaprenyl pyrophosphate phosphatase | -1.57 |
Fatty acid and phospholipid metabolism | |||
fabB b | Â | 3-oxoacyl-(acyl carrier protein) synthase | -1.51 |
yieE b | yieE F | Predicted phosphopantetheinyl transférase | -1.53 |
Transcription | |||
basR | basRS b | DNA-binding response regulator in two-component regulatory system with BasS | -1.68 |
crl | Â | Curlin genes transcriptional activatory protein | -2.52 |
fimB | Â | Type 1 fimbriae regulatory protein/Inversion of on/off regulator of fimA | -1.66 |
pdhR b | pdhR - aceEF - lpdA | Transcriptional regulator for pyruvate dehydrogenase complex | -3.42 |
rpoD | rpsU - dnaG - rpoD | RNA polymerase sigma factor | -1.65 |
Cellular processes | |||
c1936 f | Â | Type 1 fimbrial protein (homologue) | -3.23 |
fimA c | fimAIC DFGH | Major type 1 subunit fimbrin (pilin) | -2.10 |
ydeQ b | Â | Predicted fimbrial-like adhesin protein (F9 fimbriae) | -1.57 |
ydeR | ydeRST b | Hypothetical fimbrial-like protein (F9 fimbriae) | -2.21 |
Regulatory function | |||
oxyS e | Â | Global regulatory RNA | -1.82 |
Central intermediary metabolism | |||
iscR | iscR S U A | NifU-like protein/Scaffold protein | -1.62 |
Unknown function | |||
c3759 b,f | parC- c3759 | Hypothetical protein | -1.72 |
pqiA | pqiA B | Paraquat-inducible membrane protein | -1.70 |
yhcN | Â | Unknown | -7.82 |
yjbC | ybjC-nfsA-rimK-ybjN | Hypothetical protein | -1.54 |
ybcU | Â | Bor protein homolog from lambdoid prophage DLP12 | -1.62 |
z5852 | Â | Hypothetical protein | -1.52 |
Biosynthesis of cofactors, prosthetic groups and carriers | |||
thiC | thiCEFSGH | Thiamine biosynthesis protein | -3.30 |
Mobile and extrachromosomal element functions | |||
hfq | yjeFE-amiB-mutL - miaA - hfq - hflX K C | RNA-binding protein | -1.56 |
z3347 f | Â | Unknown protein encoded within prophage CP-933V | -1.65 |
z1876 f | Â | Putative endolysin of prophage CP-933X | -1.85 |