From: Global transcriptional responses to the bacteriocin colicin M in Escherichia coli
Category/Gene symbol | Gene accession No. | Gene description | 30Â min log2ratio | 60Â min log2ratio |
---|---|---|---|---|
Envelope stress regulators/systems | Â | Â | Â | Â |
rcsA | 946467 | DNA-binding transcriptional activator, co-regulator with RcsB | 3.38 | 6.13 |
cpxP | 2847688 | inhibitor of the cpx response; periplasmic adaptor protein | 1.57 | 2.61 |
pspA | 945887 | regulatory protein for phage-shock-protein operon | 1.35 | 1.18 |
pspB | 945893 | DNA-binding transcriptional regulator of psp operon | 1.32 | 1.47 |
pspC | 945499 | DNA-binding transcriptional activator | 1.14 | 1.52 |
pspD | 945635 | peripheral inner membrane phage-shock protein | 0.83 | 1.78 |
pspG | 948557 | phage shock protein G | 1.55 | 2.29 |
Colanic acid biosynthetic process | Â | Â | Â | Â |
wza | 946558 | lipoprotein required for capsular polysaccharide translocation through the outer membrane | 3.59 | 7.12 |
wzb | 946564 | protein-tyrosine phosphatase | 2.44 | 6.33 |
wzc | 946567 | protein-tyrosine kinase | 1.52 | 6.72 |
wcaA | 946570 | predicted glycosyl transferase | 0.93 | 5.7 |
wcaB | 946573 | predicted acyl transferase | 0.69 | 5.73 |
wcaC | 946579 | predicted glycosyl transferase | 0.56 | 5.47 |
wcaD | 946550 | predicted colanic acid polymerase | 0.78 | 7.23 |
wcaE | 946543 | predicted glycosyl transferase | 1.25 | 7.26 |
wcaF | 946578 | predicted acyl transferase | 0.97 | 7.21 |
gmd | 946562 | GDP-D-mannose dehydratase, NAD(P)-binding | 0.71 | 6.65 |
fcl | 946563 | bifunctional GDP-fucose synthetase: GDP-4-dehydro-6-deoxy-D-mannose epimerase/GDP-4-dehydro-6-L-deoxygalactose reductase | 0.32 | 6.57 |
gmm | 946559 | GDP-mannose mannosyl hydrolase | 0.3 | 6.15 |
wcaI | 946588 | predicted glycosyl transferase | 0.3 | 5.92 |
cpsG | 946574 | phosphomannomutase | 0.09 | 5.15 |
cpsB | 946580 | mannose-1-phosphate guanyltransferase | 0.26 | 5.1 |
wcaJ | 946583 | predicted UDP-glucose lipid carrier transferase | 0.11 | 4.82 |
wzxC | 946581 | predicted colanic acid exporter | 0.1 | 4.45 |
wcaK | 946569 | Colanic acid biosynthesis protein | −0.12 | 4.45 |
wcaL | 946565 | predicted glycosyl transferase | −0.13 | 3.63 |
manA | 944840 | mannose-6-phosphate isomerase | 0.19 | 1.05 |
ugd | 946571 | UDP-glucose 6-dehydrogenase | 0.46 | 4.36 |
wcaM | 946561 | colanic acid biosynthesis protein | −0.01 | 2.71 |
galU | 945730 | glucose-1-phosphate uridylyltransferase | 0.44 | 1.4 |
Extracellular polysaccharide distinct from colanic acid | Â | Â | Â | Â |
yjbE | 948534 | predicted protein | 1.55 | 5.74 |
yjbF | 948533 | predicted lipoprotein | 1.73 | 5.67 |
yjbG | 948526 | conserved protein | 0.67 | 4.29 |
yjbH | 948527 | predicted porin | 0.66 | 5.23 |
Peptidoglycan synthesis | Â | Â | Â | Â |
anmK | 946810 | anhydro-N-acetylmuramic acid kinase | 0.16 | 1.17 |
mrcB | 944843 | fused glycosyl transferase and transpeptidase | 0.47 | 1.01 |
ycfS | 945666 | L,D-transpeptidase linking Lpp to murein | 0.77 | 2 |
Osmotic stress response | Â | Â | Â | Â |
osmB | 945866 | lipoprotein | 2.41 | 2.95 |
osmC | 946043 | osmotically inducible, stress-inducible membrane protein | 0.44 | 1.15 |
opgB | 948888 | phosphoglycerol transferases I and II | 0.12 | 1.27 |
opgC | 946944 | membrane protein required for succinylation of osmoregulated periplasmic glucans (OPGs) | 0.31 | 1.85 |
ivy | 946530 | inhibitor of vertebrate C-lysozyme | 1.55 | 1.26 |
mliC | 946811 | inhibitor of C-lysozyme, membrane-bound; predicted lipoprotein | 2.17 | 3.92 |
ybdG | 946243 | predicted mechanosensitive channel | 0.69 | 1.26 |
dppB | 948063 | dipeptide/heme transporter | −0.29 | 3.29 |
dppF | 948056 | dipeptide transporter | −0.1 | 2.33 |
dppC | 948064 | dipeptide/heme transporter | −0.09 | 2.33 |
dppD | 948065 | dipeptide/heme transporter | −0.09 | 2.1 |
dppA | 948062 | dipeptide transporter | 0.02 | 1.13 |
Other stress responses | Â | Â | Â | Â |
ydeI | 946068 | conserved protein | 1.99 | 3.96 |
treR | 948760 | DNA-binding transcriptional repressor | 0.65 | 1.88 |
ibpA | 948200 | heat shock chaperone | −0.01 | 1.78 |
ibpB | 948192 | heat shock chaperone | 0.02 | 2.9 |
hslJ | 946525 | heat-inducible lipoprotein involved in novobiocin resistance | 2.33 | 3.32 |
yhbO | 947666 | predicted intracellular protease | 2.29 | 2.67 |
iraM | 945729 | RpoS stabilizer during Mg starvation, anti-RssB factor | 0.33 | 1.6 |
creD | 948868 | inner membrane protein | 5.66 | 4.96 |
cbrB | 948231 | inner membrane protein, creBC regulon | 5.2 | 4.29 |
cbrA | 948197 | predicted oxidoreductase with FAD/NAD(P)-binding domain | 4.3 | 3.35 |
cbrC | 948230 | conserved protein, UPF0167 family | 3.77 | 2.8 |
spy | 946253 | envelope stress induced periplasmic protein | 1.71 | 2.99 |
htpX | 946076 | predicted endopeptidase | 0.27 | 1.01 |
yggG | 945173 | heat shock protein binding to Era protein; predicted peptidase | 1.01 | 1.82 |
Biofilm formation | Â | Â | Â | Â |
ycfJ | 945977 | predicted protein | 4.77 | 5.8 |
rprA | 2847671 | ncRNA | 3.86 | 4.85 |
omrA | 2847746 | ncRNA | 0.36 | 1.76 |
omrB | 2847747 | ncRNA | 0.77 | 1.74 |
bdm | 946041 | biofilm-dependent modulation protein | 4.49 | 4.21 |
ydeH | 946075 | diguanylate cyclase, required for pgaD induction | 1.38 | 1.68 |
Cell motility | Â | Â | Â | Â |
fliZ | 946833 | RpoS antagonist; putative regulator of FliA activity | −0.41 | −1.05 |
fliE | 946446 | flagellar basal-body component | −0.66 | −1.07 |
fliG | 946451 | flagellar motor switching and energizing component | −0.28 | −1.07 |
flgN | 945634 | export chaperone for FlgK and FlgL | −0.29 | −1.12 |
flgA | 946300 | assembly protein for flagellar basal-body periplasmic P ring | −0.09 | −1.17 |
flgF | 945639 | flagellar component of cell-proximal portion of basal-body rod | −0.29 | −1.21 |
flgM | 946684 | anti-sigma factor for FliA (sigma 28) | −0.27 | −1.23 |
fliA | 948824 | RNA polymerase, sigma 28 (sigma F) factor | −0.21 | −1.45 |
flgD | 945813 | flagellar hook assembly protein | −0.33 | −1.61 |
flgE | 945636 | flagellar hook protein | −0.05 | −1.72 |
flgC | 946687 | flagellar component of cell-proximal portion of basal-body rod | −0.04 | −2.14 |
flgB | 945678 | flagellar component of cell-proximal portion of basal-body rod | −0.19 | −2.4 |
flhC | 947280 | DNA-binding transcriptional dual regulator with FlhD | −0.76 | −2.54 |
flhD | 945442 | DNA-binding transcriptional dual regulator with FlhC | −0.76 | −2.54 |
Amino acid transport/acid resistance | Â | Â | Â | Â |
glnP | 945621 | glutamine transporter subunit | −0.23 | −1.17 |
gadB | 946058 | glutamate decarboxylase B, PLP-dependent | 0.03 | −1.18 |
glnQ | 945435 | glutamine transporter subunit | −0.15 | −1.25 |
glnG | 948361 | fused DNA-binding response regulator in two-component regulatory system with GlnL: response regulator/sigma54 interaction protein | −0.15 | −1.32 |
gadA | 948027 | glutamate decarboxylase A, PLP-dependent | −0.23 | −1.64 |
gadE | 948023 | DNA-binding transcriptional activator | 0.13 | −1.38 |
slp | 948022 | outer membrane lipoprotein | −0.18 | −1.91 |
hdeB | 948026 | acid-resistance protein | 0.13 | −1.17 |
hdeD | 948024 | acid-resistance membrane protein | −0.01 | −1.04 |
Poorly characterized | Â | Â | Â | Â |
ymgD | 945732 | predicted protein | 3.45 | 3.65 |
ymgG | 945728 | conserved protein, UPF0757 family | 3.87 | 3.55 |
yfdC | 944801 | predicted inner membrane protein | 1.02 | 2.25 |
yjbJ | 948553 | conserved protein, UPF0337 family | 0.97 | 1.19 |
yaaX | 944747 | predicted protein | 1.59 | 4.12 |
yegS | 946626 | phosphatidylglycerol kinase, metal-dependent | 0.81 | 1.65 |
yaiY | 945223 | inner membrane protein, DUF2755 family | 3.94 | 5.22 |