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Table 1 Genes with modulated expression after exposure to colicin M over time, 30 and 60 min

From: Global transcriptional responses to the bacteriocin colicin M in Escherichia coli

Category/Gene symbol Gene accession No. Gene description 30 min log2ratio 60 min log2ratio
Envelope stress regulators/systems     
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     
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     
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     
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     
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     
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     
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     
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     
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     
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
  1. (bold indicates genes with gene expression log2 ratio (fold change) ≥1 and ≤−1, denoting fold change ≥2 or ≤−2, and with p≤0.05, and italic indicates genes with p≥0.05).