Table 1.

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

Category/Gene symbol	Gene accession No.	Gene description	30 min log2 ratio	60 min log2 ratio
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

(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).