TABLE 3.

Selected subset of genes that are delayed in the letS(T311M) mutant compared to the WT

Family	Gene IDa	Gene name	Paris strain ID	Lens strain ID	Description	Fold change at the indicated OD600 valueb
						2	3
Regulation	lpg0277		lpp0351	lpl0329	Regulatory protein (EAL domain)	−3.2	—
	lpg1168		lpp1170	lpl1176	Regulatory protein (GGDEF and EAL domains)	−3.4	—
	lpg2457		lpp2523	lpl2376	Two-component response regulator (crystallized)	−2.4	—
	lpg2732	lqsR	lpp2788	lpl2657	LqsR response regulator	−2.5	—
	lpg0586		lpp0636	lpl0620	Putative transcriptional regulator	—	−5.4
	lpg1114ac		lpp1115	lpl1119	KaiB-like circadian clock protein	—	−2.1
	lpg1115	kaiC2	lpp1116	lpl1120a	Putative circadian clock protein KaiC	—	−2.5
	lpg1577	rpoE	lpp1535	lpl1448	Sigma factor RpoE (σ24)	—	−3.9
	lpg1796		lpp1760	lpl1760	LysR family transcriptional regulator	—	−2.0
	lpg2132		lpp2071	lpl2061	Regulatory protein (GGDEF domain)	—	−2.5
	lpg2145		lpp2083	lpl2073	Putative two-component response regulator	—	−2.9
	lpg2146	stuC	lpp2084	lpl2074	Sensor histidine kinase	—	−2.8
	lpg2181	arcB	lpp2133	lpl2108	Putative histidine kinase/response regulator	—	−2.5
	lpg2524				LuxR family transcriptional regulator	—	−2.9
Flagellum biosynthesis	lpg1218	flgD	lpp1226	lpl1226	Flagellar basal-body rod modification protein	−2.4	—
	lpg1219	flgE	lpp1227	lpl1227	Flagellar hook protein	−6.1	—
	lpg1220	flgF	lpp1228	lpl1228	Flagellar biosynthesis protein	−4.3	—
	lpg1221	flgG	lpp1229	lpl1229	Flagellar biosynthesis protein	−2.1	—
	lpg1222	flgH	lpp1230	lpl1230	Flagellar L-ring protein precursor	−2.3	—
	lpg1223	flgI	lpp1231	lpl1231	Flagellar P-ring protein precursor	−2.9	—
	lpg1224	flgJ	lpp1232	lpl1232	Flagellar biosynthesis protein	−2.6	—
	lpg1225	flgK	lpp1233	lpl1233	Flagellar hook-associated protein	−4.9	—
	lpg1226	flgL	lpp1234	lpl1234	Flagellar hook-associated protein	−4.4	—
	lpg1340	flaA	lpp1294	lpl1293	Flagellin	—	−4.0
Type IV pilus	lpg0627	pilE	lpp0681	lpl0664	Type IV pilin	—	−2.6
	lpg0628		lpp0682	lpl0665	Type IV fimbrial biogenesis PilY1-related protein	—	−3.4
	lpg0629		lpp0683	lpl0666	Tfp pilus assembly protein PilX	—	−2.9
	lpg0631		lpp0685	lpl0668	Type IV fimbrial biogenesis protein PilV	—	−3.8
	lpg0632		lpp0686	lpl0669	Type IV fimbrial pilin related protein	—	−7.5
Virulence	lpg0910	enhA2	lpp0972	lpl0942	Similar to enhanced entry protein EnhA	—	−3.7
	lpg1355	sidG	lpp1309		SidG; substrate of the Dot/Icm T4SS	—	−2.9
	lpg1386	enhA3	lpp1341	lpl1337	Similar to enhanced entry protein EnhA	—	−3.8
	lpg2157	sdeA	lpp2096	lpl2085	SdeA; substrate of the Dot/Icm T4SS	—	−3.1
	lpg2862	legC8			Cytotoxic glucosyltransferase	—	−4.3
Eukaryotic-like	lpg0625		lpp0679	lpl0662	Similar to unknown eukaryotic proteins	—	−2.8
	lpg1158		lpp1160		Some similarity with eukaryotic proteins	—	−3.0
	lpg1491		lpp1447		Some similarity with eukaryotic proteins	—	−3.0
Putatively involved in PHB synthesis	lpg0560	phaB1	lpp0620	lpl0603	Acetoacetyl-coenzyme A reductase	−2.8	—
	lpg1059	phaB3	lpp2322	lpl1056	Acetoacetyl-coenzyme A reductase	−2.2	—
Unknown	lpg0012		lpp0012	lpl0012	Unknown	−3.2	−2.6
	lpg1174ac		lpp1177	lpl1183	Unknown	−5.8	−8.5
	lpg0741		lpp0806	lpl0777	Unknown	—	−5.5
	lpg1895		lpp1864	lpl1859	Unknown	—	−6.0
	lpg2569				Unknown	—	−5.9
	lpg2803		lpp2849	lpl2718	Unknown	—	−6.4

^aID, identifier.

^b—, no statistically significant difference in expression was detected between WT and letS(T311M) mutant bacteria.

^cThese genes were not predicted in the Philadelphia-1 strain. Their identifiers therefore became that of the gene located upstream on the chromosome with the addition of the letter “a.” For exact location and orientation of these genes, see Table S2 in the supplemental material.