Table 2.

The 50 nonribosomal genes most highly expressed in vivo in this study

ORFc	Gene	Annotation	Ranka		Fold changeb
			In vivo	In vitro
PMI1035		Translation initiation factor IF-3	9	3	−1.33
PMI0765	ompF	Outer membrane porin	13	3	−1.25
PMI3251	tufB	Elongation factor Tu	13	6	−1.23
PMI3275	secY	Preprotein translocase SecY subunit	23	20	1.03
PMI3280	rpoA	DNA-directed RNA polymerase alpha chain	26	19	−1.32
PMI2792	tufB	Elongation factor Tu	28	29	−1.16
PMI0856		Conserved hypothetical protein	29	36	−1.85
PMI0862	acpP	Acyl carrier protein	33	16	−1.66
PMI0263	mrpA	Major mannose-resistant/Proteus-like fimbria	37	3,040	13,806.33
PMI0785	ompA	Outer membrane protein A	37	50	1.21
PMI1676	cspC	Cold shock-like protein	39	9	−2.09
PMI2771	hupA	DNA-binding protein HU-alpha (HU-2)	52	60	−1.39
PMI3375	priB	Primosomal replication protein N	52	34	−1.61
PMI2793	fusA	Elongation factor G (EF-G)	52	80	1.17
PMI0716	ihfB	Integration host factor beta-subunit	57	53	−1.25
PMI0384	rimM	16S rRNA processing protein	59	59	−1.28
PMI2284	tsf	Elongation factor Ts	59	75	−1.00
PMI3059	atpE	ATP synthase C chain	59	57	−1.47
PMI1213	ahpC	Alkyl hydroperoxide reductase subunit C	62	165	6.14
PMI3062	atpA	ATP synthase alpha chain	62	68	−1.07
PMI3415	secG	Protein export membrane protein	66	71	−1.05
PMI0073	ahpC	Putative alkyl hydroperoxide reductase	67	104	1.83
PMI3063	atpG	ATP synthase gamma chain	68	70	−1.14
PMI0385	trmD	tRNA (guanine-N1)-methyltransferase	69	65	−1.69
PMI0585	pal	Peptidoglycan-associated lipoprotein	71	46	−2.60
PMI3060	atpF	ATP synthase B chain	71	60	−1.39
PMI1504	gapA	Glyceraldehyde 3-phosphate dehydrogenase A	72	81	1.33
PMI0118	hupB	DNA-binding protein HU-beta	75	76	−1.70
PMI3064	atpD	ATP synthase beta chain	75	69	−1.18
PMI3065	atpC	ATP synthase epsilon chain	78	84	−1.22
PMI3061	atpH	ATP synthase delta chain	81	83	−1.15
PMI2544	groS	10-kDa chaperonin	82	66	−1.26
PMI3057	atpI	ATP synthase protein I	82	85	−1.35
PMI3296		Conserved hypothetical protein	83	96	−1.11
PMI0418	cspE	Putative cold shock protein	84	69	−2.52
PMI0861	fabG	3-Oxoacyl-[acyl-carrier protein] reductase	85	79	−1.67
PMI1039	pheT	Phenylalanyl-tRNA synthetase beta chain	93	103	1.06
PMI2784	rpoC	DNA-directed RNA polymerase beta′ subunit	93	95	−1.15
PMI1898	grcA	Autonomous glycyl radical cofactor	95	788	19.18
PMI3622	fis	DNA-binding protein Fis	96	90	−1.37
PMI1034	thrS	Threonyl-tRNA synthetase	96	90	−1.27
PMI0114	tig	Trigger factor	98	98	−1.15
PMI1828	ptsH	Phosphotransferase system phosphocarrier protein	100	683	16.77
PMI1488	hns	DNA-binding protein (histone-like structuring protein)	100	93	−1.41
PMI3364	miaA	tRNA delta(2)-isopentenylpyrophosphate transferase	102	137	−1.11
PMI2833		Putative endoribonuclease	103	124	−1.02
PMI0842		TonB-dependent receptor	104	913	17.18
PMI3058	atpB	ATP synthase A chain	106	77	−1.66
PMI0243	fbaA	Fructose-bisphosphate aldolase class II	110	144	1.61
PMI0691	infA	Translation initiation factor IF-1	111	101	−1.60

^aMedian expression rank across nine microarrays (including ribosomal genes): 1 is most highly expressed, and 3,719 is most weakly expressed.

^bMedian fold change in vivo compared to LB broth across nine microarrays.

^cORF, open reading frame.