TABLE 1.

E. coli lipoprotein genes and their expression in microarray and RT-PCR analyses^a

Gene	Blattner no.	Analysis result for growth condition
		Aerobic		Anaerobic		Anaerobic + nitrate
		Microarrayb	RT-PCR	Microarrayb	RT-PCR	Microarrayb	RT-PCR
yaeF	b0193	2.85 A	822.74	3.8 A	904.07	5.2 M	709.66
yafL	b0227	13.9 A	149.00	16.15 A	129.12	8.95 A	126.31
yaiW	b0378	39.75 A	1,094.73	39.75 A	1,218.82	46.05 A	1,153.40
ybfP	b0689	4.35 A	112.50	17.9 A	207.54	11.75 A	304.80
ymcA	b0984	2.25 A	370.83	6.05 A	466.07	16.35 M	972.86
ycdR	b1023	0.3 A	38.25	1.2 A	77.86	0.7 A	31.79
ycjN	b1310	12.2 A	23.84	13.1 A	46.44	11.6 A	47.93
wza	b2062	8.65 A	85.28	4.35 A	59.48	4.55 A	75.04
yehR	b2123	1.85 A	250.38	4.65 A	325.93	4.75 A	414.85
yohG	b2138	8.85 A	82.18	19 A	128.07	13.7 A	133.48
yfbK	b2270	15.35 A	19.51	11.6 A	29.78	5.1 A	39.77
ypdI	b2376	0.45 A	108.74	0.35 A	238.47	0.55 A	364.14
yfgH	b2505	5.5 A	256.39	4.1 A	255.68	8.45 A	223.25
yfjS	b2636	3.9 A	165.50	1.8 A	112.20	0.9 A	119.93
yghG	b2971	1.65 A	123.61	1.15 A	82.76	1.1 A	162.09
yghH	b3014	12.6 A	907.25	11.95 A	1,012.54	9.05 A	753.22
acrE	b3265	0.7 A	62.24	0.85 A	58.61	1.35 A	59.62
yiaD	b3552	47.05 M	952.14	24.5 A	603.81	31.35 A	680.38
yiiG	b3896	3.8 A	72.07	3.35 A	107.60	4.8 A	118.86
yjbH	b4029	14.3 A	81.04	14.2 A	147.49	13.35 A	212.67
yjcP	b4080	3.25 A	44.44	4.75 A	81.48	3.85 A	147.26
yaaY	b0024	5.55 A	416.62	10.5 M	998.73	12.9 P	1,417.36
yajI	b0412	20.25 A	300.04	28.65 P	417.83	23.7 A	357.06
ybfN	b0682	15.6 M	357.89	18.55 P	576.64	14.95 M	465.00
yccZ	b0983	25.95 A	341.56	23.15 M	268.29	61.95 P	672.07
ymcC	b0986	15.1 M	192.77	16 M	267.76	47.05 P	2,090.53
csgG	b1037	2.8 A	408.03	18.35 P	1,182.28	12.6 A	581.54
yfiL	b2602	10.35 A	495.61	11.3 A	570.68	11.05 P	368.30
yghJ	b2974	26.6 P	443.18	11.6 A	218.09	9.9 A	187.63
yhiU	b3513	19.4 A	80.34	109.6 P	2,151.94	31.2 A	295.74
yjbF	b4027	27.8 A	58.37	29.9 A	54.12	25 P	45.37
yafT	b0217	15.35 P	344.12	13.7 M	207.16	18.6 P	258.22
ylcB	b0572	83.3 P	2,207.72	11.75 P	128.07	10.25 A	64.35
ybjP	b0865	23.3 P	1,027.23	17.7 A	986.19	58.35 P	1,965.78
yfhM	b2520	22 A	490.08	65.3 P	1,712.68	58.95 P	795.13
slp	b3506	5.6 A	228.51	170.3 P	10,280.10	41.25 P	1,755.04
cutF	b0192	49.65 P	3,464.82	50 P	3,315.12	68.95 P	3,713.77
yaeC	b0197	569.75 P	5,357.99	673.1 P	9,794.30	604.75 P	9,094.88
dniR	b0211	211 P	14,770.97	332.75 P	26,075.12	288.65 P	18,758.77
cyoA	b0432	1,508.05 P	97,254.40	933.95 P	64,118.31	975.1 P	61,809.18
yajG	b0434	467.95 P	18,182.95	322.2 P	11,028.77	286.75 P	8,052.42
ybaY	b0453	43.3 P	10,698.22	52.85 P	19,343.93	137.5 P	8,323.34
acrA	b0463	266 P	21,274.95	262.05 P	20,837.08	256.6 P	10,104.47
ybbC	b0498	12.75 P	1,414.58	23 P	2,338.44	36.15 P	2,893.17
fepG	b0589	68.8 P	5,840.72	57.9 P	4,170.60	70.8 P	7,139.73
rlpA	b0633	172.2 P	8,577.58	173.4 P	6,234.43	168.75 P	3,118.40
rlpB	b0641	336.65 P	16,256.17	344.35 P	18,380.11	280.8 P	13,556.01
ybgE	b0735	80.55 P	4,025.33	625.2 P	37,117.42	622.35 P	26,673.41
pal	b0741	1,088.75 P	85,844.86	858.3 P	72,334.53	737.95 P	48,684.70
ybhC	b0772	184.35 P	4,837.29	152.35 P	4,447.57	133.55 P	3,426.66
yliB	b0830	94.75 P	4,305.95	239 P	16,813.26	195.8 P	8,175.31
yceK	b1050	27 P	2,825.53	32.9 P	4,227.41	35.8 P	5,551.83
yceB	b1063	69.45 P	585.53	101.15 P	1,133.21	106.3 P	481.83
flgH	b1079	431.6 P	22,619.34	274.5 P	12,798.09	115.15 P	5,517.09
ycfL	b1104	90.75 P	8,457.11	121.55 P	11,679.68	160.85 P	12,752.51
ycfM	b1105	113.6 P	3,414.83	185.75 P	6,983.48	225.45 P	9,351.10
lolB	b1209	151.55 P	7,612.79	205.95 P	11,120.93	285.6 P	13,613.65
osmB	b1283	49.1 P	1,493.47	132.65 P	5,617.43	98.75 P	3,191.80
ynbE	b1382	16.25 P	1,639.73	19.4 P	1,998.16	20.3 P	1,368.70
ydcL	b1431	38.25 P	1,839.59	31.85 P	1,342.37	63.35 P	2,357.52
yddW	b1491	13.2 P	327.56	23.5 P	651.77	16.2 P	372.78
ydeK	b1510	34 P	1,152.62	47.85 P	3,366.87	47.3 P	3,367.11
slyB	b1641	1,177.4 P	60,695.57	1,052.75 P	61,458.84	1,110.9 P	78,871.69
lpp	b1677	2,142.5 P	652,557.12	1,581.5 P	488,494.78	1,501.85 P	374,766.64
nlpC	b1708	75 P	2,709.71	78.35 P	3,360.72	72.35 P	3,052.40
osmE	b1739	45.55 P	3,368.38	63.3 P	4,086.45	219.75 P	14,538.54
yoaF	b1793	48.6 P	1,424.51	45.65 P	1,424.32	47.3 P	1,586.21
yeaY	b1806	107.7 P	4,334.04	86 P	2,973.40	130.3 P	2,282.15
yebF	b1847	136.6 P	3,104.08	132.2 P	3,019.95	197.15 P	5,182.22
yecR	b1904	126.4 P	14,835.41	25.95 P	1,935.43	17.15 P	940.23
yedD	b1928	172.1 P	12,536.98	171.3 P	11,952.42	160.55 P	19,869.35
spr	b2175	587.4 P	46,027.52	233.45 P	17,688.27	220.05 P	14,997.48
rtn	b2176	56.55 P	952.64	50.45 P	874.74	48.65 P	664.40
yojL	b2214	46.1 P	872.69	59.3 P	1,142.29	61.25 P	877.69
vacJ	b2346	220.5 P	3,966.98	167.4 P	3,049.50	159.7 P	2,716.95
yfeY	b2432	96.85 P	6,019.97	114.6 P	6,788.17	245.15 P	12,690.81
nlpB	b2477	354 P	11,015.25	426.5 P	16,943.41	392.3 P	10,879.40
yfgL	b2512	313.4 P	21,018.48	293.95 P	23,681.22	328.35 P	27,646.47
yfiH	b2593	85.1 P	4,998.32	95.3 P	6,011.15	101.95 P	5,639.94
yfiO	b2595	332.25 P	15,555.04	343.8 P	17,027.70	376.75 P	16,355.48
yfiB	b2605	64.05 P	3,947.83	77.95 P	3,417.15	73.05 P	4,036.95
mltB	b2701	41.95 P	560.42	65.95 P	600.54	71.65 P	656.93
nlpD	b2742	1,018.55 P	54,658.96	1,397.25 P	93,860.15	1,480.25 P	57,912.34
ygdI	b2809	10.9 P	593.84	15.5 P	1,113.41	52.8 P	2,160.82
mltA	b2813	64 P	1,918.08	75.35 P	2,154.47	91.3 P	1,910.28
ygdR	b2833	49.05 P	1,914.44	50.15 P	1,576.61	60.65 P	2,155.33
ygeR	b2865	42.3 P	501.07	50.1 P	573.73	48.2 P	348.11
mltC	b2963	126.6 P	3,392.37	101.15 P	2,259.74	99.35 P	1,746.64
yraP	b3150	119.05 P	5,530.13	108.25 P	6,152.70	174.3 P	8,350.46
nlpI	b3163	1,415.7 P	197,056.23	1,460.15 P	299,438.99	1,470.4 P	281,225.58
yhdV	b3267	28 P	582.55	28.45 P	815.84	21 P	260.17
yhfL	b3369	11.8 P	338.64	11.45 P	478.89	12.05 P	406.85
nlpA	b3661	62.9 P	2,889.24	78 P	4,949.62	94.3 P	5,323.51
blc	b4149	31.25 P	1,599.72	22.8 P	1,090.51	56.25 P	1,189.99
yjfO	b4189	26.9 P	968.41	19.9 P	963.99	25.45 P	966.50
fecD	b4288	15.85 P	593.54	11.85 P	392.53	12.3 P	336.81
rcsf	b0196	220.45 P		232.75 P		263.2 P
borD	b0557	98.2 P		117.5 P		62.85 P
ybjR	b0867	48.35 P		49.85 P		71.2 P
ycaL	b0909	15.1 P		23.95 P		23.2 P
mltE	b1193	106.5 P		104.2 P		89.6 P
hslJ	b1379	35.1 P		75.15 P		77 P
ynfC	b1585	25 P		17 P		19.5 P
smpA	b2617	199.45 P		196.35 P		257.5 P
yggG	b2936	47.3 P		32.8 P		34.25 P
yidQ	b3688	86.85 P		164.35 P		227 P
yidX	b3696	8.6 P		6.4 P		7.85 P
yjeI	b4144	228.5 P		182.9 P		216.4 P

^aGenes are divided into four groups based on the microarray expression profile described in the text. RT-PCR measurements were made as described in the text, and data are expressed as the gene copy number in the presence of reverse transcriptase minus the gene copy number in the absence of reverse transcriptase and are normalized to 10 μg of mRNA. Each value is the average for two experiments.

^bmRNA status as determined by analysis with Affynaetrix Suite 5.0 software: P, present with 95% confidence; A, absent; M, marginal (present with 94% confidence).