TABLE 1.

MALDI-TOF MS analysis of aerobic versus anaerobic proteins identified from 2-D gels, in order of PA number from www.pseudomonas.com

Protein no.	Protein name	Gene	PA no.	PseudoCAP functional class	Expectation value	Coverage (%)	Mass (kDa)/pI	Aerobic vs anaerobic growtha	Growth in nitrate vs nitrite in absence of oxygena
29	Succinate-semialdehyde dehydrogenase	gabD	PA0265	Central intermediary metabolism; amino acid biosynthesis and metabolism; carbon compound catabolism	0.042	6.4	51.9/5.6	3.6	0.4
15	Transketolase	tktA	PA0548	Energy metabolism	0.05	7.7	72.6/5.2	2.5	3.0
7	Organic solvent tolerance protein OstA	ostA	PA0595	Membrane proteins; transport of small molecules	0.07	5.7	104.6/5.4	ND	Not detectable with nitrite
30	Probable DNA-binding stress protein		PA0862	Hypothetical, unclassified, unknown	0.011	25.0	17.5/5.0	0.6	0.28
34	N-Succinylglutamate 5-semialdehyde dehydrogenase	aruC	PA0895	Amino acid biosynthesis and metabolism	0.022	8.1	43.8/5.6	5.3	0.15
5	Flagellin type B	fliC	PA1092		0.004	13.3	49.2/5.4	0.14	0.14
13	Ribonucleoside reductase	nrdA	PA1156	Nucleotide biosynthesis and metabolism	0.028	7.9	107.6/5.6	0.33	9.7
33	Hypothetical protein		PA1191	Hypothetical, unclassified, unknown	0.017	17.8	23.0/6.3	1.4	Not detectable with nitrate
37	Glutamate-asparaginase	ansB	PA1337	Amino acid biosynthesis and metabolism	0.0	13.0	38.6/6.7	11.7	0.14
16	Succinate dehydrogenase	sdhA	PA1583	Energy metabolism	0.05	9.3	64.1/6.0	5.6	1.9
21	2-Oxoglutarate dehydrogenase	sucA	PA1585	Amino acid biosynthesis and metabolism; energy metabolism	0.001	7.1	106.4/6.1	2.2	2.5
35	Succinyl-CoA synthetase β chain	sucC	PA1588	Energy metabolism	0.19	10.6	41.8/5.8	3.0	0.7
27	Outer membrane protein OprF	oprF	PA1777	Membrane proteins; transport of small molecules	0.001	22.9	37.9/5.0	1.1	2.4
40	Aconitate hydratase 2	acnB	PA1787	Energy metabolism	0.005	7.9	94.2/5.2	5.3	1.1
24	Trigger factor	tig	PA1800	Cell division; chaperones and heat shock proteins	0.0	24.8	48.6/4.8	10.8	0.16
1	Isocitrate dehydrogenase	icd	PA2623	Carbon compound catabolism; amino acid biosynthesis and metabolism; energy metabolism	0.169	9.8	45.7/5.1	3.1	Not detectable with nitrite
28	Translation elongation factor P	efp	PA2851	Translation, posttranslational modification, degradation	0.008	21.3	21.1/4.8	NDA	Not present under anaerobic conditions
32	Leucine dehydrogenase	ldh	PA3418		0.008	7.6	35.9/5.6	1.5	Not detectable with nitrate
25	Hypothetical protein		PA3515	Hypothetical, unclassified, unknown	0.024	14.3	40.1/5.1	14.7	0.05
4	Probable peroxidase		PA3529	Adaptation, protection; putative enzymes	0.0	31.5	21.9/5.4	0.5	0.3
36	Elongation factor Ts	tsf	PA3655	Translation, posttranslational modification, degradation	0.5	14.2	30.7/5.2	4.8	0.14
26	l-Cysteine desulfurase	iscS	PA3814	Amino acid biosynthesis and metabolism; biosynthesis of cofactors, prosthetic groups, and carriers	0.004	11.6	44.8/5.7	7.6	0.5
2	Respiratory nitrate reductase β-subunit (isoform 1)	narH	PA3874	Energy metabolism	0	20.3	59.11/5.8	ND	Not detectable with nitrite
10	Respiratory nitrate reductase β-subunit (isoform 2)	narH	PA3874	Energy metabolism	0.0	15.8	59.1/5.7	ND	2.2
3	Conserved hypothetical protein		PA3944	Hypothetical, unclassified, unknown	0.029	9.9	21.9/5.4	0.8	Not detectable with nitrate
17	DNA-directed RNA polymerase α chain	rpoA	PA4238	Transcription, RNA processing and degradation	0.0	23.1	36.8/4.9	0.6	1.1
38	Elongation factor Tu	tufA	PA4265	Translation, posttranslational modification, degradation	0.0	25.4	43.7/5.2	8.6	0.14
41	Elongation factor G	fusA1	PA4266	Translation, posttranslational modification, degradation	0.033	10.2	78.1/5.1	4.3	0.6
20	Secretion protein SecA	secA	PA4403	Protein secretion/export apparatus	0.004	7.1	104.1/5.4	2.0	3.6
18	Rod shape-determining protein MrqqqqeB	mreB	PA4481	Cell wall/lipopolysaccharide/ capsule; cell division	0.001	20.3	37.2/5.3	0.9	4.1
6	Hypothetical protein		PA4495	Hypothetical, unclassified, unknown	0.07	16.5	24.9/5.8	ND	Not detectable with nitrate
43	Serine hydroxymethyltransferase	glyA3	PA4602	Amino acid biosynthesis and metabolism	0.068	9.8	45.4/5.7	2.6	0.5
42	DnaK protein	dnaK	PA4761	DNA replication, recombination, modification, and repair; adaptation and protection; chaperones and heat shock proteins	0.016	10.8	68.5/4.8	0.7	0.4
31	Probable transcriptional regulator		PA4902	Transcriptional regulators	0.029	12.4	33.6/6.1	0.54	Not detectable with nitrate
14	Pyruvate dehydrogenase	aceE	PA5015	Amino acid biosynthesis and metabolism; energy metabolism	0.0	18.5	99.9/5.6	4.1	0.4
44	Ornithine carbamoyltransferase	arcB	PA5172	Amino acid biosynthesis and metabolism	0.054	13.4	38.6/6.1	0.7	0.6
22	Probable transcarboxylase subunit		PA5435	Central intermediary metabolism	0.032	8.2	66.3/5.6	3.5	0.48
19	Hypothetical protein		PA5496	Hypothetical, unclassified, unknown	0.0	18.3	25.3/6.0	1.8	22.0
9	Hypothetical protein		PA5497	Hypothetical, unclassified, unknown	0.0	18.7	83.3/5.8	0.15	0.12
39	ATP synthase β chain	atpD	PA5554	Energy metabolism	0.02	15.1	49.5/5.0	0.4	0.4
11	ATP synthase α chain	atpA	PA5556	Energy metabolism	0.003	17.5	55.5/5.3	0.7	0.6

^aND, not detectable under aerobic conditions. NDA, not detectable under anaerobic conditions. Note that the last two columns represent x-fold changes expressed as ratios. In the second-to-last column, we compared the overall difference between 2-D images obtained under aerobic and anaerobic conditions (independent of whether nitrate or nitrite was used). Thus, the expression ratio data show averages between aerobic nitrate and nitrite cultures versus anaerobic nitrate and nitrite cultures.