Table 3.

Identification of the proteins differentially expressed during carbon starvation^a

Protein name	Gene name	Ro no.	Genetic context	Cluster	Normalized signal intensityb
					ML	T78	T83	S88	S120	S150	S447
Benzoate catabolism
Benzoate 1,2-dioxygenase alpha subunit	benA	02384	ben	1	1.70	1.30	0.61	0.43	0.15	0.11	0.07
Benzoate 1,2-dioxygenase beta subunit	benB	02385	ben	1	1.09	0.97	0.59	0.46	0.18	0.17	0.18
Benzoate 1,2-dioxygenase reductase subunit	benC	02386	ben	1	0.98	0.81	0.35	0.21	0.02	N	N
cis-1,6-Dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase	benD	02387	ben	1	0.56	0.50	0.33	0.20	0.02	0.04	0.01
Catechol 1,2-dioxygenase	catA	02373	cat	5	3.50	3.28	2.40	1.82	0.67	0.36	0.19
Muconate cycloisomerase	catB	02372	cat	5	0.42	0.35	0.23	0.11	0.02	0.01	0.01
3-Oxoacid CoA-transferase, subunit A	pcaI	01334	pca	5	0.35	0.32	0.30	0.27	0.10	0.04	0.02
Protocatechuate dioxygenase alpha subunit	pcaG	01336	pca	5	0.26	0.28	0.25	0.18	0.04	0.05	0.05
3-Oxoacid CoA-transferase	pcaJ	01333	pca	5	0.10	0.12	0.10	0.02	0.02	0.02	0.02
Protocatechuate dioxygenase beta subunit	pcaH	01335	pca	5	0.14	0.20	0.08	0.08	0.02	0.01	0.01
Acetyl-CoA C-acyltransferase	pcaF	01340	pca	9	0.28	0.39	0.42	0.39	0.30	0.20	0.02
3-Carboxy-cis,cis-muconate cycloisomerase	pcaB	01337	pca	9	0.10	0.11	0.07	0.08	0.08	0.07	N
3-Oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylase	pcaL	01338	pca	9	0.21	0.20	0.10	0.06	0.08	0.06	0.03
Transcriptional regulator, IclR family	pcaR	01339	pca	9	0.03	0.04	0.05	0.06	0.05	0.03	0.02
Other catabolic enzymes
Biphenyl 2,3-dioxygenase alpha subunit	bphAa	08060	bph	6	N	N	N	N	0.48	0.54	0.15
cis-3-Phenylcyclohexa-3,5-diene-1,2-diol dehydrogenase	bphB2	10126	bph/etb	6	N	N	N	N	0.03	0.03	0.13
2,6-Dioxo-6-phenylhexa-3-enoate hydrolase	bphD1	10136	bph/etb	6	N	N	N	N	0.10	0.08	0.03
Ethylbenzene dioxygenase alpha subunit	etbAa1	10133	bph/etb	6	N	N	N	N	0.47	0.45	0.26
2-Hydroxy-6-oxohepta-2,4-dienoate hydrolase	etbD1	08044	bph/etb	6	0.01	0.01	0.02	0.01	0.24	0.29	0.18
2,6-Dioxo-6-phenylhexa-3-enoate hydrolase	etbD2	10146	bph/etb	6	0.01	0.01	0.02	0.02	0.27	0.26	0.10
Phthalate 3,4-dioxygenase, ferredoxin reductase subunit	padAd1	08162/12013	pad	3	0.02	0.03	0.07	0.09	0.03	0.02	N
Phthalate ester hydrolase	patE	08169	pat	3	0.04	0.04	0.09	0.12	0.07	0.06	0.03
Propane monooxygenase hydroxylase large subunit	prmA	00441	Cluster with phenol hydroxylase and GroEL	2	0.02	0.03	0.03	0.04	0.13	0.68	0.38
Probable 1,3-propanediol dehydrogenase		06057	ATP-dependent protease	2	0.05	0.03	0.15	0.24	0.24	0.56	0.29
Other catabolic enzymes
CODH, medium subunit	coxM2	04975	CODH	6	0.09	0.11	0.08	0.12	0.22	0.20	0.19
CODH, maturation factorc	coxF3	05229	CODH	6	N	N	N	N	0.17	0.38	0.49
CODH, medium subunitc	coxM3	05230	CODH	6	0.04	0.07	0.03	0.04	0.18	0.20	0.43
CODH, large subunitc	coxL3	05232	CODH	6	N	N	0.05	0.04	0.17	0.20	0.46
Central metabolism
6-Phosphofructokinase	pfkA	06479	Amidotransferase gat	5	0.02	0.04	0.03	0.03	0.01	N	N
Pyruvate kinase	pyk1	01007	Glutamate synthase	5	0.29	0.29	0.29	0.27	0.30	0.18	0.19
Dihydrolipoyl dehydrogenasee	dldH1	02140	Hypothetical	1	0.09	0.04	N	N	N	N	N
Citrate synthase		04998	Peptidylprolyl isomerase	7	0.03	0.05	0.05	0.05	0.03	0.02	N
Citrate synthase	citA4	04993, 08812	Phosphoserine transaminase	4	0.09	0.09	0.03	0.01	0.02	0.01	0.004
Isocitrate dehydrogenasee		06238	Arabinose efflux	4	0.16	0.10	0.02	N	N	N	N
Succinate dehydrogenase	sdhA2	06246	sdh	4	0.60	0.45	0.33	0.31	0.32	0.19	0.27
Succinate-CoA ligase, alpha subunit	sucD	05573	suc	7	1.00	0.85	0.85	0.80	0.67	0.58	0.42
Succinate-CoA ligase, beta subunit	sucC	05574	suc	7	1.07	0.82	0.79	1.03	0.92	0.58	0.50
Malate dehydrogenase	fabF	06000	Single gene	7	0.20	0.24	0.25	0.16	0.06	0.02	0.06
Isocitrate lyase		02122	Lipid metabolism	2	0.20	0.22	0.74	0.75	0.59	0.38	0.46
Fumarate hydratasee		08824	Succinate dehydrogenase	2	N	N	0.01	0.01	0.01	0.02	0.02
Glucose-6-phosphate 1-dehydrogenase	zwf4	07184	Pentose phosphate pathway	2	0.03	0.02	0.03	0.04	0.05	0.05	0.11
Phosphogluconate dehydrogenase	gnd3	07246	RNA helicase	2	0.08	0.06	0.15	0.23	0.39	0.43	0.50
Stress response
Chaperonin GroL2c,e	groL2	02146	Universal stress protein	9	0.83	0.69	0.60	0.60	0.65	0.63	N
Chaperone protein GroELc,e	groEL	06190	10-kDa chaperonin	9	0.81	0.67	1.20	0.93	0.71	0.63	0.34
Chaperonin GroL1c,e	groL1	00448	Propane monooxygenase	2	N	N	0.61	0.37	0.11	1.45	N
Heat shock protein Hsp70 DnaK1c,e	dnaK1	05497	Chaperones: grpE1, dnaJ2	8	1.01	1.10	0.71	0.72	1.07	1.99	1.36
Universal stress proteinc,e		02263	Universal stress protein, oxidoreductase	3	0.03	0.03	0.06	0.06	0.05	0.03	0.03
Universal stress proteinc,e		04893	Pseudouridylate synthase	8	0.08	0.06	0.06	0.12	0.12	0.19	0.18
Catalased,e	katE	04309	Fe(3+) uptake regulator	7	0.02	0.05	0.05	0.07	0.04	0.01	0.02
Superoxide dismutasee	sodA	04009	Amidotransferase	2	1.08	0.90	1.10	1.19	1.40	1.38	1.62
Heme superoxide dismutasec		06860	Heme biosynthesis, oxidoreductase	10	0.19	0.19	0.18	0.26	0.25	0.31	0.39
ATP-dependent Clp proteased,e	clpP	01371	clpX, FKBP-type bacterial trigger factor	10	0.25	0.25	0.40	0.41	0.30	0.43	0.50
Prolyl aminopeptidasec,e		01171	panB, coenzyme metabolism	8	0.01	0.03	0.03	0.02	0.01	0.09	N
Cell division initiation protein		01080	Cell division	6	0.002	0.005	0.01	0.07	0.11	0.08	0.03
Transcription
RNA polymerase sigma factor G	sigG	05361	ArsR	2	0.07	0.07	0.11	0.13	0.17	0.14	0.18

^aProtein identification was accepted if the MASCOT-generated probability-based Mowse score in the RHA1 protein database was greater than 55 (P < 0.05) and at least 3 peptides were identified. When the MASCOT score was below the threshold, the protein ID was accepted only if the theoretical and experimental pI and MW agreed. N, not detected.

^bSpot signal intensities were normalized and averaged over three biological replicates.

^cProteins reported to be regulated by MglA (21).

^dProteins reported to be regulated by SigB (4).

^eProteins reported to be affected by starvation in references 4, 7, 14, 21, 25, 50, and 55.