. 2012 Nov 23;11:152. doi: 10.1186/1475-2859-11-152

Table 1.

Functional classification and relative fold change of K. oxytoca BAS-10 proteins differentially expressed during anaerobic growth in FEC

Spot	Protein name	Acronym	NCBI code	Theor. pI/Mr (kDa)	Exp. pI/Mr (kDa)	Functional class^a	Relative fold change^b(−O₂FEC Vs +O₂FEC)	Relative fold change^b(−O₂FEC Vs -O₂NAC)
1	NADP-specific glutamate dehydrogenase	GLDH	376386651	6.73/49	6.26/45	Amino Acid Metabolism	1	2.6
5^*	Nitrogen regulatory protein P-II 2	GlnK	376394829	5.84/12	5.62/13	Amino Acid Metabolism	−3.2	−8.7
6	Nitrogen regulatory protein P-II 2	GlnK	376394829	5.84/12	5.62/13	Amino Acid Metabolism	1	−2.7
7	Nitrogen regulatory protein P-II 2	GlnK	376394829	5.84/12	5.20/13	Amino Acid Metabolism	1	−2.2
3^*	Ketol-acid reductoisomerase	IlvC	376396684	5.25/54	5.04/54	Amino Acid Metabolism	2.3	2.2
4	D-3-phosphoglycerate dehydrogenase	PHGDH	365906793	6.06/44	5.92/46	Amino Acid Metabolism	1	−2.7
8	Major outer membrane lipoprotein 1	Lpp	376401994	9.36/8	4.16/12	Cell wall	1	3.4
9	Major outer membrane lipoprotein 1	Lpp	376401995	9.36/9	4.04/12	Cell wall	1	3.4
10	Major outer membrane lipoprotein 1	Lpp	376401994	9.36/8	4.44/12	Cell wall	1	1.7
37	Aerobic respiration control protein ArcA	ARCA	376394332	5.30/27	5.04/29	Central carbon metabolism	1.9	1
19^*	Glucose-specific phosphotransferase enzyme IIA component	EIIA^Glc	376399349	4.73/18	4.6/22	Central carbon metabolism	−1.9	−1.7
20^*	Glucose-specific phosphotransferase enzyme IIA component	EIIA^Glc	376399349	4.73/18	4.62/20	Central carbon metabolism	−1.5	−1.4
17^*	Hypothetical protein HMPREF9694_04828 (dihydrolipoyllysine-residue succinyltransferase, E2 component)	SucB	376395176	5.74/44	5.39/54	Central carbon metabolism	−2.8	−3.6
41	Succinyl-CoA synthetase subunit alpha	A-SCS	365909192	5.89/30	5.65/30	Central carbon metabolism	−3.9	1
33	Succinyl-CoA synthetase subunit beta	B-SCS	365909191	5.35/42	5.05/43	Central carbon metabolism	−1.8	1
42	Fumarate hydratase class II	FH	376401593	6.02/50	5.92/46	Central carbon metabolism	1	−2.7
2^*	Fumarate reductase flavoprotein subunit	FrdA	376396036	5.60/66	5.44/77	Central carbon metabolism	2.1	2.6
22^*	Malate dehydrogenase	MDH	376398117	5.57/33	5.34/34	Central carbon metabolism	−3.1	−2.7
23^*	Malate dehydrogenase	MDH	376398117	5.57/33	5.08/29	Central carbon metabolism	−1.9	−2.7
14	Citrate lyase beta subunit	CitE	376376734	5.33/31	4.87/29	Central carbon metabolism	1.9	1
26	Citrate lyase beta subunit	CitE	376376734	5.33/31	5.07/31	Central carbon metabolism	4.9	1
36^*	Citrate lyase beta subunit	CitE	376376734	5.33/31	5.19/29	Central carbon metabolism	3.0	2.4
15^*	Citrate lyase, alpha subunit	CitF	365908401	5.94/55	5.98/55	Central carbon metabolism	8.7	9.0
16^*	Citrate lyase, alpha subunit	CitF	365908401	5.94/55	5.89/55	Central carbon metabolism	14.1	11
24^*	Oxaloacetate decarboxylase alpha chain	OadA	376376739	5.44/63	5.04/64	Central carbon metabolism	10.4	8.7
25^*	Oxaloacetate decarboxylase alpha chain	OadA	376376739	5.44/63	4.7/43	Central carbon metabolism	3.7	2.8
81^*	Oxaloacetate decarboxylase alpha chain	OadA	376376739	5.44/63	4.74/43	Central carbon metabolism	4.0	2.4
29^*	Pyruvate formate lyase	PFL	376393708	5.63/85	5.09/80	Central carbon metabolism	2.7	12.4
30^*	Pyruvate formate lyase	PFL	376393708	5.63/85	5.3/80	Central carbon metabolism	2.1	15.4
31^*	Pyruvate formate lyase	PFL	376393708	5.63/85	5.37/80	Central carbon metabolism	2.9	12.1
32^*	Pyruvate formate lyase	PFL	376393708	5.63/85	5.44/77	Central carbon metabolism	2.7	12.4
35^*	Pyruvate formate lyase	PFL	376393708	5.63/85	5.16/43	Central carbon metabolism	2.3	3.4
27^*	Phosphotrans-acetylase	PTA	365911544	5.26/77	5.27/65	Central carbon metabolism	3.6	2.7
12^*	Acetate kinase A/propionate kinase 2	ACK	365911543	5.84/44	5.39/27	Central carbon metabolism	4.1	1.7
46^*	Triosephosphate isomerase	TIM	376397984	5.82/26	5.5/26	Central carbon metabolism	1.6	1.5
38^*	Pyruvate kinase	PK	365911037	6.00/52	5.78/55	Central carbon metabolism	1.9	1.9
21^*	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH	376401359	6.33/36	6.2/31	Central carbon metabolism	2.2	1.5
28	Pyruvate dehydrogenase subunit E1	PDH	365908482	5.47/100	5.52/67	Central carbon metabolism	2.4	1
40	3-Methyl-2-oxobutanoate hydroxymethyltransferase	PanB	365908516	5.64/28	5.34/29	Cofactor biosynthesis	1	−2.5
49	6,7-Dimethyl-8-ribityllumazine synthase	RibH	365908789	5.12/16	4.87/14	Cofactor biosynthesis	1	−2
51	DNA protection during starvation protein	DPS	376393609	5.72/19	5.61/16	DNA ricombination, replication and repair	−1.5	1
50	DNA-binding protein HU-alpha	HU-2	376396790	9.40/9	9.07/11	DNA ricombination, replication and repair	1	−2.3
52^*	ATP synthase subunit beta	ATPβ	376397178	4.93/50	4.81/51	Energy metabolism	2.5	2.2
53^*	ABC transporter arginine-binding protein 1	ArtJ	376393664	6.90/27	5.98/25	Membrane Transport	4.9	7.4
57^*	Glutamate and aspartate transporter subunit	DEBP	365909131	8.61/33	7.85/30	Membrane Transport	−7.7	−6.7
58^*	Glutamine-binding periplasmic protein	GlnH	376388520	8.74/27	5.81/26	Membrane Transport	−1.9	−2.4
59^*	Glutamine-binding periplasmic protein	GlnH	376388520	8.74/27	7.8/25	Membrane Transport	−3.1	−6.2
60^*	Glutamine-binding periplasmic protein	GlnH	376388520	8.74/27	6.87/25	Membrane Transport	−2.3	−3.8
34^*	Leucine ABC transporter subunit substrate-binding protein LivK	LivK	365907255	5.71/40	5.03/42	Membrane Transport	3.0	3.5
61^*	Maltose ABC transporter periplasmic protein	MBP	365907919	6.88/43	5.96/40	Membrane Transport	−7	−14
56^*	D-galactose-binding periplasmic protein	MGLB	376381367	6.14/36	5.42/29	Membrane Transport	−2.6	−2.5
13	Outer membrane protein A	OmpA	376393752	5.98/38	4.98/31	Membrane Transport	2.7	1
39	Outer membrane protein A	OmpA	376393752	5.98/38	5.5/28	Membrane Transport	1	−1.6
43	Outer membrane protein A	OmpA	376393752	5.98/38	4.78/32	Membrane Transport	1	−1.5
44	Outer membrane protein A	OmpA	376393752	5.98/38	4.86/32	Membrane Transport	1	−1.6
62	Outer membrane protein A	OmpA	376393752	5.98/38	5.17/32	Membrane Transport	1	−2.3
63	Outer membrane protein A	OmpA	376393752	5.98/38	5.03/32	Membrane Transport	1	−3.1
64	Outer membrane protein A	OmpA	376393752	5.98/38	5.39/22	Membrane Transport	1	−5
88	Outer membrane protein A	OmpA	376393752	5.98/38	5.46/27	Membrane Transport	1	−3.7
45	Outer membrane protein W	OmpW	365909926	6.17/23	5.2/22	Membrane Transport	−4.0	1
18^*	Hypothetical protein HMPREF9694_01670 (tricarboxylic transport)	TctC	376400424	8.61/35	6.7/26	Membrane Transport	−6.5	−5.0
48^*	Hypothetical protein HMPREF9694_01670 (tricarboxylic transport)	TctC	376400424	8.61/35	7.8/29	Membrane Transport	−4.1	−8.0
71^*	Hypothetical protein HMPREF9694_01670 (tricarboxylic transport)	TctC	376400424	8.61/35	8.37/29	Membrane Transport	−10	−6.2
65^*	Carbamoyl phosphate synthase small subunit	CPSase	365908404	5.79/42	5.4/42	Nucleotide metabolism	−2	−3.3
66^*	Multifunctional nucleoside diphosphate kinase	NdK	365911711	5.55/15	5.38/14	Nucleotide Metabolism	−2.6	−4.2
67^*	Nucleoside diphosphate kinase	NdKs	376399440	5.55/15	5.42/14	Nucleotide Metabolism	−1.8	−4.1
89	Isochorismatase hydrolase		365909686	5.61/24	5.36/26	Other	−1.6	1
68	Adenosine-3'(2'),5'-bisphosphate nucleotidase	CysQ	365908080	5.67/28	5.31/29	Other	1	−2.1
72	Alkyl hydroperoxide reductase subunit C	AHPC	376395087	5.03/21	4.95/23	Oxido reduction	−2.3	1
76	Superoxide dismutase [Fe]	FeSOD	376402095	5.75/21	5.49/22	Oxido reduction	1	3.1
73	Superoxide dismutase [Mn]	MnSOD	376396893	6.23/23	5.84/25	Oxido reduction	1	−2.6
74^*	Superoxide dismutase [Mn]	MnSOD	376396893	6.23/23	6.01/24	Oxido reduction	−2.8	−6.3
75^*	Superoxide dismutase [Mn]	MnSOD	376396893	6.23/23	5.62/24	Oxido reduction	−2	−4.5
11	Thiol peroxidase	TPX	376401245	4.67/18	4.8/19	Oxido reduction	1	−1.9
79	Chaperonin	CHA10	376396016	5.38/10	4.97/16	Protein metabolism	1	−3.2
82^*	Elongation factor G	EF-G	365907166	5.17/77	5.62/50	Protein metabolism	1.8	1.9
86^*	Ribosomal protein L1	RPL1	376396770	9.56/25	7.77/27	Protein metabolism	−2	−2.2
87^*	Ribosomal protein L1	RPL1	206564980	9.56/25	7.56/28	Protein metabolism	−1.7	−2.1
80	Ribosomal protein L13	RPL13	365907069	9.60/16	8.84/16	Protein metabolism	1	−3.9
85^*	Peptidyl-prolyl cis-trans isomerase SurA	SurA	365908414	6.42/47	5.68/48	Protein metabolism	−2.1	−2.3
78	Autonomous glycyl radical cofactor	GrcA	365911773	4.82/14	4.71/12	Stress response	−1.9	1
69^*	Osmotically-inducible protein Y	OSMY	376376350	8.67/21	5.84/22	Stress response	−3.0	−3.7
47	Universal stress protein F	USF	376401205	5.46/16	5.11/14	Stress response	−1.5	1

Fold change refers to normalized spot volumes as calculated by in silico analysis of 2D-DIGE protein maps. Positive and negative values stand for up- and down-regulation in anaerobic growth on FEC, respectively. Protein spots differentially abundant in anaerobic FEC with the respect to both aerobic FEC and anaerobic NAC are marked by an asterisk.

^aFunctional classification was performed according to KEGG database (http://www.genome.jp/kegg/).

^bRelative fold change was measured according to the criteria reported in the experimental section. FEC: Fe(III)-citrate containing medium. NAC: Na(I)-citrate containing medium. +O₂: aerobiosis. -O₂: anaerobiosis.