. 2013 Dec 11;4:379. doi: 10.3389/fmicb.2013.00379

Table 2.

Differentially expressed genes in ΔhmgA compared with WT V. campbellii.

Gene ID	Annotation	pval	WT^a	ΔhmgA	Change^b	qRT-PCR^c	Function^e
M892_05385	Pyruvate-formate lyase	3.12E-06	2.45	1.11	2.21		C
M892_06250	2-oxoglutarate dehydrogenase	5.20E-04	1.29	0.67	1.93		C
M892_06265	Succinate dehydrogenase	1.59E-04	0.82	0.37	2.22		C
M892_06275	Citrate synthase	1.57E-06	2.31	0.72	3.21		C
M892_08460	Ubiquinol-cytochrome c reductase	1.12E-05	1.45	0.61	2.38		C
M892_08470	Ubiquinol-cytochrome c reductase, iron-sulfur subunit	4.80E-06	1.36	0.86	1.58	2.50	C
M892_10625	ATP synthase subunit alpha	1.24E-04	2.17	1.55	1.40		C
M892_13885	Aconitate hydratase	2.42E-06	2.21	1.12	1.97		C
M892_17240	Cytochrome c-type protein NrfB	1.17E-06	1.24	0.04	31.00		C
M892_17245	Nitrite reductase, Fe-S protein NrfC	1.73E-06	1.24	0.02	62.00	1.58	C
M892_23815	acyl-CoA dehydrogenase, short-chain specific EtfA	6.43E-06	1.72	0.52	3.31	5.30	C
M892_23820	Electron transfer flavoprotein subunit beta EtfB	5.49E-05	1.69	0.73	2.32		C
M892_23825	Electron transfer flavoprotein-ubiquinone oxidoreductase EtfD	5.04E-04	0.85	0.24	3.54		C
M892_24165	Trimethylamine-N-oxide reductase 1	3.42E-06	2.20	1.19	1.85		C
M892_08360	Cell division GTPase	2.15E-05	1.42	0.9	1.58		D
M892_08365	Cell division protein FtsA	3.06E-04	1.13	0.79	1.43		D
M892_03740	Aspartate aminotransferase	2.04E-04	0.90	0.32	2.81		E
M892_03990	Phosphoribosyl-AMP cyclohydrolase	2.70E-05	1.57	0.87	1.80		E
M892_03995	Imidazoleglycerol-phosphate synthase	4.98E-04	1.51	1.04	1.45		E
M892_12425	Argininosuccinate lyase	1.13E-06	1.94	1.00	1.94		E
M892_13555	Aspartokinase	2.04E-04	0.92	0.07	13.14		E
M892_16070	Lactoylglutathione lyase	5.98E-08	3.09	2.02	1.53		E
M892_27505	Sodium/proline symporter PutP	1.13E-06	2.02	0.78	2.59		E
M892_27510	Delta 1-pyrroline-5-carboxylate dehydrogenase PutC	5.98E-08	3.20	1.87	1.71	4.18	E
M892_27515	Proline dehydrogenase PutB	2.10E-07	3.04	1.27	2.39		E
M892_10225	2-keto-3-deoxy-6-phosphogluconate aldolase	9.40E-04	1.12	0.42	2.67		G
M892_13305	Fructose-bisphosphate aldolase	8.05E-04	2.17	1.05	2.07	1.23	G
M892_19270	Enolase	8.81E-04	0.73	0.06	12.17		G
M892_20700	Phosphomannomutase	2.06E-04	1.86	0.69	2.70		G
M892_09970	Delta-aminolevulinic acid dehydratase	1.28E-04	0.60	0.00	UD^d		H
M892_15785	Glyceraldehyde 3-phosphate dehydrogenase	5.76E-05	2.46	1.37	1.80	6.60	I
M892_24035	3-hydroxyacyl-CoA dehydrogenase IvdG	1.22E-04	0.78	0.25	3.12		I
M892_24040	3-hydroxyisobutyrate dehydrogenase IvdF	5.61E-06	1.73	0.70	2.47		I
M892_24045	Enoyl-CoA hydratase/isomerase IvdE	9.29E-06	2.06	0.66	3.12		I
M892_24050	3-hydroxyisobutyryl-CoA hydrolase IvdD	2.15E-05	1.73	0.36	4.81		I
M892_24055	Branched-chain acyl-CoA dehydrogenase IvdC	1.59E-04	1.12	0.46	2.43		I
M892_24060	Methylmalonate-semialdehyde dehydrogenase IvdB	1.49E-06	2.18	0.55	3.96	2.49	I
M892_24065	3-ketoacyl-CoA thiolase IvdA	1.98E-05	1.94	0.79	2.46		I
M892_24075	Isovaleryl-CoA dehydrogenase LiuA	3.91E-06	2.13	0.87	2.45		I
M892_24080	Methylcrotonyl-CoA carboxylase carboxyl transferase LiuB	5.84E-05	1.46	0.66	2.21		I
M892_24525	Polyhydroxyalkanoic acid synthase PhaC	1.27E-05	1.05	0.10	10.50		I
M892_24530	PHA granule-associated protein PhaD	5.48E-05	3.07	0.57	5.39		I
M892_24535	Acetyl-CoA acetyltransferase PhaA	4.29E-06	3.25	0.95	3.42	6.61	I
M892_24540	Acetoacetyl-CoA reductase PhaB	9.29E-06	2.97	0.83	3.58		I
M892_16425	Acyl carrier protein	8.93E-06	4.07	1.59	2.56		I
M892_02880	Ribosomal protein L35	5.66E-04	2.01	1.40	1.44		J
M892_02885	Bacterial protein translation initiation factor 3	1.83E-05	2.95	2.39	1.23		J
M892_07900	Ribosome-associated protein Y	6.25E-05	4.21	2.97	1.42		J
M892_12355	Translation elongation factor	8.45E-04	1.71	0.60	2.85		J
M892_12355	Translation elongation factor	4.38E-07	3.54	2.41	1.47		J
M892_12355	Translation elongation factor	1.01E-05	3.41	2.02	1.69		J
M892_14350	Translation elongation factor	1.34E-05	1.90	0.81	2.35		J
M892_08765	Transcriptional regulator	5.57E-07	3.21	1.93	1.66		K
M892_12185	Ribonuclease R	1.24E-05	1.87	0.86	2.17		K
M892_13795	Quorum sensing regulator LuxR	2.78E-05	1.98	0.62	3.19	3.57	K
M892_02740	Bacterial nucleoid DNA-binding protein	1.59E-09	2.83	1.07	2.64		L
M892_11585	DNA-binding protein	2.08E-07	1.37	0.13	10.54		L
M892_12540	Replicative DNA helicase	7.48E-05	1.11	0.63	1.76		L
M892_06105	Membrane-bound lytic murein transglycosylase B	2.70E-05	1.36	0.85	1.60		M
M892_08355	UDP-3-O-3-hydroxymyristoyl N-acetylglucosamine deacetylase	5.65E-04	2.28	1.56	1.46		M
M892_08935	UDP-N-acetylmuramate-L-alanyl-gamma-D-glutamyl-m eso-diaminopimelate ligase	1.23E-04	1.05	0.48	2.19		M
M892_12935	UDP-N-acetylglucosamine 1-carboxyvinyltransferase	4.02E-04	1.06	0.60	1.77		M
M892_14045	Outer membrane protein OmpU	7.81E-05	1.24	0.41	3.02		M
M892_20750	Outer membrane protein OmpA	4.16E-05	3.20	1.66	1.93		M
M892_25630	Outer membrane lipoprotein	1.39E-10	4.43	1.51	2.93		M
M892_00180	Heat shock protein HslJ	5.20E-04	1.95	0.58	3.36		O
M892_00340	Glutaredoxin	4.76E-04	1.29	0.61	2.11		O
M892_07710	Antioxidant, AhpC/Tsa family	2.08E-07	2.20	0.28	7.86		O
M892_07875	ClpB protein	8.45E-04	1.25	0.37	3.38		O
M892_09255	Peptidase	5.78E-04	1.79	0.39	4.59		O
M892_11900	Chaperonin GroEL	1.70E-06	1.14	0.16	7.13		O
M892_12155	Serine protease	1.59E-04	1.45	0.58	2.50		O
M892_05540	Cation transport ATPase	4.53E-06	1.34	0.63	2.13		P
M892_15095	Arsenate reductase	5.66E-04	1.36	0.79	1.72		P
M892_12915	Putative ABC superfamily transport protein	5.26E-05	0.41	0.02	20.50		Q
M892_12920	ABC-type transport system, auxiliary component	1.17E-06	1.86	0.49	3.80		Q
M892_01320	Immunogenic protein	1.77E-05	1.63	0.41	3.98		R
M892_12140	RNA-binding protein Hfq	1.46E-06	2.94	1.96	1.50		R
M892_18180	Ecotin precursor	6.37E-05	1.51	0.99	1.53		R
M892_26640	Hemolysin	6.13E-08	1.93	0.54	3.57		R
M892_05800	Lipoprotein-related protein	6.13E-08	1.20	0.24	5.00		S
M892_08695	Hypothetical protein	3.42E-05	1.09	0.40	2.73		S
M892_13325	Hypothetical protein	4.02E-07	3.90	1.96	1.99		S
M892_24630	Hypothetical protein	7.09E-04	0.78	0.23	3.39		S
M892_05410	Putative serine protein kinase	5.29E-06	2.33	0.44	5.30		T
M892_10150	Universal stress protein	1.95E-04	2.37	1.25	1.90		T
M892_12235	Cyclic AMP receptor protein	1.76E-04	1.24	0.59	2.10		T
M892_13400	Negative regulator of sigma E activity	3.29E-05	2.29	1.48	1.55		T
M892_13405	Periplasmic negative regulator of sigma E	1.17E-05	1.51	0.88	1.72		T
M892_13560	Carbon storage regulator	1.18E-04	1.75	1.05	1.67		T
M892_20245	Universal stress protein A	1.03E-09	3.31	1.71	1.94		T
M892_05075	Translocation protein TolB	3.03E-05	1.18	0.65	1.82		U
M892_05460	ABC transporter, ATP-binding protein	6.12E-04	1.16	0.53	2.19		V
M892_07350	Type I site-specific deoxyribonuclease specificity subunit	7.70E-04	1.94	1.20	1.62		V
M892_07355	Type I restriction-modification system, methyltransferase subunit	1.57E-06	2.19	1.34	1.63		V
M892_20315	Beta-lactamase	1.56E-05	1.48	0.49	3.02		V
M892_03945	Hypothetical protein	5.33E-05	0.36	0.00	UD
M892_05165	Gonadoliberin III-related protein	9.73E-05	0.78	0.1	7.80
M892_05170	Hypothetical protein	2.71E-07	1.11	0.32	3.47
M892_05480	Hypothetical protein	1.76E-04	0.98	0.30	3.27
M892_07360	Phage transcriptional regulator AlpA	2.58E-04	2.02	0.83	2.43
M892_10485	NADH dehydrogenase subunit II-related protein	1.66E-08	3.75	2.87	1.31
M892_12930	BolA/YrbA family protein	2.75E-04	0.85	0.07	12.14
M892_13365	Hypothetical protein	1.73E-04	3.25	1.17	2.78
M892_15830	Hypothetical protein	7.46E-05	1.24	0.30	4.13
M892_16465	Hypothetical protein	7.48E-05	1.52	0.27	5.63
M892_17010	Hypothetical protein	2.32E-08	2.16	0.35	6.17
M892_18970	Hypothetical protein	2.82E-05	1.39	0.25	5.56
M892_19525	Putative lipoprotein	1.86E-08	4.17	1.09	3.83
M892_19565	Muconate cycloisomerase I	2.36E-04	1.64	0.41	4.00
M892_19745	Hypothetical protein	3.75E-04	0.39	0.00	UD
M892_20825	Fatty acid reductase LuxC	9.07E-06	2.64	1.23	2.15
M892_20830	Myristoyl-ACP-specific thioesterase LuxD	1.01E-05	2.98	1.28	2.33
M892_20835	Alkanal monooxygenase alpha chain LuxA	4.02E-07	4.00	1.78	2.25
M892_20840	Alkanal monooxygenase beta chain LuxB	3.43E-04	4.84	2.08	2.33	4.81
M892_20845	Long-chain-fatty-acid luciferin-component ligase LuxE	5.14E-05	2.83	0.87	3.25
M892_20850	NAD(P)H-dependent FMN reductase LuxG	4.58E-06	1.78	0.81	2.20
M892_22630	Peptidase	1.03E-04	1.74	1.05	1.66
M892_22965	Positive response regulator for Pho regulon	3.60E-06	2.16	0.82	2.63
M892_24070	Transcriptional regulator LiuR	0.0003	0.25	0.00	UD
M892_24215	Putative GTPase	4.14E-05	1.14	0.50	2.28
M892_24655	Hypothetical protein	3.22E-05	4.11	1.48	2.78
M892_25115	Transcriptional regulator LuxT	2.58E-04	2.96	2.25	1.32
M892_25430	Azurin	5.16E-04	1.88	1.20	1.57
M892_25755	ATP-dependent protease	7.73E-04	0.75	0.26	2.88
M892_25795	Predicted transcriptional regulator protein	8.83E-07	2.37	0.26	9.12
M892_26535	Putative lipoprotein	1.86E-08	1.76	0.19	9.26
M892_26800	Hypothetical protein	7.73E-05	1.29	0.68	1.90

Average signal intensity log₂ values from three experiments.

Transcript ratio between WT and ΔhmgA.

Transcript ratio between WT and ΔhmgA from qRT-PCR data. qRT-PCR Ct values were derived from the average of duplicates from two independent biological samples.

Undivisible as no transcript was detected from ΔhmgA.

COG functional categories: C, energy production and conversion. D, cell cycle control, cell division and chromosome partitioning; E, amino acid transport ad metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; M, cell wall/membrane/envelop biogenesis; O, post-translational modification, protein turnover and chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion and vesicular transport; V, defense mechanisms.