Table 3.

The transcriptome analysis of the genes involved in nitrogen metabolism in Methylacidiphilum fumariolicum SolV.

Enzyme	Gene name	GenBank identifier	Expression level (RPKM)a
			H2/${\text{NH}}_4^{+}$	CH4/${\text{NO}}_3^{-}$	Cells at μmaxb
Glutamine synthetase type I (EC 6.3.1.2)	glnA	Mfumv2_1420	764	893	2,065
Glutamine synthetase regulatory protein PII	glnB	Mfumv2_1419	943	719	883
[Protein-PII] uridylyltransferase (EC 2.7.7.59)	glnD	Mfumv2_1837	124	136	156
Nitrogen regulatory protein PII	glnK	Mfumv2_1285	371	125	193
Alanine dehydrogenase (EC 1.4.1.1)	ald	Mfumv2_2049	107	106	171
Glutamate dehydrogenase (EC 1.4.1.2; EC 1.4.1.4)	gdhA	Mfumv2_0663	227	231	421
Glutamate synthase [NADPH] large chain (EC 1.4.1.13)	gltB	Mfumv2_2397	906	696	1,300
Glutamate synthase beta chain	gltD	Mfumv2_1978	192	328	198
Ornithine-acetylornithine aminotransferase (EC 2.6.1.11)	argD1	Mfumv2_1148	279	271	627
Ornithine-acetylornithine aminotransferase (EC 2.6.1.11)	argD2	Mfumv2_0135	145	273	357
Argininosuccinate lyase (EC 4.3.2.1)	argH	Mfumv2_2465	78	68	203
Ornithine carbamoyltransferase (EC 2.1.3.3)	argF	Mfumv2_0136	161	239	278
Argininosuccinate synthase (EC 6.3.4.5)	argG	Mfumv2_1907	666	654	645
Carbamoyl-phosphate synthase small chain (EC 6.3.5.5)	carA	Mfumv2_1926	318	350	453
Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)	carB	Mfumv2_0408	347	674	514
Ammonium-Ammonia transporter	amtB	Mfumv2_1275	294	1,082	391
Nitrate ABC transporter, nitrate-binding protein	tauA	Mfumv2_1299	28	41	34
Assimilatory nitrate reductase catalytic subunit (EC 1.7.99.4)	nasC	Mfumv2_1297	20	105	13
Nitrate-nitrite transporter	nasA	Mfumv2_1294	67	321	23
Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)	nirB	Mfumv2_1296	140	854	19
Nitrite reductase [NAD(P)H], small subunit (EC 1.7.1.4)	nirD	Mfumv2_1295	63	308	33
Signal transduction histidine kinase with PAS domain	ntrB	Mfumv2_0271	275	180	291
Signal transduction response regulator, NtrC family	ntrC1	Mfumv2_1349	98	84	103
Sigma-54 dependent transcriptional regulator-response regulator	ntrC2	Mfumv2_1221	65	59	100
Transcriptional regulator, NifA subfamily, Fis Family	ntrC3	Mfumv2_2103	581	400	533
Sigma-54 dependent transcriptional regulator-response regulator	ntrC4	Mfumv2_0272	264	387	293
Hydroxylamine dehydrogenase (EC 1.7.2.6)	haoA	Mfumv2_2472	402	109	351
Hydroxylamine dehydrogenase associated protein	haoB	Mfumv2_2471	179	163	302
Nitric-oxide reductase subunit B (EC 1.7.99.7)	norB	Mfumv2_0037	125	84	178
Nitric-oxide reductase subunit C (EC 1.7.99.7)	norC	Mfumv2_0036	429	372	197
Copper-containing nitrite reductase (EC 1.7.2.1)	nirK	Mfumv2_1973	379	520	136
DNA-binding response regulator, NarL family	mxaB	Mfumv2_1738	163	291	288
DNA-binding response regulator, LuxR family	citB1	Mfumv2_1799	7,016	4,126	1,063
DNA-binding response regulator, LuxR family	citB2	Mfumv2_0457	137	133	307

^aThe mRNA expression is shown as RPKM according to Mortazavi et al. (2008). Changes in expression in the continuous cultures (H₂/${\mathrm{NH}}_4^{+}$ and CH₄/${\mathrm{NO}}_3^{-}$) compared to batch culture cells growing at μ_max are demonstrated by shading [up-regulation >2-fold dark gray; down-regulation <0.5 (light gray)].

^bCells grown on CH₄ with ${\mathrm{NH}}_4^{+}$ as N-source.