Table 3.

Transcription of genes involved in nitrogen metabolism in “Ca. M. fumariolicum” strain SolV.

Enzyme	Gene name	GenBank identifier	Expression level (RPKM)
			Cells at μmax	N2 fixing cells	O2 limited cells
Glutamine synthetase	glnA	Mfum_90015	1542	1052	725
Glutamine synthetase regulatory protein PII	glnB	Mfum_90016	1039	1701	914
UTP:GlnB (Protein PII) uridylyltransferase	glnD	Mfum_230007	169	111	145
Nitrogen regulatory protein PII	glnK	Mfum_140026	166	60	203
Alanine dehydrogenase	ald	Mfum_290047	248	279	256
Glutamate dehydrogenase	gdhA	Mfum_810044	436	182	500
Glutamate synthase alpha chain	gltB	Mfum_940063	1343	1360	1355
Glutamate synthase beta chain	gltD	Mfum_270076	133	114	125
Ornithine/acetylornithine aminotransferase	argD1	Mfum_190040	736	736	410
	argD2	Mfum_1010035	383	421	410
Argininosuccinate lyase	argH	Mfum_970020	226	186	107
Ornithine carbamoyltransferase	argF	Mfum_1010036	286	267	375
Argininosuccinate synthase	argG	Mfum_270005	725	527	678
Carbamoyl-phosphate synthase small chain	carA	Mfum_270024	450	340	479
Carbamoyl-phosphate synthase large chain	carB	Mfum_700048	395	267	504
Ammonium transporter	amtB	Mfum_430001_160001a	343	1143	420
Nitrate ABC transporter, nitrate-binding protein	tauA	Mfum_140012	28	117	33
Nitrate transporter	nasA	Mfum_140017	22	26	16
Assimilatory nitrate reductase large subunit	bisC	Mfum_140014	13	14	8
Assimilatory nitrite reductase	nirB	Mfum_140015	14	40	13
Ferredoxin subunit of nitrite reductase	nirD	Mfum_140016	32	18	16
Signal transduction histidine kinase with PAS domain	ntrB	Mfum_920004	283	294	250
Signal transduction response regulator, NtrC family	ntrC1	Mfum_110018	90	76	67
	ntrC2	Mfum_170043	116	110	111
	ntrC3	Mfum_260013	623	361	525
	ntrC4	Mfum_920003	225	154	216
Hydroxylamine oxidoreductase	haoA	Mfum_970027	357	124	568
Nitric oxide reductase B subunit	norB	Mfum_970100	261	120	342
Nitric oxide reductase subunit C	norC	Mfum_970099	192	93	139
Nitrite reductase (NO-forming)	nirK	Mfum_270071	72	63	200
DNA-binding response regulator, NarL family	mxaB	Mfum_1030004	232	74	142
DNA-binding response regulator, LuxR family	citB1	Mfum_790006	1760	5611	4679
DNA-binding response regulator, LuxR family	citB2	Mfum_580001	394	200	239

The mRNA expression is expressed as RPKM according to Mortazavi et al. (2008). Changes in expression in the chemostat cultures (N₂ fixing cells or O₂ limited cells) compared to batch culture cells growing at μ_max are indicated by shading: up regulation >2 times (dark gray), down regulation <0.5 (light gray). ^aMfum_430001 and Mfum_160001 encode the N- and C-terminal part, respectively.