Table 4.

The transcriptome analysis of the genes involved in the methane oxidation pathway of Methylacidiphilum fumariolicum SolV.

Enzyme	Gene name	GenBank identifier	Expression level (RPKM)a
			H2/${\text{NH}}_4^{+}$	CH4/${\text{NO}}_3^{-}$	Cells at μmaxb
Particulate CH4 monooxygenase_1 (EC 1.14.13.25)	pmoC1	Mfumv2_1796	47,785	34,734	207
	pmoA1	Mfumv2_1795	9,772	3,775	41
	pmoB1	Mfumv2_1794	9,550	5,003	164
Particulate CH4 monooxygenase_2 (EC 1.14.13.25)	pmoC2	Mfumv2_1793	18,136	5,462	37,218
	pmoA2	Mfumv2_1792	2,383	1,119	21,207
	pmoB2	Mfumv2_1791	2,139	1,265	14,899
Particulate CH4 monooxygenase_3 (EC 1.14.13.25)	pmoC3	Mfumv2_1606	539	209	181
	pmoA3	Mfumv2_1605	143	17	57
	pmoB3	Mfumv2_1604	58	13	28
Methanol dehydrogenase XoxF-type (EC 1.1.99.8)	xoxF	Mfumv2_1183	6,220	5,291	6,041
Extracellular solute-binding protein family 3	xoxJ	Mfumv2_1184	714	1,057	1,478
Cytochrome c1 protein fused with XoxJ	xoxGJ	Mfumv2_1185	611	829	1,042
Coenzyme PQQ precursor peptide	ppqA	Mfumv2_1461a	2,920	1,919	2,133
Coenzyme PQQ synthesis proteins	pqqB	Mfumv2_1461	1,308	588	620
	pqqC	Mfumv2_1462	1,165	560	622
	pqqD	Mfumv2_0766	144	242	60
	pqqD	Mfumv2_1463	451	153	249
	pqqE	Mfumv2_1464	747	514	509
	pqqF	Mfumv2_0519	408	680	718
NADPH:quinone oxidoreductase (EC 1.6.5.5)	qor1	Mfumv2_1937	253	287	315
	qor2	Mfumv2_2088	338	300	432
	qor3	Mfumv2_0618	60	12	130
Zn-dependent alcohol dehydrogenase (EC 1.1.1.1)	adh1	Mfumv2_2176	160	154	208
	adh2	Mfumv2_0724	252	218	288
Aldehyde dehydrogenase (EC 1.2.1.3)	dhaS1	Mfumv2_2408	130	317	108
	dhaS2	Mfumv2_0597	1,310	1,503	1,125
Dihydropteroate synthase (EC 2.5.1.15)	folP1	Mfumv2_0503	161	233	167
	folP2	Mfumv2_2400	126	95	208
Formate–tetrahydrofolate ligase (EC 6.3.4.3)	fhs	Mfumv2_2082	396	457	282
Methylenetetrahydrofolate dehydrogenase (NADP+) (EC 1.5.1.5) - methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9)	folD	Mfumv2_1033	257	173	261
GTP cyclohydrolase I (EC 3.5.4.16) type 2	folE	Mfumv2_0074	1,485	1,477	795
NAD-dependent formate dehydrogenase alpha subunit	fdsA	Mfumv2_1457	568	665	1,342
NAD-dependent formate dehydrogenase beta subunit	fdsB	Mfumv2_1458	569	435	1,149
NAD-dependent formate dehydrogenase gamma subunit	fdsC	Mfumv2_1459	475	240	672
NAD-dependent formate dehydrogenase delta subunit	fdsD	Mfumv2_1456	593	979	588
NAD-dependent formate dehydrogenase (EC 1.2.1.2)	fdh	Mfumv2_1567	738	863	1,110
Methylamine dehydrogenase light chain (EC 1.4.99.3)	mauA	Mfumv2_0350	119	450	108
Methylamine dehydrogenase heavy chain (EC 1.4.99.3)	mauB	Mfumv2_0347	99	135	235

^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.