TABLE 2.

Relative expression of CBB cycle-associated genes and (for comparison) key catabolic genes in “Ca. Methylomirabilis oxyfera”^a

Open reading frame identifier	Gene name	Encoded protein	ECb no.	Relative expressionc
damo_0174	cbbF1	Fructose-1,6-bisphosphatase II	3.1.3.11	8.3
damo_0175	cbbA	Fructose-bisphosphate aldolase II, CBB cycle subtype	4.1.2.13	9.8
damo_0176	cbbE	Ribulose-phosphate 3-epimerase	5.1.3.1	8.8
damo_0339	cbbG1	Glyceraldehyde 3-phosphate dehydrogenase	1.2.1.12	9.4
damo_0340	cbbK	Phosphoglycerate kinase, 5′ end	2.7.2.3	9.1
damo_0341	cbbK	Phosphoglycerate kinase, 3′ end	2.7.2.3	8.3
damo_0342	tpiA	Triosephosphate isomerase	5.3.1.1	9.0
damo_0804	oxyR	LysR-type transcriptional activator		7.5
damo_0861	oxyR	LysR-type transcriptional activator		8.7
damo_2116	cbbP1	Phosphoribulokinase	2.7.1.19	3.9
damo_2163	cbbF2	Fructose-1,6-bisphosphatase II	3.1.3.11	9.6
damo_2164	rpiA	Ribulose-5-phosphate isomerase A	5.3.1.6	8.1
damo_2165	cbbL	Ribulose-1,6-bisphosphate carboxylase/oxygenase, large chain	4.1.1.39	9.3
damo_2166	cbbS	Ribulose-1,6-bisphosphate carboxylase/oxygenase, small chain	4.1.1.39	10.1
damo_2167	cbbX	Ribulose-1,6-bisphosphate carboxylase/oxygenase activase, AAA ATPase		9.9
damo_2168	ppcA	Phosphoenolpyruvate carboxylase	4.1.1.31	9.3
damo_2170	cynT	Carbonic anhydrase	4.2.1.1	10.3
damo_2650	cbbF3	Fructose-1,6-bisphosphatase II	3.1.3.11	9.6
damo_2651	cbbT	Transketolase	2.2.1.1	7.9
damo_2652	cbbG2	Glyceraldehyde-3-phosphate-dehydrogenase	1.2.1.12	7.9
damo_2653	cbbP2	Phosphoribulokinase	2.7.1.19	9.9
damo_2986	cbbF4	Fructose-1,6-bisphosphatase II	3.1.3.11	9.1
damo_0134	mxaF3	Methanol dehydrogenase, large subunit	1.1.99.8	10.3
damo_0136	mxaJ3	Hypothetical protein involved in methanol dehydrogenase	1.1.99.8	8.7
damo_0138	mxaG3	Cytochrome c1 involved in methanol dehydrogenase	1.1.99.8	9.7
damo_0454	fae	Formaldehyde-activating enzyme	4.3.−.−	14.6
damo_0455	mtdB	Methylenetetrahydromethanopterine dehydrogenase	1.5.1.−	10.4
damo_0456	fwdD	Formylmethanofuran dehydrogenase	1.2.99.5	10.6
damo_0457	fhcB	Formyltransferase/hydrolase complex, subunit β		9.7
damo_0458	fhcA	Formyltransferase/hydrolase complex, subunit α		10.0
damo_0459	fhcD	Formyltransferase/hydrolase complex, subunit ε		10.0
damo_0460	fhcC	Formyltransferase/hydrolase complex, subunit γ		10.6
damo_0461	mch	Methenyltetrahydromethanopterin cyclohydrolase	3.5.4.27	8.3
damo_0853	fdhA2	Formate dehydrogenase, subunit α	1.2.1.2	8.1
damo_0854	fdhB2/C2	Formate dehydrogenase, subunits β and γ	1.6.99.5	8.0
damo_1134	fwdD2	Formylmethanofuran dehydrogenase	1.2.99.5	8.3
damo_1135	fhcB2	Formyltransferase/hydrolase complex, subunit β, 5′ end		7.5
damo_1136	fhcB2	Formyltransferase/hydrolase complex, subunit β, 3′ end		8.3
damo_1852	folD	5,10-Methylene-tetrahydrofolate dehydrogenase; 5,10-methenyl-tetrahydrofolate cyclohydrolase	1.5.1.5; 3.5.4.9	8.3
damo_2415	nirS	Nitrite reductase, cytochrome cd1 type	1.7.2.1	12.0
damo_2434	norZ2	Putative nitric oxide dismutase		11.7
damo_2437	norZ3	Putative nitric oxide dismutase		13.6
damo_2448	pmoB	Particulate methane monooxygenase, subunit α	1.14.13.25	11.4
damo_2450	pmoA	Particulate methane monooxygenase, subunit β	1.14.13.25	12.3
damo_2451	pmoC	Particulate methane monooxygenase, subunit γ	1.14.13.25	0.0

^aThe transcriptome analysis was performed on the basis of data published previously (38). The presented data refer to the anoxic period.

^bEC, enzyme nomenclature designation.

^cRelative expression was determined from log₂(RPKM + 1), where RPKM is reads per kilobase per million mapped reads.