. 2018 Apr 1;19(4):1049. doi: 10.3390/ijms19041049

Table 3.

List of 93 genes positively controlled by RpoN and belonging to an over-represented eggNOG category (Fischer test, p-value < 0.01). Genes harboring a putative RpoN-box in their promoter region are shown in bold.

Locus ID ¹	Description ¹	Gene Name	log₂FC (rpoN mt nod vs. wt nod) ²
Cell wall/membrane/envelope biogenesis
Bphy_0649	RND efflux system outer membrane lipoprotein		−5.0
Bphy_0919	NLP/P60 protein		−1.6
Bphy_1282	OmpW family protein		−2.6
Bphy_1546	phospholipase C		−2.1
Bphy_1681	group 1 glycosyl transferase		−2.2
Bphy_1689	exopolysaccharide transport protein family		−3.2
Bphy_1690	polysaccharide export protein		−4.3
Bphy_1691	exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase		−3.4
Bphy_2283	mannose-1-phosphate guanylyltransferase		−2.9
Bphy_2316	dTDP-4-dehydrorhamnose reductase		−2.3
Bphy_2460	group 1 glycosyl transferase		−2.5
Bphy_2464	group 1 glycosyl transferase		−3.1
Bphy_2468	putative glycosyl transferase		−2.1
Bphy_2469	group 1 glycosyl transferase		−3.1
Bphy_2470	NAD-dependent epimerase/dehydratase		−3.2
Bphy_2471	GDP-mannose 4,6-dehydratase		−3.8
Bphy_2472	exopolysaccharide transport protein family		−3.7
Bphy_2473	polysaccharide export protein		−2.7
Bphy_2474	undecaprenyl-phosphate glucose phosphotransferase		−3.8
Bphy_2475	mannose-1-phosphate guanylyltransferase		−3.2
Bphy_2670	polypeptide-transport-associated domain-containing protein		−1.5
Bphy_2671	d-alanine:d-alanine ligase	ddl	−3.0
Bphy_2672	UDP-N-acetylmuramate-l-alanine ligase	murC	−1.8
Bphy_2678	UDP-N-acetylmuramoylalanyl-d-glutamate-2	murE	−1.6
Bphy_3069	lytic transglycosylase		−1.9
Bphy_3557	glycosyl transferase family protein		−2.3
Bphy_4515	porin		−2.0
Bphy_5347	NAD-dependent epimerase/dehydratase		−4.7
Bphy_7633	d-alanine:d-alanine ligase		−3.7
Bphy_7707	glycosyl transferase family protein		−3.6
Bphy_7819	porin		−2.9
Energy production and conversion
Bphy_1284	aldehyde dehydrogenase		−1.8
Bphy_1649	alkanesulfonate monooxygenase		−3.2
Bphy_2012	PIG3 family NAD(P)H quinone oxidoreductase		−1.9
Bphy_2272	FAD linked oxidase domain-containing protein		−2.8
Bphy_3029	F0F1 ATP synthase subunit α		−1.5
Bphy_3031	F0F1 ATP synthase subunit B		−1.6
Bphy_3032	F0F1 ATP synthase subunit C		−2.6
Bphy_3646	cytochrome o ubiquinol oxidase subunit IV	cyoD	−3.9
Bphy_3647	cytochrome o ubiquinol oxidase, subunit III	cyoC	−5.1
Bphy_3648	cytochrome o ubiquinol oxidase, subunit I	cyoB	−4.0
Bphy_3649	ubiquinol oxidase, subunit II	cyoA	−4.2
Bphy_3759	transketolase central region		−2.3
Bphy_3760	pyruvate dehydrogenase (acetyl-transferring)		−2.5
Bphy_4125	acylphosphatase		−2.8
Bphy_4520	formate dehydrogenase, γ subunit		−1.3
Bphy_5148	AraC family transcriptional regulator		−1.8
Bphy_5156	l-lactate dehydrogenase (cytochrome)		−1.9
Bphy_5235	alkanesulfonate monooxygenase		−3.5
Bphy_5641	glycolate oxidase iron-sulfur subunit	glcF	−2.5
Bphy_6505	formylmethanofuran dehydrogenase subunit A		−3.5
Bphy_7231	cytochrome c class I		−2.6
Bphy_7232	xenobiotic (desulfurization)monooxygenase subunit A		−2.9
Bphy_7263	Ni/Fe-hydrogenase, b-type cytochrome subunit		−2.8
Bphy_7264	nickel-dependent hydrogenase large subunit		−4.2
Bphy_7265	hydrogenase (NiFe) small subunit	*hydA*	−4.3
Bphy_7406	aldehyde dehydrogenase		−5.6
Bphy_7729	nitrogenase MoFe cofactor biosynthesis protein	*nifE*	−4.6
Bphy_7730	nitrogenase molybdenum-cofactor biosynthesis protein	*nifN*	−2.9
Bphy_7733	ferredoxin III, nif-specific		−5.0
Bphy_7737	electron-transferring-flavoprotein dehydrogenase		−4.2
Bphy_7738	electron transfer flavoprotein α/β-subunit		−4.5
Bphy_7739	electron transfer flavoprotein α/β-subunit		−5.2
Bphy_7754	nitrogenase molybdenum-iron protein α chain	*nifD*	−4.3
Bphy_7755	nitrogenase molybdenum-iron protein β chain	*nifK*	−4.0
Bphy_7803	electron transfer flavoprotein α subunit		−3.5
Bphy_7804	electron transfer flavoprotein α/β-subunit		−3.1
Inorganic ion transport and metabolism
Bphy_0141	CutC family protein		−3.2
Bphy_0257	ammonium transporter	*amtB*	−2.1
Bphy_1627	sulfate ABC transporter inner membrane subunit	cysW	−1.7
Bphy_1629	sulfate ABC transporter periplasmic sulfate-binding protein		−1.7
Bphy_1647	ABC transporter-like protein		−2.9
Bphy_1648	transport systems inner membrane component		−2.7
Bphy_2231	sulfate adenylyltransferase large subunit		−2.2
Bphy_2235	sulfite reductase		−2.0
Bphy_3602	ABC transporter related		−1.7
Bphy_3603	ABC transporter periplasmic ligand-binding protein		−2.4
Bphy_5040	NlpA lipoprotein		−4.0
Bphy_5227	ABC-type glycine betaine transport system		−2.8
Bphy_5229	aliphatic sulfonate ABC transporter periplasmic protein		−3.7
Bphy_5232	rhodanese domain-containing protein		−4.0
Bphy_5473	Dyp-type peroxidase family protein		−1.9
Bphy_5555	sulfatase		−1.6
Bphy_6080	taurine ABC transporter, periplasmic binding protein		−4.6
Bphy_7233	ABC transporter related		−3.2
Bphy_7234	transport systems inner membrane component		−3.7
Bphy_7235	transport systems inner membrane component		−3.0
Bphy_7236	ABC sulfate ester transporter, periplasmic protein		−2.5
Bphy_7645	transport systems inner membrane component		−2.6
Bphy_7646	transport systems inner membrane component		−3.1
Bphy_7647	ABC transporter related		−3.1
Bphy_7753	nitrogenase reductase	*nifH₁*	−5.2
Bphy_7808	nitrogenase reductase	*nifH₂*	−5.2

¹ Locus identifier and description was extracted from the GenBank files (NC_010622.1, NC_010623.1, NC_010625.1, NC_010627.1); ² log₂ of the fold change (FC) in expression of P. vulgaris nodules induced by an rpoN mutant (rpoN mt nod) versus the wild type (wt nod); RND: resistance-nodulation-division; dTDP: deoxythymidine diphosphate; NAD: nicotinamide adenine dinucleotide; GDP: guanosine diphosphate; UDP: uridine diphosphate; FAD: Flavin adenine dinucleotide; ABC: ATP-binding cassette.