. 2024 Jan 22;90(2):e01374-23. doi: 10.1128/aem.01374-23

TABLE 1.

Expression change of genes involved in nodulation and nitrogen metabolism module in the free-living ΔbjaR₁ mutant compared with wild-type cells

Gene ID^a	Gene names^b	Description^c	Ratio^d	Function or pathway involved
BjaI/BjaR₁ quorum sensing
blr1063	bjaI	Putative autoinducer synthase	0.19*	IV- HSL synthesis
Nodulation genes set (or module)
bll1475	nodQ	NodQ bifunctional enzyme	2.11
bll1630	nolK	GDP-fucose synthetase	1.86
bll1631	noeL	GDP-mannose 4,6-dehydratase	2.25
blr1632	nodM	Putative glucosamine synthase	1.28
bll1714	nodW	Two component regulator	0.94
bll1715	nodV	Two component regulator	0.79
bll2019	nolA	Transcriptional regulatory protein	0.65
bll2021	nodD2	Transcriptional regulatory protein	0.28*
bll2023	nodD1	LysR family transcriptional regulator	1.44
blr2024	nodY		4.39*
blr2025	nodA	Acyl transferase	3.13*
blr2026	nodB	Chitooligosaccharide deacetylase	2.30
blr2027	nodC	Chitin synthase	2.65*
blr2028	nodS	N-methyl transferase	1.65
blr2029	nodU	6-O-carbamoyl transferase	2.37
blr2030	nodI	Transporter of Nod Factor	2.33
blr2031	nodJ	Lipooligosaccharide transport system permease protein	1.65
blr2033	nolN	Nol N protein	1.87
blr2034	nolO	Carbamoyltransferase	2.46
blr2035	nodZ	NodZ protein	1.84
blr2062	noeI	2-O-methyltransferase	1.98
blr4773	nwsA	Two component regulator	1.48
blr4774	nwsB	Two component regulator	1.51
Nitrogen metabolism module
blr0613	amtB	Ammonium transpoter	0.10*	Uptake of NH₄⁺ - N
blr1327		Nitronate monooxygenase	3.10*	Transformation of nitronate to nitrile
blr2803 ~ blr2805	nrtA/B/C	ABC transporter nitrate-binding protein	0.28 ~ 0.40*	Nitrate assimilation
blr2808		Putative nitrite reductase	0.41	Transformation of NO ^- - N to ammonia 2
blr2809	nasA	Nitrate reductase large subunit	0.31*	Assimilatory nitrate reduction
blr3214	norC	Nitric oxide reductase subunit C	0.24*	Denitrification
blr3215	norB	Nitric oxide reductase subunit B	0.37*	Denitrification
blr3397	nit	Nitrilase	0.15*	Transformation of nitrile - N to ammonia
blr4169	glnII	Glutamine synthetase II	0.28*	Glutamine synthesis
bll4571	nirA	Putative ferredoxin—nitrite reductase	0.35*	Assimilatory nitrate reduction
bll4798		Putative glutaminase	0.33*	Glutamine synthesis
blr4949	glnA	Glutamine synthetase I	2.04	Glutamine synthesis
bll5731	cyns	Probable cyanate hydratase	0.26*	Reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide
bll5732 ~ blr5734	nrtA/B/C	ABC transporter nitrate-binding protein	0.18 ~ 0.26*	Nitrate assimilation
blr6402		Nitrilase	0.19*	Transformation of nitrile - N to ammonia
bsr7036	napE	Periplasmic nitrate reductase	0.04*
blr7037	napD	Periplasmic nitrate reductase	0.03*
blr7038	napA	Periplasmic nitrate reductase large	0.02*	Dissimitory nitrate reduction to nitrite
blr7039	napB	Periplasmic nitrate reductase small	0.03*	Dissimitory nitrate reduction to nitrite
blr7040	napC	Cytochrome C-type protein	0.02*
blr7089	nirK	Respiratory nitrite reductase	0.02*	Nitrite reductase (NO-forming)
blr0314	nosR	Nitrous oxide reductase expression	0.24*	Nitrous oxide reductase regulator
blr0606	glnK	Nitrogen regulatory protein P-II 2	3.39*	Nitrogen regulation factor
blr0612	glnK	Nitrogen regulatory protein P-II 2	0.12*	Nitrogen regulation factor
blr0723	rpoN ₂	RNA polymerase sigma-54 subunit	0.47	Nitrogen regulation sigma factor
blr1883	rpoN ₁	RNA polymerase sigma-54 subunit	0.04*	Nitrogen regulation sigma factor
blr4486	nifR	Nitrogen regulation protein	0.31*
blr4487	ntrB	Two-component sensor histidine kinase	0.31*	Global nitrogen regulatory system
blr4488	ntrC	Two-component sensor histidine kinase	0.40*
blr4948	glnB	Nitrogen regulatory protein P-II 1	0.38*	Nitrogen regulation factor
blr7084	nnrR	Transcriptional regulatory protein	0.03*	Nitrogen oxide reductase regulator

^{^a}

Nomenclature according to Kaneko et al (2002).

^{^b}

Gene name according to the EMBL-EBI database.

^{^c}

Gene description according to GeneBank.

^{^d}

The transcript ratio of genes in the ΔbjaR₁ mutant compared with those in the wild-type cells freely grown in the liquid yeast-extract mannitol (YEM) medium. Before RNA isolation, genistein was added to the culture with a final concentration of 5.0 μM for 12 h. “*” indicating the significantly up- or down-regulated genes with the transcription ratio values ≥ 2.5 or ≤ 0.4, respectively.