TABLE 2.

Lipid/glycerol metabolism and regulatory genes showing increased expression during chemotaxis toward PE

PA no. or function	Genea	Protein annotation	Mean fold increaseb
Lipid/glycerol metabolism
PA0026	plcB†	PlcB, extracellular PLC	2.6
PA0182		3-Oxoacyl (acyl carrier protein) reductase	2
PA0208		Acyl-CoA:acetate/3-ketoacid CoA transferase	12.5
PA0209		Triphosphoribosyl-dephospho-CoA synthetase	6.7
PA0211	accD	AccD, acetyl-CoA carboxylase beta subunit	6.7
PA0214	fabD	FabD, acyl-carrier-protein	5.7
PA0358		1-Acyl-sn-glycerol-3-phosphate acyltransferase	2.3
PA0482	aceB†	AceB, malate synthase, glyoxylate shunt	2.0
PA0506	fadE*	FadE, acyl-CoA dehydrogenase, β-oxidation	2
PA0507	fadE*	FadE, acyl-CoA dehydrogenases, β-oxidation	2.7
PA0508	fadE*	FadE, acyl-CoA dehydrogenases, β-oxidation	2.6
PA0743	mmsB	MmsB, 3-hydroxyisobutyrate dehydrogenase	2.0
PA0744	fadN*	FadN, enoyl-CoA hydratase, β-oxidation	2
PA0745	fadN*	FadN, enoyl-CoA hydratase, β-oxidation	2
PA0746	fadE*	FadE, acyl-CoA dehydrogenases, β-oxidation	2
PA0792	prpD	PrpD methylcitrate dehydratase, propionate catabolism	2
PA0795	prpC (gltA)	PrpC (GltA), methylcitrate synthase	2.8
PA0796	prpB†	PrpB, methylisocitrate lyase	2.7
PA0797	fadR (gntR)	FadR-like regulator, GntR class of transcriptional regulators	2.4
PA0887	acs	Acs, acyl-coenzyme A synthetases/AMP-fatty acid ligase	3.9
PA1137		Crotonyl-CoA reductase	4.6
PA1288	fadL†	FadL, LCFA transport protein	2
PA1736		Acetyl-CoA acyltransferase	2.8
PA1737	fadB*	FadB 3-hydroxyacyl-CoA dehydrogenase, β-oxidation	2.6
PA2011	liuE	LiuE, 3-hydroxy-3-methylglutaryl-CoA lyase	4.2
PA2012	liuD	LiuD, alpha subunit of geranoyl-CoA carboxylase	7.7
PA2013	fadN*	FadN, enoyl-CoA hydratase, β-oxidation	3.9
PA2014	liuB	LiuB, methylmalonyl-CoA decarboxylase alpha subunit	4.6
PA2015	liuA	LiuA, isovaleryl-CoA dehydrogenase	4.1
PA2142	fabG	FabG, 3-oxoacyl-(acyl-carrier-protein) reductase	2
PA2552	fadE*	FadE, acyl-CoA dehydrogenases, β-oxidation	4.7
PA2553	paaJ	PaaJ, acetyl-CoA acetyltransferase	7.0
PA2554	fabG	FabG, 3-oxoacyl-(acyl-carrier-protein) reductase	5.9
PA2555	acs	Acs, acyl-coenzyme A synthetases/AMP-fatty acid ligases	6.0
PA2557	fadD (caiC)	FadD (CaiC), acyl-CoA synthetases	5.7
PA2634	aceA†	AceA, isocitrate lyase, glyoxylate shunt	5.0
PA2764	mhpC	MhpC, acyl transferase	2.5
PA2862	lipA†	LipA, lipases, serine active site	8.9
PA2863	lipH	LipH, lipase chaperone for LipA and LipC	4.9
PA2887		3-Oxoacyl-(acyl-carrier-protein) reductase	2.1
PA2888		Acetyl-CoA carboxylase	2.0
PA2889	caiA*	CaiA, acyl-CoA dehydrogenases, β-oxidation	2.0
PA3013	fadA*	FadA, 3-ketoacyl-CoA thiolase, β-oxidation	2.0
PA3014	fadB*	FadB, 3-hydroxyacyl-CoA dehydrogenase, β-oxidation	2.0
PA3267		1-Acyl-sn-glycerol-3-phosphate acyltransferase	2.0
PA3277	fabG	FabG, 3-oxoacyl-(acyl-carrier-protein) reductase	2.2
PA3300	fadD2	FadD2, LCFA CoA ligase	2.0
PA3415		Probable dihydrolipoamide acetyltransferase	2.0
PA3427	fabG	FabG, 3-oxoacyl-(acyl-carrier-protein) reductase, putative	2.9
PA3429	mhpC	MhpC, predicted hydrolases or acyltransferases	2.5
PA3567		Crotonyl-CoA reductase	4.6
PA3568		Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases	4.8
PA3569	mmsB	MmsB, 3-hydroxyisobutyrate dehydrogenase	2.4
PA3581	glpF	GlpF, glycerol uptake facilitator	4.4
PA3582	glpK	GlpK, glycerol kinase	2.5
PA3994	mhpC	MhpC, predicted acyltransferases	3.4
PA4148	fabG	FabG, dehydrogenases with different specificities	3.9
PA4152	mhpC	MhpC, predicted hydrolase or acyltransferases	3.7
PA4198	caiC	CaiC, acyl-CoA synthetases	2.3
PA4338		Predicted acyltransferases	2.0
PA4589	fadL†	FadL, LCFA transport protein	2.8
PA4733	acsA	AcsA, acetate CoA ligase	3.1
PA4813	lipC†	LipC, lipase	9.6
PA5112	estA†	EstA, lipase, G-D-S-L family, serine active site	2.6
Regulatory genes
PA0176	tar	Tar, methyl-accepting chemotaxis protein	2.1
PA1285	marR	MarR, transcriptional regulators	2.0
PA1300	rpoE	RpoE, sigma 24 homolog	2.0
PA1354		Transcription factor, NusG proteins	2
PA1363	rpoE	RpoE, sigma 24 homolog	2
PA1437	ompR	OmpR, response regulators, CheY-like receiver domain and winged-helix DNA-binding domain	2.4
PA1438	baeS	BaeS, signal transduction histidine kinase	2
PA1760	gerE	GerE, bacterial regulatory proteins, LuxR family	2.7
PA1912	rpoE	RpoE, sigma 24 homolog	2.4
PA1976	baeS	BaeS, signal transduction histidine kinase	8.2
PA1978	citB	CitB, response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain	6.3
PA1979		Signal transduction histidine kinase; part of operon with PA1980	6.3
PA1989	citB	CitB, response regulator containing a CheY-like receiver domain and HTH DNA-binding domain, PhoB-like	6.8
PA1992	baeS	BaeS, signal transduction histidine kinase	5.3
PA2016	liuR	LiuR, transcriptional regulator of liuABCDE genes, SoxR-like	3.8
PA2072		Diguanylate cyclase GGDEF domain and EAL domain	2
PA2137	atoC	AtoC, response regulator containing CheY-like receiver	2.3
PA2556	araC	AraC type regulator	2.4
PA3133	tetR	Bacterial regulatory proteins, TetR family	2.2
PA3233		Predicted signal transduction; cAMP-binding and CBS domains	4.5
PA4094	araC	Transcriptional regulator AraC type	3.7
PA4203	lysR	LysR type, transcriptional regulator	2.5
PA4147	acoR	AcoR, transcriptional activator of acetoin/glycerol metabolism	5.1
PA4290	tar	Tar, methyl-accepting chemotaxis protein	3.5
PA4436	araC	Transcriptional regulator, AraC type	2.1
PA4787	araC	Transcriptional regulator, AraC type	2
PA5324	araC	Transcriptional regulator, AraC type	2.9
PA5550	glpR	GlpR, transcriptional regulators of sugar metabolism	3.6

^a†, gene was mutated in this study to determine whether it is required for P. aeruginosa to preferentially move up a PE or LCFA gradient. *, gene is associated with β-oxidation.

^bAll genes listed showed an average of a twofold or greater increase (P ≤ 0.004) in expression in P. aeruginosa twitching toward PE, compared to P. aeruginosa twitching in the absence of PE. Four independent comparisons with each condition were run on separate days. Cells were harvested for RNA at 16 h after inoculation to the twitching plates.