. 2012 Oct 24;7(10):e44637. doi: 10.1371/journal.pone.0044637

Table 1. Selection of targets of the CbrAB/Crc system implicated by the transcriptome analysis.

ORF^a	Gene	LB^b			BSM^b + succinate			Description	CA motif (location)^c
		crc vs. wt	cbr vs. wt	crcZ vs. wt	crc vs. wt	cbrB vs. wt	crcZ vs. wt
PA0755	opdH	5,9			2,05			cis-aconitate porin OpdH	AAGAACAA (−25 to −18)
PA0866	*aroP2*	4,73						aromatic amino acid transport protein	AACAAUAA (−33 to −12)
PA0887	*acsA*	−3,41	−2,51	−3,27	7,98	2,88	3,62	acetyl-coenzyme A synthetase	AACAAAAACAA (−35 to −25)
PA0996	pqsA		−3,55	−3,49	−2,01	−18,34	−16,67	probable coenzyme A ligase
PA0997	pqsB		−3,72	−3,49	−2,11	−33,37	−56,5	PqsB protein
PA0998	pqsC		−3,73	−3,89	−2,01	−25,21	−40,64	PqsC protein
PA0999	pqsD		−3,77	−3,38	−2	−23,39	−34,65	3-oxoacyl-[acyl-carrier-protein] synthase III
PA1000	pqsE		−2,79	−2,58	−2,09	−18,62	−22,18	quinolone signal response protein
PA1001	phnA		−3,58	−3,28	−2,08	−18,69	−23,34	anthranilate synthase component I
PA1002	phnB		−2,04		−2,01	−11,69	−11,46	anthranilate synthase component II
PA1003	pqsR						−2,48	transcriptional regulator PqsR (MvfR)
PA1070	braG		−2,28	−3,76			−3,22	branched-chain amino acid transport protein BraG
PA1071	braF		−2,37	−4,02	2,08		−2,91	branched-chain amino acid transport protein BraF
PA1072	braE		−2,21	−3,11	2,33		−3,05	branched-chain amino acid transport protein BraE
PA1073	braD		−2,88		2,5		−5,56	branched-chain amino acid transport protein BraD
PA1074	braC		−2,11	−3,6	2,14		−2,41	branched-chain amino acid transport protein BraC
PA1342		−2,68		−2,38				probable binding protein component ofABC transporter	AAUAAAAA (−33 to −26)
PA1617					2,44			probable AMP-binding enzyme	AACAACAACAA (−23 to −13)
PA1894					5,83		−4,24	hypothetical protein
PA1895					4,27		−3,07	hypothetical protein
PA1984	exaC		−2,76		3,84		−3,37	NAD+ dependent aldehyde dehydrogenase ExaC
PA1985	pqqA		11,34	8,74				pyrroloquinoline quinone biosynthesis protein A
PA1986	pqqB		2,47	2,52				pyrroloquinoline quinone biosynthesis protein B
PA1987	pqqC		3,86	3,7				pyrroloquinoline quinone biosynthesis protein C
PA1988	pqqD		3,7	4,02				pyrroloquinoline quinone biosynthesis protein D
PA1989	pqqE		2,72	2,77				pyrroloquinoline quinone biosynthesis protein E
PA2247	*bkdA1*		−2,36	−3,81	3,23			2-oxoisovalerate dehydrogenase (alpha subunit)
PA2248	bkdA2		−2,6	−3,51				2-oxoisovalerate dehydrogenase (beta subunit)
PA2249	bkdB		−2,48	−3,22				branched-chain alpha-keto acid dehydrogenase
PA2250	lpdV		−2,62	−3,07				lipoamide dehydrogenase-Val
PA2533					2,13			probable sodium:alanine symporter	AACAAGAAUAA (−20 to −10)
PA3038			−4,13		16,75	2,11		probable porin	AAUAACAA (−7 to +1)
PA3190		−7,43		−7,81				probable binding protein component ofABC sugar transporter	AAUAACAA (−24 to −17)
PA3366	*amiE*	4,65	2,04					aliphatic amidase	AACAACAA (−20 to −13)
PA3452	mqoA	4,87	3,12					malate:quinone oxidoreductase
PA3570	mmsA				2,23			methylmalonate-semialdehyde dehydrogenase	AACAAUAA (−37 to −30)
PA3875	narG	−6,01	−4,46	−4,79				respiratory nitrate reductase alpha chain	AAGAAGAA (+34 to +41)
PA4139					−3,37	2,87	4,72	hypothetical protein
PA4147	acoR				3,38			transcriptional regulator AcoR	AACAACAA (−30 to −23)
PA4150	acoA				2,77			probable dehydrogenase E1 component	AACAACAA (−9 to −2)
PA4151	acoB				4,1			acetoin catabolism protein AcoB	AACAAGAA (−22 to −15)
PA4306	flp				−2,9	−6,66	−8,64	Type IVb pilin, Flp	AACAAGAA (−22 to −15)
PA4496			−2,54	−2,55	2,9	−2,73	−8,18	probable binding protein component of ABC transporter
PA4500			−3,29	−3,94	2,03			probable binding protein component of ABC transporter	AAAAAGAAAAAA (−22 to −11)
PA4501	opdD		−2,53		2,64			glycine-glutamate dipeptide porin OpdP	AACAAUAA (−37 to −30)
PA4770	lldP				2,96			L-lactate permease	AACAACAA (−25 to −18)
PA4913					6,89		−2,07	probable binding protein component of ABC transporter	AACAACAA (−53 to −46)
PA5112	*estA*			−2,25	2		−2,23	esterase EstA	AAAAACAA (−24 to −17)
PA5153			−2.42	−2.55	2.92		−2.28	probable periplasmic binding protein
PA5167	dctP		−4,35	−4,05	3,37		−6,85	probable c4-dicarboxylate-binding protein	AAGAACAA (−20 to −13)
PA5168	dctQ		−2,19	−2,12	6,54		−6,4	probable dicarboxylate transporter	AAUAAGAA (−20 to −13)
PA5169	dctM		−2,41	−2,2	6,72		−10,69	probable C4-dicarboxylate transporter
PA5220					2,38		−4,08	hypothetical protein	AAGAACAACAAGAA (−31 to −18)
PA5348					5,54		−3,03	probable DNA-binding protein	AACAACAA (−26 to −19)

The numbers represents ORF according to www. pseudomonas.com. [45].

Fold changes observed after growth in LB and BSM + succinate, respectively. Positive values indicate that transcripts were more abundant in the mutant than in the wild type. Negative values indicate that transcripts were less abundant in the mutant than in the wild type.

The locations of the CA-motif are given according to the start codon (A of the ATG = +1).