Table 2. List of genes differentially expressed in the rpfF_Bc and cepR mutant, using the wild type as baseline.

Locus ID CCEa	Orthologues J2315b	Descriptionc	Gene name	wt vs rpfF d	wt vs rpfF compl e	wt vs cepR
CCE49231	BCAL0124	Transcriptional activator FlhD		3.7	1.5	0.5
CCE53285	BCAL0831	Phasin family protein		2.8	0.7	3.2
CCE52825	BCAL0833	Acetoacetyl-Coa reductase		4.3	1.1	3.0
CCE51553	BCAL1063	Succinylarginine dihydrolase		2.8	1.4	0.5
CCE50476	BCAL2353	Sulfate permease		18.4	0.9	2.2
CCE51244	BCAL3285	Nitric oxide dioxygenase; flavohemoprotein		6.5	0.6	25.8
CCE46722	BCAM0184	Fucose-Binding lectin protein	bclB	181.0	0.5	5.1
CCE46721	BCAM0185	Fucose-Binding lectin protein	bclC	73.5	0.7	3.3
CCE46720	BCAM0186	Fucose-Binding lectin protein	bclA	274.4	0.5	9.0
CCE46715	BCAM0191	Non-ribosomal peptide synthetase		5.3	0.9	12.8
CCE46713	BCAM0192			9.2	1.5	46.8
CCE46712	BCAM0193			17.1	2.3	47.7
CCE46711	BCAM0194			8.0	1.6	52.2
CCE46710	BCAM0195	Non-ribosomal peptide synthetase		6.5	1.4	34.0
CCE46709	BCAM0196			6.1	0.9	37.7
CCE50917	BCAM0835	Transcriptional regulator, AraC family protein		4.9	1.2	4.3
CCE48735	BCAM1005	Acyltransferase		4.6	0.6	2.2
CCE48728	BCAM1010	Utp–Glucose-1-Phosphate uridylyltransferase		39.4	0.5	2.4
CCE46959	BCAM1745	Atpase		0.01	0.8	0.4
CCE50321	BCAM1871	3-Hydroxy-3-Methylglutaryl-Coenzyme A reductase		3.5	0.8	32.5
CCE53256	BCAM2060	Natural resistance-associated macrophage protein		0.1	0.8	0.4
CCE53120	BCAM2140	Type I secretion membrane fusion protein		16.0	0.9	3.1
CCE53119	BCAM2141	ABC transporter protein		16.0	0.9	4.4
CCE53118	BCAM2142			14.9	1.0	5.3
CCE53117	BCAM2143	Calcium ion binding protein		12.1	0.8	5.1
CCE53089	BCAM2169	Outer membrane autotransporter protein		2.6	0.9	2.1
CCE53021	BCAM2227	Pyochelin biosynthetic protein		na	na	2.2
CCE52940	BCAM2307	Metalloendopeptidase	zmpB	3.7	1.4	8.7
CCE52939	BCAM2308	Aminopeptidase		4.0	1.5	5.3
CCE52108	BCAS0292		aidA'	3.2	0.9	138.1
CCE52109	BCAS0293		aidA	4.0	0.8	167.2

^aNomenclature according to GenBank file CAFQ01000001.1.

^bOrthologs were identified as described in the Material and Methods section.

^cDescription according to EggNOG categories.

^dFold change (FC) of expression, comparing wild type strain with rpfF mutant grown in LB medium until an OD of 2.

^eFold change (FC) of expression, comparing wild type strain with complemented rpfF mutant grown in LB medium until an OD of 2.

^fFold change (FC) of expression comparing wild type strain with cepR mutant grown in LB medium until an OD of 2 [11].

na, not applicable because the read number in the mutant or complemented strains is equal 0.