Table 1. List of genes and proteins differentially expressed using RNA-Seq and proteomics in the rpfF_Bc mutant compared to the wild type.

				RNA Seq		Proteomics
Locus ID CCEa	Orthologues J2315b	Descriptionc	Gene name	wt vs rpfF d	wt vs rpfF comple	wt vs rpfF f	wt vs rpfF complg
CCE49245	BCAL0111	O-linked N-acetylglucosamine transferase		3.0	2.1	na	2.8
CCE46674	BCAL0249	50S ribosomal protein L6		0.4	0.9	1.6	1.5
CCE48190	BCAL0524	Flagellar motor switch protein		5.1	3.2	3.9	1.4
CCE48189	BCAL0525	Flagellar MS-ring protein		4.2	6.5	2.9	1.6
CCE53354	BCAL0762	Methyl-Apting chemotaxis protein		4.6	1.4	2.7	0.9
CCE53285	BCAL0831	Phasin family protein		2.9	0.7	3.2	1.4
CCE51557	BCAL1059	Bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein		2.8	1.6	0.5	0.8
CCE50475	BCAL2352	Carbonic anhydrase		4.3	1.0	7.0	1.1
CCE49840	BCAL3041	Protein involved in carbohydrate transport		4.5	2.0	0.5	1.6
CCE51244	BCAL3285	Nitric oxide dioxygenase; flavohemoprotein		6.7	0.6	na	0.8
CCE46722	BCAM0184	Fucose-Binding lectin protein	bclB	183.0	0.5	na	0.8
CCE46720	BCAM0186	Fucose-Binding lectin protein	bclA	280.2	0.5	na	1.1
CCE46715	BCAM0191	Non-ribosomal peptide synthetase		5.2	0.9	na	0.7
CCE46713	BCAM0192			9.4	1.5	na	1.2
CCE46711	BCAM0194			7.9	1.6	na	0.4
CCE46710	BCAM0195	Non-ribosomal peptide synthetase		6.6	1.4	na	0.8
CCE46709	BCAM0196			5.9	0.9	14.0	0.9
CCE50899	BCAM0853	Transposase		3.1	0.8	10.0	0.7
CCE50898	BCAM0854	Mannose-6-phosphate isomerase		8.3	0.4	na	0.4
CCE50892	BCAM0859	Protein involved in capsule organization		31.8	0.4	na	0.7
CCE48736	BCAM1004	Gdp-Mannose 4,6-dehydratase		4.3	0.3	na	0.5
CCE47169	BCAM1572	Methyl-Apting chemotaxis protein		3.0	1.2	3.0	1.5
CCE46959	BCAM1745	Atpase		0.01	0.8	0.2	2.2
CCE53120	BCAM2140	Type I secretion membrane fusion protein		15.8	1.0	na	1.4
CCE53119	BCAM2141	ABC transporter protein		16.0	0.9	na	1.0
CCE53117	BCAM2143	Calcium ion binding protein	bapA	12.2	0.8	41.5	0.7
CCE53024	BCAM2224	Protein involved in siderophore transport		31.5	28.0	na	na
CCE53019	BCAM2230	Non-ribosomal peptide synthetase		11.8	7.9	na	na
CCE46201	BCAM2627	Protein involved in iron ion transport		6.2	11.0	10.0	10.0

^aNomenclature according to GenBank file CAFQ01000001.1.

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

^cDescription according to the EggNOG classification.

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

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

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

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

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