. 2019 Aug 1;85(16):e00966-19. doi: 10.1128/AEM.00966-19

TABLE 3.

Selected differentially expressed genes

Regulation	Genes differentially expressed in the following comparisons^a:
Regulation	W3110 grown with benzoate vs no benzoate	A1-1 vs W3110 grown with benzoate	C3-1 vs W3110 grown with benzoate	G5-1 vs W3110 grown with benzoate	G5-2 vs W3110 grown with benzoate
Upregulated	aceABEFK	acs	cspB	cvpA	*ompF*
	*appAB*	glcDE	ompG	fadB	ompL
	*asr*	*ompF*	ompL	glcDE	wcaADK
	cyoABCDE		pspB	ompL	*ymgG*
	dppCB		phoE	phoE
	*gadABC*			phoH
	*gadEF*
	*hdeB*
	hyaBF
	*hycABCDEFG*
	*marRAB*
	*mdtEF*
	*narHJ*
	oppABCD
	*slp*
Downregulated	cadAB	*appBC*	flu	dctR	artP
	flgBCDEFG	dctR	*gadABC*	*gadABC*	*asr*
	fliAFN	flu	*hycACDEFGH*	*gadEF*	flu
	fruAK	*gadABC*	pepN	*hdeABD*	gltIK
	*ompF*	*gadEF*	*slp*	*hycACDEFGH*	*hycCDEFG*
	*ymgG*	*mdtEF*		*mdtEF*	*marRB*
		*hycBCDEFGH*		*slp*	*slp*
		*hdeABD*		sufABCD	yahK
		*narHIJ*		yahK	yeeR
		*slp*		yhiDM
		yeeR		wrbA
		yhiDM
		ymgG

Differential expression was indicated by a log₂ fold change in expression of ≥1 and a P value of <0.01. All strains were cultured to log phase at pH 6.5 in 5 mM sodium benzoate, except for the W3110 control culture, which was cultured without benzoate. Boldface without underlining indicates genes upregulated by benzoate in W3110 but knocked down in benzoate-evolved strains (A1-1, C3-1, G5-1, G5-2). Boldface with underlining indicates genes that were downregulated by benzoate in W3110 and that had increased expression in benzoate-evolved strains.