TABLE 3.

Genes affected by Wal-OFF conditions

Gene, changed ≥4-fold	Operona	Gene name	Annotation	Log2 fold change			Cell wall associationc
				CRISPRi		WalR OEb
				No Xyl	Low Xyl
cd630_05140	05140	cwpV	Hemagglutinin/adhesin	4.69	2.74	NCd	SPI
cd630_20160	20160		Hypothetical protein	4.18	1.65	−2.19
cd630_11700	11700		Hypothetical protein	3.52	1.83	NC
cd630_11710	11710	etfB4	Electron transfer flavoprotein alpha	3.30	1.40	NC
cd630_11720	11720	etfA4	Electron transfer flavoprotein alpha	2.58	1.24	NC
cd630_11730	11730		FAD-linked oxidase	2.17	1.08	NC
cd630_08320	08320	aksA	trans-Homoaconitate synthase	3.11	2.02	NC
cd630_08330	08330	acnB	Aconitate hydratase	3.06	2.05	NC
cd630_08340	08340	icd	Isocitrate dehydrogenase	3.07	2.16	NC
cd630_17290	17290		Sodium:phosphate symporter	2.76	0.45	−1.46	Membrane
cd630_13840	13840		LamB/YcsF family protein	2.17	0.88	NC
cd630_13850	13850		Hypothetical protein	2.36	1.15	NC	Membrane
cd630_13860	13860		Allophanate hydrolase subunit 1	2.52	1.28	NC
cd630_13870	13870		Allophanate hydrolase subunit 2	2.60	1.14	NC
cd630_24260	24260	buk1	Butyrate kinase	2.45	NC	−1.41
	24250	ptb2	Phosphate butyryltransferase	1.65	NC
cd630_24240	24240		Pyridoxal phosphate-dependent transferase	2.55	NC	−1.15
	24230		Putative transporter	1.17	NC		Membrane
cd630_07650	07650	srlEa	PTS, IIB N-terminal component	2.17	NC	NC
cd630_07660	07660	srlEb	PTS, IIB C-terminal component	2.29	NC	NC	Membrane
cd630_07670	07670	srlB	PTS, IIA subunit	2.27	NC	NC	Membrane
cd630_07680	07680	srlD	Sorbitol-6-phosphate dehydrogenase	2.35	NC	NC
	00350		Transcriptional regulator	1.46	0.55	−0.86
cd630_00360	00360	acoA	Acetoin dehydrogenase E1 alpha	2.20	0.94	NC
cd630_00370	00370	acoB	Acetoin dehydrogenase E1 beta	2.29	0.91	NC
cd630_00380	00380	acoC	Acetoin dehydrogenase E2	2.20	0.72	NC
cd630_00390	00390	acoL	Acetoin dehydrogenase E3	2.04	0.83	−0.57
cd630_30010	30010		Hydrolase/isomerase/hydratase	2.25	NC	NC
cd630_23920	23920		tRNA-binding protein	2.15	1.65	−1.77
cd630_30960	30960	bglA3	6-Phospho-beta-glucosidase	2.13	NC	NC
cd630_30950	30950	bglA2	6-Phospho-beta-glucosidase	2.07	NC	NC
cd630_25150	25150		Aspartate aminotransferase	2.12	2.38	−1.76
	24291		Flavo/ferredoxin oxidoreductase delta	1.19	NC	NC
cd630_24290	24290		Flavo/ferredoxin oxidoreductase alpha	2.11	NC	−0.91
	24280		Flavo/ferredoxin oxidoreductase beta	1.66	NC	NC
	24270		Flavo/ferredoxin oxidoreductase gamma	1.50	NC	NC
cd630_30040	30040	kdgT2	2-Keto-3-deoxygluconate permease	2.08	0.33	0.93	Membrane
cd630_30020	30020	uxaA	d-Galactate dehydratase/altronate hydrolase	2.06	0.25	NC
cd630_32630	32630	pstC	Phosphate ABC transporter, PstC	2.03	NC	NC	Membrane
	32620	pstA	Phosphate ABC transporter, PstA	1.03	NC	NC	Membrane
	32610	pstB	Phosphate ABC transporter, ATP binding	1.80	NC	NC
	32600	phoU	Phosphate uptake regulator	1.25	NC	NC
	30980	bglG1	PTS, antiterminator	0.95	NC	NC
cd630_30970	30970	bglF2	PTS, subunit IIABC	2.01	NC	−0.76	Membrane
cd630_28540	28540	dltD	d-Alanine transferase	−1.52	−2.41	1.03	Membrane
cd630_28530	28530	dltA	d-Ala–d-ala carrier protein ligase 1	−1.34	−2.27	0.84
cd630_28520	28520	dltB	d-Alanyl transferase	−1.34	−2.23	0.49	Membrane
	28510	dltC	d-Ala–d-ala carrier protein ligase 2	−1.27	−1.89	NC
cd630_09000	09000	opuCA	ABC transporter ATP-binding protein	−1.69	−2.36	1.46	Membrane
cd630_09010	09010	opuCC	ABC transporter permease	−1.68	−2.40	1.27
cd630_05190	05190		Hypothetical protein	−2.00	−2.59	0.57	Membrane
	05260		Aminobenzoyl-glutamate transporter	NDe	ND	ND
cd630_05250	05250		Peptidase	−2.15	−1.08	NC
cd630_17671 cd630_17680	17671 17680		Hypothetical protein Membrane protein	−2.18 −2.23	−1.99 −2.18	NC 0.56	Membrane
cd630_17810	17810	walA	Lipoprotein	−2.76	−5.14	NC	SPII
cd630_17820	17820	walR	TC response regulator	−2.51	−3.91	3.81
cd630_17830	17830	walK	TC sensor histidine kinase	−2.33	−4.03	NC	Membrane
cd630_17840	17840	truA2	tRNA pseudouridine synthase A	−2.34	−3.92	NC
cd630_05300	05300		Membrane protein	−2.47	NC	NC	Membrane
	05290		Membrane protein	NC	NC	NC	Membrane
	05280		Amidohydrolase	NC	NC	0.92
cd630_28620	28620		Peptidase	−2.53	−1.43	2.29

^aLists other operon members in order.

^bFold change comparing WalR overexpression to negative-control strain.

^cPredictions by SignalP (SPI, predicted to be a substrate of signal peptidase I; SPII, predicted to be a substrate of signal peptidase II) and by BUSCA (membrane). The BUSCA prediction is given only for those genes that were not already predicted to be SPI or SPII substrates by SignalP.

^dNC, no change, i.e., the fold change was close to 1 and the P value was >0.05.

^eND, CD630_05260 is a pseudogene that was not detected by the RNA-seq analysis tool.