. 2020 Dec 17;11:517462. doi: 10.3389/fmicb.2020.517462

TABLE 2.

Selected downregulated genes upon TRQ treatment.

		Sampling time^c
ORF^a	Gene^b	EXP	STA	QS^d	Protein description^e
PA0122	rahU	−3.6	−2.7	+	RahU
PA0284		1.8	−1.7		Hypothetical protein
PA0713		−1.5	−1.9	+	Hypothetical protein
PA0852	cbpD	−1.6	−3.8	+	Chitin-binding protein CbpD precursor
PA0852.1		−1.6	−3.8		Uncharacterized protein
PA0977			−1.5		Hypothetical protein
PA0997	pqsB	−4.1	−1.8	+	PqsB
PA0998	pqsC	−4.2	−1.7	+	PqsC
PA0999	pqsD	−4.1	−1.6	+	3-Oxoacyl-[acyl-carrier-protein] synthase III
PA1000	pqsE	−3.8	−1.5	+	Quinolone signal response protein
PA1216		−2.6	−2.2	+	Hypothetical protein
PA1217		−2.5	−1.8	+	Probable 2-isopropylmalate synthase
PA1218		−2.3	−1.4	+	Hypothetical protein
PA1245	aprX		−1.8	+	AprX
PA1246	aprD		−1.4	+	Alkaline protease secretion protein AprD
PA1247	aprE		−1.6	+	Alkaline protease secretion protein AprE
PA1248	aprF		−1.4	+	Alkaline protease secretion outer membrane protein AprF precursor
PA1249	aprA		−3.1	+	Alkaline metalloproteinase precursor
PA1250	aprI		−1.4	+	Alkaline proteinase inhibitor AprI
PA1384	galE		−1.3		UDP-glucose 4-epimerase
PA1784		−1.2	−1.6	+	Hypothetical protein
PA1837			−2		Hypothetical protein
PA1838	cysI		−1.5		Sulfite reductase
PA1869	acp1	−2.4	−2.2	+	Acp1
PA1871	lasA	−2	−3.4	+	LasA protease precursor
PA1899	phzA2	−2.1	−2.8		Probable phenazine biosynthesis protein
PA1900	phzB2	−3.2	−5.6		Probable phenazine biosynthesis protein
PA1901	phzC2	−2.8	−3.7	+	Phenazine biosynthesis protein PhzC
PA1902	phzD2	−4	−4	+	Phenazine biosynthesis protein PhzD
PA1903	phzE2	−3.9	−3.5	+	Phenazine biosynthesis protein PhzE
PA1904	phzF2	−3.7	−3.5	+	Probable phenazine biosynthesis protein
PA1905	phzG2	−3.3	−3.4	+	Probable pyridoxamine 5′-phosphate oxidase
PA1927	metE		−1.3	+	5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
PA2030			−1.6	+	Hypothetical protein
PA2031			−1.7	+	Hypothetical protein
PA2062			−2.4		Probable pyridoxal-phosphate dependent enzyme
PA2066		−1.1	−1.6	+	Hypothetical protein
PA2067		−1.4	−1.8	+	Probable hydrolase
PA2068		−2.6	−1.9	+	Probable major facilitator superfamily (MFS) transporter
PA2069		−2.8	−3.7	+	Probable carbamoyl transferase
PA2193	hcnA	−2.3	−3	+	Hydrogen cyanide synthase HcnA
PA2194	hcnB	−2.2	−2.9	+	Hydrogen cyanide synthase HcnB
PA2195	hcnC	−2.4	−3	+	Hydrogen cyanide synthase HcnC
PA2204		1.6	−2.1		Probable binding protein component of ABC transporter
PA2274			−2.2	+	Hypothetical protein
PA2300	chiC	−2.6	−4.5	+	Chitinase
PA2302	ambE		−2.1	+	AmbE
PA2303	ambD		−2.1	+	AmbD
PA2304	ambC		−2.1	+	AmbC
PA2305	ambB		−2	+	AmbB
PA2328		−1.5	−1.8	+	Hypothetical protein
PA2329		−1.6	−2.3	+	Probable ATP-binding component of ABC transporter
PA2330		−1.7	−2.7	+	Hypothetical protein
PA2331		−1.5	−3.3	+	Hypothetical protein
PA2381		−1	−2.5		Hypothetical protein
PA2459			−1.4		Hypothetical protein
PA2564		−2.3	−1.5	+	Hypothetical protein
PA2565		−2.3	−1.5	+	Hypothetical protein
PA2566		−2.3	−1.7	+	Conserved hypothetical protein
PA2570	lecA	−3.5	−3.6	+	LecA
PA2588			−1.7	+	Probable transcriptional regulator
PA3361	lecB	−5.6	−3.3	+	Fucose-binding lectin PA-IIL
PA3450	lsfA		−2.1		1-Cys peroxiredoxin LsfA
PA3478	rhlB	−3.2	−3.3	+	Rhamnosyltransferase chain B
PA3479	rhlA	−3.7	−3.8	+	Rhamnosyltransferase chain A
PA3520		−2.2	−2.4	+	Hypothetical protein
PA3724	lasB	−1.7	−1.7	+	Elastase LasB
PA3734		−2.3	−1.6	+	Hypothetical protein
PA3813	iscU		−1.4		Probable iron-binding protein IscU
PA3814	iscS		−1.3		L-Cysteine desulfurase (pyridoxal phosphate-dependent)
PA3869			−1.4		Hypothetical protein
PA3884			−1.4		Hypothetical protein
PA3928		−1.4	−1.8		Hypothetical protein
PA3929	cioB	−1.2	−1.9		Cyanide insensitive terminal oxidase
PA3930	cioA	−1.4	−2.1		Cyanide insensitive terminal oxidase
PA4078		−2.1	−3.9	+	Probable non-ribosomal peptide synthetase
PA4079			−1.4		NaD(P)H-dependent carbonyl reductase
PA4129		−2.1	−2.1	+	Hypothetical protein
PA4130		−2.5	−2	+	Probable sulfite or nitrite reductase
PA4131		−2.3	−1.9	+	Probable iron–sulfur protein
PA4132		−1.9	−1.9	+	Conserved hypothetical protein
PA4133		−4.2	−2.5	+	Cytochrome c oxidase subunit (cbb3-type)
PA4134		−4.1	−2.3	+	Hypothetical protein
PA4141		−2.5	−2.5	+	Hypothetical protein
PA4205	mexG	1.3	−3.5	+	Hypothetical protein
PA4206	mexH		−2	+	Probable resistance-nodulation-cell division efflux membrane protein
PA4208	opmD		−1.3	+	Probable outer membrane protein precursor
PA4209	phzM	−3.7	−3.2	+	Probable phenazine-specific methyltransferase
PA4210	phzA1	−3.6	−2.2	+	Probable phenazine biosynthesis protein
PA4211	phzB1	−5.8	−4.9	+	Probable phenazine biosynthesis protein
PA4212	phzC1	−2.9	−3.7	+	Phenazine biosynthesis protein PhzC
PA4213	phzD1	−4	−4	+	Phenazine biosynthesis protein PhzD
PA4214	phzE1	−3.9	−3.5	+	Phenazine biosynthesis protein PhzE
PA4215	phzF1	−3.7	−3.5	+	Probable phenazine biosynthesis protein
PA4216	phzG1	−3.4	−3.4	+	Probable pyridoxamine 5′-phosphate oxidase
PA4217	phzS	−4.3	−3.8	+	Flavin-containing monooxygenase
PA4442	cysN	1.7	−1.9	+	ATP sulfurylase GTP-binding subunit/APS kinase
PA5220		−2.1	−1.8	+	Hypothetical protein

^aPA numbers are from http://www.pseudomonas.com; ORF, open reading frame. ^bGenes are obtained from http://www.pseudomonas.com. ^cThe ratios (log2 ratio) represent expression levels in PAO1 cultures supplemented with 1/4 TRQ relative to that of the control at exponential phase (EXP) and stationary phase (STA). ^dThese genes were identified as QS regulated in previous transcriptome studies. ^eProteins are described from http://www.pseudomonas.com.