TABLE 2.

E. coli genes transiently upregulated (cluster 6) and downregulated (cluster 5) by NaF in a dose-dependent manner^a

General categories	Operons	Functional subcategories	Transcriptional/translational regulators		Terminators
			Activator	Repressor	and REPs
Upegulated genes (Cluster 6)
Cell envelope stress	pspA B CD E	Inner membrane stress	RpoN
Osmotic stress adaptation	proP (osmosensing transporter)	Uptake of zwitterionic osmolytes (l-proline:proton symport, glycine betaine:proton symport)	Fis, CRP, RpoS		REP326
	betIBA, betT	Biosynthesis of the osmoprotectant glycine betaine from choline	Cra, RpoS	BetI,
				p-ArcA
	proV WX	Glycine betaine ABC transporter	IHF, RpoS	H-NS	REP193a-b
	otsBA, treF	Trehalose (osmoprotectant) metabolism	RpoS, ppGpp
	osmC	Organic peroxidase activated by osmotic pressure	Na-NhaR	H-NS	REPt122
			pRcsB, ppGpp leu-Lrp
	osmY	Periplasmic chaperone	ppGpp, RpoS	H-NS, CRP, Fis, IHF, FliZ, pArcA
	osmB	Osmotic stress	RpoS, P-RcsB, Nac, ppGpp
	(lipoprotein)
	ybaY	Osmotic stress	FliA
	(lipoprotein)
Signal transduction systems	phoPQ	Phoqp Two-Component Signal Transduction System, magnesium-dependent	p-PhoP, RpoE	GcvB, MicA
	mgrB	Phoq kinase inhibitor	PhoP
	rstAB	Rstba Two-Component Signal Transduction System	PhoP
	yeaGH	Putative yeagh Two-component	ppGpp, NtrC		REP134
		Signal transduction system
Metabolism	ilvX G MED A	Isoleucine	ppGpp	Lrp, GcvB	REP285
	ivbL-ilvBN	&	ppGpp, cAMP-CRP	GcvB	Rho-ind. terminator
	ilvC	Valine biosynthesis	IlvY
	ilvE alaC	l-alanine biosynthesis II	ppGpp, InfA(B) SgrR	Lrp Nac
	aroG, aroF-tyrA	3-dehydroquinate biosynthesis I	pCpxR	TyrR, Lrp	REP70
	trpD (anthranilate synthase subunit TrpD) gltD astCADBE	l-glutamine degradation I / l-glutamate biosynthesis, l-tryptophan biosynthesis l-glutamine degradation I Ammonia assimilation cycle III l-glutamate biosynthesis I l-arginine degradation II (AST pathway)	SoxR TrpR, RydC Leu-Lrp, AdiY, RpoS, InfA, HdfR arg_ArgR p-NtrC, RpoS, RpoN	TyrR, Nac GcvB Fe2+-Fur, FNR, Nac, cAMP-CRP, Arg-ArgR Lrp, Rob	REPt190
	talA-tktB	Pentose phosphate pathway (nonoxidative branch)	pCreB, ppGpp, DksA		REP179a-c
	maeA acnA	Glyoxylate cycle, TCA cycle I (prokaryotic) mixed acid fermentation gluconeogenesis I Glyoxylate cycle / TCA cycle I	Cra, CRP, ppGpp, MarA, Rob, SoxS	FnrS pArc, Fnr
	ybdR	Oxidoreductase		Nac
	(putative alcohol dehydrogenase YbdR)
Lipid biosynthesis	pgpC	Cardiolipin biosynthesis I	RpoH	NsrR
	ybhP-cslB-ybhN	Cardiolipin biosynthesis I	ppGpp
Amine and polyamine degradation	puuDRCBE,	Putrescine degradation II	RpoS	puuR, p-ArcA	REPv112a-b
				cAMP-CRP
	puuA	Putrescine degradation II		puuR, p-ArcA, Fnr
	puuP	Putrescine:H+ symporter puup	RpoN, RpoS	puuR, p-ArcA, Fnr	REPv111
Peptidoglycan maturation	ldtE	L, d-transpeptidase ldte	ppGpp
	dacC		ppGpp	ArgR, pBolA	REPt81
Acquisition of iron Metabolite damage control	entCEBA	Enterobactin biosynthesis	cAMP-CRP	Fe2+-Fur
	yqjH (nfeF)	Adaptation to iron starvation		Fe2+-Fur, NfeR	5′ REP228a-b
	exbBD	Transport of iron-siderophore complexes		Fe2+-Fur	REP222a-d
					REPv222e
	feoABC	Ferrous iron transport	Fnr, pOmpR	Fe2+-Fur, pArcA, NagC
	fhuF	Ferric-siderophore reductase		Nac, Fe2+-Fur, OxyR
	efe U O B ybgl-pxpBC A	Ferrous iron transport system protein efeo 5-oxoprolinase		CpxR	REP95ab
Iron homeostasis	suf A B C D SE	Iron-sulfur cluster assembly	ppGpp, OxyR, IscR, OxyR, InfA	Fe2+-Fur,
				NsrR
Transcription factors	mhpR	Catabolism of aromatic compounds	cAMP-CRP
	DNA-binding transcriptional activator MhpR
DNA & protein repair	yhbO	Protein/nucleic acid deglycase 2	ppGpp	Rob
Control of cell division and morphology	fic drpB	Cell filamentation induced by camp Cell division protein drpb	RpoS RpoE
Miscellaneous	modF	Molybdenum uptake			REP71
	mgtA	Transport of Mg2+	pPhoP		REP339a REPv339b
	(Mg2+ importing P-type ATPase)
	mgtS	Interacts with the Mg2+ transporter, mgta to promote intracellular Mg2+ accumulation Transport of ammonium	pPhoP, Nac GadX, pNtrC	Fnr, Fe2+-Fur	REPt42
	(MgtS is a small, inner membrane protein) amtB
	ldcC	Aminopropylcadaverine biosynthesis		GlaR
	lysine decarboxylase 2	Cadaverine biosynthesis, l-lysine degradation I
	glpD	Aerobic glycerol 3-phosphate dehydrogenase	cAMP-CRP	pArcA, GlpR, FnrS	REPv256a REP256b
	bdm	Positive regulation of bacterial-type flagellum assembly	RcsB
	(biofilm-dependent modulation protein)
	slyB clpA mlaF EDCB	Outer membrane lipoprotein slyb Clpa ATP-dependent protease specificity component and chaperone Intermembrane phospholipid transport system, ATP binding subunit mlaf	MarA	pPhoB	REP244
	sodA (superoxide dismutase reduces iron toxicity)	Oxidative stress	SoxR, SoxS, cAMP-CRP, MarA, Rob	ArcA, Fe2+-Fur, Fur, InfAB FnrS, RyhB
	yghA	NADP+-dependent aldehyde reductase	ppGpp	pBasR	REPt222a-e
	yrbL truB pepB bax yfdC yqjE	Protein kinase-like domain-containing protein yrbl tRNA pseudouridine55 synthase Aminopeptidase B Putative glycoside hydrolase Bax Inner membrane protein yfdc Inner membrane protein yqje	PhoP, SoxS, SoxR Fis	Arg-ArgR cAMP-CRP GlaR	REP183b REP268a-d
	ytjA ybjX	DUF1328 domain-containing protein ytja DUF535 domain-containing protein ybjx	YieP, FliA	Nac
	yldA	Protein ylda
	ycfJ ycgB ymjE ybhG yobA-yebZ-yebY zntA fdoH	PF05433 family protein ycfj PF04293 family protein ycgb Protein ymje Copd family protein Copper-sequestering Zn2+/Cd2+/Pb2+ exporting P-type ATPase Formate dehydrogenase O subunit β	Leu-Lrp ppGpp RpoS, RpoN ZntR	Nac, Lrp pArcA, Fnr, PuuR CecR sRNA FnrS sRNA SdhX	REPv111 REPv297b REPv297b
Downregulated genes (Cluster 5)
CENTRAL CARBON METABOLISM  Glycolysis
Gluconeogenesis I	gapA-yeaD	Glyceraldehyde-3-phosphate dehydrogenase gapa	cAMP-CRP, RpoE, RpoS RpoS	Cra	REPt133 REPt303
Glycolysis II (from fructose 6-phosphate)	ybhA	Putative aldose 1-epimerase YeaD pyridoxal phosphate/fructose-1,6-bisphosphate phosphatase
Glycolysis I (from glucose 6-phosphate)  Pentose phosphate pathway (nonoxidative branch) I	tpiA	Triose-phosphate isomerase
	fbp	Fructose-1,6-bisphosphatase 1
	tktA	Transketolase 1
TCA cycle	sdhCD AB	Succinate dehydrogenase	Nac, cAMP-CRP, Fe2+-Fur	pArcA, pCpxR, Fnr, RyhB, Spf
Glycerol degradation	dhaKLM		DhaR, RpoS		REPt107
5-phosphoribosyl 1-pyrophosphate biosynthesis	prs	Ribose-phosphate diphosphokinas		PurR
FATTY ACID METABOLISM
Fatty acid biosynthesis initiation (type II)	accA	Acetyl-coa carboxyltransferase subunit α	FadR pCpxR, GadE, RpoE FadR
	fabF
	fabZ
	fabB
	ispU	Ditrans, polycis-undecaprenyl-diphosphate synthase ([2E,6E]-farnesyl-diphosphate specific)
	accA	Acetyl-coa carboxyltransferase subunit α	FadR
Lipoate biosynthesis and incorporation I	yebD-lipB	Lipoyl(octanoyl) transferase
Phosphopantothenate biosynthesis I	panB	3-methyl-2-oxobutanoate hydroxymethyltransferase
L-ornithine biosynthesis I	argCBH			argArgR argArgR argArgR, Lrp	REP207
	argF
	argA
L-aspartate biosynthesis (+ 3 others)	aspC	Aspartate aminotransferase	Leu-Lrp	Fe2+-Fur, Fnr
L-homoserine biosynthesis  l-lysine biosynthesis I	lysC	Aspartate kinase III	ArgP
	dapB	4-hydroxy-tetrahydrodipicolinate reductase	ArgP	Nac
L-histidine biosynthesis	hisG	ATP phosphoribosyltransferase	ppGpp, DksA
β-alanine biosynthesis III	panD	Aspartate 1-decarboxylase proenzyme		GcvB
L-arginine biosynthesis I (via l-ornithine)  Folate transformations III	argG		cAMP-CRP DksA, ppGpp pArcA, Fis, RutR	argArgR argArgR InfAB, PepA, RutR, argArgR SAM-MetJ
	argI
	carAB metF
L-methionine biosynthesis I	metA		RpoE pPhoP	SAM-MetJ SAM-MetJ	REP306
	metB
S-adenosyl-l-methionine biosynthesis	metK metJ			SAM-MetJ Fe2+-Fur	REP215 REP305ab
S-adenosyl-l-methionine salvage I
dTDP-N-acetylthomosamine biosynthesis	rfbACX		GlaR	Nac
dTDP-β-l-rhamnose biosynthesis	rfbBD
CMP-3-deoxy-d-manno-octulosonate biosynthesis	kdsA	3-deoxy-d-manno-octulosonate 8-phosphate synthase	GlaR	Nac
Acetate and ATP formation from acetyl-CoA I mixed acid fermentation ethanolamine utilization l-threonine degradation I	ackA	Acetate kinase	pArcA, pCreB, Fnr, Nac, RpoE	SdhX
L-glutamine degradation I  ammonia assimilation cycle III	glsB	Glutaminase 2
Chorismate biosynthesis from 3-dehydroquinate	aroK B	Shikimate kinase 1	ArgR
Tetrahydromonapterin biosynthesis	folX	Dihydroneopterin triphosphate 2′-epimerase		FnrS
Peptidoglycan maturation (meso-diaminopimelate containing)	dacA	D-alanyl-d-alanine carboxypeptidase daca
	rlpA	Rare lipoprotein RlpA
	lptE	Lipopolysaccharide assembly protein LptE
	murB	UDP-N-acetylenolpyruvoylglucosamine reductase
	lpp	Murein lipoprotein		pOmpR, MicL-S
	yafK(dpaA)	Peptidoglycan meso-diaminopimelic acid protein amidase A	Nac
	mepS	Peptidoglycan endopeptidase/peptidoglycan L, d-carboxypeptidase
	mipA	MltA-interacting protein	pPhoB
Peptidoglycan recycling I	emtA	Lytic murein transglycosylase E
(Aminomethyl)phosphonate degradation	ppa	Inorganic pyrophosphatase
ENERGY PRODUCTION
	cydA B	Cytochrome bd-I subunit 1	Nac, pArcA, Cra	H-NS, Fnr
	cydX	Cytochrome bd-I accessory subunit CydX
	atpIB EFHAGD	ATP biosynthesis
	hybAO	Hydrogenase 2 iron-sulfur protein		pNarL, pArcA
	ykgE	Putative lactate utilization oxidoreductase YkgE	Leu-Lrp,	YieP, Nac
	adhE	Fused acetaldehyde-coa dehydrogenase and iron-dependent alcohol dehydrogenase	Fis, Fnr, RpoS	Leu-Lpr, Cra, pNarL
	ldhA	D-lactate dehydrogenase	RpoE, leu-Lrp
	aldA	Aldehyde dehydrogenase A, NAD-linked	Mar, Rob, SoxS, cAMP-CRP	pArcA, DnaA, Fnr
The SecYEG-SecDF-YajC-YidC holo-translocon (HTL) protein secretase/insertase
cytochrome c biogenesis	yajC	Sec translocon accessory complex subunit YajC		ppGpp
	secG	Sec translocon subunit SecG		Nac
System I type	yidC	Membrane protein insertase YidC			REPv281
	yidD	Membrane protein insertion efficiency factor
	dsbA	Thiol:disulfide oxidoreductase DsbA	pCpxR	Nac
Protein translocation	tat A B C	Twin arginine protein translocation system-tatb protein
Translation
Ribosome proteins	rplK	50S ribosomal subunit protein L11		DksA, ppGpp, RplA
	rplM-rpsI	50S ribosomal subunit protein L13, 30S ribosomal subunit protein S9	SrmB	cAMP-CRP, RplM, DksA, Fis, Fnr
	rpmB-rpmG	50S ribosomal subunit protein L28, 50S ribosomal subunit protein L33		YfeC, DksA
	rpmH-rnpA(RNaseP)	50S ribosomal subunit protein L34	Nac	YfeC, DksA ppGpp
	rpsU rpsT	30S ribosomal subunit protein S21 30S ribosomal subunit protein S20		YfeC, DksA, LexA DksA
	rplS rplT	50S ribosomal subunit protein L19 50S ribosomal subunit protein L20		DksA, Fnr RplT, DksA, Fnr, NsrR
	rpsO	30S ribosomal subunit protein S15	Fis, RpsA	argArgR, ppGpp, cAMP-CRP, RpsO
	rpmE rpmF	50S ribosomal subunit protein L31 50S ribosomal subunit protein L32	RpoH	ppGpp, RpmE
	rpmA, rplU	50S ribosomal subunit protein L27	MlrI	DksA, ppGpp	REP243
	rplY	50S ribosomal subunit protein L25		RplY, DksA, ppGpp	REP159
	prmB	Ribosomal protein L3 N5-glutamine methyltransferase		Nac
	rimO	Ribosomal protein S12 methylthiotransferase rimo
Translation factors	infC	Translation initiation factor IF-3		DksA, NsrR
	infA	Translation initiation factor IF-1		ppGpp, YeiE
	rsfS-rmlH
	rrf frr	Ribosome recycling factor Ribosome-recycling factor		ppGpp ppGpp
	prfC	Peptide chain release factor RF3		ppGpp, Nac
	efp	Protein chain elongation factor EF-P		ppGpp
	yhbY	Ribosome assembly factor yhby		Leu-Lrp
	arfA	Alternative ribosome-rescue factor A
Regulation of translation	csrB	Small regulatory RNA csrb	DksA, ppGpp, pUvrY, InfAB
Protein folding	grpE	Nucleotide exchange factor grpe	cAMP-CRP, RpoE
	groS	Cochaperonin groes	Nac, RpoE,	Leu-Lrp
	degP hdeAB-yhiD	Periplasmic serine endoprotease degp Energy-independent periplasmic chaperone	pCpxR GadY, pRcsB, pPhoB, pTor, ppGpp, RpoS	H-NS GadW, GadX, pLrp, FliZ, H-NS, MarA
	fkbA	Peptidyl-prolyl cis-trans isomerase fkpa	ppGpp, RpoE
	ppiA	Peptidyl-prolyl cis-trans isomerase A	pCpxR	CytR, cAMP-CRP
	narW	Narw, putative private chaperone for narz nitrate reductase subunit	pOmpR
Protein processing	prc	Tail-specific protease
	bepA	Β-barrel assembly enhancing protease	RpoE
TRANSPORT
	ompF	Outer membrane porin F	cAMP-CRP, EnvY, Fe2+-Fur, pPhoB	InfBA, pOmpR, Nac, pCpxR, pRstA, MicF, RybB
	bamD	Outer membrane protein assembly factor bamd	RpoE
Cu+/Ag+ export	cusCFBA		pPhoB. pHprR, pCusR
	cusRS	DNA-binding transcriptional activator cusr	pPhoB. pHprR, pCusR		REP261
	pitA	Metal phosphate:H+ symporter pita	Fnr	MgrR
	rcnB	Periplasmic protein involved in nickel/cobalt export	RpoE	RcnR, Fe2+-Fur
Transport of K+	kdp F A BC	Potassium ion importing Kdp atpase	pKdpE	pArcA
	dctA	C4 dicarboxylate/orotate:H+ symporter	cAMP-CRP, DcuR	pArcA
	dauA	Erobic C4-dicarboxylate transporter daua		YieP
	dppA	Dipeptide ABC transporter periplasmic binding protein	pArcA, InfAB	Leu-Lrp, Nac, Fnr	REPv266b
Transport of thiamine	thiB PQ	Thiamine ABC transporter periplasmic binding protein	DksA, ppGpp	SgrR	REP7ab
Transport of l-aspartate  Transport of l-glutamate	gltI	Glutamate/aspartate ABC transporter periplasmic binding protein	FhlC-FhlD
Transport of spermidine	potD	Spermidine preferential ABC transporter periplasmic binding protein
Transport of d-ribopyranose	rbsDACBK R		cAMP-CRP	YidZ, RbsR, DsrA
Transport of d-galactopyranose	mglBAC		cAMP-CRP, RpoS	Nac, FlhCD, GalR, GalS	REP156abc
L-arginine ABC transporter	artJ	Periplasmic binding protein	RpoS	argArgR leu-Lrp, ArgR	REP83a-b
	artPI QM	ATP binding subunit
	plaP	Putrescine:H+ symporter plap
	lysP	Lysine:H+ symporter	ArgP	Leu-Lrp, Nac
	dtpA	Dipeptide/tripeptide:H+ symporter dtpa	pOmpR	Leu-Lrp, GadX
L-methionine/d-methionine ABC transporter  Exporters	metN I Q alaE	l-alanine exporter	GlaR, Leu-Lrp,	SAM-MetJ
	yohJ	Putative 3-hydroxypropanoate export protein yohj		YieP
PTS systems
	ptsHI-crr	Phosphocarrier protein hpr		Cra, cAMP-CRP, Mic, NagC
	yeeX(tmaR)	PTS system regulator tmar
Galactitol-specific PTS enzyme	gatABCD	Galactitol-specific PTS enzyme	cAMP-CRP	Nac, pArcA, GatR
Mannose-specific PTS enzyme	manXY Z	Mannose-specific PTS enzyme	cAMP-CRP	Cra, Mlc, NagC, DicF, SgrS
	ptsG	Glucose-specific PTS enzyme IIBC component	cAMP-CRP, SoxS	Fis, pArcA, Mlc
Xanthine:proton symport	xanP	Xanthine:H+ symporter xanp
Redox proteins / systems	trxB	Thioredoxin reductase (NADPH)		Nac, Leu-Lrp
	grxD	Glutaredoxin 4		NsrR, RyhB	REPt127
	bcp	Thiol peroxidase
	tpx	Lipid hydroperoxide peroxidase		pArcA, Fnr
STRESS RESISTANCE	hdeD	Acid resistance membrane protein	GadE, GadX, pRcsB, pPhoP, ppGpp, RpoS	H-NS
	yqgB	Acid stress response protein yqgb	Nac
	yfgG	Nickel/cobalt stress response protein yfgg
	ychF	Redox-responsive atpase ychf		OxyR, ppGpp
	sodB	Superoxide dismutase (Fe)		cAMP-CRP, InfAB, NsrR, FnrS, RyhB	REPv128ab
	opgG	Osmoregulated periplasmic glucans biosynthesis protein G	RpoE
	uspF	Universal stress protein F	YeiE
	ydiY	Acid-inducible putative outer membrane protein ydiy		Nac
SIGNAL TRANSDUCTION SYSTEMS	rcsF	Sensor lipoprotein rcsf
	dgcP	Diguanylate cyclase dgcp
CELL DIVISION/RECOMBINATION/DNA REPLICATION
	cpoB	Cell division coordinator cpob		Leu-Lrp, MicA
	ftsB	Cell division protein ftsb
	mreB	Dynamic cytoskeletal protein mreb		pBolA
	mioC rdgC	Flavoprotein mioc Nucleoid-associated protein rdgc		AsnC, MraZ, Nac, ppGpp
	holE	DNA polymerase III subunit θ		Nac
RNA AND DNA METABOLISM
Pyrimidine deoxyribonucleotides de novo biosynthesis II	dcd	Dctp deaminase	RbsR
	nrdA	Ribonucleoside-diphosphate reductase 1, α subunit dimer	Fis, ArgP, cAMP-CRP	NrdR, H-NS, DnaA	REP164a-e
	dut-slmA	Dutp diphosphatas			REPt275
UMP	pyrC	Dihydroorotase		PurR, Fe2+-Fur
biosynthesis I
Guanosine ribonucleotides de novo biosynthesis	guaB A	Inosine 5′-monophosphate dehydrogenase	cAMP-CRP	PurR, Fis, DnaA
Guanine and guanosine salvage III  Adenine and adenosine salvage V	gsk	Inosine/guanosine kinase			REP46ab
	gpt	Xanthine-guanine phosphoribosyltransferase		Leu-Lrp
UTP and CTP de novo biosynthesis	adk	Adenylate kinase			REPt45
Inosine-5′-phosphate biosynthesis I	purHD		pPhoP	PurR, RbsR
	hflD-purB	Lysogenization regulator, adenylosuccinate lyase		PurR	REPt106
5-aminoimidazole ribonucleotide biosynthesis II	purT	Phosphoribosylglycinamide formyltransferase 2	Lrp	PurR	REPt136
	purL	Phosphoribosylformylglycinamide synthetase		PurR
	purF	Amidophosphoribosyltransferase		PurR
	pur M N	Phosphoribosylglycinamide formyltransferase 1		PurR, Fnr
Interconversion of nucleotides	guaC	GMP reductase
	udk	Uridine/cytidine kinase	RbsR
TRANSCRIPTION	rpoE	RNA polymerase sigma factor rpoe (sigma 24 factor)	cAMP-CRP, DksA, GlrR, NtrC, RcsB, ppGpp, RpoN, RpoE, RpoS	pCpxR, InfAB
	rpoZ	RNA polymerase subunit ω		Nac, DksA
	hns	Transcription factor	CspA, Fis, GadX	H-NS, ppGpp, DsrA
	dusB-fis	Transcription factor Fis	InfAB, cAMP-CRP	DksA, ppGpp, Fis
	nusG	Transcription termination / antitermination factor nusg		OxyS
	cspE	Transcription antiterminator and regulator of RNA stability cspe	cAMP-CRP	DinJ-YafQ
	yeiP	Elongation factor P-like protein yeip	cAMP-CRP
	dksA	RNA polymerase-binding transcription factor dksa	cAMP-CRP	DksA, ppGpp
	crp	DNA-binding transcriptional dual regulator CRP	Cra, cAMP-CRP	ppGpp, Fis
	rseAB C	Anti-sigma-E factor rsea	cAMP-CRP, DksA, GlrR, NtrC, RcsB, ppGpp, RpoN, RpoE, RpoS	pCpxR, InfAB
	idlP	Irad leader peptide	ppGpp, Fnr	DksA, DnaA
	lrp	DNA-binding transcriptional dual regulator Lrp	ppGpp, GadE	Lrp, H-NS, Nac, NsrR, ArgR, GcvB, MicF, DsrA
	pdhR	DNA-binding transcriptional dual regulator pdhr	pOmpR, GlaR, cAMP-CRP, RpoS	Fnr, Cra, PdhR, pBtsR
	btsR	DNA-binding transcriptional dual regulator btsr
	mraZ	DNA-binding transcriptional repressor mraz		MraZ, PdhR
	marA	DNA-binding transcriptional dual regulator mara	cAMP-CRP, pCpxR, Fis, MarA, Rob, SoxS	AcrR, Cra
	dicA	DNA-binding transcriptional dual regulator dica	DicA
	narP	DNA-binding transcriptional dual regulator narp	RpoE	RprA, SdsN
	hupA	Transcriptional dual regulator HU-α (HU-2)	Nac, cAMP-CRP, Fis
	hupB	DNA-binding protein HU-β	cAMP-CRP	Fis
	adiY	DNA-binding transcriptional activator adiy	H-NS	SgrS
	uvrY	DNA-binding transcriptional activator uvry	DeaD	Nac, LexA
	ssrS	6s rna	Fis, RpoS	H-NS, Lrp, StpA, 6S RNA
RNA turnover	pcnB	Poly(A) polymerase I		DksA, ppGpp
	rnc-era	Ribonuclease III
	rppH	RNA pyrophosphohydrolase
	yicC	Putative RNase adaptor protein yicc
tRNA and rRNAs	valUXY-lysV		Fis	B2401
	serV-argVYZQ			B2695
	lysT-valT-lysW-valZ-lysY-lysQ		Fis	B0743
	metT-LeuW-glnUW-metU-glnVX		Fis	Lrp, ppGpp, b0673 ppGpp	REP60ab
	thrU-tyrU-glyT-thrT		Fis Fis	ppGpp ppGpp
	glyVXY
	glyW-cysT-leuZ
	aspT, serX
	tyrTV		Fis	ppGpp
	aspU lysZ	Trna-Lys(UUU)
	hisR	Trna-His(GUG)	DksA, Fis	DksA-ppGpp
	aspU	Trna-Asp(GUC)
	rrsA-ileT-alaT-rrlA-rrfA	Ribosomal RNA operon A		DksA, ppGpp	REP292
	rrsB-gltT-rrlB-rrfB	Ribosomal RNA operon B	Fis, RpoE	DksA, H-NS
	rrsC-gltU-rrlC-rrfC	Ribosomal RNA operon C	Fis, RpoE	DksA, H-NS
	rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF	Ribosomal RNA operon D	Fis, RpoE	DksA, H-NS
	rrsE-gltV-rrlE-rrfE	Ribosomal RNA operon E	Fis, RpoE	DksA, H-NS
	rrsG-gltW-rrlG-rrfG	Ribosomal RNA operon G	Fis, RpoE	DksA, H-NS
	rrsH-ileV-alaV-rrlH-rrfH	Ribosomal RNA operon H	Fis, RpoE	DksA, H-NS
RNA modifying enzymes	ndk-rlmN			pArcA
	rsmA	16S rrna m62a1518, m62a1519 dimethyltransferase	Fis, RpoE		REP5
	rlmH	23S rrna m3ψ1915 methyltransferase
	rlmI	23S rrna m5c1962 methyltransferase
	rluC	23S rrna pseudouridine955/2504/2580 synthase		ppGpp
	rluE	23S rrna pseudouridine2457 synthase	Nac
	rlhA	23S rrna 5-hydroxycytidine C2501 synthase
	trmA	Trna m5u54 methyltransferase	Fis, RpoH
	ppnP	Nucleoside phosphorylase ppnp
	proQ	RNA chaperone proq
tRNA Ligases	cysS	Cysteine—trna ligase		GlaR, Nac	REPt53
	asnS	Asparagine—trna ligase
	glnS	Glutamine—trna ligase	RpoH
	proS	Proline—trna ligase
	argS	Arginine—trna ligase		Leu-Lrp, ppGpp
	tyrS	Tyrosine—trna ligase
	mnmA	Trna-specific 2-thiouridylase		leu-Lrp
	mnmG metG	5-carboxymethyl-aminomethyluridine-trna synthase subunit mnmg Methionine—trna ligase	RpoS	AsnC, Nac, ppGpp
tRNA maturation	rph	Truncated RNase PH
	suhB	Nus factor suhb
Miscellaneous	ybgE ybgC-tolQ-TolR ycaC	PF09600 family protein ybge Tol-Pal system Putative hydrolase ycac	Nac pBaeR	Nac Fnr, Nac
	ycaD	Putative transporter ycad		Nac
	ybhC	Outer membrane lipoprotein ybhc			REP72abcd
	yajQ	Nucleotide binding protein yajq			REP40a
	tamAB-ytfP
	ytfP	Γ-glutamylamine cyclotransferase family protein ytfp		Nac
	yhdV	Lipoprotein yhdv	Leu-Lrp	Nac
	yajG	Putative lipoprotein yajg
	ytiD	Protein ytid	ppGpp	DksA, DnaA
	yidB	DUF937 domain-containing protein yidb	GlaR
	coaA	Pantothenate kinase / pantetheine kinase
	rclB	DUF1471 domain-containing protein rclb	RclR, RpoE	CsrA
	yqhA	UPF0114 family protein yqha
	yagN	CP4-6 prophage; protein yagn
	yqgC	Protein yqgc
	glgS	Surface composition regulator	Rob, ppGpp, cAMP-CRP
	yfcD	Putative Nudix hydrolase yfcd		ArgR, PurR
	cvpA	Colicin V production protein
	sixA	Phosphohistidine phosphatase sixa
	yfdH	CPS-53 (kple1) prophage; bactoprenol glucosyl transferase
	yfhL	Putative 4Fe-4S cluster-containing protein yfhl		Nac
	ratA	Ribosome association toxin rata
	rnlA	CP4-57 prophage; RNase LS, toxin of the rnlab toxin-antitoxin system		IscR
	yecN	MAPEG family inner membrane protein yecn
	ftnA	Ferritin iron-storage complex	Fe2+-Fur	H-NS
	ftnB	Putative ferritin-like protein	pCpxR, Nac
	yecJ	DUF2766 domain-containing protein yecj
	yedL	Putative acetyltransferase yedl		Nac
	mtfA	Mlc titration factor		Nac
	ymiA	Uncharacterized protein ymia		YjjQ
	yciX	Uncharacterized protein ycix
	ldrB	Small toxic polypeptide ldrb
	ldrC	Small toxic polypeptide ldrc
	ymjA	DUF2543 domain-containing protein ymja		Nac
	yhaM	Rac prophage; protein ynam
	ynfS	Qin prophage; protein ynfs
	ydiH	Uncharacterized protein ydih
	yoaJ yobB	Uncharacterized protein yoaj Putative carbon-nitrogen hydrolase family protein yobb		Nac, pOmpR

^aThe genes in cluster 5 and 6 that were insignificantly affected by NaF are in bold. Transcriptional/translational regulation and presence of REP-elements are indicated according to the EcoCyc database (https://ecocyc.org/). The global regulators Fis, Crp, Lrp, H-NS, and RpoE are indicated by gray shading.