RegulonDB

Regulon
Regulated gene(s)	alaT, alaU, alaV, argI, argS, argT, argX, bolA, cfa, crp, csgD, csgE, csgF, csgG, cspA, cspD, dksA, dnaA, dnaN, dusB, efp, fadD, fadL, fimB, fis, fkpA, flu, folK, frr, ftsA, ftsK, ftsQ, ftsZ, gabD, gabP, gabT, gadA, gadX, glaH, glgA, glgC, glgP, glnU, glnV, glnW, glnX, glsA, gltT, gltU, gltV, gltW, gluQ, glyT, grxB, hisJ, hisM, hisP, hisQ, hisR, hmp, hns, idlP, ileT, ileU, ileV, ilvB, ilvD, ilvE, ilvG, ilvH, ilvI, ilvL, ilvM, ilvN, ilvX, iraD, iraP, isrC, ivbL, leuA, leuB, leuC, leuD, leuL, leuO, leuT, leuW, leuX, lhgD, livJ, lrp, mazE, mazF, mazG, metT, metU, metV, metW, metZ, mioC, mnmG, pcnB, pnp, proM, pyrB, pyrI, pyrL, qorA, queA, recF, relA, rmf, rpmE, rpoE, rpoS, rpsB, rpsO, rrfA, rrfB, rrfC, rrfD, rrfE, rrfF, rrfG, rrfH, rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, rrlH, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH, rseA, rseB, rseC, rsmG, serW, setA, sgrR, sgrS, sgrT, speC, sra, sroA, sroD, tff, thiB, thiP, thiQ, thrT, thrU, thrV, tpr, trxA, tsf, tufB, tyrT, tyrU, tyrV, uspA, uspB, uspD, uspE, ybaT, yiiS, ytiC, ytiD Read more >
Multifun term(s) of regulated gene(s)	MultiFun Term (List of genes associated to the multifun term) tRNA (33) alaT, alaU, alaV, argX, glnU, glnV, glnW, glnX, gltT, gltU, gltV, gltW, glyT, hisR, ileT, ileU, ileV, leuT, leuW, leuX, metT, metU, metV, metW, metZ, proM, serW, thrT, thrU, thrV, tyrT, tyrU, tyrV translation (33) dksA, efp, frr, mazF, rmf, rpmE, rpsB, rpsO, rrfA, rrfB, rrfC, rrfD, rrfE, rrfF, rrfG, rrfH, rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, rrlH, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH, sra, tsf, tufB ribosomes (28) relA, rmf, rpmE, rpsB, rpsO, rrfA, rrfB, rrfC, rrfD, rrfE, rrfF, rrfG, rrfH, rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, rrlH, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH, sra rRNA, stable RNA (22) rrfA, rrfB, rrfC, rrfD, rrfE, rrfF, rrfG, rrfH, rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, rrlH, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH Transcription related (14) bolA, crp, csgD, cspA, dnaA, fis, gadX, hns, leuO, lrp, rpoE, rseA, rseB, rseC other (mechanical, nutritional, oxidative stress) (12) hisJ, hisM, hisP, hisQ, iraD, mazE, mazF, rpoE, rseA, rseB, rseC, setA isoleucine/valine (12) ilvA, ilvB, ilvD, ilvE, ilvH, ilvI, ilvL, ilvM, ilvN, ivbL, livJ, lrp activator (11) bolA, crp, csgD, cspA, dnaA, fis, gadX, hns, leuO, lrp, sgrR membrane (10) csgF, ftsA, ftsK, gabP, hisM, hisQ, rseC, setA, thiP, uspB leucine (9) ilvE, leuA, leuB, leuC, leuD, leuL, leuO, livJ, lrp repressor (8) bolA, crp, csgD, dnaA, fis, hns, lrp, sgrR starvation (6) dksA, mazE, mazF, mazG, rseB, rseC RNA modification (6) dusB, gluQ, mnmG, pcnB, queA, rsmG cell division (5) bolA, ftsA, ftsK, ftsQ, ftsZ nucleoproteins, basic proteins (5) dnaA, fis, hns, lrp, tpr adaptations (5) iraP, uspA, uspB, uspD, uspE sigma factors, anti-sigmafactors (5) rpoE, rpoS, rseA, rseB, rseC ABC superfamily, periplasmic binding component (4) argT, hisJ, livJ, thiB operon (4) cspA, fimB, leuO, lrp DNA replication (4) cspD, dnaA, dnaN, mioC ribosomal proteins (4) rpmE, rpsB, rpsO, sra temperature extremes (3) cspA, rpoE, rseA translation attenuation and efficiency (3) dksA, frr, mazF DNA recombination (3) fimB, fis, recF cytoplasmic polysaccharides (3) glgA, glgC, glgP ABC superfamily, membrane component (3) hisM, hisQ, thiP thiamin (3) thiB, thiP, thiQ arginine (2) argI, argT osmotic pressure (2) bolA, tufB fimbri, pili (2) csgF, fimB DNA structure level (2) cspD, fimB fatty acids (2) fadD, fadL prophage genes and phage related functions (2) fadL, flu aminobutyrate catabolism (2) gabD, gabT putrescine catabolism (2) gabD, gabT carbon compounds (2) gabP, glgP pH (2) gadA, glsA amino acids (2) glaH, lhgD thioredoxin, glutaredoxin (2) grxB, trxA ABC superfamily ATP binding cytoplasmic component (2) hisP, thiQ posttranscriptional (2) iraD, iraP RNA related (2) isrC, sroA defense/survival (2) mazE, mazF cell killing (2) mazE, mazF drug resistance/sensitivity (2) mazE, mazF RNA degradation (2) mazF, pnp pyrimidine biosynthesis (2) pyrI, pyrL inhibition / activation of enzymes (2) pyrI, sgrT unknown (2) relA, uspA radiation (2) uspD, uspE amino acid -activation (1) argS lysine (1) argT murein (1) bolA fatty acids and phosphatidic acid (1) cfa global (1) crp Accessory Factors Involved in Transport (1) csgE Channel-type Transporters (1) csgG regulon (1) dnaA phospholipid (1) fadD Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (1) fadL pilus (1) fimB chaperoning, repair (refolding) (1) fkpA folic acid (1) folK Transporters of Unknown Classification (1) ftsK SOS response (1) ftsK Porters (Uni-, Sym- and Antiporters) (1) gabP metabolism (1) glsA unassigned reversible reactions (1) hmp alanine (1) ilvE biotin (1) mioC RNA (1) pnp pyrimidine ribonucleotide biosynthesis (1) pyrB electron carriers (1) qorA DNA repair (1) recF nucleotide and nucleoside conversions (1) relA stimulon (1) rpoE Electrochemical potential driven transporters (1) setA antisense RNA (1) sgrS polyamine biosynthesis (1) speC DNA sites (1) tff detoxification (1) uspB Putative uncharacterized transport protein (1) ybaT Read more >
Regulated operon(s)	argI, argS, argT-hisJQMP, argX-hisR-leuT-proM, asnC-mioC-mnmG-rsmG, bdm-sra, bolA, cfa, crp, csgDEFG, cspA, cspD, dnaAN-recF, dusB-fis, efp, fadD-sroD, fadL, fimB, fkpA, frr, ftsK, gadAXW, glaH-lhgD-gabDTP, glgBXCAP, glsA-ybaT, grxB, hmp, hns, ilvIH, ilvLXGMEDA, infA-serW, iraP, isrC-flu, ivbL-ilvBN-uhpABC, leuLABCD, leuO, leuX, livJ, lrp, metT-leuW-glnUW-metU-glnVX, metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp, metZWV, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, nlpD-rpoS, pcnB-folK, pyrLBI, qorA, queA, relA-mazEFG, rmf, rpmE, rrsA-ileT-alaT-rrlA-rrfA, rrsB-gltT-rrlB-rrfB, rrsC-gltU-rrlC-rrfC, rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF, rrsE-gltV-rrlE-rrfE, rrsG-gltW-rrlG-rrfG, rrsH-ileV-alaV-rrlH-rrfH, rseD-rpoE-rseABC, sfsA-dksA-gluQ, sgrR-sroA-thiBPQ, sgrST-setA, speC, tff-rpsB-tsf, thrU-tyrU-glyT-thrT-tufB, tyrTV-tpr, uspA, uspB, uspE, yiiS-uspD, ytiCD-idlP-iraD Read more >
First gene in the operon(s)	argI, argS, argT, argX, bolA, cfa, crp, csgD, glaH, cspA, cspD, dksA, dnaA, dusB, efp, fadD, fadL, fimB, fkpA, frr, ftsK, ftsQ, ftsZ, gadA, glgC, glsA, grxB, hmp, hns, ilvI, ilvL, ytiC, idlP, iraP, isrC, ivbL, leuL, leuO, leuX, livJ, lrp, mazE, metT, metZ, mioC, mnmG, pcnB, pyrL, qorA, queA, relA, rmf, rpmE, rpoE, rpoS, tff, rpsO, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH, rseA, sgrR, sgrS, speC, sra, thrU, trxA, tyrT, uspA, uspB, uspE, yiiS Read more >
Simple and complex regulatory phrases	Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor binding sites (TFBSs) arrangements

Functional conformation	Function	Promoter	Sigma factor	Central Rel-Pos	Distance to first Gene	Genes	Sequence	LeftPos	RightPos	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	References
ppGpp	activation	argIp	Sigma70	nd	nd	argI	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
ppGpp	inhibition	argSp	Sigma70	nd	nd	argS	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[2]
ppGpp	inhibition	argTp	Sigma54	nd	nd	argT, hisJ, hisQ, hisM, hisP	nd nd	nd	nd	[EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[3], [4]
ppGpp	inhibition	argXp	Sigma70	nd	nd	argX, hisR, leuT, proM	nd nd	nd	nd	[EXP-IDA]	W	[5]
ppGpp	activation	bolAp	Sigma38	nd	nd	bolA	nd nd	nd	nd	[EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[2], [6]
ppGpp	activation	cfap	Sigma38	nd	nd	cfa	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[6]
ppGpp	inhibition	crpp2	nd	nd	nd	crp	nd nd	nd	nd	[EXP-IEP]	W	[7]
ppGpp	activation	csgDp3	Sigma38	nd	nd	csgD, csgE, csgF, csgG	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[8]
ppGpp	activation	csiDp	Sigma38	nd	nd	glaH, lhgD, gabD, gabT, gabP	nd nd	nd	nd	[EXP-IEP-MICROARRAY]	W	[2]
ppGpp	inhibition	cspAp1	Sigma70	nd	nd	cspA	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[9]
ppGpp	activation	cspDp	Sigma70	nd	nd	cspD	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[8]
ppGpp	inhibition	dksAp2	Sigma70	nd	nd	dksA, gluQ	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[10]
ppGpp	inhibition	dnaAp1	nd	nd	nd	dnaA, dnaN, recF	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[11]
ppGpp	inhibition	dnaAp2	Sigma70	nd	nd	dnaA, dnaN, recF	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[11]
ppGpp	inhibition	dusBp	Sigma70	nd	nd	dusB, fis	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[12]
ppGpp	inhibition	efpp	Sigma70	nd	nd	efp	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[2]
ppGpp	activation	fadDp	Sigma70	nd	nd	fadD, sroD	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[13]
ppGpp	activation	fadLp	Sigma38	nd	nd	fadL	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[6]
ppGpp	activation	fimBp2	nd	nd	nd	fimB	nd nd	nd	nd	[EXP-IDA], [EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[14]
ppGpp	activation	fkpAp1	Sigma24	nd	nd	fkpA	nd nd	nd	nd	[EXP-IEP]	W	[15], [16]
ppGpp	activation	flup	Sigma70	nd	nd	isrC, flu	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[17]
ppGpp	inhibition	frrp	Sigma70	nd	nd	frr	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[2]
ppGpp	activation	ftsKp1	Sigma70	nd	nd	ftsK	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[18]
ppGpp	activation	ftsQp	Sigma38	nd	nd	ftsQ, ftsA, ftsZ	nd nd	nd	nd	[EXP-IMP]	W	[19], [20]
ppGpp	activation	ftsZp3	nd	nd	nd	ftsZ	nd nd	nd	nd	[EXP-IMP]	W	[19], [20]
ppGpp	activation	ftsZp4	nd	nd	nd	ftsZ	nd nd	nd	nd	[EXP-IMP]	W	[19], [20]
ppGpp	activation	gadAp2	Sigma38	nd	nd	gadA, gadX	nd nd	nd	nd	[EXP-IEP-MICROARRAY]	W	[2]
ppGpp	activation	glgCp1	Sigma70	nd	nd	glgC, glgA, glgP	nd nd	nd	nd	[EXP-IMP]	W	[21]
ppGpp	activation	glgCp2	nd	nd	nd	glgC, glgA, glgP	nd nd	nd	nd	[EXP-IMP]	W	[21]
ppGpp	activation	glsAp	Sigma38	nd	nd	glsA, ybaT	nd nd	nd	nd	[EXP-IEP-MICROARRAY]	W	[2]
ppGpp	activation	grxBp	Sigma70	nd	nd	grxB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[22]
ppGpp	activation	hmpp	Sigma38	nd	nd	hmp	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[23]
ppGpp	inhibition	hnsp	Sigma70	nd	nd	hns	nd nd	nd	nd	[EXP-IDA-PURIFIED-PROTEIN], [EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[24]
ppGpp	activation	idlPp	Sigma38	nd	nd	idlP, iraD	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[25]
ppGpp	inhibition	ilvIp2	nd	nd	nd	ilvI, ilvH	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[26]
ppGpp	activation	ilvLp2	Sigma70	nd	nd	ilvL, ilvX, ilvG, ilvM, ilvE, ilvD, ilvA	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[27]
ppGpp	activation	iraDp1	Sigma70	nd	nd	ytiC, ytiD, idlP, iraD	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[25]
ppGpp	activation	iraPp1	Sigma70	nd	nd	iraP	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[28]
ppGpp	activation	ivbLp	Sigma70	nd	nd	ivbL, ilvB, ilvN	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[27]
ppGpp	activation	leuLp1	Sigma70	nd	nd	leuL, leuA, leuB, leuC, leuD	nd nd	nd	nd	[EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[27], [29]
ppGpp	activation	leuOp	Sigma70	nd	nd	leuO	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[30]
ppGpp	inhibition	leuXp	Sigma70	nd	nd	leuX	nd nd	nd	nd	[EXP-IEP]	W	[3]
ppGpp	activation	livJp	Sigma70	nd	nd	livJ	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
ppGpp	activation	lrpp	Sigma70	nd	nd	lrp	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[31]
ppGpp	inhibition	mazEp1	nd	nd	nd	mazE, mazF, mazG	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[32], [33]
ppGpp	inhibition	metTp	Sigma70	nd	nd	metT, leuW, glnU, glnW, metU, glnV, glnX	nd nd	nd	nd	[EXP-IEP]	W	[3]
ppGpp	inhibition	metZp	Sigma70	nd	nd	metZ, metW, metV	nd nd	nd	nd	[COMP-HINF], [EXP-IDA]	W	[34]
ppGpp	inhibition	mioCp	nd	nd	nd	mioC	nd nd	nd	nd	[EXP-IEP]	W	[35]
ppGpp	inhibition	mnmGp2	Sigma38	nd	nd	mnmG, rsmG	nd nd	nd	nd	[EXP-IEP]	W	[35]
ppGpp	inhibition	pcnBp	Sigma38	nd	nd	pcnB, folK	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[36]
ppGpp	inhibition	pcnBp4	Sigma38	nd	nd	pcnB, folK	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[36]
ppGpp	inhibition	pyrLp2	nd	nd	nd	pyrL, pyrB, pyrI	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[37]
ppGpp	activation	qorAp	nd	nd	nd	qorA	nd nd	nd	nd	[EXP-IEP]	W	[2], [38]
ppGpp	inhibition	queAp	nd	nd	nd	queA	nd nd	nd	nd	[EXP-IEP-MICROARRAY]	W	[2]
ppGpp	activation	relAp2	Sigma70	nd	nd	relA, mazE, mazF	nd nd	nd	nd	[EXP-IMP]	W	[39]
ppGpp	activation	rmfp	nd	nd	nd	rmf	nd nd	nd	nd	[EXP-IEP]	W	[40]
ppGpp	inhibition	rpmEp2	Sigma32	nd	nd	rpmE	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[2]
ppGpp	activation	rpoEp	Sigma24	nd	nd	rpoE, rseA, rseB, rseC	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[41]
ppGpp	activation	rpoEp2a	Sigma70	nd	nd	rpoE, rseA, rseB, rseC	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[41]
ppGpp	inhibition	rpoSp	Sigma70	nd	nd	rpoS	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[42]
ppGpp	inhibition	rpsBp	Sigma70	nd	nd	tff, rpsB, tsf	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[43]
ppGpp	inhibition	rpsOp	nd	nd	nd	rpsO, pnp	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[2]
ppGpp	inhibition	rrsAp	Sigma32	nd	nd	rrsA, ileT, alaT, rrlA, rrfA	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsAp1	Sigma70	nd	nd	rrsA, ileT, alaT, rrlA, rrfA	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsBp	Sigma32	nd	nd	rrsB, gltT, rrlB, rrfB	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsBp1	Sigma70	nd	nd	rrsB, gltT, rrlB, rrfB	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsCp	Sigma32	nd	nd	rrsC, gltU, rrlC, rrfC	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsCp1	Sigma70	nd	nd	rrsC, gltU, rrlC, rrfC	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsDp	Sigma32	nd	nd	rrsD, ileU, alaU, rrlD, rrfD, thrV, rrfF	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsDp1	Sigma70	nd	nd	rrsD, ileU, alaU, rrlD, rrfD, thrV, rrfF	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsEp1	Sigma70	nd	nd	rrsE, gltV, rrlE, rrfE	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsEp3	Sigma32	nd	nd	rrsE, gltV, rrlE, rrfE	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsGp	Sigma32	nd	nd	rrsG, gltW, rrlG, rrfG	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsGp1	Sigma70	nd	nd	rrsG, gltW, rrlG, rrfG	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsHp	Sigma32	nd	nd	rrsH, ileV, alaV, rrlH, rrfH	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	inhibition	rrsHp1	Sigma70	nd	nd	rrsH, ileV, alaV, rrlH, rrfH	nd nd	nd	nd	[EXP-IMP]	W	[44]
ppGpp	activation	rseAp3	Sigma24	nd	nd	rseA, rseB, rseC	nd nd	nd	nd	[EXP-IEP]	W	[16]
ppGpp	inhibition	serWp2	Sigma70	nd	nd	serW	nd nd	nd	nd	[COMP-HINF]	W	[45]
ppGpp	activation	sgrRp	Sigma70	nd	nd	sgrR, sroA, thiB, thiP, thiQ	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[46]
ppGpp	activation	sgrSp2	Sigma38	nd	nd	sgrS, sgrT, setA	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[46]
ppGpp	inhibition	speCp	Sigma38	nd	nd	speC	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP]	W	[47]
ppGpp	activation	srap	Sigma38	nd	nd	sra	nd nd	nd	nd	[EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[2], [48]
ppGpp	inhibition	thrUp	Sigma70	nd	nd	thrU, tyrU, glyT, thrT, tufB	nd nd	nd	nd	[EXP-IEP], [EXP-IMP]	W	[49]
ppGpp	activation	trxAp1	Sigma70	nd	nd	trxA	nd nd	nd	nd	[EXP-IMP]	W	[50]
ppGpp	activation	trxAp2	Sigma70	nd	nd	trxA	nd nd	nd	nd	[EXP-IMP]	W	[50]
ppGpp	inhibition	tyrTp	Sigma70	nd	nd	tyrT, tyrV, tpr	nd nd	nd	nd	[EXP-IEP]	W	[51]
ppGpp	activation	uspAp1	Sigma70	nd	nd	uspA	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[13], [52]
ppGpp	activation	uspBp	Sigma38	nd	nd	uspB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[6]
ppGpp	activation	uspEp	nd	nd	nd	uspE	nd nd	nd	nd	[EXP-IEP]	W	[53]
ppGpp	activation	yiiSp	Sigma24	nd	nd	yiiS, uspD	nd nd	nd	nd	[EXP-IEP]	W	[53]

Evolutionary conservation of regulatory elements

Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.

Promoter-target gene evolutionary conservation

Evidence
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IEP] Inferred from expression pattern
[EXP-IDA] Inferred from direct assay
[EXP-IEP-MICROARRAY] Expression microarray evidence
[EXP-IMP] Inferred from mutant phenotype
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[COMP-HINF] Inferred by a human based on computational evidence

Reference(s)
[1] Barker MM., Gaal T., Josaitis CA., Gourse RL., 2001, Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro., J Mol Biol 305(4):673-88
[2] Traxler MF., Summers SM., Nguyen HT., Zacharia VM., Hightower GA., Smith JT., Conway T., 2008, The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli., Mol Microbiol 68(5):1128-48
[3] Rowley KB., Elford RM., Roberts I., Holmes WM., 1993, In vivo regulatory responses of four Escherichia coli operons which encode leucyl-tRNAs., J Bacteriol 175(5):1309-15
[4] Toulokhonov II., Shulgina I., Hernandez VJ., 2001, Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N terminus of the beta'-subunit., J Biol Chem 276(2):1220-5
[5] Lyzen R., Maitra A., Milewska K., Kochanowska-Lyzen M., Hernandez VJ., Szalewska-Palasz A., 2016, The dual role of DksA protein in the regulation of Escherichia coli pArgX promoter., Nucleic Acids Res 44(21):10316-10325
[6] Kvint K., Farewell A., Nystrom T., 2000, RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s)., J Biol Chem 275(20):14795-8
[7] Johansson J., Balsalobre C., Wang SY., Urbonaviciene J., Jin DJ., Sonden B., Uhlin BE., 2000, Nucleoid proteins stimulate stringently controlled bacterial promoters: a link between the cAMP-CRP and the (p)ppGpp regulons in Escherichia coli., Cell 102(4):475-85
[8] Yamanaka K., Inouye M., 1997, Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli., J Bacteriol 179(16):5126-30
[9] Brandi A., Giangrossi M., Giuliodori AM., Falconi M., 2016, An Interplay among FIS, H-NS, and Guanosine Tetraphosphate Modulates Transcription of the Escherichia coli cspA Gene under Physiological Growth Conditions., Front Mol Biosci 3:19
[10] Chandrangsu P., Lemke JJ., Gourse RL., 2011, The dksA promoter is negatively feedback regulated by DksA and ppGpp., Mol Microbiol 80(5):1337-48
[11] Chiaramello AE., Zyskind JW., 1990, Coupling of DNA replication to growth rate in Escherichia coli: a possible role for guanosine tetraphosphate., J Bacteriol 172(4):2013-9
[12] Mallik P., Paul BJ., Rutherford ST., Gourse RL., Osuna R., 2006, DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli., J Bacteriol 188(16):5775-82
[13] Kvint K., Hosbond C., Farewell A., Nybroe O., Nystrom T., 2000, Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor., Mol Microbiol 35(2):435-43
[14] Aberg A., Shingler V., Balsalobre C., 2008, Regulation of the fimB promoter: a case of differential regulation by ppGpp and DksA in vivo., Mol Microbiol 67(6):1223-41
[15] Costanzo A., Ades SE., 2006, Growth phase-dependent regulation of the extracytoplasmic stress factor, sigmaE, by guanosine 3',5'-bispyrophosphate (ppGpp)., J Bacteriol 188(13):4627-34
[16] Costanzo A., Nicoloff H., Barchinger SE., Banta AB., Gourse RL., Ades SE., 2008, ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms., Mol Microbiol 67(3):619-32
[17] Cabrer-Panes JD., Fernandez-Coll L., Fernandez-Vazquez J., Gaviria-Cantin TC., El Mouali Y., Åberg A., Balsalobre C., 2020, ppGpp mediates the growth phase-dependent regulation of agn43, a phase variable gene, by stimulating its promoter activity., Environ Microbiol Rep 12(4):444-453
[18] Diez A., Gustavsson N., Nystrom T., 2000, The universal stress protein A of Escherichia coli is required for resistance to DNA damaging agents and is regulated by a RecA/FtsK-dependent regulatory pathway., Mol Microbiol 36(6):1494-503
[19] Vinella D., Bouloc P., D'Ari R., 1993, GTPase enters the ring., Curr Biol 3(1):65-6
[20] Vinella D., Joseleau-Petit D., Thevenet D., Bouloc P., D'Ari R., 1993, Penicillin-binding protein 2 inactivation in Escherichia coli results in cell division inhibition, which is relieved by FtsZ overexpression., J Bacteriol 175(20):6704-10
[21] Romeo T., Preiss J., 1989, Genetic regulation of glycogen biosynthesis in Escherichia coli: in vitro effects of cyclic AMP and guanosine 5'-diphosphate 3'-diphosphate and analysis of in vivo transcripts., J Bacteriol 171(5):2773-82
[22] Potamitou A., Neubauer P., Holmgren A., Vlamis-Gardikas A., 2002, Expression of Escherichia coli glutaredoxin 2 is mainly regulated by ppGpp and sigmaS., J Biol Chem 277(20):17775-80
[23] Membrillo-Hernandez J., Cook GM., Poole RK., 1997, Roles of RpoS (sigmaS), IHF and ppGpp in the expression of the hmp gene encoding the flavohemoglobin (Hmp) of Escherichia coli K-12., Mol Gen Genet 254(5):599-603
[24] Brandi A., Giangrossi M., Fabbretti A., Falconi M., 2020, The hns Gene of Escherichia coli Is Transcriptionally Down-Regulated by (p)ppGpp., Microorganisms 8(10)
[25] Merrikh H., Ferrazzoli AE., Lovett ST., 2009, Growth phase and (p)ppGpp control of IraD, a regulator of RpoS stability, in Escherichia coli., J Bacteriol 191(24):7436-46
[26] Baccigalupi L., Marasco R., Ricca E., De Felice M., Sacco M., 1995, Control of ilvIH transcription during amino acid downshift in stringent and relaxed strains of Escherichia coli., FEMS Microbiol Lett 131(1):95-8
[27] Durfee T., Hansen AM., Zhi H., Blattner FR., Jin DJ., 2008, Transcription profiling of the stringent response in Escherichia coli., J Bacteriol 190(3):1084-96
[28] Bougdour A., Gottesman S., 2007, ppGpp regulation of RpoS degradation via anti-adaptor protein IraP., Proc Natl Acad Sci U S A 104(31):12896-901
[29] Reimers JM., Schmidt KH., Longacre A., Reschke DK., Wright BE., 2004, Increased transcription rates correlate with increased reversion rates in leuB and argH Escherichia coli auxotrophs., Microbiology 150(Pt 5):1457-66
[30] Fang M., Majumder A., Tsai KJ., Wu HY., 2000, ppGpp-dependent leuO expression in bacteria under stress., Biochem Biophys Res Commun 276(1):64-70
[31] Landgraf JR., Wu J., Calvo JM., 1996, Effects of nutrition and growth rate on Lrp levels in Escherichia coli., J Bacteriol 178(23):6930-6
[32] Aizenman E., Engelberg-Kulka H., Glaser G., 1996, An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death., Proc Natl Acad Sci U S A 93(12):6059-63
[33] Gross M., Marianovsky I., Glaser G., 2006, MazG - a regulator of programmed cell death in Escherichia coli., Mol Microbiol 59(2):590-601
[34] Nagase T., Ishii S., Imamoto F., 1988, Differential transcriptional control of the two tRNA(fMet) genes of Escherichia coli K-12., Gene 67(1):49-57
[35] Ogawa T., Okazaki T., 1991, Concurrent transcription from the gid and mioC promoters activates replication of an Escherichia coli minichromosome., Mol Gen Genet 230(1-2):193-200
[36] Nadratowska-Wesolowska B., Slominska-Wojewodzka M., Lyzen R., Wegrzyn A., Szalewska-Palasz A., Wegrzyn G., 2010, Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors., Mol Genet Genomics 284(4):289-305
[37] Donahue JP., Turnbough CL., 1990, Characterization of transcriptional initiation from promoters P1 and P2 of the pyrBI operon of Escherichia coli K12., J Biol Chem 265(31):19091-9
[38] Chang DE., Smalley DJ., Conway T., 2002, Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model., Mol Microbiol 45(2):289-306
[39] Goodman C., 2012, Regulation: positively alarming., Nat Chem Biol 8(9):738
[40] Izutsu K., Wada A., Wada C., 2001, Expression of ribosome modulation factor (RMF) in Escherichia coli requires ppGpp., Genes Cells 6(8):665-76
[41] Gopalkrishnan S., Nicoloff H., Ades SE., 2014, Co-ordinated regulation of the extracytoplasmic stress factor, sigmaE, with other Escherichia coli sigma factors by (p)ppGpp and DksA may be achieved by specific regulation of individual holoenzymes., Mol Microbiol 93(3):479-93
[42] Gentry DR., Hernandez VJ., Nguyen LH., Jensen DB., Cashel M., 1993, Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp., J Bacteriol 175(24):7982-9
[43] Aseev LV., Koledinskaya LS., Boni IV., 2014, Dissecting the extended "-10" Escherichia coli rpsB promoter activity and regulation in vivo., Biochemistry (Mosc) 79(8):776-84
[44] Paul BJ., Barker MM., Ross W., Schneider DA., Webb C., Foster JW., Gourse RL., 2004, DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP., Cell 118(3):311-22
[45] Cummings HS., Sands JF., Fraser J., Hershey JW., 1994, Characterization and expression of a gene encoding serine tRNA5 from Escherichia coli., Biochimie 76(1):83-7
[46] Kessler JR., Cobe BL., Richards GR., 2017, Stringent Response Regulators Contribute to Recovery from Glucose Phosphate Stress in Escherichia coli., Appl Environ Microbiol 83(24)
[47] Holtta E., Janne J., Pispa J., 1974, The regulation of polyamine synthesis during the stringent control in Escherichia coli., Biochem Biophys Res Commun 59(3):1104-11
[48] Izutsu K., Wada C., Komine Y., Sako T., Ueguchi C., Nakura S., Wada A., 2001, Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase., J Bacteriol 183(9):2765-73
[49] Mizushima-Sugano J., Kaziro Y., 1985, Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent control., EMBO J 4(4):1053-8
[50] Lim CJ., Daws T., Gerami-Nejad M., Fuchs JA., 2000, Growth-phase regulation of the Escherichia coli thioredoxin gene., Biochim Biophys Acta 1491(1-3):1-6
[51] Travers AA., Lamond AI., Mace HA., Berman ML., 1983, RNA polymerase interactions with the upstream region of the E. coli tyrT promoter., Cell 35(1):265-73
[52] Farewell A., Diez AA., DiRusso CC., Nystrom T., 1996, Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes., J Bacteriol 178(22):6443-50
[53] Gustavsson N., Diez A., Nystrom T., 2002, The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage., Mol Microbiol 43(1):107-17

RegulonDB