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DksA DNA-binding transcriptional dual regulator

Summary:
The DksA protein binds directly to RNA polymerase, affecting transcript elongation and potentiating allosterically the effect of the alarmone ppGpp on transcription initiation 15294156. 29478808. DksA binding to the RNA polymerase (RNAP) secondary channel interferes with the proper ribonucleotide positioning in the RNAP active site, decreasing open complex stability but only at promoters with intrinsically unstable open complexes, such as the ribosomal promoters 25916853 DksA together with ppGpp is required for regulation of transcription of ribosomal RNA promoters Paul BJ,2004. DksA and ppGpp independently reduce transcription of the rrsBp1 promoter. The additions of both ppGpp and DksA have independent cumulative effects on transcription inhibition of the rrsBp1 promoter 25916853
DksA is involved in translational regulation of RpoS Brown L,2002.
dksA mutants have pleiotropic phenotypes. A null mutant is viable Kang PJ,1990. A dksA mutant exhibited a defect in induction of RpoS production upon entry into stationary phase 12193624 or in the presence of ppGpp Brown L,2002. A dksA mutant exhibited a complex phenotype with respect to ppGpp regulation Brown L,2002.
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Transcription factor

Gene name:

Genome position:

160149-160604

Length:

456 bp / 151 aa

Operon name:

TU(s) encoding the TF:

Transcription unit	Promoter
dksA-gluQ	dksAp3
dksA-yadB	dksAp1
dksA-yadB	dksAp2
sfsA-dksA	sfsAp

Regulon
Regulated gene(s)	alaT, alaU, alaV, argX, dksA, fimB, gltT, gltU, gltV, gltW, gluQ, hisR, idlP, ileT, ileU, ileV, iraD, leuT, proM, rpoE, 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, rybB, setA, sgrR, sgrS, sgrT, sroA, thiB, thiP, thiQ, thrV, ytiC, ytiD
Multifun term(s) of regulated gene(s)	MultiFun Term (List of genes associated to the multifun term) translation (23) dksA, rrfA, rrfB, rrfC, rrfD, rrfE, rrfF, rrfG, rrfH, rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, rrlH, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH 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 ribosomes (22) rrfA, rrfB, rrfC, rrfD, rrfE, rrfF, rrfG, rrfH, rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, rrlH, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH tRNA (15) alaT, alaU, alaV, argX, gltT, gltU, gltV, gltW, hisR, ileT, ileU, ileV, leuT, proM, thrV other (mechanical, nutritional, oxidative stress) (6) iraD, rpoE, rseA, rseB, rseC, setA Transcription related (4) rpoE, rseA, rseB, rseC sigma factors, anti-sigmafactors (4) rpoE, rseA, rseB, rseC starvation (3) dksA, rseB, rseC membrane (3) rseC, setA, thiP thiamin (3) thiB, thiP, thiQ temperature extremes (2) rpoE, rseA RNA related (2) rybB, sroA translation attenuation and efficiency (1) dksA fimbri, pili (1) fimB DNA recombination (1) fimB DNA structure level (1) fimB operon (1) fimB pilus (1) fimB RNA modification (1) gluQ posttranscriptional (1) iraD stimulon (1) rpoE Electrochemical potential driven transporters (1) setA activator (1) sgrR repressor (1) sgrR antisense RNA (1) sgrS inhibition / activation of enzymes (1) sgrT ABC superfamily, periplasmic binding component (1) thiB ABC superfamily, membrane component (1) thiP ABC superfamily ATP binding cytoplasmic component (1) thiQ Read more >
Regulated operon(s)	argX-hisR-leuT-proM, fimB, 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, rybB, sfsA-dksA-gluQ, sgrR-sroA-thiBPQ, sgrST-setA, ytiCD-idlP-iraD
First gene in the operon(s)	argX, dksA, fimB, idlP, ytiC, rpoE, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH, rseA, rybB, sgrR, sgrS
Simple and complex regulatory phrases	Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation

Transcription factor binding sites (TFBSs) arrangements

	Functional conformation	Function	Promoter	Sigma factor	Central Rel-Pos	Distance to first Gene	Genes	Sequence	LeftPos	RightPos	Evidence (Confirmed, Strong, Weak)	References
	DksA	activation	argXp	Sigma70	nd	nd	argX, hisR, leuT, proM	nd nd	nd	nd	[IDA]	[1]
	DksA	inhibition	dksAp2	Sigma70	nd	nd	dksA, gluQ	nd nd	nd	nd	[APPH], [GEA], [IMP]	[2], [3]
	DksA	activation	fimBp2	nd	nd	nd	fimB	nd nd	nd	nd	[APPH], [GEA]	[4]
	DksA	inhibition	iraDp1	Sigma70	nd	nd	ytiC, ytiD, idlP, iraD	nd nd	nd	nd	[GEA], [IMP]	[5]
	DksA	inhibition	iraDp2	Sigma38, Sigma70	nd	nd	idlP, iraD	nd nd	nd	nd	[GEA], [IMP]	[5]
	DksA	activation	rpoEp2a	Sigma70, Sigma24	nd	nd	rpoE, rseA, rseB, rseC	nd nd	nd	nd	[GEA]	[6]
	DksA	inhibition	rrsAp1	Sigma32, Sigma70	nd	nd	rrsA, ileT, alaT, rrlA, rrfA	nd nd	nd	nd	[APPH], [GEA]	[7]
	DksA	inhibition	rrsBp1	Sigma32, Sigma70	nd	nd	rrsB, gltT, rrlB, rrfB	nd nd	nd	nd	[APPH], [GEA]	[7]
	DksA	inhibition	rrsCp1	Sigma32, Sigma70	nd	nd	rrsC, gltU, rrlC, rrfC	nd nd	nd	nd	[APPH], [GEA]	[7]
	DksA	inhibition	rrsDp1	Sigma32, Sigma70	nd	nd	rrsD, ileU, alaU, rrlD, rrfD, thrV, rrfF	nd nd	nd	nd	[APPH], [GEA]	[7]
	DksA	inhibition	rrsEp	Sigma32, Sigma70	nd	nd	rrsE, gltV, rrlE, rrfE	nd nd	nd	nd	[APPH], [GEA]	[7]
	DksA	inhibition	rrsGp1	Sigma32, Sigma70	nd	nd	rrsG, gltW, rrlG, rrfG	nd nd	nd	nd	[APPH], [GEA]	[7]
	DksA	inhibition	rrsHp1	Sigma32, Sigma70	nd	nd	rrsH, ileV, alaV, rrlH, rrfH	nd nd	nd	nd	[APPH], [GEA]	[7]
	DksA	activation	rseAp3	Sigma24	nd	nd	rseA, rseB, rseC	nd nd	nd	nd	[BPP], [IEP]	[8]
	DksA	activation	rybBp	Sigma24	nd	nd	rybB	nd nd	nd	nd	[BPP], [IEP]	[8]
	DksA	activation	sgrRp	Sigma70	nd	nd	sgrR, sroA, thiB, thiP, thiQ	nd nd	nd	nd	[GEA]	[9]
	DksA	activation	sgrSp	Sigma70, Sigma38	nd	nd	sgrS, sgrT, setA	nd nd	nd	nd	[GEA]	[9]

Evolutionary conservation of regulatory elements

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

Promoter-target gene evolutionary conservation

Evidence
[IDA] Inferred from direct assay
[APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
[BPP] Binding of purified proteins
[IEP] Inferred from expression pattern

Reference(s)
[1] 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
[2] Chandrangsu P., Lemke JJ., Gourse RL., 2011, The dksA promoter is negatively feedback regulated by DksA and ppGpp., Mol Microbiol 80(5):1337-48
[3] Edwards AN., Patterson-Fortin LM., Vakulskas CA., Mercante JW., Potrykus K., Vinella D., Camacho MI., Fields JA., Thompson SA., Georgellis D., Cashel M., Babitzke P., Romeo T., 2011, Circuitry linking the Csr and stringent response global regulatory systems., Mol Microbiol 80(6):1561-80
[4] 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
[5] 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
[6] 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
[7] 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
[8] 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
[9] 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)

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