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NsrR DNA-binding transcriptional repressor

Synonyms: NsrR-nitric oxide, NsrR, NsrR-[2Fe-2S]reduced, NsrR-[2Fe-2S]2+ oxidized


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NsrR     nd nd
NsrR-[2Fe-2S]2+ oxidized Non-Functional Covalent Apo [BPP], [IPI] [1]
NsrR-[2Fe-2S]reduced Functional Covalent Holo [BPP], [IPI] [1]
NsrR-nitric oxide     nd nd
Evolutionary Family: Rrf2
Connectivity class: Local Regulator
Gene name: nsrR
  Genome position: 4406190-4406615
  Length: 426 bp / 141 aa
Operon name: nsrR-rnr-rlmB-yjfIJ
TU(s) encoding the TF:
Transcription unit        Promoter
nsrR-rnr-rlmB-yjfI
nsrRp


Regulon       
Regulated gene(s) aceE, aceF, bamE, bdcA, cdd, dkgB, dsdC, feaB, feaR, fhlA, fliA, fliZ, grxD, hcp, hcr, hmp, hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI, hypA, hypB, hypC, hypD, hypE, ihfA, infC, lrp, mepH, mhpT, ndh, norR, nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG, pgpC, pheM, pheS, pheT, rfe, rffC, rffG, rffH, rffM, rffT, rplT, rpmI, rybB, sodB, sufA, sufB, sufC, sufD, sufE, sufS, tadA,
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Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (15)
anaerobic respiration (11)
enterobacterial common antigen (surface glycolipid) (11)
surface antigens (ECA, O antigen of LPS) (11)
fermentation (10)
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Regulated operon(s) bamE, bdcA, cdd, dkgB, dsdC, feaB, feaR, fliAZ-tcyJ, grxD, hcp-hcr, hmp, hycABCDEFGHI, hypABCDE-fhlA, lrp, mepH, mhpT, ndh, norR, nrfABCDEFG, pdhR-aceEF-lpd, pgpC-tadA, rfe-wzzE-wecBC-rffGHC-wecE-wzxE-rffT-wzyE-rffM, rybB, sodB, sufABCDSE, tehAB, thrS-infC-rpmI-rplT-pheMST-ihfA, tsgA, waaH, ydbD, yeaE, yeaR-yoaG, ygbA, ytfE
First gene in the operon(s) aceE, bamE, bdcA, cdd, dkgB, dsdC, feaB, feaR, fliA, fliA, grxD, hcp, hmp, hycA, hypA, hypA, lrp, mepH, mhpT, ndh, norR, nrfA, pgpC, rfe, rybB, sodB, sufA, tehA, thrS, thrS, tsgA, waaH, ydbD, yeaE, yeaR, ygbA, ytfE
Simple and complex regulons ArcA,FNR,Fis,Fur,IHF,NsrR,PdhR
ArcA,FNR,NsrR
CRP,CytR,NsrR
CRP,FeaR,NsrR
CRP,IHF,NsrR
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NsrR,-](34)


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
  NsrR-nitric oxide repressor aceEp Sigma70 -81.0 -129.0 aceE, aceF
aattatccagAAGATGTTGTAaatcaagcgc
122883 122893 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor bamEp Sigma24 67.0 -53.0 bamE
gtctattatcATCGGCATATTacagatgagc
2753547 2753557 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor bdcAp Sigma70 -18.0 -29.0 bdcA
aacagttttgTAATGCATGTTacataataaa
4474077 4474087 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor cddp Sigma70 9.0 -17.0 cdd
gttatcccatTACATGATTATgaggcaacgc
2231822 2231832 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor dkgBp Sigma38 -11.0 -80.0 dkgB
cgcaaaaatcCTCTGCATTTTacgctctttt
229082 229092 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor dkgBp Sigma38 64.0 -6.0 dkgB
tagcattaaaAGAGGCATATTatggctatcc
229156 229166 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor dsdCp Sigma70 14.0 -104.0 dsdC
tcaatggagtGATTTACATCTaaaaatgaag
2477728 2477738 [GEA], [HIBSCS] [2]
  NsrR repressor feaBp1 Sigma70 -184.0 -211.0 feaB
tcgctctgtgAAATGTATTTTtattgttgca
1447303 1447313 [GEA], [HIBSCS] [2], [3]
  NsrR-nitric oxide repressor feaRp2 Sigma70 2.0 -25.0 feaR
tgcaacaataAAAATACATTTcacagagcga
1447303 1447313 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor fliAp1 Sigma70 -207.0 -237.0 fliA, fliZ, tcyJ
ctacaagttgAATTGCAATTTattgaatttg
2002021 2002031 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor fliAp1 Sigma70 7.0 -24.0 fliA, fliZ, tcyJ
aatcatgccgATAACTCATATaacgcagggc
2001808 2001818 [GEA], [HIBSCS], [SM] [2]
  NsrR-nitric oxide repressor fliAp2 Sigma28 -218.0 -237.0 fliA, fliZ, tcyJ
ctacaagttgAATTGCAATTTattgaatttg
2002021 2002031 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor fliAp2 Sigma28 -5.0 -24.0 fliA, fliZ, tcyJ
aatcatgccgATAACTCATATaacgcagggc
2001808 2001818 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor grxD Sigma70 -13.0 -74.0 grxD
aagcgtgatgAAAATGTTATTttccgatgcc
1734170 1734180 [GEA], [HIBSCS] [2]
  NsrR repressor hcpp nd 6.0 -26.0 hcp, hcr
taaccttaaaCATGTATATTAAATATAACtttaaaaggt
913831 913849 [BCE], [GEA], [HIBSCS], [SM] [2], [4], [5]
  NsrR-nitric oxide repressor hmpAp Sigma38 -38.0 -76.0 hmp
aaaacaccaaAGAACCATTTAcattgcaggg
2685754 2685764 [GEA], [HIBSCS] [2]
  NsrR repressor hmpAp Sigma38 2.0 -37.0 hmp
tttttataagATGCATTTGAGATACATCAattaagatgc
2685789 2685807 [AIBSCS], [GEA] [6]
  NsrR-nitric oxide repressor hmpAp Sigma38 20.0 -19.0 hmp
tacatcaattAAGATGCAAAAaaaggaagac
2685811 2685821 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor hycAp Sigma54 -70.0 -96.0 hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI
cacggcgacgAAATTCATCTTtagcttaaaa
2850526 2850536 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor hypAp Sigma54 -96.0 -116.0 hypA, hypB, hypC, hypD, hypE, fhlA
ttttaagctaAAGATGAATTTcgtcgccgtg
2850526 2850536 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor lrpp Sigma70 52.0 -216.0 lrp
catgcatgtaAATACCATGTTtaccgtgcta
932374 932384 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor mhpTp Sigma32 -484.0 -557.0 mhpT
actgccgagaACGTGCATTTTgtatgcccat
374897 374907 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor ndhp Sigma70 6.0 -88.0 ndh
ctcaatagcgAAGAACATTTTcattgctgta
1165992 1166002 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor norRp nd 21.0 2.0 norR
cagtgaggcaAAGATGAGTTTttccgttgat
2832282 2832292 [GEA], [HIBSCS] [2]
  NsrR repressor nrfAp Sigma70 -121.0 -214.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
ttctttgaggAACATGCAGTTatgcatgctg
4287545 4287555 [GEA], [HIBSCS] [2], [5]
  NsrR-nitric oxide repressor nrfAp Sigma70 -63.0 -156.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
taactctaaaGTGGTATTTTACATGCACTtacaattgat
4287599 4287617 [BCE], [GEA], [HIBSCS], [SM] [2], [7]
  NsrR-nitric oxide repressor pgpCp Sigma32 131.0 42.0 pgpC, tadA
ttttttgactTAGATGGAACAttgcatcagc
2698503 2698513 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor rfep Sigma70 -1.0 -117.0 rfe, wzzE, wecB, wecC, rffG, rffH, rffC, wecE, wzxE, rffT, wzyE, rffM
catgttatgcAATTTGCATATcaaatggtta
3967794 3967804 [GEA], [HIBSCS] [2]
  NsrR repressor rybBp Sigma24 nd nd rybB nd nd [GEA] [8]
  NsrR-nitric oxide repressor sodBp Sigma70 -37.0 -92.0 sodB
gcaacagggtAAGTTCATCTTttgtctcacc
1735281 1735291 [AIBSCS], [GEA] [2]
  NsrR-nitric oxide repressor sufAp Sigma70 -68.0 -100.0 sufA, sufB, sufC, sufD, sufS, sufE
aaagcaggcaAAAAGCATGTTttacggtaaa
1764481 1764491 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor sufAp Sigma70 -6.0 -38.0 sufA, sufB, sufC, sufD, sufS, sufE
cattatcactAACATGCTGTTatacgctgaa
1764419 1764429 [GEA], [HIBSCS] [2]
  NsrR repressor tehAp nd -1.0 -38.0 tehA, tehB
aattccataaAATGCATTTCAAATATACTttataaatta
1500526 1500544 [AIBSCS], [GEA], [HIBSCS] [2], [6]
  NsrR-nitric oxide repressor tehAp nd 28.0 -10.0 tehA, tehB
taaattaaacAAAATGAGTAAgaagatgcag
1500558 1500568 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor thrSp nd 80.0 -84.0 thrS, infC, rpmI, rplT, pheM, pheS, pheT, ihfA
atttgttggcTAGATGGTTTCgcaatgaact
1802649 1802659 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor tsgAp nd -64.0 -113.0 tsgA
atcacctcttAAAATGCAATTtagcaaccga
3492450 3492460 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor ydbDp Sigma38 39.0 -40.0 ydbD
acaaaagggaAAGATGCATTTcccttttttt
1475099 1475109 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor ydhOp Sigma70 -61.0 -139.0 mepH
tagctttcacTGCTGCATTTTtttgcgctcg
1734291 1734301 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor yeaEp Sigma70 5.0 -84.0 yeaE
caaattctgaTAATGCATCTTtccagggcat
1865715 1865725 [GEA], [HIBSCS] [2]
  NsrR repressor yeaRp Sigma70 -32.0 -78.0 yeaR, yoaG
taaccaataaATGGTATTTAAAATGCAAAttatcaggcg
1880017 1880035 [AIBSCS], [GEA] [9]
  NsrR-nitric oxide repressor ygbAp nd -118.0 -140.0 ygbA
ggttccgggaAAGATGCTGTTttgcagcttt
2856941 2856951 [GEA], [HIBSCS] [2]
  NsrR repressor ygbAp nd -7.0 -29.0 ygbA
ttaagattaaGATGTAATATAAATACATCttaatgaggt
2856826 2856844 [AIBSCS], [GEA], [HIBSCS] [2], [6]
  NsrR-nitric oxide repressor ygbAp nd -1.0 -23.0 ygbA
gatgtaatatAAATACATCTTaatgaggtgg
2856824 2856834 [GEA], [HIBSCS] [2]
  NsrR-nitric oxide repressor yibDp1 Sigma70 -115.0 -183.0 waaH
taatctgttaAATATGTAAAAtcctgtcagt
3790259 3790269 [GEA], [HIBSCS] [2]
  NsrR repressor ytfEp nd -12.0 -38.0 ytfE
ttgccttaaaGATGCATTTAAAATACATCttatcttatt
4432012 4432030 [AIBSCS], [GEA], [HIBSCS], [SM] [2], [5], [6]


Alignment and PSSM for NsrR TFBSs    

Aligned TFBS of NsrR   
  Sequence
  AGAAGATGTTGTAA
  GTAAAATGCAGAGG
  AAAAGAGGCATATT
  AGAACGTGCATTTT
  TAAACATGTATATT
  TAAACATGGTATTT
  TGAAAATGTTCTTC
  GTGAAATGTATTTT
  GAAAGATGCATTTC
  ATAAAATGCATTTC
  ACAAAATGAGTAAG
  TGAAAATGTTATTT
  AAAAAATGCAGCAG
  AAAAGATGAACTTA
  CTAACATGCTGTTA
  AAAACATGCTTTTT
  GCTAGATGGTTTCG
  GAAAGATGCATTAT
  TTAAAATGCAAATT
  GTTATATGAGTTAT
  ATAAATTGCAATTC
  ATTACATGATTATG
  TTTAGATGTAAATC
  TGTAAATGGTTCTT
  ATAAGATGCATTTG
  TTAAGATGCAAAAA
  CTTAGATGGAACAT
  GTAATATGCCGATG
  CAAAGATGAGTTTT
  TAAAGATGAATTTC
  TTAAGATGTATTTA
  GAAAGATGCTGTTT
  TTAAAATGCAATTT
  TAAATATGTAAAAT
  TTGATATGCAAATT
  GGAACATGCAGTTA
  TTTACATGCACTTA
  TAAAGATGCATTTA
  GTAACATGCATTAC

Position weight matrix (PWM).   
A	11	13	30	39	11	37	0	0	6	25	10	11	9	8
C	3	2	0	0	9	0	0	0	21	1	3	3	1	7
G	10	6	2	0	15	1	1	39	4	3	7	0	1	7
T	15	18	7	0	4	1	38	0	8	10	19	25	28	17

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] Tucker NP., Hicks MG., Clarke TA., Crack JC., Chandra G., Le Brun NE., Dixon R., Hutchings MI., 2008, The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster., PLoS ONE. 3(11):e3623

 [2] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol. 73(4):680-94

 [3] Rankin LD., Bodenmiller DM., Partridge JD., Nishino SF., Spain JC., Spiro S., 2008, Escherichia coli NsrR regulates a pathway for the oxidation of 3-nitrotyramine to 4-hydroxy-3-nitrophenylacetate., J Bacteriol. 190(18):6170-7

 [4] Chismon DL., Browning DF., Farrant GK., Busby SJ., 2010, Unusual organization, complexity and redundancy at the Escherichia coli hcp-hcr operon promoter., Biochem J. 430(1):61-8

 [5] Filenko N., Spiro S., Browning DF., Squire D., Overton TW., Cole J., Constantinidou C., 2007, The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase., J Bacteriol. 189(12):4410-7

 [6] Bodenmiller DM., Spiro S., 2006, The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator., J Bacteriol. 188(3):874-81

 [7] Browning DF., Lee DJ., Spiro S., Busby SJ., 2010, Down-regulation of the Escherichia coli K-12 nrf promoter by binding of the NsrR nitric oxide-sensing transcription repressor to an upstream site., J Bacteriol. 192(14):3824-8

 [8] Thompson KM., Rhodius VA., Gottesman S., 2007, {sigma}E Regulates and Is Regulated by a Small RNA in Escherichia coli., J Bacteriol. 189(11):4243-56

 [9] Lin HY., Bledsoe PJ., Stewart V., 2007, Activation of yeaR-yoaG Operon Transcription by Nitrate-responsive Regulator NarL is Independent of Oxygen-responsive Regulator Fnr in Escherichia coli K-12., J Bacteriol. 189(21):7539-48



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