RegulonDB RegulonDB 10.9: Sigmulon Form
   

Sigma54 Sigmulon in Escherichia coli K-12 genome




Sigma Factor      
Name: Sigma54     
Synonyms: RpoN
Gene name: rpoN
Sigmulon regulators:
Sigmulon Genes:


Transcribed promoters    
  Promoter Name TSS Position Transcribed Gene(s) Distance from TSS
to gene		 Promoter Sequence Box
(-12) 		Box
(-24) 		Evidence Code(s) Reference(s)
  acrDp2 2587550 acrD 45 atttacattaactcctttttttctccacgattggctcgtaccttgccgctacagtgaagcAagtcaagcctacaacgatac
                                -24         -12             +1                    		TGCCG TGGCTC [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  actPp 4284935 actP 33 gatctcctttgttctcaccggtatctacatctggcgggcgaacggcgaattcgaccgtctTaataatgaagtcctgcatga
                                -24         -12             +1                    		GGCGA TGGCGG [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  argTp 2427849 hisP, hisM, hisQ, hisJ, argT 58 tatttaacgttgaatgttactgttgtcgtcaagatggcataagacctgcatgaaagagccTgcaaacacacaacacaatac
                                   -24         -12          +1                    		TGCAT TGGCAT [AIPP]
[ICWHO] 		[3]
[1]
[4]
[5]
  aslBp 3982781 aslB 177 aaaaagcagtatttcggcgagtagcgcagcttggtagcgcaactggtttgggaccagtggGtcggaggttcgaatcctctc
                                -24         -12             +1                    		TGGTT TGGTAG [AIPP]
[ICWHO]
[IEP] 		[1]
[2]
  astCp2 1832044 astE, astB, astD, astA, astC 62 tagcctccgccgtttatgcacttttatcactggctggcacgaaccctgcaatctacatttAcagcgcaaacattacttatt
                                   -24         -12          +1                    		TGCAA TGGCAC [CV(RPF/TIM)]
[HIPP]
[ICWHO]
[RPF]
[TIM] 		[6]
[1]
[7]
  atoDp 2323412 atoD, atoA, atoE, atoB 35 attagttaaataactaaatccaataatctcattctggcactccccttgctattgcctgacTgtacccacaacggtgtatgc
                                   -24         -12          +1                    		TGCTA TGGCAC [AIPP]
[ICWHO]
[IMP] 		[1]
[8]
[4]
  chaCp 1272422 chaC 85 agttaaagctattcgtgcggtgttgccttgcaagtggtccgtggattgcatattgtcccgTtagtggtttcaaaatgagca
                                   -24         -12          +1                    		TGCAT TGGTCC [AIPP]
[ICWHO]
[IEP] 		[1]
[4]
[9]
  dcuDp2 3374583 dcuD 286 acatcctatcacaggattgaaagtaggggaaaatggcagggttttctctttgtgcctcatCattaccataattaacggaat
                                  -24         -12           +1                    		CTCTT TGGCAG [HIPP]
[ICWHO] 		[1]
[10]
  ddpXp 1563107 ddpF, ddpD, ddpC, ddpB, ddpA, ddpX 31 ttaagccagcattctggcgcttatcccggcatggcatgagatctgcataagcggaaagcgCagcaatttttgtcttataca
                                -24         -12             +1                    		TGCAT TGGCAT [AIPP]
[HIPP]
[ICWHO]
[IEP] 		[1]
[4]
[2]
  emrDp 3853845 emrD 77 catattctgccgctaaacaattccccattcctggcgtatatctggctaacattcatcaatGtgatagattcctctcccgca
                                -24         -12             +1                    		GGCTA TGGCGT [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  fdhFp 4299407 fdhF 41 cccgtaatatcagggaatgaccccacataaaatgtggcataaaagatgcatactgtagtcGagagcgcgtatgcgtgattt
                                   -24         -12          +1                    		TGCAT TGGCAT [ICWHO]
[TIM] 		[11]
[1]
[12]
  flhDp2 1978577 flhC, flhD 380 aacctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaaTcggtggagctgcatgacaaa
                                -24         -12             +1                    		CGCTG TGGGAC [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  glmYp1 2691340 glmY 0 ataatcagtacgttaccaaactattttctttattggcacagttactgcataatagtaaccAgtggctcattcaccgactta
                                  -24         -12           +1                    		TGCAT TGGCAC [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM] 		[1]
[13]
[14]
[15]
  glnAp2 4058107 glnG, glnL, glnA 73 gcatgataacgccttttaggggcaatttaaaagttggcacagatttcgctttatctttttTacggcgacacggccaaaata
                                   -24         -12          +1                    		CGCTT TGGCAC [ICWHO]
[TIM] 		[1]
[16]
[17]
[18]
  glnHp2 848047 glnQ, glnP, glnH 43 gccgcatctcgaaaaatcaaggagttgcaaaactggcacgattttttcatatatgtgaatGtcacgcaggggatcgtcccg
                                  -24         -12           +1                    		TTCAT TGGCAC [ICWHO]
[RS-EPT-CBR]
[TIM] 		[1]
[19]
[14]
  glnKp 472556 glnK, amtB 42 ttaacttcctgctctctttctcgtttttcatttctggcacaccgcttgcaataccttcttCgtgtagcagaaccattaccg
                                   -24         -12          +1                    		TGCAA TGGCAC [AIPP]
[HIPP]
[ICWHO] 		[1]
[4]
[20]
  glpQp 2351124 glpQ 113 ggtggcggcgagcgcgattgttggctacaccgtggacttcttcggctgggatggcggcttTatggtaatgattggcggcag
                                 -24         -12            +1                    		GCTGG TGGACT [ICWHO]
[RSE]
[TIM] 		[21]
  gltIp null gltL, gltK, gltJ, sroC, gltI       [AIPP] [4]
  gnsAp 1052004 gnsA 63 ataacctgttgattattgaatctttcggggagatggcttataacatttcttacctgaccaGggtaccgggaaccaacacct
                                  -24         -12           +1                    		TTTCT TGGCTT [ICWHO]
[RSE]
[TIM] 		[21]
  htpGp3 494817 htpG 303 tcggtccggatgatatcgggcttgatcgtctggaacagcgtctggcagaggaaaaaatcaCtgaagtgatcctcgccacca
                               -24          -12             +1                    		GGCAG TGGAAC [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  hycAp 2850461 hycI, hycH, hycG, hycF, hycE, hycD, hycC, hycB, hycA 26 ttaaaaatctctttaataacaataaattaaaagttggcacaaaaaatgcttaaagctggcAtctctgttaaacgggtaacc
                                   -24         -12          +1                    		TGCTT TGGCAC [ICWHO]
[RS-EPT-CBR]
[TIM] 		[1]
[22]
[14]
  hydNp 2838132 hypF, hydN 27 aattaatttccttaaataacagtaaattaaaaactggcatgatttgtgaatgtatcggcgCattaactgtcattgctggag
                                   -24         -12          +1                    		TGAAT TGGCAT [HIPP]
[ICWHO]
[TIM] 		[1]
[23]
  hyfAp 2601171 hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB 30 cataacttattgaatatattgagttaatcagaatggcatcctttatgcaatatgaaatgcAatgtttcatatcattttcaa
                                  -24         -12           +1                    		TGCAA TGGCAT [HIPP]
[ICWHO]
[TIM] 		[1]
[24]
  hypAp 2850627 hypA, hypB, hypC, hypD, hypE, fhlA 20 catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata
                                   -24         -12          +1                    		TGCTT TGGCAC [ICWHO]
[TIM] 		[1]
[25]
  ibpBp 3866981 ibpB 84 gcgaaaaaaccgcgccgtatcgaaatcaactaattccctaaggccgcctggcgcggcctgAcatctccatgctcgccgtca
                                          -24          -12  +1                    		GGCCT GGCCGC [ICWHO]
[TIM] 		[1]
[26]
  nacp 2061978 nac 45 ttggttagcttgtacatcaacaccaaaataaaactggcaagcatcttgcaatctggttgtAagtaatggcggcacttgggc
                                   -24         -12          +1                    		TGCAA TGGCAA [HIPP]
[ICWHO]
[TIM] 		[1]
[27]
  nikAp2 3613439 nikA, nikB, nikC, nikD, nikE, nikR 228 agccatcgttaaacagcgtggcggcagcgcctggcaaatcgtcagcgtagacagcacctaTcactcctcgctgtcagtcag
                                -24         -12             +1                    		AGCGT TGGCAA [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  norVp 2832439 norV, norW 37 ttatttatagagtaaaaacaatcagataaaaaactggcacgcaatctgcaattagcaagaCatctttttagaacacgctga
                                   -24         -12          +1                    		TGCAA TGGCAC [AIPP]
[HIPP]
[ICWHO]
[IEP]
[TIM] 		[1]
[4]
[28]
[2]
  patAp2 3219458 patA 36 gtgtttatcccgattttcgcgatcgcagccggagtggcgcaatccctgcaatacttaaatCggtatcatgtgatacgcgag
                                   -24         -12          +1                    		TGCAA TGGCGC [AIPP]
[ICWHO]
[TIM] 		[1]
[29]
  potFp1 893736 potF, potG, potH, potI 48 gttctcttttcttacaccgcgccgataaaaaatatgcacgtttattgcatatctttcagtGtgacaacttttgttcgtttg
                                  -24         -12           +1                    		TGCAT ATGCAC [AIPP]
[ICWHO] 		[1]
[4]
  prpBp 348646 prpB, prpC, prpD, prpE 36 tgaaattaaacatttaattttattaaggcaattgtggcacaccccttgctttgtctttatCaacgcaaataacaagttgat
                                   -24         -12          +1                    		TGCTT TGGCAC [AIPP]
[ICWHO] 		[1]
[4]
  pspAp 1368038 pspA, pspB, pspC, pspD, pspE 41 aatcagatctttataaatcaaaaagataaaaaattggcacgcaaattgtattaacagttcAgcaggacaatcctgaacgca
                                   -24         -12          +1                    		TGTAT TGGCAC [AIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM] 		[1]
[14]
[30]
  pspGp 4262816 pspG 24 gggcgttttgctgttaaatcaatagattatttttggcatgattcttgtaatgccagcaagAgatttcatatttgggagagc
                                  -24         -12           +1                    		TGTAA TGGCAT [ICA]
[ICWHO]
[RPF] 		[1]
[31]
  puuPp 1359373 puuP, ymjE 32 gtaatccagacatttcccggatgtcgcgttatggagcgcgggcggcaacgggcttccgttAacgattaagactgtgacgag
                                -24         -12             +1                    		GGCAA TGGAGC [AIPP]
[HIPP]
[ICWHO]
[IEP] 		[1]
[4]
[2]
  radDp 2280622 radD 10 ctaataacatccctcaagggaaaaagatccatggcatactattagcagaataatctacctAcgcgagaccatgatttttac
                                -24         -12             +1                    		AGCAG TGGCAT [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  relAp3 2913700 relA 49 tggatatgttcccacacacgggacatctggaatcgatggtacttttctcgcgcgttaaatAgttgcgatttgccgatttcg
 		    [TIM] [32]
  relAp4 2914318 relA 667 ccgcaccgctaagttcggcagatcgcgaaaaactggaacgcttttcgcattctgaaggccTggatctgtatctcgcccccg
 		    [TIM] [32]
  rhaDp 4094385 rhaD 113 gattgccggatgcggcacaagtgccttatcaggcctacaggtcggcaatagttgtaggccTgataagacgcgacagcgtcg
                               -24          -12             +1                    		GGCAA AGGCCT [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  rpoHp6 3600813 rpoH 30 aacagtgaatgataacctcgttgctcttaagctctggcacagttgttgctaccactgaagCgccagaagatatcgattgag
                                   -24         -12          +1                    		TGCTA TGGCAC [CV(RPF/TIM)]
[HIPP]
[ICWHO]
[RPF]
[TIM] 		[1]
[33]
[34]
  rseDp 2710339 rseC, rseB, rseA, rpoE, rseD 175 aacatggtttggtcagcatagcatcatgttgtgcggataaacacctgctattttaatattTgttacagttgctaaacacgc
                                  -24         -12           +1                    		TGCTA CGGATA [IHBCE]
[TIM] 		[35]
  rtcBp 3558107 rtcA, rtcB 28 tgaattaaaaaattaagctgcttatttaattttctggcacgacggttgcaattatcaggaCagcaaacaacgaaaagagaa
                                   -24         -12          +1                    		TGCAA TGGCAC [HIPP]
[ICWHO]
[TIM] 		[36]
[1]
  rtcRp null rtcR       [HIPP] [36]
  rutAp 1074026 rutG, rutF, rutE, rutD, rutC, rutB, rutA 15 aacagattaataacattaactttttaaaaactggcatccgctttgcaaacaagccaatacGcggctgaaaaggatatgcag
                                -24         -12             +1                    		TGCAA TGGCAT [AIPP]
[HIPP]
[ICWHO]
[IEP] 		[1]
[4]
[2]
  xapBp3 2524375 xapB 390 taacgatgatcgttttggagagcgcttcttctcactggcaaatgcctacgatgcggaataCcgcgcactgttacaaaaagt
                                    -24         -12         +1                    		ACGAT TGGCAA [ICWHO]
[RSE]
[TIM] 		[21]
  xdhAp2 3000265 xdhA, xdhB, xdhC 80 cctacctcccctaacgcttatcgtcgtttctggcgtaaatcttgcctgcttagactaaatCtttgccataagaaccaaatg
                               -24         -12              +1                    		TGCCTG TGGCG [HIPP]
[IEP]
[TIM] 		[37]
[2]
  yaaUp 45592 yaaU 215 cacattgttgtgaaggccgatgctgataaacaggcgctggagctgctggtgaaagcgtgcCccgcaggtctgtacaagaag
                                      -24         -12       +1                    		TGAAA TGGAGC [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  yahEp 335739 yahE 186 cagaccaaccatgtaggctggacgccgctactggaagcgattgtgcttaatgatggtggtAttaaacagcaggcgattgtg
                                -24         -12             +1                    		TGCTT TGGAAG [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  yeaGp1 1866815 yeaG, yeaH 93 atcaccgggcacgttgttctcatcgtcgataaaatggcatgagagttgctgtgttttagcAagagacgtcgttcagtttac
                                   -24         -12          +1                    		TGCTG TGGCAT [AIPP]
[ICWHO] 		[1]
[4]
  ygfKp 3015992 ygfK, ssnA 68 cctcacatttttttatatttcccgccaaacctggcaagagtggtgcgattgttgctctatCcccctaaaccaccggatttc
                                -24         -12             +1                    		TGCGA TGGCAA [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  yhdWp 3418972 yhdW, yhdX, yhdY, yhdZ 70 cagcttattgcgacgcgaaatcgtgcgcaaaagctggcactacttttgcttataagaggaTggccacagacaggtaaaaga
 		    [AIPP] [4]
  yhjCp 3672136 rcdB 278 aaaacaattttgaggatttccttatattggtggttagtacgcatgcaattaaaaatgaaaTtccgcgaccacaagccaaaa
                               -24          -12             +1                    		TGCAA TGGTTA [HIPP]
[ICWHO]
[IEP] 		[1]
[2]
  zraPp 4201712 zraP 24 gccagattacccgtcatatcagcgtttcatcgttggcacggaagatgcaatacccgaagtAagacaaccactggaggatta
                                  -24         -12           +1                    		TGCAA TGGCAC [AIPP]
[HIPP]
[ICWHO] 		[1]
[38]
[4]
  zraSp 4201905 zraS, zraR 21 tgtgttacagcgcagggtaagcgctgataaaagatggcatgatttctgctgtcagaaaggGatgagcaggcaaagaagaag
                                   -24         -12          +1                    		TGCTG TGGCAT [AIPP]
[HIPP]
[ICWHO] 		[1]
[38]
[4]
Evidence: [HIPP] Human inference of promoter position
[ICWHO] Inferred computationally without human oversight
[IEP] Inferred from expression pattern
[AIPP] Automated inference of promoter position
[CV(RPF/TIM)] cross validation(RPF/TIM)
[RPF] RNA polymerase footprinting
[TIM] Transcription initiation mapping
[IMP] Inferred from mutant phenotype
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[RSE] RNA-seq evidence
[ICA] Inferred by computational analysis
[IHBCE] Inferred by a human based on computational evidence


Reference(s)    

 [1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [2] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [3] Barrios H., Valderrama B., Morett E., 1999, Compilation and analysis of sigma(54)-dependent promoter sequences., Nucleic Acids Res 27(22):4305-13

 [4] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [5] Schmitz G., Durre P., Mullenbach G., Ames GF., 1987, Nitrogen regulation of transport operons: analysis of promoters argTr and dhuA., Mol Gen Genet 209(2):403-7

 [6] Fraley CD., Kim JH., McCann MP., Matin A., 1998, The Escherichia coli starvation gene cstC is involved in amino acid catabolism., J Bacteriol 180(16):4287-90

 [7] Kiupakis AK., Reitzer L., 2002, ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli., J Bacteriol 184(11):2940-50

 [8] Matta MK., Lioliou EE., Panagiotidis CH., Kyriakidis DA., Panagiotidis CA., 2007, Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon., J Bacteriol 189(17):6324-32

 [9] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [10] Janausch IG., Unden G., 1999, The dcuD (former yhcL) gene product of escherichia coli as a member of the DcuC family of C4-dicarboxylate carriers: lack of evident expression, Arch Microbiol 172(4):219-26

 [11] Birkmann A., Zinoni F., Sawers G., Bock A., 1987, Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli., Arch Microbiol 148(1):44-51

 [12] Schlensog V., Lutz S., Bock A., 1994, Purification and DNA-binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli., J Biol Chem 269(30):19590-6

 [13] Reichenbach B., Gopel Y., Gorke B., 2009, Dual control by perfectly overlapping sigma 54- and sigma 70- promoters adjusts small RNA GlmY expression to different environmental signals., Mol Microbiol 74(5):1054-70

 [14] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [15] Vogel J., Bartels V., Tang TH., Churakov G., Slagter-Jager JG., Huttenhofer A., Wagner EG., 2003, RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria., Nucleic Acids Res 31(22):6435-43

 [16] Ninfa AJ., Reitzer LJ., Magasanik B., 1987, Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers., Cell 50(7):1039-46

 [17] Reitzer LJ., Movsas B., Magasanik B., 1989, Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase., J Bacteriol 171(10):5512-22

 [18] Tian ZX., Li QS., Buck M., Kolb A., Wang YP., 2001, The CRP-cAMP complex and downregulation of the glnAp2 promoter provides a novel regulatory linkage between carbon metabolism and nitrogen assimilation in Escherichia coli., Mol Microbiol 41(4):911-24

 [19] Nohno T., Saito T., 1987, Two transcriptional start sites found in the promoter region of Escherichia coli glutamine permease operon, glnHPQ., Nucleic Acids Res 15(6):2777

 [20] van Heeswijk WC., Hoving S., Molenaar D., Stegeman B., Kahn D., Westerhoff HV., 1996, An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli., Mol Microbiol 21(1):133-46

 [21] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

 [22] Lutz S., Bohm R., Beier A., Bock A., 1990, Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli., Mol Microbiol 4(1):13-20

 [23] Maier T., Binder U., Bock A., 1996, Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism., Arch Microbiol 165(5):333-41

 [24] Skibinski DA., Golby P., Chang YS., Sargent F., Hoffman R., Harper R., Guest JR., Attwood MM., Berks BC., Andrews SC., 2002, Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR., J Bacteriol 184(23):6642-53

 [25] Lutz S., Jacobi A., Schlensog V., Bohm R., Sawers G., Bock A., 1991, Molecular characterization of an operon (hyp) necessary for the activity of the three hydrogenase isoenzymes in Escherichia coli., Mol Microbiol 5(1):123-35

 [26] Kuczynska-Wisnik D., Laskowska E., Taylor A., 2001, Transcription of the ibpB heat-shock gene is under control of sigma(32)- and sigma(54)-promoters, a third regulon of heat-shock response., Biochem Biophys Res Commun 284(1):57-64

 [27] Muse WB., Bender RA., 1998, The nac (nitrogen assimilation control) gene from Escherichia coli., J Bacteriol 180(5):1166-73

 [28] Tucker NP., D'Autr?aux B., Studholme DJ., Spiro S., Dixon R., 2004, DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria., J Bacteriol 186(19):6656-60

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