RegulonDB RegulonDB 10.10: 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]
[IHBCE] 		[1]
[2]
  actPp 4284935 actP 33 gatctcctttgttctcaccggtatctacatctggcgggcgaacggcgaattcgaccgtctTaataatgaagtcctgcatga
                                -24         -12             +1                    		GGCGA TGGCGG [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[2]
  argTp 2427849 hisP, hisM, hisQ, hisJ, argT 58 tatttaacgttgaatgttactgttgtcgtcaagatggcataagacctgcatgaaagagccTgcaaacacacaacacaatac
                                   -24         -12          +1                    		TGCAT TGGCAT [AIBSCS]
[AIPP]
[ICWHO] 		[3]
[1]
[4]
[5]
  aslBp 3982781 aslB 177 aaaaagcagtatttcggcgagtagcgcagcttggtagcgcaactggtttgggaccagtggGtcggaggttcgaatcctctc
                                -24         -12             +1                    		TGGTT TGGTAG [AIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[2]
  astCp2 1832044 astE, astB, astD, astA, astC 62 tagcctccgccgtttatgcacttttatcactggctggcacgaaccctgcaatctacatttAcagcgcaaacattacttatt
                                   -24         -12          +1                    		TGCAA TGGCAC [APIORCISFBSCS]
[CV(RPF/TIM)]
[HIPP]
[ICWHO]
[RPF]
[TIM] 		[6]
[1]
[7]
  atoDp 2323412 atoD, atoA, atoE, atoB 35 attagttaaataactaaatccaataatctcattctggcactccccttgctattgcctgacTgtacccacaacggtgtatgc
                                   -24         -12          +1                    		TGCTA TGGCAC [AIBSCS]
[AIPP]
[ICWHO]
[IMP] 		[1]
[8]
[4]
  chaCp 1272422 chaC 85 agttaaagctattcgtgcggtgttgccttgcaagtggtccgtggattgcatattgtcccgTtagtggtttcaaaatgagca
                                   -24         -12          +1                    		TGCAT TGGTCC [AIBSCS]
[AIPP]
[ICWHO]
[IEP] 		[1]
[4]
[9]
  dcuDp2 3374583 dcuD 286 acatcctatcacaggattgaaagtaggggaaaatggcagggttttctctttgtgcctcatCattaccataattaacggaat
                                  -24         -12           +1                    		CTCTT TGGCAG [APIORCISFBSCS]
[HIPP]
[ICWHO] 		[1]
[10]
  ddpXp1 1563107 ddpF, ddpD, ddpC, ddpB, ddpA, ddpX 31 ttaagccagcattctggcgcttatcccggcatggcatgagatctgcataagcggaaagcgCagcaatttttgtcttataca
                                -24         -12             +1                    		TGCAT TGGCAT [AIBSCS]
[AIPP]
[HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[4]
[2]
  emrDp 3853845 emrD 77 catattctgccgctaaacaattccccattcctggcgtatatctggctaacattcatcaatGtgatagattcctctcccgca
                                -24         -12             +1                    		GGCTA TGGCGT [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[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]
[IHBCE] 		[1]
[2]
  glmYp1 2691340 glmY 0 ataatcagtacgttaccaaactattttctttattggcacagttactgcataatagtaaccAgtggctcattcaccgactta
                                  -24         -12           +1                    		TGCAT TGGCAC [HIPP]
[ICWHO]
[IDA]
[IHBCE]
[IMP]
[RS-EPT-CBR]
[TIM] 		[1]
[13]
[14]
[15]
[16]
  glnAp2 4058107 glnG, glnL, glnA 73 gcatgataacgccttttaggggcaatttaaaagttggcacagatttcgctttatctttttTacggcgacacggccaaaata
                                   -24         -12          +1                    		CGCTT TGGCAC [ICWHO]
[TIM] 		[1]
[17]
[18]
[19]
  glnHp2 848047 glnQ, glnP, glnH 43 gccgcatctcgaaaaatcaaggagttgcaaaactggcacgattttttcatatatgtgaatGtcacgcaggggatcgtcccg
                                  -24         -12           +1                    		TTCAT TGGCAC [ICWHO]
[RS-EPT-CBR]
[TIM] 		[1]
[20]
[14]
  glnKp 472556 glnK, amtB 42 ttaacttcctgctctctttctcgtttttcatttctggcacaccgcttgcaataccttcttCgtgtagcagaaccattaccg
                                   -24         -12          +1                    		TGCAA TGGCAC [AIBSCS]
[AIPP]
[HIPP]
[ICWHO] 		[1]
[4]
[21]
  glpQp 2351124 glpQ 113 ggtggcggcgagcgcgattgttggctacaccgtggacttcttcggctgggatggcggcttTatggtaatgattggcggcag
                                 -24         -12            +1                    		GCTGG TGGACT [ICWHO]
[RSE]
[TIM] 		[22]
  gltIp2 null gltL, gltK, gltJ, sroC, gltI       [AIBSCS]
[AIPP] 		[4]
  gnsAp1 1052004 gnsA 63 ataacctgttgattattgaatctttcggggagatggcttataacatttcttacctgaccaGggtaccgggaaccaacacct
                                  -24         -12           +1                    		TTTCT TGGCTT [ICWHO]
[RSE]
[TIM] 		[22]
  htpGp3 494817 htpG 303 tcggtccggatgatatcgggcttgatcgtctggaacagcgtctggcagaggaaaaaatcaCtgaagtgatcctcgccacca
                               -24          -12             +1                    		GGCAG TGGAAC [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[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]
[23]
[14]
  hydNp 2838132 hypF, hydN 27 aattaatttccttaaataacagtaaattaaaaactggcatgatttgtgaatgtatcggcgCattaactgtcattgctggag
                                   -24         -12          +1                    		TGAAT TGGCAT [APIORCISFBSCS]
[HIPP]
[ICWHO]
[TIM] 		[1]
[24]
  hyfAp 2601171 hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB 30 cataacttattgaatatattgagttaatcagaatggcatcctttatgcaatatgaaatgcAatgtttcatatcattttcaa
                                  -24         -12           +1                    		TGCAA TGGCAT [APIORCISFBSCS]
[HIPP]
[ICWHO]
[TIM] 		[1]
[25]
  hypAp 2850627 hypA, hypB, hypC, hypD, hypE, fhlA 20 catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata
                                   -24         -12          +1                    		TGCTT TGGCAC [ICWHO]
[TIM] 		[1]
[26]
  ibpBp 3866981 ibpB 84 gcgaaaaaaccgcgccgtatcgaaatcaactaattccctaaggccgcctggcgcggcctgAcatctccatgctcgccgtca
                                          -24          -12  +1                    		GGCCT GGCCGC [ICWHO]
[TIM] 		[1]
[27]
  nacp 2061978 nac 45 ttggttagcttgtacatcaacaccaaaataaaactggcaagcatcttgcaatctggttgtAagtaatggcggcacttgggc
                                   -24         -12          +1                    		TGCAA TGGCAA [APIORCISFBSCS]
[HIPP]
[ICWHO]
[TIM] 		[1]
[28]
  nikAp2 3613439 nikA, nikB, nikC, nikD, nikE, nikR 228 agccatcgttaaacagcgtggcggcagcgcctggcaaatcgtcagcgtagacagcacctaTcactcctcgctgtcagtcag
                                -24         -12             +1                    		AGCGT TGGCAA [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[2]
  norVp 2832439 norV, norW 37 ttatttatagagtaaaaacaatcagataaaaaactggcacgcaatctgcaattagcaagaCatctttttagaacacgctga
                                   -24         -12          +1                    		TGCAA TGGCAC [AIBSCS]
[AIPP]
[HIPP]
[ICWHO]
[IEP]
[IHBCE]
[TIM] 		[1]
[4]
[29]
[2]
  patAp2 3219458 patA 36 gtgtttatcccgattttcgcgatcgcagccggagtggcgcaatccctgcaatacttaaatCggtatcatgtgatacgcgag
                                   -24         -12          +1                    		TGCAA TGGCGC [AIPP]
[ICWHO]
[IEP]
[TIM] 		[1]
[30]
[31]
[32]
  potFp1 893736 potF, potG, potH, potI 48 gttctcttttcttacaccgcgccgataaaaaatatgcacgtttattgcatatctttcagtGtgacaacttttgttcgtttg
                                  -24         -12           +1                    		TGCAT ATGCAC [AIBSCS]
[AIPP]
[ICWHO] 		[1]
[4]
  prpBp 348646 prpB, prpC, prpD, prpE 36 tgaaattaaacatttaattttattaaggcaattgtggcacaccccttgctttgtctttatCaacgcaaataacaagttgat
                                   -24         -12          +1                    		TGCTT TGGCAC [AIBSCS]
[AIPP]
[ICWHO] 		[1]
[4]
  pspAp 1368038 pspA, pspB, pspC, pspD, pspE 41 aatcagatctttataaatcaaaaagataaaaaattggcacgcaaattgtattaacagttcAgcaggacaatcctgaacgca
                                   -24         -12          +1                    		TGTAT TGGCAC [AIPP]
[ICWHO]
[IHBCE]
[IMP]
[RS-EPT-CBR]
[TIM] 		[1]
[14]
[33]
  pspGp 4262816 pspG 24 gggcgttttgctgttaaatcaatagattatttttggcatgattcttgtaatgccagcaagAgatttcatatttgggagagc
                                  -24         -12           +1                    		TGTAA TGGCAT [ICA]
[ICWHO]
[RPF] 		[1]
[34]
  puuPp 1359373 puuP, ymjE 32 gtaatccagacatttcccggatgtcgcgttatggagcgcgggcggcaacgggcttccgttAacgattaagactgtgacgag
                                -24         -12             +1                    		GGCAA TGGAGC [AIBSCS]
[AIPP]
[HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[4]
[2]
  radDp 2280622 radD 10 ctaataacatccctcaagggaaaaagatccatggcatactattagcagaataatctacctAcgcgagaccatgatttttac
                                -24         -12             +1                    		AGCAG TGGCAT [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[2]
  relAp3 2913700 relA 49 tggatatgttcccacacacgggacatctggaatcgatggtacttttctcgcgcgttaaatAgttgcgatttgccgatttcg
 		    [IDA]
[IHBCE]
[TIM] 		[35]
  relAp4 2914318 relA 667 ccgcaccgctaagttcggcagatcgcgaaaaactggaacgcttttcgcattctgaaggccTggatctgtatctcgcccccg
 		    [IDA]
[TIM] 		[35]
  rhaDp 4094385 rhaD 113 gattgccggatgcggcacaagtgccttatcaggcctacaggtcggcaatagttgtaggccTgataagacgcgacagcgtcg
                               -24          -12             +1                    		GGCAA AGGCCT [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[2]
  rpoHp6 3600813 rpoH 30 aacagtgaatgataacctcgttgctcttaagctctggcacagttgttgctaccactgaagCgccagaagatatcgattgag
                                   -24         -12          +1                    		TGCTA TGGCAC [APIORCISFBSCS]
[CV(RPF/TIM)]
[HIPP]
[ICWHO]
[IDA]
[IMP]
[RPF]
[TIM] 		[1]
[36]
[37]
[38]
[39]
  rseDp 2710339 rseC, rseB, rseA, rpoE, rseD 175 aacatggtttggtcagcatagcatcatgttgtgcggataaacacctgctattttaatattTgttacagttgctaaacacgc
                                  -24         -12           +1                    		TGCTA CGGATA [IDA]
[IEP]
[IHBCE]
[IPI]
[TIM] 		[40]
  rtcBp 3558107 rtcA, rtcB 28 tgaattaaaaaattaagctgcttatttaattttctggcacgacggttgcaattatcaggaCagcaaacaacgaaaagagaa
                                   -24         -12          +1                    		TGCAA TGGCAC [APIORCISFBSCS]
[HIPP]
[ICWHO]
[TIM] 		[41]
[1]
  rtcRp null rtcR       [APIORCISFBSCS]
[HIPP] 		[41]
  rutAp 1074026 rutG, rutF, rutE, rutD, rutC, rutB, rutA 15 aacagattaataacattaactttttaaaaactggcatccgctttgcaaacaagccaatacGcggctgaaaaggatatgcag
                                -24         -12             +1                    		TGCAA TGGCAT [AIBSCS]
[AIPP]
[HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[4]
[2]
  xapBp3 2524375 xapB 390 taacgatgatcgttttggagagcgcttcttctcactggcaaatgcctacgatgcggaataCcgcgcactgttacaaaaagt
                                    -24         -12         +1                    		ACGAT TGGCAA [ICWHO]
[RSE]
[TIM] 		[22]
  xdhAp2 3000265 xdhA, xdhB, xdhC 80 cctacctcccctaacgcttatcgtcgtttctggcgtaaatcttgcctgcttagactaaatCtttgccataagaaccaaatg
                               -24         -12              +1                    		TGCCTG TGGCG [HIPP]
[IEP]
[IHBCE]
[TIM] 		[42]
[2]
  yaaUp 45592 yaaU 215 cacattgttgtgaaggccgatgctgataaacaggcgctggagctgctggtgaaagcgtgcCccgcaggtctgtacaagaag
                                      -24         -12       +1                    		TGAAA TGGAGC [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[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 [AIBSCS]
[AIPP]
[ICWHO] 		[1]
[4]
  ygfKp 3015992 ygfK, ssnA 68 cctcacatttttttatatttcccgccaaacctggcaagagtggtgcgattgttgctctatCcccctaaaccaccggatttc
                                -24         -12             +1                    		TGCGA TGGCAA [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[2]
  yhdWp 3418972 yhdW, yhdX, yhdY, yhdZ 70 cagcttattgcgacgcgaaatcgtgcgcaaaagctggcactacttttgcttataagaggaTggccacagacaggtaaaaga
 		    [AIBSCS]
[AIPP] 		[4]
  yhjCp 3672136 rcdB 278 aaaacaattttgaggatttccttatattggtggttagtacgcatgcaattaaaaatgaaaTtccgcgaccacaagccaaaa
                               -24          -12             +1                    		TGCAA TGGTTA [HIPP]
[ICWHO]
[IEP]
[IHBCE] 		[1]
[2]
  zraPp 4201712 zraP 24 gccagattacccgtcatatcagcgtttcatcgttggcacggaagatgcaatacccgaagtAagacaaccactggaggatta
                                  -24         -12           +1                    		TGCAA TGGCAC [AIBSCS]
[AIPP]
[HIPP]
[ICWHO] 		[1]
[43]
[4]
  zraSp 4201905 zraS, zraR 21 tgtgttacagcgcagggtaagcgctgataaaagatggcatgatttctgctgtcagaaaggGatgagcaggcaaagaagaag
                                   -24         -12          +1                    		TGCTG TGGCAT [AIBSCS]
[AIPP]
[HIPP]
[ICWHO] 		[1]
[43]
[4]
Evidence: [HIPP] Human inference of promoter position
[ICWHO] Inferred computationally without human oversight
[IEP] Inferred from expression pattern
[IHBCE] Inferred by a human based on computational evidence
[AIBSCS] Automated inference based on similarity to consensus sequences
[AIPP] Automated inference of promoter position
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[CV(RPF/TIM)] cross validation(RPF/TIM)
[RPF] RNA polymerase footprinting
[TIM] Transcription initiation mapping
[IMP] Inferred from mutant phenotype
[IDA] Inferred from direct assay
[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
[IPI] Inferred from physical interaction


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] Urban JH., Papenfort K., Thomsen J., Schmitz RA., Vogel J., 2007, A Conserved Small RNA Promotes Discoordinate Expression of the glmUS Operon mRNA to Activate GlmS Synthesis., J Mol Biol 373(3):521-8

 [16] 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

 [17] 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

 [18] 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

 [19] 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

 [20] 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

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