RegulonDB RegulonDB 10.9: Operon Form
   

yhgH-nfuA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yhgH-nfuA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: gntXY
Gene(s): yhgH, nfuA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Porco A., et al., 1998
Promoter
Name: gntXp
+1: 3544667
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 215
Sequence: ctaaccaaatggctttatcaggtgcctgttgcagcacggcttcggccatatcagcaagtgAcagcgcaccaaatccccggc
                      -35                        -10        +1                   
Note(s): A σ32-dependent promoter was suggested to be located upstream of gntX Wade JT,2006, but it is unknown whether this promoter is the same as gntXp. An overlapping of σ factors, σ32/σ70, was observed in some promoters Wade JT,2006.
Evidence: [AIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
[1] Porco A., et al., 1998
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator gntXp 3544615 3544636 -41.5 gcctaaccaaATGGCTTTATCAGGTGCCTGTTGcagcacggct nd [AIBSCS] [3]
[GntR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GntR repressor gntXp 3544642 3544661 -15.0 ctgttgcagcACGGCTTCGGCCATATCAGCAagtgacagcg nd [AIBSCS] nd


Transcription unit       
Name: nfuA
Synonym(s): gntY
Gene(s): nfuA   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [4] Nonaka G., et al., 2006
Promoter
Name: nfuAp2
+1: 3545458
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 166
Sequence: cgcaacctgaaaaatgcctttcgtcttgaattgcccgtgcaaggtcgccatatggtgattGtggatgatgtcgttaccacc
                          -35                 -10           +1                   
Evidence: [AIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[4] Nonaka G., et al., 2006
[5] Salgado H, et al., 2012


Transcription unit          
Name: nfuA
Synonym(s): gntY
Gene(s): nfuA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: nfuAp1
+1: 3545596
Distance from start of the gene: 28
Sequence: caggtctggtgcctttgtcgaaccttgtagagcctcgatgatgggcgtattataaccaacTaaaatagtcaactattaggc
Evidence: [TIM]
Reference(s): [6] Giel JL., et al., 2006
TF binding sites (TFBSs)
[IscR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IscR repressor nfuAp1 3545587 3545611 4.0 tgggcgtattATAACCAACTAAAATAGTCAACTATTaggccattac nd [BPP], [GEA] [6]


Evidence    

 [AIPP] Automated inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis


Reference(s)    

 [1] Porco A., Alonso G., Isturiz T., 1998, The gluconate high affinity transport of GntI in Escherichia coli involves a multicomponent complex system., J Basic Microbiol 38(5-6):395-404

 [2] 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

 [3] Peekhaus N., Conway T., 1998, Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex., J Bacteriol 180(7):1777-85

 [4] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [5] 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.

 [6] Giel JL., Rodionov D., Liu M., Blattner FR., Kiley PJ., 2006, IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli., Mol Microbiol 60(4):1058-75

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