RegulonDB RegulonDB 10.8: Operon Form
   

gapA-yeaD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: gapA
Gene(s): gapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: gapAp7
+1: 1862240
Distance from start of the gene: 531
Sequence: agtctttgatataacgaatggattcttcacttaccggttcgtagaaactgggccagccacAgccggaatcatacttggttt
Evidence: [TIM]
Reference(s): [1] Shimada T., et al., 2005


Transcription unit       
Name: gapA
Gene(s): gapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: gapAp6
+1: 1862247
Distance from start of the gene: 524
Sequence: gatataacgaatggattcttcacttaccggttcgtagaaactgggccagccacagccggaAtcatacttggtttgggaatg
Evidence: [TIM]
Reference(s): [1] Shimada T., et al., 2005


Transcription unit          
Name: gapA
Gene(s): gapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: gapAp4
+1: 1862526
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 245
Sequence: tgactgattctaacaaaacattaacaccaactggcaaaattttgtcctaaacttgatctcGacgaaatggctgcacctaaa
                     -35                        -10         +1                   
Note(s): The gapAp4 promoter does not have a -35 promoter sequence, and it has been suggested that it either requires a transcriptional activator or it represents a secondary RNA polymerase-binding site.
Evidence: [HIPP]
[TIM]
Reference(s): [2] Charpentier B., et al., 1994
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor gapAp4 1862001 1862018 -516.5 tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]
remote Cra repressor gapAp4 1862683 1862700 166.5 ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]


Transcription unit          
Name: gapA
Gene(s): gapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: gapAp3
+1: 1862597
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 174
Sequence: tgcacctaaatcgtgatgaaaatcacatttttatcgtaattgccctttaaaattcggggcGccgaccccatgtggtctcaa
                      -35                       -10         +1                   
Note(s): Utilization of the gapAp3 promoter is subject to catabolic repression. A potential -10 promoter sequence of the RNA polymerase σ70 is found, and instead of a -35 sequence there is evidence of a potential cAMP-CRP-binding site.
Evidence: [HIPP]
[TIM]
Reference(s): [2] Charpentier B., et al., 1994
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 gapAp3 1862545 1862566 -41.5 gctgcacctaAATCGTGATGAAAATCACATTTttatcgtaat nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [2]
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor gapAp3 1862001 1862018 -587.5 tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]
remote Cra repressor gapAp3 1862683 1862700 95.5 ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]


Transcription unit          
Name: gapA-yeaD
Gene(s): gapA, yeaD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITC] Inferred through co-regulation
Reference(s): [3] Nonaka G., et al., 2006
Promoter
Name: gapAp2
+1: 1862618
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 153
Sequence: atcacatttttatcgtaattgccctttaaaattcggggcgccgaccccatgtggtctcaaGcccaaaggaagagtgaggcg
                         -35                 -10            +1                   
Note(s): The sole effect of transcription of the gapAp2 promoter during heat shock is to maintain the gapA gene transcription level.
Evidence: [AIPP]
[CV(TA/TIM)]
[HIPP]
[IDA]
[TIM]
Reference(s): [4] Charpentier B., et al., 1998
[2] Charpentier B., et al., 1994
[3] Nonaka G., et al., 2006
[5] Olvera L., et al., 2009
[6] Wade JT., et al., 2006
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor gapAp2 1862001 1862018 -608.5 tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]
remote Cra repressor gapAp2 1862683 1862700 74.5 ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]


Transcription unit          
Name: gapA
Gene(s): gapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: gapAp1
+1: 1862735
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 36
Sequence: gtcgcaatgattgacacgattccgcttgacgctgcgtaaggtttttgtaattttacaggcAaccttttattcactaacaaa
                          -35                    -10        +1                   
Note(s): gapAp1 utilization is very strong at the beginning of the exponential phase and seems to depend upon growth phase. Glucose stimulates the gapAp1 activity.
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[HIPP]
[HTIM]
[IMP]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Charpentier B., et al., 1998
[2] Charpentier B., et al., 1994
[5] Olvera L., et al., 2009
[7] Salgado H, et al., 2012
[8] Thouvenot B., et al., 2004
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor gapAp1 1862001 1862018 -725.5 tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]
proximal Cra repressor gapAp1 1862683 1862700 -43.5 ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [1]


Transcription unit       
Gene(s): yeaD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.5 1863790 1863819 gtgatctaaaAAGAGCGACTTCGGTCGCTCTTTTTTTTAcctgataaaa
  anti-terminator -4.7 1863765 1863801 tctccaaataAGTTGAGATGACACTGTGATCTAAAAAGAGCGACTTcggtcgctct
  anti-anti-terminator -6.2 1863725 1863773 accggttactCCAACAAAGTTCTGGACCTGATCGCTCACATCTCCAAATAAGTTGAGAtgacactgtg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIPP] Automated inference of promoter position

 [CV(TA/TIM)] cross validation(TA/TIM)

 [IDA] Inferred from direct assay

 [CV(RS-EPT-CBR/TA)] cross validation(RS-EPT-CBR/TA)

 [HTIM] High-throughput transcription initiation mapping

 [IMP] Inferred from mutant phenotype

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


Reference(s)    

 [1] Shimada T., Fujita N., Maeda M., Ishihama A., 2005, Systematic search for the Cra-binding promoters using genomic SELEX system., Genes Cells 10(9):907-18

 [2] Charpentier B., Branlant C., 1994, The Escherichia coli gapA gene is transcribed by the vegetative RNA polymerase holoenzyme E sigma 70 and by the heat shock RNA polymerase E sigma 32., J Bacteriol 176(3):830-9

 [3] 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

 [4] Charpentier B., Bardey V., Robas N., Branlant C., 1998, The EIIGlc protein is involved in glucose-mediated activation of Escherichia coli gapA and gapB-pgk transcription., J Bacteriol 180(24):6476-83

 [5] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [6] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [7] 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.

 [8] Thouvenot B., Charpentier B., Branlant C., 2004, The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants., Biochem J 383(Pt 2):371-82

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