RegulonDB RegulonDB 10.9: Operon Form
   

acnB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: acnB
Gene(s): acnB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of acnB is enhanced during and after the switch from aerobic to anaerobic growth conditions 21980479
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for acnB . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cunningham L., et al., 1997
Promoter
Name: acnBp
+1: 131519
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 96
Sequence: tttatgttgcttttttgtaaacagattaacacctcgtcaaaatcctgctattctgcccgtTgcggtactgggcatttaccc
                          -35                    -10        +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [1] Cunningham L., et al., 1997
[2] Huerta AM., et al., 2003
[3] Mendoza-Vargas A., et al., 2009
Terminator(s)
Type: rho-independent
Sequence: acgacacaatGCCCGGTGAATGAGATTCCCGGGCatttttttat
Reference(s): [4] Benjamin JA., et al., 2014
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-Phosphorylated repressor acnBp 131342 131356 -170.0 gaggcggtagTTTAAATTTTGACTAAtcttgggatt nd [APIORCISFBSCS], [GEA] [1]
remote ArcA-Phosphorylated repressor acnBp 131369 131383 -143.0 cttgggattcGTTGAGAAAGGTGATTatcaccatgc nd [APIORCISFBSCS], [GEA] [1]
remote ArcA-Phosphorylated repressor acnBp 131373 131387 -139.0 ggattcgttgAGAAAGGTGATTATCAccatgcgaat nd [APIORCISFBSCS], [GEA] [1]
remote ArcA-Phosphorylated repressor acnBp 131393 131407 -119.0 ttatcaccatGCGAATTAACGAAGTTtttacggagg nd [EME], [AIBSPD], [APIORCISFBSCS], [CCE], [GEA] [1], [6]
remote ArcA-Phosphorylated repressor acnBp 131399 131413 -113.0 ccatgcgaatTAACGAAGTTTTTACGgagggaaaca nd [APIORCISFBSCS], [GEA] [1]
proximal ArcA-Phosphorylated repressor acnBp 131455 131469 -57.0 gattcagccaCTTTTTTATGTTGCTTttttgtaaac nd [APIORCISFBSCS], [GEA] [1]
proximal ArcA-Phosphorylated repressor acnBp 131464 131478 -48.0 acttttttatGTTGCTTTTTTGTAAAcagattaaca nd [EME], [AIBSPD], [APIORCISFBSCS], [CCE], [GEA] [1], [6]
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 acnBp 131471 131492 -37.5 tatgttgcttTTTTGTAAACAGATTAACACCTCgtcaaaatcc nd [APIORCISFBSCS], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Cra1 repressor acnBp nd nd nd nd nd [BPP], [GEA], [IGI] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis repressor acnBp 131340 131354 -171.5 aagaggcggtAGTTTAAATTTTGACTaatcttggga nd [APIORCISFBSCS], [GEA] [1]
proximal Fis repressor acnBp 131438 131452 -73.5 tctagaccatCCTTAACGATTCAGCCacttttttat nd [APIORCISFBSCS], [GEA] [1]
proximal Fis repressor acnBp 131482 131496 -29.5 tttgtaaacaGATTAACACCTCGTCAaaatcctgct nd [APIORCISFBSCS], [GEA] [1]
Note(s): 1Direct FruR binding to acnB has been determined, even though a repressive effect is observed. The different effect of FruR on acnA (activating) and acnB (repressing) is yet unclear. It may be related to the preferential use of one of the two enzymes in the citric and glyoxylate cycles or stress response (see Cunningham L,1997).12Direct FruR binding to acnB has been determined, even though a repressive effect is observed. The different effect of FruR on acnA (activating) and acnB (repressing) is yet unclear. It may be related to the preferential use of one of the two enzymes in the citric and glyoxylate cycles or stress response (see Cunningham L,1997).
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA RyhB acnB repressor 131596 131624 GAGAGCGAGGAGAACCGUCGUGCUAGAAG TRANSLATION-BLOCKING, MRNA-DEGRADATION [IMP] [4], [5]


Transcription unit       
Name: acnB
Gene(s): acnB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: acnBp2
+1: 131564
Distance from start of the gene: 51
Sequence: tgctattctgcccgttgcggtactgggcatttaccctacaaactgctgtctcacaggagcGtgaagagaatcgcctgccgc
Evidence: [HTTIM]    
Reference(s): [3] Mendoza-Vargas A., et al., 2009


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [7] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.1 131367 131412 tcttgggattCGTTGAGAAAGGTGATTATCACCATGCGAATTAACGAAGTTTTTAcggagggaaa
  anti-terminator -7.0 131339 131385 aagaggcggtAGTTTAAATTTTGACTAATCTTGGGATTCGTTGAGAAAGGTGATTAtcaccatgcg
  anti-anti-terminator -4.3 131314 131346 cgcaggtgctGTGAATCCGAGTATAAAGAGGCGGTAGTTTAAattttgacta
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"





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