RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: aceBAK
Synonym(s): OP00001, ace
Gene(s): aceB, aceA, aceK   Genome Browser M3D Gene expression COLOMBOS
Note(s): The genes of the aceBAK operon are expressed to varying degrees due to two facts: first, they are differentially regulated at the translational level and second, there is a putative premature transcriptional termination in the region preceding the aceK gene Cozzone AJ, El-Mansi M,2005 For review see Cozzone AJ, El-Mansi M,2005
IclR represses aceBAK transcription through two mechanisms Yamamoto K,2003 (1) binding to the proximal site, overlapping the -35 promoter box and preventing the RNA polymerase binding; (2) binding to the distal site after the RNA polymerase has bound to the promoter and formed the open complex, avoiding the polymerase escape of the promoter through its interaction with the α-subunits. Perhaps the IclR binding at both sites forms a intermolecular bridge that leads to a DNA loop structure and thus enhances the aceBAK repression Yamamoto K,2003
While glyoxylate favors the inactive dimeric state of IclR, pyruvate increases the binding of IclR to the aceBp promoter by stabilizing the active tetrameric form of the protein Lorca GL, Ezersky A, Lunin VV, Walker JR, Altamentova S, Evdokimova E, Vedadi M, Bochkarev A, Savchenko A,2007.
Under conditions of glucose excess, the protein IclR is a stronger repressor of the aceBAK operon than is the ArcA protein Waegeman H, Beauprez J, Moens H, Maertens J, De Mey M, Foulquié-Moreno MR, Heijnen JJ, Charlier D, Soetaert W,2011
Under nitrogen-rich growth conditions, the expression of the aceA gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, but under nitrogen-limited growth conditions, the gene expression was decreased in a cyoA mutant. However, under both nitrogen-limited and nitrogen-rich growth conditions, the expression of aceA is increased in mutants for Fnr and Fur. It is unknown if the effects of the transcriptional regulators act directly on the gene expression Kumar R,2011
The functional conformation of IclR has been proposed to be a dimer Negre D,1992or tetramer Donald LJ, Hosfield DJ, Cuvelier SL, Ens W, Standing KG, Duckworth HW,2001 In 1996, Pan et al. proposed that IclR binds to a binding site of 15 bp (TGGAAATtATTTCCA) in the intergenic region of the aceBAK operon Pan B,1996. Footprinting experiments showed that IclR binds, as a dimer and monomer, to two regions upstream of the transcription start site of aceB Yamamoto K,2003. Pan et al. identified one specific site, of 7 bp, for IclR at the distal site, effectively characterized by footprinting at bp -122 relative to the transcription start site of aceBAK Yamamoto K,2003 According to this evidence, the curator assigned five possible binding sites of 7 bp for iclR, located at -26, -53, -104, -131, and -141, which are included in the regions protected in footprinting experiments.
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid did not affect the expression of aceAB, whereas it did affect other genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
The aceBAK operon expression is induced when the flux signal for ATP generation diminishes as the growth rate also diminishes El-Mansi M, Phue JN, Shiloach J,2021. Its expression is induced in the presence of pyruvate or acetate El-Mansi M, Phue JN, Shiloach J,2021.
Evidence: [PM] Polar mutation
Reference(s): [1] LaPorte DC., et al., 1985
[2] Maloy SR., et al., 1982
Promoter
Name: aceBp
+1: 4215402
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 76
Sequence: tatttttaattaaaatggaaattgtttttgattttgcattttaaatgagtagtcttagttGtgctgaacgaaaagagcaca
                            -35                   -10       +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[4] Yamamoto K., et al., 2003
TF binding sites (TFBSs)
[ArcA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-phosphorylated repressor aceBp nd nd nd nd nd [RBM], [BPP] [10]
[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-cyclic-AMP repressor aceBp 4215361 4215382 -30.5 ttaaaatggaAATTGTTTTTGATTTTGCATTTtaaatgagta nd [GEA], [AIBSCS] [9]
[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 activator aceBp 4215227 4215244 -166.5 tgatagtcgaTCGTTAAGCGATTCAGCAccttacctca nd [GEA], [BPP], [SM] [5], [6]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator aceBp 4215237 4215249 -159.0 tcgttaagcgATTCAGCACCTTAcctcaggcac nd [GEA], [BPP] [7]
proximal IHF activator aceBp 4215324 4215336 -72.0 ttcatattgtTATCAACAAGTTAtcaagtattt nd [GEA], [BPP] [7]
[IclR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IclR-pyruvate repressor aceBp 4215258 4215264 -141.0 tacctcaggcACCTTCGggtgcctttt nd [GEA], [APIORCISFBSCS], [BPP] [4]
remote IclR-pyruvate repressor aceBp 4215268 4215274 -131.0 accttcgggtGCCTTTTttatttccga nd [GEA], [APIORCISFBSCS], [BPP] [4]
remote IclR-pyruvate repressor aceBp 4215277 4215283 -122.0 tgccttttttATTTCCGaaacgtacct nd [GEA], [APIORCISFBSCS], [BPP] [4]
remote IclR-pyruvate repressor aceBp 4215295 4215301 -104.0 aacgtacctcAGCAGGTgaataaattt nd [GEA], [APIORCISFBSCS], [BPP] [4]
proximal IclR-pyruvate repressor aceBp 4215346 4215352 -53.0 atcaagtattTTTAATTaaaatggaaa nd [GEA], [APIORCISFBSCS], [BPP] [4], [8]
proximal IclR-pyruvate repressor aceBp 4215357 4215372 -38.0 ttaattaaaaTGGAAATTGTTTTTGAttttgcattt nd [GEA], [APIORCISFBSCS], [BPP] [4], [8]
proximal IclR-pyruvate repressor aceBp 4215373 4215379 -26.0 ttgtttttgaTTTTGCAttttaaatga nd [GEA], [APIORCISFBSCS], [BPP] [4], [8]


Transcription unit       
Name: aceK
Gene(s): aceK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [11] Zaslaver A., et al., 2006
Promoter
Name: aceKp
+1: Unknown
Evidence: [IEP]
Reference(s): [11] Zaslaver A., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.1 4215254 4215280 ccttacctcaGGCACCTTCGGGTGCCTTTTTTATTTccgaaacgta
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    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [RBM] Reaction blocked in mutant

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [SM] Site mutation

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

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] LaPorte DC., Thorsness PE., Koshland DE., 1985, Compensatory phosphorylation of isocitrate dehydrogenase. A mechanism for adaptation to the intracellular environment., J Biol Chem 260(19):10563-8

 [2] Maloy SR., Nunn WD., 1982, Genetic regulation of the glyoxylate shunt in Escherichia coli K-12., J Bacteriol 149(1):173-80

 [3] 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

 [4] Yamamoto K., Ishihama A., 2003, Two different modes of transcription repression of the Escherichia coli acetate operon by IclR., Mol Microbiol 47(1):183-94

 [5] Ramseier TM., Negre D., Cortay JC., Scarabel M., Cozzone AJ., Saier MH., 1993, In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium., J Mol Biol 234(1):28-44

 [6] Son YJ., Phue JN., Trinh LB., Lee SJ., Shiloach J., 2011, The role of Cra in regulating acetate excretion and osmotic tolerance in E. coli K-12 and E. coli B at high density growth., Microb Cell Fact 10:52

 [7] Resnik E., Pan B., Ramani N., Freundlich M., LaPorte DC., 1996, Integration host factor amplifies the induction of the aceBAK operon of Escherichia coli by relieving IclR repression., J Bacteriol 178(9):2715-7

 [8] Pan B., Unnikrishnan I., LaPorte DC., 1996, The binding site of the IclR repressor protein overlaps the promoter of aceBAK., J Bacteriol 178(13):3982-4

 [9] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [10] Iuchi S., Lin EC., 1988, arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways., Proc Natl Acad Sci U S A 85(6):1888-92

 [11] 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

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