RegulonDB RegulonDB 10.8: Operon Form
   

ymiC-acnA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: acnA
Gene(s): ymiC, acnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expresion of the acnA gene is induced under oxidative stress, although this induction is not early after the stress is generated Lu C,2003.
SoxS is a regulator that participates in controlling several genes involved in the response to oxidative stress. SoxS facilitates the binding of RNA polymerase to some promoters, including the acnA promoter, during low iron availability Fuentes AM,2001
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cunningham L., et al., 1997
Promoter
Name: acnAp1
+1: 1335424
Sigma Factor: Sigma38, Sigma70
Distance from start of the gene: 148
Sequence: aatgttccgtcgttattccagacgactggcaactaacatcgcagcagcaagcctttatagAactgtttgctgaagatgatc
                          -35                    -10        +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Cunningham L., et al., 1997


Transcription unit          
Name: acnA
Gene(s): acnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expresion of the acnA gene is induced under oxidative stress, although this induction is not early after the stress is generated Lu C,2003.
SoxS is a regulator that participates in controlling several genes involved in the response to oxidative stress. SoxS facilitates the binding of RNA polymerase to some promoters, including the acnA promoter, during low iron availability Fuentes AM,2001
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cunningham L., et al., 1997
Promoter
Name: acnAp2
+1: 1335781
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 50
Sequence: tcttttatcaatttgggttgttatcaaatcgttacgcgatgtttgtgttatctttaatatTcaccctgaagagaatcaggg
                                -35                    -10  +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Cunningham L., et al., 1997
[2] Mendoza-Vargas A., et al., 2009
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
proximal ArcA-Phosphorylated repressor acnAp2 1335740 1335754 -34.0 aatttgggttGTTATCAAATCGTTAcgcgatgttt nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [1]
[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 acnAp2 1335730 1335751 -40.5 ctcttttatcAATTTGGGTTGTTATCAAATCGttacgcgatg nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [1]
[Cra,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Cra1 activator acnAp2 nd nd nd nd nd [GEA] [1]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor acnAp2 1335734 1335747 -40.5 tttatcaattTGGGTTGTTATCAAatcgttacgc nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [1]
[MarA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarA activator acnAp2 1335720 1335740 -51.5 aaggtttctcCTCTTTTATCAATTTGGGTTGttatcaaatc nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [3], [4]
[Rob,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator acnAp2 1335720 1335740 -51.5 aaggtttctcCTCTTTTATCAATTTGGGTTGttatcaaatc nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [3]
[SoxS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator acnAp2 1335720 1335740 -51.5 aaggtttctcCTCTTTTATCAATTTGGGTTGttatcaaatc nd [APIORCISFBSCS], [BPP], , [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IHBCE], [3], [4], [5]
Note(s): 1Even though the FruR site has not been determined for the acnA gene, the FruR effect in its transcription is correlated. It has been proposed that FruR affects the acnAp2 promoter because this is responsible for the basal level of acnA during exponential growth as well as redox stress Cunningham L,1997. 7Even though the FruR site has not been determined for the acnA gene, the FruR effect in its transcription is correlated. It has been proposed that FruR affects the acnAp2 promoter because this is responsible for the basal level of acnA during exponential growth as well as redox stress Cunningham L,1997.


Transcription unit       
Name: acnA
Gene(s): acnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the gene acnA is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013
Evidence: [IC] Inferred by curator
Promoter
Name: acnAp3
+1: 1335827
Distance from start of the gene: 4
Sequence: gttatctttaatattcaccctgaagagaatcagggcttcgcaaccctgtcattaaggaggAgctatgtcgtcaaccctacg
Evidence: [HTIM]
Reference(s): [2] Mendoza-Vargas A., et al., 2009


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  ryhB antisense post-transcriptional regulation repressor       [GEA]
[HIFS]
[IMP]		 [6]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

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

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

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

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

 [CEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [RE] RNA-seq evidence

 [HTIM] High-throughput transcription initiation mapping


Reference(s)    

 [1] Cunningham L., Gruer MJ., Guest JR., 1997, Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli., Microbiology 143 ( Pt 12):3795-805

 [2] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [3] Martin RG., Rosner JL., 2002, Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data., Mol Microbiol 44(6):1611-24

 [4] Martin RG., Rosner JL., 2011, Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli., J Bacteriol 193(2):506-15

 [5] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [6] Masse E., Gottesman S., 2002, A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli., Proc Natl Acad Sci U S A 99(7):4620-5

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