RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ahpCF
Gene(s): ahpC, ahpF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Expression of ahpC is activated by OxyR. This is also true for the expression of the divergently transcribed dsbG. The intergenic region between dsbG and ahpC carries two binding sites for OxyR, a dsbG-proximal site, located 54 bp upstream of the dsbG start codon, and an ahpC-proximal site, located 290 bp upstream of the dsbG start codon Zheng M,2001
The OxyR-regulated ahpCF operon is upregulated by methylglyoxal (MG), based on ChIP-chip analysis with DNA-RNAP occupancy Ozyamak E,2013
Northern blotting and primer extension assays showed that OxyR binding to the ahpC-proximal site leads to the induction of both dsbG and ahpC transcripts, while OxyR binding to the dsbG-proximal site leads to the induction of a second ahpC transcript. This transcript of ahpC and the transcript of dsbG overlap by over 100 nucleotides. Zheng M,2001
Jung IL,2003demonstrated that both the oxyR and ahpC genes, which codify a transcriptional regulator and a product essential for the detoxification against H2O2-induced stress, respectively, were absolutely dependent on polyamines during entry into the stationary phase. These data suggest that polyamines directly participates in the defense mechanism against oxidative stress.
Six RNA processing sites (PSSs) have been identified in the ahpCF operon by high-throughput screening of PSSs Lacoux C,2020.
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Ferrante AA., et al., 1995
Promoter
Name: ahpCp2
+1: 638693
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 252
Sequence: taggtaagagcttagatcaggtgattgccctttgtttatgagggtgttgtaatccatgtcGttgttgcatttgtaagggca
                         -35                       -10      +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Zheng M., et al., 2001
TF binding sites (TFBSs)
[OxyR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR activator ahpCp2 638609 638625 -76.0 aaagtcgagtAAAAGGCATAACCTATCactgtcatag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal OxyR activator ahpCp2 638632 638648 -53.0 tatcactgtcATAGGTAAGAGCTTAGAtcaggtgatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [3], [4]


Transcription unit          
Name: ahpCF
Synonym(s): OP00101, ahpC
Gene(s): ahpC, ahpF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Expression of ahpC is activated by OxyR. This is also true for the expression of the divergently transcribed dsbG. The intergenic region between dsbG and ahpC carries two binding sites for OxyR, a dsbG-proximal site, located 54 bp upstream of the dsbG start codon, and an ahpC-proximal site, located 290 bp upstream of the dsbG start codon Zheng M,2001
Northern blotting and primer extension assays showed that OxyR binding to the ahpC-proximal site leads to the induction of both dsbG and ahpC transcripts, while OxyR binding to the dsbG-proximal site leads to the induction of a second ahpC transcript. This transcript of ahpC and the transcript of dsbG overlap by over 100 nucleotides. Zheng M,2001
Jung IL,2003demonstrated that both the oxyR and ahpC genes, which codify a transcriptional regulator and a product essential for the detoxification against H2O2-induced stress, respectively, were absolutely dependent on polyamines during entry into the stationary phase. These data suggest that polyamines directly participates in the defense mechanism against oxidative stress.
The OxyR-regulated ahpCF operon is upregulated by methylglyoxal (MG), based on ChIP-chip analysis with DNA-RNAP occupancy Ozyamak E,2013
The transcription of the gene ahpC is enhanced under high oxygen saturation (300%) Baez A,2013
Six RNA processing sites (PSSs) have been identified in the ahpCF operon by high-throughput screening of PSSs Lacoux C,2020.
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Ferrante AA., et al., 1995
Promoter
Name: ahpCp1
+1: 638921
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: atcgatttgataatggaaacgcattagccgaatcggcaaaaattggttaccttacatctcAtcgaaaacacggaggaagta
                        -35                     -10         +1                   
Note(s): This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, and induced from 10 to 15 minutes Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[5] Salgado H, et al., 2012
[6] Tartaglia LA., et al., 1989
TF binding sites (TFBSs)
[MetJ,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MetJ-S-adenosyl-L-methionine repressor ahpCp1 638930 638945 17.5 catcgaaaacACGGAGGAAGTATAGAtgtccttgat nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [11]
proximal MetJ-S-adenosyl-L-methionine repressor ahpCp1 638940 638955 27.5 acggaggaagTATAGATGTCCTTGATtaacaccaaa nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [11]
[OxyR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR activator ahpCp1 638847 638863 -66.0 tacgaaggttGTAAGGTAAAACTTATCgatttgataa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [6], [7], [8], [9]
proximal OxyR activator ahpCp1 638869 638885 -44.0 ttatcgatttGATAATGGAAACGCATTagccgaatcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [6], [7], [8], [9], [10]


Transcription unit       
Name: ahpF
Gene(s): ahpF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Promoter
Name: ahpFp
+1: 639002
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 751
Sequence: tagatgtccttgattaacaccaaaattaaaccttttaaaaaccaggcattcaaaaacggcGaattcatcgaaatcaccgaa
                            -35                   -10       +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[12] Rhodius VA., et al., 2005


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.8 639646 639672 cctaattcttCGGGTGCTGCGGCACCCGATTTTCTTccccgcacca
  anti-terminator -4.4 639635 639652 tcggaaattcACCTAATTCTTCGGGTGctgcggcacc
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    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-CHIP-SEQ-MANUAL] ChIP-seq evidence used in manual assertion

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position


Reference(s)    

 [1] Ferrante AA., Augliera J., Lewis K., Klibanov AM., 1995, Cloning of an organic solvent-resistance gene in Escherichia coli: the unexpected role of alkylhydroperoxide reductase., Proc Natl Acad Sci U S A 92(17):7617-21

 [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] Zheng M., Wang X., Doan B., Lewis KA., Schneider TD., Storz G., 2001, Computation-directed identification of OxyR DNA binding sites in Escherichia coli., J Bacteriol 183(15):4571-9

 [4] 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

 [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] Tartaglia LA., Storz G., Ames BN., 1989, Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress., J Mol Biol 210(4):709-19

 [7] Campos E., Montella C., Garces F., Baldoma L., Aguilar J., Badia J., 2007, Aerobic L-ascorbate metabolism and associated oxidative stress in Escherichia coli., Microbiology 153(Pt 10):3399-408

 [8] Tartaglia LA., Gimeno CJ., Storz G., Ames BN., 1992, Multidegenerate DNA recognition by the OxyR transcriptional regulator., J Biol Chem 267(3):2038-45

 [9] Toledano MB., Kullik I., Trinh F., Baird PT., Schneider TD., Storz G., 1994, Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection., Cell 78(5):897-909

 [10] Storz G., Tartaglia LA., Ames BN., 1990, Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation., Science 248(4952):189-94

 [11] Liu R., Blackwell TW., States DJ., 2001, Conformational model for binding site recognition by the E.coli MetJ transcription factor., Bioinformatics 17(7):622-33

 [12] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

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