RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: grcA
Gene(s): grcA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Green J., et al., 1998
Promoter
Name: grcAp2
+1: 2716506
Distance from start of the gene: 57
Sequence: tttaaatcaaagattcaagggtgtttgaggagtatatatacactcaagcaacaatggtttTaccaattggccgcgacaggc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Vesper O., et al., 2011


Transcription unit          
Name: grcA
Synonym(s): yfiD
Gene(s): grcA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the grcA ( yfiD ) gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011
The expression of the gene grcA is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 but the transcription may be activated by Fnr, whose gene is also upregulated under these conditions. This increased expression of grcA is in agreement with the increased formate production observed under acidic conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Green J., et al., 1998
Promoter
Name: grcAp1
+1: 2716523
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 74
Sequence: tgtgtggtttttattgatttaaatcaaagattcaagggtgtttgaggagtatatatacacTcaagcaacaatggttttacc
                                                       -10  +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [1] Green J., et al., 1998
TF binding sites (TFBSs)
[ArcA,+] 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 ArcA-phosphorylated activator grcAp1 2716598 2716612 -82.0 tgatgtaaaaCAATAAAATCCATTTgcgaccatac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
remote ArcA-phosphorylated activator grcAp1 2716615 2716629 -99.0 ttcacacccgCATAAGTTGATGTAAaacaataaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
[CRP,+] 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 CRP-cyclic-AMP activator grcAp1 2716553 2716574 -40.5 atgtgtggttTTTATTGATTTAAATCAAAGATtcaagggtgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[FNR,+] 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 FNR activator grcAp1 2716557 2716570 -40.5 gtggtttttaTTGATTTAAATCAAagattcaagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4], [6], [8]
[FNR,-] 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 FNR repressor grcAp1 2716557 2716570 -40.5 gtggtttttaTTGATTTAAATCAAagattcaagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4], [6], [8]
remote FNR repressor grcAp1 2716610 2716623 -93.5 cccgcataagTTGATGTAAAACAAtaaaatccat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4], [5], [6]
[Fis,+] 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 Fis activator grcAp1 2716526 2716540 -10.0 aagggtgtttGAGGAGTATATATACactcaagcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
remote Fis activator grcAp1 2716633 2716647 -117.0 aatgtaaattGGTAAAATTTCACACccgcataagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
remote Fis activator grcAp1 2716675 2716689 -159.0 acaaaatcatGCTCATTTTTTAGACttaaacgagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
[Fur,-] 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
nd Fur-Fe2+ repressor grcAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[PdhR,-] 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 PdhR repressor grcAp1 2716499 2716515 17.0 actcaagcaaCAATGGTTTTACCAATTggccgcgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]


Evidence    

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

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

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

 [EXP-IMP] Inferred from mutant phenotype

 [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.

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Green J., Baldwin ML., Richardson J., 1998, Downregulation of Escherichia coli yfiD expression by FNR occupying a site at -93.5 involves the AR1-containing face of FNR., Mol Microbiol 29(4):1113-23

 [2] Vesper O., Amitai S., Belitsky M., Byrgazov K., Kaberdina AC., Engelberg-Kulka H., Moll I., 2011, Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli., Cell 147(1):147-57

 [3] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [4] Wyborn NR., Messenger SL., Henderson RA., Sawers G., Roberts RE., Attwood MM., Green J., 2002, Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products., Microbiology 148(Pt 4):1015-26

 [5] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [6] Marshall FA., Messenger SL., Wyborn NR., Guest JR., Wing H., Busby SJ., Green J., 2001, A novel promoter architecture for microaerobic activation by the anaerobic transcription factor FNR., Mol Microbiol 39(3):747-53

 [7] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [8] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions., Biotechnol Bioeng 92(2):147-59

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