RegulonDB RegulonDB 11.1: Operon Form
   

ycgZ-ymgA-ariR-ymgC operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ycgZ-ymgA-ariR-ymgC
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ycgZ-ymgA-ariR-ymgC
Gene(s): ycgZ, ymgA, ariR, ymgC   Genome Browser M3D Gene expression COLOMBOS
Note(s): ycgZ-ymgA-ariR-ymgC constitutes an operon. YmgA and AriR activate production of the biofilm matrix substance colanic acid as well as acid resistance genes and the biofilm-associated bdm gene and they downregulate adhesive curli fimbriae Domka J,2007. Majdalani N, Gottesman S,2007. Lee J, Page R, García-Contreras R, Palermino JM, Zhang XS, Doshi O, Wood TK, Peti W,2007. Attila C, Ueda A, Wood TK,2009 YcgZ appears to counteract the activities of YmgA and YmgB Tschowri N,2009
Expression of this operon is under the control of σ38 (rpoS) RNA polymerase and repressed by ycgE, which is transcribed divergently on the opposite strand Tschowri N,2009. Weber H,2005
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Tschowri N., et al., 2009
Promoter
Name: ycgZp
+1: 1215752
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: gcaaaaaattaatttatcattctgtacacatatttcgtacaagtttgctattgttacttcActtaacattgattaacattt
                         -35                -10             +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Gama-Castro S., et al., 2008
[1] Tschowri N., et al., 2009
[3] Tschowri N., et al., 2012
TF binding sites (TFBSs)
[BluR,-] 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 BluR repressor ycgZp 1215713 1215733 -29.5 atttatcattCTGTACACATATTTCGTACAAgtttgctatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [3]
[MarA,+] 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 MarA activator ycgZp 1215683 1215698 -62.0 atatgcattaGCACTAATTGCAAAAAattaatttat nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]


Transcription unit          
Name: ycgZ-ymgA-ariR-ymgC
Gene(s): ycgZ, ymgA, ariR, ymgC   Genome Browser M3D Gene expression COLOMBOS
Note(s): ycgZ-ymgA-ariR-ymgC constitutes an operon. YmgA and AriR activate production of the biofilm matrix substance colanic acid as well as acid resistance genes and the biofilm-associated bdm gene and they downregulate adhesive curli fimbriae Domka J,2007. Majdalani N, Gottesman S,2007. Lee J, Page R, García-Contreras R, Palermino JM, Zhang XS, Doshi O, Wood TK, Peti W,2007. Attila C, Ueda A, Wood TK,2009 YcgZ appears to counteract the activities of YmgA and YmgB Tschowri N,2009
Expression of this operon is under the control of σ38 (rpoS) RNA polymerase and repressed by ycgE, which is transcribed divergently on the opposite strand Tschowri N,2009. Weber H,2005
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Tschowri N., et al., 2009
Promoter
Name: ycgZp2
+1: 1215752
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 37
Sequence: gcaaaaaattaatttatcattctgtacacatatttcgtacaagtttgctattgttacttcActtaacattgattaacattt
                         -35                -10             +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Gama-Castro S., et al., 2008
[5] Huerta AM., et al., 2003
[1] Tschowri N., et al., 2009
[3] Tschowri N., et al., 2012
TF binding sites (TFBSs)
[BluR,-] 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 BluR repressor ycgZp2 1215713 1215733 -29.5 atttatcattCTGTACACATATTTCGTACAAgtttgctatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [3]
[MarA,+] 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 MarA activator ycgZp2 1215683 1215698 -62.0 atatgcattaGCACTAATTGCAAAAAattaatttat nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]


Transcription unit       
Name: ymgC
Gene(s): ymgC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Transcription unit       
Name: ycgZ
Gene(s): ycgZ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Transcription unit       
Name: ymgA-ariR
Gene(s): ymgA, ariR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Transcription unit       
Name: ariR
Gene(s): ariR   Genome Browser M3D Gene expression COLOMBOS


Evidence    

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

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

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

 [EXP-IEP] Inferred from expression pattern

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Tschowri N., Busse S., Hengge R., 2009, The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli., Genes Dev 23(4):522-34

 [2] Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola MI., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta AM., Trevino-Quintanilla L., Collado-Vides J., 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation., Nucleic Acids Res 36(Database issue):D120-4

 [3] Tschowri N., Lindenberg S., Hengge R., 2012, Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli., Mol Microbiol 85(5):893-906

 [4] Kettles RA., Tschowri N., Lyons KJ., Sharma P., Hengge R., Webber MA., Grainger DC., 2019, The Escherichia coli MarA protein regulates the ycgZ-ymgABC operon to inhibit biofilm formation., Mol Microbiol 112(5):1609-1625

 [5] 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

RegulonDB