RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: yccA
Gene(s): yccA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under NlpE outer membrane lipoprotein overexpression, the transcription of the yccA gene is increased by CpxR Raivio TL,2013
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for yccA. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yccAp
+1: 1031443
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: gtaaagatgggtaaaacttctgggtgcccttacgcattatcattatgctgcttaattaatTacatctgtcatagagagtga
                       -35                       -10        +1                   
Note(s): This promoter appears to have more transcriptional sites at positions 1031444/5/6/7/8, as determined by high-throughput screening of maps of promoters Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Yamamoto K., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ctggcggcagTGTAACAAAAAACAAAGCCCCGCATAAAGCGAGGCTATGAAAGTGTTAGCGGGTGagattaatcg
Reference(s): [3] Feng CQ., et al., 2019
[4] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CpxR,+] 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 CpxR-phosphorylated activator yccAp 1031495 1031496 -53.0 tgcgtaaagaTgggtaaaact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.7 1031582 1031616 caaataagatAAGGGGTTAGCTAAATGCTAACCCCTTTTTCTTTtgcctgtcga
  anti-terminator -6.7 1031605 1031649 agggttccagAGTTCGAATCTCTGCGCTTCCGCCAAATAAGATAAGGGGTTAGCtaaatgctaa
  anti-anti-terminator -4.3 1031636 1031652 gaaagggttcCAGAGTTCGAATCTCTgcgcttccgc
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-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [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-CHIP-EXO] high throughput ChIP-exo evidence

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


Reference(s)    

 [1] 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

 [2] Yamamoto K., Ishihama A., 2006, Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli., Biosci Biotechnol Biochem 70(7):1688-95

 [3] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [4] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [5] Raivio TL., Leblanc SK., Price NL., 2013, The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity., J Bacteriol 195(12):2755-67

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