RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: alaS
Gene(s): alaS   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for alaS . 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: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Putney SD., et al., 1981
Promoter
Name: alaSp
+1: 2822090
Distance from start of the gene: 79
Sequence: tttgccgactgaacgcatacggtattttacttcccagtcaagaaaacttatcttattcccActtttcagttaccagcccgg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Putney SD., et al., 1981
[1] Putney SD., et al., 1981
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[AlaS,-] 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 AlaS-L-alanine repressor alaSp 2822080 2822114 -6.5 ttacttcccaGTCAAGAAAACTTATCTTATTCCCACTTTTCAGTTaccagcccgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4]


Evidence    

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

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Putney SD., Schimmel P., 1981, An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription., Nature 291(5817):632-5

 [2] Putney SD., Melendez DL., Schimmel PR., 1981, Cloning, partial sequencing, and in vitro transcription of the gene for alanine tRNA synthetase., J Biol Chem 256(1):205-11

 [3] 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.

 [4] Banerjee B., Ganguli S., Banerjee R., 2019, Biophysical characterization of interaction between E. coli alanyl-tRNA synethase with its promoter DNA., Protein Pept Lett


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