RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: alaE
Synonym(s): ygaW
Gene(s): alaE   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on DNA microarray analysis and Fourier transform-infrared spectroscopy, an Escherichia coli strain was exposed to 10 adverse conditions. Expression of three genes, ygaW, rmf, and ghrA, was significantly changed under each of these conditions (except in the presence of the disinfectant benzalkonium chloride) Moen B,2009
L-leucine and L-alanine regulate expression of the alaE gene Ihara K,2017.
The mdtEF-tolC, malEFG, gadBC, treBC, entCEBA-ybdB, hdeAB-yhiD, and alaE operons were differentially regulated after induction of the nonnative organic acid citramalate Webb J,2019
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: alaEp
+1: 2799084
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 80
Sequence: aaactgactaaataaaaatttttcactaattgattagtcatagccagcgatatacgctatGcgaaaatgcagatggcaatg
                               -35                   -10    +1                   
Note(s): A region of 60 bp protected for Lrp transcriptional regulation was identified upstream of the alaE gene, based on EMSA and footprinting analysis. Two sites for Lrp that were previously identified as regulating the divergent stpA gene Sonden B,1996. Free A,1997were associated with the region protected by Lrp in the alaE gene at the -58 and -9 positions with respect to the alaEp promoter Ihara K,2017.
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Ihara K., et al., 2017
TF binding sites (TFBSs)
[Lrp,+] 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 Lrp-L-leucine activator alaEp 2799019 2799034 -58.0 atattttatcTACAAAAACTGACTAAataaaaattt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3], [4]
proximal Lrp-L-leucine activator alaEp 2799068 2799083 -9.0 tagtcatagcCAGCGATATACGCTATgcgaaaatgc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [3], [4]


Evidence    

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

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

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

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

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

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

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


Reference(s)    

 [1] Ihara K., Sato K., Hori H., Makino Y., Shigenobu S., Ando T., Isogai E., Yoneyama H., 2017, Expression of the alaE gene is positively regulated by the global regulator Lrp in response to intracellular accumulation of l-alanine in Escherichia coli., J Biosci Bioeng 123(4):444-450

 [2] Free A., Dorman CJ., 1997, The Escherichia coli stpA gene is transiently expressed during growth in rich medium and is induced in minimal medium and by stress conditions., J Bacteriol 179(3):909-18

 [3] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [4] Sonden B., Uhlin BE., 1996, Coordinated and differential expression of histone-like proteins in Escherichia coli: regulation and function of the H-NS analog StpA., EMBO J 15(18):4970-80

RegulonDB