RegulonDB RegulonDB 11.1: Operon Form
   

lexA-dinF operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: lexA-dinF
Synonym(s): OP00046, lexA
Gene(s): lexA, dinF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Two known and one putative LexA transcription factor binding sites (TFBS) were identified in the regulatory region of the lexAp promoter Little JW,1981. Brent R,1981. Lewis LK,1994 Recently, it was demonstrated that the putative TFBS, located 50 bp upstream of the transcriptional start site of lexAp, is nonfunctional; therefore, it was removed from this database, leaving only two TFBSs regulating lexA-dinF expression, although apparently only one of these sites would be sufficient to cause repression of lexAp Kozuch BC,2020.
Upstream of the lexA gene there is a site for dynamic methylation that is methylated during stationary phase Lewis EB, Chen E, Culyba MJ,2022. Although this methylation site overlaps with a LexA binding site, it does not affect the regulation by LexA, Lewis EB, Chen E, Culyba MJ,2022. However, binding of LexA to DNA diminishes the methylation of that site Lewis EB, Chen E, Culyba MJ,2022.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Krueger JH., et al., 1983
Promoter
Name: lexAp
+1: 4257087
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: ctctggtttattgtgcagtttatggttccaaaatcgccttttgctgtatatactcacagcAtaactgtatatacacccagg
                          -35                    -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Miki T., et al., 1981
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[LexA,-] 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 LexA repressor lexAp 4257068 4257087 -9.0 aatcgcctttTGCTGTATATACTCACAGCAtaactgtata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]
proximal LexA repressor lexAp 4257089 4257108 13.0 ctcacagcatAACTGTATATACACCCAGGGggcggaatga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

 [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-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Krueger JH., Elledge SJ., Walker GC., 1983, Isolation and characterization of Tn5 insertion mutations in the lexA gene of Escherichia coli., J Bacteriol 153(3):1368-78

 [2] 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

 [3] Miki T., Ebina Y., Kishi F., Nakazawa A., 1981, Organization of the lexA gene of Escherichia coli and nucleotide sequence of the regulatory region., Nucleic Acids Res 9(3):529-43

 [4] 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.

 [5] Kozuch BC., Shaffer MG., Culyba MJ., 2020, The Parameter-Fitness Landscape of lexA Autoregulation in Escherichia coli., mSphere 5(4)

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