RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: luxS
Gene(s): luxS   Genome Browser M3D Gene expression COLOMBOS
Note(s): Udekwu, in 2010, identified several transcription start sites upstream of luxS; however, he considered that only two promoters are the producers of primary transcripts Udekwu KI.,2010 One of them was also identified by De Lay (2009) De Lay N,2009
The transcription start site for luxS lies within the divergent gene for
micA. The luxS mRNA and the MicA sRNA share 15 bp of complementary
sequence and may facilitate posttranscriptional regulation of luxS by Mi
cA De Lay N,2009
The transcription of the luxS gene is repressed after 24 h of coculture with microcapsules of Lactobacillus rhamnosus Song H, Zhang J, Qu J, Liu J, Yin P, Zhang G, Shang D,2019.
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Lay N., et al., 2009
Promoter
Name: luxSp2
+1: 2814816
Distance from start of the gene: 83
Sequence: agaaaaaggccactcgtgagtggccaaaatttcatctctgaattcagggatgatgataacAaatgcgcgtctttcatatac
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] De Lay N., et al., 2009
[2] Salgado H, et al., 2012
[3] Udekwu KI. 2010
TF binding sites (TFBSs)
[UvrY,+] 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
nd UvrY-phosphorylated activator luxSp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA CyaR luxS repressor 2814731 2814745 CAUUUAGCCACCUCC nd [EXP-IEP], [EXP-IMP-SITE-MUTATION] [1]


Transcription unit       
Name: luxS
Gene(s): luxS   Genome Browser M3D Gene expression COLOMBOS
Note(s): Udekwu, in 2010, identified several transcription start sites upstream of luxS; however, he considered that only two promoters are the producers of primary transcripts Udekwu KI.,2010 One of them was also identified by De Lay (2009) De Lay N,2009.
The transcription of the luxS gene is repressed after 24 h of coculture with microcapsules of Lactobacillus rhamnosus Song H, Zhang J, Qu J, Liu J, Yin P, Zhang G, Shang D,2019.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Lay N., et al., 2009
Promoter
Name: luxSp1
+1: 2815065
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 332
Sequence: tgcttcgataatcccgatctgactttctctgcccgtatcttaaggtctatgattgatactGgtattggcggaacaggcaaa
                               -35                   -10    +1                   
Note(s): The activity of the luxSp1 promoter is increased during entry into stationary phase and appears to depend on σ38 Udekwu KI.,2010.
The DNA sequence of the luxSp1 promoter of E. coli is conserved in Shigella flexneri, Salmonella typhimurium, and Photorabdus luminescens Udekwu KI.,2010.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Huerta AM., et al., 2003
[3] Udekwu KI. 2010


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-IEP] Inferred from expression pattern

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-AINF] Inferred computationally without human oversight

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

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


Reference(s)    

 [1] De Lay N., Gottesman S., 2009, The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior., J Bacteriol 191(2):461-76

 [2] 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.

 [3] Udekwu KI., 2010, Transcriptional and post-transcriptional regulation of the Escherichia coli luxS mRNA; involvement of the sRNA MicA., PLoS One 5(10):e13449

 [4] Mitra A., Herren CD., Patel IR., Coleman A., Mukhopadhyay S., 2016, Integration of AI-2 Based Cell-Cell Signaling with Metabolic Cues in Escherichia coli., PLoS One 11(6):e0157532

 [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

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