RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: lysU
Gene(s): lysU   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Clark RL., et al., 1990
[2] Leveque F., et al., 1991
Promoter
Name: lysUp2
+1: 4354797
Distance from start of the gene: 80
Sequence: tttattagtgatatcaacttgaggtaagcgttagtttcgataagataaactgagttactaAtagtcgaggcagataataca
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Clark RL., et al., 1990
[2] Leveque F., et al., 1991
[3] Salgado H, et al., 2012


Transcription unit          
Name: lysU
Synonym(s): OP00312
Gene(s): lysU   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Clark RL., et al., 1990
[2] Leveque F., et al., 1991
[4] Oshima T., et al., 1995
Promoter
Name: lysUp1
+1: 4354805
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 88
Sequence: gatggttatttattagtgatatcaacttgaggtaagcgttagtttcgataagataaactgAgttactaatagtcgaggcag
                                -35                        -+1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Clark RL., et al., 1990
[5] Huerta AM., et al., 2003
[2] Leveque F., et al., 1991
[3] Salgado H, et al., 2012
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 repressor lysUp1 4354856 4354870 -58.0 catttaaaccATTTTGATGGTTATTtattagtgat nd [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.8 4354725 4354763 taccgatctgTCTCTTTATCTACGCTAAATTGAAAGCTGGATTTAGAGgaaccaaaat
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-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

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

 [COMP-AINF] Inferred computationally without human oversight

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

 [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-SEQ] high throughput ChIP-seq evidence

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Clark RL., Neidhardt FC., 1990, Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior., J Bacteriol 172(6):3237-43

 [2] Leveque F., Gazeau M., Fromant M., Blanquet S., Plateau P., 1991, Control of Escherichia coli lysyl-tRNA synthetase expression by anaerobiosis., J Bacteriol 173(24):7903-10

 [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] Oshima T., Ito K., Kabayama H., Nakamura Y., 1995, Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp., Mol Gen Genet 247(5):521-8

 [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

 [6] 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)

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