RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: livJ
Synonym(s): OP00255
Gene(s): livJ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Adams MD., et al., 1990
[2] Haney SA., et al., 1992
Promoter
Name: livJp
+1: 3599762
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 104
Sequence: attgttaataaactgtcaaaatagctattccaatatcataaaaatcgggtatgttttagcAgagtatgctgctaaagcacg
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Adams MD., et al., 1990
[3] Huerta AM., et al., 2003
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
remote Lrp-L-leucine repressor livJp 3599883 3599894 -127.0 tggatgagagTCCGGGGTTTTTgttttttggg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [4], [5], [6], [7]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp activation livJp nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IMP] 		[8]
[9]
  ppGpp activation livJp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [10]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IMP] Inferred from mutant phenotype
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [8] Lee JH., et al., 2012
[9] Paul BJ., et al., 2005
[10] Barker MM., et al., 2001


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Adams MD., Wagner LM., Graddis TJ., Landick R., Antonucci TK., Gibson AL., Oxender DL., 1990, Nucleotide sequence and genetic characterization reveal six essential genes for the LIV-I and LS transport systems of Escherichia coli., J Biol Chem 265(20):11436-43

 [2] Haney SA., Platko JV., Oxender DL., Calvo JM., 1992, Lrp, a leucine-responsive protein, regulates branched-chain amino acid transport genes in Escherichia coli., J Bacteriol 174(1):108-15

 [3] 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

 [4] Fraenkel YM., Mandel Y., Friedberg D., Margalit H., 1995, Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon., Comput Appl Biosci 11(4):379-87

 [5] 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)

 [6] Lin R., D'Ari R., Newman EB., 1992, Lambda placMu insertions in genes of the leucine regulon: extension of the regulon to genes not regulated by leucine., J Bacteriol 174(6):1948-55

 [7] Tchetina E., Newman EB., 1995, Identification of Lrp-regulated genes by inverse PCR and sequencing: regulation of two mal operons of Escherichia coli by leucine-responsive regulatory protein., J Bacteriol 177(10):2679-83

 [8] Lee JH., Lennon CW., Ross W., Gourse RL., 2012, Role of the coiled-coil tip of Escherichia coli DksA in promoter control., J Mol Biol 416(4):503-17

 [9] Paul BJ., Berkmen MB., Gourse RL., 2005, DksA potentiates direct activation of amino acid promoters by ppGpp., Proc Natl Acad Sci U S A 102(22):7823-8

 [10] Barker MM., Gaal T., Josaitis CA., Gourse RL., 2001, Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro., J Mol Biol 305(4):673-88

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