RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: lsrRK
Gene(s): lsrK, lsrR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Wang L., et al., 2005
Promoter
Name: lsrRp
+1: 1601257
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 16
Sequence: ccatcacagatataaatgagcaagaactgaacaattgcattaaagatttaaatatgttcaAagtgaagaatgaattatgac
                                -35                       -1+1                   
Note(s): Wang et al. demonstrated in 2005 that lrsK could be transcribed together with lrsR Wang L,2005.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Wang L., et al., 2005
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator lsrRp 1601307 1601328 -60.5 cgtagagtcaAACTGTGGTTGCCATCACAGATataaatgagc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] C [1], [3]
remote CRP-cyclic-AMP activator lsrRp 1601378 1601399 -131.5 ttgcacatatTTCCGACGAATAGATCACAATTtatgctattt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
[LsrR,-] 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 LsrR repressor lsrRp 1601261 1601290 -18.5 gagcaagaacTGAACAATTGCATTAAAGATTTAAATATGTtcaaagtgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [4], [5]


Transcription unit       
Name: lsrK
Gene(s): lsrK   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the lsrK 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] Inferred computationally without human oversight
[EXP-IEP] Inferred from expression pattern
Reference(s): [1] Wang L., et al., 2005


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [EXP-IEP] Inferred from expression pattern

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Wang L., Li J., March JC., Valdes JJ., Bentley WE., 2005, luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling., J Bacteriol 187(24):8350-60

 [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] Wang L., Hashimoto Y., Tsao CY., Valdes JJ., Bentley WE., 2005, Cyclic AMP (cAMP) and cAMP receptor protein influence both synthesis and uptake of extracellular autoinducer 2 in Escherichia coli., J Bacteriol 187(6):2066-76

 [4] Wu M., Tao Y., Liu X., Zang J., 2013, Structural basis for phosphorylated autoinducer-2 modulation of the oligomerization state of the global transcription regulator LsrR from Escherichia coli., J Biol Chem 288(22):15878-87

 [5] Xue T., Zhao L., Sun H., Zhou X., Sun B., 2009, LsrR-binding site recognition and regulatory characteristics in Escherichia coli AI-2 quorum sensing., Cell Res 19(11):1258-68

RegulonDB