RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: fadL
Synonym(s): OP00109
Gene(s): fadL   Genome Browser M3D Gene expression COLOMBOS
Note(s): OmpR binds at least four regions of DNA near the fadL promoter, two upstream and two downstream from the transcriptional start site. Only the phosphorylated form of OmpR binds the DNA. It is not clear whether binding of OmpR to all four sites is necessary for repression, or whether binding to each site affects transcription in a different way.
Cross talk has been observed between global regulators controlling the fatty acid transport genes Feng Y,2012
Although there are two FadR sites in both the fadL and fadD-sroD operons, these operons modestly regulate FadR expression, which shows that the number of binding sites does not determine regulatory strength Feng Y,2012
FadR and ArcA control fadL and fadD-sroD expression under anaerobic conditions, and their effects are additive Feng Y,2012
Under NlpE outer membrane lipoprotein overexpression, the transcription of the fadL gene is decreased Raivio TL,2013
Evidence: [IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Black PN. 1991
Promoter
Name: fadLp
+1: 2461205
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 101
Sequence: tttgaaaaaagatagaaacatacttgcaacattccagctggtccgacctatactctcgccActggtctgatttctaagatg
                        -35                 -10             +1                   
Evidence: [HIPP]
[ICWHO]
[IEP]
[TIM]
Reference(s): [1] Black PN. 1991
[2] Farewell A., et al., 1998
[3] Higashitani A., et al., 1993
[4] Huerta AM., et al., 2003
[5] Kvint K., et al., 2000
[6] Lelong C., et al., 2007
TF binding sites (TFBSs)
[ArcA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-phosphorylated repressor fadLp 2461160 2461174 -38.0 aaaaagatagAAACATACTTGCAACattccagctg nd [AIBSCS], [BPP] nd
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator fadLp 2461037 2461059 -157.5 gcaaaatcggATAAGTGACCGAAATCACACTTAaaaatgatct nd [GEA], [BPP] [10]
[FadR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FadR repressor fadLp 2461180 2461196 -17.0 gcaacattccAGCTGGTCCGACCTATActctcgccac nd [GEA], [APIORCISFBSCS], [BCE], [BPP] [10]
proximal FadR repressor fadLp 2461205 2461221 9.0 tactctcgccACTGGTCTGATTTCTAAgatgtacctc nd [APIORCISFBSCS], [BCE], [BPP] [10]
[OmpR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote OmpR-phosphorylated repressor fadLp 2461046 2461065 -149.5 gataagtgacCGAAATCACACTTAAAAATGatctaaaaca nd [APIORCISFBSCS], [SM] nd
proximal OmpR-phosphorylated repressor fadLp 2461135 2461154 -60.5 atcgcgtttcTTAGATCATATTTGAAAAAAgatagaaaca nd [GEA], [APIORCISFBSCS] [3]
remote OmpR-phosphorylated repressor fadLp 2461264 2461283 69.5 gttacagcacGTAACATAGTTTGTATAAAAataaatcatt nd [GEA], [APIORCISFBSCS] [3]
remote OmpR-phosphorylated repressor fadLp 2461314 2461333 119.5 tcatgagccaGAAAACCCTGTTTACAAAGTctgctctcgc nd [GEA], [APIORCISFBSCS] [3]
[PhoP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PhoP-phosphorylated activator fadLp 2461005 2461023 -191.5 ttccggaaagTGCTGCTCCAGTTGTTAATtctgcaaaat nd [GEA], [AIBSCS] [9]
[Rob,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Rob repressor fadLp nd nd nd nd nd [GEA], [BPP] [11]
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 RybB fadL repressor 2461288 2461304 AUCAUUGAGGUUAUGGU nd [IEP], [IMP], [IPI] [7], [8]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation fadLp nd   [GEA] [5]
Evidence: [GEA] Gene expression analysis
Reference(s): [5] Kvint K., et al., 2000


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IEP] Inferred from expression pattern

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BCE] Binding of cellular extracts

 [SM] Site mutation

 [IMP] Inferred from mutant phenotype

 [IPI] Inferred from physical interaction


Reference(s)    

 [1] Black PN., 1991, Primary sequence of the Escherichia coli fadL gene encoding an outer membrane protein required for long-chain fatty acid transport., J Bacteriol 173(2):435-42

 [2] Farewell A., Kvint K., Nystrom T., 1998, Negative regulation by RpoS: a case of sigma factor competition., Mol Microbiol 29(4):1039-51

 [3] Higashitani A., Nishimura Y., Hara H., Aiba H., Mizuno T., Horiuchi K., 1993, Osmoregulation of the fatty acid receptor gene fadL in Escherichia coli., Mol Gen Genet 240(3):339-47

 [4] 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

 [5] Kvint K., Farewell A., Nystrom T., 2000, RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s)., J Biol Chem 275(20):14795-8

 [6] Lelong C., Aguiluz K., Luche S., Kuhn L., Garin J., Rabilloud T., Geiselmann J., 2007, The Crl-RpoS regulon of Escherichia coli., Mol Cell Proteomics 6(4):648-59

 [7] Gogol EB., Rhodius VA., Papenfort K., Vogel J., Gross CA., 2011, Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon., Proc Natl Acad Sci U S A 108(31):12875-80

 [8] Lalaouna D., Carrier MC., Semsey S., Brouard JS., Wang J., Wade JT., Masse E., 2015, A 3' external transcribed spacer in a tRNA transcript acts as a sponge for small RNAs to prevent transcriptional noise., Mol Cell 58(3):393-405

 [9] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

 [10] Feng Y., Cronan JE., 2012, Crosstalk of Escherichia coli FadR with global regulators in expression of fatty acid transport genes., PLoS One 7(9):e46275

 [11] Wang Z., Xue T., Hu D., Ma Y., 2020, A Novel Butanol Tolerance-Promoting Function of the Transcription Factor Rob in Escherichia coli., Front Bioeng Biotechnol 8:524198

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