RegulonDB RegulonDB 11.1: Operon Form
   

fadD-sroD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: fadD-sroD
Gene(s): sroD, fadD   Genome Browser M3D Gene expression COLOMBOS
Note(s): 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
Both ppGpp and the cAMP-CRP complex are required to override FadR repression of the fadD gene Kvint K,2000
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Black PN., et al., 1992
[2] Zhang JR., et al., 1989
Promoter
Name: fadDp
+1: 1889807
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 61
Sequence: cgcttcgcaaccttttcgttgggtaattatcaagctggtatgatgagttaatattatgttAacggcatgtatatcatttgg
                                -35                      -10+1                   
Note(s): The fadDp promoter is significantly affected by ectopic production of a nanoRNase during stationary-phase growth Vvedenskaya IO,2012
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [1] Black PN., et al., 1992
[3] Farewell A., et al., 1998
[4] Huerta AM., et al., 2003
[5] Vvedenskaya IO., et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gtgggcgtcaAAAAAAACGCCGGATTAACCGGCGTCTgacgactgac
Reference(s): [2] Zhang JR., et al., 1989
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor fadDp 1889807 1889821 -7.0 ggtatgatgaGTTAATATTATGTTAacggcatgta nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [8], [9]
[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 fadDp 1889856 1889877 -59.5 gataaaaataAATAGTGACGCGCTTCGCAACCttttcgttgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7]
[FadR,-] 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 FadR repressor fadDp 1889819 1889835 -20.0 gtaattatcaAGCTGGTATGATGAGTTaatattatgt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1], [6]
remote FadR repressor fadDp 1889905 1889921 -106.0 aagaaacagcGGCTGGTCCGCTGTTTCtgcattctta nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1], [6]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation fadDp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [10]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [10] Kvint K., et al., 2000


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-CHIP-CHIP] high throughput ChIP-chip evidence

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

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


Reference(s)    

 [1] Black PN., DiRusso CC., Metzger AK., Heimert TL., 1992, Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase., J Biol Chem 267(35):25513-20

 [2] Zhang JR., Deutscher MP., 1989, Analysis of the upstream region of the Escherichia coli rnd gene encoding RNase D. Evidence for translational regulation of a putative tRNA processing enzyme., J Biol Chem 264(30):18228-33

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

 [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] Vvedenskaya IO., Sharp JS., Goldman SR., Kanabar PN., Livny J., Dove SL., Nickels BE., 2012, Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs., Genes Dev 26(13):1498-507

 [6] 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

 [7] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [8] Cho BK., Knight EM., Palsson BO., 2006, Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA., Microbiology 152(Pt 8):2207-19

 [9] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

 [10] Kvint K., Hosbond C., Farewell A., Nybroe O., Nystrom T., 2000, Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor., Mol Microbiol 35(2):435-43

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