RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: fucPIKUR
Synonym(s): OP00171, fucPIK
Gene(s): fucP, fucI, fucK, fucU, fucR   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Chen YM., et al., 1989
Promoter
Name: fucPp
+1: 2934119
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 116
Sequence: ctagctaataagtgtgaccgccgtcatattacagagcgttttttatttgaaaatgaatccAtgagttcatttcagacaggc
                       -35                  -10             +1                   
Evidence: [ICWHO]
[NTAS]
Reference(s): [2] Huerta AM., et al., 2003
[3] Podolny V., et al., 1999
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP1 activator fucPp 2934028 2934049 -80.5 tttcgattatTAAAGTGATGGTAGTCACATAAAgtcaccttct nd [AIBSCS], [BPP], [GEA] [3], [4]
proximal CRP-cAMP2 activator fucPp 2934068 2934089 -40.5 tctagctaatAAGTGTGACCGCCGTCATATTACagagcgtttt nd [BPP], [GEA], [SM] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FucR-L-fuculose-1-P activator fucPp nd nd nd nd nd [BPP], [GEA], [IGI] [3]
Note(s): 1In the intergenic regulatory region the fucPIK and fucAO operons, there exist other potential CRP-binding sites, which are located at positions -80.5, -289.5, -297.5, and -387.5 relative to the transcription start site.
2In the intergenic regulatory region the fucPIK and fucAO operons, there exist other potential CRP-binding sites, which are located at positions -80.5, -289.5, -297.5, and -387.5 relative to the transcription start site.1In the intergenic regulatory region the fucPIK and fucAO operons, there exist other potential CRP-binding sites, which are located at positions -80.5, -289.5, -297.5, and -387.5 relative to the transcription start site.
2In the intergenic regulatory region the fucPIK and fucAO operons, there exist other potential CRP-binding sites, which are located at positions -80.5, -289.5, -297.5, and -387.5 relative to the transcription start site.


Transcription unit       
Name: fucU
Gene(s): fucU   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [5] Li Z., et al., 2019
Promoter
Name: fucUp
+1: 2938837
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 51
Sequence: ggtatggcgtaggggaatttaacagcccggaagaagcccgcgcacagattcattatcagtAccgttatttctacccgcaaa
                                                   -10      +1                   
Evidence: [RSE]
[TIM]
Reference(s): [5] Li Z., et al., 2019


Transcription unit       
Name: fucR
Gene(s): fucR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [6] Zaslaver A., et al., 2006
Promoter
Name: fucRp
+1: Unknown
Evidence: [IEP]
Reference(s): [6] Zaslaver A., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.3 2934062 2934106 caccttctagCTAATAAGTGTGACCGCCGTCATATTACAGAGCGTTTTTTATTTgaaaatgaat
  terminator -16.0 2937391 2937431 cccggtcgctCCGGCTACCGGGCCTGAACAAGCAAGAGTGGTTAGCCGGAtaagcaatgt
  terminator -14.1 2939324 2939342 ataccggtacGCCCGCATGACGCGGGCGgttatcgaat
  anti-terminator -10.9 2934037 2934080 taaagtgatgGTAGTCACATAAAGTCACCTTCTAGCTAATAAGTGTGACCGCCgtcatattac
  anti-anti-terminator -4.6 2934032 2934055 attattaaagTGATGGTAGTCACATAAAGTCACcttctagcta
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"




Reference(s)    

 [1] Chen YM., Lu Z., Lin EC., 1989, Constitutive activation of the fucAO operon and silencing of the divergently transcribed fucPIK operon by an IS5 element in Escherichia coli mutants selected for growth on L-1,2-propanediol., J Bacteriol 171(11):6097-105

 [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] Podolny V., Lin EC., Hochschild A., 1999, A cyclic AMP receptor protein mutant that constitutively activates an Escherichia coli promoter disrupted by an IS5 insertion., J Bacteriol 181(24):7457-63

 [4] 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

 [5] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

 [6] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [7] Beisel CL., Storz G., 2011, The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli., Mol Cell 41(3):286-97

 [8] Beisel CL., Updegrove TB., Janson BJ., Storz G., 2012, Multiple factors dictate target selection by Hfq-binding small RNAs., EMBO J 31(8):1961-74


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