RegulonDB RegulonDB 10.9: Operon Form
   

relBE-hokD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: relBE-hokD
Gene(s): hokD, relE, relB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bech FW., et al., 1985
Promoter
Name: relBp
+1: 1645903
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: cgactactttctgacttccttcgtgacttgccctaagcatgttgtagtgcgatacttgtaAtgacatttgtaattacaaga
                            -35                    -10      +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [1] Bech FW., et al., 1985
[2] Belliveau NM., et al., 2018
[3] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: aaaaacaaaaACCCGCCGAAGCGGGTtaagtgcggg
Reference(s): [1] Bech FW., et al., 1985
TF binding sites (TFBSs)
[RelB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RelB repressor relBp 1645885 1645897 13.5 tgtaatgacaTTTGTAATTACAAgaggtgtaag nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal RelB repressor relBp 1645897 1645908 1.5 tagtgcgataCTTGTAATGACATttgtaattac nd [APIORCISFBSCS], [BPP], [GEA], [SM] [2], [4]
[RelBE,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RelB-RelE repressor relBp 1645871 1645882 28.0 aattacaagaGGTGTAAGACATgggtagcatt nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal RelB-RelE repressor relBp 1645885 1645897 13.5 tgtaatgacaTTTGTAATTACAAgaggtgtaag nd [APIORCISFBSCS], [BPP], [GEA] [4]
proximal RelB-RelE repressor relBp 1645897 1645908 1.5 tagtgcgataCTTGTAATGACATttgtaattac nd [APIORCISFBSCS], [BPP], [GEA], [SM] [2], [4]
proximal RelB-RelE repressor relBp 1645911 1645922 -13.5 ccctaagcatGTTGTAGTGCGATacttgtaatg nd [APIORCISFBSCS], [BPP], [GEA] [4]


Transcription unit       
Name: relBE
Gene(s): relE, relB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


Transcription unit       
Name: hokD
Gene(s): hokD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [5] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -7.0 1645277 1645304 aggtgacactTCTGCTTTGCGTTGACAGGAGAAGCAGgctatgaagc
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"


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

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

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Bech FW., Jorgensen ST., Diderichsen B., Karlstrom OH., 1985, Sequence of the relB transcription unit from Escherichia coli and identification of the relB gene., EMBO J 4(4):1059-66

 [2] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [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] Li GY., Zhang Y., Inouye M., Ikura M., 2008, Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module., J Mol Biol 380(1):107-19

 [5] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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