RegulonDB RegulonDB 10.9: Operon Form
   

ivbL-ilvBN-uhpABC operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ivbL-ilvBN-uhpABC
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: uhpB
Gene(s): uhpB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [1] Li Z., et al., 2019
Promoter
Name: uhpBp
+1: 3850294
Distance from start of the gene: 158
Sequence: gatattgccattaaactggcatccggtcgtcaggacccgctaaccaaacgtgaacgccagGtggcggaaaaactggcgcaa
Evidence: [RSE]
[TIM]
Reference(s): [1] Li Z., et al., 2019


Transcription unit          
Name: ivbL-ilvBN
Synonym(s): OP00040, ilvB, ilvBN, w3608-ilvBN
Gene(s): ilvN, ilvB, ivbL   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ilvLBN operon, which codes for one of the enzymes involved in isoleucine
and valine biosynthesis, is thought to be subject to transcriptional regulation by two mechanisms.
The primary mechanism appears to be attenuation mediated by valine and leucine availability.
This mode of regulation is presumed to exist based on the presence of the ivbL leader
region and the folllowing terminator. Transcription is also positively regulated
by the binding of CRP at the promoter, modulated by the abundance of alarmone and ppGpp
Friden P,1982. Friden P,1984.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITCR] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [2] Friden P., et al., 1985
[3] Tsui P., et al., 1990
Promoter
Name: ivbLp
+1: 3853023
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: cctcaattttcccttgctgaaaaattttccattgtctcccctgtaaagctgtgcttgtatAaatattgttaaacacaaaac
                  -35                        -10            +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [4] Friden P., et al., 1982
[5] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: ctggcgggtaAAAAAAATACGCGCTTACCTTAACGATAAGCGCGatgttgttca
TF binding sites (TFBSs)
[CRP,+] Phrase
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 ivbLp 3853076 3853097 -64.0 aattcagtacAAAACGTGATCAACCCCTCAATTttcccttgct nd [APIORCISFBSCS], [BPP] [4]
Note(s): 1An interesting characteristic of the regulation of the ilvLBN operon is that even though CRP can activate it,
attenuation can trump any activation by CRP and absolutely stop ilvLBN transcription Friden P,1984.
1An interesting characteristic of the regulation of the ilvLBN operon is that even though CRP can activate it,
attenuation can trump any activation by CRP and absolutely stop ilvLBN transcription Friden P,1984.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation ivbLp nd   [GEA] [6]
Evidence: [GEA] Gene expression analysis
Reference(s): [6] Durfee T., et al., 2008


Transcription unit          
Name: ivbL
Gene(s): ivbL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [4] Friden P., et al., 1982
[7] Hauser CA., et al., 1985
Promoter
Name: ivbLp
+1: 3853023
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: cctcaattttcccttgctgaaaaattttccattgtctcccctgtaaagctgtgcttgtatAaatattgttaaacacaaaac
                  -35                        -10            +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [4] Friden P., et al., 1982
[5] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: cttaaacgaaAAACCCCGCCCGGTTTGCGCCGGCGGGGTTTTGGAATCGTGTGTTGTTCCAGTCCCTACGGCGCATTGCCGACGACCACCACCACACGCACGACGACCACTGCGGCGGATGGCGCAGTTGGTAGTAGTTTTGCGTTGAGCATGGAAGTagtcattggg
Reference(s): [7] Hauser CA., et al., 1985
TF binding sites (TFBSs)
[CRP,+] Phrase
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 ivbLp 3853076 3853097 -64.0 aattcagtacAAAACGTGATCAACCCCTCAATTttcccttgct nd [APIORCISFBSCS], [BPP] [4]
Note(s): 1An interesting characteristic of the regulation of the ilvLBN operon is that even though CRP can activate it,
attenuation can trump any activation by CRP and absolutely stop ilvLBN transcription Friden P,1984.
1An interesting characteristic of the regulation of the ilvLBN operon is that even though CRP can activate it,
attenuation can trump any activation by CRP and absolutely stop ilvLBN transcription Friden P,1984.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation ivbLp nd   [GEA] [6]
Evidence: [GEA] Gene expression analysis
Reference(s): [6] Durfee T., et al., 2008


Transcription unit       
Name: ivbL-ilvBN-uhpABC
Gene(s): uhpC, uhpB, uhpA, ilvN, ilvB, ivbL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [8] Park JH., et al., 2007


Transcription unit       
Name: uhpABC
Gene(s): uhpC, uhpB, uhpA   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [9] Merkel TJ., et al., 1992
[10] Weston LA., et al., 1987
[11] Weston LA., et al., 1988


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.4 3850744 3850779 tgaacaacatCGCGCTTATCGTTAAGGTAAGCGCGTATTTTTTTTacccgccagg
  terminator -16.6 3852832 3852862 gattccaaaaCCCCGCCGGCGCAAACCGGGCGGGGTTTTTcgtttaagca
  terminator -12.4 3853115 3853142 gcgactgacgAAACCTCGCTCCGGCGGGGTTTTTTGTtatctgcaat
  anti-terminator -21.2 3850769 3850844 gtaatcagtcCGATCCGACGATGTTTAACAAGATCGCGGTGTTTTTTCAGTAACCGCTCAAGGCTTGAACAACATCGCGCTTATCgttaaggtaa
  anti-terminator -21.5 3852850 3852899 tcgtcggcaaTGCGCCGTAGGGACTGGAACAACACACGATTCCAAAACCCCGCCGGCGCaaaccgggcg
  anti-terminator -18.25 3853133 3853195 gtatactttcAGTGTTGACATAATACAGTGTGCTTTGCGGTTACCAGCCGCAGGCGACTGACGAAACCTCGCtccggcgggg
  anti-anti-terminator -12.4 3852885 3852932 ccgccgcagtGGTCGTCGTGCGTGTGGTGGTGGTCGTCGGCAATGCGCCGTAGGGACtggaacaaca
  anti-anti-terminator -12.4 3853166 3853218 attgcgcgttCTGCGCGGAACACGTATACTTTCAGTGTTGACATAATACAGTGTGCTTTGCGgttaccagcc
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    

 [RSE] RNA-seq evidence

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

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

 [BPP] Binding of purified proteins


Reference(s)    

 [1] 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

 [2] Friden P., Donegan J., Mullen J., Tsui P., Freundlich M., Eoyang L., Weber R., Silverman PM., 1985, The ilvB locus of Escherichia coli K-12 is an operon encoding both subunits of acetohydroxyacid synthase I., Nucleic Acids Res 13(11):3979-93

 [3] Tsui P., Freundlich M., 1990, Integration host factor bends the DNA in the Escherichia coli ilvBN promoter region., Mol Gen Genet 223(2):349-52

 [4] Friden P., Newman T., Freundlich M., 1982, Nucleotide sequence of the ilvB promoter-regulatory region: a biosynthetic operon controlled by attenuation and cyclic AMP., Proc Natl Acad Sci U S A 79(20):6156-60

 [5] 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

 [6] Durfee T., Hansen AM., Zhi H., Blattner FR., Jin DJ., 2008, Transcription profiling of the stringent response in Escherichia coli., J Bacteriol 190(3):1084-96

 [7] Hauser CA., Sharp JA., Hatfield LK., Hatfield GW., 1985, Pausing of RNA polymerase during in vitro transcription through the ilvB and ilvGEDA attenuator regions of Escherichia coli K12., J Biol Chem 260(3):1765-70

 [8] Park JH., Lee KH., Kim TY., Lee SY., 2007, Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation., Proc Natl Acad Sci U S A 104(19):7797-802

 [9] Merkel TJ., Nelson DM., Brauer CL., Kadner RJ., 1992, Promoter elements required for positive control of transcription of the Escherichia coli uhpT gene., J Bacteriol 174(9):2763-70

 [10] Weston LA., Kadner RJ., 1987, Identification of uhp polypeptides and evidence for their role in exogenous induction of the sugar phosphate transport system of Escherichia coli K-12., J Bacteriol 169(8):3546-55

 [11] Weston LA., Kadner RJ., 1988, Role of uhp genes in expression of the Escherichia coli sugar-phosphate transport system., J Bacteriol 170(8):3375-83

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