RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ilvL
Gene(s): ilvL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Lawther RP., et al., 1980
[2] Lawther RP., et al., 1987
Promoter
Name: ilvLp1
+1: 3950218
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 104
Sequence: aaattgaatttttttcactcactattttatttttaaaaaacaacaatttatattgaaattAttaaacgcatcataaaaatc
                          -35                    -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Adams CW., et al., 1985
[4] Huerta AM., et al., 2003
[2] Lawther RP., et al., 1987
[5] Pagel JM., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: agaaaagacaAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTtttttgacct
Reference(s): [1] Lawther RP., et al., 1980
TF binding sites (TFBSs)
[IHF,-] 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 IHF repressor ilvLp1 3950195 3950207 -17.0 tatttttaaaAAACAACAATTTAtattgaaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]
remote IHF repressor ilvLp1 3950421 3950433 210.0 aaaggcttagAGATCAAGCCTTAacgaactaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-PCR-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6]


Transcription unit          
Name: ilvLXG_1G_2MEDA
Synonym(s): ilvGMEDA, ilvLGGMEDA, ilvLGMEDA, ilvLG_1G_2MEDA
Gene(s): ilvL, ilvX, ilvG, ilvM, ilvE, ilvD, ilvA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ilvLGMEDA operon, which codes for four of the five enzymes required for isoleucine and valine biosynthesis, is primarily regulated by attenuation in response to the abundance of the end products of those pathways Subrahmanyam CS, Noti JD, Umbarger HE,1980. It is also regulated by transcriptional regulators IHF and Lrp.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [7] Driver RP., et al., 1985
[2] Lawther RP., et al., 1987
[8] Parekh BS., et al., 1997
[9] Sameshima JH., et al., 1989
Promoter
Name: ilvLp1
+1: 3950218
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 104
Sequence: aaattgaatttttttcactcactattttatttttaaaaaacaacaatttatattgaaattAttaaacgcatcataaaaatc
                          -35                    -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Adams CW., et al., 1985
[4] Huerta AM., et al., 2003
[2] Lawther RP., et al., 1987
[5] Pagel JM., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: tgcctcaattAGCGGCTCATGTAGCCGCTttttctgcgc
Reference(s): [9] Sameshima JH., et al., 1989
Type: rho-dependent
Sequence: ggttacgcacCGGTTCGGGGCTGTTTTCCAGCACCACTTCCGGCAACAATGCCACGCCACAGCCGAGTGCCAccatcgatac
Reference(s): [9] Sameshima JH., et al., 1989
TF binding sites (TFBSs)
[IHF,-] 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 IHF repressor ilvLp1 3950195 3950207 -17.0 tatttttaaaAAACAACAATTTAtattgaaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]
remote IHF repressor ilvLp1 3950421 3950433 210.0 aaaggcttagAGATCAAGCCTTAacgaactaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-PCR-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6]


Transcription unit          
Name: ilvL
Gene(s): ilvL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Lawther RP., et al., 1980
[2] Lawther RP., et al., 1987
Promoter
Name: ilvLp2
+1: 3950290
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: ataaaaatcggccaaaaaatatcttgtactatttacaaaacctatggtaactctttaggcAttccttcgaacaagatgcaa
                        -35                     -10         +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [4] Huerta AM., et al., 2003
[2] Lawther RP., et al., 1987
[5] Pagel JM., et al., 1991
[10] Parekh BS., et al., 1996
[11] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: agaaaagacaAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTtttttgacct
Reference(s): [1] Lawther RP., et al., 1980
TF binding sites (TFBSs)
[IHF,+] 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 IHF activator ilvLp2 3950195 3950207 -89.0 tatttttaaaAAACAACAATTTAtattgaaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5], [6], [10], [12], [13]
remote IHF activator ilvLp2 3950421 3950433 138.0 aaaggcttagAGATCAAGCCTTAacgaactaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-PCR-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [6], [13]
[Lrp,-] 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
remote Lrp-L-leucine repressor ilvLp2 3950451 3950462 167.5 aagacccccgCACCGAAAGGTCcgggggtttt nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] W [14], [15]
remote Lrp repressor ilvLp2 3950482 3950496 200.0 tttttgacctTAAAAACATAACCGAggagcagaca nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] W [14], [15]
remote Lrp repressor ilvLp2 3950514 3950528 232.0 acaatgaataACAGCACAAAATTCTgtttctcaag nd [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [14], [15]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation ilvLp2 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [16]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [16] Durfee T., et al., 2008


Transcription unit          
Name: ilvLXG_1G_2MEDA
Synonym(s): ilvGMEDA, ilvLGGMEDA, ilvLGMEDA, ilvLG_1G_2MEDA
Gene(s): ilvL, ilvX, ilvG, ilvM, ilvE, ilvD, ilvA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ilvLGMEDA operon, which codes for four of the five enzymes required for isoleucine and valine biosynthesis, is primarily regulated by attenuation in response to the abundance of the end products of those pathways Subrahmanyam CS, Noti JD, Umbarger HE,1980. It is also regulated by transcriptional regulators IHF and Lrp.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [7] Driver RP., et al., 1985
[2] Lawther RP., et al., 1987
[8] Parekh BS., et al., 1997
[9] Sameshima JH., et al., 1989
Promoter
Name: ilvLp2
+1: 3950290
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: ataaaaatcggccaaaaaatatcttgtactatttacaaaacctatggtaactctttaggcAttccttcgaacaagatgcaa
                        -35                     -10         +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [4] Huerta AM., et al., 2003
[2] Lawther RP., et al., 1987
[5] Pagel JM., et al., 1991
[10] Parekh BS., et al., 1996
[11] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tgcctcaattAGCGGCTCATGTAGCCGCTttttctgcgc
Reference(s): [9] Sameshima JH., et al., 1989
Type: rho-dependent
Sequence: ggttacgcacCGGTTCGGGGCTGTTTTCCAGCACCACTTCCGGCAACAATGCCACGCCACAGCCGAGTGCCAccatcgatac
Reference(s): [9] Sameshima JH., et al., 1989
TF binding sites (TFBSs)
[IHF,+] 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 IHF activator ilvLp2 3950195 3950207 -89.0 tatttttaaaAAACAACAATTTAtattgaaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5], [6], [10], [12], [13]
remote IHF activator ilvLp2 3950421 3950433 138.0 aaaggcttagAGATCAAGCCTTAacgaactaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-PCR-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [6], [13]
[Lrp,-] 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
remote Lrp-L-leucine repressor ilvLp2 3950451 3950462 167.5 aagacccccgCACCGAAAGGTCcgggggtttt nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] W [14], [15]
remote Lrp repressor ilvLp2 3950482 3950496 200.0 tttttgacctTAAAAACATAACCGAggagcagaca nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] W [14], [15]
remote Lrp repressor ilvLp2 3950514 3950528 232.0 acaatgaataACAGCACAAAATTCTgtttctcaag nd [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [14], [15]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation ilvLp2 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [16]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [16] Durfee T., et al., 2008


Transcription unit       
Name: ilvEDA
Gene(s): ilvE, ilvD, ilvA   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ilvE . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [17] Calhoun DH., et al., 1985
[7] Driver RP., et al., 1985
[9] Sameshima JH., et al., 1989
Promoter
Name: ilvEp3
+1: 3952388
Distance from start of the gene: 96
Sequence: aaaatataaatatcgaattgaccgttgccagcccacggtcggtcgacttactgtttagtcAgttaaataaactggtggacg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [17] Calhoun DH., et al., 1985
[18] Lisser S., et al., 1993
[11] Salgado H, et al., 2012
[19] Wek RC., et al., 1986
Terminator(s)
Type: rho-independent
Sequence: tgcctcaattAGCGGCTCATGTAGCCGCTttttctgcgc
Reference(s): [9] Sameshima JH., et al., 1989
Type: rho-dependent
Sequence: ggttacgcacCGGTTCGGGGCTGTTTTCCAGCACCACTTCCGGCAACAATGCCACGCCACAGCCGAGTGCCAccatcgatac
Reference(s): [9] Sameshima JH., et al., 1989


Transcription unit       
Name: ilvA
Gene(s): ilvA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [20] Lopes JM., et al., 1989
Promoter
Name: ilvAp
+1: 3955235
Distance from start of the gene: 96
Sequence: ggcgcgtcgtgaagcgcaggacgctcgaggtgacaaagcctggacgccgaaaaatcgtgaAcgtcaggtctcctttgccct
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [20] Lopes JM., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: tgcctcaattAGCGGCTCATGTAGCCGCTttttctgcgc
Reference(s): [9] Sameshima JH., et al., 1989
Type: rho-dependent
Sequence: ggttacgcacCGGTTCGGGGCTGTTTTCCAGCACCACTTCCGGCAACAATGCCACGCCACAGCCGAGTGCCAccatcgatac
Reference(s): [9] Sameshima JH., et al., 1989


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-PCR-MANUAL] ChIP-PCR evidence used in manual assertion

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence


Reference(s)    

 [1] Lawther RP., Hatfield GW., 1980, Multivalent translational control of transcription termination at attenuator of ilvGEDA operon of Escherichia coli K-12., Proc Natl Acad Sci U S A 77(4):1862-6

 [2] Lawther RP., Wek RC., Lopes JM., Pereira R., Taillon BE., Hatfield GW., 1987, The complete nucleotide sequence of the ilvGMEDA operon of Escherichia coli K-12., Nucleic Acids Res 15(5):2137-55

 [3] Adams CW., Rosenberg M., Hatfield GW., 1985, Analysis of in vivo RNA transcription products of the ilvGEDA attenuator region of Escherichia coli K12., J Biol Chem 260(14):8538-44

 [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] Pagel JM., Hatfield GW., 1991, Integration host factor-mediated expression of the ilvGMEDA operon of Escherichia coli., J Biol Chem 266(3):1985-96

 [6] Tsui P., Freundlich M., 1988, Integration host factor binds specifically to sites in the ilvGMEDA operon in Escherichia coli., J Mol Biol 203(3):817-20

 [7] Driver RP., Lawther RP., 1985, Physical analysis of deletion mutations in the ilvGEDA operon of Escherichia coli K-12., J Bacteriol 162(2):598-606

 [8] Parekh BS., Hatfield GW., 1997, Growth rate-related regulation of the ilvGMEDA operon of Escherichia coli K-12 is a consequence of the polar frameshift mutation in the ilvG gene of this strain., J Bacteriol 179(6):2086-8

 [9] Sameshima JH., Wek RC., Hatfield GW., 1989, Overlapping transcription and termination of the convergent ilvA and ilvY genes of Escherichia coli., J Biol Chem 264(2):1224-31

 [10] Parekh BS., Hatfield GW., 1996, Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model., Proc Natl Acad Sci U S A 93(3):1173-7

 [11] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [12] Pagel JM., Winkelman JW., Adams CW., Hatfield GW., 1992, DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli., J Mol Biol 224(4):919-35

 [13] Parekh BS., Sheridan SD., Hatfield GW., 1996, Effects of integration host factor and DNA supercoiling on transcription from the ilvPG promoter of Escherichia coli., J Biol Chem 271(34):20258-64

 [14] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [15] Rhee KY., Parekh BS., Hatfield GW., 1996, Leucine-responsive regulatory protein-DNA interactions in the leader region of the ilvGMEDA operon of Escherichia coli., J Biol Chem 271(43):26499-507

 [16] 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

 [17] Calhoun DH., Wallen JW., Traub L., Gray JE., Kung HF., 1985, Internal promoter in the ilvGEDA transcription unit of Escherichia coli K-12., J Bacteriol 161(1):128-32

 [18] Lisser S., Margalit H., 1993, Compilation of E. coli mRNA promoter sequences., Nucleic Acids Res 21(7):1507-16

 [19] Wek RC., Hatfield GW., 1986, Examination of the internal promoter, PE, in the ilvGMEDA operon of E. coli K-12., Nucleic Acids Res 14(6):2763-77

 [20] Lopes JM., Lawther RP., 1989, Physical identification of an internal promoter, ilvAp, in the distal portion of the ilvGMEDA operon., Gene 76(2):255-69

RegulonDB