RegulonDB RegulonDB 10.9: Operon Form
   

lptD-surA-pdxA-rsmA-apaGH operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: lptD-surA-pdxA-rsmA-apaGH
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: apaGH
Gene(s): apaH, apaG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Blanchin-Roland S., et al., 1986
Promoter
Name: apaGp
+1: 52034
Distance from start of the gene: 428
Sequence: aacctgccttataacatctccacgccgttgatgttccatctgtttagctatactgatgccAttgccgacatgcactttatg
Evidence: [HIPP]
[IMP]
[RS-EPT-CBR]
Reference(s): [1] Blanchin-Roland S., et al., 1986
[2] Salgado H, et al., 2012


Transcription unit       
Name: rsmA-apaGH
Synonym(s): ksgA-apaGH, rsmA-apaG-apaH
Gene(s): apaH, apaG, rsmA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [3] Roa BB., et al., 1989
Promoter
Name: rsmAp
+1: 52588
Distance from start of the gene: 158
Sequence: aacgccgacgccgtgctggcgatgtaccacgatcagggtcttcccgtgctaaaataccagGgcttcgggcgcggtgtgaac
Evidence: [TIM]
Reference(s): [3] Roa BB., et al., 1989


Transcription unit       
Name: imp
Gene(s): lptD   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: impp1
+1: 57156
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 47
Sequence: gacgctattcggacaggattaacactagcgtagagatgacgagtacgttagtctctgaccGtttgtcacgcgcaacgttac
                         -35                     -10        +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Ohtsu I., et al., 2004
[2] Salgado H, et al., 2012


Transcription unit       
Name: imp
Gene(s): lptD   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: impp2
+1: 57241
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 132
Sequence: cgttttccggctgcggtcaattgtgggacatcgcctataatttgcattatcatacctgtcAttcaatgccgtgcctaacac
                     -35                        -10         +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Ohtsu I., et al., 2004
[2] Salgado H, et al., 2012


Transcription unit       
Name: imp-surA-pdxA
Gene(s): pdxA, surA, lptD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [6] Dartigalongue C., et al., 2001
Promoter
Name: impp3
+1: 57336
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 227
Sequence: ggccacgccaatgatttttccccaatactgcatatattccccaaatcgacacacggatatCagggctatctcccacaatat
                              -35                    -10    +1                   
Note(s): This promoter was identified by Dartigalongue et al. Dartigalongue C,2001, but Ohtsu et al. Ohtsu I,2004 could not detect it, noting that the contribution of this promoter to imp gene expression was very small, if any.
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [6] Dartigalongue C., et al., 2001
[4] Huerta AM., et al., 2003


Transcription unit          
Name: pdxA-rsmA
Synonym(s): pdxA-ksgA
Gene(s): rsmA, pdxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [7] Pease AJ., et al., 2002
Promoter
Name: pdxAp
+1: Unknown
Evidence: [NTAS]
[TASES]
Reference(s): [7] Pease AJ., et al., 2002
[3] Roa BB., et al., 1989
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis activator pdxAp nd nd nd nd nd [BPP], [GEA], [IGI] [7]


Transcription unit       
Name: surA-pdxA-rsmA-apaGH
Synonym(s): surA-pdxA-ksgA-apaGH
Gene(s): apaH, apaG, rsmA, pdxA, surA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PM] Polar mutation
Reference(s): [3] Roa BB., et al., 1989
[8] Tormo A., et al., 1990
Promoter
Name: surAp
+1: Unknown
Sigma Factor: Sigma24 Sigmulon
Evidence: [NTAS]
[TASES]
Reference(s): [7] Pease AJ., et al., 2002
[3] Roa BB., et al., 1989
[8] Tormo A., et al., 1990


Transcription unit          
Name: pdxA-rsmA-apaGH
Synonym(s): pdxA-ksgA-apaG-apaH
Gene(s): apaH, apaG, rsmA, pdxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [7] Pease AJ., et al., 2002
Promoter
Name: pdxAp
+1: Unknown
Evidence: [NTAS]
[TASES]
Reference(s): [7] Pease AJ., et al., 2002
[3] Roa BB., et al., 1989
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fis activator pdxAp nd nd nd nd nd [BPP], [GEA], [IGI] [7]


Evidence    

 [HIPP] Human inference of promoter position

 [IMP] Inferred from mutant phenotype

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

 [TIM] Transcription initiation mapping

 [ICWHO] Inferred computationally without human oversight

 [NTAS] Non-traceable author statement

 [TASES] Traceable author statement to experimental support

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IGI] Inferred from genetic interaction


Reference(s)    

 [1] Blanchin-Roland S., Blanquet S., Schmitter JM., Fayat G., 1986, The gene for Escherichia coli diadenosine tetraphosphatase is located immediately clockwise to folA and forms an operon with ksgA., Mol Gen Genet 205(3):515-22

 [2] 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.

 [3] Roa BB., Connolly DM., Winkler ME., 1989, Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12., J Bacteriol 171(9):4767-77

 [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] Ohtsu I., Kakuda N., Tsukagoshi N., Dokyu N., Takagi H., Wachi M., Aono R., 2004, Transcriptional Analysis of the ostA/imp Gene Involved in Organic Solvent Sensitivity in Escherichia coli., Biosci Biotechnol Biochem 68(2):458-61

 [6] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem 276(24):20866-75

 [7] Pease AJ., Roa BR., Luo W., Winkler ME., 2002, Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12., J Bacteriol 184(5):1359-69

 [8] Tormo A., Almiron M., Kolter R., 1990, surA, an Escherichia coli gene essential for survival in stationary phase., J Bacteriol 172(8):4339-47

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