RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit       
Name: bolA
Gene(s): bolA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Aldea M., et al., 1989
Promoter
Name: bolAp2
+1: 454349
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 123
Sequence: ctggtaaaagaaacactgatgcgaggcctgtgtttcaatctttaaatcagtaaacttcatAcgcttgacggaaaaaccagg
                              -35                  -10      +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Aldea M., et al., 1989
[2] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: gattttatgaAAAACGGCCTGCGGGCCGTTTTgttttgtctg
Reference(s): [1] Aldea M., et al., 1989


Transcription unit          
Name: bolA
Gene(s): bolA   Genome Browser M3D Gene expression COLOMBOS
Note(s): bolA gene expression levels are higher in biofilms than in exponential-phase planktonic cells Dong T, Yu R, Schellhorn H,2011 bolA facilitates biofilm development through σS Dong T, Yu R, Schellhorn H,2011
The bolA and rpoS genes are expressed in response to sudden changes in the environment Dong T, Yu R, Schellhorn H,2011
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Aldea M., et al., 1989
[3] Bohannon DE., et al., 1991
Promoter
Name: bolAp1
+1: 454434
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 38
Sequence: aacctaaatatttgttgttaagctgcaatggaaacggtaaaagcggctagtatttaaaggGatggatgacatctcagcgtt
                       -35                      -10         +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [1] Aldea M., et al., 1989
[3] Bohannon DE., et al., 1991
[2] Huerta AM., et al., 2003
[4] Kvint K., et al., 2000
[5] Maciag A., et al., 2011
[6] Nguyen LH., et al., 1997
[7] Salgado H, et al., 2012
[8] Yamamoto K., et al., 2000
Terminator(s)
Type: rho-independent
Sequence: gattttatgaAAAACGGCCTGCGGGCCGTTTTgttttgtctg
Reference(s): [1] Aldea M., et al., 1989
TF binding sites (TFBSs)
[H-NS,-] 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
nd H-NS repressor bolAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [9]
[OmpR,-] 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 OmpR-phosphorylated repressor bolAp1 454377 454396 -47.5 aggacgaaacCTAAATATTTGTTGTTAAGCtgcaatggaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8]


Transcription unit          
Name: bolA
Gene(s): bolA   Genome Browser M3D Gene expression COLOMBOS
Note(s): bolA gene expression levels are higher in biofilms than in exponential-phase planktonic cells Dong T, Yu R, Schellhorn H,2011 bolA facilitates biofilm development through σS Dong T, Yu R, Schellhorn H,2011
The bolA and rpoS genes are expressed in response to sudden changes in the environment Dong T, Yu R, Schellhorn H,2011
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Aldea M., et al., 1989
[3] Bohannon DE., et al., 1991
Promoter
Name: bolAp
+1: 454434
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 38
Sequence: aacctaaatatttgttgttaagctgcaatggaaacggtaaaagcggctagtatttaaaggGatggatgacatctcagcgtt
                       -35                 -10              +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [1] Aldea M., et al., 1989
[3] Bohannon DE., et al., 1991
[2] Huerta AM., et al., 2003
[10] Izutsu K., et al., 2001
[4] Kvint K., et al., 2000
[5] Maciag A., et al., 2011
[6] Nguyen LH., et al., 1997
[7] Salgado H, et al., 2012
[8] Yamamoto K., et al., 2000
Terminator(s)
Type: rho-independent
Sequence: gattttatgaAAAACGGCCTGCGGGCCGTTTTgttttgtctg
Reference(s): [1] Aldea M., et al., 1989
TF binding sites (TFBSs)
[H-NS,-] 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
nd H-NS repressor bolAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [9]
[OmpR,-] 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 OmpR-phosphorylated repressor bolAp 454377 454396 -47.5 aggacgaaacCTAAATATTTGTTGTTAAGCtgcaatggaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation bolAp nd   [EXP-IEP]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] 		[4]
[11]
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [4] Kvint K., et al., 2000
[11] Traxler MF., et al., 2008


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

 [EXP-IEP] Inferred from expression pattern

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

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

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

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


Reference(s)    

 [1] Aldea M., Garrido T., Hernandez-Chico C., Vicente M., Kushner SR., 1989, Induction of a growth-phase-dependent promoter triggers transcription of bolA, an Escherichia coli morphogene., EMBO J 8(12):3923-31

 [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] Bohannon DE., Connell N., Keener J., Tormo A., Espinosa-Urgel M., Zambrano MM., Kolter R., 1991, Stationary-phase-inducible "gearbox" promoters: differential effects of katF mutations and role of sigma 70., J Bacteriol 173(14):4482-92

 [4] Kvint K., Farewell A., Nystrom T., 2000, RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s)., J Biol Chem 275(20):14795-8

 [5] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [6] Nguyen LH., Burgess RR., 1997, Comparative analysis of the interactions of Escherichia coli sigma S and sigma 70 RNA polymerase holoenzyme with the stationary-phase-specific bolAp1 promoter., Biochemistry 36(7):1748-54

 [7] 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.

 [8] Yamamoto K., Nagura R., Tanabe H., Fujita N., Ishihama A., Utsumi R., 2000, Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes., FEMS Microbiol Lett 186(2):257-62

 [9] Barth M., Marschall C., Muffler A., Fischer D., Hengge-Aronis R., 1995, Role for the histone-like protein H-NS in growth phase-dependent and osmotic regulation of sigma S and many sigma S-dependent genes in Escherichia coli., J Bacteriol 177(12):3455-64

 [10] Izutsu K., Wada C., Komine Y., Sako T., Ueguchi C., Nakura S., Wada A., 2001, Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase., J Bacteriol 183(9):2765-73

 [11] Traxler MF., Summers SM., Nguyen HT., Zacharia VM., Hightower GA., Smith JT., Conway T., 2008, The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli., Mol Microbiol 68(5):1128-48

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