RegulonDB RegulonDB 11.1: Operon Form
   

talA-tktB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: talA-tktB
Gene(s): talA, tktB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the operon talA-tktB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Harinarayanan R., et al., 2008
Promoter
Name: talAp2
+1: 2578570
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 96
Sequence: aatgttttggtaataatcctataacactgatgttacctgcttaatccagcaataccatgcCtgtctgctatgcttttttga
                              -35             -10           +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Lacour S., et al., 2004
[4] Maciag A., et al., 2011


Transcription unit       
Name: talA-tktB
Gene(s): talA, tktB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Harinarayanan R., et al., 2008
Promoter
Name: talAp1
+1: 2578588
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 78
Sequence: ctataacactgatgttacctgcttaatccagcaataccatgcctgtctgctatgctttttTgatgcgtttagcgaaatttc
                             -35              -10           +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Lacour S., et al., 2004
[4] Maciag A., et al., 2011


Transcription unit          
Name: talA
Gene(s): talA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: talAp
+1: 2578608
Distance from start of the gene: 58
Sequence: gcttaatccagcaataccatgcctgtctgctatgcttttttgatgcgtttagcgaaatttCtcagaagtgtgaattaacgc
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [5] Mendoza-Vargas A., et al., 2009
TF binding sites (TFBSs)
[CreB,+] 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 CreB-phosphorylated activator talAp 2578388 2578406 -211.5 ttggttgttcCTTTCACGTAACGTTCACAaataaagtgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]


Transcription unit          
Name: tktB
Gene(s): tktB   Genome Browser M3D Gene expression COLOMBOS
Note(s): tktB is positively regulated by ppGpp in RpoS-dependent and -independent modes Harinarayanan R,2008
The expression of tktB is increased by PhoB under acidic growth conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [7] Iida A., et al., 1993
Promoter
Name: tktBp
+1: 2579308
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 328
Sequence: gtggtggaagaagatccgggcgttaaatcggtgcgcaatatctacgactactataagcaaCaccactatgaaaccattgtg
                           -35              -10             +1                   
Note(s): Jung et al. in 2005 found that the tktB gene is positively regulated by RpoS in stationary phase and is mainly controlled at the transcription level Jung IL,2005
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
Reference(s): [2] Huerta AM., et al., 2003
[8] Jung IL., et al., 2005
TF binding sites (TFBSs)
[PhoB,+] 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 PhoB-phosphorylated activator tktBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [9]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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


Reference(s)    

 [1] Harinarayanan R., Murphy H., Cashel M., 2008, Synthetic growth phenotypes of Escherichia coli lacking ppGpp and transketolase A (tktA) are due to ppGpp-mediated transcriptional regulation of tktB., Mol Microbiol 69(4):882-94

 [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] Lacour S., Landini P., 2004, SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences., J Bacteriol 186(21):7186-95

 [4] 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

 [5] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [6] Avison MB., Horton RE., Walsh TR., Bennett PM., 2001, Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media., J Biol Chem 276(29):26955-61

 [7] Iida A., Teshiba S., Mizobuchi K., 1993, Identification and characterization of the tktB gene encoding a second transketolase in Escherichia coli K-12., J Bacteriol 175(17):5375-83

 [8] Jung IL., Phyo KH., Kim IG., 2005, RpoS-mediated growth-dependent expression of the Escherichia coli tkt genes encoding transketolases isoenzymes., Curr Microbiol 50(6):314-8

 [9] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

RegulonDB