RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: cbpAM
Gene(s): cbpM, cbpA   Genome Browser M3D Gene expression COLOMBOS
Note(s): CbpM accumulates in late stationary phase; cbpM may be encoded in an operon together with cbpA
Chae C,2004.

The cbpAM operon is mainly transcribed at the transition from exponential growth to stationary phase by σS and Lrp (in the absence of leucine). The effect of Lrp on this operon could be indirect, since Lrp requires σS to activate the cbpAM operon Chenoweth MR,2008
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Chae C., et al., 2004
Promoter
Name: cbpAp2
+1: 1063828
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 53
Sequence: tttcaataacatattctgtgttggcatatgaaattttgaggattaccctacacttataggAgttaccttacaggggttcct
                                 -35                  -10   +1                   
Note(s): The cbpA gene is transcribed by two promoters: one of them is σ38 dependent and is the most efficient; the other promoter is σ70 dependent Singh SS,2011
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
[4] Singh SS., et al., 2011
[5] Yamashino T., et al., 1994


Transcription unit       
Name: cbpAM
Gene(s): cbpM, cbpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Chae C., et al., 2004
[5] Yamashino T., et al., 1994
Promoter
Name: cbpAp1
+1: 1063833
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 58
Sequence: gatgatttcaataacatattctgtgttggcatatgaaattttgaggattaccctacacttAtaggagttaccttacagggg
                                      -35                  -+1                   
Note(s): The cbpAp1 promoter contains an unusual DNA structure (i.e, DNA curvature) Yamashino T,1994 A mutation in the -18G position, with respect to the transcriptional start site, in this promoter, causes an increasing effect on transcription. The biggest effect is seen when the G at position 18 is replaced by a T Singh SS,2011
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[4] Singh SS., et al., 2011
[5] Yamashino T., et al., 1994


Transcription unit          
Name: cbpA-cbpM
Gene(s): cbpM, cbpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Chae C., et al., 2004
Promoter
Name: cbpAp4
+1: 1063919
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 144
Sequence: tggttcaactatcaaaaatcgctcaccctttttcacctgtttaaaatatgttcagcaaccCatcttgatggcgacctcctc
                         -35                   -10          +1                   
Evidence: [COMP-HINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Chintakayala K., et al., 2013
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor cbpAp4 1063927 1063941 -15.0 tttttcacctGTTTAAAATATGTTCagcaacccat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]


Transcription unit          
Name: cbpA-cbpM
Gene(s): cbpM, cbpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Chae C., et al., 2004
Promoter
Name: cbpAp6
+1: 1064037
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 262
Sequence: ttccaggcctgtttcaaataattatttgcagtgcaactaattccatgtatattactacccAtatatagcgtctataaaatt
                              -35                    -10    +1                   
Evidence: [COMP-HINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Chintakayala K., et al., 2013
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor cbpAp6 1063927 1063941 104.0 tttttcacctGTTTAAAATATGTTCagcaacccat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]


Transcription unit          
Name: cbpA-cbpM
Gene(s): cbpM, cbpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Chae C., et al., 2004
Promoter
Name: cbpAp
+1: 1064037
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 262
Sequence: ttccaggcctgtttcaaataattatttgcagtgcaactaattccatgtatattactacccAtatatagcgtctataaaatt
                              -35                    -10    +1                   
Evidence: [COMP-HINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Chintakayala K., et al., 2013
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor cbpAp 1063927 1063941 104.0 tttttcacctGTTTAAAATATGTTCagcaacccat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA] Inferred from direct assay

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

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

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

 [COMP-HINF] Inferred by a human based on computational evidence

 [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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Chae C., Sharma S., Hoskins JR., Wickner S., 2004, CbpA, a DnaJ homolog, is a DnaK co-chaperone, and its activity is modulated by CbpM., J Biol Chem 279(32):33147-53

 [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] 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.

 [4] Singh SS., Typas A., Hengge R., Grainger DC., 2011, Escherichia coli σâ·â° senses sequence and conformation of the promoter spacer region., Nucleic Acids Res 39(12):5109-18

 [5] Yamashino T., Kakeda M., Ueguchi C., Mizuno T., 1994, An analogue of the DnaJ molecular chaperone whose expression is controlled by sigma s during the stationary phase and phosphate starvation in Escherichia coli., Mol Microbiol 13(3):475-83

 [6] Chintakayala K., Singh SS., Rossiter AE., Shahapure R., Dame RT., Grainger DC., 2013, E. coli Fis protein insulates the cbpA gene from uncontrolled transcription., PLoS Genet 9(1):e1003152

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