RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit       
Name: clpB
Gene(s): clpB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The clpB gene is upregulated by short-term (30 min) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Based on ChIP-chip and consensus sequences (Virtual Footprint), a site of NsrR negatively controlling the clpB gene has been identified Partridge JD,2009 However, this site is far from the clpB promoter, at -2674 bp from the TSS.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Kitagawa M., et al., 1991
[2] Squires CL., et al., 1991
Promoter
Name: clpBp2
+1: 2734205
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 32
Sequence: ttttcacattaatctggtcaataaccttgaataattgagggatgacctcatttaatctccAgtagcaactttgatccgtta
                                -35                -10      +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[1] Kitagawa M., et al., 1991
[4] Nonaka G., et al., 2006
[5] Salgado H, et al., 2012
[2] Squires CL., et al., 1991
[6] Wade JT., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ttttccgtctAACTTATAGACAAAAACGAGCCCCGAAGGGCTCGTTTTATCATTTACTGGACGGCgacaatccgg
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001


Transcription unit       
Name: clpB
Gene(s): clpB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The clpB gene is upregulated by short-term (30 min) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Based on ChIP-chip and consensus sequences (Virtual Footprint), a site of NsrR negatively controlling the clpB gene has been identified Partridge JD,2009 However, this site is far from the clpB promoter, at -2674 bp from the TSS.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Kitagawa M., et al., 1991
[2] Squires CL., et al., 1991
Promoter
Name: clpBp
+1: 2734205
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: ttttcacattaatctggtcaataaccttgaataattgagggatgacctcatttaatctccAgtagcaactttgatccgtta
                                -35                       -1+1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[1] Kitagawa M., et al., 1991
[4] Nonaka G., et al., 2006
[5] Salgado H, et al., 2012
[2] Squires CL., et al., 1991
[6] Wade JT., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ttttccgtctAACTTATAGACAAAAACGAGCCCCGAAGGGCTCGTTTTATCATTTACTGGACGGCgacaatccgg
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern

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


Reference(s)    

 [1] Kitagawa M., Wada C., Yoshioka S., Yura T., 1991, Expression of ClpB, an analog of the ATP-dependent protease regulatory subunit in Escherichia coli, is controlled by a heat shock sigma factor (sigma 32)., J Bacteriol 173(14):4247-53

 [2] Squires CL., Pedersen S., Ross BM., Squires C., 1991, ClpB is the Escherichia coli heat shock protein F84.1., J Bacteriol 173(14):4254-62

 [3] 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

 [4] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [5] 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.

 [6] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [7] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [8] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

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