RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: ibpB
Gene(s): ibpB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ibpB gene is upregulated by short-term (30 min) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Kuczynska-Wisnik D., et al., 2001
Promoter
Name: ibpBp
+1: 3866981
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 84
Sequence: gcgaaaaaaccgcgccgtatcgaaatcaactaattccctaaggccgcctggcgcggcctgAcatctccatgctcgccgtca
                                          -24          -12  +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[1] Kuczynska-Wisnik D., et al., 2001
TF binding sites (TFBSs)
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator ibpBp 3867006 3867018 -31.0 gccgtatcgaAATCAACTAATTCcctaaggccg nd [AIBSCS] nd


Transcription unit       
Name: ibpAB
Synonym(s): hslTS
Gene(s): ibpB, ibpA   Genome Browser M3D Gene expression COLOMBOS
Note(s): It has a palindromic sequence followed by seven thymine residues downstream from the ibpB coding region. This is typical of rho-independent transcription terminators.
The bicistronic ibpAB transcript is processed by RNAse E, giving rise to monocistronic ibpA (509 nt) and ibpB (584 nt) transcripts, the monocistronic ibpB transcript is further processed to yield short 3' -terminal ibpB fragments. The 5' end of the monocistronic ibpB fragment has been mapped to position 3865032 Gaubig LC,2011.
The mRNA produced by the ibpAB operon has been observed mainly in the poles of the cell during stress conditions Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [3] Allen SP., et al., 1992
[4] Chuang SE., et al., 1993
[5] Kitagawa M., et al., 2000
[1] Kuczynska-Wisnik D., et al., 2001
Promoter
Name: ibpAp
+1: 3867518
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 96
Sequence: tgcaaaaaaaagtccgctgataaggcttgaaaagttcatttccagacccatttttacatcGtagccgatgaggacgcgcct
                           -35                -10           +1                   
Evidence: [AIBSCS]
[AIPP]
[HIPP]
[ICWHO]
[IDA]
[IEP]
[TIM]
Reference(s): [3] Allen SP., et al., 1992
[4] Chuang SE., et al., 1993
[6] Gaubig LC., et al., 2011
[2] Huerta AM., et al., 2003
[1] Kuczynska-Wisnik D., et al., 2001
[7] Nonaka G., et al., 2006
[8] Wade JT., et al., 2006


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIPP] Automated inference of promoter position

 [HIPP] Human inference of promoter position

 [IDA] Inferred from direct assay

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Kuczynska-Wisnik D., Laskowska E., Taylor A., 2001, Transcription of the ibpB heat-shock gene is under control of sigma(32)- and sigma(54)-promoters, a third regulon of heat-shock response., Biochem Biophys Res Commun 284(1):57-64

 [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] Allen SP., Polazzi JO., Gierse JK., Easton AM., 1992, Two novel heat shock genes encoding proteins produced in response to heterologous protein expression in Escherichia coli., J Bacteriol 174(21):6938-47

 [4] Chuang SE., Burland V., Plunkett G., Daniels DL., Blattner FR., 1993, Sequence analysis of four new heat-shock genes constituting the hslTS/ibpAB and hslVU operons in Escherichia coli., Gene 134(1):1-6

 [5] Kitagawa M., Matsumura Y., Tsuchido T., 2000, Small heat shock proteins, IbpA and IbpB, are involved in resistances to heat and superoxide stresses in Escherichia coli., FEMS Microbiol Lett 184(2):165-71

 [6] Gaubig LC., Waldminghaus T., Narberhaus F., 2011, Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon., Microbiology 157(Pt 1):66-76

 [7] 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

 [8] 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

 [9] null, null, null, null


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