RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: elaB
Gene(s): elaB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of elaB is induced in the stationary phase when the cells are growing principally in minimal medium rather than LB medium. elaB expression contributes to cell survival under oxidative and heat shock stress conditions. On the other hand, the deletion of elaB increased the formation of persister cells Guo Y,2017
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: elaBp
+1: 2381053
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 26
Sequence: ttgggatggcacgcgaggtaattcaggcgtaatcaacaacccttgtctatagttagtgacAggttttacgcaaatggagaa
                      -35                     -10           +1                   
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[ICA]
[IEP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Guo Y., et al., 2019
[2] Guo Y., et al., 2017
[3] Salgado H, et al., 2012
[4] Zaslaver A., et al., 2006
TF binding sites (TFBSs)
[OxyR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR1 activator elaBp 2381061 2381107 -31.0 cacattgggaTGGCACGCGAGGTAATTCAGGCGTAATCAACAACCCTTGTCTATAGTtagtgacagg nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
[OxyR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR1 repressor elaBp 2381061 2381107 -31.0 cacattgggaTGGCACGCGAGGTAATTCAGGCGTAATCAACAACCCTTGTCTATAGTtagtgacagg nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
Note(s): 1
During the exponential phase and under oxidative stress, elaB expression is induced in an OxyR- and RpoS-dependent way, but during stationary phase, elaB does not need OxyR or RpoS to induce its expression; even OxyR represses the expression of elaB under these growth conditions Guo Y,2019.
In addition to the TFBS located at -31 from the TSS, there is another TFBS located at -358.5 from the TSS of the promoter of elaB that could bind to OxyR. However, it appears not to be important for elaB regulation by OxyR, because when this site is mutated no changes in expression are observed Guo Y,2019
1
During the exponential phase and under oxidative stress, elaB expression is induced in an OxyR- and RpoS-dependent way, but during stationary phase, elaB does not need OxyR or RpoS to induce its expression; even OxyR represses the expression of elaB under these growth conditions Guo Y,2019.
In addition to the TFBS located at -31 from the TSS, there is another TFBS located at -358.5 from the TSS of the promoter of elaB that could bind to OxyR. However, it appears not to be important for elaB regulation by OxyR, because when this site is mutated no changes in expression are observed Guo Y,2019
1
During the exponential phase and under oxidative stress, elaB expression is induced in an OxyR- and RpoS-dependent way, but during stationary phase, elaB does not need OxyR or RpoS to induce its expression; even OxyR represses the expression of elaB under these growth conditions Guo Y,2019.
In addition to the TFBS located at -31 from the TSS, there is another TFBS located at -358.5 from the TSS of the promoter of elaB that could bind to OxyR. However, it appears not to be important for elaB regulation by OxyR, because when this site is mutated no changes in expression are observed Guo Y,2019

2
During the exponential phase and under oxidative stress, elaB expression is induced in an OxyR- and RpoS-dependent way, but during stationary phase, elaB does not need OxyR or RpoS to induce its expression; even OxyR represses the expression of elaB under these growth conditions Guo Y,2019.
In addition to the TFBS located at -31 from the TSS, there is another TFBS located at -358.5 from the TSS of the promoter of elaB that could bind to OxyR. However, it appears not to be important for elaB regulation by OxyR, because when this site is mutated no changes in expression are observed Guo Y,2019


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

 [ICA] Inferred by computational analysis

 [IEP] Inferred from expression pattern

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

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Guo Y., Li Y., Zhan W., Wood TK., Wang X., 2019, Resistance to oxidative stress by inner membrane protein ElaB is regulated by OxyR and RpoS., Microb Biotechnol 12(2):392-404

 [2] Guo Y., Liu X., Li B., Yao J., Wood TK., Wang X., 2017, Tail-Anchored Inner Membrane Protein ElaB Increases Resistance to Stress While Reducing Persistence in Escherichia coli., J Bacteriol 199(9)

 [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] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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