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RelB DNA-binding transcriptional repressor

Synonyms: RelB
RelB is a DNA-binding transcriptional regulator which belongs to the ribbon-helix-helix (RHH) family of transcription factors [3]and it is an antitoxin that prevents the lethal action of the toxin [] RelB is part of the relBE-hokD operon, which specifies a toxin-antitoxin system, and it is autoregulated by its own products, RelB and RelE [3] On the other hand, relE encodes a cytotoxin that is lethal or inhibitory to host cells [] and it also encodes a cofactor that enhances the repressor activity of RelB [3] The relBE-hokD operon is induced upon entering nutritional starvation conditions, such as the stringent response or acid starvation [] while the level of RelB antitoxin is reduced as a result of Lon-dependent proteolysis.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RelB Functional   [APPH] [1]
Evolutionary Family: RelB, RelE
Connectivity class: Local Regulator
Gene name: relB
  Genome position: 1645633-1645872
  Length: 240 bp / 79 aa
Operon name: relBE-hokD
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) hokD, relB, relE
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
RNA degradation (2)
translation attenuation and efficiency (2)
cell killing (2)
prophage genes and phage related functions (1)
Transcription related (1)
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Regulated operon(s) relBE-hokD
First gene in the operon(s) relB
Simple and complex regulons RelB,RelB-RelE
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation    

Transcription factor binding sites (TFBSs) arrangements

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  RelB repressor relBp Sigma70 1.5 -30.5 relB, relE, hokD
1645897 1645908 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [2], [3]
  RelB repressor relBp Sigma70 13.5 -18.5 relB, relE, hokD
1645885 1645897 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3]

Alignment and PSSM for RelB TFBSs    

Aligned TFBS of RelB   

Position weight matrix (PWM). RelB matrix-quality result   
A	0	0	1	3	0	1	4	0	4	3	2	1	1	0	0
C	1	0	2	0	1	0	0	3	0	1	1	0	0	0	3
G	3	2	0	1	0	0	0	1	0	0	1	0	2	2	1
T	0	2	1	0	3	3	0	0	0	0	0	3	1	2	0

;	consensus.strict             	GgcattACAaatggC
;	consensus.strict.rc          	GCCATTTGTAATGCC
;	consensus.IUPAC              	SkcrytASAmvtgkS
;	consensus.IUPAC.rc           	SMCABKTSTARYGMS
;	consensus.regexp             	[CG][gt]c[ag][ct]tA[CG]A[ac][acg]tg[gt][CG]
;	consensus.regexp.rc          	[CG][AC]CA[CGT][GT]T[CG]TA[AG][CT]G[AC][CG]

PWM logo   


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


 [APPH] Assay of protein purified to homogeneity

 [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


 [1] Hindermann W., Mentzel T., Katenkamp D., 1999, [Tyrosine-rich crystalloids in a myoepithelioma of the minor salivary glands in the smooth palate]., Pathologe 20(5):288-91

 [2] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [3] Li GY., Zhang Y., Inouye M., Ikura M., 2008, Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module., J Mol Biol 380(1):107-19

 [4] Bech FW., Jorgensen ST., Diderichsen B., Karlstrom OH., 1985, Sequence of the relB transcription unit from Escherichia coli and identification of the relB gene., EMBO J 4(4):1059-66