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mRNA interferase toxin RelE



Escherichia coli (strain K12)
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli


Toxic component of a type II toxin-antitoxin (TA) module (PubMed:9767574). A sequence-specific, ribosome-dependent mRNA endoribonuclease that inhibits translation during amino acid starvation (the stringent response). In vitro acts by cleaving mRNA with high codon specificity in the ribosomal A site between positions 2 and 3. The stop codon UAG is cleaved at a fast rate while UAA and UGA are cleaved with intermediate and slow rates. In vitro mRNA cleavage can also occur in the ribosomal E site after peptide release from peptidyl-tRNA in the P site as well as on free 30S subunits (PubMed:12526800). In vivo cuts frequently in the first 100 codons, most frequently after the second and third base and rarely near the stop codon (PubMed:21324908). Overexpression of RelE results in the inhibition of bacterial growth and a sharp decrease in colony-forming ability which is neutralized by the labile cognate antitoxin RelB. Overexpression also sharply increases persisters (cells that neither grow nor die in the presence of bactericidal agents and are largely responsible for high levels of biofilm tolerance to antimicrobials) (PubMed:15576765). mRNA interferases play a role in bacterial persistence to antibiotics; overexpression of this protein induces persisters resistant to ciprofloxacin and ampicillin (PubMed:21788497). Plays a role in dormancy when expressed in high-density cells in the absence of antitoxin RelB; amino acid starvation and an unidentified extracellular factor promote dormancy, while expression of antitoxin RelB restores cell culturability (PubMed:22210768). Acts with RelB as a corepressor of relBE transcription, considerably increasing the repression of RelB alone. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity (PubMed:9767574, PubMed:19747491, PubMed:18501926, PubMed:22981948).15 Publications
Seems to be a principal mediator of cell death in liquid media (PubMed:19707553). Implicated in hydroxy radical-mediated cell death induced by hydroxyurea treatment (PubMed:20005847).2 Publications
Cross-talk can occur between different TA modules. Ectopic expression of this toxin induces transcription of 7 tested TA modules (dinJ/yafQ, hicAB, mazEF, mqsRA, prlF(sohA)/yhaV, relBEF and yefM/yoeB) with specific cleavage of the relBEF mRNA produced immediately upstream and within the relB coding sequence. The cleaved mRNA can be translated into RelE, leading to a positive feedback cycle of RelE expression. The relBEF operon is required for transcription of the mazEF TA module operon during amino acid starvation.1 Publication


There are estimated to be 550-1100 RelB and 50-100 RelE molecules in rapidly growing cells of MG1655; as they have quite high affinity for each other (dissociation constant of 0.33 nM) there is probably less than 1 free RelE molecule per cell. The RelB2-RelE complex has a half-life of over 70 minutes.1 Publication


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei52Proton acceptor1 Publication1
Sitei54Transition state stabilizer1 Publication1
Sitei61Transition state stabilizer1 Publication1
Active sitei81Proton donor1 Publication1

GO - Molecular functioni

  • bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding Source: CollecTF
  • endoribonuclease activity Source: EcoCyc
  • ribosome binding Source: EcoCyc
  • rRNA binding Source: UniProtKB-KW
  • transcription regulatory region sequence-specific DNA binding Source: CollecTF

GO - Biological processi

  • cellular response to amino acid starvation Source: EcoCyc
  • mRNA catabolic process Source: EcoCyc
  • negative regulation of translation Source: EcoCyc
  • response to antibiotic Source: EcoCyc
  • transcription, DNA-templated Source: UniProtKB-KW


Molecular functionEndonuclease, Hydrolase, Nuclease, Repressor, RNA-binding, rRNA-binding, Toxin
Biological processAntibiotic resistance, Stress response, Transcription, Transcription regulation

Enzyme and pathway databases


Names & Taxonomyi

Protein namesi
Recommended name:
mRNA interferase toxin RelE (EC:3.1.-.-)
Alternative name(s):
Endoribonuclease RelE
Toxin RelE
Gene namesi
Ordered Locus Names:b1563, JW1555
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11131. relE.

Subcellular locationi

GO - Cellular componenti

  • protein-DNA complex Source: CollecTF

Pathology & Biotechi

Disruption phenotypei

Cells missing relBE have a higher steady-state level of translation during amino acid starvation than wild-type cells. They survive antibiotic treatment in log phase better than wild-type cells. Cells missing mazE-mazF survive hydroxyurea treatment better than wild-type; further disruption of relE-relB and tonB yields even better survival (PubMed:20005847). mRNA interferases play a role in bacterial persistence to antibiotics; as 10 mRNA interferases are successively deleted reduced levels of persisters are generated (PubMed:21788497).4 Publications


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52K → A: Reduces mRNA cleavage rate constant 2100-fold. Reduces mRNA cleavage rate constant 1000000-fold; when associated with F-87. 1 Publication1
Mutagenesisi54K → A: Reduces mRNA cleavage rate constant 2700-fold. 1 Publication1
Mutagenesisi61R → A: Reduces mRNA cleavage rate constant 2700000-fold. 2 Publications1
Mutagenesisi81 – 83RER → AEA: Significant reduction in endonuclease activity, still binds RelB. 1 Publication3
Mutagenesisi81R → A: Reduces mRNA cleavage rate constant 60000-fold, significantly less translation inhibition which is countered by RelB. Almost complete loss of mRNA cleavage; when associated with F-87. 3 Publications1
Mutagenesisi87Y → A: Reduces mRNA cleavage rate constant 180000-fold. 2 Publications1
Mutagenesisi87Y → F: Reduces mRNA cleavage rate constant 130-fold. Almost complete loss of mRNA cleavage; when associated with A-81 (Ref.20). Reduces mRNA cleavage rate constant 1000000-fold; when associated with A-52 (Ref.18). 2 Publications1
Mutagenesisi90 – 95AVKRIL → VTVTVT: Does not inhibit translation. 1 Publication6

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000972451 – 95mRNA interferase toxin RelEAdd BLAST95

Proteomic databases




By amino acid starvation, by glucose starvation and by chloramphenicol; induction is independent of ppGpp. Autorepressed by RelB, RelE acts as a corepressor (PubMed:9767574, PubMed:19747491, PubMed:18501926, PubMed:22981948). Member of the relBEF operon (PubMed:2990907). Operon induced by ectopic expression of toxins HicA, HipA, MazF, MqsR and itself, but not by YafQ (PubMed:23432955).8 Publications

Gene expression databases



Subunit structurei

Forms an RelB2-RelE2 heterotetramer (PubMed:18501926, PubMed:22981948). Also forms an RelB2-RelE heterotrimer (PubMed:18532983, PubMed:19747491). The RelB2-RelE complex is probably the one that binds DNA and represses transcription, possibly as 2 heterotrimers, 1 bound to each of 2 operators (PubMed:22981948, PubMed:19747491). RelE occupies the A site of the 70S ribosome, making extensive contacts with the 16S rRNA. Its presence blocks access of tRNAs and translation factors. RelB bound to RelE prevents RelE from entering the ribosomal A site and thus inhibits its endonuclease activity (PubMed:19297318).6 Publications

Protein-protein interaction databases

BioGridi4260243. 139 interactors.
IntActiP0C077. 11 interactors.


Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 7Combined sources4
Helixi9 – 17Combined sources9
Helixi20 – 35Combined sources16
Helixi40 – 42Combined sources3
Beta strandi45 – 47Combined sources3
Beta strandi50 – 54Combined sources5
Turni56 – 59Combined sources4
Beta strandi60 – 67Combined sources8
Helixi68 – 70Combined sources3
Beta strandi72 – 80Combined sources9
Helixi82 – 84Combined sources3
Helixi85 – 94Combined sources10

3D structure databases

Select the link destinations:
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum

Miscellaneous databases


Family & Domainsi

Sequence similaritiesi

Belongs to the RelE toxin family.Curated

Phylogenomic databases

eggNOGiENOG4105K4U. Bacteria.
COG2026. LUCA.

Family and domain databases

InterProiView protein in InterPro
IPR035095. RelE-like_dom.
IPR007712. RelE/ParE_toxin.
PfamiView protein in Pfam
PF05016. ParE_toxin. 1 hit.
SUPFAMiSSF143011. SSF143011. 1 hit.
TIGRFAMsiTIGR02385. RelE_StbE. 1 hit.


Sequence statusi: Complete.

P0C077-1 [UniParc]FASTAAdd to basket

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Mass (Da):11,225
Last modified:April 1, 1988 - v1

Sequence databases

Select the link destinations:
Links Updated
X02405 Genomic DNA. Translation: CAA26251.1.
U00096 Genomic DNA. Translation: AAC74636.1.
AP009048 Genomic DNA. Translation: BAA15262.1.
PIRiB22830. QQECR1.
RefSeqiNP_416081.1. NC_000913.3.
WP_000323025.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74636; AAC74636; b1563.
BAA15262; BAA15262; BAA15262.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiRELE_ECOLI
AccessioniPrimary (citable) accession number: P0C077
Secondary accession number(s): P07008
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: July 5, 2017
This is version 99 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program


Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome


  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families