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Escherichia coli K-12 substr. MG1655 Protein: RelB-antitoxin and DNA-binding transcriptional repressor



Gene: relB Accession Numbers: EG10836 (EcoCyc), b1564, ECK1558

Synonyms: RC

Regulation Summary Diagram: ?

Component of: RelB-RelE antitoxin/toxin complex and DNA-binding transcriptional repressor (extended summary available)

Subunit composition of RelB-antitoxin and DNA-binding transcriptional repressor = [RelB]4
         RelB Qin prophage; antitoxin of the RelE-RelB toxin-antitoxin system and DNA binding transcriptional repressor = RelB

Summary:
RelB is the antitoxin of the RelE-RelB toxin-antitoxin system [Gotfredsen98]. RelB also represses transcription of relBEF [Gotfredsen98]. The RelE toxin inhibits protein translation by catalyzing cleavage of mRNA in the A site of the ribosome [Pedersen03]. RelB production relieves established RelE-mediated translation inhibition and inhibition of cell growth, indicating that growth inhibition is not irreversible [Pedersen02]. The activity of tmRNA, SsrA, counteracts RelE-mediated translation inhibition [Pedersen03, Christensen03a].

The RelE-RelB system is involved in regulation of cell growth under conditions with limited nutrients [Mosteller78, Diderichsen80, Christensen01, Pedersen03, Christensen03a]. A Tn10 insertion in ydfV restores colony-forming ability to an rne mutant. The suppression phenotype is reversed by overexpression of relB, but not ydfV [Tamura12].

RelE and RelB exhibit a physical interaction, and RelE physically interacts with ribosomes [Galvani01].

Regulation has been described [Bech85, Christensen01]. When cells are starved of amino acids, Lon protease degrades RelB; RelB degradation derepresses transcription of relBE; RelE accumulates in excess compared with its RelB antitoxin; and this free RelE causes translation inhibition [Christensen01].

Mutations in the relB locus were initially identified by a "delayed relaxed" phenotype [Lavalle65, Diderichsen77].

Review: [Yamaguchi11]

Locations: cytosol

Map Position: [1,643,657 <- 1,643,896] (35.43 centisomes)
Length: 240 bp / 79 aa

Molecular Weight of Polypeptide: 9.071 kD (from nucleotide sequence), 9.0 kD (experimental) [Bech85 ]

Unification Links: ASAP:ABE-0005224 , CGSC:305 , DIP:DIP-48258N , EchoBASE:EB0829 , EcoGene:EG10836 , EcoliWiki:b1564 , OU-Microarray:b1564 , PortEco:relB , PR:PRO_000023711 , Pride:P0C079 , Protein Model Portal:P0C079 , RefSeq:NP_416082 , RegulonDB:EG10836 , SMR:P0C079 , String:511145.b1564 , UniProt:P0C079

Relationship Links: InterPro:IN-FAMILY:IPR007337 , PDB:Structure:2K29 , PDB:Structure:2KC8 , PDB:Structure:4FXE , Pfam:IN-FAMILY:PF04221

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Gotfredsen98]
GO:2000143 - negative regulation of DNA-templated transcription, initiation Inferred from experiment [Gotfredsen98]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Galvani01]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection cell killing
information transfer RNA related RNA degradation
information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation posttranscriptional translation attenuation and efficiency
regulation type of regulation transcriptional level repressor

DNA binding site length: 12 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TTGTAATTACAA, TTGTAATGACAa

Regulated Transcription Units (1 total): ?

Notes:

Essentiality data for relB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Credits:
Created 21-Apr-2011 by Peralta M , UNAM


Subunit of: RelB-RelE antitoxin/toxin complex and DNA-binding transcriptional repressor

Synonyms: RelBE

Subunit composition of RelB-RelE antitoxin/toxin complex and DNA-binding transcriptional repressor = [RelB]4[RelE]4
         RelB Qin prophage; antitoxin of the RelE-RelB toxin-antitoxin system and DNA binding transcriptional repressor = RelB
         Qin prophage; toxin of the RelE-RelB toxin-antitoxin system and cofactor to enhance the repressor activity of RelB = RelE (extended summary available)

Summary:
RelB is a DNA-binding transcriptional regulator which belongs to the ribbon-helix-helix (RHH) family of transcription factors [Anantharaman03a, Cherny07, Li08a] and it is an antitoxin that prevents the lethal action of the toxin [Gotfredsen98]. 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 [Gotfredsen98, Li08a, Galvani01]. On the other hand, relE encodes a cytotoxin that is lethal or inhibitory to host cells [Gotfredsen98], and it also encodes a cofactor that enhances the repressor activity of RelB [Gotfredsen98, Li08a, Galvani01].

The relBE-hokD operon is induced upon entering nutritional starvation conditions, such as the stringent response or acid starvation [Christensen01, Pistolese02], while the level of RelB antitoxin is reduced as a result of Lon-dependent proteolysis. Consequently, RelE toxin is liberated, leading to cell growth arrest and eventually cell death [Grady03]. The expression of the relBE-hokD operon under these conditions may have some as-yet-uncovered beneficial function [Gotfredsen98].

RelB and RelE form a high-affinity complex with a 2:1 stoichiometry when RelB is in excess [Overgaard08, Overgaard09a]. This interaction of RelE with RelB is essential for regulating the expression of the relBE-hokD operon and for neutralizing the toxic activity of RelE [Galvani01]. The ReB2-RelE complex represses transcription of the relBE-hokD operon [Li08a] via strong cooperative binding to the relB promoter region [Gotfredsen98, Overgaard09a]. The 24-bp operator contains a hexad repeat (5'-[A/T]TGT[A/C]A-3') that is repeated twice on each strand [Li08a, Li09, Overgaard09a]. The spacing between each half-site was found to be essential for cooperative interactions [Overgaard09a] between two RelB2-RelE heterotrimers. Only RelB makes contacts to the DNA and the RHH motif of RelB recognizes the four hexad repeats within the bipartite binding site. High affinity for DNA is only achieved in the presence of RelE [Li08a], which stabilizes the tetrameric form of RelB [Li08a].

When RelE is in excess, relBE transcription is stimulated [Overgaard08]. It has been suggested, that excess RelE leads to the formation of a RelE2-RelB2 complex that does not bind to the operator [Overgaard08, Overgaard09a].

RelB possesses a well-folded core domain at its N terminus followed by a flexible region at its C terminus, a pattern typical of other antitoxins [Li08a]. The C terminus is responsible for dimerization of the dimeric core domain in the assembly of the RelB tetramer [Li08a], and the N terminus is responsible for binding to the relB promoter region via its RHH domain [Overgaard08, Li08a].

By using a low-toxicity mutant of RelE, RelER81A/R83A, the protein could be purified for structural studies. RelER81A/R83A exhibits an α/β-sandwich fold. Its C-terminal helix 4 lies next to a conserved positive charged cluster, the putative mRNA-binding site of RelE toxin. In a complex of RelER81A/R83A with a C-terminal peptide of RelB (RelBc), this helix is displaced by helix 3 of RelBc, resulting in the neutralization of the positively charged cluster of RelE [Li09].

The RelB-RelE complex in Pyrococcus horikoshii is heterotetrameric (RelB-RelE)2 [Takagi05], whereas in E. coli a RelB4-RelE4 complex may form a tight association with two adjacent binding sites on the promoter, which could involve either DNA bending or DNA-induced protein conformational change [Li08a].

Several homologs have been identified on the chromosome of E. coli K-12 as well as on those of other organisms, such as Haemophilus influenzae and Vibrio cholerae, and in the E. coli plasmid P307 [Gotfredsen98]. Bacterial relBE systems are conserved in archaea, such as in Methanococcus jannaschii, Archaeoglobus fulgidus, and P. horikoshii OT3 [Gerdes00]. Alignment of the RelB homologs showed that these proteins are considerably more divergent than the RelE homologs [Gotfredsen98].

The sequence alignment of the RelB homologs shows that these proteins are considerably more divergent than the RelE homologs [Gotfredsen98].

Mutations in the relB gene confer a so-called delayed relaxed phenotype upon host cells [Lavalle65, Diderichsen77, Bech85], in which synthesis of stable RNA resumes approximately 10 min after the initiation of amino acid starvation [Gotfredsen98]. These findings provided the first sign that the stringent response system might be connected to the MazEF and RelBE systems through the translation apparatus [Wilson05].

GO Terms:

Biological Process: GO:0006276 - plasmid maintenance Inferred from experiment [Gotfredsen98]

Credits:
Created 03-Apr-2009 by Santos-Zavaleta A , UNAM
Last-Curated ? 03-Apr-2009 by Santos-Zavaleta A , UNAM

DNA binding site length: 12 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (1 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 7
[Li08a, UniProt11]
Alternate sequence: R → A; UniProt: Loss of DNA binding.
Mutagenesis-Variant 39
[Bech85, UniProt11]
Alternate sequence: A → T; UniProt: In relB101; a delayed relaxed phenotype.
Mutagenesis-Variant 45
[Bech85, UniProt11]
Alternate sequence: P → T; UniProt: In relB35; a delayed relaxed phenotype.
Alternate sequence: P → L; UniProt: In relB102; a delayed relaxed phenotype.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1564 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10836; confirmed by SwissProt match.


References

Anantharaman03a: Anantharaman V, Aravind L (2003). "New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system." Genome Biol 4(12);R81. PMID: 14659018

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bech85: 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. PMID: 2990907

Cherny07: Cherny I, Overgaard M, Borch J, Bram Y, Gerdes K, Gazit E (2007). "Structural and thermodynamic characterization of the Escherichia coli RelBE toxin-antitoxin system: indication for a functional role of differential stability." Biochemistry 46(43);12152-63. PMID: 17924660

Christensen01: Christensen SK, Mikkelsen M, Pedersen K, Gerdes K (2001). "RelE, a global inhibitor of translation, is activated during nutritional stress." Proc Natl Acad Sci U S A 98(25);14328-33. PMID: 11717402

Christensen03a: Christensen SK, Gerdes K (2003). "RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA." Mol Microbiol 48(5);1389-400. PMID: 12787364

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Diderichsen77: Diderichsen B, Fiil NP, Lavalle R (1977). "Genetics of the relB locus in Escherichia coli." J Bacteriol 131(1);30-3. PMID: 326765

Diderichsen80: Diderichsen B, Desmarez L (1980). "Variations in phenotype of relB mutants of Escherichia coli and the effect of pus and sup mutations." Mol Gen Genet 180(2);429-37. PMID: 6162075

Galvani01: Galvani C, Terry J, Ishiguro EE (2001). "Purification of the RelB and RelE proteins of Escherichia coli: RelE binds to RelB and to ribosomes." J Bacteriol 183(8);2700-3. PMID: 11274135

Gerdes00: Gerdes K (2000). "Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress." J Bacteriol 182(3);561-72. PMID: 10633087

Gotfredsen98: Gotfredsen M, Gerdes K (1998). "The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family." Mol Microbiol 29(4);1065-76. PMID: 9767574

Grady03: Grady R, Hayes F (2003). "Axe-Txe, a broad-spectrum proteic toxin-antitoxin system specified by a multidrug-resistant, clinical isolate of Enterococcus faecium." Mol Microbiol 47(5);1419-32. PMID: 12603745

Hindermann99: 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. PMID: 10501926

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lavalle65: Lavalle R (1965). "[New mutants for regulation of RNA synthesis]." Bull Soc Chim Biol (Paris) 47(8);1567-70. PMID: 5321960

Li08a: 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. PMID: 18501926

Li09: Li GY, Zhang Y, Inouye M, Ikura M (2009). "Inhibitory mechanism of Escherichia coli RelE-RelB toxin-antitoxin module involves a helix displacement near an mRNA interferase active site." J Biol Chem 284(21);14628-36. PMID: 19297318

Mosteller78: Mosteller RD (1978). "Evidence that glucose starvation-sensitive mutants are altered in the relB locus." J Bacteriol 133(2);1034-7. PMID: 342488

Overgaard08: Overgaard M, Borch J, Jorgensen MG, Gerdes K (2008). "Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity." Mol Microbiol 69(4);841-57. PMID: 18532983

Overgaard09a: Overgaard M, Borch J, Gerdes K (2009). "RelB and RelE of Escherichia coli Form a Tight Complex That Represses Transcription via the Ribbon-Helix-Helix Motif in RelB." J Mol Biol. PMID: 19747491

Pedersen02: Pedersen K, Christensen SK, Gerdes K (2002). "Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins." Mol Microbiol 2002;45(2);501-10. PMID: 12123459

Pedersen03: Pedersen K, Zavialov AV, Pavlov MY, Elf J, Gerdes K, Ehrenberg M (2003). "The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site." Cell 112(1);131-40. PMID: 12526800

Pistolese02: Pistolese GR, Ippoliti A, Mauriello A, Pistolese C, Pocek M, Simonetti G (2002). "Postoperative regression of retroperitoneal fibrosis in patients with inflammatory abdominal aortic aneurysms: evaluation with spiral computed tomography." Ann Vasc Surg 16(2);201-9. PMID: 11972253

Takagi05: Takagi H, Kakuta Y, Okada T, Yao M, Tanaka I, Kimura M (2005). "Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects." Nat Struct Mol Biol 12(4);327-31. PMID: 15768033

Tamura12: Tamura M, Kers JA, Cohen SN (2012). "Second-site suppression of RNase E essentiality by mutation of the deaD RNA helicase in Escherichia coli." J Bacteriol 194(8);1919-26. PMID: 22328678

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wilson05: Wilson DN, Nierhaus KH (2005). "RelBE or not to be." Nat Struct Mol Biol 12(4);282-4. PMID: 15809644

Yamaguchi11: Yamaguchi Y, Park JH, Inouye M (2011). "Toxin-antitoxin systems in bacteria and archaea." Annu Rev Genet 45;61-79. PMID: 22060041


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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