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Escherichia coli K-12 substr. MG1655 Protein: MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity



Gene: mazF Accession Numbers: EG11249 (EcoCyc), b2782, ECK2776

Synonyms: chpAK, chpA

Regulation Summary Diagram: ?

Component of: MazE-MazF antitoxin/toxin complex and DNA-binding transcriptional repressor (summary available)

Subunit composition of MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity = [MazF]2
         MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity = MazF

Summary:
MazF is a toxin that is counteracted by the MazE antitoxin [Masuda93, Aizenman96]. MazF exhibits sequence-specific ribonuclease activity toward single- or double-stranded RNA regions [MunozGomez04], and the resulting degradation of cellular mRNA causes global translation inhibition [Zhang03d]. MazF exhibits RNase activity toward tmRNA, and tmRNA is involved in release of MazF-mediated cell growth inhibition [Christensen03a]. MazF also stimulates DNA binding by MazE [Zhang03e].

In complex with MazE, MazF is a negative DNA-binding transcriptional regulator of cell growth. It regulates its own synthesis by negatively controlling the expression of the mazEF operon [Marianovsky01]. MazF belongs to the PemK family.

The MazEF system causes a "programmed cell death" response to stresses including starvation [Aizenman96] and antibiotics [Sat01]. The antitoxin, MazE, is subject to degradation by ClpAP protease complex and exhibits a short (30 minute) half life, whereas the toxin, MazF, is much more stable [Aizenman96]. Overproduction of MazE has no effect in the absence of MazF [Aizenman96].

Published reports disagree about whether MazF causes cell lysis in the absence of MazE [Aizenman96] or whether the toxin causes reversible inhibition of cell growth, inhibiting translation and replication without causing cell inviability [Pedersen02]. The MazE-MazF system mediates the toxicity of guanosine 3',5'-bispyrophosphate (rapid relA induction), which is associated with amino acid deprivation [Aizenman96]; cell death caused by the antibiotics rifampicin, chloramphenicol, and spectinomycin [Sat01]; and the thymineless death (TLD) response to thymine starvation [Sat03].

The structure of the MazE-MazF complex is presented at 1.7 Å resolution [Kamada03]. The complex is hexameric and is comprised of a MazE homodimer sandwiched between MazF homodimers [Kamada03]. It is proposed that the MazE monomer is less stably folded than the homodimer and that dimerization and associated structural changes may have an important role in protein activity [Lah03].

Protein-protein interactions in the MazE-MazF complex are discussed [Kamada03, Zhang03e]. MazE and MazF comigrate during native gel electrophoresis [Aizenman96]. The MazE N terminus may be involved in interaction with MazF [SantosSierra97]. The MazE-DNA interaction has been characterized [Lah03].

Homology and genomic organization of similar antitoxin/toxin systems among bacteria has been reviewed [Mittenhuber99]. MazF has similarity to episomal PemK [Masuda93].

Transcription of mazF is induced by starvation of amino acids [Christensen03a]. Transcription of the mazEF "addiction module" is repressed by high concentrations of guanosine 3',5'-bispyrophosphate (ppGpp), suggesting that amino acid starvation induces lethality via RelA and the MazE-MazF system [Aizenman96]. Thymine deprivation also represses mazEF transcription [Sat03]. An autoinhibitory effect on transcription has been observed and an inversion mechanism also contributes to transcriptional regulation [Marianovsky01]. The lambda RexB protein has an inhibitory effect on ClpP-mediated proteolysis of MazE, increasing survival of lysogenized cells under conditions of amino acid deprivation [EngelbergKulka98].

Reviews: [Mittenhuber99, delaCuevaMendez03, Yamaguchi11]

Gene Citations: [Metzger88, Gross06]

Locations: cytosol

Map Position: [2,908,778 <- 2,909,113] (62.69 centisomes)
Length: 336 bp / 111 aa

Molecular Weight of Polypeptide: 12.098 kD (from nucleotide sequence)

Molecular Weight of Multimer: 12.1 kD (experimental) [Yamaguchi11a]

pI: 8.4 [Yamaguchi11a]

Unification Links: ASAP:ABE-0009119 , CGSC:33287 , DisProt:DP00299 , EchoBASE:EB1229 , EcoGene:EG11249 , EcoliWiki:b2782 , ModBase:P0AE70 , OU-Microarray:b2782 , PortEco:chpA , PR:PRO_000022284 , Protein Model Portal:P0AE70 , RefSeq:NP_417262 , RegulonDB:EG11249 , SMR:P0AE70 , String:511145.b2782 , Swiss-Model:P0AE70 , UniProt:P0AE70

Relationship Links: InterPro:IN-FAMILY:IPR003477 , InterPro:IN-FAMILY:IPR011067 , PDB:Structure:1UB4 , PDB:Structure:3NFC , Pfam:IN-FAMILY:PF02452

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0030308 - negative regulation of cell growth Inferred from experiment [Aizenman96]
GO:0043488 - regulation of mRNA stability Inferred from experiment [Christensen03a]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred from experiment [Christensen03a]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11]
GO:0009372 - quorum sensing Inferred by computational analysis [UniProtGOA11]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004521 - endoribonuclease activity Inferred from experiment [Christensen03a]
GO:0005515 - protein binding Inferred from experiment [Aizenman96]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations other (mechanical, nutritional, oxidative stress)
cell processes adaptations starvation
cell processes defense/survival
cell processes protection cell killing
cell processes protection drug resistance/sensitivity
information transfer protein related translation
information transfer RNA related RNA degradation
regulation type of regulation posttranscriptional translation attenuation and efficiency

Essentiality data for mazF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of: MazE-MazF antitoxin/toxin complex and DNA-binding transcriptional repressor

Synonyms: MazE-MazF "addiction module", MazFE, MazEF

Subunit composition of MazE-MazF antitoxin/toxin complex and DNA-binding transcriptional repressor = [(MazF)2]2[(MazE)2]
         MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity = (MazF)2
                 MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity = MazF
         MazE antitoxin of the MazF-MazE toxin-antitoxin system = (MazE)2
                 MazE antitoxin of the MazF-MazE toxin-antitoxin system = MazE

Summary:
MazF is a toxin that is counteracted by the MazE antitoxin [Aizenman96]. The mazEF system causes a "programmed cell death" response to stresses including starvation [Aizenman96] and antibiotics [Sat01]. The antitoxin, MazE, is subject to degradation by ClpP-ClpA protease complex and exhibits a short (30 minute) half life, whereas the toxin, MazF, is much more stable [Aizenman96].

The structure of the MazE-MazF complex is presented at 1.7 A resolution [Kamada03]. The complex is hexameric and is comprised of a MazE homodimer sandwiched between MazF homodimers [Kamada03].

Review: [delaCuevaMendez03, Yamaguchi11a].

Enzymes inhibited by MazE-MazF antitoxin/toxin complex and DNA-binding transcriptional repressor, sorted by the type of inhibition, are:

Inhibitor (Mechanism unknown) of: nucleoside triphosphate pyrophosphohydrolase [Gross06]

DNA binding site length: 25 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: gTATcTAcAATnnanATTGATATATAC

Regulated Transcription Units (2 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 24
[Li06d, UniProt11]
Alternate sequence: E → A; UniProt: Greatly reduces toxicity, about 10- fold less RNA cleavage activity.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2782 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11249; confirmed by SwissProt match.


References

Aizenman96: Aizenman E, Engelberg-Kulka H, Glaser G (1996). "An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death." Proc Natl Acad Sci U S A 1996;93(12);6059-63. PMID: 8650219

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

Christensen03a: Christensen SK, Pedersen K, Hansen FG, Gerdes K (2003). "Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA." J Mol Biol 332(4);809-19. PMID: 12972253

delaCuevaMendez03: de la Cueva-Mendez G (2003). "Distressing bacteria: structure of a prokaryotic detox program." Mol Cell 11(4);848-50. PMID: 12718870

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

EngelbergKulka98: Engelberg-Kulka H, Reches M, Narasimhan S, Schoulaker-Schwarz R, Klemes Y, Aizenman E, Glaser G (1998). "rexB of bacteriophage lambda is an anti-cell death gene." Proc Natl Acad Sci U S A 1998;95(26);15481-6. PMID: 9860994

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Gross06: Gross M, Marianovsky I, Glaser G (2006). "MazG - a regulator of programmed cell death in Escherichia coli." Mol Microbiol 59(2);590-601. PMID: 16390452

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

Kamada03: Kamada K, Hanaoka F, Burley SK (2003). "Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition." Mol Cell 11(4);875-84. PMID: 12718874

Lah03: Lah J, Marianovsky I, Glaser G, Engelberg-Kulka H, Kinne J, Wyns L, Loris R (2003). "Recognition of the intrinsically flexible addiction antidote MazE by a dromedary single domain antibody fragment. Structure, thermodynamics of binding, stability, and influence on interactions with DNA." J Biol Chem 2003;278(16);14101-11. PMID: 12533537

Li06d: Li GY, Zhang Y, Chan MC, Mal TK, Hoeflich KP, Inouye M, Ikura M (2006). "Characterization of dual substrate binding sites in the homodimeric structure of Escherichia coli mRNA interferase MazF." J Mol Biol 357(1);139-50. PMID: 16413577

Marianovsky01: Marianovsky I, Aizenman E, Engelberg-Kulka H, Glaser G (2001). "The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome." J Biol Chem 2001;276(8);5975-84. PMID: 11071896

Masuda93: Masuda Y, Miyakawa K, Nishimura Y, Ohtsubo E (1993). "chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100." J Bacteriol 1993;175(21);6850-6. PMID: 8226627

Metzger88: Metzger S, Dror IB, Aizenman E, Schreiber G, Toone M, Friesen JD, Cashel M, Glaser G (1988). "The nucleotide sequence and characterization of the relA gene of Escherichia coli." J Biol Chem 1988;263(30);15699-704. PMID: 2844820

Mittenhuber99: Mittenhuber G (1999). "Occurrence of mazEF-like antitoxin/toxin systems in bacteria." J Mol Microbiol Biotechnol 1999;1(2);295-302. PMID: 10943559

MunozGomez04: Munoz-Gomez AJ, Santos-Sierra S, Berzal-Herranz A, Lemonnier M, Diaz-Orejas R (2004). "Insights into the specificity of RNA cleavage by the Escherichia coli MazF toxin." FEBS Lett 567(2-3);316-20. PMID: 15178344

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

SantosSierra97: Santos-Sierra S, Giraldo R, Diaz-Orejas R (1997). "Functional interactions between homologous conditional killer systems of plasmid and chromosomal origin." FEMS Microbiol Lett 1997;152(1);51-6. PMID: 9228770

Sat01: Sat B, Hazan R, Fisher T, Khaner H, Glaser G, Engelberg-Kulka H (2001). "Programmed cell death in Escherichia coli: some antibiotics can trigger mazEF lethality." J Bacteriol 2001;183(6);2041-5. PMID: 11222603

Sat03: Sat B, Reches M, Engelberg-Kulka H (2003). "The Escherichia coli mazEF suicide module mediates thymineless death." J Bacteriol 2003;185(6);1803-7. PMID: 12618443

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."

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

Yamaguchi11a: Yamaguchi Y, Inouye M (2011). "Regulation of growth and death in Escherichia coli by toxin-antitoxin systems." Nat Rev Microbiol 9(11);779-90. PMID: 21927020

Zhang03d: Zhang Y, Zhang J, Hoeflich KP, Ikura M, Qing G, Inouye M (2003). "MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli." Mol Cell 12(4);913-23. PMID: 14580342

Zhang03e: Zhang J, Zhang Y, Inouye M (2003). "Characterization of the interactions within the mazEF addiction module of Escherichia coli." J Biol Chem 278(34);32300-6. PMID: 12810711

Other References Related to Gene Regulation

Goodman12: Goodman C (2012). "Regulation: positively alarming." Nat Chem Biol 8(9);738. PMID: 22907080

KolodkinGal09: Kolodkin-Gal I, Engelberg-Kulka H (2009). "The stationary-phase sigma factor sigma(S) is responsible for the resistance of Escherichia coli stationary-phase cells to mazEF-mediated cell death." J Bacteriol 191(9);3177-82. PMID: 19251848

Lin13: Lin CY, Awano N, Masuda H, Park JH, Inouye M (2013). "Transcriptional Repressor HipB Regulates the Multiple Promoters in Escherichia coli." J Mol Microbiol Biotechnol 23(6);440-447. PMID: 24089053

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Montero09: Montero M, Eydallin G, Viale AM, Almagro G, Munoz FJ, Rahimpour M, Sesma MT, Baroja-Fernandez E, Pozueta-Romero J (2009). "Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes." Biochem J 424(1);129-41. PMID: 19702577

Nakagawa06: Nakagawa A, Oshima T, Mori H (2006). "Identification and characterization of a second, inducible promoter of relA in Escherichia coli." Genes Genet Syst 81(5);299-310. PMID: 17159291

Traxler08: Traxler MF, Summers SM, Nguyen HT, Zacharia VM, Hightower GA, Smith JT, Conway T (2008). "The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli." Mol Microbiol 68(5);1128-48. PMID: 18430135


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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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