|Gene:||prfA||Accession Numbers: EG10761 (EcoCyc), b1211, ECK1199|
Synonyms: ups?, sueB, uar
Release factor 1 (RF1) is one of two class 1 codon-specific factors in E. coli that facilitate the release of the growing polypeptide chain at stop codons. RF1 recognizes the termination codons UAG and UAA [Capecchi67, Scolnick68, Capecchi70, Beaudet70, Martin88]. Termination is highly precise; RF1 is able to discriminate against related sense codons by 3 to 6 orders of magnitude and without requiring energy-driven error correction [Freistroffer00]. The discriminator site consists of a tripeptide which appears to be functionally equivalent to the anticodon of tRNA [Ito00]. An E. coli cell is variously estimated to contain between 500 and 4900 molecules of RF1 and reaches the highest RF1 content at a high growth rate [Klein71, Adamski94].
RF1-mediated termination is sensitive to the codon-anticodon interaction of the wobble base at the last amino acid residue of the peptide chain and the tRNA at the ribosomal P-site [Zhang96a]. Interactions between RF1 and the ribosome have been mapped [Moffat91, Van03a]. The universally conserved tripeptide sequence GGQ is thought to interact with the peptidyl-transferase center of the ribosome and may be functionally equivalent to the CCA end of tRNA [Zavialov02, Mora03].
RF1 is post-translationally modified by N5 methylation by PrmC in vitro, most likely at position Gln235 within the conserved GGQ sequence [Nakahigashi02, HeurgueHamard02]. Methylation is required for normal translation termination activity of RF1 [Mora07]. A crystal structure of the complex between RF1, PrmC, and S-adenosyl-homocysteine, the product of the methyl transfer reaction, has been solved at 3.1 Å resolution [Graille05]. A small-angle X-ray scattering solution structure of RF1 alone shows an open structure, similar to its structure when RF1 is associated with the ribosome [Vestergaard05]. The conserved His197 residue is required for ribosomal A site binding and peptide release [Field10].
Certain mutations in prfA lead to suppression of the UAG and UAA stop codons and are conditionally lethal [Ryden84]. An allele of rpsL suppresses this phenotype, indicating that RF1 and L7/L12 interact [Zhang94]. The N-terminal domain of RF1 is not required for its activity [Mora03a]. Temperature sensitive growth of the prfA1 allele can be suppressed by a lack of the 5-methylaminomethyl-2-thiouridine modification of the wobble base of certain tRNAs [Isak09]. RF1 and the toxin RelE functionally interact; certain prfA mutants display increased sensitivity to RelE [DiagoNavarro09].
Overexpression of RF1 accelerates peptidyl-tRNA turnover from termination-paused ribosomes [Janssen09].
Expression of RF1 increases with the growth rate; the regulation is controlled at the hemA1 promoter [Dahlgren04].
PrfA: "protein release factor A" [Ryden86]
Gene Citations: [Verkamp89]
|Map Position: [1,264,235 -> 1,265,317] (27.25 centisomes, 98°)||Length: 1083 bp / 360 aa|
Molecular Weight of Polypeptide: 40.517 kD (from nucleotide sequence), 44 kD (experimental) [Klein71 ]
Unification Links: ASAP:ABE-0004066 , CGSC:14922 , DIP:DIP-35936N , EchoBASE:EB0754 , EcoGene:EG10761 , EcoliWiki:b1211 , Mint:MINT-1219241 , ModBase:P0A7I0 , OU-Microarray:b1211 , PortEco:prfA , PR:PRO_000023588 , Pride:P0A7I0 , Protein Model Portal:P0A7I0 , RefSeq:NP_415729 , RegulonDB:EG10761 , SMR:P0A7I0 , String:511145.b1211 , Swiss-Model:P0A7I0 , UniProt:P0A7I0
Relationship Links: InterPro:IN-FAMILY:IPR000352 , InterPro:IN-FAMILY:IPR004373 , InterPro:IN-FAMILY:IPR005139 , InterPro:IN-FAMILY:IPR014720 , PDB:Structure:2B3T , Pfam:IN-FAMILY:PF00472 , Pfam:IN-FAMILY:PF03462 , Prosite:IN-FAMILY:PS00745 , Smart:IN-FAMILY:SM00937
In Paralogous Gene Group: 72 (3 members)
|Biological Process:||GO:0006415 - translational termination
[GOA06, GOA01, Ryden84, DiagoNavarro09]
GO:0006412 - translation [UniProtGOA11]
|Molecular Function:||GO:0016149 - translation release factor activity, codon specific
[GOA06, GOA01, Scolnick68, Mora07]
GO:0043022 - ribosome binding [Field10]
GO:0003747 - translation release factor activity [GOA01]
|Cellular Component:||GO:0005829 - cytosol
GO:0005737 - cytoplasm [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]
|MultiFun Terms:||information transfer → protein related → translation|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
|Feature Class||Location||Common Name||Citations||Comment|
|Sequence-Conflict||72 -> 91|
10/20/97 Gene b1211 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10761; confirmed by SwissProt match.
Adamski94: Adamski FM, McCaughan KK, Jorgensen F, Kurland CG, Tate WP (1994). "The concentration of polypeptide chain release factors 1 and 2 at different growth rates of Escherichia coli." J Mol Biol 238(3);302-8. PMID: 8176726
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
Craigen85: Craigen WJ, Cook RG, Tate WP, Caskey CT (1985). "Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2." Proc Natl Acad Sci U S A 82(11);3616-20. PMID: 3889910
DiagoNavarro09: Diago-Navarro E, Mora L, Buckingham RH, Diaz-Orejas R, Lemonnier M (2009). "Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE." Mol Microbiol 71(1);66-78. PMID: 19019162
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
DincbasRenqvist00: Dincbas-Renqvist V, Engstrom A, Mora L, Heurgue-Hamard V, Buckingham R, Ehrenberg M (2000). "A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation." EMBO J 19(24);6900-7. PMID: 11118225
Freistroffer00: Freistroffer DV, Kwiatkowski M, Buckingham RH, Ehrenberg M (2000). "The accuracy of codon recognition by polypeptide release factors." Proc Natl Acad Sci U S A 97(5);2046-51. PMID: 10681447
Graille05: Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH (2005). "Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC." Mol Cell 20(6);917-27. PMID: 16364916
HeurgueHamard02: Heurgue-Hamard V, Champ S, Engstrom A, Ehrenberg M, Buckingham RH (2002). "The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors." EMBO J 21(4);769-78. PMID: 11847124
Isaacs11: Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM (2011). "Precise manipulation of chromosomes in vivo enables genome-wide codon replacement." Science 333(6040);348-53. PMID: 21764749
Isak09: Isak G, Ryden-Aulin M (2009). "Hypomodification of the wobble base in tRNAGlu, tRNALys, and tRNAGln suppresses the temperature-sensitive phenotype caused by mutant release factor 1." J Bacteriol 191(5);1604-9. PMID: 19103926
Johnson11a: Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD, Schmitz RJ, Xiang Z, Ecker JR, Briggs SP, Wang L (2011). "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat Chem Biol 7(11);779-86. PMID: 21926996
Moffat91: Moffat JG, Timms KM, Trotman CN, Tate WP (1991). "Interaction of the release factors with the Escherichia coli ribosome: structurally and functionally-important domains." Biochimie 73(7-8);1113-20. PMID: 1742355
Mora03: Mora L, Heurgue-Hamard V, Champ S, Ehrenberg M, Kisselev LL, Buckingham RH (2003). "The essential role of the invariant GGQ motif in the function and stability in vivo of bacterial release factors RF1 and RF2." Mol Microbiol 47(1);267-75. PMID: 12492870
Mora03a: Mora L, Zavialov A, Ehrenberg M, Buckingham RH (2003). "Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli." Mol Microbiol 50(5);1467-76. PMID: 14651631
Mora07: Mora L, Heurgue-Hamard V, de Zamaroczy M, Kervestin S, Buckingham RH (2007). "Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo." J Biol Chem 282(49);35638-45. PMID: 17932046
Nakahigashi02: Nakahigashi K, Kubo N, Narita S, Shimaoka T, Goto S, Oshima T, Mori H, Maeda M, Wada C, Inokuchi H (2002). "HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination." Proc Natl Acad Sci U S A 99(3);1473-8. PMID: 11805295
Ryden84: Ryden SM, Isaksson LA (1984). "A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors." Mol Gen Genet 193(1);38-45. PMID: 6419024
Strohmaier95: Strohmaier H, Remler P, Renner W, Hogenauer G (1995). "Expression of genes kdsA and kdsB involved in 3-deoxy-D-manno-octulosonic acid metabolism and biosynthesis of enterobacterial lipopolysaccharide is growth phase regulated primarily at the transcriptional level in Escherichia coli K-12." J Bacteriol 177(15);4488-500. PMID: 7543480
Vestergaard05: Vestergaard B, Sanyal S, Roessle M, Mora L, Buckingham RH, Kastrup JS, Gajhede M, Svergun DI, Ehrenberg M (2005). "The SAXS Solution Structure of RF1 Differs from Its Crystal Structure and Is Similar to Its Ribosome Bound Cryo-EM Structure." Mol Cell 20(6);929-38. PMID: 16364917
Zavialov02: Zavialov AV, Mora L, Buckingham RH, Ehrenberg M (2002). "Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3." Mol Cell 10(4);789-98. PMID: 12419223
Zhang94: Zhang S, Ryden-Aulin M, Kirsebom LA, Isaksson LA (1994). "Genetic implication for an interaction between release factor one and ribosomal protein L7/L12 in vivo." J Mol Biol 242(5);614-8. PMID: 7932718
Choi96: Choi P, Wang L, Archer CD, Elliott T (1996). "Transcription of the glutamyl-tRNA reductase (hemA) gene in Salmonella typhimurium and Escherichia coli: role of the hemA P1 promoter and the arcA gene product." J Bacteriol 1996;178(3);638-46. PMID: 8550494
Darie94: Darie S, Gunsalus RP (1994). "Effect of heme and oxygen availability on hemA gene expression in Escherichia coli: role of the fnr, arcA, and himA gene products." J Bacteriol 1994;176(17);5270-6. PMID: 8071201
Melville96: Melville SB, Gunsalus RP (1996). "Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes." Proc Natl Acad Sci U S A 93(3);1226-31. PMID: 8577745
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