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Escherichia coli K-12 substr. MG1655 Polypeptide: peptide chain release factor RF1



Gene: prfA Accession Numbers: EG10761 (EcoCyc), b1211, ECK1199

Synonyms: ups?, sueB, uar

Regulation Summary Diagram: ?

Summary:
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 [Zhang96c]. Interactions between RF1 and the ribosome have been mapped [Moffat91, Van03]. 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 [Zhang94a]. 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].

While prfA is essential for growth, strains with null mutations in prfA were constructed in certain genetic backgrounds [Mukai10, Johnson11a], or are expected to be viable [Isaacs11].

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]

Reviews: [Craigen87, Kisselev03]

Citations: [Shaw07]

Gene Citations: [Verkamp89]

Locations: cytosol

Map Position: [1,264,235 -> 1,265,317] (27.25 centisomes)
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)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006415 - translational termination Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Ryden84, DiagoNavarro09]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0016149 - translation release factor activity, codon specific Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Scolnick68, Mora07]
GO:0043022 - ribosome binding Inferred from experiment [Field10]
GO:0003747 - translation release factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer protein related translation

Essentiality data for prfA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Last-Curated ? 09-Nov-2011 by Keseler I , SRI International


Sequence Features

Feature Class Location Common Name Citations Comment
Sequence-Conflict 72 -> 91  
[Li89, UniProt10a]
Alternate sequence: PEMREMAQDELREAKEKSEQ → LRYLLYLRLFVVLFRHVVGD; UniProt: (in Ref. 7);
Mutagenesis-Variant 197 H197A
[Field10]
His197 is essential for ribosomal A site binding and peptide release [Field10].
Sequence-Conflict 211  
[Strohmaier95, UniProt10a]
Alternate sequence: D → E; UniProt: (in Ref. 3; AAC43437);
Mutagenesis-Variant 235  
[HeurgueHamard02, UniProt12]
Alternate sequence: Q → A; UniProt: Loss of methylation.
Alternate sequence: Q → E; UniProt: Loss of methylation.
Methylation-Modification 235  
[HeurgueHamard02, DincbasRenqvist00, UniProt12]
UniProt: N5-methylglutamine.
Sequence-Conflict 241  
[Craigen85, UniProt10a]
Alternate sequence: D → G; UniProt: (in Ref. 1; AAA24519);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1211 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10761; confirmed by SwissProt match.


References

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

Beaudet70: Beaudet AL, Caskey CT (1970). "Release factor translation of RNA phage terminator codons." Nature 227(5253);38-40. PMID: 5422622

Capecchi67: Capecchi MR (1967). "Polypeptide chain termination in vitro: isolation of a release factor." Proc Natl Acad Sci U S A 58(3);1144-51. PMID: 5233840

Capecchi70: Capecchi MR, Klein HA (1970). "Release factors mediating termination of complete proteins." Nature 226(5250);1029-33. PMID: 4911223

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

Craigen87: Craigen WJ, Caskey CT (1987). "The function, structure and regulation of E. coli peptide chain release factors." Biochimie 69(10);1031-41. PMID: 3126822

Dahlgren04: Dahlgren A, Ryden-Aulin M (2004). "Effects of two cis-acting mutations on the regulation and expression of release factor one in Escherichia coli." Biochimie 86(7);431-8. PMID: 15308332

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

Field10: Field A, Hetrick B, Mathew M, Joseph S (2010). "Histidine 197 in release factor 1 is essential for a site binding and peptide release." Biochemistry 49(43);9385-90. PMID: 20873815

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Ito00: Ito K, Uno M, Nakamura Y (2000). "A tripeptide 'anticodon' deciphers stop codons in messenger RNA." Nature 403(6770);680-4. PMID: 10688208

Janssen09: Janssen BD, Hayes CS (2009). "Kinetics of paused ribosome recycling in Escherichia coli." J Mol Biol 394(2);251-67. PMID: 19761774

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

Kisselev03: Kisselev L, Ehrenberg M, Frolova L (2003). "Termination of translation: interplay of mRNA, rRNAs and release factors?." EMBO J 22(2);175-82. PMID: 12514123

Klein71: Klein H, Capecchi MR (1971). "Polypetide chain termination. Purification of the release factors, R1 and R2, from Escherichia coli." J Biol Chem 246(4);1055-61. PMID: 5543670

Li89: Li JM, Russell CS, Cosloy SD (1989). "Cloning and structure of the hem A gene of Escherichia coli K-12." Gene 82(2);209-17. PMID: 2684779

Martin88: Martin R, Weiner M, Gallant J (1988). "Effects of release factor context at UAA codons in Escherichia coli." J Bacteriol 170(10);4714-7. PMID: 3049546

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

Mukai10: Mukai T, Hayashi A, Iraha F, Sato A, Ohtake K, Yokoyama S, Sakamoto K (2010). "Codon reassignment in the Escherichia coli genetic code." Nucleic Acids Res 38(22);8188-95. PMID: 20702426

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

Ryden86: Ryden M, Murphy J, Martin R, Isaksson L, Gallant J (1986). "Mapping and complementation studies of the gene for release factor 1." J Bacteriol 168(3);1066-9. PMID: 3782033

Scolnick68: Scolnick E, Tompkins R, Caskey T, Nirenberg M (1968). "Release factors differing in specificity for terminator codons." Proc Natl Acad Sci U S A 61(2);768-74. PMID: 4879404

Shaw07: Shaw JJ, Green R (2007). "Two distinct components of release factor function uncovered by nucleophile partitioning analysis." Mol Cell 28(3);458-67. PMID: 17996709

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Van03: Van Dyke N, Murgola EJ (2003). "Site of functional interaction of release factor 1 with the ribosome." J Mol Biol 330(1);9-13. PMID: 12818198

Verkamp89: Verkamp E, Chelm BK (1989). "Isolation, nucleotide sequence, and preliminary characterization of the Escherichia coli K-12 hemA gene." J Bacteriol 171(9);4728-35. PMID: 2548996

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

Zhang94a: 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

Zhang96c: Zhang S, Ryden-Aulin M, Isaksson LA (1996). "Functional interaction between release factor one and P-site peptidyl-tRNA on the ribosome." J Mol Biol 261(2);98-107. PMID: 8757279

Other References Related to Gene Regulation

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