Escherichia coli K-12 substr. MG1655 Pathway: queuosine biosynthesis

Pathway diagram: queuosine biosynthesis

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Schematic showing all replicons, marked with selected genes

Genetic Regulation Schematic: ?

Genetic regulation schematic for queuosine biosynthesis

Superclasses: Biosynthesis Nucleosides and Nucleotides Biosynthesis Nucleic Acid Processing

Queuosine is an important 7-deazapurine-modified nucleoside that is present in certain tRNAs in bacteria and most eukaryotes (with the exception of mycoplasmas and yeast). It is not found in the archaea [IwataReuyl03]. Prokaryotes can synthesize queuosine de novo by a complex biosynthetic pathway, whereas eukaryotes are unable to synthesize it, and utilize a salvage system, acquiring the queuine base as a nutrient factor from their diet or from intestinal microflora [Vinayak10].

Queuosine and its derivatives occur exclusively at position 34 (the wobble position) in the anticodons of tRNAs coding for the amino acids L-histidine, L-aspartate, L-asparagine and L-tyrosine [Harada72]. Each of these tRNAs posses the anticodon sequence GUN (positions 34-36), where N can be any nucleotide. Queuosine improves accuracy of translation [Meier85, Urbonavicius01]. These tRNAs of the 'Q-family' originally contain guanine in the first position of anticodon, which is post-transcriptionally modified with queuine by an irreversible insertion during maturation.

Beside the 7-deazaguanosine core, queuosine possesses an additional adaptation - a cyclopentenediol ring attached to an aminomethyl group at position 7. The cyclopentendiol ring can be further modified by glutamylation (see glutamyl-Q tRNAAsp synthetase) [Blaise05].

The first part of the pathway leading to formation of queuosine, up to the intermediate preQ0, is described in the pathway preQ0 biosynthesis.

PreQ0 is a common intermediate, and is also found in the pathways leading to the biosynthesis of several 7-deazapurine antibiotics produced by Streptomyces species. Before it can be inserted into a tRNA, it is converted into preQ1 by the enzyme 7-cyano-7-deazaguanine reductase. This enzyme uses two NADPH molecules to reduce the nitrile group of preQ0 to an amino group [Van05]. The next enzyme, tRNA-guanine transglycosylase, catalyzes a complex reaction in which preQ1 is transferred into a target tRNA molecule, replacing the guanine base with the 7-aminomethyl-7-deazaguanine group at position 34 [Garcia93]. The enzyme recognizes the anticodon region of its substrate, and only acts on tRNAs that contain a GUN sequence [Curnow93].

The next enzyme, S-adenosylmethionine:tRNA ribosyltransferase-isomerase, transfers a ribose moiety from S-adenosyl-L-methionine to the 7-aminomethyl group of preQ1, resulting in the formation of the 2,3-epoxy-4,5-dihydroxycyclopentane ring of epoxyqueuosine and releasing adenine and L-methionine [Slany93, Slany94]. In the last step of the pathway, the eopxy bonds are reduced, generating the final queuosine residue. The reaction is catalyzed by epoxyqueuosine reductase [Miles11].

Review: [El12]

Created 24-Jan-2011 by Caspi R , SRI International
Last-Curated ? 26-Apr-2011 by Keseler I , SRI International


Blaise05: Blaise M, Becker HD, Lapointe J, Cambillau C, Giege R, Kern D (2005). "Glu-Q-tRNA(Asp) synthetase coded by the yadB gene, a new paralog of aminoacyl-tRNA synthetase that glutamylates tRNA(Asp) anticodon." Biochimie 87(9-10);847-61. PMID: 16164993

Curnow93: Curnow AW, Kung FL, Koch KA, Garcia GA (1993). "tRNA-guanine transglycosylase from Escherichia coli: gross tRNA structural requirements for recognition." Biochemistry 32(19);5239-46. PMID: 8494901

El12: El Yacoubi B, Bailly M, de Crecy-Lagard V (2012). "Biosynthesis and function of posttranscriptional modifications of transfer RNAs." Annu Rev Genet 46;69-95. PMID: 22905870

Garcia93: Garcia GA, Koch KA, Chong S (1993). "tRNA-guanine transglycosylase from Escherichia coli. Overexpression, purification and quaternary structure." J Mol Biol 231(2);489-97. PMID: 8323579

Harada72: Harada F, Nishimura S (1972). "Possible anticodon sequences of tRNA His , tRNA Asm , and tRNA Asp from Escherichia coli B. Universal presence of nucleoside Q in the first postion of the anticondons of these transfer ribonucleic acids." Biochemistry 11(2);301-8. PMID: 4550561

IwataReuyl03: Iwata-Reuyl D (2003). "Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA." Bioorg Chem 31(1);24-43. PMID: 12697167

McCarty08: McCarty RM, Bandarian V (2008). "Deciphering deazapurine biosynthesis: pathway for pyrrolopyrimidine nucleosides toyocamycin and sangivamycin." Chem Biol 15(8);790-8. PMID: 18721750

Meier85: Meier F, Suter B, Grosjean H, Keith G, Kubli E (1985). "Queuosine modification of the wobble base in tRNAHis influences 'in vivo' decoding properties." EMBO J 4(3);823-7. PMID: 2988936

Miles11: Miles ZD, McCarty RM, Molnar G, Bandarian V (2011). "Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification." Proc Natl Acad Sci U S A 108(18);7368-72. PMID: 21502530

Slany93: Slany RK, Bosl M, Crain PF, Kersten H (1993). "A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine." Biochemistry 32(30);7811-7. PMID: 8347586

Slany94: Slany RK, Bosl M, Kersten H (1994). "Transfer and isomerization of the ribose moiety of AdoMet during the biosynthesis of queuosine tRNAs, a new unique reaction catalyzed by the QueA protein from Escherichia coli." Biochimie 76(5);389-93. PMID: 7849103

Urbonavicius01: Urbonavicius J, Qian Q, Durand JM, Hagervall TG, Bjork GR (2001). "Improvement of reading frame maintenance is a common function for several tRNA modifications." EMBO J 20(17);4863-73. PMID: 11532950

Van05: Van Lanen SG, Reader JS, Swairjo MA, de Crecy-Lagard V, Lee B, Iwata-Reuyl D (2005). "From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold." Proc Natl Acad Sci U S A 102(12);4264-9. PMID: 15767583

Vinayak10: Vinayak M, Pathak C (2010). "Queuosine modification of tRNA: its divergent role in cellular machinery." Biosci Rep 30(2);135-48. PMID: 19925456

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Chen11a: Chen YC, Brooks AF, Goodenough-Lashua DM, Kittendorf JD, Showalter HD, Garcia GA (2011). "Evolution of eukaryal tRNA-guanine transglycosylase: insight gained from the heterocyclic substrate recognition by the wild-type and mutant human and Escherichia coli tRNA-guanine transglycosylases." Nucleic Acids Res 39(7);2834-44. PMID: 21131277

Chong94: Chong S, Garcia GA (1994). "A versatile and general prokaryotic expression vector, pLACT7." Biotechniques 17(4);686, 688, 690-1. PMID: 7833029

Chong95: Chong S, Curnow AW, Huston TJ, Garcia GA (1995). "tRNA-guanine transglycosylase from Escherichia coli is a zinc metalloprotein. Site-directed mutagenesis studies to identify the zinc ligands." Biochemistry 34(11);3694-701. PMID: 7893665

Curnow94: Curnow AW, Garcia GA (1994). "tRNA-guanine transglycosylase from Escherichia coli: recognition of dimeric, unmodified tRNA(Tyr)." Biochimie 76(12);1183-91. PMID: 7748954

Curnow95: Curnow AW, Garcia GA (1995). "tRNA-guanine transglycosylase from Escherichia coli. Minimal tRNA structure and sequence requirements for recognition." J Biol Chem 270(29);17264-7. PMID: 7615526

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

Dineshkumar02: Dineshkumar TK, Thanedar S, Subbulakshmi C, Varshney U (2002). "An unexpected absence of queuosine modification in the tRNAs of an Escherichia coli B strain." Microbiology 148(Pt 12);3779-87. PMID: 12480882

Eric11: Eric Thomas C, Chen YC, Garcia GA (2011). "Differential heterocyclic substrate recognition by, and pteridine inhibition of E. coli and human tRNA-guanine transglycosylases." Biochem Biophys Res Commun 410(1);34-9. PMID: 21640076

Frey89: Frey B, Janel G, Michelsen U, Kersten H (1989). "Mutations in the Escherichia coli fnr and tgt genes: control of molybdate reductase activity and the cytochrome d complex by fnr." J Bacteriol 171(3);1524-30. PMID: 2537821

Garcia09: Garcia GA, Chervin SM, Kittendorf JD (2009). "Identification of the rate-determining step of tRNA-guanine transglycosylase from Escherichia coli." Biochemistry 48(47);11243-51. PMID: 19874048

Garcia96: Garcia GA, Tierney DL, Chong S, Clark K, Penner-Hahn JE (1996). "X-ray absorption spectroscopy of the zinc site in tRNA-guanine transglycosylase from Escherichia coli." Biochemistry 35(9);3133-9. PMID: 8608154

Garcia97: Garcia GA, Chong S (1997). "Cysteine 265 is in the active site of, but is not essential for catalysis by tRNA-guanine transglycosylase (TGT) from Escherichia coli." J Protein Chem 16(1);11-7. PMID: 9055203

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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."

GoodenoughLashu03: Goodenough-Lashua DM, Garcia GA (2003). "tRNA-guanine transglycosylase from E. coli: a ping-pong kinetic mechanism is consistent with nucleophilic catalysis." Bioorg Chem 31(4);331-44. PMID: 12877882

Hoops95: Hoops GC, Townsend LB, Garcia GA (1995). "tRNA-guanine transglycosylase from Escherichia coli: structure-activity studies investigating the role of the aminomethyl substituent of the heterocyclic substrate PreQ1." Biochemistry 34(46);15381-7. PMID: 7578154

Hoops95a: Hoops GC, Townsend LB, Garcia GA (1995). "Mechanism-based inactivation of tRNA-guanine transglycosylase from Escherichia coli by 2-amino-5-(fluoromethyl)pyrrolo[2,3-d]pyrimidin-4 (3H)-one." Biochemistry 34(47);15539-44. PMID: 7492556

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

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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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