title: Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t(6)A), a universal modification of tRNA.
abstract: The tRNA modification field has a rich literature covering biochemical analysis going back more than 40 years, but many of the corresponding genes were only identified in the last decade. In recent years, comparative genomic-driven analysis has allowed for the identification of the genes and subsequent characterization of the enzymes responsible for N6-threonylcarbamoyladenosine (t(6)A). This universal modification, located in the anticodon stem-loop at position 37 adjacent to the anticodon of tRNAs, is found in nearly all tRNAs that decode ANN codons. The t(6)A biosynthesis enzymes and synthesis pathways have now been identified, revealing both a core set of enzymes and kingdom-specific variations. This review focuses on the elucidation of the pathway, diversity of the synthesis genes, and proposes a new nomenclature for t(6)A synthesis enzymes.
authors: a Genetics and Genomics Graduate Program ; University of Florida ; Gainesville , FL USA.
authors: Patrick C
authors: PC
authors: Thiaville
authors: Dirk
authors: D
authors: Iwata-Reuyl
authors: Valérie
authors: V
authors: de Crécy-Lagard
mesh_terms: D000241:Adenosine / Q000031:analogs & derivatives* / Q000096:biosynthesis; D000926:Anticodon / Q000737:chemistry / Q000378:metabolism; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D003062:Codon / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D019622:Haloferax volcanii / Q000235:genetics / Q000378:metabolism; D006801:Humans; D009690:Nucleic Acid Conformation; D012323:RNA Processing, Post-Transcriptional; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D019098:Telomerase / Q000235:genetics / Q000378:metabolism*
chemical_list: D000926:Anticodon; D019843:Archaeal Proteins; D003062:Codon; D029968:Escherichia coli Proteins; C509947:KEOPS complex, S cerevisiae; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; C426646:YrdC protein, E coli; C003268:N(6)-(N-threonylcarbonyl)adenosine; D012343:RNA, Transfer; C509186:TERT protein, human; D019098:Telomerase; D000241:Adenosine
keywords: comparative genomics; modified nucleosides; t6A; tRNA; translation; universal proteins
references: Methods Mol Biol. 2011;718:209-26
references: 21370051
references: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8
references: 21470960
references: J Struct Biol. 2011 Aug;175(2):147-58
references: 21463689
references: BMC Genomics. 2011;12 Suppl 1:S2
references: 21810204
references: Nucleic Acids Res. 2011 Aug;39(14):6148-60
references: 21459853
references: J Clin Invest. 2011 Sep;121(9):3598-608
references: 21841312
references: Endocr J. 2011;58(10):819-25
references: 21908934
references: Angew Chem Int Ed Engl. 2012 Apr 23;51(17):4046-52
references: 22383337
references: J Biol Chem. 2012 Apr 20;287(17):13666-73
references: 22378793
references: PLoS One. 2012;7(8):e43013
references: 22927945
references: Biochemistry. 2012 Nov 6;51(44):8950-63
references: 23072323
references: Annu Rev Genet. 2012;46:69-95
references: 22905870
references: Angew Chem Int Ed Engl. 2012 Dec 7;51(50):12438-43
references: 23161728
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D262-7
references: 23118484
references: Wiley Interdiscip Rev RNA. 2013 Jan-Feb;4(1):35-48
references: 23139145
references: Nat Biotechnol. 1998 Sep;16(9):851-6
references: 9743119
references: J Mol Biol. 1998 Dec 4;284(3):621-31
references: 9826503
references: Biochem J. 2004 Dec 15;384(Pt 3):577-84
references: 15324301
references: Nat Struct Mol Biol. 2004 Dec;11(12):1186-91
references: 15558052
references: Biochemistry. 2005 Jun 7;44(22):8078-89
references: 15924427
references: Mol Biol Cell. 2006 Mar;17(3):1436-50
references: 16407407
references: Cell. 2006 Mar 24;124(6):1155-68
references: 16564010
references: Mol Syst Biol. 2006;2:2006.0008
references: 16738554
references: Nucleic Acids Res. 2006;34(10):2878-86
references: 16738127
references: EMBO J. 2006 Aug 9;25(15):3576-85
references: 16874308
references: Bioinformatics. 2007 Jan 1;23(1):127-8
references: 17050570
references: J Mol Biol. 2007 Feb 9;366(1):1-13
references: 17187822
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D159-62
references: 18957446
references: Nucleic Acids Res. 2009 May;37(9):2894-909
references: 19287007
references: J Bacteriol. 2009 Aug;191(15):4732-49
references: 19376873
references: Biochem J. 2009 Nov 1;423(3):333-41
references: 19694617
references: Nucleic Acids Res. 2009 Sep;37(16):5343-52
references: 19578062
references: Philos Trans R Soc Lond B Biol Sci. 2010 Mar 12;365(1541):749-63
references: 20124342
references: BMC Genomics. 2010;11:470
references: 20701780
references: Genes Dev. 2010 Sep 1;24(17):1832-60
references: 20810645
references: J Biol Chem. 2010 Sep 10;285(37):28425-33
references: 20584901
references: Nucleic Acids Res. 2010 Oct;38(18):6195-205
references: 20472640
references: Archaea. 2010;2010:426239
references: 21234384
references: EMBO J. 2011 Mar 2;30(5):873-81
references: 21183954
references: EMBO J. 2011 Mar 2;30(5):882-93
references: 21285948
references: Nat Chem Biol. 2013 Feb;9(2):105-11
references: 23242255
references: Nucleic Acids Res. 2013 Feb 1;41(3):1953-64
references: 23258706
references: Nucleic Acids Res. 2013 Jul;41(12):6332-46
references: 23620299
references: Nucleic Acids Res. 2013 Nov;41(20):9484-99
references: 23945934
references: Chem Biol. 2014 Feb 20;21(2):174-85
references: 24315934
references: PLoS Genet. 2014 May;10(5):e1004363
references: 24809820
references: Acta Crystallogr F Struct Biol Commun. 2014 Aug;70(Pt 8):1009-14
references: 25084372
references: Nucleic Acids Res. 2014 Aug;42(14):9350-65
references: 25063302
references: Eukaryot Cell. 2014 Sep;13(9):1222-31
references: 25038083
references: J Biol Chem. 2014 Oct 24;289(43):30025-39
references: 25204654
references: Chem Biol Drug Des. 2007 Jun;69(6):395-404
references: 17581233
references: Nature. 2003 Oct 16;425(6959):686-91
references: 14562095
references: Biochemistry. 2000 Nov 7;39(44):13396-404
references: 11063577
references: Protein Sci. 2000 Dec;9(12):2557-66
references: 11206077
references: J Mol Microbiol Biotechnol. 2001 Jul;3(3):483-9
references: 11361082
references: EMBO J. 2001 Sep 3;20(17):4863-73
references: 11532950
references: Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):524-5
references: 11856843
references: J Biol Chem. 2002 May 10;277(19):16391-5
references: 11861649
references: Nature. 2003 Oct 16;425(6959):737-41
references: 14562106
references: Biochemistry. 1969 Aug;8(8):3283-9
references: 4897334
references: Biochem Biophys Res Commun. 1969 Dec 4;37(6):990-5
references: 4902784
references: Biochem Biophys Res Commun. 1972 Jan 31;46(2):831-8
references: 4550699
references: Biochem J. 1972 Apr;127(3):515-9
references: 4561775
references: J Biol Chem. 1972 Oct 25;247(20):6394-401
references: 4561935
references: FEBS Lett. 1974 Mar 1;39(3):301-6
references: 4604806
references: Biochemistry. 1974 Oct 22;13(22):4622-8
references: 4609459
references: Eur J Biochem. 1981 May;116(1):207-13
references: 6788546
references: Nucleic Acids Res. 1985 Feb 25;13(4):1341-5
references: 3889839
references: FEBS Lett. 1986 Jan 1;194(1):131-8
references: 2416594
references: Eur J Biochem. 1987 Jul 15;166(2):325-32
references: 3301339
references: Biochimie. 1991 Dec;73(12):1445-55
references: 1666843
references: RNA. 1998 Jan;4(1):24-37
references: 9436905
references: J Bacteriol. 1998 Apr;180(7):1808-13
references: 9537379