title: Convergent evolution of AUA decoding in bacteria and archaea.
abstract: Deciphering AUA codons is a difficult task for organisms, because AUA and AUG specify isoleucine (Ile) and methionine (Met), separately. Each of the other purine-ending sense co-don sets (NNR) specifies a single amino acid in the universal genetic code. In bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, are found at the first letter of the anticodon of tRNA(Ile) responsible for AUA codons. These modifications prevent base pairing with G of the third letter of AUG codon, and enable tRNA(Ile) to decipher AUA codon specifically. In addition, these modifications confer a charging ability of tRNA(Ile) with Ile. Despite their similar chemical structures, L and agm(2)C are synthesized by distinctive mechanisms and catalyzed by different classes of enzymes, implying that the analogous decoding systems for AUA codons were established by convergent evolution after the phylogenic split between bacteria and archaea-eukaryotes lineages following divergence from the last universal common ancestor (LUCA).
authors: a Department of Chemistry and Biotechnology; Graduate School of Engineering ; University of Tokyo ; Hongo , Bunkyo-ku , Tokyo , Japan.
authors: Tsutomu
authors: T
authors: Suzuki
authors: Tomoyuki
authors: T
authors: Numata
mesh_terms: D000926:Anticodon / Q000737:chemistry / Q000378:metabolism*; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D003062:Codon / Q000737:chemistry / Q000378:metabolism*; D003562:Cytidine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D005815:Genetic Code; D007532:Isoleucine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008239:Lysine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008715:Methionine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D010802:Phylogeny; D014176:Protein Biosynthesis; D011741:Pyrimidine Nucleosides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism
chemical_list: D000926:Anticodon; D003062:Codon; D011741:Pyrimidine Nucleosides; C548874:agmatidine; D007532:Isoleucine; D003562:Cytidine; D012343:RNA, Transfer; C101421:lysidine; D008715:Methionine; D008239:Lysine
references: Science. 2010 Nov 5;330(6005):835-8
references: 21051640
references: Science. 2001 May 4;292(5518):897-902
references: 11340196
references: Mol Cell. 2005 Jul 22;19(2):235-46
references: 16039592
references: Science. 2009 Oct 30;326(5953):688-94
references: 19833920
references: Mol Cell. 2003 Sep;12(3):689-98
references: 14527414
references: RNA. 2008 Jan;14(1):117-26
references: 17998287
references: Proc Natl Acad Sci U S A. 2005 May 24;102(21):7487-92
references: 15894617
references: FEMS Microbiol Lett. 2008 Oct;287(1):113-20
references: 18702616
references: Cell. 2002 Nov 27;111(5):721-32
references: 12464183
references: Nat Struct Biol. 1996 Jan;3(1):74-86
references: 8548458
references: Microbiol Rev. 1985 Mar;49(1):81-99
references: 3157043
references: J Biol Chem. 1984 Aug 10;259(15):9461-71
references: 6746655
references: Nat Chem Biol. 2010 Apr;6(4):277-82
references: 20139989
references: J Biol Chem. 1988 Jul 5;263(19):9261-7
references: 3132458
references: Nat Struct Mol Biol. 2011 Apr;18(4):432-6
references: 21378964
references: Nature. 2009 Oct 22;461(7267):1144-8
references: 19847269
references: Biochem J. 2005 Jun 1;388(Pt 2):427-33
references: 15673283
references: Amino Acids. 2008 Jan;34(1):35-45
references: 17356805
references: J Mol Biol. 1966 Aug;19(2):548-55
references: 5969078
references: Archaea. 2010;2010:426239
references: 21234384
references: Front Genet. 2014 May 01;5:114
references: 24822057
references: Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2872-7
references: 20133752
references: Structure. 2007 Dec;15(12):1642-53
references: 18073113
references: Proc Jpn Acad Ser B Phys Biol Sci. 2010;86(1):11-39
references: 20075606
references: J Bacteriol. 1991 May;173(10):3138-48
references: 1708763
references: Nature. 1988 Nov 10;336(6195):179-81
references: 3054566
references: Nucleic Acids Res. 2013 Feb 1;41(4):2621-31
references: 23295668
references: Nat Struct Mol Biol. 2011 Nov;18(11):1268-74
references: 22002222
references: Nucleic Acids Res. 2014 Feb;42(3):1904-15
references: 24194599
references: Nature. 2006 Jul 27;442(7101):419-24
references: 16871210
references: FEBS Lett. 2010 Jan 21;584(2):272-7
references: 19944692
references: Mol Microbiol. 2011 May;80(4):1062-74
references: 21435031
references: Nat Struct Mol Biol. 2011 Nov;18(11):1275-80
references: 22002223
references: Nat Struct Mol Biol. 2013 May;20(5):641-3
references: 23542153
references: Biochemistry. 2003 Feb 4;42(4):1109-17
references: 12549933
references: FEBS Lett. 2014 Aug 1;588(15):2464-9
references: 24950426
references: Proteins. 1994 Dec;20(4):347-55
references: 7731953
references: Nat Struct Mol Biol. 2006 Feb;13(2):153-9
references: 16415880