title: Molecular phylogeny of sequenced Saccharomycetes reveals polyphyly of the alternative yeast codon usage.
abstract: The universal genetic code defines the translation of nucleotide triplets, called codons, into amino acids. In many Saccharomycetes a unique alteration of this code affects the translation of the CUG codon, which is normally translated as leucine. Most of the species encoding CUG alternatively as serine belong to the Candida genus and were grouped into a so-called CTG clade. However, the "Candida genus" is not a monophyletic group and several Candida species are known to use the standard CUG translation. The codon identity could have been changed in a single branch, the ancestor of the Candida, or to several branches independently leading to a polyphyletic alternative yeast codon usage (AYCU). In order to resolve the monophyly or polyphyly of the AYCU, we performed a phylogenomics analysis of 26 motor and cytoskeletal proteins from 60 sequenced yeast species. By investigating the CUG codon positions with respect to sequence conservation at the respective alignment positions, we were able to unambiguously assign the standard code or AYCU. Quantitative analysis of the highly conserved leucine and serine alignment positions showed that 61.1% and 17% of the CUG codons coding for leucine and serine, respectively, are at highly conserved positions, whereas only 0.6% and 2.3% of the CUG codons, respectively, are at positions conserved in the respective other amino acid. Plotting the codon usage onto the phylogenetic tree revealed the polyphyly of the AYCU with Pachysolen tannophilus and the CTG clade branching independently within a time span of 30–100 Ma.
authors: Stefanie
authors: S
authors: Mühlhausen
authors: Martin
authors: M
authors: Kollmar
mesh_terms: D000595:Amino Acid Sequence; D002175:Candida / Q000235:genetics; D003062:Codon / Q000235:genetics*; D017124:Conserved Sequence; D003598:Cytoskeletal Proteins / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics; D007930:Leucine / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012694:Serine / Q000235:genetics
chemical_list: D003062:Codon; D003598:Cytoskeletal Proteins; D005656:Fungal Proteins; D012694:Serine; D007930:Leucine
references: Curr Protoc Bioinformatics. 2002 Aug;Chapter 2:Unit 2.3
references: 18792934
references: J Clin Microbiol. 2004 Dec;42(12):5624-35
references: 15583292
references: EMBO J. 1995 Jul 3;14(13):3262-7
references: 7621837
references: J Nucleic Acids. 2011;2011:623095
references: 22007289
references: BMC Evol Biol. 2004 Jan 28;4:2
references: 15005799
references: Nat Biotechnol. 2007 Mar;25(3):319-26
references: 17334359
references: BMC Res Notes. 2011 Jul 28;4:265
references: 21798037
references: Genome Res. 2009 Dec;19(12):2231-44
references: 19745113
references: Science. 2001 Aug 10;293(5532):1129-33
references: 11498589
references: Bioinformatics. 2006 Dec 1;22(23):2971-2
references: 17021158
references: J Mol Evol. 2001 Oct-Nov;53(4-5):314-26
references: 11675591
references: IMA Fungus. 2013 Dec;4(2):371-9
references: 24563843
references: Antonie Van Leeuwenhoek. 2011 Jan;99(1):13-23
references: 20838888
references: Genome Biol. 2007;8(9):R196
references: 17877792
references: MBio. 2013 Aug 30;4(4):null
references: 23800396
references: Bioinformatics. 2003 Aug 12;19(12):1572-4
references: 12912839
references: Mycoses. 1999;42 Suppl 1:12-21
references: 10592710
references: Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15386-91
references: 15494441
references: Biochim Biophys Acta. 2004 Jan 28;1660(1-2):171-99
references: 14757233
references: Acta Biochim Pol. 2000;47(2):469-80
references: 11051212
references: BMC Genomics. 2008 Sep 18;9:422
references: 18801164
references: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7329-34
references: 15123810
references: Bioinformatics. 2007 Aug 1;23(15):1875-82
references: 17519246
references: BMC Evol Biol. 2012 Jun 22;12 :95
references: 22726940
references: Nature. 2004 Jul 1;430(6995):35-44
references: 15229592
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W465-7
references: 15980513
references: C R Biol. 2011 Aug-Sep;334(8-9):607-11
references: 21819941
references: New Phytol. 2007;174(3):475-9
references: 17447903
references: Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):11079-84
references: 23776239
references: Nucleic Acids Res. 1993 Aug 25;21(17):4039-45
references: 8371978
references: Genome Res. 2004 Jun;14(6):1188-90
references: 15173120
references: PLoS One. 2007 Oct 03;2(10):e996
references: 17912373
references: BMC Genomics. 2006 Nov 29;7:300
references: 17134497
references: Syst Appl Microbiol. 1999 Feb;22(1):79-86
references: 10188281
references: Genome Biol. 2007;8(10):R206
references: 17916231
references: Protein Eng. 2000 Oct;13(10):735-8
references: 11112513
references: Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13212-7
references: 21788494
references: Bioinformatics. 2011 Apr 15;27(8):1164-5
references: 21335321
references: J Clin Microbiol. 1997 May;35(5):1216-23
references: 9114410
references: Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14091-6
references: 21825144
references: Bioinformatics. 2012 Oct 15;28(20):2689-90
references: 22908216
references: Eukaryot Cell. 2012 Jun;11(6):827
references: 22645232
references: Mycologia. 2006 Nov-Dec;98(6):1006-17
references: 17486976
references: FEMS Yeast Res. 2013 Aug;13(5):423-32
references: 23496865
references: Syst Biol. 2008 Oct;57(5):758-71
references: 18853362
references: BMC Evol Biol. 2006 Nov 22;6:99
references: 17121679
references: Mol Biol Evol. 2006 Feb;23(2):254-67
references: 16221896
references: Syst Biol. 2007 Aug;56(4):564-77
references: 17654362
references: Protein Eng. 2002 Mar;15(3):251-5
references: 11932496
references: Genome Res. 2003 Apr;13(4):544-57
references: 12670996
references: FEMS Yeast Res. 2013 Feb;13(1):23-33
references: 22978764
references: Nature. 2009 Jun 4;459(7247):657-62
references: 19465905