title: Does the genetic code have a eukaryotic origin?
abstract: In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core "house-keeping" functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables-GC and purine contents-of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern-the symmetric pattern-where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors: Zhang
authors: Z
authors: Zhang
authors: Jun
authors: J
authors: Yu
mesh_terms: D000596:Amino Acids / Q000235:genetics*; D001482:Base Composition; D003062:Codon; D004247:DNA / Q000235:genetics; D056890:Eukaryota; D019143:Evolution, Molecular; D005815:Genetic Code; D007438:Introns; D011687:Purines / Q000737:chemistry; D012313:RNA / Q000235:genetics*; D022821:RNA Splice Sites; D012326:RNA Splicing; D014633:Valine / Q000235:genetics
chemical_list: D000596:Amino Acids; D003062:Codon; D011687:Purines; D022821:RNA Splice Sites; D012313:RNA; D004247:DNA; D014633:Valine
references: Genomics Proteomics Bioinformatics. 2007 Feb;5(1):1-6
references: 17572358
references: Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80
references: 20451164
references: Genome Biol. 2011;12(4):R38
references: 21489296
references: Proc Natl Acad Sci U S A. 1981 Jun;78(6):3824-8
references: 6167991
references: Prog Biophys Mol Biol. 1972;24:107-23
references: 4566650
references: BMC Bioinformatics. 2012 Mar 22;13:43
references: 22435713
references: Genomics. 2007 Aug;90(2):186-94
references: 17532183
references: PLoS Genet. 2010 Sep 09;6(9):e1001107
references: 20838593
references: Biochem J. 1981 Oct 1;199(1):31-41
references: 7337711
references: Phys Life Rev. 2010 Sep;7(3):362-76
references: 20558115
references: Nat Genet. 2003 Apr;33(4):514-7
references: 12612582
references: Res Microbiol. 2007 May;158(4):363-70
references: 17449227
references: Adv Enzymol Relat Areas Mol Biol. 1978;47:45-148
references: 364941
references: Genomics Proteomics Bioinformatics. 2011 Apr;9(1-2):21-9
references: 21641559
references: Protein Eng. 1987 Aug-Sep;1(4):289-94
references: 3508279
references: Genomics Proteomics Bioinformatics. 2012 Apr;10(2):55-7
references: 22768979
references: Nature. 1978 Oct 19;275(5681):673-4
references: 703834
references: J Mol Biol. 1988 Apr 5;200(3):513-22
references: 3398047
references: Nucleic Acids Res. 2006 Feb 09;34(3):905-16
references: 16473848
references: Nature. 1979 Feb 8;277(5696):491-2
references: 763335
references: Res Microbiol. 2010 Dec;161(10):838-46
references: 20868744
references: Biol Direct. 2012 Jan 10;7:2
references: 22230424
references: Genomics Proteomics Bioinformatics. 2007 Dec;5(3-4):143-51
references: 18267295
references: J Mol Evol. 1989 Oct;29(4):288-93
references: 2514270
references: Proteins. 1987;2(2):130-52
references: 3447171
references: J Mol Biol. 1983 Dec 25;171(4):479-88
references: 6663622
references: Mol Biol Evol. 2008 Mar;25(3):568-79
references: 18178545
references: BMC Evol Biol. 2009 Mar 11;9:55
references: 19284596
references: Science. 1985 Aug 30;229(4716):834-8
references: 4023714
references: PLoS One. 2011 Mar 17;6(3):e17945
references: 21437290
references: J Mol Biol. 1982 May 5;157(1):105-32
references: 7108955
references: Genomics Proteomics Bioinformatics. 2012 Jun;10(3):123-6
references: 22917184
references: Nat Struct Mol Biol. 2008 Oct;15(10):1007-14
references: 18836497
references: Nucleic Acids Res. 2008 Nov;36(19):6228-36
references: 18829715
references: J Mol Biol. 1968 Dec;38(3):367-79
references: 4887876
references: Anal Biochem. 1982 Jul 15;124(1):201-8
references: 7125223
references: Am J Hum Genet. 2003 Sep;73(3):688-92
references: 12881777
references: Genome Res. 2002 Jun;12(6):851-6
references: 12045139
references: Nucleic Acids Res. 2007;35(16):5593-609
references: 17704131
references: Genome Res. 2002 May;12(5):689-700
references: 11997336
references: Biochem Biophys Res Commun. 2007 Apr 27;356(1):20-5
references: 17336933
references: PLoS One. 2008 Feb 20;3(2):e1622
references: 18286179
references: Trends Biochem Sci. 1999 Jun;24(6):241-7
references: 10366854
references: Biol Direct. 2010 Nov 08;5:63
references: 21059261
references: Biophys J. 1985 Jan;47(1):61-70
references: 3978191
references: Genomics Proteomics Bioinformatics. 2012 Feb;10(1):11-22
references: 22449397
references: Genomics Proteomics Bioinformatics. 2012 Apr;10(2):74-81
references: 22768981
references: FEBS Lett. 2010 Jan 21;584(2):325-33
references: 19944694
references: Biochemistry. 1978 Oct 3;17(20):4277-85
references: 708713
references: Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63
references: 17531802
references: Arch Biochem Biophys. 1974 Apr 2;161(2):665-70
references: 4839053
references: Microbiol Mol Biol Rev. 2003 Dec;67(4):550-73
references: 14665676
references: J Theor Biol. 1968 Nov;21(2):170-201
references: 5700434
references: Biochemistry. 1981 Feb 17;20(4):849-55
references: 7213619
references: J Electron Microsc (Tokyo). 2012;61(6):423-31
references: 23024290
references: Genomics Proteomics Bioinformatics. 2012 Feb;10(1):4-10
references: 22449396
references: Annu Rev Biochem. 2005;74:179-98
references: 15952885
references: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11295-300
references: 9736730
references: PLoS Genet. 2010 Sep 09;6(9):e1001115
references: 20838599
references: Genomics Proteomics Bioinformatics. 2012 Aug;10(4):186-96
references: 23084774
references: Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81
references: 17127215
references: J Theor Biol. 1975 Mar;50(1):167-83
references: 1127956
references: Science. 1974 Sep 6;185(4154):862-4
references: 4843792
references: J Mol Biol. 1984 Oct 15;179(1):125-42
references: 6502707
references: Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36
references: 10704480
references: Genome Biol Evol. 2012;4(1):24-7
references: 22113795
references: PLoS One. 2010 Apr 12;5(4):e10144
references: 20419085
references: Biochimie. 2007 Oct;89(10):1276-88
references: 17889982
references: Biol Direct. 2012 Jun 11;7:13
references: 22515485
references: DNA Res. 2012 Jun;19(3):245-58
references: 22378766
references: Genomics Proteomics Bioinformatics. 2012 Aug;10(4):175-80
references: 23084772
references: Genomics Proteomics Bioinformatics. 2006 Nov;4(4):203-11
references: 17531796
references: Genome Res. 2002 Aug;12(8):1185-9
references: 12176926
references: Genomics Proteomics Bioinformatics. 2010 Jun;8(2):92-102
references: 20691394
references: Genomics Proteomics Bioinformatics. 2010 Dec;8(4):211-28
references: 21382590
references: Proc Natl Acad Sci U S A. 1980 Feb;77(2):1083-6
references: 6928661