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Nucleic Acids Res. Jan 11, 1980; 8(1): r49–r62.
PMCID: PMC327256

Codon catalog usage and the genome hypothesis.

Abstract

Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis.

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Selected References

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  • Grantham R. Viral, prokaryote and eukaryote genes contrasted by mRNA sequence indexes. FEBS Lett. 1978 Nov 1;95(1):1–11. [PubMed]
  • Garel JP. Functional adaptation of tRNA population. J Theor Biol. 1974 Jan;43(1):211–225. [PubMed]
  • Osterman LA. Participation of tRNA in regulation of protein biosynthesis at the translational level in eukaryotes. Biochimie. 1979;61(3):323–342. [PubMed]
  • Fiers W, Contreras R, Duerinck F, Haegmean G, Merregaert J, Jou WM, Raeymakers A, Volckaert G, Ysebaert M, Van de Kerckhove J, et al. A-protein gene of bacteriophage MS2. Nature. 1975 Jul 24;256(5515):273–278. [PubMed]
  • Min Jou W, Haegeman G, Ysebaert M, Fiers W. Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature. 1972 May 12;237(5350):82–88. [PubMed]
  • Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, et al. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature. 1976 Apr 8;260(5551):500–507. [PubMed]
  • Escarmis C, Sastry PA, Billeter MA. Determination of the first half of the coat protein cistron of bacteriophage Qbeta as an application of a mapping procedure for RNA fragments. J Biol Chem. 1978 Dec 10;253(23):8390–8399. [PubMed]
  • Jonard G, Richards K, Mohier E, Gerlinger P. Nucleotide sequence at the 5' extremity of tobacco-mosaic-virus RNA. 2. The coding region (nucleotides 69-236). Eur J Biochem. 1978 Mar 15;84(2):521–531. [PubMed]
  • Guilley H, Jonard G, Kukla B, Richards KE. Sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA. Nucleic Acids Res. 1979 Apr;6(4):1287–1308. [PMC free article] [PubMed]
  • Guilley H, Briand JP. Nucleotide sequence of turnip yellow mosaic virus coat protein mRNA. Cell. 1978 Sep;15(1):113–122. [PubMed]
  • Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. 1977 Feb 24;265(5596):687–695. [PubMed]
  • Fiddes JC. The nucleotide sequence of a viral DNA. Sci Am. 1977 Dec;237(6):54–67. [PubMed]
  • Shaw DC, Walker JE, Northrop FD, Barrell BG, Godson GN, Fiddes JC. Gene K, a new overlapping gene in bacteriophage G4. Nature. 1978 Apr 6;272(5653):510–515. [PubMed]
  • Godson GN, Barrell BG, Staden R, Fiddes JC. Nucleotide sequence of bacteriophage G4 DNA. Nature. 1978 Nov 16;276(5685):236–247. [PubMed]
  • Beck E, Sommer R, Auerswald EA, Kurz C, Zink B, Osterburg G, Schaller H, Sugimoto K, Sugisaki H, Okamoto T, et al. Nucleotide sequence of bacteriophage fd DNA. Nucleic Acids Res. 1978 Dec;5(12):4495–4503. [PMC free article] [PubMed]
  • van Wezenbeek P, Schoenmakers JG. Nucleotide sequence of the genes III, VI and I of bacteriophage M13. Nucleic Acids Res. 1979 Jun 25;6(8):2799–2818. [PMC free article] [PubMed]
  • Hulsebos T, Schoenmakers JG. Nucleotide sequence of gene VII and of a hypothetical gene (IX) in bacteriophage M13. Nucleic Acids Res. 1978 Dec;5(12):4677–4698. [PMC free article] [PubMed]
  • Sauer RT. DNA sequence of the bacteriophage gama cI gene. Nature. 1978 Nov 16;276(5685):301–302. [PubMed]
  • Schwarz E, Scherer G, Hobom G, Kössel H. Nucleotide sequence of cro, cII and part of the O gene in phage lambda DNA. Nature. 1978 Mar 30;272(5652):410–414. [PubMed]
  • Scherer G. Nucleotide sequence of the O gene and of the origin of replication in bacteriophage lambda DNA. Nucleic Acids Res. 1978 Sep;5(9):3141–3156. [PMC free article] [PubMed]
  • Grosschedl R, Schwarz E. Nucleotide sequence of the cro-cII-oop region of bacteriophage 434 DNA. Nucleic Acids Res. 1979 Mar;6(3):867–881. [PMC free article] [PubMed]
  • Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H, Van Herreweghe J, Volckaert G, Ysebaert M. Complete nucleotide sequence of SV40 DNA. Nature. 1978 May 11;273(5658):113–120. [PubMed]
  • Reddy VB, Thimmappaya B, Dhar R, Subramanian KN, Zain BS, Pan J, Ghosh PK, Celma ML, Weissman SM. The genome of simian virus 40. Science. 1978 May 5;200(4341):494–502. [PubMed]
  • Dhar R, Seif I, Khoury G. Nucleotide sequence of the BK virus DNA segment encoding small t antigen. Proc Natl Acad Sci U S A. 1979 Feb;76(2):565–569. [PMC free article] [PubMed]
  • Valenzuela P, Gray P, Quiroga M, Zaldivar J, Goodman HM, Rutter WJ. Nucleotide sequence of the gene coding for the major protein of hepatitis B virus surface antigen. Nature. 1979 Aug 30;280(5725):815–819. [PubMed]
  • Charnay P, Mandart E, Hampe A, Fitoussi F, Tiollais P, Galibert F. Localization on the viral genome and nucleotide sequence of the gene coding for the two major polypeptides of the hepatitis B surface antigen (HBs Ag). Nucleic Acids Res. 1979 Sep 25;7(2):335–346. [PMC free article] [PubMed]
  • Farabaugh PJ. Sequence of the lacI gene. Nature. 1978 Aug 24;274(5673):765–769. [PubMed]
  • Post LE, Strycharz GD, Nomura M, Lewis H, Dennis PP. Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1697–1701. [PMC free article] [PubMed]
  • Sutcliffe JG. Nucleotide sequence of the ampicillin resistance gene of Escherichia coli plasmid pBR322. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3737–3741. [PMC free article] [PubMed]
  • Hensgens LA, Grivell LA, Borst P, Bos JL. Nucleotide sequence of the mitochondrial structural gene for subunit 9 of yeast ATPase complex. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1663–1667. [PMC free article] [PubMed]
  • Smith M, Leung DW, Gillam S, Astell CR, Montgomery DL, Hall BD. Sequence of the gene for iso-1-cytochrome c in Saccharomyces cerevisiae. Cell. 1979 Apr;16(4):753–761. [PubMed]
  • Schaffner W, Kunz G, Daetwyler H, Telford J, Smith HO, Birnstiel ML. Genes and spacers of cloned sea urchin histone DNA analyzed by sequencing. Cell. 1978 Jul;14(3):655–671. [PubMed]
  • Sures I, Lowry J, Kedes LH. The DNA sequence of sea urchin (S. purpuratus) H2A, H2B and H3 histone coding and spacer regions. Cell. 1978 Nov;15(3):1033–1044. [PubMed]
  • McReynolds L, O'Malley BW, Nisbet AD, Fothergill JE, Givol D, Fields S, Robertson M, Brownlee GG. Sequence of chicken ovalbumin mRNA. Nature. 1978 Jun 29;273(5665):723–728. [PubMed]
  • Seidman JG, Leder A, Nau M, Norman B, Leder P. Antibody diversity. Science. 1978 Oct 6;202(4363):11–17. [PubMed]
  • Hamlyn PH, Browniee GG, Cheng CC, Gait MJ, Milstein C. Complete sequence of constant and 3' noncoding regions of an immunoglobulin mRNA using the dideoxynucleotide method of RNA sequencing. Cell. 1978 Nov;15(3):1067–1075. [PubMed]
  • Bernard O, Hozumi N, Tonegawa S. Sequences of mouse immunoglobulin light chain genes before and after somatic changes. Cell. 1978 Dec;15(4):1133–1144. [PubMed]
  • Tonegawa S, Maxam AM, Tizard R, Bernard O, Gilbert W. Sequence of a mouse germ-line gene for a variable region of an immunoglobulin light chain. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1485–1489. [PMC free article] [PubMed]
  • Seidman JG, Max EE, Leder P. A kappa-immunoglobulin gene is formed by site-specific recombination without further somatic mutation. Nature. 1979 Aug 2;280(5721):370–375. [PubMed]
  • Rogers J, Clarke P, Salser W. Sequence analysis of cloned cDNA encoding part of an immunoglobulin heavy chain. Nucleic Acids Res. 1979 Jul 25;6(10):3305–3321. [PMC free article] [PubMed]
  • Konkel DA, Tilghman SM, Leder P. The sequence of the chromosomal mouse beta-globin major gene: homologies in capping, splicing and poly(A) sites. Cell. 1978 Dec;15(4):1125–1132. [PubMed]
  • Roberts JL, Seeburg PH, Shine J, Herbert E, Baxter JD, Goodman HM. Corticotropin and beta-endorphin: construction and analysis of recombinant DNA complementary to mRNA for the common precursor. Proc Natl Acad Sci U S A. 1979 May;76(5):2153–2157. [PMC free article] [PubMed]
  • Seeburg PH, Shine J, Martial JA, Baxter JD, Goodman HM. Nucleotide sequence and amplification in bacteria of structural gene for rat growth hormone. Nature. 1977 Dec 8;270(5637):486–494. [PubMed]
  • Gubbins EJ, Maurer RA, Hartley JL, Donelson JE. Construction and analysis of recombinant DNAs containing a structural gene for rat prolactin. Nucleic Acids Res. 1979 Mar;6(3):915–930. [PMC free article] [PubMed]
  • Ullrich A, Shine J, Chirgwin J, Pictet R, Tischer E, Rutter WJ, Goodman HM. Rat insulin genes: construction of plasmids containing the coding sequences. Science. 1977 Jun 17;196(4296):1313–1319. [PubMed]
  • Heindell HC, Liu A, Paddock GV, Studnicka GM, Salser WA. The primary sequence of rabbit alpha-globin mRNA. Cell. 1978 Sep;15(1):43–54. [PubMed]
  • Efstratiadis A, Kafatos FC, Maniatis T. The primary structure of rabbit beta-globin mRNA as determined from cloned DNA. Cell. 1977 Apr;10(4):571–585. [PubMed]
  • Nakanishi S, Inoue A, Kita T, Nakamura M, Chang AC, Cohen SN, Numa S. Nucleotide sequence of cloned cDNA for bovine corticotropin-beta-lipotropin precursor. Nature. 1979 Mar 29;278(5703):423–427. [PubMed]
  • Fiddes JC, Goodman HM. Isolation, cloning and sequence analysis of the cDNA for the alpha-subunit of human chorionic gonadotropin. Nature. 1979 Oct 4;281(5730):351–356. [PubMed]
  • Marotta CA, Wilson JT, Forget BG, Weissman SM. Human beta-globin messenger RNA. III. Nucleotide sequences derived from complementary DNA. J Biol Chem. 1977 Jul 25;252(14):5040–5053. [PubMed]
  • Martial JA, Hallewell RA, Baxter JD, Goodman HM. Human growth hormone: complementary DNA cloning and expression in bacteria. Science. 1979 Aug 10;205(4406):602–607. [PubMed]
  • Shine J, Seeburg PH, Martial JA, Baxter JD, Goodman HM. Construction and analysis of recombinant DNA for human chorionic somatomammotropin. Nature. 1977 Dec 8;270(5637):494–499. [PubMed]

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