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Nucleic Acids Res. Jan 10, 1981; 9(1): r43–r74.
PMCID: PMC326682

Codon catalog usage is a genome strategy modulated for gene expressivity


The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added. One sequence, that of B. mori fibroin, is dropped due to uncertainty on the starting point for translation. Frequencies of all codons are given for each gene added and for each genome type in the total bank. A new series of correspondence analyses on codon use is presented, substantiating the genome hypothesis. Internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.

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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]
  • Grantham R, Gautier C, Gouy M, Mercier R, Pavé A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980 Jan 11;8(1):r49–r62. [PMC free article] [PubMed]
  • Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980 May 10;8(9):1893–1912. [PMC free article] [PubMed]
  • Grantham R, Gautier C. Genetic distances from mRNA sequences. Naturwissenschaften. 1980 Feb;67(2):93–94. [PubMed]
  • Miyata T, Hayashida H, Yasunaga T, Hasegawa M. The preferential codon usages in variable and constant regions of immunoglobulin genes are quite distinct from each other. Nucleic Acids Res. 1979 Dec 20;7(8):2431–2438. [PMC free article] [PubMed]
  • Claverie P. Calculation of interaction energy between triplets in the RNA 11 configuration. J Mol Biol. 1971 Feb 28;56(1):75–82. [PubMed]
  • Ninio J. Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs. Biochimie. 1979;61(10):1133–1150. [PubMed]
  • Brederode FT, Koper-Zwarthoff EC, Bol JF. Complete nucleotide sequence of alfalfa mosaic virus RNA 4. Nucleic Acids Res. 1980 May 24;8(10):2213–2223. [PMC free article] [PubMed]
  • Sims J, Capon D, Dressler D. dnaG (primase)-dependent origins of DNA replication. Nucleotide sequences of the negative strand initiation sites of bacteriophages St-1, phi K, and alpha 3. J Biol Chem. 1979 Dec 25;254(24):12615–12628. [PubMed]
  • Saito H, Tabor S, Tamanoi F, Richardson CC. Nucleotide sequence of the primary origin of bacteriophage T7 DNA replication: relationship to adjacent genes and regulatory elements. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3917–3921. [PMC free article] [PubMed]
  • Dunn JJ, Studier FW. The transcription termination site at the end of the early region of bacteriophage T7 DNA. Nucleic Acids Res. 1980 May 24;8(10):2119–2132. [PMC free article] [PubMed]
  • Davies RW. DNA sequence of the int-xis-Pi region of the bacteriophage lambda; overlap of the int and xis genes. Nucleic Acids Res. 1980 Apr 25;8(8):1765–1782. [PMC free article] [PubMed]
  • Hoess RH, Foeller C, Bidwell K, Landy A. Site-specific recombination functions of bacteriophage lambda: DNA sequence of regulatory regions and overlapping structural genes for Int and Xis. Proc Natl Acad Sci U S A. 1980 May;77(5):2482–2486. [PMC free article] [PubMed]
  • Yang RC, Wu R. BK virus DNA: complete nucleotide sequence of a human tumor virus. Science. 1979 Oct 26;206(4417):456–462. [PubMed]
  • Hérissé J, Courtois G, Galibert F. Nucleotide sequence of the EcoRI D fragment of adenovirus 2 genome. Nucleic Acids Res. 1980 May 24;8(10):2173–2192. [PMC free article] [PubMed]
  • Aleström P, Akusjärvi G, Perricaudet M, Mathews MB, Klessig DF, Pettersson U. The gene for polypeptide IX of adenovirus type 2 and its unspliced messenger RNA. Cell. 1980 Mar;19(3):671–681. [PubMed]
  • Jou WM, Verhoeyen M, Devos R, Saman E, Fang R, Huylebroeck D, Fiers W, Threlfall G, Barber C, Carey N, et al. Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA. Cell. 1980 Mar;19(3):683–696. [PubMed]
  • Post LE, Nomura M. DNA sequences from the str operon of Escherichia coli. J Biol Chem. 1980 May 25;255(10):4660–4666. [PubMed]
  • Post LE, Arfsten AE, Davis GR, Nomura M. DNA sequence of the promoter region for the alpha ribosomal protein operon in Escherichia coli. J Biol Chem. 1980 May 25;255(10):4653–4659. [PubMed]
  • Sancar A, Stachelek C, Konigsberg W, Rupp WD. Sequences of the recA gene and protein. Proc Natl Acad Sci U S A. 1980 May;77(5):2611–2615. [PMC free article] [PubMed]
  • Beck E, Bremer E. Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12. Nucleic Acids Res. 1980 Jul 11;8(13):3011–3027. [PMC free article] [PubMed]
  • Movva NR, Nakamura K, Inouye M. Regulatory region of the gene for the ompA protein, a major outer membrane protein of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3845–3849. [PMC free article] [PubMed]
  • Smith DR, Calvo JM. Nucleotide sequence of the E coli gene coding for dihydrofolate reductase. Nucleic Acids Res. 1980 May 24;8(10):2255–2274. [PMC free article] [PubMed]
  • Nakamura K, Inouye M. DNA sequence of the Serratia marcescens lipoprotein gene. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1369–1373. [PMC free article] [PubMed]
  • Zieg J, Simon M. Analysis of the nucleotide sequence of an invertible controlling element. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4196–4200. [PMC free article] [PubMed]
  • Thalenfeld BE, Tzagoloff A. Assembly of the mitochondrial membrane system. Sequence of the oxi 2 gene of yeast mitochondrial DNA. J Biol Chem. 1980 Jul 10;255(13):6173–6180. [PubMed]
  • Gallwitz D, Sures I. Structure of a split yeast gene: complete nucleotide sequence of the actin gene in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1980 May;77(5):2546–2550. [PMC free article] [PubMed]
  • Tsitilou SG, Regier JC, Kafatos FC. Selection and sequence analysis of a cDNA clone encoding a known chorion protein of the A family. Nucleic Acids Res. 1980 May 10;8(9):1987–1997. [PMC free article] [PubMed]
  • Jones CW, Rosenthal N, Rodakis GC, Kafatos FC. Evolution of two major chorion multigene families as inferred from cloned cDNA and protein sequences. Cell. 1979 Dec;18(4):1317–1332. [PubMed]
  • Showalter AM, Pesciotta DM, Eikenberry EF, Yamamoto T, Pastan I, DeCrombrugghe B, Fietzek PP, Olsen BR. Nucleotide sequence of a collagen cDNA-fragment coding for the carboxyl end of pro alpha 1(I)-chains. FEBS Lett. 1980 Feb 25;111(1):61–65. [PubMed]
  • Deacon NJ, Shine J, Naora H. Complete nucleotide sequence of a cloned chicken alpha-globin cDNA. Nucleic Acids Res. 1980 Mar 25;8(6):1187–1199. [PMC free article] [PubMed]
  • Heilig R, Perrin F, Gannon F, Mandel JL, Chambon P. The ovalbumin gene family: structure of the X gene and evolution of duplicated split genes. Cell. 1980 Jul;20(3):625–637. [PubMed]
  • Perler F, Efstratiadis A, Lomedico P, Gilbert W, Kolodner R, Dodgson J. The evolution of genes: the chicken preproinsulin gene. Cell. 1980 Jun;20(2):555–566. [PubMed]
  • Sikorav JL, Auffray C, Rougeon F. Structure of the constant and 3' untranslated regions of the murine Balb/c gamma 2a heavy chain messenger RNA. Nucleic Acids Res. 1980 Jul 25;8(14):3143–3155. [PMC free article] [PubMed]
  • Wilson JT, Wilson LB, Reddy VB, Cavallesco C, Ghosh PK, deRiel JK, Forget BG, Weissman SM. Nucleotide sequence of the coding portion of human alpha globin messenger RNA. J Biol Chem. 1980 Apr 10;255(7):2807–2815. [PubMed]
  • Sures I, Goeddel DV, Gray A, Ullrich A. Nucleotide sequence of human preproinsulin complementary DNA. Science. 1980 Apr 4;208(4439):57–59. [PubMed]
  • Ullrich A, Dull TJ, Gray A, Brosius J, Sures I. Genetic variation in the human insulin gene. Science. 1980 Aug 1;209(4456):612–615. [PubMed]
  • Taniguchi T, Ohno S, Fujii-Kuriyama Y, Muramatsu M. The nucleotide sequence of human fibroblast interferon cDNA. Gene. 1980 Jun;10(1):11–15. [PubMed]
  • Heffron F, McCarthy BJ, Ohtsubo H, Ohtsubo E. DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3. Cell. 1979 Dec;18(4):1153–1163. [PubMed]

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