Codon catalog usage is a genome strategy modulated for gene expressivity - PubMed

Codon catalog usage is a genome strategy modulated for gene expressivity

R Grantham et al. Nucleic Acids Res. 1981.

Free PMC article

Abstract

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.

Similar articles

• Codon usage in bacteria: correlation with gene expressivity.

  Gouy M, Gautier C. Gouy M, et al. Nucleic Acids Res. 1982 Nov 25;10(22):7055-74. doi: 10.1093/nar/10.22.7055. Nucleic Acids Res. 1982. PMID: 6760125 Free PMC article.

• Codon catalog usage and the genome hypothesis.

  Grantham R, Gautier C, Gouy M, Mercier R, Pavé A. Grantham R, et al. Nucleic Acids Res. 1980 Jan 11;8(1):r49-r62. doi: 10.1093/nar/8.1.197-c. Nucleic Acids Res. 1980. PMID: 6986610 Free PMC article. Review.

• Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

  Grantham R, Gautier C, Gouy M. Grantham R, et al. Nucleic Acids Res. 1980 May 10;8(9):1893-912. doi: 10.1093/nar/8.9.1893. Nucleic Acids Res. 1980. PMID: 6159596 Free PMC article.

• Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria.

  Lobry JR, Chessel D. Lobry JR, et al. J Appl Genet. 2003;44(2):235-61. J Appl Genet. 2003. PMID: 12817570

• Synonymous Codons: Choose Wisely for Expression.

  Brule CE, Grayhack EJ. Brule CE, et al. Trends Genet. 2017 Apr;33(4):283-297. doi: 10.1016/j.tig.2017.02.001. Epub 2017 Mar 12. Trends Genet. 2017. PMID: 28292534 Free PMC article. Review.

Cited by

• Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria.

  Rahman S, Kosakovsky Pond SL, Webb A, Hey J. Rahman S, et al. Proc Natl Acad Sci U S A. 2021 May 18;118(20):e2023575118. doi: 10.1073/pnas.2023575118. Proc Natl Acad Sci U S A. 2021. PMID: 33972434 Free PMC article.

• Molecular cloning, nucleotide sequence, and abscisic acid induction of a suberization-associated highly anionic peroxidase.

  Roberts E, Kolattukudy PE. Roberts E, et al. Mol Gen Genet. 1989 Jun;217(2-3):223-32. doi: 10.1007/BF02464885. Mol Gen Genet. 1989. PMID: 2528055

• Is there a relationship between DNA sequences encoding peptide ligands and their receptors?

  Goldstein A, Brutlag DL. Goldstein A, et al. Proc Natl Acad Sci U S A. 1989 Jan;86(1):42-5. doi: 10.1073/pnas.86.1.42. Proc Natl Acad Sci U S A. 1989. PMID: 2536158 Free PMC article.

• Molecular characterization of the tdc operon of Escherichia coli K-12.

  Goss TJ, Schweizer HP, Datta P. Goss TJ, et al. J Bacteriol. 1988 Nov;170(11):5352-9. doi: 10.1128/jb.170.11.5352-5359.1988. J Bacteriol. 1988. PMID: 3053659 Free PMC article.

• Comparative studies of the amino acid and nucleotide sequences of pilin derived from Pseudomonas aeruginosa PAK and PAO.

  Sastry PA, Finlay BB, Pasloske BL, Paranchych W, Pearlstone JR, Smillie LB. Sastry PA, et al. J Bacteriol. 1985 Nov;164(2):571-7. doi: 10.1128/jb.164.2.571-577.1985. J Bacteriol. 1985. PMID: 2997119 Free PMC article.

References

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • PubMed Central
  • Silverchair Information Systems

• Other Literature Sources

  • The Lens - Patent Citations Database

• Medical

  • MedlinePlus Health Information