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PMID: 3118331 Published · ppublish English Comparative Study Journal Article

Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.

Nucleic acids research ·Vol. 15 ·No. 19 ·1987-10-12 ·Pages 8023-40

Shields DC, Sharp PM

Abstract

Codon usage data for 56 Bacillus subtilis genes show that synonymous codon usage in B. subtilis is less biased than in Escherichia coli, or in Saccharomyces cerevisiae. Nevertheless, certain genes with a high codon bias can be identified by correspondence analysis, and also by various indices of codon bias. These genes are very highly expressed, and a general trend (a decrease) in codon bias across genes seems to correspond to decreasing expression level. This, then, may be a general phenomenon in unicellular organisms. The unusually small effect of translational selection on the pattern of codon usage in lowly expressed genes in B. subtilis yields similar dinucleotide frequencies among different codon positions, and on complementary strands. These patterns could arise through selection on DNA structure, but more probably are largely determined by mutation. This prevalence of mutational bias could lead to difficulties in assessing whether open reading frames encode proteins.

MeSH Terms
Bacillus subtilis/genetics Codon Escherichia coli/genetics Genes, Bacterial Genes, Fungal Mutation Protein Biosynthesis RNA, Messenger Saccharomyces cerevisiae/genetics Selection, Genetic Species Specificity
Chemicals
Codon RNA, Messenger
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Shields D C
Department of Genetics, Trinity College, Dublin, Ireland.
Sharp P M
References (42)
42 references, click to expand
  1. Codon usage and tRNA content in unicellular and multicellular organisms.
    Mol Biol Evol. 1985 Jan;2(1):13-34 PMID: 3916708
  2. Codon contexts in enterobacterial and coliphage genes.
    Mol Biol Evol. 1987 Jul;4(4):426-44 PMID: 3128715
  3. Codon catalog usage and the genome hypothesis.
    Nucleic Acids Res. 1980 Jan 11;8(1):r49-r62 PMID: 6986610
  4. Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification.
    Proc Natl Acad Sci U S A. 1981 Mar;78(3):1596-600 PMID: 6940175
  5. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes.
    J Mol Biol. 1981 Feb 15;146(1):1-21 PMID: 6167728
  6. Codon selection in yeast.
    J Biol Chem. 1982 Mar 25;257(6):3026-31 PMID: 7037777
  7. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.
    J Mol Biol. 1982 Jul 15;158(4):573-97 PMID: 6750137
  8. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.
    Gene. 1982 Jun;18(3):199-209 PMID: 6751939
  9. Codon usage in bacteria: correlation with gene expressivity.
    Nucleic Acids Res. 1982 Nov 25;10(22):7055-74 PMID: 6760125
  10. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):539-49 PMID: 6694906
  11. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):551-67 PMID: 6364041
  12. Codon usage can affect efficiency of translation of genes in Escherichia coli.
    Nucleic Acids Res. 1984 Sep 11;12(17):6663-71 PMID: 6091031
  13. The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences.
    Gene. 1984 Oct;30(1-3):157-66 PMID: 6096212
  14. Sequence analysis of the spo0B locus reveals a polycistronic transcription unit.
    J Bacteriol. 1985 Feb;161(2):556-62 PMID: 3918016
  15. Escherichia coli ribosomes translate in vivo with variable rate.
    EMBO J. 1984 Dec 1;3(12):2895-8 PMID: 6396082
  16. Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains.
    J Mol Biol. 1984 Dec 15;180(3):549-76 PMID: 6084718
  17. Structure and organization of genes for transfer ribonucleic acid in Bacillus subtilis.
    Microbiol Rev. 1985 Mar;49(1):71-80 PMID: 2580221
  18. A strong sequence homology exists between the major RNA polymerase sigma factors of Bacillus subtilis and Escherichia coli.
    J Biol Chem. 1985 Jun 25;260(12):7178-85 PMID: 2987246
  19. The mosaic genome of warm-blooded vertebrates.
    Science. 1985 May 24;228(4702):953-8 PMID: 4001930
  20. Sense codons are found in specific contexts.
    J Mol Biol. 1985 Apr 20;182(4):529-40 PMID: 3892014
  21. Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations.
    J Mol Biol. 1985 May 5;183(1):1-12 PMID: 4009718
  22. Selection pressures on codon usage in the complete genome of bacteriophage T7.
    J Mol Evol. 1984-1985;21(2):150-60 PMID: 6100189
  23. Codon-defined ribosomal pausing in Escherichia coli detected by using the pyrE attenuator to probe the coupling between transcription and translation.
    Nucleic Acids Res. 1985 Jun 11;13(11):4113-23 PMID: 2989788
  24. The DNA sequence of the gene for the secreted Bacillus subtilis enzyme levansucrase and its genetic control sites.
    Mol Gen Genet. 1985;200(2):220-8 PMID: 2993818
  25. Expression of a synthetic human growth hormone gene in yeast.
    Gene. 1985;39(1):117-20 PMID: 3908222
  26. Codon usage and genome composition.
    J Mol Evol. 1985;22(4):363-5 PMID: 3936938
  27. Markedly unbiased codon usage in Bacillus subtilis.
    Gene. 1985;40(1):145-50 PMID: 3937765
  28. Codon usage and gene expression.
    Nucleic Acids Res. 1986 Apr 11;14(7):3075-87 PMID: 2938078
  29. Cloning and nucleotide sequencing of genes for three small, acid-soluble proteins from Bacillus subtilis spores.
    J Bacteriol. 1986 May;166(2):417-25 PMID: 3009398
  30. Codon usage tabulated from the GenBank genetic sequence data.
    Nucleic Acids Res. 1986;14 Suppl:r151-97 PMID: 3703684
  31. Genetic engineering of extracellular enzyme systems of Bacilli.
    Ann N Y Acad Sci. 1986;469:1-17 PMID: 3524394
  32. Constraints on codon context in Escherichia coli genes. Their possible role in modulating the efficiency of translation.
    J Mol Biol. 1986 Apr 20;188(4):555-64 PMID: 3525848
  33. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.
    Nucleic Acids Res. 1986 Jul 11;14(13):5125-43 PMID: 3526280
  34. Effect of distribution of unfavourable codons on the maximum rate of gene expression by an heterologous organism.
    J Theor Biol. 1986 May 7;120(1):99-110 PMID: 3528671
  35. Diversity in G + C content at the third position of codons in vertebrate genes and its cause.
    Nucleic Acids Res. 1986 Aug 26;14(16):6345-55 PMID: 3748815
  36. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons.
    Nucleic Acids Res. 1986 Oct 10;14(19):7737-49 PMID: 3534792
  37. Sequence analysis of the cDNA encoding human liver glycogen phosphorylase reveals tissue-specific codon usage.
    Proc Natl Acad Sci U S A. 1986 Nov;83(21):8132-6 PMID: 2877458
  38. Unusually high-level expression of a foreign gene (hepatitis B virus core antigen) in Saccharomyces cerevisiae.
    Gene. 1986;46(1):135-41 PMID: 3542716
  39. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
    Nucleic Acids Res. 1987 Feb 11;15(3):1281-95 PMID: 3547335
  40. An evolutionary perspective on synonymous codon usage in unicellular organisms.
    J Mol Evol. 1986;24(1-2):28-38 PMID: 3104616
  41. Neighboring base effects on substitution rates in pseudogenes.
    Mol Biol Evol. 1986 Jul;3(4):322-9 PMID: 3444408
  42. Is there selection against wobble in codon-anticodon pairing?
    Science. 1976 Dec 10;194(4270):1173-4 PMID: 996548
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/15.19.8023
Published
1987-10-12
Pages
8023-40
Language
English
Region
England
NLM ID
0411011
PMCID
PMC306324
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/15.19.8023 PMC Full Text View journal details
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