Literature DB >> 6760125

Codon usage in bacteria: correlation with gene expressivity.

M Gouy, C Gautier.   

Abstract

The nucleic acid sequence bank now contains over 600 protein coding genes of which 107 are from prokaryotic organisms. Codon frequencies in each new prokaryotic gene are given. Analysis of genetic code usage in the 83 sequenced genes of the Escherichia coli genome (chromosome, transposons and plasmids) is presented, taking into account new data on gene expressivity and regulation as well as iso-tRNA specificity and cellular concentration. The codon composition of each gene is summarized using two indexes: one is based on the differential usage of iso-tRNA species during gene translation, the other on choice between Cytosine and Uracil for third base. A strong relationship between codon composition and mRNA expressivity is confirmed, even for genes transcribed in the same operon. The influence of codon use of peptide elongation rate and protein yield is discussed. Finally, the evolutionary aspect of codon selection in mRNA sequences is studied.

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Year:  1982        PMID： 6760125      PMCID： PMC326988          DOI： 10.1093/nar/10.22.7055

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  35 in total

1.  Bacteriophage MS2 RNA: a correlation between the stability of the codon: anticodon interaction and the choice of code words.

Authors:  H Grosjean; D Sankoff; W M Jou; W Fiers; R J Cedergren
Journal:  J Mol Evol       Date:  1978-12-29       Impact factor: 2.395

2.  On codon usage.

Authors:  W Fiers; H Grosjean
Journal:  Nature       Date:  1979-01-25       Impact factor: 49.962

3.  Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates.

Authors:  S Pedersen; P L Bloch; S Reeh; F C Neidhardt
Journal:  Cell       Date:  1978-05       Impact factor: 41.582

4.  Transcription patterns of adjacent segments on the chromosome of Escherichia coli containing genes coding for four 50S ribosomal proteins and the beta and beta' subunits of RNA polymerase.

Authors:  P P Dennis
Journal:  J Mol Biol       Date:  1977-10-05       Impact factor: 5.469

5.  Content of elongation factor Tu in Escherichia coli.

Authors:  A V Furano
Journal:  Proc Natl Acad Sci U S A       Date:  1975-12       Impact factor: 11.205

6.  The atp operon: nucleotide sequence of the promoter and the genes for the membrane proteins, and the delta subunit of Escherichia coli ATP-synthase.

Authors:  N J Gay; J E Walker
Journal:  Nucleic Acids Res       Date:  1981-08-25       Impact factor: 16.971

7.  DNA synthesis inhibition and the induction of protein X in Escherichia coli.

Authors:  L J Gudas; A B Pardee
Journal:  J Mol Biol       Date:  1976-03-15       Impact factor: 5.469

Review 8.  Genetic relatedness in the family Enterobacteriaceae.

Authors:  K E Sanderson
Journal:  Annu Rev Microbiol       Date:  1976       Impact factor: 15.500

9.  Interaction of the operator of the tryptophan operon with repressor.

Authors:  J K Rose; C Yanofsky
Journal:  Proc Natl Acad Sci U S A       Date:  1974-08       Impact factor: 11.205

10.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system.

Authors:  T Ikemura
Journal:  J Mol Biol       Date:  1981-09-25       Impact factor: 5.469
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  422 in total

1.  Nonrandom spatial distribution of synonymous substitutions in the GP63 gene from Leishmania.

Authors:  F Alvarez-Valin; J F Tort; G Bernardi
Journal:  Genetics       Date:  2000-08       Impact factor: 4.562

2.  Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models.

Authors:  Pierre Nicolas; Laurent Bize; Florence Muri; Mark Hoebeke; François Rodolphe; S Dusko Ehrlich; Bernard Prum; Philippe Bessières
Journal:  Nucleic Acids Res       Date:  2002-03-15       Impact factor: 16.971

3.  Interactions between natural selection, recombination and gene density in the genes of Drosophila.

Authors:  Jody Hey; Richard M Kliman
Journal:  Genetics       Date:  2002-02       Impact factor: 4.562

4.  Gradients in nucleotide and codon usage along Escherichia coli genes.

Authors:  S D Hooper; O G Berg
Journal:  Nucleic Acids Res       Date:  2000-09-15       Impact factor: 16.971

5.  Use and misuse of correspondence analysis in codon usage studies.

Authors:  Guy Perrière; Jean Thioulouse
Journal:  Nucleic Acids Res       Date:  2002-10-15       Impact factor: 16.971

6.  Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis.

Authors:  Marie E Fahey; Desmond G Higgins
Journal:  J Mol Evol       Date:  2007-09-01       Impact factor: 2.395

7.  Cloning of the gene encoding the major outer membrane protein of Haemophilus influenzae type b.

Authors:  E J Hansen; F R Gonzales; N R Chamberlain; M V Norgard; E E Miller; L D Cope; S E Pelzel; B Gaddy; A Clausell
Journal:  Infect Immun       Date:  1988-10       Impact factor: 3.441

8.  Nucleotide sequence and expression of a Streptomyces griseosporeus proteinaceous alpha-amylase inhibitor (HaimII) gene.

Authors:  H Nagaso; S Saito; H Saito; H Takahashi
Journal:  J Bacteriol       Date:  1988-10       Impact factor: 3.490

9.  The signature of selection mediated by expression on human genes.

Authors:  Araxi O Urrutia; Laurence D Hurst
Journal:  Genome Res       Date:  2003-09-15       Impact factor: 9.043

10.  Incorporation of excess wild-type and mutant tRNA(3Lys) into human immunodeficiency virus type 1.

Authors:  Y Huang; J Mak; Q Cao; Z Li; M A Wainberg; L Kleiman
Journal:  J Virol       Date:  1994-12       Impact factor: 5.103
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