publication . Article . 2011

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

Maya Botzman; Hanah Margalit;
Open Access
  • Published: 01 Oct 2011 Journal: Genome Biology, volume 12, page R109 (issn: 1465-6906, Copyright policy)
  • Publisher: Springer Nature
Abstract
Background It is widely acknowledged that synonymous codons are used unevenly among genes in a genome. In organisms under translational selection, genes encoding highly expressed proteins are enriched with specific codons. This phenomenon, termed codon usage bias, is common to many organisms and has been recognized as influencing cellular fitness. This suggests that the global extent of codon usage bias of an organism might be associated with its phenotypic traits. Results To test this hypothesis we used a simple measure for assessing the extent of codon bias of an organism, and applied it to hundreds of sequenced prokaryotes. Our analysis revealed a large varia...
Subjects
free text keywords: Research, Organism, Codon usage bias, Human genetics, Phenotype, Biology, Genetics, Phylogenetics, Gene, Genome, Phenotypic trait
Related Organizations
38 references, page 1 of 3

Grantham, R, Gautier, C, Gouy, M, Mercier, R, Pave, A. Codon catalog usage and the genome hypothesis.. Nucleic Acids Res. 1980; 8: r49-r62 [OpenAIRE] [PubMed]

Gouy, M, Gautier, C. Codon usage in bacteria: correlation with gene expressivity.. Nucleic Acids Res. 1982; 10: 7055-7074 [OpenAIRE] [PubMed] [DOI]

Bennetzen, JL, Hall, BD. Codon selection in yeast.. J Biol Chem. 1982; 257: 3026-3031 [PubMed]

Post, LE, Nomura, M. DNA sequences from the str operon of Escherichia coli.. J Biol Chem. 1980; 255: 4660-4666 [PubMed]

Ikemura, T. 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.. J Mol Biol. 1981; 151: 389-409 [OpenAIRE] [PubMed] [DOI]

Ikemura, T. Codon usage and tRNA content in unicellular and multicellular organisms.. Mol Biol Evol. 1985; 2: 13-34 [OpenAIRE] [PubMed]

Dong, H, Nilsson, L, Kurland, CG. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.. J Mol Biol. 1996; 260: 649-663 [OpenAIRE] [PubMed] [DOI]

Chen, SL, Lee, W, Hottes, AK, Shapiro, L, McAdams, HH. Codon usage between genomes is constrained by genome-wide mutational processes.. Proc Natl Acad Sci USA. 2004; 101: 3480-3485 [OpenAIRE] [PubMed] [DOI]

Hershberg, R, Petrov, DA. General rules for optimal codon choice.. PLoS Genet. 2009; 5: e1000556 [OpenAIRE] [PubMed] [DOI]

Supek, F, Skunca, N, Repar, J, Vlahovicek, K, Smuc, T. Translational selection is ubiquitous in prokaryotes.. PLoS Genet. 2010; 6: e1001004 [OpenAIRE] [PubMed] [DOI]

Lithwick, G, Margalit, H. Hierarchy of sequence-dependent features associated with prokaryotic translation.. Genome Res. 2003; 13: 2665-2673 [OpenAIRE] [PubMed] [DOI]

Ghaemmaghami, S, Huh, WK, Bower, K, Howson, RW, Belle, A, Dephoure, N, O'Shea, EK, Weissman, JS. Global analysis of protein expression in yeast.. Nature. 2003; 425: 737-741 [OpenAIRE] [PubMed] [DOI]

Lafay, B, Atherton, JC, Sharp, PM. Absence of translationally selected synonymous codon usage bias in Helicobacter pylori.. Microbiology. 2000; 146: 851-860 [OpenAIRE] [PubMed]

Sharp, PM, Bailes, E, Grocock, RJ, Peden, JF, Sockett, RE. Variation in the strength of selected codon usage bias among bacteria.. Nucleic Acids Res. 2005; 33: 1141-1153 [OpenAIRE] [PubMed] [DOI]

Andersson, SG, Kurland, CG. Codon preferences in free-living microorganisms.. Microbiol Rev. 1990; 54: 198-210 [OpenAIRE] [PubMed]

38 references, page 1 of 3
Any information missing or wrong?Report an Issue