Purifying Selection: Action on Silent Sites

Abstract

The role of selection on silent‐site evolution in humans is controversial. Mounting evidence suggests that selection for optimal base composition, codon usage or both may be common.

Keywords: silent substitutions; silent sites; selection; codon usage bias; weak selection; codon bias; population genetics

References

Akashi (1999) Within‐ and between‐species DNA sequence variation and the ‘footprint’ of natural selection. Gene 238: 39–51.

Akashi H (2001) Gene expression and molecular evolution. Current Opinion in Genetics and Development 11: 660–666.

Alvarez‐Valin F, Jabbari K and Bernardi G (1998) Synonymous and nonsynonymous substitutions in mammalian genes: intragenic correlations. Journal of Molecular Evolution 46: 37–44.

Andersson SG and Kurland CG (1990) Codon preferences in free‐living microorganisms. Microbiological Reviews 54: 198–210.

Andre S, Seed B, Eberle J et al. (1998) Increased immune response elicited by DNA vaccination with a synthetic gp120 sequence with optimized codon usage. Journal of Virology 72: 1497–1503.

Bennetzen JL and Hall BD (1982) Codon selection in yeast. Journal of Biological Chemistry 257: 3026–3031.

Bernardi G (1995) The human genome: organization and evolutionary history. Annual Review of Genetics 29: 445–476.

Bustamante CD, Nielsen R and Hartl DL (2002) A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Molecular Biology and Evolution 19: 110–117.

Coghlan A and Wolfe KH (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16: 1131–1145.

DeBry RW and Marzluff WF (1994) Selection on silent sites in the rodent H3 histone gene family. Genetics 138: 191–202.

Duret L and Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of the USA 96: 4482–4487.

Duret L and Mouchiroud D (2000) Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Molecular Biology and Evolution 17: 68–74.

Duret L, Semon M, Piganeau G, Mouchiroud D and Galtier N (2002) Vanishing GC‐rich isochores in mammalian genomes. Genetics 162: 1837–1847.

Eyre‐Walker AC (1991) An analysis of codon usage in mammals: selection or mutation bias? Journal of Molecular Evolution 33: 442–449.

Eyre‐Walker A (1999) Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152: 675–683.

Eyre‐Walker A and Hurst LD (2001) The evolution of isochores. Nature Reviews Genetics 2: 549–555.

Gouy M and Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Research 10: 7055–7074.

Grantham R, Gautier C, Gouy M, Jacobzone M and Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Research 9: r43–r74.

Grosjean H and Fiers W (1982) Preferential codon usage in prokaryotic genes: the optimal codon–anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18: 199–209.

Hartl DL, Moriyama EN and Sawyer SA (1994) Selection intensity for codon bias. Genetics 138: 227–234.

Hurst LD and Pal C (2001) Evidence for purifying selection acting on silent sites in BRCA1. Trends in Genetics 17: 62–65.

Iida K and Akashi H (2000) A test of translational selection at ‘silent’ sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 261: 93–105.

Ikemura T (1981) 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. Journal of Molecular Biology 151: 389–409.

Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution 2: 13–34.

Karlin S and Burge C (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends in Genetics 11: 283–290.

Kim CH, Oh Y and Lee TH (1997) Codon optimization for high‐level expression of human erythropoietin (EPO) in mammalian cells. Gene 199: 293–301.

Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275–276.

Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge, UK: Cambridge University Press.

King JL and Jukes TH (1969) Non‐Darwinian evolution. Science 164: 788–798.

Konu O and Li MD (2002) Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. Journal of Molecular Evolution 54: 35–41.

Lander ES, Linton LM, Birren B et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.

Liu HX, Cartegni L, Zhang MQ and Krainer AR (2001) A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nature Genetics 27: 55–58.

Narum DL, Kumar S, Rogers WO et al. (2001) Codon optimization of gene fragments encoding Plasmodium falciparum merozoite proteins enhances DNA vaccine protein expression and immunogenicity in mice. Infection and Immunity 69: 7250–7253.

Orban TI and Olah E (2001) Purifying selection on silent sites – a constraint from splicing regulation? Trends in Genetics 17: 252–253.

Sharp PM, Averof M, Lloyd AT, Matassi G and Peden JF (1995) DNA sequence evolution: the sounds of silence. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 349: 241–247.

Smith NG and Eyre‐Walker A (2001) Synonymous codon bias is not caused by mutation bias in G+C‐rich genes in humans. Molecular Biology and Evolution 18: 982–986.

Urrutia AO and Hurst LD (2001) Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159: 1191–1199.

Zhou J, Liu WJ, Peng SW, Sun XY and Frazer I (1999) Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability. Journal of Virology 73: 4972–4982.

Further Reading

Akashi H (1999) Within‐ and between‐species DNA sequence variation and the ‘footprint’ of natural selection. Gene 238: 39–51.

Andersson SG and Kurland CG (1990) Codon preferences in free‐living microorganisms. Microbiological Reviews 54: 198–210.

Bernardi G (1995) The human genome: organization and evolutionary history. Annual Review of Genetics 29: 445–476.

Bustamante CD, Nielsen R and Hartl DL (2002) A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Molecular Biology and Evolution 19: 110–117.

Gorlov IP, Kimmel M and Amos CI (2006) Strength of the purifying selection against different categories of the point mutations in the coding regions of the human genome. Human Molecular Genetics 15: 1143–1150.

Iida K and Akashi H (2000) A test of translational selection at ‘silent’ sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 261: 93–105.

Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution 2: 13–34.

Karlin S and Burge C (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends in Genetics 11: 283–290.

Orban TI and Olah E (2001) Purifying selection on silent sites – a constraint from splicing regulation? Trends in Genetics 17: 252–253.

Parmley JL, Chamary JV and Hurst LD (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Molecular Biology and Evolution 23: 301–309.

Sharp PM, Averof M, Lloyd AT, Matassi G and Peden JF (1995) DNA sequence evolution: the sounds of silence. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 349: 241–247.

Smith NG and Eyre‐Walker A (2001) Synonymous codon bias is not caused by mutation bias in G+C‐rich genes in humans. Molecular Biology and Evolution 18: 982–986.

Subramanian S and Kumar S (2006) Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Molecular Biology and Evolution 23: 2283–2287.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Nielsen, R, and Akashi, H(Dec 2007) Purifying Selection: Action on Silent Sites. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006114.pub2]