Silent (Synonymous) SNPs: Should We Care About Them?

  • Ryan Hunt
  • Zuben E. Sauna
  • Suresh V. Ambudkar
  • Michael M. Gottesman
  • Chava Kimchi-Sarfaty
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 578)

Abstract

One of the surprising findings of the Human Genome Project was that single nucleotide polymorphisms (SNPs), which, by definition, have a minor allele frequency greater than 1%, occur at higher rates than previously suspected. When occurring in the gene coding regions, SNPs can be synonymous (i.e., not causing a change in the amino acid) or nonsynonymous (when the amino acid is altered). It has long been assumed that synonymous SNPs are inconsequential, as the primary sequence of the protein is retained. A number of studies have questioned this assumption over the last decade, showing that synonymous mutations are also under evolutionary pressure and they can be implicated in disease. More importantly, several of the mechanisms by which synonymous mutations alter the structure, function, and expression level of proteins are now being elucidated. Studies have demonstrated that synonymous polymorphisms can affect messenger RNA splicing, stability, and structure as well as protein folding. These changes can have a significant effect on the function of proteins, change cellular response to therapeutic targets, and often explain the different responses of individual patients to a certain medication.

Key words

Single nucleotide polymorphism messenger RNA splicing messenger RNA stability messenger RNA structure protein folding synonymous mutations nonsynonymous mutations codon frequency codon usage 

Notes

Acknowledgments

This research was supported, in part, by the Intramural Research Program of the National Institutes of Health, National Cancer Institute. Special thanks are expressed to George Leiman, NCI, NIH, and Geetha S., CBER, FDA, for editorial assistance.

References

  1. 1.
    Collins, F. S., Brooks, L. D. and Chakravarti, A. (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8, 1229–1231.PubMedGoogle Scholar
  2. 2.
    Glazier, A. M., Nadeau, J. H. and Aitman, T. J. (2002) Finding genes that underlie complex traits. Science 298, 2345–2349.PubMedCrossRefGoogle Scholar
  3. 3.
    Goldstein, D. B. and Weale, M. E. (2001) Population genomics: Linkage disequilibrium holds the key. Curr. Biol. 11, R576–579.PubMedCrossRefGoogle Scholar
  4. 4.
    Gumus-Akay, G., Rustemoglu, A., Karadag, A. and Sunguroglu, A. (2008) Genotype and allele frequencies of MDR1 gene C1236T polymorphism in a Turkish population. Genet. Mol. Res. 7, 1193–1199.PubMedCrossRefGoogle Scholar
  5. 5.
    Sauvage, C., Bierne, N., Lapegue, S. and Boudry, P. (2007) Single nucleotide polymorphisms and their relationship to codon usage bias in the pacific oyster crassostrea gigas. Gene 406, 13–22.PubMedCrossRefGoogle Scholar
  6. 6.
    Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P. and Burge, C. B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476.PubMedCrossRefGoogle Scholar
  7. 7.
    Hart, M. C. and Cooper, J. A. (1999) Vertebrate isoforms of actin capping protein beta have distinct functions in vivo. J. Cell. Biol. 147, 1287–1298.PubMedCrossRefGoogle Scholar
  8. 8.
    Xing, Y., Xu, Q. and Lee, C. (2003) Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. FEBS Lett. 555, 572–578.PubMedCrossRefGoogle Scholar
  9. 9.
    Egan, M. F., Straub, R. E., Goldberg, T. E., Yakub, I., Callicott, J. H., Hariri, A. R., Mattay, V. S., Bertolino, A., Hyde, T. M., Shannon-Weickert, C., Akil, M., Crook, J., Vakkalanka, R. K., Balkissoon, R., Gibbs, R. A., Kleinman, J. E. and Weinberger, D. R. (2004) Variation in GRM3 affects cognition, prefrontal glutamate, and risk for schizophrenia. Proc. Natl. Acad. Sci. U.S.A. 101, 12604–12609.PubMedCrossRefGoogle Scholar
  10. 10.
    Marti, S. B., Cichon, S., Propping, P. and Nothen, M. (2002) Metabotropic glutamate receptor 3 (GRM3) gene variation is not associated with schizophrenia or bipolar affective disorder in the German population. Am. J. Med. Genet. 114, 46–50.PubMedCrossRefGoogle Scholar
  11. 11.
    Norton, N., Williams, H. J., Dwyer, S., Ivanov, D., Preece, A. C., Gerrish, A., Williams, N. M., Yerassimou, P., Zammit, S., O'Donovan, M. C. and Owen, M. J. (2005) No evidence for association between polymorphisms in GRM3 and schizophrenia. BMC Psychiatry 5, 23.PubMedCrossRefGoogle Scholar
  12. 12.
    Sartorius, L. J., Weinberger, D. R., Hyde, T. M., Harrison, P. J., Kleinman, J. E., and Lipska, B. K. (2008) Expression of a GRM3 splice variant is increased in the dorsolateral prefrontal cortex of individuals carrying a schizophrenia risk SNP. Neuropsychopharmacology 33, 2626–2634.PubMedCrossRefGoogle Scholar
  13. 13.
    Nielsen, K. B., Sorensen, S., Cartegni, L., Corydon, T. J., Doktor, T. K., Schroeder, L. D., Reinert, L. S., Elpeleg, O., Krainer, A. R., Gregersen, N., Kjems, J. and Andresen, B. S. (2007) Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: A synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. Am. J. Hum. Genet. 80, 416–432.PubMedCrossRefGoogle Scholar
  14. 14.
    Yakub, I., Lillibridge, K. M., Moran, A., Gonzalez, O. Y., Belmont, J., Gibbs, R. A. and Tweardy, D. J. (2005) Single nucleotide polymorphisms in genes for 2'-5'-oligoadenylate synthetase and RNAse L in patients hospitalized with West Nile virus infection. J. Infect. Dis. 192, 1741–1748.PubMedCrossRefGoogle Scholar
  15. 15.
    Cartegni, L., Chew, S. L. and Krainer, A. R. (2002) Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rev. Genet. 3, 285–298.PubMedCrossRefGoogle Scholar
  16. 16.
    Fedetz, M., Matesanz, F., Caro-Maldonado, A., Fernandez, O., Tamayo, J. A., Guerrero, M., Delgado, C., Lopez-Guerrero, J. A. and Alcina, A. (2006) OAS1 gene haplotype confers susceptibility to multiple sclerosis. Tissue Antigens 68, 446–449.PubMedCrossRefGoogle Scholar
  17. 17.
    Solis-Anez, E., Delgado-Luengo, W., Borjas-Fuentes, L., Zabala, W., Arraiz, N., Pineda, L., Portillo, M. G., Gonzalez-Ferrer, S., Chacin, J. A., Pena, J., Montiel, C., Morales, A., Rojas de Atencio, A., Canizales, J., Gonzalez, R., Miranda, L. E., Abreu, N., and Delgado, J. (2007) [Molecular analysis of the GABRB3 gene in autistic patients: An exploratory study]. Invest Clin. 48, 225–242.PubMedGoogle Scholar
  18. 18.
    Ross, J. (1995) mRNA stability in mammalian cells. Microbiol. Rev. 59, 423–450.PubMedGoogle Scholar
  19. 19.
    Capon, F., Allen, M. H., Ameen, M., Burden, A. D., Tillman, D., Barker, J. N. and Trembath, R. C. (2004) A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. Hum. Mol. Genet. 13, 2361–2368.PubMedCrossRefGoogle Scholar
  20. 20.
    Jones, P. M. and George, A. M. (2004) The abc transporter structure and mechanism: Perspectives on recent research. Cell. Mol. Life. Sci. 61, 682–699.PubMedCrossRefGoogle Scholar
  21. 21.
    Niemi, M., Arnold, K. A., Backman, J. T., Pasanen, M. K., Godtel-Armbrust, U., Wojnowski, L., Zanger, U. M., Neuvonen, P. J., Eichelbaum, M., Kivisto, K. T. and Lang, T. (2006) Association of genetic polymorphism in ABCC2 with hepatic multidrug resistance-associated protein 2 expression and pravastatin pharmacokinetics. Pharmacogenet. Genomics 16, 801–808.PubMedCrossRefGoogle Scholar
  22. 22.
    Shen, L. X., Basilion, J. P. and Stanton, V. P., Jr. (1999) Single-nucleotide polymorphisms can cause different structural folds of mRNA. Proc. Natl. Acad. Sci. U.S.A. 96, 7871–7876.PubMedCrossRefGoogle Scholar
  23. 23.
    Diatchenko, L., Slade, G. D., Nackley, A. G., Bhalang, K., Sigurdsson, A., Belfer, I., Goldman, D., Xu, K., Shabalina, S. A., Shagin, D., Max, M. B., Makarov, S. S., and Maixner, W. (2005) Genetic basis for individual variations in pain perception and the development of a chronic pain condition. Hum. Mol. Genet. 14, 135–143.PubMedCrossRefGoogle Scholar
  24. 24.
    Nackley, A. G., Shabalina, S. A., Tchivileva, I. E., Satterfield, K., Korchynskyi, O., Makarov, S. S., Maixner, W. and Diatchenko, L. (2006) Human catechol-o-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314, 1930–1933.PubMedCrossRefGoogle Scholar
  25. 25.
    Anfinsen, C. B. (1973) Principles that govern the folding of protein chains. Science 181, 223–230.PubMedCrossRefGoogle Scholar
  26. 26.
    Kimura, M. (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267, 275–276.PubMedCrossRefGoogle Scholar
  27. 27.
    Chamary, J. V., Parmley, J. L. and Hurst, L. D. (2006) Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 7, 98–108.PubMedCrossRefGoogle Scholar
  28. 28.
    Drummond, D. A. and Wilke, C. O. (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134, 341–352.PubMedCrossRefGoogle Scholar
  29. 29.
    Purvis, I. J., Bettany, A. J., Santiago, T. C., Coggins, J. R., Duncan, K., Eason, R. and Brown, A. J. (1987) The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. J. Mol. Biol. 193, 413–417.PubMedCrossRefGoogle Scholar
  30. 30.
    Komar, A. A., Lesnik, T. and Reiss, C. (1999) Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett. 462, 387–391.PubMedCrossRefGoogle Scholar
  31. 31.
    Kimchi-Sarfaty, C., Oh, J. M., Kim, I. W., Sauna, Z. E., Calcagno, A. M., Ambudkar, S. V. and Gottesman, M. M. (2007) A “Silent” Polymorphism in the MDR1 gene changes substrate specificity. Science 315, 525–528.PubMedCrossRefGoogle Scholar
  32. 32.
    Ivanov, I. G., Saraffova, A. A. and Abouhaidar, M. G. (1997) Unusual effect of clusters of rare arginine (AGG) codons on the expression of human interferon alpha 1 gene in Escherichia coli. Int. J. Biochem. Cell. Biol. 29, 659–666.PubMedCrossRefGoogle Scholar
  33. 33.
    Parmley, J. L. and Hurst, L. D. (2007) How do synonymous mutations affect fitness? Bioessays 29, 515–519.PubMedCrossRefGoogle Scholar
  34. 34.
    Bukau, B., Weissman, J. and Horwich, A. (2006) Molecular chaperones and protein quality control. Cell 125, 443–451.PubMedCrossRefGoogle Scholar
  35. 35.
    Ambudkar, S. V., Dey, S., Hrycyna, C. A., Ramachandra, M., Pastan, I. and Gottesman, M. M. (1999) Biochemical, cellular, and pharmacological aspects of the multidrug transporter. Annu. Rev. Pharmacol. Toxicol. 39, 361–398.PubMedCrossRefGoogle Scholar
  36. 36.
    Pauli-Magnus, C. and Kroetz, D. L. (2004) Functional implications of genetic polymorphisms in the multidrug resistance gene MDR1 (ABCB1). Pharm. Res. 21, 904–913.PubMedCrossRefGoogle Scholar
  37. 37.
    Kimchi-Sarfaty, C., Marple, A. H., Shinar, S., Kimchi, A. M., Scavo, D., Roma, M. I., Kim, I. W., Jones, A., Arora, M., Gribar, J., Gurwitz, D., and Gottesman, M. M. (2007) Ethnicity-related polymorphisms and haplotypes in the human ABCB1 gene. Pharmacogenomics 8, 29–39.PubMedCrossRefGoogle Scholar
  38. 38.
    Tsai, C. J., Sauna, Z. E., Kimchi-Sarfaty, C., Ambudkar, S. V., Gottesman, M. M. and Nussinov, R. (2008) Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J. Mol. Biol. 383, 281–291.PubMedCrossRefGoogle Scholar
  39. 39.
    Komar, A. A. (2009) A pause for thought along the co-translational folding pathway. Trends Biochem. Sci. 34, 16–24.PubMedCrossRefGoogle Scholar
  40. 40.
    Clarke, D. T., Doig, A. J., Stapley, B. J. and Jones, G. R. (1999) The alpha-helix folds on the millisecond time scale. Proc. Natl. Acad. Sci. U.S.A. 96, 7232–7237.PubMedCrossRefGoogle Scholar
  41. 41.
    Kiho, Y. and Rich, A. (1964) Induced enzyme formed on bacterial polyribosomes. Proc. Natl. Acad. Sci. U.S.A. 51, 111–118.PubMedCrossRefGoogle Scholar
  42. 42.
    Fedorov, A. N. and Baldwin, T. O. (1995) Contribution of cotranslational folding to the rate of formation of native protein structure. Proc. Natl. Acad. Sci. U.S.A. 92, 1227–1231.PubMedCrossRefGoogle Scholar
  43. 43.
    Fedorov, A. N. and Baldwin, T. O. (1997) Cotranslational protein folding. J. Biol. Chem. 272, 32715–32718.PubMedCrossRefGoogle Scholar
  44. 44.
    Batey, S., Scott, K. A. and Clarke, J. (2006) Complex folding kinetics of a multidomain protein. Biophys. J. 90, 2120–2130.PubMedCrossRefGoogle Scholar
  45. 45.
    Kowarik, M., Kung, S., Martoglio, B. and Helenius, A. (2002) Protein folding during cotranslational translocation in the endoplasmic reticulum. Mol. Cell. 10, 769–778.PubMedCrossRefGoogle Scholar
  46. 46.
    Sauna, Z. E., Kimchi-Sarfaty, C., Ambudkar, S. V. and Gottesman, M. M. (2007) The sounds of silence: Synonymous mutations affect function. Pharmacogenomics 8, 527–532.PubMedCrossRefGoogle Scholar
  47. 47.
    Schumacher, M. A. and Brennan, R. G. (2003) Deciphering the molecular basis of multidrug recognition: Crystal structures of the staphylococcus aureus multidrug binding transcription regulator QacR. Res. Microbiol. 154, 69–77.PubMedCrossRefGoogle Scholar
  48. 48.
    Keller, I., Bensasson, D. and Nichols, R. A. (2007) Transition-transversion bias is not universal: A counter example from grasshopper pseudogenes. PLoS Genet. 3, e22.PubMedCrossRefGoogle Scholar
  49. 49.
    Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C. R., Lim, E. P., Kalyanaraman, N., Nemesh, J., Ziaugra, L., Friedland, L., Rolfe, A., Warrington, J., Lipshutz, R., Daley, G. Q. and Lander, E. S. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22, 231–238.PubMedCrossRefGoogle Scholar
  50. 50.
    Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science 273, 1516–1517.PubMedCrossRefGoogle Scholar
  51. 51.
    Lander, E. S. (1996) The new genomics: Global views of biology. Science 274, 536–539.PubMedCrossRefGoogle Scholar
  52. 52.
    Lazarou, J., Pomeranz, B. H. and Corey, P. N. (1998) Incidence of adverse drug reactions in hospitalized patients: A meta-analysis of prospective studies. JAMA 279, 1200–1205.PubMedCrossRefGoogle Scholar
  53. 53.
    Higgs, P. G. and Ran, W. (2008) Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage. Mol. Biol. Evol. 25, 2279–2291.PubMedCrossRefGoogle Scholar
  54. 54.
    Hurst, L. D. (2002) The ka/ks ratio: Diagnosing the form of sequence evolution. Trends Genet. 18, 486.PubMedCrossRefGoogle Scholar
  55. 55.
    Schattner, P. and Diekhans, M. (2006) Regions of extreme synonymous codon selection in mammalian genes. Nucleic Acids Res. 34, 1700–1710.PubMedCrossRefGoogle Scholar
  56. 56.
    Charmary, J. V. and Hurst, L. D. (2009) How Trivial DNA Changes Can Hurt Health. Sci Am. 30, 46–53.Google Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2003 2009

Authors and Affiliations

  • Ryan Hunt
    • 1
  • Zuben E. Sauna
    • 1
  • Suresh V. Ambudkar
    • 2
  • Michael M. Gottesman
    • 2
  • Chava Kimchi-Sarfaty
    • 1
  1. 1.Laboratory of Hemostasis, Division of HematologyCenter for Biologics Evaluation and Research, Food and Drug AdministrationBethesdaUSA
  2. 2.Laboratory of Cell BiologyNational Cancer Institute, National Institutes of HealthBethesdaUSA

Personalised recommendations