An ancient frame-shifting event in the highly conserved KPNA gene family has undergone extensive compensation by natural selection in vertebrates

BioSystems

Volumn 105, Issue 3, 2011, Pages 210-215

  Bozorgmehr, Joseph Esfandiar Hannon ^a  

^a NONE   (United Kingdom)

Author keywords

Compensatory mutation; Gene duplication; Karyopherins; Molecular adaptation

Indexed keywords

KARYOPHERIN;

BIOCHEMICAL COMPOSITION; COMPENSATION; DIVERGENCE; EVOLUTIONARY THEORY; GENE EXPRESSION; KARYOLOGY; MOLECULAR ANALYSIS; MUTATION; NATURAL SELECTION; OPTIMIZATION; PRESERVATION; VERTEBRATE;

ARTICLE; FRAMESHIFT MUTATION; GENE; GENE DUPLICATION; GENE MUTATION; GENE SEQUENCE; GENETIC CONSERVATION; KPNA GENE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NATURAL SELECTION; NONHUMAN; VERTEBRATE;

VERTEBRATA;

EID: 79961126441     PISSN: 03032647     EISSN: 18728324     Source Type: Journal    
DOI: 10.1016/j.biosystems.2011.04.006     Document Type: Article

References (54)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215(3):403-410.
2. Collins D.W., Jukes T.H. Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomics 1994, 20(3):386-396.
3. Davis B.H., Poon A.F., Whitlock M.C. Compensatory mutations are repeatable and clustered within proteins. Proc. Biol. Sci. 2009, 276(1663):1823-1827.
4. Dingwall C., Laskey R.A. Protein import into the cell nucleus. Annu. Rev. Cell Biol. 1986, 2:367-390.
5. Dyson H.J., Wright P.E., Scheraga H.A. The role of hydrophobic interactions in initiation and propagation of protein folding. Proc. Natl. Acad. Sci. U.S.A. 2006, 103(35):13057-13061.
6. Edger P.P., Pires J.C Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res. 2009, 17(5):699-717.
7. Fagotto F., Glück U., Gumbiner B.M. Nuclear localization signal-independent and importin/karyopherin-independent nuclear import of beta-catenin. Curr. Biol. 1998, 8(4):181-190.
8. Galtier N., Duret L. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet. 2007, 6:273-277.
9. Gibson T.A., Goldberg D.S. Questioning the ubiquity of neofunctionalization. PLoS Comput. Biol. 2009, 1:e1000252.
10. Goldfarb D.S., Corbett A.H., Mason D.A., Harreman M.T., Adam S.A. Importin alpha: a multipurpose nuclear-transport receptor. Trends Cell Biol. 2004, 14(9):505-514.
11. Gu Z., Steinmetz L.M., Gu X., Scharfe C., Davis R.W., Li W.H. Role of duplicate genes in genetic robustness against null mutations. Nature 2003, 421(6918):63-66.
12. Hanada K., Kuromori T., Myouga F., Toyoda T., Li W.H., Shinozaki K. Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis. Genome Biol. Evol. 2009, 1:409-414.
13. Hartl D.L., Taubes C.H. Compensatory nearly neutral mutations: selection without adaptation. J. Theor. Biol. 1996, 182:303-309.
14. Hillier, et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432(7018):695-716.
15. Hodges R.S., Zhou N.E., Kay C.M., Semchuk P.D. Synthetic model proteins: contribution of hydrophobic residues and disulfide bonds to protein stability. Pept. Res. 1990, 3(3):123-137.
16. Hsiao T.L., Vitkup D. Role of duplicate genes in robustness against deleterious human mutations. PLoS Genet. 2008, 4(3):e1000014.
17. Hughes A.L., Ota T., Nei M. Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol. Biol. Evol. 1990, 7:515-524.
18. Hughes A.L., Packer B., Welch R., Bergen A.W., Chanock S.J., Yeager M. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. U.S.A. 2003, 100(26):15754-15757.
19. Innan H., Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat. Rev. Genet. 2010, 11:97-108.
20. Jordan I., Wolf Y., Koonin E. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol. Biol. 2004, 4:22.
21. Kelley J.B., Talley A.M., Spencer A., Gioeli D., Paschal B.M. Karyopherin alpha7 (KPNA7), a divergent member of the importin alpha family of nuclear import receptors. BMC Cell. Biol. 2010, 11:63.
22. Khachane A.N., Harrison P.M. Strong association between pseudogenization mechanisms and gene sequence length. Biol. Direct 2009, 4:38.
23. Köhler M., Speck C., Christiansen M., Bischoff F.R., Prehn S., Haller H., Görlich D., Hartmann E. Evidence for distinct substrate specificities of importin alpha family members in nuclear protein import. Mol. Cell. Biol. 1999, 19(11):7782-7791.
24. Li X., Sun L., Jin Y. Identification of karyopherin-alpha 2 as an Oct4 associated protein. J. Genet. Genomics 2008, 35(12):723-728.
25. Lin K., Simossis V.A., Taylor W.R., Heringa J. A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 2005, 21(2):152-159.
26. Lynch M., Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics 2000, 154(1):459-473.
27. Maltsev N., Glass E.M., Ovchinnikova G., Gu Z. Molecular mechanisms involved in robustness of yeast central metabolism against null mutations. J. Biochem. 2005, 137(2):177-187.
28. Mason D.A., Stage D.E., Goldfarb D.S. Evolution of the metazoan-specific importin alpha gene family. J Mol Evol. 2009, 68(4):351-365.
29. Modesto S.P., Anderson J.S. The phylogenetic definition of reptilia. Syst. Biol. 2004, 53(5):815-821.
30. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3(5):418-426.
31. Newmeyer D.D. The nuclear pore complex and nucleocytoplasmic transport. Curr. Opin. Cell Biol. 1993, 5(3):395-407.
32. Ohno S Evolution by Gene Duplication 1970, Springer-Verlag, New York.
33. Qian W., Liao B.Y., Chang A.Y., Zhang J. Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet. 2010, 0:00.
34. Raes J., Van de Peer Y Functional divergence of proteins through frameshift mutations. Trends Genet. 2005, 21(8):428-431.
35. Relf W.A., Martin D.R., Sriprakash KS Antigenic diversity within a family of M proteins from group A streptococci: evidence for the role of frameshift and compensatory mutations. Gene 1994, 144(1):25-30.
36. Resch A.M., Carmel L., Mariño-Ramírez L., Ogurtsov A.Y., Shabalina S.A., Rogozin I.B., Koonin E.V. Widespread positive selection in synonymous sites of mammalian genes. Mol. Biol. Evol. 2007, 24(8):1821-1831.
37. Rice P., Longden I., Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000, 16(6):276-277.
38. Roth C., Rastogi S., Arvestad L., Dittmar K., Light S., Ekman D., Liberles D.A. Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. J. Exp. Zool. B Mol. Dev. Evol. 2006, 10.1002/jez.b.21124.
39. Samuel D., Kumar T.K., Ganesh G., Jayaraman G., Yang P.W., Chang M.M., Trivedi V.D., Wang S.L., Hwang K.C., Chang D.K., Yu C. Proline inhibits aggregation during protein refolding. Protein Sci. 2000, 9(2):344-352.
40. Santiveri C.M.A., Jiménez A. Tryptophan residues: scarce in proteins but strong stabilizers of beta-hairpin peptides. Pept. Sci. 2010, 9999.
41. Scherer S.W., Okamura K., Feuk L., Marquès-Bonet T., Navarro A. Frequent appearance of novel protein-coding sequences by frameshift translation. Genomics 2006, 88:690-697.
42. Shiba K., Takahashi Y., Noda T Creation of libraries with long ORFs by polymerization of a microgene. Proc. Natl. Acad. Sci. U.S.A. 1997, 94(8):3805-3810.
43. Smith Temple F., Waterman Michael S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197.
44. Teichmann S.A., Babu M.M. Gene regulatory network growth by duplication. Nat. Genet. 2004, 36(5):492-496.
45. Thompson J.D., Higgins D.G., Gibson T.J., CLUSTAL W Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22(22):4673-4680.
46. Vavouri T., Semple J.I., Lehner B Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution. Trends Genet. 2008, 24:485-488.
47. Vogel C., Orozco M., Teichmann S.A., de la Cruz X., Talavera D. The (in) dependence of alternative splicing and gene duplication. PloS Comput. Biol. 2007, 3(3).
48. Weis K., Ryder U., Lamond A.I. The conserved aminoterminal domain of hSRPla is essential for nuclear protein import. EMBO J. 1996, 15:1818-1825.
49. Yang Z., Yoder A. Estimation of the transition/transversion rate bias and species sampling. J. Mol. Evol. 1999, 48:274-283.
50. Yang Z PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 1997, 13:555-556.
51. Zhang J. Evolution by gene duplication: an update. Trends Ecol. Evol. 2003, 18(6):292-298.
52. Zhang J. Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J. Mol. Evol. 2000, 50:56-68.
53. Zhao H., Li Q., Li J., Zeng C., Hu S., Yu J. The study of neighboring nucleotide composition and transition/transversion bias. Sci. China C Life Sci. 2006, 49(4):395-402.
54. Zannini L., Lecis D., Lisanti S., Benetti R., Buscemi G., Schneider C., Delia D. Karyopherin-alpha2 protein interacts with Chk2 and contributes to its nuclear import. J Biol Chem. 2003, 278(43):42346-42351.