Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins

Methods in Enzymology

Volumn 395, Issue , 2005, Pages 652-670

  Chang, Belinda S W ^a   Ugalde, Juan A ^a   Matz, Mikhail V ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; MESSENGER RNA; OLIGONUCLEOTIDE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

CHROMATOPHORE; CONTROLLED STUDY; GENE SYNTHESIS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOSPHORYLATION; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FUNCTION; REVIEW;

EID: 19944399387     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)95034-9     Document Type: Article

References (72)

1. Adachi J., Hasegawa M. "MOLPHY." 1994;Institute of Statistical Mechanics, Tokyo, Japan
2. Adachi J., Hasegawa M. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:1996;459-468
3. Adey N.B., Tollefsbol T.O., Sparks A.B., Edgell M.H., Hutchison C.A. III. Molecular resurrection of an extinct ancestral promoter for mouse L1. Proc. Natl. Acad. Sci. USA. 91:1994;1569-1573
4. Bielawski J.P., Yang Z. Maximum likelihood methods for detecting adaptive evolution after gene duplication. J. Struct. Funct. Genomics. 3:2003;201-212
5. Buckley T.R. Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Syst. Biol. 51:2002;509-523
6. Cao Y., Adachi J., Yano T.-A., Hasegawa M. Phylogenetic place of guinea pigs: No support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences. Mol. Biol. Evol. 11:1994;593-604
7. Chandrasekharan U.M., Sanker S., Glynias M.J., Karnik S.S., Husain A. Angiotensin II - forming activity in a reconstructed ancestral chymase. Science. 271:1996;502-505
8. Chang B.S., Donoghue M.J. Phylogenetic reconstruction of the origin of rod opsins from cone opsin ancestors. submitted. 2005
9. Chang B.S., Kazmi M.A., Sakmar T.P. Synthetic gene technology: Applications to ancestral gene reconstruction and structure-function studies of receptors. Methods Enzymol. 343:2002a;274-294
10. Chang B.S.W., Donoghue M.J. Recreating ancestral proteins. Trends Ecol. Evol. 15:2000;109-114
11. Chang B.S.W., Jonsson K., Kazmi M., Donoghue M.J., Sakmar T.P. Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol. 19:2002b;1483-1489
12. Cunningham C.W., Omland K.E., Oakley T.H. Reconstructing ancestral character states: A critical reappraisal. Trends Ecol. Evol. 13:1998;361-366
13. Dayhoff M.O. A model of evolutionary change in proteins. Matrices for detecting distant relationships. Dayhoff M.O. "Atlas of Protein Sequence and Structure," Vol. 5(Suppl. 3):1978;345-358 National Biomedical Research Foundation, Washington, DC
14. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:1981;368-376
15. Felsenstein J. "PHYLIP: Phylogeny Inference Package." 1991;University of Washington, Seattle, WA
16. Ferretti L., Karnik S.S., Khorana H.G., Nassal M., Oprian D.D. Total synthesis of a gene for bovine rhodopsin. Proc. Natl. Acad. Sci. USA. 83:1986;599-603
17. Galtier N., Gouy M. Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:1998;871-879
18. Gaucher E.A., Thomson J.M., Burgan M.F., Benner S.A. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature. 425:2003;285-288
19. Goldman N. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:1993;345-361
20. Goldman N., Whelan S. A novel use of equilibrium frequencies in models of sequence evolution. Mol. Biol. Evol. 19:2002;1821-1831
21. Goldman N., Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:1994;725-736
22. Griswold K.E., Mahmood N.A., Iverson B.L., Georgiou G. Effects of codon usage versus putative 5′-mRNA structure on the expression of Fusarium solani cutinase in the Escherichia coli cytoplasm. Protein Exp. Purif. 27:2003;134-142
23. Hasegawa M., Fujiwara M. Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol. Phylogenet. Evol. 2:1993;1-5
24. Heim R., Prasher D.C., Tsien R.Y. Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. 91:1994;12501-12504
25. Huelsenbeck J.P. Is the Felsenstein zone a fly trap? Syst. Biol. 46:1997;69-74
26. Huelsenbeck J.P. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst. Biol. 47:1998;519-537
27. Huelsenbeck J.P., Bollback J.P. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50:2001;351-366
28. Huelsenbeck J.P., Larget B., Miller R.E., Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51:2002;673-688
29. Huelsenbeck J.P., Rannala B. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science. 276:1997;227-232
30. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:2001;754-755
31. Jermann T.M., Opitz J.G., Stackhouse J., Benner S.A. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature. 374:1995;57-59
32. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comp. Appl. Biosci. 8:1992;275-282
33. Jukes T.H., Cantor C.R. Evolution of protein molecules. Munro H.N. "Mammalian Protein Metabolism" 1969;21-132 Academic Press, New York
34. Kane J.F. Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr. Opin. Biotech. 6:1995;494-500
35. Karnik S.S., Nassal M., Doi T., Jay E., Sgaramella V., Khorana H.G. Structure-function studies on bacteriorhodopsin. II. Improved expression of the bacterio-opsin gene in Escherichia coli. J. Biol. Chem. 262:1987;9255-9263
36. Kelmanson I.V., Matz M.V. Molecular basis and evolutionary origins of color diversity in great star coral Montastrea cavernosa (Scleractinia: Faviida). Mol. Biol. Evol. 20:2003;1125-1133
37. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:1980;111-120
38. Kishino H., Miyata T., Hasegawa M. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31:1990;151-160
39. Koshi J.M., Goldstein R.A. Probabilistic reconstruction of ancestral protein sequences. J. Mol. Evol. 42:1996;313-320
40. Labas Y.A., Gurskaya N.G., Yanushevich Y.G., Fradkov A.F., Lukyanov K.A., Lukyanov S.A., Matz M.V. Diversity and evolution of the green fluorescent protein family. Proc. Natl. Acad. Sci. 99:2002;4256-4261
41. Lewis P.O. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. Soltis P.S., Soltis D.E., Doyle J.J. "Molecular Systematics of Plants II: DNA Sequencing" 1998;132-163 Kluwer, Boston
42. Lippincott-Schwartz J., Patterson G.H. Development and use of fluorescent protein markers in living cells. Science. 300:2003;87-91
43. Maddison W.P. Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees. Syst. Biol. 44:1995;474-481
44. Maddison W.P., Maddison D.R. "MacClade." 1993;Sinauer Associates, Sunderland, MA
45. Malcolm B.A., Wilson K.P., Matthews B.W., Kirsch J.F., Wilson A.C. Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature. 345:1990;86-89
46. Matz M.V., Lukyanov K.A., Lukyanov S.A. Family of the green fluorescent protein: Journey to the end of the rainbow. Bioessays. 24:2002;953-959
47. Muse S.V., Gaut B.S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:1994;715-724
48. Nielsen R., Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:1998;929-936
49. Omland K.E. The assumptions and challenges of ancestral state reconstructions. Syst. Biol. 48:1999;604-611
50. Posada D., Crandall K.A. MODELTEST: Testing the model of DNA substitution. Bioinformatics. 14:1998;817-818
51. Roth M.E., Feng L., McConnell K.J., Schaffer P.J., Guerra C.E., Affourtit J.P., Piper K.R., Guccione L., Hariharan J., Ford M.J., Powell S.W., Krishnaswamy H., Lane J., Intrieri G., Merkel J.S., Perbost C., Valerio A., Zolla B., Graham C.D., Hnath J., Michaelson C., Wang R., Ying B., Halling C., Parman C.E., Raha D., Orr B., Jedrzkiewicz B., Liao J., Tevelev A., Mattessich M.J., Kranz D.M., Lacey M., Kaufman J.C., Kim J., Latimer D.R., Lizardi P.M. Expression profiling using a hexamer-based universal microarray. Nat. Biotechnol. 22:2004;418-426
52. Shagin D.A., Barsova E.V., Yanushevich Y.G., Fradkov A.F., Lukyanov K.A., Labas Y.A., Semenova T.N., Ugalde J.A., Meyers A., Nunez J.M., Widder E.A., Lukyanov S.A., Matz M.V. GFP-like proteins as ubiquitous metazoan superfamily: Evolution of functional features and structural complexity. Mol. Biol. Evol. 21:2004;841-850
53. Sharp P.M., Cowe E., Higgins D.G., Shields D.C., Wolfe K.H., Wright F. Codon usage patterns in Escherichia-coli, Bacillus-subtilis, Saccharomyces-cerevisiae, Schizosaccharomyces-pombe, Drosophila-melanogaster and Homo-Sapiens - a review of the considerable within-species diversity. Nucleic Acids Res. 16:1988;8207-8211
54. Sinclair G., Choy F.Y.M. Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris. Prot. Exp. Purif. 26:2002;96-105
55. Stewart C.-B. Active ancestral molecules. Nature. 374:1995;12-13
56. Sun H.M., Merugu S., Gu X., Kang Y.Y., Dickinson D.P., Callaerts P., Li W.H. Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies. Mol. Biol. Evol. 19:2002;1490-1500
57. Swofford D.L. "PAUP*, Phylogenetic Analysis Using Parsimony (*and Other Methods)." 2002;Sinauer, Sunderland, MA
58. Swofford D.L., Olsen G.J., Waddell P.J., Hillis D.M. Phylogenetic Inference. Hillis D.M., Moritz C., Mable B.K. "Molecular Systematics" 1996;407-514 Sinauer, Sunderland, MA
59. Tavare L. Some probabilistic and statistical problems of the analysis of DNA sequences. Lect. Math. Life Sci. 17:1986;57-86
60. Thornton J.W. Resurrecting ancient genes: Experimental analysis of extinct molecules. Nat. Rev. Gen. 5:2004;366-375
61. Thornton J.W., Need E., Crews D. Resurrecting the ancestral steroid receptor: Ancient origin of estrogen signaling. Science. 301:2003;1714-1717
62. Ugalde J.A., Chang B.S., Matz M.V. Evolution of coral pigments recreated. Science. 305:(5689):2004;1433
63. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:1994;306-314
64. Yang Z. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:1997;555-556
65. Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:1998;568-573
66. Yang Z., Bielawski J.P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15:2000;496-503
67. Yang Z., Goldman N., Friday A. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11:1994;316-324
68. Yang Z., Kumar S., Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics. 141:1995;1641-1650
69. Yang Z., Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:2002;908-917
70. Yang Z., Swanson W.J. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19:2002;49-57
71. Yang Z.H., Nielsen R., Goldman N., Pedersen A.M.K. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155:2000;431-449
72. Zhang J.Z., Rosenberg H.F. Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proc. Natl. Acad. Sci. 99:2002;5486-5491