A novel method for detecting intramolecular coevolution: Adding a further dimension to selective constraints analyses

Genetics

Volumn 173, Issue 1, 2006, Pages 9-23

  Fares, Mario A ^a   Travers, Simon A A ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN; GAG PROTEIN; HEAT SHOCK PROTEIN 90;

AMINO ACID SEQUENCE; ARTICLE; COEVOLUTION; CONTROLLED STUDY; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; GENE PRODUCTS, GAG; GROEL PROTEIN; HIV-1; HSP90 HEAT-SHOCK PROTEINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEINS; SELECTION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33744457709     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.053249     Document Type: Article

References (64)

1. ANÉ, C., J. G. BURLEIGH, M. M. MCMAHON and M. J. Sanderson, 2004 Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol. 22: 914-924.
2. BEREZIN, C., F. GLASER, J. ROSENBERG, I. PAZ, T. PUPKO et al., 2004 ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20: 1322-1324.
3. BERGLUND, A.-C., B. WALLNER, A. ELOFSSON and D. A. LIBERLES, 2005 Tertiary windowing to detect positive diversifying selection. J. Mol. Evol. 60: 499-504.
4. BOISVERT, D. C., J. WANG, Z. OTWINOWSKI, A. L. HORWICH and P. B. SIGLER, 1996 The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATP gamma S. Nat. Struct. Biol. 3: 170-177.
5. BRAIG, K., Z. OTWINOWSKI, R. HEGDE, D. C. BOISVERT, A. JOACHIMIAK et al., 1994 The crystal structure of the bacterial chaperonin GroEL at 2.8Å. Nature 371: 578-586.
6. BRAIG, K., P. D. ADAMS and A. T. BRÜNGER, 1995 Conformational variability in the refined structure of the chaperonin GroEL at 2.8Å resolution. Nat. Struct. Biol. 2: 1083-1094.
7. BUCHNER, J., 1999 Hsp90 & Co. - a holding for folding. Trends Biochem. Sci. 24: 136-141.
8. CAPLAN, A. J., 1999 Hsp90's secrets unfold: new insights from structural and functional studies. Trends Cell Biol. 9: 262-268.
9. CHADLI, A., I. BOUHOUCHE, W. SULLIVAN, B. STENSGARD, N. MCMAHON et al., 2000 Dimerization and N-terminal domain proximity underlie the function of themolecular chaperone heat shock protein 90. Proc. Natl. Acad. Sci. USA 97: 12524-12529.
10. CHELVANAYAGAM, G., A. EGGENSCHWILER, L. KNECHT, G. H. CONNET and S. A. BENNER, 1997 An analysis of simultaneous variation in protein structures. Protein Eng. 10: 307-316.
11. CHEN, S., W. P. SULLIVAN, D. O. TOFT and D. F. SMITH, 1998 Differential interactions of p23 and the TPR-containing proteins Hop, Cyp40, FKBP52 and FKBP51 with Hsp90 mutants. Cell Stress Chaperones 3: 118-129.
12. CLARK, A. G., and T. H. KAO, 1991 Excess nonsynonymous substitution of shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proc. Natl. Acad. Sci. USA 88: 9823-9827.
13. DEUERLING, E., A. SCHULZE-SPECKING, T. TOMOYASU, A. MOGK and B. BUKAU, 1999 Trigger factor and DnaK cooperate in folding of newly synthesized proteins. Nature 400: 693-696.
14. DIMMIC, M. W., and M. J. HUBISZ, 2005 Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics 21: i126-i135.
15. DUTHEIL, J., T. PUPKO, A. JEAN-MARIE and N. GALTIER, 2005 A model-based approach for detecting co-evolving positions in a molecule. Mol. Biol. Evol. 22: 1919-1928.
16. FARES, M. A., 2004 SWAPSC: sliding-window analysis procedure to detect selective constraints. Bioinformatics 20: 2867-2868.
17. FARES, M. A., S. F. ELENA, J. ORTIZ, A. MOYA and E. BARRIO, 2002a A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol. Evol. 55: 509-521.
18. FARES, M. A., E. BARRIO, B. SABATER-MUNOZ and A. MOYA, 2002b The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection. Mol. Biol. Evol. 19: 1162-1170.
19. FARES, M. A., A. MOYA and E. BARRIO, 2004 GroEL and the maintenance of bacterial endosymbiosis. Trends Genet. 20: 413-416.
20. FITCH, W. M., and E. MARKOWITZ, 1970 An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4: 579-593.
21. FUJITA, N., S. SATO, A. ISHIDA and T. TSURUO, 2002 Involvement of Hsp90 in signaling and stability of 3-phosphoinositide-dependent kinase-1. J. Biol. Chem. 277: 10346-10353.
22. FUKAMI-KOBAYASHI, K., D. R. SCHREIBER and S. A. BENNER, 2002 Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J. Mol. Biol. 319: 729-743.
23. GALTIER, N., 2004 Sampling properties of the bootstrap support in molecular phylogeny: influence of nonindependence among sites. Syst. Biol. 53: 38-46.
24. GLOOR, G. B., L. C. MARTIN, L. M. WAHL and S. D. DUMN, 2005 Mutual information in protein multiple sequence alignment reveals two classes of coevolving positions. Biochemistry 44: 7156-7165.
25. GÖBEL, U.,C. SANDER, R. SCHNEIDER and A. VALENCIA, 1994 Correlated mutations and residue contacts in proteins. Proteins 18: 309-317.
26. GOTTLINGER, H. G., J. G. SODROSKI and W. A. HASELTINE, 1989 Role of capsid precursor processing and myristoylation in morphogenesis and infectivity of human immunodeficiency virus type I. Proc. Natl. Acad. Sci. USA 86: 5781-5785.
27. HENIKOFF, S., and J. G. HENIKOFF, 1992 Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89: 10915-10919.
28. HERBECK, J. T., D. J. FUNK, P. H. DEGNAN and J. J. WERNEGREEN, 2003 A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL. Genetics 165: 1651-1660.
29. HUGHES, A. L., and M. NEI, 1988 Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
30. JEANMOUGIN, F., J. D. THOMPSON, M. GOUY, D. G. HIGGINS and T. J. GIBSON, 1998 Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23: 403-405.
31. JONES, D. T., W. R. TAYLOR and J. M. THORNTON, 1992 The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8: 275-282.
32. JOHNSON, B. D., A. CHADLI, S. J. FELTS, I. BOUNHOUCHE, M. G. CATELLI et al., 2000 Hsp90 chaperone activity requires the full-length protein and interaction among its multiple domains. J. Biol. Chem. 275: 32499-32507.
33. KIMURA, M., 1983 The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK.
34. KORBER, B. T., R. M. FARBER, D. H. WOLPERT and A. S. LAPEDES, 1993 Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA 8: 1549-1560.
35. LANDRY, S. J., J. ZEILSTRA-RYALLS, O. FAYET, C. GEORGOPOULOS and L. M. GIERASCH, 1993 Characterization of a functionally important mobile domain in GroES. Nature 364: 255-258.
36. LOCKHART, P. J., M. A. STEEL, A. C. BARBROOK, D. H. HUSON, M. A. CHARLESTON et al., 1998 A covariatoid model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15: 1183-1188.
37. LOCKLESS, W., and R. RANGANATHAN, 1999 Evolutionary conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
38. MAYER, M. P., and B. BUKAU, 1999 Molecular chaperones: the busy life of Hsp90. Curr. Biol. 9: R322-R325.
39. MEYER, P., C. PRODROMOU, B. HU, C. VAUGHAN, S. M. ROE et al., 2003 Structural and functional analysis of the middle segment of hsp90: implications for ATP hydrolysis and client protein and cochaperone interactions. Mol. Cell 11: 647-658.
40. NEHER, E., 1994 How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. USA 91: 98-102.
41. PAZOS, F., M. HELMER-CITTERICH, G. AUSIELLO and A. VALENCIA, 1997 Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271: 511-523.
42. POLLOCK, D. D., and W. R. TAYLOR, 1997 Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10: 647-657.
43. POLLOCK, D. D., W. R. TAYLOR and N. GOLDMAN, 1999 Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol. 287: 187-198.
44. PRATT, W. B., 1998 The hsp90-based chaperone system: involvement in signal transduction from a variety of hormone and growth factor receptors. Proc. Soc. Exp. Biol. Med. 217: 420-434.
45. PRITCHARD, L., and M. J. DUFTON, 2000 Do proteins learn to evolve? The hopfield network as a basis for the understanding of protein evolution. J. Theor. Biol. 202: 77-86.
46. PRITCHARD, L., P. M. O. BLADON, J. J. MITCHELL and M. J. DUFTON, 2001 Evaluation of a novel method for the identification of coevolving protein residues. Protein Eng. 14: 549-555.
47. PRODROMOU, C., S. M. ROE, R. O'BRIEN, J. E. LADBURY, P. W. PIPER et al., 1997 Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Cell 90: 65-75.
48. PRODROMOU, C., G. SILIGARDI, R. O'BRIEN, D. N. WOOLFSON, L. REGAN et al., 1999 Regulation of Hsp90 ATPase activity by the tetratricopeptide repeat (TPR)-domain co-chaperones. EMBO J. 18: 754-762.
49. ROBERTSON, D. L., J. P. ANDERSON, J. A. BRADAC, J. K. CARR, B. FOLEY et al., 2000 HIV-1 nomenclature proposal. Science 288: 55-56.
50. SHINDYALOV, I. N., N. A. KOLCHANOV and C. SANDER, 1994 Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7: 349-358.
51. SÖTI, C., A. RACZ and P. CSERMELY, 2002 A nucleotide-dependent molecular switch controls ATP binding at the C-terminal domain of Hsp90. N-terminal nucleotide binding unmasks a C-terminal binding pocket. J. Biol. Chem. 277: 7066-7075.
52. SÜEL, G. M., S. W. LOCKLESS, A. A. WALL and R. RANGANATHAN, 2003 Evolutionary conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10: 59-69.
53. SUZUKI, Y., 2004 Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Mol. Biol. Evol. 21: 2352-2359.
54. SUZUKI, Y., and T. GOJOBORI, 1999 A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16: 1315-1328.
55. SWOFFORD, D. L., 1998 PAUP *. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA.
56. TAYLOR, W. R., and K. HATRICK, 1994 Compensating changes in protein multiple sequence alignments. Protein Eng. 7: 341-348.
57. THULASIRAMAN, V., C. F. YANG and J. FRYDMAN, 1999 In vivo newly translated polypeptides are sequestered in a protected folding environment. EMBO J. 18: 85-95.
58. TILLIER, E. R., and R. A. COLLINS, 1995 Neighbor-joining and maximum-likelihood with rna sequences - addressing the interdependence of sites. Mol. Biol. Evol. 12: 7-15.
59. TILLIER, E. R., and T. W. LUI, 2003 Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics 19: 750-755.
60. TRAVERS, S. A., M. J. O'CONNELL, G. P. MCCORMACK and J. O. MCINERNEY, 2005 Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes. J. Virol. 79: 1836-1841.
61. TUFFLEY, C., and M. STEEL, 1998 Modelling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147: 63-91.
62. WAIN-HOBSON, S., P. SONIGO, O. DANOS, S. COLE and M. ALIZON, 1985 Nucleotide sequence of the AIDS virus, LAV. Cell 40: 9-17.
63. YANG, W., J. P. BIELAWSKI and Z. YANG, 2003 Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J. Mol. Evol. 57: 212-221.
64. YANG, Z., R. NIELSEN, N. GOLDMAN and A.-M. K. PEDERSEN, 2000 Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 153: 1077-1089.