The core domain of retrotransposon integrase in Hordeum: Predicted structure and evolution

Molecular Biology and Evolution

Volumn 15, Issue 9, 1998, Pages 1135-1144

  Suoniemi, Annu ^a   Tanskanen, Jaakko ^a   Pentikäinen, Olli ^b,c   Johnson, Mark S ^b,c   Schulman, Alan H ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF TURKU   (Finland)

^c ÅBO AKADEMI UNIVERSITY   (Finland)

Author keywords

Barley; Hordeum vulgare; Integrase; Molecular evolution; Retrotransposon; Tertiary structure

Indexed keywords

INTEGRASE;

ARTICLE; AVIAN SARCOMA VIRUS; BARLEY; CRYSTAL STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; RETROPOSON; RNA TRANSLATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AVES; AVIAN SARCOMA VIRUS; EMBRYOPHYTA; HORDEUM; HORDEUM VULGARE SUBSP. VULGARE; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0031874963     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026021     Document Type: Article

References (53)

1. BACON, D. J., and W. F. ANDERSON. 1988. A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6: 219-220.
2. BAKER, T. A., and L. LUO. 1994. Identification of residues in the Mu transposase essential for catalysis. Proc. Natl. Acad. Sci. USA 91:6654-6658.
3. BUJACZ, G., M. JASKOLSKI, J. ALEXANDRATOS, A. WLODAWER, G. MERKEL, R. A. KATZ, and A. M. SKALKA. 1995. High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J. Mol. Biol. 253:333-346.
4. _. 1996. The catalytic domain of avian sarcoma virus integrase: conformation of the active site residues in the presence of divalent cations. Structure 4:89-96.
5. CANNON, P. M., E. B. BYLES, S. M. KINGSMAN, and A. J. KINGSMAN. 1996. Conserved sequences in the carboxy terminus of integrase that are essential for human immunodeficiency virus type I replication. J. Virol. 70:651-657.
6. DYDA, F., A. B. HICKMAN, T. M. JENKINS, A. ENGELMAN, R. CRAIGIE, and D. R. DAVIES. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266:1981-1986.
7. FLAVELL, A. J., D. B. SMITH, and A. KUMAR. 1992. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol. Gen. Genet. 231:233-242.
8. GAUT, B. S., and M. T. CLEGG. 1991. Molecular evolution of alcohol dehydrogenase 1 in members of the grass family. Proc. Natl. Acad. Sci. USA 88:2060-2064.
9. GENETICS COMPUTER GROUP. 1994. Program manual for the Wisconsin Sequence Analysis Package. Version 8. Madison, Wis.
10. GOJOBORI, T., and S. YOKOYAMA. 1985. Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and its cellular homologues. Proc. Natl. Acad. Sci. USA 82: 4198-4201.
11. HICKMAN, A. B., I. PALMER, A. ENGELMAN, R. CRAIGIE, and P. WINGFIELD. 1994. Biophysical and enzymatic properties of the catalytic domain of HIV-1 integrase. J. Biol. Chem. 269:29279-29287.
12. HUANG, X. 1992. A contig assembly program based on sensitive detection of fragment overlaps. Genomics 14:18-25.
13. JOHNSON, M. S., A.-M. HOFFRÉN, and V. COCKCROFT. 1995. Macromolecular modeling for the 21st century. Kemia Kemi 22:691-695.
14. JOHNSON, M. S., A. C. W. MAY, M. A. RODIONOV, and J. P. OVERINGTON. 1996. Discrimination of common protein folds: applications of structural information to sequence/ structure comparisons. Methods Enzymol. 266:575-598.
15. JOHNSON, M. S., and J. P. OVERINGTON. 1993. A structural basis for the comparison of sequences: an evaluation of scoring methodologies. J. Mol. Biol. 233:716-738.
16. JOHNSON, M. S., J. P. OVERINGTON, and T. L. BLUNDELL. 1993. Alignment and searching for common folds using a data bank of structural templates. J. Mol. Biol. 231:735-752.
17. JOHNSON, M. S., A. ŠALI, and T. L. BLUNDELL. 1990. Phylogenetic relationships from three-dimensional structures of proteins. Methods Enzymol. 183:670-690.
18. JOHNSON, M. S., N. SRINIVASAN, R. SOWDHAMINI, and T. L. BLUNDELL. 1994. Knowledge-based modeling. CRC Crit. Rev. Biochem. Mol. Biol. 29:1-68.
19. JACOBSEN, N., and R. VON BOTHMER. 1992. Supraspecific groups in the genus Hordeum. Hereditas 116:21-24.
20. JØRGENSEN, R. B. 1986. Relationships in the barley genus (Hordeum): an electrophoretic examination of proteins. Hereditas 104:273-291.
21. KANKAANPÄÄ, J., L. MANNONEN, and A. H. SCHULMAN. 1996. The genome sizes of Hordeum species show considerable variation. Genome 39:730-735.
22. KRAULIS, P. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallogr. 24:946-950.
23. KULKOSKY, J., K. S. JONES, R. A. KATZ, J. P. G. MACK, and A. M. SKALKA. 1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12:2331-2338.
24. MCALLISTER, B. F., and J. H. WERREN. 1997. Phylogenetic analysis of a retrotransposon with implications for strong evolutionary constraints on reverse transcriptase. Mol. Biol. Evol. 14:69-80.
25. MANNINEN, I., and A. H. SCHULMAN. 1993. BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol. Biol. 22:829-846.
26. MARILLIA, E. F., and G. J. SCOLES. 1996. The use of RAPD markers in Hordeum phylogeny. Genome 39:646-654.
27. MATSUOKA, Y., and K. TSUNEWAKI. 1996. Wheat retrotransposon families identified by reverse transcriptase domain analysis. Mol. Biol. Evol. 13:1384-1392.
28. MERRITT, E. A., and M. E. P. MURPHY. 1994. Raster3D version 2.0 - a program for photorealistic molecular graphics. Acta Crystallogr. D 50:869-873.
29. MIZUUCHI, K. 1992. Transpositional recombination: mechanistic insights from studies of Mu and other elements. Annu. Rev. Biochem. 61:1011-1051.
30. MOORE, S. P., and D. J. GARFINKEL. 1994. Expression and partial purification of enzymatically active recombinant Ty1 integrase in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 91:1843-1847.
31. MOORE, S. P., M. POWERS, and D. J. GARFINKEL. 1995. Substrate specificity of Ty1 integrase. J. Virol. 69:4683-4692.
32. NEVO, E., D. ZOHARY, A. H. D. BROWN, and M. HABER. 1979. Genetic diversity and environmental associations of wild barley, Hordeum spontaneum, in Israel. Evolution 33:815-833.
33. PEARCE, S. R., G. HARRISON, J. S. HESLOP-HARRISON, A. J. FLAVELL, and A. KUMAR. 1997. Characterisation and genomic organisation of Ty1-copia group retrotransposons in rye (Secale cereale). Genome 40:1-9.
34. PEARCE, S. R., G. HARRISON, D. LI, J. S. HESLOP-HARRISON, A. KUMAR, and A. J. FLAVELL. 1996. The Ty1-copia group of retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol. Gen. Genet. 205:305-315.
35. POLARD, P., and M. CHANDLER. 1995. Bacterial transposases and retroviral integrases. Mol. Microbiol. 15:13-23.
36. RICE, P., and K. MIZUUCHI. 1995. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell 82:209-220.
37. ROST, B., and C. SANDER. 1994. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72.
38. ŠALI, A., J. P. OVERINGTON, M. S. JOHNSON, and T. L. BLUNDELL. 1990. From comparisons of protein sequences and structures to protein modeling and design. Trends Biochem. Sci. 15:235-240.
39. SANDMEYER, S. B. 1992. Yeast retrotransposons. Curr. Opin. Genet. Dev. 2:705-711.
40. SMITH, T. F., M. S. WATERMAN, and W. M. FITCH. 1981. Comparative biosequence metrics. J. Mol. Evol. 18:38-46.
41. SUONIEMI, A., K. ANAMTHAWAT-JÓNSSON, T. ARNA, and A. H. SCHULMAN. 1996. Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol. Biol. 30:1321-1329.
42. SUONIEMI, A., A. NARVANTO, and A. SCHULMAN. 1996. The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol. Biol. 31:295-306.
43. SUONIEMI, A., D. SCHMIDT, and A. H. SCHULMAN. 1997. BARE-1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites. Genetica 100: 219-230.
44. SUTCLIFFE, M. J., I. HANEEF, D. CARNEY, and T. L. BLUNDELL. 1987. Knowledge-based modeling of homologous proteins, part I: three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1:377-385.
45. SUTCLIFFE, M. J., F. R. HAYES, and T. L. BLUNDELL. 1987. Knowledge-based modeling of homologous proteins, part II: rules for the conformations of substituted sidechains. Protein Eng. 1:385-392.
46. SVITASHEV, S., T. BRYNGELSSON, A. VERSHININ, C. PEDERSEN, T. SÄLL, and R. VON BOTHMER. 1994. Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences. Theor. Appl. Genet. 89:801-810.
47. VAN GENT, D. C., C. VINK, A. A. M. OUDE GROENEGER, and R. H. A. PLASTERK. 1993. Complementation between HIV integrase proteins mutated in different domains. EMBO J. 12:3261-3267.
48. VANDERWIEL, P. L., D. F. VOYTAS, and J. F. WENDEL. 1993. Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium l.). J. Mol. Evol. 36:429-447.
49. VINCENT, K. A., V. ELLISON, S. A. CHOW, and P. O. BROWN. 1993. Characterization of human immunodeficiency virus type 1 integrase expressed in Escherichia coli and analysis of variants with amino-terminal mutations. J. Virol. 67:425-437.
50. VOYTAS, D. F., M. P. CUMMINGS, A. K. KONIECZNY, F. M. AUSUBEL, and S. R. RODERMEL. 1992. Copia-like retrotransposons are ubiquitous among plants. Proc. Natl. Acad. Sci. USA 89:7124-7128.
51. WANG, S., Q. ZHANG, P. J. MAUGHAN, and M. A. SAGHAI MAROOF. 1997. Copia-like retrotransposons in rice: sequence heterogeneity, species distribution and chromosomal locations. Plant Mol. Biol. 33:1051-1058.
52. WESSLER, S. R., T. E. BUREAU, and S. E. WHITE. 1995. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5:814-821.
53. ZHOU, J., and A. KLEINHOFS. 1996. Molecular evolution of nitrate reductase genes. J. Mol. Evol. 42:432-442.