Genes of the Pseudoviridae (Ty1/copia retrotransposons)

Molecular Biology and Evolution

Volumn 19, Issue 11, 2002, Pages 1832-1845

  Peterson Burch, Brooke D ^a   Voytas, Daniel F ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

env; gag; pol; Pseudoviridae; Retrotransposon

Indexed keywords

GAG PROTEIN; INTEGRASE; PROTEINASE; RNA DIRECTED DNA POLYMERASE; VIRUS PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; DNA FLANKING REGION; GENE SEQUENCE; GENETIC ANALYSIS; LONG TERMINAL REPEAT; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; RETROPOSON; SEQUENCE ANALYSIS; TRANSPOSON; VIRUS GENOME; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PROTEIN CONFORMATION; STRUCTURAL GENE; VIRUS GENE;

ARABIDOPSIS THALIANA; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENES, GAG; GENES, POL; GENES, VIRAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN CONFORMATION; RETROELEMENTS; VIRAL PROTEINS;

EID: 0036854310     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004008     Document Type: Article

References (76)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Atwood, A., J. H. Lin, and H. L. Levin. 1996. The retrotransposon Tf1 assembles virus-like particles that contain excess Gag relative to integrase because of a regulated degradation process. Mol. Cell. Biol. 16:338-346.
3. Avedisov, S. N., and Y. V. Ilyin. 1994. Identification of spliced RNA species of Drosophila melanogastergypsy retrotransposon. New evidence for retroviral nature of the gypsy element. FEBS Lett. 350:147-150.
4. Bailey, T. L., and C. Elkan. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2:28-36.
5. Boeke, J. D., T. Eickbush, S. B. Sandmeyer, and D. F. VoyTas. 2000a. Metaviridae. Pp. 359-367 in M. H. V. Van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carsten, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. Mcgeoch, C. R. Pringle, and R. B. WickNer, eds. Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, New York.
6. -. 2000b. Pseudoviridae. Pp. 349-357 in M. H. V. Van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carsten, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. Mcgeoch, C. R. Pringle, and R. B. Wickner, eds. Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, New York.
7. Boeke, J. D., and J. P. Stoye. 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. Pp. 343-436 in J. M. Coffin, S. H. Hughes, and H. E. Varmus, eds. Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
8. Bowen, N. J., and J. F. Mcdonald. 1999. Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res. 9:924-935.
9. -. 2001. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 11:1527-1540.
10. Braiterman, L. T., G. M. Monokian, D. J. Eichinger, S. L. Merbs, A. Gabriel, and J. D. Boeke. 1994. In-frame linker insertion mutagenesis of yeast transposon Ty1: Phenotypic analysis. Gene 139:19-26.
11. Brierley, C., and A. J. Flavell. 1990. The retrotransposon copia controls the relative levels of its gene products posttranscriptionally by differential expression from its two major mRNAs. Nucleic Acids Res. 18:2947-2951.
12. Brill, L. M., R. S. Nunn, T. W. Kahn, M. Yeager, and R. N. Beachy. 2000. Recombinant tobacco mosaic virus movement protein is an RNA-binding, alpha-helical membrane protein. Proc. Natl. Acad. Sci. USA 97:7112-7117.
13. Brown, P. O. 1997. Integration. Pp. 161-204 in J. M. Coffin, S. H. Hughes, and H. E. Varmus, eds. Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
14. Chen, J. C., J. Krucinski, L. J. Miercke, J. S. Finer-Moore, A. H. Tang, A. D. Leavitt, and R. M. Stroud. 2000. Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding. Proc. Natl. Acad. Sci. USA 97:8233-8238.
15. Colot, V., and J. L. Rossignol. 1999. Eukaryotic Dna methylation as an evolutionary device. Bioessays 21:402-411.
16. Cristofari, G., D. Ficheux, and J. L. Darlix. 2000. The GAG-like protein of the yeast Ty1 retrotransposon contains a nucleic acid chaperone domain analogous to retroviral nucleocapsid proteins. J. Biol. Chem. 275:19210-19217.
17. Cuff, J. A., and G. J. Barton. 2000. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40:502-511.
18. Eickbush, T. H. 1994. Origin and evolutionary relationships of retroelements. Pp. 121-157 in S. S. Morse, ed. The Evolutionary Biology of Viruses. Raven Press, New York.
19. Eijkelenboom, A. P., R. Sprangers, K. Hard, R. A. Puras Lutzke, R. H. Plasterk, R. Boelens, and R. Kaptein. 1999. Refined solution structure of the C-terminal DNA-binding domain of human immunovirus-1 integrase. Proteins 36:556-564.
20. Frame, I. G., J. F. Cutfield, and R. T. Poulter. 2001. New BEL-like LTR-retrotransposons in Fugu rubripes, Caenorhabditis elegans, and Drosophila melanogaster. Gene 263:219-230.
21. Gabriel, A., and E. H. Mules. 1999. Fidelity of retrotransposon replication. Ann. NY Acad. Sci. 870:108-118.
22. Garfinkel, D. J., A. M. Hedge, S. D. Youngren, and T. D. Copeland. 1991. Proteolytic processing of pol-TYB proteins from the yeast retrotransposon Ty1. J. Virol. 65:4573-4581.
23. Gesteland, R. F., and J. F. Atkins. 1996. Recoding: Dynamic reprogramming of translation. Annu. Rev. Biochem. 65:741-768.
24. Gulnik, S., J. W. Erickson, and D. Xie. 2000. Hiv protease: Enzyme function and drug resistance. Vitam. Horm. 58:213-256.
25. Haren, L., B. Ton-hoang, and M. Chandler. 1999. Integrating DNA: Transposases and retroviral integrases. Annu. Rev. Microbiol. 53:245-281.
26. Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89:10915-10919.
27. Henikoff, S., J. G. Henikoff, W. J. Alford, and S. Pietro-Kovski. 1995. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 163:GC17-GC26.
28. Hogue, C. W. 1997. Cn3D: A new generation of three-dimensional molecular structure viewer. Trends Biochem. Sci. 22:314-316.
29. Hunter, E., J. Casey, B. Hahn, M. Hayami, B. Korber, R. Kurth, J. Neil, A. Rethwilm, P. Sonigo, and J. Stoye. 2000. Retroviridae. Pp. 369-387 in M. H. V. Van Regen-Mortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carsten, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. Mcgeoch, C. R. Pringle, and R. B. Wickner, eds. Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, New York.
30. Irwin, P. A., and D. F. Voytas. 2001. Expression and processing of proteins encoded by the Saccharomyces retrotransposon Ty5. J. Virol. 75:1790-1797.
31. Jackson, R. J. 2000. A comparative view of initiation site selection mechanisms. Pp. 127-183 in N. Sonenberg, J. W. B. Hershey, and M. B. Mathews, eds. Translational Control of Gene Expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
32. Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
33. Jordan, I. K., L. V. Matyunina, and J. F. Mcdonald. 1999. Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc. Natl. Acad. Sci. USA 96:12621-12625.
34. Kapitonov, V. V., and J. Jurka. 1999. Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107:27-37.
35. Kay, B. K., M. P. Williamson, and M. Sudol. 2000. The importance of being proline: The interaction of proline-rich motifs in signaling proteins with their cognate domains. FASEB J. 14:231-241.
36. Kenna, M. A., C. B. Brachmann, S. E. Devine, and J. D. Boeke. 1998. Invading the yeast nucleus: A nuclear localization signal at the C terminus of Ty1 integrase is required for transposition in vivo. Mol. Cell. Biol. 18:1115-1124.
37. Kim, A., C. Terzian, P. Santamaria, A. Pelisson, N. Purd'homme, and A. Bucheton. 1994. Retroviruses in invertebrates: The gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91:1285-1289.
38. Kim, J. M., S. Vanguri, J. D. Boeke, A. Gabriel, and D. F. Voytas. 1998. Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8:464-478.
39. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics Analysis Software, Arizona State University, Tempe, Ariz.
40. Laten, H. M., A. Majumdar, and E. A. Gaucher. 1998. SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein. Proc. Natl. Acad. Sci. USA 95:6897-6902.
41. Lerat, E., and P. Capy. 1999. Retrotransposons and retroviruses: Analysis of the envelope gene. Mol. Biol. Evol. 16:1198-1207.
42. Malik, H. S., and T. H. Eickbush. 1999. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J. Virol. 73:5186-5190.
43. -. 2001. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 11:1187-1197.
44. Malik, H., S. Henikoff, and T. Eickbush. 2000. Poised for contagion: Evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res. 10:1307-1318.
45. Manninen, I., and A. H. Schulman. 1993. Bare-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol. Biol. 22:829-846.
46. Marracci, S., R. Batistoni, G. Pesole, L. Citti, and I. Nardi. 1996. Gypsy/Ty3-like elements in the genome of the terrestrial Salamander hydromantes (Amphibia, Urodela). J. Mol. Evol. 43:584-593.
47. Marsano, R. M., R. Moschetti, C. Caggese, C. Lanave, P. Barsanti, and R. Caizzi. 2000. The complete Tirant transposable element in Drosophila melanogaster shows a structural relationship with retrovirus-like retrotransposons. Gene 247:87-95.
48. Martin-Rendon, E., G. Marfany, S. Wilson, D. J. Ferguson, S. M. Kingsman, and A. J. Kingsman. 1996. Structural determinants within the subunit protein of Ty1 virus-like particles. Mol. Microbiol. 22:667-679.
49. McClure, M. A., T. K. Vasi, and W. M. Fitch. 1994. Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol. 11:571-592.
50. Melcher, U. 2000. The '30K' superfamily of viral movement proteins. J. Gen. Virol. 81 Pt 1:257-266.
51. Merkulov, G. V., K. M. Swiderek, C. B. Brachmann, and J. D. Boeke. 1996. A critical proteolytic cleavage site near the C-terminus of the yeast retrotransposon Ty1 Gag protein. J. Virol. 70:5548-5556.
52. Monokian, G. M., L. T. Braiterman, and J. D. Boeke. 1994. In-frame linker insertion mutagenesis of yeast transposon Ty1: Mutations, transposition and dominance. Gene 139:9-18.
53. 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.
54. Moore, S. P., L. A. Rinckel, and D. J. Garfinkel. 1998. A Ty1 integrase nuclear localization signal required for retrotransposition. Mol. Cell. Biol. 18:1105-1114.
55. Nielsen, A. L., M. Oulad-Abdelghani, J. A. Ortiz, E. Remboutsika, P. Chambon, and R. Losson. 2001. Heterochromatin formation in mammalian cells: Interaction between histones and HP1 proteins. Mol. Cell. 7:729-739.
56. Orlinsky, K. J., J. Gu, M. Hoyt, S. Sandmeyer, and T. M. Menees. 1996. Mutations in the Ty3 major homology region affect multiple steps in Ty3 retrotransposition. J. Virol. 70:3440-3448.
57. Peterson-Burch, B. D., D. A. Wright, H. M. Laten, and D. F. Voytas. 2000. Retroviruses in plants? Trends Genet. 16:151-152.
58. SanMiguel, P., A. Tikhonov, Y. K. Jin et al. (11 co-authors). 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768.
59. Schneider, T. D., and R. M. Stephens. 1990. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18:6097-6100.
60. Song, S. U., T. Gerasimova, M. Kurkulos, J. D. Boeke, and V. G. Corces. 1994. An env-like protein encoded by a Drosophila retroelement: Evidence that gypsy is an infectious retrovirus. Genes Dev. 8:2046-2057.
61. Swanstrom, R., and J. W. Wills. 1997. Synthesis, assembly and processing of viral proteins. Pp. 263-334 in J. Coffin, S. H. Hughes, and H. E. Varmus, eds. Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
62. Swofford, D. 1999. PAUP 4.0. 4.0 Edition. Smithsonian Institution, Washington D.C.
63. Tatusova, T. A., and T. L. Madden. 1999. Blast 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174:247-250.
64. Telesnitsky, A., and S. P. Goff. 1997. Reverse transcriptase and the generation of retroviral DNA. Pp. 121-160 in J. Coffin, S. H. Hughes, and H. E. Varmus, eds. Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
65. Terol, J., M. C. Castillo, M. Bargues, M. Perez-Alonso, and R. De Frutos. 2001. Structural and evolutionary analysis of the copia-like elements in the Arabidopsis thaliana genome. Mol. Biol. Evol. 18:882-892.
66. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
67. Tusnady, G. E., and I. Simon. 1998. Principles governing amino acid composition of integral membrane proteins: Application to topology prediction. J. Mol. Biol. 283:489-506.
68. Vogt, V. M. 1997. Retroviral virions and genomes. Pp. 27-70 in J. Coffin, S. H. Hughes, and H. E. Varmus, eds. Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
69. Voytas, D. F., and J. D. Boeke. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae. Pp. 631-662 in N. L. Craig, R. Craigie, M. Gellert, and A. M. Lambowitz, eds. Mobile DNA II. American Society for Microbiology, Washington, D.C.
70. Wolf, E., P. S. Kim, and B. Berger. 1997. Multicoil: A program for predicting two- and three-stranded coiled coils. Protein Sci. 6:1179-1189.
71. Wright, D. A., and D. F. Voytas. 1998. Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. Genetics 149:703-715.
72. -. 2002. Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res. 12:122-131.
73. Xie, W., X. Gai, Y. Zhu, D. C. Zappulla, R. Sternglanz, and D. F. Voytas. 2001. Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol. Cell. Biol. 21:6606-6614.
74. Xiong, Y., and T. H. Eickbush. 1988. Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol. Biol. Evol. 5:675-690.
75. -. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9:3353-3362.
76. Yoshioka, K., H. Honma, M. Zushi, S. Kondo, S. Togashi, T. Miyake, and T. Shiba. 1990. Virus-like particle formation of Drosophilacopia through autocatalytic processing. EMBO J. 9:535-541.