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Chapter 27 : Ty3, a Position-Specific, Gypsy-Like Element in Saccharomyces cerevisiae

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Abstract:

Ty3 is one of five types of long terminal repeat (LTR) retrotransposons (Ty1 to Ty5) in . These elements are classified in the family . The Ty elements of yeast provide useful model systems for understanding the retrovirus life cycle and the diversities of retroelement functions. The other LTR elements in are copialike elements in the genus . The similarity of Ty3 reverse transcriptase (RT) to retroviral RT, the nature of the minus- and plus-strand primer features, and the existence of minus- and plus-strand reverse transcription intermediates all argue that Ty3 replication is similar to that of retroviruses. In cells activated for Ty1 transposition, Ty3 insertions are readily detectable. These results argue that Ty3 insertion is highly specific for pol III-transcribed genes. One of the objectives of studying yeast retrotransposons is the identification of host factors that are involved in the life cycles of retroelements including retroviruses. Ty1 and Ty3 both rely on frameshifting for protein expression, but use distinct mechanisms. Development of varied and quantitative assays for transposition is facilitating use of the genomic resources in a high-throughput format. The combined use of these resources will make this an exciting time to realize the potential of the yeast elements as model systems for understanding the complex interactions between retroelements and their hosts.

Citation: Sandmeyer S, Aye M, Menees T. 2002. Ty3, a Position-Specific, Gypsy-Like Element in Saccharomyces cerevisiae, p 663-683. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch27

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Figure 1

The Ty3 life cycle. (A) Replication of the Ty3 element. The integrated Ty3 DNA is 5351 bp in length. The upstream and downstream LTRs are divided into repeat regions present at the 5′and 3′ends of the RNA (R) and regions present uniquely (downstream and upstream of R) at the 5′and 3′ends (U5 and U3, respectively). The RNA primes minus-strand reverse transcription from tRNA(i), which is predicted to bind to a 5′-3′bipartite split between the upstream and U3 regions of the transcript. The first template switch occurs so that the minus-strand strong stop anneals to the 3′end of the genomic RNA. Plus-strand reverse transcription is primed, after RNaseHcleavage at the end of the polypurine tract (PPT), just upstream of the U3 region and templated from the nascent minus-strand cDNA. A second template switch transfers the plus-strand strong-stop DNA to the 5′end of the genomic RNA. Experimental data support the existence of the bipartite PBS, minusstrand and plus-strand species, and priming positions of the minus and plus strands, and are described in the text. Other aspects of the model are based on retrovirus replication. After replication, the extrachromosomal Ty3 is 2 bp longer at each end. As in retroviruses, the Ty3 DNA is processed by IN so that 2 nt are removed from each 3′end (indicated by arrowheads). These ends are transferred to positions 5 nt apart in the target DNA, resulting after repair in the characteristic 5-bp repeat at both ends of the insertion. (B) Ty3 proteins. The Ty3 RNA is first translated into Ty3 polyproteins. The inferred position of translation initiation is indicated by AUG. The inferred position of termination of translation of the ORF is indicated by UAA. Most ribosomes terminate at the end of the reading frame. A percentage, however, frameshift at the sequence GCGAGUU and proceed into the reading frame to produce a Gag3-Pol3p fusion protein. Gag3p and Gag3-Pol3p polyproteins are processed by Ty3 PR into the structural and catalytic proteins that support Ty3 replication (as indicated in panel B, top). The amino-terminal processing sites of NC, PR, RT, and IN have been inferred from the amino-terminal sequences of these proteins ( ) and are shown in the right portion of the bottom panel. A protein domain, J, of about 10 kDa is inferred to occur between the PR and RT domains. It has not been detected.

Citation: Sandmeyer S, Aye M, Menees T. 2002. Ty3, a Position-Specific, Gypsy-Like Element in Saccharomyces cerevisiae, p 663-683. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch27
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Image of Figure 2
Figure 2

Assays for Ty3 transposition. (A) Ty3 Helper mobilization of a donor Ty3. In this assay, the Ty3 donor element is genetically marked. This can be with a gene that is expressed in the donor context or which is silent in the donor context and activated during transposition. If the marker gene, such as is expressed from the donor plasmid, then after transposition the plasmid must be counter selected to distinguish cells that have acquired a genomic copy of An example of the latter assay is the use of the gene containing an artificial intron () first used to study Ty1 transposition ( ). In this case is in the antisense orientation relative to Ty3 and is disrupted by a sense intron, which is spliced from the Ty3 transcript, rendering the gene active after reverse transcription and integration. In cases where the marker renders the marked element incompetent for transposition, the defect is complemented in vivo by the expression of Ty3 proteins from a transposition-competent helper Ty3. (B) Suppressor activation. This assay exploits the target specificity of Ty3 for selection of retrotransposition events. After induction of Ty3 expression, Ty3 cDNA integrates into the target plasmid containing divergent tRNA genes. Because of the closeness of the two tRNA genes, assembly of transcription initiation complex on one gene interferes with the other. Ty3 integration into the intergenic region activates expression of the suppressor tRNA gene (). This expression is detected on the selective medium as the suppression of nonsense ochre alleles of and (C) PCR amplification of integrated element DNA. This assay relies on one primer in the internal domain of Ty3 and one primer on the target plasmid. Insertion of Ty3 into the plasmid or genomic locus creates a template for PCR that results in amplification of a fragment diagnostic of a joined element and test target sequence.

Citation: Sandmeyer S, Aye M, Menees T. 2002. Ty3, a Position-Specific, Gypsy-Like Element in Saccharomyces cerevisiae, p 663-683. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch27
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Figure 3

Ty3 integration targets. Ty3 insertions occur close to the transcription initiation sites of genes transcribed by pol III. This has been demonstrated for tRNA, 5S, and U6 genes. (A) A tRNA gene (tDNA) target of Ty3 integration. Internal promoter elements box A and box B are shown. Bent arrow indicates the site of transcription initiation used for integration. TFIIIC is composed of six subunits and is shown binding over the A and B boxes of the tDNA. TFIIIC loads the initiation factor TFIIIB onto a position upstream of the transcription initiation site. TFIIIB is composed of three subunits (described in the text). Brf and TBP comprise the B′factor. In vitro TFIIIC and TFIIIB are required for Ty3 integration. (B) SNR6 target of Ty3 integration. TATA box, internal box A, and downstream box B promoter elements are shown. In vivo TFIIIC binds through contacts at the B and A boxes and loads TFIIIB (46). In vitro, in reactions with recombinant proteins, TFIIIB can bind and mediate transcription by pol III or integration by Ty3.

Citation: Sandmeyer S, Aye M, Menees T. 2002. Ty3, a Position-Specific, Gypsy-Like Element in Saccharomyces cerevisiae, p 663-683. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch27
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References

/content/book/10.1128/9781555817954.chap27
1. Aye, M.,, S. L. Dildine,, J. A. Claypool,, S. Jourdain,, and S. B. Sandmeyer. 2001. A truncation mutant of the 95-kilodalton subunit of transcription factor IIIC reveals asymmetry in Ty3 integration. Mol. Cell. Biol. 21:78397851.
1.a. Barnes, G.,, and D. Rio. 1997. DNA double-strand-break sensitivity, DNA replication, and cell cycle arrest phenotypes of Ku-deficient Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 94:867872.
2. Bartholomew, B.,, G. A. Kassavetis,, B. R. Braun,, and E. P. Geiduschek. 1990. The subunit structure of Saccharomyces cerevisiae transcription factor IIIC probed with a novel photocrosslinking reagent. EMBO J. 9:21972205.
3. Belcourt, M. F.,, and P. J. Farabaugh. 1990. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell 62:339352.
4. Bilanchone, V. W.,, J. A. Claypool,, P. T. Kinsey,, and S. B. Sandmeyer. 1993. Positive and negative regulatory elements control expression of the yeast retrotransposon Ty3. Genetics 134:685700.
5. Boeke, J. D.,, and S. E. Devine. 1998. Yeast retrotransposons: finding a nice quiet neighborhood. Cell 93:10871089.
6. Boeke, J. D.,, D. J. Eichinger,, and G. Natsoulis. 1991. Doubling Ty1 element copy number in Saccharomyces cerevisiae: host genome stability and phenotypic effects. Genetics 129: 10431052.
7. Boeke, J. D.,, T. H. Eickbush,, S. B. Sandmeyer,, and D. F. Voytas,. 2000. Metaviridae. 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 (ed.), Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, N.Y..
8. Boeke, J. D.,, D. J. Garfinkel,, C. A. Styles,, and G. R. Fink. 1985. Ty elements transpose through an RNA intermediate. Cell 40:491500.
9. Bor, Y. C.,, F. D. Bushman,, and L. E. Orgel. 1995. In vitro integration of human immunodeficiency virus type 1 cDNA into targets containing protein-induced bends. Proc. Natl. Acad. Sci. USA 92:1033410338.
10. Boulton, S. J.,, and S. P. Jackson. 1996. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 15:50935103.
11. Boulton, S. J.,, and S. P. Jackson. 1996. Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res. 24:46394648.
12. Brodeur, G. M.,, S. B. Sandmeyer,, and M. V. Olson. 1983. Consistent association between sigma elements and tRNA genes in yeast. Proc. Natl. Acad. Sci. USA 80:32923296.
13. Brow, D. A.,, and C. Guthrie. 1988. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature 334: 213218.
14. Brow, D. A.,, and C. Guthrie. 1990. Transcription of a yeast U6 snRNA gene requires a polymerase III promoter element in a novel position. Genes Dev. 4:13451356.
15. Bryk, M.,, M. Banerjee,, M. Murphy,, K. E. Knudsen,, D. J. Garfinkel,, and M. J. Curcio. 1997. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11: 255269.
16. Burnol, A.-F.,, F. Margottin,, P. Schultz,, M.-C. Marsolier,, P. Oudet,, and A. Sentenac. 1993. Basal promoter and enhancer element of yeast U6 snRNA gene. J. Mol. Biol. 233:644658.
17. Burns, N.,, B. Grimwade,, P. B. Ross-Macdonald,, E.-Y. Choi,, K. Finberg,, G. S. Roeder,, and M. Snyder. 1994. Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8: 10871105.
18. Chalker, D. L.,, and S. B. Sandmeyer. 1990. Transfer RNA genes are genomic targets for de novo transposition of the yeast retrotransposon Ty3. Genetics 126:837850.
19. Chalker, D. L.,, and S. B. Sandmeyer. 1992. Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev. 6:117128.
20. Chalker, D. L.,, and S. B. Sandmeyer. 1993. Sites of RNA polymerase III transcription initiation and Ty3 integration at the U6 gene are positioned by the TATA box. Proc. Natl. Acad. Sci. USA 90:49274931.
21. Chapman, K. B.,, and J. D. Boeke. 1991. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 65:483492.
22. Clark, D. J.,, V. W. Bilanchone,, L. J. Haywood,, S. L. Dildine,, and S. B. Sandmeyer. 1988. A yeast sigma composite element, Ty3, has properties of a retrotransposon. J. Biol. Chem. 263: 14131423.
23. Claypool, J. 1999. Identification of factors that reduce Ty3 transposition. Ph.D. dissertation. University of California, Irvine.
24. Claypool, J. A.,, H. S. Malik,, T. H. Eickbush,, and S. B. Sandmeyer. 2001. Ten-kilodalton domain in Ty3 Gag3-Pol3p between PR and RT is dispensable for Ty3 transposition. J. Virol. 75:15571560.
25. Coffin, J. M.,, S. H. Hughes,, and H. E. Varmus (ed.). 1997. Retroviruses. Cold Spring Harbor Laboratory Press, Plainview, N.Y..
26. Connolly, C. M.,, and S. B. Sandmeyer. 1997. RNA polymerase III interferes with Ty3 integration. FEBS Lett. 405:305311.
27. Conte, D., Jr.,, E. Barber,, M. Banerjee,, D. J. Garfinkel,, and M. J. Curcio. 1998. Posttranslational regulation of Ty1 retrotransposition by mitogen-activated protein kinase Fus3. Mol. Cell. Biol. 18:25022513.
28. Craven, R. C.,, A. E. Leure-DuPree, Jr.,, R. A. Weldon,, and J. W. Wills. 1995. Genetic analysis of the major homology region of the Rous sarcoma virus Gag protein. J. Virol. 69: 42134227.
29. Cristofari, G.,, C. Gabus,, D. Ficheux,, M. Bona,, S. F. Le Grice,, and J. L. Darlix. 1999. Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro. J. Biol. Chem. 274:3664336648.
30. Curcio, M. J.,, and D. J. Garfinkel. 1991. Regulation of retrotransposition in Saccharomyces cerevisiae. Mol. Microbiol. 5:18231829.
31. Curcio, M. J.,, and D. J. Garfinkel. 1991. Single-step selection for Ty1 element retrotransposition. Proc. Natl. Acad. Sci. USA 88:936940.
32. Curcio, M. J.,, and R. H. Morse. 1996. Tying together integration and chromatin. Trends Genet. 12:436438.
33. Daniel, R.,, R. A. Katz,, and A. M. Skalka. 1999. A role for DNA-PK in retroviral DNA integration. Science 284: 644647.
34. del Rey, F.,, T. F. Donahue,, and G. R. Fink. 1983. The histidine tRNA genes of yeast. J. Biol. Chem. 258:81758182.
35. Dorfman, T.,, A. Bukovsky,, A. Ohagen,, S. Hoglund,, and H. G. Gottlinger. 1994. Functional domains of the capsid protein of human immunodeficiency virus type 1. J. Virol. 68: 81808187.
35.a. Downs, J. A.,, and S. P. Jackson. 1999. Involvement of DNA end-binding protein Ku in Ty element retrotransposition. Mol. Cell. Biol. 19:62606268.
36. Engelman, A.,, K. Mizuuchi,, and R. Craigie. 1991. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67:12111221.
37. Esposito, D.,, and R. Craigie. 1999. HIV integrase structure and function. Adv. Virus Res. 52:319333.
38. Fan, H.,, A. L. Sakulich,, J. L. Goodier,, X. Zhang,, J. Qin,, and R. J. Maraia. 1997. Phosphorylation of the human La antigen on serine 366 can regulate recycling of RNA polymerase III transcription complexes. Cell 88:707715.
39. Farabaugh, P. J.,, H. Zhao,, S. Pande,, and A. Vimaladithan. 1993. Translational frameshifting expresses the POL3 gene of retrotransposon Ty3 of yeast. Cell 74:93103.
40. Finley, D.,, E. Ozkaynak,, and A. Varshavsky. 1987. The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell 48:10351046.
41. Fleig, U. N.,, R. D. Pridmore,, and P. Philippsen. 1986. Construction of LYS2 cartridges for use in genetic manipulations of Saccharomyces cerevisiae. Gene 46:237245.
42. Gabrielsen, O. S.,, E. Hornes,, L. Korsnes,, A. Ruet,, and T. B. Oyen. 1989. Magnetic DNA affinity purification of yeast transcription factor tau: a new purification principle for the ultrarapid isolation of near homogeneous factor. Nucleic Acids Res. 17:62536267.
43. Gabus, C.,, D. Ficheux,, M. Rau,, G. Keith,, S. Sandmeyer,, and J.-L. Darlix. 1998. The yeast Ty3 retrotransposon contains a 5′/3′ bipartite primer binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7. EMBO J. 17:48734880.
44. Gallay, P.,, T. Hope,, D. Chin,, and D. Trono. 1997. HIV- 1 infection of nondividing cells through the recognition of integrase by the importin/karyopherin pathway. Proc. Natl. Acad. Sci. USA 94:98259830.
45. Garfinkel, D. J.,, J. D. Boeke,, and G. R. Fink. 1985. Ty element transposition: reverse transcriptase and virus-like particles. Cell 42:507517.
46. Geiduschek, E. P.,, and G. A. Kassavetis. 2001. The RNA polymerase III transcription apparatus. J. Mol. Biol. 310: 126.
47. Gerlach, V. L.,, S. K. Whitehall,, E. P. Geiduschek,, and D. A. Brow. 1995. TFIIIB placement on a yeast U6 RNA gene in vivo is directed primarily by TFIIIC rather than by sequencespecific DNA contacts. Mol. Cell. Biol. 15:14551466.
48. Ghavidel, A.,, D. J. Hockman,, and M. C. Schultz. 1999. A review of progress towards elucidating the role of protein kinase CK2 in polymerase III transcription: regulation of the TATA binding protein. Mol. Cell. Biochem. 191:143148.
49. Goffeau, A.,, B. G. Barrell,, H. Bussey,, R. W. Davis,, B. Dujon,, H. Feldmann,, J. D. Hoheisel,, C. Jacq,, M. Johnston,, E. J. Louis,, H. W. Mewes,, Y. Murakakmi,, P. Philippsen,, H. Tettelin,, and S. G. Oliver. 1996. Life with 6000 Genes. Science 274:546567.
50. Guarente, L.,, and T. Mason. 1983. Heme regulates transcription of the cyc1 gene of S. cerevisiae via an upstream activation site. Cell 32:12791286.
51. Hansen, L. J.,, D. L. Chalker,, K. J. Orlinsky,, and S. B. Sandmeyer. 1992. Ty3GAG3 and POL3 genes encode the components of intracellular particles. J. Virol. 66:14141424.
52. Hansen, L. J.,, D. L. Chalker,, and S. B. Sandmeyer. 1988. Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses. Mol. Cell. Biol. 8: 52455256.
53. Hansen, L. J.,, and S. B. Sandmeyer. 1990. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J. Virol. 64:25992607.
54. Hsieh, Y.,, Z. Wang,, R. Kovelman,, and R. G. Roeder. 1999. Cloning and characterization of two evolutionarily conserved subunits (TFIIIC102 and TFIIIC63) of human TFIIIC and their involvement in functional interactions with TFIIIB and RNA polymerase III. Mol. Cell. Biol. 19:49444952.
55. Hull, M. W.,, J. Erickson,, M. Johnston,, and D. R. Engelke. 1994. tRNA genes as transcriptional repressor elements. Mol. Cell. Biol. 14:12661277.
56. Joazeiro, C. A. P.,, G. A. Kassavetis,, and E. P. Geiduschek. 1994. Identical components of yeast transcription factor IIIB are required and sufficient for transcription of TATA boxcontaining and TATA-less genes. Mol. Cell. Biol. 14:27982808.
57. Johnson, M. S.,, M. A. McClure,, D.-F. Feng,, J. Gray,, and R. F. Doolittle. 1986. Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with non-viral enzymes. Proc. Natl. Acad. Sci. USA 83:76487652.
58. Karst, S. M.,, M. L. Rutz,, and T. M. Menees. 2000. The yeast retrotransposons Ty1 and Ty3 require the RNA Lariat debranching enzyme, Dbr1p, for efficient accumulation of reverse transcripts. Biochem. Biophys. Res. Commun. 268:112117.
59. Karst, S. M.,, N. Sadeghi,, and T. M. Menees. 1999. Cell cycle control of reverse transcriptase activity for the yeast retrotransposon Ty3. Biochem. Biophys. Res. Commun. 254: 679684.
60. Kassavetis, G. A.,, C. Bardeleben,, A. Kumar,, E. Ramirez,, and E. P. Geiduschek. 1997. Domains of the Brf component of RNA polymerase III transcription factor IIIB (TFIIIB): functions in assembly of TFIIIB-DNA complexes and recruitment of RNA polymerase to the promoter. Mol. Cell. Biol. 17: 52995306.
61. Kassavetis, G. A.,, A. Kumar,, G. A. Letts,, and E. P. Geiduschek. 1998. A post-recruitment function for the RNA polymerase III transcription-initiation factor IIIB. Proc. Natl. Acad. Sci. USA 95:91969201.
62. Kassavetis, G. A.,, A. Kumar,, E. Ramirez,, and E. P. Geiduschek. 1998. Functional and structural organization of Brf, the TFIIB-related component of the RNA polymerase III transcription initiation complex. Mol. Cell. Biol. 18:55875599.
63. Kassavetis, G. A.,, G. A. Letts,, and E. P. Geiduschek. 1999. A minimal RNA polymerase III transcription system. EMBO J. 18:50425051.
64. Kassavetis, G. S.,, J. A. Blanco,, T. E. Johnson,, and E. P. Geiduschek. 1992. Formation of open and elongating transcription complexes by RNA polymerase III. J. Mol. Biol. 226: 4758.
65. Katz, R. A.,, K. Gravuer,, and A. M. Skalka. 1998. A preferred target DNA structure for retroviral integrase in vitro. J. Biol. Chem. 273:2419024195.
66. Ke, N.,, X. Gao,, J. B. Keeney,, J. D. Boeke,, and D. F. Voytas. 1999. The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription. RNA 5:929938.
67. Keeney, J. B.,, K. B. Chapman,, V. Lauermann,, D. F. Voytas,, S. U. Astrom,, U. von Pawel-Rammingen,, A. Bystrom,, and J. D. Boeke. 1995. Multiple molecular determinants for retrotransposition in a primer tRNA. Mol. Cell. Biol. 15:217226.
68. Kenna, M. A.,, C. Baker 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. 18:11151124.
69. Khan, E.,, J. P. Mack,, R. A. Katz,, J. Kulkosky,, and A. M. Skalka. 1991. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res. 19:851860.
70. 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. 8:464478.
71. Kinsey, P.,, and S. Sandmeyer. 1995. Ty3 transposes in mating populations of yeast: a novel transposition assay for Ty3. Genetics 139:8194.
72. Kinsey, P. T.,, and S. B. Sandmeyer. 1991. Adjacent pol II and pol III promoters: transcription of the yeast retrotransposon Ty3 and a target tRNA gene. Nucleic Acids Res. 19: 13171324.
73. Kirchner, J.,, C. M. Connolly,, and S. B. Sandmeyer. 1995. Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267:14881491.
74. Kirchner, J.,, and S. B. Sandmeyer. 1993. Proteolytic processing of Ty3 proteins is required for transposition. J. Virol. 67: 1928.
75. Kirchner, J.,, and S. B. Sandmeyer. 1996. Ty3 integrase mutants defective in reverse transcription or 3′ end processing of extrachromosomal Ty3 DNA. J. Virol. 70:47374747.
76. Kirchner, J.,, S. B. Sandmeyer,, and D. B. Forrest. 1992. Transposition of a Ty3 GAG3-POL3 fusion mutant is limited by availability of capsid protein. J. Virol. 66:60816092.
77. Kukolj, G.,, R. A. Katz,, and A. M. Skalka. 1998. Characterization of the nuclear localization signal in the avian sarcoma virus integrase. Gene 223:157163.
78. Kumar, A.,, A. Grove,, G. A. Kassavetis,, and E. P. Geiduschek. 1998. Transcription factor IIIB: the architecture of its DNA complex, and its roles in initiation of transcription by RNA polymerase III. Cold Spring Harbor Symp. Quant. Biol. 63: 121129.
79. Kumar, A.,, G. A. Kassavetis,, E. P. Geiduschek,, M. Hambalko,, and C. J. Brent. 1997. Functional dissection of the B′ component of RNA polymerase III transcription factor IIIB: a scaffolding protein with multiple roles in assembly and initiation of transcription. Mol. Cell. Biol. 17:18681880.
80. Lauermann, V.,, K. Nam,, J. Trambley,, and J. D. Boeke. 1995. Plus-strand strong-stop DNA synthesis in retrotransposon Ty1. J. Virol. 69:78457850.
81. Leavitt, A. D.,, L. Shiue,, and H. E. Varmus. 1993. Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase functions in vitro. J. Biol. Chem. 268: 21132119.
82. Lee, B. S.,, C. P. Lichtenstein,, B. Faiola,, L. A. Rinckel,, W. Wysock,, M. J. Curcio,, and D. J. Garfinkel. 1998. Posttranslational inhibition of Ty1 retrotransposition by nucleotide excision repair/transcription factor TFIIH subunits SsI2p and Rad3p. Genetics 148:17431761.
82.a. Lin, S. S.,, M. H. Nymark-McMahon,, L. Yieh,, and S. B. Sandmeyer. 2001. Integrase mediates nuclear localization of Ty3. 21:78267838.
83. Malik, H. S.,, and T. H. Eickbush. 1999. Modular evolution of the integrase domain in the Ty3/gypsy class of LTR retrotransposons. J. Virol. 73:51865190.
84. Maraia, R. J. 1996. Transcription termination factor La is also an initiation factor for RNA polymerase III. Proc. Natl. Acad. Sci. USA 93:33833387.
85. Margottin, F.,, G. Dujardin,, M. Gerard,, J.-M. Egly,, J. Huet,, and A. Sentenac. 1991. Participation of the TATA factor in transcription of the yeast U6 gene by RNA polymerase C. Science 251:424426.
86. Masuda, T.,, V. Planelles,, P. Krogstad,, and I. S. Chen. 1995. Genetic analysis of human immunodeficiency virus type 1 integrase and the U3 att site: unusual phenotype of mutants in the zinc finger-like domain. J. Virol. 69:66876696.
87. Menees, T.,, and B. S. Sandmeyer. 1996. Cellular stress inhibits transposition of the yeast retrovirus-like element Ty3 by a ubiquitin-dependent block of virus-like particle formation. Proc. Natl. Acad. Sci. USA 93:56295634.
88. Menees, T. M.,, and S. B. Sandmeyer. 1994. Transposition of the yeast retroviruslike element Ty3 is dependent on the cell cycle. Mol. Cell. Biol. 14:82298240.
89. Moore, S. P.,, L. A. Rinckel,, and D. J. Garfinkel. 1998. A Ty1 integrase nuclear localization signal required for retrotransposition. Mol. Cell. Biol. 18:11051114.
90. Muller, H.-P.,, and H. E. Varmus. 1994. DNAbending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes. EMBO J. 13: 47044714.
91. Nam, K.,, R. H. Hudson,, K. B. Chapman,, K. Ganeshan,, M. J. Damha,, and J. D. Boeke. 1994. Yeast lariat debranching enzyme. Substrate and sequence specificity. J. Biol. Chem. 269:2061320621.
92. Natsoulis, G.,, W. Thomas,, M.-C. Roghmann,, F. Winston,, and J. D. Boeke. 1989. Ty1 transposition in Saccharomyces cerevisiae is nonrandom. Genetics 123:269279.
93. Nymark-McMahon, M. H.,, and S. B. Sandmeyer. 1999. Mutations in nonconserved domains of Ty3 integrase affect multiple stages of the Ty3 life cycle. J. Virol. 73:453465.
94. Orlinsky, K.,, J. Gu,, M. Hoyt,, S. Sandmeyer,, and T. Menees. 1996. Mutations in the Ty3 major homology region affect viruslike particle morphogenesis. J. Virol. 70:34403448.
95. Orlinsky, K. J. 1994. Ty3 virus like particle morphogenesis: particle formation and genomic RNA packaging. Ph.D. dissertation. University of California, Irvine.
96. Orlinsky, K. J.,, and S. B. Sandmeyer. 1994. The Cys-His motif of Ty3 NC can be contributed by Gag3 or Gag3-Pol3 polyproteins. J. Virol. 68:41524166.
97. Parsons, M. C.,, and P. A. Weil. 1992. Cloning of TFC1, the Saccharomyces cerevisiae gene encoding the 95-kDa subunit of transcription factor TFIIIC. J. Biol. Chem. 267: 28942901.
98. Patarca, R.,, and W. A. Haseltine. 1985. A major retroviral core protein related to EPA and TIMP. Nature 318:390.
99. Pryciak, P. M.,, A. Sil,, and H. E. Varmus. 1992. Retroviral integration into minichromosomes in vitro. EMBO J. 11: 291303.
100. Pryciak, P. M.,, and H. E. Varmus. 1992. Nucleosomes, DNAbinding proteins, and DNA sequence modulate retroviral integration target site selection. Cell 69:769780.
101. Rausch, J. W.,, M. K. Le Grice,, M. H. Nymark-McMahon,, J. T. Miller,, and S. F. Le Grice. 2000. Interaction of p55 reverse transcriptase from the Saccharomyces cerevisiae retrotransposon Ty3 with conformationally distinct nucleic acid duplexes. J. Biol. Chem. 275:1387913887.
102. Sandmeyer, S. 1998. Targeting transposition: at home in the genome. Genome Res. 8:416418.
103. Sandmeyer, S. B.,, V. W. Bilanchone,, D. J. Clark,, P. Morcos,, G. F. Carle,, and G. M. Brodeur. 1988. Sigma elements are position-specific for many different yeast tRNA genes. Nucleic Acids Res. 16:14991515.
104. Sandmeyer, S. B.,, and T. M. Menees. 1996. Morphogenesis at the retrotransposon-retrovirus interface: Gypsy and Copia families in yeast and Drosophila. Curr. Top. Microbiol. Immunol. 214:261296.
105. Sandmeyer, S. B.,, and M. V. Olson. 1983. Insertion of a repetitive element at the same position in the 5′-flanking regions of two dissimilar yeast tRNA genes. Proc. Natl. Acad. Sci. USA 79:76747678.
106. Seol, J. H.,, R. M. Feldman,, W. Zachariae,, A. Shevchenko,, C. C. Correll,, S. Lyapina,, Y. Chi,, M. Galova,, J. Claypool,, S. Sandmeyer,, K. Nasmyth,, R. J. Deshaies,, A. Shevchenko,, and R. J. Deshaies. 1999. Cdc53/cullin and the essential Hrt1 RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34. Genes Dev. 13: 16141626.
107. Seufert, W.,, and S. Jentsch. 1990. Ubiquitin-conjugating enzymes UBC4 and UBC5 mediate selective degradation of short-lived and abnormal proteins. EMBO J. 9:543550.
108.Reference deleted.
109. Skalka, A. M., 1993. Endonuclease activity associated with reverse transcriptase of avian sarcoma-leukosis viruses, p. 193204. In A. M. Skalka, and S. P. Goff (ed.), Reverse Transcriptase. Cold Spring Harbor Laboratory Press, Plainview, N.Y..
110. Smith, J. S.,, and J. D. Boeke. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11: 241254.
111. Strambio-de-Castillia, C.,, and E. Hunter. 1992. Mutational analysis of the major homology region of Mason-Pfizer monkey virus by use of saturation mutagenesis. J. Virol. 66: 70217032.
112. Sundararajan, A.,, W. A. Michaud,, Q. Qian,, G. Stahl,, and P. J. Farabaugh. 1999. Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. Mol. Cell 4:10051015.
113. Swanson, R. N.,, C. Conesa,, O. Lefebvre,, C. Carles,, A. Ruet,, E. Quemeneur,, J. Gagnon,, and A. Sentenac. 1991. Isolation of TFC1, a gene encoding one of two DNA-binding subunits of yeast transcription factor tau (TFIIIC). Proc. Natl. Acad. Sci. USA 88:48874891.
114. Trentin, B.,, N. Rebeyrotte,, and R. Z. Mamoun. 1998. Human T-cell leukemia virus type 1 reverse transcriptase (RT) originates from the pro and pol open reading frames and requires the presence of RT-RNase H (RH) and RT-RHintegrase proteins for its activity. J. Virol. 72:65046510.
115. Van Arsdell, S. W.,, G. L. Stetler,, and J. Thorner. 1987. The yeast repeated element sigma contains a hormone-inducible promoter. Mol. Cell. Biol. 7:749759.
116. Vimaladithan, A.,, and P. J. Farabaugh. 1994. Special peptidyl- tRNA molecules can promote translational frameshifting without slippage. Mol. Cell. Biol. 14:81078116.
117. Werner, S.,, and B. M. Wohrl. 1999. Soluble Rous sarcoma virus reverse transcriptases alpha, alphabeta, and beta purified from insect cells are processive DNA polymerases that lack an RNase H 3′→ 5′ directed processing activity. J. Biol. Chem. 274:2632926336.
118. Werner-Washburne, M.,, D. E. Stone,, and E. A. Craig. 1987. Complex interactions among members of an essential subfamily of hsp70 genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 7:25682577.
119. White, R. J. 1998. RNA Polymerase III Transcription. Springer-Verlag and R. G. Landes, Berlin, Germany.
120. Wilhelm, M.,, T. Heyman,, S. Friant,, and F. X. Wilhelm. 1997. Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts. Nucleic Acids Res. 25:21612166.
121. Wilke, C. M.,, and J. Adams. 1992. Fitness effects of Ty transposition in Saccharomyces cerevisiae. Genetics 131:3142.
122. Wills, J. W.,, and R. C. Craven. 1991. Form, function, and use of retroviral Gag proteins. AIDS 5:639654.
123. Winston, F.,, C. Dollard,, E. A. Malone,, J. Clare,, J. G. Kapakos,, P. Farabaugh,, and P. L. Minehart. 1987. Three genes are required for trans-activation of Ty transcription in yeast. Genetics 115:649656.
124. Winston, F.,, K. J. Durbin,, and G. R. Fink. 1984. The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae. Cell 39:657682.
125. Wu, X.,, H. Liu,, H. Xiao,, J. A. Conway,, E. Hehl,, G. V. Kalpana,, V. Prasad,, and J. C. Kappes. 1999. Human immunodeficiency virus type 1 integrase protein promotes reverse transcription through specific interactions with the nucleoprotein reverse transcription complex. J. Virol. 73:21262135.
126. Xu, H.,, and J. D. Boeke. 1991. Inhibition of Ty1 transposition by mating pheromones in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:27362743.
127. Yang, Z. N.,, T. C. Mueser,, F. D. Bushman,, and C. C. Hyde. 2000. Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase. J. Mol. Biol. 296:535548.
128. Yieh, L. 2000. Host mediators of Ty3 transposition. Ph.D. dissertation. University of California, Irvine.
129. Yieh, L.,, G. Kassavetis,, E. P. Geiduschek,, and S. B. Sandmeyer. 2000. The Brf and TBP subunits of the RNA polymerase III transcription factor IIIB mediate position-specific integration of the gypsy-like element, Ty3. J. Biol. Chem. 275: 2976729771.
130. Yoo, C. J.,, and S. L. Wolin. 1994. La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth. Mol. Cell. Biol. 14:54125424.
131. Yoo, C. J.,, and S. L. Wolin. 1997. The yeast La protein is required for the 3′ endonucleolytic cleavage that matures tRNA precursors. Cell 89:393402.
132. Zeyl, C.,, G. Bell,, and D. M. Green. 1996. Sex and the spread of retrotransposon Ty3 in experimental populations of Saccharomyces cerevisiae. Genetics 143:15671577.

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