Ty16, a novel Ty3/gypsy-like retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica

Yeast

Volumn 22, Issue 12, 2005, Pages 979-991

  Kovalchuk, Andriy ^a   Senam, Senam ^a,b   Mauersberger, Stephan ^a   Barth, Gerold ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b YOGYAKARTA STATE UNIVERSITY   (Indonesia)

Author keywords

Retrotransposon; Ty16; Ty3 gypsy; Yarrowia lipolytica

Indexed keywords

ARTICLE; CONTROLLED STUDY; FUNGAL STRAIN; FUNGUS ISOLATION; GENE SEQUENCE; GENOME; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; RETROPOSON; RIBOSOMAL FRAMESHIFTING; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; WILD TYPE; YARROWIA LIPOLYTICA; AMINO ACID SEQUENCE; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PROTEIN SYNTHESIS; SEQUENCE HOMOLOGY; YARROWIA;

FUNGI; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES EXIGUUS; YARROWIA LIPOLYTICA;

FUNGAL DNA; FUNGAL PROTEIN; RNA DIRECTED DNA POLYMERASE;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA, FUNGAL; FUNGAL PROTEINS; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PROTEIN BIOSYNTHESIS; RETROELEMENTS; RNA-DIRECTED DNA POLYMERASE; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TERMINAL REPEAT SEQUENCES; YARROWIA;

EID: 25844527243     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/yea.1287     Document Type: Article

References (52)

1. Altschul SF, Madden TL, Schaffer AA, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Anaya N, Roncero MI. 1995. Skippy, a retrotransposon from the fungal plant pathogen Fusarium oxysporum. Mol Gen Genet 249: 637-647.
3. Barth G, Gaillardin C. 1996. Yarrowia lipolytica. In Nonconventional Yeasts in Biotechnology, Wolf K (ed.). Springer: Berlin, Heidelberg, New York; 313-388.
4. Barth G, Gaillardin C. 199. Physiology and genetics of the dimorphic fungus Yarrowia lipolytica. FEMS Microbiol Rev 19: 219-237.
5. Boeke JD, Sandmeyer SB. 1991. Yeast transposable elements. In The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis and Energetics, Broach JR (ed.). Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY; 193-261.
6. Boeke JD, Stoye JP. 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In Retroviruses, Coffin JM, Hughes SH, Varmus HE (eds). Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY; 343-435.
7. Casaregola S, Neuveglise C, Lepingle A, et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica. FEBS Lett 487: 95-100.
8. Casaregola S, Neuveglise C, Bon E, Gaillardin C. 2002. Ylli, a non-LTR retrotransposon L1 family in the dimorphic yeast Yarrowia lipolytica. Mol Biol Evol 19: 664-677.
9. Chalker DL, Sandmeyer SB. 1992. Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev 6: 117-128.
10. Covey SN. 1986. Amino acid sequence homology in gag region of reverse transcribing elements and the coat protein gene of cauliflower mosaic virus. Nucleic Acids Res 14: 623-633.
11. Cryer DR, Eccleshall R, Marmur J. 1975. Isolation of yeast DNA. Methods Cell Biol 12: 39-44.
12. Curcio MJ, Derbyshire KM. 2003. The outs and ins of transposition: from Mu to Kangaroo. Nat Rev Mol Cell Biol 4: 865-877.
13. Devine SE, Boeke JD. 1996. Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes Dev 10: 620-633.
14. Dujon B, Sherman DJ, Fischer G, et al. 2004. Genome evolution in yeasts. Nature 430: 35-44.
15. Dunn BM, Goodenow MM, Gustchina A, Wlodawer A. 2002. Retroviral proteases. Genome Biol 3: 1-7.
16. Falquet L, Pagni M, Bucher P, et al. 2002. The PROSITE database, its status in 2002. Nucleic Acids Res 30: 235-238.
17. Farabaugh PJ. 1996. Programmed translational frameshiffing. Annu Rev Genet 30: 507-528.
18. Farman ML, Tosa Y, Nitta N, Leong SA. 1996. MAGGY, a retrotransposon in the genome of the rice blast fungus Magnaporthe grisea. Mol Gen Genet 251: 665-674.
19. Felsenstein J. 1993. PHYLIP Manual, version 3.5. University of Washington: Seattle, WA.
20. Fingerman EG, Dombrowski PG, Francis CA, Sniegowski PD. 2003. Distribution and sequence analysis of a novel Ty3-like element in natural Saccharomyces paradoxus isolates. Yeast 20: 761-770.
21. Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF. 2003. Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA 9: 1422-1430.
22. Goodwin TJ, Poulter RT. 2000. Multiple LTR-retrotransposon families in the asexual yeast Candida albicans. Genome Res 10: 174-191.
23. Goodwin TJ, Poulter RT. 2001a. The DIRS1 group of retrotransposons. Mol Biol Evol 18: 2067-2082.
24. Goodwin TJ, Poulter RT. 2001b. The diversity of retrotransposons in the yeast Cryptococcus neoformans. Yeast 18: 865-880.
25. Goodwin TJ, Poulter RT. 2002. A group of deuterostome Ty3/ gypsy-like retrotransposons with Ty1/copia-like pol-domain orders. Mol Genet Genom 267: 481-491.
26. Hansen LJ, Sandmeyer SB. 1990. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J Virol 64: 2599-2607.
27. Juretzek T, Le Dall MT, Mauersberger S, et al. 2001. Vectors for gene expression and amplification in the yeast Yarrowia lipolytica. Yeast 18: 97-113.
28. Keogh RS, Seoighe C, Wolfe KH. 1998. Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast 14: 443-457.
29. Khan E, Mack JP, Katz RA, Kulkosky J, Skalka AM. 1991. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res 19: 851-860.
30. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. 1998. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8: 464-478.
31. Kujau M, Weber H, Barth G. 1992. Characterization of mutants of the yeast Yarrowia lipolytica defective in acetyl-coenzyme A synthetase. Yeast 8: 193-203.
32. Kurtzman CP, Robnett CJ. 1998. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequence. Antonie Van Leeuwenhoek 73: 331-371.
33. Le Dall MT, Nicaud JM, Gaillardin C. 1994. Multiple-copy integration in the yeast Yarrowia lipolytica. Curr Genet 26: 38-44.
34. Levin HL, Weaver DC, Boeke JD. 1990. Two related families of retrotransposons from Schizosaccharomyces pombe. Mol Cell Biol 10: 6791-6798.
35. Malik HS, Eickbush TH. 1999. Modular evolution of the integrase domain in the Ty3/gypsy class of LTR retrotransposons. J Virol 73: 5186-5190.
36. Malik HS, Eickbush TH. 2001. Phylogenetie analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11: 1187-1197.
37. Marchler-Bauer A, Bryant SH. 2004. CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32: W327-331.
38. Marin I, Llorens C. 2000. Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol Biol Evol 17: 1040-1049.
39. McHale MT, Roberts IN, Noble SM, et al. 1992. Cfr-I: an LTR-retrotransposon in Cladosporium fulvum, a fungal pathogen of tomato. Mol Gen Genet 233: 337-347.
40. Miller JH. 1972. Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press: Cold Spring Harbour, NY.
41. Neuveglise C, Feldmann H, Bon E, Gaillardin C, Casaregola S. 2002. Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Res 12: 930-943.
42. Page RD. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
43. Rogozin IB, Kochetov AV, Kondrashov FA, Koonin EV, Milanesi L. 2001. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinformatics 17: 890-900.
44. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbour Laboratory Press: Cold Spring Harbour, NY.
45. Schmid-Berger N, Schmid B, Barth G. 1994. Ylt1, a highly repetitive retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica. J Bacteriol 176: 2477-2482.
46. Senam S, Barth G. 2003. Detection and activation of the Ylt1 retrotransposon in the yeast Yarrowia lipolytica. In Nonconventional Yeasts in Genetics, Biochemistry and Biotechnology: Practical Protocols, Wolf K, Breunig K, Barth G (eds). Springer: Berlin, Heidelberg, New York; 357-364.
47. Smith RF, Wiese BA, Wojzynski MK, Davison DB, Worley KC. 1996. BCM Search Launcher - an integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res 6: 454-462.
48. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
49. Wickerham LJ, Kurtzman CP, Herman AI. 1969. Sexuality in Candida lipolytica. In Recent Trends in Yeast Research. Miner Institute: Chazy, NY; 81-92.
50. Woodcock DM, Crowther PJ, Doherty J, et al. 1989. Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res 17: 3469-3478.
51. Wright DA, Voytas DF. 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.
52. Xiong Y, Eickbush TH. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9: 3353-3362.