Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation

PLoS ONE

Volumn 6, Issue 3, 2011, Pages

  Galeote, Virginie ^a   Bigey, Frédéric ^a   Beyne, Emmanuelle ^a   Novo, Maite ^a   Legras, Jean Luc ^a   Casaregola, Serge ^b   Dequin, Sylvie ^a  

^a SPO   (France)

^b UMR1319 MICALIS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; EXTRACHROMOSOMAL DNA; FUNGAL DNA;

ARTICLE; CONTROLLED STUDY; FUNGAL GENOME; FUNGAL STRAIN; GENE AMPLIFICATION; GENE DOSAGE; GENE INSERTION; GENETIC VARIABILITY; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; SACCHAROMYCES CEREVISIAE; WINE; ZYGOSACCHAROMYCES; ZYGOSACCHAROMYCES BAILII; BIOLOGICAL MODEL; CHROMOSOME; CHROMOSOME BREAKAGE; DIPLOIDY; EXTRACHROMOSOMAL INHERITANCE; GENE EXPRESSION REGULATION; GENETICS; MICROBIOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PULSED FIELD GEL ELECTROPHORESIS; SOUTHERN BLOTTING;

SACCHAROMYCES CEREVISIAE; ZYGOSACCHAROMYCES BAILII;

BASE SEQUENCE; BLOTTING, SOUTHERN; CHROMOSOME BREAKPOINTS; CHROMOSOMES, FUNGAL; DIPLOIDY; DNA, CIRCULAR; DNA, FUNGAL; ELECTROPHORESIS, GEL, PULSED-FIELD; EVOLUTION, MOLECULAR; EXTRACHROMOSOMAL INHERITANCE; GENE AMPLIFICATION; GENE DOSAGE; GENETIC VARIATION; GENOME, FUNGAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; SACCHAROMYCES CEREVISIAE; WINE; ZYGOSACCHAROMYCES;

EID: 79952523291     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017872     Document Type: Article

References (61)

1. Keeling PJ, Palmer JD, (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9: 605-618.
2. Marcet-Houben M, Gabaldon T, (2010) Acquisition of prokaryotic genes by fungal genomes. Trends Genet 26: 5-8.
3. Keeling PJ, (2009) Functional and ecological impacts of horizontal gene transfer in eukaryotes. Curr Opin Genet Dev 19: 613-619.
4. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, et al. (2004) Genome evolution in yeasts. Nature 430: 35-44.
5. Fitzpatrick DA, O'Gaora P, Byrne KP, Butler G, (2010) Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. BMC Genomics 11: 290.
6. Hall C, Brachat S, Dietrich FS, (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4: 1102-1115.
7. Rolland T, Neuveglise C, Sacerdot C, Dujon B, (2009) Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes. PLoS One 4: e6515.
8. Liti G, Barton DB, Louis EJ, (2006) Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174: 839-850.
9. Muller LA, McCusker JH, (2009) A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae. FEMS Yeast Res 9: 143-152.
10. Kavanaugh LA, Fraser JA, Dietrich FS, (2006) Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment. Mol Biol Evol 23: 1879-1890.
11. Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ, (2006) Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr Biol 16: 1857-1864.
12. Novo M, Bigey F, Beyne E, Galeote V, Gavory F, et al. (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci U S A 106: 16333-16338.
13. Galeote V, Novo M, Salema-Oom M, Brion C, Valerio E, et al. (2010) FSY1, an horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain encodes a high affinity fructose/H+ symporter. Microbiology 156: 3754-3761.
14. Broach JR, Li YY, Feldman J, Jayaram M, Abraham J, et al. (1983) Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol 47: 1165-1173.
15. Van Houten JV, Newlon CS, (1990) Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol Cell Biol 10: 3917-3925.
16. Moore JK, Haber JE, (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 16: 2164-2173.
17. Liti G, Carter DM, Moses AM, Warringer J, Parts L, et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337-341.
18. Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L, (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342-345.
19. Fay JC, Benavides JA, (2005) Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet 1: 66-71.
20. Legras JL, Merdinoglu D, Cornuet JM, Karst F, (2007) Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol Ecol 16: 2091-2102.
21. Koszul R, Fischer G, (2009) A prominent role for segmental duplications in modeling Eukaryotic genomes. Comptes Rendus Biologies 332: 254-266.
22. Dujon B, (2010) Yeast evolutionary genomics. Nat Rev Genet 11: 512-524.
23. Gresham D, Usaite R, Germann SM, Lisby M, Botstein D, et al. (2010) Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus. Proc Natl Acad Sci U S A 107: 18551-18556.
24. Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, et al. (2000) Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25: 333-337.
25. Libuda DE, Winston F, (2006) Amplification of histone genes by circular chromosome formation in Saccharomyces cerevisiae. Nature 443: 1003-1007.
26. Moore IK, Martin MP, Dorsey MJ, Paquin CE, (2000) Formation of circular amplifications in Saccharomyces cerevisiae by a breakage-fusion-bridge mechanism. Environ Mol Mutagen 36: 113-120.
27. Campbell JL, Newlon CS, (1991) Chromosomal DNA replication. In: Broach JR, Pringle JRP, Jones EWJ, editors. The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics Cold Spring Harbor, New York Cold Spring Harbor laboratory Press pp. 41-146.
28. Araki H, Jearnpipatkul A, Tatsumi H, Sakurai T, Ushio K, et al. (1985) Molecular and functional organization of yeast plasmid pSR1. J Mol Biol 182: 191-203.
29. Toh-e A, Araki H, Utatsu I, Oshima Y, (1984) Plasmids resembling 2-micrometers DNA in the osmotolerant yeasts Saccharomyces bailii and Saccharomyces bisporus. J Gen Microbiol 130: 2527-2534.
30. Toh-e A, Utatsu I, (1985) Physical and functional structure of a yeast plasmid, pSB3, isolated from Zygosaccharomyces bisporus. Nucleic Acids Res 13: 4267-4283.
31. Utatsu I, Sakamoto S, Imura T, Toh-e A, (1987) Yeast plasmids resembling 2 micron DNA: regional similarities and diversities at the molecular level. J Bacteriol 169: 5537-5545.
32. Daley JM, Palmbos PL, Wu D, Wilson TE, (2005) Nonhomologous end joining in yeast. Annu Rev Genet 39: 431-451.
33. Hourcade D, Dressler D, Wolfson J, (1973) The amplification of ribosomal RNA genes involves a rolling circle intermediate. Proc Natl Acad Sci U S A 70: 2926-2930.
34. Horowitz H, Haber JE, (1985) Identification of autonomously replicating circular subtelomeric Y' elements in Saccharomyces cerevisiae. Mol Cell Biol 5: 2369-2380.
35. Paques F, Haber JE, (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 63: 349-404.
36. Wood V, Rutherford KM, Ivens A, Rajandream MA, Barrell B, (2001) A re-annotation of the Saccharomyces cerevisiae genome. Comp Funct Genomics 2: 143-154.
37. McVey M, Lee SE, (2008) MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends in Genetics 24: 529-538.
38. Ma JL, Kim EM, Haber JE, Lee SE, (2003) Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double-strand breaks lacking overlapping end sequences. Mol Cell Biol 23: 8820-8828.
39. Ricchetti M, Fairhead C, Dujon B, (1999) Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402: 96-100.
40. Sacerdot C, Casaregola S, Lafontaine I, Tekaia F, Dujon B, et al. (2008) Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts. FEMS Yeast Res 8: 846-857.
41. Yu X, Gabriel A, (1999) Patching broken chromosomes with extranuclear cellular DNA. Mol Cell 4: 873-881.
42. Frank AC, Wolfe KH, (2009) Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes. Eukaryot Cell 8: 1521-1531.
43. Kuttler F, Mai S, (2007) Formation of non-random extrachromosomal elements during development, differentiation and oncogenesis. Semin Cancer Biol 17: 56-64.
44. Cohen Z, Lavi S, (2009) Replication independent formation of extrachromosomal circular DNA in mammalian cell-free system. PLoS One 4: e6126.
45. van Loon N, Miller D, Murnane JP, (1994) Formation of extrachromosomal circular DNA in HeLa cells by nonhomologous recombination. Nucleic Acids Res 22: 2447-2452.
46. Damon C, Vallon L, Zimmermann S, Z. Haider M, Galeote V, et al. A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryoties. ISME J: In press.
47. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
48. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
49. Bidenne C, Blondin B, Dequin S, Vezinhet F, (1992) Analysis of the chromosomal DNA polymorphism of wine strains of Saccharomyces cerevisiae. Curr Genet 22: 1-7.
50. Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, et al. (2009) Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res 7: 7.
51. Edgar RC, (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
52. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
53. Tajima F, Nei M, (1984) Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1: 269-285.
54. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
55. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
56. Doniger SW, Kim HS, Swain D, Corcuera D, Williams M, et al. (2008) A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet 4: e1000183.
57. Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, et al. (2007) Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A 104: 12825-12830.
58. Borneman AR, Forgan AH, Pretorius IS, Chambers PJ, (2008) Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res 8: 1185-1195.
59. Hoffman CS, Winston F, (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57: 267-272.
60. Hill JE, Myers AM, Koerner TJ, Tzagoloff A, (1986) Yeast/E. coli shuttle vectors with multiple unique restriction sites. Yeast 2: 163-167.
61. Guldener U, Heck S, Fielder T, Beinhauer J, Hegemann JH, (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24: 2519-2524.