Lager yeasts possess dynamic genomes that undergo rearrangements and gene amplification in response to stress

Current Genetics

Volumn 53, Issue 3, 2008, Pages 139-152

  James, Tharappel C ^a   Usher, Jane ^a   Campbell, Susan ^a,b   Bond, Ursula ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Adaptive evolution; Competitive genomic hybridisations; Environmental stress; Gross chromosomal rearrangements

Indexed keywords

RIBOSOME RNA;

ARTICLE; CHROMOSOMAL INSTABILITY; CHROMOSOME 12; CHROMOSOME REARRANGEMENT; CONTROLLED STUDY; ENVIRONMENTAL STRESS; FERMENTATION; FUNGAL STRAIN; FUNGUS MUTANT; GENE AMPLIFICATION; GENE LOCUS; GENOME; HEAT TOLERANCE; HIGH TEMPERATURE; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TELOMERE; YEAST;

ENVIRONMENT; FERMENTATION; GENE AMPLIFICATION; GENE EXPRESSION REGULATION, FUNGAL; GENE REARRANGEMENT; GENOME, FUNGAL; KARYOTYPING; NUCLEIC ACID HYBRIDIZATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES PASTORIANUS;

EID: 39649104571     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-007-0172-8     Document Type: Article

References (43)

1. Andalis AA, Storchova Z, Styles C, Galitski T, Pellman D, Fink GR (2004) Defects arising from whole-genome duplications in Saccharomyces cerevisiae. Genetics 167:1109-1121
2. Ansanay Galeote V, Alexandre H, Bach B, Delobel P, Dequin S, Blondin B (2007) Sfl1p acts as an activator of the HSP30 gene in Saccharomyces cerevisiae. Curr Genet 52:55-63
3. Attfield PV (1997) Stress tolerance: The key to effective strains of industrial baker's yeast. Nat Biotechnol 15:1351-1357
4. Biemont C, Vieira C (2006) Genetics: Junk DNA as an evolutionary force. Nature 443:521-524
5. Blieck L, Toye G, Dumortier F, Verstrepen KJ, Delvaux FR, Thevelein JM, Van Dijck P (2007) Isolation and characterization of brewer's yeast variants with improved fermentation performance under high-gravity conditions. Appl Environ Microbiol 73:815-824
6. Bond U (1988) Heat shock but not other stress inducers leads to the disruption of a sub-set of snRNPs and inhibition of in vitro splicing in HeLa cells. EMBO J 7:3509-3518
7. Bond U, Blomberg A (2006) Yeasts in food and beverages. Springer, Heidleberg
8. Bond U, Neal C, Donnelly D, James TC (2004) Aneuploidy and copy number breakpoints in the genome of lager yeasts mapped by microarray hybridisation. Curr Genet 45:360-370
9. Brosnan MP, Donnelly D, James TC, Bond U (2000) The stress response is repressed during fermentation in brewery strains of yeast. J Appl Microbiol 88:746-755
10. Butler DK, Gillespie D, Steele B (2002) Formation of large palindromic DNA by homologous recombination of short inverted repeat sequences in Saccharomyces cerevisiae. Genetics 161:1065-1075
11. Carrasco P, Querol A, del Olmo M (2001) Analysis of the stress resistance of commercial wine yeast strains. Arch Microbiol 175:450-457
12. Casaregola S, Nguyen HV, Lapathitis G, Kotyk A, Gaillardin C (2001) Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. Int J Syst Evol Microbiol 51:1607-1618
13. Casey GP (1986) Molecular and genetic analysis of chromosomes X in Saccharomyces carlsbergensis. Carlsberg Res Commun 51:343-362
14. Despons L, Wirth B, Louis VL, Potier S, Souciet JL (2006) An evolutionary scenario for one of the largest yeast gene families. Trends Genet 22:10-15
15. Fablet M, Rebollo R, Biemont C, Vieira C (2007) The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes. Gene 390:84-91
16. Feldman M, Levy AA (2005) Allopolyploidy - a shaping force in the evolution of wheat genomes. Cytogenet Genome Res 109:250-258
17. French SL, Osheim YN, Cioci F, Nomura M, Beyer AL (2003) In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol Cell Biol 23:1558-1568
18. Galhardo RS, Hastings PJ, Rosenberg SM (2007) Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 42:399-435
19. Grauslund M, Didion T, Kielland-Brandt MC, Andersen HA (1995) BAP2, a gene encoding a permease for branched-chain amino acids in Saccharomyces cerevisiae. Biochim Biophys Acta 1269:275-280
20. Huang D, Koshland D (2003) Chromosome integrity in Saccharomyces cerevisiae: The interplay of DNA replication initiation factors, elongation factors, and origins. Genes Dev 17:1741-1754
21. Hunt CR, Dix DJ, Sharma GG, Pandita RK, Gupta A, Funk M, Pandita TK (2004) Genomic instability and enhanced radiosensitivity in Hsp70.1- and Hsp70.3-deficient mice. Mol Cell Biol 24:899-911
22. Kaiser C, Michaelis S, Mitchel LA (1994) Methods in yeast genetics, a laboratory manual. Cold Spring Harbour, Cold Spring Harbour
23. Kobayashi T, Horiuchi T, Tongaonkar P, Vu L, Nomura M (2004) SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast. Cell 117:441-453
24. Kodama Y, Kielland-Brandt MC, Hansen J (2005) Lager brewing yeast. Springer, Berlin
25. Laun P, Ramachandran L, Jarolim S, Herker E, Liang P, Wang J, Weinberger M, Burhans DT, Suter B, Madeo F et al (2005) A comparison of the aging and apoptotic transcriptome of Saccharomyces cerevisiae. FEMS Yeast Res 5:1261-1272
26. Leh-Louis V, Wirth B, Despons L, Wain-Hobson S, Potier S, Souciet JL (2004) Differential evolution of the Saccharomyces cerevisiae DUP240 paralogs and implication of recombination in phylogeny. Nucleic Acids Res 32:2069-2078
27. Liti G, Louis EJ (2005) Yeast evolution and comparative genomics. Ann Rev Microbiol 59:135-153
28. Liu L, Trimarchi JR, Navarro P, Blasco MA, Keefe DL (2003) Oxidative stress contributes to arsenic-induced telomere attrition, chromosome instability, and apoptosis. J Biol Chem 278:31998-32004
29. Mable BK, Otto SP (2001) Masking and purging mutations following EMS treatment in haploid, diploid and tetraploid yeast (Saccharomyces cerevisiae). Genet Res 77:9-26
30. Mayer VW, Aguilera A (1990) High levels of chromosome instability in polyploids of Saccharomyces cerevisiae. Mutat Res 231:177-186
31. Nilsson-Tillgren T, Gjermansen C, Kielland-Brandt MC, Petersen JGL, Holmberg S (1981) Genetic differences between Saccharomyces carlsbergensis and S. cerevisiae. Analysis of chromosome III by single chromosome transfer. Carlsberg Res Commun 46:65-76
32. Opresko PL, Fan J, Danzy S, Wilson DM 3rd, Bohr VA (2005) Oxidative damage in telomeric DNA disrupts recognition by TRF1 and TRF2. Nucleic Acids Res 33:1230-1239
33. Rainieri S, Kodama Y, Kaneko Y, Mikata K, Nakao Y, Ashikari T (2006) Pure and mixed genetic lines of Saccharomyces bayanus and Saccharomyces pastorianus and their contribution to the lager brewing strain genome. Appl Environ Microbiol 72:3968-3974
34. Sanchez Y, Taulien J, Borkovich KA, Lindquist S (1992) Hsp104 is required for tolerance to many forms of stress. EMBO J 11:2357-2364
35. Scholes DT, Kenny AE, Gamache ER, Mou Z, Curcio MJ (2003) Activation of a LTR-retrotransposon by telomere erosion. Proc Natl Acad Sci USA 100:15736-15741
36. Shitsukawa N, Tahira C, Kassai K-i, Hirabayashi C, Shimizu T, Takumi S, Mochida K, Kawaura K, Ogihara Y, Murai K (2007) Genetic and epigenetic alteration among three homoeologous genes of a class E MADS Box Gene in hexaploid wheat. Plant Cell 19:1723-1737
37. Sinclair DA, Guarente L (1997) Extrachromosomal rDNA circles - a cause of aging in yeast. Cell 91:1033-1042
38. Storchova Z, Breneman A, Cande J, Dunn J, Burbank K, O'Toole E, Pellman D (2006) Genome-wide genetic analysis of polyploidy in yeast. Nature 443:541-547
39. Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ, Amon A (2007) Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science 317:916-924
40. VanHulle K, Lemoine FJ, Narayanan V, Downing B, Hull K, McCullough C, Bellinger M, Lobachev K, Petes TD, Malkova A (2007) Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements. Mol Cell Biol 27:2601-2614
41. Volff JN (2006) Turning junk into gold: Domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28:913-922
42. Ziv S, Brenner O, Amariglio N, Smorodinsky NI, Galron R, Carrion DV, Zhang W, Sharma GG, Pandita RK, Agarwal M et al (2005) Impaired genomic stability and increased oxidative stress exacerbate different features of Ataxia-telangiectasia. Hum Mol Genet 14:2929-2943
43. Zuzuarregui A, Carrasco P, Palacios A, Julien A, del Olmo M (2005) Analysis of the expression of some stress induced genes in several commercial wine yeast strains at the beginning of vinification. J Appl Microbiol 98:299-307