Presentation is loading. Please wait.

Presentation is loading. Please wait.

Genome Evolution in Yeast Gilles Fischer 27 th January 2009 | European Course on.

Similar presentations


Presentation on theme: "Genome Evolution in Yeast Gilles Fischer 27 th January 2009 | European Course on."— Presentation transcript:

1 Genome Evolution in Yeast Gilles Fischer 27 th January 2009 | European Course on

2 INTRODUCTION: Comparative genomics Yeasts as model organisms GENOME EVOLUTION: DNA duplications Chromosome dynamics Nucleotide composition

3 A brief introduction to the field of Comparative Genomics Vendrely and Vendrely (1950): "Il ne fait aucun doute que l'étude systématique de la teneur absolue du noyau en acide désoxyribonucléique, à travers de nombreuses espèces animales puisse fournir des suggestions intéressantes en ce qui concerne le problème de l'évolution" Comparing genomes is a very old idea… DNA carries the genetic information: Avery (1943) and Hershey-Chase (1952) "Tout ce qui est vrai pour le colibacille est vrai pour l'éléphant" Jacques Monod:

4 identicaldivergentdifferent time or quantity of evolutionary changes A brief introduction to the field of Comparative Genomics Looking for differencesLooking for similarities

5 identicaldivergentdifferent time or quantity of evolutionary changes A brief introduction to the field of Comparative Genomics Looking for differencesLooking for similarities NEED FOR ADEQUATELY RELATED ORGANSIMS

6 Looking for differences Looking for similarities A brief introduction to the field of Comparative Genomics Genome sequences Bio-informatics Rules governing genome evolution Mechanistic hypotheses Genetic screens functional genomics Experimental Biology Molecular mechanisms

7 Looking for differences Looking for similarities A brief introduction to the field of Comparative Genomics Genome sequences Bio-informatics Rules governing genome evolution Mechanistic hypotheses Genetic screens functional genomics Experimental Biology Molecular mechanisms SMALL GENOMES AND EXPERIMENTALLY TRACTABLE

8 Eukaryotic micro-organisms classified in the kingdom Fungi About 1,500 species currently described (only 1% of all yeast) Yeasts are unicellular, typically measuring 3–4 µm in diameter (up to over 40 µm) Saccharomyces cerevisiae used in baking and fermenting alcoholic beverages for thousands of years Other species of yeast, such as Candida albicans, are opportunistic human pathogens Yeasts have recently been used to generate electricity in microbial fuel cells and produce ethanol for the biofuel industry. Yeasts are found in both divisions Ascomycota and Basidiomycota The budding yeasts ("true yeasts") are classified in the Saccharomycotina subphylum Organisms with small genomes, phylogenetically related and experimentally tractable = YEASTS A brief introduction to the field of Yeast Genomics

9 Organisms with small genomes, phylogenetically related and experimentally tractable = YEASTS A brief introduction to the field of Yeast Genomics The Tree of Eukaryotes (Keeling et al., 2005)

10 A brief introduction to the field of Yeast Genomics The genome of S. cerevisiae André Goffeau 8 years, 120 labs, 641 people Life with 6000 genes Science (1996) The first eukaryotic genome sequence: Saccharomyces paradoxus Saccharomyces mikatae Saccharomyces cerevisiae Saccharomyces kudriavzevii Saccharomyces bayanus Saccharomyces pastorianus Saccharomyces exiguus Saccharomyces servazzii Saccharomyces castellii Candida glabrata Vanderwaltozyma polyspora Zygosaccharomyces rouxii Lachancea thermotolerans Lachancea waltii Lachancea kluyveri Kluyveromyces lactis Kluyveromyces marxianus Eremothecium gossypii Saccharomycodes ludwigii Brettanomyces bruxellensis Pichia angusta Candida lusitaniae Debaryomyces hansenii Pichia stipitis Pichia sorbitophila Candida guilliermondii Candida tropicalis Candida parapsilosis Lodderomyces elongisporus Candida albicans Candida dubliniensis Arxula adeninivorans Yarrowia lipolytica Schizosaccharomyces pombe Saccharomycotina

11 Saccharomyces paradoxus Saccharomyces mikatae Saccharomyces cerevisiae Saccharomyces kudriavzevii Saccharomyces bayanus Saccharomyces pastorianus Saccharomyces exiguus Saccharomyces servazzii Saccharomyces castellii Candida glabrata Vanderwaltozyma polyspora Zygosaccharomyces rouxii Lachancea thermotolerans Lachancea waltii Lachancea kluyveri Kluyveromyces lactis Kluyveromyces marxianus Eremothecium gossypii Saccharomycodes ludwigii Brettanomyces bruxellensis Pichia angusta Candida lusitaniae Debaryomyces hansenii Pichia stipitis Pichia sorbitophila Candida guilliermondii Candida tropicalis Candida parapsilosis Lodderomyces elongisporus Candida albicans Candida dubliniensis Arxula adeninivorans Yarrowia lipolytica Schizosaccharomyces pombe Saccharomycotina A brief introduction to the field of Yeast Genomics Whole Genome Duplication Extensive loss of transposable elements and spliceosomal introns Gain of mating type cassettes and small centromeres frequent tandem duplications Gain of Megasatellites Gain of HO gene

12 # genes # tRNA # introns 12,1 12,3 9,8 11,3 10,4 10,7 12,1 20,5 size (Mb) # chr Genome annotation Yarrowia lipolytica Saccharomyces cerevisiae Candida glabrata Lachancea kluyveri (WashU seq center M. Jonhston) Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii A brief introduction to the field of Yeast Genomics

13 Yarrowia lipolytica Saccharomyces cerevisiae Candida glabrata Lachancea kluyveri Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii MYr MYr 100 MYr Berbee and Taylor, 2006; James et al., * amino acid identity % Evolutionary scale Mus musculus Takifugu rubripes Tetraodon negroviridis Homo sapiens 100 * MYr 100 MYr 550 MYr Ciona intestinalis * Dujon et al., et * Jaillon et al., Nature, 2004 A brief introduction to the field of Yeast Genomics

14 Yarrowia lipolytica Saccharomyces cerevisiae Candida glabrata Lachancea kluyveri (WashU seq center M. Jonhston) Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii mean family size Genome redundancy YALI SACE LAKL DEHA KLLA LATH ZYRO CAGL WGD Wolfe and Shields, important level of redundancy (in all eukaryotic phyla) - Gene order changes (differential loss of duplicates, translocation breakpoints) - several mechanisms of duplication A brief introduction to the field of Yeast Genomics

15 - Small, compact and specialized: - small intergenic sequences - few transposable elements - few introns - limited RNA interference -Large evolutionary scale - High level of genome redundancy - Numerous evolutionary novelties in all clades - High number of sequenced genomes Yeast Genomes ===> good model organisms to study genome evolution

16 Most eukaryotic genomes contain high proportion of duplicated genes Duplicated Genes 43% 65% 49% 40% 50% S. c. A. t. C. e. D. m. H. s. s. duplication Gene dosage increase Genetic robustness Gain of a new function Specialization of the 2 copies Loss of function (most frequent fate ) PseudogenizationNeofunctionalization Conservation Degeneration Complementation ===> Strong evolutionary potential Genome evolution: DNA duplications

17 CGH SDs containing between 1 to 22 genes No homology at the junctions (microhomologies) Gresham et al., PLoS Genet 2008 Adaptation to sulfate-limited conditions in chemostats for 200 generations: Genome evolution: DNA duplications Adaptative value of DNA duplications:

18 3days - YPD - 30° and so on… RPL20B XV XIII RPL20A ==> WT growth rate RPL20B XV XIII ==>slow growth rpl20A délétion ??? RPL20B ==> WT growth rate A duplication assay: Genome evolution: DNA duplications

19 I VI III IX V - VIII XI X XIV II V, XIII VII, XV IV - XII XV Karyotype Hybridization RPL20B Molecular combing direct tandem PCR and sequence Despite the selection of a single gene duplication event, only large segmental duplications were recovered Molecular characterization of segmental duplications: Comparative Genomic Hybridization 143 kb RPL20B Genome evolution: DNA duplications A duplication assay:

20 Inter-chromosomalIntra-chromosomal strainrate of SDs (/cell/division) type of SDsbreakpoint sequences (%) LTRs (300bp) microhomologies (2 to 11 bp) microsatellites (poly A/T or répét trinucleotides) WT (1) pol (<0.07) REPLICATION clb57x (730) CPT3 x (320) rad523 x (3) DSB REPAIR rad52 rad1 dnl4 8 x (0.8) Genome evolution: DNA duplications Molecular mechanisms: Koszul et al. EMBO J., 2004 TTT T TT time (min) Lately replicated regions tRNAs LTRs microsatellites a connection with replication? Raghuraman et al. Science, 2001

21 Clb5 Replication-based mechanisms Inter-chromosomalIntra-chromosomal strainrate of SDs (/cell/division) type of SDsbreakpoint sequences (%) LTRs microhomologies microsatellites WT (1) clb57x (730) defect in the firing of late replication origins (Schwob et al, 1993) S-phase lasts twice longer (Epstein et al, 1992) Rad9-dependent activation of the replication checkpoint indicative of DNA damages (Gibson et al, 2004) RPL20B lies in Clb5-dependent region (CDR; McCune et al, 2008) replication perturbations strongly induce SD formation Bloom and Cross, 2007 Pol32 Nick McElhinny, Cell 2008 pol (<0.07) Pol32 is required for initiating BIR reaction (Lydeard et al, 2007) SDs are generated through replication-based mechanisms

22 Broken forks as precursor lesions leading to SDs strainrate of SDs (/cell/division) type of SDsbreakpoint sequences (%) WT (1) CPT3 x (320) Top1 CPT Top1 =>broken forks promote SD formation Inter-chromosomalIntra-chromosomal LTRs microhomologies microsatellites Replication-based mechanisms

23 pas dhomologies, religature simple NHEJ Dnl4 Resection Rad52 Rad1 MMEJ SSABIR SDSADSBR Rad51 The DSB repair pathways Pol32 Microhomologies (5-12pb) >30pb dhomologies HR

24 Two different replication-based mechanisms strainrate of SDs (/cell/division) type of SDsbreakpoint sequences (%) WT (1) HR-dependent rad523 x (3) => ====> HR-independent Inter-chromosomalIntra-chromosomal LTRs microhomologies microsatellites => HR-mediated SDs result from BIR Rad51-independent => Non HR-mediated SDs result from ?

25 Dnl4 Resection Rad52 Rad1 The DSB repair pathways X X X

26 strainrate of SDs (/cell/division) type of SDsbreakpoint sequences (%) WT (1) rad523 x (3) MMIR: microhomology microsatellite-induced replication Inter-chromosomalIntra-chromosomal LTRs microhomologies microsatellites rad52 rad1 dnl4 8 x (0.8) SD are still being formed in the absence of all known DSB repair pathways existence of a new DSB repair pathway? HR requires Rad52 MMEJ requires Rad1 NHEJ requires Dnl4 Sequences found at breakpoints: microhomologies between 2 and 11 bp poly (A/T) trinucleotide repeats (GTT) 3-20 Formation of chimeric genes at breakpoints (in 13 out of 26 junctions) Extremely high density of microhomologies and microsatelites in the genome often intragenic

27 Dnl4 Resection Rad52 Rad1 The DSB repair pathways X X X

28 Dnl4 Resection Rad52 Rad1 The DSB repair pathways X X X A new pathway? MMIR Microhomology/microsatellites Induced Replication - independent from all known DSB repair pathways (HR, NHEJ, MMEJ) - dependent from Pol32 - Replication template switching between microhomologies and microsatellites

29 SDs are spontaneously generated at high frequency: SD/cell/division for the RPL20B locus SDs arise from two alternative replication-based mechanisms: BIR and MMIR MMIR represents a new mechanism different from known DSB repair pathways (HR, NHEJ): between microhomologie (between 2 to 11 nt) and microsatellites (poly A/T, trinucleotide repeats) independent from Rad52 requires Pol32 MMIR induces the formation of chimerical genes at the rearrangement junctions Conclusions Genome evolution: DNA duplications

30 Hastings et al, Nature Review Genetics, 2009 In human, FoSTeS/MMBIR: Complex structural variations:- Lissencephaly (Nagamani et al., J. Med Genet 2009) - Miller-Dieker syndrome - Charcot-Marie-Tooth disease (Lupski and Chance, 2005) - Pelizaeus Merzbacher disease (Lee et al., Cell 2007) - XLMR syndrome (Bauters et al., Genome Res 2008) - SDs and CNVs (Kim et al., Genome Res 2008) Genome evolution: DNA duplications

31 Genome evolution: Chromosome Dynamics translocations Inversions duplications deletions rates of rearrangements Species 1 Species 2 # # x -Duplications: high evolutionary potential (creation of new genes, adaptation, specialization,…) - Translocations, inversions, deletions: very low evolutionary potential? (Loss of genes, deregulation of gene expression, modification of sub-nuclear architecture,…)

32 S. paradoxus S. kudriavzevii S. cariocanus S. mikatae S. bayanus S. cerevisiae Saccharomyces sensu stricto complex: - monophyletic group - very closely related species - hybrids viable but sterile - 16 chromosomes Genome evolution: Chromosome Dynamics Yarrowia lipolytica S. serevisiae S. bayanus Candida glabrata Lachancea kluyveri Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii Sensu stricto

33 S. paradoxus S. kudriavzevii S. cariocanus S. mikatae S. bayanus S. cerevisiae Fischer et al., Nature 2000 S. cerevisiaeS. paradoxusS. cariocanusS. mikataeS. kudriavzeviiS. bayanus S. cerevisiaeS. paradoxusS. cariocanusS. mikataeS. kudriavzeviiS. bayanus Genome evolution: Chromosome Dynamics (4) (2) only few translocations: low reorganization recombination between repeated sequences no chromosomal speciation variable rate of rearrangements? (0)

34 C. glabrataK. lactisD. hansenii S. cerevisiae chr VIII ADGIJ %77% 11% 5% Y. lipolytica S. bayanus % Yarrowia lipolytica S. serevisiae S. bayanus Candida glabrata Lachancea kluyveri Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii Sensu stricto Genome evolution: Chromosome Dynamics

35 C. glabrataK. lactisD. hansenii S. cerevisiae chr VIII ADGIJ %77% 11% 5% Y. lipolytica S. bayanus % Genome evolution: Chromosome Dynamics

36 C. glabrataK. lactisD. hansenii S. cerevisiae chr VIII ADGIJ %77% Y. lipolytica S. bayanus % Fischer Fischer et al., PLoS Genet 2006 F. Brunet Genome evolution: Chromosome Dynamics

37 C. glabrataK. lactisD. hansenii S. cerevisiae chr VIII ADGIJ %77% 11% 5% Y. lipolytica S. bayanus % Genome evolution: Chromosome Dynamics

38 C. glabrataK. lactisD. hansenii S. cerevisiae chr VIII ADGIJ %77% 11% 5% Y. lipolytica S. bayanus % Genome evolution: Chromosome Dynamics

39 Saccharomyces cerevisiae Candida glabrata Lachancea kluyveri Lachancea thermotolerans Zygosaccharomyces rouxii at genome scale: S.cerevisiae C. glabrata - comprehensive reshuffling translocations, 104 inversions - no homologous chromosomes "UNSTABLE" GENOMES "STABLE" GENOMES Genome evolution: Chromosome Dynamics L. kluyveri L. thermotolerans -moderate reshuffling -91 translocations, 22 inversions - large chromosomal segments (up to 670 kb) Mean amino acid identity: 58% Mean amino acid identity: 65%

40 Quantitative estimation of the relative genome stability: GOC (gene order conservation) species 1 species 2 ? =5 If yes: +1 If no: 0 Rocha, Trends Genet, 2003, GOC = # neighboring orthologues Total # orthologues - GOL : Gene Order Loss = 1 - GOC - Rate of rearrangements = GOL Dist phylogénétique ( ( mean rate Genome evolution: Chromosome Dynamics

41 Yarrowia lipolytica Saccharomyces cerevisiae Candida glabrata Lachancea kluyveri (WashU seq center M. Jonhston) Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii WGD Rearrangement branch rate S. cerevisiae C. glabrata Z. rouxii K. lactis L. kluyveri L. thermot D. hansenii Species instability scale Genome evolution: Chromosome Dynamics Fischer et al., PLoS Genet 2006

42 Y. lipolytica S. serevisiae S. bayanus Candida glabrata Lachancea kluyveri (WashU seq center M. Jonhston) Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii Sensu stricto low massive Unstable genome Stable genomes differential gene loss No synteny moderate TGA expansion Genome evolution: Chromosome Dynamics

43 High level of chromosome plasticity Hundreds of translocations and inversions Gene order is not very constrained Highly variable rates of chromosome rearrangements between lineages but also within a given lineage Is there a selective advantage associated to these rearrangements? Are they accumulated by genetic drift? usually considered as deleterious few examples of the adaptative role of rearrangements (proliferation of cancer cells (ONeil and Look, 2007), growth advantage of translocated yeast cells (Colson et al, 2004), adaptative gene loss (Domergue, 2005). Creation of genetic novelties requires chromosome plasticity? Conclusions Genome evolution: Chromosome Dynamics

44 Base substitution mutations: CT transitions : cytosine deamination Kreutzer and Essigmann, PNAS, 1998 GT transversions : 8-oxo-guanine Shibutani et al., Nature, 1991 Global AT-enrichment Biased Gene Conversion (BGC): Global GC-enrichment ATGC mutations Duret and Galtier, Annu Rev Genomics Human Genet, 2009 GC% Yarrowia lipolytica Saccharomyces cerevisiae Candida glabrata Lachancea kluyveri Debaryomyces hansenii Kluyveromyces lactis Lachancea thermotolerans Zygosaccharomyces rouxii Eremothecium gossypii52.0 The Génolevures Consortium, Genome Res., 2009 > < Marsolier-Kergoat and Yeramian, Genetics, 2009 not in yeast? Genome evolution: Nucleotide composition

45 ABCDEFG GC% Mb 39.1 ABCDEFGH 47.3 Lachancea thermotolerans Zygosaccharomyces rouxii ABC D EFGH Mb GC% Lachancea kluyveri C-left 1 Mb

46 DNA GC% in C-left: GC% out of C-left: global GC increase RNA 1 st 2 nd 3 rd AAAAAA strong bias in codon usage GC% in C-left: GC% out of C-left: Protein AGPRINKF GC% in synonymous codons relative use in C-left bias in protein composition Payen et al., Genome Res., 2009 Genome evolution: Nucleotide composition

47 E. gossypii K. lactis L. thermotolerans L. waltii L. kluyveri Z. rouxii C. glabrata S. cerevisiae Payen et al., Genome Res., 2009 C-left has the same phylogentic origin than the rest of the genome Alignments of universally conserved proteins : 17 families (6688 residues) outside C-left 19 families (4631 residues) in C-left Genome evolution: Nucleotide composition Phylogeny:

48 LATH_G LATH_E LATH_C LATH_A LATH_F LAKL_C LAWA_S27LAWA_S56LAWA_S55LAWA_S kb C-left share a common ancestral origin with the genomes of L. waltii (LAWA) and L. thermotolerans (LATH) Genome evolution: Nucleotide composition Synteny:

49 - Design of custom microarrays (Agilent 2 x 105k): 200bp fragments G1 S G2 DNA Cy3 DNA Cy5 - Time course analysis of copy number variation during S-phase: Genome evolution: Nucleotide composition Replication:

50 ChrA ChrB Genome evolution: Nucleotide composition Replication:

51 ChrC ChrD Genome evolution: Nucleotide composition Replication:

52 Global GC increase (codon usage bias and protein composition bias) harbors a normal gene density Phylogenetic origin consistent with the rest of the genome presents a very high level of synteny conservation with sister species genomes encompasses the MAT locus but has lost the silent cassettes HMR and HML is devoid of Transposable Elements (203 insertions in the rest of the genome) harbors the same compositional bias in all 11 L. kluyveri strains tested The replication program is modified (more origins and delayed firing) => a cause or a consequence of the unusual GC composition? Meiotic recombination and BGC? Genome evolution: Nucleotide composition Conclusions L. kluyveri offers a unique opportunity to understand the mechansims of evolution of genome nucleotide composition

53 Merci - Plateforme Puces ADN, Génopole PasteurOdile Sismeiro, Jean-Yves Coppé - Génopole Pasteur-Ile de France Christiane Bouchier, Lionel Frangeul - Centre National de Séquençage, Evry Jean-Luc SoucietUniv. Louis Pasteur, Strasbourg Jean Weissenbach, Patrick Winker - Génolevures consortium: - Unité de Génétique Moléculaire des Levures, Institut Pasteur Celia Payen Romain Koszul - Unité de Génomique des Microorganismes, équipe Biologie des Génomes Nicolas Agier Guénola Drillon


Download ppt "Genome Evolution in Yeast Gilles Fischer 27 th January 2009 | European Course on."

Similar presentations


Ads by Google