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Denis BAURAIN Département Des Sciences De La Vie Université De Liège Société Royale Des Sciences De Liège 20 Septembre 2012 Plan De L’Exposé

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Denis BAURAIN Département Des Sciences De La Vie Université De Liège Société Royale Des Sciences De Liège 20 Septembre 2012 Plan De L’Exposé L’évolution des Eucaryotes Denis BAURAIN Département des Sciences de la Vie Université de Liège Société Royale des Sciences de Liège 20 septembre 2012 Plan de l’exposé 1. Qu’est-ce qu’un Eucaryote ? 2. Quelle est la diversité des Eucaryotes ? 3. Quelles sont les relations de parenté entre les grands groupes d’Eucaryotes ? 4. D’où viennent les Eucaryotes ? Qu’est-ce1 qu’un Eucaryote ? Eukaryotic Cells définition ultrastructurale : organelles spécifiques • noyau (1) • nucléole (2) • RE (5, 8) • Golgi (6) • centriole(s) (13) • mitochondrie(s) (9) • chloroplaste(s) • ... http://en.wikipedia.org/ A eukaryotic gene is arranged in a patchwork of coding (exons) and non-coding sequences (introns). Introns are eliminated while exons are spliced together to yield the mature mRNA used for protein synthesis. http://reflexions.ulg.ac.be/ Gene DNA Transcription Exon1 Exon2 Exon3 Exon4 Exon5 Exon6 pre-mRNA Alternatif splicing mature mRNA Translation Protein In many Eukaryotes, almost all genes can lead to different proteins through a process termed alternative splicing. http://reflexions.ulg.ac.be/ REVIEWS Box 2 | Endosymbiotic evolution and the tree of genomes Intracellular endosymbionts that originally descended from free-living prokaryotes have been important in the evolution of eukaryotes by giving rise to two cytoplasmic organelles. Mitochondria arose from α-proteobacteria and chloroplasts arose from cyanobacteria. Both organelles have made substantial contributions to the complement of genes that are found in eukaryotic nuclei today. The figure shows a schematic diagram of the evolution of eukaryotes, highlighting the incorporation of mitochondria and chloroplasts into the eukaryotic lineage through endosymbiosis and the subsequent co-evolution of the nuclear and organelle genomes. The host that acquired plastids probably possessed two flagella113. The nature of the host cell that acquired the mitochondrion (lower right) is fiercely debated among cell evolutionists. The host is generally accepted by most to have an affinity to ARCHAEBACTERIA but beyond that, biologists cannot agree as to the nature of its intracellular organization (prokaryotic, eukaryotic Endosymbiotic Organelles120 or intermediate), its age, its biochemical lifestyle or how many and what kind of genes it possessed . The host is usually assumed to have been unicellular and to have lacked mitochondria. Eukaryotes Plants Early diversification of Origin of Lynn Margulis algal/plant lineages and plastids gene transfer to the host Ancient protozoon origines endosymbiotiques de la Early diversification of eukaryotic lineages and gene transfer to the host mitochondrie et du chloroplaste Ancient cyanobacterium Origin of mitochondria Ancient The host proteobacterium that acquired mitochondria Cyanobacteria Proteobacteria Archaebacteria Timmis et al. (2004) Nat Rev Genet 5:123-135 the term ‘NUMTS’ was coined to designate these nuclear divergence indicates recurrent transfer events, from stretches of mtDNA26.Numts have been found in the ancient to contemporary. The human genome has at 27 28,29 ARCHAEBACTERIA nuclear genomes of grasshoppers ,primates and least 296 different numts of between 106 bp and 14,654 An ancient group of organisms shrimps30, and are often mistaken for bona fide bp (90% of the mitochondrial genome) that cover the that have ribosomes and cell mtDNA31,32. entire mtDNA circle34.Other studies tallied 612 mtDNA membranes that distinguish Eukaryotic genome sequences have more fully insertions in the human genome35,a greater number them from eubacteria. They sometimes show exposed the scale of integrated mitochondrial and because different sequence conservation criteria for 36 environmentally extreme cpDNA in the nuclear genome. Fragments of organelle identifying numts are used in different studies .Older ecology. DNA are becoming recognized as a normal attribute of numts are more abundant in the human genome than nearly all eukaryotic chromosomes. For example, the recent INTEGRANTS, indicating that mtDNA can be ampli- NUMT yeast genome contains tracts with 80–100% similarity fied once inserted36,37 and many are organized as tandem An acronym to describe nuclear 35 integrants of mitochondrial to mtDNA that range in size from 22 to 230 base pairs repeats .Barely detectable numts are present in DNA. (bp) integrated at 34 sites33.This range of sequence Plasmodium32,but highly conserved numts have now NATURE REVIEWS | GENETICS VOLUME 5 | FEBRUARY 2004 | 125 262 DANIEL GRZEBYK ET AL. Table 2. The protein-coding gene nomenclature in algal rarachniophyte plastids appear to have been acquired chloroplast genomes (adapted from Stoebe et al. 1998). from secondary endosymbiosis of chlorophytes (van de Peer et al. 1996, Bhattacharya and Medlin 1998, Gene code Protein function Palmer and Delwiche 1998, Turmel et al. 1999). Ac- accA,B,D Acetyl-CoA carboxylase cordingly, the set of genes retained in secondary en- acpP Acyl carrier protein apcA,B,D,E,F Allophycocyanin phycobilisome dosymbiotic plastids is almost totally included in the argB Acetylglutamate kinase primary lineage from which they descended (Fig. 1). atpA,B,D,E,F,G,H,I ATP synthase The only exceptions are a small number of genes re- bas1 Thiol-specific antioxidant protein tained in secondary plastids that may not be present bioY Biotin synthase carA Carbamoyl phosphate synthetase inGenome their related extant primary plastids: minD and Reduction cbbX Red type Calvin cycle operon minE in cryptophytes (Fig. 1), ycf66 in diatoms, and ccsA Heme attachment to plastid cytochrome c ycf13 and ycf67 in euglenophytes. These genes are rel- cemA Envelope membrane protein REVIEWS chlB,I,L,N Protochlorophyllide reductase ics from ancestral primary plastids that were later lost. clpC/P Caseinolytic-like protease (Clp) cpcA,B,G Phycocyanin phycobilisome gene retention and losses in chloroplast Mitochondrion-to-nucleus transfers. In yeast, a recombi- cpeA,B Phycoerythrin genomes reflect evolutionary patterns nant plasmid, which was introduced into a genome- crtE Geranylgeranyl pyrophosphate synthetase cysA,T Probable transport proteins Whereas Chloroplastthe presence genome reductionof specific genes provides clues lacking mitochondrion, was shown to relocate to the dfr Drug sensory protein about the originand gene of transfer plastids, to the nucleus plastid gene losses, which nucleus as an EPISOME (that is, not recombined into nuclear DNA) at a frequency of 2 x 10–5 per cell per dnaB DNA-replication helicase are effectivelyPhotosynthetic irreversible, electron also provide evolutionary dnaK Hsp 70-type chaperone transport, respiration, ATPase generation80chloroplastes.A lower frequency (5 x 10–6 per cell per gen- information. There are 200 or fewer protein-coding dsbD Thiol:disulfide interchange protein Functional eration) of episomal relocation was observed when the Translation categories fabH ␤-Ketoacyl-acyl carrier protein synthase III genes in primary plastids. Assuming that the number plasmid was integrated into the mitochondrial chromo- fdx 2[4Fe-4S] ferredoxin of genes in Otherthe original primary ur-plastid was similar 81 ftrB Ferredoxin-thioredoxin reductase some .In these experiments, the released DNA was epi- ftsH,W Division proteins to that found in the extant cyanobacterium Synechocys- somal, indicating that release of DNA from the yeast glnB Nitrogen regulatory protein tis PCC6803 (3168 protein-coding genes; Kaneko et mitochondrion is frequent, but integration might be rare gltB Glutamate synthase (GOGAT) al. 1996), more than 93% of the ancestral endosym- in yeast nuclei because of their characteristically high level groEL,ES Chaperonins 60 and 10 kDa biont genome was lost or transferred to the host nu- of reliance on homologous recombination for DNA hemA 5-Aminolevulinic acid synthase cleus in the primary plastid lineages (Fig. 2). Green incorporation. Newer work indicates that mtDNA escape hisH Histidinol-phosphate aminotransferase in yeast occurs through an intracellular mechanism that I-CvuI DNA endonuclease plastids exhibit the most numerous gene losses, either depends on the composition of the growth medium and ilvB,H Acetohydroxyacid synthase specific losses or those in common with glaucophytes. infA,B,C Translational initiation factors the genetic state of the mitochondrial genome, and is Subsequently, patterns of gene losses occurred differ- independent of an RNA intermediate82. minD,E Homologues of bacterial cell division Genome reduction regulators ently at phylum level radiations within primary lin- mntA,B Manganese transport system proteins eages and at radiations accompanying secondary sym- Chloroplast-to-nucleus transfers in higher plants.Only moeB Molybdopterin biosynthesis protein biotic events. Between 1% and 10% of the remaining more recently has it been possible to quantify the process nadA Quinolinate synthase of chloroplast-to-nucleus DNA transfer. To determine nblA Phycobilisome degradation protein plastid genes were lost at phylum level radiations the frequency of plastid DNA transfer and integrative ndhA-J NADH-plastoquinone oxidoreductase within Evolutionaryrhodophytes and chlorophytes. A larger num- ndhK NADH-ubiquinone oxidoreductase ber of timethe remaining primary plastid genes were lost recombination into the higher plant nuclear genome, the ntcA Global nitrogen transcriptional regulator plastome of tobacco was transformed with a neomycin odpA,B Pyruvate dehydrogenase E1 component at radiations linked to secondary symbiotic events. For phosphotransferase gene (neoSTLS2) that was tailored
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